Current Issues in Molecular Biology doi: 10.3390/cimb48060595

Authors: Xiaoxuan Pan Xin Chen Chunyuan Zhang Xin Ma Jieru Han

This review argues that protein lactylation—a lactate-driven posttranslational modification—serves as the long-sought molecular bridge that coordinates these two hallmarks in gastric cancer (GC). Far from being a passive metabolic byproduct, lactylation operates as a central molecular hub with a dual function: intracellularly, it directly drives malignant phenotypes by modifying key oncoproteins such as YAP and metabolic enzymes; extracellularly, it remodels the tumor immune microenvironment by polarizing tumor-associated macrophages toward an immunosuppressive M2 phenotype, upregulating PD-L1 expression, and impairing CD8+ T-cell function. We propose that these two arms constitute a self-reinforcing metabolic–epigenetic–immunological circuit, wherein lactylation both originates from and perpetuates the Warburg effect, creating a vicious cycle that sustains malignancy and immune evasion. This framework positions lactylation not merely as a mechanistic detail, but as a unifying principle that integrates metabolic reprogramming, epigenetic regulation, and immune suppression in GC. We critically evaluate the current landscape of lactylation “writers,” “erasers,” and “readers”; highlight the translational potential of targeting this pathway; and identify the conceptual and technical bottlenecks that must be overcome—including the lack of causality in current studies, the absence of specific research tools, and the unresolved heterogeneity of lactylation across cell types and disease stages. By reframing lactylation as an actionable hub rather than a downstream consequence, this review provides a roadmap for advancing lactylation-based precision medicine in GC.

Current Issues in Molecular Biology doi: 10.3390/cimb48060594

Authors: Fumihiro Nishimura Manabu Sasada Fumio Fukai Kyoko Imanaka-Yoshida Akihiro Sudo Masahiro Hasegawa

Osteoarthritis (OA) is highly prevalent worldwide. Fibronectin (FN) has been associated with OA pathology; however, its role remains unexplored. In this study, we hypothesized that FNIII14 induces chondrocyte apoptosis by inactivating β1 integrin and aimed to clarify the role of FNIII14 in OA pathology. Immunohistochemistry, immunofluorescence, flow cytometry, a 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium assay, a terminal deoxynucleotidyl transferase deoxyuridine triphosphate nick-end labeling assay, real-time quantitative polymerase chain reaction, and Western blotting were performed using cartilage obtained from patients who underwent total knee arthroplasty. In a mouse model, FNIII14 or phosphate-buffered saline was administered to the knees, and cartilage degeneration and synovitis were evaluated using the Mankin and Synovitis scores, respectively. Statistical significance was determined using the Mann–Whitney U or Kruskal–Wallis test (p < 0.05). FNIII14 was detected in highly degenerated OA cartilage, with decreased β1 integrin activity, suppressed cell proliferation, and induced apoptosis in chondrocytes. FNIII14 decreased the gene expression of cartilage-specific markers and anabolic factors and increased inflammatory cytokine gene expression and phosphorylation of extracellular signal-regulated protein kinase-1/2. FNIII14 induced cartilage degeneration in mouse knees with almost no synovitis. Regulation of FNIII14 production and action may play an important role in suppressing cartilage degeneration in human OA.

Current Issues in Molecular Biology doi: 10.3390/cimb48060593

Authors: Yihan Wang Mengchen Lv Ying Li

Cadmium (Cd) is one of the most toxic heavy metals in the environment, and it severely represses photosynthesis, growth, development and nutrient uptake in photosynthetic organisms. Excessive cadmium (Cd) taken up by plants seriously threatens global food security and human health. Therefore, designing an eco-friendly and sustainable strategy that can reduce the accumulation of Cd in plants is a major challenge. Phosphorus (P), as an essential nutrient for plant growth, has been shown to play a pivotal role in mediating Cd-induced stress response. However, the molecular mechanisms underlying the crosstalk between phosphate signaling and Cd stress response remain largely uncharacterized, especially the role of the core phosphate homeostasis regulator Phosphate Starvation Response 1 (PSR1). Here, we used the model green microalga Chlamydomonas reinhardtii to investigate the physiological and transcriptomic responses to Cd stress in wild type (WT, CC-125) and PSR1 loss-of-function mutant (Crpsr1, CC-4267). Our results showed that the Crpsr1 mutant exhibited significantly enhanced Cd tolerance compared with WT under P-sufficient conditions, with a better growth phenotype and a significantly lower Cd accumulation. Transcriptome analysis revealed distinct gene expression profiles between WT and the Crpsr1 mutant in response to Cd treatment. Gene Ontology (GO) enrichment analysis showed that differentially expressed genes (DEGs) were mainly involved in primary metabolism, protein kinase activity, ion binding and transmembrane transport, which are critical processes for mitigating Cd stress. Notably, key genes associated with iron uptake and homeostasis were significantly upregulated in the Crpsr1 mutant under Cd stress, indicating a potential regulatory link between PSR1, iron homeostasis and Cd tolerance. Taken together, our findings establish a functional association between the central phosphate signaling regulator PSR1 and Cd stress response in green microalgae, and provide novel candidate genes and regulatory networks for developing engineered microalgae with enhanced Cd phytoremediation capacity.

Current Issues in Molecular Biology doi: 10.3390/cimb48060592

Authors: Pei-Yi Chen Je-Wen Liou Ming-Jiuan Wu Jui-Hung Yen

Disruption of cholesterol homeostasis is closely associated with hypercholesterolemia, dyslipidemia, atherosclerotic cardiovascular disease (ASCVD), and metabolic disorders such as metabolic dysfunction-associated fatty liver disease (MAFLD). Intestinal and hepatic cholesterol absorption are central to maintaining systemic cholesterol balance, with Niemann–Pick C1-Like 1 (NPC1L1) acting as a key transporter that mediates cholesterol uptake in enterocytes and hepatocytes. Aberrant NPC1L1 expression or activity promotes excessive cholesterol accumulation in both plasma and liver, thereby contributing to dyslipidemia and hepatic steatosis. Consequently, NPC1L1 has emerged as an important therapeutic target for reducing cholesterol absorption and improving lipid homeostasis. Although ezetimibe is currently the only clinically approved NPC1L1 inhibitor, its limited efficacy as monotherapy highlights the need for alternative or complementary therapeutic strategies. Growing evidence indicates that natural phytochemicals, particularly polyphenols and flavonoids, can modulate NPC1L1 at both transcriptional and functional levels. These compounds not only suppress intestinal cholesterol absorption but also attenuate hepatic lipid accumulation, ultimately improving circulating lipid profiles. This review summarizes recent advances in understanding the role of NPC1L1 in cholesterol metabolism and highlights the emerging therapeutic potential of phytochemicals as novel complementary approaches for the prevention and treatment of lipid metabolic disorders.

Current Issues in Molecular Biology doi: 10.3390/cimb48060591

Authors: Saba Iordanishvili Nazibrola Chiradze Dodo Agladze Marine Kikvidze Revaz Solomonia Vincenzo Lagani

Blood lipid responses to diet vary substantially between individuals, limiting the effectiveness of uniform dietary recommendations, and genetic variation may contribute to this heterogeneity through gene–diet interactions. This systematic review and meta-analysis evaluated nutrigenetic interactions affecting blood lipid traits. Web of Science Core Collection and MEDLINE were searched in April 2026 to identify human studies testing interactions between dietary exposures—including macronutrient composition, fat quantity, fat type [polyunsaturated fatty acids (PUFA), monounsaturated fatty acids (MUFA), and saturated fatty acids (SFA)], carbohydrate, and protein—and lipid-related genes. Interaction p-values were synthesized using a weighted Stouffer’s Z method with Benjamini–Hochberg false discovery rate correction. Twenty studies (n = 20), comprising approximately 9800 participants, met the inclusion criteria. The most consistent evidence was observed for CETP, APOE, and APOB, particularly in relation to broader macronutrient composition and fat-related exposures, while ABCA1 and APOA5 showed significant but more limited evidence. PUFA was the most consistent specific dietary exposure. In contrast, ABCG5, ABCG8, and CYP7A1 lacked sufficient data for meta-analysis, highlighting major gaps in the current literature. Overall, the findings support the view that lipid responses to diet are partly genotype-dependent, while also underscoring the need for larger, better harmonized studies to clarify and extend the current evidence base.

Current Issues in Molecular Biology doi: 10.3390/cimb48060590

Authors: Li Wang Yaoxing Wang Mingkai Shao Tao Wang Wanbao Zheng Jun Cao Renwen Luo Youyan Tu Yiting Xia Yiming Wei Ning Liu Wenjie Lu Youzhi Xu

In the original publication [...]

Current Issues in Molecular Biology doi: 10.3390/cimb48060589

Authors: Arzu Ay Nevra Alkanli Gokay Taylan Esra Ergin

Chronic inflammation mediated by cytokines is central to the pathogenesis of coronary artery disease (CAD). This exploratory study aimed to investigate potential associations between functional gene variations of the cytokines interleukin 18 (IL-18) and interleukin 8 (IL-8) and the CAD susceptibility within a specific regional cohort, while accounting for common clinical comorbidities. Genotype distributions of IL-18 (−607 C/A, −137 G/C) and IL-8 (+781 C/T) were analyzed in a cohort of 102 patients with angiographically confirmed CAD and 102 healthy controls. Genotyping was performed using PCR, allele-specific PCR, and RFLP techniques. Multivariate logistic regression was utilized to assess potential independent associations, adjusting for age and traditional clinical risk factors. In this specific cohort, after adjusting for age, hypertension, diabetes, cholesterol, family history, and smoking, the IL-18 (−137 G/C) CC genotype was observed more frequently in CAD patients (adjusted odds ratio [AOR] = 6.15, 95% CI = 2.10–18.05, p = 0.001). An exploratory analysis of genotype combinations suggested that the IL-18 (−607/−137) CA-CC profile may be linked to an increased risk (AOR = 3.65, p = 0.028), while tentative protective trends were noted for certain IL-18/IL-8 combinations. Notably, a significant deviation from a Hardy–Weinberg equilibrium (HWE) was observed in the control group for the IL-18 loci, which represents a substantial methodological limitation that may influence these risk estimates. Our preliminary findings suggest that specific IL-18 and IL-8 variations may contribute to CAD susceptibility independently of traditional risk factors in the studied population. However, given the modest sample size and the observed HWE deviation, these associations should be regarded as suggestive rather than definitive. While these genetic variations underscore the importance of cytokine pathways in cardiovascular research, they do not currently support clinical implementation for risk stratification. Large-scale, multi-center prospective studies are necessary to validate these preliminary signals and evaluate their long-term scientific utility.

Current Issues in Molecular Biology doi: 10.3390/cimb48060588

Authors: Diana Basharova Ayazhan Bekbayeva Gulnara Svyatova Aizhan Darmeshova Elena Zholdybayeva

Background: Alport syndrome is a hereditary disorder caused by defects in the type IV collagen network. Although exon variants are primarily associated with Alport syndrome, the clinical significance of intronic variants remains incompletely characterized. The aim of this study was to characterize the clinical and molecular features of a familial case of Alport syndrome associated with the intronic variant c.1588-2A>G and to assess its impact using in silico tools. Case description: Two affected siblings presented with hematuria, proteinuria, and renal biopsy demonstrated focal global and segmental glomerulosclerosis, findings consistent with Alport syndrome. Whole-exome sequencing was subsequently performed in patients. The variant (NM_033380.2, c.1588-2A>G) in intron 23 of the COL4A5 gene was identified in both probands. SpliceAI analysis demonstrated a complete loss of the canonical acceptor site and a high probability of cryptic site activation. Conclusion: The evidence suggests a likely pathogenic role of the COL4A5 c.1588-2A>G variant in Alport syndrome.

Current Issues in Molecular Biology doi: 10.3390/cimb48060587

Authors: Quan Gu Wenyang Zhang Ziping Chen Na Li Shuwen Xu

Although previous studies have indicated that heme oxygenase 1 (HO1/HY1) regulates the flowering time via the photoperiod pathway, the specific mechanism is still elusive. Here, we found that the Arabidopsis hy1-100 mutant displayed early flowering, and the characteristic expression patterns of several master genes involved in the autonomous pathway were altered. Notably, the transcript levels of FLOWERING LOCUS C (AtFLC) gene declined developmentally in both wild-type and hy1-100 mutant, with a more pronounced fold reduction observed in the mutant. Genetic evidence further underlined that hy1-100/FLCOE plants partially reversed the early flowering phenomenon of hy1-100 mutant, suggesting that AtHO1 regulated flowering at least partially through the AtFLC-involved autonomous pathway, as supported by changes in FLOWERING LOCUS T (AtFT) and SUPPRESSOR OF OVEREXPRESSION OF CO1 (AtSOC1) transcripts. Further analysis of hy1-100/ft mutants revealed that hy1-100/ft and ft mutants displayed similar late flowering phenotypes, accompanied by downregulated APETALA1 (AtAP1) and AtSOC1, indicating that AtFT played a crucial role in AtHO1-regulated flowering. Two key conclusions are drawn: first, the loss of AtHO1 function promotes early flowering in Arabidopsis, which was genetically linked to the autonomous pathway regulating AtFLC expression; second, AtFT was an essential downstream factor mediating AtHO1-regulated flowering.

Current Issues in Molecular Biology doi: 10.3390/cimb48060586

Authors: Marko Mladenović Bojana Banović Đeri Ana Nikolić Dragana Dudić Slaven Prodanović Sanja Z. Perić Nikola Grčić

Knowledge of population structure and genetic relationship among inbred lines is essential for exploiting heterosis in maize breeding programs. This study evaluated the concordance between 25k Illumina® Infinum Maize SNP (Single Nucleotide Polymorphism) Array (25k SNP array)-derived and ribonucleic acid (RNA)-sequencing (seq)-derived markers in estimating genetic relatedness and population structure within the Maize Research Institute “Zemun Polje” (MRIZP) breeding program. A panel of 28 elite MRIZP maize inbred lines, along with two public lines, was analyzed. For the RNA-seq data, three alternative SNP datasets were generated based on heterozygous-site handling (ALL, HOM, and FINAL) to assess their impact on downstream genetic inference. These approaches had distinct effects on clustering resolution and genetic relationship structure. The FINAL dataset, in which heterozygous positions were recoded as missing values and re-filtered, was selected as the most balanced dataset for comparative analyses with 25k SNP array data. Only a limited number of overlapping SNP positions were identified between RNA-seq and 25k SNP array datasets (six in ALL, two in FINAL, and none in HOM), all located within coding regions. Despite this minimal overlap, distance-based analyses revealed partial concordance in genetic relationship patterns and population structure between platforms. Genetic distances estimated from 25k SNP array markers were consistent with pedigree records and provided more informative insights than pedigree data alone. Population structure inferred from 25k SNP array data showed high concordance with previously defined heterotic groups, correctly assigning 29 out of 30 lines (96.67%) to their expected clusters. In contrast, RNA-seq-derived SNPs showed moderate concordance with expected heterotic groupings (56.67%), indicating that transcriptome-derived markers capture part of the underlying breeding structure, but do not fully resolve heterotic group separation. Overall, these results support the 25k SNP array as a robust tool for assessing genetic relatedness and population structure in maize breeding programs, while RNA-seq-derived SNPs provide complementary but less reliable information for routine heterotic assignment.

Current Issues in Molecular Biology doi: 10.3390/cimb48060585

Authors: Kenta Hosomi Mitsuaki Ishida Kensuke Nakanishi Kohei Taniguchi Jun Arima Atsushi Tomioka Mitsuhiro Asakuma Sang-Woong Lee Ko Fujimori Yoshinobu Hirose

Acinar-to-ductal metaplasia (ADM)—a process involving the dedifferentiation or transdifferentiation of pancreatic acinar cells—is recognized as an initial event in pancreatic tumorigenesis. Studies in mouse models have revealed that tuft cells, which are chemosensory epithelial cells, appear in ADM following tissue injury, and tuft cell-produced prostaglandin (PG) D2 may suppress inflammation and tumorigenesis. However, the presence and role of tuft cells in the human pancreas remain unclear. Therefore, in this study, we investigated the presence of tuft cells and PGD2 production in human ADM. We analyzed ADM lesions from consecutive patients undergoing surgical resection for pancreatic tumors using dual immunohistochemical staining for POU domain class 2 transcription factor 3 (POU2F3) and hematopoietic PGD synthase (H-PGDS). All 29 patients (13 men and 16 women) with diagnoses including pancreatic ductal adenocarcinoma and intraductal papillary mucinous neoplasms exhibited ADM in regions of obstructive pancreatitis. Immunohistochemical analysis showed that 67.3% of ADM lesions contained POU2F3- and/or H-PGDS-positive cells. Among these, 85.5% of POU2F3-positive cells co-expressed H-PGDS, and 76.2% of H-PGDS-positive cells were POU2F3-positive. These findings indicate that tuft cells present in human ADM produce PGD2, suggesting a role in tissue repair. Tuft cells may represent a potential therapeutic target in pancreatitis, warranting further investigation into their functional role in ADM.

Current Issues in Molecular Biology doi: 10.3390/cimb48060583

Authors: Shifang Zhang Guo Hu Yuan Guo Xudong Chang Haijun Li Yingzhu Liu

The brown frog (Rana dybowskii) is an important cold-temperate amphibian species in northeastern China, with considerable ecological and resource value. Because its survival, metabolism, and reproduction are highly sensitive to environmental temperature, elucidating the molecular mechanism’s underlying temperature response is of great significance for understanding environmental adaptation and reproductive regulation in amphibians. In this study, R. dybowskii was used as the experimental model, and a multi-tissue transcriptomic analysis was conducted on the brain, liver, spleen, ovary, oviduct, and testis from both females and males under 2 °C and 12 °C conditions to characterize tissue- and sex-specific responses to temperature variation. The results showed that the global transcriptomic landscape of R. dybowskii was primarily driven by tissue type, whereas temperature effects were mainly manifested within individual tissues. The liver, brain, and spleen exhibited pronounced temperature responsiveness in both sexes, with the liver mainly showing metabolic reprogramming-related functional changes. Intersection analysis further revealed that temperature-responsive genes included not only conserved modules shared across tissues but also a large number of tissue-specific genes. Reproductive tissues displayed more pronounced functional divergence: the ovary showed relatively limited transcriptional changes and remained comparatively stable; the oviduct underwent marked transcriptional remodeling, with upregulated genes mainly involved in glycosylation and macromolecule processing, whereas downregulated genes were primarily associated with ribosomes, translation, and RNA splicing; the testis was likewise highly sensitive to temperature changes, with upregulated genes mainly enriched in amino acid metabolism, mitochondrial function, and DNA repair, while downregulated genes were mainly related to cellular structure and intercellular junctions. Collectively, these findings indicate that the molecular adaptation of R. dybowskii to temperature variation is characterized by strong tissue specificity and sex-biased responses in reproductive tissues. This study provides a transcriptomic basis for elucidating the molecular responses to short-term temperature variation is important for understanding environmental sensitivity and reproductive regulation in amphibians.

Current Issues in Molecular Biology doi: 10.3390/cimb48060584

Authors: Caiyun Sun Shi Tang Binlong Chen Mo-Zi-Li Adu

Fingered citron volatile oil is a volatile oil with a fresh and slightly floral aroma, extracted from fresh fingered citron. It is one of the natural perfume essential oils. At present, scholars at home and abroad mainly focus their research on fingered citron volatile oil on optimizing extraction processes, component analysis, pharmacological effects, and other aspects. With the continuous development and application of fingered citron volatile oil and related products, the research scope of fingered citron volatile oil is becoming increasingly extensive. As a narrative review, this paper summarizes and compares eight distinct extraction techniques for fingered citron volatile oil and clarifies the merits and drawbacks of each method. Steam distillation is one of the most employed approaches for volatile oil extraction in laboratory settings, whereas mechanical pressing is extensively applied and serves as the dominant and preferred industrial process for fingered citron volatile oil production. This paper also reviews its potential biological activities, including antidepressant, anti-anxiety, and sleep-improving effects, as well as the development and application of related products. Fingered citron volatile oil has been applied in products such as cigarettes and insecticides. Studying the chemical components of fingered citron volatile oil can not only help research its medicinal mechanisms but also promote the development of natural spices, providing a useful reference for the further utilization of fingered citron volatile oil in the future.

Current Issues in Molecular Biology doi: 10.3390/cimb48060582

Authors: Yanni Cao Xiaohui Li Jiangshan Liu Junyuan Zhang Kangcheng Xu Hao Lin Yuxian Liu

Background: Breast cancer (BRCA) is a common malignant tumor that seriously threatens women’s health. Studies have shown that histone modifications (HMs) play a vital role in the occurrence and development of BRCA. This study aims to explore the distribution patterns of HMs in the mammary epithelial cell line (HMEC) and breast cancer cell line (MCF-7), and their potential associations with gene expression, patient prognosis, and drug efficacy. Methods: First, the distribution of histone modification (HM) signals in HMEC and MCF-7 cell lines was analyzed. Multiple algorithms were then used to predict the effects of different HMs and their modified regions on gene expression in the two cell lines. Based on four key regions identified from this analysis, 268 HM-related immune-related genes (H_IRGs) were screened, followed by functional enrichment and pathway analysis. Subsequently, Cox and LASSO regression analyses were performed on the H_IRGs to construct a risk scoring model. Results: The random forest algorithm showed the best predictive performance (AUC = 0.92) and identified three key HMs (H3K4me2, H3K27me3, and H3K36me3) and four key regions that strongly influenced gene expression. A risk scoring model was constructed from 11 key IRGs (BCL2A1, PSME2, STC2, ESRRG, CRISP3, IL13RA1, LCN1, EED, CLEC10A, SLURP1, and FGF12). This model effectively predicted patients’ survival in both the training and validation cohorts. Conclusions: In summary, our research results provide a theoretical basis for the occurrence and development of BRCA, and the 11 key IRGs discovered are expected to become potential biomarkers for BRCA prognostic assessment and treatment response prediction.

Current Issues in Molecular Biology doi: 10.3390/cimb48060581

Authors: Dragana Zaklan Nikola Martić Bojana Andrejić Višnjić Milana Bosanac Snežana Hadžistević Aleksandar Rašković Nebojša Pavlović

Carnosine is widely recognized for its antioxidant and cytoprotective properties and is being increasingly used in dietary supplements. However, its effects in drug-induced liver injury remain insufficiently studied. This study aimed to investigate and compare the hepatoprotective and antioxidative effects of pure carnosine and an antioxidant-enriched commercial carnosine supplement in a murine model of paracetamol-induced hepatotoxicity. Adult male Swiss Webster mice were pretreated orally for seven days with carnosine or a commercial carnosine supplement prior to a single hepatotoxic dose of paracetamol. The serum biochemical parameters, hepatic oxidative stress markers, histopathology, and immunohistochemical expression of CYP2E1, COX-2, and Iba1 were evaluated 24 h after paracetamol administration. Paracetamol increased serum aminotransferases, lipid peroxidation, CYP2E1 expression, and histological liver injury. Pure carnosine pretreatment tended to exacerbate biochemical liver injury, whereas the commercial supplement attenuated lipid peroxidation, preserved bilirubin levels, and reduced histological damage. Both formulations decreased CYP2E1 expression and were associated with less necrosis and COX-2 immunoreactivity compared with paracetamol alone. Antioxidant enzyme activities and macrophage markers showed no consistent intergroup differences. These findings indicate that carnosine may not consistently exert hepatoprotective effects in acute drug-induced liver injury and that accompanying antioxidants may critically modify its biological actions.

Current Issues in Molecular Biology doi: 10.3390/cimb48060579

Authors: Marcos Antônio Denk Isabella Cristina Mendes Rossa Luize Kremer Gamba Anna Clara Faidiga Silva Julia Letícia de Bortolo Paulo Cesar Lock Silveira Camila da Costa Júlio Cesar Francisco Luiz César Guarita-Souza

Background/Objectives: Acute myocardial infarction (AMI) remains a major cause of global morbidity and mortality and is a leading factor in the development of heart failure. This study investigated the regenerative potential of decellularized human amniotic membrane (HAM) and Wharton’s jelly (WJ) in a rat model of left ventricular dysfunction induced by acute myocardial infarction (AMI). Methods: Twenty-three rats underwent left anterior descending coronary artery ligation and were randomized into three groups: control (saline), WJ (decellularized WJ), and HAM (decellularized HAM). Results: After 30 days, echocardiographic, histopathological, and immunohistochemical assessments were performed. No significant differences in ventricular function were observed among groups. However, the HAM-treated group showed a significant reduction in myocardial fibrosis compared with the control (p = 0.009), suggesting attenuation of post-infarction remodeling. Despite the absence of measurable functional recovery, HAM demonstrated potential to promote more favorable tissue organization. Study limitations include the lack of a sham-operated group, short follow-up period, and absence of quantitative decellularization validation. Conclusions: Overall, the results indicate that decellularized HAM may act as a structural modulator of myocardial remodeling, warranting further studies with longer follow-up and combination approaches, such as cell-based or growth factor-enhanced therapies.

Current Issues in Molecular Biology doi: 10.3390/cimb48060578

Authors: Bingpeng Yang Yanhui Wang Yufei Teng Yan Liu Xinjun Fan Qianrui Yang Na Li Binwen Shi Wanchao Zhu Shutu Xu Wenqian Mei Jiquan Xue

Plant height is a fundamental quantitative phenotypic trait affecting maize (Zea mays) planting density and is an important focus in the breeding of varieties suitable for mechanical harvesting. In this study, we found a natural extreme dwarf mutant designated as d25, whose dwarf phenotype is controlled by a single recessive gene. The phenotype was restored by spraying with gibberellic acid 3 (GA3), which indicated that the mutant phenotype of the d25 mutant resulted from mutations in genes involved in the gibberellin (GA) metabolic pathway. Additionally, performing bulked segregant analysis on 30 extreme phenotypic plants in the F2 population (d25 × P002), we located one major quantitative trait locus (QTL) at chromosome 3 from 9.3 to 11 Mb. In combination with transcriptome sequencing analysis of d25 and WT plants, we identified the cloned typical plant height-related gene D1, whose expression was significantly higher in d25 mutant plants than that in WT plants. Further analysis revealed that a 275 bp structural variant spanning exonic and intronic regions of the D1 gene accounted for the dwarf phenotype in the d25 mutant. Protein prediction revealed that this variant site alters the translated protein sequence of this region, thereby modifying its function and impairing the critical pathway responsible for hormone synthesis, resulting in reduced plant height. These findings indicate that the d25 mutant may be a novel mutant allele of the D1 gene affecting maize plant development.

Current Issues in Molecular Biology doi: 10.3390/cimb48060580

Authors: Xiao Han Xiaojie Zhang Rui Wang Lili Gu Wenxian Yang Yiqiang Ren Zhenwei Ren

The PIN-LIKES (PILS) gene family is crucial for regulating auxin homeostasis and stress adaptation in plants; nevertheless, a comprehensive study on this family in alfalfa (Medicago sativa) remains insufficient. This research found 46 MsPILS genes within the tetraploid alfalfa genome and categorized them into four subfamilies. The genes are irregularly allocated throughout 16 chromosomes, with tandem duplications acting as a primary catalyst for family expansion. Analysis indicated that all MsPILS proteins contain the conserved Mem_trans domain. The promoter study revealed that MsPILS genes had many cis-elements that respond to abiotic stressors and hormones. qRT-PCR research indicated that MsPILS genes exhibit variable expression across several tissues and respond to multiple abiotic stressors. Protein–protein interaction (PPI) research revealed PIN3, PIN5, and PIN6 as principal interacting partners of the MsPILS proteins. Subcellular localization studies indicated that MsPILS1c is in the nucleus, plasma membrane, and endoplasmic reticulum (ER). This research offers significant genetic resources and a theoretical framework for elucidating the activities of PILS genes and for molecular breeding aimed at improving stress tolerance in alfalfa.

Current Issues in Molecular Biology doi: 10.3390/cimb48060577

Authors: Jesús Alonso Gándara-Mireles Elio Aarón Reyes Espinoza Verónica Loera-Castañeda Lourdes Patricia Córdova Hurtado Antonio Emilio González Font Julio Cesar Grijalva Ávila Ignacio Villanueva Fierro Ismael Lares-Asseff Cynthia Mora Muñoz Gabriela Velasco Villa Hugo Payán Gándara Leslie Patrón-Romero Horacio Almanza-Reyes

Doxorubicin (Dox) is a cornerstone in the treatment of pediatric acute lymphoblastic leukemia (ALL), but its use is limited by dose-dependent cardiotoxicity. Oxidative stress, arising from mitochondrial dysfunction, enzymatic generation of reactive oxygen species, and cardiotoxic metabolites, has been implicated as a central mechanism, with interindividual variability partly influenced by genetic factors. This study evaluated oxidative DNA damage 8-hydroxy-2′-deoxyguanosine (8-OHdG) as an integrative marker of redox-related pathways in Dox-induced cardiotoxicity. In a prospective case–control study, 93 pediatric patients with ALL treated with Dox and 63 controls were included. Cardiotoxicity was assessed by serial echocardiography, and 8-OHdG levels were measured by ELISA. Genotyping of ABCC1 rs3743527, NCF4 rs1883112, and CBR3 rs1056892 was performed, and multivariable analyses were conducted. Dox-treated patients showed higher 8-OHdG levels than controls, and patients with cardiotoxicity (n = 11) had higher levels than those without. A higher frequency and severity of cardiotoxicity was observed in female patients, although this finding should be interpreted cautiously. Although allele frequencies did not reach statistical significance, distinct distribution patterns were observed between groups. These findings suggest that 8-OHdG may function as an integrative marker of redox dysfunction associated with Dox-induced cardiotoxicity.

Current Issues in Molecular Biology doi: 10.3390/cimb48060576

Authors: Bilian Hu Yuting Dai Can Cheng Jihua Zhou Fuan Niu Bin Sun Anpeng Zhang Liming Cao Huangwei Chu

Boro II (BT), the first cytoplasmic male sterility (CMS) system in rice, is widely used in three-line japonica hybrid rice production. Accurate detection of maintainer-seed contamination in BT-type CMS seed lots is critical for ensuring genetic purity and hybrid seed quality. In this study, we developed a SYBR Green-based quantitative real-time PCR (qPCR) assay for the detection and quantification of maintainer-seed contamination in BT-type CMS seed lots. Maintainer-specific primers targeting a mitochondrial sequence unique to the maintainer line, together with an endogenous reference targeting a conserved mitochondrial sequence present in both maintainer and CMS lines, were validated for specificity. A standard curve was constructed using defined CMS–maintainer seed mixtures (0.1–5% contamination), and ΔCt values were converted to relative abundance (2−ΔCt). The assay exhibited high specificity, reproducibility, and sensitivity, with a strong linear relationship between 2−ΔCt values and actual contamination levels (R2 > 0.99). Performance testing using simulated contamination samples (0.2–3.13%) demonstrated accurate quantification with acceptable recovery rates. This method provides a rapid, robust, and reliable tool for routine genetic purity testing and quality control in BT-type CMS hybrid rice seed production.

Current Issues in Molecular Biology doi: 10.3390/cimb48060575

Authors: Eirini Ilia Dimitrios Papoutsis Vasiliki Michou Aikaterini Itziou

Background: Long-term exposure to ambient air pollution during pregnancy has been strongly associated with oxidative-stress-mediated adverse maternal and fetal outcomes. Aim: The present study aimed to evaluate systemic oxidative stress and antioxidant capacity in pregnant women residing in a highly polluted area (Kozani) compared with a less polluted region (Grevena) in Western Macedonia, Greece. Methods: Oxidative stress was assessed using derivatives of reactive oxygen metabolites (d-ROMs), while antioxidant capacity was evaluated through biological antioxidant potential (BAP). Results: The findings of the study demonstrated that pregnant women in the polluted area exhibited elevated d-ROMs levels and significantly reduced BAP levels compared with controls. Although unadjusted oxidative stress differences were not statistically significant, adjusted analyses revealed significantly higher oxidative stress in the exposed group. These results suggest that air pollution exposure is associated with systemic redox homeostasis, primarily through depletion of antioxidant defenses. Conclusions: This study provides novel biomonitoring evidence linking environmental exposure to redox imbalance during pregnancy. As Western Macedonia transitions to a post-lignite era, the decrease in air pollution is anticipated to lead to significant improvements in public health, while these findings establish an important baseline for evaluating the effectiveness of environmental and public health interventions.

Current Issues in Molecular Biology doi: 10.3390/cimb48060574

Authors: Nada Tawfig Hashim Rasha Babiker Muhammed Mustahsen Rahman Riham Mohammed Vivek Padmanabhan Md Sofiqul Islam Nallan C. S. K. Chaitanya Bakri Gobara Shadi El Bahra

Periodontal disease is a chronic inflammatory condition driven by polymicrobial biofilms whose interaction with the host immune response drives the destruction of tooth-supporting tissues. Within these communities, bacterial cell–cell communication—particularly quorum sensing (QS)—coordinates virulence factor expression, biofilm maturation, and interspecies behaviour, allowing pathogens to mount population-dependent attacks on the host. Disrupting these signals has therefore drawn growing attention as an anti-virulence strategy for biofilm-associated oral infection. Quorum quenching (QQ)—the inhibition or disruption of QS pathways—prevents bacteria from coordinating these virulence-related activities. The candidate inhibitors investigated to date fall into three broad classes: conventional antibiotics used at sub-inhibitory concentrations, plant-derived natural compounds, and synthetic molecules designed to interfere with signal synthesis, signal reception, or signal transduction. In experimental work on periodontal pathogens, agents from each class reduce biofilm formation, suppress virulence factor production, and disrupt microbial communication within polymicrobial biofilms. Clinical translation, however, lags behind the laboratory evidence. Most data still come from in vitro systems and animal models, and the ecological complexity of the oral biofilm makes therapeutic targeting difficult: signals that drive virulence in pathogens also support cooperation among commensals. Toxicity profiles, pharmacokinetics, and well-powered clinical trials are needed before quorum-quenching agents can be considered for routine periodontal care. Even with these caveats, targeting bacterial communication offers a different therapeutic logic from conventional antimicrobials: attenuating virulence rather than killing cells, and so exerting weaker selective pressure for resistance. Further dissection of QS networks in oral biofilms—and the rational design of quenching agents that act on pathogenic rather than commensal signalling—may yield useful adjuncts to current periodontal therapy.

Current Issues in Molecular Biology doi: 10.3390/cimb48060573

Authors: Gian Carlos Nascimento Melina Laura Moretti Pinheiro Brenda Veridiane Dias Raphael Ocelli Pinheiro Maria Aparecida Vasconcelos Paiva Brito Afonso Henrique de Oliveira Júnior Lara Louzada Aguiar Rodinei Augusti Julio Onesio-Ferreira Melo Rafael Bastos Teixeira Ana Cardoso Clemente Filha Ferreira de Paula

Medicinal plants have attracted increasing scientific interest due to the diversity of bioactive compounds reported across different species. They may represent complementary sources of bioactive compounds alongside conventional antimicrobials, which may pose risks to animal health and compromise treatment efficacy. Considering the importance of alternative compounds, we aimed to evaluate the antimicrobial activity in vitro of medicinal plants Stryphnodendron adstringens (Mart.) Coville, known as barbatimão, Baccharis crispa Spreng, known as carqueja and Azadirachta indica, known as neem. S. adstringens (Mart.) Coville and B. crispa Spreng were used as extract and obtained from plants collected in the municipality of Bambuí, state of Minas Gerais, Brazil. A. indica was evaluated as extract and oil, and the crushed leaves and oil were purchased from a commercial company. Antimicrobial activity was determined by the minimum bactericidal concentration (MBC) test-against Staphylococcus aureus, Streptococcus agalactiae, Streptococcus uberis, Escherichia coli, and Salmonella spp., isolated from bovine mastitis. The bacteria were submitted to the MBC test at concentrations of 100, 50, 25, 12.5, 6.25, 3.12, 1.56, 0.78, 0.39, 0.19 and 0.09 mg/mL. The bacteria evaluated were sensitive to most plant extracts for at least one of the concentrations evaluated, except for Gram-negative bacteria, Escherichia coli, and Salmonella spp. There was no activity of B. crispa Spreng extract and A. indica against E. coli and neither of B. crispa Spreng extract against Salmonella spp. even at the highest concentration evaluated. S. adstringens (Mart.) Coville was considered the extract with the highest activity against the bacteria evaluated and S. uberis the most susceptible to antimicrobial action. The results indicate detectable antimicrobial activity of the evaluated extracts and oil, suggesting their potential relevance as complementary sources of bioactive compounds for further investigation, rather than as direct alternatives to conventional antibiotic therapies. Paper spray mass spectrometry (PS-MS) was employed as an exploratory phytochemical screening approach, and all metabolite assignments reported herein should be regarded as tentative or putative annotations under the analytical conditions used, consistent with MSI Level 3 confidence.

Current Issues in Molecular Biology doi: 10.3390/cimb48060572

Authors: Mark Okot Aneesa Ahmed Colin W. Wright Md Talat Nasim

Pulmonary arterial hypertension (PAH) is a progressive, fatal disease of the pulmonary vasculature characterized by obliterative remodeling of small pulmonary arteries, leading to sustained elevation of pulmonary vascular resistance, right ventricular failure, and premature death. The diagnostic gold standard remains right heart catheterization, requiring a mean pulmonary artery pressure greater than 20 mmHg at rest, a pulmonary arterial wedge pressure of 15 mmHg or below, and a pulmonary vascular resistance exceeding 2 Wood units. PAH is an autosomal dominant disorder with markedly incomplete penetrance of approximately 20–30%, indicating that germline mutations alone are insufficient to cause disease. Disease manifestation requires additional “second hits”, including chronic hypoxia, systemic inflammation, hemodynamic stress, hormonal influences, and common genetic modifiers such as single-nucleotide polymorphisms (SNPs). This genetic and environmental complexity underpins the broad clinical heterogeneity observed across PAH subtypes, which include idiopathic PAH, heritable PAH, and disease associated with connective tissue disorders, HIV infection, portal hypertension, congenital heart disease, schistosomiasis, and drug or toxin exposure. This review provides a comprehensive and critical appraisal of the molecular-genetic architecture of PAH. Thirty genes have now been implicated in disease pathogenesis, spanning seven functional categories: receptors of the TGF-β/BMP signaling family (BMPR2, ACVRL1, ENG, BMPR1B); circulating BMP ligands (GDF2, BMP10); transcription factors (TBX4, SOX17, KLF4, FOXF1, SMAD1, SMAD4, SMAD9); membrane and polyamine transporters (ATP13A3, AQP1); potassium channel regulators (KCNA5, KCNK3, ABCC8); metabolic and mitochondrial genes (EIF2AK4, NFU1, GGCX); signaling receptors and structural proteins (NOTCH3, KDR, CAV1, PLEKHH2); vasoactive and extracellular matrix regulators (KLK1, CBLN2, CD248); and epigenetic regulators (TET2, TOPBP1). Among these, BMPR2 is the dominant contributor, accounting for 53–86% of heritable PAH and 14–35% of idiopathic cases. The remaining genes each account for fewer than 5% of cases individually, collectively reflecting a broad landscape of rare and ultra-rare genetic contributions. For each gene, we critically evaluate the strength of genetic evidence, pathogenic mechanisms, degree of mechanistic resolution, and clinical relevance. We further discuss the contribution of emerging technologies, including whole-genome sequencing, single-cell and spatial transcriptomics, multi-omics integration, iPSC-derived vascular models, and artificial intelligence, to expanding the PAH genetic architecture beyond single-gene discovery. A key theme across this landscape is convergence: despite mechanistic diversity at the gene level, most PAH-associated variants ultimately impair endothelial quiescence, promote smooth muscle proliferation, and drive apoptosis resistance through disruption of BMP signaling amplitude, transcriptional stability, ion channel homeostasis, metabolic integrity, or epigenetic regulation. This convergence supports both a unified therapeutic rationale and a precision medicine framework for genotype-stratified intervention in PAH.

Current Issues in Molecular Biology doi: 10.3390/cimb48060570

Authors: Changli Yang Qi Jia Yongxia Zhao Lin Qin Daopeng Tan Yuqi He

Dendrobium nobile Lindl. is a valuable medicinal orchid in traditional Chinese medicine. It abounds in alkaloids with extensive pharmacological properties, holding promising prospects for pharmaceutical development. In this review, the relevant literature was systematically retrieved from PubMed, Web of Science and CNKI using the keywords Dendrobium nobile Lindl., alkaloids, dendrobine, pharmacological activities and biosynthetic pathways. We comprehensively summarize the chemical composition, pharmacological effects, biosynthetic routes, clinical application potential and research prospects of alkaloids derived from D. nobile. The main alkaloid components including dendrobine, dendramine and nobilonine are classified into dendrobine, dendroxine and nobiline structural types. This paper further elaborates the anti-inflammatory, antioxidant and neuroprotective effects of these alkaloids, as well as their regulatory mechanisms on apoptosis-associated proteins and signaling cascades. Key enzymes and regulatory genes participating in the mevalonate pathway-mediated biosynthesis of sesquiterpenoid alkaloids are also discussed. Collectively, this review provides a theoretical basis and reference for subsequent basic research and therapeutic development of D. nobile alkaloids.

Current Issues in Molecular Biology doi: 10.3390/cimb48060571

Authors: Andria Kotsoni Evelina Ioannou Evangelia Barmparousi Lefteris C. Zacharia

β2-adrenergic receptor (β2-AR) agonists have been implicated in neuroprotection, yet their mechanisms remain obscure. We examined whether salbutamol (SA, short-acting) or formoterol (FO, long-acting) protect PC-12 cells from okadaic acid (OA), and evaluated receptor dependence, antioxidant capacity, and apoptotic signaling. Viability was quantified with crystal violet and MTT assays. OA reduced viability to approximately 60%, and SA or FO (0.1–10 µM) improved survival, which reached 76–83% at 10 µM (p < 0.05). β2-AR blockage with ICI-118,551, and ADRB2 mRNA knockdown did not abolish protection by FO or SA, suggesting a possible β2-AR-independent protective component. However, as knockdown was not confirmed at the protein level and signaling was not directly assessed, the evidence remains provisional. FO, but not SA, exhibited direct antioxidant activity in the DPPH assay, but both at 50 μΜ lowered H2O2-induced intracellular reactive oxygen species (from 167.9% to baseline, p < 0.05). Both compounds reduced the OA-induced expression of selected pro-apoptotic transcripts, although these mRNA data do not establish the functional inhibition of apoptosis. FO reduced fold change relative to untreated control from 5.8 to 2.6 for Bax, and 6.4 to 3.4 for Bak, whereas SA achieved a significant reduction only for Bax, from 5.8 to 4.4. Taken together, SA and FO offer a partial protection to PC-12 cells from OA cytotoxicity through pathways suggesting a β2-AR-independent protective component, with FO showing additional antioxidant properties and a reduced expression of selected pro-apoptotic transcripts. These findings provide preliminary evidence that select β2 agonists may exert cytoprotective effects that are consistent with, but do not establish, a receptor-independent component. These findings warrant further protein-level and functional validation.

Current Issues in Molecular Biology doi: 10.3390/cimb48060569

Authors: Zhijun Fan Yi Li Shuting Geng Yu Si Yuerong Yang Huali Yu Xue Hu Jianhai Jiang

N-acetylneuraminate pyruvate lyase (NPL) is a key enzyme in sialic acid catabolism that links sialylation to cellular metabolism, but its role in cancer cell metabolic adaptation is poorly defined. In particular, it remains unclear whether NPL contributes to ATP maintenance in hepatocellular carcinoma (HCC) under nutrient stress through its role in sialic acid catabolism. HCC is a highly lethal malignancy characterized by extensive metabolic reprogramming. Here, we investigated whether NPL links sialic acid catabolism to ATP maintenance in HCC cells under glucose deprivation. Glucose deprivation induced NPL expression in Huh7 and PLC/PRF/5 cells, which is consistent with an adaptive response to energetic stress. Stable NPL knockdown reduced intracellular ATP levels. Consistently, cell growth was significantly reduced, as assessed by Cell Counting Kit-8 (CCK-8) and colony formation assays. These effects were more pronounced in the absence of glucose. Exogenous pyruvate partially restored ATP levels and the growth inhibition caused by NPL knockdown, particularly in the absence of glucose. This rescue further suggests that NPL may support ATP maintenance under glucose deprivation partly through pyruvate metabolism. Together, these findings indicate that NPL contributes to maintaining intracellular ATP levels during glucose deprivation, thereby supporting HCC cell adaptation to metabolic stress. To extend these biological findings to potential therapeutic exploration, we performed virtual screening and molecular docking using a U.S. Food and Drug Administration (FDA)-approved drug library. Candidate compounds predicted to bind NPL were identified, providing a basis for further validation and optimization.

Current Issues in Molecular Biology doi: 10.3390/cimb48060568

Authors: Ya Zhu Xiaochun Zhang Chao Jin Heying Jin

Inflammatory bowel disease (IBD) is associated with skeletal muscle loss and mitochondrial dysfunction, which may compromise therapeutic responsiveness. We investigated whether progressive resistance training could improve muscle oxidative phosphorylation gene expression and enhance the efficacy of anti-TNF-α therapy (infliximab) in a dextran sulfate sodium (DSS)-induced colitis mouse model. Male C57BL/6 mice with subacute DSS-induced colitis were assigned to control, DSS, DSS + resistance training, DSS + anti-TNF-α, and DSS + resistance training + anti-TNF-α groups (n = 6 each). Resistance training consisted of 8 weeks of progressive ladder climbing; anti-TNF-α was administered at weeks 0, 2, and 6. Outcomes included body weight, disease activity, muscle function, histology, serum cytokines, muscle transcriptomics, and qPCR. DSS caused weight loss, functional decline, elevated proinflammatory cytokines, suppressed mitochondrial gene expression, and muscle inflammation. Resistance training or anti-TNF-α alone partially restored performance and mitochondrial gene expression while reducing inflammation. Their combination yielded superior effects (p < 0.01), normalizing histology. These findings suggest that resistance training may improve muscle metabolic status and attenuate systemic inflammation, thereby contributing to enhanced anti-TNF-α therapy outcomes in this preclinical model. Further studies are warranted to elucidate the underlying mechanisms and evaluate the translational potential.

Current Issues in Molecular Biology doi: 10.3390/cimb48060567

Authors: Claudia Moriello Nicola Alessio Rosario Finamore Chiara De Rosa Chiara Schiraldi Caterina Manna Stefania D’Angelo Pasquale Perrone

Oxidative stress plays a central role in the development of cardiovascular diseases (CVDs) and is strongly influenced by environmental toxicants such as heavy metals. Mercury (Hg) is a well-known pro-oxidant agent capable of disrupting cellular redox homeostasis, promoting reactive oxygen species (ROS) generation, and inducing structural and functional alterations in circulating blood cells. In particular, erythrocytes (RBC) are highly susceptible to oxidative damage due to their continuous exposure to oxygen and limited antioxidant repair mechanisms. In this study, we investigated the protective effects of polyphenolic extracts obtained from two tomato (Solanum lycopersicum) cultivars, Piccadilly and Piennolo, against HgCl2-induced oxidative stress in human RBC. Chemical characterization revealed that Piennolo extracts contained higher levels of total polyphenols, flavonoids, and ortho-diphenols compared with Piccadilly samples. Despite these differences, both extracts showed comparable antioxidant capacity. In RBC exposed to HgCl2, tomato extracts significantly reduced ROS production, lipid peroxidation (TBARS), methemoglobin formation, and sulfhydryl depletion, while restoring intracellular glutathione levels. Importantly, pretreatment with the extracts markedly decreased phosphatidylserine externalization, indicating preservation of membrane phospholipid asymmetry and a reduction in the procoagulant phenotype induced by oxidative stress. Overall, these findings suggest that bioactive compounds present in polyphenol-rich tomato extracts exert protective effects on RBC through antioxidant and membrane-stabilizing mechanisms.

Current Issues in Molecular Biology doi: 10.3390/cimb48060566

Authors: Camille Jacques Flora Marchand Mathias Chatelais Elías Hurtado-Gaitán Joana M. Buades Ilaria Floris

The micro-immunotherapy medicine (MIM) 2LEID-N® was developed to sustain immune response, notably in the framework of respiratory infections. This pilot study investigated the potential effects of one capsule of this MIM, referred to as 2LEID-N-9 throughout the manuscript, containing IL-12 (5 CH), IFN-γ (6 CH), and TNF-α (5 CH). Phagocytosis and surface marker expression were assessed using flow cytometry, and cytokine secretion was assessed by ELISA. Cellular models included human monocyte-derived macrophages, peripheral blood mononuclear cells (PBMCs) from healthy donors, and THP-1 cells. Liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS/MS) was used to detect the actives. Compared with vehicle control, 2LEID-N-9 showed a trend towards the enhanced phagocytic activity of macrophages. In PBMCs, 2LEID-N-9 upregulated the secretion of several cytokines, including IL-2, IL-4, IL-13, IFN-γ, and TNF-α in both basal and CD3/CD28-stimulated conditions. Notably, a tendency towards increased secretion of TNF-α was found in LPS-stimulated THP-1 cells. The presence of the three actives, as assessed by LC-HRMS/MS, combined with the functional data, provide promising exploratory evidence of immunomodulatory effects and tendencies towards the stimulation of innate and adaptive immune cells, warranting further investigation.

Current Issues in Molecular Biology doi: 10.3390/cimb48060565

Authors: Ahmet Ali Berber Cansu Akbulut Esra Yıldız Sinem Öztürk Şefika Nur Demir Nurcan Berber

This study evaluates the cytotoxic and genotoxic-like potential of an ipfencarbazone-based herbicide formulation (IPF-BH; commercial product Hokuto, containing 250 g/L of the triazolinone herbicide ipfencarbazone) in human peripheral lymphocytes in vitro across a concentration range of 62.5–1000 µg/mL. Cytotoxicity was monitored via the mitotic index (MI), while cytogenetic damage was assessed using the cytokinesis-block micronucleus (MN) assay and the alkaline comet assays. Comparisons were performed using one-way ANOVA, followed by Dunnett’s post hoc test, against the negative control. Results indicated a concentration-dependent cytotoxic effect, with a marked reduction in MI observed at all tested concentrations (p < 0.001). MN frequency was significantly elevated at concentrations ≥125 µg/mL, whereas the 62.5 µg/mL concentration did not induce significant micronuclei formation. The comet assay revealed increased DNA damage parameters (tail length, tail intensity (%), and tail moment) across the tested concentration range, albeit with a non-monotonic profile for tail length and tail intensity. These findings suggest that IPF-BH exposure is associated with marked cytotoxicity and a genotoxic response in this in vitro model at concentrations within the OECD 487-acceptable cytotoxicity window, together with cytotoxicity-associated genotoxic-like effects at strongly cytotoxic concentrations in human peripheral lymphocytes under in vitro conditions. Because IPF-BH is a commercial formulation, and no direct mechanistic endpoints (e.g., reactive oxygen species, mitochondrial transmembrane potential, lipid peroxidation, glutathione) were measured, and because the present design was performed without exogenous metabolic activation (no S9 supplementation), the observed effects cannot be unambiguously attributed to ipfencarbazone alone or to a defined mechanism of action; extrapolation to in vivo genotoxicity requires complementary +S9 and rodent in vivo follow-up studies.

Current Issues in Molecular Biology doi: 10.3390/cimb48060564

Authors: Luyao Qi Jiale Feng Xinyi Tan Meng Yang Lilian Ji Weicheng Hu

Sebacic acid (SA), a ten-carbon medium-chain dicarboxylic acid, has emerged as a multifunctional bioactive metabolite with potential applications in metabolic regulation and regenerative medicine. Evidence indicates that SA exerts anti-inflammatory effects by modulating nuclear factor kappa B (NF-kB), mitogen-activated protein kinase (MAPK), and signal transducer and activator of transcription (STAT) pathways, improves glucose homeostasis by enhancing mitochondrial function and suppressing hepatic gluconeogenesis, and contributes to lipid metabolism via peroxisomal and mitochondrial β-oxidation. Beyond metabolic regulation, SA promotes bone repair by stimulating osteoblast differentiation and inhibiting osteoclast activity, and supports muscle regeneration by enhancing energy supply, cell proliferation, and the microenvironment. SA also serves as a monomer for poly (glycerol sebacate) (PGS), enabling its use in biodegradable tissue engineering scaffolds. This review synthesizes current experimental and preclinical findings on the biological functions of SA, elucidates the underlying molecular mechanisms, and highlights its translational potential for the treatment of metabolic disorders and tissue regeneration.

Current Issues in Molecular Biology doi: 10.3390/cimb48060563

Authors: Yu Liu Hao Liang Xiaxiang Zhang Qiang Zhang Nanqing Liu

The fructose 1,6-bisphosphate aldolase (FBA) gene family plays crucial roles in plant energy metabolism, growth, development, and abiotic stress responses, as it modulates antioxidant synthesis and soluble sugar accumulation to enhance plant cadmium tolerance. Seashore paspalum (Paspalum vaginatum Sw.), a halophytic perennial C4 turfgrass renowned for its exceptional cadmium tolerance, is ideal for phytoremediation of cadmium-contaminated soil. FBA family genes have been identified in several grass species, such as maize, rice, and wheat, but systematic investigations into FBA family genes and their functions in seashore paspalum remain scarce. In this study, seven class I FBAs (named as PvFBA1–PvFBA7) and one class II FBA (named as PvFBA8) in seashore paspalum were identified. The physicochemical properties, evolutionary relationships, gene structures, conserved domains, protein structures, cis-acting regulatory elements, chromosomal localizations, and collinearity relationships of eight PvFBAs were analyzed. These analyses suggested that PvFBA genes had highly conserved domains and belonged to ultra-conserved core genes. Expression pattern analysis indicated that the PvFBA gene family was dynamically responsive to cadmium stress. PvFBA6 and PvFBA7 were highly expressed in leaves, whereas PvFBA1 and PvFBA3 showed almost no expression. The RT-qPCR results suggested that the expression levels of PvFBA5 and PvFBA6 were highly consistent with the FPKM value trends analyzed in the transcriptomic data. Collectively, this study not only provides a theoretical foundation for the understanding of the evolution of the PvFBA gene family but also offers potential candidate genes for enhancing cadmium stress tolerance in plants.

Current Issues in Molecular Biology doi: 10.3390/cimb48060562

Authors: Xiaoyan He Ying Liang Chunli Wang Xinghao Li Shuangshuang Qin Linxuan Li Guili Wei Danfeng Tang Zhanjiang Zhang Fan Wei

Sophora tonkinensis Gagnep. is an important medicinal shrub native to the karst regions of southwestern China, where long-term overharvesting and habitat fragmentation have markedly reduced wild resources. Although recent phytochemical, transcriptomic, and chloroplast genomic studies have improved understanding of this species, its maternally inherited population structure has remained unclear. To address this gap, we developed nine novel chloroplast simple sequence repeat (cpSSR) markers and used them to genotype 274 individuals from eighteen wild populations. A total of 41 alleles were detected, with 2–10 alleles per locus, indicating moderate to high polymorphism at the species level. By combining the nine cpSSR loci, we further identified 25 chlorotypes, including 19 private chlorotypes. Within-population chloroplast diversity was generally low, and five populations were monomorphic, whereas HJSE and LYNG retained comparatively high chlorotype diversity. Genetic differentiation among populations was extremely strong (mean FST = 0.808), whereas historical gene flow was very limited (Nm = 0.112), and AMOVA showed that 85% of total chloroplast variation occurred among populations. Taken together, chlorotype network analysis, chlorotype geographic distribution, UPGMA, PCoA, and exploratory STRUCTURE analysis supported three geographically structured chloroplast groups, indicating long-term restriction of seed-mediated dispersal across the fragmented karst landscape. These newly developed cpSSR markers and the derived chlorotype framework provide a practical basis for tracing maternal lineages, prioritizing conservation units, guiding ex situ germplasm sampling, and informing future breeding of this nationally protected species. Overall, the present results describe chloroplast-based maternal structure rather than total genome-wide diversity in S. tonkinensis.

Current Issues in Molecular Biology doi: 10.3390/cimb48060561

Authors: Mónica Vázquez-Del Mercado Beatriz Teresita Martín-Márquez Erika Aurora Martínez-García Marcelo Heron Petri

The prostaglandin D2 receptor (PTGDR) -441 C/T polymorphism has been previously associated with inflammatory diseases such as asthma. The goal of this study was to explore the association of this polymorphism with idiopathic inflammatory myopathies (IIM) and their clinical features. Seventy-two healthy subjects (HS) and forty-eight patients with IIM from Guadalajara and Mexico were recruited over three years. Clinical features and enzymes used for diagnostics and follow-up, such as creatine phosphokinase (CPK), lactate dehydrogenase (LDH), aspartate transaminase (AST), and alanine aminotransferase (ALT), were collected at the recruitment point and from the chart at the diagnostic point. PCR-ARMS was used to define genotypes. The Chi-square test was used to compare genotype and allele frequencies and clinical features between IIM patients and healthy subjects. A one-way ANOVA on ranks was performed to compare enzymatic levels. The allele distribution was not in Hardy–Weinberg equilibrium in the controls. There was no difference in age or gender distribution between the groups. The polymorphic (T) allele was more common in the IIM group than in the HS group. At the same time, the wild-type (CC) genotype presented more clinical features, such as heliotrope rash, fever, dyspnea, and weight loss, than the TT genotype. No significant differences were found regarding the enzyme levels. To further understand the role of this polymorphism in IIM, a bigger sample size is required along with mechanistical studies. Nevertheless, the polymorphic allele of the PTGDR -441 C/T polymorphism suggests susceptibility to IIM, whereas the wild-type CC genotype is associated with more clinical features.

Current Issues in Molecular Biology doi: 10.3390/cimb48060560

Authors: Ivo Nikolaev Sirakov Kalina Shishkova Raina Gergova Stefan Dimitrov Gergov Elena Tasheva-Terzieva

Type 2 diabetes is a multifactorial metabolic disease characterized by chronic hyperglycemia, insulin resistance, and persistent low-grade inflammation. All of these factors lead to dysregulation of the immune system. Of particular interest is the interaction between immune dysregulation in type 2 diabetes and oncogenic viruses such as Human papillomavirus (HPV) and Epstein–Barr virus (EBV), which play an essential role in the etiology of Head and neck cancer on the one hand and have mechanisms for escaping the immune response on the other. The aim of the present study is to perform an analysis of patients with head and neck cancer divided into two groups, with and without diabetes, aimed at studying the relationship between type 2 diabetes and the established viral status. It was found that for all viruses proven by us, the frequency of positive tests for them was higher in the group with type 2 diabetes compared to the group of patients without diabetes. The study provides new insights and suggestions for a significant association between type 2 diabetes mellitus, increased prevalence of EBV, and some low-risk HPV genotypes in patients with head and neck tumors. Continuing from our previous study, the association between EBV and HPV44, after strict statistical adjustment, highlights their potential biological and clinical significance within the oncogenic environment in the presence of type 2 diabetes.

Current Issues in Molecular Biology doi: 10.3390/cimb48060559

Authors: Eun-Ji You Boyong Kim

Fermentation is widely used to enhance the bioactivity of herbal phytochemicals through microbial bioconversion. Rehmannia glutinosa contains catalpol, an iridoid glycoside with metabolic and immunomodulatory potential; however, its efficacy in the unfermented form is limited. This study investigated whether fermentation enhances catalpol production and improves metabolic and immune-regulating functions via glucagon-like peptide-1 receptor (GLP-1R) signaling. Rehmannia glutinosa extract was fermented under optimized conditions, and catalpol and iridoid precursor levels were quantified to assess bioconversion efficiency. Biological effects were evaluated in intestinal epithelial cells, macrophages, and an Artemia model, focusing on glucose transport, GLP-1 secretion, dipeptidyl peptidase-4 (DPP-4) expression, mucosal defense, and GLP-1R/protein kinase A/cAMP response element-binding protein (PKA/CREB) signaling. Fermentation significantly increased catalpol content while reducing iridoid precursors. The fermented extract suppressed intestinal glucose absorption by downregulating sodium–glucose cotransporter 1 (SGLT1) and glucose transporter 2 (GLUT2). It also enhanced GLP-1 secretion and reduced DPP-4 expression, leading to activation of GLP-1R/PKA/CREB signaling. This activation increased mucin 2 (MUC2) expression and promoted anti-inflammatory.

Current Issues in Molecular Biology doi: 10.3390/cimb48060558

Authors: Jirong Liu Nanyan Mao Yaru Cui Yiyao Bao Chao Tang

Multisystem inflammatory syndrome in children (MIS-C) is a severe systemic inflammatory complication triggered by prior SARS-CoV-2 infection. It predominantly affects the cardiovascular system, and coronary artery injury, myocardial dysfunction, and myocardial ischemia are closely associated with disease severity and clinical outcomes. This article reviews the immunopathological characteristics and clinical manifestations of MIS-C-related coronary artery lesions, including coronary artery dilation and aneurysm formation, as well as the key pathophysiological mechanisms leading to myocardial ischemia. Based on recent clinical and translational research, we summarize current approaches to diagnosis, risk stratification, acute medical management, and long-term follow-up strategies. By synthesizing updated evidence, this review aims to provide theoretical support and practical clinical guidance for the early identification, timely intervention, and optimized management of affected children, ultimately improving their long-term cardiovascular prognosis.

Current Issues in Molecular Biology doi: 10.3390/cimb48060557

Authors: Michail Varras Fani-Niki Varra Viktoria-Konstantina Varra Panagiotis Theodosis-Nobelos

Autoimmune diseases are characterized by chronic inflammation, immune dysregulation, and excessive oxidative stress, which collectively contribute to a progressive tissue damage and organ dysfunction. Although conventional immunosuppressive and anti-inflammatory therapies remain the main therapeutic approach, their clinical efficacy is often limited by poor pharmacokinetic properties, low tissue selectivity, systemic toxicity, and adverse effects following long-term administration. In this context, antioxidant-based nanoformulations have emerged as promising multi-target therapeutic strategies for the modulation of oxidative and inflammatory pathways involved in autoimmune disorders. This review focuses on polymeric and non-polymeric nanoformulations designed to improve the solubility, stability, bioavailability, controlled release, and targeted delivery of antioxidant and anti-inflammatory agents for autoimmune disease treatment. Recent advances in nanocarrier systems applications, including nanogels, poly(lactic-co-glycolic acid) (PLGA), polyethylene glycol (PEG), polymethacrylate, chitosan, hyaluronic acid, hydroxyapatite (HAP), lipid-based and ROS-responsive nanosystems, are discussed. The therapeutic potential of nanoencapsulated steroidal and non-steroidal anti-inflammatory drugs, antioxidant compounds, enzymes, inorganic elements, and nucleic acid-binding systems is evaluated through preclinical and limited clinical evidence. Many of these reported nanoformulations exhibit enhanced therapeutic efficacy, improved tissue targeting, reduced systemic toxicity, and the ability to simultaneously modulate oxidative stress and inflammatory signaling pathways. Despite the encouraging findings, important challenges remain regarding clinical translation, long-term safety, reproducibility, and large-scale production. In overall, antioxidant nanoformulations represent a promising and evolving platform for the development of more effective and targeted therapies against autoimmune diseases.

Current Issues in Molecular Biology doi: 10.3390/cimb48060556

Authors: Jintana Sirivarasai Sorsia Muttrarak Prapimporn Chattranukulchai Shantavasinkul Sittiruk Roytrakul Waraporn Malilas Pachara Panpunuan Piyamitr Sritara

Coffee consumption has been associated with metabolic and cardiovascular health, but the molecular mechanisms underlying these associations remain unclear. This study investigated the association between coffee intake and circulating proteomic profiles across metabolic conditions using a pooled-serum, exploratory design. Participants were classified into four groups: normal weight (NW), normal weight with coffee intake (NWC), obese with hypertension (OBHT), and obese with hypertension with coffee intake (OBHTC). Differentially expressed proteins (DEPs) were identified using volcano plot criteria (|log2FC| ≥ 1, FDR < 0.05), followed by Reactome pathway enrichment, Gene Ontology (GO) molecular function, and Enrichr-derived protein–protein interaction (PPI) analyses. Results: In NW vs. NWC, coffee intake was associated with proteins enriched in receptor-mediated signaling and phosphoinositide pathways. In OBHT vs. OBHTC, DEPs were linked to mitochondrial respiration and oxidoreductase activity. The NW vs. OBHT comparison showed downregulation of metabolic and signaling proteins with enrichment of mitochondrial and stress-response functions. In NWC vs. OBHTC, proteins related to cytokine signaling and vascular function were reduced, while redox-associated regulators were increased. PPI networks highlighted interconnected hubs integrating signaling, metabolism, and immune responses. Conclusion: These findings suggest context-dependent proteomic patterns associated with coffee intake. Given the pooled design and small sample size, results are hypothesis-generating and require validation.

Current Issues in Molecular Biology doi: 10.3390/cimb48060555

Authors: Zitong Pan Yi Wang Jieya Zhang Xiaoran Bian Huaxue Zhang Jiahao Pan Xinyu Wang Dadong Guo

Regulatory T cells (Tregs, CD4+ CD25+ Foxp3+) play a crucial role as a core cell subset in maintaining immune homeostasis in the ocular immune-privileged microenvironment. This review systematically summarizes the stage-specific regulatory mechanisms of Treg cells in common inflammatory diseases such as keratitis, uveitis, and dry eye syndrome, including intercellular interactions, signal pathway mediation, and cytokine network regulation, as well as key experimental evidence (animal/cell models and clinical sample data) and research progress in targeted therapy. Studies have shown that Treg cells maintain ocular immune balance by secreting anti-inflammatory cytokines (such as IL-10 and TGF-β), regulating signaling pathways (STAT, PI3K/AKT, SIRT1, etc.), and interacting with immune cells (macrophages, dendritic cells). Their functions are regulated by multiple factors such as cytokine networks, epigenetic modifications, and delivery vectors. Targeted interventions based on Treg cells (cell therapy, drug intervention, and signaling pathway regulation) and combined treatment strategies have shown good anti-inflammatory potential. This article, in light of current research limitations (such as insufficient analysis of cell heterogeneity and the disconnect between basic and clinical research), proposes future research directions, providing a theoretical basis for the understanding of the pathogenesis of inflammatory eye diseases and the development of new immunomodulatory therapies, and establishing a complete research framework of “mechanism–evidence–treatment”.

Current Issues in Molecular Biology doi: 10.3390/cimb48060554

Authors: Krastena Nikolova Ivan Antonov Victoria Ilieva Valentina Gavazova Daniela Virovska Denitsa Nencheva Silviya Abarova

In this study, we investigated the interaction of a dapagliflozin-containing medicinal product (the commercial drug Forxiga®) with human serum albumin (HSA) at different temperatures using steady-state fluorescence spectroscopy, competitive displacement assays, UV–Vis absorption spectroscopy, and thermodynamic analysis. Increasing concentrations of Forxiga induced a gradual, concentration-dependent quenching of the intrinsic fluorescence of HSA (λex=284 nm; λemmax≈334–339 nm), indicating perturbation of the microenvironment surrounding Trp-214 located in subdomain IIA. Stern–Volmer analysis showed that the quenching constants were temperature-dependent. Meanwhile, the high apparent bimolecular quenching constants suggested a predominantly static quenching mechanism associated with ground-state complex formation. By performing a modified Scatchard-type double-logarithmic analysis, we identified a primary binding site, particularly at lower temperatures. Van’t Hoff analysis revealed negative enthalpy and entropy changes. This indicates that the interaction was spontaneous and exothermic, mainly driven by hydrogen bonding and van der Waals forces. The competitive displacement assays confirmed preferential binding at Sudlow’s site I, in proximity to Trp-214. Additionally, the UV–Vis spectroscopy, supported by ligand-induced perturbation of aromatic residues, confirmed the absence of significant inner-filter effects. Differential scanning calorimetry suggested partial thermal stabilization of HSA upon ligand binding. This finding is consistent with the formation of a stabilized protein–ligand complex. These results suggest that Forxiga forms a relatively stable ground-state complex with HSA, primarily at Sudlow’s site I, and that the interaction is influenced by temperature-dependent conformational changes in the protein.

Current Issues in Molecular Biology doi: 10.3390/cimb48060553

Authors: Rogelio Frank Jiménez-Ortega Rosa M. Salgado Berenice Rivera-Paredez Nelly Patiño Tania Hilario-Huerta Silvia Arenas-Díaz Rafael Velázquez-Cruz Alberto Hidalgo-Bravo

Osteosarcoma is the most common primary bone tumor in children, adolescents, and young adults, and metastasis remains the main determinant for a poor outcome. We conducted an exploratory retrospective cohort study using formalin-fixed, paraffin-embedded tissue from 97 patients with histopathologically confirmed osteosarcoma treated between 2005 and 2019 to evaluate telomere maintenance mechanisms. To assess alternative lengthening of telomeres (ALT), colocalization of telomeric DNA and promyelocytic leukemia protein (TEL–PML) was evaluated as a tissue-based proxy. TEL–PML colocalization was assessed using combined PML immunofluorescence and telomere DNA PNA-FISH. Furthermore, telomerase reverse transcriptase (TERT) expression was evaluated by immunohistochemistry in relation to metastasis and disease progression. Logistic regression models were adjusted for age, sex, and smoking. TEL–PML was evaluable in 45/97 cases, including 10 positive and 35 negative tumors; the remaining samples were non-evaluable because of non-determinable signal or predominant necrosis. TERT immunohistochemistry was scorable in 58/97 cases, of which 33 were positive. TEL–PML evaluability was associated with amputation specimens, whereas TERT positivity was associated with non-osteoblastic histology and was inversely associated with age. Neither TEL–PML nor TERT was significantly associated with metastasis, recurrence, or death. Exploratory time-to-metastasis curves suggested an earlier increase of metastatic events among TEL–PML-positive cases. However, the small number of positive tumors precludes definitive prognostic interpretation. These hypothesis-generating findings indicate that TEL–PML assessment is feasible in osteosarcoma, but it is strongly influenced by tissue adequacy. On the other hand, TERT immunohistochemistry appears to reflect subtype- and age-related heterogeneity rather than providing robust outcome stratification in this cohort.

Current Issues in Molecular Biology doi: 10.3390/cimb48060552

Authors: Tian Xia Changhe Wei Xiaofan Chen

Chimeric antigen receptor T-cell (CAR-T) therapy has emerged as the most transformative cellular immunotherapy modality, with its evolutionary trajectory intrinsically coupled to advances in immune receptor structure–function paradigms. Recent technological breakthroughs have yielded unprecedented mechanistic insights into immune receptors. Cryo-electron microscopy, single-cell omics, and structural biology have revealed the molecular architecture and functional dynamics of key receptors, including T-cell receptors (TCRs) and B-cell receptors (BCRs). This comprehensive review systematically integrates the latest discoveries in immune receptor structure–function relationships, emphasizing the mechanistic underpinnings of receptor diversity generation, signal transduction networks, and their direct translational impact on CAR-T therapeutic optimization. We critically examine the innovative design principles governing fourth-generation CAR-T cells, delineate breakthrough strategies for overcoming solid tumor immunoresistance, and analyze the synergistic potential of CAR-T and TCR-T technological convergence. Particular attention is devoted to elucidating how fundamental immune receptor research can be harnessed to address the tripartite challenges of safety, efficacy, and persistence that currently constrain CAR-T clinical applications. This review establishes a mechanistic framework for developing next-generation CAR-T technologies grounded in immune receptor biology and provides strategic insights for accelerating cellular immunotherapy clinical translation.

Current Issues in Molecular Biology doi: 10.3390/cimb48060551

Authors: Lucía Ceballos-Romero Soraya Herrera-Espejo Daniel Atassi Pilar Sánchez-Suero Jerónimo Pachón José Miguel Cisneros María Eugenia Pachón-Ibáñez

Rapid detection of Pseudomonas aeruginosa and its virulence factor ExoU is essential for improving patient outcomes. In this study, a CRISPR–Cas13a-based diagnostic assay combined with recombinase polymerase amplification (RPA) was developed to detect P. aeruginosa and the exoU gene in blood samples. The assay demonstrated robust amplification, with detection limits of 6 log10 and 8 log10 CFU/mL in Luria–Bertani medium and blood, respectively, and a 100% specificity, without cross-reactivity against four Gram-negative bacilli and Staphylococcus aureus reference strains. The utilisation of a fluorescence-based readout facilitated unambiguous discrimination between P. aeruginosa and P. aeruginosa/exoU+ isolates vs. negative controls. In conclusion, these results support the potential of RPA/CRISPR-Cas13a diagnostics for the rapid identification of P. aeruginosa and its ExoU virulence factor. Further optimisation and clinical validation are required to confirm its utility as a bedside diagnostic test, where its application would speed up clinical decisions in the treatment of these infections.

Current Issues in Molecular Biology doi: 10.3390/cimb48060550

Authors: Zengxun Ni Zineng Zhou Feipeng Jia Jingcheng Wu Junhao Qiu Kangrui Yuan Zhicheng Jia

Hypoxia is a prevalent pathophysiological condition. Prolonged exposure to hypobaric hypoxia can lead to maladaptation, increasing the risk of chronic hypoxic diseases such as high-altitude polycythemia (HAPC). Dauricine, an alkaloid derived from the root of Menispermum dauricum DC, has been demonstrated to possess anti-hypoxic properties; however, its underlying molecular mechanisms remain elusive. In this study, a potential multi-target anti-hypoxic mechanism of dauricine was proposed and computationally evaluated using an integrated approach combining network pharmacology, molecular docking, and molecular dynamics simulations. Common targets between dauricine and hypoxia-related genes were identified through network pharmacology screening. A protein–protein interaction (PPI) network was constructed to identify core targets, followed by Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Molecular docking was subsequently employed to evaluate the binding affinities between dauricine and the candidate core targets, while molecular dynamics simulations were performed to assess the dynamic stability of the resulting complexes. Additionally, the drug-likeness and safety profiles of dauricine were assessed. The results suggest that dauricine may exert its anti-hypoxic effects by modulating candidate core targets, including ESR1, PIK3CA, and MTOR, and by acting on key signaling pathways such as PI3K-Akt, MAPK, and mTOR. This study provides a theoretical foundation for the further investigation of dauricine as a multi-target candidate for intervention in hypoxia and establishes a bioinformatics basis for subsequent experimental validation.

Current Issues in Molecular Biology doi: 10.3390/cimb48060549

Authors: Jeeyoung Kim Ye-Won Jo Weon Jeong Bang Kwang Won Lee Yung Hyup Joo Sung Hyeon Lee Chang-Seok Lee

This study evaluated olive leaf extract (OLE) as a multifunctional dermocosmetic candidate for sebum-related and inflammatory responses relevant to oily and acne-prone skin using an axis-aligned in vitro panel: (i) sebocyte lipogenesis, (ii) inflammatory mediator production in keratinocytes, and (iii) fibroblast-mediated collagen gel contraction. In addition, supportive mechanistic evidence for the sebum-related effects of OLE was obtained by examining signaling proteins associated with sebocyte lipogenesis, including PPAR-γ and SREBP-1. As a result, OLE significantly inhibited linoleic acid-induced lipid accumulation in SEB-1 sebocytes without cytotoxicity. In HaCaT keratinocytes, OLE significantly reduced the production of pro-inflammatory cytokines, including IL-8, TNF-α, and PGE2, induced by Cutibacterium acnes or UVB. In dermal fibroblast-containing collagen gels, OLE enhanced fibroblast-mediated gel contraction. Additionally, analysis of the main mechanisms of lipid inhibition using SEB-1 sebocytes revealed that OLE exerts a dual regulatory role in lipid synthesis and inflammation by downregulating AKT and ERK phosphorylation and inhibiting PPAR-γ and SREBP-1 expression. Furthermore, among the tested extracts, the 70% ethanol extract (OLE70) exhibited the strongest antioxidant activity, the greatest gel contraction response, and the highest content of oleuropein, a major bioactive phenolic compound derived from olive. Like OLE, oleuropein also showed sebum-regulatory activity by reducing lipid accumulation in SEB-1 sebocytes, an inhibitory effect on IL-8 expression in HaCaT keratinocytes, and an inhibitory effect on the expression of PPAR-γ and SREBP-1, which are involved in sebum secretion. Taken together, these findings suggest that OLE and its major phenolic constituent, oleuropein, may modulate sebum-related, inflammatory, oxidative, and dermal remodeling-associated responses in skin cell models. These results should be interpreted as exploratory and provide a basis for further mechanistic and translational investigation.

Current Issues in Molecular Biology doi: 10.3390/cimb48060548

Authors: Sara AlSrayea Maryam H. Alrashid Nasmah K. Bastaki Jasem Al-Barrak

Colorectal cancer (CRC) and non-Hodgkin lymphoma (NHL) are among the most prevalent cancer types globally by incidence and mortality. Both types are influenced differentially by chronic inflammation. Central to this inflammation are inflammatory genes that are meticulously regulated by nuclear factor kappa B (NF-κB) and tumor necrosis factor-α (TNF-α). NF-κB is negatively regulated by IκBα (encoded by NFKBIA), while TNF-α’s actions can be modulated by ghrelin (encoded by GHRL). We investigated four single nucleotide polymorphisms (SNPs) in NFKB1 (rs4648068), NFKBIA (rs2233406), TNF-α (rs1800629), and GHRL (rs1629816) as biomarkers for CRC and NHL risk in a cohort of Kuwaiti individuals. DNA samples from patients and controls were collected and genotyped for all SNPs, and their association with CRC or NHL risk was assessed. While rs4648068 showed a modest association with increased CRC risk, it had no significant impact on NHL risk. Conversely, rs2233406 increased NHL risk without affecting CRC risk. Interestingly, while rs1800629 showed a protective effect against NHL, it showed an increased risk for CRC. Finally, rs1629816 was associated with greater NHL but not CRC risk. Our findings suggests that variations of these inflammatory genes may be useful indicators for predicting cancer risk but might have unpredictable effects on cancer susceptibility, depending on the cancer type.

Current Issues in Molecular Biology doi: 10.3390/cimb48060547

Authors: Marina Giannaki Elena Parmigiani Karin Burger Verdon Taylor Claudio Giachino

Interferons (IFNs) play fundamental roles in cancer immunity. We have previously shown that conditional ablation of Notch pathway genes in a mouse model of glioma results in impaired IFNγ signaling and immunosuppressive tumors. However, it remained unclear whether the interaction between the Notch and IFN signaling pathways could be leveraged to counteract immune evasion in glioma. Here, we investigated whether expression of the intrinsically active Notch intracellular domain (NICD) could enhance IFN responses in glioma cells. Using a doxycycline (Dox)-inducible system, we overexpressed (OE) NICD in U-251MG human glioma cells. NICD-OE dramatically potentiated STAT1 phosphorylation in response to stimulation with either IFNγ or IFNα. Moreover, NICD-OE induced the expression of the transcription factor IRF1, a regulator of IFN signaling responses. Notably, NICD-OE in U-251MG human glioma cells boosted the IFNγ-dependent transcription of the CXCL9 and CXCL10 genes, which encode cytokines that regulate T cell function. Accordingly, NICD-OE in vivo promoted cytotoxic T lymphocyte recruitment to the tumor and reduced tumor cell proliferation in a murine glioma model. Hence, we have identified a signaling network that could be exploited to enhance anti-tumor immunity in glioma subtypes.

Current Issues in Molecular Biology doi: 10.3390/cimb48060546

Authors: Yuexi Liu Yukun Yuan Xiaoyi Shi Rongsi Sun Xiaolan Ding

Vitiligo is a chronic, acquired autoimmune disorder characterized by white skin patches resulting from the loss of epidermal melanocytes. Vitiligo may arise through multiple mechanisms, including genetic susceptibility, oxidative stress, autoimmune dysfunction, and environmental factors. Treatment strategies have focused on inhibiting melanocyte loss and stimulating repigmentation. Mitogen-activated protein kinase (MAPK) pathways regulate various cellular processes, including differentiation, survival, and inflammatory responses. The dysregulated MAPK pathways play distinct roles in the development of vitiligo through a complex interplay of melanogenesis, oxidative stress, and autoimmune responses within different cells, thereby leading to melanocyte damage. Thus, therapeutic targeting of MAPK pathways has the potential to mitigate oxidative stress-induced damage and inhibit the exaggerated autoimmunity, thereby controlling disease progression and supporting repigmentation. This review provides an overview of MAPK signaling across the multicellular network in vitiligo pathogenesis and summarizes agents that may provide new perspectives for therapeutic intervention.

Current Issues in Molecular Biology doi: 10.3390/cimb48060545

Authors: Zeliha Emrence Seyma Punar Vahideh Zarerajabi Sena Uslu Neslihan Abaci Sema Sirma Ekmekci

Breast cancer remains a leading cause of cancer-related mortality worldwide, with epigenetic mechanisms like N6 methyladenosine (m6A) modification playing a crucial role in tumorigenesis. The interaction between microRNAs and m6A regulators, such as the methyltransferase METTL14, is increasingly recognized as a key pathway in oncogenesis. This study investigated whether miR-30c-2-3p regulates METTL14 expression to influence global m6A levels and cell migration in breast epithelial (MCF12A) and breast cancer (MCF7) cell lines. Following transfection with miR-30c-2-3p mimics, successful overexpression was confirmed in both cell lines. Subsequent RT-qPCR and Western blotting analyses demonstrated that METTL14 mRNA and protein levels were significantly reduced at 24 and 48 h post-transfection (p < 0.05). Concurrently, global m6A RNA methylation levels decreased, with a more pronounced reduction observed in MCF12A cells (p < 0.001). Functionally, wound healing assays revealed that miR-30c-2-3p significantly inhibited migration, reducing wound closure by 30–44% in MCF7 cells and by 66–72% in MCF12A cells. These findings reveal a novel regulatory axis involving miR-30c-2-3p, METTL14, and m6A, suggesting that miR-30c-2-3p functions as a tumor suppressor and represents a promising biomarker and therapeutic target in breast cancer.

Current Issues in Molecular Biology doi: 10.3390/cimb48060544

Authors: Monia Cecati Arianna Vignini

Despite remarkable advances in cancer therapy, treatment resistance, tumor heterogeneity, and therapy-associated toxicity remain major obstacles in achieving durable clinical responses [...]

Current Issues in Molecular Biology doi: 10.3390/cimb48060543

Authors: Bin Xu Shizhen Lu Rongge Xia Qi Han Zhiqi Zhu Xinpeng Chen Huiying Shi Wencong Wu Wanqun Xing Jingjing Lu

SIRT2 (Sirtuin 2) is an NAD+-dependent deacetylase that exerts crucial regulatory effects on immune homeostasis and macrophage activation. While chronic cold exposure is a known predisposing factor for pulmonary dysfunction, the precise mechanisms by which SIRT2 potentially modulates lung macrophage polarization under cold stress remains poorly understood. In this study, we evaluated the protective capacity of SIRT2 using both wild-type (WT) and Sirt2-knockout (Sirt2−/−) murine models subjected to chronic cold exposure (4 °C for 3 h daily over 21 days). Our results demonstrated that Sirt2 deficiency significantly exacerbated cold-induced pulmonary histopathological damage and increased the secretion of pro-inflammatory cytokines (TNF-α, IL-1β, and IL-6) (p < 0.05). Furthermore, chronic cold stress triggered a macrophage-centered inflammatory response, a process wherein SIRT2 was found to curtail M1 pro-inflammatory polarization. To further investigate these mechanisms, in vitro experiments were conducted using the mouse alveolar macrophage cell line MH-S. While LPS was utilized as a canonical inflammatory stimulus to mimic the injury environment, SIRT2 overexpression was found to reverse the LPS-induced increase in M1 markers and attenuate inflammatory cytokine secretion. These findings suggest that SIRT2 maintains intracellular homeostasis by modulating macrophage plasticity and plays a protective role in the development of chronic cold stimulus-induced lung injury. Consequently, SIRT2 activation may represent a potential therapeutic pathway for the treatment of environment-related respiratory diseases.

Current Issues in Molecular Biology doi: 10.3390/cimb48060542

Authors: LinShu Liu Adrienne B. Narrowe Jenni Firrman Karley K. Mahalak Venkateswari J. Chetty Johanna M. S. Lemons Aurélien Baudot Pieter Van den Abbeele

Perfluorooctanoic acid (PFOA) is an environmentally persistent chemical that enters the gastrointestinal tract (GIT) via the food chain, posing a harmful, long-term threat to human health. In response to this challenge, research on the PFOA-GIT interaction is thriving. Currently, studies on the effect of PFOA on the epithelial cells of the GIT and those on its influence on the microbial community are often implemented separately, and less attention has been paid to the combinational effects of the chemical, the gut microbiome and metabolome. In the present study, we co-cultured fecal samples from healthy adults aged 25–70 in the ex vivo SIFR® simulator, adding PFOA at 10 mg/L to represent the accumulated effects of long-term exposure. The results obtained from bacterial cell counting by flow cytometry and shotgun metagenomic sequencing revealed that PFOA was broadly disruptive to the microbiome and that Pseudomonadota emerged as the dominant phylum by replacing Bacteriodota and Bacillota, including key members of short-chain fatty acid-producing groups. Bacterial culture media with and without PFOA were collected and used in human colonoid cell culture for TEER and transcription measurement. It was shown that the PFOA-impacted microbial culture had stronger effects on the cell’s protective functions, in terms of tissue junction tightening, mucin biosynthesis, and immune response, than either untreated bacterial culture or PFOA alone. The results point out the possibility that the combination of PFOA and PFOA-impacted bacterial metabolites more strongly induces a change in epithelial cells’ protective function than either one alone.

Current Issues in Molecular Biology doi: 10.3390/cimb48060541

Authors: Changgeng Shang Hu Huang Yu Chen Renying Zhuo Hongsuo Shu Zhengquan He

The GRAS transcription factor family plays a pivotal role in plant stress adaptation, yet its systematic characterization and the underlying drought-responsive mechanisms remain poorly elucidated in Populus deltoides. Here, a genome-wide identification and analysis of GRAS genes in P. deltoides was performed, and a total of 92 family members were identified and classified into 12 distinct subfamilies through phylogenetic analysis. Evolutionary analysis revealed a high degree of conservation between the GRAS proteins of P. deltoides and those of Arabidopsis thaliana, Oryza sativa, and Solanum lycopersicum. Genomic duplication events, including 90 segmental and 11 tandem duplications, were identified as the primary drivers of GRAS family expansion. Promoter cis-element analysis uncovered an enrichment of stress-responsive elements (MBS, ABRE) and phytohormone-related motifs (e.g., TATC-box). Transcriptomic profiling further revealed distinct drought-inducible expression patterns of GRAS genes: PdeGRAS49 exhibited rapid upregulation at the early stage of drought exposure (1–3 h), whereas DELLA subfamily members PdeGRAS51 and PdeGRAS59 reached their expression peaks at 6–9 h, and PdeGRAS34 and PdeGRAS77 maintained sustained activation throughout 12–24 h. Moreover, the drought-inducible expression patterns of five DELLA genes were confirmed by qRT-PCR validation. Collectively, this study provides crucial genomic insights into the GRAS family and valuable candidate gene resources, which lay a foundation for molecular breeding of drought-tolerant P. deltoides cultivars via manipulating GRAS-mediated regulatory mechanisms.

Current Issues in Molecular Biology doi: 10.3390/cimb48050540

Authors: Chandana Sooranahalli Charles Bouchard Omer Iqbal

Necroptosis has been implicated in the pathogenesis of Stevens–Johnson syndrome and toxic epidermal necrolysis (SJS/TEN), with prior studies demonstrating tissue-level involvement of receptor-interacting protein kinases RIPK1 and RIPK3. However, their systemic expression in the circulatory compartment remains incompletely characterized. The objective of this study is to evaluate circulating levels of RIPK1 and RIPK3 in patients with SJS/TEN and explore their potential association with diseases. Serum samples from patients with SJS/TEN and control groups were analyzed for RIPK1 and RIPK3 levels using ELISA. Group differences were assessed using non-parametric statistical methods. Circulating levels of RIPK1 and RIPK3 were elevated in patients with SJS/TEN compared with controls. These findings were consistent across analyses; however, variability within groups and overlap between cohorts were observed. These results suggest an association between increased circulating RIPK1 and RIPK3 levels and SJS/TEN. Given the limited sample size, heterogeneous control populations, and lack of functional or phosphorylation-specific assays, these findings should be considered exploratory. Further studies incorporating larger cohorts and mechanistic validation are needed to clarify the role of necroptosis-related pathways in the systemic manifestations of SJS/TEN.

Current Issues in Molecular Biology doi: 10.3390/cimb48050539

Authors: Chan-Yen Kuo

Inflammation is increasingly recognized as a dynamic and interconnected regulatory network rather than a linear signaling cascade, in which immune signaling, oxidative stress, metabolic adaptation, and tissue-specific microenvironmental factors collectively shape inflammatory responses [...]

Current Issues in Molecular Biology doi: 10.3390/cimb48050538

Authors: Lu Li Kexin Ji Fengqi Du Nini Jin He Li Xinqi Liu

Citrus flavonoid intake is associated with beneficial effects on endothelial function. Our previous randomized control trial demonstrated that the concentration of Hesperetin-7-O-glucuronide (H7G) was positively correlated with the improvement in endothelial function in overweight and obese participants following blood orange juice consumption. To explore the underlying mechanism by which H7G improves endothelial function, we investigated the regulation of H7G on endothelial function in a permanent human endothelial cell line (EA. hy926 cells) under normal and oxidative conditions treated with high-oxidation low-density lipoprotein. The results indicated that H7G improved the expression of nitric oxide synthase 3 (NOS3), heme oxygenase 1 (HMOX1) ad glutamate cysteine ligase catalytic (GCLC), and inhibited the expression of endothelin-1 (EDN1), through the upregulation of miR-660-5p and inhibition of miR-21-5p. In summary, H7G improves endothelial cell function via the upregulation of miR-660-5p and the inhibition of miR-21-5p.

Current Issues in Molecular Biology doi: 10.3390/cimb48050537

Authors: Maria Giovanna Rizzo

We are pleased to present this Special Issue of Current Issues in Molecular Biology, entitled “Osteoclastogenesis and Osteogenesis: Physiological and Molecular Responses to Xenobiotics and Biomaterials” [...]

Current Issues in Molecular Biology doi: 10.3390/cimb48050536

Authors: Zhen Chen Shanshan Wang Yuzong Chen

Severe COVID-19 is characterized by profound thromboinflammatory and immune disturbances, but the network-level relationships among complement–coagulation dysregulation, humoral immune remodeling, and iron-associated immune regulation remain incompletely understood. Here, we performed integrative proteomic and transcriptomic analyses across peripheral blood and lung microenvironments using weighted gene co-expression network analysis (WGCNA), differential network analysis (DiNA), and immune deconvolution. Proteomic network analysis identified a disease-associated module enriched in complement activation, coagulation cascades, platelet degranulation, and acute inflammatory responses. Hub proteins, including C9, LBP, vWF, and F11, were prioritized based on module association and intramodular connectivity. Notably, C9 and LBP were repeatedly identified across WGCNA, DiNA, and differential expression analyses, underscoring their robust association with severe COVID-19-associated molecular network remodeling. Transcriptomic and CIBERSORTx-based immune deconvolution analyses showed altered immune-cell composition in blood and lung tissues, including B-cell and plasma-cell-associated changes. Notably, TFRC displayed cell-type-associated expression changes in naïve B cells and plasma cells, suggesting a potential link between iron-associated immune regulation and humoral immune remodeling. Collectively, these computational findings highlight coordinated complement–coagulation dysregulation, humoral immune remodeling, and TFRC-associated iron-related immune alterations in severe COVID-19, and prioritize TFRC, C9, and LBP as candidate molecular indicators requiring further experimental and clinical validation.

Current Issues in Molecular Biology doi: 10.3390/cimb48050534

Authors: Shaqraa Musawi

Alpha-fetoprotein (AFP) is a glycoprotein primarily produced by the fetal liver and yolk sac during development. It is a multifaceted biomarker with significant applications in the prenatal screening of congenital abnormalities, cancer, and other disorders. The level of AFP in maternal blood may indicate several obstetric concerns and complications during pregnancy. Atypical AFP levels are commonly utilized as a biomarker for detecting fetal anomalies, placental complications, and other pregnancy-related issues. These findings raise concerns regarding the effectiveness of screening maternal serum alpha-fetoprotein (MS-AFP) as a primary indicator of pregnancy problems and underscore the need for further investigation into the functional role of AFP throughout pregnancy. The measurement of MS-AFP has been utilized for the past four decades. It is anticipated that MS-AFP measurement will continue to be utilized as a component of integrated or sequential tests for chromosomal abnormalities and may serve as a prognostic indicator for adverse obstetric outcomes. Critically, whether AFP functions solely as a passive marker or plays active biological roles in pregnancy physiology and pathology remains unresolved, necessitating additional mechanistic investigation and discourse. This review consolidates critical data from numerous studies on AFP, focusing specifically on its diagnostic and prognostic applications for congenital abnormalities and problems during pregnancy. This review also identifies key research gaps regarding the functional biology of AFP, particularly whether AFP functions as a passive biomarker or an active participant in the pathophysiology of adverse pregnancy outcomes.

Current Issues in Molecular Biology doi: 10.3390/cimb48050535

Authors: Bernardo L. Rapoport Ronald Anderson Daniel van Tonder Teresa Smit Theresa M. Rossouw Carol-Ann Benn Helen C. Steel

Triple-negative breast cancer is an aggressive and heterogeneous type of invasive breast cancer (BC) in which the cancer cells lack estrogen and progesterone receptors, as well as expression of the human epidermal growth factor 2 protein. This cancer tends to grow and spread faster than other BC subtypes, and is associated with a poor prognosis due to early visceral and neurological recurrences. Multidisciplinary management includes surgery, chemotherapy, radiation therapy, and immunotherapy with targeted immune checkpoint inhibitors (ICIs). The introduction of ICIs has improved outcomes in patients with TNBC, particularly in the metastatic and neoadjuvant settings. Despite these advances, a significant proportion of patients either do not respond to treatment or develop resistance to it. TNBC mortality remains high, underscoring the urgent need to identify novel prognostic and predictive biomarkers to overcome resistance to immunotherapy. Following a brief overview of the clinical features and established biomarkers of TNBC, the current review focuses on immune checkpoint proteins (ICPs) beyond PD-1 and PD-L1, and on the potential use of soluble ICPs rather than the well-established membrane-bound assays. These soluble ICPs are produced through the alternative splicing of messenger (m)RNA or the cleavage/shedding of membrane-bound proteins. This is followed by an overview of current treatment and novel predictive targets in TNBC. Additionally, the involvement of the B- and T-lymphocyte attenuator (BTLA)/herpes virus entry mediator (HVEM)/CD160 pathway and its role in the pathogenesis of BC and TNBC are reviewed, highlighting the potential use of BTLA and HVEM as biomarkers.

Current Issues in Molecular Biology doi: 10.3390/cimb48050533

Authors: Attila Farsang

Infectious diseases have always posed a significant threat to both humankind and our livestock [...]

Current Issues in Molecular Biology doi: 10.3390/cimb48050532

Authors: Suman Basak

Proteomics has become central to pharmacological research by providing quantitative readouts of protein abundance, post-translational modifications, interactions, and spatial context. However, proteomic datasets are high-dimensional, heterogeneous, and frequently affected by missingness, batch effects, and limited cohort size. Artificial intelligence (AI) and machine learning (ML) can help convert these complex data into decision-relevant outputs for target identification, biomarker discovery, pharmacodynamic monitoring, and drug repurposing. This review critically compares supervised learning, ensemble methods, dimensionality reduction, clustering, deep learning, graph learning, survival modeling, causal inference, and calibration approaches in proteomics-driven drug discovery. We also summarize major software ecosystems for mass-spectrometry processing, targeted assays, spectrum prediction, phosphoproteomics, structure modeling, and reproducible workflows. Emphasis is placed on model selection, benchmarking, missing-data handling, batch correction, interpretability, uncertainty, experimental validation, and translational readiness. Finally, we highlight emerging directions, including contrastive learning, diffusion models, graph-based integration, and federated analytics.

Current Issues in Molecular Biology doi: 10.3390/cimb48050531

Authors: Burcu Biltekin Yusuf Elgormus Ayhan Bilir

Background and Objectives: Potential anti-neoplastic effects of resveratrol, which has antioxidant features combined with clomipramine, which has antineoplastic features, or with gemcitabine, used as a nucleoside analog widely used in chemotherapy, were evaluated together and individually on the HL-60 leukemia cells in this in vitro screening study. Materials and Methods: HL-60 cells were treated with gemcitabine, clomipramine, resveratrol, or their combinations at concentrations ranging from 1 to 200 µM. Cell viability was assessed at 24, 48, and 72 h using the trypan blue exclusion method, and results are expressed as a percentage of time-matched untreated controls. Cell proliferation was further evaluated by bromodeoxyuridine (BrdU) immunohistochemical labeling. All experiments were performed in triplicate, and statistical analyses were conducted using one-way analysis of variance (ANOVA) with post hoc comparisons. Results: Gemcitabine markedly reduced HL-60 cell viability at all concentrations and time points (p < 0.001), indicating strong time-dependent cytotoxicity, with a significant drop in BrdU proliferation index at 48 h (p < 0.001). Clomipramine exhibited a biphasic response: high concentrations decreased viability (p < 0.05), while low concentrations allowed partial recovery by 72 h. Resveratrol showed concentration-dependent cytotoxicity, with reduced viability at high concentration and near-control levels at low concentration by 72 h; BrdU indices remained significantly lower than control (p < 0.001). Combination treatments with gemcitabine showed no additive cytotoxic or antiproliferative effects (p > 0.05). A transient enhanced effect was observed in the clomipramine + resveratrol group at 24 h (p < 0.01 vs. clomipramine; p < 0.05 vs. gemcitabine). Conclusions: Gemcitabine, clomipramine, and resveratrol all exhibited inhibitory effects on cell proliferation in HL-60 cell cultures. However, the combination treatments did not show additional cytotoxicity or additive effects. These findings suggest that while each of these compounds individually has the potential to inhibit cell growth, their combined application does not enhance the cytotoxic effects beyond those observed with single treatments. These findings highlight the necessity of a rational approach when considering novel drug combinations.

Current Issues in Molecular Biology doi: 10.3390/cimb48050530

Authors: Yanshi Hu Zixuan Wang Yueming Hu Cong Feng Qiuyu Fang Ming Chen

Transcriptomic meta-analysis enhances biological veracity and reproducibility of differentially expressed genes (DEGs) by integrating multiple independent studies, yet prevailing p-value or effect-size integration approaches exhibit limited power to resolve subtle yet vital gene signatures. This study presents AWmeta, an adaptively weighted framework that unifies both meta-analytical paradigms for the first time. Benchmarked on 35 Parkinson’s and Crohn’s disease datasets spanning diverse tissues and adaptively down-weighting underpowered studies, AWmeta yields higher-fidelity DEGs with markedly reduced false positives and achieves more truthful gene differential expression quantification across individual studies at both gene and study levels over the random-effects model (REM). Resilience experiments demonstrate AWmeta’s remarkable stability and robustness against external and internal perturbations. Crucially, AWmeta prioritizes more tissue-contextual genes of Parkinson’s and Crohn’s disease with genuine pathological importance than those from REM and constituent studies. Functional enrichment analysis further verifies that these screened gene signatures capture higher contextual coherence in all analyzed disease tissues. AWmeta harmonizes heterogeneous transcriptomic datasets into reliable DEG identification and mechanistic insights, serving as an indispensable tool for precision transcriptomic integration.

Current Issues in Molecular Biology doi: 10.3390/cimb48050529

Authors: José Manuel Pérez de la Lastra Celia María Curieses Andrés Elena Bustamante Munguira Celia Andrés Juan Eduardo Pérez Lebeña

Polyphenols act in humans through authentic metabolites, including regio-isomeric glucuronides/sulphates, O-methylated forms, and microbiota products (urolithins, γ-valerolactones, equol), that reach targets by spatiotemporally gated exposure. Vectorial transport (MRP2/BCRP/P-gp), enterohepatic cycling, and β-glucuronidase hubs create early, surface-proximal microbursts of aglycone/catechol, whereas microbiota metabolites arrive systemically 6–24 h later. Signalling emerges from a continuum of weak noncovalent modulation, conditionally gated electrophile/redox relays (catechol → o-quinone, reversible Michael adduction plus signalling-range H2O2), and PTM cascades (phosphorylation → acylation → proteostasis) that reprogram NRF2/Keap1, NF-κB/IKK, AMPK/MAPK/PI3K-Akt, SIRT1/HDACs, PPARγ, AhR, and TFEB according to where and when metabolites appear. We provide methods and standards to dose isomer-resolved metabolites at physiological free concentrations (nM-low µM) in transport-competent systems, with PK-informed sampling across seconds–minutes, 15/60/240 min, and 6–24 h, and we outline a research agenda (reference panels, spatial exposure atlases, metabotype-stratified trials, safety windows). Framed this way, polyphenols shift from vague “antioxidants” to programmable dietary signals that enable precision nutrition targeting transcription-factor and proteostasis programmes in vivo.

Current Issues in Molecular Biology doi: 10.3390/cimb48050528

Authors: Ioana-Laura Olteanu Ciprian Pușcașu Corina Andrei Anca Zanfirescu

Endometriosis is a chronic, estrogen-dependent disorder defined by ectopic endometrial-like tissue growth, persistent inflammation, and aberrant innervation. Emerging evidence indicates that disease progression and symptom severity are driven by a reciprocal interaction between hormonal dysregulation and neuroinflammatory signaling. This narrative review synthesizes human-based mechanistic and clinical evidence on the hormonal–neuroinflammatory interface in endometriosis, drawing on peer-reviewed publications retrieved from PubMed and Scopus through November 2025. The publications comprised studies using data from patient-derived tissues, primary endometriotic cells, and clinical cohorts. Several convergent molecular nodes at this interface were identified: the prostaglandin E2–prostaglandin E receptor 2/prostaglandin E receptor 4–aromatase axis, estrogen receptor beta—nuclear factor kappa B signaling, interleukin-6/signal transducer and activator of transcription 3-mediated fibrosis, neurotrophin pathways, transient receptor potential channels (TRPV1/TRPA1), and neurokinin 1 receptor signaling. In this integrated model, endocrine dysfunction fuels neuroinflammation, which in turn impairs steroid responsiveness. This cycle explains the frequent pain–lesion mismatch and the persistence of symptoms despite standard hormonal suppression. Targeting these druggable interface pathways enables better patient stratification and more effective combination therapies for endometriosis.

Current Issues in Molecular Biology doi: 10.3390/cimb48050527

Authors: Abrar Akbar Rita Rahmeh Mohamed Kishk Anisha Shajan

Bordetella petrii is an environmentally versatile Gram-negative bacterium with hydrocarbon-degrading capabilities, yet its genetic and metabolic characteristics remain poorly characterized. This study investigated the genomic features of a PAH-degrading Bordetella petrii strain P003 isolated from contaminated oil in Kuwait using bioinformatic approaches. The genome of B. petrii P003 was sequenced and analyzed for genomic islands, comparative genomics, and PAH degradation pathways. The draft genome assembly of B. petrii P003 was 5,011,660 bp with 49 contigs and 68.67% GC content. It contained 4687 coding sequences, 5 rRNAs, and 56 tRNAs. Prediction of genomic islands (GIs) revealed that strain P003 possessed 99 GIs, whereas the reference B. pertii DSM 12,804 had 58 unique GIs. Comparative genomics showed 279 locally collinear blocks with the reference strain. The P003 genome encoded multiple genes involved in PAH, naphthalene, and benzoate degradation pathways, including an 8-gene PAH operon (pht4, ph2, pht5, pht3, pcaG, pcaH, nahAb/nagAb/ndoA/nbzA). We found that pcaG and pcaH encode the enzymes responsible for the breakdown of PAH, protocatechuate 3,4-dioxygenase, alpha and beta subunits (EC: 1.13.11.3). The genomic analysis of B. petrii P003 provides insights into its PAH degradation capabilities and potential for bioremediation applications. The strain possesses an expanded repertoire of aromatic compound degradation genes compared to reference strains, suggesting enhanced metabolic versatility for degrading environmental pollutants.

Current Issues in Molecular Biology doi: 10.3390/cimb48050526

Authors: Rhea Sharma Daniel H. Shain

Polycystic ovarian syndrome (PCOS) affects over 116 million women globally and is typically linked with excess androgens such as testosterone. Many patients, however, display classic PCOS symptoms despite normal serum androgen. One proposed mechanism for these cases involves a shortened CAG (i.e., encodes glutamine) repeat length in the androgen receptor (AR) gene, which increases AR activity without elevating testosterone. Fewer glutamine repeats alter the AR’s N-terminal domain and may contribute to strengthened interactions with co-activators and enhanced transcription of androgen-regulated genes. Heightened AR activity in hypothalamus neurons stimulates increased pulsatile release of gonadotropin-releasing hormone (GnRH), which disrupts pituitary secretion dynamics and favors luteinizing hormone (LH) over follicle-stimulating hormone (FSH). This altered LH/FSH ratio leads to impaired folliculogenesis, anovulation and other hallmark PCOS symptoms. Targeting AR activity directly, for example by using compounds that covalently modify the AR N-terminal domain to suppress activity, may therefore offer a more precise treatment strategy for PCOS.

Current Issues in Molecular Biology doi: 10.3390/cimb48050525

Authors: Hsin-Yi Shih Chien-Chih Chen

Tumor hypoxia has been implicated in treatment resistance and disease progression in esophageal squamous cell carcinoma (ESCC), yet its relationship with post-neoadjuvant pathological staging remains unclear. This study evaluated the association between hypoxia-inducible factor-1α (HIF-1α) expression and pathological stage following neoadjuvant concurrent chemoradiotherapy (CCRT). We retrospectively analyzed 55 patients with ESCC treated with standardized neoadjuvant CCRT followed by curative esophagectomy. Immunohistochemical staining was performed on surgical specimens to assess tumor (HIF-T%) and stromal (HIF-N%) HIF-1α expression, and correlations with postoperative pathological stage were analyzed. Tumor HIF-1α expression was significantly higher in patients with pathological stage III disease compared with stage I–II disease (40% vs. 15%, p = 0.023). Increasing trends in tumor HIF-T% were observed across higher T and N classifications, although these did not reach statistical significance. Stromal HIF-1α expression was not associated with pathological stage. These findings demonstrate that elevated tumor HIF-1α expression is associated with advanced pathological stage following neoadjuvant CCRT in ESCC, supporting the role of hypoxia-related signaling in treatment resistance. HIF-1α may serve as a clinically relevant biomarker of residual disease burden, although further validation in larger cohorts is warranted.

Current Issues in Molecular Biology doi: 10.3390/cimb48050524

Authors: Elizabeth Thurmond Eliza J. Roeth Kristen Noyes Madeline Boyer Ethan Evans Benjamin T. Bikman Paul R. Reynolds Juan A. Arroyo

Semaglutide, a long-acting glucagon-like peptide-1 receptor agonist (GLP-1RA), has transformed obesity and diabetes management. However, its expanding use among reproductive-age women raises concerns about potential effects on early placental development. We examined semaglutide’s impact on two human trophoblast cell lines: Swan71 (invasive extravillous) and BeWO (syncytiotrophoblast-like). Cells were treated with semaglutide (100 nM) for 24 h, and proliferation, viability, mitochondrial respiration, oxidative stress, signaling pathways, and invasiveness were evaluated. Semaglutide significantly reduced proliferation in Swan71 cells and increased it in BeWO cells, with no significant change in viability for Swan71 and a slight increase for BeWO. Western blot analysis revealed altered phosphorylation of key signaling proteins, including mTOR, p70S6K, 4EBP1, AKT, and ERK, as well as increased AMPK phosphorylation, indicating a shift toward catabolic signaling. Reactive oxygen species (ROS) accumulation increased markedly, accompanied by altered oxygen consumption rates—reduced in Swan71 cells and elevated in BeWO cells. Functionally, semaglutide suppressed Swan71 invasion through Matrigel by approximately three-fold. These findings suggest that semaglutide induces oxidative and metabolic stress in trophoblasts and is associated with altered mTOR-mediated signaling and reduced invasive potential. Such cellular alterations may contribute to compromised placental development and uterine vascular remodeling if exposure occurs near conception. While clinical data remain limited, this study provides mechanistic insight supporting caution in the use of semaglutide during the periconception period and underscores the need for targeted reproductive safety studies.

Current Issues in Molecular Biology doi: 10.3390/cimb48050523

Authors: Jiahui Zhang Xue Zhong Mingxin Cao Jiajing Xu Mengchao Qin Frédéric Francis Lanqin Xia

The grain aphid, Sitobion miscanthi, poses a serious threat to cereal crops worldwide, leading to considerable yield losses and demanding annual insecticide applications during the grain-filling stage. As a sustainable alternative, we explored host-induced gene silencing (HIGS) targeting an aphid-specific gene. In this study, we identified SmDSR32, a novel gene encoding a salivary peptide in S. miscanthi, and validated its suitability for RNAi. Transgenic wheat lines expressing SmDSR32-dsRNA were generated. Aphids feeding on these lines showed a 20-fold reduction in SmDSR32 transcript levels compared with controls. This silencing disrupted normal feeding behavior in electropenetrography (EPG) analyses, characterized by a 1.94-fold prolongation of intercellular probing and a 61% shortening of phloem ingestion. Consequently, aphid performance was severely compromised, with at least a 56.7% decrease in survival, a shortening of 5 days in lifespan, and a reduction of 9–10 individuals in aphid progeny production. Impressively, upon being transferred to wild-type plants, both the surviving aphids and their progeny sustained fitness deficits, with a 30% reduction in survival still observed in the first generation. These findings validate SmDSR32 as a potent RNAi target and establish HIGS targeting essential salivary genes as a promising strategy for sustainable aphid management in wheat.

Current Issues in Molecular Biology doi: 10.3390/cimb48050521

Authors: Jiangtao Fan Pengpeng Gong Yujia Liu Mengke Dou Qing Li Qiuhong Hu Yong Wang Gang Wang Xiong Huang

Basic leucine zipper (bZIP) transcription factors are widely involved in plant growth, development, environmental adaptation, and secondary metabolism. However, the bZIP gene family in Taxus yunnanensis has not been systematically characterized, and its potential involvement in shading-responsive regulation of paclitaxel biosynthesis remains unclear. In this study, a genome-wide analysis was performed to identify and characterize the bZIP family in T. yunnanensis. Phylogenetic analysis, conserved motif and domain identification, promoter cis-element analysis, chromosomal localization, and expression profiling were conducted to investigate their structural features and regulatory potential. A total of 18 TyubZIP genes were identified and classified into 10 subfamilies. These genes exhibited variation in physicochemical properties but showed conserved structural features and nuclear localization. Promoter analysis revealed abundant light-responsive, hormone-related, and stress-related cis-elements. Expression profiling indicated tissue-specific expression patterns and diverse responses to shading treatment. WGCNA further identified candidate TyubZIP genes potentially associated with paclitaxel biosynthesis. Among them, TyuHY5 was selected for functional analysis. Subcellular localization and transcriptional assays demonstrated that TyuHY5 can bind to the promoter of TyuDBTNBT and positively regulate its activity. These findings provide the first genome-wide characterization of the bZIP family in T. yunnanensis and identify TyuHY5 as a shading-responsive candidate regulator of paclitaxel biosynthesis, providing insights that may inform the genetic improvement and cultivation strategies of Taxus for enhanced paclitaxel production.

Current Issues in Molecular Biology doi: 10.3390/cimb48050522

Authors: Tuba Gül Mücahit Seçme

Background and Objectives: Neuroblastoma represents the most common extracranial solid tumor in childhood and is associated with a poor prognosis in high-risk cases. Amygdalin, a naturally occurring cyanogenic glycoside, has been reported to exhibit anti-tumor properties in various cancer models; however, its effects on neuroblastoma cells remain insufficiently characterized. The present study was conducted with the objective of investigating the effects of amygdalin on cell proliferation, apoptosis, and invasion in SH-SY5Y neuroblastoma cells in vitro. Materials and Methods: The SH-SY5Y neuroblastoma cells were cultivated under the optimal conditions for their growth. The cytotoxic effect of amygdalin was determined using the CCK8 assay, which is dose- and time-dependent. Total RNA isolation was performed using Trizol. Subsequently, a process of cDNA synthesis was initiated. The real-time PCR method was utilized to ascertain alterations in the expression levels of mRNA molecules associated with apoptosis, namely Bax, Bcl2, caspase-3, caspase-7, caspase-8, caspase-9, caspase-10, NFkB, and invasion-related genes MMP2, MMP9, TIMP1, and TIMP3. Furthermore, alterations in NFkB levels were examined through the utilization of the ELISA method. Results: The IC50 value of amygdalin in SH-SY5Y cells was determined to be 112.7 µM at 24 h. Amygdalin demonstrated a dose-dependent cytotoxic effect on neuroblastoma cells. Furthermore, the study revealed that the drug induced apoptosis through the upregulation of BAX and BID, and the downregulation of BCL-2 and NF-κB. This process led to a reduction in cell proliferation. Furthermore, the study demonstrated an anti-invasive effect through the downregulation of MMP9 and the upregulation of TIMP1 and TIMP3. In addition, a substantial decrease in NF-κB protein concentration was observed. Conclusions: These findings demonstrate that amygdalin exerts anti-proliferative, pro-apoptotic, and anti-invasive effects in SH-SY5Y neuroblastoma cells in vitro. Amygdalin may represent a promising natural compound for further investigation as a potential therapeutic agent in neuroblastoma.

Current Issues in Molecular Biology doi: 10.3390/cimb48050520

Authors: Lian Xia Zhaoguo Zhou Chen Luo Yan Yang Daike Zou Hanyue Zhang Kaizhi Hu Xianqin Luo

Kidney stone disease is a common urinary system disorder with a continuously rising global incidence, posing a major public health challenge. As a classic traditional Chinese medicine for the treatment of kidney stones, Lysimachia christinae Hance (LCH) has not yet been fully elucidated in terms of its pharmacological mechanism. In this study, a rat model of calcium oxalate kidney stones and a calcium oxalate monohydrate (COM)-induced injury model of human renal tubular epithelial (HK-2) cells were established. Combined with transcriptomic analysis and experimental verification, the therapeutic effect and underlying molecular mechanism of LCH against kidney stones were systematically explored. Results demonstrated that LCH extract significantly reduced serum levels of blood urea nitrogen (BUN) and creatinine (Cr), as well as renal tissue levels of kidney injury molecule-1 (KIM-1) and cystatin-C (Cys-C) in rats with calcium oxalate crystal-induced renal injury, and diminished calcium oxalate crystal deposition and adhesion in rat renal tissues as well as HK-2 cells, thus exerting a robust renoprotective effect. Mechanistically, transcriptome sequencing indicated that the anti-nephrolithiasis effect of LCH was closely related to the inhibition of oxidative stress and ferroptosis. LCH extract reversed CaOx crystal-induced upregulation of NADPH oxidase 2 (NOX2) and downregulation of superoxide dismutase 2 (SOD2), reduced intracellular oxygen species (ROS) levels, downregulated the expression of transferrin receptor 1 (TFR1) and acyl-CoA synthetase long-chain family member 4 (ACSL4) while upregulating that of ferritin heavy chain 1 (FTH1), solute carrier family 7 member 11 (SLC7A11) and glutathione peroxidase 4 (GPX4), and diminished intracellular iron accumulation, thereby effectively ameliorating crystal-mediated renal injury. The present study demonstrates that the therapeutic effect of LCH on kidney stones is closely related to the regulation of the NOX2/ROS signaling axis and ferroptosis, providing novel theoretical evidence for its clinical application.

Current Issues in Molecular Biology doi: 10.3390/cimb48050519

Authors: Siyi He Zhongyu Ren Lan Wu Yinping Xie Limin Sun Ling Xiao Gaohua Wang

Women are twice as likely to suffer from major depressive disorder (MDD). The underlying mechanism between estrogen and depression is still unknown. We used ovariectomized rats to simulate menopausal status and established a depression model of chronic and acute stress. The therapeutic effects of estrogen were systematically studied through behavioral testing, Western blotting, ELISA, LC-MS, and cell experiments. In chronic stress, OVX rats showed depressive-like behaviors, and elevated hippocampal ER, BDNF, IL-1β/IL-18, and body weight. ERT reduced depression-like behavior by 64% to 76% in the behavioral test. ERT also reversed the molecules without affecting GPR30. In acute stress, ERT reduced depression-like behavior by 20% to 58% in the behavioral test. OVX decreased ER, BDNF, P2X7, IL-1β/IL-18, spine density, and microglia and increased the expression of GPR30. ERT reversed all the above. ERT normalized metabolic abnormalities caused by CUMS. Our study demonstrates that estrogen deficiency contributes to the onset and progression of depression in a rat model of menopause-like estrogen deficiency. Estrogen replacement therapy appears to alleviate depressive-like behaviors by reducing brain inflammation and supporting the brain’s adaptive capacities through ER. Furthermore, the dual function positions GPR30 as a promising potential target for future treatments of menopausal depression, and GPR30 regulates neuroinflammation and neuroplasticity through the NLRP3/P2X7/IL-1β pathway.

Current Issues in Molecular Biology doi: 10.3390/cimb48050518

Authors: Peng Tang Jing Yang Haoyi Wang Meiqi Zhang Miao Tian Yuqin Zhao Ming Liu Rui Wang

The persistence of an immunosuppressive microenvironment remains a formidable challenge for cancer immunotherapy, particularly in tumors with immune-excluded or immune-desert phenotypes. Increasing evidence indicates that chronic inflammation and tumor progression are intrinsically linked through shared signaling hubs, including NF-κB and PI3K/Akt. Osthole, a natural coumarin compound, has been reported to exhibit both potent anti-inflammatory and antitumor activities; however, whether these effects reflect a coordinated regulation of the inflammation–cancer axis remains unclear. In this study, we deployed an integrative framework founded on network pharmacology, molecular docking, and rigorous molecular dynamics simulations, complemented by literature-based evidence synthesis, to computationally explore the potential mechanisms underlying Osthole’s dual activities. Our analysis revealed that Osthole’s predicted targets are significantly enriched in signaling pathways bridging inflammatory and oncogenic processes, most notably the PI3K/Akt, NF-κB, and TGF-β/Smad pathways. Crucially, MD simulations provided supportive computational evidence, suggesting that Osthole forms stable, energetically favorable complexes with core protein hubs (AKT1, RELA, and TGFB1) under the simulated conditions. Evidence from representative inflammatory and tumor models supports the biological plausibility of these predictions, including suppression of pro-inflammatory signaling, mitigation of maladaptive tissue remodeling, and induction of apoptosis. Furthermore, in hepatocellular carcinoma models, Osthole-mediated apoptosis appeared linked to HMGB1-related inflammatory signaling, highlighting its potential to modulate the local immune niche. Collectively, this convergence of systems-level predictions and dynamic structural evidence identifies Osthole as a promising multi-target candidate for the coordinated regulation of inflammation-associated tumor progression, providing a robust rationale for further experimental validation.

Current Issues in Molecular Biology doi: 10.3390/cimb48050517

Authors: Ergin Bilgin Deniz Baklacı Tuba Çandar

Background and Objectives: The primary objective of this study was to elucidate the diagnostic significance of systemic inflammatory indices and C1q/TNF-related proteins (CTRP3 and CTRP5) in acute facial paralysis, with a focus on identifying independent metabolic and immunological predictors. Materials and Methods: This retrospective analysis included 64 individuals (25 patients with acute facial paralysis and 39 healthy controls). Complete blood count–derived indices (neutrophil-to-lymphocyte ratio [NLR] and platelet-to-lymphocyte ratio [PLR]), serum albumin, and serum CTRP3/CTRP5 levels (ELISA) were compared between groups. Independent predictors were assessed using binary logistic regression, and discriminative performance was evaluated by ROC analysis. Results: Compared with controls, the facial paralysis group showed lower albumin (p < 0.001) and lymphocyte counts (p = 0.010), higher neutrophil counts (p = 0.012), and elevated NLR (p < 0.001) and PLR (p = 0.026). CTRP3 levels were significantly lower in patients (p = 0.002), whereas CTRP5 did not differ between groups (p = 0.853). In a parsimonious multivariable logistic regression model adjusted for NLR and CTRP3, NLR remained the only independent predictor (OR = 2.54, p = 0.004). ROC analysis showed an AUC of 0.753 for NLR and a raw AUC of 0.265 for CTRP3 (p = 0.002). An AUC significantly below 0.5 indicates that lower CTRP3 levels are associated with facial paralysis, which is statistically equivalent to an inverse predictor. Conclusions: Acute facial paralysis is characterized by a systemic inflammatory shift and reduced CTRP3 levels. Given the modest sample size, these findings should be strictly considered hypothesis-generating, suggesting that the depletion of anti-inflammatory defenses and increased inflammatory burden may play a role in the acute phase.

Current Issues in Molecular Biology doi: 10.3390/cimb48050516

Authors: Nikolaos Martinos Christos Kroupis Maria Gypari Georgios Kranidiotis Christos Karakoidas Marina Konstantinou Andreas C. Lazaris Georgia-Eleni Thomopoulou

Background/Objectives: Histologic mucosal healing is an increasingly recognized therapeutic target in inflammatory bowel disease (IBD), yet reliable non-invasive correlates remain limited. This study aimed to evaluate circulating cytokine patterns as detectability-based immune signals across the spectrum of histologic disease activity. Methods: In this prospective cross-sectional study, 59 patients with IBD and 36 healthy controls were enrolled. Serum interleukin-10 (IL-10) and interleukin-23 (IL-23) were quantified by ELISA. Histologic activity was graded using the Geboes score. Associations were assessed using non-parametric methods and multivariable logistic regression with Firth penalization. Results: IL-10 demonstrated apparent separation across histologic states, primarily driven by reduced detectability in active inflammation, and was inversely associated with histologic severity. IL-10 remained associated with histologic status, although estimates should be interpreted cautiously. Detectable IL-23 was confined to moderate-to-severe inflammation and did not show graded discrimination, with interpretation limited by the small number of detectable observations. Conclusions: IL-10 and IL-23 exhibit complementary patterns, reflecting detectability-based regulatory signaling and a severity-dependent inflammatory threshold, respectively, without evidence of independent clinical utility for IL-23 in the present dataset. These findings are exploratory and require validation in larger prospective cohorts.

Current Issues in Molecular Biology doi: 10.3390/cimb48050515

Authors: Alexandre Tavartkiladze Levan Tavartkiladze Russel J. Reiter Michel Burnier Dinara Kasradze Nana Okrostsvaridze Pati Revazishvili Revaz Turmanidze

Circadian desynchronization is increasingly linked to metabolic, immune, neurocognitive, and oncological disease, but integrated clinical phenotyping across endocrine, microbiome, metabolic, and neuroimaging domains remains limited. We conducted a prospective, single-centre, observational study in 179 symptomatic patients referred for chronic multisystem features consistent with circadian dysregulation and 107 practically healthy controls. Circadian melatonin status was assessed using fractionated 24 h urinary 6-sulfatoxymelatonin (aMT6s) and standardized dim-light plasma sampling at daytime (14:00–16:00) and nocturnal (02:00–04:00) windows. Microbiome composition was assessed by 16S rRNA sequencing, urolithin A by targeted metabolomics, and putative glymphatic/perivascular clearance by MRI-derived DTI-ALPS index, perivascular space scoring, and white-matter-hyperintensity (WMH) volumetry. Patients showed markedly reduced nocturnal melatonin output and loss of day–night contrast (night aMT6s 10.2 vs. 40.6 ng/mL; urinary aMT6s day/night ratio 0.81 vs. 0.14; plasma nocturnal melatonin 12.7 vs. 54.4 pg/mL; all p < 0.0001), accompanied by altered cortisol day–night patterning. Patients also showed reduced microbiome diversity, depletion of Gordonibacter and Ellagibacter, lower plasma urolithin A, higher WMH volume and perivascular space scores, and a lower DTI-ALPS index. Age distributions broadly overlapped in the individual-level dataset, and key biomarkers were not significantly correlated with chronological age within the patient cohort; however, this finding is interpreted as an exploratory absence of detectable age gradient within the symptomatic cohort, not as proof of biological age-independence. Overall, the data support a coherent cross-sectional association among blunted nocturnal melatonin rhythmicity, dysbiosis/urolithin depletion, and MRI markers compatible with impaired perivascular clearance. The MGM axis framework should be regarded as hypothesis-generating; causal direction, melatonin receptor involvement, and AQP4-related mechanisms require longitudinal and mechanistic validation.

Current Issues in Molecular Biology doi: 10.3390/cimb48050514

Authors: Rida-e-Zainab Kayani Komal Aman Tajamul Hussain Hazir Rahman Ziaur Rahman Ahmed Muhammad Ajaz Muhammad Latif Salman Alrokayan

Background: Microbial derivatives are pivotal in research because of their structural heterogeneity and diverse biological significance, including antitumor and antimicrobial activities. Aims and Objectives: This study aimed to evaluate the molecular characterization, antibacterial effects on multidrug-resistant (MDR) gastrointestinal pathogens, and potential anticancer activity of soil bacterial isolates. Methodology: Two bacterial isolates, Bacillus subtilis (B. subtilis) and Bacillus paralicheniformis (B. paralicheniformis), were characterized for their metabolic profiles and antimicrobial efficacy. Evolutionary relationships were determined using Sanger sequencing and MEGA-7 software. Secondary metabolites were characterized using Gas Chromatography–Mass Spectrometry (GC-MS), potentially contributing to the development of novel therapeutic agents. Results:B. subtilis and B. paralicheniformis were identified as microbial strains, with 11 and 28 compounds isolated from their extracts, respectively, and evaluated for their efficacy against gastrointestinal pathogens. The extracts also demonstrated potential anticancer effects, with significant DPPH-scavenging activity. B. subtilis exhibited higher Superoxide Dismutase (SOD) activity, suggesting the presence of antioxidant bioactive compounds. This study also documented alterations in the apoptotic and anti-apoptotic gene expression patterns in HCT-116 cells treated with the extracts. Notably, the increase in BAK and BAX expression suggests a possible link to the apoptotic response in HCT-116 cells. Conclusions: This study highlights the diversity of bacterial communities in soil that produce numerous secondary metabolites with therapeutic potential, including antibacterial and anticancer properties.

Current Issues in Molecular Biology doi: 10.3390/cimb48050513

Authors: Oksana V. Sazonova Dmitry N. Fedorin Alexander T. Eprintsev Abir U. Igamberdiev

The expression of two genes, Fum1 and Fum2, encoding the mitochondrial and cytosolic forms of fumarase (EC 4.2.1.2); the methylation of individual CpGs of their promoters; and fumarase activity were studied in sunflower (Helianthus annuus L.) leaves depending on irradiation and salinity. Fumarase activity was twice as high in darkness compared to irradiation by white light and red light, while far-red light applied after darkness or after red light reverted the activity to the values in darkness, which indicates the involvement of phytochrome. Using qRT-PCR, it was demonstrated that this corresponded to the pattern of expression of the Fum1 gene, while the expression of the Fum2 gene was higher upon irradiation by white and red light, and lower in darkness and under far-red light. Under the application of 150 mM NaCl for 1, 3, 6, 12, and 24 h, fumarase activity increased fivefold from the start of incubation to 6 h, and then decreased after 12 h. These changes were associated with the transcriptional regulation of the Fum1 and Fum2 genes. Changes in the methylation status of the analyzed CpGs in their gene promoters, detected via semi-quantitative methylation-specific PCR, were associated with differences in their expression. The higher methylation levels of the analyzed CpGs in the Fum1 gene promoter under different light conditions and in the Fum2 gene promoter under salinity corresponded to low levels of their transcripts in sunflower leaves. It is suggested that the mitochondrial and cytosolic forms of fumarase are regulated by light and salinity at the gene expression level, presumably through changes in the methylation status of individual CpGs in their promoters.

Current Issues in Molecular Biology doi: 10.3390/cimb48050512

Authors: Nan Liu Yi Zheng Xiaojun Xu

Minimal residual disease (MRD) is the most robust independent prognostic biomarker for pediatric acute lymphoblastic leukemia (ALL). Conventional MRD detection assays suffer from insufficient sensitivity and inherent technical limitations, failing to identify ultra-low-level leukemic blasts and thereby contributing to disease relapse. Next-generation sequencing (NGS)-based MRD detection (NGS-MRD) overcomes these drawbacks by targeting immunoglobulin (Ig)/T-cell receptor (TCR) gene rearrangements and enabling the precise quantification of residual leukemic clones. In recent years, NGS-MRD has undergone extensive technological optimization in target panel design, result interpretation and sample type expansion, and has been validated for its clinical utility in therapeutic threshold definition, prognostic stratification, post-therapy monitoring and treatment adjustments in pediatric ALL. This review synthesizes the latest technological refinements and clinical applications of NGS-MRD in pediatric ALL, critically discusses the current challenges that limit its routine clinical use, and proposes future research directions to address these issues.

Current Issues in Molecular Biology doi: 10.3390/cimb48050510

Authors: Guliziremu Ainiwaer Xiaoxuan Zhang Mukatansi Tayier Xin Luo

Background: The development of Slow Transit Constipation (STC) is associated with intestinal barrier damage. Coreopsis tinctoria Nutt. (CT) is effective in treating STC, but the mechanisms are unclear. Methods: We investigated three CT extracts—traditional aqueous extract, and an aqueous extract from supercritical fluid extraction, with or without lipophilic components—on intestinal transit in a loperamide-induced STC rat model. The potential therapeutic targets of CT for STC were initially predicted using an integrated approach of network pharmacology and molecular docking. The therapeutic effect of CT was evaluated in a STC rat model by assessing defecation parameters (fecal count, water content, intestinal transit), colon histology (H&E and AB-PAS staining), inflammatory markers (ELISA), and target protein expression (Western blotting and immunohistochemistry). In parallel, an LPS-induced IEC-6 cell injury model was used to investigate intestinal barrier protection, analyzing cell viability (CCK-8), apoptosis (flow cytometry and Western blotting), migration (scratch assay), and protein expression (Western blotting). Results: Docking and enrichment analysis highlighted hub targets (TNF, AKT1, Caspase3, STAT3, and BCL-2) and the PI3K/AKT pathway. In vivo, CT treatment improved defecation function, reduced colonic damage, and decreased markers of inflammation and apoptosis in STC rats. It also up-regulated ZO-1 and Occludin, lowered serum markers of intestinal permeability D-lactate (D-LA) and Diamine oxidase (DAO), and restored intestinal barrier function. Furthermore, CT reduced Caspase3 expression and increased the expression of proteins such as BCL-2, PI3K, and P-AKT/AKT. These findings were further supported by in vitro experiments. Conclusions: CT improves STC and its associated intestinal barrier damage by activating the PI3K/AKT pathway and suppressing inflammation and apoptosis, among which the aqueous extract from supercritical fluid extraction combined with the lipophilic fraction exhibits the best efficacy.

Current Issues in Molecular Biology doi: 10.3390/cimb48050511

Authors: Deepika Lal Jaswinder Singh Maras Rakhi Maiwall Anupam Kumar Chhagan Bihari

Background and Aims: Anemia is seen in nearly >70% of patients with cirrhosis and is often non-responsive to nutritional supplements; therefore, we assessed the erythropoiesis and associated alteration in bone marrow (BM). Methods: It is a cross-sectional study. Flow cytometry was performed to assess the hematopoietic stem cells (HSCs) and erythroid population of 60 patients with cirrhosis compared with patients with 7 non-cirrhotic portal fibrosis (NCPF) and 3 controls. Proteomics were performed of the pure CD71 erythroid population taken from patients with cirrhosis to decipher the internal abnormalities supported by validation experiments. Real Time PCR, colony assay and heme quantification, cytokine array, and ELISA were performed to assess erythropoietic stimulating agents (ESA), inflammatory cytokines, and growth factors as an external factor affecting erythropoiesis. Results: We found a decrease in intermediate erythroid progenitors [IEPs; CD71+ CD235a+], conversely early erythroid precursors [EEP; CD71+ CD235a−] and late erythroid progenitors [LEP; CD71− CD235a+] were increased (p < 0.05) in cirrhotic and NCPF as compared to control. However, unlike NCPF, cirrhosis exhibited decreased CD71+ transferrin receptor (TfR1) expression over erythroid cells and increased immature erythrocytes (p < 0.05) in peripheral circulation. In vitro culture of erythroid precursors showed impaired differentiation and maturation that was confirmed by the reduced (p < 0.05) number of erythroid colonies (BFU-E). Proteomics analysis showed downregulated proteins associated with hemoglobin synthesis, ROS detoxification, translation, and mitochondrial activity. Furthermore, we found an altered expression of genes related to erythropoiesis and hemoglobin synthesis and increase (p < 0.05) in inflammatory cytokines such as IL-5, TRAIL-R2, TGF-α, and TGF-β in BM. Conclusions: This study suggests that the dysregulated erythropoiesis observed in patients with cirrhosis having anemia is maintained despite adequate nutrition.

Current Issues in Molecular Biology doi: 10.3390/cimb48050509

Authors: Yaqing Yang Mingzi Shi Yaxin Liu Xiaomei Gao Hui Li Laming Pei

Maize (Zea mays L.) is a vital global crop whose productivity is severely threatened by abiotic stresses. Epicuticular waxes provide a hydrophobic barrier that protects land plants from environmental stresses. However, the role of key wax biosynthetic enzymes, such as aldehyde decarbonylase CER1, in maize stress adaptation remains unclear. In this study, we performed a functional characterization of ZmCER1 in maize. Our results show that the overexpression of ZmCER1 in both Arabidopsis and maize substantially improved tolerance to these abiotic stresses. Under stress conditions, the transgenic plants displayed better growth performance, elevated activities of antioxidant enzymes, and reduced levels of oxidative damage markers. Additionally, the alkane content—especially that of C29 and C31—was significantly increased in the ZmCER1OE lines. Through a yeast two-hybrid screening (Y2H screening), we identified the peroxisomal membrane protein ZmPEX14 as an interacting partner of ZmCER1, and the interaction was further confirmed by luciferase complementation (LUC) and bimolecular fluorescence complementation (BiFC) assays. We propose a model wherein ZmCER1 enhances stress tolerance not only by reinforcing the cuticular wax barrier but also by potentially regulating reactive oxygen species (ROS) detoxification via association with ZmPEX14. Collectively, our findings establish ZmCER1 as a key regulator of abiotic stress tolerance in maize and a promising candidate for the molecular breeding of stress-resilient crops.

Current Issues in Molecular Biology doi: 10.3390/cimb48050508

Authors: Darrell O. Ricke

Background/Objectives: Kawasaki’s disease (KD) is a leading cause of heart disease in children. The multisystem inflammatory syndrome (MIS) associated with the SARS-CoV-2 virus is similar to KD. The etiologies of KD and MIS are unknown. Both diseases are associated with pathogens and immunizations. Methods: The Vaccine Adverse Event Reporting System (VAERS) was retrospectively examined for etiology insights into both KD and MIS. Results: Statistically significant, elevated AE MIS safety signals were observed for several COVID-19 Pfizer-BioNTech manufacturing lots. Elevated AE MIS normalized frequencies were observed in children of all ages. Immediate-onset AE KD safety signals were detected for specific vaccines and coadministered combinations of these vaccines (including specific live, attenuated virus vaccines and other specific vaccines) for young infants; a subset of these safety signals has a male sex bias, whereas others appear to be unbiased. Conclusions: Both KD and MIS are hypothesized to involve two activation pathways. The first pathway is hypothesized to involve high titers of immune complexes that activate Fc receptors on mast cells, platelets, and other immune cells. Immune complex titers higher than primary immune response levels are hypothesized to be required to activate low-affinity IgGFcγR2α receptors on immune cells and platelets. IVIG treatment is hypothesized to directly compete with immune complex binding to FcγR2α receptors. The second hypothesized pathway is proposed to directly activate mast cells and other immune cells without involving immune complexes and Fc receptors; lack of Fc receptor competition by immune complexes is hypothesized as a possible explanation for IVIG nonresponders for KD and MIS, worthy of future studies. The proposed etiology models for both KD and MIS may be consistent with being novel mast cell activation syndromes (MCAS). MIS is hypothesized to be KD-associated with the SARS-CoV-2 virus or the COVID-19 spike protein (MIS-V).

Current Issues in Molecular Biology doi: 10.3390/cimb48050507

Authors: Theophilus Bhatti Hong-Yi Xiang Jihyun Lee Ji-Yeong Bae Jinu Kim

Rubus buergeri Miq., a wild species native to Jeju Island (Republic of Korea), is a relatively understudied plant with potential as a source of bioactive phenolic compounds. This study investigated the phytochemical composition of R. buergeri extract (RBE) and evaluated its antioxidant and anti-inflammatory activities using a bioactivity-guided fractionation approach. Antioxidant capacity was assessed by 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), and ferric reducing antioxidant power assays (FRAP), along with total phenolic content determination, while anti-inflammatory activity was evaluated by measuring nitric oxide (NO) production and inflammatory gene expression in lipopolysaccharide (LPS)-stimulated RAW 264.7 macrophages. RBE exhibited high phenolic content and strong antioxidant activity; its ethyl acetate and n-butanol fractions demonstrated the greatest antioxidant activities and significantly inhibited LPS-induced NO production. Furthermore, RBE suppressed LPS-induced mRNA expression of Nos2, Ptgs2, Tnfa, Il1b, and Il6, indicating coordinated inhibition of inflammatory responses. Ultra-high-performance liquid chromatography (UHPLC) analysis identified ellagic acid, ethyl gallate, and epicatechin as major phenolic constituents, with ellagic acid and ethyl gallate showing stronger inhibitory effects on NO production and inflammatory gene expression than epicatechin. These findings suggest that the phenolic constituents of R. buergeri modulate NO-associated inflammatory responses and support its potential as a source of anti-inflammatory phytochemicals.

Current Issues in Molecular Biology doi: 10.3390/cimb48050506

Authors: Wafa Khelaifia Ines Gouaref Fatma Zohra Djaballah-Ider Nabila Bouterfas Chafia Touil-Boukoffa Assia Galleze

Survivors of childhood leukemia are at increased risk of long-term skeletal complications, including reduced bone mineral density (BMD). Vitamin D deficiency and genetic variations in the vitamin D receptor (VDR) gene are important factors influencing bone health, yet their combined effects remain insufficiently studied, particularly in North African populations. This case-control study included 130 survivors of childhood acute lymphoblastic leukemia (ALL) in remission (age range: 5–26 years) and 110 age- and sex-matched healthy controls recruited from Beni Messous Hospital. BMD was assessed at the lumbar spine and femoral neck using dual-energy X-ray absorptiometry and expressed as z-scores. Serum 25-hydroxyvitamin D levels were measured, and VDR polymorphisms (FokI, ApaI, and BsmI) were analyzed using PCR-RFLP. Hypovitaminosis D was observed in 43.85% of patients at diagnosis and 23.07% after remission. Survivors had significantly lower BMD compared with controls at both the lumbar spine (z-score: −4.26 ± 0.75 vs. 0 ± 1, p < 0.001) and femoral neck (−3.78 ± 0.45 vs. 0 ± 1, p < 0.001). Reduced BMD for age was identified in 30% of patients. Variant genotypes TT (FokI), AA (BsmI), and CC (ApaI) were more frequent in patients and were associated with lower BMD (p < 0.0001). These findings suggest that hypovitaminosis D and VDR polymorphisms may be associated with bone health in survivors of childhood leukemia. The coexistence of these factors may contribute to interindividual variability in BMD.

Current Issues in Molecular Biology doi: 10.3390/cimb48050505

Authors: Gabriel Augusto Marques Rossi Fábio Parra Sellera Eliana Guedes Stehling João Pedro Rueda Furlan

Aminoglycoside resistance is commonly mediated by enzymatic modification, target alteration, or efflux mechanisms; however, acquired resistance has not been characterized in radiation-resistant Deinococcus species. Here, we investigated the occurrence and genomic context of acquired aminoglycoside resistance genes in all publicly available Deinococcus radiodurans genomes. A total of 19 genomes were screened using ResFinder and CARD, followed by comparative genomic analyses. The aadA1 gene was identified in two genomes, being located on the plasmid pSP1 in strain R1 dM1, a known shuttle vector used for genetic manipulation. In contrast, aadA1 was found on a chromosomal contig in strain DRR11, suggesting a possible assembly artifact. Additionally, the aph(3′)-Ia gene was detected in three genomes within a conserved chromosomal region that lacks this gene in reference strains. Sequence similarity analyses indicated that aph(3′)-Ia is associated with laboratory vectors, being consistent with a potential non-natural origin. Considering the high recombination capacity and genomic plasticity of D. radiodurans, these findings suggest that the detected aminoglycoside resistance genes may be derived from laboratory constructs, potentially combined with assembly inconsistencies or chromosomal integration events. Therefore, this study highlights the importance of integrating genomic context with molecular and evolutionary plausibility to avoid misinterpretation of antimicrobial resistance in extremophiles and model organisms, and underscores the importance of complementary raw-read analyses to distinguish natural acquisition from technical or laboratory-derived origins.

Current Issues in Molecular Biology doi: 10.3390/cimb48050504

Authors: I-Chang Lai De-Yi Liu Shih-Chan Hsu Shu-Jui Kuo

In the published article [...]

Current Issues in Molecular Biology doi: 10.3390/cimb48050503

Authors: Buang Matseke Daniel Tswaledi Kokoette Bassey

Background: Momordica balsamina L. is widely used in traditional medicine for the management of diabetes in South Africa and globally. This study evaluated the in vitro antidiabetic and cytotoxic effects of M. balsamina leaf extracts and identified bioactive compounds potentially responsible for its activity. Methods: Leaves were sequentially extracted using solvents of increasing polarity. Phytochemical composition was determined using standard colorimetric assays, while gas chromatography–mass spectrometry (GC–MS) was employed for compound identification. Antioxidant activity was evaluated using dot blot, DPPH radical scavenging, hydrogen peroxide scavenging, and ferric reducing power assays. Antidiabetic potential was assessed using α-amylase, α-glucosidase, and β-glucosidase inhibitory assays, with acarbose as the reference drug. Cytotoxicity was determined by using the MTT assay on Vero and HEK-293 cell lines. Results: Phytochemical screening revealed alkaloids, flavonoids, terpenoids, saponins, glycosides, and steroids. GC–MS analysis identified compounds associated with antidiabetic activity, including vanillin, 2,4-di-tert-butylphenol, oleic acid, phytol, and hexadecenoic acid. All extracts exhibited antioxidant activity, with the ethyl acetate extract showing the strongest effect. Enzyme inhibition was concentration dependent. The dichloromethane and ethyl acetate extracts showed stronger α-amylase inhibition (IC50 = 0.149 and 0.146 mg/mL) than acarbose (0.209 mg/mL). For α-glucosidase, acarbose showed the highest activity, while extracts displayed moderate inhibition. In β-glucosidase assays, both extracts were more active than acarbose. Both extracts were non-cytotoxic up to 500 µg/mL. Conclusions: These findings support the traditional use of M. balsamina and highlight its potential as a safe source of antidiabetic agents, warranting further investigation.

Current Issues in Molecular Biology doi: 10.3390/cimb48050501

Authors: Hazrat Bilal Imran Khan Ayesha Yaseen Xiaopeng Zhang Xuexue Liu Jian Zhao Jing Li Ata Ur Rehman Lei Sun Xiao Yu

The gut–heart axis plays a role in cardiac injury due to the disruption of barriers, endotoxemia, and inflammatory signaling; yet, it is not clear whether sodium butyrate (SB) is capable of alleviating isoprenaline-induced myocardial injury through coordinated intestinal, microbial, and metabolic restoration. This study used male Sprague-Dawley rats, which were grouped into control, control + SB, isoprenaline (ISO)-induced myocardial injury, and ISO + SB groups. We evaluated cardiac biomarkers of injury, oxidative stress, histopathologic, intestinal barrier (16S rRNA sequencing), and serum metabolomics (LC-MS). SB treatment decreased serum cardiac troponin I, creatine kinase-MB, and lactate dehydrogenase; relieved oxidative stress; and lowered myocardial necrosis and fibrosis. It re-established colonic architecture, upregulated the expression of ZO-1 (zonula occludens-1) and claudin-1, and reduced endotoxin in the bloodstream. SB also prevented the production of proinflammatory cytokines such as TNF-α, IL-6, and IL-1β; cardiac TLR4; IκBα degradation; and NF-κB p 65 phosphorylation. In addition, SB altered the gut microbiota in favor of beneficial commensals, including Ligilactobacillus and Bifidobacterium, and reduced Desulfovibrio. It normalized key circulating metabolites and enriched cardiometabolic pathways, and the patterns of correlation suggested the coordinated remodeling of the microbiome–metabolome. These findings reveal that SB prevents myocardial injury caused by ISO through strengthening gut barrier protection, alleviating endotoxemia, inhibiting TLR4/NF-κB, and remodeling the microbiome–metabolome axis, indicating its potential for use as a gut-targeted cardioprotective intervention.

Current Issues in Molecular Biology doi: 10.3390/cimb48050502

Authors: Jakub Wnuk Wiktoria Skowron Anna Długaszek Joanna Sadurska Łukasz Pietrzyński Jacek Kabut Iwona Gisterek-Grocholska

Pancreatic cancer (PC) is considered one of the deadliest cancers worldwide, and the number of PC-related deaths is expected to increase. Early diagnosis of PC is crucial for improving treatment outcomes. Despite improvements in overall survival (OS) in metastatic and unresectable PC due to systemic therapy, there is still a need to search for novel therapies and factors predictive of response to treatment. Cancer profiling based on genome sequencing can be used to develop targeted therapies and improve prognostics and treatment outcomes. Therefore, this review was conducted to evaluate the clinical value of molecular subtyping in pancreatic cancer as a prognostic and predictive factor in pancreatic cancer. Due to its limitations, including the lack of a registered protocol and risk of bias assessment for the included studies and those whose results were not included, this study should be considered a narrative review with a structured search strategy rather than a systematic review.

Current Issues in Molecular Biology doi: 10.3390/cimb48050500

Authors: Dimitra Ioannidou Ioulietta Samartza Georgios Tsoktouridis Andreas D. Drouzas Nikos Krigas

Crete, a major Mediterranean biodiversity hotspot, hosts many local endemic, threatened and/or protected plant taxa (species and subspecies). Besides their ecological and conservation significance, these unique phytogenetic resources hold significant economic potential for sustainable utilization. Since DNA barcoding is critical for conservation, taxonomy, and plant-derived product authentication, we studied 15 local Cretan endemic taxa using three chloroplast DNA (cpDNA) regions (rbcL, trnL, trnH-psbA). A comparative analysis against GenBank (NCBI) records revealed significant new data: (i) the first genetic information for five taxa (Centaurea redempta subsp. redempta, Galium fruticosum, Micromeria hispida, Salix kaptarae, Teucrium cuneifolium); (ii) new marker-specific sequences for seven taxa (Helichrysum heldreichii, Scutellaria hirta, Sesleria doerfleri, Staehelina petiolata, Teucrium alpestre, Campanula pelviformis, Phlomis lanata); and (iii) novel genotypes of already represented markers for three species (Phlomis lanata, Scutellaria sieberi, Staehelina petiolata). Phylogenetic analyses were performed for all three molecular markers across selected members of Scutellaria section Scutellaria, Teucrium section Polium, and Campanula section Quinqueloculares. The overall results indicated that, amongst the studied species, the trnH-psbA marker is more suitable for species-level identification, whereas the rbcL and trnL markers were more helpful to genus-level identification within Lamiaceae and Campanulaceae. These results enrich the DNA barcoding reference library and form a concrete contribution towards the protection, conservation and traceability of Crete’s unique botanical heritage.

Current Issues in Molecular Biology doi: 10.3390/cimb48050499

Authors: Jiayu Liu Yuxin Wang Zhao Gao Tongtan Liu Ao Xu Wenxuan Li Mei Li Xiaomeng Song Baorui Guo Huadong Wang Wenying Lv Jianning Zhang

Glioblastoma (GBM) remains the most aggressive primary malignant brain tumor in adults, with limited survival benefit from the current standard of care consisting of maximal safe resection, radiotherapy, and temozolomide-based chemotherapy. The highly infiltrative growth pattern, profound intratumoral heterogeneity, and strongly immunosuppressive tumor microenvironment together contribute to therapeutic resistance and frequent recurrence. In this context, oncolytic herpes simplex virus (oHSV) has emerged as a promising therapeutic platform for glioblastoma because of its dual capacity to directly lyse tumor cells and stimulate antitumor immune responses. In addition, the large viral genome and well-characterized biology of herpes simplex virus enable extensive genetic engineering to improve tumor selectivity, safety, and immunomodulatory function. In this review, we summarize the molecular design strategies that have driven the development of oHSV for glioblastoma, including attenuation of neurovirulence, enhancement of tumor-selective replication, and arming with immune-stimulatory transgenes. We further discuss the major biological barriers within the GBM tumor microenvironment that continue to limit therapeutic efficacy, with particular attention given to representative engineered oHSV platforms and the lessons learned from preclinical and early-phase clinical studies. A dedicated section examines these barriers in detail, including restricted intratumoral viral spread, antiviral innate immunity, and immunosuppressive myeloid cell dominance. We also review current efforts to improve outcomes through rational combination strategies with radiotherapy, immune checkpoint blockade, cytokine modulation, and other multimodal approaches. Although encouraging advances have been achieved, the clinical translation of oHSV therapy for glioblastoma still faces substantial challenges in patient selection, delivery optimization, response assessment, and treatment integration. A deeper understanding of virus–host–tumor interactions and more precise engineering of viral platforms may help unlock the full potential of oHSV-based therapy. Overall, oHSV represents one of the most compelling translational approaches in glioblastoma and provides a valuable framework for the development of mechanism-driven viro-immunotherapy in neuro-oncology.

Current Issues in Molecular Biology doi: 10.3390/cimb48050498

Authors: Ane Larrea Mariyem Naji Marina Gulak Maria Torrecilla Gabriel Barreda-Gómez

High-level athletic performance requires the implementation of personalized strategies based on the analysis of metabolic pathways involved in energy production: phosphagen, glycolytic, and oxidative pathways. In this context, mitochondria play an essential role as the central regulator of energy production, being closely linked to these three pathways. Exercise boosts cellular respiration, which can also be optimized by nutritional interventions and targeted supplementation, promoting mitochondrial biogenesis, reducing oxidative stress and increasing ATP production. These metabolic adaptations improve athletic performance, accelerate recovery processes, and reduce the risk of injury, adapting to the physiological characteristics of each athlete. Moreover, some of these metabolic adaptations converge on specific targets whose expression or activity is also altered in mental disorders. Therefore, the aim of this review is to analyze mitochondrial adaptations induced by exercise and supplementation, evaluating their impact on the phosphagen, glycolytic, and oxidative metabolic pathways, as well as their relationship with optimizing performance and recovery in high-level athletes, with special attention to their potential application to mental health.

Current Issues in Molecular Biology doi: 10.3390/cimb48050497

Authors: Ana Yanina Bustos Juan José Carol Paz Jorge Nicolás Gómez Ana Estela Ledesma

The rapid characterization of lactic acid bacteria (LAB) with probiotic and technological properties is crucial for functional food design. In this study, fourteen LAB strains belonging to the species Lactiplantibacillus (L.) plantarum, Lentilactobacillus (L.) parabuchneri, and Leuconostoc (L.) mesenteroides were differentiated using Raman spectroscopy. By integrating Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA), we achieved a clear inter-generic separation while simultaneously enabling the intra-specific grouping of L. plantarum strains. Our results demonstrate that the Raman spectral fingerprint, coupled with supervised chemometric models, successfully categorized the strains into three distinct clusters based on their macromolecular profiles. Specifically, the analysis provided high-resolution differentiation between genera and, more importantly, allowed for the fine-scale clustering of diverse L. plantarum isolates. This highlights Raman spectroscopy as a robust, non-destructive tool for the rapid identification and taxonomic classification of LAB, offering a high-throughput alternative to traditional molecular methods for strain-level discrimination.

Current Issues in Molecular Biology doi: 10.3390/cimb48050496

Authors: Hilal Oğuz Soydinç Sena Şen Murat Serilmez Senem Karabulut

Colorectal cancer (CRC) remains a major cause of cancer-related morbidity and mortality worldwide. Metastasis regulators and matrix metalloproteinases have been implicated in tumor progression; however, their clinical significance in CRC remains incompletely defined. In this study, the prognostic value of MACC1 and MMP8 expression levels was investigated. A total of 140 patients diagnosed with CRC and 48 healthy controls were included. Serum levels of MACC1 and MMP8 were measured using ELISA. Clinicopathological parameters were recorded, and their associations with biomarker expression were analyzed. Both MACC1 and MMP8 levels demonstrated moderate diagnostic performance with comparable area under the curve values. A strong positive correlation between MACC1 and MMP8 expression was observed. MACC1 expression was significantly associated with metastasis status and tumor stage, whereas MMP8 expression was associated with tumor localization. In survival analyses, established clinicopathological factors, particularly tumor stage and metastasis status, were identified as the primary determinants of overall survival. In multivariate analysis, tumor stage remained the only consistent independent prognostic factor, while MMP8 showed a modest independent association in a separate model. MACC1 did not retain independent prognostic significance. Although MACC1 and MMP8 may have diagnostic and biological relevance in CRC, their prognostic utility appears limited compared to established clinical parameters. Further large-scale prospective studies are needed.