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Current and Emerging Therapeutic Strategies for the Treatment of Duchenne Muscular Dystrophy -
When Bones Blur the Lines: Ancient DNA Validation of Morphological Sex Estimation Traits and the Challenges of Population-Specific Dimorphism -
From Longevity Genetics to Precision Interventions: Integrating Nutrigenomics and Epigenetic Mechanisms of Ageing -
Clinical Applications of Liquid Biopsy in Colorectal Cancer: A Focus on Registered Clinical Trials -
Pharmacogenetic Analysis of Variants in IL-6 Signaling and Response to Modern Therapeutic Approaches in Greek Patients with Atopic Dermatitis
Journal Description
Genes
Genes
is a peer-reviewed, open access journal of genetics and genomics published monthly online by MDPI. The Epigenetics Society (ES) and the Spanish Society for Nitrogen Fixation (SEFIN) are affiliated with Genes, and their members receive discounts on the article processing charges.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, SCIE (Web of Science), PubMed, MEDLINE, PMC, Embase, PubAg, and other databases.
- Journal Rank: JCR - Q2 (Genetics and Heredity) / CiteScore - Q2 (Genetics (clinical))
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 13.3 days after submission; acceptance to publication is undertaken in 3.7 days (median values for papers published in this journal in the first half of 2026).
- Recognition of Reviewers: Reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.
Impact Factor:
3.1 (2025);
5-Year Impact Factor:
3.3 (2025)
Latest Articles
Expanding the Phenotypic Spectrum of PRKD1 Gain-of-Function Syndrome: Congenital Heart Disease, Bilateral Carotid Dissections, and Ectodermal Dysplasia in an Adult Patient
Genes 2026, 17(9), 1048; https://doi.org/10.3390/genes17091048 (registering DOI) - 30 Aug 2026
Abstract
Background: PRKD1-related congenital heart defects and ectodermal dysplasia syndrome (CHDED) is a rare multisystem developmental disorder caused by heterozygous gain-of-function variants in PRKD1. Reported phenotypes include congenital heart defects, ectodermal abnormalities, limb anomalies, and neurodevelopmental impairment, while vascular manifestations remain poorly
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Background: PRKD1-related congenital heart defects and ectodermal dysplasia syndrome (CHDED) is a rare multisystem developmental disorder caused by heterozygous gain-of-function variants in PRKD1. Reported phenotypes include congenital heart defects, ectodermal abnormalities, limb anomalies, and neurodevelopmental impairment, while vascular manifestations remain poorly characterized. We report an adult patient with a de novo PRKD1 variant and bilateral carotid artery dissections. Methods: Clinical, cardiovascular, neurological, and genetic evaluations were performed, including SNP-microarray and trio whole-exome sequencing with additional analysis of genes associated with heritable thoracic aortic and connective tissue disorders. Results: The patient was diagnosed at 35 years of age with a de novo PRKD1 c.1808G>A p.(Arg603His) variant. He had childhood-onset congenital heart disease, ectodermal and skeletal abnormalities, hearing impairment, infertility, and learning difficulties. In adulthood, he developed bilateral carotid artery dissections and mild aortic dilatation. No additional pathogenic or likely pathogenic variants were identified in the evaluated connective tissue and heritable aortic disease genes. The PRKD1 variant was absent or extremely rare in population databases and had supporting functional evidence for a gain-of-function effect. Conclusions: This case raises the possibility of a previously unrecognized vascular manifestation of PRKD1-related CHDED. Although a biological association is plausible, causality cannot be established from a single case. Further clinical and functional studies are needed to determine whether vascular fragility is a recurrent feature of PRKD1-related disease. This case also highlights the importance of considering rare genetic syndromes in patients with unexplained arteriopathy and congenital heart disease.
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(This article belongs to the Special Issue Advances in Genetic Insights into Cardiovascular Diseases)
Open AccessArticle
The Inhibition of Histone Lysine Demethylases Affects Head and Neck Cancer Cell Growth and Response to Cisplatin
by
Dawid Dorna, Robert Kleszcz, Violetta Krajka-Kuźniak and Jarosław Paluszczak
Genes 2026, 17(9), 1047; https://doi.org/10.3390/genes17091047 (registering DOI) - 30 Aug 2026
Abstract
Background/Objectives: Head and neck squamous cell carcinomas (HNSCC) are a heterogenous group of tumors, which are usually treated with surgery and radiotherapy, while chemotherapy (e.g., cisplatin), anti-EGFR, or immune checkpoint inhibitors are used to treat locoregionally advanced and recurrent cases. However, survival
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Background/Objectives: Head and neck squamous cell carcinomas (HNSCC) are a heterogenous group of tumors, which are usually treated with surgery and radiotherapy, while chemotherapy (e.g., cisplatin), anti-EGFR, or immune checkpoint inhibitors are used to treat locoregionally advanced and recurrent cases. However, survival outcomes are still unsatisfactory, and novel augmenting treatments are required. Recently, histone lysine demethylases (KDMs) emerged as promising anti-cancer targets. In order to further characterize KDM4–6 as pharmacological targets in HNSCC, we evaluated changes in KDM4/5/6 expression in HNSCC patients, and we experimentally assessed the biological effects of inhibitors of KDM4/5/6 in HNSCC cell lines. Methods: We used online tools (TIMER, GEPIA3, UALCAN) to analyze TCGA data from HNSCC patients. Then, we used resazurin assay to assess the effect of ML324, GSK-J4, and JIB-04 (the inhibitors of KDM4, KDM6, and KDM4–6, respectively) on cell viability in two-dimensional (2D) and three-dimensional (3D) culture of FaDu, SCC-152, and Detroit-562 cells. The potential for cisplatin sensitization was also assessed. Gene/protein expression was evaluated by qPCR and antibody array. Results: We found that the majority of the analyzed KDMs were overexpressed in HNSCC, except KDM4C, KDM5D, and KDM6A. All three studied inhibitors significantly reduced cell viability in 2D and 3D cell cultures. Moreover, the pre-treatment of cells with KDM inhibitors showed moderate potential for cisplatin sensitization. In addition, the chemicals significantly reduced the expression of pluripotency markers, especially SOX2. Conclusions: In conclusion, KDM4–6 inhibitors significantly affected HNSCC cell growth, and exerted the potential for epigenetic priming in combination with cisplatin.
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(This article belongs to the Special Issue Decoding the Epigenomic Basis of Gene Regulation in Cancer)
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Open AccessArticle
Insight into Essential and Complex Autism Spectrum Disorders: Clinical Characteristics, Chromosomal Microarray Analysis, and Risk Factors
by
Beyhan Tüysüz, Evrim Çifçi Sunamak, Gizem Durcan, Birol Öztürk, Dilek Uludağ Alkaya, Hazal Cansu Çulpan, Mehmet Barış Korkmaz, Burak Doğangün and Ertuğrul Kıykım
Genes 2026, 17(9), 1045; https://doi.org/10.3390/genes17091045 (registering DOI) - 30 Aug 2026
Abstract
Background/Objectives: Autism spectrum disorder (ASD) can present with either an essential or a complex phenotype. The aim of this study was to compare clinical characteristics and the diagnostic yield of copy number variations (CNVs) in essential and complex phenotypes, and to evaluate risk
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Background/Objectives: Autism spectrum disorder (ASD) can present with either an essential or a complex phenotype. The aim of this study was to compare clinical characteristics and the diagnostic yield of copy number variations (CNVs) in essential and complex phenotypes, and to evaluate risk factors. Methods: A total of 163 Turkish children (126 boys, 37 girls) who met the DSM-5 diagnostic criteria for ASD were evaluated. Chromosomal microarray analysis was performed. Results: Among the patients, 21.5% had a complex phenotype and 78.5% had an essential phenotype. Overall, 13.7% of the patients had a developmental/intelligence quotient (DQ/IQ) below 50, most of whom had a complex phenotype. In contrast, 15.3% of the patients had a DQ/IQ of 70 or higher, all of whom had an essential phenotype. The frequency of verbal individuals was 30.5% and did not differ between the two phenotypes. Pathogenic CNVs were identified in 7.4%; 17.1% of the complex group and 4.7% of the essential group. CNVs of uncertain significance that were potentially causal because they included an ASD-associated gene were present in 12.3% of individuals. CNV positivity was significantly higher in individuals with an IQ below 50; interestingly, it was similar between the verbal and non-verbal groups. Besides ultra-rare CNVs, recurrent CNVs associated with ASD were identified. A novel pathogenic CNV was identified at 2q13.33, including NPHP1 and BUB1, both of which are expressed in the brain and are potentially associated with ASD. Advanced parental age and preterm birth were identified as possible risk factors. Conclusions: Deep phenotyping is important for the management of both essential and complex phenotypes and allows the identification of patients with a higher probability of having CNVs. Reporting novel or rare CNVs contributes to clarifying the pathogenesis of ASD.
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(This article belongs to the Section Genetic Diagnosis)
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Open AccessArticle
Integrative Transcriptomic Analysis and Single-Cell Characterization Identify RTN4 as a Candidate PBMC-Derived Hub Gene Associated with COPD and Coronary Artery Disease
by
Yongle Xu, Shan Shan, Hanhan Liu and Tao Ren
Genes 2026, 17(9), 1046; https://doi.org/10.3390/genes17091046 (registering DOI) - 29 Aug 2026
Abstract
Background: Chronic obstructive pulmonary disease (COPD) is associated with systemic inflammation and increased cardiovascular comorbidity, yet peripheral blood molecular markers for cardiovascular comorbidity-related stratification in COPD remain poorly defined. Methods: In this study, PBMC transcriptomic datasets from a COPD cohort (GSE42057) and a
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Background: Chronic obstructive pulmonary disease (COPD) is associated with systemic inflammation and increased cardiovascular comorbidity, yet peripheral blood molecular markers for cardiovascular comorbidity-related stratification in COPD remain poorly defined. Methods: In this study, PBMC transcriptomic datasets from a COPD cohort (GSE42057) and a CAD cohort (GSE113079) were analyzed using weighted gene co-expression network analysis (WGCNA) to identify disease-associated modules, followed by overlapping gene screening. Machine-learning models were then applied to prioritize the shared genes. External validation was performed in an independent COPD cohort (GSE54837) and an independent CAD cohort (GSE250283). Immune-cell deconvolution and single-cell transcriptomic analysis of a CAD dataset (GSE269269) were further used to characterize the immune and cellular context of the leading candidate. Finally, RT–qPCR was performed in an institutional PBMC cohort for experimental validation. Results: A total of 169 shared genes were identified, with enrichment in immune, mitochondrial, oxidative phosphorylation, and metabolic pathways. RTN4 was the most consistently validated candidate across COPD and CAD cohorts and was associated with poorer lung function, advanced GOLD stages, and monocyte-related immune patterns. In CAD single-cell data, RTN4-associated signals were mainly localized to monocytes, particularly intermediate monocytes under plaque rupture conditions, with enrichment of immune, antigen-presentation, oxidative-stress, and metabolic pathways. RT–qPCR confirmed increased RTN4 mRNA expression in COPD and a further increase in patients with COPD and comorbid CAD despite comparable FEV1% predicted between the two COPD groups. Conclusions: These findings suggest that elevated RTN4 expression may serve as a PBMC-derived, monocyte-associated candidate molecular feature related to COPD–CAD comorbidity.
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(This article belongs to the Section Bioinformatics)
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Open AccessArticle
Genome-Wide Characterization, Stress-Responsive Expression, and QTLome Integration of the DUF1645 Gene Family in Rice (Oryza sativa L.)
by
Peipei Su, Zhiqun Que, Xin Song and Gehong Wang
Genes 2026, 17(9), 1044; https://doi.org/10.3390/genes17091044 (registering DOI) - 29 Aug 2026
Abstract
Background: Domain of Unknown Function 1645 (DUF1645) is a conserved but poorly characterized plant gene family whose evolutionary history and roles in stress adaptation remain unclear. We performed an integrated genomic, evolutionary, transcriptomic, and Quantitative Trait Locus (QTL) characterization of the DUF1645
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Background: Domain of Unknown Function 1645 (DUF1645) is a conserved but poorly characterized plant gene family whose evolutionary history and roles in stress adaptation remain unclear. We performed an integrated genomic, evolutionary, transcriptomic, and Quantitative Trait Locus (QTL) characterization of the DUF1645 family in rice (Oryza sativa). Methods and Results: We identified 14 intronless, non-redundant OsDUF1645 genes distributed across eight chromosomes. Phylogenetic and collinearity analyses suggested that family expansion within Poaceae involved ancestral segmental and localized tandem duplication events. Promoter analysis identified stress- and phytohormone-responsive cis-acting elements, including ABRE, MBS, and MeJA-associated motifs. Public transcriptome datasets revealed diverse OsDUF1645 expression patterns under abiotic and hormonal treatments. Integration with the Quantitative Trait Loci Annotation Rice Online (Q-TARO) QTLome identified physical co-localization of multiple OsDUF1645 loci with stress- and agronomic-trait QTLs, including salinity-, drought-, root architecture-, and water-deficit-associated regions. On Chromosome 1, OsDUF1645.1, OsDUF1645.2, OsDUF1645.3, and OsDUF1645.4 overlapped QTL intervals associated with salinity-related physiological traits, including Na+ uptake and Na+ balance, and drought-related root traits. On Chromosome 5, the tandemly arranged OsDUF1645.8, OsDUF1645.9, and OsDUF1645.10 co-localized with QTLs related to root architecture and water-deficit responses. qRT-PCR validation under salinity, osmotic stress, and cadmium exposure confirmed distinct stress-responsive expression profiles; OsDUF1645.6 exhibited broad multi-stress responsiveness, whereas OsDUF1645.3 was downregulated under several conditions. Conclusions: The OsDUF1645 family exhibits substantial functional diversification, supported by distinct regulatory architectures, expression profiles, and QTL associations. These findings provide a framework for prioritizing OsDUF1645 candidates for functional validation and their potential application in molecular breeding and development of climate-resilient rice cultivars.
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(This article belongs to the Section Plant Genetics and Genomics)
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Open AccessArticle
Clinical Insights into RELA-Associated Disease: From Genotype to Phenotype and Exploring Treatment
by
Chun Pan, Cuifang Zheng, Yuhuan Wang, Jieru Shi, Lin Wang and Ying Huang
Genes 2026, 17(9), 1043; https://doi.org/10.3390/genes17091043 (registering DOI) - 29 Aug 2026
Abstract
Background/Objectives: RELA encodes the p65 subunit of NF-κB and plays a critical role in immune regulation, epithelial protection, and anti-apoptotic signaling. Pathogenic RELA variants cause monogenic immune dysregulation with heterogeneous clinical manifestations. However, genotype–phenotype relationships and optimal treatment strategies remain incompletely defined.
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Background/Objectives: RELA encodes the p65 subunit of NF-κB and plays a critical role in immune regulation, epithelial protection, and anti-apoptotic signaling. Pathogenic RELA variants cause monogenic immune dysregulation with heterogeneous clinical manifestations. However, genotype–phenotype relationships and optimal treatment strategies remain incompletely defined. Methods: We conducted a comprehensive literature-based analysis of reported individuals with RELA variants and additionally described a family carrying a RELA c.706C>T (p.R236*) variant, including a clinically affected proband and his variant-positive father with isolated vitiligo. Clinical, immunological, genetic, endoscopic, and therapeutic data were extracted and summarized using a module-based phenotypic framework. Exploratory analyses were performed to examine potential genotype–phenotype patterns and reported treatment responses. Results: A total of 72 individuals with RELA variants, including the proband and his variant-positive father from the present family, were analyzed. RELA-associated disease exhibited marked clinical heterogeneity, encompassing mucocutaneous, systemic inflammatory, autoimmune, gastrointestinal, hematologic, allergic/eosinophilic, and infection-related manifestations. Exploratory analyses suggested that truncating or splice-site variants were more frequently observed among individuals with mucocutaneous lesions, whereas missense variants appeared to be more common among those with autoimmune manifestations. Tumor necrosis factor (TNF) inhibitors were among the therapies associated with favorable reported responses. In the present family, the proband presented with early-onset Behçet-like intestinal inflammation and achieved clinical and endoscopic remission after thalidomide and dose-escalated infliximab treatment. Conclusions: This study expands the clinical spectrum of RELA-associated disease and highlights preliminary variant-related clinical patterns that require confirmation in larger independent cohorts. The available treatment experience suggests that TNF blockade may be considered as a therapeutic option in selected patients, although comparative efficacy cannot be established from the available data.
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(This article belongs to the Section Human Genomics and Genetic Diseases)
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Open AccessArticle
Transcriptional Heterogeneity Underlying Cancer Cell Migration Converges on Shared Regulatory Programs
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Ismael Ortiz, Paul V. Taufalele, Victor L. Dunagan, Samantha S. Hodge, Jing Wang, Qi Liu and Cynthia A. Reinhart-King
Genes 2026, 17(9), 1042; https://doi.org/10.3390/genes17091042 (registering DOI) - 29 Aug 2026
Abstract
Background/Objectives: Cancer cell migration is a hallmark of cancer and is associated with metastasis. While large-scale functional screens have identified regulators of migration, less is known about how intrinsic transcriptional heterogeneity drives highly migratory phenotypes within individual cancer models or whether these
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Background/Objectives: Cancer cell migration is a hallmark of cancer and is associated with metastasis. While large-scale functional screens have identified regulators of migration, less is known about how intrinsic transcriptional heterogeneity drives highly migratory phenotypes within individual cancer models or whether these transcriptional changes are conserved across different models of varying tissues of origin. This study aims to define shared and cell line-specific transcriptional programs associated with cancer cell migration and analyze their relevance to patient datasets. Methods: Five cancer cell lines across three cancer types (breast, colorectal, and melanoma) were subjected to transwell-based migratory sorting to isolate highly and weakly migratory subpopulations. Bulk RNA sequencing, differential gene expression analysis, Gene Ontology (GO) enrichment, and upstream regulator prediction were performed. Public tumor datasets were analyzed to evaluate gene expression and its association with patient survival. Results: EVA1A was consistently upregulated in all highly migratory (HM) subpopulations. Multiple GO terms were enriched across all cell lines, often driven by distinct gene signatures, indicating convergence at the level of biological processes despite transcriptional divergence. TEAD4 was predicted as an upstream regulator, and increased TEAD4 nuclear localization was observed in four of the five HM subpopulations. EVA1A and TEAD4 expression were elevated in tumors relative to normal tissues, with cancer type-dependent survival outcomes. Conclusions: Migratory selection was accompanied by extensive transcriptional change within each model, yet across five models spanning three tissue types these changes converged on shared biological processes rather than shared genes. Migration-associated phenotypes may therefore be better defined by pathway-level than single-gene analyses, and the clinical relevance of regulatory nodes such as TEAD4 appears conditional on cancer type.
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(This article belongs to the Special Issue From Genes to Systems: Genetic and Epigenetic Control of the Metastatic Cascade)
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Open AccessArticle
The Evolutionary Plasticity, Conservation of Functional Motifs, and Structural—Functional Architecture of the ras85D 3′ UTR in Drosophila
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Aleksey M. Kulikov, Ekaterina A. Sivoplyas and Oleg E. Lazebny
Genes 2026, 17(9), 1041; https://doi.org/10.3390/genes17091041 (registering DOI) - 29 Aug 2026
Abstract
Background/Objectives: The 3′ untranslated region (3′ UTR) integrates cleavage and polyadenylation signals, microRNA targets, RNA-binding-protein sites, and RNA secondary structure, but the organizational levels that remain conserved during long-term sequence evolution are poorly understood. Methods: We analyzed the ras85D 3′ UTR in 37
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Background/Objectives: The 3′ untranslated region (3′ UTR) integrates cleavage and polyadenylation signals, microRNA targets, RNA-binding-protein sites, and RNA secondary structure, but the organizational levels that remain conserved during long-term sequence evolution are poorly understood. Methods: We analyzed the ras85D 3′ UTR in 37 drosophilid taxa. Substitution rates were estimated by maximum likelihood and RelTime; insertions and deletions were reconstructed with ARPIP and summarized as insertion–deletion evolutionary localizations (IELs). Mobile-element candidates were detected with CENSOR/Repbase, and evolutionarily conserved motifs (ECMs) with MEME/MAST. Functional and structural annotations were integrated for Drosophila melanogaster, Drosophila yakuba, and Drosophila virilis and tested using permutation-based coverage, distance, boundary-neighborhood, and multilayer architecture analyses. Results: The 2247-column alignment yielded 959 block events (710 deletions and 249 insertions). Among 63 positive-length ingroup branches, 16 were deletion-enriched, three were insertion-enriched, and one showed bidirectional turnover. Thirty-four IELs projected to 27 D. melanogaster loci and were associated with ECMs. The final registry contained 390 primary functional objects and 1135 RNAfold-predicted structural segments. Predicted weakly conserved miRNA target sites were depleted in ECM_15 and ECM_11, whereas none of 12 Functional Distance tests was significant. APA objects were enriched near predicted structural-segment boundaries (O/E = 5.21; FDR = 0.00761). SAME_MULTILOOP_INTERVAL showed reduced between-context variance (0.276× null; FDR = 0.0233), and the DIFFERENT_MULTILOOP_ARMS − SAME_MULTILOOP_INTERVAL contrast was significant (p = 0.00149; FDR = 0.00447). Conclusions: The ras85D 3′ UTR evolves as a mosaic system in which extensive deletion-biased sequence turnover coexists with conserved regulatory landmarks, recurrently remodeled local neighborhoods, and context-dependent structural–functional architectures.
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(This article belongs to the Special Issue Insights into RNA Coding and Transcriptional Regulation)
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Open AccessCase Report
Illustrative Variant-Positive Molecular Autopsy Series: Autopsy-Led Concordance of Loeys–Dietz Spectrum Findings in Eight Florida Sudden Deaths
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Juan Fernández-Cadena, Edwin W. Naylor and Arindam Bhattacharjee
Genes 2026, 17(9), 1040; https://doi.org/10.3390/genes17091040 (registering DOI) - 29 Aug 2026
Abstract
Background/Objectives: Molecular autopsy increasingly identifies rare variants in heritable aortopathy and Loeys–Dietz spectrum genes among sudden-death decedents, yet classification and causal attribution remain challenging when a syndromic diagnosis was never established during life. We reviewed eight unrelated Florida medical examiner decedents ascertained by
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Background/Objectives: Molecular autopsy increasingly identifies rare variants in heritable aortopathy and Loeys–Dietz spectrum genes among sudden-death decedents, yet classification and causal attribution remain challenging when a syndromic diagnosis was never established during life. We reviewed eight unrelated Florida medical examiner decedents ascertained by sudden or unexpected death under medical examiner jurisdiction, including laboratory-reported heterozygous missense variants spanning the Loeys–Dietz syndrome (LDS)/familial thoracic aortic aneurysm and dissection (FTAAD) gene spectrum (TGFBR1, TGFBR2, TGFB2, and SMAD3). None had a premortem clinical diagnosis of LDS; ascertainment was therefore a variant-positive molecular autopsy series, not clinically diagnosed LDS. This illustrative series of eight cases cannot estimate prevalence, diagnostic yield, penetrance, or incidental-finding frequency. Methods: Autopsy (±premortem) phenotype–variant concordance was graded as strong, limited, discordant, or not assessable without treating death as evidence of pathogenicity or equating laboratory detection with clinical LDS diagnosis. Grades were assigned by the authors using predefined rules, were not blinded to laboratory class, and were reconciled by consensus discussion; inter-rater reliability was not quantified. Population, computational, and ClinVar annotations, together with multi-axis molecular triangulation, were retained as supplementary context only. Results: Laboratory classifications were pathogenic in one case (TGFBR1 p.Arg487Gln, Case 1), likely pathogenic in another (TGFBR2 p.Glu428Asp, Case 3), and variants of uncertain significance (VUS) in the remaining cases. Strong phenotype–variant concordance mapped to two aortic-catastrophe decedents (Cases 1 and 3), limited concordance to two cases (Cases 4 and 5), and discordant presentations to four (Cases 2, 6, 7, and 8), including pulmonary thromboembolism without aortopathy, infant sudden death with competing cardiomyopathy-gene context, and ethanol-related death with a normal aorta (SMAD3 Case 8). Conclusions: In this illustrative variant-positive series, 2/8 cases had strong autopsy-led concordance, 2/8 limited, and 4/8 discordant. Autopsy-led concordance grading distinguished two LDS-spectrum variants with strong phenotype–variant concordance for fatal ascending aortic catastrophe from six variants with limited or discordant support. Rare variants in TGFBR1, TGFBR2, TGFB2, or SMAD3 should not be conflated with an LDS diagnosis or with the cause of death without concordant autopsy evidence.
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(This article belongs to the Section Human Genomics and Genetic Diseases)
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Open AccessArticle
Functional Characterization of the PAX8 p.Leu264Pro Variant Identified in a Patient with a Müllerian Duct Anomaly
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Lin He, Liangzhe Li, Yuxiao Li, Yujun Sun, Zhi Zheng, Chunfang Chu and Lin Li
Genes 2026, 17(9), 1039; https://doi.org/10.3390/genes17091039 (registering DOI) - 29 Aug 2026
Abstract
Background/Objectives: Müllerian duct anomalies (MDAs) are congenital structural abnormalities of the female reproductive tract with heterogeneous and incompletely defined genetic contributions. PAX8 is a developmental transcription factor implicated in thyroid and urogenital development. This study assessed the functional consequences of a rare PAX8
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Background/Objectives: Müllerian duct anomalies (MDAs) are congenital structural abnormalities of the female reproductive tract with heterogeneous and incompletely defined genetic contributions. PAX8 is a developmental transcription factor implicated in thyroid and urogenital development. This study assessed the functional consequences of a rare PAX8 variant identified by whole-exome sequencing (WES) in an MDA cohort, without presuming a causal relationship. Methods: WES was performed in 150 patients with MDAs. The PAX8 c.791T>C (p.Leu264Pro) variant was evaluated using computational predictions, cellular assays, and RNA sequencing in a 293FT transient-overexpression model. Results: The heterozygous p.Leu264Pro variant was identified in one patient with a complex septate uterine, cervical, and vaginal anomaly and was absent from 120 controls. Parental samples were unavailable. No statistically significant difference in construct-derived PAX8 mRNA abundance was detected between PAX8-WT and PAX8-L264P, and both proteins showed predominantly nuclear localization. In the direct PAX8-WT-versus-L264P RNA-seq comparison, 76 transcripts had nominal p values below 0.05, but none remained significant after Benjamini–Hochberg correction, and no gene met the prespecified differential-expression criteria. AK5, RCBTB2, and IFT88 were identified as candidate PAX8-responsive genes in this experimental system. Conclusions: No major functional difference was detected between PAX8-WT and L264P under the tested conditions; however, these findings do not establish functional equivalence or exclude smaller, tissue-specific, or developmental-stage-specific effects. The p.Leu264Pro variant remains a variant of uncertain significance with respect to MDAs, and the functional results were not used as benign evidence under ACMG/AMP criterion BS3.
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(This article belongs to the Section Genetic Diagnosis)
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Open AccessArticle
Genetic Differentiation Between Black Grouse (Lyrurus tetrix, Linnaeus, 1758) Populations from the Sudetes and the Carpathians
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Anna Santorek, Artur Pałucki, Tomasz Zwijacz-Kozica, Sebastian Szczepański, Michał Ciach and Robert Rutkowski
Genes 2026, 17(9), 1038; https://doi.org/10.3390/genes17091038 (registering DOI) - 29 Aug 2026
Abstract
Background/Objectives: The black grouse (Lyrurus tetrix) is experiencing a rapid decline across much of Europe. In Poland, the Carpathians and Sudetes constitute two of the last important strongholds of this endangered species; however, the genetic relationships between populations inhabiting these mountain
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Background/Objectives: The black grouse (Lyrurus tetrix) is experiencing a rapid decline across much of Europe. In Poland, the Carpathians and Sudetes constitute two of the last important strongholds of this endangered species; however, the genetic relationships between populations inhabiting these mountain systems remain poorly understood. Methods: A total of 579 non-invasive samples were collected in the Jizera Mountains and Giant Mountains (Sudetes), as well as in the Tatra Mountains and the Orava–Nowy Targ Basin (Carpathians). Microsatellite genotyping at nine loci identified 122 individuals. Genetic diversity and population genetic structure were assessed using F-statistics, AMOVA, STRUCTURE, PCoA and DAPC. Results: Significant genetic differentiation was detected among populations, with substantially lower differentiation within the mountain regions than between the Sudetes and Carpathians. Analyses consistently identified two major genetic groups corresponding to the Sudetes and Carpathians. The highest genetic diversity was recorded in the Tatra Mountains. Some individuals from this population displayed genetic signatures consistent with possible connectivity to neighbouring populations outside the study area, although this hypothesis requires testing with additional reference samples from these populations. Conclusions: The results demonstrate strong genetic structuring of black grouse populations in southern Poland and suggest limited contemporary gene flow between the Sudetes and Carpathians mountain ranges. The observed differentiation supports treating the Sudeten and Carpathian populations as separate Management Units. The Tatra Mountains constitute an important reservoir of genetic diversity and may play a key role in maintaining genetic connectivity within the Carpathian population.
Full article
(This article belongs to the Special Issue Conservation Genetics of Birds)
Open AccessArticle
Transcriptional Response of Rice Phytocystatin Family Genes to Cold Stress
by
Mingbo Li, Tingting Yang, Deyu Kong and Jin Xu
Genes 2026, 17(9), 1037; https://doi.org/10.3390/genes17091037 (registering DOI) - 29 Aug 2026
Abstract
Background/Objectives: Phytocystatins are plant-specific inhibitors of papain-like cysteine proteinases that participate in plant development and responses to biotic and abiotic stresses. The roles of rice (Oryza sativa L.) phytocystatins under cold stress remain poorly understood. Xiaomagu (XMG), a cold-tolerant japonica rice landrace,
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Background/Objectives: Phytocystatins are plant-specific inhibitors of papain-like cysteine proteinases that participate in plant development and responses to biotic and abiotic stresses. The roles of rice (Oryza sativa L.) phytocystatins under cold stress remain poorly understood. Xiaomagu (XMG), a cold-tolerant japonica rice landrace, provides valuable material for exploring phytocystatin transcript responses to low-temperature stress. This study characterizes 12 rice phytocystatin genes isolated from XMG and investigates their transcript profiles under cold and abscisic acid (ABA) treatments. Methods: Twelve phytocystatin genes were isolated from the cold-tolerant japonica rice landrace Xiaomagu. Sequence characterization and conserved domain analysis were performed for these phytocystatin family members. Real-time quantitative PCR was performed to examine transcript abundance of phytocystatin genes: low-temperature stress was applied to leaf and root tissues, while ABA treatment was carried out for leaf tissues only. Results: Conserved domain analysis revealed structural differences among the identified phytocystatin members. Real-time quantitative PCR detected distinct transcriptional responses to cold stress among these phytocystatin genes. In leaves, OsCST1, OsCST8, and OsCST12 were up-regulated, whereas OsCST11 was down-regulated. In roots, OsCST2, OsCST3, OsCST6, and OsCST12 showed increased transcript levels, while OsCST1 and OsCST11 were down-regulated. OsCST2, OsCST6, and OsCST11 exhibited significantly altered transcript abundance under ABA treatment. Conclusions: This study characterizes transcript-level responses of 12 phytocystatin genes from the cold-tolerant rice landrace Xiaomagu (XMG) under cold and ABA treatments. The detected expression changes reflect stress-responsive transcriptional regulation of rice phytocystatin family genes. Further in planta functional assays and comparisons with cold-sensitive genotypes are needed to elucidate their precise roles in rice cold adaptation.
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(This article belongs to the Section Plant Genetics and Genomics)
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Open AccessArticle
Integrated Multi-Omics Analysis Reveals Lipid Metabolism as a Key Contributor to the Growth–Meat Quality Trade-Off Among Genetically Divergent Chicken Breeds
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Ying Li, Rongqin Huang, Li Zhang, Haiping Xu, Chenglong Luo, Wen Luo and Zongliang Du
Genes 2026, 17(9), 1036; https://doi.org/10.3390/genes17091036 (registering DOI) - 29 Aug 2026
Abstract
Background: Improving meat quality while maintaining growth efficiency remains a major challenge in poultry production. However, the molecular mechanisms underlying breed-specific meat quality variation remain unclear. This study aimed to investigate how breed-specific growth patterns influence meat quality and elucidate metabolic and transcriptional
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Background: Improving meat quality while maintaining growth efficiency remains a major challenge in poultry production. However, the molecular mechanisms underlying breed-specific meat quality variation remain unclear. This study aimed to investigate how breed-specific growth patterns influence meat quality and elucidate metabolic and transcriptional mechanisms involved. Methods: Pectoralis major meat quality traits and multi-omics profiles were characterized in three genetically distinct chicken breeds—the fast-growing Small White-Feathered chicken (XBJ), the slow-growing Huiyang Bearded chicken (HXJ), and the layer-type Hy-Line Brown chicken (HLH)—at 50, 180, and 300 days of age. Twelve birds per breed per age were used for phenotypic measurement (n = 108 in total), and eight birds per breed per age were subjected to metabolomic and transcriptomic profiling. Phenotypes were analyzed using linear mixed-effects models with breed, age, and their interaction as fixed effects and pen nested within breed as a random effect, followed by Tukey-adjusted pairwise comparisons (p < 0.05). Differential metabolites were screened by OPLS-DA (VIP > 1, p < 0.05), and differentially expressed genes were identified using DESeq2 (|log2FC| ≥ 1, FDR < 0.05). Integrative analyses were performed to identify key genes, metabolites, and pathways associated with meat quality. Results: Phenotypic evaluation revealed a breed-dependent growth–meat quality trade-off, with XBJ exhibiting superior growth but poorer water-holding capacity and meat color, whereas HXJ and HLH showed better tenderness and color at the expense of growth. Metabolomic analysis revealed lipid metabolism as a major contributor to breed-specific divergence, with triglyceride-driven divergence predominating at early and middle stages, whereas later-stage differences involved glycerophospholipid and amino acid metabolism. Transcriptomic analysis revealed significant breed-specific differences in expressed genes at 50 and 180 days, enriched in pathways related to muscle structure, ECM remodeling, and energy metabolism, consistent with metabolic and phenotypic divergence. Integrated analyses identified 28 candidate genes and 71 core metabolites associated with meat quality traits, with PLIN1 and SLC1A6 emerging as key regulators associated with TG species, drip loss, shear force, and BMW. Conclusions: These findings reveal molecular mechanisms underlying the growth–meat quality trade-off and highlight lipid metabolic regulation as a key contributor to meat quality variation. The identified gene–metabolite networks provide insights for molecular breeding to improve chicken meat quality.
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(This article belongs to the Section Animal Genetics and Genomics)
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Open AccessReview
Circulating Tumor Function: A Systems Biology Framework for Liquid Biopsy in Genitourinary Cancers
by
Roxana Andra Coman, Andreea Nutu, Lia-Raluca Olari, Stefan Strilciuc, Dana Monica Iancu and Ioana Berindan-Neagoe
Genes 2026, 17(9), 1035; https://doi.org/10.3390/genes17091035 (registering DOI) - 29 Aug 2026
Abstract
Liquid biopsy enables minimally invasive detection and longitudinal monitoring of tumor-derived material in blood and urine. In genitourinary cancers, most applications have focused on genomic alterations in circulating tumor DNA (ctDNA), together with circulating tumor cells (CTCs), extracellular vesicles (EVs), and cell-free RNAs.
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Liquid biopsy enables minimally invasive detection and longitudinal monitoring of tumor-derived material in blood and urine. In genitourinary cancers, most applications have focused on genomic alterations in circulating tumor DNA (ctDNA), together with circulating tumor cells (CTCs), extracellular vesicles (EVs), and cell-free RNAs. These measurements are clinically informative but are often interpreted as isolated, predominantly descriptive biomarkers and therefore incompletely represent the adaptive processes that determine progression and treatment response. We propose circulating tumor function (CTF) as a systems biology framework for integrating tumor-derived and host-derived genomic, regulatory, metabolic, redox, and immune signals obtained through serial liquid biopsy. CTF is not a single analyte or assay; rather, it is an inference model intended to generate interpretable functional states, including proliferative activity, immune evasion, metastatic potential, metabolic stress, and therapeutic adaptation. We review the contributions and limitations of ctDNA, ncRNA networks, EV-mediated signaling, redox biomarkers, and tumor–host crosstalk in prostate, bladder, renal, and testicular cancers. We also outline the analytical and clinical validation required to determine whether integrated CTF models provide incremental value over established single-analyte approaches. This framework may help reposition liquid biopsy from molecular detection toward functional precision oncology.
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(This article belongs to the Special Issue Application of Molecular or Genetic Markers in Liquid Biopsy for Urogenital Cancers)
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Open AccessReview
Activating Transcription Factor 3 in Pain: A Molecular Regulator and Emerging Biomarker
by
Mario García-Domínguez
Genes 2026, 17(9), 1034; https://doi.org/10.3390/genes17091034 (registering DOI) - 29 Aug 2026
Abstract
Pain is a complex process involving dynamic transcriptional changes in cells of the PNS and CNS following injury or inflammation. Among stress-inducible transcription factors, ATF3 has emerged as one of the most robust molecular markers of neuronal injury, particularly in sensory neurons of
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Pain is a complex process involving dynamic transcriptional changes in cells of the PNS and CNS following injury or inflammation. Among stress-inducible transcription factors, ATF3 has emerged as one of the most robust molecular markers of neuronal injury, particularly in sensory neurons of the DRG. Although ATF3 is widely used as an indicator of axonal damage in experimental pain models, its functional contribution to the initiation, maintenance, and resolution of pain remains poorly understood. Recent transcriptomic and functional studies suggest that ATF3 not only reflects neuronal stress but also orchestrates gene expression programs involved in axonal regeneration, neuroimmune communication, ion channel remodeling, and nociceptor plasticity. Moreover, ATF3 expression has been identified in non-neuronal cell populations, including Schwann cells and satellite glial cells, indicating broader roles in peripheral nerve repair and neuroinflammation. Despite the growing body of experimental evidence, the literature remains fragmented, and no consensus has yet been reached as to whether ATF3 primarily promotes adaptive regeneration or directly contributes to maladaptive pain signaling. This review aims to provide a comprehensive and critical overview of the current understanding of ATF3 biology in pain, building on evidence from transcriptomic and molecular analyses, experimental models of neuropathic, inflammatory, and cancer-associated pain, and emerging mechanistic insights into its role in pain-related neuronal plasticity. This review examines the regulation of ATF3 expression, its downstream transcriptional targets, its interactions with inflammatory signaling pathways, and its potential value as a therapeutic target. By consolidating current evidence and highlighting existing knowledge gaps, this review seeks to clarify the multifaceted role of ATF3 in pain pathophysiology.
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(This article belongs to the Special Issue Genetic Regulation of Neurons and Behavioral Genetics)
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Open AccessArticle
Promoter DNA Methylation Metrics and Gene Expression in Human CD3+ T Cells: Sensitivity to Analytical Choices
by
Ragıp Onur Öztornacı
Genes 2026, 17(9), 1033; https://doi.org/10.3390/genes17091033 - 28 Aug 2026
Abstract
Background/Objectives: Promoter DNA methylation is conventionally summarised as a regional mean. Two alternatives have been proposed to capture information the mean discards: the concurrence ratio derived from partially methylated bisulfite reads (CAMDA) and single-CpG Shannon (β-) entropy. Benchmarks of such metrics typically
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Background/Objectives: Promoter DNA methylation is conventionally summarised as a regional mean. Two alternatives have been proposed to capture information the mean discards: the concurrence ratio derived from partially methylated bisulfite reads (CAMDA) and single-CpG Shannon (β-) entropy. Benchmarks of such metrics typically report one coefficient per metric on a single gene set at a single aggregation scale. We asked how far that comparison depends on analytical choices that are rarely reported. Methods: Matched whole-genome bisulfite sequencing (WGBS) and RNA-seq from one donor of human CD3+ T cells were analysed. Promoter windows spanning −1000 to +500 bp around the transcription start site (TSS) were divided into fifteen 100 bp bins; all three metrics were computed on an identical CpG set and correlated with log2(FPKM) by Spearman’s ρ. The comparison was repeated across annotation source, quantification level, coverage threshold, aggregation scheme, the treatment of zero-expression transcripts and CpG island status, with metric differences assessed by paired bootstrap over promoters and over chromosomes. Results: Across a grid of five analytical choices, the mean methylation coefficient ranged from −0.145 to −0.593 and the ordering of the metrics reversed between configurations. At the 100 bp bin scale, the largest difference between metrics was 0.037; aggregating the same CpGs to the whole promoter opened differences of up to 0.31, so the apparent superiority of a metric is itself a function of the aggregation scale. CAMDA exceeded the regional mean consistently but modestly, with the advantage largest in distal upstream bins and indistinguishable from zero adjacent to the TSS. β-Entropy is a strictly monotone function of the folded measure 1 − 2|β − 0.5|; at the 100 bp scale, the mean of per-CpG entropy tracked the folding transform of regional mean methylation to within 0.002 in every bin, while at the whole-promoter scale, the two separated by 0.041. Within CpG islands, the regional mean weakened (ρ = −0.246) while CAMDA did not (−0.494). Conclusions: In this single-donor dataset, analytical design affected the estimated coupling more than the choice of summary metric. The observed range is dataset-specific and should not be interpreted as a transferable numerical estimate. Rather, these results show that evaluating plausible analytical configurations can provide important context when comparing promoter methylation summary metrics.
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(This article belongs to the Section Molecular Genetics and Genomics)
Open AccessArticle
Genome-Wide Analysis of Alternative Splicing Identifies a Prognostic Signature in ER-Positive Breast Cancer
by
Ahmed M. Basudan, Yazeed Alshuweishi, Hamood AlSudais and Mohammad A. Alfhili
Genes 2026, 17(9), 1032; https://doi.org/10.3390/genes17091032 - 28 Aug 2026
Abstract
Background/Objectives: Alternative splicing (AS) contributes substantially to transcriptomic diversity and has emerged as an important regulator of cancer progression. However, the genome-wide characterization of AS events specific to estrogen receptor (ER)-positive breast cancer remains limited. This study aims to comprehensively profile AS in
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Background/Objectives: Alternative splicing (AS) contributes substantially to transcriptomic diversity and has emerged as an important regulator of cancer progression. However, the genome-wide characterization of AS events specific to estrogen receptor (ER)-positive breast cancer remains limited. This study aims to comprehensively profile AS in ER-positive breast cancer and identify a prognostic AS signature associated with patient outcome. Methods: Clinical and splicing data (Percent Spliced In values) were obtained from The Cancer Genome Atlas (TCGA) for 737 ER-positive samples. Prognostic AS events were identified using Cox regression analysis. The Least Absolute Shrinkage Selection Operator (LASSO) model was used to construct an AS-based prognostic signature, and a standardized risk score was calculated for each sample. The signature was then evaluated by Kaplan–Meier (KM) analysis and receiver operating characteristic (ROC) curves, in addition to other methods to validate model performance. Furthermore, transcript-level annotation and RNA expression correlation were performed to evaluate biological relevance. Results: Profiling identified 6276 AS events across 4457 genes, with exon skipping (ES) representing the most prevalent class (34.4%). Model analysis established a novel five-event AS prognostic signature (comprising DNAJC14, BAZ2B, PCDHAC1, PCDHA7, and DAPL1). The signature significantly stratified patients into high-risk and low-risk groups for both disease-free survival (DFS; p < 0.001) and overall survival (OS; p < 0.001). HER2-specific analysis demonstrated more consistent performance in HER2-negative patients for both DFS (p < 0.001) and OS (p = 0.018). The model achieved area under the curve (AUC) of 0.804 for 60-month follow-up supporting long-term prognostic performance. Additionally, the signature demonstrated stable and reliable discrimination with a concordance index (C-index) of approximately 0.73 across multiple validation methods. Conclusions: The study identified AS signature with promising prognostic value in ER-positive breast cancer. This highlights the potential of splicing-based models to refine risk stratification beyond conventional gene expression analysis.
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(This article belongs to the Special Issue Alternative Splicing in Genetic Disorders and Cancer)
Open AccessArticle
Shared Genetic Basis of Autoimmune Diseases and Follicular Lymphoma by Mendelian Randomization and Multi-Omics
by
Chendong Jiang, Zhan Sun, Zhanyan Gao, Jie Wang, Jun Liang and Yang Feng
Genes 2026, 17(9), 1031; https://doi.org/10.3390/genes17091031 - 28 Aug 2026
Abstract
Background/Objectives: Epidemiological studies link autoimmune diseases (AIDs) to follicular lymphoma (FL) risk, but their shared genetic architecture and causal mechanisms remain unclear. Methods: A two-sample Mendelian randomization (MR) analysis was employed to assess causal relationships between 15 AIDs and FL. Pleiotropic
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Background/Objectives: Epidemiological studies link autoimmune diseases (AIDs) to follicular lymphoma (FL) risk, but their shared genetic architecture and causal mechanisms remain unclear. Methods: A two-sample Mendelian randomization (MR) analysis was employed to assess causal relationships between 15 AIDs and FL. Pleiotropic loci were identified through the Pleiotropy Analysis under Composite Null (PLACO). Bayesian colocalization analysis, functional mapping, and Multi-marker Analysis of GenoMic Annotation were applied to fine-map shared genetic variants and identify their target genes. Summary data-based MR was used with multitissue expression quantitative trait locus data to infer causal effects of gene expression. HyPrColoc analysis was applied to decipher shared genetic regulation of immune cell phenotypes. Results: MR revealed that rheumatoid arthritis increased FL risk (ORIVW = 1.55, nominal p = 7.16 × 10−5, FDR-corrected p = 1.07 × 10−3), whereas composite autoimmune disease reduced FL risk (ORIVW = 0.70, nominal p = 4.61 × 10−5, FDR-corrected p = 6.92 × 10−4). Hypothyroidism showed only a nominally suggestive protective trend (ORIVW = 0.88, nominal p = 0.015), which did not survive Benjamini–Hochberg multiple-testing correction (FDR-corrected p = 0.075). Fifty-five pleiotropic loci shared between FL and AIDs were identified, among which key loci such as 1p36.32, 6p21.32, 17p13.1, and 11q23.3 exhibited strong colocalization evidence. Core pleiotropic genes (e.g., TNFRSF14, MMEL1, CXCR5, and RNASET2) were prioritized, which implicated pathways related to MHC class II antigen presentation, interferon signaling, and T cell activation. HyPrColoc analysis demonstrated that these loci colocalized with the expression of immune receptors, including BAFF-R on B cells and HVEM (TNFRSF14) on naïve CD8+ T cells. Conclusions: Our study identifies divergent causal effects of selected AIDs on FL risk and demonstrates localized pleiotropy at key loci, providing novel insights into shared immunogenetic mechanisms.
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(This article belongs to the Section Human Genomics and Genetic Diseases)
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Open AccessArticle
BSA-Seq-Based QTL Mapping for the Height of the First Fruiting Branch Node of Cotton and the Development of Molecular Markers
by
Fuxiang Zhao, Tao Yang, Xuwen Wang, Gang Wang, Jinxin Qiao, Xianhui Kong, Li Liu, Wanli Han and Yu Yu
Genes 2026, 17(9), 1030; https://doi.org/10.3390/genes17091030 - 28 Aug 2026
Abstract
The height of the first fruiting branch node (HFFBN) is a core indicator for mechanical harvesting of cotton, and the development of molecular markers for this trait is important for accelerating the breeding process. In this study, using bulked segregant analysis coupled with
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The height of the first fruiting branch node (HFFBN) is a core indicator for mechanical harvesting of cotton, and the development of molecular markers for this trait is important for accelerating the breeding process. In this study, using bulked segregant analysis coupled with whole-genome sequencing (BSA-seq), one quantitative trait locus (QTL) associated with the HFFBN was mapped; a molecular marker, qFBH7, associated with the HFFBN of cotton was developed; and its application value was systematically evaluated. A total of 20 lines with extreme phenotypes were selected from the recombinant inbred lines constructed using upland cotton Z3-146 and Z3-147 as parental lines. The screened lines with extreme phenotypes were used to construct the extreme high-HFFBN pool and the extreme low-HFFBN pool, which were subsequently used for BSA-seq. Using the upland cotton genome as a reference, relevant QTLs were mapped by BSA-seq. One relevant candidate region was identified, with a total length of 2.25 Mb. The validation experiments revealed that the genotyping results of the KASP_FBH7_03 molecular marker in the parental lines Z3-146 and Z3-147 were completely consistent with the BSA-seq data: Z3-146 had the TT genotype, and Z3-147 had the CC genotype. Among the 66 samples from the natural population, there was a significant difference (p < 0.05) in the HFFBN between the CC and TT genotypes, and the mean HFFBN of the TT genotype was greater than that of the CC genotype. In summary, the KASP_FBH7_03 molecular marker can be effectively used for selective breeding for the HFFBN of cotton, and the TT genotype has a positive regulatory effect on the HFFBN. This study not only provides resources for breeding cotton varieties suited to mechanical harvesting but also offers a robust tool for molecular marker-assisted selection.
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(This article belongs to the Special Issue Genetic Studies on Cotton Stress Resistance, Quality Traits, and Drought Response Mechanisms)
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Open AccessArticle
Hepatocyte-Specific RORα Deficiency Accelerates Liver Regeneration by Unleashing ME1-Driven Glycolysis
by
Hongmei Zhang, Shanshan Yang, Ming Yi, Qiuyue Guan, Dan Ding, Xiaoqian Yu, Yin Liu, Dan Deng, Yuxi Feng and Zhiguang Su
Genes 2026, 17(9), 1029; https://doi.org/10.3390/genes17091029 - 28 Aug 2026
Abstract
Background/Objectives: Hepatocyte proliferation during liver regeneration requires precise transcriptional coordination of metabolic reprogramming, but the key regulators governing this process remain largely unknown. Methods: Hepatocyte-specific retinoic acid receptor-related orphan receptor α (RORα) knockout (RORα-LKO) mice were generated and subjected to two-thirds partial
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Background/Objectives: Hepatocyte proliferation during liver regeneration requires precise transcriptional coordination of metabolic reprogramming, but the key regulators governing this process remain largely unknown. Methods: Hepatocyte-specific retinoic acid receptor-related orphan receptor α (RORα) knockout (RORα-LKO) mice were generated and subjected to two-thirds partial hepatectomy (PHx). Liver regeneration was assessed by liver-to-body weight ratio, histology, and proliferation markers (PCNA, Ki67, cyclin D1). Metabolic changes were evaluated by untargeted metabolomics, Seahorse extracellular flux analysis, and glycolytic enzyme activity assays. The molecular mechanism was investigated through RNA-seq analysis, qPCR, Western blotting, dual-luciferase reporter assays, CUT&Tag-qPCR, and pharmacological inhibition. Results: RORα expression was transiently upregulated during the early phase and declined at the peak of hepatocyte proliferation. RORα-LKO mice exhibited accelerated liver recovery and increased hepatocyte proliferation following a partial hepatectomy, without enhanced inflammation or fatty acid oxidation. Mechanistically, RORα directly binds to the promoter of Me1 to repress its transcription. Loss of RORα upregulates ME1, enhances glycolysis, and increases ATP production. Pharmacological inhibition of ME1 reversed these effects. Conclusions: The RORα–ME1 axis links transcriptional repression to metabolic reprogramming and may represent a therapeutic target for liver regeneration.
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(This article belongs to the Special Issue Feature Papers: Molecular Genetics and Genomics 2026)
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