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16 pages, 1373 KB  
Article
MCAM (CD146) Gene Encodes Chicken Blood Alloantigen System H
by Janet E. Fulton, Amy M. McCarron, Anna Wolc, Brandi A. Sparling, Lowdan Ali, Courtney Jaeger and Robert L. Taylor
Genes 2026, 17(4), 412; https://doi.org/10.3390/genes17040412 - 31 Mar 2026
Viewed by 300
Abstract
Background/Objectives: Alloantigen H is one of thirteen systems in the chicken. Little is known about this system which has two serological alleles. The objectives of this study were (1) to identify the genetic region encoding the chicken alloantigen H, and (2) to develop [...] Read more.
Background/Objectives: Alloantigen H is one of thirteen systems in the chicken. Little is known about this system which has two serological alleles. The objectives of this study were (1) to identify the genetic region encoding the chicken alloantigen H, and (2) to develop DNA detection-based methods to aid H system allele identification. Methods: SNP genotypes from Axiom chicken SNP arrays were established for samples with known H system serological types. Sources of DNA included two elite Hy-Line White Leghorn lines segregating for alloantigen H, non-pedigreed samples from the Northern Illinois University (NIU) DNA bank, plus inbred line samples. Sequence information was also available for the commercial and inbred lines. Results: GWAS results from the elite Hy-Line lines and NIU DNA bank samples showed a very strong peak in the same 4.20–4.30 Mbp region on chromosome 24. Predicted cell membrane expression and the presence of non-synonymous SNP were criteria to identify candidate genes. Seven genes in this region have membrane-associated products: MCAM (CD146), THY1, MFRP, CLDN25, KCNJ14L, ABCG4, and PDZD3. However, only MCAM had an SNP variation that matched the serological haplotypes. Lines known to be segregating for the H system had concordance rates between serological results and SNP haplotype of 95% for both the elite HYL lines and 99% for the NIU samples, indicating that the MCAM (CD146) gene encodes the chicken H blood system. Conclusions: The gene product is a cell adhesion molecule affecting multiple activities including angiogenesis, development, cell differentiation, cell migration, signaling transduction, and immune responses. Long, short, and soluble isoforms are found in chickens. The described DNA-based typing methods facilitate future investigations to examine H haplotype frequencies in lines with identified differential responses such as growth or immune responses. Determining H haplotype association with egg production, feed conversion, and other traits with economic importance will aid in determining the significance of this immune-related gene in overall poultry health. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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22 pages, 509 KB  
Review
The Molecular Basis of Neonatal Diabetes Mellitus and Transient Hyperglycemia in the Neonate
by Niki Dermitzaki, Anastasios Serbis, Maria Baltogianni, Chrysoula Kosmeri, Foteini Balomenou, Chrysanthi Maria Tsiogka and Vasileios Giapros
Appl. Sci. 2026, 16(6), 2649; https://doi.org/10.3390/app16062649 - 10 Mar 2026
Viewed by 267
Abstract
Neonatal diabetes mellitus (NDM) is a rare monogenic disorder characterized by persistent hyperglycemia requiring insulin therapy, typically diagnosed within the first six months of life, and may be transient οr permanent. However, hyperglycemia in the neonatal population may be observed outside the NDM [...] Read more.
Neonatal diabetes mellitus (NDM) is a rare monogenic disorder characterized by persistent hyperglycemia requiring insulin therapy, typically diagnosed within the first six months of life, and may be transient οr permanent. However, hyperglycemia in the neonatal population may be observed outside the NDM range. This narrative review aims to provide an overview of the genetic and molecular mechanisms underlying NDM, including both transient and permanent forms on the one hand and the developmental and regulatory pathways contributing to transient hyperglycemic states in neonates on the other. A comprehensive literature search of PubMed, Scopus, and Google Scholar was conducted, focusing on genetic and molecular mechanisms associated with NDM and transient neonatal hyperglycemia. Mutations in more than 40 genes or chromosomal loci have been implicated in the pathogenesis of NDM, affecting the development and function of pancreatic beta-cells, as well as insulin synthesis and secretion. Abnormalities of the 6q24 locus have been recognized as the most common cause of transient NDM, whereas mutations in genes encoding ATP-sensitive potassium (KATP) channels, particularly KCNJ11, are more commonly identified in permanent NDΜ cases. Transient hyperglycemia may occur in preterm and/or critically ill neonates due to immaturity and transient beta-cell dysregulation, insulin resistance, epigenetic modifications, or drug administration. In NDM cases, the clinical course, the presence of extra-pancreatic manifestations, and the optimal treatment depend on the causative gene. Therefore, genetic diagnosis is imperative, as it can facilitate individualized management strategies, long-term follow-up, and genetic counselling. Full article
(This article belongs to the Special Issue Advanced Studies in Molecular and Metabolic Mechanisms of Diabetes)
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16 pages, 262 KB  
Article
Genetic Variants in Potassium Channel Genes and Their Clinical Implications in Kazakhstani Patients with Cardiac Arrhythmias
by Ayaulym Chamoieva, Saule Rakhimova, Zhannur Abilova, Ainur Akhmetova, Gulbanu Akilzhanova, Madina Zhalbinova, Asset Daniyarov, Kenes Akilzhanov, Askhat Molkenov, Ulykbek Kairov, Anargul Kuanysheva, Nurlan Shaimardanov, Ayan Abdrakhmanov, Makhabbat Bekbossynova and Ainur Akilzhanova
J. Pers. Med. 2026, 16(2), 60; https://doi.org/10.3390/jpm16020060 - 26 Jan 2026
Viewed by 564
Abstract
Background/Objectives: Cardiac arrhythmias are among the leading causes of sudden cardiac death (SCD). Pathogenic variants in potassium channel genes play a key role in inherited arrhythmia syndromes, yet their contribution in Central Asian populations remains poorly characterized. Methods: We performed targeted [...] Read more.
Background/Objectives: Cardiac arrhythmias are among the leading causes of sudden cardiac death (SCD). Pathogenic variants in potassium channel genes play a key role in inherited arrhythmia syndromes, yet their contribution in Central Asian populations remains poorly characterized. Methods: We performed targeted next-generation sequencing (NGS) using a 96-gene custom Haloplex panel in 79 Kazakhstani patients with clinically diagnosed arrhythmias, including atrioventricular block, sick sinus syndrome, and atrial fibrillation. Detected variants in potassium channel genes were classified according to ACMG guidelines and correlated with clinical phenotypes. Results: A total of 52 variants were identified across 11 potassium channel genes. Two likely pathogenic variants (KCNH2 p.Cys66Gly and p.Arg176Trp) and six variants of uncertain significance (VUS) in KCNQ1, KCNE2, KCNE3, and KCNJ8 were detected. Two novel previously unreported variants were found in KCNE5 and KCND3. Patients harboring pathogenic variants commonly presented with early-onset arrhythmias or a positive family history of cardiovascular disease. Carriers of KCNH2 variants exhibited mild QT prolongation and recurrent syncope. Conclusions: This is the first genetic study of potassium channel gene mutations in Kazakhstani patients with cardiac arrhythmias. The detection of pathogenic and novel variants highlights the clinical utility of integrating genetic testing into diagnostic and management pathways for arrhythmia syndromes. Population-specific genomic data are essential for improving risk stratification, guiding medication safety, and enabling cascade family screening in Central Asia. Full article
19 pages, 1159 KB  
Review
The Genetic Landscape and Precision Medicine in Neonatal Diabetes Mellitus: From Molecular Mechanisms to Clinical Management
by Yuanyuan Meng, Lina Zhu, Guanping Dong and Chao Tang
Curr. Issues Mol. Biol. 2026, 48(1), 104; https://doi.org/10.3390/cimb48010104 - 19 Jan 2026
Cited by 1 | Viewed by 649
Abstract
Neonatal Diabetes Mellitus (NDM) is a rare, heterogeneous monogenic disorder typically presenting within the first six months of life. Unlike type 1 or type 2 diabetes, NDM is caused by single-gene mutations that disrupt pancreatic β-cell function or development. With the advent of [...] Read more.
Neonatal Diabetes Mellitus (NDM) is a rare, heterogeneous monogenic disorder typically presenting within the first six months of life. Unlike type 1 or type 2 diabetes, NDM is caused by single-gene mutations that disrupt pancreatic β-cell function or development. With the advent of next-generation sequencing, the genetic spectrum of NDM has expanded significantly, necessitating a shift from symptomatic management to precision medicine. This narrative review summarizes the genetic basis and pathogenic mechanisms of NDM, categorizing them into three major pathways: (1) ATP-sensitive potassium (KATP) channelopathies (e.g., ABCC8, KCNJ11), where gain-of-function mutations inhibit insulin secretion; (2) Transcription factor defects (e.g., GLIS3, PAX6, GATA6), which impair pancreatic development and often present with syndromic features; and (3) Endoplasmic reticulum (ER) stress-mediated β-cell apoptosis, exemplified by WFS1 mutations. Furthermore, we highlight the clinical complexity of these mutations, including the “biphasic phenotype” observed in ABCC8 and HNF1A variants. Understanding these molecular mechanisms is critical for clinical decision-making. We discuss the transformative impact of genetic diagnosis in treatment, particularly the successful transition from insulin to oral sulfonylureas in patients with KATP channel mutations, and emphasize the importance of early genetic testing to optimize glycemic control and prevent complications. Full article
(This article belongs to the Section Molecular Medicine)
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25 pages, 7503 KB  
Article
Naringin Mitigates PEDV-Induced Intestinal Damage in Suckling Piglets by Modulating Inflammatory, Antiviral, and Metabolic and Transport Pathways
by Yanyan Zhang, Muzi Li, Zongyun Li, Zhonghua Li, Lei Wang, Di Zhao, Tao Wu, Dan Yi and Yongqing Hou
Biomolecules 2026, 16(1), 48; https://doi.org/10.3390/biom16010048 - 28 Dec 2025
Viewed by 745
Abstract
This study evaluated the protective effects of naringin (NG) against intestinal injury in 7-day-old piglets infected with porcine epidemic diarrhea virus (PEDV). Eighteen piglets (Duroc × Landrace × Large, body weight = 2.58 ± 0.05 kg) were divided into three treatment groups based [...] Read more.
This study evaluated the protective effects of naringin (NG) against intestinal injury in 7-day-old piglets infected with porcine epidemic diarrhea virus (PEDV). Eighteen piglets (Duroc × Landrace × Large, body weight = 2.58 ± 0.05 kg) were divided into three treatment groups based on similar body weights and equal numbers of males and females: the blank control group (CON group), the PEDV infection group (PEDV group), and the NG intervention + PEDV infection group (NG + PEDV group) (n = 6 per group). The experiment lasted for 11 days, comprising a pre-feeding period from days 0 to 3 and a formal experimental period from days 4 to 10. On days 4–10 of the experiment, piglets in the NG + PEDV group were orally administered NG (10 mg/kg). On Day 8 of the experiment, piglets in the PEDV and NG + PEDV groups were inoculated with PEDV (3 mL, 106 50% tissue culture infective dose (TCID50) per milliliter). On day 11 of the experiment, piglets were euthanized for sample collection. PEDV infection caused significant intestinal damage, including a decreased (p < 0.05) villus height in the duodenum and ileum and an increased (p < 0.05) crypt depth in all intestinal segments. This intestinal damage was accompanied by an impaired absorptive function, as indicated by reduced (p < 0.05) serum D-xylose. Further results showed that PEDV compromised the intestinal antioxidant capacity by decreasing (p < 0.05) glutathione peroxidase and catalase activities, and it stimulated the intestinal inflammatory response by upregulating (p < 0.05) the expression of key inflammatory genes, including regenerating family member 3 gamma (REG3G; duodenum, jejunum, colon), S100 calcium binding protein A9 (S100A9; ileum, colon), interleukin 1 beta (IL-1β; ileum, colon), and S100 calcium binding protein A8 (S100A8; colon). PEDV also suppressed the intestinal lipid metabolism pathway by downregulating (p < 0.05) the ileal expression of Solute Carrier Family 27 Member 4 (SLC27A4), Microsomal Triglyceride Transfer Protein (MTTP), Apolipoprotein A4 (APOA4), Apolipoprotein C3 (APOC3), Diacylglycerol O-Acyltransferase 1 (DGAT1), and Cytochrome P450 Family 2 Subfamily J Member 34 (CYP2J34). Moreover, PEDV suppressed the intestinal antiviral ability by downregulating (p < 0.05) interferon (IFN) signaling pathway genes, including MX dynamin like GTPase 1 (MX1) and ISG15 ubiquitin like modifier (ISG15) in the duodenum; weakened intestinal water and ion transport by downregulating (p < 0.05) aquaporin 10 (AQP10) and potassium inwardly rectifying channel subfamily J member 13 (KCNJ13) in the duodenum, aquaporin 7 (AQP7) and transient receptor potential cation channel subfamily V member 6 (TRPV6) in the ileum, and TRPV6 and transient receptor potential cation channel subfamily M member 6 (TRPM6) in the colon; and inhibited intestinal digestive and absorptive function by downregulating (p < 0.05) phosphoenolpyruvate carboxykinase 1 (PCK1) in the duodenum and sucrase-isomaltase (SI) in the ileum. Notably, NG effectively counteracted these detrimental effects. Moreover, NG activated the IFN signaling pathway in the jejunum and suppressed PEDV replication in the colon. In conclusion, NG alleviates PEDV-induced intestinal injury by enhancing the antioxidant capacity, suppressing inflammation, normalizing the expression of metabolic and transport genes, and improving the antiviral ability. Full article
(This article belongs to the Section Natural and Bio-derived Molecules)
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16 pages, 3267 KB  
Article
Whole-Genome Resequencing Analysis Reveals the Local Ancestry and Selection of Kongshan Cattle
by Mengmeng Bai, Kai Yang, Xiaohui Ma, Chenqi Bian, Wei Wang, Jun Yi, Ningbo Chen, Chuzhao Lei and Xiaoting Xia
Biology 2025, 14(12), 1778; https://doi.org/10.3390/biology14121778 - 12 Dec 2025
Viewed by 818
Abstract
Kongshan cattle is an indigenous breed from Sichuan Province, China, characterized by their excellent meat quality, high fertility, strong disease resistance, and remarkable environmental adaptability. However, their genomic diversity has not been systematically studied. In this work, we performed whole-genome sequencing of 30 [...] Read more.
Kongshan cattle is an indigenous breed from Sichuan Province, China, characterized by their excellent meat quality, high fertility, strong disease resistance, and remarkable environmental adaptability. However, their genomic diversity has not been systematically studied. In this work, we performed whole-genome sequencing of 30 Kongshan cattle from a breeding farm and integrated these data with 113 representative commercial and indigenous cattle breeds worldwide to investigate their population structure and genetic diversity. We further analyzed the ancestral contributions to the development of the breed. The population structure revealed that Kongshan cattle possess four types of ancestral components: East Asian indicine (0.5974), East Asian taurine (0.3464), European taurine (0.0483), and Indian indicine (0.0079). The population also exhibits high nucleotide diversity, second only to pure East Asian indicine cattle. We inferred the ancestry of each variable site in the genome and, in combination with integrated haplotype score analysis, identified candidate genes related to meat quality (ME1, ENPP2, GPD2, PDZRN4, and TMTC2), immunity (MCM6, MAP3K6, PIP4K2A, CDC6, CDC25B, PTAFR, ZC3H10, and NEK6), and environmental adaptability (KCNJ15, BECN1, AOC2, DUSP5, and ST3GAL4). These findings provide valuable insights into the evolutionary history and ancestral origins of Kongshan cattle and contribute to the broader understanding, conservation, and sustainable utilization of indigenous Chinese cattle genetic resources. Full article
(This article belongs to the Section Bioinformatics)
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19 pages, 1128 KB  
Article
Barriers, Limitations, and Experiences with Clinical Trials—Treatment in Rare Diseases with Prader–Willi Syndrome as an Example
by Merlin G. Butler, Spencer Silvey and Harold J. P. van Bosse
Genes 2025, 16(12), 1436; https://doi.org/10.3390/genes16121436 - 1 Dec 2025
Cited by 1 | Viewed by 738
Abstract
Background/Objectives: Developing and implementing clinical trials for rare diseases is complicated by the incomplete understanding of the varied genotype and subsequent phenotypic differences of a condition, particularly when low numbers of subjects are enrolled in a study. Moreover, a small-scale clinical study [...] Read more.
Background/Objectives: Developing and implementing clinical trials for rare diseases is complicated by the incomplete understanding of the varied genotype and subsequent phenotypic differences of a condition, particularly when low numbers of subjects are enrolled in a study. Moreover, a small-scale clinical study may indicate a positive outcome but have too small of a sampling population to adequately evaluate unwanted outcomes. Prader–Willi syndrome (PWS) is one such genetic disorder with varied subtypes and heterogeneity, where little progress has been made in treatment discoveries. Recently, the FDA approved diazoxide choline for treating key features of hyperphagia and obesity associated with PWS based on clinical trial experience. Diazoxide choline activates the ATP-sensitive potassium channel (KATP) of pancreatic beta cells, inhibiting the release of insulin. One of the subunits of KATP is the protein Kir6.2, the gene product of KCNJ11. Methods: Web-based programs and datasets were used to study the gene and protein functional enrichments of Kir6.2 and KCNJ11, including shared gene and/or protein–protein interactions, and biological processes and functions. Results: Four essential domains of related functions were identified: (1) apoptosis, protein degradation, and inflammation; (2) the coupling of G proteins needed for KATP channel activation; (3) glucose metabolism and control; and (4) the maintenance of intracellular ionic homeostasis. Conclusions: Cellular metabolism in the pancreas is linked to membrane excitability by KATP, which regulates insulin production, energy production and storage, appetite regulation, and fatty acid synthesis. As such, diazoxide choline may influence several biological systems beyond pancreatic and metabolic functions. Full article
(This article belongs to the Special Issue Molecular Basis in Rare Genetic Disorders)
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14 pages, 515 KB  
Article
High Polyunsaturated Fatty Acid Intake Attenuates the Genetic Risk of Higher Waist Circumference in a Sri Lankan Adult Population
by Padmini Sekar, Julie A. Lovegrove, Shelini Surendran and Karani Santhanakrishnan Vimaleswaran
Nutrients 2025, 17(17), 2866; https://doi.org/10.3390/nu17172866 - 4 Sep 2025
Cited by 1 | Viewed by 1350
Abstract
Background: Metabolic diseases, like type 2 diabetes mellitus and obesity, show a growing public health concern in Sri Lanka. Genetic predisposition and diet contribute to metabolic disease risk, but there are limited investigations into the impact of gene–diet interactions on metabolic disease risk [...] Read more.
Background: Metabolic diseases, like type 2 diabetes mellitus and obesity, show a growing public health concern in Sri Lanka. Genetic predisposition and diet contribute to metabolic disease risk, but there are limited investigations into the impact of gene–diet interactions on metabolic disease risk in the Sri Lankan population. In this study, we examined whether a metabolic genetic risk score (GRS), constructed from 10 single nucleotide polymorphisms (SNPs), interacts with dietary factors to influence metabolic health indicators in Sri Lankan adults. Methods: This cross-sectional study included 105 generally healthy adults aged 25–50 years from the GOOD (Genetics of Obesity and Diabetes) study. Anthropometric, biochemical, and dietary data using food frequency questionnaires were collected using validated methods. Genotyping was performed using the KASP® assay. The unweighted GRS was calculated by summing risk alleles across 10 SNPs in the TCF7L2, CAPN10, FTO KCNJ11, and MC4R genes. Gene–diet interaction analysis was conducted using regression models adjusted for confounders. Results: A statistically significant interaction was identified between the 10-SNP metabolic GRS and polyunsaturated fatty acid (PUFA) intake on waist circumference (P(interaction) = 0.00009). Participants with a high GRS (≥6 risk alleles) and higher PUFA intake (≥3.1 g/day) exhibited significantly lower waist circumference (p = 0.047). Conclusions: This study provides novel insights to understand gene–diet interactions affecting metabolic traits in Sri Lankans. The findings suggest that higher PUFA intake may mitigate genetic susceptibility to central obesity, highlighting the importance of personalized dietary recommendations for metabolic disease prevention. Further studies in larger cohorts are warranted to confirm this finding. Full article
(This article belongs to the Section Lipids)
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10 pages, 1271 KB  
Article
More than a Diagnosis: How Prenatal Identification of Cantú Syndrome Transformed a Family’s Medical Narrative
by Isidoro Narbona-Arias, Marta Blasco-Alonso, Susana Monís-Rodriguez, Cristina Gómez Muñoz, Ernesto González-Mesa, Daniel María Lubián-López and Jesús Jiménez-López
J. Clin. Med. 2025, 14(17), 6017; https://doi.org/10.3390/jcm14176017 - 26 Aug 2025
Viewed by 1762
Abstract
Background/Objectives: Cantú syndrome is a rare autosomal dominant genetic disorder caused by gain-of-function variants in the ABCC9 or KCNJ8 genes. Although its phenotypic expression is variable and can go unnoticed postnatally, certain ultrasound findings may raise suspicion during pregnancy. This article presents a [...] Read more.
Background/Objectives: Cantú syndrome is a rare autosomal dominant genetic disorder caused by gain-of-function variants in the ABCC9 or KCNJ8 genes. Although its phenotypic expression is variable and can go unnoticed postnatally, certain ultrasound findings may raise suspicion during pregnancy. This article presents a case of prenatal diagnosis through exome sequencing, which also enabled retrospective diagnosis in the mother and a previously undiagnosed child, highlighting the clinical and emotional value of diagnostic certainty in fetal medicine. Methods: We conducted a descriptive observational study based on a case identified at the Fetal Medicine Unit of the Regional University Hospital of Málaga. The patient underwent high-resolution ultrasound and trio-based exome sequencing (fetus and both parents). Results: Prenatal exome sequencing revealed a heterozygous pathogenic variant in ABCC9, consistent with Cantú syndrome, identified simultaneously in the fetus and the mother as part of a trio-based analysis, confirming maternal inheritance. The same variant was later detected in the patient’s older daughter, who had been under pediatric evaluation for a suggestive phenotype but had not received a genetic diagnosis until this study. The prenatal diagnosis allowed for obstetric and neonatal planning, genetic counselling, and a reinterpretation of the clinical and emotional meaning of previous pregnancies. Conclusions: Prenatal diagnosis of Cantú syndrome enables anticipation of perinatal complications, planned clinical interventions, and also provides emotional relief and a coherent narrative for families. In scenarios of variable phenotypic expressivity, fetal medicine may represent a gateway to family diagnosis, with significant clinical and psychosocial implications. Full article
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54 pages, 9063 KB  
Article
Cell Settling, Migration, and Stochastic Cancer Gene Expression Suggest Potassium Membrane Flux May Initiate pH Reversal
by Marie E. Beckner
Biomolecules 2025, 15(8), 1177; https://doi.org/10.3390/biom15081177 - 16 Aug 2025
Viewed by 3046
Abstract
Attraction of glioblastoma cells to potassium was suspected when glioblastoma cells clustered around dying cells and migrated towards serum (high [K+]) and increased potassium. Potassium channel proteins (KCN family, 90 members) mediating alterations in the transmembrane flux may provide K+ [...] Read more.
Attraction of glioblastoma cells to potassium was suspected when glioblastoma cells clustered around dying cells and migrated towards serum (high [K+]) and increased potassium. Potassium channel proteins (KCN family, 90 members) mediating alterations in the transmembrane flux may provide K+ that releases H+ bound to inner membranes in cancer cells for cytosolic proton transfer, possibly conformational in water (Grotthuss), to extrusion sites. Cell settling and migration assay results led to collecting 70 studies, unbiased by the authors for inclusion of KCN genes, that detected KCN differentially expressed genes (DEGs). Of 53 KCN DEGs found among 29 malignancies, 62.3% encoded H+-sensitive proteins. KCN DEGs encoding H+-sensitive proteins were more prevalent in 50 studies involving one or more categories (seven oncogenes and histone/DNA modifiers) versus those with none; p = 0.0325. Pertinent genes for lactate outflow, etc., had relatively normal levels of expression. Brain tumors in REMBRANDT (database) showed altered expression of KCN genes encoding H+-sensitive proteins in glioblastomas versus less invasive oligodendrogliomas of patients on anti-seizure medications, with less KCNJ16/Kir5.1; p = 5.32 × 10−8 in glioblastomas. Altered H+-sensitive potassium flux via the KCN family, downstream of oncogenes and histone/DNA modifiers, putatively incites proton transfers for H+ release during pH reversal (pHi > pHe) in cancer. Full article
(This article belongs to the Collection Feature Papers in Chemical Biology)
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22 pages, 3541 KB  
Article
Explainable Machine Learning Models for Glioma Subtype Classification and Survival Prediction
by Olga Vershinina, Victoria Turubanova, Mikhail Krivonosov, Arseniy Trukhanov and Mikhail Ivanchenko
Cancers 2025, 17(16), 2614; https://doi.org/10.3390/cancers17162614 - 9 Aug 2025
Cited by 3 | Viewed by 2195
Abstract
Background/Objectives: Gliomas are complex and heterogeneous brain tumors characterized by an unfavorable clinical course and a fatal prognosis, which can be improved by an early determination of tumor kind. Here, we developed explainable machine learning (ML) models for classifying three major glioma [...] Read more.
Background/Objectives: Gliomas are complex and heterogeneous brain tumors characterized by an unfavorable clinical course and a fatal prognosis, which can be improved by an early determination of tumor kind. Here, we developed explainable machine learning (ML) models for classifying three major glioma subtypes (astrocytoma, oligodendroglioma, and glioblastoma) and predicting survival rates based on RNA-seq data. Methods: We analyzed publicly available datasets and applied feature selection techniques to identify key biomarkers. Using various ML models, we performed classification and survival analysis to develop robust predictive models. The best-performing models were then interpreted using Shapley additive explanations (SHAP). Results: Thirteen key genes (TERT, NOX4, MMP9, TRIM67, ZDHHC18, HDAC1, TUBB6, ADM, NOG, CHEK2, KCNJ11, KCNIP2, and VEGFA) proved to be closely associated with glioma subtypes as well as survival. Support Vector Machine (SVM) turned out to be the optimal classification model with the balanced accuracy of 0.816 and the area under the receiver operating characteristic curve (AUC) of 0.896 for the test datasets. The Case-Control Cox regression model (CoxCC) proved best for predicting survival with the Harrell’s C-index of 0.809 and 0.8 for the test datasets. Using SHAP we revealed the gene expression influence on the outputs of both models, thus enhancing the transparency of the prediction generation process. Conclusions: The results indicated that the developed models could serve as a valuable practical tool for clinicians, assisting them in diagnosing and determining optimal treatment strategies for patients with glioma. Full article
(This article belongs to the Section Methods and Technologies Development)
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16 pages, 654 KB  
Article
Effect of Pharmacogenetics on Renal Outcomes of Heart Failure Patients with Reduced Ejection Fraction (HFrEF) in Response to Dapagliflozin
by Neven Sarhan, Mona F. Schaalan, Azza A. K. El-Sheikh and Bassem Zarif
Pharmaceutics 2025, 17(8), 959; https://doi.org/10.3390/pharmaceutics17080959 - 24 Jul 2025
Cited by 1 | Viewed by 1310
Abstract
Background/Objectives: Heart failure with reduced ejection fraction (HFrEF) is associated with significant renal complications, affecting disease progression and patient outcomes. Sodium-glucose co-transporter-2 (SGLT2) inhibitors have emerged as a key therapeutic strategy, offering cardiovascular and renal benefits in these patients. However, interindividual variability [...] Read more.
Background/Objectives: Heart failure with reduced ejection fraction (HFrEF) is associated with significant renal complications, affecting disease progression and patient outcomes. Sodium-glucose co-transporter-2 (SGLT2) inhibitors have emerged as a key therapeutic strategy, offering cardiovascular and renal benefits in these patients. However, interindividual variability in response to dapagliflozin underscores the role of pharmacogenetics in optimizing treatment efficacy. This study investigates the influence of genetic polymorphisms on renal outcomes in HFrEF patients treated with dapagliflozin, focusing on variations in genes such as SLC5A2, UMOD, KCNJ11, and ACE. Methods: This prospective, observational cohort study was conducted at the National Heart Institute, Cairo, Egypt, enrolling 200 patients with HFrEF. Genotyping of selected single nucleotide polymorphisms (SNPs) was performed using TaqMan™ assays. Renal function, including estimated glomerular filtration rate (eGFR), Kidney Injury Molecule-1 (KIM-1), and Neutrophil Gelatinase-Associated Lipocalin (NGAL) levels, was assessed at baseline and after six months of dapagliflozin therapy. Results: Significant associations were found between genetic variants and renal outcomes. Patients with AA genotype of rs3813008 (SLC5A2) exhibited the greatest improvement in eGFR (+7.2 mL ± 6.5, p = 0.004) and reductions in KIM-1 (−0.13 pg/mL ± 0.49, p < 0.0001) and NGAL (−6.1 pg/mL ± 15.4, p < 0.0001). Similarly, rs12917707 (UMOD) TT genotypes showed improved renal function. However, rs5219 (KCNJ11) showed no significant impact on renal outcomes. Conclusions: Pharmacogenetic variations influenced renal response to dapagliflozin in HFrEF patients, particularly in SLC5A2 and UMOD genes. These findings highlighted the potential of personalized medicine in optimizing therapy for HFrEF patients with renal complications. Full article
(This article belongs to the Section Clinical Pharmaceutics)
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19 pages, 8300 KB  
Article
Genome-Wide Association Study and RNA-Seq Analysis Uncover Candidate Genes Controlling Growth Traits in Red Tilapia (Oreochromis spp.) Under Hyperosmotic Stress
by Bingjie Jiang, Yifan Tao, Wenjing Tao, Siqi Lu, Mohamed Fekri Badran, Moustafa Hassan Lotfy Saleh, Rahma Halim Mahmoud Aboueleila, Pao Xu, Jun Qiang and Kai Liu
Int. J. Mol. Sci. 2025, 26(13), 6492; https://doi.org/10.3390/ijms26136492 - 5 Jul 2025
Cited by 1 | Viewed by 1875
Abstract
Growth traits are the most important economic traits in red tilapia (Oreochromis spp.) production, and are the main targets for its genetic improvement. Increasing salinity levels in the environment are affecting the growth, development, and molecular processes of aquatic animals. Red tilapia [...] Read more.
Growth traits are the most important economic traits in red tilapia (Oreochromis spp.) production, and are the main targets for its genetic improvement. Increasing salinity levels in the environment are affecting the growth, development, and molecular processes of aquatic animals. Red tilapia tolerates saline water to some degree. However, few credible genetic markers or potential genes are available for choosing fast-growth traits in salt-tolerant red tilapia. This work used genome-wide association study (GWAS) and RNA-sequencing (RNA-seq) to discover genes related to four growth traits in red tilapia cultured in saline water. Through genotyping, it was determined that 22 chromosomes have 12,776,921 high-quality single-nucleotide polymorphisms (SNPs). One significant SNP and eight suggestive SNPs were obtained, explaining 0.0019% to 0.3873% of phenotypic variance. A significant SNP peak associated with red tilapia growth traits was located on chr7 (chr7-47464467), and plxnb2 was identified as the candidate gene in this region. A total of 501 differentially expressed genes (DEGs) were found in the muscle of fast-growing individuals compared to those of slow-growing ones, according to a transcriptome analysis. Combining the findings of the GWAS and RNA-seq analysis, 11 candidate genes were identified, namely galnt9, esrrg, map7, mtfr2, kcnj8, fhit, dnm1, cald1, plxnb2, nuak1, and bpgm. These genes were involved in ‘other types of O-glycan biosynthesis’, ‘glycine, serine and threonine metabolism’, ‘glycolysis/gluconeogenesis’, ‘mucin-type O-glycan biosynthesis’ and ‘purine metabolism signaling’ pathways. We have developed molecular markers to genetically breed red tilapia that grow quickly in salty water. Our study lays the foundation for the future marker-assisted selection of growth traits in salt-tolerant red tilapia. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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20 pages, 1660 KB  
Article
Phenotypes and the Importance of Genetic Analysis in Adult Patients with Nephrolithiasis and/or Nephrocalcinosis: A Single-Center Experience
by Elena Emanuela Rusu, Bogdan Marian Sorohan, Robert Pandele, Andreea Popescu, Raluca Bobeica, Sonia Balanica, Diana Silvia Zilisteanu, Alexandru Iordache, Adrian Lungu and Gener Ismail
Genes 2025, 16(5), 501; https://doi.org/10.3390/genes16050501 - 27 Apr 2025
Cited by 3 | Viewed by 2464
Abstract
Background: Molecular analysis in patients with nephrolithiasis (NL) and/or nephrocalcinosis (NC) enables more accurate evaluation of underlying etiologies. The existing clinical evidence regarding genetic testing in adults with NL comprises only a few cohort studies. Materials and Methods: We retrospectively analyzed 49 adult [...] Read more.
Background: Molecular analysis in patients with nephrolithiasis (NL) and/or nephrocalcinosis (NC) enables more accurate evaluation of underlying etiologies. The existing clinical evidence regarding genetic testing in adults with NL comprises only a few cohort studies. Materials and Methods: We retrospectively analyzed 49 adult patients diagnosed with NL and/or NC from a single center, on whom we performed a genetic test using a nephrolithiasis panel. We reviewed the phenotype of the patients and compared the cases with positive and negative molecular diagnosis. Results: In total, 49 adult patients with NL and/or NC underwent genetic testing. Of the tested patients, 29 (59.2%) patients had 24 abnormal variants in 14 genes. Mendelian diseases were diagnosed in 14 (28.6%) cases: cystinuria (SLC3A1, SLC7A9; n = 4), hereditary distal renal tubular acidosis (SLC4A1; n = 3), Dent disease (CLCN5; n = 2), familial hypomagnesaemia with hypercalciuria and nephrocalcinosis (CLDN16; n = 1), infantile hypercalcemia type 1 (CYP24A1; n = 1), primary hyperoxaluria type 1 (AGXT; n = 1), Bartter syndrome type 2 (KCNJ1; n = 1), and autosomal dominant tubulointerstitial kidney disease (UMOD; n = 1). Eight (16.3%) patients had pathogenic or likely pathogenic monoallelic variants as predisposing factors for NL and/or NC, and seven (14.3%) had biallelic or monoallelic variants of uncertain significance. Patients with positive genetic tests had a lower estimated glomerular filtration rate (p = 0.03) and more frequent NL associated with NC (p = 0.007) and were unlikely to have arterial hypertension (p = 0.03) when compared with patients with negative tests. Conclusions: Our study shows an increased effectiveness of molecular diagnosis and highlights the benefits of genetic testing. NL associated with NC and the presence of chronic kidney disease are the characteristics that should prompt the clinician to suspect an inherited form of NL and/or NC. Full article
(This article belongs to the Special Issue Genes and Gene Therapies in Chronic Renal Disease)
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15 pages, 3692 KB  
Article
Comparative Transcriptome Profiling of Ileal and Cecal Tissues Between Pekin Ducks and Shaoxing Ducks
by Dandan Wang, Zhengyu Hu, Ayong Zhao, Tao Zeng, Tiantian Gu, Wenwu Xu, Yong Tian, Lizhi Lu and Li Chen
Genes 2025, 16(5), 488; https://doi.org/10.3390/genes16050488 - 25 Apr 2025
Cited by 1 | Viewed by 854
Abstract
Background: Pekin ducks are well-known meat-type ducks, whereas Shaoxing ducks are bred for their egg-laying abilities. Growth and development of poultry species is well studied; however, very little is known regarding differences in intestinal gene expression between Pekin and Shaoxing ducks. Methods [...] Read more.
Background: Pekin ducks are well-known meat-type ducks, whereas Shaoxing ducks are bred for their egg-laying abilities. Growth and development of poultry species is well studied; however, very little is known regarding differences in intestinal gene expression between Pekin and Shaoxing ducks. Methods: To investigate intestinal differences between Pekin and Shaoxing ducks, we conducted transcriptome analysis on ileal and cecal tissues from five 42-day-old ducks per breed, raised under identical housing and feeding conditions to minimize environmental influences. Results: The results showed that a total of 379 differentially expressed genes (DEGs) with p < 0.05 and |log2FoldChange| > 1 were identified in the ileum when Pekin ducks were compared to Shaoxing ducks, among which 158 were upregulated and 221 were downregulated. Compared to Shaoxing ducks, a total of 367 DEGs with p < 0.05 and |log2FoldChange| > 1 were identified in the ceca of Pekin ducks, among which 204 were upregulated and 163 were downregulated. Among these DEGs, nine genes were reported to be associated with growth and metabolism, namely, P2RX6, KCNJ6, CASQ2, EHHADH, ACSBG1, ELOVL4, AIF1L, VILL, and FABP1. Functional enrichment analyses using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases indicated that the DEGs were significantly involved in pathways such as calcium signaling, unsaturated fatty acid biosynthesis, fatty acid degradation, and tryptophan metabolism. Conclusions: In conclusion, our study identified transcriptome differences in the intestines of meat-type and laying-type ducks, offering insights into the genetic basis of their growth and metabolic differences. Future studies should validate key genes and explore environmental influences on gene expression. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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