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Keywords = single-nucleotide polymorphism

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16 pages, 8063 KB  
Article
Identification of Potential Roles of Bestrophin 3 in the Growth Performance of Ortiental River Prawn Macrobrachium nipponense by RNA Interference
by Shubo Jin, Zijian Gao, Hongtuo Fu, Yiwei Xiong, Hui Qiao, Wenyi Zhang and Sufei Jiang
Int. J. Mol. Sci. 2026, 27(12), 5338; https://doi.org/10.3390/ijms27125338 (registering DOI) - 13 Jun 2026
Abstract
Macrobrachium nipponense is an economically important freshwater prawn species in China, where larger individuals have higher commercial value than smaller ones. Previous studies indicated that bestrophin 3 (BEST3) may play a regulatory role in the growth performance of this species. Therefore, [...] Read more.
Macrobrachium nipponense is an economically important freshwater prawn species in China, where larger individuals have higher commercial value than smaller ones. Previous studies indicated that bestrophin 3 (BEST3) may play a regulatory role in the growth performance of this species. Therefore, the present study investigated the potential functions of the BEST3 gene in the growth of M. nipponense by using quantitative real-time PCR (qPCR) and RNA interference (RNAi), and also searched for growth-related single-nucleotide polymorphisms (SNPs) within this gene. qPCR results revealed that Mn-BEST3 expression was widely detected across all tested tissues, suggesting that this gene may serve multiple functions in M. nipponense. Notably, its highest expression was observed in muscle tissue, which was significantly greater than that in all other tested tissues (p < 0.05), implicating a potential role for this gene in growth regulation. Further qPCR analysis confirmed that the synthesized dsBEST3 effectively reduced Mn-BEST3 expression. The body mass gain percentage in the dsBEST3-injected group was significantly lower than that in the dsGFP-injected control group, with differences becoming significant from Day 12 onward in both males and females (p < 0.05). These findings indicate that Mn-BEST3 plays a positive role in regulating growth in M. nipponense. Finally, three SNPs were identified in the coding region of this gene. The associations of these three SNPs with growth performance, including body weight and total length, were further validated using 50 male and 50 female prawns derived from a full-sib family at approximately 5 months post-hatching. Among them, one SNP (S31_23192836) was found to be associated with growth performance in both male prawns and female prawns. Overall, this study confirmed the positive regulatory role of BEST3 in the growth of M. nipponense and identified growth-related SNPs within this gene. These results improve our understanding of the molecular mechanisms underlying growth regulation and support the production of populations with superior growth traits through marker-assisted selection. Full article
(This article belongs to the Special Issue Molecular Genetics and Genomics of Aquatic Crustaceans)
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19 pages, 480 KB  
Article
Clock Gene Variants Are Associated with Energy and Macronutrient Intake in Early Childhood and Adulthood
by Zachary J. Ribau, Sanjeena Subedi, Lori Ann Vallis, Hannah J. Coyle-Asbil, Angela Annis, Madeline Nixon, Lyn Hillyer, Alison M. Duncan, Jess Haines and David W. L. Ma
Nutrients 2026, 18(12), 1906; https://doi.org/10.3390/nu18121906 (registering DOI) - 12 Jun 2026
Abstract
Background/Objectives: Obesity remains a global health concern, and personalized prevention strategies that consider genetic predispositions can enhance existing strategies. Research suggests that variation in circadian rhythm-related genes, or clock genes, may influence obesity risk, in part through effects on dietary behaviour. However, associations [...] Read more.
Background/Objectives: Obesity remains a global health concern, and personalized prevention strategies that consider genetic predispositions can enhance existing strategies. Research suggests that variation in circadian rhythm-related genes, or clock genes, may influence obesity risk, in part through effects on dietary behaviour. However, associations between single-nucleotide polymorphisms (SNPs) in clock genes and dietary outcomes remain understudied, particularly in children. Therefore, we investigated cross-sectional associations between clock gene SNPs and dietary outcomes using baseline data from 226 adults (138 females, 88 males) aged 26–50 y and 168 children (90 females, 78 males) aged 2–6 y from the Guelph Family Health Study. Methods: DNA was extracted from saliva and genotyped using the Illumina Global Diversity Array, and dietary intake was assessed using the Automated Self-Administered 24 h Dietary Assessment Tool. Nine SNPs representing 8 clock genes were selected based on prior associations with dietary and obesity-related outcomes. Generalized Estimating Equations were used to test associations, adjusted for multiple comparisons with the Benjamini–Hochberg false discovery rate (FDR) procedure. Results: Ten nominal associations were identified (p < 0.05), and 2 remained significant after FDR correction (Padj < 0.05); among children, rs2314339-T (NR1D1) was associated with a lower percentage of energy from protein (β = −2.4%, Padj = 0.003) and rs11605924-A (CRY2) with higher energy intake (β = 118.0 kcal, Padj = 0.044). Conclusions: Findings suggest that clock gene SNPs may influence dietary habits from early childhood. Future longitudinal and functional studies are needed to clarify whether these variants can inform precision nutrition strategies for obesity prevention. Full article
(This article belongs to the Section Nutrigenetics and Nutrigenomics)
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21 pages, 3765 KB  
Systematic Review
The Role of lncRNA Polymorphisms in Digestive System Cancers: A Systematic Review and Meta-Analysis
by Krisztina Varajti, Szimonetta Lohner, László Czina, Márk Kovács-Valasek, Afshin Zand, Tímea Varjas and István Kiss
Cancers 2026, 18(12), 1916; https://doi.org/10.3390/cancers18121916 - 12 Jun 2026
Abstract
Background: Gastrointestinal (GI) cancers, particularly colorectal, gastric, and liver cancers, account for a major global burden of incidence and mortality and remain important targets for genetic susceptibility research. Long non-coding RNAs (lncRNAs) can regulate gene expression and are increasingly studied in carcinogenesis. Numerous [...] Read more.
Background: Gastrointestinal (GI) cancers, particularly colorectal, gastric, and liver cancers, account for a major global burden of incidence and mortality and remain important targets for genetic susceptibility research. Long non-coding RNAs (lncRNAs) can regulate gene expression and are increasingly studied in carcinogenesis. Numerous case–control studies have investigated associations between lncRNA polymorphisms and cancer risk, but findings are inconsistent. This study systematically evaluated the association between lncRNA single nucleotide polymorphisms (SNPs) and GI cancer susceptibility. Methods: A systematic literature search from Embase, Medline, Scopus, and Web of Science databases identified 174 potentially extractable studies. Eligible studies were case–control or cross-sectional studies published up to 8 May 2026; case reports, reviews, and meta-analyses were excluded. After screening for identical cancer type, identical SNP, and sufficient statistical data, only variants supported by at least three independent case–control studies were eligible for meta-analysis. Seven SNPs across six lncRNAs, comprising 23 studies (15,131 cases and 20,969 controls), were selected. Because of the limited number of eligible studies, subgroup analyses could not be performed consistently. Odds ratios (ORs) with 95% confidence intervals (CIs) were assessed under allelic, dominant, and recessive genetic models using fixed- or random-effects models according to heterogeneity. Results: In the primary analyses restricted to homogenous Chinese populations, H19 rs3024270 was significantly associated with hepatocellular carcinoma under allelic (OR = 1.22, 95% CI: 1.05–1.42, p = 0.01) and dominant models (OR = 1.22, 95% CI: 1.03–1.45, p = 0.02). Exploratory analyses including mixed populations identified additional associations, with the strongest observed for MEG3 rs7158663 and colorectal cancer, showing significant risk elevation under allelic (OR = 1.42, 95% CI: 1.25–1.63, p < 0.00001), dominant (OR = 1.42, 95% CI: 1.20–1.68, p < 0.0001), and recessive models (OR = 1.98, 95% CI: 1.46–2.68, p < 0.0001). PRNCR1 rs16901946 showed a significant association with gastric cancer under the dominant model (OR = 1.20, 95% CI: 1.02–1.41, p = 0.03), while GAS5 rs145204276 demonstrated a recessive-model association with gastric cancer (OR = 1.30, 95% CI: 1.16–1.46, p < 0.0001). In contrast, GAS5 rs145204276 in colorectal cancer; H19 rs2839698 and MALAT1 rs619586 in hepatocellular carcinoma yielded heterogeneous or unstable pooled estimates. Findings should be interpreted cautiously due to the limited number of studies, heterogeneity, and potential publication bias. Conclusions: Among the primary analyses, H19 rs3024270 showed the most consistent association with HCC susceptibility. Exploratory analyses identified candidate variants, including MEG3 rs7158663, PRNCR1 rs16901946, and GAS5 rs145204276. Population-specific effects and study heterogeneity remain important limitations. PROSPERO registration number for this study: CRD42023389742. Full article
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16 pages, 792 KB  
Article
KL-6 as a Biomarker for Adult Patients with Cystic Fibrosis and the Impact of MUC1 Genotype
by Sarah Ricken, Sarah Dietz-Terjung, Gerhard Weinreich, Jose Ortiz, Michaela Schedel, Svenja Straßburg, Christian Taube, Matthias Welsner, Francesco Bonella and Sivagurunathan Sutharsan
J. Clin. Med. 2026, 15(12), 4555; https://doi.org/10.3390/jcm15124555 - 12 Jun 2026
Abstract
Background/Objectives: Krebs von den Lungen-6 (KL-6) is a mucin-like glycoprotein that is elevated in a variety of lung diseases and used as a diagnostic and prognostic biomarker in people with cystic fibrosis (pwCF). Single nucleotide polymorphisms (SNPs) in mucin-1 (MUC1) [...] Read more.
Background/Objectives: Krebs von den Lungen-6 (KL-6) is a mucin-like glycoprotein that is elevated in a variety of lung diseases and used as a diagnostic and prognostic biomarker in people with cystic fibrosis (pwCF). Single nucleotide polymorphisms (SNPs) in mucin-1 (MUC1) influence KL-6 serum concentration. This study investigated the relationship between serum KL-6 concentrations in pwCF and a MUC1 SNP and its longitudinal dynamics. Methods: The study included pwCF (n = 174) and healthy controls (n = 30). In pwCF, 365 samples were collected for longitudinal analyses; KL-6 levels were measured and the MUC1 SNP rs4072037 was genotyped in pwCF and controls. Cross-sectional and longitudinal associations between KL-6, genotype, and clinical parameters, such as infectious exacerbation, body mass index, inflammatory values and lung function, were analyzed using linear mixed-effects models. Results: Serum KL-6 was significantly elevated in pwCF compared with controls (458 ± 357 vs. 283 ± 103 U/mL; p < 0.001). Homozygous G/G carriers exhibited higher baseline KL-6 than A/A carriers (627 ± 673 vs. 397 ± 148 U/mL; p < 0.001), while heterozygous individuals showed intermediate levels. Longitudinally, the MUC1 SNP and interindividual differences in vital capacity (ppFVC) primarily determined baseline KL-6 levels, explaining 52.5% of variance. Short-term intraindividual fluctuations were largely driven by infectious exacerbations independent of genotype, accounting for ~10% of within-subject variance. Conclusions: PwCF generally showed elevated serum KL-6 levels and reflected both stable interindividual differences, mainly driven by the MUC1 SNP and ppFVC. Dynamic intraindividualchanges were associated with infectious exacerbations. Given the influence of MUC1 polymorphisms (e.g., rs4072037) on KL-6 concentration, personalized interpretation based on the genotype status may be informative in pwCF. Full article
(This article belongs to the Section Respiratory Medicine)
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10 pages, 213 KB  
Article
A Greek Case–Control Replication Study of IKZF1 rs4132601 and CDKN2A rs3731217 in Childhood Acute Lymphoblastic Leukemia
by Ioannis Kyriakidis, Spyridoula D. Katsarou, Maria I. Zervou, Nikolaos Katzilakis, Maria Stratigaki, Iordanis Pelagiadis and Eftichia Stiakaki
Genes 2026, 17(6), 682; https://doi.org/10.3390/genes17060682 - 10 Jun 2026
Viewed by 127
Abstract
Background/Objectives: Inherited variants in IKZF1 and CDKN2A/2B are among the most consistently reported germline susceptibility markers for childhood acute lymphoblastic leukemia (ALL). Nonetheless, effect sizes differ across ancestry groups, age ranges, and immunophenotypic subtypes, making well-characterized population-specific replication studies valuable for refining ancestry-specific [...] Read more.
Background/Objectives: Inherited variants in IKZF1 and CDKN2A/2B are among the most consistently reported germline susceptibility markers for childhood acute lymphoblastic leukemia (ALL). Nonetheless, effect sizes differ across ancestry groups, age ranges, and immunophenotypic subtypes, making well-characterized population-specific replication studies valuable for refining ancestry-specific evidence. This study examined two sentinel variants with historical relevance, IKZF1 rs4132601 and CDKN2A rs3731217, within a pediatric Greek cohort. Methods: A case–control study with retrospective case ascertainment and control recruitment through routine pediatric visits was conducted, comprising 50 children and adolescents with ALL and 91 healthy controls from Crete, Greece. Constitutional DNA was isolated from peripheral blood samples collected during remission in cases, while controls provided peripheral blood for targeted germline genotyping. Genotyping was performed using PCR-restriction fragment length polymorphism analysis. We evaluated Hardy–Weinberg equilibrium and genotype and allele distributions and analyzed the data using logistic regression models. Results: Control minor allele frequencies were broadly compatible with public European reference data. Neither IKZF1 rs4132601 nor CDKN2A rs3731217 showed a significant association with susceptibility to childhood ALL under either genotype-based or additive models. Results remained consistent after excluding T-cell ALL cases. Exploratory genotype-phenotype analyses did not reveal robust associations with clinical or molecular features. Conclusions: In this first Greek pediatric assessment of IKZF1 rs4132601 and CDKN2A rs3731217, no significant association with ALL susceptibility was observed. Within the constraints of limited statistical power, these negative findings provide population-specific evidence, refine regional allele-frequency and effect-size estimates, highlight the limitations of relying on single historical sentinel single-nucleotide polymorphisms (SNPs), and support future ancestry-informed and polygenic approaches in southeastern European cohorts. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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35 pages, 1834 KB  
Article
Complete Genomes of Human Papillomavirus Type 16 Viruses Isolated from Cases of Cervical Neoplasia and Squamous Cell Carcinomas Followed in Latvia in 2012–2024
by Juris Jansons, Nikita Zrelovs, Arta Spridzane, Marija Nazarenko, Liba Sokolovska, Karina Biserova, Daira Krisane, Austra Breiksa-Vaivode, Daria Avdoshina, Beatrise Orlova, Marta Petrovska, Serhii Kalman, Stefan Petkov, Valery Ilinsky, Anna Ilinskaya, Jurijs Nazarovs, Androniks Mitildzans and Maria Isaguliants
Vaccines 2026, 14(6), 517; https://doi.org/10.3390/vaccines14060517 - 9 Jun 2026
Viewed by 74
Abstract
Background: Persistent high-risk human papillomavirus (hrHPV) infection causes over 99% of cervical precancers and cancers worldwide, with HPV genotype 16 (HPV16) responsible for 50% of the cases. Latvia ranks among the top EU countries for cervical cancer incidence and mortality. In the general [...] Read more.
Background: Persistent high-risk human papillomavirus (hrHPV) infection causes over 99% of cervical precancers and cancers worldwide, with HPV genotype 16 (HPV16) responsible for 50% of the cases. Latvia ranks among the top EU countries for cervical cancer incidence and mortality. In the general Latvian population, 4.2% of women are hrHPV-infected, mostly with HPV16. However, information on the circulating HPV16 isolates is missing. Objectives: To study the genomic variability of the Latvian HPV16 isolates, compare them with HPV16 in Europe and across the globe, reveal features associated with the severity of cervical disease and uncover eventual sequence changes due to the national HPV vaccination. Methods: DNA was extracted from the formalin-fixed paraffin-embedded cervical tissues of women diagnosed with cervical intraepithelial neoplasia (CIN) stages I-III and squamous cell carcinoma (SCC) grades 1–3, collected between 2012 and 2024. Samples positive for HPV16 were subjected to whole genome sequencing (WGS) on the Illumina platform (n = 16) or Sanger sequencing of the E6/E7 coding region (n = 31). A consensus HPV16 sequence was generated, and single nucleotide polymorphisms (SNPs) and eventual amino acid substitutions (AAS) were analysed. Results: Complete genomes of 16 HPV16 variants were reconstructed, with 13 related to the European sublineage A1 and 3 to the sublineage A2 references. Sequences showed high conservation; still 93 non-redundant variants were identified. The highest variability was observed for the capsid protein L2, and the lowest, for oncoprotein E7. The prevalence of SNPs and AAS in the Latvian HPV16 variants, specifically in capsid protein L1, did not increase with time, showing no effect of HPV vaccination. Associations between HPV16 sequence features and severity of cervical disease were limited to AAS E6:L90V, which was significantly more common in SCC grade 2/3 than in CINII/III cases (p = 0.015). Conclusions: Highly conserved HPV16 genomes circulating in Latvia harbour a series of unique as well as common nonsynonymous SNPs with respective AAS, with one, AAS E6:L90V, associating with disease severity. No HPV vaccine escape variants were detected. Deciphering complete genomes of HPV16 from CIN and SCC cases in Latvia informs public authorities performing HPV vaccination and is useful for the management of HPV-associated cervical diseases. Full article
(This article belongs to the Special Issue Chronic Viral Infections and Cancer: Openings for Vaccines and Cure)
13 pages, 1417 KB  
Article
Evidence for Genotype-Associated Differences in Disease Severity and Limitations of Serotype-Based Classification in Glaesserella parasuis Revealed by Whole-Genome Sequencing in Japan
by Manao Ozawa, Motoshi Kawano and Shoko Iwamoto
Pathogens 2026, 15(6), 619; https://doi.org/10.3390/pathogens15060619 - 9 Jun 2026
Viewed by 142
Abstract
We conducted whole-genome sequencing to investigate serotypes, virulence-associated genes, antimicrobial resistance determinants, and genetic relationships among Glaesserella parasuis isolates from diseased pigs in Japan, focusing on underrecognized aspects of disease epidemiology and control. Although Glässer’s disease is well recognized in swine production, its [...] Read more.
We conducted whole-genome sequencing to investigate serotypes, virulence-associated genes, antimicrobial resistance determinants, and genetic relationships among Glaesserella parasuis isolates from diseased pigs in Japan, focusing on underrecognized aspects of disease epidemiology and control. Although Glässer’s disease is well recognized in swine production, its epidemiology remains incompletely understood, particularly regarding the relationship between serotype, genotype, and pathogenicity. Serotypes 5 or 12 (5/12) (28.9%) were predominant, followed by serotype 7 (10.8%). Phylogenetic analysis based on core-genome single nucleotide polymorphisms and cluster analysis classified the isolates into three genetic groups, with no clear association between serotype and genetic grouping. One genetic group tended to exhibit a lower proportion of severe clinical cases compared with the others, with a statistically significant difference observed in one comparison but not in the other. These findings provide evidence suggesting genotype-associated differences in disease severity, indicating that pathogenic potential may be more closely linked to genetic background than to serotype. These findings suggest a potential limitation of serotype-based vaccine strategies. Although 86.7% of isolates lacked antimicrobial resistance genes, resistance determinants were identified on contigs predicted to be of plasmid origin. These results indicate that antimicrobial resistance, while not widespread, may be underestimated and could disseminate. Overall, our findings highlight underexplored aspects of Glässer’s disease relevant to improving control and prevention. Full article
(This article belongs to the Special Issue Neglected Infectious Diseases of Swine)
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13 pages, 1419 KB  
Article
Phenotypic Characterization and DNA Fingerprinting of Tianbao Melon Using Genome-Wide SNPs
by Yumeng Ren, Xiaofeng Su, Wenjing Dong, Minghe Hu, Houshun Ma, Qian Zhao, Wenhao Jiang, Shengkai Zhang, Sen Chai, Xiaoli Liu, Xiaofeng Liu, Kexiang Wang and Kuipeng Xu
Horticulturae 2026, 12(6), 714; https://doi.org/10.3390/horticulturae12060714 - 9 Jun 2026
Viewed by 208
Abstract
The Tianbao melon (Cucumis melo subsp. agrestis) is a highly valued regional horticultural crop, yet its sustainable development is severely constrained by a narrow genetic base and widespread varietal admixture in the market. In this study, a panel of 32 Tianbao [...] Read more.
The Tianbao melon (Cucumis melo subsp. agrestis) is a highly valued regional horticultural crop, yet its sustainable development is severely constrained by a narrow genetic base and widespread varietal admixture in the market. In this study, a panel of 32 Tianbao melon accessions was systematically evaluated by integrating field-based phenotypic assessment with genome-wide single-nucleotide polymorphism (SNP) analysis via whole-genome resequencing. Phenotypic analysis based on ten quantitative traits revealed low overall morphological variability, indicating limited discriminatory power of morphological traits alone. In contrast, 173,497 high-quality SNPs uncovered substantial hidden genetic differentiation, partitioning the accessions into four distinct genotypic groups. Notably, accessions TB-17 and TB-27, though nearly indistinguishable morphologically, exhibited clear genetic divergence in both phylogenetic and principal component analyses. Furthermore, a panel of 20 core SNPs with conserved flanking sequences was selected, generating unique molecular fingerprint profiles for all 32 accessions and achieving high discriminatory resolution (pairwise differences ranging from 10 to 13 SNPs). These findings demonstrate that the integration of phenotypic and genome-wide SNP data provides a robust framework for genetic diversity assessment and DNA fingerprinting in Tianbao melon, offering a scientific basis for cultivar identification, intellectual property protection, and precision breeding to support sustainable development of the regional melon industry. Full article
(This article belongs to the Special Issue Germplasm Resources and Genetics Improvement of Watermelon and Melon)
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15 pages, 1702 KB  
Article
Evaluation of TAB2/SUMO4 Region Polymorphisms in Childhood and Adult-Onset Type 1 Diabetes Mellitus in a Southern Brazilian Population
by Mateus Santana Lopes, Pedro Henrique Barato Plocharski, Paula Rothbarth Silva, Suzana Nesi-França, Rosângela Roginski Réa, Glaucio Valdameri, Vivian Rotuno Moure, Marcel Henrique Marcondes Sari, Geraldo Picheth and Fabiane Gomes de Moraes Rego
Endocrines 2026, 7(2), 25; https://doi.org/10.3390/endocrines7020025 - 8 Jun 2026
Viewed by 166
Abstract
Background/Objective: Type 1 diabetes (T1D) is a complex autoimmune disease characterized by the destruction of insulin-producing pancreatic beta cells. The TAB2/SUMO4 locus has been implicated in T1D susceptibility through a biochemical mechanism involving NFκB. Given that alterations in NFκB activity have been linked [...] Read more.
Background/Objective: Type 1 diabetes (T1D) is a complex autoimmune disease characterized by the destruction of insulin-producing pancreatic beta cells. The TAB2/SUMO4 locus has been implicated in T1D susceptibility through a biochemical mechanism involving NFκB. Given that alterations in NFκB activity have been linked to the etiology of T1D, this study evaluated the association between single nucleotide polymorphisms (SNPs) in the TAB2/SUMO4 region (rs6942381, rs237027, rs237025, and rs7896) and T1D in a population from southern Brazil. Methods: Two T1D groups, each comprising 150 with childhood-onset (aged ≤14 years) and 150 with adulthood-onset (aged >18 years) were compared with healthy controls (165 children aged ≤14 years and 150 adults aged >18 years, respectively). Genotyping of SNPs in the TAB2/SUMO4 region was performed using real-time PCR. Results: All polymorphisms were in Hardy–Weinberg equilibrium. The genotype and allele frequencies of the studied polymorphisms in the TAB2/SUMO4 region did not differ among groups in either children or adults. The MAF of the children and adults controls are respectively for rs6942381 49.1% (95% CI 44–54%) and 48.0% (95% CI 42–52%), rs237027 12.4% (95% CI 9–16%) and 11.7% (95% CI 8–15%), rs237025 45.5% (95% CI 40–51%) and 46.0% (95% CI 41–52%) and rs7896 18.2% (95% CI 14–22%) and 24.3% (95% CI 19–29%). The haplotype frequencies were also similar between groups. The observed minor allele frequencies were similar to those reported in European populations. Conclusions: TAB2/SUMO4 locus polymorphisms (rs6942381, rs237027, rs237025, and rs7896) were not associated with childhood- or adulthood-onset T1D in the studied population. Full article
(This article belongs to the Special Issue Recent Advances in Type 1 Diabetes)
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25 pages, 3682 KB  
Article
Effect of Genetic Architecture and Partitioning of Training Population on GEBVs, SNP Effects and GWAS: A Simulation Study
by Gaurav Dutta, Hélène Wilmot, Elizabeth D. Schifano and Breno Fragomeni
Genes 2026, 17(6), 670; https://doi.org/10.3390/genes17060670 - 7 Jun 2026
Viewed by 487
Abstract
Background/Objectives: Inconsistency of results in genome-wide association studies (GWAS) has been a challenge for animal breeders and geneticists. Understanding how different training subset configurations influence genomic estimated breeding values (GEBVs) and GWAS is essential for optimizing genomic evaluations. This study aimed to evaluate [...] Read more.
Background/Objectives: Inconsistency of results in genome-wide association studies (GWAS) has been a challenge for animal breeders and geneticists. Understanding how different training subset configurations influence genomic estimated breeding values (GEBVs) and GWAS is essential for optimizing genomic evaluations. This study aimed to evaluate the impact of training population partitioning and QTL architecture on prediction accuracy, GEBV and SNP-effect correlations, and on the consistency of GWAS. Methods: A simulated population consisting of ten breeding generations was partitioned and evaluated on four training scenarios: animal ID, sex, generations, and generation correct.blocks. Moreover, four distinct genetic architectures were simulated, representing combinations of two QTL counts (100 and 1000) and two effect-size distributions (normal and gamma). Phenotypes were available for 10,000 individuals, which were genotyped for 50,000 SNP markers. Results: Across generation blocks, accuracy increased from earlier to more recent generations. GEBV correlations were consistently higher than SNP-effect correlations across scenarios. Adjacent generation blocks showed stronger correlations than distant blocks. Architectures with 1000 QTL yielded higher accuracy than 100 QTL architectures, while effect distribution had limited influence. Manhattan plots showed stable major QTL peaks across subsets. However, reduced peak magnitudes with more noise signals were observed in smaller training sets. Training population size and genetic distance strongly influenced genomic prediction performance. GEBVs were more stable than individual SNP-effect estimates across training configurations. Conclusions: These findings provide insights for interpreting why GWAS results fluctuate more than breeding values due to limited dimensionality of genomic information. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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17 pages, 5092 KB  
Article
Novel Potential Risk Loci for Migraine in the Portuguese Population
by Rodrigo De Marco, Kevin Pucci, Mariana Santos, Raquel Gil-Gouveia, Bruno Cavadas, Alda Sousa, Miguel Alves-Ferreira, Luísa Azevedo, Carolina Lemos and Andreia Dias
Int. J. Mol. Sci. 2026, 27(12), 5165; https://doi.org/10.3390/ijms27125165 - 6 Jun 2026
Viewed by 235
Abstract
Common forms of migraine are complex disorders characterized by significant clinical diversity. Their genetic basis has been extensively studied but remains unclear. This study represents the first pilot genome-wide association study (GWAS) integrating a polygenic risk score (PRS) in the Portuguese population, designed [...] Read more.
Common forms of migraine are complex disorders characterized by significant clinical diversity. Their genetic basis has been extensively studied but remains unclear. This study represents the first pilot genome-wide association study (GWAS) integrating a polygenic risk score (PRS) in the Portuguese population, designed to identify migraine susceptibility loci through a case–control study and unravel population-specific variants. Genotyping data was acquired with Applied Biosystems Axiom™ PMDA array, producing 12,035,248 single-nucleotide polymorphisms (SNPs) post-imputation, providing a comprehensive scope for GWAS analysis. PRS models were created and tested using a k-folds cross-validation framework and the optimal significance threshold was assessed. We detected 12 potential risk loci corresponding to 12 lead SNPs (RP11-204N11.2, CTA-481E9.4/CTA-481E9.3, RAP1A, TIGD4, CADPS2, RP11-46E17.6, RP4-569D19.5, RP11-398K14.1, PCBP1-AS1, TCF15, IL6R and UNC13A). The top three variants (RP11-204N11.2, CTA-481E9.4/CTA-481E9.3 and RAP1A) were also supported by the PRS model. We highlight that several variants present putative biological relevance to migraine pathophysiology, reinforcing the importance of neurotransmitter release, synaptic transmission and the involvement of vascular components in migraine pathophysiology. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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20 pages, 519 KB  
Article
A Multi-Locus and Machine Learning-Based Assessment of SNCA Variants in Alzheimer’s Disease
by Hatice Segmen and Mustafa Yildiz
Int. J. Mol. Sci. 2026, 27(11), 5143; https://doi.org/10.3390/ijms27115143 - 5 Jun 2026
Viewed by 119
Abstract
This study investigates the role of single nucleotide polymorphisms (SNPs) in the SNCA gene, encoding alpha-synuclein, in Alzheimer’s disease (AD). A case–control study was conducted including 95 AD patients and 97 healthy controls. Four SNCA polymorphisms (rs2583988, rs2619363, rs2619364, rs10005233) were analyzed using [...] Read more.
This study investigates the role of single nucleotide polymorphisms (SNPs) in the SNCA gene, encoding alpha-synuclein, in Alzheimer’s disease (AD). A case–control study was conducted including 95 AD patients and 97 healthy controls. Four SNCA polymorphisms (rs2583988, rs2619363, rs2619364, rs10005233) were analyzed using logistic regression, haplotype estimation, genotype combination analysis, and Random Forest modeling. Significant associations were identified for rs2583988, rs2619364, and rs2619363, while rs10005233 showed no association. The rs2583988 C allele and rs2619364 G allele were more frequent in patients, suggesting increased disease risk. Linkage disequilibrium analysis revealed weak correlations (low r2), indicating largely independent genetic effects. Multivariate logistic regression showed that clinical parameters, rather than genetic variants, were independently associated with AD. Multi-locus genotype analysis demonstrated that specific SNP combinations were linked to increased disease risk. Firth regression confirmed associations in low-frequency genotypes. The outcomes derived from the Random Forest methodology were classified as exploratory and not as proof of clinical predictive utility, attributed to the limited sample size, the absence of external validation, and the educational imbalance. Ordinal logistic regression indicated no association between SNCA variants and cognitive severity, while education had a protective effect. The selected SNCA variants showed exploratory associations with AD in this cohort; however, they failed to maintain their validity as independent predictors in multivariate logistic regression analysis. Before drawing any conclusions regarding screening or risk stratification, these findings require independent replication, correction for multiple testing and functional validation. Full article
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32 pages, 2377 KB  
Review
Per- and Polyfluoroalkyl Substances Exposure and Ischemic Heart Disease: Emerging Evidence from the Literature
by Francesca Gorini, Alessandro Tonacci, Mariangela Palazzo, Elisa Bustaffa, Fabrizio Minichilli and Andrea Borghini
Antioxidants 2026, 15(6), 718; https://doi.org/10.3390/antiox15060718 - 5 Jun 2026
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Abstract
Ischemic heart disease (IHD) is a chronic and progressive condition characterized by reduced blood flow, mainly due to atherosclerosis. It is currently the leading cause of mortality among cardiovascular diseases. In recent years, per- and polyfluoroalkyl substances (PFAS), a group of ubiquitous and [...] Read more.
Ischemic heart disease (IHD) is a chronic and progressive condition characterized by reduced blood flow, mainly due to atherosclerosis. It is currently the leading cause of mortality among cardiovascular diseases. In recent years, per- and polyfluoroalkyl substances (PFAS), a group of ubiquitous and highly persistent environmental contaminants, have emerged as potential risk factors for IHD. PFAS are well-established endocrine disruptors and have been associated with hypercholesterolemia, hypertriglyceridemia, and insulin resistance. Despite the limited number of epidemiological studies and inconsistent findings from occupational settings, accumulating evidence suggests that elevated exposure to certain PFAS compounds may increase the risk of IHD and vascular dysfunction, including processes related to atherosclerosis development, sometimes with dose–response relationships and sex-specific patterns. Mechanistic evidence supports this link, indicating that PFAS exposure induces molecular and cellular alterations relevant to cardiovascular pathophysiology, including increased oxidative stress and vascular inflammation, and disruption of lipid metabolism. In addition, PFAS may affect epigenetic regulation, telomere length, and mitochondrial DNA copy number, which are emerging biomarkers associated with atherosclerosis and IHD and may indicate early cardiovascular vulnerability. Future research integrating innovative approaches and advanced analytical techniques may help address current knowledge gaps and clarify the mechanistic pathways linking PFAS exposure to clinical cardiovascular outcomes. Full article
(This article belongs to the Section Health Outcomes of Antioxidants and Oxidative Stress)
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16 pages, 575 KB  
Article
Population-Specific Exploration of MIR146A Gene Polymorphism in Acute Renal Rejection: A Cross-Sectional, Case–Control Study
by Nor Elhouda Nacer, Soumia Missoum, Houssem Eddine Ouarhlent, Seddam Hares, Asma Ribouh and Ghania Belaaloui
Int. J. Mol. Sci. 2026, 27(11), 5105; https://doi.org/10.3390/ijms27115105 - 4 Jun 2026
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Abstract
Acute renal allograft rejection (AR) is immune-mediated. Recent evidence highlights some microRNAs as immune modulators. Few and conflicting studies have studied the impact of the MIR146A gene single-nucleotide polymorphism rs2910164 (C>G) on AR. We explored the association of rs2910164 with AR in a [...] Read more.
Acute renal allograft rejection (AR) is immune-mediated. Recent evidence highlights some microRNAs as immune modulators. Few and conflicting studies have studied the impact of the MIR146A gene single-nucleotide polymorphism rs2910164 (C>G) on AR. We explored the association of rs2910164 with AR in a single-center cohort of 533 kidney transplant recipients (KTRs) by genotyping cases with biopsy-proven late AR (AR group, n = 35) and matched control KTRs without AR (non-AR group, n = 60). Genotyping was performed with real-time PCR. Multivariable logistic regression and Firth penalized logistic regression, as a sensitivity analysis, were used to adjust for confounding factors. Donor–recipient age difference was significantly higher in the AR group than in the non-AR group (23.37 ± 11.29 vs. 14.83 ± 10.54, p < 0.001). Recipient mean age in the AR group is lower than in the non-AR group (27.51 ± 10.34 vs. 32.83 ± 9.76 years, p = 0.014), while the opposite is observed with the donor mean age (49.57 ± 10.37 vs. 43.27 ± 10.27 years, p = 0.005). AR was associated with preformed donor-specific antibodies (DSAs) (45.7% vs. 8.3%, p = 0.000, OR = 9.263, 95% CI (2.988–28.720)), and with two HLA-A* mismatches (17.1% vs. 3.3%, p = 0.048, OR = 6.000, 95% CI (1.139–31.595)). Moreover, post-transplant viral infections, particularly with CMV and SARS-CoV-2, were associated with AR (p < 0.05). However, rs2910164 was not associated with AR across all the tested genetic models (p > 0.05). Our study provides population-specific negative association data on rs2910164 and AR. Larger multicentric studies and future meta-analyses are needed to clarify whether any effect is modest or context-dependent. Full article
(This article belongs to the Special Issue Advances in Kidney Transplantation)
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20 pages, 1375 KB  
Article
Genetic Variability in the IGF-1 Axis Modulates Cancer-Associated Cachexia and Prognosis
by Mariana Moreira Pires, Inês Guerra de Melo, Ana Carolina Leão Silva, Virgínia Rocha Dias, Cláudia Silva, Maria Paula Silva, Joana M. O. Santos, Tiago Ferreira, Valéria Tavares and Rui Medeiros
Cancers 2026, 18(11), 1822; https://doi.org/10.3390/cancers18111822 - 2 Jun 2026
Viewed by 355
Abstract
Background: Cancer-associated cachexia (CAC) is a multifactorial syndrome driven by a profound metabolic and inflammatory dysregulation. Due to the central role of the insulin-like growth factor 1 (IGF-1) pathway in regulating muscle mass, energy metabolism, and inflammation, this study evaluated the relevance of [...] Read more.
Background: Cancer-associated cachexia (CAC) is a multifactorial syndrome driven by a profound metabolic and inflammatory dysregulation. Due to the central role of the insulin-like growth factor 1 (IGF-1) pathway in regulating muscle mass, energy metabolism, and inflammation, this study evaluated the relevance of five IGF-1 axis-related single-nucleotide polymorphisms (SNPs), namely IGF1 rs6220, insulin-like growth factor 1 receptor (IGF1R) rs2016347 and rs2684788, growth hormone receptor (GHR) rs6873545, and insulin receptor substrate 1 (IRS1) rs1801278. Methods: The impact of these variants on CAC onset and overall survival (OS) was assessed in a cohort of 140 cancer patients. Results: While overall-cohort analyses did not reach statistical significance, exploratory analyses suggested potential associations between the IGF1 rs6220 GG and GHR rs6873545 CC genotypes and increased CAC risk in male patients. A trend for higher CAC prevalence was also noted in younger patients (<63 years) with the rs6873545 CC genotype. For pre-CAC and CAC patients, exploratory subgroup analyses on patients’ OS were conducted following no significant results in the overall cohort. Among older patients and those with high prognostic nutritional index (PNI; >44.2), the IGF1 rs6220 G allele was associated with longer OS. Conversely, the IGF1R rs2016347 G allele and rs2684788 T allele were linked to poorer OS across multiple pre-CAC and CAC subgroups. The effects of GHR rs6873545 varied across subgroups, suggesting context-dependent activity. Conclusions: This study highlights the functional heterogeneity of IGF-1 axis-related genetic variants, indicating potential to serve as predictors of CAC. Given the exploratory nature of these findings, validation in larger cohorts is required to confirm the associations found. Full article
(This article belongs to the Section Cancer Pathophysiology)
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