Human molecular genetics最新文献

{"title":"Droplet digital PCR as a first-line detection tool in the genetic diagnosis of vascular anomalies.","authors":"Tara K Lane, Natasha J Brown, Timothy E Green, Denisse Garza, Michelle G de Silva, Mark F Bennett, Caitlin Tubb, Sian M W Macdonald, Adam Gascoigne, Roderic J Phillips, John Slavin, Colleen D'Arcy, Duncan MacGregor, Amelia Clifford, Lydia Pathmanathan, Susan J Robertson, Phillip Bekhor, Jodie Simpson, Samuel Gooley, Ingrid E Scheffer, Samuel F Berkovic, Anthony J Penington, Michael S Hildebrand","doi":"10.1093/hmg/ddag109","DOIUrl":"https://doi.org/10.1093/hmg/ddag109","url":null,"abstract":"<p><p>Targeted precision therapies are increasingly used in the treatment of individuals with vascular anomalies (VAs). This increases the need for rapid, accurate and inexpensive genetic diagnosis. Droplet digital polymerase chain reaction (ddPCR) is an alternative to next-generation sequencing (NGS), permitting rapid, highly sensitive interrogation of recurrent pathogenic mosaic variants. We examined the feasibility of ddPCR as a primary diagnostic tool in a large cohort of individuals with VAs. Lesional tissue was collected for ddPCR of up to 46 recurrent pathogenic variants across 16 genes associated with VAs. Specimens were assessed on a subset of assays for each individual based on clinical phenotype. Most individuals who had negative ddPCR results went on to high-depth gene panel or deep exome NGS, or Sanger sequencing. Here we report the phenotypic and molecular findings for 78 newly recruited and tested individuals in addition to the 60 individuals already reported from our cohort. The overall diagnostic yield for our cohort when combined with individuals previously reported was 104/138 (75%). Of 138 individuals tested, recurrent pathogenic variants were detected in 71 (51%) on ddPCR. Variants were most frequently identified in PIK3CA (n = 28), TEK (n = 18), GNAQ (n = 12), or MAP2K1 (n = 7). In a further 33 individuals, pathogenic variants were identified on NGS or Sanger sequencing. Our findings indicate that ddPCR is an efficient method achieving a high diagnostic yield in our cohort when used prior to sequencing.</p>","PeriodicalId":13070,"journal":{"name":"Human molecular genetics","volume":"35 21","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149227767","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gene regulatory behaviors of mutant CRX proteins demonstrated with late-stage human retinal organoids.","authors":"Nathaniel K Mullin, Andrew P Voigt, Deepak A Lamba, Kathleen R Chirco","doi":"10.1093/hmg/ddag107","DOIUrl":"10.1093/hmg/ddag107","url":null,"abstract":"<p><p>Variants in the transcription factor CRX cause a spectrum of retinal degenerative disorders including Leber congenital amaurosis 7 (LCA7). LCA7-associated variants exert a dominant effect in developing photoreceptor cells, leading to cellular dysfunction and poor to absent visual acuity in patients. Here, we dissect the allelic heterogeneity of LCA7 using multimodal single-cell gene expression and chromatin accessibility analysis of retinal organoids. We generated mature (240 day) retinal organoids from patient-derived iPSCs carrying missense (K88Q) and nonsense (T155fs) variants, as well as from CRISPR-corrected control lines. We show that these variants, while both causing LCA7, produce unique transcriptional changes in human photoreceptors. Furthermore, the K88Q variant causes aberrant chromatin accessibility at sites typically bound by non-photoreceptor retinal transcription factors, indicating a partial derangement of normal retinal cell fate programming. This work demonstrates the gene regulatory mechanisms of pathogenicity of two disease-causing CRX variants in human retinal cells.</p>","PeriodicalId":13070,"journal":{"name":"Human molecular genetics","volume":"35 21","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13669955/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149193247","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The monogenic forms of obesity in Saudi families.","authors":"Sultanah Turki Almolafikh, Ali A Alshatwi, Razan Orfali, Haya AlSaud","doi":"10.1093/hmg/ddag054","DOIUrl":"https://doi.org/10.1093/hmg/ddag054","url":null,"abstract":"<p><strong>Background: </strong>Obesity is a multifactorial disorder with a substantial yet incompletely defined genetic component. Rare monogenic variants, particularly in consanguineous populations, may account for part of the 'missing heritability.'</p><p><strong>Objectives: </strong>To delineate the genetic contribution to severe obesity in individuals from Saudi Arabia by pinpointing known and novel monogenic variants in families presenting with extreme phenotypes.</p><p><strong>Methods: </strong>Eight multiplex Saudi families (each comprising 9 members; range: lean body weight to severe obesity) were enrolled. Adults had a BMI of ≥30 kg/m2; children exceeded the 90th percentile (overweight) or the 97th percentile (obese). Whole-exome sequencing (WES) was performed on samples collected from two children in each family, including one child with obesity and one control child without obesity. Variant calling files were filtered for quality, frequency < 1%, and predicted functional impact. Candidate loci were prioritized using Moon (Diploid) software and manual curation, then validated by Sanger sequencing.</p><p><strong>Results: </strong>Initial filtering revealed 40 rare, potentially pathogenic variants in 35 genes shared among affected relatives. Prioritization highlighted 28 variants in 19 candidate genes, encompassing established obesity-related genes (e.g. LEPR, MC4R, BDNF) and putative novel loci linked to appetite regulation, lipid metabolism, and energy balance. Segregation analysis identified both heterozygous and homozygous variants across affected individuals, reflecting variability in inheritance patterns. Seven previously reported candidate genes did not show pathogenic variants in this cohort. Carriers of prioritized variants exhibited significantly higher BMI z-scores than non-carriers (P < 0.01), underscoring a clear genotype-phenotype correlation.</p><p><strong>Conclusion: </strong>This study broadens the catalog of genes associated with obesity in the Saudi population and demonstrates the value of studying extreme phenotypes in consanguineous families. Both previously recognized and novel variants were identified in association with severe, early-onset obesity, reflecting genetic heterogeneity across families rather than a single underlying mechanism. These findings provide a foundation for improved genetic characterization, tailored counseling, and future functional studies.</p>","PeriodicalId":13070,"journal":{"name":"Human molecular genetics","volume":"35 21","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149223931","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"VPS13C regulates triglyceride homeostasis and adipocyte differentiation.","authors":"Antwi-Boasiako Oteng, Ayo P Doumatey, Ashton F Oliver, Karlijn A C Meeks, Lin Lei, Elisabeth F Heuston, Binta Jalloh, Bayu Sisay, Abdel Elkahloun, Adebowale A Adeyemo, Charles N Rotimi","doi":"10.1093/hmg/ddag108","DOIUrl":"https://doi.org/10.1093/hmg/ddag108","url":null,"abstract":"<p><strong>Background: </strong>Hypertriglyceridemia is a major risk factor for cardiometabolic diseases. VPS13C is a genome-wide significant locus for triglyceride with an incomplete understanding of its functional role in triglyceride biology. In this study, we investigated the transcriptomic associations and functional roles of VPS13C in triglyceride metabolism.</p><p><strong>Methods: </strong>We analyzed VPS13C expression in subcutaneous adipose tissue and assessed fasting serum lipid levels (including total cholesterol and triglycerides) in participants from the Africa America Diabetes Mellitus (AADM) study. In parallel, we conducted functional studies in 3T3-L1 mouse adipocytes, where Vps13c was knocked down using siRNA. We then evaluated markers of adipogenesis, lipogenesis, and triglyceride metabolism.</p><p><strong>Results: </strong>In human subjects, VPS13C expression in subcutaneous adipose tissue was inversely associated with fasting triglyceride levels but showed non-significant correlation with total cholesterol. In 3T3-L1 cells, Vps13c knockdown impaired adipocyte differentiation, evidenced by reduced lipid droplet formation and lower intracellular levels of triglycerides, glycerol, and fatty acids. This knockdown also led to significant downregulation of Pparg expression and suppression of PPARγ-mediated pathways, as well as genes involved in adipogenesis and lipogenesis.</p><p><strong>Conclusion: </strong>VPS13C is associated with circulating triglyceride levels and plays a critical role in adipocyte differentiation, adipogenesis and lipogenesis. These findings suggest that VPS13C may play an important role in triglyceride-related metabolic disorders.</p>","PeriodicalId":13070,"journal":{"name":"Human molecular genetics","volume":"35 21","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149206768","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Modeling patient variants of Cnot1 and Cdc42bpb results in distinct forms of congenital diaphragmatic hernia in mice.","authors":"Eric L Bogenschutz, Cynthia Carpenter, Ameleen Wong, Kristina Palmer, Aalekh S Mehta, Yannick Ledermann, Caleb Heffner, Kathy J Snow, Carol Bult, Yufeng Shen, Patricia K Donahoe, Samuel P Rowbotham, Frances A High, Wendy K Chung, Stephen A Murray","doi":"10.1093/hmg/ddag106","DOIUrl":"10.1093/hmg/ddag106","url":null,"abstract":"<p><p>Congenital diaphragmatic hernia (CDH) is a severe congenital anomaly characterized by impairment of both diaphragm and lung development in utero. CDH presents as a spectrum of forms and severities, with diaphragm defects arising in the dorsal/posterior region typically correlating with more severe pulmonary disease and higher risk of mortality than those appearing in ventral/anterior regions. The genetic etiology underlying CDH is complex, with many implicated genes showing variable expressivity and incomplete penetrance in both human patients and mouse models. Here we present in vivo validation of two genes previously unassociated with CDH: the CDC42-interacting kinase CDC42BPB; and CNOT1, a scaffolding protein of the CCR4-NOT protein complex, critical for mRNA regulation through modifications such as deadenylation. Each gene was found to have a damaging, de novo missense variant in a recent large-scale CDH patient sequencing screen. Loss of Cdc42bpb leads to ventral diaphragmatic hernias, heart septal defects, and minor lung epithelial differentiation defects in mouse embryos. Installation of the orthologous patient-specific missense variant through CRISPR/Cas9 editing leads to less severe ventral diaphragm defects. Mouse embryos with either one or two copies of the orthologous Cnot1 variant, c.1867C > T (p.R623W), develop dorsal diaphragmatic hernias with low (<50%) penetrance, and mutants showed alterations in mRNA isoform expression consistent with the molecular role of Cnot1 in RNA splicing. These results underscore the power of in vivo functional modeling to validate genes and patient-specific variants uncovered by patient sequencing, reveal two previously unrecognized genetic causes of CDH, and highlight the heterogeneity of different patient anatomic presentations.</p>","PeriodicalId":13070,"journal":{"name":"Human molecular genetics","volume":"35 21","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13665469/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149180769","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Immune-related DNA methylation signatures, age prediction, and cross-tissue assessment via biologically informed neural networks.","authors":"Xi Cheng, Cuipei Wu, Xiaohe Yang, Rui Liu","doi":"10.1093/hmg/ddag110","DOIUrl":"https://doi.org/10.1093/hmg/ddag110","url":null,"abstract":"<p><p>Immune-related DNA methylation patterns may provide interpretable markers of biological ageing and disease relevance. This exploratory study integrated four Illumina HumanMethylation450 and MethylationEPIC datasets comprising paediatric peripheral-blood leukocytes (GSE36054; 192 retained after quality control), infant buccal cells (n = 542), neuronal nuclei (n = 58), and peripheral blood from a polybrominated-biphenyl exposure cohort (n = 659). The paediatric peripheral-blood dataset served as the primary modelling cohort, with infant buccal cells providing an independent early-life cross-tissue reference. Processing included cohort-specific quality control and normalisation, batch adjustment, empirical-Bayes differential methylation analysis, pathway enrichment, repeated 10-fold cross-validation, biologically informed neural-network modelling, feature attribution, cross-tissue assessment, gene-ablation analysis, disease mapping, and two-sample Mendelian randomisation. IL6, CXCR4, CDK11 and CREBBP showed the strongest coherent methylation signals and stable predictive contributions, whereas BCLAF1 contributed less consistently. These loci mapped to cytokine-receptor interaction, chemokine signalling, G2/M checkpoint regulation, histone acetylation, and apoptosis-related pathways. The neural network achieved a cross-validated mean absolute error of 1.87 years and R2 of 0.781; removing the polybrominated-biphenyl-associated feature filter yielded comparable performance (MAE 1.91 years; R2 = 0.772). Prioritised features also showed cross-tissue consistency in infant buccal cells. Mendelian randomisation identified genetically supported associations of IL6 methylation with preterm birth and lower mean birth weight and of CXCR4 methylation with preterm birth after multiplicity correction. These associations do not establish that methylation itself causes the outcomes. The findings prioritise immune-related methylation features across paediatric blood and infant buccal contexts within an interpretable framework for age-related methylation and outcome-oriented molecular investigation.</p>","PeriodicalId":13070,"journal":{"name":"Human molecular genetics","volume":"35 21","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149227728","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DUOXA2-mediated thyroid hormone synthesis is indispensable for postnatal maturation of auditory function.","authors":"Wen Li, Min Wang, Luhan Jiang, Yulong Zhao, Shizheng Lu, Hao Liu, Cheng Xu, Zhenzu Li, Guodong Hong, Ziyi Liu, Hui Liu, Xiuli Bi, Xiaoxu Zhao, Yunhao Wu, Siwei Guo, Yu Xiao, Shuyuan Shen, Tao Xin, Xiaolong Fu","doi":"10.1093/hmg/ddag104","DOIUrl":"https://doi.org/10.1093/hmg/ddag104","url":null,"abstract":"<p><p>More than 500 genes associated with hearing loss have been identified, yet the pathogenic mechanisms underlying most deafness-causing mutations remain to be clarified, hindering the development of viable clinical therapeutic strategies. Clinical studies indicated that patients with DUOXA2 mutations present mucosal immune dysregulation and hypothyroidism. In addition, genetics screening in mouse models linked Duoxa2 deficiency to severe deafness, yet its pathogenic mechanism remains elusive. In this study, we demonstrated that Duoxa2 is essential for normal auditory function and clarified its underlying mechanism by establishing the Duoxa2 conditional knockout (cKO) mouse model. We found that Duoxa2 deficiency impairs the structure and function of outer hair cells (OHCs) and stria vascularis (SV), core auditory components, via disrupted thyroid hormone synthesis. Duoxa2 cKO mice exhibited disorganized stereociliary bundles in OHCs, altered distribution patterns of the critical KCNQ4, aberrant ribbon synapse localization, and capillary dilation within the intermediate cell layer of SV. Notably, Atoh1-Cre drivers not only express Cre recombinase in hair cells but also show high expression in thyroid. This finding elucidates the reduced thyroid hormone levels in Atoh1-Duoxa2-/- mice and reveals an indirect mechanism affecting cochlear function. While postnatal thyroid hormone supplementation completely reversed these pathological changes, the effect was minimal in adulthood. Our findings provided insights into the intrinsic link between distinct thyroid disorders and hearing impairment and offered evidence for clinical intervention in patients with DUOXA2 variants.</p>","PeriodicalId":13070,"journal":{"name":"Human molecular genetics","volume":"35 21","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149181646","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MEF2C promoter variants in patent ductus arteriosus: a genetic and functional study.","authors":"Shao-Jie Wang, Huan-Xin Chen, Qin Yang, Guo-Wei He","doi":"10.1093/hmg/ddag097","DOIUrl":"https://doi.org/10.1093/hmg/ddag097","url":null,"abstract":"<p><p>Patent ductus arteriosus (PDA) is a common congenital heart disease (CHD) with a complex genetic basis. The transcription factor MEF2C plays a critical role in cardiac development, but the role of promoter region variants in PDA has not been explored. This study aimed to identify MEF2C promoter variants in PDA patients and investigate their functional consequences. We sequenced the MEF2C promoter region in 318 children with PDA and 306 healthy controls. Identified variants were subjected to dual-luciferase reporter assays in A7r5 vascular smooth muscle cells to assess transcriptional activity. Bioinformatics (JASPAR) and electrophoretic mobility shift assays (EMSA) were used to predict and validate changes in transcription factor binding. Seventeen variants were identified, of which seven were present exclusively in PDA patients. Three variants were novel. Dual-luciferase assays showed that six variants significantly altered promoter activity compared to wild-type (range 69.6%-82.3%). JASPAR prediction revealed that these variants affected binding sites for 16 transcription factors, including GATA1, GATA2, GATA3, STAT3, ZEB1 and E2F1. EMSA confirmed altered DNA-protein binding patterns for all six variants, and super-shift assays further validated that the g.24571 A > G variant specifically disrupts GATA3 binding. This is the first study to identify functionally relevant MEF2C promoter variants in PDA. Our findings suggest that dysregulation of MEF2C through promoter variants may contribute to PDA pathogenesis by disrupting critical transcription factor interactions. These results extend the genetic landscape of PDA beyond coding regions and provide new insights into the molecular mechanisms of CHD.</p>","PeriodicalId":13070,"journal":{"name":"Human molecular genetics","volume":"35 20","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149060563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Explaining the unexplained admixture mapping signals via rare variants: the HCHS/SOL.","authors":"Xueying Chen, Maria Argos, Bing Yu, Eric Boerwinkle, Qibin Qi, Robert Kaplan, Nora Franceschini, Tamar Sofer","doi":"10.1093/hmg/ddag098","DOIUrl":"10.1093/hmg/ddag098","url":null,"abstract":"<p><p>In admixed populations, formed by a mixing of two or more previously isolated populations, genomic segments can be traced to their ancestral populations ('ancestries'). Admixture mapping (AM) associates local ancestry with outcomes in admixed populations, detecting signals when causal variants differ in frequency or effect across ancestral populations. Prior work showed that adjusting for nearby GWAS-identified common variants does not fully explain some AM signals. Here, we assessed two approaches to explain the previously unexplained AM signal: (1) including sets of rare variants; (2) increasing the genomic region considered when searching for common variants. We studied these hypotheses comprehensively using a whole-genome sequencing dataset coupled with metabolomics from the Hispanic Community Health Study/Study of Latinos. From 16 genomic regions of interest, we identified 35 rare-variant sets associated with metabolite levels, of which 4 associations replicated. The locations of identified rare variant sets are either within the same gene or in proximity to adjusted common variants. Overall, our study provides new insight into the genetic architecture underlying AM signals via evaluating the contributions of common and rare variant sets. By integrating rare-variant analysis within the AM framework, our work highlights the potential interplay between variant types and establishes a novel strategy to guide future fine-mapping and causal variant identification in admixed populations. Yet the detected rare variants appear to explain only a small fraction of the AM signal, while inclusion of common variants from a larger genomic region appears to explain most of the AM signals.</p>","PeriodicalId":13070,"journal":{"name":"Human molecular genetics","volume":"35 20","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13626212/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149060494","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic and epigenetic contributors to cleft laterality: evidence from monozygotic mirror twins and replication cohorts.","authors":"Aline L Petrin, Waheed Awotoye, Christina E Spencer, Ligiane A Machado-Paula, Luke Hovey, Henry Keen, Michael Chimenti, Patrick Breheny, Fang Qian, Shareef Dabdoub, James C Thomas, Azeez Butali, Jeffrey C Murray, Shankar Rengasamy Venugopalan, Lina M Moreno-Uribe","doi":"10.1093/hmg/ddag088","DOIUrl":"10.1093/hmg/ddag088","url":null,"abstract":"<p><p>Nonsyndromic cleft lip (nsCL) exhibits a non-random laterality pattern, with left-sided clefts occurring twice as frequently as right-sided clefts. The molecular mechanisms underlying this laterality bias remain poorly understood. We performed whole-genome sequencing and methylation profiling on a family comprising monozygotic twins with mirror-image nsCL, their affected mother, and unaffected father and brother. We conducted three independent replications via publicly available whole genome data; genome-wide methylation analysis in 38 individuals with unilateral cleft; and validation of methylation results in the top 3 candidate genes in 385 unrelated individuals with unilateral nonsyndromic cleft lip with or without cleft palate (nsCL/P) (DNA from blood or saliva). We identified a variant in FGF20 (p.Ile79Val) shared by the twins and their mother. We observed laterality and severity-associated methylation differences in three main genes. ARID5B showed higher methylation in left clefts (saliva, P = .001; blood, P = .032). ZFP57 demonstrated a strong cleft-extent effect, with cleft lip and palate (CLP) showing markedly higher methylation than cleft lip only (CL) (LCLP vs. RCL padj = 0.0004; LCLP vs. LCL padj = 0.019). HOOK2 displayed a cross-tissue cleft-extent effect in the opposite direction-CLP subtypes were hypomethylated relative to CL-only subtypes in blood (P < .0001) and saliva (P = .0008). This study provides evidence that DNA methylation patterns play a role in both the laterality and severity of cleft lip. ARID5B provides a consistent laterality signal across tissues, while ZFP57 and HOOK2 track palatal involvement independently of side. Together, these findings suggest that epigenetic variation acts downstream of genetic predisposition to shape cleft phenotypes.</p>","PeriodicalId":13070,"journal":{"name":"Human molecular genetics","volume":"35 19","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13626208/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148944817","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}