Human molecular genetics最新文献

{"title":"The genetic architecture of hip shape and its role in the development of hip osteoarthritis and fracture.","authors":"Benjamin G Faber, Monika Frysz, Jaiyi Zheng, Huandong Lin, Kaitlyn A Flynn, Raja Ebsim, Fiona R Saunders, Rhona Beynon, Jennifer S Gregory, Richard M Aspden, Nicholas C Harvey, Claudia Lindner, Timothy Cootes, David M Evans, George Davey Smith, Xin Gao, Sijia Wang, John P Kemp, Jonathan H Tobias","doi":"10.1093/hmg/ddae169","DOIUrl":"10.1093/hmg/ddae169","url":null,"abstract":"<p><strong>Objectives: </strong>Hip shape is thought to be an important causal risk factor for hip osteoarthritis and fracture. We aimed to identify genetic determinants of hip shape and use these to assess causal relationships with hip osteoarthritis.</p><p><strong>Methods: </strong>Statistical hip shape modelling was used to derive 10 hip shape modes (HSMs) from DXA images in UK Biobank and Shanghai Changfeng cohorts (ntotal = 43 485). Genome-wide association study meta-analyses were conducted for each HSM. Two-sample Mendelian randomisation (MR) was used to estimate causal effects between HSM and hip osteoarthritis using hip fracture as a positive control.</p><p><strong>Results: </strong>Analysis of the first 10 HSMs identified 203 independent association signals (P < 5 × 10-9). Hip shape SNPs were also associated (P < 2.5 × 10-4) with hip osteoarthritis (n = 26) and hip fracture (n = 4). Fine mapping implicated SMAD3 and PLEC as candidate genes that may be involved in the development of hip shape and hip osteoarthritis. MR analyses suggested there was no causal effect between any HSM and hip osteoarthritis, however there was evidence that HSM2 (more obtuse neck-shaft angle) and HSM4 (wider femoral neck) have a causal effect on hip fracture (ORIVW method 1.27 [95% CI 1.12-1.44], P = 1.79 × 10-4 and ORIVW 0.74 [0.65-0.84], P = 7.60 × 10-6 respectively).</p><p><strong>Conclusions: </strong>We report the largest hip shape GWAS meta-analysis that identifies hundreds of novel loci, some of which are also associated with hip osteoarthritis and hip fracture. MR analyses suggest hip shape may not cause hip osteoarthritis but is implicated in hip fractures. Consequently, interventions targeting hip shape in older adults to prevent hip osteoarthritis may prove ineffective.</p>","PeriodicalId":13070,"journal":{"name":"Human molecular genetics","volume":" ","pages":"207-217"},"PeriodicalIF":3.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11792254/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142686895","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":"Development of a riboflavin-responsive model of riboflavin transporter deficiency in zebrafish.","authors":"Catherine M Choueiri, Jarred Lau, Emily O'Connor, Alicia DiBattista, Brittany Y Wong, Sally Spendiff, Rita Horvath, Izabella Pena, Alexander MacKenzie, Hanns Lochmüller","doi":"10.1093/hmg/ddae171","DOIUrl":"10.1093/hmg/ddae171","url":null,"abstract":"<p><p>Riboflavin transporter deficiency (RTD) is a rare and progressive neurodegenerative disease resulting from the disruption of RFVT2- and RFVT3- mediated riboflavin transport caused by biallelic mutations in SLC52A2 and SLC52A3, respectively. The resulting impaired mitochondrial metabolism leads to sensorimotor neurodegeneration and symptoms including muscle weakness, respiratory difficulty, and sensorineural deafness. Although over 70% of patients with RTD improve following high-dose riboflavin supplementation, remaining patients either stabilise or continue to deteriorate. This may be due to the rapid excretion of central nervous system (CNS) riboflavin by organic anion transporter 3 (OAT-3), highlighting the need for alternative or supplemental RTD treatments. Probenecid is a promising therapeutic candidate for RTD due to its known inhibitory effect on OAT-3. Therefore, this study aimed to generate morpholino-mediated knockdowns of human SLC52A3 ortholog slc52a3 in zebrafish larvae for use in therapeutic screening of riboflavin and probenecid. Knockdown of slc52a3 resulted in an RTD-like phenotype indicative of altered neurodevelopment, hearing loss, and reduced mobility. This RTD-like phenotype overlaps with the phenotype of CRISPR/Cas9-mediated knockout of slc52a3 in zebrafish, is maintained following slc52a3 morpholino + p53 morpholino co-injection, and is rescued following slc52a3 morpholino + human SLC52A3 mRNA co-injection, indicating specificity of the knockdown. Riboflavin treatment alone ameliorates locomotor activity and hearing ability in slc52a3 morphants. Riboflavin and probenecid co-treatment provides an additional small benefit to hearing but not to locomotion. Our findings demonstrate that this model recapitulates both the RTD phenotype and the riboflavin-responsiveness of RTD patients, and possible therapeutic benefit conferred by probenecid warrants further investigation.</p>","PeriodicalId":13070,"journal":{"name":"Human molecular genetics","volume":" ","pages":"265-276"},"PeriodicalIF":3.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142828373","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":"Constructing methylation-driven ceRNA networks unveil tumor heterogeneity and predict patient prognosis.","authors":"Xinyu Li, Chuo Peng, Hongyu Liu, Mingjie Dong, Shujuan Li, Weixin Liang, Xia Li, Jing Bai","doi":"10.1093/hmg/ddae176","DOIUrl":"10.1093/hmg/ddae176","url":null,"abstract":"<p><p>Cancer development involves a complex interplay between genetic and epigenetic factors, with emerging evidence highlighting the pivotal role of competitive endogenous RNA (ceRNA) networks in regulating gene expression. However, the influence of ceRNA networks by aberrant DNA methylation remains incompletely understood. In our study, we proposed DMceNet, a computational method to characterize the effects of DNA methylation on ceRNA regulatory mechanisms and apply it across eight prevalent cancers. By integrating methylation and transcriptomic data, we constructed methylation-driven ceRNA networks and identified a dominant role of lncRNAs within these networks in two key ways: (i) 17 cancer-shared differential methylation lncRNAs (DMlncs), including PVT1 and CASC2, form a Common Cancer Network (CCN) affecting key pathways such as the G2/M checkpoint, and (ii) 24 cancer-specific DMlncs construct unique ceRNA networks for each cancer type. For instance, in LUAD and STAD, hypomethylation drives DMlncs like PCAT6 and MINCR, disrupting the Wnt signaling pathway and apoptosis. We further investigated the characteristics of these methylation-driven ceRNA networks at the cellular level, revealing how methylation-driven dysregulation varies across distinct cell populations within the tumor microenvironment. Our findings also demonstrate the prognostic potential of cancer-specific ceRNA relationships, highlighting their relevance in predicting patient survival outcomes. This integrated transcriptomic and epigenomic analysis provides new insights into cancer biology and regulatory mechanisms.</p>","PeriodicalId":13070,"journal":{"name":"Human molecular genetics","volume":" ","pages":"251-264"},"PeriodicalIF":3.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11792255/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142739499","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":"Dysregulation of alternative splicing is a transcriptomic feature of patient-derived fibroblasts from CAG repeat expansion spinocerebellar ataxias.","authors":"Asmer Aliyeva, Claudia D Lennon, John D Cleary, Hannah K Shorrock, J Andrew Berglund","doi":"10.1093/hmg/ddae174","DOIUrl":"10.1093/hmg/ddae174","url":null,"abstract":"<p><p>The spinocerebellar ataxias (SCAs) are a genetically heterogeneous group of rare dominantly inherited neurodegenerative diseases characterized by progressive ataxia. The most common mutation seen across the SCAs is a CAG repeat expansion, causative for SCA1, 2, 3, 6, 7, 12 and 17. We recently identified dysregulation of alternative splicing as a novel, presymptomatic transcriptomic hallmark in mouse models of SCAs 1, 3 and 7. In order to understand if dysregulation of alternative splicing is a transcriptomic feature of patient-derived cell models of CAG SCAs, we performed RNA sequencing and transcriptomic analysis in patient-derived fibroblast cell lines of SCAs 1, 3 and 7. We identified widespread and robust dysregulation of alternative splicing across all CAG expansion SCA lines investigated, with disease relevant pathways affected, such as microtubule-based processes, transcriptional regulation, and DNA damage and repair. Novel disease-relevant alternative splicing events were validated across patient-derived fibroblast lines from multiple CAG SCAs and CAG containing reporter cell lines. Together this study demonstrates that dysregulation of alternative splicing represents a novel and shared pathogenic process in CAG expansion SCA1, 3 and 7 and can potentially be used as a biomarker across patient models of this group of devastating neurodegenerative diseases.</p>","PeriodicalId":13070,"journal":{"name":"Human molecular genetics","volume":" ","pages":"239-250"},"PeriodicalIF":3.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11792238/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142715972","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":"A replication study of novel fetal hemoglobin-associated genetic variants in sickle cell disease-only cohorts.","authors":"Yann Ilboudo, Nicolas Brosseau, Ken Sin Lo, Hicham Belhaj, Stéphane Moutereau, Kwesi Marshall, Marvin Reid, Abdullah Kutlar, Allison E Ashley-Koch, Marilyn J Telen, Philippe Joly, Frédéric Galactéros, Pablo Bartolucci, Guillaume Lettre","doi":"10.1093/hmg/ddaf015","DOIUrl":"https://doi.org/10.1093/hmg/ddaf015","url":null,"abstract":"<p><p>Sickle cell disease (SCD) is the most common monogenic disease in the world and is caused by mutations in the β-globin gene (HBB). Notably, SCD is characterized by extreme clinical heterogeneity. Inter-individual variation in fetal hemoglobin (HbF) levels strongly contributes to this patient-to-patient variability, with high HbF levels associated with decreased morbidity and mortality. Genetic association studies have identified and replicated HbF levels-associated variants at three loci: BCL11A, HBS1L-MYB, and HBB. In SCD patients, genetic variation at these three loci accounts for ~ 50% of HbF heritability. Genome-wide association studies (GWAS) in non-anemic and SCD patients of multiple ancestries have identified 20 new HbF-associated variants. However, these genetic associations have yet to be replicated in independent SCD cohorts. Here, we validated the association between HbF levels and variants at five of these new loci (ASB3, BACH2, PFAS, ZBTB7A, and KLF1) in up to 3740 SCD patients. By combining CRISPR inhibition and single-cell transcriptomics, we also showed that sequences near non-coding genetic variants at BACH2 (rs4707609) and KLF1 (rs2242514, rs10404876) can control the production of the β-globin genes in erythroid HUDEP-2 cells. Finally, we analyzed whole-exome sequence data from 1354 SCD patients but could not identify rare genetic variants of large effect on HbF levels. Together, our results confirm five new HbF-associated loci that can be functionally studied to develop new strategies to induce HbF expression in SCD patients.</p>","PeriodicalId":13070,"journal":{"name":"Human molecular genetics","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143065356","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":"Correction to: Expanded CAG/CTG repeats resist gene silencing mediated by targeted epigenome editing.","authors":"","doi":"10.1093/hmg/ddae167","DOIUrl":"10.1093/hmg/ddae167","url":null,"abstract":"","PeriodicalId":13070,"journal":{"name":"Human molecular genetics","volume":" ","pages":"204"},"PeriodicalIF":3.1,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11780871/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142619281","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":"Correction to: Pathomechanisms of Monoallelic variants in TTN causing skeletal muscle disease.","authors":"","doi":"10.1093/hmg/ddae181","DOIUrl":"10.1093/hmg/ddae181","url":null,"abstract":"","PeriodicalId":13070,"journal":{"name":"Human molecular genetics","volume":" ","pages":"205"},"PeriodicalIF":3.1,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11780837/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142828370","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 regulation of miRNAs using curcumin and other polyphenols during the prevention and treatment of Alzheimer's disease.","authors":"XiYun Wang, Sale Zhang, Ying Li, Yu Zhang","doi":"10.1093/hmg/ddae154","DOIUrl":"10.1093/hmg/ddae154","url":null,"abstract":"<p><p>Alzheimer's disease (AD), a prevalent neurodegenerative disorder, predominantly affects individuals over the age of 65 and poses significant challenges in terms of effective management and treatment. The disease's pathogenesis involves complex molecular pathways including misfolded proteins accumulation, neuroinflammation, and synaptic dysfunction. Recent insights have highlighted the role of microRNAs (miRNAs) as critical regulators within these pathways, where they influence gene expression and contribute to the pathophysiological landscape of AD. Notably, emerging research has demonstrated that polyphenols, including curcumin, might modulate miRNA activity, thus offering a novel approach to mitigate AD symptoms and progression. This review explores the potential mechanisms through which polyphenols regulate miRNA expression and activity, specifically focusing on autophagy enhancement and inflammation reduction in the context of AD. We provide a detailed examination of key studies linking miRNA dysregulation to AD pathogenesis and discuss how polyphenols might correct these aberrations. The findings presented here underscore the therapeutic potential of polyphenols in AD treatment via miRNA modulation, pointing to new directions in disease management strategies and highlighting the need for targeted research into miRNA-based interventions.</p>","PeriodicalId":13070,"journal":{"name":"Human molecular genetics","volume":" ","pages":"117-127"},"PeriodicalIF":3.1,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142675672","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":"BMP4-GPX4 can improve the ferroptosis phenotype of retinal ganglion cells and enhance their differentiation ability after retinal stem cell transplantation in glaucoma with high intraocular pressure.","authors":"Chuankai Fang, Di He, Yafen Qian, Xiaomei Shen","doi":"10.1093/hmg/ddaf011","DOIUrl":"https://doi.org/10.1093/hmg/ddaf011","url":null,"abstract":"<p><p>Activation of bone morphogenetic protein (BMP) 4 signaling promotes the survival of retinal ganglion cell (RGC) after acute injury. In this study, we investigated the role of the BMP4 signaling pathway in regulating the degeneration of retinal ganglion cells (RGCs) in a mouse glaucoma model and its potential application in retinal stem cell. Our results demonstrate that BMP4-GPX4 not only reduces oxidative stress and iron accumulation but also promotes neuroprotective factors that support the survival of transplanted RSCs into the host retina. These findings suggest a novel therapeutic approach for glaucoma involving the modulation of the BMP4-GPX4 pathway to protect RGCs and improve visual function through enhanced RSC differentiation.</p>","PeriodicalId":13070,"journal":{"name":"Human molecular genetics","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143058956","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":"De novo missense variants in the PP2A regulatory subunit PPP2R2B in a neurodevelopmental syndrome: potential links to mitochondrial dynamics and spinocerebellar ataxias.","authors":"Priyanka Sandal, Chian Ju Jong, Ronald A Merrill, Grace J Kollman, Austin H Paden, Eric G Bend, Jennifer Sullivan, Rebecca C Spillmann, Vandana Shashi, Anneke T Vulto-van Silfhout, Rolph Pfundt, Bert B A de Vries, Pan P Li, Louise S Bicknell, Stefan Strack","doi":"10.1093/hmg/ddae166","DOIUrl":"10.1093/hmg/ddae166","url":null,"abstract":"<p><p>The heterotrimeric protein phosphatase 2A (PP2A) complex catalyzes about half of Ser/Thr dephosphorylations in eukaryotic cells. A CAG repeat expansion in the neuron-specific protein PP2A regulatory subunit PPP2R2B gene causes spinocerebellar ataxia type 12 (SCA12). We established five monoallelic missense variants in PPP2R2B (four confirmed as de novo) as a cause of intellectual disability with developmental delay (R149P, T246K, N310K, E37K, I427T). In addition to moderate to severe intellectual disability and developmental delay, affected individuals presented with seizures, microcephaly, aggression, hypotonia, as well as broad-based or stiff gait. We used biochemical and cellular assays, including a novel luciferase complementation assay to interrogate PP2A holoenzyme assembly and activity, as well as deregulated mitochondrial dynamics as possible pathogenic mechanisms. Cell-based assays documented impaired ability of PPP2R2B missense variants to incorporate into the PP2A holoenzyme, localize to mitochondria, induce fission of neuronal mitochondria, and dephosphorylate the mitochondrial fission enzyme dynamin-related protein 1. AlphaMissense-based pathogenicity prediction suggested that an additional seven unreported missense variants may be pathogenic. In conclusion, our studies identify loss-of-function at the PPP2R2B locus as the basis for syndromic intellectual disability with developmental delay. They also extend PPP2R2B-related pathologies from neurodegenerative (SCA12) to neurodevelopmental disorders and suggests that altered mitochondrial dynamics may contribute to mechanisms.</p>","PeriodicalId":13070,"journal":{"name":"Human molecular genetics","volume":" ","pages":"193-203"},"PeriodicalIF":3.1,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11780858/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142675668","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}