Pub Date : 2025-09-30DOI: 10.1016/j.ajhg.2025.09.008
Esra Erkut,Cherith Somerville,Marci L B Schwartz,Laura McDonald,Qiliang Ding,Olivia M Moran,Xin Chen,Roozbeh Manshaei,Anne-Sophie Riedijk,Marie-Therese Schnürer,Daniel C Koboldt,Stylianos E Antonarakis,Emma C Bedoukian,Xavier Blanc,Laura K Conlin,Helen Cox,Karin E M Diderich,Bri Dingmann,Christèle Dubourg,Frances Elmslie,Luis F Escobar,Rachel Gosselin,Maria J Guillen Sacoto,Cynthia D Haag,Lisa Herzig,Ramanand Jeeneea,Priti Kenia,Konstantinos Kolokotronis,Anna M Kopps,Christin Kupper,Hayley Lees,Jacqueline Leonard,Jonathan Levy,Rebecca Littlejohn,Demian Mayer,Scott D McLean,Nikhil Pattani,Laurence Perrin,Véronique Pingault,Chloé Quelin,Emmanuelle Ranza,Anita Rauch,Sara L Reichert,Joana Rosmaninho-Salgado,Cara Skraban,Sérgio Sousa,Melissa Stuebben,Paolo Zanoni,Raymond H Kim,Ian C Scott,Rebekah K Jobling
Syndromic cardiac malformations can result in morbidity, yet their genetic etiology is only understood for a subset of individuals. Genome sequencing efforts in congenital anomaly cohorts may identify disease-associated variants in previously unrecognized genes. Through international matchmaking efforts, we identified eighteen individuals in total with de novo or loss-of-function variants in EIF3A (n = 4) or EIF3B (n = 14). The clinical phenotype varied but predominantly included cardiac defects, craniofacial dysmorphisms, mild developmental delays, and behavioral abnormalities. These genes encode core subunits of the eukaryotic initiation factor 3 (eIF3) complex, which plays a critical role in binding mRNA transcripts to the 40S ribosomal subunit during translation initiation. Both genes are highly constrained against loss of function, and animal models have demonstrated that disruptions in the eIF3 complex result in a range of developmental defects, including cardiovascular malformations. Additionally, EIF3B is located within the minimally overlapping region implicated in cardiac anomalies associated with 7p22.3 microdeletions. We sought to further study the role of these genes in syndromic congenital heart disease. To explore their functional impact, we generated zebrafish models with mutations in the orthologous eif3s10 and eif3ba genes, which resulted in developmental abnormalities, including thin heart tubes, lack of craniofacial cartilage, and embryonic lethality. We propose that pathogenic variants in EIF3A, as well as pathogenic variants or microdeletions involving EIF3B, cause a distinct autosomal-dominant neurodevelopmental syndrome characterized by cardiovascular and craniofacial manifestations.
{"title":"A cardiovascular, craniofacial, and neurodevelopmental disorder caused by loss-of-function variants in the eIF3 complex component genes EIF3A and EIF3B.","authors":"Esra Erkut,Cherith Somerville,Marci L B Schwartz,Laura McDonald,Qiliang Ding,Olivia M Moran,Xin Chen,Roozbeh Manshaei,Anne-Sophie Riedijk,Marie-Therese Schnürer,Daniel C Koboldt,Stylianos E Antonarakis,Emma C Bedoukian,Xavier Blanc,Laura K Conlin,Helen Cox,Karin E M Diderich,Bri Dingmann,Christèle Dubourg,Frances Elmslie,Luis F Escobar,Rachel Gosselin,Maria J Guillen Sacoto,Cynthia D Haag,Lisa Herzig,Ramanand Jeeneea,Priti Kenia,Konstantinos Kolokotronis,Anna M Kopps,Christin Kupper,Hayley Lees,Jacqueline Leonard,Jonathan Levy,Rebecca Littlejohn,Demian Mayer,Scott D McLean,Nikhil Pattani,Laurence Perrin,Véronique Pingault,Chloé Quelin,Emmanuelle Ranza,Anita Rauch,Sara L Reichert,Joana Rosmaninho-Salgado,Cara Skraban,Sérgio Sousa,Melissa Stuebben,Paolo Zanoni,Raymond H Kim,Ian C Scott,Rebekah K Jobling","doi":"10.1016/j.ajhg.2025.09.008","DOIUrl":"https://doi.org/10.1016/j.ajhg.2025.09.008","url":null,"abstract":"Syndromic cardiac malformations can result in morbidity, yet their genetic etiology is only understood for a subset of individuals. Genome sequencing efforts in congenital anomaly cohorts may identify disease-associated variants in previously unrecognized genes. Through international matchmaking efforts, we identified eighteen individuals in total with de novo or loss-of-function variants in EIF3A (n = 4) or EIF3B (n = 14). The clinical phenotype varied but predominantly included cardiac defects, craniofacial dysmorphisms, mild developmental delays, and behavioral abnormalities. These genes encode core subunits of the eukaryotic initiation factor 3 (eIF3) complex, which plays a critical role in binding mRNA transcripts to the 40S ribosomal subunit during translation initiation. Both genes are highly constrained against loss of function, and animal models have demonstrated that disruptions in the eIF3 complex result in a range of developmental defects, including cardiovascular malformations. Additionally, EIF3B is located within the minimally overlapping region implicated in cardiac anomalies associated with 7p22.3 microdeletions. We sought to further study the role of these genes in syndromic congenital heart disease. To explore their functional impact, we generated zebrafish models with mutations in the orthologous eif3s10 and eif3ba genes, which resulted in developmental abnormalities, including thin heart tubes, lack of craniofacial cartilage, and embryonic lethality. We propose that pathogenic variants in EIF3A, as well as pathogenic variants or microdeletions involving EIF3B, cause a distinct autosomal-dominant neurodevelopmental syndrome characterized by cardiovascular and craniofacial manifestations.","PeriodicalId":7659,"journal":{"name":"American journal of human genetics","volume":"1 1","pages":""},"PeriodicalIF":9.8,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145203857","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-29DOI: 10.1016/j.ajhg.2025.09.006
Anmol Singh,Cristina Alarcon,Edith A Nutescu,Travis J O'Brien,Matthew Tuck,Li Gong,Teri E Klein,David O Meltzer,Julie A Johnson,Larisa H Cavallari,Minoli A Perera
African Americans (AAs) are underrepresented in pharmacogenomics research, which has led to a significant gap in knowledge. Through admixture, AAs can inherit specific loci from either their African or European ancestors, known as local ancestry (LA). A previous study in AAs identified SNPs located in the CYP2C cluster that are associated with warfarin dose. However, LA was not considered in that study. Here, we conducted an ancestry-adjusted genome-wide association study (GWAS) in the AA International Warfarin Pharmacogenomics Consortium (IWPC) cohort (n = 340). We replicated top associations in the independent ACCOuNT cohort of AAs (n= 309) and validated associations in a warfarin pharmacokinetic study in AAs (n = 63). We performed RNA sequencing (RNA-seq) of AA hepatocytes carrying each genotype to assess expression and splicing of CYP2C9 and CYP2C19. We identified 6 genome-wide significant SNPs (p < 5E-8) in the CYP2C locus (lead SNP, rs7906871 [p = 3.14E-8]). These associations were replicated (p ≤ 2.76E-5) and validated with a pharmacokinetic association for S-warfarin concentration in plasma (p = 0.048). rs7906871 explains 6.0% of the variability in warfarin dose in AAs. Multivariate regression demonstrated that rs7906871 and known genetic, clinical, and demographic factors explain 37% of dose variability, greater than previously reported in AAs. RNA-seq analysis identified a significant alternate exon inclusion event between exons 6 and 7 in CYP2C19 for carriers of rs7906871. In conclusion, we have found and replicated a CYP2C variant associated with warfarin dose requirement with functional consequences to CYP2C19. CYP2C19 is involved in the metabolism of 10%-15% of commonly prescribed drugs today. This finding could have broader impacts for drug response and pharmacogenomics.
{"title":"Local ancestry-informed GWAS of warfarin dose requirement in African Americans identifies a CYP2C19 splicing QTL.","authors":"Anmol Singh,Cristina Alarcon,Edith A Nutescu,Travis J O'Brien,Matthew Tuck,Li Gong,Teri E Klein,David O Meltzer,Julie A Johnson,Larisa H Cavallari,Minoli A Perera","doi":"10.1016/j.ajhg.2025.09.006","DOIUrl":"https://doi.org/10.1016/j.ajhg.2025.09.006","url":null,"abstract":"African Americans (AAs) are underrepresented in pharmacogenomics research, which has led to a significant gap in knowledge. Through admixture, AAs can inherit specific loci from either their African or European ancestors, known as local ancestry (LA). A previous study in AAs identified SNPs located in the CYP2C cluster that are associated with warfarin dose. However, LA was not considered in that study. Here, we conducted an ancestry-adjusted genome-wide association study (GWAS) in the AA International Warfarin Pharmacogenomics Consortium (IWPC) cohort (n = 340). We replicated top associations in the independent ACCOuNT cohort of AAs (n= 309) and validated associations in a warfarin pharmacokinetic study in AAs (n = 63). We performed RNA sequencing (RNA-seq) of AA hepatocytes carrying each genotype to assess expression and splicing of CYP2C9 and CYP2C19. We identified 6 genome-wide significant SNPs (p < 5E-8) in the CYP2C locus (lead SNP, rs7906871 [p = 3.14E-8]). These associations were replicated (p ≤ 2.76E-5) and validated with a pharmacokinetic association for S-warfarin concentration in plasma (p = 0.048). rs7906871 explains 6.0% of the variability in warfarin dose in AAs. Multivariate regression demonstrated that rs7906871 and known genetic, clinical, and demographic factors explain 37% of dose variability, greater than previously reported in AAs. RNA-seq analysis identified a significant alternate exon inclusion event between exons 6 and 7 in CYP2C19 for carriers of rs7906871. In conclusion, we have found and replicated a CYP2C variant associated with warfarin dose requirement with functional consequences to CYP2C19. CYP2C19 is involved in the metabolism of 10%-15% of commonly prescribed drugs today. This finding could have broader impacts for drug response and pharmacogenomics.","PeriodicalId":7659,"journal":{"name":"American journal of human genetics","volume":"17 1","pages":""},"PeriodicalIF":9.8,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145194735","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
This study explores the impact of mutations in the exon 2 of the von Hippel-Lindau (VHL) gene, associated with erythrocytosis or von Hippel-Lindau disease. We analyzed 15 missense and synonymous genetic variants to assess their effects on splicing and VHL protein stability. Using in silico predictions and functional assays, we found that some specific mutations impact splicing and reduce protein stability, allowing their clinical classification as pathogenic. This study revealed exonic-splicing regulatory regions. Notably, by performing RNA-protein pull-down, we identified two RNA-binding proteins, hnRNPF and hnRNPAB, as key regulators of VHL splicing. Our findings reveal the limitations of current splicing-prediction tools in recognizing exonic-splicing enhancer (ESE) or silencer (ESS) sequences and suggest that mutations can differentially affect disease phenotypes by influencing both splicing and protein stability. These insights enhance our understanding of the molecular mechanisms underlying VHL-associated disorders and expand the landscape of regulatory elements and protein factors involved in VHL splicing regulation.
{"title":"Unraveling the impact of VHL exon 2 mutations in erythrocytosis or von Hippel-Lindau disease identified RNA-binding proteins involved in VHL splicing.","authors":"Valéna Karaghiannis,Loïc Schmitt,Franck Chesnel,Emilie-Fleur Gautier,Marjorie Leduc,Morgane Le Gall,Salam Idriss,Sophie Couvé,Anne Barlier,Guillaume Sarrabay,Nada Maaziz,Bruno Cassinat,Laurence Legros,Vincent Thibaud,Stéphane Richard,François Girodon,Julie Miro,Sylvie Tuffery-Giraud,Yannick Arlot,Betty Gardie","doi":"10.1016/j.ajhg.2025.09.002","DOIUrl":"https://doi.org/10.1016/j.ajhg.2025.09.002","url":null,"abstract":"This study explores the impact of mutations in the exon 2 of the von Hippel-Lindau (VHL) gene, associated with erythrocytosis or von Hippel-Lindau disease. We analyzed 15 missense and synonymous genetic variants to assess their effects on splicing and VHL protein stability. Using in silico predictions and functional assays, we found that some specific mutations impact splicing and reduce protein stability, allowing their clinical classification as pathogenic. This study revealed exonic-splicing regulatory regions. Notably, by performing RNA-protein pull-down, we identified two RNA-binding proteins, hnRNPF and hnRNPAB, as key regulators of VHL splicing. Our findings reveal the limitations of current splicing-prediction tools in recognizing exonic-splicing enhancer (ESE) or silencer (ESS) sequences and suggest that mutations can differentially affect disease phenotypes by influencing both splicing and protein stability. These insights enhance our understanding of the molecular mechanisms underlying VHL-associated disorders and expand the landscape of regulatory elements and protein factors involved in VHL splicing regulation.","PeriodicalId":7659,"journal":{"name":"American journal of human genetics","volume":"73 1","pages":""},"PeriodicalIF":9.8,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145140239","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-23DOI: 10.1016/j.ajhg.2025.08.012
Austin W Reynolds,Haiko Schurz,Gillian Meeks,Simon Gravel,Justin W Myrick,Stacy Edington,Fernando L Mendez,Cedric J Werely,Paul D van Helden,Eileen G Hoal,G David Poznik,Minju Kim,Caitlin Uren,Peter A Underhill,Marlo Möller,Brenna M Henn
The colonial-period arrival of Europeans in southern Africa is associated with strong sex-biased migration by which male settlers displaced Indigenous Khoekhoe and San men. Concurrently, the importation of enslaved individuals from South Asia, Indonesia, and eastern Africa likely contributed to female-biased migration. Using genetic data from over 1,400 individuals, we examine the spatial and temporal spread of sex-biased migration from the Cape to the northern edges of the historic colonial frontier. In all regions, admixture patterns were sex biased, with evidence of a greater male contribution of European ancestry and greater female contribution of Khoe-San ancestry. While admixture among Khoe-San, European, equatorial African, and Asian groups has likely been continuous from the founding of Cape Town to the present day, we find that Khoe-San groups further north experienced a single pulse of European admixture 6-8 generations ago. European admixture was followed by additional Khoe-San gene flow, potentially reflecting an aggregation of Indigenous groups due to disruption by colonial interlopers. Male migration into the northern frontier territories was not a homogenous group of expanding Afrikaners and slaves. The Nama exhibit distinct founder effects and derive 15% of their Y chromosome haplogroups from Asian lineages, a pattern absent in the ≠Khomani San. Khoe-San ancestry from the paternal line is greatly diminished in populations from Cape Town, the Cederberg Mountains, and Upington but remains more frequent in self-identified Indigenous ethnic groups. Strikingly, we estimate that Khoe-San Y chromosomes were experiencing unprecedented population growth at the time of European arrival. Our findings shed light on the patterns of admixture and population history of South Africa as the colonial frontier expanded.
{"title":"The Indian Ocean slave trade and colonial expansion resulted in strong sex-biased admixture in South Africa.","authors":"Austin W Reynolds,Haiko Schurz,Gillian Meeks,Simon Gravel,Justin W Myrick,Stacy Edington,Fernando L Mendez,Cedric J Werely,Paul D van Helden,Eileen G Hoal,G David Poznik,Minju Kim,Caitlin Uren,Peter A Underhill,Marlo Möller,Brenna M Henn","doi":"10.1016/j.ajhg.2025.08.012","DOIUrl":"https://doi.org/10.1016/j.ajhg.2025.08.012","url":null,"abstract":"The colonial-period arrival of Europeans in southern Africa is associated with strong sex-biased migration by which male settlers displaced Indigenous Khoekhoe and San men. Concurrently, the importation of enslaved individuals from South Asia, Indonesia, and eastern Africa likely contributed to female-biased migration. Using genetic data from over 1,400 individuals, we examine the spatial and temporal spread of sex-biased migration from the Cape to the northern edges of the historic colonial frontier. In all regions, admixture patterns were sex biased, with evidence of a greater male contribution of European ancestry and greater female contribution of Khoe-San ancestry. While admixture among Khoe-San, European, equatorial African, and Asian groups has likely been continuous from the founding of Cape Town to the present day, we find that Khoe-San groups further north experienced a single pulse of European admixture 6-8 generations ago. European admixture was followed by additional Khoe-San gene flow, potentially reflecting an aggregation of Indigenous groups due to disruption by colonial interlopers. Male migration into the northern frontier territories was not a homogenous group of expanding Afrikaners and slaves. The Nama exhibit distinct founder effects and derive 15% of their Y chromosome haplogroups from Asian lineages, a pattern absent in the ≠Khomani San. Khoe-San ancestry from the paternal line is greatly diminished in populations from Cape Town, the Cederberg Mountains, and Upington but remains more frequent in self-identified Indigenous ethnic groups. Strikingly, we estimate that Khoe-San Y chromosomes were experiencing unprecedented population growth at the time of European arrival. Our findings shed light on the patterns of admixture and population history of South Africa as the colonial frontier expanded.","PeriodicalId":7659,"journal":{"name":"American journal of human genetics","volume":"28 1","pages":""},"PeriodicalIF":9.8,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145134341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-23DOI: 10.1016/j.ajhg.2025.09.003
Emma P Wilson,K Alaine Broadaway,Victoria A Parsons,Swarooparani Vadlamudi,Narisu Narisu,Sarah M Brotman,Kevin W Currin,Heather M Stringham,Michael R Erdos,Ryan Welch,Jeffrey K Holtzman,Timo A Lakka,Markku Laakso,Jaakko Tuomilehto,Michael Boehnke,Heikki A Koistinen,Francis S Collins,Stephen C J Parker,Laura J Scott,Karen L Mohlke
Identifying genetic variants that regulate gene expression can help uncover mechanisms underlying complex traits. We performed a meta-analysis of skeletal muscle expression quantitative trait locus (eQTL) using data from 1,002 individuals from two studies. A stepwise analysis identified 18,818 conditionally distinct signals for 12,283 genes, and 35% of these genes contained two or more signals. Colocalization of these eQTL signals with 26 muscular and cardiometabolic trait genome-wide association studies (GWASs) identified 2,252 GWAS-eQTL colocalizations that nominated 1,342 candidate genes. Notably, 22% of the GWAS-eQTL colocalizations involved non-primary eQTL signals. Additionally, 37% of the colocalized GWAS-eQTL signals corresponded to the closest protein-coding gene, while 44% were located >50 kb from the transcription start site of the nominated gene. To assess tissue specificity for a heterogeneous trait, we compared colocalizations with type 2 diabetes (T2D) signals across muscle, adipose, liver, and islet eQTLs; we identified 551 candidate genes for 309 T2D signals representing 36% of T2D signals tested and over 100 more than were detected with any one tissue alone. We then functionally validated the allelic regulatory effect of an eQTL variant for INHBB linked to T2D in both muscle and adipose tissue. Together, these results further demonstrate the value of skeletal muscle eQTLs in elucidating mechanisms underlying complex traits.
{"title":"Skeletal muscle eQTL meta-analysis implicates genes in the genetic architecture of muscular and cardiometabolic traits.","authors":"Emma P Wilson,K Alaine Broadaway,Victoria A Parsons,Swarooparani Vadlamudi,Narisu Narisu,Sarah M Brotman,Kevin W Currin,Heather M Stringham,Michael R Erdos,Ryan Welch,Jeffrey K Holtzman,Timo A Lakka,Markku Laakso,Jaakko Tuomilehto,Michael Boehnke,Heikki A Koistinen,Francis S Collins,Stephen C J Parker,Laura J Scott,Karen L Mohlke","doi":"10.1016/j.ajhg.2025.09.003","DOIUrl":"https://doi.org/10.1016/j.ajhg.2025.09.003","url":null,"abstract":"Identifying genetic variants that regulate gene expression can help uncover mechanisms underlying complex traits. We performed a meta-analysis of skeletal muscle expression quantitative trait locus (eQTL) using data from 1,002 individuals from two studies. A stepwise analysis identified 18,818 conditionally distinct signals for 12,283 genes, and 35% of these genes contained two or more signals. Colocalization of these eQTL signals with 26 muscular and cardiometabolic trait genome-wide association studies (GWASs) identified 2,252 GWAS-eQTL colocalizations that nominated 1,342 candidate genes. Notably, 22% of the GWAS-eQTL colocalizations involved non-primary eQTL signals. Additionally, 37% of the colocalized GWAS-eQTL signals corresponded to the closest protein-coding gene, while 44% were located >50 kb from the transcription start site of the nominated gene. To assess tissue specificity for a heterogeneous trait, we compared colocalizations with type 2 diabetes (T2D) signals across muscle, adipose, liver, and islet eQTLs; we identified 551 candidate genes for 309 T2D signals representing 36% of T2D signals tested and over 100 more than were detected with any one tissue alone. We then functionally validated the allelic regulatory effect of an eQTL variant for INHBB linked to T2D in both muscle and adipose tissue. Together, these results further demonstrate the value of skeletal muscle eQTLs in elucidating mechanisms underlying complex traits.","PeriodicalId":7659,"journal":{"name":"American journal of human genetics","volume":"13 1","pages":""},"PeriodicalIF":9.8,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145134391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-22DOI: 10.1016/j.ajhg.2025.09.001
Johnny Bou-Rouphael,Auriane Cospain,Thomas Courtin,Boris Keren,Corentine Marie,Marion Lesieur-Sebellin,Delphine Heron,Jean-Madeleine de Sainte Agathe,Solveig Heide,Elodie Lejeune,Chloe Quelin,François Lecoquierre,Mathilde Nizon,Bertrand Isidor,Thomas Besnard,Benjamin Cogne,Xenia Latypova,Jonathan Levy,Pascal Joset,Katharina Steindl,Maria Palomares-Bralo,Fernando Santos-Simarro,Mary Ann Thomas,Amina Abubakar,Sally Ann Lynch,Amelie J Müller,Tobias B Haack,Martin Zenker,Michael Parker,Emma Clossick,Michael Spiller,Renarta Crookes,Muriel Holder-Espinasse,Allan Bayat,Rikke S Møller,Tomasz Stanislaw Mieszczanek,Pierre de la Grange,Julien Buratti,Pierre Marijon,Sabir Ataf,Ryan Gavin,Carlos Parras,Bassem A Hassan,Cyril Mignot,Laïla El Khattabi
Alternative splicing is highly prevalent in the brain where it orchestrates key processes such as neurogenesis and synaptogenesis, both essential for the nervous system's complexity and plasticity. Dysregulation of splicing has increasingly been linked to neurodevelopmental disorders. Here, we describe unrelated individuals carrying de novo, likely deleterious heterozygous variants in Splicing Factor 1 (SF1), all presenting with neurodevelopmental disorders of variable severity, frequently accompanied by autistic traits and other non-specific features. SF1 is a core component of pre-mRNA processing, facilitating early spliceosome assembly at the 3' splice site and regulating alternative splicing. We conducted functional studies in neural progenitor cells, which showed that SF1 downregulation alters gene expression and alternative splicing programs, particularly in genes involved in neuronal differentiation, synaptic transmission, and axonal guidance, processes fundamental to brain development. Together, these findings establish SF1 dysfunction as an additional spliceosomopathy contributing to neurodevelopmental disorders and underscore its essential role in human neurodevelopment and disease.
{"title":"Heterozygous pathogenic variants in the splicing factor SF1 lead to a large spectrum of neurodevelopmental disorders.","authors":"Johnny Bou-Rouphael,Auriane Cospain,Thomas Courtin,Boris Keren,Corentine Marie,Marion Lesieur-Sebellin,Delphine Heron,Jean-Madeleine de Sainte Agathe,Solveig Heide,Elodie Lejeune,Chloe Quelin,François Lecoquierre,Mathilde Nizon,Bertrand Isidor,Thomas Besnard,Benjamin Cogne,Xenia Latypova,Jonathan Levy,Pascal Joset,Katharina Steindl,Maria Palomares-Bralo,Fernando Santos-Simarro,Mary Ann Thomas,Amina Abubakar,Sally Ann Lynch,Amelie J Müller,Tobias B Haack,Martin Zenker,Michael Parker,Emma Clossick,Michael Spiller,Renarta Crookes,Muriel Holder-Espinasse,Allan Bayat,Rikke S Møller,Tomasz Stanislaw Mieszczanek,Pierre de la Grange,Julien Buratti,Pierre Marijon,Sabir Ataf,Ryan Gavin,Carlos Parras,Bassem A Hassan,Cyril Mignot,Laïla El Khattabi","doi":"10.1016/j.ajhg.2025.09.001","DOIUrl":"https://doi.org/10.1016/j.ajhg.2025.09.001","url":null,"abstract":"Alternative splicing is highly prevalent in the brain where it orchestrates key processes such as neurogenesis and synaptogenesis, both essential for the nervous system's complexity and plasticity. Dysregulation of splicing has increasingly been linked to neurodevelopmental disorders. Here, we describe unrelated individuals carrying de novo, likely deleterious heterozygous variants in Splicing Factor 1 (SF1), all presenting with neurodevelopmental disorders of variable severity, frequently accompanied by autistic traits and other non-specific features. SF1 is a core component of pre-mRNA processing, facilitating early spliceosome assembly at the 3' splice site and regulating alternative splicing. We conducted functional studies in neural progenitor cells, which showed that SF1 downregulation alters gene expression and alternative splicing programs, particularly in genes involved in neuronal differentiation, synaptic transmission, and axonal guidance, processes fundamental to brain development. Together, these findings establish SF1 dysfunction as an additional spliceosomopathy contributing to neurodevelopmental disorders and underscore its essential role in human neurodevelopment and disease.","PeriodicalId":7659,"journal":{"name":"American journal of human genetics","volume":"2 1","pages":""},"PeriodicalIF":9.8,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145127151","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Allele-specific silencing by RNA interference offers a promising therapeutic approach for dominant inherited diseases through specific silencing of the mRNA produced by the mutated allele. Here, we report the development of such a strategy for Schuurs-Hoeijmakers syndrome (SHMS), a rare neurodevelopmental disorder characterized by intellectual disability, abnormal craniofacial features, and congenital malformations without available treatment. Most cases of SHMS are caused by a recurrent de novo heterozygous missense mutation (c.607C>T [p.Arg203Trp]) in the PACS1 gene, which encodes PACS1 (phosphofurin acid cluster sorting 1), a multifunctional sorting protein. Through an in vitro screening of fibroblasts derived from affected individuals, we identified several small interfering RNA (siRNA) sequences that specifically silence the PACS1 transcript harboring the recurrent PACS1 mutation while sparing the wild-type mRNA. Furthermore, transcriptomic analysis of SHMS fibroblasts revealed alterations in extracellular matrix organization in mutant cells, including elevated COL8A1 expression and extracellular deposition. Treatment with the best selected allele-specific siRNA corrected the COL8A1 dysregulation. Altogether, this study provides the proof of concept of allele-specific RNA interference therapeutic for SHMS in cells derived from affected individuals and highlights a pathophysiological mechanism involving extracellular matrix dysfunction in this disorder. These results strengthen the allele-specific silencing approach as a robust, safe, and efficient therapy for dominant inherited diseases.
{"title":"Allele-specific RNAi therapy corrects an extracellular matrix defect in Schuurs-Hoeijmakers syndrome.","authors":"Lylia Mekzine,Natalia Pinzón,Kamel Mamchaoui,Maria Kondili,Bruno Cadot,Marc Bitoun,Delphine Trochet","doi":"10.1016/j.ajhg.2025.07.010","DOIUrl":"https://doi.org/10.1016/j.ajhg.2025.07.010","url":null,"abstract":"Allele-specific silencing by RNA interference offers a promising therapeutic approach for dominant inherited diseases through specific silencing of the mRNA produced by the mutated allele. Here, we report the development of such a strategy for Schuurs-Hoeijmakers syndrome (SHMS), a rare neurodevelopmental disorder characterized by intellectual disability, abnormal craniofacial features, and congenital malformations without available treatment. Most cases of SHMS are caused by a recurrent de novo heterozygous missense mutation (c.607C>T [p.Arg203Trp]) in the PACS1 gene, which encodes PACS1 (phosphofurin acid cluster sorting 1), a multifunctional sorting protein. Through an in vitro screening of fibroblasts derived from affected individuals, we identified several small interfering RNA (siRNA) sequences that specifically silence the PACS1 transcript harboring the recurrent PACS1 mutation while sparing the wild-type mRNA. Furthermore, transcriptomic analysis of SHMS fibroblasts revealed alterations in extracellular matrix organization in mutant cells, including elevated COL8A1 expression and extracellular deposition. Treatment with the best selected allele-specific siRNA corrected the COL8A1 dysregulation. Altogether, this study provides the proof of concept of allele-specific RNA interference therapeutic for SHMS in cells derived from affected individuals and highlights a pathophysiological mechanism involving extracellular matrix dysfunction in this disorder. These results strengthen the allele-specific silencing approach as a robust, safe, and efficient therapy for dominant inherited diseases.","PeriodicalId":7659,"journal":{"name":"American journal of human genetics","volume":"6 1","pages":""},"PeriodicalIF":9.8,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145089909","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genomic sequencing is essential for both biomedical research and clinical practice. While single-cell RNA sequencing (scRNA-seq) provides insights into biological processes at the cellular level, bulk RNA sequencing remains widely used for its scalability and cost-effectiveness. To explore biological heterogeneity, research efforts have been made toward inferring single-cell-like cellular compositions from bulk samples, i.e., deconvolving bulk samples into multiple cell types. However, existing deconvolution methods face two major limitations: (1) reliance on predefined gene signature matrices without accounting for inter-sample variability and (2) susceptibility to noise within biological systems. Here, we propose a cellular-component analysis (CCA) framework by leveraging a genomic-interaction-encoded image representation of RNA-seq data for substantially improved pattern discovery. The framework incorporates sample-specific gene-expression variability and derives signature patterns by utilizing a convolutional variational autoencoder and Gaussian mixture model. An image-domain linear decomposition of bulk RNA-seq data based on these sample-specific, interpretable gene-signature patterns is then performed for CCA and other downstream tasks, such as cancer subtype classification and biomarker discovery. We demonstrate that the proposed technique improves decomposition accuracy by over 14.1% in average Pearson correlation compared to existing techniques by using both simulation and experimental datasets. This approach offers an effective solution for tissue heterogeneity analysis and lays a foundation for a range of clinical and biological applications.
{"title":"Unveiling tissue heterogeneity through genomic interaction-encoded image representation of RNA-sequencing data.","authors":"Junyan Liu,Zixia Zhou,Yizheng Chen,Md Tauhidul Islam,Lei Xing","doi":"10.1016/j.ajhg.2025.08.021","DOIUrl":"https://doi.org/10.1016/j.ajhg.2025.08.021","url":null,"abstract":"Genomic sequencing is essential for both biomedical research and clinical practice. While single-cell RNA sequencing (scRNA-seq) provides insights into biological processes at the cellular level, bulk RNA sequencing remains widely used for its scalability and cost-effectiveness. To explore biological heterogeneity, research efforts have been made toward inferring single-cell-like cellular compositions from bulk samples, i.e., deconvolving bulk samples into multiple cell types. However, existing deconvolution methods face two major limitations: (1) reliance on predefined gene signature matrices without accounting for inter-sample variability and (2) susceptibility to noise within biological systems. Here, we propose a cellular-component analysis (CCA) framework by leveraging a genomic-interaction-encoded image representation of RNA-seq data for substantially improved pattern discovery. The framework incorporates sample-specific gene-expression variability and derives signature patterns by utilizing a convolutional variational autoencoder and Gaussian mixture model. An image-domain linear decomposition of bulk RNA-seq data based on these sample-specific, interpretable gene-signature patterns is then performed for CCA and other downstream tasks, such as cancer subtype classification and biomarker discovery. We demonstrate that the proposed technique improves decomposition accuracy by over 14.1% in average Pearson correlation compared to existing techniques by using both simulation and experimental datasets. This approach offers an effective solution for tissue heterogeneity analysis and lays a foundation for a range of clinical and biological applications.","PeriodicalId":7659,"journal":{"name":"American journal of human genetics","volume":"17 1","pages":""},"PeriodicalIF":9.8,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145083354","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-09DOI: 10.1016/j.ajhg.2025.08.015
Hammad Yousaf,Maayke A de Koning,Kamal Khan,Kelly L Gilmore,Mariëtte J V Hoffer,Georgios Kellaris,Sophie Lanone,Maylis Dagouassat,Farid Ullah,Phebe N Adama van Scheltema,Delphine Heron,Yline Capri,Alma Kuechler,Bernd Schweiger,Monique C Haak,Boris Keren,Frederic Tran Mau Them,Cacha M P C D Peeters-Scholte,Frank J Kaiser,Tamara T Koopmann,Hailiang Mei,Binnaz Yalcin,Christel Depienne,Neeta L Vora,Gijs W E Santen,Erica E Davis
Fetal brain anomalies identified by prenatal ultrasound and/or magnetic resonance imaging represent a considerable healthcare burden with ∼1-2/1,000 live births. To identify the underlying etiology, trio prenatal exome sequencing or genome sequencing (ES/GS) has emerged as a comprehensive diagnostic paradigm with a reported diagnostic rate up to ∼32%. Here, we report five unrelated families with six affected individuals that presented neuroanatomical, craniofacial, and skeletal anomalies, all harboring rare, bi-allelic deleterious variants in SNAPIN, which encodes SNARE-associated protein. SNAPIN is a ubiquitously expressed component of the autophagy-lysosomal pathway that catalyzes retrograde axonal transport and synaptic transmission. To investigate the role of SNAPIN in brain development, we generated zebrafish gene ablation models, which recapitulated human-relevant disease phenotypes. Two independent, genetically stable snapin mutants exhibited pre-adulthood lethality, reduced overall length, disproportionately smaller head size, and altered brain morphology. Transcriptomic profiling of snapin mutant zebrafish heads revealed an early and progressive transcriptomic shift marked by autophagy activation with concomitant downregulation of structural and neurodevelopmental genes. Assessment of brain cellular ultrastructure with electron microscopy and light chain 3 (LC3)-II immunoblotting revealed retrograde vesicle transport defects, with an accumulation of late endosomes and autophagosomes. Together, these findings support bi-allelic pathogenic variants in SNAPIN as a likely cause for a severe neurodevelopmental syndrome and expand the growing list of autophagy-lysosome pathway regulators essential for human brain development.
{"title":"Bi-allelic deleterious variants in SNAPIN, which encodes a retrograde dynein adaptor, cause a prenatal-onset neurodevelopmental disorder.","authors":"Hammad Yousaf,Maayke A de Koning,Kamal Khan,Kelly L Gilmore,Mariëtte J V Hoffer,Georgios Kellaris,Sophie Lanone,Maylis Dagouassat,Farid Ullah,Phebe N Adama van Scheltema,Delphine Heron,Yline Capri,Alma Kuechler,Bernd Schweiger,Monique C Haak,Boris Keren,Frederic Tran Mau Them,Cacha M P C D Peeters-Scholte,Frank J Kaiser,Tamara T Koopmann,Hailiang Mei,Binnaz Yalcin,Christel Depienne,Neeta L Vora,Gijs W E Santen,Erica E Davis","doi":"10.1016/j.ajhg.2025.08.015","DOIUrl":"https://doi.org/10.1016/j.ajhg.2025.08.015","url":null,"abstract":"Fetal brain anomalies identified by prenatal ultrasound and/or magnetic resonance imaging represent a considerable healthcare burden with ∼1-2/1,000 live births. To identify the underlying etiology, trio prenatal exome sequencing or genome sequencing (ES/GS) has emerged as a comprehensive diagnostic paradigm with a reported diagnostic rate up to ∼32%. Here, we report five unrelated families with six affected individuals that presented neuroanatomical, craniofacial, and skeletal anomalies, all harboring rare, bi-allelic deleterious variants in SNAPIN, which encodes SNARE-associated protein. SNAPIN is a ubiquitously expressed component of the autophagy-lysosomal pathway that catalyzes retrograde axonal transport and synaptic transmission. To investigate the role of SNAPIN in brain development, we generated zebrafish gene ablation models, which recapitulated human-relevant disease phenotypes. Two independent, genetically stable snapin mutants exhibited pre-adulthood lethality, reduced overall length, disproportionately smaller head size, and altered brain morphology. Transcriptomic profiling of snapin mutant zebrafish heads revealed an early and progressive transcriptomic shift marked by autophagy activation with concomitant downregulation of structural and neurodevelopmental genes. Assessment of brain cellular ultrastructure with electron microscopy and light chain 3 (LC3)-II immunoblotting revealed retrograde vesicle transport defects, with an accumulation of late endosomes and autophagosomes. Together, these findings support bi-allelic pathogenic variants in SNAPIN as a likely cause for a severe neurodevelopmental syndrome and expand the growing list of autophagy-lysosome pathway regulators essential for human brain development.","PeriodicalId":7659,"journal":{"name":"American journal of human genetics","volume":"12 1","pages":""},"PeriodicalIF":9.8,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145031927","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-08DOI: 10.1016/j.ajhg.2025.08.014
Charlie F Rowlands,Sophie Allen,Alice Garrett,Miranda Durkie,George J Burghel,Rachel Robinson,Alison Callaway,Joanne Field,Bethan Frugtniet,Sheila Palmer-Smith,Jonathan Grant,Judith Pagan,Trudi McDevitt,Katie Snape,Helen Hanson,Terri McVeigh,Clare Turnbull,
Multiplex assays of variant effect (MAVEs) provide promising new sources of functional evidence, potentially empowering improved classification of germline genomic variants, particularly rare missense variants, which are commonly assigned as variants of uncertain significance (VUSs). However, paradoxically, quantification of clinically applicable evidence strengths for MAVEs requires construction of "truthsets" comprising missense variants already robustly classified as pathogenic and benign. In this study, we demonstrate how benign truthset size is the primary driver of applicable functional evidence toward pathogenicity (PS3). We demonstrate, when using existing ClinVar classifications as a source of benign missense truthset variants, that only 19.8% (23/116) of established cancer susceptibility genes had a PS3 evidence strength of "strong" attainable when simulating validation for a hypothetical new MAVE (also applying favorable assumption of perfect concordance). We describe a systematic framework for benign truthset construction in which all possible missense variants in a gene of interest are concurrently assessed for assignation of (likely) benignity via established ACMG/AMP combination rules, including population frequency, in silico evidence codes, and case-control signal. We apply this framework to eight hereditary breast and ovarian cancer genes, demonstrating that systematically generated benign missense truthsets allow maximum application of PS3 at greater (or equivalent) strength-reaching "moderate" for CHEK2 and "strong" for the other seven genes-than those derived from ClinVar ≥2∗ classifications alone. We propose, given many genes have few existing benign-classified missense variants, that the application of this systematic framework to disease genes more broadly will be important for leveraging full value from MAVEs.
{"title":"Availability of benign missense variant \"truthsets\" for validation of functional assays: Current status and a systematic approach.","authors":"Charlie F Rowlands,Sophie Allen,Alice Garrett,Miranda Durkie,George J Burghel,Rachel Robinson,Alison Callaway,Joanne Field,Bethan Frugtniet,Sheila Palmer-Smith,Jonathan Grant,Judith Pagan,Trudi McDevitt,Katie Snape,Helen Hanson,Terri McVeigh,Clare Turnbull, ","doi":"10.1016/j.ajhg.2025.08.014","DOIUrl":"https://doi.org/10.1016/j.ajhg.2025.08.014","url":null,"abstract":"Multiplex assays of variant effect (MAVEs) provide promising new sources of functional evidence, potentially empowering improved classification of germline genomic variants, particularly rare missense variants, which are commonly assigned as variants of uncertain significance (VUSs). However, paradoxically, quantification of clinically applicable evidence strengths for MAVEs requires construction of \"truthsets\" comprising missense variants already robustly classified as pathogenic and benign. In this study, we demonstrate how benign truthset size is the primary driver of applicable functional evidence toward pathogenicity (PS3). We demonstrate, when using existing ClinVar classifications as a source of benign missense truthset variants, that only 19.8% (23/116) of established cancer susceptibility genes had a PS3 evidence strength of \"strong\" attainable when simulating validation for a hypothetical new MAVE (also applying favorable assumption of perfect concordance). We describe a systematic framework for benign truthset construction in which all possible missense variants in a gene of interest are concurrently assessed for assignation of (likely) benignity via established ACMG/AMP combination rules, including population frequency, in silico evidence codes, and case-control signal. We apply this framework to eight hereditary breast and ovarian cancer genes, demonstrating that systematically generated benign missense truthsets allow maximum application of PS3 at greater (or equivalent) strength-reaching \"moderate\" for CHEK2 and \"strong\" for the other seven genes-than those derived from ClinVar ≥2∗ classifications alone. We propose, given many genes have few existing benign-classified missense variants, that the application of this systematic framework to disease genes more broadly will be important for leveraging full value from MAVEs.","PeriodicalId":7659,"journal":{"name":"American journal of human genetics","volume":"72 1","pages":""},"PeriodicalIF":9.8,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145025701","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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