Human Genetics最新文献

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VCAT: an integrated variant function annotation tools. VCAT:综合变异功能注释工具。
IF 3.8 2区 生物学
Human Genetics Pub Date : 2024-08-27 DOI: 10.1007/s00439-024-02699-6
Bi Huang, Cong Fan, Ken Chen, Jiahua Rao, Peihua Ou, Chong Tian, Yuedong Yang, David N Cooper, Huiying Zhao
{"title":"VCAT: an integrated variant function annotation tools.","authors":"Bi Huang, Cong Fan, Ken Chen, Jiahua Rao, Peihua Ou, Chong Tian, Yuedong Yang, David N Cooper, Huiying Zhao","doi":"10.1007/s00439-024-02699-6","DOIUrl":"https://doi.org/10.1007/s00439-024-02699-6","url":null,"abstract":"<p><p>The development of sequencing technology has promoted discovery of variants in the human genome. Identifying functions of these variants is important for us to link genotype to phenotype, and to diagnose diseases. However, it usually requires researchers to visit multiple databases. Here, we presented a one-stop webserver for variant function annotation tools (VCAT, https://biomed.nscc-gz.cn/zhaolab/VCAT/ ) that is the first one connecting variant to functions via the epigenome, protein, drug and RNA. VCAT is also the first one to make all annotations visualized in interactive charts or molecular structures. VCAT allows users to upload data in VCF format, and download results via a URL. Moreover, VCAT has annotated a huge number (1,262,041,068) of variants collected from dbSNP, 1000 Genomes projects, gnomAD, ICGC, TCGA, and HPRC Pangenome project. For these variants, users are able to searcher their functions, related diseases and drugs from VCAT. In summary, VCAT provides a one-stop webserver to explore the potential functions of human genomic variants including their relationship with diseases and drugs.</p>","PeriodicalId":13175,"journal":{"name":"Human Genetics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142080183","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}
引用次数: 0
Integrative genomic analyses identify neuroblastoma risk genes involved in neuronal differentiation. 整合基因组分析确定了参与神经元分化的神经母细胞瘤风险基因。
IF 3.8 2区 生物学
Human Genetics Pub Date : 2024-08-27 DOI: 10.1007/s00439-024-02700-2
Matilde Tirelli, Ferdinando Bonfiglio, Sueva Cantalupo, Annalaura Montella, Marianna Avitabile, Teresa Maiorino, Sharon J Diskin, Achille Iolascon, Mario Capasso
{"title":"Integrative genomic analyses identify neuroblastoma risk genes involved in neuronal differentiation.","authors":"Matilde Tirelli, Ferdinando Bonfiglio, Sueva Cantalupo, Annalaura Montella, Marianna Avitabile, Teresa Maiorino, Sharon J Diskin, Achille Iolascon, Mario Capasso","doi":"10.1007/s00439-024-02700-2","DOIUrl":"https://doi.org/10.1007/s00439-024-02700-2","url":null,"abstract":"<p><p>Genome-Wide Association Studies (GWAS) have been decisive in elucidating the genetic predisposition of neuroblastoma (NB). The majority of genetic variants identified in GWAS are found in non-coding regions, suggesting that they can be causative of pathogenic dysregulations of gene expression. Nonetheless, pinpointing the potential causal genes within implicated genetic loci remains a major challenge. In this study, we integrated NB GWAS and expression Quantitative Trait Loci (eQTL) data from adrenal gland to identify candidate genes impacting NB susceptibility. We found that ZMYM1, CBL, GSKIP and WDR81 expression was dysregulated by NB predisposing variants. We further investigated the functional role of the identified genes through computational analysis of RNA sequencing (RNA-seq) data from single-cell and whole-tissue samples of NB, neural crest, and adrenal gland tissues, as well as through in vitro differentiation assays in NB cell cultures. Our results indicate that dysregulation of ZMYM1, CBL, GSKIP, WDR81 may lead to malignant transformation by affecting early and late stages of normal program of neuronal differentiation. Our findings enhance the understanding of how specific genes contribute to NB pathogenesis by highlighting their influence on neuronal differentiation and emphasizing the impact of genetic risk variants on the regulation of genes involved in critical biological processes.</p>","PeriodicalId":13175,"journal":{"name":"Human Genetics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142080182","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}
引用次数: 0
Structure-informed protein language models are robust predictors for variant effects. 结构信息蛋白质语言模型是变异效应的稳健预测器。
IF 3.8 2区 生物学
Human Genetics Pub Date : 2024-08-08 DOI: 10.1007/s00439-024-02695-w
Yuanfei Sun, Yang Shen
{"title":"Structure-informed protein language models are robust predictors for variant effects.","authors":"Yuanfei Sun, Yang Shen","doi":"10.1007/s00439-024-02695-w","DOIUrl":"10.1007/s00439-024-02695-w","url":null,"abstract":"<p><p>Emerging variant effect predictors, protein language models (pLMs) learn evolutionary distribution of functional sequences to capture fitness landscape. Considering that variant effects are manifested through biological contexts beyond sequence (such as structure), we first assess how much structure context is learned in sequence-only pLMs and affecting variant effect prediction. And we establish a need to inject into pLMs protein structural context purposely and controllably. We thus introduce a framework of structure-informed pLMs (SI-pLMs), by extending masked sequence denoising to cross-modality denoising for both sequence and structure. Numerical results over deep mutagenesis scanning benchmarks show that our SI-pLMs, even when using smaller models and less data, are robustly top performers against competing methods including other pLMs, which shows that introducing biological context can be more effective at capturing fitness landscape than simply using larger models or bigger data. Case studies reveal that, compared to sequence-only pLMs, SI-pLMs can be better at capturing fitness landscape because (a) learned embeddings of low/high-fitness sequences can be more separable and (b) learned amino-acid distributions of functionally and evolutionarily conserved residues can be of much lower entropy, thus much more conserved, than other residues. Our SI-pLMs are applicable to revising any sequence-only pLMs through model architecture and training objectives. They do not require structure data as model inputs for variant effect prediction and only use structures as context provider and model regularizer during training.</p>","PeriodicalId":13175,"journal":{"name":"Human Genetics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141906463","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}
引用次数: 0
Assessing predictions on fitness effects of missense variants in HMBS in CAGI6. 评估 CAGI6 中 HMBS 的错义变异对健康影响的预测。
IF 3.8 2区 生物学
Human Genetics Pub Date : 2024-08-07 DOI: 10.1007/s00439-024-02680-3
Jing Zhang, Lisa Kinch, Panagiotis Katsonis, Olivier Lichtarge, Milind Jagota, Yun S Song, Yuanfei Sun, Yang Shen, Nurdan Kuru, Onur Dereli, Ogun Adebali, Muttaqi Ahmad Alladin, Debnath Pal, Emidio Capriotti, Maria Paola Turina, Castrense Savojardo, Pier Luigi Martelli, Giulia Babbi, Rita Casadio, Fabrizio Pucci, Marianne Rooman, Gabriel Cia, Matsvei Tsishyn, Alexey Strokach, Zhiqiang Hu, Warren van Loggerenberg, Frederick P Roth, Predrag Radivojac, Steven E Brenner, Qian Cong, Nick V Grishin
{"title":"Assessing predictions on fitness effects of missense variants in HMBS in CAGI6.","authors":"Jing Zhang, Lisa Kinch, Panagiotis Katsonis, Olivier Lichtarge, Milind Jagota, Yun S Song, Yuanfei Sun, Yang Shen, Nurdan Kuru, Onur Dereli, Ogun Adebali, Muttaqi Ahmad Alladin, Debnath Pal, Emidio Capriotti, Maria Paola Turina, Castrense Savojardo, Pier Luigi Martelli, Giulia Babbi, Rita Casadio, Fabrizio Pucci, Marianne Rooman, Gabriel Cia, Matsvei Tsishyn, Alexey Strokach, Zhiqiang Hu, Warren van Loggerenberg, Frederick P Roth, Predrag Radivojac, Steven E Brenner, Qian Cong, Nick V Grishin","doi":"10.1007/s00439-024-02680-3","DOIUrl":"10.1007/s00439-024-02680-3","url":null,"abstract":"<p><p>This paper presents an evaluation of predictions submitted for the \"HMBS\" challenge, a component of the sixth round of the Critical Assessment of Genome Interpretation held in 2021. The challenge required participants to predict the effects of missense variants of the human HMBS gene on yeast growth. The HMBS enzyme, critical for the biosynthesis of heme in eukaryotic cells, is highly conserved among eukaryotes. Despite the application of a variety of algorithms and methods, the performance of predictors was relatively similar, with Kendall's tau correlation coefficients between predictions and experimental scores around 0.3 for a majority of submissions. Notably, the median correlation (≥ 0.34) observed among these predictors, especially the top predictions from different groups, was greater than the correlation observed between their predictions and the actual experimental results. Most predictors were moderately successful in distinguishing between deleterious and benign variants, as evidenced by an area under the receiver operating characteristic (ROC) curve (AUC) of approximately 0.7 respectively. Compared with the recent two rounds of CAGI competitions, we noticed more predictors outperformed the baseline predictor, which is solely based on the amino acid frequencies. Nevertheless, the overall accuracy of predictions is still far short of positive control, which is derived from experimental scores, indicating the necessity for considerable improvements in the field. The most inaccurately predicted variants in this round were associated with the insertion loop, which is absent in many orthologs, suggesting the predictors still heavily rely on the information from multiple sequence alignment.</p>","PeriodicalId":13175,"journal":{"name":"Human Genetics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141897332","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}
引用次数: 0
GBF1 deficiency causes cataracts in human and mouse. GBF1 缺乏会导致人类和小鼠白内障。
IF 3.8 2区 生物学
Human Genetics Pub Date : 2024-08-07 DOI: 10.1007/s00439-024-02697-8
Weimin Jia, Chenming Zhang, Yalin Luo, Jing Gao, Chao Yuan, Dazhi Zhang, Xiaopei Zhou, Yongyao Tan, Shuang Wang, Zhuo Chen, Guigang Li, Xianqin Zhang
{"title":"GBF1 deficiency causes cataracts in human and mouse.","authors":"Weimin Jia, Chenming Zhang, Yalin Luo, Jing Gao, Chao Yuan, Dazhi Zhang, Xiaopei Zhou, Yongyao Tan, Shuang Wang, Zhuo Chen, Guigang Li, Xianqin Zhang","doi":"10.1007/s00439-024-02697-8","DOIUrl":"https://doi.org/10.1007/s00439-024-02697-8","url":null,"abstract":"<p><p>Any opacification of the lens can be defined as cataracts, and lens epithelium cells play a crucial role in guaranteeing lens transparency by maintaining its homeostasis. Although several causative genes of congenital cataracts have been reported, the mechanisms underlying lens opacity remain unclear. In this study, a large family with congenital cataracts was collected and genetic analysis revealed a pathological mutation (c.3857 C > T, p.T1287I) in the GBF1 gene; all affected individuals in the family carried this heterozygous mutation, while unaffected family members did not. Functional studies in human lens epithelium cell line revealed that this mutation led to a reduction in GBF1 protein levels. Knockdown of endogenous GBF1 activated XBP1s in the unfolded protein response signal pathway, and enhances autophagy in an mTOR-independent manner. Heterozygous Gbf1 knockout mice also displayed typic cataract phenotype. Together, our study identified GBF1 as a novel causative gene for congenital cataracts. Additionally, we found that GBF1 deficiency activates the unfolded protein response and leads to enhanced autophagy, which may contribute to lens opacity.</p>","PeriodicalId":13175,"journal":{"name":"Human Genetics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141897333","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}
引用次数: 0
Genome-wide assessment of shared genetic landscape of idiopathic pulmonary fibrosis and its comorbidities. 特发性肺纤维化及其并发症的全基因组共享遗传景观评估。
IF 3.8 2区 生物学
Human Genetics Pub Date : 2024-08-06 DOI: 10.1007/s00439-024-02696-9
Yuanhao Yang, Yong H Sheng, Patricia Carreira, Tong Wang, Huiying Zhao, Ran Wang
{"title":"Genome-wide assessment of shared genetic landscape of idiopathic pulmonary fibrosis and its comorbidities.","authors":"Yuanhao Yang, Yong H Sheng, Patricia Carreira, Tong Wang, Huiying Zhao, Ran Wang","doi":"10.1007/s00439-024-02696-9","DOIUrl":"https://doi.org/10.1007/s00439-024-02696-9","url":null,"abstract":"<p><p>Idiopathic pulmonary fibrosis (IPF) is a progressive interstitial lung disease accompanied by both local and systemic comorbidities. Genetic factors play a role in the development of IPF and certain associated comorbidities. Nevertheless, it is uncertain whether there are shared genetic factors underlying IPF and these comorbidities. To bridge this knowledge gap, we conducted a systematic investigation into the shared genetic architecture between IPF and ten prevalent heritable comorbidities (i.e., body mass index [BMI], coronary artery disease [CAD], chronic obstructive pulmonary disease [COPD], gastroesophageal reflux disease, lung cancer, major depressive disorder [MDD], obstructive sleep apnoea, pulmonary hypertension [PH], stroke, and type 2 diabetes), by utilizing large-scale summary data from their respective genome-wide association studies and multi-omics studies. We revealed significant (false discovery rate [FDR] < 0.05) and moderate genetic correlations between IPF and seven comorbidities, excluding lung cancer, MDD and PH. Evidence suggested a partially putative causal effect of IPF on CAD. Notably, we observed FDR-significant genetic enrichments in lung for the cross-trait between IPF and CAD and in liver for the cross-trait between IPF and COPD. Additionally, we identified 65 FDR-significant genes over-represented in 20 biological pathways related to the etiology of IPF, BMI, and COPD, including inflammation-related mucin gene clusters. Several of these genes were associated with clinically relevant drugs for the treatment of IPF, CAD, and/or COPD. Our results underscore the pervasive shared genetic basis between IPF and its common comorbidities and hold future implications for early diagnosis of IPF-related comorbidities, drug repurposing, and the development of novel therapies for IPF.</p>","PeriodicalId":13175,"journal":{"name":"Human Genetics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141893355","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}
引用次数: 0
T1R2/T1R3 polymorphism affects sweet and fat perception: Correlation between SNP and BMI in the context of obesity development. T1R2/T1R3多态性影响甜味和脂肪感知:肥胖发展过程中 SNP 与 BMI 之间的相关性。
IF 3.8 2区 生物学
Human Genetics Pub Date : 2024-08-06 DOI: 10.1007/s00439-024-02690-1
Vinithra Ponnusamy, Gowtham Subramanian, Keerthana Vasanthakumar, Karthi Muthuswamy, Prabha Panneerselvan, Vasanth Krishnan, Selvakumar Subramaniam
{"title":"T1R2/T1R3 polymorphism affects sweet and fat perception: Correlation between SNP and BMI in the context of obesity development.","authors":"Vinithra Ponnusamy, Gowtham Subramanian, Keerthana Vasanthakumar, Karthi Muthuswamy, Prabha Panneerselvan, Vasanth Krishnan, Selvakumar Subramaniam","doi":"10.1007/s00439-024-02690-1","DOIUrl":"https://doi.org/10.1007/s00439-024-02690-1","url":null,"abstract":"<p><p>Genetic variations in taste receptors are associated with gustatory perception and obesity, which in turn affects dietary preferences. Given the increasing tendency of people with obesity choosing sweet, high-fat meals, the current study assessed the cross-regulation of two polymorphisms of the sweet taste receptor (T1R2/T1R3), rs35874116 and rs307355, on fat sensitivity in Indian adults. We investigated the association between taste sensitivity and BMI in the T1R2, T1R3, and CD36 polymorphic and non-polymorphic groups. The general labelled magnitude scale (gLMS) was used to assess the taste sensitivity of 249 participants in addition to anthropometric data. TaqMan Probe-based RT-PCR was employed to determine the polymorphisms. Additionally, the colorimetric method utilizing 3, 5-dinitro salicylic acid was used to evaluate the participants' salivary amylase activity. The mean detection thresholds for linoleic acid (LA) and sucrose were greater in individuals with obesity (i.e., 0.97 ± 0.08 mM and 0.22 ± 0.02 M, respectively) than in healthy adults (p < 0.0001), indicating lower sensitivity. Moreover, it was found that a greater proportion of persons with obesity fall into the polymorphic groups (i.e., 52% with genotype CD36 AA, 44% with genotype T1R2 CC, and 40% with genotype T1R3 TT). All three single nucleotide polymorphisms support the Hardy-Weinberg equilibrium (p = 0.78). The Pearson correlation analysis between LA and the sucrose detection threshold revealed a significant (p < 0.0001) positive relationship with an r value of 0.5299. Moreover, salivary amylase activity was significantly (p < 0.05) higher in the polymorphic sub-groups. The results of our study imply that genetic variations in T1R2/T1R3 receptors affect perception of both sweetness and fat, which may have an effect on obesity.</p>","PeriodicalId":13175,"journal":{"name":"Human Genetics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141897334","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}
引用次数: 0
Scalable approaches for generating, validating and incorporating data from high-throughput functional assays to improve clinical variant classification. 生成、验证和纳入高通量功能测定数据的可扩展方法,以改进临床变异分类。
IF 3.8 2区 生物学
Human Genetics Pub Date : 2024-08-01 DOI: 10.1007/s00439-024-02691-0
Samskruthi Reddy Padigepati, David A Stafford, Christopher A Tan, Melanie R Silvis, Kirsty Jamieson, Andrew Keyser, Paola Alejandra Correa Nunez, John M Nicoludis, Toby Manders, Laure Fresard, Yuya Kobayashi, Carlos L Araya, Swaroop Aradhya, Britt Johnson, Keith Nykamp, Jason A Reuter
{"title":"Scalable approaches for generating, validating and incorporating data from high-throughput functional assays to improve clinical variant classification.","authors":"Samskruthi Reddy Padigepati, David A Stafford, Christopher A Tan, Melanie R Silvis, Kirsty Jamieson, Andrew Keyser, Paola Alejandra Correa Nunez, John M Nicoludis, Toby Manders, Laure Fresard, Yuya Kobayashi, Carlos L Araya, Swaroop Aradhya, Britt Johnson, Keith Nykamp, Jason A Reuter","doi":"10.1007/s00439-024-02691-0","DOIUrl":"10.1007/s00439-024-02691-0","url":null,"abstract":"<p><p>As the adoption and scope of genetic testing continue to expand, interpreting the clinical significance of DNA sequence variants at scale remains a formidable challenge, with a high proportion classified as variants of uncertain significance (VUSs). Genetic testing laboratories have historically relied, in part, on functional data from academic literature to support variant classification. High-throughput functional assays or multiplex assays of variant effect (MAVEs), designed to assess the effects of DNA variants on protein stability and function, represent an important and increasingly available source of evidence for variant classification, but their potential is just beginning to be realized in clinical lab settings. Here, we describe a framework for generating, validating and incorporating data from MAVEs into a semi-quantitative variant classification method applied to clinical genetic testing. Using single-cell gene expression measurements, cellular evidence models were built to assess the effects of DNA variation in 44 genes of clinical interest. This framework was also applied to models for an additional 22 genes with previously published MAVE datasets. In total, modeling data was incorporated from 24 genes into our variant classification method. These data contributed evidence for classifying 4043 observed variants in over 57,000 individuals. Genetic testing laboratories are uniquely positioned to generate, analyze, validate, and incorporate evidence from high-throughput functional data and ultimately enable the use of these data to provide definitive clinical variant classifications for more patients.</p>","PeriodicalId":13175,"journal":{"name":"Human Genetics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11303574/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141859632","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}
引用次数: 0
The missing link: ARID1B non-truncating variants causing Coffin-Siris syndrome due to protein aggregation. 缺失的一环:ARID1B非截断变异因蛋白质聚集而导致科芬-西里斯综合征。
IF 3.8 2区 生物学
Human Genetics Pub Date : 2024-08-01 Epub Date: 2024-07-19 DOI: 10.1007/s00439-024-02688-9
Elisabeth Bosch, Esther Güse, Philipp Kirchner, Andreas Winterpacht, Mona Walther, Marielle Alders, Jennifer Kerkhof, Arif B Ekici, Heinrich Sticht, Bekim Sadikovic, André Reis, Georgia Vasileiou
{"title":"The missing link: ARID1B non-truncating variants causing Coffin-Siris syndrome due to protein aggregation.","authors":"Elisabeth Bosch, Esther Güse, Philipp Kirchner, Andreas Winterpacht, Mona Walther, Marielle Alders, Jennifer Kerkhof, Arif B Ekici, Heinrich Sticht, Bekim Sadikovic, André Reis, Georgia Vasileiou","doi":"10.1007/s00439-024-02688-9","DOIUrl":"10.1007/s00439-024-02688-9","url":null,"abstract":"<p><p>ARID1B is the most frequently mutated gene in Coffin-Siris syndrome (CSS). To date, the vast majority of causative variants reported in ARID1B are truncating, leading to nonsense-mediated mRNA decay. In the absence of experimental data, only few ARID1B amino acid substitutions have been classified as pathogenic, mainly based on clinical data and their de novo occurrence, while most others are currently interpreted as variants of unknown significance. The present study substantiates the pathogenesis of ARID1B non-truncating/NMD-escaping variants located in the SMARCA4-interacting EHD2 and DNA-binding ARID domains. Overexpression assays in cell lines revealed that the majority of EHD2 variants lead to protein misfolding and formation of cytoplasmic aggresomes surrounded by vimentin cage-like structures and co-localizing with the microtubule organisation center. ARID domain variants exhibited not only aggresomes, but also nuclear aggregates, demonstrating robust pathological effects. Protein levels were not compromised, as shown by quantitative western blot analysis. In silico structural analysis predicted the exposure of amylogenic segments in both domains due to the nearby variants, likely causing this aggregation. Genome-wide transcriptome and methylation analysis in affected individuals revealed expression and methylome patterns consistent with those of the pathogenic haploinsufficiency ARID1B alterations in CSS cases. These results further support pathogenicity and indicate two approaches for disambiguation of such variants in everyday practice. The few affected individuals harbouring EHD2 non-truncating variants described to date exhibit mild CSS clinical traits. In summary, this study paves the way for the re-evaluation of previously unclear ARID1B non-truncating variants and opens a new era in CSS genetic diagnosis.</p>","PeriodicalId":13175,"journal":{"name":"Human Genetics","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11303441/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141723537","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}
引用次数: 0
Automatized detection of uniparental disomies in a large cohort. 自动检测大型群组中的单亲畸形。
IF 3.8 2区 生物学
Human Genetics Pub Date : 2024-08-01 Epub Date: 2024-07-16 DOI: 10.1007/s00439-024-02687-w
Johanna Moch, Maximilian Radtke, Thomas Liehr, Thomas Eggermann, Christian Gilissen, Rolph Pfundt, Galuh Astuti, Julia Hentschel, Isabell Schumann
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