Przemyslaw Szafranski, Tomasz Gambin, Michal Kadlof, Michał Denkiewicz, Dariusz Plewczynski, Hyun Jeong Kim, Gail Deutsch, Nahir Cortes-Santiago, Salmo Raskin, Paweł Stankiewicz
{"title":"涉及TBX4的CNV缺失在三个患有肺发育障碍的已故兄弟姐妹及其轻度影响的母亲和祖父中的高度可变表达性","authors":"Przemyslaw Szafranski, Tomasz Gambin, Michal Kadlof, Michał Denkiewicz, Dariusz Plewczynski, Hyun Jeong Kim, Gail Deutsch, Nahir Cortes-Santiago, Salmo Raskin, Paweł Stankiewicz","doi":"10.1111/cge.70010","DOIUrl":null,"url":null,"abstract":"<p><p>Single nucleotide variants (SNVs) and copy-number variant (CNV) deletions involving TBX4 have been associated with pulmonary arterial hypertension, ischiocoxopodopatellar syndrome, and lethal lung developmental disorders (LLDDs). Thus far, all large CNV deletions encompassing entire TBX4 have been found to have arisen de novo. Here, we present a three-generation family with three neonate siblings who died within 35-66 days due to histopathologically diagnosed LLDD. Whole-genome sequencing identified an ~108-kb CNV deletion encompassing TBX4 in all three infants. The deletion was also found in their mother with a history of pneumonia and persistent thick upper airway secretions and in the maternal grandfather who had surgically corrected genu valgum. RT-qPCR from the proband's lung biopsy showed a decrease of TBX4 transcript level greater than 50%, suggesting additional deregulation of TBX4 expression. Computational analyses of the TBX4 super-enhancer identified 15 candidate noncoding hypomorphic SNVs transmitted to the children exclusively from their father and absent in their mother and maternal grandfather. We show that SNV rs35827636T > C, previously proposed as potentially hypomorphic in an unrelated AcDys patient, reduced transcriptional activity of the TBX4 promoter in an episomal reporter assay. Moreover, Hi-C analysis predicted inter-TAD interaction between the TBX4 super-enhancer and its promoter-proximal region. Our data further demonstrate complex compound inheritance of LLDDs and resulting challenges for genetic counseling.</p>","PeriodicalId":10354,"journal":{"name":"Clinical Genetics","volume":" ","pages":""},"PeriodicalIF":2.3000,"publicationDate":"2025-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12269481/pdf/","citationCount":"0","resultStr":"{\"title\":\"Highly Variable Expressivity of a CNV Deletion Involving TBX4 in Three Deceased Siblings With Lung Developmental Disorder and Their Mildly Affected Mother and Grandfather.\",\"authors\":\"Przemyslaw Szafranski, Tomasz Gambin, Michal Kadlof, Michał Denkiewicz, Dariusz Plewczynski, Hyun Jeong Kim, Gail Deutsch, Nahir Cortes-Santiago, Salmo Raskin, Paweł Stankiewicz\",\"doi\":\"10.1111/cge.70010\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Single nucleotide variants (SNVs) and copy-number variant (CNV) deletions involving TBX4 have been associated with pulmonary arterial hypertension, ischiocoxopodopatellar syndrome, and lethal lung developmental disorders (LLDDs). Thus far, all large CNV deletions encompassing entire TBX4 have been found to have arisen de novo. Here, we present a three-generation family with three neonate siblings who died within 35-66 days due to histopathologically diagnosed LLDD. Whole-genome sequencing identified an ~108-kb CNV deletion encompassing TBX4 in all three infants. The deletion was also found in their mother with a history of pneumonia and persistent thick upper airway secretions and in the maternal grandfather who had surgically corrected genu valgum. RT-qPCR from the proband's lung biopsy showed a decrease of TBX4 transcript level greater than 50%, suggesting additional deregulation of TBX4 expression. Computational analyses of the TBX4 super-enhancer identified 15 candidate noncoding hypomorphic SNVs transmitted to the children exclusively from their father and absent in their mother and maternal grandfather. We show that SNV rs35827636T > C, previously proposed as potentially hypomorphic in an unrelated AcDys patient, reduced transcriptional activity of the TBX4 promoter in an episomal reporter assay. Moreover, Hi-C analysis predicted inter-TAD interaction between the TBX4 super-enhancer and its promoter-proximal region. Our data further demonstrate complex compound inheritance of LLDDs and resulting challenges for genetic counseling.</p>\",\"PeriodicalId\":10354,\"journal\":{\"name\":\"Clinical Genetics\",\"volume\":\" \",\"pages\":\"\"},\"PeriodicalIF\":2.3000,\"publicationDate\":\"2025-06-21\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12269481/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Clinical Genetics\",\"FirstCategoryId\":\"3\",\"ListUrlMain\":\"https://doi.org/10.1111/cge.70010\",\"RegionNum\":3,\"RegionCategory\":\"医学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"GENETICS & HEREDITY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Clinical Genetics","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.1111/cge.70010","RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
Highly Variable Expressivity of a CNV Deletion Involving TBX4 in Three Deceased Siblings With Lung Developmental Disorder and Their Mildly Affected Mother and Grandfather.
Single nucleotide variants (SNVs) and copy-number variant (CNV) deletions involving TBX4 have been associated with pulmonary arterial hypertension, ischiocoxopodopatellar syndrome, and lethal lung developmental disorders (LLDDs). Thus far, all large CNV deletions encompassing entire TBX4 have been found to have arisen de novo. Here, we present a three-generation family with three neonate siblings who died within 35-66 days due to histopathologically diagnosed LLDD. Whole-genome sequencing identified an ~108-kb CNV deletion encompassing TBX4 in all three infants. The deletion was also found in their mother with a history of pneumonia and persistent thick upper airway secretions and in the maternal grandfather who had surgically corrected genu valgum. RT-qPCR from the proband's lung biopsy showed a decrease of TBX4 transcript level greater than 50%, suggesting additional deregulation of TBX4 expression. Computational analyses of the TBX4 super-enhancer identified 15 candidate noncoding hypomorphic SNVs transmitted to the children exclusively from their father and absent in their mother and maternal grandfather. We show that SNV rs35827636T > C, previously proposed as potentially hypomorphic in an unrelated AcDys patient, reduced transcriptional activity of the TBX4 promoter in an episomal reporter assay. Moreover, Hi-C analysis predicted inter-TAD interaction between the TBX4 super-enhancer and its promoter-proximal region. Our data further demonstrate complex compound inheritance of LLDDs and resulting challenges for genetic counseling.
期刊介绍:
Clinical Genetics links research to the clinic, translating advances in our understanding of the molecular basis of genetic disease for the practising clinical geneticist. The journal publishes high quality research papers, short reports, reviews and mini-reviews that connect medical genetics research with clinical practice.
Topics of particular interest are:
• Linking genetic variations to disease
• Genome rearrangements and disease
• Epigenetics and disease
• The translation of genotype to phenotype
• Genetics of complex disease
• Management/intervention of genetic diseases
• Novel therapies for genetic diseases
• Developmental biology, as it relates to clinical genetics
• Social science research on the psychological and behavioural aspects of living with or being at risk of genetic disease