Browsing by Author "Krantz, Ian"

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    Heterozygous loss-of-function SMC3 variants are associated with variable and incompletely penetrant growth and developmental features
    (medRxiv, 2023-09-28) Ansari, Morad; Faour, Kamli N. W.; Shimamura, Akiko; Grimes, Graeme; Kao, Emeline M.; Denhoff, Erica R.; Blatnik, Ana; Ben-Isvy, Daniel; Wang, Lily; Helm, Benjamin M.; Firth, Helen; Breman, Amy M.; Bijlsma, Emilia K.; Iwata-Otsubo, Aiko; de Ravel, Thomy J. L.; Fusaro, Vincent; Fryer, Alan; Nykamp, Keith; Stühn, Lara G.; Haack, Tobias B.; Korenke, G. Christoph; Constantinou, Panayiotis; Bujakowska, Kinga M.; Low, Karen J.; Place, Emily; Humberson, Jennifer; Napier, Melanie P.; Hoffman, Jessica; Juusola, Jane; Deardorff, Matthew A.; Shao, Wanqing; Rockowitz, Shira; Krantz, Ian; Kaur, Maninder; Raible, Sarah; Kliesch, Sabine; Singer-Berk, Moriel; Groopman, Emily; DiTroia, Stephanie; Ballal, Sonia; Srivastava, Siddharth; Rothfelder, Kathrin; Biskup, Saskia; Rzasa, Jessica; Kerkhof, Jennifer; McConkey, Haley; O'Donnell-Luria, Anne; Sadikovic, Bekim; Hilton, Sarah; Banka, Siddharth; Tüttelmann, Frank; Conrad, Donald; Talkowski, Michael E.; FitzPatrick, David R.; Boone, Philip M.; Medical and Molecular Genetics, School of Medicine
    Heterozygous missense variants and in-frame indels in SMC3 are a cause of Cornelia de Lange syndrome (CdLS), marked by intellectual disability, growth deficiency, and dysmorphism, via an apparent dominant-negative mechanism. However, the spectrum of manifestations associated with SMC3 loss-of-function variants has not been reported, leading to hypotheses of alternative phenotypes or even developmental lethality. We used matchmaking servers, patient registries, and other resources to identify individuals with heterozygous, predicted loss-of-function (pLoF) variants in SMC3, and analyzed population databases to characterize mutational intolerance in this gene. Here, we show that SMC3 behaves as an archetypal haploinsufficient gene: it is highly constrained against pLoF variants, strongly depleted for missense variants, and pLoF variants are associated with a range of developmental phenotypes. Among 13 individuals with SMC3 pLoF variants, phenotypes were variable but coalesced on low growth parameters, developmental delay/intellectual disability, and dysmorphism reminiscent of atypical CdLS. Comparisons to individuals with SMC3 missense/in-frame indel variants demonstrated a milder presentation in pLoF carriers. Furthermore, several individuals harboring pLoF variants in SMC3 were nonpenetrant for growth, developmental, and/or dysmorphic features, some instead having intriguing symptomatologies with rational biological links to SMC3 including bone marrow failure, acute myeloid leukemia, and Coats retinal vasculopathy. Analyses of transcriptomic and epigenetic data suggest that SMC3 pLoF variants reduce SMC3 expression but do not result in a blood DNA methylation signature clustering with that of CdLS, and that the global transcriptional signature of SMC3 loss is model-dependent. Our finding of substantial population-scale LoF intolerance in concert with variable penetrance in subjects with SMC3 pLoF variants expands the scope of cohesinopathies, informs on their allelic architecture, and suggests the existence of additional clearly LoF-constrained genes whose disease links will be confirmed only by multi-layered genomic data paired with careful phenotyping.
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    Heterozygous loss-of-function SMC3 variants are associated with variable growth and developmental features
    (Elsevier, 2024) Ansari, Morad; Faour, Kamli N. W.; Shimamura, Akiko; Grimes, Graeme; Kao, Emeline M.; Denhoff, Erica R.; Blatnik, Ana; Ben-Isvy, Daniel; Wang, Lily; Helm, Benjamin M.; Firth, Helen; Breman, Amy M.; Bijlsma, Emilia K.; Iwata-Otsubo, Aiko; de Ravel, Thomy J. L.; Fusaro, Vincent; Fryer, Alan; Nykamp, Keith; Stühn, Lara G.; Haack, Tobias B.; Korenke, G. Christoph; Constantinou, Panayiotis; Bujakowska, Kinga M.; Low, Karen J.; Place, Emily; Humberson, Jennifer; Napier, Melanie P.; Hoffman, Jessica; Juusola, Jane; Deardorff, Matthew A.; Shao, Wanqing; Rockowitz, Shira; Krantz, Ian; Kaur, Maninder; Raible, Sarah; Dortenzio, Victoria; Kliesch, Sabine; Singer-Berk, Moriel; Groopman, Emily; DiTroia, Stephanie; Ballal, Sonia; Srivastava, Siddharth; Rothfelder, Kathrin; Biskup, Saskia; Rzasa, Jessica; Kerkhof, Jennifer; McConkey, Haley; Sadikovic, Bekim; Hilton, Sarah; Banka, Siddharth; Tüttelmann, Frank; Conrad, Donald F.; O'Donnell-Luria, Anne; Talkowski, Michael E.; FitzPatrick, David R.; Boone, Philip M.; Medical and Molecular Genetics, School of Medicine
    Heterozygous missense variants and in-frame indels in SMC3 are a cause of Cornelia de Lange syndrome (CdLS), marked by intellectual disability, growth deficiency, and dysmorphism, via an apparent dominant-negative mechanism. However, the spectrum of manifestations associated with SMC3 loss-of-function variants has not been reported, leading to hypotheses of alternative phenotypes or even developmental lethality. We used matchmaking servers, patient registries, and other resources to identify individuals with heterozygous, predicted loss-of-function (pLoF) variants in SMC3, and analyzed population databases to characterize mutational intolerance in this gene. Here, we show that SMC3 behaves as an archetypal haploinsufficient gene: it is highly constrained against pLoF variants, strongly depleted for missense variants, and pLoF variants are associated with a range of developmental phenotypes. Among 14 individuals with SMC3 pLoF variants, phenotypes were variable but coalesced on low growth parameters, developmental delay/intellectual disability, and dysmorphism, reminiscent of atypical CdLS. Comparisons to individuals with SMC3 missense/in-frame indel variants demonstrated an overall milder presentation in pLoF carriers. Furthermore, several individuals harboring pLoF variants in SMC3 were nonpenetrant for growth, developmental, and/or dysmorphic features, and some had alternative symptomatologies with rational biological links to SMC3. Analyses of tumor and model system transcriptomic data and epigenetic data in a subset of cases suggest that SMC3 pLoF variants reduce SMC3 expression but do not strongly support clustering with functional genomic signatures of typical CdLS. Our finding of substantial population-scale LoF intolerance in concert with variable growth and developmental features in subjects with SMC3 pLoF variants expands the scope of cohesinopathies, informs on their allelic architecture, and suggests the existence of additional clearly LoF-constrained genes whose disease links will be confirmed only by multilayered genomic data paired with careful phenotyping.
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    HNRNPC haploinsufficiency affects alternative splicing of intellectual disability-associated genes and causes a neurodevelopmental disorder
    (Elsevier, 2023) Niggl, Eva; Bouman, Arjan; Briere, Lauren C.; Hoogenboezem, Remco M.; Wallaard, Ilse; Park, Joohyun; Admard, Jakob; Wilke, Martina; Harris-Mostert, Emilio D. R. O.; Elgersma, Minetta; Bain, Jennifer; Balasubramanian, Meena; Banka, Siddharth; Benke, Paul J.; Bertrand, Miriam; Blesson, Alyssa E.; Clayton-Smith, Jill; Ellingford, Jamie M.; Gillentine, Madelyn A.; Goodloe, Dana H.; Haack, Tobias B.; Jain, Mahim; Krantz, Ian; Luu, Sharon M.; McPheron, Molly; Muss, Candace L.; Raible, Sarah E.; Robin, Nathaniel H.; Spiller, Michael; Starling, Susan; Sweetser, David A.; Thiffault, Isabelle; Vetrini, Francesco; Witt, Dennis; Woods, Emily; Zhou, Dihong; Genomics England Research Consortium; Undiagnosed Diseases Network; Elgersma, Ype; van Esbroeck, Annelot C. M.; Medical and Molecular Genetics, School of Medicine
    Heterogeneous nuclear ribonucleoprotein C (HNRNPC) is an essential, ubiquitously abundant protein involved in mRNA processing. Genetic variants in other members of the HNRNP family have been associated with neurodevelopmental disorders. Here, we describe 13 individuals with global developmental delay, intellectual disability, behavioral abnormalities, and subtle facial dysmorphology with heterozygous HNRNPC germline variants. Five of them bear an identical in-frame deletion of nine amino acids in the extreme C terminus. To study the effect of this recurrent variant as well as HNRNPC haploinsufficiency, we used induced pluripotent stem cells (iPSCs) and fibroblasts obtained from affected individuals. While protein localization and oligomerization were unaffected by the recurrent C-terminal deletion variant, total HNRNPC levels were decreased. Previously, reduced HNRNPC levels have been associated with changes in alternative splicing. Therefore, we performed a meta-analysis on published RNA-seq datasets of three different cell lines to identify a ubiquitous HNRNPC-dependent signature of alternative spliced exons. The identified signature was not only confirmed in fibroblasts obtained from an affected individual but also showed a significant enrichment for genes associated with intellectual disability. Hence, we assessed the effect of decreased and increased levels of HNRNPC on neuronal arborization and neuronal migration and found that either condition affects neuronal function. Taken together, our data indicate that HNRNPC haploinsufficiency affects alternative splicing of multiple intellectual disability-associated genes and that the developing brain is sensitive to aberrant levels of HNRNPC. Hence, our data strongly support the inclusion of HNRNPC to the family of HNRNP-related neurodevelopmental disorders.