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Long-read single-cell RNA transcriptomics reveals a signature of PIK3CA mutation in a human capillary malformation

ABSTRACT: PIK3CA-related overgrowth syndromes (PROS) are caused by somatic variants that result in constitutive activation of the phosphatidylinositol-3-kinase/AKT/mTOR pathway. Promising responses to molecularly targeted therapy have been reported, however identification of an appropriate agent can be hampered by the mosaic nature and low variant allele frequency of the causal variant. Moreover, our understanding of the molecular repercussions of these variants at the single cell level remain limited. Here we report in vitro expansion of affected tissue followed by exome sequencing and combined 3’ whole transcriptome and targeted long-read single cell RNA-sequencing in a patient with clinical symptoms consistent with Megalencephaly-Capillary Malformation Syndrome (MCAP, a PROS condition). This approach identified a targetable PIK3CA variant restricted to a PAX3+ fibroblast population. These studies highlight the utility of novel next-generation sequencing strategies in the management of suspected syndromes of somatic mosaicism and provide insight into the underlying pathophysiology of a debilitating genetic syndrome.

ORGANISM(S): Homo sapiens

PROVIDER: GSE253153 | GEO | 2024/07/19

REPOSITORIES: GEO

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Isogenic patient-derived human iPSCs, wild-type or heterozygous for PIK3CA-E418K

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Immune-interacting lymphatic endothelial subtype at capillary terminals drives lymphatic malformation

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The microcephaly-capillary malformation syndrome.

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High-dose oncogenic PIK3CA drives constitutive cellular stemness through increased NODAL/TGFb signaling

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2021-03-03 | PXD014719 | Pride

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Project description:Genome-directed oncology has the potential to revolutionize patient treatment, but is limited by an abundance of rare, uncharacterized and therapeutically uninformative somatic variants. To accelerate characterization of the “long tail” of rare somatic variants, we quantified the activity and drug responsiveness of virtually all possible (99.84%) missense variants in the Ser/Thr kinase MAPK1/ERK2. We identified recurrent and rare hypermorphic and loss-of-function alleles, revealing that variant activity is uncorrelated with mutational frequency. Somatic ERK2 variants displayed variable responses to RAF-, MEK- and ERK-directed therapies, potentially informing clinical treatment strategies for patients whose tumors harbor these alterations. A subset of recurrent and rare somatic variants co-localized on ERK2 protein-protein interfaces, yet engendered contrasting phenotypes based on their specific sub-domain localization. The approach presented here represents an allele-characterization framework that compliments existing computational efforts and supports current and future somatic variant discovery efforts, advancing the promise of genome-guided treatment strategies.

2017-12-01 | GSE79989 | GEO

Capillary malformation-arteriovenous malformation, a new clinical and genetic disorder caused by RASA1 mutations.

Project description:Capillary malformation (CM), or "port-wine stain," is a common cutaneous vascular anomaly that initially appears as a red macular stain that darkens over years. CM also occurs in several combined vascular anomalies that exhibit hypertrophy, such as Sturge-Weber syndrome, Klippel-Trenaunay syndrome, and Parkes Weber syndrome. Occasional familial segregation of CM suggests that there is genetic susceptibility, underscored by the identification of a large locus, CMC1, on chromosome 5q. We used genetic fine mapping with polymorphic markers to reduce the size of the CMC1 locus. A positional candidate gene, RASA1, encoding p120-RasGAP, was screened for mutations in 17 families. Heterozygous inactivating RASA1 mutations were detected in six families manifesting atypical CMs that were multiple, small, round to oval in shape, and pinkish red in color. In addition to CM, either arteriovenous malformation, arteriovenous fistula, or Parkes Weber syndrome was documented in all the families with a mutation. We named this newly identified association caused by RASA1 mutations "CM-AVM," for capillary malformation-arteriovenous malformation. The phenotypic variability can be explained by the involvement of p120-RasGAP in signaling for various growth factor receptors that control proliferation, migration, and survival of several cell types, including vascular endothelial cells.

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Patients with a Kabuki syndrome phenotype demonstrate DNA methylation abnormalities.

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2018-06-27 | GSE116300 | GEO

Diffuse capillary malformation with overgrowth contains somatic PIK3CA variants.

Project description:Diffuse capillary malformation with overgrowth (DCMO) is a clinical diagnosis describing patients with multiple, extensive capillary malformations (CMs) associated with overgrowth and foot anomalies. The purpose of the study was to identify somatic variants in DCMO. Skin containing CM and overgrown subcutaneous adipose tissue was collected from patients with DCMO. Exons from 447 cancer-related genes were sequenced using OncoPanel. Variant-specific droplet digital PCR (ddPCR) independently confirmed the variants and determined variant allele frequencies (VAF). One subject contained a somatic PIK3CA p.G106V variant. A second patient had a PIK3CA p.D350G variant. VAF was 27% to 29% in skin and 16% to 28% in subcutaneous adipose. Variants were enriched in endothelial cells (VAF 50%-51%) compared to nonendothelial cells (1%-8%). DCMO is associated with somatic PIK3CA variants and should be considered on the PIK3CA-related overgrowth spectrum (PROS). Variants are present in both skin and subcutaneous adipose and are enriched in endothelial cells.

| S-EPMC8128061 | biostudies-literature

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