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Defining the transcriptome of PIK3CA-altered cells in a human capillary malformation using single cell long-read

Michelle A Wedemeyer1,2,3,4, Tianli Ding1, Elizabeth A R Garfinkle1

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|October 25, 2024
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Summary

PIK3CA-related overgrowth spectrum disorders involve PIK3CA gene variants. This study used advanced single-cell sequencing to identify a targetable PIK3CA variant in Megalencephaly-Capillary Malformation Syndrome, revealing its specific cellular expression.

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Area of Science:

  • Genetics and Molecular Biology
  • Developmental Biology
  • Medical Genetics

Background:

  • PIK3CA-related overgrowth spectrum (PROS) disorders stem from somatic mosaic PIK3CA variants activating the PI3K/AKT/mTOR pathway.
  • Targeted therapy shows promise for PROS, but mosaicism complicates variant identification and treatment selection.
  • Understanding the molecular effects, including gene expression changes, of these variants is crucial.

Purpose of the Study:

  • To characterize the molecular basis of Megalencephaly-Capillary Malformation Syndrome (MCAP), a PROS condition.
  • To identify targetable genetic variants and their cellular expression patterns in MCAP.
  • To explore the utility of advanced single-cell sequencing techniques in understanding PROS disorders.

Main Methods:

  • In vitro expansion of human capillary malformation tissue from an MCAP patient.
  • Exome sequencing to identify genetic variants.
  • Single-cell RNA-sequencing (scRNA-seq) and targeted long-read scRNA-seq for transcriptomic profiling.
  • Analysis of gene expression in specific cell populations.

Main Results:

  • A targetable PIK3CA variant was identified in the MCAP patient.
  • The PIK3CA variant expression was found to be restricted to PAX3+ fibroblast and undifferentiated keratinocyte populations.
  • Single-cell sequencing methods revealed unique transcriptomic profiles and cell types associated with MCAP.

Conclusions:

  • Next-generation single-cell sequencing effectively elucidates transcriptomic profiles and cell types in MCAP.
  • This approach aids in understanding the molecular intricacies of PROS conditions.
  • Identifying specific cellular expression of targetable variants like PIK3CA is vital for advancing precision medicine in MCAP and other PROS disorders.