# Genotype-informed single cell transcriptomic profiling of mosaic brain tissue

> **NIH NIH R21** · UNIV OF NORTH CAROLINA CHAPEL HILL · 2024 · $268,410

## Abstract

Somatic variants that arise during embryonic corticogenesis and result in brain mosaicism are increasingly
recognized as significant contributors to the genetic risk of neurodevelopmental and neuropsychiatric conditions.
The discovery of disease-causing somatic variants in the brain has not only contributed to the identification of
novel genes and refined our understanding of the underlying genetic architecture of a range of neuropsychiatric
diseases, but they also provide powerful research tools that can be used to understand how cell-type-specific
changes contribute to disease pathophysiology. In this study, we seek to use single-cell genomic approaches in
mosaic human brain tissue to establish which cell types harbor the disease-causing somatic variants and to
determine cell-type-specific transcriptomic changes associated with the variant. While single-cell genomics
approaches have been used to inform many novel aspects of pathophysiology across a range of diseases, no
studies to our knowledge consider genotype and use deep single-cell RNA sequencing to study variant-
associated transcriptomic changes in specific cell types from mosaic human brain tissue. Here, we propose to
perform a proof-of-concept study to establish the extent to which genotype-informed comprehensive single-cell
RNA sequencing of mosaic human brain tissue is reproducible and can inform novel aspects of disease
pathophysiology. We will accomplish this goal using hemimegalencephaly, a severe brain malformation causing
overgrowth of one cerebral hemisphere that is caused by a single highly penetrant, brain tissue-specific somatic
variant in either AKT3, MTOR, or PIK3CA, as our prototype. We will isolate both DNA and RNA from single nuclei
from therapeutically resected mosaic brain tissue of each individual, genotype the DNA to classify each isolated
cell as variant-positive or variant-negative, and then perform RNA sequencing to determine cell-type-specific
variant burden and define the transcriptomic changes associated with the variant in specific cell types. We will
analyze three individuals with genetically diagnosed hemimegalencephaly caused by the same pathogenic
somatic variant for each of the three known disease genes to allow for comparisons across individuals and
genes. Comparisons of variant-positive to variant-negative cells in hemimegalencephaly cases, along with
variant-negative cells from age-matched neurotypical control brain tissue, within like cell types, will allow us to
identify cell type-specific cell-autonomous and non-cell-autonomous transcriptomic changes associated with the
variant. We hypothesize that these studies will reveal reproducible convergent and divergent cell-type-specific
disease mechanisms across individuals with the same pathogenic variants and across genes implicated in the
same brain malformation. If successful, we will establish a powerful research approach that leverages somatic
mosaicism to inform cell types involved in disease, iden...

## Key facts

- **NIH application ID:** 10904476
- **Project number:** 1R21NS133873-01A1
- **Recipient organization:** UNIV OF NORTH CAROLINA CHAPEL HILL
- **Principal Investigator:** Erin L HEINZEN
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $268,410
- **Award type:** 1
- **Project period:** 2024-06-01 → 2026-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10904476

## Citation

> US National Institutes of Health, RePORTER application 10904476, Genotype-informed single cell transcriptomic profiling of mosaic brain tissue (1R21NS133873-01A1). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10904476. Licensed CC0.

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