# Generating hiPSC-derived ATRT models to investigate cell of origin and identify therapeutic vulnerabilities

> **NIH NIH F31** · UNIVERSITY OF CALIFORNIA, SAN DIEGO · 2024 · $41,755

## Abstract

Project Summary
Atypical teratoid rhabdoid tumors (ATRTs) are aggressive pediatric brain cancers that lack standardized
treatment regimens. After radiotherapy treatments, survivors suffer from long-term neurocognitive defects. Thus,
there is a critical need for dissecting the underlying biology of ATRTs to identify novel therapeutic strategies.
ATRTs are driven by a differentiation block caused by biallelic inactivation of SMARCB1 with no other recurrent
mutations, resulting in dysregulated cells that fail to terminally differentiate and consequently acquire oncogenic
states. Naturally, neural progenitor cells (NPCs) are suspected to be the cells of origin for ATRTs, as their stalled
differentiation has been implicated in pediatric brain tumorigenesis. However, ATRTs present unique features
that imply a cell of origin that is not restricted to the central nervous system (CNS). Despite being driven by only
SMARCB1 loss, ATRTs are comprised of three molecular subgroups, with different clinical outcomes, of which
only one displays neural features: ATRT-Sonic hedgehog (SHH). Furthermore, ATRTs are molecularly identical
to extracranial malignant rhabdoid tumors (MRTs). As a potential explanation for these nonneural features, the
neural crest cell (NCC) is a putative cell of origin for both ATRTs and extracranial MRTs, as it emerges from the
neuroectoderm but then migrates throughout the embryo. Therefore, the hypotheses of this proposal are that
SMARCB1 loss interacts with cell identity and anatomical location during tumorigenesis, and that there are
targetable vulnerabilities that can enable SMARCB1-depleted cells to overcome their differentiation block.
Previously, the Furnari lab engineered human induced pluripotent stem cells (hiPSCs) with DOX-inducible
SMARCB1 knockdown (KD hiPSCs). NPCs derived from these hiPSCs, that were differentiated without
SMARCB1 expression (KD NPCs), exhibited an ATRT-SHH transcriptome, presented a block in neuronal
differentiation, and formed orthotopic tumors. This hiPSC-derived SMARCB1 knockdown platform will be
leveraged to investigate the hypotheses of this proposal. To unveil interactions between cell identity and
SMARCB1 loss, RNAseq analyses will be performed on hiPSCs that were differentiated, with or without
SMARCB1 expression, into NPCs and NCCs. To characterize interactions between anatomical location and
SMARCB1 loss during tumorigenesis, KD NPCs and NCCs will be engrafted intracranially and subcutaneously.
Resulting tumors will be analyzed via RNAseq. Since KD NPCs are unable to differentiate further into NCAM+
neurons, a high-throughput, pooled CRISPR screen will be performed on KD NPCs to identify targetable
vulnerabilities that can overcome their differentiation block. Candidate genes will be validated in vitro via IPTG
inducible knockdown and drug treatment studies, followed by in vivo validation by treating orthotopically
engrafted KD NPC brain tumors with candidate drugs. If successful, this proposal ...

## Key facts

- **NIH application ID:** 10996034
- **Project number:** 1F31CA294873-01
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN DIEGO
- **Principal Investigator:** Clark Gold Wang
- **Activity code:** F31 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $41,755
- **Award type:** 1
- **Project period:** 2024-07-01 → 2026-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10996034

## Citation

> US National Institutes of Health, RePORTER application 10996034, Generating hiPSC-derived ATRT models to investigate cell of origin and identify therapeutic vulnerabilities (1F31CA294873-01). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10996034. Licensed CC0.

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