# Organoid-based Discovery of Oncogenic Drivers and Treatment Resistance Mechanisms

> **NIH NIH U01** · STANFORD UNIVERSITY · 2020 · $946,509

## Abstract

PROJECT SUMMARY/ABSTRACT
The deluge of multi-scale “omics” data from The Cancer Genome Atlas Project (TCGA)
and other cancer profiling projects has revealed remarkable genetic and epigenetic
complexity and tremendous intrapatient variation. Accordingly, a particularly acute need
exists for accurate, scalable human cancer models that can functionally interrogate
these extensive datasets, identify driver oncogenic events from benign passengers and
characterize their relevance to treatment response.
 For the last four years the Stanford Cancer Target Discovery and Development
(CTD2) Center has pursued human “organoid” culture methods for cancer modeling and
driver oncogene discovery. Primary 3D organoid cultures afford the unusual opportunity
to initiate cancer de novo within the epi/genetic “tabula rasa” of cultured primary human
wild-type tissue, versus the corresponding and often poorly-defined complexity of long-
passaged 2D cancer cell lines. This creates a highly defined baseline for cancer
modeling and functional driver oncogene validation that is leveraged throughout.
 Our overall approach applies state-of-the-art systems biology and robust
computational resources to large-scale cancer profiling datasets, thus nominating
candidate drivers that undergo direct functional evaluation in human organoid culture.
This experimental scope leverages a highly synergistic team of Calvin Kuo (reporting PI,
organoids), Hanlee Ji (multi-PI, cancer ITH, genomics), Christina Curtis (multi-PI, tumor
evolution, cancer systems biology), Olivier Gevaert (cancer systems biology,
epigenetics) and Michael Bassik (high-throughput functional genomics). Accordingly,
Aims 1 and 2 couple bioinformatic prioritization of TCGA copy number alteration (CNA)
and methylation data for driver discovery via organoid-based barcoded lentiviral screens
and orthogonal cDNA, shRNA and CRISPR approaches. Aim 3 exploits the ability to
longitudinally observe de novo genomic and epigenomic evolution in oncogene-
engineered wild-type organoids to nominate networks of cooperating oncogenes that
undergo iterative organoid functional validation. Lastly, Aim 4 explores the utility of
organoids to model de novo treatment resistance, using archetypal targeted and
chemotherapy perturbagens as proof-of-principle and employing single cell RNA-
seq/intratumoral heterogeneity and exome sequencing endpoints.

## Key facts

- **NIH application ID:** 10009281
- **Project number:** 5U01CA217851-04
- **Recipient organization:** STANFORD UNIVERSITY
- **Principal Investigator:** Christina N Curtis
- **Activity code:** U01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $946,509
- **Award type:** 5
- **Project period:** 2017-09-01 → 2022-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10009281

## Citation

> US National Institutes of Health, RePORTER application 10009281, Organoid-based Discovery of Oncogenic Drivers and Treatment Resistance Mechanisms (5U01CA217851-04). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10009281. Licensed CC0.

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