A CRISPR/Cas9-Engineered <i>ARID1A</i> -Deficient Human Gastric Cancer Organoid Model Reveals Essential and Nonessential Modes of Oncogenic Transformation

Abstract

Mutations in <i>ARID1A</i> rank among the most common molecular aberrations in human cancer. However, oncogenic consequences of <i>ARID1A</i> mutation in human cells remain poorly defined due to lack of forward genetic models. Here, CRISPR/Cas9-mediated <i>ARID1A</i> knockout (KO) in primary <i>TP53^-/-</i> human gastric organoids induced morphologic dysplasia, tumorigenicity, and mucinous differentiation. Genetic WNT/β-catenin activation rescued mucinous differentiation, but not hyperproliferation, suggesting alternative pathways of <i>ARID1A</i> KO-mediated transformation. <i>ARID1A</i> mutation induced transcriptional regulatory modules characteristic of microsatellite instability and Epstein-Barr virus-associated subtype human gastric cancer, including <i>FOXM1</i>-associated mitotic genes and <i>BIRC5/</i>survivin. Convergently, high-throughput compound screening indicated selective vulnerability of <i>ARID1A</i>-deficient organoids to inhibition of BIRC5/survivin, functionally implicating this pathway as an essential mediator of <i>ARID1A</i> KO-dependent early-stage gastric tumorigenesis. Overall, we define distinct pathways downstream of oncogenic <i>ARID1A</i> mutation, with nonessential WNT-inhibited mucinous differentiation in parallel with essential transcriptional <i>FOXM1/BIRC5</i>-stimulated proliferation, illustrating the general utility of organoid-based forward genetic cancer analysis in human cells. SIGNIFICANCE: We establish the first human forward genetic modeling of a commonly mutated tumor suppressor gene, <i>ARID1A</i>. Our study integrates diverse modalities including CRISPR/Cas9 genome editing, organoid culture, systems biology, and small-molecule screening to derive novel insights into early transformation mechanisms of <i>ARID1A</i>-deficient gastric cancers.<i>See related commentary by Zafra and Dow, p. 1327</i>.<i>This article is highlighted in the In This Issue feature, p. 1307</i>.