bioRxiv : the preprint server for biologyMay 18, 2026

Key weaknesses in diverse patient-derived prostate cancer models identified using single-cell analysis and gene editing

CRISPR Gene Editing Weekly Brief ↗PubMed ↗DOI ↗

Updated Jun 27, 2026

Abstract

Essence

Single-cell multiomics plus CRISPR screening can reveal lineage-specific vulnerabilities in heterogeneous prostate cancer organoids.

Evidence

Patient-derived organoid resource and functional-genomics study profiled more than 190,000 cells across 22 CRPC and NEPC organoids and coupled the atlas to subtype-resolved pooled CRISPR-Cas9 screens.

Caveat

The target dependencies, including AHR in a hybrid stem-like/ASCL1 population, are derived from 3D human tumor models rather than clinical treatment outcomes.

Simplified

Lineage plasticity and tumor heterogeneity limit the effectiveness of targeted therapies, yet the functional dependencies used to nominate therapeutic targets are often derived from homogeneous systems that fail to capture this complexity. Here, we establish a framework to resolve state-specific genetic vulnerabilities by integrating single-cell multiomics (RNA and ATAC) with pooled CRISPR-Cas9 screening across a large panel of patient-derived organoids (PDOs) from castrate-resistant prostate cancer (CRPC) and neuroendocrine prostate cancer (NEPC). We generate a single-cell multiome atlas spanning >190,000 cells across 22 PDOs, defining seven lineage states-including intermediate and plastic populations not resolved by bulk profiling-and demonstrate that these lineage programs robustly classify independent transcriptomic datasets from prostate cancer patient tumors. By systematically coupling this atlas to subtype-resolved CRISPR screens, we construct a functional dependency map linking cell state in heterogeneous 3D human tumor models. We show that intratumoral heterogeneity fundamentally reshapes the interpretation of gene essentiality, whereby gene-level depletion reflects the composite behavior of co-existing subpopulations, and identify a general principle in which resistant "limiting" populations disproportionately determine aggregate fitness effects. This framework reveals both canonical and previously unrecognized lineage-restricted dependencies within highly plastic tumor and NEPC states, including a therapeutically targetable dependency on the aryl hydrocarbon receptor (AHR) in a novel hybrid stem-like/ASCL1 population. Together, these data establish an extensive multi-dimensional prostate cancer resource, identify novel lineage-resolved biology, and provide a generalizable strategy for interpreting functional genomics in heterogeneous human tumors.

Funding

Competing interests

Competing Interests. S.Z consults for Guidepoint and Gerson Lehram Group. C.L.S. is a cofounder of ORIC Pharmaceuticals and is a co-inventor of the prostate cancer drugs enzalutamide and apalutamide, covered by US patents 7,709,517; 8,183,274; 9,126,941; 8,445,507; 8,802,689; and 9,388,159 filed by the University of California. C.L.S. is on the scientific advisory boards for the following biotechnology companies: Beigene, Blueprint Medicines, Column Group, Foghorn, Housey Pharma, Nextech, PMV Pharma and ORIC.

PubMed