Multiomic assessments of LNCaP and derived cell strains reveal determinants of prostate cancer pathobiology
Arnab Bose, Armand Bankhead III, Ilsa Coleman, Thomas Persse, Wanting Han, Patricia Galipeau, Brian Hanratty, Tony Chu, Jared Lucas, Dapei Li, Rabeya Bilkis, Pushpa Itagi, Sajida Hassan, Mallory Beightol, Minjeong Ko, Ruth Dumpit, Michael Haffner, Colin Pritchard, Gavin Ha, Peter S. Nelson
Arnab Bose, Armand Bankhead III, Ilsa Coleman, Thomas Persse, Wanting Han, Patricia Galipeau, Brian Hanratty, Tony Chu, Jared Lucas, Dapei Li, Rabeya Bilkis, Pushpa Itagi, Sajida Hassan, Mallory Beightol, Minjeong Ko, Ruth Dumpit, Michael Haffner, Colin Pritchard, Gavin Ha, Peter S. Nelson
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Research Article Cell biology Oncology

Multiomic assessments of LNCaP and derived cell strains reveal determinants of prostate cancer pathobiology

Abstract

A cornerstone of research to improve cancer outcomes involves studies of model systems to identify causal drivers of oncogenesis, understand mechanisms leading to metastases, and develop new therapeutics. Although most cancer types are represented by large cell line panels that reflect diverse neoplastic genotypes and phenotypes found in patients, prostate cancer is notable for a very limited repertoire of models that recapitulate the pathobiology of human disease. Of these, the lymph node carcinoma of the prostate (LNCaP) cell line has served as the major resource for basic and translational studies. Here, we delineated the molecular composition of LNCaP and multiple substrains through analyses of whole-genome sequences, transcriptomes, chromatin structure, androgen receptor (AR) cistromes, and functional studies. Our results determined that LNCaP exhibits substantial subclonal diversity, ongoing genomic instability, and phenotype plasticity. Several oncogenic features were consistently present across strains, but others were unexpectedly variable, such as ETV1 expression, Y chromosome loss, a reliance on WNT and glucocorticoid receptor activity, and distinct AR alterations maintaining AR pathway activation. These results document the inherent molecular heterogeneity and ongoing genomic instability that drive diverse prostate cancer phenotypes and provide a foundation for the accurate interpretation and reproduction of research findings.

Authors

Arnab Bose, Armand Bankhead III, Ilsa Coleman, Thomas Persse, Wanting Han, Patricia Galipeau, Brian Hanratty, Tony Chu, Jared Lucas, Dapei Li, Rabeya Bilkis, Pushpa Itagi, Sajida Hassan, Mallory Beightol, Minjeong Ko, Ruth Dumpit, Michael Haffner, Colin Pritchard, Gavin Ha, Peter S. Nelson

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Figure 5

Y chromosome and transcriptional heterogeneity within the LNCaP_FGC line.

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Y chromosome and transcriptional heterogeneity within the LNCaP_FGC line...
(A) Single-cell RNA-Seq (sc-RNA-Seq) UMAP of LNCaP_FGC cells where colors represent clusters identified using Seurat FindClusters with resolution set to 0.5. (B) scRNA-Seq UMAP of LNCaP_FGC where colors represent clusters defined by cell cycle phase: G1 (n = 883 cells), G2/M (n = 513cells), and S (n = 454 cells). (C) Cell cycle progression (CCP) signature score in LNCaP cells partitioned by cell cycle. Wilcoxon P values show significant differences between cells in phases of the cell cycle. (D) Androgen receptor (AR) activity score in LNCaP_FGC cells partitioned by cell cycle. AR scores quantified per cell by the average log-transformed count of AR signature genes with median counts greater than 0. Wilcoxon P values shown. (E and F) Volcano plot demonstrating genes differentially expressed in LNCaP_FGC cells in G1 (E) or S (F) versus cells in different phases of the cell cycle. Genes denoted by red color are significantly differentially expressed (log2 fold change > 0, q value < 0.05, G1 expressed > 50%). (G and H) sc-RNA-Seq UMAP of LNCaP_FGC cells following regression of cell cycle–associated effects with cells annotated by cycle phase (H). (I) sc-RNA-Seq UMAP of LNCaP_FGC highlighting ETV1 expression; 33% of cells lacked ETV1. (J) Volcano plot demonstrating genes differentially expressed in LNCaP_FGC cells assigned to cluster 5 versus other clusters from G. (K) Heatmap of transcript abundance of genes on the Y chromosome and signature scores. Genes with detectable expression in at least 1 sample are listed on the right side of the plot. (L and M) UMAP of (L) LNCaP_FGC and (M) LNCaP_C4-2B, where cells colored blue have negligible expression of all Y chromosome genes (≤ 1 read mapping to any Y chromosome gene, with a maximum of 5 total reads mapping to Y chromosome genes). Data were downsampled to be comparable (1,850 cells, 19,000 average reads). UMAP, uniform manifold approximation and projection.