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Supplementary Figure 1 from Whole-Genome and Transcriptional Analysis of Treatment-Emergent Small-Cell Neuroendocrine Prostate Cancer Demonstrates Intraclass Heterogeneity

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posted on 2023-04-03, 16:41 authored by Rahul R. Aggarwal, David A. Quigley, Jiaoti Huang, Li Zhang, Tomasz M. Beer, Matthew B. Rettig, Rob E. Reiter, Martin E. Gleave, George V. Thomas, Adam Foye, Denise Playdle, Paul Lloyd, Kim N. Chi, Christopher P. Evans, Primo N. Lara, Felix Y. Feng, Joshi J. Alumkal, Eric J. Small

Supplementary Figure 1. A gene set reported by Beltran and colleagues to distinguish adenocarcinoma and neuroendocrine tumors separated WGS t-SCNC and neuroendocrine samples, confirming the neuroendocrine phenotype of the t-SCNC samples.

Funding

U.S. Army Department of Defense Prostate Cancer Program

Prostate Cancer Foundation Special Challenge Award

Prostate Cancer Foundation Young Investigator Award

Pacific Northwest Prostate Cancer SPORE

NCI

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ARTICLE ABSTRACT

Therapeutic resistance in metastatic castration-resistant prostate cancer (mCRPC) can be accompanied by treatment-emergent small-cell neuroendocrine carcinoma (t-SCNC), a morphologically distinct subtype. We performed integrative whole-genome and -transcriptome analysis of mCRPC tumor biopsies including paired biopsies after progression, and multiple samples from the same individual. t-SCNC was significantly less likely to have amplification of AR or an intergenic AR-enhancer locus, and demonstrated lower expression of AR and its downstream transcriptional targets. Genomic and transcriptional hallmarks of t-SCNC included biallelic loss of RB1, elevated expression levels of CDKN2A and E2F1, and loss of expression of the AR and AR-responsive genes including TMPRSS2 and NKX3-1. We identified three tumors that converted from adenocarcinoma to t-SCNC and demonstrate spatial and temporal intrapatient heterogeneity of metastatic tumors harboring adenocarcinoma, t-SCNC, or mixed expression phenotypes, with implications for treatment strategies in which dual targeting of adenocarcinoma and t-SCNC phenotypes may be necessary. The t-SCNC phenotype is characterized by lack of AR enhancer gain and loss of RB1 function, and demonstrates both interindividual and intraindividual heterogeneity.Visual Overview: http://mcr.aacrjournals.org/content/molcanres/17/6/1235/F1.large.jpg.

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