Single-Cell RNA-seq Reveals a Subpopulation of Prostate Cancer Cells with Enhanced Cell-Cycle–Related Transcription and Attenuated Androgen Response

Abstract

Increasing evidence suggests the presence of minor cell subpopulations in prostate cancer that are androgen independent and poised for selection as dominant clones after androgen deprivation therapy. In this study, we investigated this phenomenon by stratifying cell subpopulations based on transcriptome profiling of 144 single LNCaP prostate cancer cells treated or untreated with androgen after cell-cycle synchronization. Model-based clustering of 397 differentially expressed genes identified eight potential subpopulations of LNCaP cells, revealing a previously unappreciable level of cellular heterogeneity to androgen stimulation. One subpopulation displayed stem-like features with a slower cell doubling rate, increased sphere formation capability, and resistance to G-M arrest induced by a mitosis inhibitor. Advanced growth of this subpopulation was associated with enhanced expression of 10 cell-cycle-related genes (, and ) and decreased dependence upon androgen receptor signaling. analysis of RNA-seq data from The Cancer Genome Atlas further demonstrated that concordant upregulation of these genes was linked to recurrent prostate cancers. Analysis of receiver operating characteristic curves implicates aberrant expression of these genes and could be useful for early identification of tumors that subsequently develop biochemical recurrence. Moreover, this single-cell approach provides a better understanding of how prostate cancer cells respond heterogeneously to androgen deprivation therapies and reveals characteristics of subpopulations resistant to this treatment. Illustrating the challenge in treating cancers with targeted drugs, which by selecting for drug resistance can drive metastatic progression, this study characterized the plasticity and heterogeneity of prostate cancer cells with regard to androgen dependence, defining the character or minor subpopulations of androgen-independent cells that are poised for clonal selection after androgen-deprivation therapy. .

Epigenetic analysis identifies factors driving racial disparity in prostate cancer

“…Several studies had reported association of interleukin signaling and inflammation to be more prevalent in AA and over‐activation of PI3K/AKT pathway in AA men compared with CA men . Furthermore, we found cell cycle signaling was downregulated in AAs in line with a recent study that reported enhanced cell cycle‐related transcription in specific subpopulation of CA derived PCa cell‐line . Finally, amino‐acid metabolism pathways were observed to be associated with genes upregulated in CA men (MC3), which was in line with previously reported study that showed higher amino acid metabolism in CA derived PCa cell lines treated with androgens …”

“…Several studies had reported association of interleukin signaling and inflammation to be more prevalent in AA 17,52 and over-activation of PI3K/AKT pathway in AA men compared with CA men. 53 Furthermore, we found cell cycle signaling was downregulated in AAs in line with a recent study that 54 Finally, amino-acid metabolism pathways were observed to be associated with genes upregulated in CA men (MC3), which was in line with previously reported study that showed higher amino acid metabolism in CA derived PCa cell lines treated with androgens. 55 To establish a premise for a larger study in the future, we carried out a pilot RRBS study using a small cohort of PCa tumors derived from AA (three samples) and CA men (three samples).…”

Epigenetic analysis identifies factors driving racial disparity in prostate cancer

“…Our observations are similar to these findings. Furthermore, we found cell cycle signaling was downregulated in AAs whereas a recent study shows enhanced cell cycle related transcription in specific subpopulation of CA derived prostate cancer cell-line [50]. Finally, similar to our observation of amino-acid metabolism to be associated with CA, Putluri et al, 2011 reported higher amino acid metabolism in CA derived prostate cancer cell lines treated with androgens [51].…”

Gene expression profiles define molecular subtypes of prostate cancer bone metastases with different outcomes and morphology traceable back to the primary tumor

“…In the current study, approximately 13% of the samples showed an intermediate subtype with characteristics of both MetA and MetB, and in the validation cohort (Quigley et al, 2018), this was observed in about 14%. In the LNCaP cell line, single-cell sequencing has demonstrated the existence of multiple subclones where some appear similar to MetA, whereas others are more MetB-like with high cell proliferation and reduced androgen dependency (Horning et al, 2018). Collectively, this suggests that the luminal-derived MetA subtype may be able to dedifferentiate in to the more aggressive MetB subtype, possibly driven by altered AR-activity.…”