Single-cell RNA-seq reveals a subpopulation of prostate cancer cells with enhanced cell cycle-related transcription and attenuated androgen response

Increasing evidence indicates that minor subpopulations intrinsic to androgen-independence are present in prostate cancer cells, poised to become clonal dominance under prolonged androgen-deprivation selection. To stratify different subpopulations, we conduct transcriptome profiling of 144 single LNCaP prostate cancer cells treated and untreated with androgen after cell cycle synchronization. At least eight subpopulations of LNCaP cells are identified, revealing a previously unappreciable level of cellular heterogeneity to androgen stimulation. One subpopulation displays stem-like features, the advanced growth of which depends more on enhanced expression of 10 cell cycle-related genes and less on androgen-dependent signaling. Concordant upregulation of these genes appears to be linked to recurrent prostate cancers and can be used for early detection of tumors that subsequently develop androgen independence. Moreover, this single-cell approach provides a better understanding of how cancer cells respond heterogeneously to androgen-deprivation therapies and to reveal which subpopulations are resistant to this treatment. For each of 3 treatment groups, forty eight LNCaP single cells and 1 representative bulk cell RNA sample (1ng) were collected for SMART-seq2 amplification and later single-cell RNA-seq (total 144 single cells and 3 bulk cell samples). All of the treatment groups were harvested from after synchronizing the cells at the G1/S phase with a double thymidine block and androgen depriving the cells for ~24 hours. Treatment groups 2 and 3 were cultured in the absence and presence of androgen (1 nM R1881) for 12 hours, respectively. Treatment group 1 was a baseline comparison treatment group and was collected right after cell synchronization and androgen deprivation (considered 0 hour).