American Association for Cancer Research
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Supplementary Figure S1-10 from Single-Cell RNA-seq Reveals a Subpopulation of Prostate Cancer Cells with Enhanced Cell-Cycle–Related Transcription and Attenuated Androgen Response

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posted on 2023-03-31, 01:20 authored by Aaron M. Horning, Yao Wang, Che-Kuang Lin, Anna D. Louie, Rohit R. Jadhav, Chia-Nung Hung, Chiou-Miin Wang, Chun-Lin Lin, Nameer B. Kirma, Michael A. Liss, Addanki P. Kumar, LuZhe Sun, Zhijie Liu, Wei-Ting Chao, Qianben Wang, Victor X. Jin, Chun-Liang Chen, Tim H.-M. Huang

Supplementary Figure S1: Time-course expression analysis of LNCaP cells reveals dynamic and heterogeneous responses to androgen stimulation. Supplementary Figure S2: Cell cycle progression of LNCaP cells treated with or without R1881 after cell synchronization by double thymidine block (DTB). Supplementary Figure S3: The summary of aligned and unaligned single-cell RNA-seq reads counts. Supplementary Figure S4: Correlation of single-cell RNA-seq ensemble reads with representative bulk RNA-seq reads. Supplementary Figure S5: Venn diagrams illustrating the comparison of differentially expressed genes found in single- and bulk-cell LNCaP experiments. Supplementary Figure S6: The Mclust algorithm defines likely subgroups using a "model-based" approach. Supplementary Figure S7: Each cell within each subcluster exhibits a similar gene expression profile. Supplementary Figure S8: Gleason score and biochemical recurrence status compared to each subcluster''s gene expression profile. Supplementary Figure S9: Differential expression of 10 genes in LNCaP''s 8.1 subpopulation of cells. Supplementary Figure S10: High single-cell expression of 10 genes in PC3 similar to 12hr-R1881 LNCaP cells.

Funding

NIH

CPRIT

Cancer Therapy and Research Center Foundation

Max and Minnie Tomerlin Voelcker Fund

Alice P. McDermott Endowment

Cancer Biology Training Program

National Cancer Institute

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ARTICLE 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 G2–M arrest induced by a mitosis inhibitor. Advanced growth of this subpopulation was associated with enhanced expression of 10 cell-cycle–related genes (CCNB2, DLGAP5, CENPF, CENPE, MKI67, PTTG1, CDC20, PLK1, HMMR, and CCNB1) and decreased dependence upon androgen receptor signaling. In silico 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.Significance: 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. Cancer Res; 78(4); 853–64. ©2017 AACR.