Keratin Profiling by Single-Cell RNA-Sequencing Identifies Human Prostate Stem Cell Lineage Hierarchy and Cancer Stem-Like Cells

Abstract

Single prostate stem cells can generate stem and progenitor cells to form prostaspheres in 3D culture. Using a prostasphere-based label retention assay, we recently identified keratin 13 (KRT13)-enriched prostate stem cells at single-cell resolution, distinguishing them from daughter progenitors. Herein, we characterized the epithelial cell lineage hierarchy in prostaspheres using single-cell RNA-seq analysis. Keratin profiling revealed three clusters of label-retaining prostate stem cells; cluster I represents quiescent stem cells (PSCA, CD36, SPINK1, and KRT13/23/80/78/4 enriched), while clusters II and III represent active stem and bipotent progenitor cells (KRT16/17/6 enriched). Gene set enrichment analysis revealed enrichment of stem and cancer-related pathways in cluster I. In non-label-retaining daughter progenitor cells, three clusters were identified; cluster IV represents basal progenitors (KRT5/14/6/16 enriched), while clusters V and VI represent early and late-stage luminal progenitors, respectively (KRT8/18/10 enriched). Furthermore, MetaCore analysis showed enrichment of the “cytoskeleton remodeling–keratin filaments” pathway in cancer stem-like cells from human prostate cancer specimens. Along with common keratins (KRT13/23/80/78/4) in normal stem cells, unique keratins (KRT10/19/6C/16) were enriched in cancer stem-like cells. Clarification of these keratin profiles in human prostate stem cell lineage hierarchy and cancer stem-like cells can facilitate the identification and therapeutic targeting of prostate cancer stem-like cells.

Single-Cell Transcriptome Analysis Identifies Subclusters with Inflammatory Fibroblast Responses in Localized Scleroderma

“…Other cells were also clustered using known markers, as follows: keratinocytes were identified by cell cluster expression of KRT1 [ 26 ], KRT14 [ 27 ], and KRT5 [ 28 ]; pericytes [ 29 ] by RGS5, CSPG4, and PDGFRB; T cells by CD3D [ 30 ], CD3E, CD8A, and CD4 [ 31 ]; macrophages by CD163 [ 32 ] and AIF1 [ 33 ]; dendritic cells (DCs) [ 34 ] by CD1C and FCER1A; natural killer (NK) cells by NKG7 [ 35 ]; melanocytes by PMEL [ 36 ]; B cells by IGJ and MS4A1 [ 37 ]; mast cells by TPSAB1 [ 38 ]; eccrine cells by AQP5 [ 39 ] and DCD [ 30 ]; and endothelial and lymphatic endothelial cells by ACKR1 [ 30 ] and LYVE1, respectively [ 40 ]. Further comparison of the 9192 total skin fibroblasts comprised of patient- and control-derived samples identified 12 distinct subclusters, which were annotated using the top DEGs and references to literature ( Figure 2 , Figure 3 and Figure S2 ; Table S3 ).…”

“…Other cells were also clustered using known markers, as follows: keratinocyte identified by cell cluster expression of KRT1 [26], KRT14 [27], and KRT5 [28]; pe [29] by RGS5, CSPG4, and PDGFRB; T cells by CD3D [30], CD3E, CD8A, and CD macrophages by CD163 [32] and AIF1 [33]; dendritic cells (DCs) [34] by CD1 FCER1A; natural killer (NK) cells by NKG7 [35]; melanocytes by PMEL [36]; B cells and MS4A1 [37]; mast cells by TPSAB1 [38]; eccrine cells by AQP5 [39] and DCD [3 endothelial and lymphatic endothelial cells by ACKR1 [30] and LYVE1, respective These total cells analyzed with Seurat provided unsupervised clustering of 43 cell populations (Figure S1A), all of which included both healthy and LS disbursement (Figure S1B), and then were categorized into 14 main groups of cells using annotations from published gene expression profiles for the different cell types (Figure S1C) (Table S2). Our primary cells of interest, the fibroblasts, were characterized by COL1A1, COL1A2, and PDGFRA expression identified within these clusters (Figure S1D).…”

A Kaleidoscope of Keratin Gene Expression and the Mosaic of Its Regulatory Mechanisms

“…One of the markers of cancer progression and other pathologies is the appearance or upregulation of several keratin genes, including K17, K19, K6/16, etc. Keratins are not only routinely used for cancer diagnostics, but are also applicable for the prediction of invasiveness and aggressiveness of the tumor cell [ 242 , 243 , 244 , 245 , 246 , 247 , 248 , 249 , 250 , 251 , 252 , 253 , 254 , 255 , 256 , 257 , 258 , 259 ]. Following the aberrant expression, the reorganization of the keratin cytoskeleton affects the cell motility, survival, and resistance to external factors, which results in tumor treatment responsiveness [ 260 , 261 , 262 , 263 , 264 , 265 , 266 , 267 , 268 , 269 ].…”

Endocrine-disrupting chemicals and epigenetic reprogramming in developmental origin of uterine fibroids

“…Identifying and elucidating the biology of these stem cells have great significance for understanding normal myometrial function, as well as diseases such as UFs. 2 However, despite the remarkable advances in defining the cellular hierarchy in other hormonally regulated tissues, such as the breast 3 and prostate, 4 , 5 little is known about the molecular mechanism underlying the cellular origin and initial steps in UF tumorigenesis.…”