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Single-cell RNA sequencing identifies extracellular matrix gene expression by pancreatic circulating tumor cells.

Ting DT, Wittner BS, Ligorio M, Vincent Jordan N, Shah AM, Miyamoto DT, Aceto N, Bersani F, Brannigan BW, Xega K, Ciciliano JC, Zhu H, MacKenzie OC, Trautwein J, Arora KS, Shahid M, Ellis HL, Qu N, Bardeesy N, Rivera MN, Deshpande V, Ferrone CR, Kapur R, Ramaswamy S, Shioda T, Toner M, Maheswaran S, Haber DA - Cell Rep (2014)

Bottom Line: To define their composition, we compared genome-wide expression profiles of CTCs with matched primary tumors in a mouse model of pancreatic cancer, isolating individual CTCs using epitope-independent microfluidic capture, followed by single-cell RNA sequencing.Mouse as well as human pancreatic CTCs exhibit a very high expression of stromal-derived extracellular matrix (ECM) proteins, including SPARC, whose knockdown in cancer cells suppresses cell migration and invasiveness.The aberrant expression by CTCs of stromal ECM genes points to their contribution of microenvironmental signals for the spread of cancer to distant organs.

View Article: PubMed Central - PubMed

Affiliation: Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA.

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Targeted Analysis of Single-Cell RNA-Seq Data(A) Expression heatmap of epithelial, hematopoietic, and endothelial markers in primary tumors and classical epithelial CTCs (CTC-c). Scale in log10(rpm).(B–D) Epithelial and mesenchymal genes differentially expressed in CTCs versus tumors.Boxplot of epithelial genes that are (B) downregulated or mesenchymal genes that are (C) upregulated or (D) downregulated in CTCs (red) versus tumors (blue). Bar represents median, and boxplot represents quartiles; scale in log10(rpm).
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Figure 3: Targeted Analysis of Single-Cell RNA-Seq Data(A) Expression heatmap of epithelial, hematopoietic, and endothelial markers in primary tumors and classical epithelial CTCs (CTC-c). Scale in log10(rpm).(B–D) Epithelial and mesenchymal genes differentially expressed in CTCs versus tumors.Boxplot of epithelial genes that are (B) downregulated or mesenchymal genes that are (C) upregulated or (D) downregulated in CTCs (red) versus tumors (blue). Bar represents median, and boxplot represents quartiles; scale in log10(rpm).

Mentions: Interrogation of single cells isolated by CD45 depletion from tumor-bearing mice, using the epithelial, hematopoietic, and endothelial markers, revealed notable differences among the three major candidate CTC groupings (clusters 1, 3, and 7; Figures 3A and S3). Cluster 3 showed strong expression of epithelial markers, consistent with a “classical” CTC phenotype (denoted CTC-c). A subset of these cells expressed Cd34, an endothelial progenitor marker that is also found in mesenchymal cells including MEFs (Figures 3A and S3) and stromal cells (Krause et al., 1994), but other characteristic endothelial lineage markers were absent. Clusters 1 and 7 were more complex, with the former noteworthy for enrichment of platelet markers CD41 (Itga2b) and CD61 (Itgb3) (hence denoted CTC-plt) and the latter having a prominent cellular proliferation signature (CTC-pro).


Single-cell RNA sequencing identifies extracellular matrix gene expression by pancreatic circulating tumor cells.

Ting DT, Wittner BS, Ligorio M, Vincent Jordan N, Shah AM, Miyamoto DT, Aceto N, Bersani F, Brannigan BW, Xega K, Ciciliano JC, Zhu H, MacKenzie OC, Trautwein J, Arora KS, Shahid M, Ellis HL, Qu N, Bardeesy N, Rivera MN, Deshpande V, Ferrone CR, Kapur R, Ramaswamy S, Shioda T, Toner M, Maheswaran S, Haber DA - Cell Rep (2014)

Targeted Analysis of Single-Cell RNA-Seq Data(A) Expression heatmap of epithelial, hematopoietic, and endothelial markers in primary tumors and classical epithelial CTCs (CTC-c). Scale in log10(rpm).(B–D) Epithelial and mesenchymal genes differentially expressed in CTCs versus tumors.Boxplot of epithelial genes that are (B) downregulated or mesenchymal genes that are (C) upregulated or (D) downregulated in CTCs (red) versus tumors (blue). Bar represents median, and boxplot represents quartiles; scale in log10(rpm).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4230325&req=5

Figure 3: Targeted Analysis of Single-Cell RNA-Seq Data(A) Expression heatmap of epithelial, hematopoietic, and endothelial markers in primary tumors and classical epithelial CTCs (CTC-c). Scale in log10(rpm).(B–D) Epithelial and mesenchymal genes differentially expressed in CTCs versus tumors.Boxplot of epithelial genes that are (B) downregulated or mesenchymal genes that are (C) upregulated or (D) downregulated in CTCs (red) versus tumors (blue). Bar represents median, and boxplot represents quartiles; scale in log10(rpm).
Mentions: Interrogation of single cells isolated by CD45 depletion from tumor-bearing mice, using the epithelial, hematopoietic, and endothelial markers, revealed notable differences among the three major candidate CTC groupings (clusters 1, 3, and 7; Figures 3A and S3). Cluster 3 showed strong expression of epithelial markers, consistent with a “classical” CTC phenotype (denoted CTC-c). A subset of these cells expressed Cd34, an endothelial progenitor marker that is also found in mesenchymal cells including MEFs (Figures 3A and S3) and stromal cells (Krause et al., 1994), but other characteristic endothelial lineage markers were absent. Clusters 1 and 7 were more complex, with the former noteworthy for enrichment of platelet markers CD41 (Itga2b) and CD61 (Itgb3) (hence denoted CTC-plt) and the latter having a prominent cellular proliferation signature (CTC-pro).

Bottom Line: To define their composition, we compared genome-wide expression profiles of CTCs with matched primary tumors in a mouse model of pancreatic cancer, isolating individual CTCs using epitope-independent microfluidic capture, followed by single-cell RNA sequencing.Mouse as well as human pancreatic CTCs exhibit a very high expression of stromal-derived extracellular matrix (ECM) proteins, including SPARC, whose knockdown in cancer cells suppresses cell migration and invasiveness.The aberrant expression by CTCs of stromal ECM genes points to their contribution of microenvironmental signals for the spread of cancer to distant organs.

View Article: PubMed Central - PubMed

Affiliation: Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA.

Show MeSH
Related in: MedlinePlus