Single-Cell RNA Sequencing Identifies Extracellular Matrix Gene Expression by Pancreatic Circulating Tumor Cells

Abstract

Circulating tumor cells (CTCs) are shed from primary tumors into the bloodstream, mediating the hematogenous spread of cancer to distant organs. 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. CTCs clustered separately from primary tumors and tumor-derived cell lines, showing low-proliferative signatures, enrichment for the stem-cell-associated gene Aldh1a2, biphenotypic expression of epithelial and mesenchymal markers, and expression of Igfbp5, a gene transcript enriched at the epithelial-stromal interface. 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.

References 49

1. 1.

   Adany R, Heimer R, Caterson B, Sorrell JM, Iozzo RV. Altered expression of chondroitin sulfate proteoglycan in the stroma of human colon carcinoma. Hypomethylation of PG-40 gene correlates with increased PG-40 content and mRNA levels. J Biol Chem. 1990;265:11389-11396.

   Not in our library

2. 2.

   Bardeesy N, Aguirre AJ, Chu GC, Cheng KH, Lopez LV, Hezel AF, Feng B, Brennan C, Weissleder R, Mahmood U, et al. Both p16(Ink4a) and the p19(Arf)-p53 pathway constrain progression of pancreatic adenocarcinoma in the mouse. Proc Natl Acad Sci USA. 2006;103:5947-5952.

   Not in our library10.1073/pnas.0601273103

3. 3.

   Boström P, Sainio A, Kakko T, Savontaus M, Söderström M, Järveläinen H. Localization of decorin gene expression in normal human breast tissue and in benign and malignant tumors of the human breast. Histochem Cell Biol. 2013;139:161-171.

   Not in our library10.1007/s00418-012-1026-0

4. 4.

   Breitling R, Armengaud P, Amtmann A, Herzyk P. Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments. FEBS Lett. 2004;573:83-92.

   Not in our library10.1016/j.febslet.2004.07.055

5. 5.

   Brembeck FH, Rustgi AK. The tissue-dependent keratin 19 gene transcription is regulated by GKLF/KLF4 and Sp1. J Biol Chem. 2000;275:28230-28239.

   Not in our library10.1074/jbc.m004013200

6. 6.

   Cann GM, Gulzar ZG, Cooper S, Li R, Luo S, Tat M, Stuart S, Schroth G, Srinivas S, Ronaghi M, et al. mRNA-Seq of single prostate cancer circulating tumor cells reveals recapitulation of gene expression and pathways found in prostate cancer. PLoS ONE. 2012;7:e49144.

   Not in our library10.1371/journal.pone.0049144

7. 7.

   Carvalho FL, Simons BW, Antonarakis ES, Rasheed Z, Douglas N, Villegas D, Matsui W, Berman DM. Tumorigenic potential of circulating prostate tumor cells. Oncotarget. 2013;4:413-421.

   Not in our library10.18632/oncotarget.895

8. 8.

   Feig C, Gopinathan A, Neesse A, Chan DS, Cook N, Tuveson DA. The pancreas cancer microenvironment. Clin Cancer Res. 2012;18:4266-4276.

   Not in our library10.1158/1078-0432.ccr-11-3114

9. 9.

   Fidler IJ. The pathogenesis of cancer metastasis: the ‘seed and soil’ hypothesis revisited. Nat Rev Cancer. 2003;3:453-458.

   Not in our library10.1038/nrc1098

10. 10.

    Hao X, Sun B, Hu L, Lähdesmäki H, Dunmire V, Feng Y, Zhang SW, Wang H, Wu C, Wang H, et al. Differential gene and protein expression in primary breast malignancies and their lymph node metastases as revealed by combined cDNA microarray and tissue microarray analysis. Cancer. 2004;100:1110-1122.

    Not in our library10.1002/cncr.20095

11. 11.

    Henke A, Grace OC, Ashley GR, Stewart GD, Riddick AC, Yeun H, O’Donnell M, Anderson RA, Thomson AA. Stromal expression of decorin, Semaphorin6D, SPARC, Sprouty1 and Tsukushi in developing prostate and decreased levels of decorin in prostate cancer. PLoS ONE. 2012;7:e42516.

    Not in our library10.1371/journal.pone.0042516

12. 12.

    Hunzelmann N, Schönherr E, Bonnekoh B, Hartmann C, Kresse H, Krieg T. Altered immunohistochemical expression of small proteoglycans in the tumor tissue and stroma of basal cell carcinoma. J Invest Dermatol. 1995;104:509-513.

    Not in our library10.1111/1523-1747.ep12605979

13. 13.

    Infante JR, Matsubayashi H, Sato N, Tonascia J, Klein AP, Riall TA, Yeo C, Iacobuzio-Donahue C, Goggins M. Peritumoral fibroblast SPARC expression and patient outcome with resectable pancreatic adenocarcinoma. J Clin Oncol. 2007;25:319-325.

    Not in our library10.1200/jco.2006.07.8824

14. 14.

    Iozzo RV, Cohen I. Altered proteoglycan gene expression and the tumor stroma. EXS. 1994;70:199-214.

    Not in our library10.1007/978-3-0348-7545-5_12

15. 15.

    Johnson SK, Haun RS. Insulin-like growth factor binding protein-5 influences pancreatic cancer cell growth. World J Gastroenterol. 2009;15:3355-3366.

    Not in our library10.3748/wjg.15.3355

16. 16.

    Johnson SK, Dennis RA, Barone GW, Lamps LW, Haun RS. Differential expression of insulin-like growth factor binding protein-5 in pancreatic adenocarcinomas: identification using DNA microarray. Mol Carcinog. 2006;45:814-827.

    Not in our library10.1002/mc.20203

17. 17.

    Kalluri R, Weinberg RA. The basics of epithelial-mesenchymal transition. J Clin Invest. 2009;119:1420-1428.

    Not in our library10.1172/jci39104

18. 18.

    Krause DS, Ito T, Fackler MJ, Smith OM, Collector MI, Sharkis SJ, May WS. Characterization of murine CD34, a marker for hematopoietic progenitor and stem cells. Blood. 1994;84:691-701.

    Not in our library

19. 19.

    Labelle M, Begum S, Hynes RO. Direct signaling between platelets and cancer cells induces an epithelial-mesenchymal-like transition and promotes metastasis. Cancer Cell. 2011;20:576-590.

    Not in our library10.1016/j.ccr.2011.09.009

20. 20.

    Minn AJ, Gupta GP, Siegel PM, Bos PD, Shu W, Giri DD, Viale A, Olshen AB, Gerald WL, Massagué J. Genes that mediate breast cancer metastasis to lung. Nature. 2005;436:518-524.

    Not in our library10.1038/nature03799

21. 21.

    Mu Y, Chen Y, Zhang G, Zhan X, Li Y, Liu T, Li G, Li M, Xiao Z, Gong X, Chen Z. Identification of stromal differentially expressed proteins in the colon carcinoma by quantitative proteomics. Electrophoresis. 2013;34:1679-1692.

    Not in our library10.1002/elps.201200596

22. 22.

    Muzumdar MD, Tasic B, Miyamichi K, Li L, Luo L. A global double-fluorescent Cre reporter mouse. Genesis. 2007;45:593-605.

    Not in our library10.1002/dvg.20335

23. 23.

    Naba A, Clauser KR, Hoersch S, Liu H, Carr SA, Hynes RO. The matrisome: in silico definition and in vivo characterization by proteomics of normal and tumor extracellular matrices. Mol Cell Proteomics. 2012;11.

    Not in our library10.1074/mcp.m111.014647

24. 24.

    Nash MA, Deavers MT, Freedman RS. The expression of decorin in human ovarian tumors. Clin Cancer Res. 2002;8:1754-1760.

    Not in our library

25. 25.

    Neesse A, Michl P, Frese KK, Feig C, Cook N, Jacobetz MA, Lolkema MP, Buchholz M, Olive KP, Gress TM, Tuveson DA. Stromal biology and therapy in pancreatic cancer. Gut. 2011;60:861-868.

    Not in our library10.1136/gut.2010.226092

26. 26.

    Neesse A, Frese KK, Bapiro TE, Nakagawa T, Sternlicht MD, Seeley TW, Pilarsky C, Jodrell DI, Spong SM, Tuveson DA. CTGF antagonism with mAb FG-3019 enhances chemotherapy response without increasing drug delivery in murine ductal pancreas cancer. Proc Natl Acad Sci USA. 2013;110:12325-12330.

    Not in our library10.1073/pnas.1300415110

27. 27.

    Neesse A, Frese KK, Chan DS, Bapiro TE, Howat WJ, Richards FM, Ellenrieder V, Jodrell DI, Tuveson DA. SPARC independent drug delivery and antitumour effects of nab-paclitaxel in genetically engineered mice. Gut. 2014;63:974-983.

    Not in our library10.1136/gutjnl-2013-305559

28. 28.

    Neuzillet C, Tijeras-Raballand A, Cros J, Faivre S, Hammel P, Raymond E. Stromal expression of SPARC in pancreatic adenocarcinoma. Cancer Metastasis Rev. 2013;32:585-602.

    Not in our library10.1007/s10555-013-9439-3

29. 29.

    Olive KP, Jacobetz MA, Davidson CJ, Gopinathan A, McIntyre D, Honess D, Madhu B, Goldgraben MA, Caldwell ME, Allard D, et al. Inhibition of Hedgehog signaling enhances delivery of chemotherapy in a mouse model of pancreatic cancer. Science. 2009;324:1457-1461.

    Not in our library10.1126/science.1171362

30. 30.

    Ozkumur E, Shah AM, Ciciliano JC, Emmink BL, Miyamoto DT, Brachtel E, Yu M, Chen PI, Morgan B, Trautwein J, et al. Inertial focusing for tumor antigen-dependent and -independent sorting of rare circulating tumor cells. Sci Transl Med. 2013;5:179ra147.

    Not in our library10.1126/scitranslmed.3005616

31. 31.

    Pantel K, Brakenhoff RH, Brandt B. Detection, clinical relevance and specific biological properties of disseminating tumour cells. Nat Rev Cancer. 2008;8:329-340.

    Not in our library10.1038/nrc2375

32. 32.

    Prasad NB, Biankin AV, Fukushima N, Maitra A, Dhara S, Elkahloun AG, Hruban RH, Goggins M, Leach SD. Gene expression profiles in pancreatic intraepithelial neoplasia reflect the effects of Hedgehog signaling on pancreatic ductal epithelial cells. Cancer Res. 2005;65:1619-1626.

    Not in our library10.1158/0008-5472.can-04-1413

33. 33.

    Provenzano PP, Cuevas C, Chang AE, Goel VK, Von Hoff DD, Hingorani SR. Enzymatic targeting of the stroma ablates physical barriers to treatment of pancreatic ductal adenocarcinoma. Cancer Cell. 2012;21:418-429.

    Not in our library10.1016/j.ccr.2012.01.007

34. 34.

    Ramsköld D, Luo S, Wang YC, Li R, Deng Q, Faridani OR, Daniels GA, Khrebtukova I, Loring JF, Laurent LC, et al. Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nat Biotechnol. 2012;30:777-782.

    Not in our library10.1038/nbt.2282

35. 35.

    Rasheed ZA, Matsui W. Biological and clinical relevance of stem cells in pancreatic adenocarcinoma. J Gastroenterol Hepatol. 2012;27(Suppl 2):15-18.

    Not in our library10.1111/j.1440-1746.2011.07015.x

36. 36.

    Rasheed ZA, Yang J, Wang Q, Kowalski J, Freed I, Murter C, Hong SM, Koorstra JB, Rajeshkumar NV, He X, et al. Prognostic significance of tumorigenic cells with mesenchymal features in pancreatic adenocarcinoma. J Natl Cancer Inst. 2010;102:340-351.

    Not in our library10.1093/jnci/djp535

37. 37.

    Rasheed ZA, Matsui W, Maitra A, Grippo PJ, Munshi HG. Pathology of pancreatic stroma in PDAC. Pancreatic Cancer and Tumor Microenvironment. 2012.

    Not in our library

38. 38.

    Rhim AD, Mirek ET, Aiello NM, Maitra A, Bailey JM, McAllister F, Reichert M, Beatty GL, Rustgi AK, Vonderheide RH, et al. EMT and dissemination precede pancreatic tumor formation. Cell. 2012;148:349-361.

    Not in our library10.1016/j.cell.2011.11.025

39. 39.

    Sato N, Fukushima N, Maehara N, Matsubayashi H, Koopmann J, Su GH, Hruban RH, Goggins M. SPARC/osteonectin is a frequent target for aberrant methylation in pancreatic adenocarcinoma and a mediator of tumor-stromal interactions. Oncogene. 2003;22:5021-5030.

    Not in our library10.1038/sj.onc.1206807

40. 40.

    Takahashi K, Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell. 2006;126:663-676.

    Not in our library10.1016/j.cell.2006.07.024

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