Single-cell dissection of transcriptional heterogeneity in human colon tumors (original) (raw)

• Reya, T., Morrison, S.J., Clarke, M.F. & Weissman, I.L. Stem cells, cancer, and cancer stem cells. Nature 414, 105–111 (2001).
  Article CAS Google Scholar
• Jordan, C.T., Guzman, M.L. & Noble, M. Cancer stem cells. N. Engl. J. Med. 355, 1253–1261 (2006).
  Article CAS Google Scholar
• Dalerba, P., Cho, R.W. & Clarke, M.F. Cancer stem cells: models and concepts. Annu. Rev. Med. 58, 267–284 (2007).
  Article CAS Google Scholar
• Shackleton, M., Quintana, E., Fearon, E.R. & Morrison, S.J. Heterogeneity in cancer: cancer stem cells versus clonal evolution. Cell 138, 822–829 (2009).
  Article CAS Google Scholar
• Campbell, L.L. & Polyak, K. Breast tumor heterogeneity: cancer stem cells or clonal evolution? Cell Cycle 6, 2332–2338 (2007).
  Article CAS Google Scholar
• Marusyk, A. & Polyak, K. Tumor heterogeneity: causes and consequences. Biochim. Biophys. Acta 1805, 105–117 (2010).
  CAS Google Scholar
• Kirkland, S.C. Clonal origin of columnar, mucous, and endocrine cell lineages in human colorectal epithelium. Cancer 61, 1359–1363 (1988).
  Article CAS Google Scholar
• Odoux, C. et al. A stochastic model for cancer stem cell origin in metastatic colon cancer. Cancer Res. 68, 6932–6941 (2008).
  Article CAS Google Scholar
• Vermeulen, L. et al. Single-cell cloning of colon cancer stem cells reveals a multi-lineage differentiation capacity. Proc. Natl. Acad. Sci. USA 105, 13427–13432 (2008).
  Article CAS Google Scholar
• Sato, T. et al. Paneth cells constitute the niche for Lgr5 stem cells in intestinal crypts. Nature 469, 415–418 (2011).
  Article CAS Google Scholar
• Warren, L., Bryder, D., Weissman, I.L. & Quake, S.R. Transcription factor profiling in individual hematopoietic progenitors by digital RT-PCR. Proc. Natl. Acad. Sci. USA 103, 17807–17812 (2006).
  Article CAS Google Scholar
• Guo, G. et al. Resolution of cell fate decisions revealed by single-cell gene-expression analysis from zygote to blastocyst. Dev. Cell 18, 675–685 (2010).
  Article CAS Google Scholar
• White, A.K. et al. High-throughput microfluidic single-cell RT-qPCR. Proc. Natl. Acad. Sci. USA 108, 13999–14004 (2011).
  Article CAS Google Scholar
• Jiao, Y.F., Nakamura, S., Sugai, T., Yamada, N. & Habano, W. Serrated adenoma of the colorectum undergoes a proliferation versus differentiation process: new conceptual interpretation of morphogenesis. Oncology 74, 127–134 (2008).
  Article Google Scholar
• Wielenga, V.J. et al. Expression of CD44 in Apc and Tcf mutant mice implies regulation by the WNT pathway. Am. J. Pathol. 154, 515–523 (1999).
  Article CAS Google Scholar
• Prall, F. et al. CD66a (BGP), an adhesion molecule of the carcinoembryonic antigen family, is expressed in epithelium, endothelium, and myeloid cells in a wide range of normal human tissues. J. Histochem. Cytochem. 44, 35–41 (1996).
  Article CAS Google Scholar
• Barker, N. et al. Identification of stem cells in small intestine and colon by marker gene Lgr5. Nature 449, 1003–1007 (2007).
  Article CAS Google Scholar
• Becker, L., Huang, Q. & Mashimo, H. Immunostaining of Lgr5, an intestinal stem cell marker, in normal and premalignant human gastrointestinal tissue. Scientific World Journal 8, 1168–1176 (2008).
  Article CAS Google Scholar
• Merlos-Suarez, A. et al. The intestinal stem cell signature identifies colorectal cancer stem cells and predicts disease relapse. Cell Stem Cell 8, 511–524 (2011).
  Article CAS Google Scholar
• Sahoo, D., Dill, D.L., Gentles, A.J., Tibshirani, R. & Plevritis, S.K. Boolean implication networks derived from large scale, whole genome microarray datasets. Genome Biol. 9, R157 (2008).
  Article Google Scholar
• Hoglund, P. et al. Mutations of the down-regulated in adenoma (DRA) gene cause congenital chloride diarrhoea. Nat. Genet. 14, 316–319 (1996).
  Article CAS Google Scholar
• Fischer, H., Stenling, R., Rubio, C. & Lindblom, A. Differential expression of aquaporin 8 in human colonic epithelial cells and colorectal tumors. BMC Physiol. 1, 1 (2001).
  Article CAS Google Scholar
• Koslowski, M., Sahin, U., Dhaene, K., Huber, C. & Tureci, O. MS4A12 is a colon-selective store-operated calcium channel promoting malignant cell processes. Cancer Res. 68, 3458–3466 (2008).
  Article CAS Google Scholar
• Noah, T.K., Kazanjian, A., Whitsett, J. & Shroyer, N.F. SAM pointed domain ETS factor (SPDEF) regulates terminal differentiation and maturation of intestinal goblet cells. Exp. Cell Res. 316, 452–465 (2010).
  Article CAS Google Scholar
• Gregorieff, A. et al. The ets-domain transcription factor Spdef promotes maturation of goblet and paneth cells in the intestinal epithelium. Gastroenterology 137, 1333–1345 (2009).
  Article CAS Google Scholar
• van der Flier, L.G. et al. Transcription factor achaete scute-like 2 controls intestinal stem cell fate. Cell 136, 903–912 (2009).
  Article CAS Google Scholar
• Ezhkova, E. et al. Ezh2 orchestrates gene expression for the stepwise differentiation of tissue-specific stem cells. Cell 136, 1122–1135 (2009).
  Article CAS Google Scholar
• Park, I.K. et al. Bmi-1 is required for maintenance of adult self-renewing haematopoietic stem cells. Nature 423, 302–305 (2003).
  Article CAS Google Scholar
• Sangiorgi, E. & Capecchi, M.R. Bmi1 is expressed in vivo in intestinal stem cells. Nat. Genet. 40, 915–920 (2008).
  Article CAS Google Scholar
• Zeng, Y.A. & Nusse, R. Wnt proteins are self-renewal factors for mammary stem cells and promote their long-term expansion in culture. Cell Stem Cell 6, 568–577 (2010).
  Article CAS Google Scholar
• Beider, K., Abraham, M. & Peled, A. Chemokines and chemokine receptors in stem cell circulation. Front. Biosci. 13, 6820–6833 (2008).
  Article CAS Google Scholar
• Jensen, K.B. et al. Lrig1 expression defines a distinct multipotent stem cell population in mammalian epidermis. Cell Stem Cell 4, 427–439 (2009).
  Article CAS Google Scholar
• Dalla-Favera, R., Wong-Staal, F. & Gallo, R.C. Onc gene amplification in promyelocytic leukaemia cell line HL-60 and primary leukaemic cells of the same patient. Nature 299, 61–63 (1982).
  Article CAS Google Scholar
• Hoey, T. et al. DLL4 blockade inhibits tumor growth and reduces tumor-initiating cell frequency. Cell Stem Cell 5, 168–177 (2009).
  Article CAS Google Scholar
• Park, S.Y., Gonen, M., Kim, H.J., Michor, F. & Polyak, K. Cellular and genetic diversity in the progression of in situ human breast carcinomas to an invasive phenotype. J. Clin. Invest. 120, 636–644 (2010).
  Article CAS Google Scholar
• Losi, L., Baisse, B., Bouzourene, H. & Benhattar, J. Evolution of intratumoral genetic heterogeneity during colorectal cancer progression. Carcinogenesis 26, 916–922 (2005).
  Article CAS Google Scholar
• Dalerba, P. et al. Phenotypic characterization of human colorectal cancer stem cells. Proc. Natl. Acad. Sci. USA 104, 10158–10163 (2007).
  Article CAS Google Scholar
• Oien, K.A. Pathologic evaluation of unknown primary cancer. Semin. Oncol. 36, 8–37 (2009).
  Article CAS Google Scholar
• Lugli, A., Tzankov, A., Zlobec, I. & Terracciano, L.M. Differential diagnostic and functional role of the multi-marker phenotype CDX2/CK20/CK7 in colorectal cancer stratified by mismatch repair status. Mod. Pathol. 21, 1403–1412 (2008).
  Article CAS Google Scholar
• Sahoo, D., Dill, D.L., Tibshirani, R. & Plevritis, S.K. Extracting binary signals from microarray time-course data. Nucleic Acids Res. 35, 3705–3712 (2007).
  Article CAS Google Scholar
• Jorissen, R.N. et al. Metastasis-associated gene expression changes predict poor outcomes in patients with dukes stage B and C colorectal cancer. Clin. Cancer Res. 15, 7642–7651 (2009).
  Article CAS Google Scholar
• Smith, J.J. et al. Experimentally derived metastasis gene expression profile predicts recurrence and death in patients with colon cancer. Gastroenterology 138, 958–968 (2010).
  Article CAS Google Scholar
• Guastadisegni, C., Colafranceschi, M., Ottini, L. & Dogliotti, E. Microsatellite instability as a marker of prognosis and response to therapy: a meta-analysis of colorectal cancer survival data. Eur. J. Cancer 46, 2788–2798 (2010).
  Article CAS Google Scholar
• Bardia, A. et al. Adjuvant chemotherapy for resected stage II and III colon cancer: comparison of two widely used prognostic calculators. Semin. Oncol. 37, 39–46 (2010).
  Article CAS Google Scholar
• Dalerba, P. et al. Reconstitution of human telomerase reverse transcriptase expression rescues colorectal carcinoma cells from in vitro senescence: evidence against immortality as a constitutive trait of tumor cells. Cancer Res. 65, 2321–2329 (2005).
  Article CAS Google Scholar
• Ringner, M. What is principal component analysis? Nat. Biotechnol. 26, 303–304 (2008).
  Article CAS Google Scholar
• O'Doherty, U., Swiggard, W.J. & Malim, M.H. Human immunodeficiency virus type 1 spinoculation enhances infection through virus binding. J. Virol. 74, 10074–10080 (2000).
  Article CAS Google Scholar
• Wang, G.P. et al. DNA bar coding and pyrosequencing to analyze adverse events in therapeutic gene transfer. Nucleic Acids Res. 36, e49 (2008).
  Article Google Scholar
• Ishizawa, K. et al. Tumor-initiating cells are rare in many human tumors. Cell Stem Cell 7, 279–282 (2010).
  Article CAS Google Scholar
• Quintana, E. et al. Efficient tumour formation by single human melanoma cells. Nature 456, 593–598 (2008).
  Article CAS Google Scholar