Ht, The NetherlandsAbstractCancer is frequently viewed as a caricature of regular developmental processes, however the extent by which its cellular heterogeneity truly recapitulates multi-lineage differentiation processes of regular tissues remains unknown. Here, we implement “single-cell PCR gene-expression analysis” (SINCE-PCR) to dissect the cellular composition of main human standard colon and colon cancer epithelia. We show that human colon cancer tissues include distinct cell populations whose transcriptional identities mirror those in the distinctive cellular lineages of regular colon. By producing monoclonal tumor xenografts from injection of a single-cell (n = 1), we show that transcriptional diversity of cancer tissues is largely explained by in vivo multi-lineage differentiation, not merely by clonal genetic heterogeneity. Lastly, we show that perturbations in gene-expression programs linked to multi-lineage differentiation strongly associate with patient survival. Guided by SINCE-PCR data, we develop two-gene classifier systems (KRT20 vs CA1, MS4A12, CD177, SLC26A3) that predict clinical outcomes with hazard-ratios superior to pathological grade and comparable to microarray-derived multi-gene expression signatures.Users might view, print, copy, download and text and data- mine the content material in such documents, for the purposes of academic investigation, topic constantly for the complete Conditions of use: http://nature.com/authors/editorial_policies/license.html#terms Correspondence to: Stephen R. Quake, Ph.D., Professor of Bioengineering and Applied Physics, Stanford University, Clark Center, E350Q, 318 Campus Drive, Stanford, California, 94305, phone (650) 736-7890, fax(650) 736-1961, [email protected]. These authors contributed equally to the study. AUTHOR CONTRIBUTIONS P.D., T.K., D.S., M.F.C. and S.R.Q. conceived the study and designed the experiments. P.S.R., M.E.R., A.A.L., M.Z., N.F.N, M. v. d. W. and H.C. supplied intellectual guidance inside the design and style of selected experiments. P.D., T.K., D.S., P.S.R., A.A.L., S.S., J.O., D.M.J., D.Q., J.W., Y.S. and S.H. performed the experiments. P.D., T.K., D.S., N.F.N., Y.S., M.F.C. and S.R.Q analyzed the data and/or provided intellectual guidance in their interpretation. J.B., A.A.S. and B.V. supplied samples and reagents. P.D., T.K., D.S., M.F.C. and S.R.Q. wrote the paper.Dalerba et al.PageThe in vivo cellular composition of solid tissues is often hard to investigate inside a comprehensive and quantitative way. Methods for instance N-Acetylneuraminic acid Epigenetic Reader Domain immunohistochemistry and flow cytometry are restricted by the availability of antigen-specific monoclonal antibodies and by the little quantity of parallel measurements that may be performed on each person cell. Conventional high-throughput assays, for instance gene-expression arrays, when performed on whole tissues, give information on average gene expression levels, and can be only indirectly Random Inhibitors products correlated to quantitative modifications in cellular subpopulations. These limitations grow to be particularly hard to overcome when studying minority populations, like stem cells, whose identification is produced elusive by their low numbers and by the lack of exclusive markers. In addition, in pathological states, for example cancer, it can be frequently impossible to establish no matter whether perturbations in gene expression detected in complete tissues are due to modifications in the relative composition of diverse cell sorts or to aberrations in the gene-expression profile of mutated cells. As an example, despite the fact that.