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Single-cell dissection of transcriptional heterogeneity in human colon tumors

Nature Biotechnology volume 29, pages 1120–1127 (2011)Cite this article

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Abstract

Cancer is often viewed as a caricature of normal developmental processes, but the extent to which its cellular heterogeneity truly recapitulates multilineage differentiation processes of normal tissues remains unknown. Here we implement single-cell PCR gene-expression analysis to dissect the cellular composition of primary human normal colon and colon cancer epithelia. We show that human colon cancer tissues contain distinct cell populations whose transcriptional identities mirror those of the different cellular lineages of normal colon. By creating monoclonal tumor xenografts from injection of a single (n = 1) cell, we demonstrate that the transcriptional diversity of cancer tissues is largely explained by in vivo multilineage differentiation and not only by clonal genetic heterogeneity. Finally, we show that the different gene-expression programs linked to multilineage differentiation are strongly associated with patient survival. We develop two-gene classifier systems (KRT20 versus CA1, MS4A12, CD177, SLC26A3) that predict clinical outcomes with hazard ratios superior to those of pathological grade and comparable to those of microarray-derived multigene expression signatures.

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Figure 1: Single-cell PCR gene-expression analysis of human normal colon epithelium.
Figure 2: Single-cell PCR gene-expression analysis of human colon tumor tissues.
Figure 3: Analysis of a monoclonal human colon cancer xenograft obtained from injection of a single (n = 1) cell in NOD/SCID/IL2Rγ−/− mice.
Figure 4: KRT20 and top-crypt genes can be used as prognostic markers in colorectal cancer patients.

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Acknowledgements

This study was supported by National Institutes of Health (NIH) grants U54-CA126524 and P01-CA139490 (to S.R.Q. and M.F.C.), the NIH Director's Pioneer Awards (to S.R.Q.) and a grant from the Ludwig foundation (to M.F.C.). P.D. was supported by a training grant from the California Institute for Regenerative Medicine (CIRM) and by a BD Biosciences Stem Cell Research Grant (Summer 2011). T.K. was supported by a fellowship from the Machiah Foundation. D.S. was supported by NIH grant K99-CA151673, by Department of Defense grant W81XWH-10-1-0500 and a grant from the Siebel Stem Cell Institute and the Thomas and Stacey Siebel Foundation. We wish to thank R. Tibshirani, D. Witten, L. Warren, R.A. White III, E. Gilbert, P. Lovelace, M. Palmor, C. Donkers and S.P. Miranda for helpful discussion and technical support in many moments during the completion of this study.

Author information

Author notes

  1. Piero Dalerba, Tomer Kalisky, Debashis Sahoo, Michael F Clarke and Stephen R Quake: These authors contributed equally to this work.

Authors and Affiliations

  1. Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, USA

    Piero Dalerba, Debashis Sahoo, Pradeep S Rajendran, Michael E Rothenberg, Sopheak Sim, Darius M Johnston, Dalong Qian, Maider Zabala, Shigeo Hisamori, Yohei Shimono & Michael F Clarke

  2. Department of Medicine, Division of Oncology, Stanford University, Stanford, California, USA

    Piero Dalerba & Michael F Clarke

  3. Department of Bioengineering, Stanford University, Stanford, California, USA

    Tomer Kalisky, Anne A Leyrat, Jennifer Okamoto, Darius M Johnston, Norma F Neff, Jianbin Wang & Stephen R Quake

  4. Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University, Stanford, California, USA

    Michael E Rothenberg

  5. Howard Hughes Medical Institute, Chevy Chase, Maryland, USA

    Jennifer Okamoto, Darius M Johnston & Stephen R Quake

  6. Tissue Bank, Stanford University, Stanford, California, USA

    Janet Bueno

  7. Department of Surgery, Stanford University, Stanford, California, USA

    Andrew A Shelton & Brendan Visser

  8. Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, The Netherlands

    Marc van de Wetering & Hans Clevers

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  1. Piero Dalerba
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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. provided intellectual guidance in the design 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., 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. provided samples and reagents. P.D., T.K., D.S., M.F.C. and S.R.Q. wrote the paper.

Corresponding authors

Correspondence to Michael F Clarke or Stephen R Quake.

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Competing interests

S.R.Q. is a founder, consultant and shareholder of Fluidigm. S.R.Q. and M.F.C. are founders, consultants and shareholders of QuantiCell. The authors have filed a patent application based on the results described in this study.

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Dalerba, P., Kalisky, T., Sahoo, D. et al. Single-cell dissection of transcriptional heterogeneity in human colon tumors. Nat Biotechnol 29, 1120–1127 (2011). https://doi.org/10.1038/nbt.2038

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