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Profiling Cell Type Abundance and Expression in Bulk Tissues with CIBERSORTx

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Stem Cell Transcriptional Networks

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2117))

Abstract

CIBERSORTx is a suite of machine learning tools for the assessment of cellular abundance and cell type-specific gene expression patterns from bulk tissue transcriptome profiles. With this framework, single-cell or bulk-sorted RNA sequencing data can be used to learn molecular signatures of distinct cell types from a small collection of biospecimens. These signatures can then be repeatedly applied to characterize cellular heterogeneity from bulk tissue transcriptomes without physical cell isolation. In this chapter, we provide a detailed primer on CIBERSORTx and demonstrate its capabilities for high-throughput profiling of cell types and cellular states in normal and neoplastic tissues.

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Acknowledgments

We would like to thank B. Chen, B. Nabet, and M. Matusiak for assistance in beta-testing CIBERSORTx. This work was supported by grants from the 2019 AACR-AstraZeneca Lymphoma Research Fellowship (C.B.S., 19-40-12-STEE), the National Cancer Institute (A.M.N., R00CA187192; A.A.A., U01CA194389; A.A.A., R01CA188298), the Stinehart-Reed foundation (A.M.N., A.A.A.), the Stanford Bio-X Interdisciplinary Initiatives Seed Grants Program (IIP) (A.M.N.), the Virginia and D.K. Ludwig Fund for Cancer Research (A.M.N., A.A.A.), the US Department of Defense (A.M.N., W81XWH-12-1-0498), anonymous donors (A.A.A., A.M.N.), the Shanahan and Bronzini Family Funds (A.A.A.), the V Foundation for Cancer Research (A.A.A.), the Leukemia and Lymphoma Society (A.A.A.), and the Damon Runyon Cancer Research Foundation (A.A.A.), the American Society of Hematology (A.A.A.).

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Authors and Affiliations

  1. Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA

    Chloé B. Steen, Chih Long Liu & Ash A. Alizadeh

  2. Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA

    Chih Long Liu, Ash A. Alizadeh & Aaron M. Newman

  3. Center for Cancer Systems Biology, Stanford University, Stanford, CA, USA

    Ash A. Alizadeh

  4. Division of Hematology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA

    Ash A. Alizadeh

  5. Department of Biomedical Data Science, Stanford University, Stanford, CA, USA

    Aaron M. Newman

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  1. Chloé B. Steen
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  2. Chih Long Liu
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  3. Ash A. Alizadeh
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  4. Aaron M. Newman
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Corresponding authors

Correspondence to Ash A. Alizadeh or Aaron M. Newman .

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Editors and Affiliations

  1. Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA

    Benjamin L. Kidder

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Steen, C.B., Liu, C.L., Alizadeh, A.A., Newman, A.M. (2020). Profiling Cell Type Abundance and Expression in Bulk Tissues with CIBERSORTx. In: Kidder, B. (eds) Stem Cell Transcriptional Networks. Methods in Molecular Biology, vol 2117. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0301-7_7

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  • DOI: https://doi.org/10.1007/978-1-0716-0301-7_7

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