DIY: Visualizing the immune landscape of tumors using transcriptome and methylome data

Steven F Gameiro; Farhad Ghasemi; John W Barrett; James Koropatnick; Anthony C Nichols; Joe S Mymryk; Saman Maleki Vareki

doi:10.1016/bs.mie.2019.05.040

DIY: Visualizing the immune landscape of tumors using transcriptome and methylome data

Methods Enzymol. 2020:636:49-76. doi: 10.1016/bs.mie.2019.05.040. Epub 2019 Jul 9.

Authors

Steven F Gameiro¹, Farhad Ghasemi², John W Barrett², James Koropatnick³, Anthony C Nichols⁴, Joe S Mymryk⁵, Saman Maleki Vareki⁶

Affiliations

¹ Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada.
² Department of Otolaryngology, Head & Neck Surgery, The University of Western Ontario, London, ON, Canada.
³ Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada; Department of Oncology, The University of Western Ontario, London, ON, Canada; Department of Pathology, The University of Western Ontario, London, ON, Canada; Department of Physiology and Pharmacology, The University of Western Ontario, London, ON, Canada; London Regional Cancer Program, Lawson Health Research Institute, London, ON, Canada.
⁴ Department of Otolaryngology, Head & Neck Surgery, The University of Western Ontario, London, ON, Canada; Department of Oncology, The University of Western Ontario, London, ON, Canada; London Regional Cancer Program, Lawson Health Research Institute, London, ON, Canada.
⁵ Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada; Department of Otolaryngology, Head & Neck Surgery, The University of Western Ontario, London, ON, Canada; Department of Oncology, The University of Western Ontario, London, ON, Canada; London Regional Cancer Program, Lawson Health Research Institute, London, ON, Canada. Electronic address: jmymryk@uwo.ca.
⁶ Department of Oncology, The University of Western Ontario, London, ON, Canada; London Regional Cancer Program, Lawson Health Research Institute, London, ON, Canada. Electronic address: saman.malekivareki@lhsc.on.ca.

PMID: 32178827
DOI: 10.1016/bs.mie.2019.05.040

Abstract

The importance of the immune system in combating many different types of malignancies has been firmly established. Indeed, the success of immune checkpoint-blocking antibodies in cancer treatment has focused the attention of many researchers on the tumor immune microenvironment. As one consequence, the analysis of the number, type, and activation status of tumor-infiltrating leukocytes (TILs) has become an area of great interest. Detailed knowledge of the immunological profile of a given tumor has the potential to predict patient response to therapy and overall survival. This chapter is intended to summarize the steps necessary for basic comparative analysis of the infiltration and activation status of immune cells in various human solid tumors, using freely available data obtained from The Cancer Genome Atlas (TCGA).

Keywords: Gene expression analysis; Immune landscape; Immune markers; Immunogenomics; TCGA; Tumor-infiltrating leukocytes.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Epigenome
Humans
Lymphocytes, Tumor-Infiltrating
Neoplasms* / genetics
Transcriptome*
Tumor Microenvironment / genetics

Abstract

Publication types

MeSH terms

Grants and funding