Localization of T cell clonotypes using the Visium spatial transcriptomics platform

• Type of Material: Article
• Authors: William Hudson, Emory University; Lisa Sudmeier, Emory University
• Language: English
• Date: 2022-06-17
• Publisher: Elsevier BV
• Publication Version: Final Published Version
• Copyright Statement: © 2022 The Author(s)
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1016/j.xpro.2022.101391
• Title of Journal or Parent Work: STAR Protocols
• Volume: 3
• Issue: 2
• Start Page: 101391
• End Page: 101391
• Grant/Funding Information: W.H.H. is supported by K99AI153736 from the National Institutes of Health (NIH).; The Yerkes Nonhuman Primate Genomics Core is supported in part by NIH P51OD011132, and Visium gene expression sequencing data was acquired on an Illumina NovaSeq6000 funded by NIH S10OD026799; L.J.S. is supported by a Conquer Cancer Young Investigator Award, a Radiological Society of North America Resident Research Award, and the Nell W. and William Simpson Elkin Fellowship from Emory University.; Research reported in this publication was also supported by the National Cancer Institute of the National Institutes of Health under Award Number P50CA217691. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health or the American Society of Clinical Oncology® or Conquer Cancer®.
• Keywords: Sequence analysis; T-Lymphocytes; Clone Cells; Molecular Biology; Humans; Immunology; Transcriptome
• Research Categories: Health Sciences, Immunology; Biology, Microbiology; Health Sciences, Oncology

Abstract

We present a protocol to localize T cell receptor clones using the Visium spatial transcriptomics platform. This approach permits simultaneous localization of both gene expression and T cell clonotypes in situ within tissue sections. T cell receptor sequences identified by this protocol are readily recapitulated by single-cell sequencing. This technique enables detailed studies of the spatial organization of the human T cell repertoire, such as the localization of infiltrating T cell clones within the tumor microenvironment. For complete details on the use and execution of this protocol, please refer to Sudmeier et al. (2022).