Localization of T cell clonotypes using the Visium spatial transcriptomics platform

William H Hudson; Lisa J Sudmeier

doi:10.1016/j.xpro.2022.101391

Localization of T cell clonotypes using the Visium spatial transcriptomics platform

STAR Protoc. 2022 Jun 10;3(2):101391. doi: 10.1016/j.xpro.2022.101391. eCollection 2022 Jun 17.

Authors

William H Hudson^{1

2}, Lisa J Sudmeier^{3

4}

Affiliations

¹ Emory Vaccine Center, Atlanta, GA, USA.
² Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA.
³ Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA.
⁴ Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA.

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).

Keywords: Immunology; Molecular Biology; Sequence analysis.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Clone Cells
Humans
T-Lymphocytes*
Transcriptome* / genetics

Abstract

Publication types

MeSH terms

Grant support