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Localization of T cell clonotypes using spatial transcriptomics

View ORCID ProfileWilliam H. Hudson, View ORCID ProfileLisa J. Sudmeier
doi: https://doi.org/10.1101/2021.08.03.454999
William H. Hudson
1Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322
2Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322
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  • For correspondence: william.hudson@emory.edu
Lisa J. Sudmeier
3Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322
4Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322
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Abstract

Spatial transcriptomics is an emerging technology that measures gene expression while preserving spatial information. Here, we present a method to determine localization of specific T cell clones by obtaining T cell receptor (TCR) sequences from spatial transcriptomics assays. Our method uses an existing commercial spatial transcriptomics platform and open-source software for analysis, allowing simple and inexpensive integration with archived samples and existing laboratory workflows. Using human brain metastasis samples, we show that TCR sequences are readily obtained from human tumor tissue and that these sequences are recapitulated by single-cell sequencing methods. This technique will permit detailed studies of the spatial organization of the human T cell repertoire, such as the identification of tumor-infiltrating and tumor-excluded T cell clones.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted August 05, 2021.
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Localization of T cell clonotypes using spatial transcriptomics
William H. Hudson, Lisa J. Sudmeier
bioRxiv 2021.08.03.454999; doi: https://doi.org/10.1101/2021.08.03.454999
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Localization of T cell clonotypes using spatial transcriptomics
William H. Hudson, Lisa J. Sudmeier
bioRxiv 2021.08.03.454999; doi: https://doi.org/10.1101/2021.08.03.454999

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