Key Points
Single-cell–based rhesus-specific Ig and TCR repertoire sequencing is established.
All rhesus Ig and TCR isotypes and chain types are recovered.
Abstract
Recent advancements in microfluidics and high-throughput sequencing technologies have enabled recovery of paired H and L chains of Igs and VDJ and VJ chains of TCRs from thousands of single cells simultaneously in humans and mice. Despite rhesus macaques being one of the most well-studied model organisms for the human adaptive immune response, high-throughput single-cell immune repertoire sequencing assays are not yet available due to the complexity of these polyclonal receptors. We used custom primers that capture all known rhesus macaque Ig and TCR isotypes and chains that are fully compatible with a commercial solution for single-cell immune repertoire profiling. Using these rhesus-specific assays, we sequenced Ig and TCR repertoires in >60,000 cells from cryopreserved rhesus PBMCs, splenocytes, and FACS-sorted B and T cells. We were able to recover every Ig isotype and TCR chain, measure clonal expansion in proliferating T cells, and pair Ig and TCR repertoires with gene expression profiles of the same single cells. Our results establish the ability to perform high-throughput immune repertoire analysis in rhesus macaques at the single-cell level.
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Footnotes
This work was supported by the U.S. Department of Health and Human Services (HHS), National Institutes of Health (NIH), National Institute of Allergy and Infectious Diseases (NIAID) (Contract HHSN272201800008C) and by the Washington National Primate Research Center Core (Grant P51 OD010425 to M.G. and Grant R21AI120713 to X.P. from the HHS, NIH, NIAID, Office of the Director). The nonhuman primate work has also been funded by multiple awards from the HHS, NIH, NIAID, including Grants R38AI40297 (to B.I.S.) and U19AI131471 (to A.D.K.).
The online version of this article contains supplemental material.
Abbreviations used in this article
- DC
- dendritic cell
- IRS
- immune repertoire sequencing
- NP
- nonproliferating
- P
- proliferating
- QC
- quality-control
- scIRS
- single-cell immune repertoire sequencing
- UMAP, uniform manifold approximation and projection; UMI
- unique molecular identifier
- UTR
- untranslated region
- Received August 19, 2021.
- Accepted November 17, 2021.
- Copyright © 2022 by The American Association of Immunologists, Inc.
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