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Virus-specific TRM cells of both donor and recipient origin reside in human kidney transplants
Daphne M. Hullegie-Peelen, Hector Tejeda Mora, Dennis A. Hesselink, Eric M.J. Bindels, Thierry P.P. van den Bosch, Marian C. Clahsen-van Groningen, Marjolein Dieterich, Sebastiaan Heidt, Robert C. Minnee, Georges M.G.M. Verjans, Martin J. Hoogduijn, Carla C. Baan
Daphne M. Hullegie-Peelen, Hector Tejeda Mora, Dennis A. Hesselink, Eric M.J. Bindels, Thierry P.P. van den Bosch, Marian C. Clahsen-van Groningen, Marjolein Dieterich, Sebastiaan Heidt, Robert C. Minnee, Georges M.G.M. Verjans, Martin J. Hoogduijn, Carla C. Baan
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Research Article Immunology Transplantation

Virus-specific TRM cells of both donor and recipient origin reside in human kidney transplants

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Abstract

Tissue-resident lymphocytes (TRLs) are critical for local protection against viral pathogens in peripheral tissue. However, it is unclear if TRLs perform a similar role in transplanted organs under chronic immunosuppressed conditions. In this study, we aimed to characterize the TRL compartment in human kidney transplant nephrectomies and examine its potential role in antiviral immunity. The TRL compartment of kidney transplants contained diverse innate, innate-like, and adaptive TRL populations expressing the canonical residency markers CD69, CD103, and CD49a. Chimerism of donor and recipient cells was present in 43% of kidney transplants and occurred in all TRL subpopulations. Paired single-cell transcriptome and T cell receptor (TCR) sequencing showed that donor and recipient tissue–resident memory T (TRM) cells exhibit striking similarities in their transcriptomic profiles and share numerous TCR clonotypes predicted to target viral pathogens. Virus dextramer staining further confirmed that CD8 TRM cells of both donor and recipient origin express TCRs with specificities against common viruses, including CMV, EBV, BK polyomavirus, and influenza A. Overall, the study results demonstrate that a diverse population of TRLs resides in kidney transplants and offer compelling evidence that TRM cells of both donor and recipient origin reside within this TRL population and may contribute to local protection against viral pathogens.

Authors

Daphne M. Hullegie-Peelen, Hector Tejeda Mora, Dennis A. Hesselink, Eric M.J. Bindels, Thierry P.P. van den Bosch, Marian C. Clahsen-van Groningen, Marjolein Dieterich, Sebastiaan Heidt, Robert C. Minnee, Georges M.G.M. Verjans, Martin J. Hoogduijn, Carla C. Baan

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Figure 4

Analysis of TCR clonality of donor and recipient TRM cells.

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Analysis of TCR clonality of donor and recipient TRM cells.
Single-cell ...
Single-cell TCR-Seq was performed in parallel with the scRNA-Seq of chimeric kidney transplant nephrectomy samples (n = 4; study sample identifiers G1, G9, G10, and G22). (A) UMAP visualization of TCR expansion in donor (left) and recipient (right) TRM cells. Different colors represent different degrees of TCR expansion. The range between the parentheses indicates the frequency of the expressed clonotype across the samples (×). (B and C) Clonotype size distribution across donor and recipient TRM cells (B) and per cell cluster (C). The proportion of clonotype size is indicated on the y axis. The number of cells within each clonotype size group is shown in the graph. (D) Shannon and inversed Pielou’s scores are shown for different cell clusters (left) and for donor and recipient TRM cells (right). Box-and-whisker plots show the median, IQR, minimum, and maximum values (excluding outliers). (E and G) Analysis of clonal overlap between different cell clusters (E) and samples (G). Numbers indicate the absolute number of shared unique clonotypes. (F) Venn diagram showing the unique clonotypes for recipient and donor TRM cells. The overlap indicates the number of shared unique clonotypes. (H) The top 10 unique clonotypes among donor and recipient TRM cells for each sample. The proportion of clonotypes is indicated on the y axis. Each color represents a unique clonotype. Colored bands connect the shared bar plot segments between donor and recipient. The sequence reads of the clonotypes are shown next to the graphs.

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