SARS-CoV2 mRNA-vaccination-induced Immunological Memory in Human Non-Lymphoid and Lymphoid Tissues

Tissue-resident lymphocytes provide organ-adapted protection against invading pathogens. Whereas their biology has been examined in great detail in various infection models, their generation and functionality in response to vaccination has not been comprehensively analyzed in humans. We therefore studied SARS-CoV2 mRNA-vaccine-specific T cells in surgery specimens of kidney, liver, lung, bone marrow and spleen in comparison to paired blood samples from largely virus-naïve individuals. As opposed to lymphoid tissues, non-lymphoid organs harbored significantly elevated frequencies of Spike-specific CD4+ T cells compared to paired peripheral blood showing hallmarks of tissue residency and an expanded memory pool. Organ-derived, vaccine-specific T helper (Th) cells were characterized by increased portions of multifunctional cells over those detected in blood. Single-cell RNA sequencing revealed functional rather than organ-specific clusters of Spike-reactive Th cells, indicating similar diversification programs across tissues. T cell receptor (TCR) repertoire analysis indicated that the TCR sequence is a major determinant of transcriptomic state in tissue-resident, vaccine-specific CD4+ T cells. In summary, our data demonstrate that SARS-CoV2 vaccination entails acquisition of tissue memory and residency features in organs distant from the inoculation site, thereby contributing to our understanding of how local tissue protection might be accomplished. One sentence summary SARS-CoV2 mRNA vaccination-induced CD4+ Th cells reside in both human lymphoid and non-lymphoid organs showing distinct adaptations in tissues with respect to memory differentiation, retention and function. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement KK is supported by grants from the Deutsche Forschungsgemeinschaft (KO-2270/7-1, KO-2270/4-1, KO-2270/8-1), Wilhelm-Sander Stiftung (2022.035.1), Zentrales Innovationsprogramm Mittelstand (KK5463201BA2) and unconditional project funding from Chiesi GmbH. The funder was not involved in the study design, collection, analysis, interpretation of data, the writing of this article or the decision to submit it for publication. ES is enrolled in the Charite Clinician Scientist Program funded by the Charite-Universitaetsmedizin Berlin and the Berlin Institute of Health. SL is supported by the German Ministry for Education and Research through the Medical Informatics Initiative (junior research group Medical Omics, 01ZZ2001). HS received funding from the Ministry for Science, Research, and Arts of Baden-Wuerttemberg, Germany and the European Commission (HORIZON2020 Project SUPPORT-E, no. 101015756). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The study was approved by the local Ethics Committee of the Charite-Universitaetsmedizin Berlin (EA4/066/19, EA1/353/16, EA4/115/21) and University Hospital Leipzig (322/17-ek, 237/22-ek) and was conducted in compliance with the declarations of Helsinki and Istanbul. All patients provided written informed consent. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All cellular data needed to evaluate the conclusions in the paper are present in the paper or the Supplementary Materials. Upon publication, scRNA-Seq data will be available at EGA for non-commercial research, subject to controlled access according to EU and German data protection regulations. This study did not use any unique codes, and all analyses were performed in R and Python using standard protocols from previously published packages as indicated. Requests for materials should be directed to K.K., A.S. or S.L. * CDR3 : complementarity-determining region COVID-19 : corona virus disease 2019 MNC : mononuclear cells MMR : measles, mumps, and rubella SARS-CoV2 : severe acute respiratory syndrome coronavirus type 2 TCR : T cell receptor Th cell : T helper cell Trm : tissue resident memory T cell UMAP : Uniform Manifold Approximation and Projection