Distinct organization of adaptive immunity in the long-lived rodent Spalax galili

. 2021 Feb ; 1 (2) : 179-189. [epub] 20210208

Jazyk angličtina Země Spojené státy americké Médium print-electronic

Typ dokumentu časopisecké články, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/pmid37118630
Odkazy

PubMed 37118630
DOI 10.1038/s43587-021-00029-3
PII: 10.1038/s43587-021-00029-3
Knihovny.cz E-zdroje

A balanced immune response is a cornerstone of healthy aging. Here, we uncover distinctive features of the long-lived blind mole-rat (Spalax spp.) adaptive immune system, relative to humans and mice. The T-cell repertoire remains diverse throughout the Spalax lifespan, suggesting a paucity of large long-lived clones of effector-memory T cells. Expression of master transcription factors of T-cell differentiation, as well as checkpoint and cytotoxicity genes, remains low as Spalax ages. The thymus shrinks as in mice and humans, while interleukin-7 and interleukin-7 receptor expression remains high, potentially reflecting the sustained homeostasis of naive T cells. With aging, immunoglobulin hypermutation level does not increase and the immunoglobulin-M repertoire remains diverse, suggesting shorter B-cell memory and sustained homeostasis of innate-like B cells. The Spalax adaptive immune system thus appears biased towards sustained functional and receptor diversity over specialized, long-lived effector-memory clones-a unique organizational strategy that potentially underlies this animal's extraordinary longevity and healthy aging.

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Jameson, S. C. & Masopust, D. Understanding subset diversity in T cell memory. Immunity 48, 214–226 (2018). PubMed DOI PMC

Gasper, D. J., Tejera, M. M. & Suresh, M. CD4 T-cell memory generation and maintenance. Crit. Rev. Immunol. 34, 121–146 (2014). PubMed DOI PMC

Kurosaki, T., Kometani, K. & Ise, W. Memory B cells. Nat. Rev. Immunol. 15, 149–159 (2015). PubMed DOI

McHeyzer-Williams, M., Okitsu, S., Wang, N. & McHeyzer-Williams, L. Molecular programming of B cell memory. Nat. Rev. Immunol. 12, 24–34 (2011). PubMed DOI PMC

Grimsholm, O. et al. The interplay between CD27(dull) and CD27(bright) B cells ensures the flexibility, stability, and resilience of human B cell memory. Cell Rep. 30, 2963–2977 (2020). PubMed DOI

Britanova, O. V. et al. Dynamics of individual T cell repertoires: from cord blood to centenarians. J. Immunol. 196, 5005–5013 (2016). PubMed DOI

Rose, N. R. Infection, mimics, and autoimmune disease. J. Clin. Invest. 107, 943–944 (2001). PubMed DOI PMC

Kivity, S., Agmon-Levin, N., Blank, M. & Shoenfeld, Y. Infections and autoimmunity—friends or foes? Trends Immunol. 30, 409–414 (2009). PubMed DOI

Van Den Berg, H. A., Molina-Paris, C. & Sewell, A. K. Specific T-cell activation in an unspecific T-cell repertoire. Sci. Prog. 94, 245–264 (2011). DOI

Goronzy, J. J. & Weyand, C. M. Successful and maladaptive T cell aging. Immunity 46, 364–378 (2017). PubMed DOI PMC

Minato, N., Hattori, M. & Hamazaki, Y. Physiology and pathology of T-cell aging. Int. Immunol. 32, 223–231 (2020). PubMed DOI PMC

Turner, D. L. & Farber, D. L. Mucosal resident memory CD4 T cells in protection and immunopathology. Front. Immunol. 5, 331 (2014). PubMed DOI PMC

Tacutu, R. et al. Human ageing genomic resources: new and updated databases. Nucleic Acids Res. 46, D1083–D1090 (2018). PubMed DOI

Ruby, J. G., Smith, M. & Buffenstein, R. Naked mole-rat mortality rates defy gompertzian laws by not increasing with age. eLife 7, e31157 (2018). PubMed DOI PMC

Edrey, Y. H., Hanes, M., Pinto, M., Mele, J. & Buffenstein, R. Successful aging and sustained good health in the naked mole rat: a long-lived mammalian model for biogerontology and biomedical research. ILAR J. 52, 41–53 (2011). PubMed DOI

Gorbunova, V. et al. Cancer resistance in the blind mole rat is mediated by concerted necrotic cell death mechanism. Proc. Natl Acad. Sci. USA 109, 19392–19396 (2012). PubMed DOI PMC

Tian, X. et al. High-molecular-mass hyaluronan mediates the cancer resistance of the naked mole rat. Nature 499, 346–349 (2013). PubMed DOI PMC

Manov, I. et al. Pronounced cancer resistance in a subterranean rodent, the blind mole-rat, Spalax: in vivo and in vitro evidence. BMC Biol. 11, 91 (2013). PubMed DOI PMC

Gorbunova, V., Seluanov, A., Zhang, Z., Gladyshev, V. N. & Vijg, J. Comparative genetics of longevity and cancer: insights from long-lived rodents. Nat. Rev. Genet. 15, 531–540 (2014). PubMed DOI PMC

Schmidt, H. et al. Hypoxia tolerance, longevity and cancer-resistance in the mole rat Spalax—a liver transcriptomics approach. Sci. Rep. 7, 14348 (2017). PubMed DOI PMC

Altwasser, R. et al. The transcriptome landscape of the carcinogenic treatment response in the blind mole rat: insights into cancer resistance mechanisms. BMC Genomics 20, 17 (2019). PubMed DOI PMC

Fang, X. et al. Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax. Nat. Commun. 5, 3966 (2014). PubMed DOI

Bolotin, D. A. et al. MiXCR: software for comprehensive adaptive immunity profiling. Nat. Methods 12, 380–381 (2015). PubMed DOI

Lanning, D. K., Esteves, P. J. & Knight, K. L. The remnant of the European rabbit (Oryctolagus cuniculus) IgD gene. PLoS ONE 12, e0182029 (2017). PubMed DOI PMC

Izraelson, M. et al. Comparative analysis of murine T-cell receptor repertoires. Immunology 153, 133–144 (2018). PubMed DOI

Posnett, D. N., Sinha, R., Kabak, S. & Russo, C. Clonal populations of T cells in normal elderly humans: the T cell equivalent to “benign monoclonal gammapathy”. J. Exp. Med. 179, 609–618 (1994). PubMed DOI

Messaoudi, I., Lemaoult, J., Guevara-Patino, J. A., Metzner, B. M. & Nikolich-Zugich, J. Age-related CD8 T cell clonal expansions constrict CD8 T cell repertoire and have the potential to impair immune defense. J. Exp. Med. 200, 1347–1358 (2004). PubMed DOI PMC

Mogilenko, D. A. et al. Comprehensive profiling of an aging immune system reveals clonal GZMK PubMed DOI

Franckaert, D. et al. Premature thymic involution is independent of structural plasticity of the thymic stroma. Eur. J. Immunol. 45, 1535–1547 (2015). PubMed DOI PMC

Gui, J., Mustachio, L. M., Su, D. M. & Craig, R. W. Thymus size and age-related thymic involution: early programming, sexual dimorphism, progenitors and stroma. Aging Dis. 3, 280–290 (2012). PubMed PMC

Bonati, A. et al. T-cell receptor beta-chain gene rearrangement and expression during human thymic ontogenesis. Blood 79, 1472–1483 (1992). PubMed DOI

Murugan, A., Mora, T., Walczak, A. M. & Callan, C. G. Jr. Statistical inference of the generation probability of T-cell receptors from sequence repertoires. Proc. Natl Acad. Sci. USA 109, 16161–16166 (2012). PubMed DOI PMC

Venturi, V. et al. A mechanism for TCR sharing between T cell subsets and individuals revealed by pyrosequencing. J. Immunol. 186, 4285–4294 (2011). PubMed DOI

Quigley, M. F. et al. Convergent recombination shapes the clonotypic landscape of the naive T-cell repertoire. Proc. Natl Acad. Sci. USA 107, 19414–19419 (2010). PubMed DOI PMC

Nizetic, D. et al. Major histocompatibility complex of the mole-rat. I. Serological and biochemical analysis. Immunogenetics 20, 443–451 (1984). PubMed DOI

Krishna, C., Chowell, D., Gonen, M., Elhanati, Y. & Chan, T. A. Genetic and environmental determinants of human TCR repertoire diversity. Immun. Ageing 17, 26 (2020). PubMed DOI PMC

Zvyagin, I. V. et al. Distinctive properties of identical twins’ TCR repertoires revealed by high-throughput sequencing. Proc. Natl Acad. Sci. USA 111, 5980–5985 (2014). PubMed DOI PMC

Tanno, H. et al. Determinants governing T cell receptor alpha/beta-chain pairing in repertoire formation of identical twins. Proc. Natl Acad. Sci. USA 117, 532–540 (2020). PubMed DOI

Logunova, N. N. et al. MHC-II alleles shape the CDR3 repertoires of conventional and regulatory naive CD4 PubMed DOI PMC

Egorov, E. S. et al. The changing landscape of naive T cell receptor repertoire with human aging. Front. Immunol. 9, 1618 (2018). PubMed DOI PMC

Garner, L. C., Klenerman, P. & Provine, N. M. Insights into mucosal-associated invariant T cell biology from studies of invariant natural killer T cells. Front. Immunol. 9, 1478 (2018). PubMed DOI PMC

Howson, L. J. et al. MAIT cell clonal expansion and TCR repertoire shaping in human volunteers challenged with Salmonella Paratyphi A. Nat. Commun. 9, 253 (2018). PubMed DOI PMC

Reantragoon, R. et al. Antigen-loaded MR1 tetramers define T cell receptor heterogeneity in mucosal-associated invariant T cells. J. Exp. Med. 210, 2305–2320 (2013). PubMed DOI PMC

Madi, A. et al. T cell receptor repertoires of mice and humans are clustered in similarity networks around conserved public CDR3 sequences. eLife 6, e22057 (2017). PubMed DOI PMC

Shugay, M. E. A. VDJdb: a curated database of T-cell receptor sequences with known antigen specificity. Nucleic Acids Res. 46, D419–D427 (2017). DOI PMC

Bedel, R. et al. Effective functional maturation of invariant natural killer T cells is constrained by negative selection and T-cell antigen receptor affinity. Proc. Natl Acad. Sci. USA 111, E119–E128 (2014). PubMed DOI

Koay, H. F. et al. Diverse MR1-restricted T cells in mice and humans. Nat. Commun. 10, 2243 (2019). PubMed DOI PMC

DeWitt, W. S. 3rd et al. Human T cell receptor occurrence patterns encode immune history, genetic background, and receptor specificity. eLife 7, e38358 (2018). PubMed DOI PMC

Pieren, D. K. J., Smits, N. A. M., van de Garde, M. D. B. & Guichelaar, T. Response kinetics reveal novel features of ageing in murine T cells. Sci. Rep. 9, 5587 (2019). PubMed DOI PMC

Fang, D. & Zhu, J. Dynamic balance between master transcription factors determines the fates and functions of CD4 T cell and innate lymphoid cell subsets. J. Exp. Med. 214, 1861–1876 (2017). PubMed DOI PMC

Elyahu, Y. et al. Aging promotes reorganization of the CD4 T cell landscape toward extreme regulatory and effector phenotypes. Sci. Adv. 5, eaaw8330 (2019). PubMed DOI PMC

Peters, M. J. et al. The transcriptional landscape of age in human peripheral blood. Nat. Commun. 6, 8570 (2015). PubMed DOI

Marquez, E. J. et al. Sexual-dimorphism in human immune system aging. Nat. Commun. 11, 751 (2020). PubMed DOI PMC

Eberl, G. et al. An essential function for the nuclear receptor RORγt in the generation of fetal lymphoid tissue inducer cells. Nat. Immunol. 5, 64–73 (2004). PubMed DOI

Garg, S. K. et al. Aging is associated with increased regulatory T-cell function. Aging Cell 13, 441–448 (2014). PubMed DOI PMC

Channappanavar, R., Twardy, B. S., Krishna, P. & Suvas, S. Advancing age leads to predominance of inhibitory receptor expressing CD4 T cells. Mech. Ageing Dev. 130, 709–712 (2009). PubMed DOI

Burchill, M. A., Yang, J., Vogtenhuber, C., Blazar, B. R. & Farrar, M. A. IL-2 receptor β-dependent STAT5 activation is required for the development of Foxp3 PubMed DOI

Williams, M. A., Tyznik, A. J. & Bevan, M. J. Interleukin-2 signals during priming are required for secondary expansion of CD8 PubMed DOI PMC

Leonard, W. J. & Wan, C. K. IL-21 signaling in immunity. F1000Res 5, 224 (2016). DOI

Skak, K., Frederiksen, K. S. & Lundsgaard, D. Interleukin-21 activates human natural killer cells and modulates their surface receptor expression. Immunology 123, 575–583 (2008). PubMed DOI PMC

Surh, C. D. & Sprent, J. Homeostasis of naive and memory T cells. Immunity 29, 848–862 (2008). PubMed DOI

Lynch, E. A., Heijens, C. A., Horst, N. F., Center, D. M. & Cruikshank, W. W. Cutting edge: IL-16/CD4 preferentially induces Th1 cell migration: requirement of CCR5. J. Immunol. 171, 4965–4968 (2003). PubMed DOI

Skundric, D. S., Cai, J., Cruikshank, W. W. & Gveric, D. Production of IL-16 correlates with CD4 PubMed DOI PMC

Fiorentino, D. F., Bond, M. W. & Mosmann, T. R. Two types of mouse T helper cell. IV. Th2 clones secrete a factor that inhibits cytokine production by Th1 clones. J. Exp. Med. 170, 2081–2095 (1989). PubMed DOI

Moore, K. W., de Waal Malefyt, R., Coffman, R. L. & O’Garra, A. Interleukin-10 and the interleukin-10 receptor. Annu. Rev. Immunol. 19, 683–765 (2001). PubMed DOI

Bagnasco, D., Ferrando, M., Varricchi, G., Passalacqua, G. & Canonica, G. W. A critical evaluation of anti-IL-13 and anti-IL-4 strategies in severe asthma. Int. Arch. Allergy Immunol. 170, 122–131 (2016). PubMed DOI

Park, H. et al. A distinct lineage of CD4 T cells regulates tissue inflammation by producing interleukin 17. Nat. Immunol. 6, 1133–1141 (2005). PubMed DOI PMC

Ivanov, I. I. et al. The orphan nuclear receptor RORγt directs the differentiation program of proinflammatory IL-17 PubMed DOI

Soares, M. V. et al. IL-7-dependent extrathymic expansion of CD45RA PubMed

Nguyen, V., Mendelsohn, A. & Larrick, J. W. Interleukin-7 and immunosenescence. J. Immunol. Res. 2017, 4807853 (2017). PubMed DOI PMC

Passtoors, W. M. et al. IL7R gene expression network associates with human healthy ageing. Immun. Ageing 12, 21 (2015). PubMed DOI PMC

Horns, F. et al. Lineage tracing of human B cells reveals the in vivo landscape of human antibody class switching. eLife 5, e16578 (2016). PubMed DOI PMC

Ventura, M. T., Casciaro, M., Gangemi, S. & Buquicchio, R. Immunosenescence in aging: between immune cells depletion and cytokines up-regulation. Clin. Mol. Allergy 15, 21 (2017). PubMed DOI PMC

Paganelli, R. et al. Changes in circulating B cells and immunoglobulin classes and subclasses in a healthy aged population. Clin. Exp. Immunol. 90, 351–354 (1992). PubMed DOI PMC

Rogosch, T. et al. IgA response in preterm neonates shows little evidence of antigen-driven selection. J. Immunol. 189, 5449–5456 (2012). PubMed DOI

de Jong, B. G. et al. Human IgG2- and IgG4-expressing memory B cells display enhanced molecular and phenotypic signs of maturity and accumulate with age. Immunol. Cell Biol. 95, 744–752 (2017). PubMed DOI PMC

Ghraichy, M. et al. Maturation of the human immunoglobulin heavy chain repertoire with age. Front. Immunol. 11, 1734 (2020). PubMed DOI PMC

Choi, Y. S., Dieter, J. A., Rothaeusler, K., Luo, Z. & Baumgarth, N. B-1 cells in the bone marrow are a significant source of natural IgM. Eur. J. Immunol. 42, 120–129 (2012). PubMed DOI

Baumgarth, N. A Hard(y) look at B-1 cell development and function. J. Immunol. 199, 3387–3394 (2017). PubMed DOI

Holodick, N. E. & Rothstein, T. L. B cells in the aging immune system: time to consider B-1 cells. Ann. N. Y. Acad. Sci. 1362, 176–187 (2015). PubMed DOI PMC

Prohaska, T. A. et al. Massively parallel sequencing of peritoneal and splenic B cell repertoires highlights unique properties of B-1 cell antibodies. J. Immunol. 200, 1702–1717 (2018). PubMed

Kosmrlj, A., Jha, A. K., Huseby, E. S., Kardar, M. & Chakraborty, A. K. How the thymus designs antigen-specific and self-tolerant T cell receptor sequences. Proc. Natl Acad. Sci. USA 105, 16671–16676 (2008). PubMed DOI PMC

Kosmrlj, A. et al. Effects of thymic selection of the T-cell repertoire on HLA class I-associated control of HIV infection. Nature 465, 350–354 (2010). PubMed DOI PMC

Stadinski, B. D. et al. Hydrophobic CDR3 residues promote the development of self-reactive T cells. Nat. Immunol. 17, 946–955 (2016). PubMed DOI PMC

Tang, A. L. et al. CTLA4 expression is an indicator and regulator of steady-state CD4 PubMed DOI

Klocke, K., Sakaguchi, S., Holmdahl, R. & Wing, K. Induction of autoimmune disease by deletion of CTLA-4 in mice in adulthood. Proc. Natl Acad. Sci. USA 113, E2383–E2392 (2016). PubMed DOI PMC

Walker, L. S. K. EFIS lecture: understanding the CTLA-4 checkpoint in the maintenance of immune homeostasis. Immunol. Lett. 184, 43–50 (2017). PubMed DOI

den Braber, I. et al. Maintenance of peripheral naive T cells is sustained by thymus output in mice but not humans. Immunity 36, 288–297 (2012). DOI

Kim, E. B. et al. Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Nature 479, 223–227 (2011). PubMed DOI PMC

Lewis, K. N. et al. Unraveling the message: insights into comparative genomics of the naked mole-rat. Mamm. Genome 27, 259–278 (2016). PubMed DOI PMC

Malik, A. et al. Genome maintenance and bioenergetics of the long-lived hypoxia-tolerant and cancer-resistant blind mole rat, Spalax: a cross-species analysis of brain transcriptome. Sci. Rep. 6, 38624 (2016). PubMed DOI PMC

Matz, M. et al. Amplification of cDNA ends based on template-switching effect and step-out PCR. Nucleic Acids Res. 27, 1558–1560 (1999). PubMed DOI PMC

Egorov, E. S. et al. Quantitative profiling of immune repertoires for minor lymphocyte counts using unique molecular identifiers. J. Immunol. 194, 6155–6163 (2015). PubMed DOI

Turchaninova, M. A. et al. High-quality full-length immunoglobulin profiling with unique molecular barcoding. Nat. Protoc. 11, 1599–1616 (2016). PubMed DOI

Weber, J. et al. PiggyBac transposon tools for recessive screening identify B-cell lymphoma drivers in mice. Nat. Commun. 10, 1415 (2019). PubMed DOI PMC

Kivioja, T. et al. Counting absolute numbers of molecules using unique molecular identifiers. Nat. Methods 9, 72–74 (2012). DOI

Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics 26, 589–595 (2010). PubMed DOI PMC

Yu, Y. et al. A rat RNA-seq transcriptomic BodyMap across 11 organs and 4 developmental stages. Nat. Commun. 5, 3230 (2014). PubMed DOI

Shugay, M. et al. Towards error-free profiling of immune repertoires. Nat. Methods 11, 653–655 (2014). PubMed DOI

Shugay, M. et al. VDJtools: unifying post-analysis of T cell receptor repertoires. PLoS Comput. Biol. 11, e1004503 (2015). PubMed DOI PMC

Tumeh, P. C. et al. PD-1 blockade induces responses by inhibiting adaptive immune resistance. Nature 515, 568–571 (2014). PubMed DOI PMC

Bolotin, D. A. et al. Antigen receptor repertoire profiling from RNA-seq data. Nat. Biotechnol. 35, 908–911 (2017). PubMed DOI PMC

Hughes, J. B., Hellmann, J. J., Ricketts, T. H. & Bohannan, B. J. Counting the uncountable: statistical approaches to estimating microbial diversity. Appl. Environ. Microbiol. 67, 4399–4406 (2001). PubMed DOI PMC

Chiu, C. H. & Chao, A. Estimating and comparing microbial diversity in the presence of sequencing errors. PeerJ 4, e1634 (2016). PubMed DOI PMC

Shugay, M. et al. Huge overlap of individual TCR beta repertoires. Front. Immunol. 4, 466 (2013). PubMed DOI PMC

Mamrot, J. et al. De novo transcriptome assembly for the spiny mouse (Acomys cahirinus). Sci. Rep. 7, 8996 (2017). PubMed DOI PMC

Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014). PubMed DOI PMC

Bushmanova, E., Antipov, D., Lapidus, A. & Prjibelski, A. D. rnaSPAdes: a de novo transcriptome assembler and its application to RNA-seq data. Gigascience 8, giz100 (2019). PubMed DOI PMC

Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat. Biotechnol. 29, 644–652 (2011). PubMed DOI PMC

Simao, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212 (2015). PubMed DOI

Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinformatics 10, 421 (2009). PubMed DOI PMC

Finn, R. D. et al. Pfam: the protein families database. Nucleic Acids Res. 42, D222–D230 (2014). PubMed DOI

Nielsen, H. Predicting secretory proteins with SignalP. Methods Mol. Biol. 1611, 59–73 (2017). PubMed DOI

Krogh, A., Larsson, B., von Heijne, G. & Sonnhammer, E. L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305, 567–580 (2001). PubMed DOI

Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012). PubMed DOI PMC

Li, B. & Dewey, C. N. RSEM: accurate transcript quantification from RNA-seq data with or without a reference genome. BMC Bioinformatics 12, 323 (2011). PubMed DOI PMC

Durinck, S., Spellman, P. T., Birney, E. & Huber, W. Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nat. Protoc. 4, 1184–1191 (2009). PubMed DOI PMC

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