Distinct organization of adaptive immunity in the long-lived rodent Spalax galili
Jazyk angličtina Země Spojené státy americké Médium print-electronic
Typ dokumentu časopisecké články, práce podpořená grantem
PubMed
37118630
DOI
10.1038/s43587-021-00029-3
PII: 10.1038/s43587-021-00029-3
Knihovny.cz E-zdroje
- MeSH
- adaptivní imunita MeSH
- imunoglobuliny metabolismus MeSH
- interleukin-7 metabolismus MeSH
- lidé MeSH
- mikroftalmičtí podzemní hlodavci MeSH
- myši MeSH
- Spalax * genetika MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- imunoglobuliny MeSH
- interleukin-7 MeSH
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.
Central European Institute of Technology Brno Czech Republic
Institute of Systematics and Ecology of Animals SB RAS Novosibirsk Russia
Pirogov Russian National Research Medical University Moscow Russia
Privolzhsky Research Medical University Nizhny Novgorod Russia
Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry Moscow Russia
Zobrazit více v PubMed
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