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

ABSTRACT 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

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Contact customer support SIMILAR CONTENT BEING VIEWED BY OTHERS HALLMARKS OF T CELL AGING Article 13 May 2021 FUNCTIONAL T CELLS ARE CAPABLE OF SUPERNUMERARY CELL DIVISION AND LONGEVITY

Article 18 January 2023 ASYMMETRIC CELL DIVISION SHAPES NAIVE AND VIRTUAL MEMORY T-CELL IMMUNITY DURING AGEING Article Open access 11 May 2021 DATA AVAILABILITY TCR and IGH profiling and

RNA-seq raw sequencing data were deposited in GenBank under BioProjects PRJNA432350 and PRJNA643223. _Spalax_ TCR and IGH gene references are available at

https://doi.org/10.5281/zenodo.4473340. Extracted TCR clonesets, gene expression data and cloneset metrics are available in figshare:

https://figshare.com/projects/Distinct_organization_of_adaptive_immunity_in_long-lived_rodent_Spalax_Galili/28773. CODE AVAILABILITY See Supplementary Note 2 for the de novo transcriptome

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of Medicine, Technion, for the MR imaging and image analysis. The work was supported by the Russian Science Foundation (grant no. 16-15-00149, to O.V.B.), the Ministry of Education and

Science of the Russian Federation (grant no. 14.W03.31.0005, to D.M.C., for part of mouse samples preparation) and the Israel Science Foundation (grant no. 1935/17, to I.S.). M.M. was

supported by the European Regional Development Fund–Project ‘MSCAfellow3@MUNI’ (grant no. CZ.02.2.69/0.0/0.0/19_074/0012727). AUTHOR INFORMATION Author notes * These authors contributed

equally: M. Izraelson, M. Metsger, A.N. Davydov. * These authors jointly supervised this work: I. Shams, O. V. Britanova, D. M. Chudakov. AUTHORS AND AFFILIATIONS * Shemyakin and Ovchinnikov

Institute of Bioorganic Chemistry, Moscow, Russia M. Izraelson, I. A. Shagina, A. S. Obraztsova, I. Z. Mamedov, T. O. Nakonechnaya, M. Shugay, D. A. Bolotin, D. B. Staroverov, G. V.

Sharonov, S. Lukyanov, O. V. Britanova & D. M. Chudakov * Privolzhsky Research Medical University, Nizhny Novgorod, Russia M. Izraelson, I. Z. Mamedov, L. N. Volchkova, T. O.

Nakonechnaya, M. Shugay, D. B. Staroverov, G. V. Sharonov, E. V. Zagaynova & D. M. Chudakov * Pirogov Russian National Research Medical University, Moscow, Russia M. Izraelson, I. A.

Shagina, I. Z. Mamedov, T. O. Nakonechnaya, M. Shugay, D. A. Bolotin, D. B. Staroverov, G. V. Sharonov, S. Lukyanov & D. M. Chudakov * Central European Institute of Technology, Brno,

Czech Republic M. Metsger, A. N. Davydov, I. Z. Mamedov & D. M. Chudakov * Institute of Evolution & Department of Evolutionary and Environmental Biology, University of Haifa, Haifa,

Israel M. A. Dronina, D. A. Miskevich & I. Shams * Institute of Systematics and Ecology of Animals SB RAS, Novosibirsk, Russia E. Y. Kondratyuk Authors * M. Izraelson View author

publications You can also search for this author inPubMed Google Scholar * M. Metsger View author publications You can also search for this author inPubMed Google Scholar * A. N. Davydov

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author inPubMed Google Scholar * L. N. Volchkova View author publications You can also search for this author inPubMed Google Scholar * T. O. Nakonechnaya View author publications You can

also search for this author inPubMed Google Scholar * M. Shugay View author publications You can also search for this author inPubMed Google Scholar * D. A. Bolotin View author publications

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author publications You can also search for this author inPubMed Google Scholar * E. Y. Kondratyuk View author publications You can also search for this author inPubMed Google Scholar * E.

V. Zagaynova View author publications You can also search for this author inPubMed Google Scholar * S. Lukyanov View author publications You can also search for this author inPubMed Google

Scholar * I. Shams View author publications You can also search for this author inPubMed Google Scholar * O. V. Britanova View author publications You can also search for this author

inPubMed Google Scholar * D. M. Chudakov View author publications You can also search for this author inPubMed Google Scholar CONTRIBUTIONS M.I., I.A.S., M.A.D., D.A.M., I.Z.M., L.N.V.,

T.O.N., D.B.S., G.V.S., E.Y.K., I.S. and O.V.B. performed wet laboratory experiments. M.I., M.M., A.N.D., A.S.O., M.S., D.A.B. and O.V.B. performed data analysis. E.V.Z., S.L., I.S., O.V.B.

and D.M.C. designed and supervised the project, designed experiments and worked on the manuscript. I.S., O.V.B. and D.M.C. are the co-senior authors. CORRESPONDING AUTHORS Correspondence to

O. V. Britanova or D. M. Chudakov. ETHICS DECLARATIONS COMPETING INTERESTS The authors declare no competing interests. ADDITIONAL INFORMATION PEER REVIEW INFORMATION _Nature Aging_ thanks

Vera Gorbunova and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. PUBLISHER’S NOTE Springer Nature remains neutral with regard to jurisdictional

claims in published maps and institutional affiliations. EXTENDED DATA EXTENDED DATA FIG. 1 PHYLOGENETIC TREE OF NUCLEOTIDE SEQUENCES OF IGVH SEGMENTS. The gene segments are highlighted in

blue for mouse, orange for _Spalax_, and green for rat. Number after asterisk corresponds to the allele name. Only functional alleles are shown. The neighbour-joining trees were constructed

with the evolutionary distances computed using the Maximum Composite Likelihood method, with a bootstrap of 1,000 replicates. EXTENDED DATA FIG. 2 PHYLOGENETIC TREE OF NUCLEOTIDE SEQUENCES

OF TRAV SEGMENTS. Gene segments are highlighted in blue for mouse, orange for _Spalax_, and green for rat. The neighbour-joining trees were constructed with the evolutionary distances

computed using the Maximum Composite Likelihood method, with a bootstrap of 1,000 replicates. The tree is drawn to scale, with branch lengths in the same units as the evolutionary distances

used to output the phylogenetic tree. Number after asterisk corresponds to the allele name. Only functional alleles are shown. EXTENDED DATA FIG. 3 ASSESSING THE SIZE OF THE THYMUS IN YOUNG

AND ADULT SPALAX. A. Histological verification of thymic tissue localization showing its connection to surrounding tissues. Paraffin-embedded tissue after PFA fixation. Hematoxylin and eosin

staining of section from young _Spalax_ (<3 years) at 20x magnification. H - heart (aorta), T - thymus. Staining was performed on two animals. A,B. Representative thymus MRI sequential

images for young (B) and old (C) _Spalax_ showing the sagittal sections. White arrows point to the thymic lobes. EXTENDED DATA FIG. 4 PHYSICOCHEMICAL CHARACTERISTICS OF TCR CDR3Β

REPERTOIRES. Mean characteristics of the five amino acid residues in the center of CDR3β are shown for the four age groups in human, mouse, and _Spalax_. The measured parameters are A,

normalized strength (strongly interacting amino acids), B, normalized volume (bulky amino acids), and C, normalized hydrophobicity (based on inverted Kidera factor 4). P-values were

calculated using two-sided Welch’s t-test. * < 0.05, ** < 0.01, *** - < 0.001, ****<0.0001. n = 19 mice and 17 _Spalax_ animals. EXTENDED DATA FIG. 5 EXPRESSION OF T-CELL-RELATED

GENES IN MOUSE AND SPALAX SPLEEN ACROSS AGE GROUPS. Expression of A, T cell transcription factors, B, checkpoint molecules, and C, naive/homeostatic genes, presented as non-normalized TPM

values (corresponding to data shown in Fig. 4b–d). A-C. P-values represent one-way ANOVA with Tukey’s test, * < 0.05, ** < 0.01, *** - < 0.001. The boxplots visualize the median,

hinges representing the 25th and 75th percentiles, and whiskers extending to the values that are no further than 1.5 × IQR from the upper or the lower hinge. n = 12 mice and 12 _Spalax_ (3

animals per age group) were used for the analysis. D,E. Expression levels of (D) basic cytokines and (E) receptors (non z-scaled data corresponding to data shown in Fig. 4e,f). The P-value

and Log-transformed fold changes (Log2FC) shown on the left represent the differential gene expression analysis results calculated between species (9 animals for each species excluding

newborn, 3 animals per age group) according to the procedure described in the Methods section. EXTENDED DATA FIG. 6 BUSCO ANALYSIS OF TRANSCRIPTOME COMPLETENESS. Cumulative percentage of

orthologues calculated using BUSCO with --auto-lineage-euk option against four transcriptome assemblies prepared by different tools (Shannon, SPAdes with kmer size of 55 and 75, Trinity).

The Final_assembly represents the result of EvidentialGene pipeline applied to the merged data from 4 different assemblies. SUPPLEMENTARY INFORMATION SUPPLEMENTARY INFORMATION Supplementary

Notes 1 and 2 and Tables 1, 3 and 4. REPORTING SUMMARY SUPPLEMENTARY TABLE Supplementary Table 2. RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE

Izraelson, M., Metsger, M., Davydov, A.N. _et al._ Distinct organization of adaptive immunity in the long-lived rodent _Spalax galili_. _Nat Aging_ 1, 179–189 (2021).

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