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Expansible residence decentralizes immune homeostasis

Abstract

In metazoans, specific tasks are relegated to dedicated organs that are established early in development, occupy discrete locations and typically remain fixed in size. The adult immune system arises from a centralized haematopoietic niche that maintains self-renewing potential1,2, and—upon maturation—becomes distributed throughout the body to monitor environmental perturbations, regulate tissue homeostasis and mediate organism-wide defence. Here we examine how immunity is integrated within adult mouse tissues, and address issues of durability, expansibility and contributions to organ cellularity. Focusing on antiviral T cell immunity, we observed durable maintenance of resident memory T cells up to 450 days after infection. Once established, resident T cells did not require the T cell receptor for survival or retention of a poised, effector-like state. Although resident memory indefinitely dominated most mucosal organs, surgical separation of parabiotic mice revealed a tissue-resident provenance for blood-borne effector memory T cells, and circulating memory slowly made substantial contributions to tissue immunity in some organs. After serial immunizations or cohousing with pet-shop mice, we found that in most tissues, tissue pliancy (the capacity of tissues to vary their proportion of immune cells) enables the accretion of tissue-resident memory, without axiomatic erosion of pre-existing antiviral T cell immunity. Extending these findings, we demonstrate that tissue residence and organ pliancy are generalizable aspects that underlie homeostasis of innate and adaptive immunity. The immune system grows commensurate with microbial experience, reaching up to 25% of visceral organ cellularity. Regardless of the location, many populations of white blood cells adopted a tissue-residency program within nonlymphoid organs. Thus, residence—rather than renewal or recirculation—typifies nonlymphoid immune surveillance, and organs serve as pliant storage reservoirs that can accommodate continuous expansion of the cellular immune system throughout life. Although haematopoiesis restores some elements of the immune system, nonlymphoid organs sustain an accrual of durable tissue-autonomous cellular immunity that results in progressive decentralization of organismal immune homeostasis.

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Fig. 1: Residence sustains organism-wide autonomous immune surveillance by T cells.
Fig. 2: The CD8+ T cell compartment expands to accommodate new and pre-existing resident memory.
Fig. 3: Tissue pliancy enables immune expansion after microbial conditioning.
Fig. 4: Tissue residence typifies organism-wide immune surveillance.

Data availability

The data that support the findings of this study are available from the corresponding author upon reasonable request. Source data are provided with this paper.

Code availability

ImageJ scripts developed for cell enumeration are available at http://github.com/wijey001/count.

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Acknowledgements

We thank members of the laboratories of D.M. and V.V. for helpful discussions; C. Klose and D. Artis for advice in identifying innate lymphoid cells; University of Minnesota Flow Cytometry Resource; University Imaging Centers (J. Mitchell and T. Pengo); and the Biosafety Level 3 Program. This study was supported by National Institutes of Health (NIH) grants R01 AI084913, R01 AI146032 (D.M.), F30 DK114942 and T32 AI007313 (S.W.) and the Howard Hughes Medical Institute Faculty Scholars program (D.M.).

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Contributions

S.W., L.K.B., M.J.P., J.M.S., O.A.A., R.R., E.M.S. and P.C.R. performed the experiments; S.W., V.V. and D.M. designed the experiments and wrote the manuscript.

Corresponding author

Correspondence to David Masopust.

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The authors declare no competing interests.

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Peer review information Nature thanks Evan Newell 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 figures and tables

Extended Data Fig. 1 Compartmentalized decay of uterine T cells concomitant with morphological changes in tissue architecture over time.

a, Representative immunofluorescence of uterine tissue. b, The frequency of P14 memory CD8+ T cells in uterine compartments was assessed by quantitative immunofluorescent microscopy at day 60 (n = 6 mice) and day 200 (n = 7 mice) after LCMV infection in one experiment. c, Representative immunofluorescence images of mouse uterine tissue at various ages, demonstrating endometrial vacuolations in older mice. d, e, Representative immunofluorescence images of mouse salivary gland at various time points demonstrating emergence of salivary gland tertiary lymphoid organs in older mice (d) and expression of peripheral node addressin (PNAd) (e). Morphology representative of n > 12 mice, PNAd staining representative of n = 5 mice (ce). Scale bar, 100 μm (a), 500 μm (c, 70 weeks in d), 200 μm (10 and 35 weeks in d, e). Statistical significance was determined by two-tailed Mann–Whitney U test (b). *P = 0.0221, **P = 0.0023 (endometrium) or **P = 0.0082 (perimetrium). Data are mean ± s.e.m.

Source data

Extended Data Fig. 2 Selective TCR ablation using Tracfl/fl mice reveals TCR-independent homeostasis of TRM cells.

a, Experimental model. Thy1.1CD45.2+ Tracfl/fl mice and Thy1.1+CD45.2+ wild-type B6 mice were infected with LCMV. After 30 days, 107 lymphocytes—isolated from secondary lymphoid organs—were transferred into naive CD45.1+ B6 mice, which were subsequently infected with LCMV. Forty days after infection, CD45.1+ mice were treated with tamoxifen to selectively ablate TCR from transferred Thy1.1CD45.2+ Tracfl/fl secondary memory T cells. b, c, LCMV-specific secondary memory T cells in peripheral blood are shown 40 days after LCMV infection (before tamoxifen treatment) (b). Data pooled from 3 independent experiments for a total of n = 8 mice (c). d, e, Selective TCR ablation of Tracfl/fl secondary memory CD8+ T cells, as measured by ex vivo peptide stimulation assay. Sixty days after tamoxifen treatment of CD45.1+ B6 recipient mice, splenocytes were isolated and stimulated in vitro with gp33–41 peptide. Cytokine production by TCR Tracfl/fl memory CD8+ T cells and TCR+ wild-type memory CD8+ T cells from spleen is shown, and reflects n = 6 mice. f, Frequency of cells that lack TCRβ expression on Tracfl/fl memory CD8+ T cells. Data pooled from 4 independent experiments for a total of n = 8–10 mice (n varies by tissue). g, Representative flow cytometry, depicting expression of tissue-resident markers on small-intestine epithelial memory CD8+ T cells 60 days after tamoxifen treatment. h, Frequency of CD69+ memory CD8+ T cells in the spleen for wild-type and TCRβ Tracfl/fl populations. Data pooled from four independent experiments, for a total of n = 10 mice. Statistical significance was determined by two-tailed Wilcoxon matched-pairs signed-rank test (e, h). *P = 0.0313. Data are mean ± s.e.m.

Source data

Extended Data Fig. 3 In vitro activation of Tracfl/fl naive T cells generates primary TRM cells that are maintained in the absence of constitutive TCR signalling.

a, Experimental model. Lymphocytes were isolated from secondary lymphoid organs of CD45.2+ Tracfl/fl mice and wild-type Thy1.1+ B6 mice, and enriched for naive CD8+ T cells via magnetic bead enrichment. T cells were activated in vitro for 3 days with anti-CD3ε and rB7-1, and 107 cells were co-transferred into naive CD45.1+ B6 mice. Thirty days later, recipient mice were treated with tamoxifen. b, Thirty days after tamoxifen treatment, transferred CD8+ T cells were evaluated for CD44 expression, as compared to endogenous CD8+ T cells, shown via representative flow cytometry of CD8+ T cells isolated from blood. c, Expression of TCRβ was evaluated for Tracfl/fl and wild-type CD8+ T cells, as shown via representative flow cytometry of peripheral blood. d, The ratio of Tracfl/fl to wild-type CD8+ T cells was quantified 30 days after tamoxifen treatment in various tissues, normalized to values from blood, and was not significantly different from 1:1. Data show n = 4 biologically independent mice from 1 experiment. Statistical significance was determined by two-tailed one-sample Wilcoxon test, using 0 as a hypothetical mean. Data are box plots showing median, IQR and extremes.

Source data

Extended Data Fig. 4 CD69 does not unequivocally distinguish long-lived TRM cells in the lung.

a, b, Representative flow cytometry (a) and graph (b), demonstrating the degree of disequilibrium among CD69+ extravascular memory P14 CD8+ T cells in tissues of separated parabiotic mice (n = 8–10), 260 days after LCMV infection from 1 experiment. Top panels in a are gated on extravascular memory CD8+ P14 T cells. Data are mean ± s.e.m.

Source data

Extended Data Fig. 5 Ex-TRM cells comprise a substantial fraction of blood-borne memory.

a, b, Longitudinal graphs depicting the frequency of host-derived memory P14 CD8+ T cells (a) or the frequency of ex-TRM cells of P14 CD8+ T cells, as calculated (b) in the peripheral blood of separated parabiotic mice from two independent experiments (n = 17). Data are mean ± s.e.m.; in b, coloured dotted lines reflect s.e.m. c, d, More than 200 days after separation of congenically distinct parabiotic P14-immune chimeric mice (n = 17), host- and donor-derived P14 CD8+ T cells were evaluated for expression of markers of antigen experience, tissue-trafficking and differentiation potential (d). Gating strategy for P14 CD8+ T cells in separated parabiotic mice shown in c is generally representative of the flow cytometry panels in Figs. 1, 2, Extended Data Figs. 24, 6.

Source data

Extended Data Fig. 6 The glycoform of CD43 recognized by 1B11 is expressed on CD8+ TRM cells.

a, b, Representative flow cytometry (a) and quantification (b) of CD43–1B11 antibody staining on memory P14 CD8+ T cells in nonlymphoid tissues of mice (n = 9) 200 days after infection with LCMV. In a, naive CD8+ T cells isolated from peripheral blood (in red) serve as basis for comparison. Data are mean ± s.e.m.

Source data

Extended Data Fig. 7 Pre-existing memory T cells retain functional potency after heterologous prime–boost immunization.

a, Sixty days after infection with LCMV, P14-immune chimeric mice were subjected to a heterologous prime–boost regimen. The ex vivo functionality of memory P14 CD8+ T cells in various tissues was compared, and found to be not significantly different (P > 0.05) between n = 4 or 5 mice (n varies by tissue) receiving heterologous prime–boost and n = 5 age-matched control mice, from one of two independent experiments with similar results. Statistical significance was determined by two-tailed Mann–Whitney U test. Data are mean ± s.e.m.

Source data

Extended Data Fig. 8 Lung or skin memory CD8+ T cells are preserved after microbial experience.

ad, P14 CD8+ T cells were transferred into naive mice, which were intranasally infected with PR8–gp33 influenza virus and, 30 days later, mice were cohoused for 45 days with mice obtained from pet shops (a). P14 CD8+ T cells from spleen (b), extravascular lung (c) and bronchoalveolar lavage (BAL) fluid (d) of cohoused mice (n = 8) were enumerated and compared to infection-matched mice housed in SPF conditions (n = 8) from 1 experiment. eg, OT-1 CD8+ T cells were transferred into naive mice, which were intravenously infected with VSV–OVA; 30 days later, mice were cohoused for 60 days with mice obtained from pet shops (e). OT-1 CD8+ T cells from spleen (f) and epidermal skin (g) of cohoused mice (n = 6) were enumerated and compared to infection-matched mice housed in SPF conditions (n = 7) from 1 experiment. Statistical significance was determined by two-tailed Mann–Whitney U test. **P = 0.0047 (b); **P = 0.0012 (f). Data are box plots showing median, IQR and extremes.

Source data

Extended Data Fig. 9 Both CD4+ and CD8+ memory T cell populations are expansible.

a, b, CD45+ cells increase in tissues after cohousing (Fig. 3). Here we examined relative frequencies of memory T cells. C57Bl/6 SPF laboratory mice were cohoused for >60 days with mice obtained from pet shops. Age-matched, conventionally housed SPF mice served as controls. The frequency of CD4+ memory T cells (a) and CD8+ memory T cells (b) as a proportion of CD45+ immune cells is depicted in various tissues in both groups of mice. Memory T cells were defined as CD44+PD1. mLN, mesenteric lymph node. Data are pooled from 2–4 independent experiments for a total of n = 4–14 mice (n varies by tissue) per group. Data are mean ± s.e.m.

Source data

Extended Data Fig. 10 Tissue residence typifies immune surveillance for many leukocyte populations.

a, Model depicting the cohousing of CD45.1+ and CD45.2+ C57Bl/6 SPF laboratory mice for >60 days with mice obtained from pet shops, followed by parabiosis of laboratory mice for 28–32 days. b, Between 28 and 32 days after parabiosis, the equilibration of leukocyte populations in peripheral blood was evaluated in n = 8–14 mice. ch, Between 28 and 32 days after parabiosis, the tissue disequilibrium of innate lymphoid cells (c, n = 3–12 mice), natural killer cells (d, n = 5–14 mice), monocytes and macrophages (e, n = 4–12 mice), CD44+PD1 memory T cells (f, n = 7–14 mice), granulocytes (g, n = 4–12 mice) and B cells (h, n = 2–14 mice) was evaluated. Data are pooled from four independent experiments and n varies dependent on tissue and population of interest (as not all cell populations were abundantly detected in each tissue or each experiment). AM, alveolar macrophages; IM, interstitial macrophages; mes LN, mesenteric lymph node. Data are mean ± s.e.m.

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Wijeyesinghe, S., Beura, L.K., Pierson, M.J. et al. Expansible residence decentralizes immune homeostasis. Nature 592, 457–462 (2021). https://doi.org/10.1038/s41586-021-03351-3

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