Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Mucosal viral infection induces a regulatory T cell activation phenotype distinct from tissue residency in mouse and human tissues

Abstract

Regulatory T cells (Tregs) mediate immune homeostasis, yet also facilitate nuanced immune responses during infection, balancing pathogen control while limiting host inflammation. Recent studies have identified Treg populations in non-lymphoid tissues that are phenotypically distinct from Tregs in lymphoid tissues (LT), including performance of location-dependent roles. Mucosal tissues serve as critical barriers to microbes while performing unique physiologic functions, so we sought to identify distinct phenotypical and functional aspects of mucosal Tregs in the female reproductive tract. In healthy human and mouse vaginal mucosa, we found that Tregs are highly activated compared to blood or LT Tregs. To determine if this phenotype reflects acute activation or a general signature of vaginal tract (VT)-residency, we infected mice with HSV-2 to discover that VT Tregs express granzyme-B (GzmB) and acquire a VT Treg signature distinct from baseline. To determine the mechanisms that drive GzmB expression, we performed ex vivo assays to reveal that a combination of type-I interferons and interleukin-2 is sufficient for GzmB expression. Together, we highlight that VT Tregs are activated at steady state and become further activated in response to infection; thus, they may exert robust control of local immune responses, which could have implications for mucosal vaccine design.

This is a preview of subscription content, access via your institution

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Fig. 1: Human regulatory T cells in the vaginal mucosa display increased activation potential compared to circulating Tregs.
Fig. 2: Vaginal tissue Tregs are highly activated compared to lymphoid tissue Tregs in healthy mice.
Fig. 3: Vaginal HSV-2 infection increases the accumulation of highly activated Tregs at the site of infection and drives increased expression of select activation markers consistent with a tissue signature.
Fig. 4: Vaginal Tregs are transcriptionally distinct from dLN Tregs and enriched for visceral adipose tissue Treg gene signature.
Fig. 5: Vaginal tissue Tregs differentially express Granzyme B after HSV-2 infection.
Fig. 6: Inflammatory cytokines induce Granzyme B expression in Tregs.
Fig. 7: IL-2 depletion in vivo decreases vaginal Treg expression of GzmB.

Data availability

The sequencing data from this publication have been deposited in the NCBI’s Gene Expression Omnibus and are accessible through the series accession number GEO: GSE189375. All scripts used for data processing and figure generation are available at GitHub: https://github.com/Brianna-Traxinger/scRNAseq_vaginalTreg_HSV-2.

References

  1. Fontenot, J. D., Gavin, M. A. & Rudensky, A. Y. Foxp3 programs the development and function of CD4+CD25+ regulatory T cells. Nat. Immunol. 4, 330–336 (2003).

    CAS  PubMed  Article  Google Scholar 

  2. Hori, S., Nomura, T. & Sakaguchi, S. Control of regulatory T cell development by the transcription factor Foxp3. Science 299, 1057–1061 (2003).

    CAS  PubMed  Article  Google Scholar 

  3. Josefowicz, S. Z. & Rudensky, A. Control of regulatory T cell lineage commitment and maintenance. Immunity 30, 616–625 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  4. Khattri, R., Cox, T., Yasayko, S. A. & Ramsdell, F. An essential role for Scurfin in CD4+CD25+ T regulatory cells. Nat. Immunol. 4, 337–342 (2003).

    CAS  PubMed  Article  Google Scholar 

  5. Williams, L. M. & Rudensky, A. Y. Maintenance of the Foxp3-dependent developmental program in mature regulatory T cells requires continued expression of Foxp3. Nat. Immunol. 8, 277–284 (2007).

    CAS  PubMed  Article  Google Scholar 

  6. Kuswanto, W. et al. Poor repair of skeletal muscle in aging mice reflects a defect in local, interleukin-33-dependent accumulation of regulatory T cells. Immunity 44, 355–367 (2016).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  7. Burzyn, D. et al. A special population of regulatory T cells potentiates muscle repair. Cell 155, 1282–1295 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  8. Feuerer, M. et al. Lean, but not obese, fat is enriched for a unique population of regulatory T cells that affect metabolic parameters. Nat. Med. 15, 930–939 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  9. Cipolletta, D. et al. PPAR-gamma is a major driver of the accumulation and phenotype of adipose tissue Treg cells. Nature 486, 549–553 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  10. Li, C. et al. TCR transgenic mice reveal stepwise, multi-site acquisition of the distinctive Fat-Treg Phenotype. Cell 174, 285–299 e212 (2018).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  11. Kalekar, L. A. et al. Regulatory T cells in skin are uniquely poised to suppress profibrotic immune responses. Sci. Immunol. 4, eaaw2910 (2019).

  12. Ali, N. et al. Regulatory T cells in skin facilitate epithelial stem cell differentiation. Cell 169, 1119–1129 e1111 (2017).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  13. Mathur, A. N. et al. Treg-cell control of a CXCL5-IL-17 inflammatory axis promotes hair-follicle-stem-cell differentiation during skin-barrier repair. Immunity 50, 655–667 e654 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  14. Sanchez Rodriguez, R. et al. Memory regulatory T cells reside in human skin. J. Clin. Invest. 124, 1027–1036 (2014).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  15. Shafiani, S., Tucker-Heard, G., Kariyone, A., Takatsu, K. & Urdahl, K. B. Pathogen-specific regulatory T cells delay the arrival of effector T cells in the lung during early tuberculosis. J. Exp. Med. 207, 1409–1420 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  16. Kolodin, D. et al. Antigen- and cytokine-driven accumulation of regulatory T cells in visceral adipose tissue of lean mice. Cell Metab. 21, 543–557 (2015).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  17. Tanoue, T., Atarashi, K. & Honda, K. Development and maintenance of intestinal regulatory T cells. Nat. Rev. Immunol. 16, 295–309 (2016).

    CAS  PubMed  Article  Google Scholar 

  18. Cosovanu, C. & Neumann, C. The many functions of Foxp3(+) regulatory T cells in the intestine. Front Immunol. 11, 600973 (2020).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  19. Noval Rivas, M. & Chatila, T. A. Regulatory T cells in allergic diseases. J. Allergy Clin. Immunol. 138, 639–652 (2016).

    CAS  PubMed  Article  Google Scholar 

  20. Singh, R. et al. Regulatory T cells in respiratory health and diseases. Pulm. Med. 2019, 1907807 (2019).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  21. Chatila, T. A. et al. JM2, encoding a fork head-related protein, is mutated in X-linked autoimmunity-allergic disregulation syndrome. J. Clin. Invest. 106, R75–R81 (2000).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  22. Verbsky, J. W. & Chatila, T. A. Immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) and IPEX-related disorders: an evolving web of heritable autoimmune diseases. Curr. Opin. Pediatr. 25, 708–714 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  23. Kearley, J., Barker, J. E., Robinson, D. S. & Lloyd, C. M. Resolution of airway inflammation and hyperreactivity after in vivo transfer of CD4+CD25+ regulatory T cells is interleukin 10 dependent. J. Exp. Med. 202, 1539–1547 (2005).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  24. Lewkowich, I. P. et al. CD4+CD25+ T cells protect against experimentally induced asthma and alter pulmonary dendritic cell phenotype and function. J. Exp. Med. 202, 1549–1561 (2005).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  25. Josefowicz, S. Z. et al. Extrathymically generated regulatory T cells control mucosal TH2 inflammation. Nature 482, 395–399 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  26. Hartl, D. et al. Quantitative and functional impairment of pulmonary CD4+CD25hi regulatory T cells in pediatric asthma. J. Allergy Clin. Immunol. 119, 1258–1266 (2007).

    CAS  PubMed  Article  Google Scholar 

  27. Arpaia, N. et al. A distinct function of regulatory T cells in tissue protection. Cell 162, 1078–1089 (2015).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  28. Belkaid, Y., Piccirillo, C. A., Mendez, S., Shevach, E. M. & Sacks, D. L. CD4+CD25+ regulatory T cells control Leishmania major persistence and immunity. Nature 420, 502–507 (2002).

    CAS  PubMed  Article  Google Scholar 

  29. Loebbermann, J. et al. Regulatory T cells expressing granzyme B play a critical role in controlling lung inflammation during acute viral infection. Mucosal Immunol. 5, 161–172 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  30. Mendez, S., Reckling, S. K., Piccirillo, C. A., Sacks, D. & Belkaid, Y. Role for CD4(+) CD25(+) regulatory T cells in reactivation of persistent leishmaniasis and control of concomitant immunity. J. Exp. Med. 200, 201–210 (2004).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  31. Shafiani, S. et al. Pathogen-specific Treg cells expand early during mycobacterium tuberculosis infection but are later eliminated in response to Interleukin-12. Immunity 38, 1261–1270 (2013).

    CAS  PubMed  Article  Google Scholar 

  32. Suvas, S., Azkur, A. K., Kim, B. S., Kumaraguru, U. & Rouse, B. T. CD4+CD25+ regulatory T cells control the severity of viral immunoinflammatory lesions. J. Immunol. 172, 4123–4132 (2004).

    CAS  PubMed  Article  Google Scholar 

  33. Gebhardt, T. et al. Memory T cells in nonlymphoid tissue that provide enhanced local immunity during infection with herpes simplex virus. Nat. Immunol. 10, 524–530 (2009).

    CAS  PubMed  Article  Google Scholar 

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

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  35. Woodward Davis, A. S. et al. The human memory T cell compartment changes across tissues of the female reproductive tract. Mucosal Immunol. 14, 862–872 (2021).

    CAS  PubMed  Article  Google Scholar 

  36. Dave, V. A. et al. Cervicovaginal Tissue Residence Confers a Distinct Differentiation Program upon Memory CD8 T Cells. J. Immunol. 206, 2937–2948 (2021).

  37. Iijima, N. & Iwasaki, A. T cell memory. A local macrophage chemokine network sustains protective tissue-resident memory CD4 T cells. Science 346, 93–98 (2014).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  38. Roychoudhury, P. et al. Tissue-resident T cell-derived cytokines eliminate herpes simplex virus-2-infected cells. J. Clin. Invest. 130, 2903–2919 (2020).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  39. Schiffer, J. T. Mucosal HSV-2 specific CD8+ T-cells represent containment of prior viral shedding rather than a correlate of future protection. Front Immunol. 4, 209 (2013).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  40. Shin, H. & Iwasaki, A. A vaccine strategy that protects against genital herpes by establishing local memory T cells. Nature 491, 463–467 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  41. Dropulic, L. K. & Cohen, J. I. The challenge of developing a herpes simplex virus 2 vaccine. Expert Rev. Vaccines 11, 1429–1440 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  42. Shin, H. & Iwasaki, A. Generating protective immunity against genital herpes. Trends Immunol. 34, 487–494 (2013).

    CAS  PubMed  Article  Google Scholar 

  43. Milman, N. et al. In situ detection of regulatory T cells in human genital herpes simplex virus type 2 (HSV-2) reactivation and their influence on spontaneous HSV-2 reactivation. J. Infect. Dis. 214, 23–31 (2016).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  44. Smigiel, K. S., Srivastava, S., Stolley, J. M. & Campbell, D. J. Regulatory T-cell homeostasis: steady-state maintenance and modulation during inflammation. Immunol. Rev. 259, 40–59 (2014).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  45. Richert-Spuhler, L. E. & Lund, J. M. The immune Fulcrum: regulatory T cells tip the balance between Pro- and Anti-inflammatory outcomes upon infection. Prog. Mol. Biol. Transl. Sci. 136, 217–243 (2015).

    PubMed  PubMed Central  Article  Google Scholar 

  46. Vick, S. C. et al. A regulatory T cell signature distinguishes the immune landscape of COVID-19 patients from those with other respiratory infections. Sci. Adv. 7, eabj0274 (2021).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  47. Brincks, E. L. et al. Antigen-specific memory regulatory CD4+Foxp3+ T cells control memory responses to influenza virus infection. J. Immunol. 190, 3438–3446 (2013).

    CAS  PubMed  Article  Google Scholar 

  48. Botta, D. et al. Dynamic regulation of T follicular regulatory cell responses by interleukin 2 during influenza infection. Nat. Immunol. 18, 1249–1260 (2017).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  49. Leon, B., Bradley, J. E., Lund, F. E., Randall, T. D. & Ballesteros-Tato, A. FoxP3+ regulatory T cells promote influenza-specific Tfh responses by controlling IL-2 availability. Nat. Commun. 5, 3495 (2014).

    PubMed  Article  CAS  Google Scholar 

  50. Lund, J. M., Hsing, L., Pham, T. T. & Rudensky, A. Y. Coordination of early protective immunity to viral infection by regulatory T cells. Science 320, 1220–1224 (2008).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  51. Soerens, A. G., Da Costa, A. & Lund, J. M. Regulatory T cells are essential to promote proper CD4 T-cell priming upon mucosal infection. Mucosal Immunol. 9, 1395–1406 (2016).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  52. Traxinger, B. R., Richert-Spuhler, L. E. & Lund, J. M. Mucosal tissue regulatory T cells are integral in balancing immunity and tolerance at portals of antigen entry. Mucosal Immunol. 15, 398–407 (2022).

    CAS  PubMed  Article  Google Scholar 

  53. Aluvihare, V. R., Kallikourdis, M. & Betz, A. G. Regulatory T cells mediate maternal tolerance to the fetus. Nat. Immunol. 5, 266–271 (2004).

    CAS  PubMed  Article  Google Scholar 

  54. Guerin, L. R. et al. Seminal fluid regulates accumulation of FOXP3+ regulatory T cells in the preimplantation mouse uterus through expanding the FOXP3+ cell pool and CCL19-mediated recruitment. Biol. Reprod. 85, 397–408 (2011).

    CAS  PubMed  Article  Google Scholar 

  55. Moldenhauer, L. M. et al. Cross-presentation of male seminal fluid antigens elicits T cell activation to initiate the female immune response to pregnancy. J. Immunol. 182, 8080–8093 (2009).

    CAS  PubMed  Article  Google Scholar 

  56. Robertson, S. A. et al. Seminal fluid drives expansion of the CD4+CD25+ T regulatory cell pool and induces tolerance to paternal alloantigens in mice. Biol. Reprod. 80, 1036–1045 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  57. Pattacini, L. et al. A pro-inflammatory CD8+ T-cell subset patrols the cervicovaginal tract. Mucosal Immunol. 12, 1118–1129 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  58. Vignali, D. A., Collison, L. W. & Workman, C. J. How regulatory T cells work. Nat. Rev. Immunol. 8, 523–532 (2008).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  59. Linehan, M. M. et al. In vivo role of nectin-1 in entry of herpes simplex virus type 1 (HSV-1) and HSV-2 through the vaginal mucosa. J. Virol. 78, 2530–2536 (2004).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  60. Anderson, K. G. et al. Intravascular staining for discrimination of vascular and tissue leukocytes. Nat. Protoc. 9, 209–222 (2014).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  61. Galkina, E. et al. Preferential migration of effector CD8+ T cells into the interstitium of the normal lung. J. Clin. Invest. 115, 3473–3483 (2005).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  62. Han, Y., Guo, Q., Zhang, M., Chen, Z. & Cao, X. CD69+ CD4+ CD25- T cells, a new subset of regulatory T cells, suppress T cell proliferation through membrane-bound TGF-beta 1. J. Immunol. 182, 111–120 (2009).

    CAS  PubMed  Article  Google Scholar 

  63. Fontenot, J. D. et al. Regulatory T cell lineage specification by the forkhead transcription factor foxp3. Immunity 22, 329–341 (2005).

    CAS  PubMed  Article  Google Scholar 

  64. Levine, A. G. et al. Stability and function of regulatory T cells expressing the transcription factor T-bet. Nature 546, 421–425 (2017).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  65. Stuart, T. et al. Comprehensive Integration of Single-. Cell Data. Cell 177, 1888–1902 e1821 (2019).

    CAS  PubMed  Google Scholar 

  66. Becht, E. et al. Dimensionality reduction for visualizing single-cell data using UMAP. Nat. Biotechnol. 37, 38–44 (2018).

  67. Finak, G. et al. MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data. Genome Biol. 16, 278 (2015).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  68. Malarkannan, S. NKG7 makes a better killer. Nat. Immunol. 21, 1139–1140 (2020).

    CAS  PubMed  Article  Google Scholar 

  69. Ng, S. S. et al. The NK cell granule protein NKG7 regulates cytotoxic granule exocytosis and inflammation. Nat. Immunol. 21, 1205–1218 (2020).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  70. Velotti, F., Barchetta, I., Cimini, F. A. & Cavallo, M. G. Granzyme B in inflammatory diseases: apoptosis, inflammation, extracellular Matrix Remodeling, Epithelial-to-Mesenchymal Transition and Fibrosis. Front. Immunol. 11, 587581 (2020).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  71. Grossman, W. J. et al. Differential expression of granzymes A and B in human cytotoxic lymphocyte subsets and T regulatory cells. Blood 104, 2840–2848 (2004).

    CAS  PubMed  Article  Google Scholar 

  72. Zhao, D. M., Thornton, A. M., DiPaolo, R. J. & Shevach, E. M. Activated CD4+CD25+ T cells selectively kill B lymphocytes. Blood 107, 3925–3932 (2006).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  73. Doebbeler, M. et al. CD83 expression is essential for Treg cell differentiation and stability. JCI Insight 3, e99712 (2018).

  74. Kohlmeier, J. E., Cookenham, T., Roberts, A. D., Miller, S. C. & Woodland, D. L. Type I interferons regulate cytolytic activity of memory CD8(+) T cells in the lung airways during respiratory virus challenge. Immunity 33, 96–105 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  75. Mackay, L. K. et al. Maintenance of T cell function in the face of chronic antigen stimulation and repeated reactivation for a latent virus infection. J. Immunol. 188, 2173–2178 (2012).

    CAS  PubMed  Article  Google Scholar 

  76. Lund, J., Sato, A., Akira, S., Medzhitov, R. & Iwasaki, A. Toll-like receptor 9-mediated recognition of Herpes simplex virus-2 by plasmacytoid dendritic cells. J. Exp. Med. 198, 513–520 (2003).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  77. Lund, J. M., Linehan, M. M., Iijima, N. & Iwasaki, A. Cutting Edge: Plasmacytoid dendritic cells provide innate immune protection against mucosal viral infection in situ. J. Immunol. 177, 7510–7514 (2006).

    CAS  PubMed  Article  Google Scholar 

  78. Cao, X. et al. Granzyme B and perforin are important for regulatory T cell-mediated suppression of tumor clearance. Immunity 27, 635–646 (2007).

    CAS  PubMed  Article  Google Scholar 

  79. Sula Karreci, E. et al. Human regulatory T cells undergo self-inflicted damage via granzyme pathways upon activation. JCI Insight 2, e91599 (2017).

  80. Sun, B., Liu, M., Cui, M. & Li, T. Granzyme B-expressing treg cells are enriched in colorectal cancer and present the potential to eliminate autologous T conventional cells. Immunol. Lett. 217, 7–14 (2020).

    CAS  PubMed  Article  Google Scholar 

  81. Gondek, D. C., Lu, L. F., Quezada, S. A., Sakaguchi, S. & Noelle, R. J. Cutting edge: contact-mediated suppression by CD4+CD25+ regulatory cells involves a granzyme B-dependent, perforin-independent mechanism. J. Immunol. 174, 1783–1786 (2005).

    CAS  PubMed  Article  Google Scholar 

  82. Salti, S. M. et al. Granzyme B regulates antiviral CD8+ T cell responses. J. Immunol. 187, 6301–6309 (2011).

    CAS  PubMed  Article  Google Scholar 

  83. Dolina, J. S. et al. Developmentally distinct CD4(+) Treg lineages shape the CD8(+) T cell response to acute Listeria infection. Proc. Natl Acad. Sci. USA 119, e2113329119 (2022).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  84. Efimova, O. V. & Kelley, T. W. Induction of granzyme B expression in T-cell receptor/CD28-stimulated human regulatory T cells is suppressed by inhibitors of the PI3K-mTOR pathway. BMC Immunol. 10, 59 (2009).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  85. Maurice, N. J., Taber, A. K. & Prlic, M. The Ugly Duckling Turned to Swan: a change in perception of bystander-activated memory CD8 T cells. J. Immunol. 206, 455–462 (2021).

    CAS  PubMed  Article  Google Scholar 

  86. Milligan, G. N. & Bernstein, D. I. Interferon-gamma enhances resolution of herpes simplex virus type 2 infection of the murine genital tract. Virology 229, 259–268 (1997).

    CAS  PubMed  Article  Google Scholar 

  87. Nakanishi, Y., Lu, B., Gerard, C. & Iwasaki, A. CD8(+) T lymphocyte mobilization to virus-infected tissue requires CD4(+) T-cell help. Nature 462, 510–513 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  88. Chu, T. et al. Bystander-activated memory CD8 T cells control early pathogen load in an innate-like, NKG2D-dependent manner. Cell Rep. 3, 701–708 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  89. Woodward Davis, A. S. et al. The human tissue-resident CCR5(+) T cell compartment maintains protective and functional properties during inflammation. Sci. Transl. Med. 11, eaaw8718 (2019).

  90. Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).

    CAS  PubMed  Article  Google Scholar 

  91. Li, B. & Dewey, C. N. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinforma. 12, 323 (2011).

    CAS  Article  Google Scholar 

  92. Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2010).

    CAS  PubMed  Article  Google Scholar 

  93. Law, C. W., Chen, Y., Shi, W. & Smyth, G. K. voom: Precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol. 15, R29 (2014).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  94. Ritchie, M. E. et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43, e47 (2015).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  95. Smyth GK. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3: Article3 (2004).

  96. Wu, D. & Smyth, G. K. Camera: a competitive gene set test accounting for inter-gene correlation. Nucleic Acids Res. 40, e133 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  97. Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587 e3529 (2021).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  98. Butler, A., Hoffman, P., Smibert, P., Papalexi, E. & Satija, R. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat. Biotechnol. 36, 411–420 (2018).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  99. Satija, R., Farrell, J. A., Gennert, D., Schier, A. F. & Regev, A. Spatial reconstruction of single-cell gene expression data. Nat. Biotechnol. 33, 495–502 (2015).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  100. Wang, T., Li, B., Nelson, C. E. & Nabavi, S. Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data. BMC Bioinforma. 20, 40 (2019).

    Article  Google Scholar 

Download references

Acknowledgements

We thank the members of the Lund and Prlic labs for their helpful input and discussions and the study participants. Select figure graphics were created with Biorender.com.

Funding

This work was funded by the National Institute of Allergy and Infectious Disease of the US National Institutes of Health (R01 AI141435 and AI131914 to J.M.L.). J.R.E. and S.C.V. were funded by the Diseases of Public Health Importance Training Grant (T32 AI007509) and B.R.T. was funded by the Viral Pathogenesis Training Grant (T32 AI083203).

Author information

Authors and Affiliations

Authors

Contributions

B.R.T., S.C.V., A.W.D., and J.R.E. performed all experiments. B.R.T. and V.V. performed data and statistical analyses. J.C. and C.T. collected the human clinical samples. B.R.T., M.P., and J.M.L. designed the study and wrote the first draft of the manuscript. All authors contributed to editing and approved the final draft.

Corresponding authors

Correspondence to Martin Prlic or Jennifer M. Lund.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Traxinger, B., Vick, S.C., Woodward-Davis, A. et al. Mucosal viral infection induces a regulatory T cell activation phenotype distinct from tissue residency in mouse and human tissues. Mucosal Immunol 15, 1012–1027 (2022). https://doi.org/10.1038/s41385-022-00542-7

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41385-022-00542-7

Search

Quick links