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Stem cell transplantation

Genetic T-cell receptor diversity at 1 year following allogeneic hematopoietic stem cell transplantation

Abstract

After allogeneic hematopoietic stem cell transplantation (HSCT), immune reconstitution leads to the development of a new T-cell repertoire. Immune reconstitution could be influenced by events such as conditioning, infections, and graft versus host disease (GVHD). Factors influencing the TCR diversity are of great interest to fine-tune the strategy for donor selection and to optimize standard of care. In this work, immunosequencing of the TCR CDR3β region was carried out in a large cohort of 116 full chimeric recipients at 1 year post-HSCT and their respective donors prior to transplantation. The repertoire overlap before and after HSCT was minimal, supporting de novo reconstitution as a primary pathway at any age. Among the parameters investigated, increased patient and/or donor age as well as positive CMV serologic status reinforced by CMV infection/reactivation were the ones significantly associated with a reduced diversity at 1 year post-HSCT. CMV-specific T-cell clones were shown to influence the clonality of the repertoire alongside the expansion of limited numbers of non-CMV T-cell populations. Interestingly, at the exception of CMV infection/reactivation, TCR diversity was not predictive of GVHD, relapse, death, or infections post-HSCT.

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References

  1. Petersdorf EW. Genetics of graft-versus-host disease: the major histocompatibility complex. Blood Rev. 2013;27:1–12.

    PubMed  CAS  Google Scholar 

  2. Fleischhauer K, Beelen DW. HLA mismatching as a strategy to reduce relapse after alternative donor transplantation. Semin Hematol. 2016;53:57–64.

    PubMed  CAS  Google Scholar 

  3. Fleischhauer K, Shaw BE. HLA-DP in unrelated hematopoietic cell transplantation revisited: challenges and opportunities. Blood. 2017;130:1089–96.

    PubMed  CAS  Google Scholar 

  4. Jameson SC. Maintaining the norm: T-cell homeostasis. Nat Rev Immunol. 2002;2:547–56.

    PubMed  CAS  Google Scholar 

  5. Degauque N, Brouard S, Soulillou JP. Cross-reactivity of TCR repertoire: current concepts, challenges, and implication for allotransplantation. Front Immunol. 2016;7:89.

    PubMed  PubMed Central  Google Scholar 

  6. DeWolf S, Sykes M. Alloimmune T cells in transplantation. J Clin Investig. 2017;127:2473–81.

    PubMed  Google Scholar 

  7. Inman CF, Eldershaw SA, Croudace JE, Davies NJ, Sharma-Oates A, Rai T, et al. Unique features and clinical importance of acute alloreactive immune responses. JCI Insight 2018;3:10.

    Google Scholar 

  8. Phan TL, Pritchett JC, Leifer C, Zerr DM, Koelle DM, Di Luca D, et al. HHV-6B infection, T-cell reconstitution, and graft-vs-host disease after hematopoietic stem cell transplantation. Bone marrow Transplant. 2018;53:1508–17.

    PubMed  Google Scholar 

  9. Mackall CL, Bare CV, Granger LA, Sharrow SO, Titus JA, Gress RE. Thymic-independent T cell regeneration occurs via antigen-driven expansion of peripheral T cells resulting in a repertoire that is limited in diversity and prone to skewing. J Immunol. 1996;156:4609–16.

    PubMed  CAS  Google Scholar 

  10. Sharon E, Sibener LV, Battle A, Fraser HB, Garcia KC, Pritchard JK. Genetic variation in MHC proteins is associated with T cell receptor expression biases. Nature genetics. 2016;48:995–1002.

  11. Chaudhry MS, Velardi E, Malard F, van den Brink MR. Immune reconstitution after allogeneic hematopoietic stem cell transplantation: Time To T Up the Thymus. J Immunol. 2017;198:40–6.

    PubMed  CAS  Google Scholar 

  12. Clave E, Busson M, Douay C, Peffault de Latour R, Berrou J, Rabian C, et al. Acute graft-versus-host disease transiently impairs thymic output in young patients after allogeneic hematopoietic stem cell transplantation. Blood. 2009;113:6477–84.

    PubMed  CAS  Google Scholar 

  13. Hakim FT, Memon SA, Cepeda R, Jones EC, Chow CK, Kasten-Sportes C, et al. Age-dependent incidence, time course, and consequences of thymic renewal in adults. J Clin Investig. 2005;115:930–9.

    PubMed  CAS  Google Scholar 

  14. Lynch HE, Goldberg GL, Chidgey A, Van den Brink MR, Boyd R, Sempowski GD. Thymic involution and immune reconstitution. Trends Immunol. 2009;30:366–73.

    PubMed  PubMed Central  CAS  Google Scholar 

  15. Weinberg K, Blazar BR, Wagner JE, Agura E, Hill BJ, Smogorzewska M, et al. Factors affecting thymic function after allogeneic hematopoietic stem cell transplantation. Blood. 2001;97:1458–66.

    PubMed  CAS  Google Scholar 

  16. Bosch M, Khan FM, Storek J. Immune reconstitution after hematopoietic cell transplantation. Curr Opin Hematol. 2012;19:324–35.

    PubMed  Google Scholar 

  17. Ogonek J, Kralj Juric M, Ghimire S, Varanasi PR, Holler E, Greinix H, et al. Immune reconstitution after allogeneic hematopoietic stem cell transplantation. Front Immunol. 2016;7:507.

    PubMed  PubMed Central  Google Scholar 

  18. Storek J, Geddes M, Khan F, Huard B, Helg C, Chalandon Y, et al. Reconstitution of the immune system after hematopoietic stem cell transplantation in humans. Semin Immunopathol 2008;30:425–37.

    PubMed  Google Scholar 

  19. Stern L, McGuire H, Avdic S, Rizzetto S, Fazekas de St Groth B, Luciani F, et al. Mass cytometry for the assessment of immune reconstitution after hematopoietic stem cell transplantation. Front Immunol. 2018;9:1672.

    PubMed  PubMed Central  Google Scholar 

  20. Lakshmikanth T, Olin A, Chen Y, Mikes J, Fredlund E, Remberger M, et al. Mass cytometry and topological data analysis reveal immune parameters associated with complications after allogeneic stem cell transplantation. Cell Rep. 2017;20:2238–50.

    PubMed  CAS  Google Scholar 

  21. Heather JM, Ismail M, Oakes T, Chain B. High-throughput sequencing of the T-cell receptor repertoire: pitfalls and opportunities. Brief Bioinform 2018;19:554–65.

    PubMed  CAS  Google Scholar 

  22. Robins H. Immunosequencing: applications of immune repertoire deep sequencing. Curr Opin Immunol. 2013;25:646–52.

    PubMed  CAS  Google Scholar 

  23. Six A, Mariotti-Ferrandiz ME, Chaara W, Magadan S, Pham HP, Lefranc MP, et al. The past, present, and future of immune repertoire biology—the rise of next-generation repertoire analysis. Front Immunol. 2013;4:413.

    PubMed  PubMed Central  Google Scholar 

  24. Cochet M, Pannetier C, Regnault A, Darche S, Leclerc C, Kourilsky P. Molecular detection and in vivo analysis of the specific T cell response to a protein antigen. Eur J Immunol. 1992;22:2639–47.

    PubMed  CAS  Google Scholar 

  25. Gorski J, Yassai M, Zhu X, Kissela B, Kissella B, Keever C, et al. Circulating T cell repertoire complexity in normal individuals and bone marrow recipients analyzed by CDR3 size spectratyping. Correlation with immune status. J Immunol. 1994;152:5109–19.

    PubMed  CAS  Google Scholar 

  26. Yew PY, Alachkar H, Yamaguchi R, Kiyotani K, Fang H, Yap KL, et al. Quantitative characterization of T-cell repertoire in allogeneic hematopoietic stem cell transplant recipients. Bone marrow Transplant. 2015;50:1227–34.

    PubMed  PubMed Central  CAS  Google Scholar 

  27. van Heijst JW, Ceberio I, Lipuma LB, Samilo DW, Wasilewski GD, Gonzales AM, et al. Quantitative assessment of T cell repertoire recovery after hematopoietic stem cell transplantation. Nat Med. 2013;19:372–7.

    PubMed  PubMed Central  Google Scholar 

  28. Suessmuth Y, Mukherjee R, Watkins B, Koura DT, Finstermeier K, Desmarais C, et al. CMV reactivation drives posttransplant T-cell reconstitution and results in defects in the underlying TCRbeta repertoire. Blood. 2015;125:3835–50.

    PubMed  PubMed Central  CAS  Google Scholar 

  29. Link-Rachner CS, Eugster A, Rucker-Braun E, Heidenreich F, Oelschlagel U, Dahl A, et al. T cell receptor alpha repertoire of CD8+ T cells following allogeneic stem cell transplantation using next-generation sequencing. Haematologica. 2019;104:622–31.

  30. Gkazi AS, Margetts BK, Attenborough T, Mhaldien L, Standing JF, Oakes T, et al. Clinical T cell receptor repertoire deep sequencing and analysis: an application to monitor immune reconstitution following cord blood transplantation. Front Immunol. 2018;9:2547.

    PubMed  PubMed Central  Google Scholar 

  31. Chalandon Y, Roosnek E, Mermillod B, Waelchli L, Helg C, Chapuis B. Can only partial T-cell depletion of the graft before hematopoietic stem cell transplantation mitigate graft-versus-host disease while preserving a graft-versus-leukemia reaction? A prospective phase II study. Biol Blood Marrow Transplant. 2006;12:102–10.

    PubMed  Google Scholar 

  32. Carlson CS, Emerson RO, Sherwood AM, Desmarais C, Chung MW, Parsons JM, et al. Using synthetic templates to design an unbiased multiplex PCR assay. Nat Commun. 2013;4:2680.

    PubMed  Google Scholar 

  33. Robins HS, Campregher PV, Srivastava SK, Wacher A, Turtle CJ, Kahsai O, et al. Comprehensive assessment of T-cell receptor beta-chain diversity in alphabeta T cells. Blood. 2009;114:4099–107.

    PubMed  PubMed Central  CAS  Google Scholar 

  34. Jurtz V, Paul S, Andreatta M, Marcatili P, Peters B, Nielsen M. NetMHCpan-4.0: improved peptide-MHC Class I interaction predictions integrating eluted ligand and peptide binding affinity data. J Immunol. 2017;199:3360–8.

    PubMed  PubMed Central  CAS  Google Scholar 

  35. Nunes E, Heslop H, Fernandez-Vina M, Taves C, Wagenknecht DR, Eisenbrey AB, et al. Definitions of histocompatibility typing terms. Blood. 2011;118:e180–3.

    PubMed  CAS  Google Scholar 

  36. Emerson RO, DeWitt WS, Vignali M, Gravley J, Hu JK, Osborne EJ, et al. Immunosequencing identifies signatures of cytomegalovirus exposure history and HLA-mediated effects on the T cell repertoire. Nat Genet 2017;49:659–65.

    PubMed  CAS  Google Scholar 

  37. Laydon DJ, Bangham CR, Asquith B. Estimating T-cell repertoire diversity: limitations of classical estimators and a new approach. Philos Trans R Soc Lond B Biol Sci. 2015;370.

  38. Rempala GA, Seweryn M. Methods for diversity and overlap analysis in T-cell receptor populations. J Math Biol. 2013;67:1339–68.

    PubMed  Google Scholar 

  39. Bentzen AK, Such L, Jensen KK, Marquard AM, Jessen LE, Miller NJ, et al. T cell receptor fingerprinting enables in-depth characterization of the interactions governing recognition of peptide-MHC complexes. Nat Biotechnol. 2018;36:1191–6.

  40. Birnbaum ME, Mendoza JL, Sethi DK, Dong S, Glanville J, Dobbins J, et al. Deconstructing the peptide-MHC specificity of T cell recognition. Cell 2014;157:1073–87.

    PubMed  PubMed Central  CAS  Google Scholar 

  41. Illing PT, Pymm P, Croft NP, Hilton HG, Jojic V, Han AS, et al. HLA-B57 micropolymorphism defines the sequence and conformational breadth of the immunopeptidome. Nat Commun. 2018;9:4693.

    PubMed  PubMed Central  Google Scholar 

  42. Ljungman P, Perez-Bercoff L, Jonsson J, Avetisyan G, Sparrelid E, Aschan J, et al. Risk factors for the development of cytomegalovirus disease after allogeneic stem cell transplantation. Haematologica. 2006;91:78–83.

    PubMed  Google Scholar 

  43. Miller HK, Braun TM, Stillwell T, Harris AC, Choi S, Connelly J, et al. Infectious Risk after Allogeneic Hematopoietic Cell Transplantation Complicated by Acute Graft-versus-Host Disease. Biol Blood Marrow Transplant. 2017;23:522–8.

    PubMed  Google Scholar 

  44. Hakki M, Riddell SR, Storek J, Carter RA, Stevens-Ayers T, Sudour P, et al. Immune reconstitution to cytomegalovirus after allogeneic hematopoietic stem cell transplantation: impact of host factors, drug therapy, and subclinical reactivation. Blood 2003;102:3060–7.

    PubMed  CAS  Google Scholar 

  45. Cantoni N, Hirsch HH, Khanna N, Gerull S, Buser A, Bucher C, et al. Evidence for a bidirectional relationship between cytomegalovirus replication and acute graft-versus-host disease. Biol Blood Marrow Transplant. 2010;16:1309–14.

    PubMed  Google Scholar 

  46. Storek J, Joseph A, Dawson MA, Douek DC, Storer B, Maloney DG. Factors influencing T-lymphopoiesis after allogeneic hematopoietic cell transplantation. Transplantation. 2002;73:1154–8.

    PubMed  Google Scholar 

  47. Toubert A, Glauzy S, Douay C, Clave E. Thymus and immune reconstitution after allogeneic hematopoietic stem cell transplantation in humans: never say never again. Tissue Antigens. 2012;79:83–9.

    PubMed  CAS  Google Scholar 

  48. Baron F, Storer B, Maris MB, Storek J, Piette F, Metcalf M, et al. Unrelated donor status and high donor age independently affect immunologic recovery after nonmyeloablative conditioning. Biol Blood Marrow Transplant. 2006;12:1176–87.

    PubMed  Google Scholar 

  49. Talvensaari K, Clave E, Douay C, Rabian C, Garderet L, Busson M, et al. A broad T-cell repertoire diversity and an efficient thymic function indicate a favorable long-term immune reconstitution after cord blood stem cell transplantation. Blood. 2002;99:1458–64.

    PubMed  CAS  Google Scholar 

  50. Fusco A, Panico L, Gorrese M, Bianchino G, Barone MV, Grieco V, et al. Molecular evidence for a thymus-independent partial T cell development in a FOXN1-/- athymic human fetus. PLoS ONE. 2013;8:e81786.

    PubMed  PubMed Central  Google Scholar 

  51. McClory S, Hughes T, Freud AG, Briercheck EL, Martin C, Trimboli AJ, et al. Evidence for a stepwise program of extrathymic T cell development within the human tonsil. J Clin Investig. 2012;122:1403–15.

    PubMed  CAS  Google Scholar 

  52. Melendez-Munoz R, Marchalik R, Jerussi T, Dimitrova D, Nussenblatt V, Beri A, et al. Cytomegalovirus infection incidence and risk factors across diverse hematopoietic cell transplantation platforms using a standardized monitoring and treatment approach: a comprehensive evaluation from a single institution. Biol Blood Marrow Transplant. 2019;25:577–86.

  53. Ogonek J, Varanasi P, Luther S, Schweier P, Kuhnau W, Gohring G, et al. Possible impact of cytomegalovirus-specific CD8(+) T cells on immune reconstitution and conversion to complete donor chimerism after allogeneic stem cell transplantation. Biol Blood Marrow Transplant. 2017;23:1046–53.

    PubMed  CAS  Google Scholar 

  54. Elkington R, Walker S, Crough T, Menzies M, Tellam J, Bharadwaj M, et al. Ex vivo profiling of CD8+-T-cell responses to human cytomegalovirus reveals broad and multispecific reactivities in healthy virus carriers. J Virol. 2003;77:5226–40.

    PubMed  PubMed Central  CAS  Google Scholar 

  55. Sylwester AW, Mitchell BL, Edgar JB, Taormina C, Pelte C, Ruchti F, et al. Broadly targeted human cytomegalovirus-specific CD4+ and CD8+ T cells dominate the memory compartments of exposed subjects. J Exp Med. 2005;202:673–85.

    PubMed  PubMed Central  CAS  Google Scholar 

  56. Camargo JF, Komanduri KV. Emerging concepts in cytomegalovirus infection following hematopoietic stem cell transplantation. Hematol Oncol Stem Cell Ther. 2017;10:233–8.

    PubMed  CAS  Google Scholar 

  57. Boeckh M, Geballe AP. Cytomegalovirus: pathogen, paradigm, and puzzle. J Clin Investig. 2011;121:1673–80.

    PubMed  CAS  Google Scholar 

  58. Fink PJ, Hendricks DW. Post-thymic maturation: young T cells assert their individuality. Nat Rev Immunol. 2011;11:544–9.

    PubMed  PubMed Central  CAS  Google Scholar 

  59. Itzykson R, Robin M, Moins-Teisserenc H, Delord M, Busson M, Xhaard A, et al. Cytomegalovirus shapes long-term immune reconstitution after allogeneic stem cell transplantation. Haematologica 2015;100:114–23.

    PubMed  PubMed Central  CAS  Google Scholar 

  60. Lugthart G, van Ostaijen-Ten Dam MM, Jol-van der Zijde CM, van Holten TC, Kester MG, Heemskerk MH, et al. Early cytomegalovirus reactivation leaves a specific and dynamic imprint on the reconstituting T cell compartment long-term after hematopoietic stem cell transplantation. Biol Blood Marrow Transplant. 2014;20:655–61.

    PubMed  CAS  Google Scholar 

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Acknowledgements

This study was supported by the Swiss National Science Foundation (grant #310030_173237/1), the Academic Society of the University of Geneva, IRGHET (International Research Group on unrelated Hematopoietic stem cell Transplantation), the Dr Henri Dubois-Ferrière Dinu Lippatti foundation and the Philantropy Settlement. The authors are grateful to Lydie Brunet for her technical expertize and to the technicians of the LNRH for their most efficient support for HLA typing. We would also like to thanks Dr José Manuel Nunes (Biosc-iGE3) for his valuable suggestions on data analysis using R.

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Buhler, S., Bettens, F., Dantin, C. et al. Genetic T-cell receptor diversity at 1 year following allogeneic hematopoietic stem cell transplantation. Leukemia 34, 1422–1432 (2020). https://doi.org/10.1038/s41375-019-0654-y

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