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Quantitative assessment of T cell repertoire recovery after hematopoietic stem cell transplantation


Delayed T cell recovery and restricted T cell receptor (TCR) diversity after allogeneic hematopoietic stem cell transplantation (allo-HSCT) are associated with increased risks of infection and cancer relapse. Technical challenges have limited faithful measurement of TCR diversity after allo-HSCT. Here we combined 5′ rapid amplification of complementary DNA ends PCR with deep sequencing to quantify TCR diversity in 28 recipients of allo-HSCT using a single oligonucleotide pair. Analysis of duplicate blood samples confirmed that we accurately determined the frequency of individual TCRs. After 6 months, cord blood–graft recipients approximated the TCR diversity of healthy individuals, whereas recipients of T cell–depleted peripheral-blood stem cell grafts had 28-fold and 14-fold lower CD4+ and CD8+ T cell diversities, respectively. After 12 months, these deficiencies had improved for the CD4+ but not the CD8+ T cell compartment. Overall, this method provides unprecedented views of T cell repertoire recovery after allo-HSCT and may identify patients at high risk of infection or relapse.

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Figure 1: Quantification of T cell repertoire recovery after allo-HSCT.
Figure 2: T cell repertoire dynamics during the first year after allo-HSCT.
Figure 3: T cell repertoire recovery by three different stem cell sources 6 and 12 months after allo-HSCT.
Figure 4: T cell repertoire recovery after allo-HSCT as a function of clinical variables.
Figure 5: Monitoring patients with poor T cell repertoire recovery after allo-HSCT.


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We thank all patients and healthy donors who volunteered to participate in this study. We thank G. Redelman-Sidi for collection of blood samples, I. Leiner for processing of blood samples, C. Ubeda-Morant for assistance with data analysis, J. Li and A. Viale of the Memorial Sloan-Kettering Cancer Center Genomics Core Laboratory for performing Roche/454 sequencing and R. Jenq for critical reading of the manuscript. This work was supported by the Netherlands Organisation for Scientific Research (NWO) (Rubicon fellowship to J.W.J.v.H.), the Asociación Española Contra el Cáncer (AECC) (PAO grant to I.C.), the US National Institutes of Health (NIH) (grants HL069929, CA023766, AI080455, AI100288 and AI101406 to M.R.M.v.d.B. and AI042135, AI039031 and CA023766 to E.G.P.) and The Tow Foundation (to E.G.P.). Additional support was received from the US Department of Defense (USAMRAA Award W81XWH-09-1-0294), the Radiation Effects Research Foundation (RERF-NIAID), The Lymphoma Foundation, Alex's Lemonade Stand, The Geoffrey Beene Cancer Research Center at Memorial Sloan-Kettering Cancer Center and The Susan and Peter Solomon Divisional Genomics Program (to M.R.M.v.d.B.), The Translational and Integrative Medicine Research Fund of Memorial Sloan-Kettering Cancer Center, Cycle for Survival, The New York Community Trust and When Everyone Survives (to M.A.P.) and The Experimental Therapeutics Center of Memorial Sloan-Kettering Cancer Center funded by W.H. Goodwin and A. Goodwin (to M.R.M.v.d.B. and M.A.P.).

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Authors and Affiliations



J.W.J.v.H. designed and performed the study, analyzed data and wrote the manuscript. I.C. collected clinical data. L.B.L. performed Roche/454 sequencing. D.W.S. compared naive and memory CD8+ T cells. G.D.W., A.M.R.G. and J.L.N. provided patient samples. M.R.M.v.d.B. designed and supervised the study. M.A.P. designed and supervised the study and provided patient samples. E.G.P. designed and supervised the study, analyzed data and wrote the manuscript.

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Correspondence to Jeroen W J van Heijst or Eric G Pamer.

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The authors declare no competing financial interests.

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van Heijst, J., Ceberio, I., Lipuma, L. et al. Quantitative assessment of T cell repertoire recovery after hematopoietic stem cell transplantation. Nat Med 19, 372–377 (2013).

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