title: Quantitative characterization of T-cell repertoire and biomarkers in kidney transplant rejection.
abstract: T-cell-mediated rejection (TCMR) remains a major cause of kidney allograft failure. The characterization of T-cell repertoire in different immunological disorders has emerged recently as a novel tool with significant implications. We herein sought to characterize T-cell repertoire using next generation sequencing to diagnose TCMR.
  
  
  
  In this prospective study, we analyzed samples from 50 kidney transplant recipients. We collected blood and kidney transplant biopsy samples at sequential time points before and post transplant. We used next generation sequencing to characterize T-cell receptor (TCR) repertoire by using illumina miSeq on cDNA synthesized from RNA extracted from six patients' samples. We also measured RNA expression levels of FOXP3, CD8, CD4, granzyme and perforin in blood samples from all 50 patients.
  
  
  
  Seven patients developed TCMR during the first three months of the study. Out of six patients who had complete sets of blood and biopsy samples two had TCMR. We found an expansion of the TCR repertoire in blood at time of rejection when compared to that at pre-transplant or one-month post transplant. Patients with TCMR (n = 7) had significantly higher RNA expression levels of FOXP3, Perforin, Granzyme, CD4 and CD8 in blood samples than those with no TCMR (n = 43) (P = 0.02, P = 0.003, P = 0.002, P = 0.017, and P = 0.01, respectively).
  
  
  
  Our study provides a potential utilization of TCR clone kinetics analysis in the diagnosis of TCMR. This approach may allow for the identification of the expanded T-cell clones associated with the rejection and lead to potential noninvasive diagnosis and targeted therapies of TCMR.
authors.affiliation: School of Pharmacy, University of Southern California, Los Angeles, CA, 90089, USA. alachkar@USC.edu.
authors.forename: Houda
authors.initials: H
authors.lastname: Alachkar
authors.affiliation: Department of Medicine, University of Chicago, Chicago, IL, 60637, USA.
authors.forename: Martin
authors.initials: M
authors.lastname: Mutonga
authors.affiliation: Department of Medicine, University of Chicago, Chicago, IL, 60637, USA.
authors.forename: Taigo
authors.initials: T
authors.lastname: Kato
authors.affiliation: Department of Medicine, Division of Nephrology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.|Kendall regional medical center, Miami, FL, 33175, USA.
authors.forename: Sowjanya
authors.initials: S
authors.lastname: Kalluri
authors.affiliation: Department of Medicine, Division of Nephrology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.|Department of Urology, Osaka University Graduate School of Medicine, Osaka, Japan.
authors.forename: Yoichi
authors.initials: Y
authors.lastname: Kakuta
authors.affiliation: Department of Urology, Osaka University Graduate School of Medicine, Osaka, Japan.
authors.forename: Motohide
authors.initials: M
authors.lastname: Uemura
authors.affiliation: Department of Urology, Osaka University Graduate School of Medicine, Osaka, Japan.
authors.forename: Ryoichi
authors.initials: R
authors.lastname: Imamura
authors.affiliation: Department of Urology, Osaka University Graduate School of Medicine, Osaka, Japan.
authors.forename: Norio
authors.initials: N
authors.lastname: Nonomura
authors.affiliation: Department of Medicine, Division of Nephrology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.|Johns Hopkins Hospital, Baltimore, MD, 21287, USA.
authors.forename: Vikas
authors.initials: V
authors.lastname: Vujjini
authors.affiliation: Department of Medicine, Division of Nephrology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.|Johns Hopkins Hospital, Baltimore, MD, 21287, USA.
authors.forename: Sami
authors.initials: S
authors.lastname: Alasfar
authors.affiliation: Department of Medicine, Division of Nephrology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.|Johns Hopkins Hospital, Baltimore, MD, 21287, USA.
authors.forename: Hamid
authors.initials: H
authors.lastname: Rabb
authors.affiliation: Department of Medicine, University of Chicago, Chicago, IL, 60637, USA.
authors.forename: Yusuke
authors.initials: Y
authors.lastname: Nakamura
authors.affiliation: Department of Medicine, Division of Nephrology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.|Johns Hopkins Hospital, Baltimore, MD, 21287, USA.
authors.forename: Nada
authors.identifier: 0000-0003-1249-2455
authors.initials: N
authors.lastname: Alachkar
mesh_terms: D000328:Adult; D000368:Aged; D015415:Biomarkers / Q000097:blood; D015704:CD4 Antigens / Q000235:genetics; D016827:CD8 Antigens / Q000235:genetics; D005260:Female; D051858:Forkhead Transcription Factors / Q000235:genetics; D020869:Gene Expression Profiling; D006084:Graft Rejection / Q000276:immunology* / Q000473:pathology; D053804:Granzymes / Q000235:genetics; D006801:Humans; D007668:Kidney / Q000473:pathology; D016030:Kidney Transplantation; D008297:Male; D008875:Middle Aged; D054353:Perforin / Q000235:genetics; D011446:Prospective Studies; D012333:RNA, Messenger / Q000097:blood*; D011948:Receptors, Antigen, T-Cell / Q000235:genetics / Q000378:metabolism*; D013601:T-Lymphocytes / Q000276:immunology* / Q000378:metabolism; D055815:Young Adult
chemical_list: D015415:Biomarkers; D015704:CD4 Antigens; D016827:CD8 Antigens; C418974:FOXP3 protein, human; D051858:Forkhead Transcription Factors; D012333:RNA, Messenger; D011948:Receptors, Antigen, T-Cell; D054353:Perforin; D053804:Granzymes
keywords: Kidney transplant; T cell mediated rejection; T cell sequencing; T-cell