TY - JOUR
T1 - Epstein-barr virus epitope-major histocompatibility complex interaction combined with convergent recombination drives selection of diverse T cell receptor α and β repertoires
AU - Gil, Anna
AU - Kamga, Larisa
AU - Chirravuri-Venkata, Ramakanth
AU - Aslan, Nuray
AU - Clark, Fransenio
AU - Ghersi, Dario
AU - Luzuriaga, Katherine
AU - Selin, Liisa K.
N1 - Funding Information:
and AI-109858 (L.K.S.); Center for Diabetes Research Core grant DR32520 (L.K.S.); the UMass Center for Clinical and Translational Science (UL1-TR001453); and a Nebraska Research Initiative grant to D.G. A.G. was supported by funding to L.K.S., and L.K. was supported by funding to K.L.
Funding Information:
This research used resources of the Advanced Photon Source, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under contract no. DE-AC02-06CH11357. Use of the Lilly Research Laboratories Collaborative Access Team (LRL-CAT) beamline at Sector 31 of the Advanced Photon Source was provided by Eli Lilly Company, which operates the facility. We have no financial conflicts.
Funding Information:
This study was supported by NIH grants AI-49320 (L.K.S. and K.L.), AI-046629 (L.K.S.),
Funding Information:
We are grateful to the study subjects for their participation; George Corey and Jessica Conrad for obtaining clinical samples; Linda Lambrecht, Robin Brody, Anita Gautam, and Jennifer Henderson for expert technical assistance; Margaret McManus for data management and critical review of the manuscript; and Raymond Welsh for critical review of the manuscript. This research used resources of the Advanced Photon Source, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under contract no. DE-AC02-06CH11357. Use of the Lilly Research Laboratories Collaborative Access Team (LRL-CAT) beamline at Sector 31 of the Advanced Photon Source was provided by Eli Lilly Company, which operates the facility. We have no financial conflicts. The contents of this publication are solely the responsibility of the authors and do not represent the official view of the NIH. L.K.S. and K.L. obtained samples and conceived the study. A.G. and L.K. contributed to study design and were primarily responsible for cell sorting and TCR sequencing. All authors contributed to data analyses. D.G. and R.C.-V. performed all computational analyses. L.K.S., K.L., L.K., A.G., and D.G. assumed primary responsibility for writing the manuscript. All authors reviewed, provided substantive input to, and approved the final manuscript. A.G. did most of the experimental work, including CD8 tetramer sorting and TCR deep sequencing; both A.G. and L.K. contributed to data analyses, making figures, and writing the manuscript. Both K.L. and L.K.S. contributed to designing the research, supervising A.G. and L.K., funding the experimental work, writing the manuscript (L.K.S. did the first revisions), analyzing the data, and designing the figures (L.K.S. made some of the original complex figures). A.N. and F.C. did some of the experimental work and helped with editing the manuscript. This study was supported by NIH grants AI-49320 (L.K.S. and K.L.), AI-046629 (L.K.S.), and AI-109858 (L.K.S.); Center for Diabetes Research Core grant DR32520 (L.K.S.); the UMass Center for Clinical and Translational Science (UL1-TR001453); and a Nebraska Research Initiative grant to D.G. A.G. was supported by funding to L.K.S., and L.K. was supported by funding to K.L
Publisher Copyright:
© 2020 Gil et al.
PY - 2020/3/1
Y1 - 2020/3/1
N2 - Recognition modes of individual T cell receptors (TCRs) are well studied, but factors driving the selection of TCR repertoires from primary through persistent human virus infections are less well understood. Using deep sequencing, we demonstrate a high degree of diversity of Epstein-Barr virus (EBV)-specific clonotypes in acute infectious mononucleosis (AIM). Only 9% of unique clonotypes detected in AIM persisted into convalescence; the majority (91%) of unique clonotypes detected in AIM were not detected in convalescence and were seeming replaced by equally diverse “de novo” clonotypes. The persistent clonotypes had a greater probability of being generated than nonpersistent clonotypes due to convergence recombination of multiple nucleotide sequences to encode the same amino acid sequence, as well as the use of shorter complementarity-determining regions 3 (CDR3s) with fewer nucleotide additions (i.e., sequences closer to germ line). Moreover, the two most immunodominant HLA-A2-restricted EBV epitopes, BRLF1109 and BMLF1280, show highly distinct antigen-specific public (i.e., shared between individuals) features. In fact, TCRα CDR3 motifs played a dominant role, while TCRβ played a minimal role, in the selection of TCR repertoire to an immunodominant EBV epitope, BRLF1. This contrasts with the majority of previously reported repertoires, which appear to be selected either on TCRβ CDR3 interactions with peptide/major histocompatibility complex (MHC) or in combination with TCRα CDR3. Understanding of how TCR-peptide-MHC complex interactions drive repertoire selection can be used to develop optimal strategies for vaccine design or generation of appropriate adoptive immunotherapies for viral infections in transplant settings or for cancer. IMPORTANCE Several lines of evidence suggest that TCRα and TCRβ repertoires play a role in disease outcomes and treatment strategies during viral infections in transplant patients and in cancer and autoimmune disease therapy. Our data suggest that it is essential that we understand the basic principles of how to drive optimum repertoires for both TCR chains, α and β. We address this important issue by characterizing the CD8 TCR repertoire to a common persistent human viral infection (EBV), which is controlled by appropriate CD8 T cell responses. The ultimate goal would be to determine if the individuals who are infected asymptomatically develop a different TCR repertoire than those that develop the immunopathology of AIM. Here, we begin by doing an in-depth characterization of both CD8 T cell TCRα and TCRβ repertoires to two immunodominant EBV epitopes over the course of AIM, identifying potential factors that may be driving their selection.
AB - Recognition modes of individual T cell receptors (TCRs) are well studied, but factors driving the selection of TCR repertoires from primary through persistent human virus infections are less well understood. Using deep sequencing, we demonstrate a high degree of diversity of Epstein-Barr virus (EBV)-specific clonotypes in acute infectious mononucleosis (AIM). Only 9% of unique clonotypes detected in AIM persisted into convalescence; the majority (91%) of unique clonotypes detected in AIM were not detected in convalescence and were seeming replaced by equally diverse “de novo” clonotypes. The persistent clonotypes had a greater probability of being generated than nonpersistent clonotypes due to convergence recombination of multiple nucleotide sequences to encode the same amino acid sequence, as well as the use of shorter complementarity-determining regions 3 (CDR3s) with fewer nucleotide additions (i.e., sequences closer to germ line). Moreover, the two most immunodominant HLA-A2-restricted EBV epitopes, BRLF1109 and BMLF1280, show highly distinct antigen-specific public (i.e., shared between individuals) features. In fact, TCRα CDR3 motifs played a dominant role, while TCRβ played a minimal role, in the selection of TCR repertoire to an immunodominant EBV epitope, BRLF1. This contrasts with the majority of previously reported repertoires, which appear to be selected either on TCRβ CDR3 interactions with peptide/major histocompatibility complex (MHC) or in combination with TCRα CDR3. Understanding of how TCR-peptide-MHC complex interactions drive repertoire selection can be used to develop optimal strategies for vaccine design or generation of appropriate adoptive immunotherapies for viral infections in transplant settings or for cancer. IMPORTANCE Several lines of evidence suggest that TCRα and TCRβ repertoires play a role in disease outcomes and treatment strategies during viral infections in transplant patients and in cancer and autoimmune disease therapy. Our data suggest that it is essential that we understand the basic principles of how to drive optimum repertoires for both TCR chains, α and β. We address this important issue by characterizing the CD8 TCR repertoire to a common persistent human viral infection (EBV), which is controlled by appropriate CD8 T cell responses. The ultimate goal would be to determine if the individuals who are infected asymptomatically develop a different TCR repertoire than those that develop the immunopathology of AIM. Here, we begin by doing an in-depth characterization of both CD8 T cell TCRα and TCRβ repertoires to two immunodominant EBV epitopes over the course of AIM, identifying potential factors that may be driving their selection.
KW - Acute infectious mononucleosis
KW - EBV
KW - Epstein-barr virus
KW - Repertoire
KW - T cell receptor
KW - TCR
UR - http://www.scopus.com/inward/record.url?scp=85082081954&partnerID=8YFLogxK
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U2 - 10.1128/mBio.00250-20
DO - 10.1128/mBio.00250-20
M3 - Article
C2 - 32184241
AN - SCOPUS:85082081954
VL - 11
JO - mBio
JF - mBio
SN - 2161-2129
IS - 2
M1 - e00250-20
ER -