Identifying patient-specific Epstein-Barr Nuclear Antigen-1 genetic variation and potential autoreactive targets relevant to multiple sclerosis pathogenesis

M. Tschochner, S. Leary, D. Cooper, K. Strautins, A. Chopra, H. Clark, L. Choo, D. Dunn, I. James, Bill M. Carroll, Allan G. Kermode, D. Nolan

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Abstract

© Copyright 2016 Tschochner et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Background: Epstein-Barr virus (EBV) infection represents a major environmental risk factor for multiple sclerosis (MS), with evidence of selective expansion of Epstein-Barr Nuclear Antigen-1 (EBNA1)-specific CD4+ T cells that cross-recognize MS-associated myelin antigens in MS patients. HLA-DRB1*15-restricted antigen presentation also appears to determine susceptibility given its role as a dominant risk allele. In this study, we have utilised standard and next-generation sequencing techniques to investigate EBNA-1 sequence variation and its relationship to HLA-DR15 binding affinity, as well as examining potential cross-reactive immune targets within the central nervous system proteome. Methods: Sanger sequencing was performed on DNA isolated from peripheral blood samples from 73 Western Australian MS cases, without requirement for primary culture, with additional FLX 454 Roche sequencing in 23 samples to identify low-frequency variants. Patient-derived viral sequences were used to predict HLA-DRB1*1501 epitopes (NetMHCII, NetMHCIIpan) and candidates were evaluated for cross recognition with human brain proteins. Results EBNA-1 sequence variation was limited, with no evidence of multiple viral strains and only low levels of variation identified by FLX technology (8.3% nucleotide positions at a 1% cutoff). In silico epitope mapping revealed two known HLA-DRB1*1501-restricted epitopes ('AEG': aa 481-496 and 'MVF': aa 562-577), and two putative epitopes between positions 502-543. We identified potential cross-reactive targets involving a number of major myelin antigens including experimentally confirmed HLA-DRB1*15-restricted epitopes as well as novel candidate antigens within myelin and paranodal assembly proteins that may be relevant to MS pathogen
Original languageEnglish
Article numbere0147567
JournalPLoS One
Volume11
Issue number2
DOIs
Publication statusPublished - 2016

Fingerprint

nuclear antigens
Nuclear Antigens
sclerosis
HLA-DRB1 Chains
Multiple Sclerosis
Epitopes
pathogenesis
epitopes
myelin sheath
Myelin Sheath
genetic variation
Antigens
antigens
Epitope Mapping
Human herpesvirus 4
antigen presentation
Epstein-Barr Virus Infections
T-cells
Antigen Presentation
Neurology

Cite this

Tschochner, M. ; Leary, S. ; Cooper, D. ; Strautins, K. ; Chopra, A. ; Clark, H. ; Choo, L. ; Dunn, D. ; James, I. ; Carroll, Bill M. ; Kermode, Allan G. ; Nolan, D. / Identifying patient-specific Epstein-Barr Nuclear Antigen-1 genetic variation and potential autoreactive targets relevant to multiple sclerosis pathogenesis. In: PLoS One. 2016 ; Vol. 11, No. 2.
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title = "Identifying patient-specific Epstein-Barr Nuclear Antigen-1 genetic variation and potential autoreactive targets relevant to multiple sclerosis pathogenesis",
abstract = "{\circledC} Copyright 2016 Tschochner et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Background: Epstein-Barr virus (EBV) infection represents a major environmental risk factor for multiple sclerosis (MS), with evidence of selective expansion of Epstein-Barr Nuclear Antigen-1 (EBNA1)-specific CD4+ T cells that cross-recognize MS-associated myelin antigens in MS patients. HLA-DRB1*15-restricted antigen presentation also appears to determine susceptibility given its role as a dominant risk allele. In this study, we have utilised standard and next-generation sequencing techniques to investigate EBNA-1 sequence variation and its relationship to HLA-DR15 binding affinity, as well as examining potential cross-reactive immune targets within the central nervous system proteome. Methods: Sanger sequencing was performed on DNA isolated from peripheral blood samples from 73 Western Australian MS cases, without requirement for primary culture, with additional FLX 454 Roche sequencing in 23 samples to identify low-frequency variants. Patient-derived viral sequences were used to predict HLA-DRB1*1501 epitopes (NetMHCII, NetMHCIIpan) and candidates were evaluated for cross recognition with human brain proteins. Results EBNA-1 sequence variation was limited, with no evidence of multiple viral strains and only low levels of variation identified by FLX technology (8.3{\%} nucleotide positions at a 1{\%} cutoff). In silico epitope mapping revealed two known HLA-DRB1*1501-restricted epitopes ('AEG': aa 481-496 and 'MVF': aa 562-577), and two putative epitopes between positions 502-543. We identified potential cross-reactive targets involving a number of major myelin antigens including experimentally confirmed HLA-DRB1*15-restricted epitopes as well as novel candidate antigens within myelin and paranodal assembly proteins that may be relevant to MS pathogen",
author = "M. Tschochner and S. Leary and D. Cooper and K. Strautins and A. Chopra and H. Clark and L. Choo and D. Dunn and I. James and Carroll, {Bill M.} and Kermode, {Allan G.} and D. Nolan",
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Tschochner, M, Leary, S, Cooper, D, Strautins, K, Chopra, A, Clark, H, Choo, L, Dunn, D, James, I, Carroll, BM, Kermode, AG & Nolan, D 2016, 'Identifying patient-specific Epstein-Barr Nuclear Antigen-1 genetic variation and potential autoreactive targets relevant to multiple sclerosis pathogenesis' PLoS One, vol. 11, no. 2, e0147567. https://doi.org/10.1371/journal.pone.0147567

Identifying patient-specific Epstein-Barr Nuclear Antigen-1 genetic variation and potential autoreactive targets relevant to multiple sclerosis pathogenesis. / Tschochner, M.; Leary, S.; Cooper, D.; Strautins, K.; Chopra, A.; Clark, H.; Choo, L.; Dunn, D.; James, I.; Carroll, Bill M.; Kermode, Allan G.; Nolan, D.

In: PLoS One, Vol. 11, No. 2, e0147567, 2016.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Identifying patient-specific Epstein-Barr Nuclear Antigen-1 genetic variation and potential autoreactive targets relevant to multiple sclerosis pathogenesis

AU - Tschochner, M.

AU - Leary, S.

AU - Cooper, D.

AU - Strautins, K.

AU - Chopra, A.

AU - Clark, H.

AU - Choo, L.

AU - Dunn, D.

AU - James, I.

AU - Carroll, Bill M.

AU - Kermode, Allan G.

AU - Nolan, D.

PY - 2016

Y1 - 2016

N2 - © Copyright 2016 Tschochner et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Background: Epstein-Barr virus (EBV) infection represents a major environmental risk factor for multiple sclerosis (MS), with evidence of selective expansion of Epstein-Barr Nuclear Antigen-1 (EBNA1)-specific CD4+ T cells that cross-recognize MS-associated myelin antigens in MS patients. HLA-DRB1*15-restricted antigen presentation also appears to determine susceptibility given its role as a dominant risk allele. In this study, we have utilised standard and next-generation sequencing techniques to investigate EBNA-1 sequence variation and its relationship to HLA-DR15 binding affinity, as well as examining potential cross-reactive immune targets within the central nervous system proteome. Methods: Sanger sequencing was performed on DNA isolated from peripheral blood samples from 73 Western Australian MS cases, without requirement for primary culture, with additional FLX 454 Roche sequencing in 23 samples to identify low-frequency variants. Patient-derived viral sequences were used to predict HLA-DRB1*1501 epitopes (NetMHCII, NetMHCIIpan) and candidates were evaluated for cross recognition with human brain proteins. Results EBNA-1 sequence variation was limited, with no evidence of multiple viral strains and only low levels of variation identified by FLX technology (8.3% nucleotide positions at a 1% cutoff). In silico epitope mapping revealed two known HLA-DRB1*1501-restricted epitopes ('AEG': aa 481-496 and 'MVF': aa 562-577), and two putative epitopes between positions 502-543. We identified potential cross-reactive targets involving a number of major myelin antigens including experimentally confirmed HLA-DRB1*15-restricted epitopes as well as novel candidate antigens within myelin and paranodal assembly proteins that may be relevant to MS pathogen

AB - © Copyright 2016 Tschochner et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Background: Epstein-Barr virus (EBV) infection represents a major environmental risk factor for multiple sclerosis (MS), with evidence of selective expansion of Epstein-Barr Nuclear Antigen-1 (EBNA1)-specific CD4+ T cells that cross-recognize MS-associated myelin antigens in MS patients. HLA-DRB1*15-restricted antigen presentation also appears to determine susceptibility given its role as a dominant risk allele. In this study, we have utilised standard and next-generation sequencing techniques to investigate EBNA-1 sequence variation and its relationship to HLA-DR15 binding affinity, as well as examining potential cross-reactive immune targets within the central nervous system proteome. Methods: Sanger sequencing was performed on DNA isolated from peripheral blood samples from 73 Western Australian MS cases, without requirement for primary culture, with additional FLX 454 Roche sequencing in 23 samples to identify low-frequency variants. Patient-derived viral sequences were used to predict HLA-DRB1*1501 epitopes (NetMHCII, NetMHCIIpan) and candidates were evaluated for cross recognition with human brain proteins. Results EBNA-1 sequence variation was limited, with no evidence of multiple viral strains and only low levels of variation identified by FLX technology (8.3% nucleotide positions at a 1% cutoff). In silico epitope mapping revealed two known HLA-DRB1*1501-restricted epitopes ('AEG': aa 481-496 and 'MVF': aa 562-577), and two putative epitopes between positions 502-543. We identified potential cross-reactive targets involving a number of major myelin antigens including experimentally confirmed HLA-DRB1*15-restricted epitopes as well as novel candidate antigens within myelin and paranodal assembly proteins that may be relevant to MS pathogen

U2 - 10.1371/journal.pone.0147567

DO - 10.1371/journal.pone.0147567

M3 - Article

VL - 11

JO - P L o S One

JF - P L o S One

SN - 1932-6203

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