An unanticipated lack of consensus cytotoxic T lymphocyte epitopes in HIV-1 databases: the contribution of prediction programs

I.M.M. Schellens; C. Kesmir; F. Miedema; D. van Baarle; J.A.M. Borghans

doi:10.1097/QAD.0b013e3282f15622

An unanticipated lack of consensus cytotoxic T lymphocyte epitopes in HIV-1 databases: the contribution of prediction programs

I.M.M. Schellens, C. Kesmir, F. Miedema, D. van Baarle, J.A.M. Borghans

Research output: Contribution to journal › Article › Academic › peer-review

Abstract

Background: Most consensus HIV-1-specific cytotoxic T lymphocytes epitopes presented via intensively studied HLA molecules are thought to be known

Objective: To identify possible novel HIV-1 epitopes for HLA-B27 and HLA-B57; two HLA types which are abundantly studied because of their correlation with slow HIV disease progression.

Methods: HIV-1 consensus subtype B sequences were analysed using peptide prediction programs based on major histocompatibility complex binding, proteasomal cleavage and TAP (transporter associated with antigen processing) transport. Recognition of the novel identified epitopes by cytotoxic T lymphocytes was tested using interferon-[gamma] ELISpot assay.

Results: In total, 22 novel epitopes predicted to be presented by either HLA-B27 or HLA-B57 were selected. Of these, 86% elicited significant immune responses in HIV-1-infected individuals.

Conclusions: These data show that numerous HIV-1 epitopes remain to be identified, and that prediction programs are powerful tools for this purpose.

Original language	English
Pages (from-to)	33-37
Number of pages	5
Journal	AIDS
Volume	22
Issue number	1
DOIs	https://doi.org/10.1097/QAD.0b013e3282f15622
Publication status	Published - 2008

Keywords

Life sciences
Biomathematics and biometrics

Access to Document

10.1097/QAD.0b013e3282f15622

unanticipatedFinal published version, 130 KB

Cite this

@article{52dcb9c5cffb4bc7baeb70f82aa117ad,

title = "An unanticipated lack of consensus cytotoxic T lymphocyte epitopes in HIV-1 databases: the contribution of prediction programs",

abstract = "Background: Most consensus HIV-1-specific cytotoxic T lymphocytes epitopes presented via intensively studied HLA molecules are thought to be knownObjective: To identify possible novel HIV-1 epitopes for HLA-B27 and HLA-B57; two HLA types which are abundantly studied because of their correlation with slow HIV disease progression.Methods: HIV-1 consensus subtype B sequences were analysed using peptide prediction programs based on major histocompatibility complex binding, proteasomal cleavage and TAP (transporter associated with antigen processing) transport. Recognition of the novel identified epitopes by cytotoxic T lymphocytes was tested using interferon-[gamma] ELISpot assay.Results: In total, 22 novel epitopes predicted to be presented by either HLA-B27 or HLA-B57 were selected. Of these, 86% elicited significant immune responses in HIV-1-infected individuals.Conclusions: These data show that numerous HIV-1 epitopes remain to be identified, and that prediction programs are powerful tools for this purpose.",

keywords = "Life sciences, Biomathematics and biometrics",

author = "I.M.M. Schellens and C. Kesmir and F. Miedema and {van Baarle}, D. and J.A.M. Borghans",

year = "2008",

doi = "10.1097/QAD.0b013e3282f15622",

language = "English",

volume = "22",

pages = "33--37",

journal = "AIDS",

issn = "0269-9370",

publisher = "Lippincott Williams & Wilkins",

number = "1",

}

TY - JOUR

T1 - An unanticipated lack of consensus cytotoxic T lymphocyte epitopes in HIV-1 databases: the contribution of prediction programs

AU - Schellens, I.M.M.

AU - Kesmir, C.

AU - Miedema, F.

AU - van Baarle, D.

AU - Borghans, J.A.M.

PY - 2008

Y1 - 2008

N2 - Background: Most consensus HIV-1-specific cytotoxic T lymphocytes epitopes presented via intensively studied HLA molecules are thought to be knownObjective: To identify possible novel HIV-1 epitopes for HLA-B27 and HLA-B57; two HLA types which are abundantly studied because of their correlation with slow HIV disease progression.Methods: HIV-1 consensus subtype B sequences were analysed using peptide prediction programs based on major histocompatibility complex binding, proteasomal cleavage and TAP (transporter associated with antigen processing) transport. Recognition of the novel identified epitopes by cytotoxic T lymphocytes was tested using interferon-[gamma] ELISpot assay.Results: In total, 22 novel epitopes predicted to be presented by either HLA-B27 or HLA-B57 were selected. Of these, 86% elicited significant immune responses in HIV-1-infected individuals.Conclusions: These data show that numerous HIV-1 epitopes remain to be identified, and that prediction programs are powerful tools for this purpose.

AB - Background: Most consensus HIV-1-specific cytotoxic T lymphocytes epitopes presented via intensively studied HLA molecules are thought to be knownObjective: To identify possible novel HIV-1 epitopes for HLA-B27 and HLA-B57; two HLA types which are abundantly studied because of their correlation with slow HIV disease progression.Methods: HIV-1 consensus subtype B sequences were analysed using peptide prediction programs based on major histocompatibility complex binding, proteasomal cleavage and TAP (transporter associated with antigen processing) transport. Recognition of the novel identified epitopes by cytotoxic T lymphocytes was tested using interferon-[gamma] ELISpot assay.Results: In total, 22 novel epitopes predicted to be presented by either HLA-B27 or HLA-B57 were selected. Of these, 86% elicited significant immune responses in HIV-1-infected individuals.Conclusions: These data show that numerous HIV-1 epitopes remain to be identified, and that prediction programs are powerful tools for this purpose.

KW - Life sciences

KW - Biomathematics and biometrics

U2 - 10.1097/QAD.0b013e3282f15622

DO - 10.1097/QAD.0b013e3282f15622

M3 - Article

SN - 0269-9370

VL - 22

SP - 33

EP - 37

JO - AIDS

JF - AIDS

IS - 1

ER -

An unanticipated lack of consensus cytotoxic T lymphocyte epitopes in HIV-1 databases: the contribution of prediction programs

Abstract

Keywords

Access to Document

Fingerprint

Cite this