Search CTL/CD8+ T-Cell Epitope Database

Found 6 matching records:

Displaying record number 60505

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HXB2 Location	Gag(77-85) p17(77-85) DNA(1018..1044)	Gag Epitope Map
Author Location	p17
Epitope	`SLYNTVATL`	Epitope Alignment
		Show epitope variants
Epitope Name	A2-SL9
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	ACS 19957: A01, A02, B08:01, B15; ACS 19885: A01, A02, B08:01, B27; ACS 19861: A01, A02, B08:01, B51; ACS 19453: A01, A02, B08:01, B38; ACS 19342: A01, A02, B08:01, B40; ACS 18840: A02, B08:01, B27; ACS 18839: A02:07, B08:01, B27; ACS 18785: A01, A02, B07, B08:01
Country	Netherlands
Experimental methods	Other, Tetramer binding
Keywords	TCR usage

Notes

Eight asymptomatic, chronic HIV-1-infected, ART-naive, HLA-A*02+, B*08+ subjects from the Amsterdam cohort were interrogated at two time points for correlations between HIV-1 epitope mutation, antigen-specific T-cell expansion i.e. TCR diversity, and repertoire of responding CTL clonotypes. Data suggest continuous bidirectional adaptation between HIV-1 and HIV-specific T-cell clonotypes at the TCR-antigenic epitope interface.
Viral epitope variation has no direct correlation with CTL repertoire and diversity, though parallel evolution of TCR repertoire, virus and CTL response was noted, independent of individual subjects. Different patterns of TCRβ evolution were observed in subjects who showed delayed progression to disease.
Epitope A2-SL9, SLYNTVATL, was at 100% wild type sequence in most subjects at time point 1 (t₁). Variants were SLYNTiATL, pLYNTVATL, SLfNaVAvL, SLfNAVAvL, SLfNTVATL.

References

Costa2015 Ana I. Costa, Dan Koning, Kristin Ladell, James E. McLaren, Bart P. X. Grady, Ingrid M. M. Schellens, Petra van Ham, Monique Nijhuis, José A. M. Borghans, Can Keşmir, David A. Price, and Debbie van Baarle. Complex T-Cell Receptor Repertoire Dynamics Underlie the CD8+ T-Cell Response to HIV-1. J. Virol., 89(1):110-119, Jan 2015. PubMed ID: 25320304. Show all entries for this paper.

Displaying record number 60506

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HXB2 Location	Gag(260-267) p24(128-135) DNA(1567..1590)	Gag Epitope Map
Author Location	p24
Epitope	`EIYKRWII`	Epitope Alignment
		Show epitope variants
Epitope Name	B8-EI8
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	ACS 19957: A01, A02, B08:01, B15; ACS 19885: A01, A02, B08:01, B27; ACS 19861: A01, A02, B08:01, B51; ACS 19453: A01, A02, B08:01, B38; ACS 19342: A01, A02, B08:01, B40; ACS 18840: A02, B08:01, B27; ACS 18839: A02:07, B08:01, B27; ACS 18785: A01, A02, B07, B08:01
Country	Netherlands
Experimental methods	Other, Tetramer binding
Keywords	TCR usage

Notes

Eight asymptomatic, chronic HIV-1-infected, ART-naive, HLA-A*02+, B*08+ subjects from the Amsterdam cohort were interrogated at two time points for correlations between HIV-1 epitope mutation, antigen-specific T-cell expansion i.e. TCR diversity, and repertoire of responding CTL clonotypes. Data suggest continuous bidirectional adaptation between HIV-1 and HIV-specific T-cell clonotypes at the TCR-antigenic epitope interface.
Viral epitope variation has no direct correlation with CTL repertoire and diversity, though parallel evolution of TCR repertoire, virus and CTL response was noted, independent of individual subjects. Different patterns of TCRβ evolution were observed in subjects who showed delayed progression to disease.
Epitope B8-EI8, EIYKRWII, was at 100% wild type sequence in most subjects at time point 1 (t₁). Variants were EIYeRWII, EIYKRWIv, EIYrRWII and dIYKRWII.

References

Displaying record number 63217

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HXB2 Location	Gag(260-267) p24(128-135)	Gag Epitope Map
Author Location
Epitope	`EIYKRWII`	Epitope Alignment
Species (MHC/HLA)	human
Immunogen	computer prediction
Experimental methods	Other
Keywords	assay or method development

Notes

DeNeuter2018 demonstrates the feasibility of accurate TCR-epitope recognition predictors based on the amino acid sequence of the TCR. Two random forest classifiers were developed & found to have good performance in analyzing 2 model epitopes: a "one-versus-one" classifier that predicts which of 2 HIV epitopes is most likely to be bound by a TCR sequence & a "one-versus-many" classifier that identifies TCRs that bind to a specific epitope.
Using data from Costa2015, these random forest classifiers were used to identify sequence-based features that likely play prominent roles in TCR-epitope recognition. For Gag epitope EIYKRWII, known to be restricted by HLA-B*08, the most discriminatory features were basicity & hydrophobicity (both average & for specific central residues in CDR3) and the isoelectric point of the CDR3.

References

DeNeuter2018 Nicolas De Neuter, Wout Bittremieux, Charlie Beirnaert, Bart Cuypers, Aida Mrzic, Pieter Moris, Arvid Suls, Viggo Van Tendeloo, Benson Ogunjimi, Kris Laukens, and Pieter Meysman. On the feasibility of mining CD8+ T cell receptor patterns underlying immunogenic peptide recognition. Immunogenetics, 70(3):159-168 doi, Mar 2018. PubMed ID: 28779185 Show all entries for this paper.

Displaying record number 60508

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HXB2 Location	Gag(263-272) p24(131-140) DNA(1576..1605)	Gag Epitope Map
Author Location	p24
Epitope	`KRWIILGLNK`	Epitope Alignment
		Show epitope variants
Epitope Name	B27-KK10
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	ACS 19957: A01, A02, B08:01, B15; ACS 19885: A01, A02, B08:01, B27; ACS 19861: A01, A02, B08:01, B51; ACS 19453: A01, A02, B08:01, B38; ACS 19342: A01, A02, B08:01, B40; ACS 18840: A02, B08:01, B27; ACS 18839: A02:07, B08:01, B27; ACS 18785: A01, A02, B07, B08:01
Country	Netherlands
Experimental methods	Other, Tetramer binding
Keywords	TCR usage

Notes

Eight asymptomatic, chronic HIV-1-infected, ART-naive, HLA-A*02+, B*08+ subjects from the Amsterdam cohort were interrogated at two time points for correlations between HIV-1 epitope mutation, antigen-specific T-cell expansion i.e. TCR diversity, and repertoire of responding CTL clonotypes. Data suggest continuous bidirectional adaptation between HIV-1 and HIV-specific T-cell clonotypes at the TCR-antigenic epitope interface.
Viral epitope variation has no direct correlation with CTL repertoire and diversity, though parallel evolution of TCR repertoire, virus and CTL response was noted, independent of individual subjects. Different patterns of TCRβ evolution were observed in subjects who showed delayed progression to disease.
Immunodominant epitope B27-KK10, KRWIILGLNK, was at 93.6% wild type sequence in subject 2 (ACS 19885) at time point 1 (t₁), decreasing to 85.7% at t₂. At t₁ it was at 28% in subject 6 (ACS 18840). Variants were eRWIILGLNK, KRWIIpGLNK, KRWIvmGLNK, KRWIImGLNK, KRWIIiGLNK, and rRWIILGLNK.

References

Displaying record number 60507

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HXB2 Location	Nef(90-97) DNA(9064..9087)	Nef Epitope Map
Author Location	Nef
Epitope	`FLKEKGGL`	Epitope Alignment
		Show epitope variants
Epitope Name	B8-FL8
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	ACS 19957: A01, A02, B08:01, B15; ACS 19885: A01, A02, B08:01, B27; ACS 19861: A01, A02, B08:01, B51; ACS 19453: A01, A02, B08:01, B38; ACS 19342: A01, A02, B08:01, B40; ACS 18840: A02, B08:01, B27; ACS 18839: A02:07, B08:01, B27; ACS 18785: A01, A02, B07, B08:01
Country	Netherlands
Experimental methods	Other, Tetramer binding
Keywords	TCR usage

Notes

Eight asymptomatic, chronic HIV-1-infected, ART-naive, HLA-A*02+, B*08+ subjects from the Amsterdam cohort were interrogated at two time points for correlations between HIV-1 epitope mutation, antigen-specific T-cell expansion i.e. TCR diversity, and repertoire of responding CTL clonotypes. Data suggest continuous bidirectional adaptation between HIV-1 and HIV-specific T-cell clonotypes at the TCR-antigenic epitope interface.
Viral epitope variation has no direct correlation with CTL repertoire and diversity, though parallel evolution of TCR repertoire, virus and CTL response was noted, independent of individual subjects. Different patterns of TCRβ evolution were observed in subjects who showed delayed progression to disease.
Epitope B8-FL8, FLKEKGGL, was at 100% wild type sequence only in subject 3 at time point 1 (t₁). Variants were FLKEtGGL, FLKErGGL, FLKEmGGL, FLKEeGGL, FLnEKGGL, lLnEKGGL, and FLrEKGGL.

References

Displaying record number 63216

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HXB2 Location	Nef(90-97)	Nef Epitope Map
Author Location
Epitope	`FLKEKGGL`	Epitope Alignment
Species (MHC/HLA)	human
Immunogen	computer prediction
Experimental methods	Other
Keywords	assay or method development

Notes

DeNeuter2018 demonstrates the feasibility of accurate TCR-epitope recognition predictors based on the amino acid sequence of the TCR. Two random forest classifiers were developed & found to have good performance in analyzing 2 model epitopes: a "one-versus-one" classifier that predicts which of 2 HIV epitopes is most likely to be bound by a TCR sequence & a "one-versus-many" classifier that identifies TCRs that bind to a specific epitope.
Using data from Costa2015, these random forest classifiers were used to identify sequence-based features that likely play prominent roles in TCR-epitope recognition. For HIV-1 epitope FLKEKGGL, known to be restricted by HLA-B*08, the most discriminatory features were TCR CDR3 sequence length, helicity & hydrophobicity (both average & for specific central residues in CDR3) and the number of lysines within CDR3.