Search CTL/CD8+ T-Cell Epitope Database

Found 9 matching records:

Displaying record number 60425

Download this epitope record as JSON.

HXB2 Location	Gag(274-282) p24(142-150) DNA(1609..1635)	Gag Epitope Map
Author Location	Gag(274-282)
Epitope	`VRMYSPVSI`	Epitope Alignment
Epitope Name	VI9
Species (MHC/HLA)	human(B*07)
Immunogen	HIV-1 infection
Experimental methods	CD8 T-cell Elispot - IFNγ, Flow cytometric T-cell cytokine assay
Keywords	rate of progression, optimal epitope, chronic infection

Notes

Correlation between HLA class I and spontaneous control of HIV-1 was significant for 7-8 epitopes when 341 chronic, HIV-infected subjects, divided into controllers and non-controllers, were tested for EliSpot responses to 257 optimally defined epitopes. 21 epitopes were associated with viral progression. Protective epitopes tend to cluster in regions of critical stability for the protein, therefore constraining escape.
VRMYSPVSI had a significantly positive association with HLA B*07; it was recognized by 6/37 B*07-positive subjects and 8/289 B*07-negative subjects.

References

Pereyra2014 Florencia Pereyra, David Heckerman, Jonathan M. Carlson, Carl Kadie, Damien Z. Soghoian, Daniel Karel, Ariel Goldenthal, Oliver B. Davis, Charles E. DeZiel, Tienho Lin, Jian Peng, Alicja Piechocka, Mary Carrington, and Bruce D. Walker. HIV Control Is Mediated in Part by CD8+ T-Cell Targeting of Specific Epitopes. J. Virol., 88(22):12937-12948, Nov 2014. PubMed ID: 25165115. Show all entries for this paper.

Displaying record number 61975

Download this epitope record as JSON.

HXB2 Location	Gag(274-282) p24(142-150) DNA(1609..1635)	Gag Epitope Map
Author Location	Gag(274-282)
Epitope	`VRMYSPVSI`	Epitope Alignment
Subtype	A, D
Species (MHC/HLA)	human(B*07:02)
Immunogen	HIV-1 infection
Patient MHC/HLA	2127: A01:01, A03:01, B07:02, B41:01, C07:01, C07:23
Country	Kenya
Experimental methods	CD8 T-cell Elispot - IFNγ, Other, Tetramer binding
Keywords	subtype comparisons, HIV exposed persistently seronegative (HEPS), assay or method development

Notes

A systematic analysis of clade A or D epitopes that bind either protective HLA-A*0101 or susceptible HLA-B*0702 using the iTopia epitope discovery system was conducted. Broad epitope and variant recognition, and immune response was seen with the susceptible HLA allele, while a focused recognition of multiple epitope subtypes was seen associated with the protective HLA allele.
Novel epitopes were discovered using the iTopia system (3 assays: peptide binding, binding affinity, and off-rate).
Four new amino acids at anchor positions P2 (Lys, Arg, Thr, Iso) and P9 (Lys, Thr, Arg, Gly) were identified for B*0702 binding, including polar basic residues K and R, showing that B*0702-restricted epitopes are more tolerant to amino acid changes than known previously.
Previously known B*0702-restricted Gag epitope VRMYSPVSI was recognized by seronegative subjects as well as HIV-1 patients and bound HLA-B*0702. 1/4 B*0702+ female subjects responded to the epitope, with a mean of 435 SFU/million cells.

References

Luo2012 Ma Luo, Christina A. Daniuk, Tamsir O. Diallo, Rupert E. Capina, Joshua Kimani, Charles Wachihi, Makubo Kimani, Thomas Bielawny, Trevor Peterson, Mark G. R. Mendoza, Sandra Kiazyk, T. Blake Ball, and Francis A. Plummer. For Protection from HIV-1 Infection, More Might Not Be Better: A Systematic Analysis of HIV Gag Epitopes of Two Alleles Associated with Different Outcomes of HIV-1 Infection. J. Virol., 86(2):1166-1180, Jan 2012. PubMed ID: 22072744. Show all entries for this paper.

Displaying record number 60423

Download this epitope record as JSON.

HXB2 Location	Gag(274-282) p24(142-150) DNA(1609..1635)	Gag Epitope Map
Author Location	Gag(274-282)
Epitope	`VRMYSPVSI`	Epitope Alignment
Epitope Name	VI9
Species (MHC/HLA)	human(B*52)
Immunogen	HIV-1 infection
Experimental methods	CD8 T-cell Elispot - IFNγ, Flow cytometric T-cell cytokine assay
Keywords	rate of progression, optimal epitope, chronic infection

Notes

Correlation between HLA class I and spontaneous control of HIV-1 was significant for 7-8 epitopes when 341 chronic, HIV-infected subjects, divided into controllers and non-controllers, were tested for EliSpot responses to 257 optimally defined epitopes. 21 epitopes were associated with viral progression. Protective epitopes tend to cluster in regions of critical stability for the protein, therefore constraining escape.
VRMYSPVSI had a significantly positive association with HLA B*52; it was recognized by 8/15 B*52-positive subjects and 14/326 B*52-negative subjects.

References

Displaying record number 60424

Download this epitope record as JSON.

HXB2 Location	Gag(274-282) p24(142-150) DNA(1609..1635)	Gag Epitope Map
Author Location	Gag(274-282)
Epitope	`VRMYSPVSI`	Epitope Alignment
Epitope Name	VI9
Species (MHC/HLA)	human(B*57)
Immunogen	HIV-1 infection
Experimental methods	CD8 T-cell Elispot - IFNγ, Flow cytometric T-cell cytokine assay
Keywords	rate of progression, optimal epitope, chronic infection

Notes

Correlation between HLA class I and spontaneous control of HIV-1 was significant for 7-8 epitopes when 341 chronic, HIV-infected subjects, divided into controllers and non-controllers, were tested for EliSpot responses to 257 optimally defined epitopes. 21 epitopes were associated with viral progression. Protective epitopes tend to cluster in regions of critical stability for the protein, therefore constraining escape.
VRMYSPVSI had a significantly positive association with HLA B*57; it was recognized by 8/94 B*57-positive subjects and 0/195 B*57-negative subjects.

References

Displaying record number 54113

Download this epitope record as JSON.

HXB2 Location	Gag(274-282) p24(142-150) DNA(1609..1635)	Gag Epitope Map
Author Location
Epitope	`VRMYSPVSI`	Epitope Alignment
Epitope Name	VI9
Species (MHC/HLA)	human(C*18)
Immunogen
Experimental methods
Keywords	optimal epitope, A-list

Notes

C. Brander notes this is a Cw*18 epitope.

References

Llano2019 Anuska Llano, Samandhy Cedeño, Sandra Silva Arrieta, and Christian Brander. The 2019 Optimal HIV CTL Epitopes Update: Growing Diversity in Epitope Length and HLA restriction. 2019. Show all entries for this paper.

Displaying record number 55722

Download this epitope record as JSON.

HXB2 Location	Gag(274-282) p24(142-150) DNA(1609..1635)	Gag Epitope Map
Author Location	Gag
Epitope	`VRMYSPVSI`	Epitope Alignment
Epitope Name	VI9-Cw18
Subtype	B, F
Species (MHC/HLA)	human(C*18)
Immunogen	HIV-1 infection
Country	Argentina
Experimental methods
Keywords	dynamics, escape, HLA associated polymorphism

Notes

Dynamics of CTL escape mutations was studied theoretically by analyzing plasma samples from 302 subjects (collected over 20 years). HLA associated polymorphisms accumulated in a subtype-specific manner.
Epitope VRMYSPVSI mutates to variant VRMYSPtSI with time.

References

Dilernia2008 Dario Alberto Dilernia, Leandro Jones, Sabrina Rodriguez, Gabriela Turk, Andrea E Rubio, Sandra Pampuro, Manuel Gomez-Carrillo, Christian Bautista, Gabriel Deluchi, Jorge Benetucci, María Beatriz Lasala, Leonardo Lourtau, Marcelo Horacio Losso, Héctor Perez, Pedro Cahn, and Horacio Salomón. HLA-Driven Convergence of HIV-1 Viral Subtypes B and F Toward the Adaptation to Immune Responses in Human Populations. PLoS ONE, 3(10):e3429, 2008. PubMed ID: 18941505. Show all entries for this paper.

Displaying record number 53975

Download this epitope record as JSON.

HXB2 Location	Gag(274-282) p24(142-150) DNA(1609..1635)	Gag Epitope Map
Author Location	( C consensus)
Epitope	`VRMYSPVSI`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human(C*18:01)
Immunogen	HIV-1 infection
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	rate of progression, optimal epitope

Notes

A comprehensive analysis of 160 class I T cell responses in 578 individuals from KwaZulu-Natal, South Africa was performed. Gag-specific responses were associated with lowering viremia, while Env, accessory and regulatory protein-specific responses were associated with higher viremia.
VRMYSPVSI is an optimal epitope.

References

Kiepiela2007 Photini Kiepiela, Kholiswa Ngumbela, Christina Thobakgale, Dhanwanthie Ramduth, Isobella Honeyborne, Eshia Moodley, Shabashini Reddy, Chantal de Pierres, Zenele Mncube, Nompumelelo Mkhwanazi, Karen Bishop, Mary van der Stok, Kriebashnie Nair, Nasreen Khan, Hayley Crawford, Rebecca Payne, Alasdair Leslie, Julia Prado, Andrew Prendergast, John Frater, Noel McCarthy, Christian Brander, Gerald H. Learn, David Nickle, Christine Rousseau, Hoosen Coovadia, James I. Mullins, David Heckerman, Bruce D. Walker, and Philip Goulder. CD8+ T-Cell Responses to Different HIV Proteins Have Discordant Associations with Viral Load. Nat. Med., 13(1):46-53, Jan 2007. PubMed ID: 17173051. Show all entries for this paper.

Displaying record number 55083

Download this epitope record as JSON.

HXB2 Location	Gag(274-282) p24(142-150) DNA(1609..1635)	Gag Epitope Map
Author Location	p24(142-150)
Epitope	`VRMYSPVSI`	Epitope Alignment
Species (MHC/HLA)	human(C*18:01)
Immunogen	peptide-HLA interaction
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, HLA binding, Intracellular cytokine staining
Keywords	optimal epitope

Notes

Novel epitopes are defined for four HLA-alleles common in South African Zulu/Xhosa populations: B*3910, B*4201, B*8101 and Cw*1801, by motif inference. HLA-A*2902 was found to overlap those of A1 and A24 supertypes.
VRMYSPVSI was the optimal epitope for HLA-Cw*1801 with variants VRMYSPVS, RMYSPVSI, VRMYSPVSIl, iVRMYSPVSI having been tested.

References

Honeyborne2006 Isobella Honeyborne, Almas Rathod, Rico Buchli, Dhanwanthie Ramduth, Eshia Moodley, Prinisha Rathnavalu, Senica Chetty, Cheryl Day, Christian Brander, William Hildebrand, Bruce D. Walker, Photini Kiepiela, and Philip J. R. Goulder. Motif Inference Reveals Optimal CTL Epitopes Presented by HLA Class I Alleles Highly Prevalent in Southern Africa. J. Immunol., 176(8):4699-4705, 15 Apr 2006. PubMed ID: 16585563. Show all entries for this paper.

Displaying record number 62811

Download this epitope record as JSON.

HXB2 Location	Gag(274-282) p24(142-150) DNA(1609..1635)	Gag Epitope Map
Author Location	p24(274-282)
Epitope	`VRMYSPVSI`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human
Immunogen	engineered
Experimental methods	Other, Relative replication capacity assay
Keywords	assay or method development, protective allele

Notes

NL4-3 Gag polyprotein random mutagenesis, high-throughput fitness profiling and in silico prediction of MHC-peptide binding affinity revealed that mutations in CTL epitopes presented by protective MHC-I alleles, vs. non-protective alleles, showed greater loss of experimental replicative capacity and lower levels of predicted reduction in MHC-I binding affinity. Together, these two variables could predict protectiveness of MHC-I alleles in a linear regression model. Analyses of intraperson viral evolution in 4 LTNP vs. 4 paired progressor subjects further supported paper conclusions.
After mutagenesis and passaging through human T cells, 58 single nucleotide mutations were observed in epitope VRMYSPVSI (known to bind to Cw18) with a log transformation of mean fitness score, relative to NL4-3, of -0.5937.

References

Du2017 Yushen Du, Tian-Hao Zhang, Lei Dai, Xiaojuan Zheng, Aleksandr M. Gorin, John Oishi, Ting-Ting Wu, Janice M. Yoshizawa, Xinmin Li, Otto O. Yang, Otoniel Martinez-Maza, Roger Detels, and Ren Sun. Effects of Mutations on Replicative Fitness and Major Histocompatibility Complex Class I Binding Affinity Are Among the Determinants Underlying Cytotoxic-T-Lymphocyte Escape of HIV-1 Gag Epitopes. mBio, 8(6), 28 Nov 2017. PubMed ID: 29184023. Show all entries for this paper.