Search CTL/CD8+ T-Cell Epitope Database

Found 8 matching records:

Displaying record number 62315

Download this epitope record as JSON.

HXB2 Location	gp160(217-226) gp120(217-226) DNA(6873..6902)	gp160 Epitope Map
Author Location	Env(217-226)
Epitope	`YCAPAGFAIL`	Epitope Alignment
		Show epitope variants
Epitope Name	YL10
Subtype	B
Species (MHC/HLA)	human(C*01)
Immunogen	HIV-1 infection
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	acute/early infection, mutation acquisition, viral fitness and reversion, viral replication

Notes

In a longitudinal study of patient 1362, escape mutations were tracked in 5 HIV Env gp120 and 2 Gag p24 CTL epitopes. Only 1/9 gp120 dominant mutations that appeared during acute infection within one year had fitness loss, 4/9 had no effect on fitness and 3/9 experienced a slight fitness increase. Meanwhile, all 4 Gag p24 mutations, which appeared in two years, decreased fitness! Thus, Gag p24 mutations are associated with significant fitness cost, but most Env escapes are fitness-neutral.
Escape mutations in Env NW9 appeared by 113 DPS (days post symptoms) and had no deleterious effects on fitness, at least a year before the emergence of escape mutations in the Gag EW10 and QW11 epitopes.

References

Troyer2009 Ryan M. Troyer, John McNevin, Yi Liu, Shao Chong Zhang, Randall W. Krizan, Awet Abraha, Denis M. Tebit, Hong Zhao, Santiago Avila, Michael A. Lobritz, M. Juliana McElrath, Sylvie Le Gall, James I. Mullins, and Eric J. Arts. Variable Fitness Impact of HIV-1 Escape Mutations to Cytotoxic T Lymphocyte (CTL) Response. PLoS Pathog., 5(4):e1000365, Apr 2009. PubMed ID: 19343217. Show all entries for this paper.

Displaying record number 55833

Download this epitope record as JSON.

HXB2 Location	gp160(217-226) gp120(217-226) DNA(6873..6902)	gp160 Epitope Map
Author Location	Env
Epitope	`YCAPAGFAIL`	Epitope Alignment
Epitope Name	YL10
Subtype	B
Species (MHC/HLA)	human(C*01)
Immunogen	HIV-1 infection
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Chromium-release assay
Keywords	binding affinity

Notes

For the first time, viral immune evasion is reported via an insertion mutation, in an ART-naive patient. A 3 aa repeat, SPT inserted within p6^Pol epitope NL8 is reported. This insertion is associated often with ART drug resistance to NRTI drugs. Thus immune pressure and drug resistance may cause HIV-1 to select the same variation.
A concomitant insertion mutation APP, is seen in p6^Gag, permitting viral budding.
Epitope YCAPAGFAIL bound its MHC I less strongly than NL8 (NSPTRREL) did its MHC I molecule.

References

Cao2008 Jianhong Cao, John McNevin, Matthew McSweyn, Yi Liu, James I. Mullins, and M. Juliana McElrath. Novel Cytotoxic T-Lymphocyte Escape Mutation by a Three-Amino-Acid Insertion in the Human Immunodeficiency Virus Type 1 p6Pol and p6Gag Late Domain Associated with Drug Resistance. J. Virol., 82(1):495-502, Jan 2008. PubMed ID: 17942528. Show all entries for this paper.

Displaying record number 54163

Download this epitope record as JSON.

HXB2 Location	gp160(217-226) gp120(217-226) DNA(6873..6902)	gp160 Epitope Map
Author Location	gp120(217-226 HIV-MN)
Epitope	`YCAPAGFAIL`	Epitope Alignment
		Show epitope variants
Epitope Name	YL10
Subtype	B
Species (MHC/HLA)	human(C*01:02)
Immunogen	HIV-1 infection
Patient MHC/HLA	PIC1362: A02:01, A25:01, B18:01, B51:01, C01:02, C12:03
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	escape, mutation acquisition, optimal epitope

Notes

T-cell immunity and the impact of selection were longitudinally studied in a patient from the time of transmission. New epitopes were detected at sites that were shown to be under positive selection. Env was found to be the major target of CTLs and most of the new epitopes were found here. One third of the sites examined were associated with epitope escape mutations from CTL. Acquisition of mutations found at high frequency in the database was suggested to be a result of reversion of CTL epitopes in the absence of immune targeting.
This is a newly defined epitope. Last position (10)in the epitope had potentially experienced positive selection. YCAPAGFAIi escape variant was found.

References

Liu2006 Yi Liu, John McNevin, Jianhong Cao, Hong Zhao, Indira Genowati, Kim Wong, Sherry McLaughlin, Matthew D. McSweyn, Kurt Diem, Claire E. Stevens, Janine Maenza, Hongxia He, David C. Nickle, Daniel Shriner, Sarah E. Holte, Ann C. Collier, Lawrence Corey, M. Juliana McElrath, and James I. Mullins. Selection on the Human Immunodeficiency Virus Type 1 Proteome following Primary Infection. J. Virol., 80(19):9519-9529, Oct 2006. PubMed ID: 16973556. Show all entries for this paper.

Displaying record number 59093

Download this epitope record as JSON.

HXB2 Location	gp160(217-226) gp120(217-226) DNA(6873..6902)	gp160 Epitope Map
Author Location	gp120(217-226)
Epitope	`YCAPAGFAIL`	Epitope Alignment
		Show epitope variants
Subtype	B
Species (MHC/HLA)	human(C*01:02)
Immunogen	HIV-1 infection
Patient MHC/HLA	PIC1362: A02:01, A25:01, B18:01, B51:01, C01:02, C12:03
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	viral fitness and reversion

Notes

CTL responses were studied in a single drug-naive individual during the first 4 years of infection. 25 CTL epitopes were identified; 17 of them underwent evolution; 15 mutant forms that escaped or partially escaped were detected.
YCAPAGFAIL was an epitope whose frequency decreased during 4 years of infection; 1 escape mutant was detected (YCAPAGFAIi).

References

Liu2007a Yi Liu, John McNevin, Hong Zhao, Denis M. Tebit, Ryan M. Troyer, Matthew McSweyn, Ananta K. Ghosh, Daniel Shriner, Eric J. Arts, M. Juliana McElrath, and James I. Mullins. Evolution of Human Immunodeficiency Virus Type 1 Cytotoxic T-Lymphocyte Epitopes: Fitness-Balanced Escape. J. Virol., 81(22):12179-12188, Nov 2007. PubMed ID: 17728222. Show all entries for this paper.

Displaying record number 61024

Download this epitope record as JSON.

HXB2 Location	gp160(217-226) gp120(217-226) DNA(6873..6902)	gp160 Epitope Map
Author Location	gp160(217-226)
Epitope	`YCAPAGFAIL`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(C*01:02)
Immunogen	HIV-1 infection
Patient MHC/HLA	10849: A23:01, A68:01, B35:43, B57:03, C01:02, C02:10
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	acute/early infection

Notes

The extent to which set-point viremia is affected by early HIV-infection T cell responses to either conserved or variable epitopes was studied. 23 ART-naive subjects were characterized for CTL responses for 6 months, postinfection. While most CTL responses (73/123) were targeted against variable HIV-1 epitopes, recognition of conserved epitopes (16/123) was associated with lower set point viremia. This was independent of HLA type and also functional avidity of the CTL response. Most of the conserved responses were targeted to Gag and Pol epitopes.
YCAPAGFAIL, restricted by Cw*0102, was recognized by 1 patient with the restricting allele.

References

Kunwar2013 Pratima Kunwar, Natalie Hawkins, Warren L. Dinges, Yi Liu, Erin E. Gabriel, David A. Swan, Claire E. Stevens, Janine Maenza, Ann C. Collier, James I. Mullins, Tomer Hertz, Xuesong Yu, and Helen Horton. Superior Control of HIV-1 Replication by CD8+ T Cells Targeting Conserved Epitopes: Implications for HIV Vaccine Design. PLoS One, 8(5):e64405, 2013. PubMed ID: 23741326. Show all entries for this paper.

Displaying record number 58152

Download this epitope record as JSON.

HXB2 Location	gp160(217-226) gp120(217-226) DNA(6873..6902)	gp160 Epitope Map
Author Location	gp120(217-226)
Epitope	`YCAPAGFAIL`	Epitope Alignment
		Show epitope variants
Epitope Name	YL10
Subtype	B
Species (MHC/HLA)	human(C*01:02)
Immunogen	HIV-1 infection
Patient MHC/HLA	PIC1362: A02:01, A25:01, B18:01, B51:01, C01:02, C12:03
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	escape, acute/early infection

Notes

CTL responses were studied in a drug-naive patient for 4 years, beginning at the time of infection. CTL recognition of 25 epitopes was observed, and 18 of them underwent mutational changes, usually indicative of escape.
Evolving epitope YCAPAGFAIL underwent strong selection during 4 years of infection.
Variant YCAPAGFAIi had replaced the wild type sequence by 400 days post-infection. Sequence changes were associated with loss of EliSpot response to the epitope.

References

Liu2011a Yi Liu, John P. McNevin, Sarah Holte, M. Juliana McElrath, and James I. Mullins. Dynamics of Viral Evolution and CTL Responses in HIV-1 Infection. PLoS One, 6(1):e15639, 2011. PubMed ID: 21283794. Show all entries for this paper.

Displaying record number 57084

Download this epitope record as JSON.

HXB2 Location	gp160(217-226) gp120(217-226) DNA(6873..6902)	gp160 Epitope Map
Author Location	gp120(217-226 DU422)
Epitope	`YCAPAGFAIL`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(C*01:02)
Immunogen	in vitro stimulation or selection
Experimental methods	CD8 T-cell Elispot - IFNγ, Chromium-release assay, Tetramer binding
Keywords	dendritic cells

Notes

Three types of myeloid dendritic cells - monocytic dendritic cells, Langerhans cells, and interstitial dermal-intestinal dendritic cells - were shown to be able to prime CD8+ T-cell responses to HIV-1. Primed monocytic dendritic cells from 2 uninfected adult donors had broad primary T-cell reactivity, reacting with 15mers containing 42 known epitopes in Gag, Env, and Nef.
One of the reactive 15mers contained optimal epitope YCAPAGFAIL, which was restricted by HLA Cw*0102.

References

Colleton2009 Bonnie A. Colleton, Xiao-Li Huang, Nada M. Melhem, Zheng Fan, Luann Borowski, Giovanna Rappocciolo, and Charles R. Rinaldo. Primary Human Immunodeficiency Virus Type 1-Specific CD8+ T-Cell Responses Induced by Myeloid Dendritic Cells. J. Virol., 83(12):6288-6299, Jun 2009. PubMed ID: 19357176. Show all entries for this paper.

Displaying record number 57162

Download this epitope record as JSON.

HXB2 Location	gp160(217-226) gp120(217-226) DNA(6873..6902)	gp160 Epitope Map
Author Location	gp120(218-226)
Epitope	`YCAPAGFAIL`	Epitope Alignment
Epitope Name	YL10
Subtype	B
Species (MHC/HLA)	human(Cw1)
Immunogen	HIV-1 infection
Patient MHC/HLA	A26, A32, B27, Cw1, Cw2
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	HIV exposed persistently seronegative (HEPS), acute/early infection

Notes

CTL responses were measured in a highly exposed patient who was seronegative for 2 years, both before and after seroconversion. CTL responses after seroconversion were stronger, and more of the responses were associated with protective HLA allele B27.
YCAPAGFAIL was part of a pool that was recognized by the HEPS patient before seroconversion; it elicited an EliSpot response after seroconversion. The patient's consensus sequence at day 24 after seroconversion was the same as the test peptide.

References

Liu2009b Yi Liu, Amanda Woodward, Haiying Zhu, Thomas Andrus, John McNevin, Jean Lee, James I. Mullins, Lawrence Corey, M. Juliana McElrath, and Tuofu Zhu. Preinfection Human Immunodeficiency Virus (HIV)-Specific Cytotoxic T Lymphocytes Failed to Prevent HIV Type 1 Infection from Strains Genetically Unrelated to Viruses in Long-Term Exposed Partners. J. Virol., 83(20):10821-10829, Oct 2009. PubMed ID: 19706711. Show all entries for this paper.