Search CTL/CD8+ T-Cell Epitope Database

Found 16 matching records:

Displaying record number 61945

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HXB2 Location	Gag(124-132) p17(124-132) DNA(1159..1185)	Gag Epitope Map
Author Location	Gag(124-132)
Epitope	`NSSKVSQNY`	Epitope Alignment
		Show epitope variants
Subtype	A, D
Species (MHC/HLA)	human(A*01:01)
Immunogen	HIV-1 infection
Patient MHC/HLA	1932: A01:01, B37:01, B81:01, C06:02, C18:01; 2297: A01:01, A30:01, B08:01, B57:03, C07:04, C18:01; ML2261: A01:01, A03:01, B27:26, B49:01, C02:02, C07:01; 2178: A01:01, A29:02, B81:01, C07:04, C08:04; 1589: A01:01, A30:02, B58:02, C06:02, C06:06; 2646: A01:01, A29:02, B45:01, B57:01, C06:02, C07:01; 893: A01:01, A24:02, B15:17, B35:02, C04:01, C*17:01
Country	Kenya
Experimental methods	CD8 T-cell Elispot - IFNγ, Other, Tetramer binding
Keywords	subtype comparisons, HIV exposed persistently seronegative (HEPS), assay or method development, novel epitope

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 A*0101-restricted Gag epitope NSSKVSQNY and 6 of its variants (4 of which were novel) were recognized by seronegative subjects as well as HIV-1 patients and bound HLA-A*0101 robustly. This epitope is located right beside the p17/p24 protease cleavage site in Gag. 7/12 A*0101+ female subjects responded to the epitope, with a mean of 79 SFU/million.

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 1997

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HXB2 Location	Gag(124-132) p17(124-132) DNA(1159..1185)	Gag Epitope Map
Author Location	p17
Epitope	`NSSKVSQNY`	Epitope Alignment
Epitope Name	Gag-NY9; p17-NY9
Subtype	B
Species (MHC/HLA)	human(B*35)
Immunogen	HIV-1 infection
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	HAART, ART

Notes

Among HIV+ individuals who carried HLA B*35, 1/21 (5%) recognized this epitope.

References

Sabbaj2003 Steffanie Sabbaj, Anju Bansal, G. Douglas Ritter, Christopher Perkins, Bradley H. Edwards, Ethan Gough, Jianming Tang, James J. Szinger, Bette Korber, Craig M. Wilson, Richard A. Kaslow, Mark J. Mulligan, and Paul A. Goepfert. Cross-Reactive CD8+ T Cell Epitopes Identified in US Adolescent Minorities. J. Acquir. Immune Defic. Syndr., 33(4):426-438, 1 Aug 2003. PubMed ID: 12869831. Show all entries for this paper.

Displaying record number 53134

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HXB2 Location	Gag(124-132) p17(124-132) DNA(1159..1185)	Gag Epitope Map
Author Location	p17(124-132)
Epitope	`NSSKVSQNY`	Epitope Alignment
Species (MHC/HLA)	human(B*35)
Immunogen	HIV-1 infection
Country	Spain
Experimental methods	CD8 T-cell Elispot - IFNγ, Flow cytometric T-cell cytokine assay, Proliferation
Keywords	HAART, ART, supervised treatment interruptions (STI)

Notes

Structured treatment interruption (STI) alone is not able to control viral replication in chronically infected patients, probably due to lack of strong, maintained T-helper cell responses. HIV-1 specific CD8+ T-cell responses were shown to increase significantly until the end of the follow up, but were not correlated with viral load.
Less than 2/9 patients recognized this epitope.

References

Plana2004 Montserrat Plana, Felipe Garcia, Annette Oxenius, Gabriel M. Ortiz, Anna Lopez, Anna Cruceta, Gabriel Mestre, Emilio Fumero, Catherine Fagard, Maria Antonia Sambeat, Ferran Segura, José M. Miró, Mireia Arnedo, L. Lopalcos, Tomas Pumarola, Bernard Hirschel, Rodney E. Phillips, Douglas F. Nixon, Teresa Gallart, and Jose M. Gatell. Relevance of HIV-1-Specific CD4+ Helper T-Cell Responses During Structured Treatment Interruptions in Patients With CD4+ T-Cell Nadir Above 400/mm3. J. Acquir. Immune Defic. Syndr., 36(3):791-799, 1 Jul 2004. PubMed ID: 15213562. Show all entries for this paper.

Displaying record number 58531

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HXB2 Location	Gag(124-132) p17(124-132) DNA(1159..1185)	Gag Epitope Map
Author Location	p17(124-132)
Epitope	`NSSKVSQNY`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(B*35)
Immunogen	HIV-1 infection
Country	Canada
Experimental methods	Other
Keywords	characterizing CD8+ T cells, elite controllers

Notes

Dual color EliSpot testing for IL-2 and IFN-γ was used to determine whether CTL restricted by MHC Class I alleles associated with slow progression to disease, viz. B*57 and B*27, had a more poly-functional profile than other CD8+ cells in a treatment-naive cohort from Montreal. B*57/B*27-restricted CTL producing IL-2 or IFN-γ or IL-2/IFN-γ, were similar in both slow progressors (SP) and progressors. Other non-protective MHC-I-restricted CTL producing both IL-2/IFN-γ, were greater in number in SP than progressors.
Within SP, peptides restricted by both protective and non-protective MHC-I alleles elicited CTL with the same functional profile. For progressors, peptides and epitopes restricted by protective B*57/B*27 alleles stimulated a higher proportion of dual-(IL-2/IFN-γ)secreting CTL.
HLA-B*35-restricted p17 optimal epitope NSSKVSQNY was tested in a dual color EliSpot and was found to elicit CTL that could produce IL-2 and/or IFN-γ.

References

Peretz2011 Yoav Peretz, Olivia Marra, Réjean Thomas, Danielle Legault, Pierre Côté, Mohamed-Rachid Boulassel, Danielle Rouleau, Jean-Pierre Routy, Rafick-Pierre Sékaly, Christos M Tsoukas, Cécile Tremblay, and Nicole F. Bernard. Relative Contribution of HIV-Specific Functional Lymphocyte Subsets Restricted by Protective and Non-Protective HLA Alleles. Viral Immunol, 24(3):189-198, Jun 2011. PubMed ID: 21668360. Show all entries for this paper.

Displaying record number 127

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HXB2 Location	Gag(124-132) p17(124-132) DNA(1159..1185)	Gag Epitope Map
Author Location	p17(124-132 LAI)
Epitope	`NSSKVSQNY`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(B35)
Immunogen	in vitro stimulation or selection
Experimental methods
Keywords

Notes

A peptide-based protocol was optimized for restimulation of CTLp using optimized peptide and IL-7 concentrations -- importantly this protocol does not stimulate a primary response, only secondary -- peptide-specific CTLp counts could be obtained via staining with peptide-Class I tetramers.
This peptide was one of the B35 presented test peptides used in control experiments showing that the assay gave no activity using lymphocytes from 21 healthy B35 seronegative donors.

References

Lalvani1997 A. Lalvani, T. Dong, G. Ogg, A. A. Patham, H. Newell, A. V. Hill, A. J. McMichael, and S. Rowland-Jones. Optimization of a Peptide-Based Protocol Employing IL-7 for In Vitro Restimulation of Human Cytotoxic T Lymphocyte Precursors. J. Immunol. Methods, 210:65-77, 1997. PubMed ID: 9502585. Show all entries for this paper.

Displaying record number 128

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HXB2 Location	Gag(124-132) p17(124-132) DNA(1159..1185)	Gag Epitope Map
Author Location	p17
Epitope	`NSSKVSQNY`	Epitope Alignment
Species (MHC/HLA)	human(B35)
Immunogen
Experimental methods
Keywords	HIV exposed persistently seronegative (HEPS), HIV-2

Notes

CTL responses in seronegative highly HIV-exposed African female sex workers in Gambia and Nairobi were studied -- these women had no delta 32 deletion in CCR5.
In Gambia there is exposure to both HIV-1 and HIV-2. CTL responses to B*35 epitopes in exposed, uninfected women are cross-reactive.
HIV-2 version of this epitope is not conserved: PPSGKGGNY, but the CTLs are cross-reactive -- this is one of five B*35 CTL epitopes in this study, and it is cross-reactive, see also RowlandJones1995.
Database note: First author "Rowland-Jones" is also found as "RowlandJones" on annotated papers in this database.

References

RowlandJones1995 S. L. Rowland-Jones, J. Sutton, K. Ariyoshi, T. Dong, F. Gotch, S. McAdam, D. Whitby, S. Sabally, A. Gallimore, T. Corrah, M. Takiguchi, T. Schultz, A. McMichael, and H. Whittle. HIV-Specific Cytotoxic T Cells in HIV-Exposed but Uninfected Gambian Women. Nat. Med., 1:59-64, 1995. Four HIV-1 and -2 cross-reactive epitopes that are presented to CTL from HIV-infected Gambians by HLA-35 were identified. These peptides could elicit HIV-specific CTLs from 3 of 6 repeatedly exposed but seronegative sex workers who carry the HLA-B35 allele. Most CTL derived from HIV-2 positive donors also recognized the HIV-2 peptide and the analogous HIV-1 peptide. PubMed ID: 7584954. Show all entries for this paper.

Rowland-Jones1999 S. L. Rowland-Jones, T. Dong, L. Dorrell, G. Ogg, P. Hansasuta, P. Krausa, J. Kimani, S. Sabally, K. Ariyoshi, J. Oyugi, K. S. MacDonald, J. Bwayo, H. Whittle, F. A. Plummer, and A. J. McMichael. Broadly Cross-Reactive HIV-Specific Cytotoxic T Lymphocytes in Highly-Exposed Persistently Seronegative Donors. Immunol. Lett., 66:9-14, 1999. PubMed ID: 10203028. Show all entries for this paper.

Displaying record number 1487

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HXB2 Location	Gag(124-132) p17(124-132) DNA(1159..1185)	Gag Epitope Map
Author Location	p17
Epitope	`NSSKVSQNY`	Epitope Alignment
Species (MHC/HLA)	human(B35)
Immunogen	HIV-1 infection
Experimental methods
Keywords	HAART, ART

Notes

CTL responses were studied by tetramer staining in 41 patients with combination therapy -- activated CD8+ T-cells decline as the viral load drops in response to therapy, but the overall level of antigen-specific cells capable of differentiating into effectors stays constant and new epitopes may be recognized.

References

Seth2001 A. Seth, J. Markee, A. Hoering, A. Sevin, D. E. Sabath, J. E. Schmitz, M. J. Kuroda, M. A. Lifton, M. S. Hirsch, A. C. Collier, N. L. Letvin, and M. J. McElrath. Alterations in T cell phenotype and human immunodeficiency virus type 1-specific cytotoxicity after potent antiretroviral therapy. J. Infect. Dis., 183(5):722-9, 1 Mar 2001. PubMed ID: 11181148. Show all entries for this paper.

Displaying record number 1564

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HXB2 Location	Gag(124-132) p17(124-132) DNA(1159..1185)	Gag Epitope Map
Author Location	p17(124-132 SF2)
Epitope	`NSSKVSQNY`	Epitope Alignment
Species (MHC/HLA)	human(B35)
Immunogen	HIV-1 infection
Experimental methods
Keywords	HAART, ART, acute/early infection

Notes

Therapy provided during acute infection resulted in a narrower CTL response, stronger T help response, and a less diverse viral population than was seen in individuals treated during chronic infection.
The breadth and specificity of the response was determined using ELISPOT by studying 19 individuals with pre-seroconversion therapy (Group 1), 11 individuals with primary infection but post-seroconversion therapy (Group 2), and 10 individuals who responded to HAART given during chronic infection (Group 3), using 259 overlapping peptides spanning p17, p24, RT, gp41, gp120 and Nef.
Previously described and newly defined optimal epitopes were tested for CTL response.
Number of HLA-B35+ individuals that had a CTL response to this epitope broken down by group: 0/2 group 1, 0/2 group 2, and 1/1 group 3.

References

Altfeld2001b M. Altfeld, E. S. Rosenberg, R. Shankarappa, J. S. Mukherjee, F. M. Hecht, R. L. Eldridge, M. M. Addo, S. H. Poon, M. N. Phillips, G. K. Robbins, P. E. Sax, S. Boswell, J. O. Kahn, C. Brander, P. J. Goulder, J. A. Levy, J. I. Mullins, and B. D. Walker. Cellular immune responses and viral diversity in individuals treated during acute and early HIV-1 infection. J. Exp. Med., 193(2):169-80, 15 Jan 2001. URL: http://www.jem.org/cgi/content/full/193/2/169. PubMed ID: 11148221. Show all entries for this paper.

Displaying record number 54878

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HXB2 Location	Gag(124-132) p17(124-132) DNA(1159..1185)	Gag Epitope Map
Author Location
Epitope	`NSSKVSQNY`	Epitope Alignment
Species (MHC/HLA)	human(B35)
Immunogen	HIV-1 infection, vaccine
Experimental methods	CD8 T-cell Elispot - IFNγ, Flow cytometric T-cell cytokine assay
Keywords	vaccine-induced immune responses, characterizing CD8+ T cells

Vaccine Details

Vaccine type	canarypox, canarypox prime with recombinant protein boost
Vaccine strain	B clade BRU, B clade LAI, B clade MN, multiple epitope immunogen
Vaccine component	Gag, gp120, gp41, Nef, Pol, Protease

Notes

CD8+ T-cell function induced by HIV-1 immunogens and natural infection was compared. Natural infections consisted of early, chronic, and long term nonprogressors.
B27- and B57-restricted CD8+ T cells from nonprogressors exhibited greater expansion than those restricted by other alleles, providing an explanation for the observed association between HLA-B27/B57 and control of HIV-1 infection.

References

Horton2006 Helen Horton, Ian Frank, Ruth Baydo, Emilie Jalbert, Justin Penn, Sean Wilson, John P. McNevin, Matthew D. McSweyn, Deborah Lee, Yunda Huang, Stephen C. De Rosa, and M. Juliana McElrath. Preservation of T Cell Proliferation Restricted by Protective HLA Alleles Is Critical for Immune Control of HIV-1 Infection. J. Immunol., 177(10):7406-7415, 15 Nov 2006. PubMed ID: 17082660. Show all entries for this paper.

Displaying record number 122

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HXB2 Location	Gag(124-132) p17(124-132) DNA(1159..1185)	Gag Epitope Map
Author Location	p17(124-132 LAI)
Epitope	`NSSKVSQNY`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(B35)
Immunogen	HIV-1 infection
Experimental methods
Keywords	review

Notes

Review of HIV CTL epitopes.

References

McMichael1994 A. J. McMichael and B. D. Walker. Cytotoxic T Lymphocytes Epitopes: Implications for HIV Vaccine. AIDS, 8S:S155-S173, 1994. Comprehensive review summarizing CTL epitopes that have known HLA type and are fine mapped to indicate epitope boundaries. Anchor residues are indicated when known for different HLA restricted epitopes. Includes a summary of the published literature, as well as much work that was in press or submitted for publication. Show all entries for this paper.

Displaying record number 123

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HXB2 Location	Gag(124-132) p17(124-132) DNA(1159..1185)	Gag Epitope Map
Author Location
Epitope	`NSSKVSQNY`	Epitope Alignment
Species (MHC/HLA)	human(B35)
Immunogen	HIV-1 infection
Experimental methods
Keywords	dynamics, acute/early infection

Notes

Three individuals with highly focused HIV-specific CTL responses were studied during acute infection using tetramers -- high frequencies of HIV-1-specific CD8+ T cells were found prior to seroconversion, and there was a close temporal relationship between the number of circulating HIV-specific T cells and viral load.
All three patients were B*2705, with HLA alleles: A1, A30/31, B*2705, B35; A1, A*0301, B7, B2705; and A*0201, A*0301, B2705, B39.
ELISPOT was used to test a panel of CTL epitopes that had been defined earlier and were appropriate for the HLA haplotypes of the study subjects -- 3/3 subjects showed a dominant response to the B*2705 epitope KRWIILGGLNK.
The subject with A*0201 had a moderately strong response to SLYNTVATL.
Weak responses were observed to A*301-RLRPGGKKK, A*301-QVPLRPMTYK, and B7-TPGPGVRYPL in the subject who was HLA A1, A*0301, B7, B*2705.
No acute response was detected to the following epitopes: A*201-ILKEPVHGV, A*301-KIRLRPGGK, A*301-AIFQSSMTK, A*301-TVYYGVPVWK, B35-EPIVGAETF, B35-HPDIVIYQY, B35-PPIPVGEIY, B35-NSSKVSQNY, B35-VPLRPMTY, B35-DPNPQEVVL.

References

Wilson2000 J. D. Wilson, G. S. Ogg, R. L. Allen, C. Davis, S. Shaunak, J. Downie, W. Dyer, C. Workman, S. Sullivan, A. J. McMichael, and S. L. Rowland-Jones. Direct Visualization of HIV-1-Specific Cytotoxic T Lymphocytes During Primary Infection. AIDS, 14:225-233, 2000. PubMed ID: 10716497. Show all entries for this paper.

Displaying record number 124

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HXB2 Location	Gag(124-132) p17(124-132) DNA(1159..1185)	Gag Epitope Map
Author Location	p17(124-132)
Epitope	`NSSKVSQNY`	Epitope Alignment
Species (MHC/HLA)	human(B35)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

A study of p17 variation considering known p17 epitopes and individuals with known HLA types revealed that p17 evolution is influenced by immune pressure from CTLs.

References

Birk1998 M. Birk, A. Vahlne, A. Sonnerborg, and M. Sallberg. Nonsynonymous Mutations within the Human Immunodeficiency Virus Type 1 p17 Gene Are Clustered to Sequences Binding to the Host Human Leukocyte Antigen Class I Molecules. AIDS Res. Hum. Retroviruses, 14:241-248, 1998. PubMed ID: 9491914. Show all entries for this paper.

Displaying record number 125

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HXB2 Location	Gag(124-132) p17(124-132) DNA(1159..1185)	Gag Epitope Map
Author Location	p17(124-132 LAI)
Epitope	`NSSKVSQNY`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(B35)
Immunogen	HIV-1 or HIV-2 infection
Country	Gambia
Experimental methods
Keywords	HIV exposed persistently seronegative (HEPS), HIV-2

Notes

Established by titration. HIV-1infected and HIV-2-infected B35+ subjects recognized both the HIV-1 (NSSKVSQNY) and HIV-2 forms (PPSGKGGNY).
Database note: First author "RowlandJones" is also found as "Rowland-Jones" on annotated papers in this database.

References

Displaying record number 57480

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HXB2 Location	Gag(124-132) p17(124-132) DNA(1159..1185)	Gag Epitope Map
Author Location	Gag(124-132)
Epitope	`NSSKVSQNY`	Epitope Alignment
Epitope Name	NY9
Subtype	B
Species (MHC/HLA)	human(B*35:01)
Immunogen	HIV-1 infection
Country	United Kingdom
Experimental methods	CD8 T-cell Elispot - IFNγ, Cytokine production, Flow cytometric T-cell cytokine assay, HLA binding
Keywords	computational epitope prediction

Notes

44 candidate B*3501-restricted epitopes were predicted by computational analysis of HIV-1 Gag. Twelve candidates had significant binding affinity for HLA-B*3501. Two previously-unknown candidates also had positive EliSpot responses among 4 chronically-infected B35-positive patients carrying subtype B HIV-1.
Previously-documented B35-restricted epitope NSSKVSQNY had a positive IFN-gamma EliSpot response in 1/4 HLA-B*3501-positive patients.

References

Westrop2009 Samantha J. Westrop, Nathali Grageda, and Nesrina Imami. Novel Approach to Recognition of Predicted HIV-1 Gag B3501-Restricted CD8 T-Cell Epitopes by HLA-B3501+ Patients: Confirmation by Quantitative ELISpot Analyses and Characterisation Using Multimers. J. Immunol. Methods, 341(1-2):76-85, 28 Feb 2009. PubMed ID: 19056394. Show all entries for this paper.

Displaying record number 126

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HXB2 Location	Gag(124-132) p17(124-132) DNA(1159..1185)	Gag Epitope Map
Author Location	p17(124-132 LAI)
Epitope	`NSSKVSQNY`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(B*35:01)
Immunogen	HIV-1 or HIV-2 infection
Experimental methods
Keywords	optimal epitope, A-list

Notes

Noted by Brander to be B*3501 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 62782

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HXB2 Location	Gag(124-132) p17(124-132) DNA(1159..1185)	Gag Epitope Map
Author Location	p17(124-132)
Epitope	`NSSKVSQNY`	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, 57 single nucleotide mutations were observed in epitope NSSKVSQNY (known to bind to B3501) with a log transformation of mean fitness score, relative to NL4-3, of -0.3546.

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.