Search CTL/CD8+ T-Cell Epitope Database

Found 14 matching records:

Displaying record number 59612

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HXB2 Location	Pol(197-205) RT(42-50) DNA(2673..2699)	Pol Epitope Map
Author Location	Pol(197-205)
Epitope	`EKEGKISKI`	Epitope Alignment
Epitope Name	EI9
Species (MHC/HLA)	human(A*68:02)
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.
EKEGKISKI had a significantly positive association with HLA A*6802; it was recognized by 4/22 A*6802-positive subjects and 4/250 A*6802-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 59610

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HXB2 Location	Pol(197-205) RT(42-50) DNA(2673..2699)	Pol Epitope Map
Author Location	Pol(197-205)
Epitope	`EKEGKISKI`	Epitope Alignment
Epitope Name	EI9
Species (MHC/HLA)	human(B*18)
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.
EKEGKISKI had a significantly positive association with HLA B*18; it was recognized by 10/19 B*18-positive subjects and 8/272 B*18-negative subjects.

References

Displaying record number 59613

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HXB2 Location	Pol(197-205) RT(42-50) DNA(2673..2699)	Pol Epitope Map
Author Location	Pol(197-205)
Epitope	`EKEGKISKI`	Epitope Alignment
Epitope Name	EI9
Species (MHC/HLA)	human(B35:01, B35:08)
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.
EKEGKISKI had a significantly positive association with HLA B*3501,B*3508; it was recognized by 3/27 B*3501,B*3508-positive subjects and 1/223 B*3501,B*3508-negative subjects.

References

Displaying record number 59611

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HXB2 Location	Pol(197-205) RT(42-50) DNA(2673..2699)	Pol Epitope Map
Author Location	Pol(197-205)
Epitope	`EKEGKISKI`	Epitope Alignment
Epitope Name	EI9
Species (MHC/HLA)	human(B35:02, B35:03, B*53:01)
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.
EKEGKISKI had a significantly positive association with HLA B*3502,B*3503,B*5301; it was recognized by 18/37 B*3502,B*3503,B*5301-positive subjects and 28/304 B*3502,B*3503,B*5301-negative subjects.

References

Displaying record number 59609

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HXB2 Location	Pol(197-205) RT(42-50) DNA(2673..2699)	Pol Epitope Map
Author Location	Pol(197-205)
Epitope	`EKEGKISKI`	Epitope Alignment
Epitope Name	EI9
Species (MHC/HLA)	human(B*49)
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.
EKEGKISKI had a significantly positive association with HLA B*49; it was recognized by 10/13 B*49-positive subjects and 18/291 B*49-negative subjects.

References

Displaying record number 59376

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HXB2 Location	Pol(197-205) RT(42-50) DNA(2673..2699)	Pol Epitope Map
Author Location
Epitope	`EKEGKISKI`	Epitope Alignment
Species (MHC/HLA)	human(B*49:01)
Immunogen	HIV-1 infection
Patient MHC/HLA	T06: A01:01, A30:04, B08:01, B49:01, C*07:01
Country	Germany
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	computational epitope prediction, optimal epitope

Notes

Peptides of 15-20 amino acids were used to compare epitopes determined experimentally versus predictions from 3 epitope prediction tools: SYFPEITHI, CTLPRED, and IEDB. The IEDB tool performed best, but none of the tools performed well. Predictions were better when the HLA restriction of the peptide was known, and when the restricting HLA was present at high frequency in the population.
EKEGKISKI was an optimal epitope experimentally mapped from the input peptide LVEICTEMEKEGKISKI.

References

Roider2014 Julia Roider, Tim Meissner, Franziska Kraut, Thomas Vollbrecht, Renate Stirner, Johannes R. Bogner, and Rika Draenert. Comparison of Experimental Fine-Mapping to In Silico Prediction Results of HIV-1 Epitopes Reveals Ongoing Need for Mapping Experiments. Immunology, 143(2):193-201, Oct 2014. PubMed ID: 24724694. Show all entries for this paper.

Displaying record number 416

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HXB2 Location	Pol(197-205) RT(42-50) DNA(2673..2699)	Pol Epitope Map
Author Location	RT(42-50 LAI)
Epitope	`EKEGKISKI`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(B51)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

Of 98 patients in cross-sectional analysis, 78% had CTL against pol -- RT was more immunogenic than Integrase and Protease (81%, 51%, and 24% of 37 patients, respectively)
New clusters of epitopes were defined utilizing different HLA molecules.

References

Haas1998 G. Haas, A. Samri, E. Gomard, A. Hosmalin, J. Duntze, J. M. Bouley, H. G. Ihlenfeldt, C. Katlama, and B. Autran. Cytotoxic T Cell Responses to HIV-1 Reverse Transcriptase, Integrase and Protease. AIDS, 12(12):1427-1436, 1998. PubMed ID: 9727563. Show all entries for this paper.

Displaying record number 52972

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HXB2 Location	Pol(197-205) RT(42-50) DNA(2673..2699)	Pol Epitope Map
Author Location	RT(42-50)
Epitope	`EKEGKISKI`	Epitope Alignment
Species (MHC/HLA)	human(B51)
Immunogen	HIV-1 infection
Patient MHC/HLA	A3, A32, B15, B51, C*03, Cw6, DQ7, DR4, DR8
Country	Netherlands
Experimental methods	CD8 T-cell Elispot - IFNγ, Flow cytometric T-cell cytokine assay
Keywords	escape

Notes

Both stable potential epitopes and epitopes with escape mutations were found in a patient with increasing viral load over a time period of 4 years. Fixation of escape mutations occurred sequentially and correlated with the rise in viral load and with the increased number of productively infected cells.
This is one of 17 potential epitopes from this individual, defined based on previously identified epitopes presented by appropriate HLA molecules. Full length genome sequence did not reveal changes in time in any of these epitopes over a four year period. Peptide pools initially revealed very little response to these epitopes, but this increased over time.

References

Geels2003 Mark J. Geels, Marion Cornelissen, Hanneke Schuitemaker, Kiersten Anderson, David Kwa, Jolanda Maas, John T. Dekker, Elly Baan, Fokla Zorgdrager, Remco van den Burg, Martijn van Beelen, Vladimir V. Lukashov, Tong-Ming Fu, William A. Paxton, Lia van der Hoek, Sheri A. Dubey, John W. Shiver, and Jaap Goudsmit. Identification of Sequential Viral Escape Mutants Associated with Altered T-Cell Responses in a Human Immunodeficiency Virus Type 1-Infected Individual. J. Virol., 77(23):12430-12440, Dec 2003. PubMed ID: 14610167. Show all entries for this paper.

Displaying record number 55044

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HXB2 Location	Pol(197-205) RT(42-50) DNA(2673..2699)	Pol Epitope Map
Author Location
Epitope	`EKEGKISKI`	Epitope Alignment
Species (MHC/HLA)	human(B51)
Immunogen	HIV-1 infection
Experimental methods	CD8 T-cell Elispot - IFNγ, HLA binding
Keywords	binding affinity, immunodominance, optimal epitope

Notes

CTL responses were tested for both HIV-1 and EBV derived epitopes restricted by HLA-A, -B and -C alleles. HLA-B alleles more frequently induce detectable responses and that the responses are generally of greater magnitude than those for HLA-A and -C alleles.
The magnitude and frequency of CTL recognition were related to each other and that TCR avidity for HLA/peptide complexes is a more important determinant for magnitude of response than peptide binding affinity to HLA.
EBV response patterns were not significantly altered by HIV coinfection.
Epitope EKEGKISKI elicited a magnitude of response of 270 SFC with a functional avidity of 0.1nM and binding affinity of 14059nM.

References

Bihl2006 Florian Bihl, Nicole Frahm, Loriana Di Giammarino, John Sidney, Mina John, Karina Yusim, Tonia Woodberry, Kaori Sango, Hannah S. Hewitt, Leah Henry, Caitlyn H. Linde, John V. Chisholm, III, Tauheed M. Zaman, Eunice Pae, Simon Mallal, Bruce D Walker, Alessandro Sette, Bette T. Korber, David Heckerman, and Christian Brander. Impact of HLA-B Alleles, Epitope Binding Affinity, Functional Avidity, and Viral Coinfection on the Immunodominance of Virus-Specific CTL Responses. J. Immunol., 176(7):4094-4101, 1 Apr 2006. PubMed ID: 16547245. Show all entries for this paper.

Displaying record number 56444

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HXB2 Location	Pol(197-205) RT(42-50) DNA(2673..2699)	Pol Epitope Map
Author Location	RT
Epitope	`EKEGKISKI`	Epitope Alignment
Epitope Name	EI9(RT)
Subtype	B
Species (MHC/HLA)	human(B51)
Immunogen	HIV-1 infection
Country	China
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	chronic infection

Notes

49 ART-naive chronically HIV-1 infected Chinese subjects' CTLs were tested with 413 OLPs in IFN-γ assays, determining optimal epitopes specific for Chinese Clade B HIV-1 sequences.
An inverse correlation was found between CTL response and viral load.
Targeted peptides have lower entropy than peptides that are not CTL targeted. This correlation is independent of HLA-restriction.
Although the tested peptide sequence contains the exact sequence of a previously described HLA-B51 optimal epitope, EKEGKISKI, none of the 15 HLA-B51 carriers responded to it (author communication and Fig.1).

References

Zhai2008 Song Zhai, Yan Zhuang, Yang Song, Shu Li, Dedong Huang, Wenzhen Kang, Xinhong Li, Qi Liao, Yanhou Liu, Zhongfang Zhao, Yichen Lu, and Yongtao Sun. HIV-1-Specific Cytotoxic T Lymphocyte (CTL) Responses Against Immunodominant Optimal Epitopes Slow the Progression of AIDS in China. Curr. HIV Res., 6(4):335-350, Jun 2008. PubMed ID: 18691032. Show all entries for this paper.

Displaying record number 59076

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HXB2 Location	Pol(197-205) RT(42-50) DNA(2673..2699)	Pol Epitope Map
Author Location	RT(42-50)
Epitope	`EKEGKISKI`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(B*51:01)
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.
EKEGKISKI was a persistent epitope, consistently present during 4 years of infection; no escape mutants were detected.

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 54320

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HXB2 Location	Pol(197-205) RT(42-50) DNA(2673..2699)	Pol Epitope Map
Author Location	RT(42-50)
Epitope	`EKEGKISKI`	Epitope Alignment
Species (MHC/HLA)	human(B*51:01)
Immunogen	HIV-1 infection
Experimental methods	CD8 T-cell Elispot - IFNγ, Chromium-release assay, Cytokine production, HLA binding, Other
Keywords	vaccine-induced immune responses, HLA cross-presentation, HLA associated polymorphism

Notes

25 CTL epitopes with sequence conservation were studied. Population protection coverage (PPC) for 5 different ethnic groups in the US was estimated by combining HLA binding predictions and known HLA frequencies. HIV-1-naive individuals mounted a better response to the epitope pools than HIV-1 infected individuals.
A more detailed evaluation of HIV-naive T-cell responses was undertaken, limiting the study to only those peptides that are restricted to A*0201. Though the peptides could cross-recognize and bind different HLA, they were able to specifically lyse only cells of the same (A*0201) HLA-restriction. Thus, the CTL response was less degenerate than peptide binding to MHC.
In addition to the published restriction above, epitope EKEGKISKI was predicted to be restricted by HLA B*2701, B*3801, B*3901, B*3909, B*4402, B*5101, B8.

References

Reche2006 Pedro A. Reche, Derin B. Keskin, Rebecca E. Hussey, Petronela Ancuta, Dana Gabuzda, and Ellis L. Reinherz. Elicitation from Virus-Naive Individuals of Cytotoxic T Lymphocytes Directed against Conserved HIV-1 Epitopes. Med. Immunol., 5:1, 2006. PubMed ID: 16674822. Show all entries for this paper.

Displaying record number 54150

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HXB2 Location	Pol(197-205) RT(42-50) DNA(2673..2699)	Pol Epitope Map
Author Location	RT(42-50 HXB2)
Epitope	`EKEGKISKI`	Epitope Alignment
Epitope Name	EI9
Subtype	B
Species (MHC/HLA)	human(B*51:01)
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.

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 61266

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HXB2 Location	Pol(197-205) RT(42-50) DNA(2673..2699)	Pol Epitope Map
Author Location	RT
Epitope	`EKEGKISKI`	Epitope Alignment
		Show epitope variants
Subtype	B
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Country	Mexico, Spain
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	drug resistance

Notes

Pol (PR-RT) CTL epitopes containing drug resistance (DR) mutations, but capable of eliciting immune response were found in ART-naive subjects. Most CTL response detected was to either a DR-containing or wild type (WT) peptide but not both. A majority of the 22 most-recognized peptides of the 218 tested were DR-containing. Capability of immune recognition and response to DR peptides was usually not associated with the presence of DR mutations in the infecting virus, but this association did exist for WT peptides.
WT Reverse Transcriptase peptide EKEGKISKI was recognized by 9/49 patients tested, with a mean magnitude of 87 SFC/10⁶cells. It overlaps a DR position, E44D, but those 9 subjects did not respond to the DR peptide.

References

Blanco-Heredia2016 Juan Blanco-Heredia, Aarón Lecanda, Humberto Valenzuela-Ponce, Christian Brander, Santiago Ávila-Rios, and Gustavo Reyes-Terán. Identification of Immunogenic Cytotoxic T Lymphocyte Epitopes Containing Drug Resistance Mutations in Antiretroviral Treatment-Naive HIV-Infected Individuals. PLoS One, 11(1):e0147571, 2016. PubMed ID: 26808823. Show all entries for this paper.