Search CTL/CD8+ T-Cell Epitope Database

Found 22 matching records:

Displaying record number 1795

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HXB2 Location	Gag(329-337) p24(197-205) DNA(1774..1800)	Gag Epitope Map
Author Location	p24(197-205)
Epitope	`DCKTILKAL`	Epitope Alignment
Species (MHC/HLA)	human(B*08)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

B*08-restricted CTL accounted for about 1/3 of the total CTL response in one individual.

References

Day2001 C. L. Day, A. K. Shea, M. A. Altfeld, D. P. Olson, S. P. Buchbinder, F. M. Hecht, E. S. Rosenberg, B. D. Walker, and S. A. Kalams. Relative dominance of epitope-specific cytotoxic T-lymphocyte responses in human immunodeficiency virus type 1-infected persons with shared HLA alleles. J. Virol., 75(14):6279-91, Jul 2001. URL: http://jvi.asm.org/cgi/content/full/75/14/6279. PubMed ID: 11413294. Show all entries for this paper.

Displaying record number 56368

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HXB2 Location	Gag(329-337) p24(197-205) DNA(1774..1800)	Gag Epitope Map
Author Location	p24(329-337)
Epitope	`DCKTILKAL`	Epitope Alignment
Epitope Name	DL9
Subtype	B
Species (MHC/HLA)	human(B*08)
Immunogen	HIV-1 infection
Country	Australia, Canada, Germany, United States
Experimental methods
Keywords	HLA associated polymorphism

Notes

98 newly infected patients were studied to track early host HLA and Gag/Pol/Nef epitope immune responses' association with viral evolution. Response hierarchies were the same as those for later infection, and 50% of the most rapidly substituting epitopes were restricted by protective HLA, e.g. Gag B*57-associated mutations which were the most rapidly reverting upon transmission to a non-B*57-host. While there are great differences in mutation rates and reversions across the HIV proteome, most early viral change is driven by immune pressure.
HLA-driven epitope evolution was seen in 80% of published CTL epitopes.
HLA-B*08-associated substitution within optimally defined epitope DCKTILKAL is at positions K3, DCkTILKAL. DL9 has a very low recognition frequency and does not escape.

References

Brumme2008 Zabrina L. Brumme, Chanson J. Brumme, Jonathan Carlson, Hendrik Streeck, Mina John, Quentin Eichbaum, Brian L Block, Brett Baker, Carl Kadie, Martin Markowitz, Heiko Jessen, Anthony D. Kelleher, Eric Rosenberg, John Kaldor, Yuko Yuki, Mary Carrington, Todd M. Allen, Simon Mallal, Marcus Altfeld, David Heckerman, and Bruce D. Walker. Marked Epitope- and Allele-Specific Differences in Rates of Mutation in Human Immunodeficiency Type 1 (HIV-1) Gag, Pol, and Nef Cytotoxic T-Lymphocyte Epitopes in Acute/Early HIV-1 Infection. J. Virol., 82(18):9216-9227, Sep 2008. PubMed ID: 18614631. Show all entries for this paper.

Displaying record number 58537

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HXB2 Location	Gag(329-337) p24(197-205) DNA(1774..1800)	Gag Epitope Map
Author Location	p24(197-205)
Epitope	`DCKTILKAL`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(B*08)
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*08-restricted p24 optimal epitope DCKTILKAL 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 59566

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HXB2 Location	Gag(329-337) p24(197-205) DNA(1774..1800)	Gag Epitope Map
Author Location	Gag(329-337)
Epitope	`DCKTILKAL`	Epitope Alignment
Epitope Name	DL9
Species (MHC/HLA)	human(B*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.
DCKTILKAL had a significantly positive association with HLA B*08; it was recognized by 3/21 B*08-positive subjects and 6/272 B*08-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 62119

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HXB2 Location	Gag(329-337) p24(197-205) DNA(1774..1800)	Gag Epitope Map
Author Location	p24(329-337 NL4-3)
Epitope	`DCKTILKAL`	Epitope Alignment
Species (MHC/HLA)	human(B*08)
Immunogen	computer prediction
Experimental methods	Other, Relative replication capacity assay
Keywords	vaccine antigen design, viral fitness and reversion

Notes

Computational models were used to translate published HIV-1 sequence data into quantitative viral fitness landscapes with peaks and valleys, that are a function of the amino acid sequences of its constituent proteins. In this case, Clade B Gag was modeled. Predictions were tested against in vitro fitness measurements and were consistent.
Epitope DCKTILKAL is used as an example where each amino acid position within the epitope is associated with a different energy cost, ΔE, and the greater the cost the higher the fitness penalty. Observed HLA-associated escape position at K331 is one of the positions (including I333) with the lowest h_i value, i.e. the least energetically costly to change.
Based on fitness costs, the authors created a rank-ordered bar chart called the "Epitope Index" and marked out immunodominant response associations on it. The epitope index reads Gag: (164-172)-B*57; (162-172)-B*57 i.e. KF11; (167-175)-A*26; (260-267)-B*08; (240-249)-B*57 i.e. TW10; (296-306)-B*14; (147-155)-B*57; (349-359)-A*11; (263-272)-B*27; (269-277)-B*15; (145-155)-A*25; (306-316)-B*44, from highest to lowest fitness costs.
Brumme2009 is not annotated in this database as epitopes were not immunologically defined, but the table of polymorphisms is available at https://www.hiv.lanl.gov/content/immunology/pdf/2010/escape_article_supplement.html. and a review of the work is available on the main page, hiv.lanl.gov under 'Tools and Data Sets', "Identifying HLA-Associated Polymorphisms in HIV-1" (PDF).

References

Ferguson2013a Andrew L. Ferguson, Jaclyn K. Mann, Saleha Omarjee, Thumbi Ndung'u, Bruce D Walker, and Arup K. Chakraborty. Translating HIV Sequences into Quantitative Fitness Landscapes Predicts Viral Vulnerabilities for Rational Immunogen Design. Immunity, 38(3):606-617, 21 Mar 2013. PubMed ID: 23521886. Show all entries for this paper.

Displaying record number 353

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HXB2 Location	Gag(329-337) p24(197-205) DNA(1774..1800)	Gag Epitope Map
Author Location	p24(329-337 LAI)
Epitope	`DCKTILKAL`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(B*08:01)
Immunogen
Experimental methods
Keywords	optimal epitope, A-list

Notes

C. Brander notes this is a B*0801 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 58432

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HXB2 Location	Gag(329-337) p24(197-205) DNA(1774..1800)	Gag Epitope Map
Author Location	Gag(329-337)
Epitope	`DCKTILKAL`	Epitope Alignment
Subtype	A1
Species (MHC/HLA)	human(B*08:01)
Immunogen	HIV-1 infection
Patient MHC/HLA	ML1992: A02:01, A30:01, B08:01, B44:15, C02:02, C04:01.; ML1857: A02:01, A66:01, B35:01, B44:18, C04:01, C16:04
Country	Kenya
Experimental methods	Other
Keywords	assay or method development

Notes

Ultra-deep parallel pyrosequencing using nested PCR was compared to and found to be vastly superior to Sanger clone-based sequencing. 96 ART-naive HIV-1 (clade A1, B, C or D) -infected subjects' HIV-Gag protein when sequenced by both methods, revealed 14,034 variations by pyrosequencing technology versus 3,632 variations by Sanger's method. These variations were located in previously experimentally determined CTL epitopes of Gag. The sequencing method chosen for a study affects genetic variations found, host-virus interactions detected and evolutionary conclusions drawn.
Parallel 454 pyrosequencing method detected sequence that generated a cosensus epitope read of DCKTILKAL from patient ML1992. When Sanger clone-based sequencing was used however, the same functional, immunogenic site output a different consensus epitope of DCK(K/R)TILKAL.
Note: Restricting HLA is a typo, A*0801. Corrected to B*08:01 by author communication, Dr. Ma Luo.

References

Liang2011 Binhua Liang, Ma Luo, Joel Scott-Herridge, Christina Semeniuk, Mark Mendoza, Rupert Capina, Brent Sheardown, Hezhao Ji, Joshua Kimani, Blake T. Ball, Gary Van Domselaar, Morag Graham, Shane Tyler, Steven J. M. Jones, and Francis A. Plummer. A Comparison of Parallel Pyrosequencing and Sanger Clone-Based Sequencing and Its Impact on the Characterization of the Genetic Diversity of HIV-1. PLoS One, 6(10):e26745, 2011. PubMed ID: 22039546. Show all entries for this paper.

Displaying record number 59565

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HXB2 Location	Gag(329-337) p24(197-205) DNA(1774..1800)	Gag Epitope Map
Author Location	Gag(329-337)
Epitope	`DCKTILKAL`	Epitope Alignment
Epitope Name	DL9
Species (MHC/HLA)	human(B*14)
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.
DCKTILKAL had a significantly positive association with HLA B*14; it was recognized by 5/33 B*14-positive subjects and 9/293 B*14-negative subjects.

References

Displaying record number 59564

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HXB2 Location	Gag(329-337) p24(197-205) DNA(1774..1800)	Gag Epitope Map
Author Location	Gag(329-337)
Epitope	`DCKTILKAL`	Epitope Alignment
Epitope Name	DL9
Species (MHC/HLA)	human(B*15:03)
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.
DCKTILKAL had a significantly positive association with HLA B*1503; it was recognized by 7/15 B*1503-positive subjects and 14/326 B*1503-negative subjects.

References

Displaying record number 59567

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HXB2 Location	Gag(329-337) p24(197-205) DNA(1774..1800)	Gag Epitope Map
Author Location	Gag(329-337)
Epitope	`DCKTILKAL`	Epitope Alignment
Epitope Name	DL9
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.
DCKTILKAL had a significantly positive association with HLA B*3502,B*3503,B*5301; it was recognized by 3/33 B*3502,B*3503,B*5301-positive subjects and 3/239 B*3502,B*3503,B*5301-negative subjects.

References

Displaying record number 54809

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HXB2 Location	Gag(329-337) p24(197-205) DNA(1774..1800)	Gag Epitope Map
Author Location
Epitope	`DCKTILKAL`	Epitope Alignment
Species (MHC/HLA)	(B8)
Immunogen
Experimental methods
Keywords	review, immunodominance, escape, vaccine antigen design

Notes

This review discusses current literature on particular CTL escape mutations that significantly impair viral fitness and argues for a concerted effort to identify these targets.
This epitope is discussed in the context of the hierarchy of recognized HLA-B8 epitopes during acute infection.

References

Altfeld2006a Marcus Altfeld and Todd M. Allen. Hitting HIV Where It Hurts: An Alternative Approach to HIV Vaccine Design. Trends Immunol., 27(11):504-510, Nov 2006. PubMed ID: 16997629. Show all entries for this paper.

Displaying record number 352

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HXB2 Location	Gag(329-337) p24(197-205) DNA(1774..1800)	Gag Epitope Map
Author Location	p24(329-337 LAI)
Epitope	`DCKTILKAL`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(B8)
Immunogen
Experimental methods
Keywords

Notes

Predicted epitope based on B8-binding motifs, from larger peptide VQNANPDCKTILKAL.

References

Sutton1993 J. Sutton, S. Rowland-Jones, W. Rosenberg, D. Nixon, F. Gotch, X.-M. Gao, N. Murray, A. Spoonas, P. Driscoll, M. Smith, A. Willis, and A. McMichael. A Sequence Pattern for Peptides Presented to Cytotoxic T Lymphocytes by HLA B8 Revealed by Analysis of Epitopes and Eluted Peptides. Eur. J. Immunol., 23:447-453, 1993. PubMed ID: 7679646. Show all entries for this paper.

Displaying record number 354

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HXB2 Location	Gag(329-337) p24(197-205) DNA(1774..1800)	Gag Epitope Map
Author Location	p24(329-337)
Epitope	`DCKTILKAL`	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human(B8)
Immunogen	HIV-1 infection
Experimental methods
Keywords	escape

Notes

In a longitudinal study of CTL response and immune escape -- the variant DCRTILKAL was also found, binds to B8, but is not recognized.

References

Nowak1995 M. A. Nowak, R. M. May, R. E. Phillips, S. Rowland-Jones, D. G. Lalloo, S. McAdam, P. Klenerman, B. Koppe, K. Sigmund, C. R. M. Bangham, and A. J. McMichael. Antigenic Oscillations and Shifting Immunodominance in HIV-1 Infections. Nature, 375:606-611, 1995. This paper presents longitudinal studies of epitope variation and corresponding CTL responses in two patients. A mathematical model was created to provide a framework to explain the observed shifts in epitope and CTLp frequencies. For discussion, see also: J. M. Coffin, Nature 375:534-535 (1995). PubMed ID: 7791879. Show all entries for this paper.

Displaying record number 355

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HXB2 Location	Gag(329-337) p24(197-205) DNA(1774..1800)	Gag Epitope Map
Author Location	p24(329-337)
Epitope	`DCKTILKAL`	Epitope Alignment
Species (MHC/HLA)	human(B8)
Immunogen
Experimental methods
Keywords

Notes

Defined as minimal epitope by titration and binding studies.

References

McAdam1995 S. McAdam, P. Klenerman, L. Tussey, S. Rowland-Jones, D. Lalloo, R. Phillips, A. Edwards, P. Giangrande, A. L. Brown, and F. Gotch. Immunogenic HIV Variant Peptides That Bind to HLA-B8 Can Fail to Stimulate Cytotoxic T Lymphocyte Responses. J. Immunol., 155:2729-2736, 1995. PubMed ID: 7544382. Show all entries for this paper.

Displaying record number 356

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HXB2 Location	Gag(329-337) p24(197-205) DNA(1774..1800)	Gag Epitope Map
Author Location	p24(197-205)
Epitope	`DCKTILKAL`	Epitope Alignment
Species (MHC/HLA)	human(B8)
Immunogen
Experimental methods
Keywords

Notes

Included in a study of the B8 binding motif.

References

Goulder1997c P. J. R. Goulder, S. W. Reid, D. A. Price, C. A. O'Callaghan, A. J. McMichael, R. E. Phillips, and E. Y. Jones. Combined Structural and Immunological Refinement of HIV-1 HLA-B8 Restricted Cytotoxic T Lymphocyte Epitopes. Eur. J. Immunol., 27:1515-1521, 1997. PubMed ID: 9209505. Show all entries for this paper.

Displaying record number 1374

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HXB2 Location	Gag(329-337) p24(197-205) DNA(1774..1800)	Gag Epitope Map
Author Location	p24(329-337)
Epitope	`DCKTILKAL`	Epitope Alignment
Epitope Name	DCK
Species (MHC/HLA)	human(B8)
Immunogen	HIV-1 infection
Experimental methods
Keywords	HAART, ART, supervised treatment interruptions (STI), immunodominance, acute/early infection

Notes

Patients who started therapy at acute HIV-1 infection (three with sustained therapy, two with limited therapy upon early infection) had strong HIV specific CD4 proliferative responses and were able to maintain a CTL response even with undetectable viral load -- three patients that had delayed initiation of HAART had no HIV specific CD4 proliferative responses and lost their CTL responses when HAART was eventually given and their viral loads became undetectable.
This epitope was recognized at a low level by only 1 of the 7/8 study subjects that were HLA B8.
Patient SC12(HLA A1, B8/39, Cw0701/0702, DR2/3, DR51/52, DQ2/6) had sustained therapy started during acute infection and maintained an immunodominant response to FLKEKGGL throughout and minor responses to GEIYKRWII, DCKTILKAL, GGKKKYKLK -- GEIYKRWII and GGKKKYKLK responses were stimulated by a brief period off therapy.

References

Oxenius2000b A. Oxenius, D. A. Price, P. J. Easterbrook, C. A. O'Callaghan, A. D. Kelleher, J. A. Whelan, G. Sontag, A. K. Sewell, and R. E. Phillips. Early highly active antiretroviral therapy for acute HIV-1 infection preserves immune function of CD8+ and CD4+ T lymphocytes. Proc. Natl. Acad. Sci. U.S.A., 97(7):3382-7, 28 Mar 2000. URL: http://www.pnas.org/cgi/content/full/97/7/3382. PubMed ID: 10737796. Show all entries for this paper.

Displaying record number 1451

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HXB2 Location	Gag(329-337) p24(197-205) DNA(1774..1800)	Gag Epitope Map
Author Location	p24(197-205)
Epitope	`DCKTILKAL`	Epitope Alignment
Species (MHC/HLA)	human(B8)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

One of the 51 HIV-1 epitopes selected by Ferrari et al. as good candidate CTL epitopes for vaccines by virtue of being conserved and presented by common HLA alleles.

References

Ferrari2000 G. Ferrari, D. D. Kostyu, J. Cox, D. V. Dawson, J. Flores, K. J. Weinhold, and S. Osmanov. Identification of highly conserved and broadly cross-reactive HIV type 1 cytotoxic T lymphocyte epitopes as candidate immunogens for inclusion in Mycobacterium bovis BCG-vectored HIV vaccines. AIDS Res. Hum. Retroviruses, 16(14):1433-43, 20 Sep 2000. PubMed ID: 11018863. Show all entries for this paper.

Displaying record number 52320

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HXB2 Location	Gag(329-337) p24(197-205) DNA(1774..1800)	Gag Epitope Map
Author Location	p24
Epitope	`DCKTILKAL`	Epitope Alignment
Epitope Name	DCK
Species (MHC/HLA)	human(B8)
Immunogen	HIV-1 infection
Experimental methods
Keywords	HAART, ART, supervised treatment interruptions (STI)

Notes

Using previously defined epitopes Oxenius2000b,Oxenius2001b in an IFNgamma Elispot assay, 13 chronically HIV-1 infected patients were studied over a period including therapy with standard treatment interruptions (STI).
STIs induced increased recognition of CTL epitopes, but there was no correlation between CTL responses with viral rebound rates, plateau viral loads, or clearance rates.

References

Oxenius2002b Annette Oxenius, Angela R. McLean, Marek Fischer, David A. Price, Sarah J. Dawson, Roland Hafner, Christine Schneider, Helen Joller, Bernard Hirschel, Rodney E. Phillips, Rainer Weber, Huldrych F. Günthard, and Swiss HIV Cohort Study Group. Human Immunodeficiency Virus-Specific CD8+ T-Cell Responses Do Not Predict Viral Growth and Clearance Rates During Structured Intermittent Antiretroviral Therapy. J. Virol., 76(20):10169-10176, Oct 2002. PubMed ID: 12239291. Show all entries for this paper.

Displaying record number 52965

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HXB2 Location	Gag(329-337) p24(197-205) DNA(1774..1800)	Gag Epitope Map
Author Location	Gag(329-337)
Epitope	`DCKTILKAL`	Epitope Alignment
Species (MHC/HLA)	humanized rabbit(B8)
Immunogen	HIV-1 infection
Patient MHC/HLA	A28, A3, B7, B8
Country	Canada
Experimental methods	Chromium-release assay, Flow cytometric T-cell cytokine assay, Proliferation
Keywords	HAART, ART, memory cells

Notes

HAART restores HIV specific immunity after advanced infection by increase of CD4+ and CD8+ T cell numbers after suppression of viral replication. However, HIV specific CTLs emerged only with detectable viral replication breakthroughs and were short-lived while CD4+ T-cell responses remained compromised, suggesting failure of generating stable CD8+ memory T-cells in the absence of HIV-specific T-helper responses.

References

Gamberg2004 Jane Gamberg, Lisa Barrett, Ian Bowmer, Constance Howley, and Michael Grant. Immune Reconstitution and Viral Stimulation Are Required to Restore HIV-Specific CD8 T Cell Responses Following Advanced Infection. J. Clin. Immunol., 24(2):115-124, Mar 2004. PubMed ID: 15024178. Show all entries for this paper.

Displaying record number 53381

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HXB2 Location	Gag(329-337) p24(197-205) DNA(1774..1800)	Gag Epitope Map
Author Location	( B consensus)
Epitope	`DCKTILKAL`	Epitope Alignment
Epitope Name	DL9
Subtype	B
Species (MHC/HLA)	human(B8)
Immunogen	HIV-1 infection
Patient MHC/HLA	A1, A3, B14, B8, Cw7, Cw8
Country	United States
Experimental methods	Chromium-release assay, Cytokine production, Flow cytometric T-cell cytokine assay, Intracellular cytokine staining
Keywords	assay or method development, memory cells, characterizing CD8+ T cells

Notes

Using a flow-cytometric cytotoxicity assay based on caspase-3 activation in dying target cells, it was shown that the subset of HIV-1-specific CD8+ T cells secreting both IFN-gamma and TNF-alpha exhibit stronger cytotoxic activity than those secreting only IFN-gamma. These cells also exhibited stronger intracellular perforin expression. No association between HIV-1-specific CD8+ T-cell maturation phenotypes and intracellular perforin expression was found.
1/9 individuals recognized this epitope.

References

Lichterfeld2004b Mathias Lichterfeld, Xu G. Yu, Michael T. Waring, Stanley K. Mui, Mary N. Johnston, Daniel Cohen, Marylyn M. Addo, John Zaunders, Galit Alter, Eunice Pae, Daryld Strick, Todd M. Allen, Eric S. Rosenberg, Bruce D. Walker, and Marcus Altfeld. HIV-1-Specific Cytotoxicity Is Preferentially Mediated by a Subset of CD8+ T Cells Producing both Interferon-gamma and Tumor Necrosis Factor-alpha. Blood, 104(2):487-394, 15 Jul 2004. PubMed ID: 15059848. Show all entries for this paper.

Displaying record number 54341

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HXB2 Location	Gag(329-337) p24(197-205) DNA(1774..1800)	Gag Epitope Map
Author Location	p24
Epitope	`DCKTILKAL`	Epitope Alignment
Epitope Name	B8-DL9(p24)
Species (MHC/HLA)	human(B8)
Immunogen	HIV-1 infection
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	rate of progression, immunodominance, early-expressed proteins

Notes

Immunodominant HIV epitopes in early, primary infection of CTLs were identified and the relative contributions of immune responses restricted to individual HLA class I molecules were studied.
This epitope-HLA combination was recognized. The most frequently recognized epitopes also elicited the greatest CTL response.
HIV-1 Epitope sequence variability was not correlated with immunodominant versus immune sub-dominant responses.
HLA-B*57 and HLA-B*27 restricted responses were the strongest in these early and acute infections - due to dominant responses to a single epitope in each case (TW10 for B*57 and KK10 for B*27).
In the presence of HLA-B*57 and HLA-B*27 restricted responses, the relative contributions of other restricting HLA dropped greatly.

References

Altfeld2006 Marcus Altfeld, Elizabeth T. Kalife, Ying Qi, Hendrik Streeck, Mathias Lichterfeld, Mary N. Johnston, Nicole Burgett, Martha E. Swartz, Amy Yang, Galit Alter, Xu G. Yu, Angela Meier, Juergen K. Rockstroh, Todd M. Allen, Heiko Jessen, Eric S. Rosenberg, Mary Carrington, and Bruce D. Walker. HLA Alleles Associated with Delayed Progression to AIDS Contribute Strongly to the Initial CD8+ T Cell Response against HIV-1. PLoS Med., 3(10):e403, Oct 2006. PubMed ID: 17076553. Show all entries for this paper.

Displaying record number 62825

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HXB2 Location	Gag(329-337) p24(197-205) DNA(1774..1800)	Gag Epitope Map
Author Location	p24(329-337)
Epitope	`DCKTILKAL`	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, 60 single nucleotide mutations were observed in epitope DCKTILKAL (known to bind to B0801) with a log transformation of mean fitness score, relative to NL4-3, of -0.6660.

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.