Search CTL/CD8+ T-Cell Epitope Database

Found 23 matching records:

Displaying record number 1317

HXB2 Location	Rev(67-75) DNA(8501..8527)	Rev Epitope Map
Author Location	Rev
Epitope	`SAEPVPLQL`	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human(B14)
Immunogen	HIV-1 infection
Experimental methods
Keywords	escape

Notes

Molecularly cloned primary NSI macrophage tropic strain 2.1 and SI non-macrophage tropic strain 1.2 were isolated from study participant ACH320 and use to infect irradiated XID mice that had been reconstituted with human PBMC from B14+ seronegative donors -- results indicate CTL may favor selective outgrowth of macrophage tropic strains.
The CTL clone TCC108 specific for SAEPVPLQL, previously described by van Baalen 1997, and van Baalen 1998, was stimulated in vitro and given to the mice to apply specific CTL pressure.
The macrophage-tropic HIV-1 strain #2.1 escaped CTL pressure more efficiently (7/14 animals) than its non-macrophage-tropic counterpart #1.2(SI) -- the latter isolate was suppressed in 13/14 animals -- macrophage may serve as a CTL sanctuary and reduced pressure on macrophage tropic HIV strains may allow additional replication to assist with acquisition of escape.
Specific HIV-1 variants selectively induced by TCC108 were for strain 1.2: SEEPVPLQL, and for strain 2.1: SAEHVPLQL, SAESVPLQL, SVEPVPLQL, SLEPVPLQL, SAEPVPFQL, and SAEPVPFQL.

References

Schutten2001 M. Schutten, C. A. van Baalen, C. Guillon, R. C. Huisman, P. H. Boers, K. Sintnicolaas, R. A. Gruters, and A. D. Osterhaus. Macrophage tropism of human immunodeficiency virus type 1 facilitates in vivo escape from cytotoxic T-lymphocyte pressure. J. Virol., 75(6):2706-9, Mar 2001. URL: http://jvi.asm.org/cgi/content/full/75/6/2706. PubMed ID: 11222694. Show all entries for this paper.

Displaying record number 1206

HXB2 Location	Rev(67-75) DNA(8501..8527)	Rev Epitope Map
Author Location	( LAI)
Epitope	`SAEPVPLQL`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	(B14)
Immunogen
Experimental methods
Keywords

References

vanBaalenPerCom2000 C. van Baalen and R. Gruters. Personal communication, 2000. Show all entries for this paper.

Displaying record number 54344

HXB2 Location	Rev(67-75) DNA(8501..8527)	Rev Epitope Map
Author Location	Rev
Epitope	`SAEPVPLQL`	Epitope Alignment
Epitope Name	B14-SL9(Rev)
Species (MHC/HLA)	human(B14)
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 contribution of immune responses restricted to individual HLA class I molecules were studied.
The most frequently recognised 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 contribution 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 52417

HXB2 Location	Rev(67-75) DNA(8501..8527)	Rev Epitope Map
Author Location	Rev(67-75)
Epitope	`SAEPVPLQL`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(B14)
Immunogen	HIV-1 infection
Experimental methods
Keywords	early-expressed proteins

Notes

CTL responses against regulatory and accessory proteins in 70 HIV-1 infected patients were studied using overlapping peptides and Elispot.
28% targeted one or more overlapping Tat peptides; 36%, Rev peptides; 33%, Vif peptides; 40%, Vpr peptides; and 2%, Vpu peptides.
All known optimally defined epitopes were summarized for the five proteins.

References

Addo2002a M. M. Addo, X. G. Yu, E. S. Rosenberg, B. D. Walker, and M. Altfeld. Cytotoxic T-Lymphocyte (CTL) Responses Directed against Regulatory and Accessory Proteins in HIV-1 Infection. DNA Cell Biol., 21(9):671-678, Sep 2002. PubMed ID: 12396610. Show all entries for this paper.

Displaying record number 52351

HXB2 Location	Rev(67-75) DNA(8501..8527)	Rev Epitope Map
Author Location	Rev(67-75)
Epitope	`SAEPVPLQL`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(B14)
Immunogen	HIV-1 infection
Experimental methods
Keywords	acute/early infection, early-expressed proteins, kinetics

Notes

Tat, Rev and Nef are the first HIV proteins expressed upon acute infection of T-cells (< 6 hours), and RT is not expressed until after 24 hours. The B14-restricted Rev-SAEPVPLQL specific CD8 T-cell clone TCC108, and the B57-restricted RT-IVLPEKDSW specific CD8 T-cell clone TCL1C11 were co-incubated with CD4+ cultures inoculated with HIV-1 at low MOI. Co-incubation with the Rev-specific CTL resulted in two logs less HIV-1 production in ten days of culture. When the RT epitope was cloned into the Nef gene of the infecting strain, another early expressed protein, it proved as effective as the Rev epitope at inhibiting viral production. A mathematical model of CTL-target interactions suggest early proteins are important for vaccine design.

References

vanBaalen2002 Carel A. van Baalen, Christophe Guillon, Minus van Baalen, Esther J. Verschuren, Patrick H. M. Boers, Albert D. M. E. Osterhaus, and Rob A. Gruters. Impact of Antigen Expression Kinetics on the Effectiveness of HIV-Specific Cytotoxic T Lymphocytes. Eur. J. Immunol., 32(9):2644-2652, Sep 2002. PubMed ID: 12207349. Show all entries for this paper.

Displaying record number 619

HXB2 Location	Rev(67-75) DNA(8501..8527)	Rev Epitope Map
Author Location	Rev(67-75 IIIB)
Epitope	`SAEPVPLQL`	Epitope Alignment
Species (MHC/HLA)	human(B14, Cw8)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

The Rev-specific CTL response studied here was from an individual infected with HIV-1 for more than 12 years without developing symptoms -- Rev and Tat are expressed early and CTL activity against these proteins has been correlated with long-term survival.
The CTL clone TCC108 specific for this epitope was studied in vitro.
CTLs added immediately after infection suppressed viral production, indicative of CTL interference with viral production prior to lysis -- CTL-mediated lysis occurred after the onset of progeny viral release, but prior to peak viral production.
Rapid selection of a E69K mutation, which abolished CTL, recognition was observed.
The epitope was originally listed as B14, but Cw8 and B14 are in linkage disequilibrium, and in this case were not distinguished (pers. comm., Christian Brander, 1999)

References

VanBaalen1998 C. A. van Baalen, M. Schutten, R. C. Huisman, P. H. Boers, R. A. Gruters, and A. D. Osterhaus. Kinetics of Antiviral Activity by Human Immunodeficiency Virus Type 1-Specific Cytotoxic T Lymphocytes (CTL) and Rapid Selection of CTL Escape Virus In Vitro. J. Virol., 72:6851-6857, 1998. PubMed ID: 9658134. Show all entries for this paper.

Displaying record number 60243

HXB2 Location	Rev(67-75) DNA(8501..8527)	Rev Epitope Map
Author Location	Rev(67-75)
Epitope	`SAEPVPLQL`	Epitope Alignment
Epitope Name	SL9
Species (MHC/HLA)	human(B*40)
Immunogen	HIV-1 infection
Experimental methods	CD8 T-cell Elispot - IFNγ, Flow cytometric T-cell cytokine assay
Keywords	rate of progression, optimal epitope

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.
SAEPVPLQL had a significantly positive association with HLA B*40; it was recognized by 2/26 B*40-positive subjects and 1/243 B*40-negative subjects.
SAEPVPLQL was significantly protective, associated with viral control when restricted by HLA-B*40 in a cohort of 245 controllers and 96 progressors that included B*57/*5801 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 60241

HXB2 Location	Rev(67-75) DNA(8501..8527)	Rev Epitope Map
Author Location	Rev(67-75)
Epitope	`SAEPVPLQL`	Epitope Alignment
Epitope Name	SL9
Species (MHC/HLA)	human(C*01)
Immunogen	HIV-1 infection
Experimental methods	CD8 T-cell Elispot - IFNγ, Flow cytometric T-cell cytokine assay
Keywords	rate of progression, optimal epitope

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.
SAEPVPLQL had a significantly positive association with HLA C*01; it was recognized by 3/31 C*01-positive subjects and 3/269 C*01-negative subjects.
SAEPVPLQL was significantly protective, associated with viral control when restricted by HLA-C*01 in a cohort of 245 controllers and 96 progressors that included B*57/*5801 subjects.

References

Displaying record number 60242

HXB2 Location	Rev(67-75) DNA(8501..8527)	Rev Epitope Map
Author Location	Rev(67-75)
Epitope	`SAEPVPLQL`	Epitope Alignment
Epitope Name	SL9
Species (MHC/HLA)	human(C*08)
Immunogen	HIV-1 infection
Experimental methods	CD8 T-cell Elispot - IFNγ, Flow cytometric T-cell cytokine assay
Keywords	rate of progression, optimal epitope

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.
SAEPVPLQL had a significantly positive association with HLA C*08; it was recognized by 4/41 C*08-positive subjects and 6/300 C*08-negative subjects.
SAEPVPLQL was significantly protective, associated with viral control when restricted by HLA-C*08 in a cohort of 245 controllers and 96 progressors that included B*57/*5801 subjects.

References

Displaying record number 61998

HXB2 Location	Rev(67-75) DNA(8501..8527)	Rev Epitope Map
Author Location	Env(2-10)
Epitope	`SAEPVPLQL`	Epitope Alignment
Species (MHC/HLA)	human(Cw*0501)
Immunogen	peptide-HLA interaction
Experimental methods	Intracellular cytokine staining, Other
Keywords	assay or method development, NK cells

Notes

Contamination of what were previously thought to be highly specific epitopes identified through HLA IP-based immunopeptidomics is exposed. A low-level of co-isolation of erroneously assigned Class I-restricted peptides is found viz. HLA class II peptides, extended peptides from HIV Gag, and peptides from the B lymphoblastoid cell line 721.221 previously thought to be Class I deficient but which actually does present HLA-Cw*0102.
9/64 C8166 cell lysate identified epitopes are actually known epitopes. SAEPVPLQL is one of them, restricted by Cw*0501.

References

Partridge2018 Thomas Partridge, Annalisa Nicastri, Anna E. Kliszczak, Louis-Marie Yindom, Benedikt M. Kessler, Nicola Ternette, and Persephone Borrow. Discrimination Between Human Leukocyte Antigen Class I-Bound and Co-Purified HIV-Derived Peptides in Immunopeptidomics Workflows. Front. Immunol., 9:912, 2018. PubMed ID: 29780384. Show all entries for this paper.

Displaying record number 1212

HXB2 Location	Rev(67-75) DNA(8501..8527)	Rev Epitope Map
Author Location	( LAI)
Epitope	`SAEPVPLQL`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(Cw*0501)
Immunogen
Experimental methods
Keywords	optimal epitope

References

Addo2001 Marylyn M. Addo, Marcus Altfeld, Eric S. Rosenberg, Robert L. Eldridge, Mary N. Philips, Kathleen Habeeb, Ashok Khatri, Christian Brander, Gregory K. Robbins, Gail P. Mazzara, Philip J. R. Goulder, and Bruce D. Walker. The HIV-1 Regulatory Proteins Tat and Rev are Freqently Targeted by cytotoxic T Lymphocytes (CTL) Derived from HIV Infected Individuals. Proc. Natl. Acad. Sci. U.S.A., 98(4):1781-1786, 13 Feb 2001. PubMed ID: 11172028. Show all entries for this paper.

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 53531

HXB2 Location	Rev(67-75) DNA(8501..8527)	Rev Epitope Map
Author Location	Rev
Epitope	`SAEPVPLQL`	Epitope Alignment
Epitope Name	SL9
Subtype	B
Species (MHC/HLA)	human(Cw5)
Immunogen	HIV-1 infection
Patient MHC/HLA	A11, A2, B18, B44, Cw12, Cw5
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	subtype comparisons, escape, characterizing CD8+ T cells, viral fitness and reversion

Notes

Two-thirds of all mutations arising in non-envelope proteins during the transition from acute to chronic infection were found to be due to either CD8 T-cell-associated selective pressures or reversion of HLA-I-associated mutations selected in a previous host.The predominance of escape mutations at highly polymorphic sites was observed across different HIV-1 clades.
One escape mutation, at position 5, SAEPgPLQL, was found not to correspond to the most polymorphic residue in the epitope.

References

Allen2005a Todd M. Allen, Marcus Altfeld, Shaun C. Geer, Elizabeth T. Kalife, Corey Moore, Kristin M. O'Sullivan, Ivna DeSouza, Margaret E. Feeney, Robert L. Eldridge, Erica L. Maier, Daniel E. Kaufmann, Matthew P. Lahaie, Laura Reyor, Giancarlo Tanzi, Mary N. Johnston, Christian Brander, Rika Draenert, Jurgen K. Rockstroh, Heiko Jessen, Eric S. Rosenberg, Simon A. Mallal, and Bruce D. Walker. Selective Escape from CD8+ T-Cell Responses Represents a Major Driving Force of Human Immunodeficiency Virus Type 1 (HIV-1) Sequence Diversity and Reveals Constraints on HIV-1 Evolution. J. Virol., 79(21):13239-13249, Nov 2005. PubMed ID: 16227247. Show all entries for this paper.

Displaying record number 1288

HXB2 Location	Rev(67-75) DNA(8501..8527)	Rev Epitope Map
Author Location	Rev( SF2)
Epitope	`SAEPVPLQL`	Epitope Alignment
Epitope Name	SL9
Species (MHC/HLA)	human(Cw5)
Immunogen	HIV-1 infection
Experimental methods
Keywords	acute/early infection

Notes

Data from patient AC13 suggest a role for this epitope in initial control of viremia in acute infection, as it is one of several subdominant CTL epitopes recognized during the initial decline in viremia.
A CTL response to SL9, SLYNTVATL, was not evident until 18 months post-presentation.

References

Goulder2001 P. J. Goulder, M. M. Addo, M. A. Altfeld, E. S. Rosenberg, Y. Tang, U. Govender, N. Mngqundaniso, K. Annamalai, T. U. Vogel, M. Hammond, M. Bunce, H. M. Coovadia, and B. D. Walker. Rapid Definition of Five Novel HLA-A*3002-Restricted Human Immunodeficiency Virus-Specific Cytotoxic T-Lymphocyte Epitopes by Elispot and Intracellular Cytokine Staining Assays. J. Virol., 75(3):1339-1347, Feb 2001. URL: http://jvi.asm.org/cgi/content/full/75/3/1339. PubMed ID: 11152507. Show all entries for this paper.

Displaying record number 52643

HXB2 Location	Rev(67-75) DNA(8501..8527)	Rev Epitope Map
Author Location	Rev(67-75)
Epitope	`SAEPVPLQL`	Epitope Alignment
Species (MHC/HLA)	human(Cw5)
Immunogen	HIV-1 infection
Patient MHC/HLA	A*0201, A1, B44, B57, Cw5, Cw6
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	binding affinity, acute/early infection, early-expressed proteins

Notes

CTL epitope responses were mapped in 21 men within 15-92 days post-HIV-1 infection. Subjects initially a showed narrow immune responses with a mean of 2.3 epitopes recognized per patient. The immune response broadened later in infection. No correlation between the plasma viral load and the number of recognized epitopes or the frequency of IFN-gamma secreting cells was observed, and there was no correlation between the functional avidity of a responses and the abundance of IFN-secreting cells that recognized the epitope. The first epitopes to be recognized tended not to be the most avid, and earliest responses tended to be directed against Nef, Tat, Vpr, and Env.
All HIV-1 proteins except Vpu were recognized, and a responses to a total of 41 optimal epitopes were characterized; 24 had been identified previously. 48% of the total T-cell responses were directed against Nef and 43% were directed against Gag.
More common HLA alleles were less frequently used in primary infection than less common alleles, for example A3, B35, B57, and B62 were more frequently recognized than A1, A2, A30, and A44.

References

Cao2003 Jianhong Cao, John McNevin, Sarah Holte, Lisa Fink, Lawrence Corey, and M. Juliana McElrath. Comprehensive Analysis of Human Immunodeficiency Virus Type 1 (HIV-1)-Specific Gamma Interferon-Secreting CD8+ T Cells in Primary HIV-1 Infection. J. Virol., 77(12):6867-6878, Jun 2003. PubMed ID: 12768006. Show all entries for this paper.

Displaying record number 53477

HXB2 Location	Rev(67-75) DNA(8501..8527)	Rev Epitope Map
Author Location	Rev(67-75)
Epitope	`SAEPVPLQL`	Epitope Alignment
		Show epitope variants
Epitope Name	SL9
Subtype	B
Species (MHC/HLA)	human(Cw5)
Immunogen	HIV-1 infection
Patient MHC/HLA	A11, A2, B18, B44, Cw12, Cw5
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Flow cytometric T-cell cytokine assay, Intracellular cytokine staining
Keywords	escape

Notes

4/14 optimal HIV-1 T-cell epitopes in a subject underwent mutation associated with dramatic loss of the original CD8 response. For 1 of the escape variants, a novel CD8 T-cell response equal in magnitude to the wildtype, was generated. CD8 T-cell recognizing the variant epitope utilized a distinct T-cell receptor and did not exhibit any cross-reactivity against the wildtype.
Escape occurred at position 5 of this epitope, saepGplql.

References

Allen2005 Todd M. Allen, Xu G. Yu, Elizabeth T. Kalife, Laura L. Reyor, Mathias Lichterfeld, Mina John, Michael Cheng, Rachel L. Allgaier, Stanley Mui, Nicole Frahm, Galit Alter, Nancy V. Brown, Mary N. Johnston, Eric S. Rosenberg, Simon A. Mallal, Christian Brander, Bruce D. Walker, and Marcus Altfeld. De Novo Generation of Escape Variant-Specific CD8+ T-Cell Responses Following Cytotoxic T-Lymphocyte Escape in Chronic Human Immunodeficiency Virus Type 1 Infection. J. Virol., 79(20):12952-12960, Oct 2005. PubMed ID: 16188997. Show all entries for this paper.

Displaying record number 1550

HXB2 Location	Rev(67-75) DNA(8501..8527)	Rev Epitope Map
Author Location	Rev(67-75 SF2)
Epitope	`SAEPVPLQL`	Epitope Alignment
Species (MHC/HLA)	human(Cw5)
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-Cw5+ individuals that had a CTL response to this epitope broken down by group: 2/6 group 1, 0/1 group 2, and 0/2 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 55496

HXB2 Location	Rev(67-75) DNA(8501..8527)	Rev Epitope Map
Author Location	Rev
Epitope	`SAEPVPLQL`	Epitope Alignment
Epitope Name	SL9
Subtype	B
Species (MHC/HLA)	human(Cw5)
Immunogen	HIV-1 infection
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Flow cytometric T-cell cytokine assay, Tetramer binding
Keywords	characterizing CD8+ T cells

Notes

T-cells were studied for exhaustion and dysfunction in chronic HIV infection. Polyfunctionality of CTL immune response to HIV-1 decreased with persistence of antigen presence over time in chronic infection. CTL exhaustion can thus be halted by reduction in viral antigen load - either by ART or through escape mutations.
PD-1, marker for activation and apoptosis increases over time, but it decreases when epitope mutations develop. CD127 however, is not impacted by viral escape.
203 days after first testing, epitope SAEPVPLQL showed no variation in a treated patient. Previously published HLA-restriction for SL9 wis HLA-Cw5.

References

Streeck2008 Hendrik Streeck, Zabrina L. Brumme, Michael Anastario, Kristin W. Cohen, Jonathan S. Jolin, Angela Meier, Chanson J. Brumme, Eric S. Rosenberg, Galit Alter, Todd M. Allen, Bruce D. Walker, and Marcus Altfeld. Antigen Load and Viral Sequence Diversification Determine the Functional Profile of HIV-1-Specific CD8+ T Cells. PLoS Med, 5(5):e100, 6 May 2008. PubMed ID: 18462013. Show all entries for this paper.

Displaying record number 52416

HXB2 Location	Rev(67-75) DNA(8501..8527)	Rev Epitope Map
Author Location	Rev(67-75)
Epitope	`SAEPVPLQL`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(Cw5, Cw8)
Immunogen	HIV-1 infection
Experimental methods
Keywords	early-expressed proteins

Notes

CTL responses against regulatory and accessory proteins in 70 HIV-1 infected patients were studied using overlapping peptides and Elispot.
28% targeted one or more overlapping Tat peptides; 36%, Rev peptides; 33%, Vif peptides; 40%, Vpr peptides; and 2%, Vpu peptides.
All known optimally defined epitopes were summarized for the five proteins.

References

Displaying record number 1274

HXB2 Location	Rev(67-75) DNA(8501..8527)	Rev Epitope Map
Author Location	Rev(69-77 BRU)
Epitope	`SAEPVPLQL`	Epitope Alignment
Epitope Name	Rev SL9
Species (MHC/HLA)	human(Cw8)
Immunogen	HIV-1 infection
Experimental methods
Keywords	HAART, ART, supervised treatment interruptions (STI), acute/early infection

Notes

Rev and Tat are expressed early in the virus life cycle and thus may be important targets for CTL against HIV early in infection and for vaccines -- therefore CTL responses against Tat and Rev were screened using overlapping peptides.
11/57 (19.3%) HIV-1+ individuals recognized at least 1 Tat peptide, and 21/57 (37%) responded to at least 1 Rev peptide.
This epitope is the first HIV-specific CTL epitope restricted by HLA-Cw5.
This epitope was recognized by 2/5 individuals expressing HLA-Cw8 and by 5/11 individuals expressing Cw5 allele, which differs from Cw8 by 4 amino acids, suggesting promiscuous presentation of the epitope between those HLA molecules.
Longitudinal data was available for 6 Rev-SL9 responders, who were treated during acute infection, and the response was stable 2 and 12 months after initiation of HAART, measurements by ELISPOT and flow-based intracellular cytokine staining (ICS) were concordant -- in two subjects the response was heightened by transient re-exposure to antigen with treatment interruption at 12 to 14 months.

References

Displaying record number 54275

HXB2 Location	Rev(67-75) DNA(8501..8527)	Rev Epitope Map
Author Location	Rev
Epitope	`SAEPVPLQL`	Epitope Alignment
Epitope Name	Cw8-SL9(Rev)
Species (MHC/HLA)	human(Cw8)
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 contribution of immune responses restricted to individual HLA class I molecules were studied.
The most frequently recognised 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 contribution of other restricting HLA dropped greatly.

References

Displaying record number 53594

HXB2 Location	Rev(67-75) DNA(8501..8527)	Rev Epitope Map
Author Location	Rev(67-75)
Epitope	`SAEPVPLQL`	Epitope Alignment
Species (MHC/HLA)	human
Immunogen	HIV-1 infection, in vitro stimulation or selection
Experimental methods	HLA binding
Keywords	assay or method development, characterizing CD8+ T cells

Notes

A new senstitive, non-readioactive assay, called fluorescent antigen-transfected target cell-CTL (FATT-CTL) assay, was developed to measure antigen-specific cytotoxicity ex vivo. Target cells were generated by nucleofection with DNA vectors encoding antigen-GFP fusion proteins. Flow cytometry was used to quantify viable and dead GFP-positive cells after coculture with different effector:target cell ratios. Cytotoxicity was detected at lower effector:target cell ratios than in standard Cr-release assay. Antigen-specific cytotoxicity was detected ex vivo in PBMCs from HIV-1 infected individuals.

References

vanBaalen2005 Carel A. van Baalen, David Kwa, Esther J. Verschuren, Mariska L. Reedijk, Adrianus C. M. Boon, Gerrie de Mutsert, Guus F. Rimmelzwaan, Albert D. M. E. Osterhaus, and Rob A. Gruters. Fluorescent Antigen-Transfected Target Cell Cytotoxic T Lymphocyte Assay for Ex Vivo Detection of Antigen-Specific Cell-Mediated Cytotoxicity. J. Infect. Dis., 192(7):1183-1190, 1 Oct 2005. PubMed ID: 16136460. Show all entries for this paper.

Displaying record number 52052

HXB2 Location	Rev(67-75) DNA(8501..8527)	Rev Epitope Map
Author Location
Epitope	`SAEPVPLQL`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Experimental methods
Keywords	epitope processing, escape

Notes

Epitopes that have been described in the literature and included in this database tend to cluster in conserved regions and be absent or rarely found in highly variable regions in Nef, Env, and p17.
While the uneven distribution of epitopes may be in part due to a limited cross-recognition of specific responses because of differences between peptides used to probe the immune response and autologous strains, regions with a paucity of defined epitopes also had higher frequencies of amino acids that tend to not be found in C-terminal positions of epitopes, and had lower cleavage prediction scores for epitope processing. This suggests that in the regions of the virus where variation is best tolerated traces of immune escape have left an imprint on the viral population. Epitopes also were concentrated in alpha-helix and turn regions in the proteins.
In the more conserved p24, and Pol proteins RT and Protease, epitopes are more evenly distributed.
What was learned from proteins where many epitopes have been defined (Gag, Pol, Env and Nef) was used to develop an algorithm to predict where epitopes would be localized in Rev, Tat, Vif, and Vpr. Predictions were made blinded, and then compared to the first 15 epitopes defined in these proteins; the epitopes were concentrated in the predicted regions.

References

Yusim2002 Karina Yusim, Can Kesmir, Brian Gaschen, Marylyn M. Addo, Marcus Altfeld, S\oren Brunak, Alexandre Chigaev, Vincent Detours, and Bette T. Korber. Clustering Patterns of Cytotoxic T-Lymphocyte Epitopes in Human Immunodeficiency Virus Type 1 (HIV-1) Proteins Reveal Imprints of Immune Evasion on HIV-1 Global Variation. J. Virol., 76(17):8757-8768, Sep 2002. PubMed ID: 12163596. Show all entries for this paper.

Displaying record number 52227

HXB2 Location	Rev(67-75) DNA(8501..8527)	Rev Epitope Map
Author Location	Rev(65-77 BH10, LAI)
Epitope	`SAEPVPLQL`	Epitope Alignment
Species (MHC/HLA)	human
Immunogen	computer prediction
Experimental methods	Other
Keywords	computational epitope prediction, T-cell crossreactivity to human proteins

Notes

This study employs an antigenic similarity matrix to compare HIV-1 antigenic determinants with human proteins.
This CTL epitope (the HIV-1 LAI fragment with high similarity to a human protein overlapping this epitope is GRSAEPVPLQLPP) has similarity with transforming growth factor beta binding protein I, fragment ARSAEPEVATAPP.
This CTL epitope (the HIV-1 LAI fragment with high similarity to a human protein overlapping this epitope is EPVPLQLPPL) also has similarity with the epidermal growth factor receptor substrate 15, fragment EPVPMSLPPA.

References

Maksiutov2002 A. Z. Maksiutov, A. G. Bachinskii, and S. I. Bazhan. [Searching for Local Similarities Between HIV-1 and Human Proteins. Application to Vaccines]. Mol Biol (Mosk), 36(3):447-459, May-Jun 2002. Article in Russian. PubMed ID: 12068630. Show all entries for this paper.