Search CTL/CD8+ T-Cell Epitope Database

Found 24 matching records:

Displaying record number 53102

HXB2 Location	gp160(770-780) gp41(259-269) DNA(8532..8564)	gp160 Epitope Map
Author Location	Env(786-778)
Epitope	`RLRDLLLIVTR`	Epitope Alignment
Species (MHC/HLA)	human(A*03)
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 of 14 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 57293

HXB2 Location	gp160(770-780) gp41(259-269) DNA(8532..8564)	gp160 Epitope Map
Author Location
Epitope	`RLRDLLLIVTR`	Epitope Alignment
Epitope Name	RR11
Subtype	B
Species (MHC/HLA)	human(A*03)
Immunogen	HIV-1 infection
Country	Barbados, Haiti, Jamaica
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	mother-to-infant transmission, elite controllers

Notes

To dissect whether the protective effect of HLA-B*57 in HIV-1 infection is due to CTL that recognize HLA-B*57-restricted epitopes or by the presence of viral-fitness attenuating mutations in such B*57 epitopes, 13 mother-infant pairs were studied. The B57 advantage is primarily through the maintenance of a fitness-attenuating mutation in p24-Gag, T242N in epitope TW10 (TSTLQEQIGW).
Regardless of parental inheritance, HLA-B57 controls VL even in infancy and even when escape mutations from B*57 positive mothers are transmitted. Mutations in p24-Gag are predominant in mismatched-HLA subject pairs and arise after vertical transmission, impacting viral fitness.
Non-B57-epitope RR11-gp160, RLRDLLLIVTR restricted by A*03, was recognized by an infant with maternally-inherited B57.

References

Schneidewind2009 Arne Schneidewind, Yanhua Tang, Mark A. Brockman, Elizabeth G. Ryland, Jacqueline Dunkley-Thompson, Julianne C. Steel-Duncan, M. Anne St. John, Joseph A. Conrad, Spyros A. Kalams, Francine Noel, Todd M. Allen, Celia D. Christie, and Margaret E. Feeney. Maternal Transmission of Human Immunodeficiency Virus Escape Mutations Subverts HLA-B57 Immunodominance but Facilitates Viral Control in the Haploidentical Infant. J. Virol., 83(17):8616-8627, Sep 2009. PubMed ID: 19515764. Show all entries for this paper.

Displaying record number 1779

HXB2 Location	gp160(770-780) gp41(259-269) DNA(8532..8564)	gp160 Epitope Map
Author Location	gp41(770-780)
Epitope	`RLRDLLLIVTR`	Epitope Alignment
Species (MHC/HLA)	human(A*03)
Immunogen	HIV-1 infection
Experimental methods
Keywords	rate of progression, acute/early infection

Notes

The CTL response to optimally defined CTL epitopes restricted by HLA class I A and B alleles in individuals who coexpressed HLA A*02, A*03, and B*07 was studied in eight HIV-1-infected subjects, two with acute infection, five with chronic, and one long-term non-progressor (LTNP)
2 to 17 epitopes were recognized in a given individual, A*02-restricted CTL response tended to be narrow and never dominated the response, and 25/27 epitopes were targeted by at least one person.
All patients recognized at least 1 A*03 epitope, up to 8 A*03 epitopes, but none was clearly dominant.

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 1780

HXB2 Location	gp160(770-780) gp41(259-269) DNA(8532..8564)	gp160 Epitope Map
Author Location	Nef(73-82)
Epitope	`RLRDLLLIVTR`	Epitope Alignment
Species (MHC/HLA)	human(A*03)
Immunogen	HIV-1 infection
Experimental methods
Keywords	rate of progression, acute/early infection

Notes

The CTL response to optimally defined CTL epitopes restricted by HLA class I A and B alleles in individuals who coexpressed HLA A*02, A*03, and B*07 was studied in eight HIV-1-infected subjects, two with acute infection, five with chronic, and one long-term non-progressor (LTNP)
2 to 17 epitopes were recognized in a given individual, A*02-restricted CTL response tended to be narrow and never dominated the response, and 25/27 epitopes were targeted by at least one person.
All patients recognized at least 1 A*03 epitope, up to 8 A*03 epitopes, but none was clearly dominant.
In two of the subjects, RLRDLLLIVTR was the dominant epitope.

References

Displaying record number 60127

HXB2 Location	gp160(770-780) gp41(259-269) DNA(8532..8564)	gp160 Epitope Map
Author Location	Env(770-780)
Epitope	`RLRDLLLIVTR`	Epitope Alignment
Epitope Name	RR11
Species (MHC/HLA)	human(A*03)
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.
RLRDLLLIVTR had a significantly positive association with HLA A*03; it was recognized by 11/62 A*03-positive subjects and 18/241 A*03-negative subjects.
RLRDLLLIVTR was significantly protective, associated with viral control when restricted by HLA-A*03 in a cohort of 245 controllers and 96 progressors.

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 58980

HXB2 Location	gp160(770-780) gp41(259-269) DNA(8532..8564)	gp160 Epitope Map
Author Location	gp41(259-269)
Epitope	`RLRDLLLIVTR`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(A*0301)
Immunogen	HIV-1 infection
Country	Australia, Canada, Spain, Switzerland
Experimental methods	Other
Keywords	mutation acquisition

Notes

Computational genome-wide scans were run to find associations between (subjects' ) host genome DNA polymorphisms, and infecting HIV-1 genome sequence variation from 1071 subjects, as well as their viral load (VL). Such genome-to-genome approaches also reveal sites of single nucleotide polymorphisms (SNPs) linked to variant HIV-1 amino acids that either limit viral efficiency or that are easily tolerated by it.
48 amino acid residues of HIV-1 were linked to human SNPs, and the variants were not antiretroviral drug resistance mutations. 50% of these viral amino acids were located within previously defined optimal epitopes, such as RLRDLLLIVTR, whose variation at position 267 is associated with SNP rs9278477.

References

Bartha2013 István Bartha, Jonathan M. Carlson, Chanson J. Brumme, Paul J. McLaren, Zabrina L. Brumme, Mina John, David W. Haas, Javier Martinez-Picado, Judith Dalmau, Cecilio López-Galíndez, Concepción Casado, Andri Rauch, Huldrych F. Günthard, Enos Bernasconi, Pietro Vernazza, Thomas Klimkait, Sabine Yerly, Stephen J. O'Brien, Jennifer Listgarten, Nico Pfeifer, Christoph Lippert, Nicolo Fusi, Zoltán Kutalik, Todd M. Allen, Viktor Müller, P. Richard Harrigan, David Heckerman, Amalio Telenti, and Jacques Fellay. A Genome-to-Genome Analysis of Associations between Human Genetic Variation, HIV-1 Sequence Diversity, and Viral Control. eLife, 2:e01123, 2013. PubMed ID: 24171102. Show all entries for this paper.

Displaying record number 1121

HXB2 Location	gp160(770-780) gp41(259-269) DNA(8532..8564)	gp160 Epitope Map
Author Location	gp41(775-785 LAI)
Epitope	`RLRDLLLIVTR`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(A*0301)
Immunogen	HIV-1 infection
Experimental methods
Keywords	optimal epitope

Notes

C. Brander notes this is an A*0301 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 863

HXB2 Location	gp160(770-780) gp41(259-269) DNA(8532..8564)	gp160 Epitope Map
Author Location	gp41(768-778 NL43)
Epitope	`RLRDLLLIVTR`	Epitope Alignment
Species (MHC/HLA)	human(A*0301)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

CD8+ T cell clone.

References

Takahashi1991 K. Takahashi, L.-C. Dai, T. R. Fuerst, W. E. Biddison, P. L. Earl, B. Moss, and F. A. Ennis. Specific Lysis of Human Immunodeficiency Virus Type 1-Infected Cells by a HLA-A3.1-Restricted CD8+ Cytotoxic T-Lymphocyte Clone That Recognizes a Conserved Peptide Sequence within the gp41 Subunit of the Envelope Protein. Proc. Natl. Acad. Sci. U.S.A., 88:10277-10281, 1991. gp41 epitope: RLRDLLLIVTR, HLA A3.1 (NL43). Synthetic peptides of RF and CDC4 were recognized by CTL clone despite non-conservative Thr to (Val or Ala) change, but an MN peptide with four natural substitutions was not recognized. PubMed ID: 1719555. Show all entries for this paper.

Displaying record number 1653

HXB2 Location	gp160(770-780) gp41(259-269) DNA(8532..8564)	gp160 Epitope Map
Author Location	gp41(775-785)
Epitope	`RLRDLLLIVTR`	Epitope Alignment
Species (MHC/HLA)	human(A3)
Immunogen	HIV-1 exposed seronegative, HIV-1 infection
Experimental methods
Keywords	HIV exposed persistently seronegative (HEPS)

Notes

ELISPOT was used to study CTL responses to a panel of 54 predefined HIV-1 epitopes in 91 HIV-1-exposed, persistently seronegative (HEPS) and 87 HIV-1-infected female Nairobi sex workers.

References

Kaul2001a R. Kaul, T. Dong, F. A. Plummer, J. Kimani, T. Rostron, P. Kiama, E. Njagi, E. Irungu, B. Farah, J. Oyugi, R. Chakraborty, K. S. MacDonald, J. J. Bwayo, A. McMichael, and S. L. Rowland-Jones. CD8(+) lymphocytes respond to different HIV epitopes in seronegative and infected subjects. J. Clin. Invest., 107(10):1303-10, May 2001. URL: http://www.jci.org/cgi/content/full/107/10/1303. PubMed ID: 11375420. Show all entries for this paper.

Displaying record number 864

HXB2 Location	gp160(770-780) gp41(259-269) DNA(8532..8564)	gp160 Epitope Map
Author Location	gp41(768-778 NL43)
Epitope	`RLRDLLLIVTR`	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human(A3)
Immunogen	HIV-1 infection
Experimental methods
Keywords	subtype comparisons

Notes

The consensus peptide of clade B is RLRDLLLIVTR.
The consensus peptide of clades A, C and E is RLRDFILIVTR and it is less reactive.
The consensus peptide of clade D is SLRDLLLIVTR and it is less reactive.

References

Cao1997a H. Cao, P. Kanki, J. L. Sankale, A. Dieng-Sarr, Gail P. Mazzara, S. Kalams, B. Korber, S. M'Boup, and B. D. Walker. CTL Cross-Reactivity among Different HIV-1 Clades: Implications for Vaccine Development. J. Virol., 71:8615-8623, 1997. PubMed ID: 9343219. Show all entries for this paper.

Displaying record number 52149

HXB2 Location	gp160(770-780) gp41(259-269) DNA(8532..8564)	gp160 Epitope Map
Author Location	gp41(769-780)
Epitope	`RLRDLLLIVTR`	Epitope Alignment
Epitope Name	A3-RR11
Subtype	B
Species (MHC/HLA)	human(A3)
Immunogen	HIV-1 infection
Patient MHC/HLA	A3, B7, Cw7
Experimental methods
Keywords	dynamics, supervised treatment interruptions (STI), acute/early infection

Notes

CTL responses in 18 acutely HIV-infected HLA-A3 (n=7) or -B7 (n=4) or both -A3 and B7 (n=7) positive individuals were studied.
One individual, AC-06, was homozygous at all three class I alleles (A3, B7, Cw7), was treated during acute infection and had supervised treatment interruptions (STI). He had only two detectable CTL responses during acute infection, but after STI this broadened to 27 distinct epitopes including 15 restricted by HLA-A3, 11 by HLA-B7, and 1 by HLA-Cw7.
0/14 HLA-A3 positive individuals had detectable A3-restricted responses to this epitope during acute infection, but only 5/15 of HLA-A3 epitopes tested were targeted during acute infection. 1/7 individuals began to have detectable responses to this epitope after STI.

References

Yu2002b Xu G. Yu, Marylyn M. Addo, Eric S. Rosenberg, William R. Rodriguez, Paul K. Lee, Cecily A. Fitzpatrick, Mary N. Johnston, Daryld. Strick, Philip J. R. Goulder, Bruce D. Walker, and Marcus Altfeld. Consistent Patterns in the Development and Immunodominance of Human Immunodeficiency Virus Type 1 (HIV-1)-Specific CD8+ T-Cell Responses Following Acute HIV-1 Infection. J. Virol., 76(17):8690-8701, Sep 2002. PubMed ID: 12163589. Show all entries for this paper.

Displaying record number 52990

HXB2 Location	gp160(770-780) gp41(259-269) DNA(8532..8564)	gp160 Epitope Map
Author Location	Env(770-780)
Epitope	`RLRDLLLIVTR`	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human(A3)
Immunogen	HIV-1 infection
Patient MHC/HLA	A3, A32, B15, B51, Cw03, Cw6, DQ7, DR4, DR8
Country	Netherlands
Experimental methods	CD8 T-cell Elispot - IFNγ, Flow cytometric T-cell cytokine assay
Keywords	rate of progression, 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 7 epitopes from this individual that varied over time, although the internal mutations did not become fixed. rlrdlllVItr variant residues were found. The V mutation arose at late time points, the I mutation arose at intermediate time points.

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 55018

HXB2 Location	gp160(770-780) gp41(259-269) DNA(8532..8564)	gp160 Epitope Map
Author Location
Epitope	`RLRDLLLIVTR`	Epitope Alignment
Species (MHC/HLA)	human(A3, A31)
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 RLRDLLLIVTR when restricted by HLA-A03 elicited a magnitude of response of 450 SFC with a functional avidity of 0.5nM and binding affinity of 9.6nM. When restricted by HLA-A31, it elicited a magnitude of response of 450 SFC with a functional avidity of 0.05nM and binding affinity of 3.8nM.

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 56428

HXB2 Location	gp160(770-780) gp41(259-269) DNA(8532..8564)	gp160 Epitope Map
Author Location	gp160
Epitope	`RLRDLLLIVTR`	Epitope Alignment
Epitope Name	RR11(gp160)
Subtype	B
Species (MHC/HLA)	human(A3, A31)
Immunogen	HIV-1 infection
Country	China
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords

Notes

49 ART-naive chronically HIV-1 infected Chinese subjects' CTLs were tested with 413 OLPs in IFN-gamma 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.
HLA-A*03-restricted epitope RLRDLLLIVTR elicited no immune response in Chinese HIV-1 positive subjects as part of peptide HRLRDLLLIVTRIVELL.
Although the tested peptide sequence HRLRDLLLIVTRIVELL contains the exact sequence of a previously described HLA-A3 epitope, RLRDLLLIVTR, none of the 3 HLA-A3 carriers responded to it (author communication and Fig.1). When tested in Chinese HLA-A31 positive subjects, this peptide did elicit an immune response.

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 55192

HXB2 Location	gp160(770-780) gp41(259-269) DNA(8532..8564)	gp160 Epitope Map
Author Location
Epitope	`RLRDLLLIVTR`	Epitope Alignment
Species (MHC/HLA)	human(A3, A31)
Immunogen	HIV-1 infection
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	supertype, HLA cross-presentation

Notes

100 HIV-infected subjects were tested for response to optimally-defined CTL epitopes regardless of the subject's HLA type. Half of all detected responses were seen in the absence of the originally reported restricting HLA class I allele, and only 3% of epitopes were recognized exclusively in the presence of their original allele. Statistical and experimental methods were used to define additional HLA alleles associated with the epitopes.
Based on a prediction of the minimum number of HLA alleles needed to cover the HLA representation in all responders to this epitope, a minimum set of 6 alleles was found: 2 alleles previously known to be associated (A03, A31) and 4 additional alleles (A02, A74, B44, Cw04).

References

Frahm2007b Nicole Frahm, Karina Yusim, Todd J. Suscovich, Sharon Adams, John Sidney, Peter Hraber, Hannah S. Hewitt, Caitlyn H. Linde, Daniel G. Kavanagh, Tonia Woodberry, Leah M. Henry, Kellie Faircloth, Jennifer Listgarten, Carl Kadie, Nebojsa Jojic, Kaori Sango, Nancy V. Brown, Eunice Pae, M. Tauheed Zaman, Florian Bihl, Ashok Khatri, Mina John, Simon Mallal, Francesco M. Marincola, Bruce D . Walker, Alessandro Sette, David Heckerman, Bette T. Korber, and Christian Brander. Extensive HLA Class I Allele Promiscuity among Viral CTL Epitopes. Eur. J. Immunol., 37(9):2419-2433, Sep 2007. PubMed ID: 17705138. Show all entries for this paper.

Displaying record number 60125

HXB2 Location	gp160(770-780) gp41(259-269) DNA(8532..8564)	gp160 Epitope Map
Author Location	Env(770-780)
Epitope	`RLRDLLLIVTR`	Epitope Alignment
Epitope Name	RR11
Species (MHC/HLA)	human(A*31)
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.
RLRDLLLIVTR had a significantly positive association with HLA A*31; it was recognized by 12/22 A*31-positive subjects and 35/319 A*31-negative subjects.
RLRDLLLIVTR was significantly protective, associated with viral control when restricted by HLA-A*31 in a cohort of 245 controllers and 96 progressors.

References

Displaying record number 52919

HXB2 Location	gp160(770-780) gp41(259-269) DNA(8532..8564)	gp160 Epitope Map
Author Location	Env
Epitope	`RLRDLLLIVTR`	Epitope Alignment
Epitope Name	RR11
Subtype	C
Species (MHC/HLA)	human(A31)
Immunogen	HIV-1 infection
Experimental methods	CD8 T-cell Elispot - IFNγ, Chromium-release assay
Keywords	epitope processing, escape

Notes

This study characterizes the N-terminal flanking position of the epitope ISPRTLNAW, and mutations in this position are thought to impact processing. The A31 epitope RLRDLLLIVTR was used as a negative control in this study.

References

Draenert2004a Rika Draenert, Sylvie Le Gall, Katja J. Pfafferott, Alasdair J. Leslie, Polan Chetty, Christian Brander, Edward C. Holmes, Shih-Chung Chang, Margaret E. Feeney, Marylyn M. Addo, Lidia Ruiz, Danni Ramduth, Prakash Jeena, Marcus Altfeld, Stephanie Thomas, Yanhua Tang, Cori L. Verrill, Catherine Dixon, Julia G. Prado, Photini Kiepiela, Javier Martinez-Picado, Bruce D. Walker, and Philip J. R. Goulder. Immune Selection for Altered Antigen Processing Leads to Cytotoxic T Lymphocyte Escape in Chronic HIV-1 Infection. J. Exp. Med., 199(7):905-915, 5 Apr 2004. PubMed ID: 15067030. Show all entries for this paper.

Displaying record number 866

HXB2 Location	gp160(770-780) gp41(259-269) DNA(8532..8564)	gp160 Epitope Map
Author Location	gp41(770-780)
Epitope	`RLRDLLLIVTR`	Epitope Alignment
Species (MHC/HLA)	human(A31)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

This epitope is processed by a TAP1/2 dependent mechanism.

References

Ferris1999 R. L. Ferris, C. Hall, N. V. Sipsas, J. T. Safrit, A. Trocha, R. A. Koup, R. P. Johnson, and R. F. Siliciano. Processing of HIV-1 Envelope Glycoprotein for Class I-Restricted Recognition: Dependence on TAP1/2 and Mechanisms for Cytosolic Localization. J. Immunol., 162:1324-1332, 1999. PubMed ID: 9973386. Show all entries for this paper.

Hammond1995 S. A. Hammond, R. P. Johnson, S. A. Kalams, B. D. Walker, M. Takiguchi, J. T. Safrit, R. A. Koup, and R. F. Siliciano. An Epitope-Selective Transporter Associated with Antigen Presentation TAP-1/2-Independent Pathway and a More General TAP-1/2-Dependent Antigen-Processing Pathway Allow Recognition of the HIV-1 Envelope Glycoprotein by CD8+ CTL. J. Immunol., 154:6140-6156, 1995. Two peptide-processing pathways are utilized for MHC class I presentation of HIV-1 Env epitopes. The previously characterized TAP-1 and TAP-2 dependent pathway can generate all Env epitopes and uses Env protein mislocalized in the cytosol to produce peptides. The second, novel pathway uses a TAP-1/2 independent pathway, and allows a subset of MHC-restricted epitopes to be processed in the endoplasmic reticulum or a Golgi compartment. PubMed ID: 7538543. Show all entries for this paper.

Displaying record number 52632

HXB2 Location	gp160(770-780) gp41(259-269) DNA(8532..8564)	gp160 Epitope Map
Author Location	gp41(770-780)
Epitope	`RLRDLLLIVTR`	Epitope Alignment
Species (MHC/HLA)	human(A31)
Immunogen	HIV-1 infection
Patient MHC/HLA	A*0201, A31, B44, B60, Cw16, Cw3
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 1199

HXB2 Location	gp160(770-780) gp41(259-269) DNA(8532..8564)	gp160 Epitope Map
Author Location	gp160(770-780 LAI)
Epitope	`RLRDLLLIVTR`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(A*3101)
Immunogen
Experimental methods
Keywords	optimal epitope

Notes

C. Brander notes this is an A*3002 epitope.

References

Displaying record number 865

HXB2 Location	gp160(770-780) gp41(259-269) DNA(8532..8564)	gp160 Epitope Map
Author Location	gp41(770-780 BH10)
Epitope	`RLRDLLLIVTR`	Epitope Alignment
Species (MHC/HLA)	human(A*3101)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

Recognized by CTL derived from acute seroconverter.
C. Brander notes that this is an A*3101 epitope in the 1999 database.

References

Safrit1994a J. T. Safrit, C. A. Andrews, T. Zhu, D. D. Ho, and R. A. Koup. Characterization of Human Immunodeficiency Virus Type 1-Specific Cytotoxic T Lymphocyte Clones Isolated during Acute Seroconversion: Recognition of Autologous Virus Sequences within a Conserved Immunodominant Epitope. J. Exp. Med., 179:463-472, 1994. HIV-1 specific CTL clones were isolated from two individuals at acute seroconversion. In one patient, two HLA A31-restricted clones recognized the same fragment of gp41, peptide RLRDLLLIVTR, but one was sensitive to a Thr to Val substitution, while the other was not. A CTL HLA A32-restricted clone from the other patient recognized the gp41 peptide VLSIVNRVRQGYSPLSFQTH. Autologous viral sequences from seroconversion were recognized by the CTL clones, but not the HIV-1 strain MN. PubMed ID: 8294860. Show all entries for this paper.

Safrit1994b J. T. Safrit, A. Y. Lee, C. A. Andrews, and R. A. Koup. A Region of the Third Variable Loop of HIV-1 gp120 Is Recognized by HLA-B7-Restricted CTLs from Two Acute Seroconversion Patients. J. Immunol., 153:3822-3830, 1994. HIV-1 envelope-specific CTL clones were isolated from the peripheral blood of two patients within weeks of seroconversion. These clones were CD8+ and restricted by the HLA-B7 molecule. The minimum epitope was defined, RPNNNTRKSI, with anchor residues at the proline and isoleucine; the anchor residues are relatively well conserved. A Serine to Arginine change at position 9 of the epitope abrogated clone recognition in one of the patients. This amino acid change is one factor that has been associated with a change from a nonsyncytium-inducing to a syncytium-inducing phenotype of HIV-1.. PubMed ID: 7523505. Show all entries for this paper.

Displaying record number 60128

HXB2 Location	gp160(770-780) gp41(259-269) DNA(8532..8564)	gp160 Epitope Map
Author Location	Env(770-780)
Epitope	`RLRDLLLIVTR`	Epitope Alignment
Epitope Name	RR11
Species (MHC/HLA)	human(A*34)
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.
RLRDLLLIVTR had a significantly positive association with HLA A*34; it was recognized by 3/11 A*34-positive subjects and 15/230 A*34-negative subjects.
RLRDLLLIVTR was significantly protective, associated with viral control when restricted by HLA-A*34 in a cohort of 245 controllers and 96 progressors.

References

Displaying record number 60126

HXB2 Location	gp160(770-780) gp41(259-269) DNA(8532..8564)	gp160 Epitope Map
Author Location	Env(770-780)
Epitope	`RLRDLLLIVTR`	Epitope Alignment
Epitope Name	RR11
Species (MHC/HLA)	human(A*74)
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.
RLRDLLLIVTR had a significantly positive association with HLA A*74; it was recognized by 6/16 A*74-positive subjects and 29/303 A*74-negative subjects.
RLRDLLLIVTR was significantly protective, associated with viral control when restricted by HLA-A*74 in a cohort of 245 controllers and 96 progressors.

References

Displaying record number 1122

HXB2 Location	gp160(770-780) gp41(259-269) DNA(8532..8564)	gp160 Epitope Map
Author Location	gp41(775-785)
Epitope	`RLRDLLLIVTR`	Epitope Alignment
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Experimental methods
Keywords	immunodominance

Notes

Only 4/11 HLA-A2+ HIV+ individuals had CTL that reacted to SLYNTVATL, calling into question whether it is immunodominant.
95 optimally-defined peptides from this database were used to screen for INFγ responses to other epitopes.
1/11 of the HLA A2+ was HLA A*0201, A31, B8, B51 and responded to this epitope that has been previously noted to be HLA A3.1, as well as seven others.

References

Betts2000 M. R. Betts, J. P. Casazza, B. A. Patterson, S. Waldrop, W. Trigona, T.-M Fu, F. Kern, L. J. Picker, and R. A. Koup. Putative Immunodominant Human Imunodeficiency Virus-Specific CD8+ T Cell Responses Cannot Be Predicted by Major Histocompatibility Complex Class I Haplotype. J. Virol., 74:9144-9151, 2000. PubMed ID: 10982361. Show all entries for this paper.