Search CTL/CD8+ T-Cell Epitope Database

Found 14 matching records:

Displaying record number 59556

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HXB2 Location	Pol(894-903) Integrase(179-188) DNA(4764..4793)	Pol Epitope Map
Author Location	Pol(894-903)
Epitope	`AVFIHNFKRK`	Epitope Alignment
Epitope Name	AK10
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, 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.
AVFIHNFKRK had a significantly positive association with HLA A*03; it was recognized by 17/61 A*03-positive subjects and 36/250 A*03-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 52528

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HXB2 Location	Pol(894-903) Integrase(179-188) DNA(4764..4793)	Pol Epitope Map
Author Location	Integrase(179-188)
Epitope	`AVFIHNFKRK`	Epitope Alignment
Species (MHC/HLA)	human(A*03:01)
Immunogen	HIV-1 infection
Experimental methods
Keywords	optimal epitope, A-list

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 59555

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HXB2 Location	Pol(894-903) Integrase(179-188) DNA(4764..4793)	Pol Epitope Map
Author Location	Pol(894-903)
Epitope	`AVFIHNFKRK`	Epitope Alignment
Epitope Name	AK10
Species (MHC/HLA)	human(A*11)
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.
AVFIHNFKRK had a significantly positive association with HLA A*11; it was recognized by 12/30 A*11-positive subjects and 53/311 A*11-negative subjects.

References

Displaying record number 55243

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HXB2 Location	Pol(894-903) Integrase(179-188) DNA(4764..4793)	Pol Epitope Map
Author Location	Integrase(179-188)
Epitope	`AVFIHNFKRK`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(A*11)
Immunogen	HIV-1 infection
Country	China
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	assay or method development, optimal epitope

Notes

HLA-A11-restricted CTL epitopes in 2 male Han Chinese subjects (one ART naive and one receiving HAART) were determined. A novel epitope was discovered and 5 other putative epitopes confirmed using 425 overlapping peptides spanning the entire HIV-1 clade B proteome. By employing intracellular cytokine staining, the authors developed a new method of mapping optimal epitopes and defining their HLA restriction efficiently. In spite of its being the most common HLA type in China, A*11-restricted epitopes were recognized less frequently than other epitopes, and A*11-restricted responses formed a mean of only 13% of the responses against HIV.
This putative epitope, AVFIHNFKRK, was detected and confirmed within overlapping peptides AVFIHNFKRKGGIGGYSA and RKGGIGGYSAGERIVDII.

References

Wang2007 Shaoyang Wang, Yongtao Sun, Song Zhai, Yan Zhuang, Shuguang Zhao, Whenzhen Kang, Xinhong Li, Dedong Huang, Xu G. Yu, Bruce D. Walker, and Marcus A. Altfeld. Identification of HLA-A11-Restricted HIV-1-Specific Cytotoxic T-Lymphocyte Epitopes in China. Curr. HIV Res., 5(1):119-128, Jan 2007. PubMed ID: 17266563. Show all entries for this paper.

Displaying record number 1727

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HXB2 Location	Pol(894-903) Integrase(179-188) DNA(4764..4793)	Pol Epitope Map
Author Location	Pol(894-903 93TH253 subtype CRF01)
Epitope	`AVFIHNFKRK`	Epitope Alignment
Epitope Name	P894-903
Subtype	CRF01_AE
Species (MHC/HLA)	human(A*11)
Immunogen	HIV-1 exposed seronegative
Experimental methods
Keywords	HIV exposed persistently seronegative (HEPS)

Notes

This was a study of HIV-1 exposed persistently seronegative (HEPS) female sex workers in Chiang Mai, northern Thailand.
HLA-A*11 is very common in this population, and was enriched among the HEPS sexworkers -- weak CTL responses were detected in 4/7 HEPS women, and CTL responses were found in 8/8 HIV+ controls, and 0/9 HIV- women that were not exposed.
This epitope was weakly reactive in the HEPS study subjects 265 who was HLA A*02/A*11 and 128 who was HLA A*11/A*33, and had been predicted to be a possible A11 epitope using Epimer in Bond2001

References

Bond2001 K. B. Bond, B. Sriwanthana, T. W. Hodge, A. S. De Groot, T. D. Mastro, N. L. Young, N. Promadej, J. D. Altman, K. Limpakarnjanarat, and J. M. McNicholl. An HLA-directed molecular and bioinformatics approach identifies new HLA-A11 HIV-1 subtype E cytotoxic T lymphocyte epitopes in HIV-1-infected Thais. AIDS Res. Hum. Retroviruses, 17(8):703-17, 20 May 2001. PubMed ID: 11429111. Show all entries for this paper.

Displaying record number 54258

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HXB2 Location	Pol(894-903) Integrase(179-188) DNA(4764..4793)	Pol Epitope Map
Author Location	Integrase
Epitope	`AVFIHNFKRK`	Epitope Alignment
Epitope Name	A11-AK10(Int)
Species (MHC/HLA)	human(A11)
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 52863

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HXB2 Location	Pol(894-903) Integrase(179-188) DNA(4764..4793)	Pol Epitope Map
Author Location	Pol
Epitope	`AVFIHNFKRK`	Epitope Alignment
Epitope Name	1264
Subtype	multiple
Species (MHC/HLA)	human(A11)
Immunogen	HIV-1 infection
Patient MHC/HLA	202001: A25, A68, B18, B27; 606001: A1, A68, B15, B40, Cw3; 523001: A11, A3, B14, B51, Cw8
Country	United States
Experimental methods	T-cell Elispot
Keywords	binding affinity, supertype, computational epitope prediction, immunodominance, HLA cross-presentation, novel epitope

Notes

Epitopes defined using sequence parsing and matching algorithm Conservatrix, and epitope prediction tool EpiMatrix, were shown to be conserved in a broad range of HIV-1 sequences derived from different parts of the world. 31 novel highly conserved HIV-1 epitopes were found, among which four were recognized as promiscuous epitopes and five as MHC supertypes.
Estimated binding probability for AVFIHNFKRK:53% Supertype epitope binding to A11, A03 and A68. Immunodominant.

References

DeGroot2003 Anne S. De Groot, Bill Jesdale, William Martin, Caitlin Saint Aubin, Hakima Sbai, Andrew Bosma, Judy Lieberman, Gail Skowron, Fadi Mansourati, and Kenneth H. Mayer. Mapping Cross-Clade HIV-1 Vaccine Epitopes Using a Bioinformatics Approach. Vaccine, 21(27-30):4486-4504, 1 Oct 2003. PubMed ID: 14505932. Show all entries for this paper.

Displaying record number 56427

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HXB2 Location	Pol(894-903) Integrase(179-188) DNA(4764..4793)	Pol Epitope Map
Author Location	Integrase
Epitope	`AVFIHNFKRK`	Epitope Alignment
Epitope Name	AK10(Integrase)
Subtype	B
Species (MHC/HLA)	human(A11, A3)
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 LKTAVQMAVFIHNFKRK contains the exact sequence of a previously described HLA-A3 optimal epitope, AVFIHNFKRK, none of the 3 HLA-A3 carriers responded to it. 4 of the 28 HLA-A11 carriers responded to the AVFIHNFKRK-containing peptide AVFIHNFKRKGGIGGYSA with average magnitude of CTL response of 150 SFC/million PBMC (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 1192

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HXB2 Location	Pol(894-903) Integrase(179-188) DNA(4764..4793)	Pol Epitope Map
Author Location	Integrase(179-188 LAI)
Epitope	`AVFIHNFKRK`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(A*11:01)
Immunogen
Experimental methods
Keywords	optimal epitope, A-list

Notes

C. Brander notes this is an A*1101 epitope.

References

Fukada1999 K. Fukada, Y. Chujoh, H. Tomiyama, K. Miwa, Y. Kaneko, S. Oka, and M. Takiguchi. HLA-A*1101-Restricted Cytotoxic T Lymphocyte Recognition of HIV-1 Pol Protein. AIDS, 13:1413-1414, 1999. PubMed ID: 10449296. Show all entries for this paper.

Displaying record number 52101

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HXB2 Location	Pol(894-903) Integrase(179-188) DNA(4764..4793)	Pol Epitope Map
Author Location	Pol(894-903)
Epitope	`AVFIHNFKRK`	Epitope Alignment
Subtype	B, CRF01_AE
Species (MHC/HLA)	human(A*11:01)
Immunogen	HIV-1 infection
Experimental methods
Keywords	subtype comparisons

Notes

Counterparts for eight known clade B HLA A*1101 epitopes were generated for clade E (CRF01). Three epitopes, identical among clade A-E, were cross-reactive and recognized by clade E infected individuals. The clade E and B analogs to three more HLA A*1101 epitopes was recognized in a clade specific manner. Two other HLA A*1101 clade B defined epitopes were found not to have stimulated a response in clade E infected individuals.
AVFIHNFKRK is commonly found in viruses representing subtypes A-E. It was strongly recognized by CTL from 4/7 E clade infected Thai subjects.

References

Fukada2002 Katsuhiko Fukada, Hiroko Tomiyama, Chantapong Wasi, Tomoko Matsuda, Shigeru Kusagawa, Hironori Sato, Shinichi Oka, Yutaka Takebe, and Masafumi Takiguchi. Cytotoxic T-cell Recognition of HIV-1 Cross-Clade and Clade-Specific Epitopes in HIV-1-Infected Thai and Japanese Patients. AIDS, 16(5):701-711, 29 Mar 2002. PubMed ID: 11964526. Show all entries for this paper.

Displaying record number 59554

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HXB2 Location	Pol(894-903) Integrase(179-188) DNA(4764..4793)	Pol Epitope Map
Author Location	Pol(894-903)
Epitope	`AVFIHNFKRK`	Epitope Alignment
Epitope Name	AK10
Species (MHC/HLA)	human(A*24)
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.
AVFIHNFKRK had a significantly positive association with HLA A*24; it was recognized by 10/31 A*24-positive subjects and 26/219 A*24-negative subjects.

References

Displaying record number 52895

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HXB2 Location	Pol(894-903) Integrase(179-188) DNA(4764..4793)	Pol Epitope Map
Author Location	Pol
Epitope	`AVFIHNFKRK`	Epitope Alignment
Epitope Name	1264
Subtype	multiple
Species (MHC/HLA)	human(A3)
Immunogen	HIV-1 infection
Patient MHC/HLA	A23, A3, B49, B57; A24, A3, B27, B57, C*18
Country	United States
Experimental methods	T-cell Elispot
Keywords	binding affinity, computational epitope prediction, novel epitope

Notes

Epitopes defined using sequence parsing and matching algorithm Conservatrix, and epitope prediction tool EpiMatrix, were shown to be conserved in a broad range of HIV-1 sequences derived from different parts of the world. 31 novel highly conserved HIV-1 epitopes were found, among which four were recognized as promiscuous epitopes and five as MHC supertypes.
Estimated binding probability for AVFIHNFKRK: 52%

References

Displaying record number 52828

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HXB2 Location	Pol(894-903) Integrase(179-188) DNA(4764..4793)	Pol Epitope Map
Author Location	Integrase(179-188)
Epitope	`AVFIHNFKRK`	Epitope Alignment
		Show epitope variants
Epitope Name	A3-AK10 Pol
Subtype	B
Species (MHC/HLA)	human(A3)
Immunogen	HIV-1 infection
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	supervised treatment interruptions (STI), escape, early treatment, superinfection

Notes

An HIV+ individual given acute ARV and undergoing STI developed a strong CTL immune response, but despite this was shown to be superinfected with second B clade virus. Some epitope variants of the second infecting virus were resistant to the initial CTL response.
The second infecting strain had the variant avfVhnfkrk. The CTL response to the second variant was zero at all timepoints. The CTL response to the first variant was low and declined over time.

References

Altfeld2002a Marcus Altfeld, Todd M. Allen, Xu G. Yu, Mary N. Johnston, Deepak Agrawal, Bette T. Korber, David C. Montefiori, David H. O'Connor, Ben T. Davis, Paul K. Lee, Erica L. Maier, Jason Harlow, Philip J. R. Goulder, Christian Brander, Eric S. Rosenberg, and Bruce D. Walker. HIV-1 Superinfection Despite Broad CD8+ T-Cell Responses Containing Replication of the Primary Virus. Nature, 420(6914):434-439, 28 Nov 2002. PubMed ID: 12459786. Show all entries for this paper.

Displaying record number 52148

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HXB2 Location	Pol(894-903) Integrase(179-188) DNA(4764..4793)	Pol Epitope Map
Author Location	Integrase(894-904)
Epitope	`AVFIHNFKRK`	Epitope Alignment
Epitope Name	A3-AK10
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.