Search CTL/CD8+ T-Cell Epitope Database

Found 20 matching records:

Displaying record number 52350

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HXB2 Location	Pol(448-456) RT(293-301) DNA(3426..3452)	Pol Epitope Map
Author Location	Pol(489-456)
Epitope	`IPLTEEAEL`	Epitope Alignment
Species (MHC/HLA)	human(B07:02, B35:01, B51:01, B53:01)
Immunogen	HIV-1 infection
Patient MHC/HLA	A24, A26, B35, B51, Cw3
Experimental methods
Keywords	supertype, HLA cross-presentation, TCR usage

Notes

The IPLTEEAEL epitope was known to be presented by both HLA-B*3501 and -B*5101 to a dual specific CTL clone. A single TCR complex bearing Valpha12.1 and Vβ5.6 was shown recognize the epitope in either HLA-B*3501 and -B*5101. Furthermore, this TCR also recognized the peptide presented by B*5301 and B*0702 in cytolytic CTL assays, demonstrating that this single TCR complex recognizes the same peptide presented by a range of HLA class I molecules.

References

Ueno2002 Takamasa Ueno, Hiroko Tomiyama, and Masafumi Takiguchi. Single T Cell Receptor-Mediated Recognition of an Identical HIV-Derived Peptide Presented by Multiple HLA Class I Molecules. J. Immunol., 169(9):4961-4969, 1 Nov 2002. PubMed ID: 12391209. Show all entries for this paper.

Displaying record number 53446

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HXB2 Location	Pol(448-456) RT(293-301) DNA(3426..3452)	Pol Epitope Map
Author Location	Pol( HXB2, LAI)
Epitope	`IPLTEEAEL`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(B15:01, B35:01)
Immunogen	HIV-1 infection
Patient MHC/HLA	A24:02, A26:01, B35:01, B51:01
Country	Japan
Experimental methods	Chromium-release assay, Cytokine production, Tetramer binding
Keywords	binding affinity, HLA cross-presentation, immunotherapy, TCR usage, characterizing CD8+ T cells

Notes

This paper described the transduction of HIV specific clone TCR genes Valpha12.1/Vbeta5.6 into primary CD8+ T cells. Epitope fine specificity and appropriate effector functions were observed in the transduced cells, although functional avidity could change due to different densities of TCR on the surface of the transduced cells. No allogenic responses were detected. This methodology could have immunotherapeutic applications.

References

Ueno2004b Takamasa Ueno, Mamoru Fujiwara, Hiroko Tomiyama, Masafumi Onodera, and Masafumi Takiguchi. Reconstitution of Anti-HIV Effector Functions of Primary Human CD8 T Lymphocytes by Transfer of HIV-Specific alpha-beta TCR Genes. Eur. J. Immunol., 34(12):3379-3388, Dec 2004. PubMed ID: 15517606. Show all entries for this paper.

Displaying record number 57585

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HXB2 Location	Pol(448-456) RT(293-301) DNA(3426..3452)	Pol Epitope Map
Author Location	RT(293-301)
Epitope	`IPLTEEAEL`	Epitope Alignment
Epitope Name	IL9
Subtype	B
Species (MHC/HLA)	(B*35)
Immunogen	HIV-1 infection
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	acute/early infection

Notes

Responses to specific B57/58, B27, and B35-restricted epitopes were tested in a cohort of 45 subjects during primary infection. The presence of certain B57/58, B27, and B35-restricted T-cell responses during primary infection better defined disease progression than the HLA genotype alone, suggesting that it is the HIV-specific CD8+ T-cells and not the presence of a particular HLA allele, that determine disease progression.
6/12 B35-positive subjects responded to IPLTEEAEL, and 37% of the patients' total response magnitude was derived from this specific response.
This epitope was 9% conserved among M-group sequences and 34% conserved among B-subtype sequences.
Prevalent responses to variable B35-restricted DL9 (DPNPQEVVL) and IL9 (IPLTEEAEL) epitopes were associated with more rapid disease progression, suggesting that these CTL responses to variable regions were ineffective at limiting disease progression.

References

Dinges2010 Warren L. Dinges, Julia Richardt, David Friedrich, Emilie Jalbert, Yi Liu, Claire E. Stevens, Janine Maenza, Ann C. Collier, Daniel E. Geraghty, Jeremy Smith, Zoe Moodie, James I. Mullins, M. Juliana McElrath, and Helen Horton. Virus-Specific CD8+ T-Cell Responses Better Define HIV Disease Progression than HLA Genotype. J. Virol., 84(9):4461-4468, May 2010. PubMed ID: 20147397. Show all entries for this paper.

Displaying record number 57320

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HXB2 Location	Pol(448-456) RT(293-301) DNA(3426..3452)	Pol Epitope Map
Author Location	Pol
Epitope	`IPLTEEAEL`	Epitope Alignment
Subtype	A, CRF02_AG, CRF06_cpx, CRF09_cpx
Species (MHC/HLA)	human(B*35)
Immunogen	HIV-1 infection
Country	Burkina Faso
Experimental methods	Other
Keywords	drug resistance

Notes

Drug-associated mutations were analyzed in HIV-1 pol gene from drug-naive patients in Burkina Faso. 12.5% of all mutations were drug resistance-associated, suggesting either transmission from an ART-treated tramsitter or prior undocumented use of ART by the subject. Subtype specific polymorphisms were also seen, some of them within CTL epitopes.
B-consensus HLA-B*35-restricted epitope IPLTEEAEL was found in subtypes CRF02.AG, A and CRF09.cpx sequences as vtLTEEAEL, but variant vPLTaEAEL was seen in subtype CFR06.cpx. 12% Burkinabe carry HLA-B*35.

References

Tebit2009 Denis M. Tebit, Lassana Sangaré, Fabrice Tiba, Yameogo Saydou, Aline Makamtse, Hermann Somlare, Guillaume Bado, Boris G. Kouldiaty, Inoussa Zabsonre, Sibiri L. Yameogo, Kanokporn Sathiandee, Joseph Y. Drabo, and Hans-Georg Kräusslich. Analysis of the Diversity of the HIV-1 pol Gene and Drug Resistance Associated Changes among Drug-Naïve Patients in Burkina Faso. J. Med. Virol., 81(10):1691-701, Oct 2009. PubMed ID: 19697403. Show all entries for this paper.

Displaying record number 57925

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HXB2 Location	Pol(448-456) RT(293-301) DNA(3426..3452)	Pol Epitope Map
Author Location	Pol(448-456)
Epitope	`IPLTEEAEL`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(B35)
Immunogen	HIV-1 infection
Patient MHC/HLA	A02:01, A24:02, B35:01, B35:03, C03:03, C04:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	acute/early infection

Notes

The study tracked changes in amino acid residues across the whole genome over time during the first year of infection in 11 individuals representing 4 donor-recipient pairs and 3 independent seroconverters. 9 of the 11 individuals were enrolled during acute infection. In most cases, a single founder virus underwent selection, primarily in env and nef. Mutations were detected in the first week, and became consensus as early as 21 days post-onset of symptoms. Putative escape mutations were often rapidly replaced with mutually-exclusive mutations nearby. Escape mutations were more frequent than reversions.
Previously-documented B35-restricted epitope IPLTEEAEL was recognized by EliSpot assay in 1 HIV-positive B35-positive patient. The patient was negative at day 25, and positive by day 144 post-seroconversion.

References

Herbeck2011 Joshua T. Herbeck, Morgane Rolland, Yi Liu, Sherry McLaughlin, John McNevin, Hong Zhao, Kim Wong, Julia N. Stoddard, Dana Raugi, Stephanie Sorensen, Indira Genowati, Brian Birditt, Angela McKay, Kurt Diem, Brandon S. Maust, Wenjie Deng, Ann C. Collier, Joanne D. Stekler, M. Juliana McElrath, and James I. Mullins. Demographic Processes Affect HIV-1 Evolution in Primary Infection before the Onset of Selective Processes. J. Virol., 85(15):7523-7534, Aug 2011. PubMed ID: 21593162. Show all entries for this paper.

Displaying record number 495

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HXB2 Location	Pol(448-456) RT(293-301) DNA(3426..3452)	Pol Epitope Map
Author Location	( SF2)
Epitope	`IPLTEEAEL`	Epitope Alignment
Species (MHC/HLA)	human(B35)
Immunogen	HIV-1 infection
Experimental methods
Keywords	rate of progression

Notes

HLA B35 is associated with rapid disease progression.
The sequences of 9 previously described HIV-1 B35 CTL epitopes were obtained in 10 HLA B35+ and 19 HLA B35- individuals.
3/9 CTL epitopes had substitutions that were more common in B35+ individuals than in B35- individuals but this was one of the six that had no B35 associated pattern of mutation.

References

Kawana1999 A. Kawana, H. Tomiyama, M. Takiguchi, T. Shioda, T. Nakamura, and A. Iwamoto. Accumulation of Specific Amino Acid Substitutions in HLA-B35-Restricted Human Immunodeficiency Virus Type 1 Cytotoxic T Lymphocyte Epitopes. AIDS Res. Hum. Retroviruses, 15:1099-1107, 1999. PubMed ID: 10461830. Show all entries for this paper.

Displaying record number 57947

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HXB2 Location	Pol(448-456) RT(293-301) DNA(3426..3452)	Pol Epitope Map
Author Location	RT(293-301)
Epitope	`IPLTEEAEL`	Epitope Alignment
Epitope Name	IL9
Subtype	A1, B, C
Species (MHC/HLA)	human(B35)
Immunogen	vaccine
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining
Keywords	vaccine-induced immune responses

Vaccine Details

Vaccine type	adenovirus
Vaccine strain	B clade HXB2, A clade 92RW020, C clade 97ZA012
Vaccine component	Env, Gag-Pol

Notes

The study evaluated vaccine-induced T-cell responses in 40 uninfected volunteers. 12 epitopes were targeted. Certain HLA alleles (B27, B57, B35, B14) were preferentially utilized, while other alleles (A02, B07) were rarely utilized. This preference was explained by 4 factors: higher affinity of specific peptides to specific HLAs, higher avidity of certain T-cell receptors, HLA and peptide interactions, and higher surface expression of certain HLAs.
4/4 B35-positive vaccinees responded to IPLTEEAEL. This epitope sequence is an exact match for 9% of M-clade and 34% of B-clade sequences in the LANL HIV sequence database.

References

Friedrich2011 David Friedrich, Emilie Jalbert, Warren L. Dinges, John Sidney, Alex Sette, Yunda Huang, M. Juliana McElrath, and Helen Horton. Vaccine-Induced HIV-Specific CD8+ T Cells Utilize Preferential HLA Alleles and Target-Specific Regions of HIV-1. J. Acquir. Immune Defic. Syndr., 58(3):248-252, 1 Nov 2011. PubMed ID: 21709567. Show all entries for this paper.

Displaying record number 57336

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HXB2 Location	Pol(448-456) RT(293-301) DNA(3426..3452)	Pol Epitope Map
Author Location	Pol(448-)
Epitope	`IPLTEEAEL`	Epitope Alignment
Epitope Name	Pol448
Subtype	B
Species (MHC/HLA)	human(B35)
Immunogen	HIV-1 infection
Country	Japan
Experimental methods	Chromium-release assay, Cytotoxicity assay, Intracellular cytokine staining, Proliferation, Tetramer binding
Keywords	binding affinity

Notes

CTL responses toward B35 optimal epitopes in Pol, Env, and Nef were characterized in chronically-infected patients. Antigenic variations that abolished TCR recognition not only resulted in escape but also eventually generated a subset of variant-specific CTLs having decreased antiviral activity.
In a tetramer analysis of IPLTEEAEL, the average response frequency of B35-positive HIV-1-infected patients was significantly above background.

References

Ueno2007 Takamasa Ueno, Yuka Idegami, Chihiro Motozono, Shinichi Oka, and Masafumi Takiguchi. Altering Effects of Antigenic Variations in HIV-1 on Antiviral Effectiveness of HIV-Specific CTLs. J. Immunol., 178(9):5513-5523, 1 May 2007. PubMed ID: 17442933. Show all entries for this paper.

Displaying record number 494

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HXB2 Location	Pol(448-456) RT(293-301) DNA(3426..3452)	Pol Epitope Map
Author Location	RT(448-456 SF2)
Epitope	`IPLTEEAEL`	Epitope Alignment
Species (MHC/HLA)	human(B35, B51)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

Binds HLA-B*3501 and B*5101.
Reviewed in Menendez-Arias1998, this epitope lies in the thumb region of RT.

References

Menendez-Arias1998 L. Menendez-Arias, A. Mas, and E. Domingo. Cytotoxic T-Lymphocyte Responses to HIV-1 Reverse Transcriptase. Viral Immunol., 11:167-181, 1998. PubMed ID: 10189185. Show all entries for this paper.

Shiga1996 H. Shiga, T. Shioda, H. Tomiyama, Y. Takamiya, S. Oka, S. Kimura, Y. Yamaguchi, T. Gojoubori, H. G. Rammensee, K. Miwa, and M. Takiguchi. Identification of Multiple HIV-1 Cytotoxic T Cell Epitopes Presented by Human Leukocyte Antigen B35 Molecule. AIDS, 10:1075-1083, 1996. PubMed ID: 8874623. Show all entries for this paper.

Displaying record number 496

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HXB2 Location	Pol(448-456) RT(293-301) DNA(3426..3452)	Pol Epitope Map
Author Location	RT(448-456 SF2)
Epitope	`IPLTEEAEL`	Epitope Alignment
Species (MHC/HLA)	human(B*35:01)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

A CTL clone responsive to this epitope was obtained.
Only 1/7 B35-positive individuals had a CTL response to this epitope.
An E to K substitution at position 5 abrogates specific lysis, but not binding to B*3501.
An I to V substitution at position 1, P to Q at position 2, and E to K at 5, abrogates specific lysis and binding to B*3501.
An I to V substitution at position 1 did not alter reactivity.
Reviewed in Menendez-Arias1998, this epitope lies in the thumb region of RT.

References

Tomiyama1997 H. Tomiyama, K. Miwa, H. Shiga, Y. I. Moore, S. Oka, A. Iwamoto, Y. Kaneko, and M. Takiguchi. Evidence of Presentation of Multiple HIV-1 Cytotoxic T Lymphocyte Epitopes by HLA-B*3501 Molecules That Are Associated with the Accelerated Progression of AIDS. J. Immunol., 158:5026-5034, 1997. PubMed ID: 9144523. Show all entries for this paper.

Displaying record number 61556

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HXB2 Location	Pol(448-456) RT(293-301) DNA(3426..3452)	Pol Epitope Map
Author Location	Pol(448-456)
Epitope	`IPLTEEAEL`	Epitope Alignment
Species (MHC/HLA)	human(B*35:01)
Immunogen	HIV-1 infection
Country	Japan
Experimental methods	CD8 T-cell Elispot - IFNγ, Chromium-release assay, Intracellular cytokine staining
Keywords	TCR usage

Notes

A previously identified Pol epitope, IPLTEEAEL, restricted by HLA-B*3501 was recognized by an αβ TCR that expresses and presents a Vδ1 molecule encoded by Vδ1JαCα transcripts due probably to a unique Vδ1Jα rearrangement. Recognition, immune response, and cytotoxicity were proven for αβCTL from an HIV-infected patient [HLA-A*2402/A*2601, HLA-B*3501/B*5101] against the epitope as presented by T2 cells in the context of classical MHC I molecule, HLA-B*3501.

References

Ueno2003 Takamasa Ueno, Hiroko Tomiyama, Mamoru Fujiwara, Shinichi Oka, and Masafumi Takiguchi. HLA Class I-Restricted Recognition of an HIV-Derived Epitope Peptide by a Human T Cell Receptor Alpha Chain Having a V-delta-1 Variable Segment. Eur. J. Immunol., 33(10):2910-2916, Oct 2003. PubMed ID: 14515275. Show all entries for this paper.

Displaying record number 53445

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HXB2 Location	Pol(448-456) RT(293-301) DNA(3426..3452)	Pol Epitope Map
Author Location	Pol( HXB2, LAI)
Epitope	`IPLTEEAEL`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(B*35:01)
Immunogen	HIV-1 infection
Patient MHC/HLA	A24:02, A26:01, B35:01, B51:01
Country	Japan
Experimental methods	Chromium-release assay, Cytokine production, Tetramer binding
Keywords	binding affinity, kinetics, TCR usage, characterizing CD8+ T cells

Notes

Two different clonotypes of CD8+ T-cells with specificity for this epitope were isolated from a chronic HIV+ patient. The clonotype with the relatively high affinity TCR had no cytolytic activity, cytokine production or proliferation in response to HIV-infected cells, while the moderate affinity clonotype had strong reactions. More than 3-fold increased duration in tetramer 1/2 life was observed with the defective clonotype. The TCRs from the two clonotypes preserved the phenotype when transduced into primary CD8+ T cells, suggesting the TCR with higher affinity was directly associated with impaired T-cell reactivity of the cells.
The high affinity impared TCR was Valpha1.1/Vbeta13.3, the moderate affinity active TCR was Valpha12.1/Vbeta5.6.

References

Ueno2004 Takamasa Ueno, Hiroko Tomiyama, Mamoru Fujiwara, Shinichi Oka, and Masafumi Takiguchi. Functionally Impaired HIV-Specific CD8 T Cells Show High Affinity TCR-Ligand Interactions. J. Immunol., 173(9):5451-547, 1 Nov 2004. PubMed ID: 15494492. Show all entries for this paper.

Displaying record number 1344

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HXB2 Location	Pol(448-456) RT(293-301) DNA(3426..3452)	Pol Epitope Map
Author Location	Pol(448-456 SF2-24)
Epitope	`IPLTEEAEL`	Epitope Alignment
Epitope Name	HIV-B35-SF2-24
Species (MHC/HLA)	human(B35:01, B51:01)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

This epitope is naturally processed and presented by both HLA-B*3501 and HLA-B*5101 and is cross-recognized by a single CTL clone.
IPLTEEAEL binds approximately four times more tightly to HLA-B*3501 than HLA-B*5101.

References

Tomiyama2000b H. Tomiyama, N. Yamada, H. Komatsu, K. Hirayama, and M. Takiguchi. A single CTL clone can recognize a naturally processed HIV-1 epitope presented by two different HLA class I molecules. Eur. J. Immunol., 30(9):2521-30, Sep 2000. PubMed ID: 11009085. Show all entries for this paper.

Displaying record number 58621

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HXB2 Location	Pol(448-456) RT(293-301) DNA(3426..3452)	Pol Epitope Map
Author Location	Pol(448-456 SF2-24)
Epitope	`IPLTEEAEL`	Epitope Alignment
Epitope Name	HIV-B35-SF2-24
Species (MHC/HLA)	human(B35:01, B51:01)
Immunogen	HIV-1 infection
Experimental methods
Keywords	optimal epitope, A-list

Notes

C. Brander noted this as an optimal B*3501 and B*5101 epitope based on data from Tomiyama2000b.

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 52980

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HXB2 Location	Pol(448-456) RT(293-301) DNA(3426..3452)	Pol Epitope Map
Author Location	RT(293-301)
Epitope	`IPLTEEAEL`	Epitope Alignment
Species (MHC/HLA)	human(B51)
Immunogen	HIV-1 infection
Patient MHC/HLA	A3, A32, B15, B51, C*03, Cw6, DQ7, DR4, DR8
Country	Netherlands
Experimental methods	CD8 T-cell Elispot - IFNγ, Flow cytometric T-cell cytokine assay
Keywords	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 17 potential epitopes from this individual, defined based on previously identified epitopes presented by appropriate HLA molecules. Full length genome sequence did not reveal changes in time in any of these epitopes over a four year period. Peptide pools initially revealed very little response to these epitopes, but this increased over time.

References

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

Displaying record number 1686

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HXB2 Location	Pol(448-456) RT(293-301) DNA(3426..3452)	Pol Epitope Map
Author Location	Pol(447-455)
Epitope	`IPLTEEAEL`	Epitope Alignment
Species (MHC/HLA)	human(B51)
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 53413

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HXB2 Location	Pol(448-456) RT(293-301) DNA(3426..3452)	Pol Epitope Map
Author Location	RT Pol(286-294)
Epitope	`IPLTEEAEL`	Epitope Alignment
		Show epitope variants
Epitope Name	IPL
Species (MHC/HLA)	human(B7)
Immunogen	HIV-1 infection
Patient MHC/HLA	A2, A68.1, B07, B35:03, C04:01, C07:02, DQ2, DQ6, DR15, DR17, DR51, DR52
Experimental methods	CD4 T-cell Elispot - IFNγ, CD8 T-cell Elispot - IFNγ, Tetramer binding
Keywords	rate of progression, immunodominance, escape

Notes

The increase in plasma viral load in a patient that progressed rapidly was preceded by positive selection of viral escape mutations in epitopes targeted by dominant HIV-1-specific CD8+ T-cell responses,and a decrease in HIV-1-specific CD4+ and CD8+ T-cell frequencies. Overall, escape variant epitopes were recognized 0-80% as efficiently as the index peptide, and the relatively efficiency of the variant epitopes increased using PBLs collected after their appearance. No changes were found in viral tropism, replication kinetics and neutralizing antibody titers so the rapid decline of the patient was attributed to loss of HIV containment due to CTL escape.
The IPL epitope was found to be under positive selection for escape mutations and it was replaced by first variant between days 297 and 369, ipltGeael. This new variant was subsequently replaced by 2 further variants, that were even more resistent to CD8+ T cell recognition between days 369 and 635, ipltAeael and ipltVeael.

References

Oxenius2004 Annette Oxenius, David A. Price, Alexandra Trkola, Charles Edwards, Emma Gostick, Hua-Tang Zhang, Philippa J. Easterbrook, Tin Tun, Andrew Johnson, Anele Waters, Edward C. Holmes, and Rodney E. Phillips. Loss of Viral Control in Early HIV-1 Infection Is Temporally Associated with Sequential Escape from CD8+ T Cell Responses and Decrease in HIV-1-Specific CD4+ and CD8+ T Cell Frequencies. J. Infect. Dis., 190(4):713-721, 15 Aug 2004. PubMed ID: 15272399. Show all entries for this paper.

Displaying record number 62845

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HXB2 Location	Pol(448-456) RT(293-301) DNA(3426..3452)	Pol Epitope Map
Author Location	RT(293-301)
Epitope	`IPLTEEAEL`	Epitope Alignment
Epitope Name	IL-9
Subtype	B, C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection, engineered
Experimental methods	Other, Relative replication capacity assay
Keywords	acute/early infection, HLA associated polymorphism, chronic infection, protective allele

Notes

The in vitro replicative capacity (RC) of recombinant subtype B NL4-3 viruses expressing subtype C RT-integrase sequences derived from recently infected patients correlated positively with log subsequent VL set point and a higher rate of CD4 decline, while the RC of NL4-3 recombinants expressing subtype C RT-integrase sequences derived from chronically infected patients correlated positively with log VL but negatively with CD4 count. Protective & risk HLA alleles were associated with lower and higher RC values, respectively, and the number of HLA-associated polymorphisms in RT correlated positively with RC while the inverse was observed for integrase. About 90% of RT-integrase polymorphisms significantly associated with altered RC occurred inside or within 5 aa of A-list epitopes (LANL HIV Database).
RT polymorphism E297K was associated with altered RC and is located 2 within best-defined A-list epitope IPLTEEAEL, IL-9, known to bind to B*3501 & B*5101.
Rare E297K occurred in 7 participant-derived recombinant viruses with a substantially reduced median RC of 0.80, while 386 analogous viruses without E297K had a median RC of 0.92, relative to unmodified NL4-3. Authors suggest E297K may be a novel fitness-costly immune-driven escape mutation.

References

Ojwach2018 Doty B. A. Ojwach, Daniel MacMillan, Tarylee Reddy, Vladimir Novitsky, Zabrina L. Brumme, Mark A. Brockman, Thumbi Ndung'u, and Jaclyn K. Mann. Pol-Driven Replicative Capacity Impacts Disease Progression in HIV-1 Subtype C Infection. J. Virol., 92(19), 1 Oct 2018. PubMed ID: 29997209. Show all entries for this paper.

Displaying record number 56208

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HXB2 Location	Pol(448-456) RT(293-301) DNA(3426..3452)	Pol Epitope Map
Author Location	RT
Epitope	`IPLTEEAEL`	Epitope Alignment
Species (MHC/HLA)	human
Immunogen	in vitro stimulation or selection, HIV-1 infection
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords

Notes

The study examined the influence of HIV-1 infection on human endogenous retroviruses (HERVs) activity and explored T cells cross-reactivity in regions of HIV-1/HERV similarity.
T cell responses to HERV peptides were identified in HIV-1 positive individuals. There was an inverse correlation between anti-HERV T cell responses and HIV-1 viral load.
HIV-1 epitope LSHFLKEKGGLEG has a corresponding HERV peptide LDLLTAEKGGLCI. These 2 peptides were used in measuring IFN-γ ELISPOT responses in HIV-1-positive and -negative individuals.

References

Garrison2007 Keith E. Garrison, R. Brad Jones, Duncan A. Meiklejohn, Naveed Anwar, Lishomwa C. Ndhlovu, Joan M. Chapman, Ann L. Erickson, Ashish Agrawal, Gerald Spotts, Frederick M. Hecht, Seth Rakoff-Nahoum, Jack Lenz, Mario A. Ostrowski, and Douglas F. Nixon. T Cell Responses to Human Endogenous Retroviruses in HIV-1 Infection. PLoS Pathog., 3(11):e165, Nov 2007. PubMed ID: 17997601. Show all entries for this paper.

Displaying record number 58103

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HXB2 Location	Pol(448-456) RT(293-301) DNA(3426..3452)	Pol Epitope Map
Author Location	Pol
Epitope	`IPLTEEAEL`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human
Immunogen	vaccine
Patient MHC/HLA	A24:03, A68:01, B35:03, B38:01, C04:01, C12:03; A01:01, A24:02, B35:03, B57:01, C04:01, C06:02
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	vaccine-induced immune responses

Vaccine Details

Vaccine type	adenovirus type 5 (Ad5), DNA prime with Ad5 boost
Vaccine strain	B clade IIIB, B clade JRFL, B clade CAM-1
Vaccine component	Gag, Nef, Pol

Notes

T-cell epitope response specificities were examined in uninfected subjects who received the Gag/Pol/Nef vaccine used in the Step trial. Variable epitopes were detected more frequently than would be expected from an unbiased sampling. The most conserved epitopes were detected at a lower frequency, similar to the frequency reported for responses to natural infection, suggesting potential epitope masking. This may be a mechanism used by the virus in both contexts to escape effective T-cell surveillance. Development of vaccine strategies that can elicit a greater breadth, and towards conserved regions of the genome in particular, are critical requirements for effective T-cell based vaccines.
All vacinees had responses to the Gag peptide pool, and most also had responses to the Nef and/or Pol pools. Subsequent mapping using 9mer minipools demonstrated that T-cell epitopes were recognized across the length of all 3 proteins. A total of 105 distinct 9mers were detected, although some of these may have been overlapping 9mers representing a single epitope.
2 vaccinees recognized 9mer IPLTEEAEL.

References

Li2011a Fusheng Li, Adam C. Finnefrock, Sheri A. Dubey, Bette T. M. Korber, James Szinger, Suzanne Cole, M. Juliana McElrath, John W. Shiver, Danilo R. Casimiro, Lawrence Corey, and Steven G Self. Mapping HIV-1 Vaccine Induced T-Cell Responses: Bias Towards Less-Conserved Regions and Potential Impact on Vaccine Efficacy in the Step Study. PLoS One, 6(6):e20479, 2011. PubMed ID: 21695251. Show all entries for this paper.