Search CTL/CD8+ T-Cell Epitope Database

Found 11 matching records:

Displaying record number 53706

HXB2 Location	Nef(106-114) DNA(9112..9138)	Nef Epitope Map
Author Location	Nef(106-114)
Epitope	`RQDILDLWI`	Epitope Alignment
		Show epitope variants
Epitope Name	RI9
Species (MHC/HLA)	human(B13)
Immunogen	HIV-1 infection
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	rate of progression, escape, variant cross-reactivity, optimal epitope

Notes

An HLA-B13-restricted optimal epitope was defined in Nef, RI9. The frequency of CTLs specific for this epitope in B13-positive patients exceeded the number of CTLs against other epitopes, indicating that this is a dominant epitope in B13-positive subjects. Three B13-positive patients who had an immunodominant response to this epitope were good controllers of their infection, with low viral loads over long periods.
In B13-positive patients with a previous diagnosis of AIDS, an RrDILDLWI escape variant was found.
This is a well conserved epitope but natural variants were tested. Peptide titation experiments indicate a V9I RQDILDLWv variant and RQDILDLWI are equally well recognized. Other natural substitutions are less well recognized: RkDILDLWI, RQeILDLWI, aQDILDLWI, RQaILDLWI, RrDILDLWv.

References

Harrer2005b Ellen G. Harrer, Silke Bergmann, Kathrin Eismann, Marion Rittmaier, Andreas Goldwich, Sandra M. Müller, Bernd M. Spriewald, and Thomas Harrer. A Conserved HLA B13-Restricted Cytotoxic T Lymphocyte Epitope in Nef is a Dominant Epitope in HLA B13-Positive HIV-1-Infected Patients. AIDS, 19(7):734-735, 29 Apr 2005. PubMed ID: 15821402. Show all entries for this paper.

Displaying record number 57580

HXB2 Location	Nef(106-114) DNA(9112..9138)	Nef Epitope Map
Author Location	Nef(106-114)
Epitope	`RQDILDLWI`	Epitope Alignment
Epitope Name	RI9
Subtype	B
Species (MHC/HLA)	(B*13)
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.
3/3 B13-positive subjects responded to RQDILDLWI, and 58% of the patients' total response magnitude was derived from this specific response.
This epitope was 5% conserved among M-group sequences and 20% conserved among B-subtype sequences.

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 54122

HXB2 Location	Nef(106-114) DNA(9112..9138)	Nef Epitope Map
Author Location	Nef(106-114)
Epitope	`RQDILDLWI`	Epitope Alignment
Species (MHC/HLA)	human(B*13)
Immunogen
Experimental methods
Keywords	optimal epitope

Notes

C. Brander notes that this is an B*13 epitope. Variant RQDILDLWv also noted.

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 60183

HXB2 Location	Nef(106-114) DNA(9112..9138)	Nef Epitope Map
Author Location	Nef(106-114)
Epitope	`RQDILDLWI`	Epitope Alignment
Epitope Name	RI9
Species (MHC/HLA)	human(B*13)
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.
RQDILDLWI had a significantly positive association with HLA B*13; it was recognized by 7/13 B*13-positive subjects and 11/296 B*13-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 61225

HXB2 Location	Nef(106-114) DNA(9112..9138)	Nef Epitope Map
Author Location	Nef(106-114)
Epitope	`RQDILDLWI`	Epitope Alignment
		Show epitope variants
Epitope Name	RI9
Subtype	B
Species (MHC/HLA)	human(B*1302)
Immunogen	HIV-1 infection
Experimental methods	Relative replication capacity assay
Keywords	class I down-regulation by Nef, escape, novel epitope

Notes

Protective HLA-B*13 was studied by following the 10 most common polymorphisms associated with it. Conserved Gag and Nef B*13-restricted epitopes were shown to have fitness costs when mutated and this makes B*13 a highly protective HLA. In addition, escape-substitutions E24Q and Q107R together, but not separately, impair the ability of Nef to downregulate the MHCI molecule. A novel B*13-restricted Gag p24 epitope GQMVHQAI was identified. Also, Gag-K436R is a compensatory mutation to escape GagI437L.
Epitope RI9, RQDILDLWI, contains the escape Q107R that in collusion with E24Q, negates Nef-mediated Class I downregulation of HLA. This mutation pair is another reason for the ability of HLA-B*13 to remain protective against HIV-1 infection.

References

Shahid2015 Aniqa Shahid, Alex Olvera, Gursev Anmole, Xiaomei T. Kuang, Laura A. Cotton, Montserrat Plana, Christian Brander, Mark A. Brockman, and Zabrina L. Brumme. Consequences of HLA-B*13-Associated Escape Mutations on HIV-1 Replication and Nef Function. J. Virol., 89(22):11557-11571, Nov 2015. PubMed ID: 26355081. Show all entries for this paper.

Displaying record number 60186

HXB2 Location	Nef(106-114) DNA(9112..9138)	Nef Epitope Map
Author Location	Nef(106-114)
Epitope	`RQDILDLWI`	Epitope Alignment
Epitope Name	RI9
Species (MHC/HLA)	human(B*1524)
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.
RQDILDLWI had a significantly positive association with HLA B*1524; it was recognized by 1/1 B*1524-positive subjects and 6/274 B*1524-negative subjects.

References

Displaying record number 60185

HXB2 Location	Nef(106-114) DNA(9112..9138)	Nef Epitope Map
Author Location	Nef(106-114)
Epitope	`RQDILDLWI`	Epitope Alignment
Epitope Name	RI9
Species (MHC/HLA)	human(B*57)
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.
RQDILDLWI had a significantly positive association with HLA B*57; it was recognized by 5/93 B*57-positive subjects and 1/181 B*57-negative subjects.

References

Displaying record number 56303

HXB2 Location	Nef(106-114) DNA(9112..9138)	Nef Epitope Map
Author Location	Nef(106-114 SF2, HXBc2/Bal R5)
Epitope	`RQDILDLWI`	Epitope Alignment
		Show epitope variants
Subtype	B
Species (MHC/HLA)	human(B7)
Immunogen	HIV-1 infection
Patient MHC/HLA	A24, A25, B18, B7, Cw12, Cw7
Country	United States
Experimental methods	Cytokine production, Degranulation, CD107a and b cell surface mobilization, Flow cytometric T-cell cytokine assay
Keywords	supervised treatment interruptions (STI), immunodominance, variant cross-reactivity, characterizing CD8+ T cells, drug resistance

Notes

A detailed analysis of 6 chronically infected patients' CTL responses to autologous virus was performed after ART and SIT (structured interruption of therapy). Qualitative responses including degranulation and production of IFN-gamma, MIP-1beta, TNF-alpha, IL-2, but not memory CD27, CD45RO and CD57 T cells correlated with extended low plasma viremia. Frequency and breadth of CTL response as well as immune escape did not influence virological outcome.
One patient exhibited drug resistance mutations K170R (to NNRTI efavirenz) and D76N, K70R (to NRTIs).
Autologous epitopes were preferentially recognized over optimal, consensus sequences.
Patients with favorable virological outcomes demonstrated CTL recognition within multiple, conserved regions of Gag and Nef.
Patients with poor virological outcomes recognized optimal epitopes with much lower frequencies, though this was not significant.
HLA-B7-restricted epitope, RQDILDLWI, elicited a response in 1 patient and is found in Nef immunodominant region IHSQRRQDILDLWIYGTQG. Patient autologous sequence was RQDILDLWv.

References

Daucher2008 Marybeth Daucher, David A. Price, Jason M. Brenchley, Laurie Lamoreaux, Julia A. Metcalf, Catherine Rehm, Elizabeth Nies-Kraske, Elizabeth Urban, Christian Yoder, Diane Rock, Julie Gumkowski, Michael R. Betts, Mark R. Dybul, and Daniel C. Douek. Virological Outcome after Structured Interruption of Antiretroviral Therapy for Human Immunodeficiency Virus Infection Is Associated with the Functional Profile of Virus-Specific CD8+ T Cells. J. Virol., 82(8):4102-4114, Apr 2008. PubMed ID: 18234797. Show all entries for this paper.

Displaying record number 60182

HXB2 Location	Nef(106-114) DNA(9112..9138)	Nef Epitope Map
Author Location	Nef(106-114)
Epitope	`RQDILDLWI`	Epitope Alignment
Epitope Name	RI9
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.
RQDILDLWI had a significantly positive association with HLA C*01; it was recognized by 13/32 C*01-positive subjects and 18/309 C*01-negative subjects.

References

Displaying record number 60184

HXB2 Location	Nef(106-114) DNA(9112..9138)	Nef Epitope Map
Author Location	Nef(106-114)
Epitope	`RQDILDLWI`	Epitope Alignment
Epitope Name	RI9
Species (MHC/HLA)	human(C*15)
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.
RQDILDLWI had a significantly positive association with HLA C*15; it was recognized by 4/21 C*15-positive subjects and 7/275 C*15-negative subjects.

References

Displaying record number 53900

HXB2 Location	Nef(106-114) DNA(9112..9138)	Nef Epitope Map
Author Location	Nef(106-114)
Epitope	`RQDILDLWI`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Country	India
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	subtype comparisons, computational epitope prediction, immunodominance

Notes

PBMCs from HIV-1 infected Indian subjects were tested for HIV-1 Gag (with C clade peptides), Nef (with B clade peptides), and Env (clade B peptides) specific T-cell responses. 5 immunodominant regions conserved across clades were identified in Gag and Nef. 3 antigenic regions were found to be recognized by CTLs in the Indian subjects; these regions were not identified as immunodominant in studies from Africa.
PBMCs from HIV-1 infected Indian subjects were tested for HIV-1 Gag (with C clade peptides), Nef (with B clade peptides), and Env (clade unspecified) specific T-cell responses. 5 immunodominant regions conserved across clades were identified in Gag and Nef. 3 antigenic regions were found to be recognized by CTLs in the Indian subjects; these regions were not identified as immunodominant in studies from Africa.
26 epitopes were predicted within reactive peptides, of which 90% were clustered in the conserved immunodominant regions of Gag and Nef.
3 of the epitopes were highly conserved across clades, and 7 novel epitopes were found.
Epitope RQDILDLWI showed some conservation to subtype B. Its HLA-restriction was predicted to be to HLA-A*24, -B*37, or -Cw*0602.

References

Thakar2005 Madhuri R. Thakar, Leena S. Bhonge, Samir K. Lakhashe, U. Shankarkumar, Suvarna S. Sane, Smita S. Kulkarni, Bharati A. Mahajan, and Ramesh S. Paranjape. Cytolytic T Lymphocytes (CTLs) from HIV-1 Subtype C-Infected Indian Patients Recognize CTL Epitopes From a Conserved Immunodominant Region of HIV-1 Gag and Nef. J. Infect. Dis., 192(5):749-759, 1 Sep 2005. PubMed ID: 16088824. Show all entries for this paper.