Use of an In Vivo FTA Assay to Assess the Magnitude, Functional Avidity and Epitope Variant Cross-Reactivity of T Cell Responses Following HIV-1 Recombinant Poxvirus Vaccination

A series of HIV-1 CRF01_AE/CRF07_BC recombinants were previously found to have emerged gradually in a superinfected patient (patient LNA819). However, the extent to which T-cell responses influenced the development of these recombinants after superinfection is unclear. In this study, we undertook a recombination structure analysis of the gag, pol, and nef genes from longitudinal samples of patient LNA819. A total of 9 pol and 5 nef CRF01_AE/CRF07_BC recombinants were detected. The quasispecies makeup and the composition of the pol and nef gene recombinants changed continuously, suggestive of continuous evolution in vivo. T-cell responses targeting peptides of the primary strain and the recombination regions were screened. The results showed that Pol-LY10, Pol-RY9, and Nef-GL9 were the immunodominant epitopes. Pol-LY10 overlapped with the recombination breakpoints in multiple recombinants. For the LY10 epitope, escape from T-cell responses was mediated by both recombination with a CRF07_BC insertion carrying the T467E/T472V variants and T467N/T472V mutations originating in the CRF01_AE strain. In pol recombinants R8 and R9, the recombination breakpoints were located ~23 amino acids upstream of the RY9 epitope. The appearance of new recombination breakpoints harboring a CRF07_BC insertion carrying a R984K variant was associated with escape from RY9-specific T-cell responses. Although the Nef-GL9 epitope was located either within or 10~11 amino acids downstream of the recombination breakpoints, no variant of this epitope was observed in the nef recombinants. Instead, a F85V mutation originating in the CRF01_AE strain was the main immune escape mechanism. Understanding the cellular immune pressure on recombination is critical for monitoring the new circulating recombinant forms of HIV and designing epitope-based vaccines. Vaccines targeting antigens that are less likely to escape immune pressure by recombination and/or mutation are likely to be of benefit to patients with HIV-1.

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Functional analysis of peripheral and intratumoral neoantigen-specific TCRs identified in a patient with melanoma

Journal for ImmunoTherapy of Cancer ◽

10.1136/jitc-2021-002754 ◽

2021 ◽

Vol 9 (9) ◽

pp. e002754

Author(s):

Eva Bräunlein ◽

Gaia Lupoli ◽

Franziska Füchsl ◽

Esam T Abualrous ◽

Niklas de Andrade Krätzig ◽

...

Keyword(s):

T Cells ◽

T Cell ◽

Immune Responses ◽

Immune Checkpoint ◽

T Cell Responses ◽

Functional Avidity ◽

Cell Responses

BackgroundNeoantigens derived from somatic mutations correlate with therapeutic responses mediated by treatment with immune checkpoint inhibitors. Neoantigens are therefore highly attractive targets for the development of therapeutic approaches in personalized medicine, although many aspects of their quality and associated immune responses are not yet well understood. In a case study of metastatic malignant melanoma, we aimed to perform an in-depth characterization of neoantigens and respective T-cell responses in the context of immune checkpoint modulation.MethodsThree neoantigens, which we identified either by immunopeptidomics or in silico prediction, were investigated using binding affinity analyses and structural simulations. We isolated seven T-cell receptors (TCRs) from the patient’s immune repertoire recognizing these antigens. TCRs were compared in vitro by multiparametric analyses including functional avidity, multicytokine secretion, and cross-reactivity screenings. A xenograft mouse model served to study in vivo functionality of selected TCRs. We investigated the patient’s TCR repertoire in blood and different tumor-related tissues over 3 years using TCR beta deep sequencing.ResultsSelected mutated peptide ligands with proven immunogenicity showed similar binding affinities to the human leukocyte antigen complex and comparable disparity to their wild-type counterparts in molecular dynamic simulations. Nevertheless, isolated TCRs recognizing these antigens demonstrated distinct patterns in functionality and frequency. TCRs with lower functional avidity showed at least equal antitumor immune responses in vivo. Moreover, they occurred at high frequencies and particularly demonstrated long-term persistence within tumor tissues, lymph nodes and various blood samples associated with a reduced activation pattern on primary in vitro stimulation.ConclusionsWe performed a so far unique fine characterization of neoantigen-specific T-cell responses revealing defined reactivity patterns of neoantigen-specific TCRs. Our data highlight qualitative differences of these TCRs associated with function and longevity of respective T cells. Such features need to be considered for further optimization of neoantigen targeting including adoptive T-cell therapies using TCR-transgenic T cells.

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Identification of Cross-Reactive CD8+ T Cell Receptors with High Functional Avidity to a SARS-CoV-2 Immunodominant Epitope and Its Natural Mutant Variants

10.1101/2020.11.02.364729 ◽

2020 ◽

Cited By ~ 1

Author(s):

Chao Hu ◽

Meiying Shen ◽

Xiaojian Han ◽

Qian Chen ◽

Luo Li ◽

...

Keyword(s):

T Cell ◽

T Cell Receptors ◽

Vaccine Development ◽

Ex Vivo ◽

T Cell Responses ◽

Cross Reactivity ◽

Functional Avidity ◽

Cell Receptors ◽

Cell Functions ◽

Cell Responses

ABSTRACTDespite the growing knowledge of T cell responses and their epitopes in COVID-19 patients, there is a lack of detailed characterizations for T cell-antigen interactions and T cell functions. Using a peptide library predicted with HLA class I-restriction, specific CD8+ T cell responses were identified in over 75% of COVID-19 convalescent patients. Among the 15 SARS-CoV-2 epitopes identified from the S and N proteins, N361-369 (KTFPPTEPK) was the most dominant epitope. Importantly, we discovered 2 N361-369-specific T cell receptors (TCRs) with high functional avidity, and they exhibited complementary cross-reactivity to reported N361-369 mutant variants. In dendritic cells (DCs) and the lung organoid model, we found that the N361-369 epitope could be processed and endogenously presented to elicit the activation and cytotoxicity of CD8+ T cells ex vivo. Our study evidenced potential mechanisms of cellular immunity to SARS-CoV-2, illuminating natural ways of viral clearance with high relevancy in the vaccine development.

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High degree of inter-clade cross-reactivity of HIV-1-specific T cell responses at the single peptide level

AIDS ◽

10.1097/01.aids.0000183126.32077.c8 ◽

2005 ◽

Vol 19 (14) ◽

pp. 1449-1456 ◽

Cited By ~ 24

Author(s):

Xu G Yu ◽

Mathias Lichterfeld ◽

Beth Perkins ◽

Elizabeth Kalife ◽

Stanley Mui ◽

...

Keyword(s):

T Cell ◽

T Cell Responses ◽

Cross Reactivity ◽

Cell Responses ◽

Peptide Level ◽

High Degree ◽

Hiv 1 ◽

Single Peptide

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HIV-1 Env DNA Vaccine plus Protein Boost Delivered by EP Expands B- and T-Cell Responses and Neutralizing Phenotype In Vivo

PLoS ONE ◽

10.1371/journal.pone.0084234 ◽

2013 ◽

Vol 8 (12) ◽

pp. e84234 ◽

Cited By ~ 20

Author(s):

Kar Muthumani ◽

Megan C. Wise ◽

Kate E. Broderick ◽

Natalie Hutnick ◽

Jonathan Goodman ◽

...

Keyword(s):

T Cell ◽

Dna Vaccine ◽

T Cell Responses ◽

Cell Responses ◽

Protein Boost ◽

Hiv 1

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In Vitro Priming Recapitulates In Vivo HIV-1 Specific T Cell Responses, Revealing Rapid Loss of Virus Reactive CD4+ T Cells in Acute HIV-1 Infection

PLoS ONE ◽

10.1371/journal.pone.0004256 ◽

2009 ◽

Vol 4 (1) ◽

pp. e4256 ◽

Cited By ~ 31

Author(s):

Rachel Lubong Sabado ◽

Daniel G. Kavanagh ◽

Daniel E. Kaufmann ◽

Karlhans Fru ◽

Ethan Babcock ◽

...

Keyword(s):

T Cells ◽

T Cell ◽

Cd4 T Cells ◽

T Cell Responses ◽

Rapid Loss ◽

Cell Responses ◽

Acute Hiv ◽

Hiv 1

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HIV-1-Based Virus-like Particles that Morphologically Resemble Mature, Infectious HIV-1 Virions

Viruses ◽

10.3390/v11060507 ◽

2019 ◽

Vol 11 (6) ◽

pp. 507 ◽

Cited By ~ 4

Author(s):

Christopher A. Gonelli ◽

Georges Khoury ◽

Rob J. Center ◽

Damian F.J. Purcell

Keyword(s):

T Cell ◽

Dna Vaccine ◽

Neutralizing Antibodies ◽

T Cell Responses ◽

Expression Vectors ◽

Virus Like Particles ◽

Cell Responses ◽

Hiv 1

A prophylactic vaccine eliciting both broad neutralizing antibodies (bNAbs) to the HIV-1 envelope glycoprotein (Env) and strong T cell responses would be optimal for preventing HIV-1 transmissions. Replication incompetent HIV-1 virus-like particles (VLPs) offer the opportunity to present authentic-structured, virion-associated Env to elicit bNAbs, and also stimulate T cell responses. Here, we optimize our DNA vaccine plasmids as VLP expression vectors for efficient Env incorporation and budding. The original vector that was used in human trials inefficiently produced VLPs, but maximized safety by inactivating RNA genome packaging, enzyme functions that are required for integration into the host genome, and deleting accessory proteins Vif, Vpr, and Nef. These original DNA vaccine vectors generated VLPs with incomplete protease-mediated cleavage of Gag and were irregularly sized. Mutations to restore function within the defective genes revealed that several of the reverse transcriptase (RT) deletions mediated this immature phenotype. Here, we made efficient budding, protease-processed, and mature-form VLPs that resembled infectious virions by introducing alternative mutations that completely removed the RT domain, but preserved most other safety mutations. These VLPs, either expressed from DNA vectors in vivo or purified after expression in vitro, are potentially useful immunogens that can be used to elicit antibody responses that target Env on fully infectious HIV-1 virions.

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In vivo electroporation in DNA-VLP prime-boost preferentially enhances HIV-1 envelope-specific IgG2a, neutralizing antibody and CD8 T cell responses

Vaccine ◽

10.1016/j.vaccine.2017.03.006 ◽

2017 ◽

Vol 35 (16) ◽

pp. 2042-2051 ◽

Cited By ~ 2

Author(s):

Xun Huang ◽

Qianqian Zhu ◽

Xiaoxing Huang ◽

Lifei Yang ◽

Yufeng Song ◽

...

Keyword(s):

T Cell ◽

T Cell Responses ◽

Neutralizing Antibody ◽

Cd8 T Cell ◽

In Vivo Electroporation ◽

Cell Responses ◽

Hiv 1

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Enhanced Cellular Immunity in Macaques following a Novel Peptide Immunotherapy

Journal of Virology ◽

10.1128/jvi.79.6.3748-3757.2005 ◽

2005 ◽

Vol 79 (6) ◽

pp. 3748-3757 ◽

Cited By ~ 23

Author(s):

S. Chea ◽

C. J. Dale ◽

R. De Rose ◽

I. A. Ramshaw ◽

S. J. Kent

Keyword(s):

T Cell ◽

Mononuclear Cells ◽

De Novo ◽

T Cell Responses ◽

Peripheral Blood Mononuclear ◽

Cell Responses ◽

Cell Immunity ◽

Immunodeficiency Virus ◽

Hiv 1

ABSTRACT Advances in treating and preventing AIDS depend on understanding how human immunodeficiency virus (HIV) is eliminated in vivo and on the manipulation of effective immune responses to HIV. During the development of assays quantifying the elimination of fluorescent autologous cells coated with overlapping 15-mer simian immunodeficiency virus (SIV) or HIV-1 peptides, we made a remarkable observation: the reinfusion of macaque peripheral blood mononuclear cells, or even whole blood, pulsed with SIV and/or HIV peptides generated sharply enhanced SIV- and HIV-1-specific T-cell immunity. Strong, broad CD4+- and CD8+-T-cell responses could be enhanced simultaneously against peptide pools spanning 87% of all SIV- and HIV-1-expressed proteins—highly desirable characteristics of HIV-specific immunity. De novo hepatitis C virus-specific CD4+- and CD8+-T-cell responses were generated in macaques by the same method. This simple technique holds promise for the immunotherapy of HIV and other chronic viral infections.

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