P1_125 The pathogenicity of T cell epitopes on human Goodpasture antigen and its critical amino acid motif

ABSTRACTAlthough parasite strain-restricted CD8 T cell responses have been described for several protozoa, the precise role of antigenic variability in immunity is poorly understood. The tick-borne protozoan parasiteTheileria annulatainfects leukocytes and causes an acute, often fatal lymphoproliferative disease in cattle. Building on previous evidence of strain-restricted CD8 T cell responses toT. annulata, this study set out to identify and characterize the variability of the target antigens. Three antigens were identified by screening expressed parasite cDNAs with specific CD8 T cell lines. In cattle expressing the A10 class I major histocompatibility complex haplotype, A10-restricted CD8 T cell responses were shown to be focused entirely on a single dominant epitope in one of these antigens (Ta9). Sequencing of the Ta9 gene from field isolates ofT. annulatademonstrated extensive sequence divergence, resulting in amino acid polymorphism within the A10-restricted epitope and a second A14-restricted epitope. Statistical analysis of the allelic sequences revealed evidence of positive selection for amino acid substitutions within the region encoding the CD8 T cell epitopes. Sequence differences in the A10-restricted epitope were shown to result in differential recognition by individual CD8 T cell clones, while clones also differed in their ability to recognize different alleles. Moreover, the representation of these clonal specificities within the responding CD8 T cell populations differed between animals. As well as providing an explanation for incomplete protection observed after heterologous parasite challenge of vaccinated cattle, these results have important implications for the choice of antigens for the development of novel subunit vaccines.

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Thyrotropin-Receptor and Thyroid Peroxidase-Specific T Cell Clones and Their Cytokine Profile in Autoimmune Thyroid Disease1

The Journal of Clinical Endocrinology & Metabolism ◽

10.1210/jcem.82.11.4336 ◽

1997 ◽

Vol 82 (11) ◽

pp. 3655-3663

Author(s):

Maria Elena Fisfalen ◽

Ellen M. Palmer ◽

Gijs A. van Seventer ◽

Keyoumars Soltani ◽

Yoshikuni Sawai ◽

...

Keyword(s):

Amino Acid ◽

T Cell ◽

Thyroid Tissue ◽

Cytokine Profile ◽

Thyroid Peroxidase ◽

Amino Acid Residues ◽

T Cell Epitopes ◽

T Cell Clones ◽

Cell Clones ◽

Ifn Γ

We studied the cytokine profile and the immune responses to thyroid antigens of specific T cell clones (TCC) isolated from patients with Hashimoto’s thyroiditis (HT) and Graves’ disease (GD). Antigen-specific TCC were reactive to thyroid peroxidase (TPO), thyroglobulin (Tg) or human recombinant TSH-receptor extracellular domain (TSH-R), and/or their respective peptides. Of the 43 clones derived from HT patients, 65% were reactive to TPO, and 59% of the 32 clones derived from GD patients were reactive to TSH-R. TPO epitopes 100–119 and 625–644 were recognized by 75% of HT-derived clones, whereas TSH-R epitopes 158–176, 207–222, and 343–362/357–376 were recognized by 85% of GD-derived TCC. The TCC were classified according to their cytokine profile into T helper cell (Th)0 [secreting interleukin (IL)-4, IL-5, interferon (IFN)-γ], Th1 (secreting IFN-γ) and Th2 (secreting IL-4 and/or IL-5). Tumor necrosis factor-β and IL-10 were produced by all subsets. The specific TCC were predominantly Th1-like cells in HT, and were Th0- and Th1-like cells in GD. Fifty three percent of Th0 clones were derived from GD patients and were reactive to TSH-R, whereas 50% of Th1 clones were derived from HT patients and were reactive to TPO or Tg. Most Th2 clones (82%) were reactive to TPO and were established from peripheral blood. All these clones produced IL-5, and 64% produced IL-4 and IL-10. Interestingly, IFN-γ was highly produced by TPO- or Tg-specific clones established from HT thyroid tissue. These results confirm at the clonal level our previous studies regarding T cell epitopes on TPO and TSH-R molecules and support the concept that immunodominant T cell epitopes are located on amino acid residues 100–119 and 625–644 of TPO in HT and amino acid residues 158–176, 207–222 and 343–362/357–376 of TSH-R in GD. Our studies also demonstrate that thyroid-specific T cells can be classified into Th0, Th1, and Th2 subsets. TPO- or Tg-specific clones with Th1 phenotype appear to be involved in the pathogenesis of HT, mediating thyroid tissue destruction, whereas TSH-R clones with Th0 phenotype may induce thyroid-stimulating autoantibodies in GD.

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INTRAHOST EVOLUTION OF THE HIV-2 CAPSID CORRELATES WITH PROGRESSION TO AIDS

10.1101/2021.12.28.21268379 ◽

2021 ◽

Author(s):

Michael Terence Boswell ◽

Jamirah Nazziwa ◽

Kimiko Kuroki ◽

Angelica Palm ◽

Sara Karlson ◽

...

Keyword(s):

Amino Acid ◽

T Cell ◽

Bayes Factor ◽

Protein Structures ◽

Sequence Diversity ◽

Evolutionary Rates ◽

Sequence Evolution ◽

T Cell Epitopes ◽

Linear Regression Models ◽

Over Time

Background: HIV-2 infection will progress to AIDS in most patients without treatment, albeit at approximately half the rate of HIV-1 infection. HIV-2 p26 amino acid variations are associated with lower viral loads and enhanced processing of T cell epitopes, which may lead to protective Gag-specific CTL responses common in slower disease progressors. Lower virus evolutionary rates, and positive selection on conserved residues in HIV-2 env have been associated with slower progression to AIDS. We therefore aimed to determine if intrahost evolution of HIV-2 p26 is associated with disease progression. Methods: Twelve treatment-naive, HIV-2 mono-infected participants from the Guinea-Bissau Police cohort with longitudinal CD4+ T cell data and clinical follow-up were included in the analysis. CD4% change over time was analysed via linear regression models to stratify participants into relative faster and slower disease progressor groups. Gag amplicons of 735 nucleotides which spanned the p26 region were amplified by PCR and sequenced. We analysed p26 sequence diversity evolution, measured site-specific selection pressures and evolutionary rates, and determined if these evolutionary parameters were associated with progression status. Amino acid polymorphisms were mapped to existing p26 protein structures. Results: In total, 369 heterochronous HIV-2 p26 sequences from 12 male patients with a median age of 30 (IQR: 28-37) years at enrolment were analysed. Faster progressors had lower CD4% and faster CD4% decline rates. Median pairwise sequence diversity was higher in faster progressors (5.7x10-3 versus 1.4x10-3 base substitutions per site, P<0.001). p26 evolved under negative selection in both groups (dN/dS=0.12). Virus evolutionary rates were higher in faster than slower progressors - synonymous rates: 4.6x10-3 vs. 2.3x10-3; and nonsynonymous rates: 6.9x10-4 vs. 2.7x10-4 substitutions/site/year, respectively. Virus evolutionary rates correlated negatively with CD4% change rates (rho = -0.8, P=0.02), but not CD4% level. However, Bayes factor (BF) testing indicated that the association between evolutionary rates and CD4% kinetics was supported by weak evidence (BF=0.5). The signature amino acid at p26 positions 6, 12 and 119 differed between faster (6A, 12I, 119A) and slower (6G, 12V, 119P) progressors. These amino acid positions clustered near to the TRIM5 alpha/p26 hexamer interface surface. Conclusions: Faster p26 evolutionary rates were associated with faster progression to AIDS and were mostly driven by synonymous substitutions. Nonsynonymous evolutionary rates were an order of magnitude lower than synonymous rates, with limited amino acid sequence evolution over time within hosts. These results indicate the HIV-2 p26 may be an attractive vaccine or therapeutic target.

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The Molecular Characteristics of T-Cell Immune Reconstitution in Leukemia Patients after Allogeneic Hematopoietic Stem Cell Transplantation.

Blood ◽

10.1182/blood.v108.11.5141.5141 ◽

2006 ◽

Vol 108 (11) ◽

pp. 5141-5141

Author(s):

Yuewen Fu ◽

De Pei Wu ◽

Aining Sun ◽

Yufeng Feng ◽

Weirong Chang ◽

...

Keyword(s):

Bone Marrow ◽

Bone Marrow Transplantation ◽

Amino Acid ◽

T Cell ◽

Hematopoietic Stem Cell Transplantation ◽

Marrow Transplantation ◽

Immune Reconstitution ◽

Cmv Infection ◽

Amino Acid Motif ◽

Hematopoietic Stem

Abstract The clinical and experimental results indicated that the T cell immune reconstitution was slow after hematopoietic stem cell transplantation. This study was To analyze the molecular characteristics of T lymphocytic clones during immune reconstitution in leukemia patients after allogeneic hematopoietic stem cell transplantation(Allo-HCST)by investigating complementarity determining region (CDR3) repertoires of T cell receptor β chain variable region (TCRVB) and made it possible to understand the relationship between the express of TCRVB and immune reconstitution. Reverse transcriptase-polymerase chain reaction(RT-PCR) amplified 24 subfamily genes of TCRVB from peripheral blood lymphocytes (PBLs) of twenty-four patients with leukemia underwent three kinds of Allo-HSCT(haploidentical bone marrow transplantation, matched sibling bone marrow transplantation and matched-unrelated PBSCT), five normal donors as control. The PCR products were further analyzed by genescane to evaluate the clonality of VB subfamily. The monoclonal bands which associated with GVHD and CMV infection were obtained through denaturation polyacrylamide gel electrophoresis and sequenced. Compared the sequences of TCRVB CDR3 gene repertoire with other sequences associated with GVHD or CMV infection which had been reported. +2~+19months after transplantation, for nine patients among them which underwent haploidentical bone marrow transplantation, there were 6~14 VB subfamilies expressed with 33% 15 VB subfamilies expressed, which 45%of them were polyclones. In the 5 patients of matched-unrelated PBSCT, there were 10~15 VB families expressed, with 45% the polyclone expression. For ten patients underwent matched sibling bone marrow transplantation, 10~16 VB subfamilies expressed and more than 48% were polyclones. Monoclones and oligoclones existed in 24 VB subfamilies, no common monoclone VB subfamilies expressed. According to the usage of VB family and polyclonal expression, Immune reconstitution in patients which underwent haploidentical BMT was later than that of other two groups (p<0.05), there were no different between other two groups (p>0.05). After Allo-HSCT, two patients detected TCRVB in +2m and +3m and found that it has tendency of adding to use VB subfamilies and increasing to express CDR3 polymorphism. Using biology-information tool, compared 23 TCRVB CDR3 molecules which related to GVHD and CMV infection and found that, different cases in the same VB subfamilies may share similarity in amino acid motif, while in different VB subfamilies none of clones appeared to share the same amino acid motif. In 1.5 years after AHSCT, the usage of TCRVB subfamilies still restricted. T-cell immune reconstitution in patients which underwent haploidentical BMT was later than that of other two groups. TCRVB CDR3 molecules which related to GVHD and CMV infection showed that different cases in the same VB subfamilies may share similarity in amino acid motif, while in different VB subfamilies none of clones appeared to share the same amino acid motif.

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Frequency of Interferon-Resistance Conferring Substitutions in Amino Acid Positions 70 and 91 of Core Protein of the Russian HCV 1b Isolates Analyzed in the T-Cell Epitopic Context

Journal of Immunology Research ◽

10.1155/2018/7685371 ◽

2018 ◽

Vol 2018 ◽

pp. 1-13 ◽

Cited By ~ 6

Author(s):

V. S. Kichatova ◽

K. K. Kyuregyan ◽

N. V. Soboleva ◽

A. A. Karlsen ◽

O. V. Isaeva ◽

...

Keyword(s):

Amino Acid ◽

T Cell ◽

Immune Escape ◽

Core Protein ◽

Significant Proportion ◽

In Silico Analysis ◽

Hla Class I ◽

T Cell Epitopes ◽

Hla Class I Molecules ◽

Negative Effect

Amino acid substitutions R70Q/H and L91M in HCV subtype 1b core protein can affect the response to interferon and are associated with the development of hepatocellular carcinoma. We found that the rate of R70Q/H in HCV 1b from Russia was 31.2%, similar to that in HCV strains from Asia (34.0%), higher than that in the European (18.0%, p=0.0010), but lower than that in the US HCV 1b strains (62.8%, p<0.0001). Substitution L91M was found in 80.4% of the Russian HCV 1b isolates, higher than in Asian isolates (43.8%, p<0.0001). Thus, a significant proportion of Russian HCV 1b isolates carry the unfavorable R70Q/H and/or L91M substitution. In silico analysis of the epitopic structure of the regions of substitutions revealed that both harbor clusters of T-cell epitopes. Peptides encompassing these regions were predicted to bind to a panel of HLA class I molecules, with substitutions impairing peptide recognition by HLA I molecules of the alleles prevalent in Russia. This indicates that HCV 1b with R70Q/H and L91M substitutions may have evolved as the immune escape variants. Impairment of T-cell recognition may play a part in the negative effect of these substitutions on the response to IFN treatment.

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A 10-Amino-Acid Linear Sequence of VP1 of Foot and Mouth Disease Virus Containing B- and T-Cell Epitopes Induces Protection in Mice

Virology ◽

10.1006/viro.1995.1519 ◽

1995 ◽

Vol 212 (2) ◽

pp. 614-621 ◽

Cited By ~ 40

Author(s):

P. Zamorano ◽

A. Wigdorovitz ◽

M. Perez-Filgueira ◽

C. Carrillo ◽

J.M. Escribano ◽

...

Keyword(s):

Amino Acid ◽

T Cell ◽

Disease Virus ◽

Foot And Mouth Disease ◽

Mouth Disease ◽

T Cell Epitopes ◽

Linear Sequence ◽

Mouth Disease Virus ◽

Foot And Mouth

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Identification of Promising CD8 and CD4 T-cell Epitopes for Peptide Vaccine Formulation Against SARS-CoV-2

10.21203/rs.3.rs-482706/v1 ◽

2021 ◽

Author(s):

Supriyo Chakraborty ◽

Bornali Deb ◽

Durbba Nath ◽

Deboja Monoswita

Keyword(s):

Amino Acid ◽

T Cell ◽

Peptide Vaccine ◽

Preventive Measure ◽

Cost Effective ◽

Cd8 T Cell ◽

Surface Glycoprotein ◽

Cd4 T Cell ◽

T Cell Epitopes ◽

Aliphatic Amino Acid

Abstract The novel virus “Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)” has been responsible for the worldwide pandemic causing huge devastation and deaths since December 2019. The disease caused by this virus is known as COVID-19. The present study is based on immunoinformatics approach to develop a multi-epitope loaded peptide vaccine to combat the COVID-19 menace. Here, we have reported the 9-mer CD8 T-cell epitopes and 15-mer CD4 T-cell epitopes, free from glycosylation sites, belonging to three proteins, viz. surface glycoprotein, membrane glycoprotein and envelope protein of this virus. Immunogenicity, aliphatic amino acid, antigenicity and hydrophilicity scores of the predicted epitopes were estimated. In addition, other physicochemical parameters namely net charge, Boman index and amino acid contents were also accounted. Out of all the epitopes, three CD8 T-cell epitopes viz. PDPSKPSKR, DPSKPSKRS and QTQTNSPRR and three CD4 T-cell epitopes viz. ASYQTQTNSPRRARS, RIGNYKLNTDHSSSS and RYRIGNYKLNTDHSS were found to be efficient targets for raising immunity in human against this virus. With the help of our identified potent epitopes, various pharma industries might initiate efforts to incorporate those epitopes with carrier protein or adjuvant to develop a multi-epitope-loaded peptide vaccine against SARS-CoV-2. The peptide vaccines are usually cost effective and therefore, could be administered as a preventive measure to combat the spread of this disease. Proper clinical trials must be conducted prior to the use of identified epitopes as vaccine candidates.

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The Clonotypic BCR IG of CLL Patients Contain Predicted T-Cell Class I Epitopes with Shared Structural Properties

Blood ◽

10.1182/blood-2021-152422 ◽

2021 ◽

Vol 138 (Supplement 1) ◽

pp. 1540-1540

Author(s):

Anna Vardi ◽

Andreas Agathangelidis ◽

Sofia Gkagkaridou ◽

Anna-Lisa Schaap-Johansen ◽

Maria Karipidou ◽

...

Keyword(s):

Clinical Trials ◽

Amino Acid ◽

T Cell ◽

Research Funding ◽

Cd8 T Cell ◽

Class I ◽

T Cell Epitopes ◽

Ighv Gene ◽

Cell Class ◽

Rank Score

Abstract Targeted therapies have revolutionized the treatment of chronic lymphocytic leukemia (CLL) with remarkable overall response rates. Against that, however, CLL remains incurable, indicating a need for novel strategies towards disease control and eventual eradication, including reinvigoration of anti-tumor immune responses. T cells in CLL display an oligoclonal profile and appear selected by restricted antigens, with recent evidence suggesting that the selecting epitopes may lie within the clonotypic B-cell receptor immunoglobulins (BcR IG). Should this prove to be the case, such neoepitopes could be exploited as idiotypic targets for cellular therapy or for peptide vaccine design, aiming to augment response to current treatments. Here we performed ad hoc prediction of putative T-cell class I neoepitopes contained within the clonotypic BcR IGs of CLL patients, with an intended bias towards major stereotyped CLL subsets. We selected 27 patients to represent the full spectrum of CLL: (i) with mutated IGHV genes (M-CLL, n=5), (ii) with unmutated IGHV genes (U-CLL, n=5), (iii) assigned to major stereotyped subsets (subset #1, n=7; subset #2, n=5; subset #4, n=5). RT-PCR was performed for the heavy (H) and the light (K/L) IG chains using subgroup-specific Leader primers for the IGHV/IGK/LV gene and universal primers annealing to the constant domain (IGHG, IGHM, IGKC, IGLC), in order to produce the full-length V-(D)-J gene rearrangement sequence, plus the start of the constant domain. PCR products were subjected to direct double-strand Sanger sequencing with a quality-optimized protocol. The amino acid sequences were subsequently parsed in peptides and subjected to NetMHCpan. The rank score was calculated, considering the 4-digit HLA-A and -B typing for each individual patient. High- and medium-binding peptides (rank score <2%) were selected. Exact matches to germline and/or proteome databases were excluded. Overall, 1,007 predicted neoepitopes were identified. All patients had predicted CD8 + T-cell epitopes within the clonotypic BcR IG, either in the heavy chain (26/27 pts, n=632 epitopes) or the light chain (26/27 pts, n=375 epitopes). The majority of the peptides resulted from somatic hypermutations (SHMs) across the IGHV gene outside the complementarity-determining region 3 (CDR3; n=538, 53.4%). With the exception of few peptides located within the FR4 region (n=11, 0.1%), the remaining (n=458, 45.5%) involved (at least part of) the CDR3, which is particularly relevant given its small length (9-27 aa) within the full sequence (331-660 aa). There was no statistically significant difference in the rank score of peptides involving the CDR3 vs. all others. Peptide clustering assigned most of the predicted neoepitopes (970/1007, 96.3%) in 54 clusters of similar length and amino acid composition. Also, it revealed similar or identical predicted neoepitopes among different patients (30 clusters of two, 10 clusters of three, 8 clusters of four, 4 clusters of five, 1 cluster of six and 1 cluster of eight). Importantly, these clusters involved: (i) shared CDR3 patterns in patients assigned to the same stereotyped subset, but also (ii) subset-specific recurrent SHMs across the rearranged IGHV gene, e.g. G-to-E SHM at position 28 in the VH CDR1 of subset #4, a recurrent SHM in this subset. Also of note, the two most highly populated clusters involved peptides within the VL CDR3, and were biased towards specific subsets; the cluster of eight patients contained 4 patients assigned to subset #1 and the cluster of six patients included 4 patients assigned to subset #2. In conclusion, in silico prediction identified a significant number of putative T-cell class I neoepitopes contained within the clonotypic BcR IG of CLL patients. The majority of these neoepitopes can be assigned to clusters based on amino acid similarity and are shared among different patients. Many of them culminate from subset-specific ('stereotyped') CDR3 patterns or recurrent SHMs, suggesting that the targeted SHM which shapes the CLL BcR IG repertoire may produce immunogenic CD8 + T-cell epitopes. Their actual immunogenicity has to be tested in ex vivo studies, currently underway by our group. Disclosures Anagnostopoulos: Abbvie: Other: clinical trials; Sanofi: Other: clinical trials ; Ocopeptides: Other: clinical trials ; GSK: Other: clinical trials; Incyte: Other: clinical trials ; Takeda: Other: clinical trials ; Amgen: Other: clinical trials ; Janssen: Other: clinical trials; novartis: Other: clinical trials; Celgene: Other: clinical trials; Roche: Other: clinical trials; Astellas: Other: clinical trials . Chatzidimitriou: Abbvie: Honoraria, Research Funding; Janssen: Honoraria, Research Funding.

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