In Silico Guided Discovery of Novel Class I and II Trypanosoma cruzi Epitopes Recognized by T Cells from Chagas’ Disease Patients

Abstract

T cell–mediated immune response plays a crucial role in controlling Trypanosoma cruzi infection and parasite burden, but it is also involved in the clinical onset and progression of chronic Chagas’ disease. Therefore, the study of T cells is central to the understanding of the immune response against the parasite and its implications for the infected organism. The complexity of the parasite–host interactions hampers the identification and characterization of T cell–activating epitopes. We approached this issue by combining in silico and in vitro methods to interrogate patients’ T cells specificity. Fifty T. cruzi peptides predicted to bind a broad range of class I and II HLA molecules were selected for in vitro screening against PBMC samples from a cohort of chronic Chagas’ disease patients, using IFN-γ secretion as a readout. Seven of these peptides were shown to activate this type of T cell response, and four out of these contain class I and II epitopes that, to our knowledge, are first described in this study. The remaining three contain sequences that had been previously demonstrated to induce CD8+ T cell response in Chagas’ disease patients, or bind HLA-A*02:01, but are, in this study, demonstrated to engage CD4+ T cells. We also assessed the degree of differentiation of activated T cells and looked into the HLA variants that might restrict the recognition of these peptides in the context of human T. cruzi infection.

T Cell Specificity: A Great Challenge in Chagas Disease

“…Peptides from those proteins ( Table 1 ) were recognized by PBMC from chronic Chagas disease patients in IFN-γ ELISPOT and tetramer assays ( 31 ). Another cruzipain epitope was described in a recent publication of our group using an in silico guided approach ( 38 ). Sequences of T. cruzi proteins characterized as T cell immunogens in the Immune Epitope Database [IEDB-, ( 67 )] were screened and the binding to a set of HLA-A and HLA-B or HLA-DRB1 molecules were predicted.…”

“…Sequences of T. cruzi proteins characterized as T cell immunogens in the Immune Epitope Database [IEDB-, ( 67 )] were screened and the binding to a set of HLA-A and HLA-B or HLA-DRB1 molecules were predicted. One out of the four novel peptides reported (namely TcCZp2, Table 1 ), revealed predominant CD8 + T cell activation in IFN-γ ELISPOT assays with PBMC depleted of CD4 + T cells ( 38 ). In addition, the predicted nested core of this peptide (TcCZp2me) allowed the identification of epitope-specific CD8 + T cells in HLA-A*31:01 + patients, with a predominant effector memory T EMRA (terminal effector T cells re-expressing CD45RA) or T EM (effector memory) cell phenotype ( 38 ).…”

“…Only a few proteins have been demonstrated to induce a recall response on CD4 + T cells from T. cruzi infected-individuals in the chronic phase of the disease ( 38 , 49 , 52 , 76 , 77 ).…”

“…A recent in silico approach also enabled the identification of potential T. cruzi -specific CD4 + epitopes from a co-chaperone GrpE and from a hypothetical protein ( 72 ). And more recently, another predictive approach developed by our group led to the discovery of peptides demonstrated to induce CD4 + T cell response in Chagas disease patients ( 38 ). In fact, these cells were the leading producers of IFN-γ in response to the novel T. cruzi peptides TcTSp3, TcTSp4 and TcTSp5 ( Table 1 ).…”

“…Notably, the IFN-γ responses against TcTSp1, TcTSp2 and TcCZp1 ( Table 1 ) were also predominantly attributed to CD4 + T cell activation, although they comprised sequences from cruzipain and TS proteins previously reported to induce CD8 + T cell response in Chagas disease or to bind HLA-A*02:01 ( 31 , 33 ). Regarding phenotype characterization, CD4 + T cells showed heterogeneous degree of maturation between chronic Chagas´ disease patient population, although central memory (T CM ) T cells seemed to be preponderant in patients with IFN-γ response against TcTSp4 ( 38 ).…”