Biology subjects

Reche, P. A.

Publications and source records attributed to Reche, P. A..

7 recordsLinked to original sources

bioRxiv2025

Treg cell epitopes from α-tubulin: discovery and immunomodulatory features

Regulatory T (Treg) cells are pivotal in maintaining self-tolerance and controlling immune responses. In this study, we investigated potential Treg cell epitopes in human -tubulin that were selected in silico for their promiscuous binding to class II human leukocyte antigens and full identity with antigens from enteric nematodes present in excretory-secretory products. We identified five Treg cell epitopes in -tubulin that were capable of stimulating and expanding IL-10 and TGF-{beta}-producing Foxp3+ Treg cells in peripheral blood mononuclear cells. We also proved that a peptide pool containing the identified Treg cell epitopes (TBL pool) suppressed the T cell responses elicited by different stimuli, including LPS, and class I and class II restricted T cell epitopes, as determined by intracellular cytokine staining assays. Similarly, this same peptide pool was able to suppress T cell responses in mixed lymphocyte reactions. Finally, we found that stimulation of naive CD4+ T cells with autologous monocyte-derived dendritic cells in the presence of the TBL pool promoted the differentiation of functional CD4+CD25highFoxP3+ T cells capable of suppressing the proliferation of CD3/CD28-activated T cells. -tubulin Treg cell epitopes could be useful for treating autoimmune and chronic inflammatory diseases by inducing Treg cells and, given the ubiquitous and copious expression of -tubulin, enable a general mechanism of immune homeostasis.

immunology↗

bioRxiv2024

HIV-1 protein coding sequences are present in relevant bacteria

Human Immunodeficiency Virus (HIV) is a retrovirus that attacks the immune system, causing acquired immunodeficiency syndrome (AIDS). Early diagnosis and treatment of HIV infected individuals are considered key to reduce HIV transmission and developing AIDS. Therefore, HIV diagnostics play an important role in the battle against AIDS. HIV tests are regarded as reliable and very specific. However, false-positive results are known to occur, usually caused by infections with unrelated pathogens leading to cross-reactive antibodies. In this work, we found through TBLASTN searches that the genome of several bacterial species, most frequently Klebsiella pneumoniae and Escherichia coli, contain segments matching HIV-1 proteins, including p24 and other proteins relevant for HIV testing, with a high degree of similarity (sequence identity > 95 %). The presence of HIV-1 in these bacteria of the human microbiota does not appear to be an artifact, since HIV-1 proteins were detected in different isolates of the same species. The proteome of other common viruses, particularly Influenza A virus and Hepatitis B virus, was also detected in bacterial genomes, but to a much lesser extent. Overall, our findings support that some bacteria can acquire HIV-1 genetic material and could interfere with HIV testing, causing false-positives.

microbiology↗

bioRxiv2023

Analysis of virus-specific B cell epitopes reveals extensive antigen processing prior to recognition

B cell epitopes must be solvent accessible for recognition by cognate B cells and antibodies. Here, we sought to study such premise for B cell epitopes targeted during infection in humans, available at the Immune Epitope Database. Most of these B cell epitopes were virus-specific linear B cell epitopes and so we focused on them, analyzing first the localization of the relevant antigens. Antigen localization could be unequivocally assigned to 26498 linear B cell epitopes. Of those, 18832 B cell epitopes belonged to antigens that remain enclosed in host cells and/or virus particles, hidden to antibody recognition, while just 7666 lie in ectodomains of viral envelope antigens and/or mature secreted antigens, visible to antibody recognition. Next, we selected B cell epitopes that mapped in antigens with known tertiary (3D-)structures and determined residue relative solvent accessibility (rRSA), comparing them with those of conformational B cell epitopes obtained from available 3D-structures of antigen-antibody complexes. rRSA values computed form linear B cell epitopes had a median value of 23.00%, while that of conformational B cell epitopes was 48.50%. Moreover, considering average rRSA values per entire epitopes (eRSA), only 32.72% of the linear B cell epitopes had eRSA values minimally comparable to those of conformational B cell epitopes. In sum, our results point that most virus-specific B cell epitopes targeted during infection are unreachable to antibody recognition on intact viral particles and/or host cells. Hence, we must conclude that antigen recognition by antibodies must be preceded by degradation/processing of viral particles and infected cells.

immunology↗

bioRxiv2020

Deconvoluting the T cell response to SARS-CoV-2: specificity versus chance- and cognate cross-reactivity

SARS-CoV-2 infection takes a mild or clinically inapparent course in the majority of humans who contract this virus. After such individuals have cleared the virus, only the detection of SARS-CoV-2-specific immunological memory can reveal the exposure, and hopefully the establishment of immune protection. With most viral infections, the presence of specific serum antibodies has provided a reliable biomarker for the exposure to the virus of interest. SARS-CoV-2 infection, however, does not reliably induce a durable antibody response, especially in sub-clinically infected individuals. Consequently, it is plausible for a recently infected individual to yield a false negative result within only a few months after exposure. Immunodiagnostic attention has therefore shifted to studies of specific T cell memory to SARS-CoV-2. Most reports published so far agree that a T cell response is engaged during SARS-CoV-2 infection, but they also state that in 20-81% of non-SARS-CoV-2-exposed individuals, T cells respond to SARS-CoV-2 antigens (mega peptide pools), allegedly due to T cell cross-reactivity with coronaviruses causing Common Cold (CCC), or other antigens. Here we show that by introducing irrelevant mega peptide pools as negative controls to account for chance cross-reactivity, and by establishing the antigen dose-response characteristic of the T cells, one can clearly discern between cognate T cell memory induced by SARS-CoV-2 infection vs. cross-reactive T cell responses in individuals who had not been infected with SARS-CoV-2.

immunology↗

bioRxiv2020

CERI, CEFX, and CPI: largely improved positive controls for testing antigen-specific T cell function in PBMC compared to CEF

Monitoring antigen-specific T cell immunity relies on functional tests that require T cells and antigen presenting cells to be uncompromised. Drawing of blood, its storage and shipment from the clinical site to the test laboratory, and the subsequent isolation, cryopreservation and thawing of peripheral blood mononuclear cells (PBMC) before the actual test is performed can introduce numerous variables that may jeopardize the results. Therefore, no T cell test is valid without assessing the functional fitness of the PBMC being utilized. This can only be accomplished through inclusion of positive controls that actually evaluate the performance of the antigen-specific T cell and antigen presenting cell (APC) compartments. CEF peptides have been commonly used to this extent. Here we show that CEF peptides fail as a positive control in nearly half of test subjects. Moreover, CEF peptides only measure CD8+ T cell functionality. More reliable alternatives for the assessment of CD8+ T cells are introduced here, as well as positive controls for the CD4+ T cell and APC compartments. In sum, we offer new tools and strategies for the assessment of PBMC functional fitness required for reliable T cell immune monitoring.

immunology↗

bioRxiv2020

Discordance between the predicted vs. the actually recognized CD8+ T cell epitopes of HCMV pp65 antigen and aleatory epitope dominance

CD8+ T cell immune monitoring aims at measuring the numbers and functions of antigen-specific CD8+ T cell populations engaged during immune responses, providing insights into the magnitude and quality of cell-mediated immunity operational in a test subject. The selection of peptides for ex vivo CD8+ T cell detection is critical, however, because for each restricting HLA class I molecule present in a human individual there is a multitude of potential epitopes within complex antigens, and HLA diversity between the test subjects predisposes CD8+ T cell responses to individualized epitope recognition profiles. We report here on a brute force CD8+ T cell epitope mapping approach for the human cytomegalovirus (HCMV) pp65 antigen on ten HLA-A*02:01-matched HCMV infected human subjects. In this approach, in each test subject, every possible CD8+ T cell epitope was systematically tested; that is 553 individual peptides that walk the sequence of the HCMV pp65 protein in steps of single amino acids. Highly individualized CD8+ T cell response profiles with aleatory epitope recognition patterns were observed. We compared the actually detected epitope utilization in each individual with epitope prediction ranking for the shared HLA-A*02:01 allele, and for additional HLA class I alleles expressed by each individual. No correlation was found between epitopes ranking on the prediction scale and their actual immune dominance. The data suggest that accurate CD8+ T cell immune monitoring might depend on the agnostic reliance on mega peptide pools, or brute force mapping, rather than individualized epitope predictions.

immunology↗

bioRxiv2019

Plasmodium falciparum immunodominant IgG epitopes in subclinical malaria

Incomplete non-sterile immunity to malaria is attained in endemic regions after recurrent infections by a large percentage of the adult population, who carry the malaria parasite asymptomatically. Although blood-stage Plasmodium falciparum rapidly elicits IgG responses, the target antigens of partially protective and non-protective IgG antibodies as well as the basis for the acquisition of these antibodies remain largely unknown. We performed IgG-immunomics to screen for P. falciparum antigens and to identify epitopes associated with exposure and clinical disease. Sera from malaria cases identified five prevalent antigens recognized by all analyzed patients IgGs. For further epitope mapping, peptide microarrays designed to cover their sequences were probed with a set of 38 sera samples from adult individuals of an endemic malaria region in Ghana. Eight 20-mer peptides with the highest affinity and frequency of recognition among the population were subsequently validated with 16 sera from the same region, segregated into patients with positive or negative subclinical detection of P. falciparum. Significant binding specificity for two immunodominant antigenic regions was uncovered within the START-related lipid transfer protein and the protein disulfide isomerase PDI8. These 20-mer peptides challenged with sera samples from children under 5 years old displayed specific IgG binding in those with detectable parasitemia, even at subclinical level. These results suggest that the humoral response against START and PDI8 antigens may be triggered even at submicroscopic parasitemia levels in children and may eventually be used to differentially diagnose subclinical malaria in children.\n\nSignificanceMalaria in Africa is a leading cause of morbidity and mortality. The reservoirs of the malaria parasite are asymptomatic patients who carry it subclinically. Identifying the parasite antigens and its fragments that trigger the most common immunity response by immunoglobulin G that partially protect people can have profound implications for both, development of a malaria vaccine and diagnosis of the subclinical parasite carriers. Antigen discovery and mapping, validated with sera from subclinical carriers, showed that immunoglobulin G responses in children against parasites START and PDI8 may eventually be used to differentially diagnose non-infected from subclinical cases. Furthermore, anti-START and anti-PDI8 endemic immunodominance provides association of these antigens with long-term acquired immunity and immune evasion to malaria.

microbiology↗