Biology subjects

Lujan, H. D.

Publications and source records attributed to Lujan, H. D..

6 recordsLinked to original sources

bioRxiv2024

Expression of IL-1R2 by Tfr prevents their IL-1-dependent proliferation and the exacerbation of allergy

The antibody response is regulated by follicular T helper (Tfh) and regulatory (Tfr) cells that control the germinal center (GC) reaction. Recent research has shown that Tfh/Tfr have a unique pattern of IL-1 receptor expression. We investigated the mechanisms by which this IL-1 axis in GCs could regulate the allergic response. To study this, we generated CD4creIL-1R1lox mice, specifically lacking IL-1R1 expression in T cells and FoxP3creIL-1R2lox mice, specifically lacking IL-1R2 expression in Tfr cells. The conditional knockout mice were compared to their respective control mice in a model of ovalbumin (OVA) sensitization and anaphylaxis, and a phenotypic and functional characterization of humoral and cellular responses was performed. While CD4creIL-1R1lox mice showed little phenotypic changes, FoxP3creIL-1R2lox mice were highly susceptible to allergic anaphylaxis and generated an increase in IgE responses that promoted basophil degranulation. Additionally, FoxP3creIL-1R2lox mice displayed significantly reduced OVA-specific IgG responses, limiting their ability to control allergy via the inhibitory IgG receptor Fc{gamma}RIIb. Although FoxP3creIL-1R2lox mice showed an overall increase in splenic T and B cell numbers, they were unable to efficiently generate proliferating GC B cells. Upon ex vivo IL-1{beta} and/or OVA re-stimulation, we observed a striking IL-1R1-dependent activation and proliferation of Tfr cells in FoxP3creIL-1R2lox splenocytes, that was neither observed in Tregs nor in Tfh. At the same time, B cell proliferation upon re-stimulation was suppressed. These findings suggest that IL-1R2 expression on Tfr cells prevents allergy by limiting excessive Tfr activation and suppressing the IgG/IgE ratio.

immunology↗

bioRxiv2022

Antibodies to protozoan variable surface antigens induce antigenic variation

The genomes of most protozoa encode families of variant surface antigens, whose mutually exclusive changes in expression allow parasitic microorganisms to evade the host immune response1,2. It is widely assumed that antigenic variation in protozoan parasites is accomplished by the spontaneous appearance within the population of cells expressing antigenic variants that escape antibody-mediated cytotoxicity1,2. Here we show, both in vitro and in animal infections, that antibodies to Variant-specific Surface Proteins (VSPs) of the intestinal parasite Giardia lamblia are not cytotoxic, inducing instead VSP clustering into liquid-ordered phase membrane microdomains that trigger a massive release of microvesicles carrying the original VSP and switch in expression to different VSPs by a calcium-dependent mechanism. Surface microvesiculization and antigenic switching are also stimulated when Trypanosoma brucei and Tetrahymena thermophila are confronted to antibodies directed to their GPI-anchored variable surface glycoproteins. This novel mechanism of surface antigen clearance throughout its release into microvesicles coupled to the stochastic induction of new phenotypic variants not only changes the current paradigm of spontaneous antigenic switching but also provides a new framework for understanding the course of protozoan infections as a host/parasite adaptive process.

microbiology↗

bioRxiv2022

MHC-I binding affinity derived metrics fail to predict tumor specific neoantigen immunogenicity

Tumor-specific antigens emerging through somatic genomic rearrangements, known as neoantigens, play a critical role in current anticancer immunotherapy. They may or may not elicit an immune response when presented on the tumor cell surface bound to the MHC-I molecule, whose strength has been assumed as an indicator of immunogenicity. Several in silico peptide-MHC-I binding affinity predictors are used to prioritize putative immunogenic neoantigens to be experimentally and clinically explored either as biomarkers or targets for anticancer vaccines. This claims for a fair evaluation of such predictors, making essential the development of appropriate databases with experimentally validated, immunogenic/non-immunogenic neoantigens. Thus far, such a database is lacking. We herein present ITSNdb, a new and curated immunogenic neoantigen database and use it to benchmark current neoantigen immunogenicity predictors. Benchmark results failed to support the application of the predicted peptide- MHC-I binding affinity or its derived metrics as a tool to estimate neoantigen immunogenicity and the tumor neoantigen burden as an immunotherapy response biomarker. Moreover, binding affinity based immunogenicity definition leads to identifying wild-type peptide counterparts as predictors of immunotherapy response. We demonstrate that MHC-I binding affinity is insufficient to define neoantigen immunogenicity, despite being necessary for neoantigen tumor cell presentation suggesting that a paradigm shift for the emergence of new rules to identify immunogenic neoantigens is required.

bioinformatics↗

bioRxiv2022

Characterization of Cysteine-rich protein families of Giardia lamblia and their role during antigenic variation.

Giardia lamblia encode several families of cysteine-rich proteins. Among these families are the Variant-specific Surface Proteins (VSPs), which are involved in the process of antigenic variation. In addition to VSPs, other Cys-rich proteins have been described, such as High Cysteine Membrane Proteins (HCMPs), High Cysteine Proteins (HCPs) and Tenascin-like Proteins (TLPs). However, these proteins are less characterized and there is no consensus on their subcellular localization, function, expression, and relationship with the VSPs. Although numerous efforts have been made to determine the distinctive characteristics of VSPs and the number of VSP genes present in the genome of Giardia, a clear profile of the VSP repertoire is still lacking. Here, we performed an exhaustive analysis of the Cys-rich families in the recently updated version of the Giardia genome, including their organization, characteristic features, evolution and levels of expression, by combining simple pattern searches and predictions with massive sequencing techniques, integrating and reanalyzing as much omics data as possible. We propose a new classification for the Cys-rich protein-encoding genes and pseudogenes that better describes their involvement in the parasite biology and define unique characteristics of the VSPs that include, besides their known features, an Initiator element/Kozak-like sequence, an extended polyadenylation signal and a unique pattern of mutually exclusive transcript accumulation. Our findings also imply that the HCMPs (now named Cys-Rich Membrane Proteins, CRMPs) are upregulated under stress conditions and might protect the parasite during VSP switching. These results contribute to a better understanding of the process of antigenic variation in this pathogen. Author SummaryThe most common cause of parasite-induced diarrhea is Giardia lamblia. This intestinal parasite causes 180 million cases of symptomatic disease (giardiasis) yearly but also many asymptomatic infections, resulting in that more than 0.5 billion people are currently colonized by the parasite. One key virulence mechanism of G. lamblia, resulting in long-term infections and frequent re-infections, is antigenic variation of Variant-specific Surface Proteins (VSPs). The cysteine-rich VSP proteins are encoded by a multi-gene family but until now the number of genes and how they are regulated has been unclear. Here a recently assembled Giardia reference genome was analyzed using different bioinformatic analyses and this revealed that there are 136 VSP genes in the Giardia genome. The analyses revealed that there are additional cysteine rich proteins in gene families with fewer members that are related to VSPs but with other roles than antigenic variation. A large number of incomplete VSP genes were also identified and they can function as a sequence reservoir for generation of VSP variability. The VSP genes have unique regulatory elements in the upstream and downstream regions, suggesting a role in regulation. Several gene expression data sets were re-analyzed and it showed that one major VSP is expressed per cell. This study is the first to reveal the organization of VSPs in Giardia and it will be the basis for further studies of the mechanism of antigenic variation in this important intestinal parasite.

microbiology↗

bioRxiv2021

A thermostable oral SARS-CoV-2 vaccine induces mucosal and protective immunity

An ideal protective vaccine against SARS-CoV-2 should not only be effective in preventing disease, but also in preventing virus transmission. It should also be well accepted by the population and have a simple logistic chain. To fulfill these criteria, we developed a thermostable, orally administered vaccine that can induce a robust mucosal neutralizing immune response. We used our platform based on retrovirus-derived enveloped virus-like particles (e-VLPs) harnessed with variable surface proteins (VSPs) from the intestinal parasite Giardia lamblia, affording them resistance to degradation and the triggering of robust mucosal cellular and antibody immune responses after oral administration. We made e-VLPs expressing various forms of the SARS-CoV-2 Spike protein (S), with or without membrane protein (M) expression. We found that prime-boost administration of VSP-decorated e-VLPs expressing a pre-fusion stabilized form of S and M triggers robust mucosal responses against SARS-CoV-2 in mice and hamsters, which translate into complete protection from a viral challenge. Moreover, they dramatically boosted the IgA mucosal response of intramuscularly injected vaccines. We conclude that our thermostable orally administered e-VLP vaccine could be a valuable addition to the current arsenal against SARS-CoV-2, in a stand-alone prime-boost vaccination strategy or as a boost for existing vaccines.

immunology↗

bioRxiv2019

MIXTURE: an improved algorithm for immune tumor microenvironment estimation based on gene expression data.

RNA sequencing has proved to be an efficient high-throughput technique to robustly characterize the presence and quantity of RNA in tumor biopsies at a given time. Importantly, it can be used to computationally estimate the composition of the tumor immune infiltrate and to infer the immunological phenotypes of those cells. Given the significant impact of anti-cancer immunotherapies and the role of the associated immune tumor microenvironment (ITME) on its prognosis and therapy response, the estimation of the immune cell-type content in the tumor is crucial for designing effective strategies to understand and treat cancer. Current digital estimation of the ITME cell mixture content can be performed using different analytical tools. However, current methods tend to over-estimate the number of cell-types present in the sample, thus under-estimating true proportions, biasing the results. We developed MIXTURE, a noise-constrained recursive feature selection for support vector regression that overcomes such limitations. MIXTURE deconvolutes cell-type proportions of bulk tumor samples for both RNA microarray or RNA-Seq platforms from a leukocyte validated gene signature. We evaluated MIXTURE over simulated and benchmark data sets. It overcomes competitive methods in terms of accuracy on the true number of present cell-types and proportions estimates with increased robustness to estimation bias. It also shows superior robustness to collinearity problems. Finally, we investigated the human immune microenvironment of breast cancer, head and neck squamous cell carcinoma, and melanoma biopsies before and after anti-PD-1 immunotherapy treatment revealing associations to response to therapy which have not seen by previous methods.

bioinformatics↗