Biology subjects

Perreault, C.

Publications and source records attributed to Perreault, C..

9 recordsLinked to original sources

bioRxiv2026

Redundant roles of YES and SRC tyrosine kinases in driving malignant peripheral nerve sheath tumors

Malignant peripheral nerve sheath tumors (MPNST) are highly aggressive soft tissue sarcomas that are largely incurable with no clinically effective systemic therapies or immunotherapies for advanced disease. Here, we identify the SRC-family kinases (SFKs) YES and SRC as redundant, essential drivers of MPNST growth. Dual inhibition of YES/SRC activity by genetic silencing or pharmacological SFK inhibitors markedly suppressed the proliferation of multiple NF1-mutant MPNST cell lines. In vivo, conditional genetic depletion of YES/SRC in MPNST cells abrogated tumor growth in subcutaneous and orthotopic models, and dasatinib treatment delayed tumor progression and improved overall survival. Integrated transcriptomic and phosphotyrosine proteomic analyses revealed that YES/SRC inactivation extensively rewires MPNST signaling, coordinately repressing multiple oncogenic signaling pathways and downstream cell cycle transcriptional programs. Unexpectedly, YES/SRC inhibition also upregulated interferon and antigen processing and presentation pathways and increased cell-surface MHC class I expression, consistent with tumor-intrinsic immune reactivation. Clinically, analysis of a large sarcoma cohort demonstrated that YES1 is significantly overexpressed in MPNST compared to benign soft tissue tumors. Collectively, our findings establish YES/SRC as non-oncogene vulnerabilities in MPNST.

cancer biology↗

bioRxiv2025

Cryptic leukemia antigens share homology with microbial epitopes and stimulate T-cell responses in healthy donors

Leukemia cells express cryptic tumor-specific antigens (TSAs) derived from aberrantly transcribed non-exomic genome sequences. These antigens are generally absent from healthy tissues yet shared across patients, making them attractive immunotherapy targets by minimizing on-target/off-tumor toxicity while offering broad applicability. However, their immunogenic potential and the nature of the T-cell repertoire they stimulate remain unknown. Cryptic antigen-specific CD8+ T cells could be expanded from healthy donor T-cell repertoires for six out of nine candidate acute leukemia cryptic TSA. T-cell receptor (TCR) and epitope sequence analysis revealed oligoclonal or near-monoclonal responses, involving shared and donor-restricted clonotypes recognizing cryptic TSAs which shared sequence homology with microbial epitopes. Orthotopic TCR replacement with cryptic TSA-specific TCR chains using a one-step CRISPR-Cas9 approach further validated the antigenic specificity and therapeutic potential of two TCRs respectively targeting cryptic TSAs from acute myeloid and lymphoid leukemia. To our knowledge, this is the first report describing functional TCRs directed against cryptic leukemia TSAs and highlights their potential as a new class of antigens for T-cell-based immunotherapies. Key pointsO_LIA high proportion of cryptic leukemia TSAs shares homology with microbial epitopes and can stimulate expansion of low-frequency T cell repertoire in healthy individuals. C_LIO_LIEx vivo expansion of cryptic TSA-specific T cells enables TCR identification that can be used to devise new T cell immunotherapies. C_LI Visual Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC="FIGDIR/small/691479v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1bd720dorg.highwire.dtl.DTLVardef@8ac6d6org.highwire.dtl.DTLVardef@104289aorg.highwire.dtl.DTLVardef@5a65e_HPS_FORMAT_FIGEXP M_FIG C_FIG ConclusionCryptic leukemia antigens elicit antigenic and specific T-cell responses and represents novel targets for TCR or BiTE immunotherapy.

immunology↗

bioRxiv2025

Transgenic Inducible MHC I Overexpression in Mouse Alveolar Type 2 Cells

The major histocompatibility complex class I (MHC I) is crucial in adaptive immunity, enabling CD8+ T cells to detect and eliminate infected and cancerous cells. Recent studies have uncovered significant variability in MHC I expression across tissues, challenging the traditional belief of uniform expression. Lung epithelial cells (LECs) express meager amounts of MHC I, which preserves the lung epithelium from excessive inflammation but renders it more susceptible to cancer and infection. Despite MHC I overexpression in various immunopathologies, its precise role in disease initiation or progression remains unclear due to the absence of suitable in vivo models for studying MHC I overexpression. This study introduces a novel mouse model with targeted surface MHC I upregulation. Leveraging a conditional Cre-lox system, we augmented Nlrc5 expression to specifically upregulate MHC I in alveolar type 2 (AT2) LECs, known for their low basal expression of MHC I and significant overexpression in disease. Our model demonstrated a rapid and sustained tenfold increase in MHC I surface expression persisting for up to a year without triggering pathology or inflammation. Comprehensive characterization and validation of this model indicated that MHC I overexpression does not serve as a primary initiator of respiratory diseases under steady-state conditions and shows a therapeutic window for increasing MHC I without significant damage to the lung epithelium. This adaptable model offers insights into the effects of tissue-specific MHC I regulation and presents new avenues for therapeutic development.

molecular biology↗

bioRxiv2024

Sex and Disease Regulate MHC I Expression in Human Lung Epithelial Cells

Major histocompatibility complex class I (MHC I) molecules present endogenous peptides to CD8+ T-cells for immunosurveillance of infections and cancers. Recent studies revealed unexpected heterogeneity in MHC I expression among cells of different lineages. While respiratory diseases rank among the leading causes of mortality, studies in mice showed that lung epithelial cells (LECs) express lower MHC I levels than all other tested cell types. The present study aimed to evaluate MHC I expression in human LECs from parenchymal explants using single-cell RNA sequencing (scRNA-seq) and immunostaining of primary human LECs. After confirming the low constitutive MHC I expression in human LECs, we observed a significant upregulation of MHC I across three chronic respiratory diseases: chronic obstructive pulmonary disease (COPD), idiopathic pulmonary fibrosis (IPF), and cystic fibrosis (CF). Additionally, we unveiled an unexpected sexual dimorphism in MHC I expression in both health and disease, with males exhibiting higher levels of MHC I under steady-state conditions. Gene expression analyses suggest that differential redox balance between sexes is instrumental in this dimorphism. Our study unveils the complex interplay between MHC I expression, sex, and respiratory diseases. Since, in other models, MHC I upregulation contributes to the development of immunopathologies, we propose that it might have a similar impact on chronic lung diseases. NEW & NOTEWORTHYThis study shows that MHC I expression is very low in healthy LECs but escalates significantly in three chronic respiratory diseases, potentially contributing to disease progression. Furthermore, sex-specific divergences in LEC MHC I levels hint at distinct susceptibilities to chronic lung inflammation between males and females. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/599895v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@44cfaborg.highwire.dtl.DTLVardef@19e1e29org.highwire.dtl.DTLVardef@1ce179aorg.highwire.dtl.DTLVardef@16f8063_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2023

Transposable elements regulate thymus development and function

Transposable elements (TE) are repetitive sequences representing [~]45% of the human and mouse genomes and are highly expressed by medullary thymic epithelial cells (mTEC). In this study, we investigated the role of TEs on T-cell development in the thymus. We performed multi-omic analyses of TEs in human and mouse thymic cells to elucidate their role in T cell development. We report that TE expression in the human thymus is high and shows extensive age- and cell lineage-related variations. TE expression correlates with multiple transcription factors in all cell types of the human thymus. Two cell types express particularly broad TE repertoires: mTECs and plasmacytoid dendritic cells (pDC). In mTECs, transcriptomic data suggest that TEs interact with transcription factors essential for mTEC development and function (e.g., PAX1 and REL), and immunopeptidomic data showed that TEs generate MHC-I-associated peptides implicated in thymocyte education. Notably, AIRE, FEZF2, and CHD4 regulate small yet non-redundant sets of TEs in murine mTECs. Human thymic pDCs homogenously express large numbers of TEs that likely form dsRNA, which can activate innate immune receptors, potentially explaining why thymic pDCs constitutively secrete IFN LJ/{beta}. This study highlights the diversity of interactions between TEs and the adaptive immune system. TEs are genetic parasites, and the two thymic cell types most affected by TEs (mTEcs and pDCs) are essential to establishing central T-cell tolerance. Therefore, we propose that orchestrating TE expression in thymic cells is critical to prevent autoimmunity in vertebrates.

immunology↗

bioRxiv2022

Autophagy degrades immunogenic endogenous retroelements induced by 5-azacytidine in acute myeloid leukemia

The hypomethylating agent 5-azacytidine (AZA) is the first-line therapy for acute myeloid leukemia (AML) patients unfit for intensive chemotherapy. Evidence suggests that the anti-tumor effect of AZA results partly from T-cell cytotoxic responses against MHC-I-associated peptides (MAPs) whose expression is induced by hypomethylation. Through a proteogenomic approach, we analyzed the impact of AZA on the transcriptome and MAP repertoire of four AML cell lines and validated salient findings in the transcriptome of 437 primary AML samples. We demonstrate that AZA caused pleiotropic changes in AML cells via perturbation of transcription, translation, and protein degradation. Overall, 1,364 MAPs were upregulated in AZA-treated cells, including several cancer-testis antigens. Increased MAP abundance was due to the upregulation of corresponding transcripts in a minority of cases and post-translational events in most cases. Furthermore, AZA-induced hypomethylation increased the abundance of numerous transcripts, of which 38% were endogenous retroelements (EREs). Upregulated ERE transcripts triggered innate immune responses but were degraded by autophagy and not processed into MAPs. Autophagy resulted from the formation of protein aggregates caused by AZA-dependent inhibition of DNMT2, a tRNA-methyl transferase enzyme. We found that autophagy inhibition had a synergistic effect with AZA on AML cell proliferation and survival, increased ERE levels and triggered pro-inflammatory responses. Finally, autophagy gene signatures were associated with a lower abundance of CD8+ T-cell markers in AML patients expressing high levels of EREs. Altogether, this work demonstrates that the impact of AZA is regulated at several levels and suggests that inhibiting autophagy could improve the immune recognition of AML blasts in patients.

immunology↗

bioRxiv2022

BamQuery: a proteogenomic tool for the genome-wide exploration of the immunopeptidome

MHC-I-associated peptides (MAPs) derive from selective yet highly diverse genomic regions, including allegedly non-protein-coding sequences, such as endogenous retroelements (EREs). Quantifying canonical (exonic) and non-canonical MAPs-encoding RNA expression in malignant and benign cells is critical for identifying tumor antigens (TAs) but represents a challenge for immunologists. We present BamQuery, a computational tool attributing an exhaustive RNA expression to MAPs of any origin (exon, intron, UTR, intergenic) from bulk and single-cell RNA-sequencing data. We show that non-canonical MAPs (including TAs) can derive from multiple different genomic regions (up to 35,343 for EREs), abundantly expressed in normal tissues. We also show that supposedly tumor-specific mutated MAPs, viral MAPs, and MAPs derived from proteasomal splicing can arise from different unmutated non-canonical genomic regions. The genome-wide approach of BamQuery allows comprehensive mapping of all MAPs in healthy and cancer tissues. BamQuery can also help predict MAP immunogenicity and identify safe and actionable TAs.

immunology↗

bioRxiv2022

Two types of human TCR differentially regulate reactivity to self and non-self antigens

Based on analyses of TCR sequences from over 1,000 individuals, we report that the TCR repertoire is composed of two ontogenically and functionally distinct types of TCRs. Their production is regulated by variations in thymic output and terminal deoxynucleotidyl transferase (TDT) activity. Neonatal TCRs derived from TDT-negative progenitors persist throughout life, are highly shared among subjects, and are polyreactive to self and microbial antigens. Thus, >50% of cord blood TCRs are responsive to SARS-CoV2 and other common pathogens. TDT- dependent TCRs present distinct structural features and are less shared among subjects. TDT- dependent TCRs are produced in maximal numbers during infancy when thymic output and TDT activity reach a summit, are more abundant in subjects with AIRE mutations, and seem to play a dominant role in graft-versus-host disease. Factors decreasing thymic output (age, male sex) negatively impact TCR diversity. Males compensate for their lower repertoire diversity via hyperexpansion of selected TCR clonotypes.

immunology↗

bioRxiv2020

Codon arrangement modulates MHC-I peptides presentation

MHC-I associated peptides (MAPs) play a central role in the elimination of virus-infected and neoplastic cells by CD8 T cells. However, accurately predicting the MAP repertoire remains difficult, because only a fraction of the transcriptome generates MAPs. In this study, we investigated whether codon arrangement (usage and placement) regulates MAP biogenesis. We developed an artificial neural network called Codon Arrangement MAP Predictor (CAMAP), predicting MAP presentation solely from mRNA sequences flanking the MAP-coding codons (MCCs), while excluding the MCC per se. CAMAP predictions were significantly more accurate when using original codon sequences than shuffled codon sequences which reflect amino acid usage. Furthermore, predictions were independent of mRNA expression and MAP binding affinity to MHC-I molecules and applied to several cell types and species. Combining MAP ligand scores, transcript expression level and CAMAP scores was particularly useful to increaser MAP prediction accuracy. Using an in vitro assay, we showed that varying the synonymous codons in the regions flanking the MCCs (without changing the amino acid sequence) resulted in significant modulation of MAP presentation at the cell surface. Taken together, our results demonstrate the role of codon arrangement in the regulation of MAP presentation and support integration of both translational and post-translational events in predictive algorithms to ameliorate modeling of the immunopeptidome. Author summaryMHC-I associated peptides (MAPs) are small fragments of intracellular proteins presented at the surface of cells and used by the immune system to detect and eliminate cancerous or virus-infected cells. While it is theoretically possible to predict which portions of the intracellular proteins will be naturally processed by the cells to ultimately reach the surface, current methodologies have prohibitively high false discovery rates. Here we introduce an artificial neural network called Codon Arrangement MAP Predictor (CAMAP) which integrates information from mRNA-to-protein translation to other factors regulating MAP biogenesis (e.g. MAP ligand score and transcript expression levels) to improve MAP prediction accuracy. While most MAP predictive approaches focus on MAP sequences per se, CAMAPs novelty is to analyze the MAP-flanking mRNA sequences, thereby providing completely independent information for MAP prediction. We show on several datasets that the integration of CAMAP scores with other known factors involved in MAP presentation (i.e. MAP ligand score and mRNA expression) significantly improves MAP prediction accuracy, and further validate CAMAP learned features using an in-vitro assay. These findings may have major implications for the design of vaccines against cancers and viruses, and in times of pandemics could accelerate the identification of relevant MAPs of viral origins.

bioinformatics↗