Biology subjects

Renard, C.

Publications and source records attributed to Renard, C..

5 recordsLinked to original sources

bioRxiv2026

DeepPhage: leveraging the power of NGS phage display data, an in-depth analysis for the identification of Eu3+-binding peptides

Summary: Phage Surface Display (PSD) is a widely used molecular technique for identifying peptides and antibodies with applications in therapeutics, diagnostics, and materials science. The use of highly diverse phage libraries enables the screening of millions of ligand variants, while the integration of Next-Generation Sequencing (NGS) provides high-throughput access to the sequence composition of selected phage populations. Despite these advances, the identification of genuine target-binding ligands remains challenging due to biases introduced during library construction, biological selection and propagation, as well as the enrichment of target-unrelated peptides (TUPs). These factors distort sequence distributions and complicate the interpretation of PSD-NGS experiments, particularly when comparing multiple libraries or selection rounds. Consequently, robust computational methods are required to distinguish biologically relevant enrichments from technical artifacts. We demonstrate DeepPhage using PSD-NGS datasets from Eu3+ biopanning experiments, in which differences in peptide composition between experimental conditions were identified and a systematic comparison of several conditions was made possible. It was developed to address the lack of comparative analysis tools for large-scale PSD-NGS experiments by combining statistical analyses with comprehensive visualisation. These features form the basis for a more reliable interpretation of phage display selection experiments. DeepPhage provides a reproducible framework for comparative PSD-NGS analysis, which supports the identification of sequence bias, library heterogeneity and potential target-binding peptides across multiple experiments. The software is freely available as an open-source command-line application, so that it can be deployed on a high computer cluster for particularly large volumes of data. Availability and implementation: DeepPhage is entirely open source and is available on GitLab https://codebase.helmholtz.cloud/phagelabs-hif/DeepPhage/-/tree/stable_release_v0.1 under the GPL v3 licence. The repository contains documentation, installation instructions, a user guide and example data. The sample data used for the demonstration is available at the online repository RODARE (https://doi.org/10.14278/rodare.4647).

bioinformatics↗

bioRxiv2024

Disruption of the epigenetic regulator BAP1 drives chromatin remodeling leading to the emergence of cells with breast cancer stem cell properties and aberrant glycosylation.

BackgroundEpigenetic regulator genes play critical roles in controlling cell identity and are frequently disrupted in breast cancers, suggesting a key driver role in this disease and its associated phenotypes. However, specific epigenetic drivers (epidrivers) of mammary cell plasticity and their mechanistic contributions to this phenotype are poorly characterized. MethodsTo identify potential epidrivers of the emergence of mesenchymal breast cancer stem cell-like phenotypes in non-tumorigenic mammary cells, we employed a CRISPR/Cas9 loss-of-function screening strategy targeting epigenetic regulator genes. This approach was followed by an in-depth validation and characterization of epigenomic, transcriptomic, proteomic and phenotypic changes resulting from the disruption of the putative epidriver gene BAP1. ResultsOur investigation revealed that loss of the histone deubiquitinase BAP1 impacts cellular processes associated with breast cancer cell plasticity such as epithelial-to-mesenchymal transition (EMT) and actin cytoskeleton organization. In addition, we unveiled that BAP1 loss resulted in an overall less permissive chromatin and downregulated gene expression, impacting programs that control cellular glycosylation and leading to decreased glycan abundance and complexity. BAP1 rescue restored the expression of several deregulated genes in a catalytic activity-dependent manner, suggesting that BAP1-mediated cell identity and glycosylation regulation are largely dependent on its histone deubiquitinase activity. ConclusionsOverall, our results point to BAP1 disruption as a driver of mammary cell plasticity and reveal a novel role of BAP1 as an epigenetic regulator of cellular glycosylation.

cancer biology↗

bioRxiv2024

Molecular and cell phenotype programs in oral epithelial cells directed by co-exposure to arsenic and smokeless tobacco

Chronic arsenic exposure can lead to various health issues, including cancer. Concerns have been mounting about the enhancement of arsenic toxicity through co-exposure to various prevalent lifestyle habits. Smokeless tobacco products are commonly consumed in South Asian countries, where their use frequently co-occurs with exposure to arsenic from contaminated groundwater. To decipher the in vitro molecular and cellular responses to arsenic and/or smokeless tobacco, we performed temporal multi-omics analysis of the transcriptome and DNA methylome remodelling in exposed hTERT-immortalized human normal oral keratinocytes (NOK), as well as arsenic and/or smokeless tobacco genotoxicity and mutagenicity investigations in NOK cells and in human p53 knock-in murine embryonic fibroblasts (Hupki MEF). RNAseq results from acute exposures to arsenic alone and in combination with smokeless tobacco extract revealed upregulation of genes with roles in cell cycle changes, apoptosis and inflammation responses. This was in keeping with global DNA hypomethylation affecting genes involved in the same processes in response to chronic treatment in NOK cells. At the phenotypic level, we observed a dose-dependent decrease in NOK cell viability, induction of DNA damage, cell cycle changes and increased apoptosis, with the most pronounced effects observed under arsenic and SLT co-exposure conditions. Live-cell imaging experiments indicated that the DNA damage likely resulted from induction of apoptosis, an observation validated by a lack of exome-wide mutagenesis in response to chronic exposure to arsenic and/or smokeless tobacco. In sum, our integrative omics study provides novel insights into the acute and chronic responses to arsenic and smokeless tobacco (co-)exposure, with both types of responses converging on several key mechanisms associated with cancer hallmark processes. The generated rich catalogue of molecular programs in oral cells regulated by arsenic and smokeless tobacco (co-)exposure may provide bases for future development of biomarkers for use in molecular epidemiology studies of exposed populations at risk of developing oral cancer.

cancer biology↗

bioRxiv2024

Human cancer genomes harbor the mutational signature of tobacco-specific nitrosamines NNN and NNK

Tobacco usage is linked to multiple cancer types and accounts for a quarter of all cancer-related deaths. Tobacco smoke contains various carcinogenic compounds, including polycyclic aromatic hydrocarbons (PAH), though the mutagenic potential of many tobacco-related chemicals remains largely unexplored. In particular, the highly carcinogenic tobacco-specific nitrosamines NNN and NNK form pre-mutagenic pyridyloxobutyl (POB) DNA adducts. In the study presented here, we identified genome-scale POB-induced mutational signatures in cell lines and rat tumors, while also investigating their role in human cancer. These signatures are characterized by T>N and C>T mutations forming from specific POB adducts damaging dT and dC residues. Analysis of 2,780 cancer genomes uncovered POB signatures in [~]180 tumors; from cancer types distinct from the ones linked to smoking-related signatures SBS4 and SBS92. This suggests that, unlike PAH compounds, the POB pathway may contribute uniquely to the mutational landscapes of certain hematological malignancies and cancers of the kidney, breast, prostate and pancreas.

genomics↗

bioRxiv2020

Mechanisms of Igf2 inhibition in thymic epithelial cells infected by coxsackievirus CV-B4

Epidemiological studies have evidenced a link between type 1 diabetes (T1D) and infections by enteroviruses, especially with coxsackievirus B4 (CV-B4). CV-B4 is able to infect human and murine thymic epithelial cells (TECs) and, in a murine TEC line, we have shown that the diabetogenic strain CV-B4 E2 decreases transcription of insulin-like growth factor 2 gene (Igf2), coding for the self-peptide of the insulin family. Here we show that in CV-B4 infection of mice alters Igf2 transcripts isoforms in TECs, followed by a decrease of pro-IGF2 precursor in the thymus. CV-B4 infection of a murine TEC line decreases Igf2 P3 promoter activity by targeting the region -68 to -22 upstream of the transcription start site (TSS) whereas Igf2 transcripts stability is not affected, pointing towards a regulation of Igf2 transcription. Our data also show that CV-B4 decreases IL-6/STAT3 signaling in vitro. This study provides new knowledge about the regulation of intrathymic Igf2 transcription by CV-B4 and reinforces the hypothesis that CV-B4 infection of the thymus could break central self-tolerance of the insulin family by decreasing Igf2 transcription and IGF2 presentation in thymus epithelium. IMPORTANCECoxsackievirus B4 represents one of the most important environmental factors associated to type 1 diabetes, autoimmune disease for which no curative treatment exist. The diabetogenic strain Coxsackievirus B4 E2 was previously shown to decrease Igf2 expression, important player for central tolerance towards insulin, in a thymic epithelial cell line. The understanding of Igf2 regulation mechanisms during coxsackievirus B4 infection represents an interest for the understanding of central tolerance development but also for Igf2 transcriptional regulation itself, still poorly understood. Here we demonstrate that, some transcripts isoforms of Igf2 are also decreased in thymic epithelial cells in vivo. Moreover, we show that this decrease is induced by an alteration of specific regions of Igf2 P3 promoter and may be linked by a decrease of STAT3 signaling. In fine we hope that this work could lead to future therapies leading to reprogramming central tolerance towards {beta} cells antigens via Igf2 expression.

microbiology↗