Biology subjects

Burel, A.

Publications and source records attributed to Burel, A..

4 recordsLinked to original sources

bioRxiv2026

Finely tuned DDA-PASEF-based immunopeptidomics workflow enhances HLA class I coverage

Mass spectrometry-based immunopeptidomics is essential for the direct identification of HLA-presented peptides, but its application to low-input and clinical samples remains challenging. In this study, we present an optimized DDA-PASEF-based workflow to improve HLA class I peptide coverage. First, we optimized a magnetic bead-based sample preparation protocol to support analysis from reduced starting material and increase compatibility with automation. We then evaluated LC gradient length and column dimensions to define complementary configurations for high-throughput and high-coverage analysis. For MS acquisition, we fine-tuned key parameters, including ion accumulation time, number of PASEF scans, ion mobility range, and polygon filtering, to improve sensitivity while maintaining a suitable cycle time and limiting pre-CID truncations. The customized polygon filter improved the detection of singly charged HLA class I peptides, thereby broadening the identified immunopeptide repertoire. Finally, TIMS2Rescore was integrated to improve confidence in peptide identification. Overall, this optimized workflow improves HLA class I immunopeptide coverage across different sample types, even from low injected sample amounts, supporting its future applicability to clinically relevant samples.

biochemistry↗

bioRxiv2024

sRNA-mediated crosstalk between cell wall stress and galactose metabolism in Staphylococcus aureus

Staphylococcus aureus is an opportunistic pathogen responsible for a wide range of diseases in humans. During infections, this bacterium is exposed to various stresses that target its cell wall, such as oxidative or acid environments as well as various cell wall-acting antimicrobials. S. aureus has effective regulatory systems for responding to environmental stresses enabling the expression of factors necessary for its survival. Bacterial small RNAs (sRNAs) play a crucial role in this adaptation process. In this study, we show that RsaOI, an S. aureus sRNA, accumulates under acid stress conditions. This response is mediated via the two-component system VraSR, which is associated with the cell wall damage response. As a component of the VraSR regulon, RsaOI contributes to the survival of S. aureus under acid stress and affects its susceptibility to glycopeptide antibiotics. Our findings reveal that RsaOI targets lacABCDFEG operon, which encodes components of tagatose pathway, a unique mechanism responsible for galactose metabolism in S. aureus. By antisense base pairing near the ribosome-binding site of lacD, RsaOI inhibits the expression of this gene, encoding tagatose-6-phosphate aldolase. This regulation disrupts the tagatose pathway, impairing galactose utilization in S. aureus. These findings highlight the role of RsaOI in the mediation between cell wall stress responses and specific metabolic pathway.

microbiology↗

bioRxiv2024

PPARgamma, a key modulator of metabolic reprogramming, stemness and chemoresistance associated with retrodifferentiation in human hepatocellular carcinomas

Human hepatocellular carcinomas (HCCs) with cancer stem cell (CSC) features are a subclass of therapeutically challenging cancers. We recently showed that retrodifferentiation of hepatic cancer cells into CSC-like cells leads to metabolic reprogramming and chemoresistance. The molecular mechanisms whereby differentiated cancer cells switch towards a CSC phenotype are poorly understood. By studying metabolic reprogramming associated with HCC cell plasticity, we identified an unsuspected role of peroxisome proliferator-activated receptor (PPAR){gamma} in hepatic CSC phenotype acquisition. Gene expression and metabolic analyses performed throughout cell differentiation/retrodifferentiation process of human HepaRG and HBG-BC2 HCC cells show that metabolic reprogramming in hepatic CSCs is associated with fragmented mitochondrial network, decreased respiration, de novo lipogenesis, fatty acid oxidation, but increased glycolysis and lipid storage. Mitochondrial genes downregulated in HepaRG-CSCs are also downregulated in the STEM HCC subclass. While PPAR is the main isoform in differentiated hepatic cells, we find high PPAR{gamma} expression in hepatic CSCs. Accordingly, nuclear localization of PPAR{gamma} is detected in human HCC tumors and PPAR{gamma}high/PPARlow expression is associated with the STEM HCC subclass and a poor outcome in human HCC cohorts. PPAR{gamma} silencing or/and inhibition of its target gene pyruvate dehydrogenase kinase 4 reactivates cell respiration, increases reactive oxygen species production and sensitizes hepatic CSCs to chemotherapy. Conversely, PPAR activation synergizes with chemotherapy to induce cell death. Targeting PPAR{gamma}, a key regulator of metabolic reprogramming and stemness in hepatic CSCs, or modulating the PPAR{gamma}/PPAR balance that finely tunes the differentiation/retrodifferentiation process in HCC deserves further investigation for antitumor therapy. Implications heading and statementPPAR{gamma}, a key regulator of metabolic reprogramming and stemness in hepatic CSC, reduces oxidative phosphorylation and reactive oxygen species production, therefore contributing to HCC chemoresistance.

cancer biology↗

bioRxiv2020

Mitochondrial Aurora kinase A induces mitophagy by interacting with MAP1LC3 and Prohibitin 2

Epithelial and haematologic tumours often show the overexpression of the serine/threonine kinase AURKA. Recently, AURKA was shown to localise at mitochondria, where it regulates mitochondrial dynamics and ATP production. Here we define the molecular mechanisms of AURKA in regulating mitochondrial turnover by mitophagy. When overexpressed, AURKA induces the disappearance of Outer Mitochondrial Membrane proteins by the proteasome. Then, AURKA triggers the degradation of Inner Mitochondrial Membrane (IMM)/matrix proteins by interacting with core components of the autophagy pathway. On the IMM, the kinase forms a tripartite complex with MAP1LC3 and the mitophagy receptor PHB2. This complex is necessary to trigger mitophagy in a PARK2/Parkin-independent manner. The formation of the tripartite complex is induced by the phosphorylation of PHB2 on Ser39, which is required for MAP1LC3 to interact with PHB2. Last, treatment with the PHB2 ligand Xanthohumol blocks AURKA-induced mitophagy by destabilising the tripartite complex. This treatment also restores normal ATP production levels. Altogether, these data provide evidence for a previously undetected role of AURKA in promoting mitophagy through the interaction with PHB2 and MAP1LC3. This work paves the way to the use of function-specific pharmacological inhibitors to counteract the effects of the overexpression of AURKA in cancer.

cell biology↗