Biology subjects

Pedeux, R.

Publications and source records attributed to Pedeux, R..

4 recordsLinked to original sources

bioRxiv2024

A Genome-wide CRISPR screen unveils WDR91 protein as a promoter of productive ASO activity

Antisense oligonucleotides (ASOs) belong to promising therapeutics for the treatment of neurologic, muscular and metabolic disorders. Several ASOs have been approved so far and more than a hundred clinical trials are currently underway covering a dozen therapeutic areas. Yet, the mechanisms of internalization and cell trafficking of these molecules remain poorly understood. Moreover, with only a small fraction of ASOs reaching the correct cellular compartment following systemic delivery, the majority of targeted diseases requires recurrent injections of ASOs. A deeper understanding of these mechanisms would guide the improvement of their potency and thus, reduce the amount of delivered ASOs and their potential side-effects. Here, using a CRISPR screen, we investigated intracellular proteins involved in ASOs efficiency using a whole genome approach and identified several potential regulators which could significantly impact ASOs potency in melanoma cells. We validated WD Repeat Domain 91 (WDR91), a regulator of endosomal maturation, as a modulator whose depletion significantly inhibits ASO productive activity. This study provides the first list of ASO modulators using a biologically relevant assay to estimate the role of these proteins. In conclusion, these data could lead to a better understanding of the mechanisms favoring productive uptake or improved endosomal escape of ASOs.

molecular biology↗

bioRxiv2022

Genomic characteristics and clinical significance of CD56+ Circulating Tumor Cells in Small Cell Lung Carcinoma

IntroductionCirculating Tumor Cells (CTC) have been studied in various solid tumors but clinical utility of CTC in Small Cell Lung Cancer (SCLC) remains unclear. The aim of the CTC-CPC study was to develop an EpCAM-independent CTC isolation method allowing isolation of a broader range of living CTC from SCLC and decipher their genomic and biological characteristics. Patients and methodsCTC-CPC is a monocentric prospective non-interventional study including treatment-naive newly diagnosed SCLC. CD56+CTC were isolated from whole blood samples, at diagnosis and relapse after first-line treatment and submitted to Whole-exome-sequencing (WES). ResultsPhenotypic study confirms tumor lineage and tumorigenic properties of isolated cells for the 4 patients analyzed with WES. WES of CD56+CTC and matched tumor biopsy reveal genomic alteration frequently impaired in SCLC. At diagnosis CD56+CTC were characterized by a high mutation load, a distinct mutational profile and a unique genomic, compared to match tumors biopsies. In addition to classical pathways altered in SCLC, we found new biological processes specifically affected in CD56+CTC at diagnosis. High numeration of CD56+CTC (>7/ml) at diagnosis was associated with ES-SCLC. Comparing CD56+CTC isolated at diagnosis and relapse, we identify differentially altered oncogenic pathways (e.g. DLL3 or MAPK pathway). ConclusionsWe report a versatile method of CD56+CTC detection in SCLC. Numeration of CD56+CTC at diagnosis is correlated with disease extension. Isolated CD56+CTC are tumorigenic and a distinct mutational profile. We report a minimal gene set as a unique signature of CD56+CTC and identify new affected biological pathways enriched in EpCAM-independent isolated CTC in SCLC.

cancer biology↗

bioRxiv2021

p97/VCP induces GLI1 to control XBP1-dependent endoplasmic reticulum stress transcriptional response

Upon accumulation of improperly folded proteins in the ER, an adaptive pathway named the UPR is triggered to restore ER homeostasis. The induction of stress genes controlling ER dynamics is a condition sine qua non for an effective UPR. Although this requirement has been extensively characterized, the transcriptional mechanism underlying this process remains in part elucidated. Here, we show that p97/VCP, an AAA+ ATPase known to modulate ER stress-induced gene expression, dynamically interacts with RUVBL2 and the mSin3A-HDAC1/2 complex. Further analysis of the mechanism defined a novel interplay between the aforementioned molecules and the transcription factor USF2 to control expression of GLI1, a primary effector of Hedgehog (Hh) signaling. Under basal conditions, GLI1 is repressed by RUVBL2-mSin3A-HDAC1/2 while upon ER stress GLI1 is induced through a mechanism requiring p97/VCP-mediated extraction of the repressor complex. Further analysis showed that GLI1 cooperate with ATF6f to activate the expression of XBP1, a transcription factor regulating the expression of genes controlling cellular stress response, under ER conditions. Overall, our work demonstrates that p97/VCP orchestrates the activation of GLI1 upon ER stress in a Hh ligand-independent fashion and defines the interplay between the newly identified p97/VCP-mSin3A-HDAC1/2 complex and the transcription factor USF2 as an essential player in this process.

cancer biology↗

bioRxiv2020

Stress-induced tyrosine phosphorylation of RtcB modulates IRE1 activity and signaling outputs.

Endoplasmic Reticulum (ER) stress is a hallmark of various diseases, which is dealt with through the activation of an adaptive signaling pathway named the Unfolded Protein Response (UPR). This response is mediated by three ER-resident sensors and the most evolutionary conserved, IRE1 signals through its cytosolic kinase and endoribonuclease (RNase) activities. IRE1 RNase activity can either catalyze the initial step of XBP1 mRNA unconventional splicing or degrade a number of RNAs through Regulated IRE1- Dependent Decay (RIDD). The balance between these two activities plays an instrumental role in cells life and death decisions upon ER stress. Until now, the biochemical and biological outputs of IRE1 RNase activity have been well documented, however, the precise mechanisms controlling whether IRE1 signaling is adaptive or pro-death (terminal) remain unclear. This prompted us to further investigate those mechanisms and we hypothesized that XBP1 mRNA splicing and RIDD activity could be co-regulated by the IRE1 RNase regulatory network. We showed that a key nexus in this pathway is the tRNA ligase RtcB which, together with IRE1, is responsible for XBP1 mRNA splicing. We demonstrated that RtcB is tyrosine phosphorylated by c-Abl and dephosphorylated by PTP1B. Moreover, we identified RtcB Y306 as a key residue which, when phosphorylated, perturbs RtcB interaction with IRE1, thereby attenuating XBP1 mRNA splicing and favoring RIDD. Our results demonstrate that the IRE1 RNase regulatory network is dynamically fine-tuned by tyrosine kinases and phosphatases upon various stresses and that the nature of the stress determines cell adaptive or death outputs.

biochemistry↗