Biology subjects

Batsche, E.

Publications and source records attributed to Batsche, E..

9 recordsLinked to original sources

bioRxiv2026

CBX3 Deletion Overcomes Ferroptosis Resistance in Colorectal Cancer by Targeting IFNγ/SLC7A11/SLC3A2 Axis

System Xc- (SLC7A11/SLC3A2) maintains redox balance by supporting glutathione synthesis, thereby preventing lipid peroxidation and ferroptosis, and represents a promising therapeutic target in cancer. In this work, we revealed that an important epigenetic regulator, CBX3 deletion significantly increased intracellular ROS and lipid ROS level following ferroptosis inducing, particularly under IFN{gamma} stimulation, thereby sensitized CRC cells to ferroptosis in vitro using human CRC cells as well as in vivo using MC38 syngenetic tumors. RNAseq with mice syngeneic tumors revealed an 11-gene oxidative stress signature downregulated in Cbx3KO tumors after combined treatment; its low expression score correlated with improved overall survival in CRC patients. Among them, Slc7a11, Ptgs2, and Cth were identified as CBX3 direct target genes. Additionally, several amino acid transporters functionally coupled to Xc- antiporter, as Slc3a2, Slc7a5, Slc1a5 and Slc6a9, all significantly decreased in Cbx3KO tumor under RSL3+IFN{gamma} treatment. Mechanistically, CBX3 binds directly to the promoter of Slc7a11 or Slc3a2 to sustain their expression and redox balance to resist ferroptosis in CRC. Knockout of CBX3 in CRC cells significantly impaired RNA polymerase II recruitment to the promoter of SLC7A11 or SLC3A2 and reduced SLC7A11 and SLC3A2 expression, an effect that was further exacerbated under IFN{gamma} stimulation but restored by STAT1 deletion. Overall, CBX3 protects CRC from oxidative stress by maintaining the functional integrity of IFN{gamma}/STAT1/SLC7A11/SLC3A2 axis, positioning CBX3 as a potential therapeutic target for enhancing ferroptosis therapies in CRC.

cancer biology↗

bioRxiv2025

Identification of CaVβ1 isoforms required for neuromuscular junction formation and maintenance

Voltage-gated Ca{superscript 2} channels (VGCCs) are regulated by four CaV{beta} subunits (CaV{beta}1-CaV{beta}4), each showing specific expression patterns in excitable cells. While primarily known for regulating VGCC function, CaV{beta} proteins also have channel-independent roles, including gene expression modulation. Among these, CaV{beta}1 is expressed in skeletal muscle as multiple isoforms. The adult isoform, CaV{beta}1D, localizes at the triad and modulates CaV1 activity during Excitation-Contraction Coupling (ECC). In this study, we investigated the lesser-known embryonic/perinatal CaV{beta}1 isoforms and their roles in neuromuscular junction (NMJ) formation, maturation, and maintenance. We found that CaV{beta}1 isoform expression is developmentally regulated through differential promoter activation. Specifically, CaV{beta}1A is expressed in embryonic muscle and reactivated in denervated adult muscle, alongside the known CaV{beta}1E isoform. Nerve injury in adult muscle triggers a shift in promoter usage, resulting in re-expression of embryonic/perinatal Cacnb1A and Cacnb1E transcripts. Functional analyses using aneural agrin-induced AChR clustering on primary myotubes demonstrated that these isoforms contribute to NMJ formation. Additionally, their expression during early postnatal development is essential for NMJ maturation and long-term maintenance. These findings reveal previously unrecognized roles of CaV{beta}1 isoforms beyond VGCC regulation, highlighting their significance in neuromuscular system development and homeostasis.

physiology↗

bioRxiv2023

Defective Integrator activity shapes the transcriptome of patients with multiple sclerosis

HP1/CBX5 is an epigenetic regulator with a suspected role in multiple sclerosis (MS). Here, using high-depth RNA sequencing on monocytes, we identified a subset of MS patients with reduced CBX5 expression, correlating with progressive stages of the disease and extensive transcriptomic alterations. Examination of rare non-coding RNA species in these patients revealed impaired maturation/degradation of U snRNAs and enhancer-RNAs, indicative of a reduced activity of the Integrator, a complex with suspected links to increased MS risk. At protein-coding genes, compromised Integrator activity manifested in reduced pre-mRNA splicing efficiency and altered expression of genes regulated by RNA polymerase II pause-release. Inactivation of Cbx5 in the mouse mirrored most of these transcriptional defects and resulted in hypersensitivity to Experimental Autoimmune Encephalomyelitis (EAE). Collectively, our observations suggested a major contribution of the Integrator complex in safeguarding against transcriptional anomalies characteristic of MS, with HP1/CBX5 emerging as an unexpected regulator of this complexs activity. These findings bring novel insights into the transcriptional aspects of MS and provide potential new criteria in patient stratification.

genomics↗

bioRxiv2022

The HP1γ epigenetic silencer dampens IFN-γ response at the gut epithelial barrier

Interferon gamma (IFN-{gamma}) plays central roles in the pathophysiology of inflammatory bowel disease (IBD), both activating inflammatory responses and immunosuppressive functions. However, the epigenetic mechanisms controlling the expression of IFN-{gamma} responsive genes at the gut epithelial barrier are not well understood. In this study, we identified the epigenetic regulator HP1{gamma} as a transcriptional repressor of the IFN-{gamma}-responsive genes STAT1 (signal transducer and activator of transcription 1) and PD-L1 (Programmed Cell Death Ligand 1). Accordingly, HP1{gamma} gene inactivation in the mouse gut epithelium resulted in an immunopathology with a long-lasting up-regulation of STAT1 and PD-L1. Colon organoids models and in vitro cell lines showed that HP1{gamma} deficiency primed STAT1 and PD-L1 expressions, ultimately sensitizing epithelial cells to IFN-{gamma} stimulation. Chromatin immunoprecipitation experiments suggest that HP1 promoter tethering is involved in the silencing of gene expression. Overall, these results identify HP1{gamma} as an epigenetic silencing pathway controlling the IFN-{gamma} response at the epithelial barrier.

immunology↗

bioRxiv2022

Influenza A virus RNA Polymerase targets the chromatin of innate immune response genes

KEY POINTSO_LIFluPol is linked to RNAs in gene body and 3-downstream regions C_LIO_LIFluPol Chromatin-targets are involved in the cell defense C_LIO_LICap-snatching could occur everywhere during transcription elongation C_LI The influenza A virus (IAV) RNA polymerase (FluPol) primes the viral transcription by using capped 5-ends << snatched >> from host nascent RNAs. However, the exact localization of the FluPol on the genome or the timing of its snatching activity remains poorly characterized. Here, we have monitored IAV infection from the perspective of the FluPol interaction with the host chromatin template. Quantification of chromatin-bound RNAs shows a significant perturbation in host transcription that correlates with a relocalization of RNA polymerase II (RNAPII) from the gene bodies to downstream intergenic regions. This extended transcription leading to the production of RNA downstream of genes (DoGs) was previously linked to the NS1-mediated inhibition of the transcriptional termination. However, immunoprecipitation of FluPol-bound RNA in the chromatin fraction revealed that FluPol remains linked to nascent host transcripts during phases of transcriptional elongation and termination, thereby extending the window of opportunity in which cap-snatching may occur. In addition, chromatin-associated FluPol was enriched at transcription termination sites, suggesting that it may participate in the virus-induced termination defects. Finally, we observed that, rather than targeting just highly expressed genes, the FluPol was preferentially recruited to promoters activated by the viral infection and enhancers. Together, these observations suggest the FluPol uses the early immune response to target regulatory elements of defense-related genes at which it interferes with the fate of the transcripts, and possibly also limits RNAPII re-initiation by impairing the termination process. Author SummaryThe influenza A virus (IAV) exploits the transcriptional machinery of the infected cells to generate its own RNAs with the viral polymerase (FluPol) hijacking cap structures from host mRNAs. This "cap snatching" requires an interaction between FluPol and the cellular RNA polymerase (RNAPII) accumulating at transcription start sites (TSS) of genes. In parallel, another IAV factor interferes the termination of gene transcription, resulting in frequent transcription downstream of genes and reduced recycling of the RNAPII. Here, employing genome-wide ChIP assays, we show that FluPol selectively targets the TSS of infection-activated genes often associated with cellular defense mechanisms, and thereby contributing to their downregulation. In addition, we show that FluPol is not only recruited to promoters and enhancers, but also within genes, where it interacts with nascent RNAs during transcription and splicing. It is further detected beyond the 3 end of the genes, suggesting that FluPol exerts a broad influence on host transcription by affecting both transcription initiation through cap-snatching and transcription re-initiation via its involvement in the virus-induced transcription-termination defect at the end of genes.

molecular biology↗

bioRxiv2020

HP1γ sets the biological age of the intestinal epithelium

Defects in RNA splicing have been linked to numerous human disorders, but remain poorly explored in inflammatory bowel disease (IBD). Here, we report that, in the gut epithelium of patients with ulcerative colitis (UC), the expression of the chromatin and alternative splicing regulator HP1{gamma} is strongly reduced. Accordingly, inactivation of the HP1{gamma} gene in the mouse gut triggered several IBD-like traits, including inflammation and dysbiosis. In parallel, we discovered that its loss of function broadly increased splicing noise, reducing requirement for canonical splicing consensus sequences, and favoring the usage of cryptic splice sites at numerous genes with key functions in gut biology. This notably resulted in the production of progerin, a noncanonical toxic splice variant of prelamin A mRNA, responsible for the Hutchinson Gilford Progeria Syndrome (HGPS) of premature aging. Likewise, production of progerin transcript was found to be a signature of colonic cells from UC patients. Thus, our study identifies HP1{gamma} as a regulator of RNA metabolism in vivo, providing a unique mechanism linking anti-inflammation and accuracy of RNA splicing in the gut epithelium. HP1 defect may confer a general disturbance in RNA splicing precision to scrutinize in IBD and more generally in accelerating aging diseases.

cell biology↗

bioRxiv2019

Reduced RNA turnover as a driver of cellular senescence

Accumulation of senescent cells is an important contributor to chronic inflammation upon aging. While cytoplasmic DNA was shown to drive the inflammatory phenotype of senescent cells, an equivalent role for RNA has never been explored. Here, we show that some senescent cells accumulate long promoter RNAs and 3 gene extensions, rich in retrotransposon sequences. Accordingly, these cells display increased expression of genes involved in detecting double stranded RNA of viral origin downstream of the interferon pathway. The RNA accumulation is correlated with signs of reduced RNA turn-over, including in some cases, reduced expression of RNA exosome subunits. Reciprocally, engineered inactivation of RNA exosome subunit Exosc3 induces expression of multiple senescence markers. A senescence-like RNA accumulation is also observed in cells exposed to oxidative stress, an important trigger of cellular senescence. Altogether, we propose that in a subset of senescent cells, repeat-containing transcripts stabilized by oxidative stress or reduced RNA exosome activity participate, possibly in combination with cytoplasmic DNA, in driving and maintaining the permanent inflammatory state characterizing cellular senescence.

molecular biology↗

bioRxiv2019

CD44 alternative splicing is a sensor of intragenic DNA methylation in tumors

DNA methylation (meDNA) is a suspected modulator of alternative splicing, while splicing in turn is involved in tumour formations nearly as frequently as DNA mutations. Yet, the impact of meDNA on tumorigenesis via its effect on splicing has not been thoroughly explored. Here, we find that HCT116 colon carcinoma cells inactivated for the DNA methylases DNMT1 and DNMT3b undergo a partial epithelial to mesenchymal transition (EMT) associated with alternative splicing of the CD44 transmembrane receptor. The skipping of CD44 variant exons is in part explained by altered expression or splicing of splicing and chromatin factors. A direct effect of meDNA on alternative splicing was sustained by transient depletion of DNMT1 and the methyl-binding genes MBD1, MBD2, and MBD3. Yet, local changes in intragenic meDNA also altered recruitment of MBD1 protein and of the chromatin factor HP1{gamma} known to alter transcriptional pausing and alternative splicing decisions. We further tested if meDNA level has sufficiently strong direct impact on the outcome of alternative splicing to have a predictive value in the MCF10A model for breast cancer progression and in patients with acute lymphoblastic leukemia (B ALL). We found that a small number of differentially spliced genes mostly involved in splicing and signal transduction is systematically correlated with local meDNA. Altogether, our observations suggest that, although DNA methylation has multiple avenues to alternative splicing, its indirect effect may be also mediated through alternative splicing isoforms of these sensors of meDNA.

molecular biology↗

bioRxiv2018

Compound signaling activates endogenous retroviruses by inducing enhancer and gene-neighborhood transcription

SummaryMultiple sclerosis (MS) is a neuroinflammatory and autoimmune disease, in which various immune cell types and autoreactive T cells exert a pathogenic activity. This disease is also associated with increased transcription of several endogenous retroviruses (HERVs) normally kept in check by heterochromatin. Here, we have uncovered an organic pollutant dieldrin that activates several HERVs associated with MS and allowing us to examine the mechanism of their activation. Dieldrin singles out by its ability to simultaneously activate the MAP kinase and the PI3K pathways, while also triggering calcium dependent peptidylarginine deiminase activity. It was this association of pathways that caused HERV activation, a phenomenon that was only part of more generally increased transcription of heterochromatic regions. The HERV transcripts were generally not polyadenylated. Some arose as a consequence of activation of HERV-based enhancers, while others were the result of unusually strong activation at some mostly transcription factor genes causing transcription to leak out of the HERV-free region that surrounds them. Altogether, our data emphasized the hazard associated with simultaneous activation of multiples signaling pathways by xenobiotics, while also providing a very general toolbox for the interpretation of HERV transcription.

molecular biology↗