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Biology subjects

Modafferi, S.

Publications and source records attributed to Modafferi, S..

4 recordsLinked to original sources

DNA damage response defects induced by the formation of TDP-43 and mutant FUS cytoplasmic inclusions and their pharmacological rescue.

Formation of cytoplasmic inclusions (CIs) of TDP-43 and FUS, along with DNA damage accumulation, is a hallmark of affected motor neurons in Amyotrophic Lateral Sclerosis (ALS). However, the impact of CIs on DNA damage response (DDR) and repair in this pathology remains unprobed. Here, we show that CIs of TDP-43 and FUSP525L, co-localizing with stress granules, lead to a dysfunctional DDR activation associated with physical DNA breakage. Inhibition of the activity of the DDR kinase ATM, but not of ATR, abolishes DDR signaling, indicating that DNA double-strand breaks (DSBs) are the primary source of DDR activation. In addition, cells with TDP-43 and FUSP525L CIs exhibit reduced DNA damage-induced RNA synthesis at DSBs. We previously showed that the two endoribonucleases DROSHA and DICER, also known to interact with TDP-43 and FUS during small RNA processing, contribute to DDR signaling at DSBs. Treatment with enoxacin, which stimulates DDR and repair by boosting the enzymatic activity of DICER, restores a proficient DDR and reduces DNA damage accumulation in cultured cells with CIs and in vivo in a murine model of ALS. In Drosophila melanogaster, Dicer-2 overexpression rescues TDP-43-mediated retinal degeneration. In summary, our results indicate that the harmful effects caused by TDP-43 and FUS proteinopathies include genotoxic stress and that the pharmacological stimulation of the DNA damage signaling and repair counteracts it.

molecular biology↗

DROSHA, DICER and Damage-Induced long ncRNA control BMI1-dependent transcriptional repression at DNA double-strand break

Genome integrity is safeguarded by the DNA damage response (DDR). Controlled transcriptional dampening of genes surrounding DNA double-strand breaks (DSBs) has been shown to facilitate DNA repair. This phenomenon, defined as DSB-induced silencing in cis (DISC), involves the DDR apical kinase ATM and the Polycomb Repressive Complex 1 (PRC1). Conversely, DSBs have also been reported to induce de novo transcription of damaged-induced long non-coding RNAs (dilncRNAs) in a MRE11-RAD50-NBS1 (MNR) complex-dependent manner. MRN also controls the recruitment to DSB of the ribonuclease DROSHA, which together with DICER, stimulates DDR signaling and DNA repair. Here, we reconcile these apparently contrasting observations by showing that dilncRNA, together with DROSHA and DICER, but not GW182-like proteins required for miRNA-mediated gene silencing, controls DISC. Indeed, similarly to ATM, MRN inhibition abolishes DISC while pharmacological enhancement of DICER ribonuclease activity by Enoxacin improves DISC. Importantly, Enoxacin administration restores DISC upon ATM inhibition, demonstrating that DICER promotes DISC independently from ATM. Differently, Enoxacin does not restore DISC upon MRN inhibition, suggesting that DICER acts downstream to dilncRNA biogenesis and DROSHA recruitment. Mechanistically, we show that DROSHA and DICER control the recruitment of the PRC1 component BMI1 at DSBs and the consequent H2A-K119 ubiquitination. Upon DSBs formation, BMI1 and DROSHA interact in an RNA-dependent manner. Indeed, BMI1 associates to dilncRNA and do so in a DROSHA- and DICER-dependent manner. Importantly, inhibition of dilncRNA function by antisense oligonucleotides or Cas13-mediated targeting is sufficient to reduce BMI1 recruitment and DISC at individual loci. We propose that dilncRNAs together with DROSHA and DICER control DISC at genomic DSB by supporting PRC1 recruitment and chromatin ubiquitination.

molecular biology↗

Multi-omics analysis of paracetamol exposure identifies dysregulated genes involved in neurotoxicity and neuronal differentiation of human embryonic stem cells

Prenatal paracetamol exposure has been associated with neurodevelopmental outcomes in childhood. Pharmacoepigenetic studies show differences in cord blood DNA methylation between paracetamol exposed and unexposed neonates. However, causal implications and impact of long-term prenatal long-term paracetamol exposure on brain development remain unclear. Using a multi-omics approach, we investigated the effects of paracetamol on a model of early human brain development. We exposed human embryonic stem cells undergoing in vitro neuronal differentiation to daily media changes with paracetamol concentrations corresponding to maternal therapeutic doses. Single-cell RNA-seq and ATAC-seq integration identified paracetamol-induced chromatin-opening changes linked to gene expression. Differentially methylated and/or expressed genes were involved in signalling, neurotransmission, and cell fate-determination trajectories. Some genes involved in neuronal injury and development-specific pathways, such as KCNE3, overlapped with differentially methylated genes previously identified in cord blood associated with prenatal paracetamol exposure. Our data suggest that paracetamol may play a causal role in impaired neurodevelopment. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=191 HEIGHT=200 SRC="FIGDIR/small/519620v2_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@e1a75forg.highwire.dtl.DTLVardef@b36a1forg.highwire.dtl.DTLVardef@fc25e4org.highwire.dtl.DTLVardef@1bb1c8_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

A multi-omics approach to visualize early neuronal differentiation in 4D

Neuronal differentiation of pluripotent stem cells is an established method to study physiology, disease and medication safety. However, the sequence of events in human neuronal differentiation and the ability of in vitro models to recapitulate early brain development are poorly understood. We developed a protocol optimized for the study of early human brain development and neuropharmacological applications. We comprehensively characterized gene expression and epigenetic profiles at four timepoints, as the cells differentiate from embryonic stem cells towards a heterogenous population of progenitors, immature and mature neurons bearing telencephalic signatures. A multi-omics roadmap of neuronal differentiation, combined with searchable interactive gene analysis tools, allows for extensive exploration of early neuronal development and the effect of medications. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=178 SRC="FIGDIR/small/478732v1_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@163539forg.highwire.dtl.DTLVardef@72c09org.highwire.dtl.DTLVardef@dc04eforg.highwire.dtl.DTLVardef@c821d2_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIMulti-omics charting a new neuronal differentiation protocol for human ES cells C_LIO_LISingle-cell analyses reveals marker genes during neuronal differentiation C_LIO_LIIdentified transcriptional waves similar to early human brain development C_LIO_LISearchable tools to visualize single-cell gene expression and chromatin state C_LI In BriefWe have developed a novel protocol for human embryonic stem cells to study neural induction and early neuronal differentiation. Multi-omics analyses uncovered cell populations, genes and transcriptional waves defining cell fate commitment. We comprehensively describe epigenetic landscapes and gene expression and provide searchable analysis tools for exploration of the data.

cell biology↗