Biology subjects

Metzakopian, E.

Publications and source records attributed to Metzakopian, E..

9 recordsLinked to original sources

bioRxiv2026

CRISPR/CAS9-MEDIATED LOSS OF VESICULAR GLUTAMATE TRANSPORTER IN SEROTONIN NEURONS OF THE DORSAL RAPHE NUCLEUS LEADS TO SYNAPTIC CHANGES AND ANXIETY-LIKE BEHAVIORS

Vesicular glutamate transporter 3 (VGluT3) is expressed in a large subset of serotonin (5-HT) neurons of the dorsal raphe nucleus (DRN), suggesting a potential for glutamate co-transmission. Although VGluT3 has been implicated in the physiology of several non-glutamatergic neuronal populations, its specific role in the organization and function of 5-HT axons remains unclear. Here, we used CRISPR-Cas9 mediated knockdown and viral overexpression of VGluT3 in DRN 5-HT neurons of adult mice to assess its contribution to synaptic architecture in the lateral hypothalamus (LHA) and to 5-HT-related behaviors. VGluT3 depletion did not significantly alter synaptic incidence or organization of 5-HT DRN terminals in the LHA. In contrast, VGluT3 overexpression increased the proportion of asymmetric synapses without changing the overall synaptic incidence. In behavioral assays, VGluT3 depletion impaired motor coordination and increased anxiety-like, repetitive, and social behavior, whereas VGluT3 overexpression selectively reduced repetitive behavior. Basal locomotion and depressive-like behaviors were unchanged by either manipulation. Together, these findings indicate that VGluT3 modulates both the structural organization and behavioral output of DRN 5-HT neurons, supporting a modulatory role for VGluT3-dependent signaling within 5-HT circuits.

neuroscience↗

bioRxiv2025

Axon-specific mRNA translation shapes dopaminergic circuit development

The precise organization of midbrain dopaminergic (mDA) projections is essential for motor and cognitive functions, and their disruption contributes to multiple brain disorders. Yet the molecular mechanism guiding the development of these projections remains poorly defined. Here, we used ribosome tagging (RiboTag) and specific mouse crossing strategies (DATIRES-Cre mice) to isolate ribosome-bound mRNAs specifically from mDA axons and to analyze their axonal translatomes across developmental stages. We found that early-stage axons are enriched in transcripts involved in axon guidance and growth, while mature axons predominantly translate mRNAs related to synaptic function. Among key candidates, we identified PlxnA4, which is locally translated into mDA axons and modulates arborization in response to Sema3a. Functional assays in vitro and in vivo revealed that Plxna4-mediated signaling regulates topographical axon targeting and innervation, particularly in the nigrostriatal pathway. Our results uncover a dynamic and compartment-specific regulation of mRNA translation in developing mDA neurons, offering mechanistic insight into circuit formation and providing new molecular targets to improve integration of grafted neurons in regenerative therapies for Parkinsons disease.

developmental biology↗

bioRxiv2023

Unravelling cell type specific response to Parkinson's Disease at single cell resolution

Parkinsons Disease (PD) is the second most common neurodegenerative disorder and is generally characterized by impaired motor functions. It currently affects 6.3 million people aged 60 years and more, worldwide. The pathological hallmarks of PD are Lewy bodies (abnormal aggregation of -synuclein inside cells), which are observed primarily in the substantia nigra (SN) region of the midbrain. It is yet not known how different cell types in SN respond during PD and what are the molecular mechanisms underlying neurodegeneration. To address this question, we generated a large-scale single cell transcriptomics dataset from human post-mortem SN tissue of 29 donors including 15 sporadic cases and 14 controls. We obtained data for a total of [~]80K nuclei, representing major cell types of the brain (including neurons, astrocytes, microglia and oligodendrocytes). Pathway and differential gene expression analysis revealed multicellular character of PD pathology involving major cellular response from neuronal and glial cells.

bioinformatics↗

bioRxiv2022

HNRNPH1 regulates the neuroprotective cold-shock protein RBM3 expression through poison exon exclusion

Enhanced expression of the cold-shock protein RNA binding motif 3 (RBM3) is highly neuroprotective both in vitro and in vivo. Whilst upstream signalling pathways leading to RBM3 expression have been described, the precise molecular mechanism of RBM3 induction during cooling remains elusive. To identify temperature-dependent modulators of RBM3, we performed a genome-wide CRISPR-Cas9 knockout screen using RBM3-reporter human iPSC-derived neurons. We found that RBM3 mRNA and protein levels are robustly regulated by several splicing factors, with heterogeneous nuclear ribonucleoprotein H1 (HNRNPH1) being the strongest positive regulator. Splicing analysis revealed that moderate hypothermia significantly represses the inclusion of a poison exon, which, when retained, targets the mRNA for nonsense-mediated decay. Importantly, we show that HNRNPH1 mediates this cold-dependent exon skipping via its interaction with a G-rich motif within the poison exon. Our study provides novel mechanistic insights into the regulation of RBM3 and provides further targets for neuroprotective therapeutic strategies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/514062v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@ef0a5org.highwire.dtl.DTLVardef@d907a5org.highwire.dtl.DTLVardef@85176aorg.highwire.dtl.DTLVardef@1c4306a_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2022

A genetic variant of the Wnt receptor LRP6 accelerates synapse degeneration during ageing and in Alzheimer's disease

Synapse loss strongly correlates with cognitive decline in Alzheimers Disease (AD), but the underlying mechanisms are poorly understood. Studies suggest that deficient Wnt signalling, a pathway required for neuronal connectivity, contributes to synapse dysfunction and loss in AD. Consistent with this idea, a variant of Lrp6, (Lrp6-val), which confers reduced Wnt signalling, has been linked to late onset AD. However, the impact of Lrp6-val on synapses in the healthy and AD brain has not been examined. Using CRISPR/Cas9 genome editing, we generated a novel knock-in mouse model carrying this Lrp6 variant to study its role in synaptic integrity. Lrp6-val mice develop normally and do not exhibit morphological brain abnormalities. Hippocampal neurons from Lrp6-val mice do not respond to Wnt7a, a Wnt ligand that promotes synaptic assembly through the Frizzled-5 (Fz5) receptor. Activation of the Wnt pathway by Wnt ligands leads to the formation of a complex between LRP6 and Fz5. In contrast, LRP6-Val impairs the formation of the LRP6-Fz5 complex elicited by Wnt7a, as detected by proximity ligation assay (PLA). We demonstrate that Lrp6-val mice exhibit structural and functional synaptic defects that become more pronounced with age, consistent with decreased canonical Wnt signalling during ageing. To investigate the contribution of this variant to AD, Lrp6-val mice were crossed to hAPPNL-G-F/NL-G-F (NL-G-F), a knock-in AD mouse model. The presence of the Lrp6-val variant significantly exacerbates synapse loss around amyloid-{beta} plaques in NL-G-F mice. Our findings uncover a novel role for the Lrp6-val variant in synapse vulnerability during ageing and its contribution to synapse degeneration in AD.

neuroscience↗

bioRxiv2021

Endoplasmic Reticulum morphological regulation by RTN4/NOGO modulates neuronal regeneration by slowing luminal transport

Cell and tissue functions rely on an elaborate intracellular transport system responsible for distributing bioactive molecules with high spatiotemporal accuracy. The tubular network of the Endoplasmic Reticulum (ER) constitutes a system for the delivery of luminal solutes it stores, including Ca2+, across the cell periphery. The physical nature and factors underlying the ERs functioning as a fluidics system are unclear. Using an improved ER transport visualisation methodology combined with optogenetic Ca2+ dynamics imaging, we observed that ER luminal transport is modulated by natural ER tubule narrowing and dilation, directly proportional to the amount of an ER membrane morphogen, Reticulon 4 (RTN4). Consequently, the ER morphoregulatory effect of RTN4 defines ERs capacity for peripheral Ca2+ delivery and thus controls axonogenesis. Excess RTN4 limited ER luminal transport, Ca2+ release and iPSC-derived cortical neurons axonal extension, while RTN4 elimination reversed the effects. SummaryIntracellular transport through the lumen of the ER network is modulated through narrowing/dilation of ER tubules by a membrane morphogen - RTN4, a process controlling axonogenesis by limiting the delivery of ER-stored Ca2+.

cell biology↗

bioRxiv2020

MicroExonator enables systematic discovery and quantification of microexons across mouse embryonic development

Microexons, exons that are [≤]30 nucleotides, were shown to play key roles in neuronal development, but are difficult to detect and quantify using standard RNA-Seq alignment tools. Here, we present MicroExonator, a novel pipeline for reproducible de novo discovery and quantification of microexons. We processed 289 RNA-seq datasets from eighteen mouse tissues corresponding to nine embryonic and postnatal stages, providing the most comprehensive survey of microexons available for mouse. We detected 2,984 microexons, 332 of which are differentially spliced throughout mouse embryonic brain development, including 29 that are not present in mouse transcript annotation databases. Unsupervised clustering of microexons alone segregates brain tissues by developmental time and further analysis suggest a key function for microexon inclusion in axon growth and synapse formation. Finally, we analysed single-cell RNA-seq data from the mouse visual cortex and we report differential inclusion between neuronal subpopulations, suggesting that some microexons could be cell-type specific.

genomics↗

bioRxiv2018

Mutations generated by repair of Cas9-induced double strand breaks are predictable from surrounding sequence

The exact DNA mutation produced by cellular repair of a CRISPR/Cas9-generated double strand break determines its phenotypic effect. It is known that the mutational outcomes are not random, and depend on DNA sequence at the targeted location. Here, we present a systematic study of this link. We created a high throughput assay to directly measure the edits generated by over 40,000 guide RNAs, and applied it in a range of genetic backgrounds and for alternative CRISPR/Cas9 reagents. In total, we gathered data for over 1,000,000,000 mutational outcomes in synthetic constructs, which mirror those at endogenous loci. The majority of reproducible mutations are insertions of a single base, short deletions, or long microhomology-mediated deletions. gRNAs have a cell-line dependent preference for particular outcomes, especially favouring single base insertions and microhomology-mediated deletions. We uncover sequence determinants of the produced mutations at individual loci, and use these to derive a predictor of Cas9 editing outcomes with accuracy close to the theoretical maximum. This improved understanding of sequence repair allows better design of editing experiments, and may lead to future therapeutic applications.

cell biology↗

bioRxiv2018

ATM orchestrates the DNA-damage response to counter toxic non-homologous end-joining at broken replication forks

Mutations in the ATM tumor suppressor confer hypersensitivity to DNA-damaging agents. To explore genetic resistance mechanisms, we performed genome-wide CRISPR-Cas9 screens in cells treated with the DNA topoisomerase poison topotecan. Thus, we establish that loss of terminal components of the non-homologous end-joining (NHEJ) machinery or the BRCA1-A complex specifically confers topotecan resistance to ATM-deficient cells. We show that hypersensitivity of ATM-mutant cells to topotecan or the poly-(ADP-ribose) polymerase inhibitor olaparib is due to delayed homologous recombination repair at DNA-replication-fork-associated double-strand breaks (DSBs), resulting in toxic NHEJ-mediated chromosome fusions. Accordingly, restoring legitimate repair in ATM-deficient cells, either by preventing NHEJ DNA ligation or by enhancing DSB-resection by BRCA1-A complex inactivation, markedly suppresses this toxicity. Our work suggests opportunities for patient stratification in ATM-deficient cancers and when using ATM inhibitors in the clinic, and identifies additional therapeutic vulnerabilities that might be exploited when such cancers evolve drug resistance.\n\nOne Sentence SummaryATM counteracts toxic NHEJ at broken replication forks

cell biology↗