Biology subjects

Amzallag, E.

Publications and source records attributed to Amzallag, E..

3 recordsLinked to original sources

bioRxiv2025

Ubiquitination regulates granulostasis and DRiP accumulation in SGs under heat stress via the E3 ligase MKRN2

Stress granules (SGs) are transient cytoplasmic biomolecular condensates that play a role in the cellular response to proteotoxic stress. It has been previously shown that ubiquitination regulates SG dynamics; however, the specific mechanisms by which ubiquitin affects SGs are not fully understood. Here, using proximity proteomics, we discover that the engagement of several E3 ubiquitin ligases in SGs is dependent on UBA1 activity. A detailed study of the E3 ubiquitin-protein ligase Makorin 2 (MKRN2) demonstrated that it is localized to SGs in a manner dependent on active ubiquitination. MKRN2 promotes both the proper formation of SGs and their disassembly following stress recovery, by preventing the accumulation of defective ribosomal products (DRiPs) within SGs. Therefore, MKRN2 is a novel regulator of SGs that mediates the maintenance of granulostasis, suggesting that the localization of a subset of E3 ligases into SGs is linked to their capacity to ubiquitinate target proteins.

cell biology↗

bioRxiv2025

TDP-43 pathology triggers SRRM4-dependent cryptic splicing of G3BP1 in ALS/FTD

Loss of nuclear TDP-43 is a defining feature of the neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), yet how this leads to selective neuronal vulnerability is poorly understood. Here, using human iPSC-derived neurons and a large multi-omics dataset of ALS/FTD patients, we demonstrate that TDP-43 pathology induces the inclusion of an in-frame cryptic exon in human G3BP1. The resulting CRYPTIC G3BP1 protein contains an additional 10-amino acids within the highly conserved NTF2L domain, which acts as a dominant negative and disrupts stress granule dynamics. We further show that cryptic exon inclusion in G3BP1 upon TDP-43 loss is enriched in neurons. Mechanistically, the loss of TDP-43 unmasks a binding site for the neuron-specific splicing regulator SRRM4 within intron 2 of G3BP1, enabling the inclusion of the cryptic exon. Collectively, our findings reveal that neuron-specific regulatory mechanisms intersect with TDP-43 -mediated splicing and suggest a mechanistic basis for the increased neuronal vulnerability observed in ALS/FTD.

neuroscience↗

bioRxiv2024

Organellomics: AI-driven deep organellar phenotyping of human neurons

Systematic assessment of organelle architectures, termed the organellome, offers valuable insights into cellular states and pathomechanisms, but remains largely uncharted. Here, we present a deep phenotypic learning based on vision transformers, resulting in the Neuronal Organellomics Vision Atlas (NOVA) model that studies confocal images of more than 30 markers of distinct membrane-bound and membraneless organelles in 11.5 million images of human neurons. Organellomics analysis quantifies perturbation-induced changes in organelle localization and morphology using a rigorous mixed-effects meta-analytic framework that accounts for sampling variance and experimental heterogeneity. Applying this approach, we delineate phenotypic alterations in neurons carrying ALS-associated mutations and uncover a physical and functional crosstalk between cytoplasmic mislocalized TDP-43, a hallmark of ALS, and processing bodies (P-bodies), membraneless organelles regulating mRNA stability. These findings are validated in patient-derived neurons and human neuropathology. NOVA establishes a scalable framework for quantitative mapping of subcellular phenotypes and provides a new avenue for investigating the neurocellular basis of disease.

systems biology↗