Biology subjects

Setti, A.

Publications and source records attributed to Setti, A..

10 recordsLinked to original sources

bioRxiv2026

nHOTAIRM1 scaffolds ANXA11-dependent assemblies to drive axonal mRNA localization in human motor neurons

Long noncoding RNAs (lncRNAs) are well recognized as regulators of neuronal development and function, yet their integration into canonical axonal transport pathways, an essential component of spatial gene regulation in highly polarized cells, remains incompletely defined. It is still unclear to what extent individual lncRNAs confer cargo selectivity and couple discrete mRNA cohorts to established transport machineries. Here we identify a cytoplasmic role for the neuronal isoform of HOTAIRM1 (nHOTAIRM1) in shaping the axonal RNA landscape of human iPSC-derived spinal motor neurons (spMNs). We show that nHOTAIRM1 associates with Annexin A11 (ANXA11), a factor linked to lysosome-coupled movement of RNA granules and engages a defined subset of MN-relevant mRNAs. Transcriptome-wide and targeted interaction assays, together with computational mapping and steric competition, support direct RNA-RNA pairing between nHOTAIRM1 and mRNAs involved in cytoskeletal organization and synaptic or vesicular functions, while spatial analyses place these RNA pairs in close proximity within the soma and neurites. Loss-of-function experiments further show that nHOTAIRM1 depletion reduces the association of these mRNAs with ANXA11-positive complexes and diminishes their enrichment in neuronal projections, an effect that is recapitulated by ANXA11 depletion. Collectively, these findings support a model in which nHOTAIRM1 contributes to the selective recruitment of cargo mRNAs into ANXA11-associated transport assemblies, thereby promoting their localization within distal neurites. More broadly, our findings provide mechanistic insight into how a lncRNA can regulate mRNA sorting and compartment-specific RNA trafficking in human spMNs.

molecular biology↗

bioRxiv2026

LINC00205 acts as a multivalent scaffold promoting FUSP525L recruitment in Amyotrophic Lateral Sclerosis stress granules

Stress granules (SG) are dynamic, membrane-less ribonucleoprotein assemblies that orchestrate cellular stress responses and rapidly disassemble upon stress relief. In Amyotrophic Lateral Sclerosis (ALS), mutations in RNA-binding proteins such as Fused in Sarcoma (FUS) impair SG dynamics, promoting the formation of aberrant and persistent granules. Although long non-coding RNAs (lncRNAs) are emerging as regulators of ribonucleoprotein organization, their mechanistic role in SG architecture and pathological remodeling remains largely unexplored. Here, we identify LINC00205 as a critical RNA regulator of pathological SG dynamics in FUSP525L-associated ALS. Using Neuroblastoma cells and human iPSC-derived Motor Neurons (MN), we show that LINC00205 is enriched in SG upon oxidative stress and directly interacts with mutant FUSP525L. Knock-out of LINC00205 selectively reduces the formation of FUSP525L-containing SG and restores physiological SG disassembly kinetics, without affecting normal SG or FUS expression levels. Mechanistically, LINC00205 acts as a multivalent RNA scaffold, directly binding mRNAs specifically enriched in pathological SG, such as PLCXD3 and PIK3CA, as well as the RNA helicase DHX36, which is preferentially associated with FUSP525L-containing SG. We demonstrate that LINC00205 promotes their specific recruitment into pathological SG, thereby contributing to the aberrant features of these assemblies. Together, our findings uncover an active lncRNA-driven mechanism that shapes the molecular composition of aberrant ALS-related SG and regulates their persistence, establishing lncRNAs as key organizers of RNA-protein assemblies under stress and providing a conceptual framework for modulating pathological condensates.

molecular biology↗

bioRxiv2026

Neuronal late endosomes serve as selective RNA hubs disrupted by ALS-linked FUS mutation

Neurons depend on tightly regulated positioning of cellular components to maintain long-distance signaling, but the mechanisms guiding specific mRNAs to distant regions remain unclear. Here we show that late endosomes function as selective RNA carriers in human motor neurons and uncover the molecular logic guiding their loading. Using APEX2-mediated proximity labeling, we identify the external transcriptome of RAB7A-positive endosomes and find a specific population of mRNAs enriched for endosomal, axonal and synaptic functions. We find that mRNAs enriched in RAB7A endosomes contain evolutionarily conserved 5'UTRs which act as localization signals, and that the RNA-binding protein GEMIN5 interacts with these regions to promote endosomal RNA recruitment. Finally, we show that in ALS-associated conditions there is a conspicuous loss of endosome-associated transcripts and the mislocalization of GEMIN5 from endosomes. These findings uncover fundamental principles of RNA compartmentalization and highlight endosomal mRNA loading as a vulnerable axis in neuronal homeostasis.

molecular biology↗

bioRxiv2025

Mutant FUS perturbs m6A regulation by repressing ALKBH5, while restoring m6A levels alleviates ALS pathology in vivo

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder marked by the progressive loss of motor neurons, where aberrant stress granule (SG) dynamics has emerged as a hallmark, especially in cases involving mutations in RNA-binding proteins such as FUS and TDP-43. We previously showed that m6A RNA modification is elevated in FUS-associated ALS and that restoring its physiological levels through METTL3 inhibition is sufficient to rescue the aberrant stress granule phenotypes in different human cellular models. Importantly, here we show that reducing m6A levels ameliorates locomotor defects and neuromuscular junction (NMJ) abnormalities in Drosophila melanogaster models of ALS expressing the human FUSP525L mutant. Moreover, we demonstrate that the increase in m6A is attributable to reduced expression of the m6A eraser ALKBH5, resulting from impaired translation caused by direct FUS binding to its transcript. We further show that ALKBH5 downregulation contributes to RNA and protein alterations observed in FUS-associated ALS, driving the abnormal SG dynamics characteristic of the disease. This study supports the hypothesis that restoring correct m6A levels could serve as a potential therapeutic strategy for ALS.

molecular biology↗

bioRxiv2025

Decoding RNA-RNA Interactions: The Role of Low-Complexity Repeats and a Deep Learning Framework for Sequence-Based Prediction

RNA-RNA interactions (RRIs) are fundamental to gene regulation and RNA processing, yet their molecular determinants remain unclear. In this work, we analyze several large-scale RRI datasets and identify low-complexity repeats (LCRs), including simple tandem repeats, as key drivers of RRIs. Our findings reveal that LCRs enable thermodynamically stable interactions with multiple partners, positioning them as key hubs in RNA-RNA interaction networks. These RRIs appear to be important for several aspects of RNA metabolism. Sequencing-based analysis of the lncRNA Lhx1os interactors validates the importance of LCRs in shaping contacts potentially involved in neuronal development. Recognizing the pivotal role of sequence determinants, we develop RIME, a deep learning model that predicts RRIs by leveraging embeddings from a nucleic acid language model. RIME outperforms traditional thermodynamics-based tools, successfully captures the role of LCRs and prioritizes high-confidence interactions, including those established by lncRNAs. RIME is freely available at https://tools.tartaglialab.com/rna_rna.

biochemistry↗

bioRxiv2023

M6A reduction relieves FUS-associated ALS granules

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease due to gradual motorneurons (MN) degeneration1. Among the processes associated to ALS pathogenesis, there is the formation of cytoplasmic inclusions produced by mutant protein aggregation, among which the RNA binding protein FUS2. In this work we show that such inclusions are significantly reduced in number and dissolve faster when the RNA m6A content is diminished as a consequence of the m6A writer METTL3 knock-down. These effects were observed both in neuronal cell lines and in iPSC-derived human motor neurons expressing mutant FUS. Importantly, stress granules formed in ALS condition showed a distinctive transcriptome with respect to control cells; interestingly, after METTL3 downregulation, it reverted to similar to control. Finally, we show that FUS inclusions are reduced also in patient-derived fibroblasts treated with STM-2457, a well characterized inhibitor of METTL3 activity, paving the way for its possible use for counteracting aggregate formation in ALS.

molecular biology↗

bioRxiv2023

ALS-associated FUS mutation reshapes the RNA and protein composition and dynamic of Stress Granules.

Stress Granules (SG) formation is a cellular protection mechanism, constituting a storage for untranslated mRNAs and RNA-binding proteins (RBPs); however, these condensates can turn into pathological aggregates, related to the onset of neurodegenerative diseases like Amyotrophic Lateral Sclerosis (ALS). This transition towards cytotoxic inclusions is triggered by ALS-causative mutations in the RBP FUS, which lead to its cytoplasmic mis-localization and accumulation in SG. Here, we describe the SG transcriptome in a neural context and describe several features for RNA recruitment in SG. We demonstrate that SG dynamics and RNA content are strongly modified by the incorporation of mutant FUS, switching to a more unstructured, AU-rich SG transcriptome. Moreover, we show that mutant FUS, together with its protein interactors and their target RNAs, are responsible for the reshaping of the mutant SG transcriptome with alterations that can be linked to neurodegeneration. Therefore, our data give a comprehensive view of the molecular differences between physiological and pathological SG in ALS conditions, showing how FUS mutations impact the RNA and protein population of these condensates.

molecular biology↗

bioRxiv2022

The long noncoding RNA Charme supervises cardiomyocytes maturation by controlling cell differentiation programs in the developing heart

Long noncoding RNAs (lncRNAs) are emerging as critical regulators of heart physiology and disease, although the studies unveiling their modes-of-action are still limited to few examples. We recently identified pCharme, a chromatin-associated lncRNA whose functional knockout in mice results in defective myogenesis and morphological remodelling of the cardiac muscle. Here, we combined Cap-Analysis of Gene Expression (CAGE), single-cell (sc)RNA sequencing and whole-mount in situ hybridization analyses to study pCharme cardiac expression. Since the early steps of cardiomyogenesis, we found the lncRNA being specifically restricted to cardiomyocytes, where it assists the formation of specific nuclear condensates containing MATR3, as well as important RNAs for cardiac development. In line with the functional significance of these activities, pCharme ablation in mice results in a delayed maturation of cardiomyocytes, which ultimately leads to morphological alterations of the myocardium and ventricular hypo-trabeculation. Since congenital anomalies in myocardium are clinically relevant in humans and predispose patients to major complications, the identification of novel genes controlling cardiac morphology becomes crucial. Our study offers unique insights into a novel lncRNA-mediated regulatory mechanism promoting cardiomyocyte maturation and bears relevance to Charme locus for future theranostic applications.

molecular biology↗

bioRxiv2021

Dietary, Cultural and Pathogens-related Selective Pressures Shaped Differential Adaptive Evolution Among Native Mexican Populations

Native American genetic ancestry has been remarkably implicated with increased risk of diverse health issues in several Mexican populations, especially in relation to the dramatic changes in environmental, dietary and cultural settings they have recently undergone. In particular, the effects of these ecological transitions and Westernization of lifestyles have been investigated so far predominantly on Admixed individuals. Nevertheless, indigenous groups, rather than admixed Mexicans, have plausibly retained the highest proportions of genetic components shaped by natural selection in response to the ancient milieu experienced by Mexican ancestors during their pre-Columbian evolutionary history. These formerly adaptive alleles/haplotypes have the potential to represent the genetic determinants of some biological traits peculiar to the Mexican people and a reservoir of loci with potential biomedical relevance. To test such a hypothesis, we used high-resolution genomic data to infer the unique adaptive evolution of 15 Native Mexican groups selected as reasonable descendants of the main pre-Columbian Mexican civilizations. A combination of haplotype-based and gene-network analyses enabled us to detect genomic signatures ascribable to polygenic adaptive traits evolved by the main genetic clusters of indigenous Mexican populations to cope with local environmental and/or cultural conditions. Some of them were also found to play a role in modulating the susceptibility/resistance of these groups to certain pathological conditions, thus providing new evidence for diverse selective pressures having contributed to shape current biological and disease-risk patterns in present-day Native and Mestizo Mexican populations.

evolutionary biology↗

bioRxiv2020

Multisensory perception, verbal, visuo-spatial and motor working memory modulation after a single open- or closed-skill exercise session in children.

Physical activity presents clear benefits for childrens cognition; this study examined the effect of a single exercise session of open- or closed-skill exercise, as opposed to a no-exercise activity on multisensory perception, i.e. the ability to appropriately merge inputs from different sensory modalities, and on working memory (verbal, visuo-spatial, and motor working memory) in 51 preadolescent children (aged 6-8). Using a semi-randomised pre-post design, participants completed a range of cognitive tasks immediately before and after an exercise session or a classroom sedentary activity. Participants were randomised, within each school, to one of the three groups (open-skill, n=16; closed-skill, n=16; classroom activity, n=19). Exercise, but not usual classroom activity, improved childrens multisensory perception, with no difference between exercise types. Results also revealed that a single open-skill session produced verbal working memory (digit span) benefits; a closed-skill exercise session benefitted motor working memory. While the relatively small number of participants should be acknowledged as limitation, these findings contribute to emerging evidence for selective cognitive benefits of exercise, and show, for the first time in children, that multisensory processing sensitivity is improved by exercise.

animal behavior and cognition↗