Biology subjects

Funes, S.

Publications and source records attributed to Funes, S..

5 recordsLinked to original sources

bioRxiv2025

SWR1C loss promotes longevity through tRNA-mediated proteostasis

The conserved SWR1C chromatin remodeling complex promotes cellular aging, yet the mechanisms linking its activity to lifespan control remain poorly defined. Although SWR1C shapes chromatin architecture and regulates non-coding RNA expression, how these activities relate to its role in aging remains unclear. Here, we combine genetic and lifespan-epistasis analyses to identify the cellular processes that underlie SWR1C-dependent chronological longevity in Saccharomyces cerevisiae. Loss of subunits specifically required for H2A.Z deposition robustly extends longevity, and this effect is functionally linked to cytosolic translation and proteostasis pathways. Lifespan profiling of ncRNA deletions reveals a substantial fraction of aging phenotypes and prevalent genetic interactions with SWR1, with tRNAs emerging as key determinants of its long-lived phenotype. The expression of specific tRNA genes is dysregulated in swr1{Delta} cells, and interactions with tyrosine-decoding tRNA genes are linked to ER proteotoxic stress, suggesting that altered tRNA pools affect proteostasis during aging. These findings establish tRNAs as central mediators of SWR1C-associated longevity, revealing a fundamental connection between chromatin remodeling, RNA biology, and proteostasis stress responses in lifespan regulation.

cell biology↗

bioRxiv2025

Metformin-induced longevity is associated with retrotransposon dynamics in yest chronological aging

The widely used antidiabetic drug metformin extends lifespan across diverse model organisms, from yeast to primates. However, the cellular mechanisms underlying its anti-aging effects remain only partially understood. Here, we combined large-scale genetic screening and high-resolution lifespan phenotyping with transcriptomic and proteomic analyses to provide a systems view of metformins impact on the chronological lifespan of Saccharomyces cerevisiae. Unexpectedly, we uncovered pronounced gene-drug interactions between metformin and chromatin-modifying factors. Specifically, deletions of Set3C histone deacetylation complex subunits phenocopied the longevity effect of metformin, with no additive benefit when combined, suggesting convergence on shared pathways. Transcriptome profiling further revealed that metformin reprogrammed stationary-phase gene expression, with Ty1-copia retrotransposons emerging as a consistently induced signature, thereby suggesting a possible mechanism for the observed interactions with Set3C regulation. Paradoxically, TYA Gag-like protein levels and retrotransposition frequency were modestly reduced, indicating an uncoupling between transcriptional activation and retromobility. Proteome analysis revealed increased abundance of mitochondrial and stress-response proteins as primary outcomes of metformin exposure, both known modulators of Ty1 dynamics in yeast. Together, our findings position chromatin regulation and retrotransposon expression as integral components of metformins pro-longevity mechanisms, expanding its influence beyond signaling, metabolism, and stress response. HighlightsO_LILarge-scale genetic screening reveals that deletions of Set3C histone deacetylase phenocopy metformin-induced longevity. C_LIO_LIMetformin consistently induces Ty1 retrotransposon transcription but reduces Gag protein abundance and retromobility. C_LIO_LIProteomic changes highlight mitochondrial and stress-response proteins as primary outcomes of metformin exposure. C_LIO_LIRetrotransposon dynamics emerge as a key component associated with metformin-induced longevity. C_LI

cell biology↗

bioRxiv2025

Exposing the core genetic drivers of chronological aging in yeast cells

The chronological lifespan of Saccharomyces cerevisiae has been pivotal in advancing our understanding of aging in eukaryotic cells. However, gaining a genome-wide perspective of this trait remains challenging due to substantial discrepancies observed across large-scale gene-deletion screens. In this study, we performed a meta-analysis to compile a ranked catalog of key processes and regulators driving chronological longevity in yeast, ensuring their robustness across diverse experimental setups. These consistent chronological aging factors were enriched in genes associated with yeast replicative lifespan and orthologs implicated in aging across other model organisms. Functional analysis revealed that the downstream cellular mechanisms underlying chronological longevity in yeast align with well-established, universal hallmarks of aging, underscoring the potential of the yeast chronological aging model to investigate conserved aging processes. Additionally, we identified transcriptional regulators associated with these consistent genetic factors, uncovering potential global and local modulators of chronological aging. Among these, Tec1, a key regulator of the filamentous growth pathway, emerged as a central hub connected to multiple aging pathways. To further elucidate the functional role of this regulator, we conducted a high-resolution lifespan-epistasis screen, demonstrating that TEC1 and mitochondrial machinery promote chronological longevity in parallel, compensating for each others impaired functions. Our findings provide an integrated view of the core genetic and functional landscape underlying aging in yeast cells.

genetics↗

bioRxiv2023

Expression of ALS-PFN1 impairs vesicular degradation in iPSC-derived microglia

Microglia play a pivotal role in neurodegenerative disease pathogenesis, but the mechanisms underlying microglia dysfunction and toxicity remain to be fully elucidated. To investigate the effect of neurodegenerative disease-linked genes on the intrinsic properties of microglia, we studied microglia-like cells derived from human induced pluripotent stem cells (iPSCs), termed iMGs, harboring mutations in profilin-1 (PFN1) that are causative for amyotrophic lateral sclerosis (ALS). ALS-PFN1 iMGs exhibited lipid dysmetabolism and deficits in phagocytosis, a critical microglia function. Our cumulative data implicate an effect of ALS-linked PFN1 on the autophagy pathway, including enhanced binding of mutant PFN1 to the autophagy signaling molecule PI3P, as an underlying cause of defective phagocytosis in ALS-PFN1 iMGs. Indeed, phagocytic processing was restored in ALS-PFN1 iMGs with Rapamycin, an inducer of autophagic flux. These outcomes demonstrate the utility of iMGs for neurodegenerative disease research and highlight microglia vesicular degradation pathways as potential therapeutic targets for these disorders.

neuroscience↗

bioRxiv2021

A reference induced pluripotent stem cell line for large-scale collaborative studies

Human induced pluripotent stem cell (iPSC) lines are a powerful tool for studying development and disease, but the considerable phenotypic variation between lines makes it challenging to replicate key findings and integrate data across research groups. To address this issue, we sub-cloned candidate iPSC lines and deeply characterised their genetic properties using whole genome sequencing, their genomic stability upon CRISPR/Cas9-based gene editing, and their phenotypic properties including differentiation to commonly-used cell types. These studies identified KOLF2.1J as an all-around well-performing iPSC line. We then shared KOLF2.1J with groups around the world who tested its performance in head-to-head comparisons with their own preferred iPSC lines across a diverse range of differentiation protocols and functional assays. On the strength of these findings, we have made KOLF2.1J and hundreds of its gene-edited derivative clones readily accessible to promote the standardization required for large-scale collaborative science in the stem cell field. SummaryThe authors of this collaborative study deeply characterized human induced pluripotent stem cell (iPSC) lines to rationally select a clonally-derived cell line that performs well across multiple modalities. KOLF2.1J was identified as a candidate reference cell line based on single-cell analysis of its gene expression in the pluripotent state, whole genome sequencing, genomic stability after highly efficient CRISPR-mediated gene editing, integrity of the p53 pathway, and the efficiency with which it differentiated into multiple target cell populations. Since it is deeply characterized and can be readily acquired, KOLF2.1J is an attractive reference cell line for groups working with iPSCs. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/472643v6_ufig1.gif" ALT="Figure 1"> View larger version (84K): org.highwire.dtl.DTLVardef@cef106org.highwire.dtl.DTLVardef@31d5d8org.highwire.dtl.DTLVardef@1ce6d8corg.highwire.dtl.DTLVardef@17a19d2_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗