Biology subjects

Gorospe, M.

Publications and source records attributed to Gorospe, M..

14 recordsLinked to original sources

bioRxiv2026

Reduced LANCL1-AS1 in old human skeletal muscle diminishes mitochondrial activity, shortens mt-mRNA poly(A) tails, and suppresses myogenesis

Regeneration of skeletal muscle preserves muscle mass and function, which decline with age. Here, we sought to identify long noncoding (lnc)RNAs involved in skeletal muscle myogenesis and potentially relevant to muscle aging. Cross-sectional analysis of skeletal muscle transcriptomes from healthy 22-through 89-year-old individuals revealed lncRNA LANCL1-AS1 among the top declining transcripts. Conversely, LANCL1-AS1 increased robustly during skeletal myogenesis and promoted myogenic differentiation in culture. Affinity pulldown by ChIRP followed by mass spectrometry revealed that LANCL1-AS1 associated with the mitochondrial protein LRPPRC, enhancing the formation of the chaperone complex LRPPRC-SLIRP, which maintains longer poly(A) tails of mitochondrial (mt-)mRNAs and stabilizes mt-mRNAs. Importantly, while myoblasts from old rhesus monkey muscle expressed lower levels of LANCL1-AS1 and mt-mRNAs, and displayed lower mitochondrial activity than young monkey myoblasts, overexpressing LANCL1-AS1 in old myoblasts restored mitochondrial activity and myogenesis. We propose that the age-associated reduction in LANCL1-AS1 contributes to impaired mitochondrial function and reduced myogenic capacity in aging skeletal muscle.

molecular biology↗

bioRxiv2026

SenCat: Cataloging human cell senescence through multiomic profiling of multiple senescent primary cell types

There is an urgent need to comprehensively catalog senescence markers across cell types in an organism in order to characterize senotypes and senescent cell heterogeneity. Here, we profiled the transcriptomes and proteomes in 14 different primary human cell types undergoing over 30 senescence paradigms to create a senescence catalog we termed SenCat. We found that, while senescent cells from all primary tissue types did not share a single unique marker, they did activate shared specific metabolic and damage-response pathways implicated in tissue repair. Machine learning analysis of the SenCat transcriptomic and proteomic datasets successfully identified independent sets of senescent human cells, and senescent-like cells in mouse lung and kidney. In sum, SenCat represents a much-needed resource to identify senescent cells across tissues in the body. HIGHLIGHTSO_LIIdentifying senescent cells in organisms in vivo remains a challenge C_LIO_LIWe created SenCat: a catalog transcriptomes and proteomes of senescent primary cells C_LIO_LIMachine learning (ML) analysis of SenCat identified robust senescence scores C_LIO_LIML-derived senescence scores uncovered senescent-like cell dynamics in vivo C_LI

molecular biology↗

bioRxiv2025

Senolytic treatment with fisetin reverses age-related endothelial dysfunction partially mediated by SASP factor CXCL12

BackgroundAdvancing age is the strongest risk factor for cardiovascular diseases (CVDs), primarily due to progressive vascular endothelial dysfunction. Cellular senescence and the senescence-associated secretory phenotype (SASP) contribute to age-related endothelial dysfunction by promoting mitochondrial oxidative stress and inflammation, which reduce nitric oxide (NO) bioavailability. However, the molecular changes in senescent endothelial cells and their role in endothelial dysfunction with aging remain incompletely unclear. As such, in this study we sought to identify the endothelial cell senescence-related signalling pathways, endothelial-derived SASP factors, and their impact on endothelial function with aging. MethodsSingle-cell transcriptomics was performed on aortas from young (6 months) and old (27 months) mice with and without in vivo senolytic treatment with fisetin (100 mg/kg/day administered in an intermittent dosing paradigm) to characterize endothelial cell senescence and transcript expression changes. Circulating levels of SASP factors were measured to validate transcriptional changes. Plasma exposure and protein addition and inhibiton experiments were conducted in isolated mouse arteries and cultured human endothelial cells to determine the causal role of the circulating SASP milieu and specific SASP factors in mediating endothelial dysfunction and underlying mechanisms-of-action. ResultsSenescent endothelial cells exhibited elevated expression of SASP factors, particularly Cxcl12, which was reversed by fisetin supplementation, with responses also reflected in circulating CXCL12 concentrations. Plasma from old mice impaired endothelial function by inducing vascular cell senescence, reducing NO, increasing mitochondrial oxidative stress, and promoting endothelial-to-mesenchymal transition--effects partially driven by CXCL12 and prevented by fisetin. ConclusionsThese results identify the SASP and CXCL12 as drivers of age-related endothelial dysfunction and establish mechanisms of senolytic intervention with fisetin supplementation. NOVELTY AND SIGNFICANCEO_ST_ABSWhat is known?C_ST_ABSO_LIAdvancing age is the primary risk factor for cardiovascular disease, in part due to progressive endothelial dysfunction. C_LIO_LICellular senescence contributes to age-related endothelial impairment through the secretion of a pro-inflammatory milieu known as the senescence-associated secretory phenotype (SASP), which can affect neighboring cells and tissue function. C_LIO_LISenolytic compounds selectively eliminate senescent cells and improve vascular function in preclinical models of aging. C_LI What new information does this article contribute?O_LIEndothelial cells are highly susceptible to senescence with aging in vivo and are selectively cleared by senolytic treatment with the natural compound fisetin. C_LIO_LISingle-cell transcriptomic profiling identifies CXCL12 as the most highly upregulated SASP factor in senescent endothelial cells and in circulation with aging, both of which are reversed by senolytic treatment with fisetin. C_LIO_LIWe identify a specific circulating SASP factor, CXCL12, as a partial mediator of endothelial dysfunction by inducing mitochondrial oxidative stress, impairing nitric oxide bioavailability, and promoting endothelial-to-mesenchymal transition (Endo, which is restored by senolytic treatment with fisetin. C_LI SummaryThis study provides novel mechanistic insight into how senescent endothelial cells and their secretory products--particularily CXCL12--contribute to age-related endothelial dysfunction. It further demonstrates that senolytic treatment with fisetin reverses these effects, highlighting a promising translational strategy for targeting vascular aging and preserving endothelial health. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=68 SRC="FIGDIR/small/670216v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@b49a8org.highwire.dtl.DTLVardef@110da92org.highwire.dtl.DTLVardef@17dbd54org.highwire.dtl.DTLVardef@1906c6_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2025

Telomere replication stress-induced DNA damage response triggers inflammatory signaling via canonical and non-canonical STING pathways

Telomeres are protected by the shelterin complex, but they are also common fragile sites and are particularly susceptible to replicative stress. We found that depletion of telomeric repeat-binding factor 1 (TRF1), a key shelterin component essential for telomere replication, in mouse embryonic fibroblasts (MEFs) activated ATR- and subsequent ATM-dependent DNA damage responses. TRF1 loss increased the formation of micronuclei and cytosolic DNA, leading to ATR-dependent micronuclear rupture and activation of the cGAS/STING pathway. ATM activation enhanced STING K63 modification, thereby boosting the STING/NF{kappa}B pathway. Inhibition of ATM or cGAS reduced the expression of the pro-inflammatory cytokine IL6, with combined inhibition further suppressing IL6 levels. Depletion or inhibition of STING alone decreased production of IL6 and IFN{beta}, with no major reduction by combined ATM and/or cGAS inhibitors. These findings indicate that STING acts epistatically with ATM- and cGAS-mediated inflammatory responses. Overall, the telomere replication stress and dysfunction triggered by loss of TRF1 promotes inflammation through the ATR/cGAS/STING and ATM/STING pathways.

genomics↗

bioRxiv2025

Molecular interactome of HNRNPU reveals regulatory networks in neuronal differentiation and DNA methylation

HNRNPU is an RNA-binding protein with diverse roles in transcriptional and post-transcriptional regulation. Pathogenic genetic variants of HNRNPU cause a severe neurodevelopmental disorder (NDD), but the underlying molecular mechanisms are unclear. Here, we comprehensively investigate the HNRNPU molecular interactome by integrating protein-protein interaction (PPI) mapping, RNA target identification, and genome-wide DNA methylation profiling in human neuroepithelial stem cells and differentiating neural cells. We identified extensive HNRNPU-centered networks, including a strong association with the mammalian SWI/SNF chromatin-remodelling complex, and uncovered a previously unrecognized role in translation. We present evidence that HNRNPU associates with mRNAs encoding proteins important for neuronal development, including several linked to NDDs. Silencing HNRNPU reprogrammed methylation dynamics at regulatory regions, particularly at active and bivalent promoters of neurodevelopmental transcription factors. Integrative analysis across PPI, RNA, and methylome datasets identified 19 converging genes at all three molecular levels, including NDD genes within the SWI/SNF complex and RNA-processing machinery such as SYNCRIP. Together, these data showcase HNRNPU as a central coordinator of RNA metabolism and epigenetic remodelling during neural differentiation, linking RNA-binding, chromatin organization, and DNA methylation to the pathogenesis of HNRNPU-related NDDs.

molecular biology↗

bioRxiv2024

Integrative single-cell analysis of neural stem/progenitor cells reveals epigenetically dysregulated interferon response in progressive multiple sclerosis

Progressive multiple sclerosis (PMS) is characterized by a primary smouldering pathological disease process associated with a superimposed inflammatory activity. Cellular and molecular processes sustaining the pathobiology of PMS remain to be identified. We previously discovered senescence signatures in neural stem/progenitor cells (NSCs) from people with PMS. Applying direct reprogramming to generate directly induced NSCs (iNSCs) from somatic fibroblasts, we retain epigenetic information and observe hypomethylation of genes associated with lipid metabolic processes and IFN signalling only in PMS lines. Single-cell/nucleus transcriptomic and epigenetic profiling reveal an inflammatory, senescent-like, IFN-responsive radial glia (RG)-like cell subcluster mainly in PMS iNSCs that is driven by IFN-associated transcription factors. Lastly, we identify a population of senescent, IFN-responsive, disease-associated RG-like cells (DARGs) in the PMS brain that share pseudotime trajectories with iNSCs in vitro. We describe the existence of a non-neurogenic, dysfunctional DARG population that has the potential to fuel smouldering inflammation in PMS.

neuroscience↗

bioRxiv2024

Cytotoxic CD4+ T cells in the bone marrow compromise healthy ageing by enhancing granulopoiesis

Neutrophils are the most abundant leukocytes in the blood, with numbers further increasing with age. Despite their essential role as a primary line of defense, neutrophils can contribute to tissue damage and age-related diseases 1 and a high neutrophil-to-lymphocyte ratio predicts all causes of mortality in the elderly 2-5. However, the precise mechanisms driving enhanced neutrophil generation during ageing remain poorly understood. Here, we show that a subset of CD4+ T cells with a cytotoxic phenotype (CD4+ CTLs) producing the chemokine CCL5 and harbouring dysfunctional mitochondria, infiltrate the bone marrow and induce granulopoiesis in aged mice. During ageing, hematopoietic stem cells upregulate CCR5, the primary receptor for CCL5, and its deficiency limits the T cell-mediated induction of granulopoiesis and neutrophil output. Treatment with the FDA-approved CCR5 inhibitor Maraviroc decreases granulopoiesis and lowers the levels of circulatory and tissue-infiltrating neutrophils, ameliorating multiple ageing biomarkers and improving functional outcomes in aged mice. These findings suggest that age-associated alterations in T cells reduce health outcomes by remodelling the bone marrow niche and enhancing neutrophil generation. Consequently, interventions to disrupt the interplay between T cells and hematopoietic stem cells hold substantial therapeutic potential to ameliorate age-associated diseases.

immunology↗

bioRxiv2023

Senescence-specific translation dysregulation desensitizes cells to stress by inhibiting activation of the integrated stress response

Senescence is a state of indefinite cell cycle arrest associated with aging, cancer, and age-related diseases. Here, using label-based mass spectrometry, ribosome profiling and nanopore direct RNA sequencing, we explore the coordinated interaction of translational and transcriptional programs of human cellular senescence. We find that translational deregulation and a corresponding maladaptive integrated stress response (ISR) is a hallmark of senescence that desensitizes senescent cells to stress. We present evidence that senescent cells maintain high levels of eIF2 phosphorylation, typical of ISR activation, but translationally repress production of the stress response transcription factor 4 (ATF4) by ineffective bypass of the inhibitory upstream open reading frames. Surprisingly, ATF4 translation remains inhibited even after acute proteotoxic and amino acid starvation stressors, resulting in a highly diminished stress response. Furthermore, absent a response, stress augments the senescence secretory phenotype, thus intensifying a proinflammatory state that exacerbates disease. Our results reveal a novel mechanism that senescent cells exploit to evade an adaptive stress response and remain viable.

molecular biology↗

bioRxiv2022

The YAP-TEAD complex promotes senescent cell survival by lowering endoplasmic reticulum stress

Sublethal cell damage can trigger a complex adaptive program known as senescence, characterized by growth arrest, resistance to apoptosis, and a senescence-associated secretory phenotype (SASP). As senescent cells accumulating in aging organs are linked to many age-associated diseases, senotherapeutic strategies are actively sought to eliminate them. Here, a whole-genome CRISPR knockout screen revealed that proteins in the YAP-TEAD pathway influenced senescent cell viability. Accordingly, treating senescent cells with a drug that inhibited this pathway, Verteporfin (VPF), selectively triggered apoptotic cell death and derepressed DDIT4, in turn inhibiting mTOR. Reducing mTOR function in senescent cells diminished endoplasmic reticulum (ER) biogenesis, causing ER stress and apoptosis due to high demands on ER function by the SASP. Importantly, VPF treatment decreased senescent cell numbers in the organs of old mice and mice exhibiting doxorubicin-induced senescence. We present a novel senolytic strategy that eliminates senescent cells by hindering ER activity required for SASP production.

cell biology↗

bioRxiv2022

Pleiotropic effects of BAFF on the senescence-associated secretome and growth arrest

Senescent cells release a variety of cytokines, proteases, and growth factors collectively known as the senescence-associated secretory phenotype (SASP). Sustained SASP contributes to a pattern of chronic inflammation associated with aging and implicated in many age-related diseases. Here, we investigated the expression and function of the immunomodulatory cytokine BAFF (B-cell activating factor), a SASP protein, in multiple senescence models. We first characterized BAFF production across different senescence models, including senescent human diploid fibroblasts (WI-38, IMR-90) and monocytic leukemia cells (THP-1), and tissues of mice induced to undergo senescence. We then identified IRF1 (interferon response factor 1) as a transcription factor required for promoting BAFF mRNA transcription in senescence. We discovered that suppressing BAFF production decreased the senescent phenotype of both fibroblasts and monocyte-derived THP-1 cells, overall reducing IL6 secretion, SA-{beta}-Gal staining, and {gamma}-H2AX accumulation. Importantly, however, the influence of BAFF on the senescence program was cell type-specific: in monocytes, BAFF promoted the early activation of NF-{kappa}B and general SASP secretion, while in fibroblasts, BAFF contributed to the production and function of TP53 (p53). We propose that BAFF is elevated across senescence models and is a potential target for senotherapy.

cell biology↗

bioRxiv2022

Circular RNAs arising from synaptic host genes are modulated by SFPQ RNA-binding protein and increased during human neuronal differentiation

BackgroundCircular RNAs (circRNAs) are emerging as a key component of the complex neural transcriptome implicated in brain development. However, the specific expression patterns and functions of circRNAs in human neuronal differentiation have not been explored. ResultsUsing total RNA sequencing analysis, we identified expressed circRNAs during the differentiation of human neuroepithelial stem (NES) cells into developing neurons and discovered that many circRNAs originated from host genes associated with synaptic function. Interestingly, when assessing population data, exons giving rise to circRNAs in our dataset had a higher frequency of genetic variants. Additionally, screening for RNA-binding protein sites identified enrichment of Splicing Factor Proline and Glutamine Rich (SFPQ) motifs in increased circRNAs, several of which were reduced by SFPQ knockdown and enriched in SFPQ ribonucleoprotein complexes. ConclusionsOur study provides an in-depth characterisation of circRNAs in a human neuronal differentiation model and highlights SFPQ as both a regulator and binding partner of circRNAs elevated during neuronal maturation.

neuroscience↗

bioRxiv2020

Spatial heterogeneity of glioblastoma cells reveals sensitivity to NAD+ depletion at tumor edge

Even after total resection of glioblastoma core lesions by surgery and aggressive post-surgical treatments, life-threatening tumors inevitably recur. A characteristic obstacle in effective treatment is high intratumoral heterogeneity, both longitudinally and spatially. Recurrence occurs predominantly at the brain parenchyma-tumor core interface, a region termed tumor edge. Given the difficulty of accessing it surgically, the composition of the tumor edge, harboring both cancerous and non-cancerous cells, remains largely unknown. Here, to identify phenotypic diversity among heterogeneous glioblastoma core and edge lesions, we uncovered the existence of three phenotypically-distinct clonal subpopulations within individual tumors from glioblastoma patients. Clones from the tumor core shared the same phenotype, exclusively generating tumor-core cells. In contrast, two distinct clonal subtypes were identified at the tumor edge: one generated only edge-lesion cells and the other expanded more broadly to establish both edge- and core-lesions. Using multiple xenograft experimental models in mouse brains, tumor edge development was found to require that both somatic and tumor cells express the NADase CD38, combinedly elevating glioblastoma malignancy. In vitro data suggested that intracellular NADase activity at the edge was provoked through intercellular communication between edge clones and normal astrocytes. Systemic treatment of tumor-bearing mice with 78c, a small-molecule CD38 inhibitor, attenuated the formation of glioblastoma edge lesions, suggesting its clinical potential to pharmacologically eliminate tumor-edge lesions. Collectively, these findings provide novel phenotypic and mechanistic insights into clonal heterogeneity within glioblastoma, particularly in the surgically unresectable, currently understudied tumor edge.

cancer biology↗

bioRxiv2020

Brain aging-dependent glioma traits reversible by NAD+/BDNF-mediated neuronal reactivation

The rise in aging population worldwide is increasing death from cancer, including glioblastoma. Here, we explore the impact of brain aging on glioma tumorigenesis. We find that glioblastoma in older patients and older mice displayed reduced neuronal signaling, including a decline of NTRK-like family member 6 (SLITRK6), a receptor for neurotrophic factor BDNF. This reduction was linked to the systemic decline of nicotinamide adenine dinucleotide (NAD+) with aging, as old mice exposed to young blood via parabiosis or supplemented with the NAD+ precursor NMN (nicotinamide mononucleotide) reverted phenotypically to young-brain responses to glioma, with reactivated neuronal signaling and reduced death from tumor burden. Interestingly, the phenotypic reversal by NMN was largely absent in old mice undergoing parabiosis with BDNF+/- young mice and in BDNF+/- mice undergoing tumor challenge, supporting the notion that the lower NAD+-BDNF signaling in the aging brain aggravated glioma tumorigenesis. We propose that the aging-associated decline in brain NAD+ worsens glioma outcomes at least in part by decreasing neuronal/synaptic activity and increasing neuroinflammation.

cancer biology↗

bioRxiv2019

Aging skeletal muscle proteomics finds changes in spliceosome, immune factors, proteostasis and mitochondria

A progressive decline of skeletal muscle strength with aging is a primary cause of mobility loss and frailty in older persons, but the molecular mechanisms of such decline are not fully understood. Here, using quantitative discovery proteomic data from skeletal muscle specimens collected from 58 healthy persons aged 20 to 87 years show that ribosomal proteins and proteins related to energetic metabolism, including those related to the TCA cycle, mitochondria respiration, and glycolysis were underrepresented in older persons. Proteins with important roles in innate and adaptive immunity, involved in proteostasis and regulation of alternative splicing were all overrepresented in muscle from older persons. Changes with aging of alternative splicing were confirmed by RNA-seq. Overall, older muscle has a profound deficit of energetic metabolism, a pro-inflammatory environment and increased proteostasis. Upregulation of the splicing machinery maybe an attempt to compensate for these changes and this could be tested in future studies.

physiology↗