Biology subjects

de Cabo, R.

Publications and source records attributed to de Cabo, R..

10 recordsLinked to original sources

bioRxiv2026

MSMICA: computational metabolite identification in untargeted metabolomics by integrating MS, retention time, and biological evidence

Mass Spectrometry Metabolomics Identification Connection Algorithm (MSMICA) is an algorithm for automated metabolite identification in untargeted liquid chromatography-high-resolution mass spectrometry (LC-HRMS) analyses. Limitations in metabolite identification can occur due to the availability and cost of standards and prevent recognition of metabolic factors impacting human health and disease. MSMICA performs mass-to-charge-ratio matching with chemical structures and clusters of LC-HRMS features for adduct and isotope forms. A local optimization is then used to integrate retention time prediction, metabolite precursor-product and transporter correlations, and biospecimen-specific abundance information for metabolite identification. Applying MSMICA to various internal and external mammalian datasets, validation results showed a 96.2 +- 5.1% correct rate of metabolite identification. When multiple LC-HRMS datasets were used, MSMICA enabled greater metabolite identifications, expanded metabolic pathway coverage, and data harmonization. Thus, MSMICA applies multiple pieces of evidence to substantially improve metabolite identification coverage and accuracy for known metabolites.

bioinformatics↗

bioRxiv2026

A novel multicellular model of the adult mouse sinoatrial node retains spontaneous electrical activity and enables live investigation of the S100B-associated cell population

Approximately half of the adult sinoatrial node (SAN) consists of non-myocyte populations, indicating that cardiac pacemaking depends on interactions within a multicellular tissue rather than on pacemaker cardiomyocytes alone. Among these, an S100B-associated cell population has been implicated in pacemaker function, yet its identity and physiological roles remain poorly understood. These cells are rare and dispersed throughout the small, structurally complex SAN, making them difficult to observe repeatedly while preserving the native multicellular environment. Here, we established a dissociated multicellular culture of adult mouse SAN tissue on soft collagen-gelatin hydrogels that retains spontaneous electrical activity and permits longitudinal live imaging of S100B-associated cells. Using an S100B-EGFP+ reporter, we identified at least six reproducible morphological and behavioral phenotypes, including migration, proliferation, phagocytic behavior, and spontaneous self-organization into three-dimensional clusters. Cultures remained spontaneously electrically active for more than 10 days in vitro, with peak activity around day 10. This multicellular culture model bridges the gap between intact SAN preparations and isolated-cell cultures, allowing repeated observation of rare S100B-associated cells within a spontaneously active multicellular environment. HighlightsO_LIThe platform enables longitudinal live imaging of rare S100B-associated cells within an diverse multicellular SAN culture. C_LIO_LILive imaging reveals at least six reproducible morphological and behavioral phenotypes of S100B-associated cells. C_LIO_LIDissociated multicellular SAN cultures remain spontaneously electrically active for more than 10 days in vitro. C_LI

cell biology↗

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

Deep and Quantitative Proteomic Profiling of Low Volume Mouse Serum Across the Lifespan

Assessing and validating circulating biomarkers is essential for the development of pre-clinical biomarkers that predict biological aging and aging-phenotypes in mice. However, comprehensive proteomics of serum, especially in longitudinal mouse studies, are limited by low volumes of samples. In this study, we develop a workflow for comprehensive and quantitative proteomic analysis of low volume mouse serum and demonstrate its utility and performance in identifying and evaluating key associations with aging phenotypes. Notably, a nanoparticle (NP)-based serum processing workflow coupled to mass spectrometry (MS) increases proteomic coverage by 3 to 6-fold across a range of volumes and provides a quantitative and reproducible (CV < 10%) pipeline for NP-based studies. In a study of 30 mice (aged 12, 24, and 30 months), we uncovered 3992 protein groups across all samples (2235 on average) in 20 {micro}L of serum and highlight novel insights into aging-associated changes in serum and associations with glucose and body composition. With 1 {micro}L additional serum, a 48-cytokine assay quantified 39 additional proteins not identified by MS. This study establishes a powerful workflow that enables deep quantitative proteomics of biologically relevant proteins in volumes feasibly obtained from mice (21 {micro}L of serum) and presents fundamental insights into the aging serum proteome.

biochemistry↗

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↗

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

Cyb5r3-based mechanism and reversal of secondary failure to sulfonylurea

Sulfonylureas (SU) are effective and affordable anti-diabetic drugs. But chronic use leads to secondary failure, limiting their utilization. The mechanism of secondary failure is unknown. Here we identify Cyb5r3 downregulation as a mechanism of SU failure and successfully reverse it. Chronic exposure to SU impairs Cyb5r3 levels and reduces islet glucose utilization with a metabolomics signature characterized by low acetyl-CoA and amino acid levels. Cyb5r3 engages in a glucose-dependent interaction that stabilizes glucokinase (Gck) to maintain glucose utilization. Accordingly, activating Gck mutations in patients with hyperinsulinemia reduce Cyb5r3 binding, whereas inactivating MODY mutations increase it, providing evidence for a role of Cyb5r3 in determining flux through Gck. The Cyb5r3 activator tetrahydroindenoindole (THII) rescues secondary failure to SU in an animal model of chronic SU treatment and restores insulin secretion from ex vivo islets. We conclude that Cyb5r3 loss-of-function is a key factor in the secondary failure to SU and a potential target for its prevention, which may lead to a rehabilitation of SU use in diabetes.

physiology↗

bioRxiv2022

Ketones facilitate transcriptional resolution of secondary DNA structures in premature aging

There is currently no established intervention for Cockayne syndrome, a disease characterized by progressive early onset neurodegeneration with features of premature aging. Here, we tested if acetyl-CoA precursors, citrate and beta-hydroxybutyrate, could reduce features of Cockayne syndrome in three model systems. We identified the gene Helicase 89B as a homologue of CSB in drosophila and found that the ketone beta-hydroxybutyrate rescued features of premature aging in Hel89B deficient flies. In mammals, loss of the citrate carrier Indy exacerbated the phenotype of Csbm/m mice which was rescued by a ketogenic diet. The rescue effect appeared to be mediated through ketone stimulated histone acetylation and facilitation of transcriptional readthrough of secondary DNA structures. These findings link a ketogenic diet with transcriptional resolution of secondary structures and DNA repair.

physiology↗

bioRxiv2018

ATP synthase K+- and H+-flux drive ATP synthesis and enable mitochondrial K+-uniporter function

ATP synthase (F1Fo) synthesizes daily our bodys weight in ATP, whose production-rate can be transiently increased several-fold. Using purified mammalian F1Fo-reconstituted proteoliposomes and isolated mitochondria, we show that F1Fo utilizes both H+- and K+-transport (because of >106-fold K+ excess vs H+) to drive ATP synthesis with the H+:K+ permeability of ~106:1. F1Fo can be upregulated by endogenous survival-related proteins (Bcl-xL, Mcl-1) and synthetic molecules (diazoxide, pinacidil) to increase its chemo-mechanical efficiency via IF1. Increasing K+- and H+-driven ATP synthesis enables F1Fo to operate as a primary mitochondrial K+-uniporter regulating energy supply-demand matching, and as the recruitable mitochondrial KATP-channel that can limit ischemia-reperfusion injury. Isolated mitochondria in the presence of K+ can sustain ~3.5-fold higher ATP-synthesis-flux (vs K+ absence) driven by a 2.7:1 K+:H+ stoichiometry with unaltered OxPhos coupling. Excellent agreement between F1Fo single-molecule and intact-mitochondria experiments is consistent with K+-transport through ATP synthase driving a major fraction of ATP synthesis.

biophysics↗