Biology subjects

Menni, C.

Publications and source records attributed to Menni, C..

10 recordsLinked to original sources

bioRxiv2026

Gut Microbiota Production of Phenylacetate Programs Vascular Niche Senescence and Drives Atherosclerosis

Vascular senescence is a key contributor to ageing-related diseases, including atherosclerosis. Initial intervention is based on aggressive management of traditional risk factors, yet microbial metabolites remain underestimated as modifiable factors. We recently identified phenylacetate (PAA), a gut microbiota-linked metabolite, as a potent accelerator of endothelial senescence, raising the question of its causal role in atherosclerosis. Here, we show that PAA promotes vascular niche senescence and perivascular adipose tissue (PVAT) dysfunction, associated with atherosclerosis in humans and mice. Furthermore, PAA administration to atherosclerosis-prone mice was sufficient to drive atherosclerosis without altering lipid profile. Mechanistically, we found that PAA induces senescence-messaging secretome, containing IL-6, from endothelial cells, which stimulates Notch1 and disrupts insulin signaling in adipocytes. Blocking the PAA-IL-6-Notch1 axis as well as senolytics rescued adipocyte senescence and dysfunction. Identification of the strong link between PAA and atherosclerosis opens new avenues for microbiome-targeted preventive and therapeutic strategies in ageing. HighlightsO_LIAge-dependent increase in gut microbial metabolite PAA causally promotes vascular niche senescence C_LIO_LIPAA indirectly accelerates PVAT senescence through endothelial senescence-messaging secretome C_LIO_LISASP upregulates Notch1 signaling, leading to PVAT dysfunction C_LIO_LISenolytic therapy restores PVAT function C_LIO_LIPAA-induced vascular niche senescence contributes to atherosclerosis progression C_LI

cell biology↗

bioRxiv2026

Reconstructing N-Glycan Profiles of Individual Glycoproteins from the Total Blood Plasma N-Glycome: Implications for Immunoglobulin G N-Glycosylation GWAS

The genetic regulation of the plasma N-glycome variation in human populations is not fully characterized, partly due to the limited sample size in glyco-genetics studies. Here, we aimed to demonstrate that protein-specific N-glycan profiles, like those of immunoglobulin G (IgG), can be accurately reconstructed from the total plasma N-glycome (TPNG), enabling us to find new regulators of this complex process re-analysing existing datasets. By testing multiple linear and non-linear machine learning approaches we built a model to reconstruct IgG N-glycans from TPNG data, training on the TwinsUK cohort and validating on CEDAR. We reconstruct GWAS summary statistics for IgG N-glycans by applying the trained linear model to plasma glycan GWAS summary statistics, i.e., as GWAS of linear combinations of plasma glycan traits. The majority of the identified loci had been implicated in IgG N-glycosylation GWAS. Additionally, we found four new loci and suggested the role of FCRLA, KDELR2, HHEX, and TCF3 in the regulation of IgG N-glycosylation. In conclusion, we showed that our method enables the creation of protein-specific N-glycome datasets, allowing for powerful meta-analyses without the need to profile new samples.

genetics↗

bioRxiv2025

Genetic regulation of fatty acid content in adipose tissue

Fatty acids are important as structural components, energy sources, and signaling mediators. While studies have extensively explored genetic regulation of fatty acids in serum and other bodily fluids, their regulation within adipose tissue, a crucial regulator of cardiovascular and metabolic health remains unclear. Here, we investigated the genetic regulation of 18 fatty acids in subcutaneous adipose tissue from 569 female twins from TwinsUK. Using twin models, the heritability of fatty acids ranged from 5% to 59%, indicating a substantial genetic regulation of fatty acid levels within adipose tissue, which was also tissue-specific in many cases. Genome-wide association studies identified ten significant loci, in SCD, ADAMTSL1, ZBTB41, SNTB1, EXOC6B, ACSL3, LINC02055, MKRN2/TSEN2, FADS1 and HAPLN across 13 fatty acids or fatty acid product-to-precursor ratios. Using adipose gene expression and methylation, which were concurrently measured in these samples, we detected five fatty acid-associated signals that colocalized with eQTL and meQTL signals, highlighting fatty acids that are regulated by molecular processes within adipose tissue. We identified strong associations of adipose fatty acids-associated loci with type 2 diabetes, body fat percentage, and cardiovascular disease. We explored links between polygenic scores of common metabolic traits and adipose fatty acid levels, and identified associations between polygenic scores of BMI, body-fat distribution and triglycerides and several fatty acids, indicating these risk scores impact local adipose tissue content. Overall, our results identified local genetic regulation of fatty acids within adipose tissue and highlighted their links with renal and cardio-metabolic health.

genetics↗

bioRxiv2025

Theobromine is Associated with Slower Epigenetic Ageing

Theobromine, a commonly consumed dietary alkaloid derived from cocoa, has been linked to extended lifespan in model organisms and to health benefits in humans. We examined associations between circulating theobromine intake, measured using serum metabolomics, and blood-based epigenetic markers of biological ageing in two European human population-based cohorts. Serum theobromine levels were significantly associated with reduced epigenetic age acceleration, as measured by GrimAge (p<2e-7) and DNAmTL (p<0.001) in over 500 individuals from the TwinsUK cohort, and both signals replicated in 1,160 individuals from the KORA cohort (p = 7.2e-08 and p = 0.007, respectively). Sensitivity analyses including covariates of other cocoa and coffee metabolites suggest that the effect is specific to theobromine. Our findings indicate that the reported beneficial links between theobromine intake on health and ageing extend to the molecular epigenetic level in humans.

genetics↗

bioRxiv2024

ESPClust: Unsupervised identification of modifiers for the effect size profile in omics association studies

High-throughput omics technologies have revolutionised the identification of associations between individual traits and underlying biological characteristics, but still use one effect-size fits all approaches. While covariates are often used, their potential as effect modifiers often remains unexplored. To bridge this gap, we introduce ESPClust, a novel unsupervised method designed to identify covariates that modify the effect size of associations between sets of omics variables and outcomes. By extending the concept of moderators to encompass multiple exposures, ESPClust analyses the effect size profile (ESP) to identify regions in covariate space with different ESP, enabling the discovery of subpopulations with distinct associations. Applying ESPClust to insulin resistance and COVID-19 symptom manifestation, we demonstrate its versatility and ability to uncover nuanced effect size modifications that traditional analyses may overlook. By integrating information from multiple exposures, ESPClust identifies effect size modifiers in datasets that are too small for traditional univariate stratified analyses. This method provides a robust framework for understanding complex omics data and holds promise for personalised medicine.

bioinformatics↗

bioRxiv2024

Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samples

Viruses are an abundant and crucial component of the human microbiome, but accurately discovering them via metagenomics is still challenging. Currently, the available viral reference genomes poorly represent the diversity in microbiome samples, and expanding such a set of viral references is difficult. As a result, many viruses are still undetectable through metagenomics even when considering the power of de novo metagenomic assembly and binning, as viruses lack universal markers. Here, we describe a novel approach to catalog new viral members of the human gut microbiome and show how the resulting resource improves metagenomic analyses. We retrieved >3,000 viral-like particles (VLP) enriched metagenomic samples (viromes), evaluated the efficiency of the enrichment in each sample to leverage the viromes of highest purity, and applied multiple analysis steps involving assembly and comparison with hundreds of thousands of metagenome-assembled genomes to discover new viral genomes. We reported over 162,000 viral sequences passing quality control from thousands of gut metagenomes and viromes. The great majority of the retrieved viral sequences ([~]94.4%) were of unknown origin, most had a CRISPR spacer matching host bacteria, and four of them could be detected in >50% of a set of 18,756 gut metagenomes we surveyed. We included the obtained collection of sequences in a new MetaPhlAn 4.1 release, which can quantify reads within a metagenome matching the known and newly uncovered viral diversity. Additionally, we released the viral database for further virome and metagenomic studies of the human microbiome.

microbiology↗

bioRxiv2023

Gut microbiota-dependent increase in phenylacetic acid induces endothelial cell senescence during aging

Endothelial cell (EC) senescence plays a crucial role in the development of cardiovascular diseases in aging population. Gut microbiota alterations are emerging as significant factors present in cellular senescence associated with aging. However, little is known about how aging-related changes in gut microbiota are causally implicated in EC senescence. Here we show that gut microbiota-dependent phenylacetic acid (PAA) and its derivative, phenylacetylglutamine (PAGln), are elevated in a human aging cohort (TwinsUK, n=7,303) and in aged mice. Metagenomic analyses revealed a marked increase in the abundance of PAA-producing microbial pathways (PPFOR and VOR), which were positively associated with the abundance of Clostridium sp. ASF356, higher circulating PAA concentrations, and endothelial dysfunction in old mice. We found that PAA potently induces EC senescence and attenuates angiogenesis. Mechanistically, PAA increases mitochondrial H2O2 generation, which aggravates IL6-mediated HDAC4 translocation and thereby upregulates VCAM1. In contrast, exogenous acetate, which was reduced in old mice, rescues the PAA-induced EC senescence and restores angiogenic capacity through markedly alleviating the SASP and epigenetic alteration. Our studies provide direct evidence of PAA-mediated crosstalk between aging gut microbiota and EC senescence and suggest a microbiota-based therapy for promoting healthy aging. HighlightsO_LIAging-related gut microbiota alterations contribute to a marked elevation of plasma PAA and PAGln in humans and mice C_LIO_LIClostridium sp. ASF356 contributes to PPFOR-mediated PAA formation in aged mice C_LIO_LIGut-derived PAA promotes endothelial senescence and impairs angiogenesis C_LIO_LIPAA induces mitochondrial H2O2 generation, by which drives epigenetic alterations and SASP in ECs C_LIO_LIAcetate rescues PAA-induced EC senescence and mitochondrial dysfunction C_LIO_LIAcetate improves angiogenesis by reducing HDAC4 phosphorylation and SASP C_LI

cell biology↗

bioRxiv2022

Characterisation of fasting and postprandial NMR metabolites: insights from the ZOE PREDICT 1 Study

BackgroundPostprandial metabolomic profiles and their inter-individual variability are not well characterised. Here we describe postprandial metabolite changes, their correlations with fasting values and their inter- and intra-individual variability following a standardised meal in the ZOE PREDICT 1 cohort. MethodsIn the ZOE PREDICT 1 study (n = 1,002 (NCT03479866)), 250 metabolites, mainly lipids, were measured by Nightingale NMR panel in fasting and postprandial (4 and 6 h after a 3.7 MJ mixed nutrient meal, with a second 2.2 MJ mixed nutrient meal at 4 h) serum samples. For each metabolite, inter- and intra-individual variability over-time was evaluated using linear mixed modelling and intraclass-correlation coefficients (ICC) calculated. ResultsPostprandially, 85% (of 250 metabolites) significantly changed from fasting at 6h (47% increased, 53% decreased; Kruskal-Wallis), with 37 measures increasing by >25%, and 14 increasing by >50%. The largest changes were observed in very large lipoprotein particles and ketone bodies. Seventy-one percent of circulating metabolites were strongly correlated (Spearmans rho >0.80) between fasting and postprandial timepoints, and 5% were weakly correlated (rho <0.50). The median ICC of the 250 metabolites was 0.91 (range 0.08-0.99). The lowest ICCs (ICC<0.40, 4% of measures) were found for glucose, pyruvate, ketone bodies ({beta}-hydroxybutyrate, acetoacetate, acetate) and lactate. ConclusionsIn this large-scale postprandial metabolomic study, circulating metabolites were highly variable between individuals following a mixed challenge meal. Findings suggest that a meal challenge may yield postprandial responses divergent from fasting measures, specifically for glycolysis, essential amino acid, ketone body and lipoprotein size metabolites.

biochemistry↗

bioRxiv2021

Large-scale genome-wide association study of food liking reveals genetic determinants and genetic correlations with distinct neurophysiological traits.

Variable preferences for different foods are among the main determinants of their intake and are influenced by many factors, including genetics. Despite considerable twins heritability, studies aimed at uncovering food-liking genetics have focused mostly on taste receptors. Here, we present the first results of a large-scale genome-wide association study of food liking conducted on 161,625 participants from UK Biobank. Liking was assessed over 139 specific foods using a 9-point hedonic scale. After performing GWAS, we used genetic correlations coupled with structural equation modelling to create a multi-level hierarchical map of food liking. We identified three main dimensions: high caloric foods defined as "Highly palatable", strong-tasting foods ranging from alcohol to pungent vegetables, defined as "Learned" and finally "Low caloric" foods such as fruit and vegetables. The "Highly palatable" dimension was genetically uncorrelated from the other two, suggesting that two independent processes underlie liking high reward foods and the Learned/Low caloric ones. Genetic correlation analysis with the corresponding food consumption traits revealed a high correlation, while liking showed twice the heritability compared to consumption. For example, fresh fruit liking and consumption showed a genetic correlation of 0.7 with heritabilities of 0.1 and 0.05, respectively. GWAS analysis identified 1401 significant food-liking associations located in 173 genomic loci, with only 11 near taste or olfactory receptors. Genetic correlation with morphological and functional brain data (33,224 UKB participants) uncovers associations of the three food-liking dimensions with non-overlapping, distinct brain areas and networks, suggestive of separate neural mechanisms underlying the liking dimensions. In conclusion, we created a comprehensive and data-driven map of the genetic determinants and associated neurophysiological factors of food liking beyond taste receptor genes.

genetics↗

bioRxiv2019

Genome-wide scan identifies novel genetic loci regulating salivary metabolite levels

Saliva, as a biofluid, is inexpensive and non-invasive to obtain, and provides a vital tool to investigate oral health and its interaction with systemic health conditions. There is growing interest in salivary biomarkers for systemic diseases, notably cardiovascular disease. Whereas hundreds of genetic loci have been shown to be involved in the regulation of blood metabolites leading to unprecedented insights into the pathogenesis of complex human diseases, little is known about the impact of host genetics on salivary metabolites. Here we report the first genome-wide association study exploring 476 salivary metabolites in 1,419 subjects of European ancestry from the TwinsUK cohort (discovery phase). A total of 14 salivary metabolites were significantly associated (p<10-10) with genetic variants that mapped to 11 distinct loci, most of which replicated in the Study of Health in Pomerania (SHIP-2) cohort. Interestingly, while only a limited number of the loci that are known to regulate blood metabolites were also associated with salivary metabolites in our study, we identified several novel saliva-specific locus-metabolite associations, including associations for the AGMAT (with the metabolites 4-guanidinobutanoate and beta-guanidinopropanoate), ATP13A5 (with the metabolite creatinine) and DPYS (with the metabolites 3-ureidopropionate and 3-ureidoisobutyrate) loci. Our study suggests that there are biological pathways which are specific to the regulation of the salivary metabolome. In addition, some of our findings may have clinical relevance, such as the utility of the pyrimidine (uracil) degradation metabolites in predicting 5-fluorouracil toxicity and the role of the agmatine pathway metabolites as biomarkers of oral health.

genetics↗