Effect of Empagliflozin on the plasma lipidome in patients with type 2 diabetes mellitus: results from the EmDia clinical trial Katrin I. Bauer, Dhanwin Baker, Raissa Lerner, Thomas Koeck, Gregor Buch, et al. Cardiovascular Diabetology, 2025 Background Sodium-glucose cotransporter 2 (SGLT2) inhibitors, such as Empagliflozin, are antidiabetic drugs that reduce glucose levels and have emerged as a promising therapy for patients with heart failure (HF), although the exact molecular mechanisms underlying their cardioprotective effects remain to be fully elucidated. The EmDia study, a randomized, double-blind trial conducted at the University Medical Center of Mainz, has confirmed the beneficial effects of Empagliflozin in HF patients after both one and twelve weeks of treatment. In this work, we aimed to assess whether changes in lipid profiles driven by Empagliflozin use in HF patients in the EmDia trial could assist in gaining a better understanding of its cardioprotective mechanisms. Methods Lipid analysis of blood plasma from 144 patients from the EmDia trial was conducted using 4D-LC-TIMS/IMS lipidomics. Lipid signatures after treatment for one and twelve weeks, respectively, were obtained with sparse group LASSO regularized regression models. Linear regression models were employed to highlight associations between significantly changed clinical traits and lipids. Results The lipid signatures after one week of treatment consisted of 37 lipids from the lipid groups lysophosphatidylcholine (LPC), phosphatidylcholine (PC), phosphatidylethanolamine (PE), sphingomyelin (SM), and triacylglycerol (TG). After twelve weeks, the signature comprised 24 lipids from the same five lipid groups, along with Ceramides (Cer). Three of five lipids altered at both time points showed consistent directional trends. Empagliflozin treatment led to significant alterations in the lipidome, including increases in both beneficial lipids, such as LPCs, and potentially harmful species, notably ceramides, which have been implicated in lipotoxicity and cardiovascular risk. Conclusion This study identified distinct lipid signatures associated with Empagliflozin treatment after both one and twelve weeks, respectively, with five lipids overlapping between signatures and three with consistent directions, revealing that some of the beneficial effects of Empagliflozin could be through lipid modulation. Notably, Empagliflozin-modulated lipids associated with changes in clinical traits and lipid-specific profiles among clinical subgroups were observed. However, challenges remain in establishing direct associations between individual lipids and clinical outcomes. Future research integrating lipidomics data with other omics datasets could provide a more comprehensive understanding of the identified lipid signatures and their potential roles in health and diseases. Trial registration ClinicalTrials.gov; NCT02932436. Registration date, 2016/10/13. Graphical abstract
A Map of the Lipid–Metabolite–Protein Network to Aid Multi-Omics Integration Uchenna Alex Anyaegbunam, Aimilia-Christina Vagiona, Vincent ten Cate, Katrin Bauer, Thierry Schmidlin, et al. Biomolecules, 2025 The integration of multi-omics data offers transformative potential for elucidating complex molecular mechanisms underlying biological processes and diseases. In this study, we developed a lipid–metabolite–protein network that combines a protein–protein interaction network and enzymatic and genetic interactions of proteins with metabolites and lipids to provide a unified framework for multi-omics integration. Using hyperbolic embedding, the network visualizes connections across omics layers, accessible through a user-friendly Shiny R (version 1.10.0) software package. This framework ranks molecules across omics layers based on functional proximity, enabling intuitive exploration. Application in a cardiovascular disease (CVD) case study identified lipids and metabolites associated with CVD-related proteins. The analysis confirmed known associations, like cholesterol esters and sphingomyelin, and highlighted potential novel biomarkers, such as 4-imidazoleacetate and indoleacetaldehyde. Furthermore, we used the network to analyze empagliflozin’s temporal effects on lipid metabolism. Functional enrichment analysis of proteins associated with lipid signatures revealed dynamic shifts in biological processes, with early effects impacting phospholipid metabolism and long-term effects affecting sphingolipid biosynthesis. Our framework offers a versatile tool for hypothesis generation, functional analysis, and biomarker discovery. By bridging molecular layers, this approach advances our understanding of disease mechanisms and therapeutic effects, with broad applications in computational biology and precision medicine.
A Systematic Review of Lipid-Focused Cardiovascular Disease Research: Trends and Opportunities Uchenna Alex Anyaegbunam, Piyush More, Jean-Fred Fontaine, Vincent ten Cate, Katrin Bauer, et al. Current Issues in Molecular Biology, 2023 Lipids are important modifiers of protein function, particularly as parts of lipoproteins, which transport lipophilic substances and mediate cellular uptake of circulating lipids. As such, lipids are of particular interest as blood biological markers for cardiovascular disease (CVD) as well as for conditions linked to CVD such as atherosclerosis, diabetes mellitus, obesity and dietary states. Notably, lipid research is particularly well developed in the context of CVD because of the relevance and multiple causes and risk factors of CVD. The advent of methods for high-throughput screening of biological molecules has recently resulted in the generation of lipidomic profiles that allow monitoring of lipid compositions in biological samples in an untargeted manner. These and other earlier advances in biomedical research have shaped the knowledge we have about lipids in CVD. To evaluate the knowledge acquired on the multiple biological functions of lipids in CVD and the trends in their research, we collected a dataset of references from the PubMed database of biomedical literature focused on plasma lipids and CVD in human and mouse. Using annotations from these records, we were able to categorize significant associations between lipids and particular types of research approaches, distinguish non-biological lipids used as markers, identify differential research between human and mouse models, and detect the increasingly mechanistic nature of the results in this field. Using known associations between lipids and proteins that metabolize or transport them, we constructed a comprehensive lipid–protein network, which we used to highlight proteins strongly connected to lipids found in the CVD-lipid literature. Our approach points to a series of proteins for which lipid-focused research would bring insights into CVD, including Prostaglandin G/H synthase 2 (PTGS2, a.k.a. COX2) and Acylglycerol kinase (AGK). In this review, we summarize our findings, putting them in a historical perspective of the evolution of lipid research in CVD.
Lithium treatment extends human lifespan: findings from the UK Biobank Elisa Araldi, Catherine R. Jutzeler, Michael Ristow Aging, 2023 Lithium is a nutritional trace element that is also used pharmacologically for the management of bipolar and related psychiatric disorders. Recent studies have shown that lithium supplementation can extend health and lifespan in different animal models. Moreover, nutritional lithium uptake from drinking water was repeatedly found to be positively correlated with human longevity. By analyzing a large observational aging cohort (UK Biobank, n = 501,461 individuals) along with prescription data derived from the National Health Services (NHS), we here find therapeutic supplementation of lithium linked to decreased mortality (p = 0.0017) of individuals diagnosed with affective disorders. Subsequent multivariate survival analyses reveal lithium to be the strongest factor in regards to increased survival effects (hazard ratio = 0.274 [0.119–0.634 CI 95%, p = 0.0023]), corresponding to 3.641 times lower (95% CI 1.577–8.407) chances of dying at a given age for lithium users compared to users of other anti-psychotic drugs. While these results may further support the use of lithium as a geroprotective supplement, it should be noted that doses applied within the UK Biobank/NHS setting require close supervision by qualified medical professionals.
Germline loss-of-function PAM variants are enriched in subjects with pituitary hypersecretion Giampaolo Trivellin, Adrian F. Daly, Laura C. Hernández-Ramírez, Elisa Araldi, Christina Tatsi, et al. Frontiers in Endocrinology, 2023 IntroductionPituitary adenomas (PAs) are common, usually benign tumors of the anterior pituitary gland which, for the most part, have no known genetic cause. PAs are associated with major clinical effects due to hormonal dysregulation and tumoral impingement on vital brain structures. PAM encodes a multifunctional protein responsible for the essential C-terminal amidation of secreted peptides.MethodsFollowing the identification of a loss-of-function variant (p.Arg703Gln) in the peptidylglycine a-amidating monooxygenase (PAM) gene in a family with pituitary gigantism, we investigated 299 individuals with sporadic PAs and 17 familial isolated PA kindreds for PAM variants. Genetic screening was performed by germline and tumor sequencing and germline copy number variation (CNV) analysis.ResultsIn germline DNA, we detected seven heterozygous, likely pathogenic missense, truncating, and regulatory SNVs. These SNVs were found in sporadic subjects with growth hormone excess (p.Gly552Arg and p.Phe759Ser), pediatric Cushing disease (c.-133T>C and p.His778fs), or different types of PAs (c.-361G>A, p.Ser539Trp, and p.Asp563Gly). The SNVs were functionally tested in vitro for protein expression and trafficking by Western blotting, splicing by minigene assays, and amidation activity in cell lysates and serum samples. These analyses confirmed a deleterious effect on protein expression and/or function. By interrogating 200,000 exomes from the UK Biobank, we confirmed a significant association of the PAM gene and rare PAM SNVs with diagnoses linked to pituitary gland hyperfunction.ConclusionThe identification of PAM as a candidate gene associated with pituitary hypersecretion opens the possibility of developing novel therapeutics based on altering PAM function.
Grainyhead 1 acts as a drug-inducible conserved transcriptional regulator linked to insulin signaling and lifespan Giovanna Grigolon, Elisa Araldi, Reto Erni, Jia Yee Wu, Carolin Thomas, et al. Nature Communications, 2022 Aging is impacted by interventions across species, often converging on metabolic pathways. Transcription factors regulate longevity yet approaches for their pharmacological modulation to exert geroprotection remain sparse. We show that increased expression of the transcription factor Grainyhead 1 (GRH-1) promotes lifespan and pathogen resistance in Caenorhabditis elegans. A compound screen identifies FDA-approved drugs able to activate human GRHL1 and promote nematodal GRH-1-dependent longevity. GRHL1 activity is regulated by post-translational lysine methylation and the phosphoinositide (PI) 3-kinase C2A. Consistently, nematodal longevity following impairment of the PI 3-kinase or insulin/IGF-1 receptor requires grh-1. In BXD mice, Grhl1 expression is positively correlated with lifespan and insulin sensitivity. In humans, GRHL1 expression positively correlates with insulin receptor signaling and also with lifespan. Fasting blood glucose levels, including in individuals with type 2 diabetes, are negatively correlated with GRHL1 expression. Thereby, GRH-1/GRHL1 is identified as a pharmacologically malleable transcription factor impacting insulin signaling and lifespan.
Targeted Suppression of miRNA-33 Using pHLIP Improves Atherosclerosis Regression Xinbo Zhang, Noemi Rotllan, Alberto Canfrán-Duque, Jonathan Sun, Jakub Toczek, et al. Circulation Research, 2022 Background: miRNA therapeutics have gained attention during the past decade. These oligonucleotide treatments can modulate the expression of miRNAs in vivo and could be used to correct the imbalance of gene expression found in human diseases such as obesity, metabolic syndrome, and atherosclerosis. The in vivo efficacy of current anti-miRNA technologies hindered by physiological and cellular barriers to delivery into targeted cells and the nature of miRNAs that allows one to target an entire pathway that may lead to deleterious off-target effects. For these reasons, novel targeted delivery systems to inhibit miRNAs in specific tissues will be important for developing effective therapeutic strategies for numerous diseases including atherosclerosis. Methods: We used pH low-insertion peptide (pHLIP) constructs as vehicles to deliver microRNA-33-5p (miR-33) antisense oligonucleotides to atherosclerotic plaques. Immunohistochemistry and histology analysis was performed to assess the efficacy of miR-33 silencing in atherosclerotic lesions. We also assessed how miR-33 inhibition affects gene expression in monocytes/macrophages by single-cell RNA transcriptomics. Results: The anti-miR-33 conjugated pHLIP constructs are preferentially delivered to atherosclerotic plaque macrophages. The inhibition of miR-33 using pHLIP-directed macrophage targeting improves atherosclerosis regression by increasing collagen content and decreased lipid accumulation within vascular lesions. Single-cell RNA sequencing analysis revealed higher expression of fibrotic genes ( Col2a1, Col3a1, Col1a2, Fn1 , etc) and tissue inhibitor of metalloproteinase 3 ( Timp3 ) and downregulation of Mmp12 in macrophages from atherosclerotic lesions targeted by pHLIP-anti-miR-33. Conclusions: This study provides proof of principle for the application of pHLIP for treating advanced atherosclerosis via pharmacological inhibition of miR-33 in macrophages that avoid the deleterious effects in other metabolic tissues. This may open new therapeutic opportunities for atherosclerosis-associated cardiovascular diseases via selective delivery of other protective miRNAs.
Type 2 diabetes risk alleles in peptidyl-glycine alpha-amidating monooxygenase influence GLP-1 levels and response to GLP-1 receptor agonists MM Umapathysivam, E Araldi, B Hastoy, AY Dawed, H Vatandaslar, ... Genome Medicine , 2026 2026 Citations: 11
Effect of Empagliflozin on the plasma lipidome in patients with type 2 diabetes mellitus: results from the EmDia clinical trial KI Bauer, D Baker, R Lerner, T Koeck, G Buch, Z Fischer, R Martens, ... Cardiovascular Diabetology 24 (1), 359 , 2025 2025 Citations: 6
Unraveling the link between cholesterol and immune system in cancer: From biological mechanistic insights to clinical evidence. A narrative review F Pecci, V Cognigni, GC Giudice, F Paoloni, L Cantini, KS Saini, ... Critical Reviews in Oncology/Hematology 209, 104654 , 2025 2025 Citations: 7
Autophagy regulator ATG7 links lipid metabolism to cell-fate decisions in kidney tubule health and disease D Nieri, SA Keller, L Pierre, F Carloni, R Pili, Z Chen, AM Ouellette, ... medRxiv, 2025.03. 26.25324675 , 2025 2025 Citations: 1
A map of the lipid–metabolite–protein network to aid multi-omics integration UA Anyaegbunam, AC Vagiona, V Ten Cate, K Bauer, T Schmidlin, ... Biomolecules 15 (4), 484 , 2025 2025 Citations: 3
Unbiased multi-omics network-based data integration allows clinically relevant outcome-predicting clustering of individuals with heart failure EE Esenkova, T Koeck, R Lerner, D Baker, KI Bauer, M Nuber, G Valentini, ... medRxiv, 2025.01. 28.25321241 , 2025 2025
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Retraction of: Lithium treatment extends human lifespan: findings from the UK Biobank E Araldi, CR Jutzeler, M Ristow Aging (Albany NY) 16 (17), 12431 , 2024 2024
Sec24D-positive ER exit sites sort raftpreferring proteins for rapid ER export I Castello-Serrano, R Ippolito, K Levental, E Araldi, I Levental FEBS OPEN BIO 14, 74-74 , 2024 2024
Effect of Empagliflozin compared to placebo on the plasma lipidome in patients with type 2 diabetes mellitus-results from the EmDia trial K Bauer, D Baker, R Lerner, Z Fischer, T Koeck, G Buch, E Esenkova, ... FEBS OPEN BIO 14, 159-159 , 2024 2024
Type 2 diabetes risk alleles in peptidyl-glycine alpha-amidating monooxygenase influence GLP-1 levels and response to GLP-1 receptor agonists E Araldi, MM Umapathysivam, B Hastoy, AY Dawed, H Vatandaslar, ... FEBS OPEN BIO 14, 467-467 , 2024 2024
Unbiased clustering and molecular characterisation of novel metabolic phenotypes in a heart failure cohort E Esenkova, T Koeck, G Valentini, P Wild, E Casiraghi, E Araldi Cardiovascular Research 120 (Supplement_1), cvae088. 087 , 2024 2024
A systematic review of lipid-focused cardiovascular disease research: trends and opportunities UA Anyaegbunam, P More, JF Fontaine, V Cate, K Bauer, U Distler, ... Current Issues in Molecular Biology 45 (12), 9904-9916 , 2023 2023 Citations: 9
Germline loss-of-function PAM variants are enriched in subjects with pituitary hypersecretion G Trivellin, AF Daly, LC Hernández-Ramírez, E Araldi, C Tatsi, RK Dale, ... Frontiers in Endocrinology 14, 1166076 , 2023 2023 Citations: 22
Effects of antidiabetic drugs on mortality risks in individuals with type 2 diabetes: A prospective cohort study of UK Biobank participants E Araldi, CR Jutzeler, M Ristow medRxiv, 2023.05. 19.23290214 , 2023 2023 Citations: 4
Lithium treatment extends human lifespan: findings from the UK Biobank E Araldi, CR Jutzeler, M Ristow Aging (Albany NY) 15 (2), 421 , 2023 2023 Citations: 22
Targeted suppression of miRNA-33 using pHLIP improves atherosclerosis regression X Zhang, N Rotllan, A Canfrán-Duque, J Sun, J Toczek, A Moshnikova, ... Circulation Research 131 (1), 77-90 , 2022 2022 Citations: 86
Grainyhead 1 acts as a drug-inducible conserved transcriptional regulator linked to insulin signaling and lifespan G Grigolon, E Araldi, R Erni, JY Wu, C Thomas, M La Fortezza, B Laube, ... Nature communications 13 (1), 107 , 2022 2022 Citations: 21
Desmosterol suppresses macrophage inflammasome activation and protects against vascular inflammation and atherosclerosis X Zhang, JG McDonald, B Aryal, A Canfrán‐Duque, EL Goldberg, E Araldi, ... Proceedings of the National Academy of Sciences 118 (47), e2107682118 , 2021 2021 Citations: 130
Targeted suppression of microRNA-33 in lesional macrophages using pH low-insertion peptides (pHLIP) improves atherosclerotic plaque regression X Zhang, N Rotllan, A Canfrán-Duque, J Toczek, A Moshnikova, S Malik, ... 2020 Citations: 1
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