About

Karsten Suhre, Ph.D., is a Professor of Physiology and Biophysics and the Director of the Bioinformatics Core at Weill Cornell Medicine-Qatar. He joined the Department of Physiology and Biophysics at Weill Cornell Medicine in March 2011. His research interests are at the intersection of metabolomics and genomics and their role in human health. Since 2006, he has focused on how genetic variation in human metabolism interacts with environmental challenges and lifestyle factors in the development of complex diseases, especially diabetes, cancer, heart, and kidney diseases. His work has demonstrated that understanding the genetic basis of metabolic individuality in humans can generate new hypotheses for biomedical and pharmaceutical research and inform individualized therapy. Suhre has contributed to setting up and supporting industry-level metabolomics and proteomics facilities in Qatar, conducting clinical studies with metabolomics read-outs, developing cell-culture based metabolomics assays for drug testing, mentoring large genome-wide association studies, and running a bioinformatics core that analyzes whole genome sequences for metabolically relevant gene losses in Mendelian disorders.

Research topics

• Immunology
• Genetics
• Biology
• Cell biology

Selected publications

• Genomic correlates of hyperthermostability revisited: a large-scale validation across 1,963 microbial genomes

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-04-22

  articleOpen access1st authorCorresponding

  Abstract In 2003, Suhre and Claverie demonstrated that the difference between the fraction of charged amino acids and the fraction of polar uncharged amino acids in a proteome (the CvP-bias) was the single genomic feature that most strongly discriminates hyperthermophilic microorganisms from their mesophilic and thermophilic counterparts. The original analysis was based on 71 completely sequenced genomes available at the time. Here, using modern genome databases — specifically the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) for curated optimal growth temperature (OGT) metadata and the NCBI RefSeq FTP archive for sequence data — the same analysis is repeated at approximately 28-fold larger scale, covering 1,963 bacterial and archaeal genomes (103 hyperthermophiles, 409 thermophiles, 1,451 mesophiles). The original finding is confirmed with high statistical confidence: CvP-bias is elevated in hyperthermophiles (mean 11.1 ± 3.1%) relative to mesophiles (5.0 ± 2.0%; ANOVA F = 496, p < 10 −170 ), with a large effect size (Cohen’s d = 2.32) and area under the receiver operating characteristic curve of 0.94 for binary hyper/meso classification. Principal component analysis confirms that the first principal component, explaining 47% of variance, is loaded by CvP-bias as a major contributor, separating hyperthermophiles from other organisms. These results establish that the CvP-bias signal identified in 2003 is not an artifact of small sample size but a genuine, robust property of hyperthermophilic proteomes.

  PublisherOA PDFDOI

• Urinary Single-Cell Transcriptomics in Kidney Transplantation: Elucidation of Donor–Recipient Cellular Dynamics and Fibrogenic Stress

  American Journal of Transplantation · 2026-05-01

  article
  PublisherDOI

• Kidney Allograft Podocyte Epithelial-to-Mesenchymal Transition Detected by Single-Cell RNA Sequencing of Urinary Cells

  American Journal of Transplantation · 2025-08-01

  article
  PublisherDOI

• Elevated Salivary Theobromine and Long‐Term Improvement of Periodontal Health in Two Cohort Studies

  Journal Of Clinical Periodontology · 2025-12-12

  articleOpen access

  BACKGROUND: Theobromine, a methylxanthine mainly found in chocolate, has been suggested to possess various health-promoting properties. This study aimed to investigate the long-term effect of salivary theobromine levels on periodontitis severity using 7- and 10-year follow-up data from the prospective Studies of Health in Pomerania (SHIP-TREND and SHIP-START). MATERIALS AND METHODS: We conducted a non-targeted metabolomics analysis of salivary methylxanthines in 679 participants from SHIP-TREND and 953 participants from SHIP-START. Inverse-probability-of-treatment-weighted generalised linear models were used to assess the relationship between salivary theobromine and periodontal variables, including bleeding on probing, probing depth and clinical attachment loss. RESULTS: Higher salivary theobromine levels were significantly associated with improved periodontal health, as evidenced by lower mean probing depth and a reduced percentage of sites with probing depth ≥ 3 mm. The results were successfully replicated in the SHIP-START data and extended to a lower clinical attachment loss. DISCUSSION: Our cohort studies suggest that elevated salivary theobromine levels are associated with improved periodontal parameters over 7 and 10 years. These results indicate the potential for theobromine-containing products to support periodontal health, warranting further investigation through randomised controlled trials.

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• N‐lactoyl amino acids are potential biomarkers for insulin resistance and diabetic complications

  Diabetes Obesity and Metabolism · 2025-07-22 · 4 citations

  articleOpen access

  AIMS: N-lactoyl amino acids (Lac-AA) are emerging as crucial players in metabolic research, with potential implications for disease mechanisms and therapeutic interventions. This study exploress the role of Lac-AA in insulin resistance, type 2 diabetes (T2D), and its complications. MATERIALS AND METHODS: A cross-sectional study was conducted using data from 2918 participants from Qatar Biobank. After quality control, 2907 individuals were retained and randomly divided into discovery (n = 1990) and validation (n = 917) cohorts. Untargeted metabolomics was employed to profile serum metabolites, and analysis was focused on three Lac-AA species. Participants were stratified into insulin-sensitive, insulin-resistant, T2D without complications and T2D with complications. Associations with clinical traits were assessed using linear regression and Spearman correlation. Diagnostic performance was evaluated using Receiver Operating Characteristic (ROC) analysis in an independent cohort (n = 60). One-sample Mendelian randomisation was performed to assess causality between genetic predisposition to T2D and Lac-AA levels. Network analysis explored metabolic pathways linked to Lac-AA. RESULTS: Lac-AA levels were significantly higher in individuals with insulin resistance and diabetic complications. These findings were robustly replicated in the validation cohort. These metabolites showed strong positive correlations with markers of poor glycaemic control independent of metformin use. ROC analysis demonstrated that Lac-AA could discriminate between insulin-resistant and insulin-sensitive individuals. Mendelian randomisation analysis indicated a potential causal association between genetic risk for T2D and increased Lac-AA, particularly in patients with complications, supporting their role as downstream biomarkers of metabolic disease severity. Gaussian graphical model analysis revealed Lac-AA as central nodes in metabolic networks, showing strong associations with mitochondrial dysfunction biomarkers. CONCLUSIONS: Lac-AA may serve as integrative biomarkers of metabolic dysfunction and diabetic complications. Further longitudinal and interventional studies are needed to clarify their mechanistic roles and clinical utility.

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• Comparative Analysis Between Olink‐PEA and Alamar‐NULISA Proteomic Technologies Applied to a Critically Ill COVID‐19 Cohort

  PROTEOMICS · 2025-02-10 · 5 citations

  article

  We aim to verify and validate low-abundant plasma proteins from severe COVID-19 cases and controls through a comparative analysis between Olink and Alamar performances. Eighty-three severe cases and 44 controls were measured for proteomics using three Olink panels and one Alamar panel, which share 94 targets. CV, pairwise correlation of intensity signals, and detectability range were compared across platforms. Statistical comparisons were performed using FDR-adjusted linear models with age as a covariate to construct differential protein abundance volcano plots between cases and controls per platform and heatmaps between our cohort and five public cohorts. Overall, pairwise comparisons (n = 94) showed strong correlations among cases (r = 0.82) and controls (r = 0.7). 60/94 proteins had mutual significance on both platforms; of which 54 showed concordant effect direction, and six showed opposite effect direction (IL-6R, IL-1R2, KITLG, TSLP, IL-17C, and IL-4R). Alamar verified 80 and 60 targets from cases and controls, respectively, along with 54 differential proteins from Olink. Compared to public cohorts measured by Olink, our Olink data showed consistent findings from 28 proteins, of which 27 were validated by Alamar.

  PublisherDOI

• Subtyping of type 2 diabetes from a large Middle Eastern biobank: Implications for precision medicine

  Molecular Metabolism · 2025-06-23 · 1 citations

  articleOpen accessCorresponding

  Type 2 diabetes (T2D) can be classified into Severe Insulin-Deficient Diabetes (SIDD), Severe Insulin-Resistant Diabetes (SIRD), Mild Obesity-related Diabetes (MOD), and Mild Age-related Diabetes (MARD). This classification can help in predicting disease complications and determining the best treatment for individuals. However, the applicability of this classification to non-European populations and sensitivity to confounding factors remain unclear. We applied k-means clustering to a large Middle Eastern biobank cohort (Qatar Biobank; QBB, comprising 13,808 individuals; 2,687 with T2D). We evaluated the efficacy of the European cluster coordinates and analyzed the impact of using actual age on clustering outcomes. We examined sex differences, analyzed insulin treatment frequency, investigated the clustering of monogenic diabetes (MD) focusing on maturity-onset diabetes of the young (MODY), and evaluated the prevalence of chronic kidney disease (CKD) and Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) among T2D subtypes. We identified the four T2D subtypes within a large Arab cohort. Data-derived centers outperformed European coordinates in classifying T2D. The use of actual age, as opposed to age of diagnosis, impacted MOD and MARD classification. Obesity prevalence was significantly higher in females. However, that did not translate to worse disease severity, as indicated by comparable levels of HbA1C and HOMA2-IR. Insulin was predominantly prescribed for individuals in SIDD and SIRD, who also displayed the highest risk of CKD, followed by MOD. Interestingly, most MODY individuals were clustered within MARD, further highlighting the need for precise classification and tailored interventions. The observed sex differences underscore the importance of tailoring treatment plans for females compared to males. Individuals who are at a higher risk of CKD and MASLD may require closer monitoring and physician oversight. Additionally, in populations without access to genetic testing, likely MODY individuals can be identified within the MARD cluster. These findings strongly support the need for a transition to more personalized, data-driven treatment approaches to minimize diabetes-related complications and improve disease outcomes. • We successfully classified 2,687 individuals with T2D into four distinct subtypes (SIDD, SIRD, MOD, MARD). • Obesity was significantly higher among females; however, this did not increase disease severity, as shown by similar levels of HbA1C and HOMA2-IR. • The prevalence of Chronic Kidney Disease (CKD) and Metabolic dysfunction–associated steatotic liver disease (MASLD) was highest in SIRD, followed by SIDD and MOD. • MODY individuals can be identified within the MARD cluster in populations without access to genetic testing.

  PublisherDOI

• Theobromine is Associated with Slower Epigenetic Ageing

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-04-19

  preprintOpen access

  Abstract 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.

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• Genomic Analysis of Date Palm Fruit Size Traits and Identification of Candidate Genes through GWAS

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-01-22 · 2 citations

  preprint

  Abstract The commercial value of economically significant fruits, including date palm fruit (dates), is influenced by various factors, such as biochemical composition and morphological features like size, shape, and visual appearance, which are key determinants of their quality and market value. Dates are typically consumed at the dry stage (Tamar), during which they exhibit a wide range of physical characteristics, such as color, length, weight, and skin appearance. Understanding the genetic basis of these traits is crucial for improving crop quality and breeding new cultivars. In this study, we integrated a genome dataset from highly diverse date cultivars with phenotypes of dry fruit such as length, width, area, and weight, identifying multiple significant genetic loci (SNPs) associated with these traits. We also identified candidate genes located near the associated SNPs that are involved in biological processes such as cell differentiation, proliferation, growth, and the regulation of signalling pathways for growth regulators like auxin and abscisic acid, as observed in other plants. Gene expression analysis reveals that many of these genes are highly expressed in the early stage of fruit development when the fruit attains its maximum size and weight. These findings will enhance our understanding of genetic determinants of fruit size particularly at the commercially important Tamar stage.

  PublisherDOI

• Individual bioenergetic capacity as a potential source of resilience to Alzheimer’s disease

  Nature Communications · 2025-02-24 · 16 citations

  articleOpen access

  Impaired glucose uptake in the brain is an early presymptomatic manifestation of Alzheimer's disease (AD), with symptom-free periods of varying duration that likely reflect individual differences in metabolic resilience. We propose a systemic "bioenergetic capacity", the individual ability to maintain energy homeostasis under pathological conditions. Using fasting serum acylcarnitine profiles from the AD Neuroimaging Initiative as a blood-based readout for this capacity, we identified subgroups with distinct clinical and biomarker presentations of AD. Our data suggests that improving beta-oxidation efficiency can decelerate bioenergetic aging and disease progression. The estimated treatment effects of targeting the bioenergetic capacity were comparable to those of recently approved anti-amyloid therapies, particularly in individuals with specific mitochondrial genotypes linked to succinylcarnitine metabolism. Taken together, our findings provide evidence that therapeutically enhancing bioenergetic health may reduce the risk of symptomatic AD. Furthermore, monitoring the bioenergetic capacity via blood acylcarnitine measurements can be achieved using existing clinical assays.

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Frequent coauthors

• Jerzy Adamski

  University of Ljubljana

  583 shared

• Gabi Kastenmüller

  Helmholtz Zentrum München

  554 shared

• Annette Peters

  Deutsches Diabetes-Zentrum e.V.

  424 shared

• Christian Gieger

  Deutsches Diabetes-Zentrum e.V.

  406 shared

• Rui Wang‐Sattler

  Center for Environmental Health

  254 shared

• Jan Krumsiek

  Cornell University

  245 shared

• Werner Römisch‐Margl

  Helmholtz Zentrum München

  178 shared

• Thomas Illig

  German Center for Lung Research

  176 shared

Education

• Habilitation, Bioinformatics

  Aix-Marseille Université

  2004

• PhD, Atmospheric Chemistry and Meteorology

  Université Paul Sabatier

  1994

• Vordiplom, Mathematics

  Universität Osnabrück

  1991

• Diplom, Physics

  Universität Osnabrück

  1991

• Exchange Student (3rd year BSc), Applied Mathematics

  University of Hull

  1989