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Unit of Integrative Metabolomics

The focus of our research is to understand the metabolic drivers of disease towards the goal of developing a quantitative phenotype of health.

Part of the:
Craig Wheelock, IMM

Our work employs mass spectrometry to perform molecular phenotyping of individuals in response to disease or environmental stressors. These efforts are combined with integrative modeling to identify biochemical pathways associated with specific disease sub-phenotypes towards the twin goals of understanding the etiology of disease processes and identifying markers of the onset as well as resolution of system-based stress.

Publications

All publications from group members

  • Journal article: REGULATORY TOXICOLOGY AND PHARMACOLOGY. 2025;162:105894
    Barnett RE; Lawson TN; Rivetti C; Barata C; Cronin MTD; Lacorte S; Lloyd GR; Weber RJM; Smith MJ; Southam AD; Biales A; Koehrn K; Campos B; Colbourne JK; Hodges G; Viant MR
  • Journal article: ERJ OPEN RESEARCH. 2025;11(6):01089-02024
    Eastwood MC; Busby J; Kolmert J; Zurita J; Dahlen S-E; Mcdowell PJ; Bradley J; Jackson D; Pavord I; Djukanovic R; Arron J; Bradding P; Brightling C; Chaudhuri R; Cowan D; Fowler S; Hardman TC; Holweg C; Lordan J; Mansur A; Robinson D; Wheelock CE; Heaney L; UK MRCRSP
  • Journal article: ARCHIVES OF TOXICOLOGY. 2025;99(8):3379-3392
    Bowen TJ; Hall AR; Lloyd GR; Smith MJ; Weber RJM; Wilson A; Pointon A; Viant MR
  • Preprint: CHEMRXIV. 2025
    Revol-Cavalier J; Hamberg M; Wheelock C
  • Journal article: BIOMEDICINE & PHARMACOTHERAPY. 2025;188:118184
    Zelkowska J; Kolmert J; Zurita J; Kisluk J; Niklinski J; Reszec J; Wheelock CE; Ciborowski M; Godzien J
  • Article: PLANT BIOLOGY. 2025;27(4):476-491
    Ni B; Klein M; Hossbach B; Feussner K; Hornung E; Herrfurth C; Hamberg M; Feussner I
  • Editorial comment: SCIENCE SIGNALING. 2025;18(887):eadw1245
    Schebb NH; Kampschulte N; Hagn G; Plitzko K; Meckelmann SW; Ghosh S; Joshi R; Kuligowski J; Vuckovic D; Botana MT; Sanchez-Illana A; Zandkarimi F; Das A; Yang J; Schmidt L; Checa A; Roche HM; Armando AM; Edin ML; Lih FB; Aristizabal-Henao JJ; Miyamoto S; Giuffrida F; Moussaieff A; Domingues R; Rothe M; Hinz C; Das US; Rund KM; Taha AY; Hofstetter RK; Werner M; Werz O; Kahnt AS; Bertrand-Michel J; Le Faouder P; Gurke R; Thomas D; Torta F; Milic I; Dias IHK; Spickett CM; Biagini D; Lomonaco T; Idborg H; Liu J-Y; Fedorova M; Ford DA; Barden A; Mori TA; Kennedy PD; Maxey K; Ivanisevic J; Gallart-Ayala H; Gladine C; Wenk M; Galano J-M; Durand T; Stark KD; Barbas C; Garscha U; Gelhaus SL; Ceglarek U; Flamand N; Griffin JL; Ahrends R; Arita M; Zeldin DC; Schopfer FJ; Quehenberger O; Julian R; Nicolaou A; Blair IA; Murphy MP; Hammock BD; Freeman B; Liebisch G; Serhan CN; Koefeler HC; Jakobsson P-J; Steinhilber D; Gelb MH; Holcapek M; Andrew R; Giera M; Fitzgerald GA; Murphy RC; Newman JW; Dennis EA; Ekroos K; Milne GL; Gijon MA; Vesper HW; Wheelock CE; O'Donnell VB
  • Journal article: AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE. 2025;211:a5285
    Wheelock CE; Smith M; Safholm J; Firsova A; Samakovlis C
  • Article: AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY. 2025;328(5):l638-l649
    Nie M; Liu J; Xiang Y; Wong A; Hendriks E; Nilsson G; Safholm J; Adner M
  • Article: MUCOSAL IMMUNOLOGY. 2025;18(4):836-847
    Morales Castro RA; Kern BC; D铆az-Basabe A; Meinen ER; Zhao D; Zhou Y; Castillo F; Monasterio G; Farcas V; Ch谩vez MN; Fransson J; Villablanca EJ
  • Article: SKELETAL MUSCLE. 2025;15(1):9
    Horwath O; Cornet L; Stroemlind H; Moberg M; Edman S; Soederlund K; Checa A; Ruas JL; Blomstrand E
  • Article: AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE. 2025;211(5):737-748
    Mendez KM; Kachroo P; Prince N; Huang M; Cote M; Chu SH; Chen Y; Sharma R; Hecker J; Chen L; Gerszten R; Clish C; Avila L; Celedon JC; Wheelock CE; Weiss ST; Mcgeachie M; Broadhurst DI; Kelly RS; Reinke SN; Lasky-Su JA
  • Article: EBIOMEDICINE. 2025;112:105534
    Sharma R; Mendez K; Begum S; Chu S; Prince N; Hecker J; Kelly RS; Chen Q; Wheelock CE; Celedon JC; Clish C; Gertszen R; Tantisira KG; Weiss ST; Lasky-Su J; Mcgeachie M
  • Preprint: RESEARCH SQUARE. 2025
    wheelock C; Botana M; Lewis R; Quaranta A; Salamin O; Revol-Cavalier J; Oakley C; Feussner I; Hamberg M; Grossman A; Suggett D; Weis V; Davy S
  • Review: CHEMICAL REVIEWS. 2025;125(1):1-90
    Revol-Cavalier J; Quaranta A; Newman JW; Brash AR; Hamberg M; Wheelock CE
  • Article: EUROPEAN RESPIRATORY JOURNAL. 2025;65(1):2400298
    Wang G; Hallberg J; Merid SK; Kumar A; Klevebro S; Habchi B; Chaleckis R; Wheelock CE; Hernandez-Pacheco N; Ekstrom S; Janson C; Kull I; Bergstrom A; Melen E
  • Book chapter: METHODS IN MOLECULAR BIOLOGY. 2025;p. 315-339
    Salamin O; Wheelock CE
  • Preprint: BIORXIV. 2024
    Botana MT; Lewis RE; Quaranta A; Salamin O; Revol-Cavalier J; Oakley CA; Feussner I; Hamberg M; Grossman AR; Suggett DJ; Weis VM; Wheelock CE; Davy SK
  • Article: MED. 2024;5(12):1485-1494.e3
    Kim M; Brustad N; Eliasen AU; Ali M; Wang T; Rasmussen MA; Ernst M; Hougaard D; Litonjua AA; Wheelock CE; Kelly RS; Chen Y; Prince N; Townsend PA; Stokholm J; Weiss ST; Bonnelykke K; Lasky-Su J; Chawes B
  • Article: SCIENCE IMMUNOLOGY. 2024;9(102):eadl1467
    Bohnacker S; Henkel FDR; Hartung F; Geerlof A; Riemer S; Prodjinotho UF; Salah EB; Mourao ASD; Bohn S; Teder T; Thomas D; Gurke R; Boeckel C; Ud-Dean M; Koenig A-C; Quaranta A; Alessandrini F; Lechner A; Spitzlberger B; Kabat AM; Pearce E; Haeggstroem JZ; Hauck SM; Wheelock CE; Jakobsson P-J; Sattler M; Voehringer D; Feige MJ; da Costa CP; Bieren JE-V
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Staff and contact

Head of Unit

All members of the group

Metabolomic Epidemiology

We are working to develop the nascent discipline of metabolomic epidemiology, the field involving the systematic use of epidemiological methods and principles to study population-based variation in the human metabolome as it associates with health-related outcomes or exposures. Towards that end, the group works extensively on developing high-throughput robust metabolomics methods that are suitable for large-scale data acquisition. As part of our efforts in this area, we work to address many of the issues that can serve as potential sources of study bias and variation, both epidemiological and metabolomic, including study design, metadata collection, patient selection, appropriate choice of biofluid/tissue, sample collection, biobanking protocols, sample storage integrity, metabolite coverage, metabolite annotation, and metabolite quality control. Accordingly, following collection and analytical consideration of these potentially influencing variables, metabolomic and epidemiological data are integrated, and appropriate interpretations can be made. These efforts are important for our work in stratified or precision medicine in which we can use individual metabotypes to identify patient sub-groups with unique disease trajectories and treatment needs towards the goal of getting the right medication to the right patient at the right time. Our primary interest is in understanding the pathophysiological and environmental drivers of obstructive lung disease with a focus on asthma, in which we are using metabolomic epidemiological approaches to identify biomarkers for stratifying asthmatics for treatment with biologics.

Lipid Mediators

We are investigating the role of bioactive lipids including octadecanoids, eicosanoids, and sphingolipids in the etiology and pathophysiology of inflammation. Our research focuses in particular on the C18-carbon containing fatty acids and their downstream biosynthetic products. Linoleic acid, and its C18 analogs from both omega-6 and omega-3 fatty acids, can be converted to multiple metabolites, collectively called octadecanoids. While there is extensive research on the biological activity of the arachidonic acid-derived eicosanoids, there is a paucity of information on the octadecanoids. This oversight is important because due to the widespread use of vegetable oils, linoleic acid is now the most highly consumed polyunsaturated fatty acid (PUFA) in the western diet. The increase of linoleic acid consumption over the last 50 years has raised concerns concerning its potential impact upon human pathophysiology, particularly in regards to the effects on chronic inflammation. Conversely, the omega-3 fatty acid alpha-linolenic acid (ALA) is generally considered to exert anti-inflammatory or pro-resolving effects, and deficiencies are associated with onset of inflammation. Work in our group focuses on identifying new octadecanoids and developing the analytical methods to quantify these compounds in multiple biological matrices. We focus in particular on characterizing the production of octadecanoids by immune cells to explore their role in the etiology of obstructive lung disease. Recent efforts include investigating the role of the gut microbiome in the production of octadecanoids and examining their physiological role in the gut-lung axis. Our primary interest can be summarized as a concerted effort to quantify lipids with a focus on understanding the role of fatty acids and their lipid mediator biosynthetic products in the etiology of disease. 

KI-SMMS Core Facility

Small Molecule Mass Spectrometry Core Facility (KI-SMMS) can assist with expert knowledge in metabolism, experimental design, and data analysis. Whether you need to perform metabolomics, lipidomics, targeted fluxomics or other types of LC-MS based experiments, we can customize our methods to your research goals and questions. Let us enhance your research with the power of targeted mass spectrometry.

LINK to Small Molecule Mass Spectrometry Core Facility (KI-SMMS)