A biological-systems-based analysis using proteomic and metabolic network inference reveals mechanistic insights into hepatic steatosis

Metabolism, vol. 178, pp. 156552

Abstract

OBJECTIVE: To delineate organ-specific and systemic drivers of metabolic dysfunction-associated steatotic liver disease (MASLD), we applied integrative causal inference across clinical, imaging, and proteomic domains in individuals with and without type 2 diabetes (T2D). METHODS: Bayesian network analyses and complementary two-sample Mendelian randomization were used to quantify causal pathways linking adipose distribution, glycemia, and insulin dynamics with liver fat in the IMI-DIRECT prospective cohort study. Data included frequently sampled metabolic challenge tests, MRI-derived abdominal and hepatic fat content, serological biomarkers, and Olink plasma proteomics from 331 adults with new-onset T2D and 964 adults without diabetes, with harmonized protocols enabling replication. RESULTS: High basal insulin secretion rate (BasalISR), estimated via C-peptide deconvolution, emerged as the primary potential causal driver of liver fat accumulation in both cohorts. BasalISR, a clearance-independent measure of β-cell insulin output distinct from peripheral insulin levels, was independently linked to hepatic steatosis. Visceral adipose tissue exhibited bidirectional associations with liver fat, suggesting a self-reinforcing metabolic loop. Of 446 analyzed proteins, 34 mapped to these metabolic networks (27 in the non-diabetes network, 18 in the T2D network, and 11 shared). Key proteins directly associated with liver fat included GUSB, ALDH1A1, LPL, IGFBP1/2, CTSD, HMOX1, FGF21, AGRP, and ACE2. Sex-stratified analyses identified GUSB in females and LEP in males as the strongest protein predictors of liver fat. CONCLUSIONS: BasalISR may better capture early β-cell-driven disturbances contributing to MASLD. These findings outline a multifactorial, sex- and disease stage-specific proteo-metabolic architecture of hepatic steatosis and identify potential biomarkers or therapeutic targets.

Authors 63

1. Natalie N. Atabaki corresponding

   University of Copenhagen · Lund University · University of Oxford · NIHR Oxford Biomedical Research Centre · Oxford Centre for Diabetes, Endocrinology and Metabolism · Novo Nordisk Foundation Center for Basic Metabolic Research

   Affiliation as printed

   Department of Clinical Science, Genetic and Molecular Epidemiology, Lund University Diabetes Centre, Helsingborg, Sweden; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; The National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre (BRC), OCDEM, Radcliffe Department of Medicine, University of Oxford, Oxford, UK. Electronic address: natalie.atabaki@med.lu.se

2. Daniel Coral

   Lund University

   Affiliation as printed

   Department of Clinical Science, Genetic and Molecular Epidemiology, Lund University Diabetes Centre, Helsingborg, Sweden

3. Hugo Pomares‐Millan

   Dartmouth–Hitchcock Medical Center · Lund University

   Affiliation as printed

   Department of Clinical Science, Genetic and Molecular Epidemiology, Lund University Diabetes Centre, Helsingborg, Sweden; Department of Epidemiology, Geisel School of Medicine at Dartmouth, Dartmouth-Hitchcock Medical Center, Lebanon, USA

4. Kieran Smith

   National Institute for Health and Care Research · University of Oxford · NIHR Oxford Biomedical Research Centre · Oxford Centre for Diabetes, Endocrinology and Metabolism

   Affiliation as printed

   The National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre (BRC), OCDEM, Radcliffe Department of Medicine, University of Oxford, Oxford, UK

5. Hamid Behjat

   Lund University

   Affiliation as printed

   Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, Lund, Sweden

6. Robert Wilhelm Koivula

   National Institute for Health and Care Research · University of Oxford · NIHR Oxford Biomedical Research Centre · Oxford Centre for Diabetes, Endocrinology and Metabolism

   Affiliation as printed

   The National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre (BRC), OCDEM, Radcliffe Department of Medicine, University of Oxford, Oxford, UK

7. Andrea Tura

   National Research Council

   Affiliation as printed

   Institute of Neuroscience, National Research Council, Padova, Italy

8. Hamish Miller

   Barts Health NHS Trust · National Institute for Health and Care Research · University of Oxford · NIHR Oxford Biomedical Research Centre

   Affiliation as printed

   The National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre (BRC), OCDEM, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; Barts Liver Centre, Queen Mary University London and Barts Health NHS Trust, London, UK

9. Katherine E. Pinnick

   National Institute for Health and Care Research · University of Oxford · NIHR Oxford Biomedical Research Centre · Oxford Centre for Diabetes, Endocrinology and Metabolism

   Affiliation as printed

   The National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre (BRC), OCDEM, Radcliffe Department of Medicine, University of Oxford, Oxford, UK

10. Leandro Z. Agudelo

    Broad Institute · Massachusetts Institute of Technology

    Affiliation as printed

    Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, USA; Broad Institute of MIT and Harvard, Cambridge, USA

11. Kristine H. Allin

    University of Copenhagen · Novo Nordisk Foundation Center for Basic Metabolic Research

    Affiliation as printed

    Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark

12. Andrew Anand Brown

    University of Dundee · Ninewells Hospital

    Affiliation as printed

    Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, Scotland, UK

13. Elizaveta Chabanova

    Herlev Hospital · Copenhagen University Hospital · Gentofte Hospital

    Affiliation as printed

    Department of Diagnostic Radiology, Copenhagen University Hospital Herlev Gentofte, Herlev, Denmark

14. Piotr Jaroslaw Chmura

    University of Copenhagen · Novo Nordisk Foundation

    Affiliation as printed

    Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark

15. Ulrik Plesner Jacobsen

    University of Copenhagen · Novo Nordisk Foundation

    Affiliation as printed

    Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark

16. Adem Y. Dawed

    University of Dundee · Ninewells Hospital

    Affiliation as printed

    Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, Scotland, UK

17. PETRA J.M. ELDERS

    Amsterdam Public Health · Amsterdam UMC Location Vrije Universiteit Amsterdam

    Affiliation as printed

    Department of General Practice, Amsterdam UMC- location Vumc, Amsterdam Public Health Research Institute, Amsterdam, the Netherlands

18. Juan J. Fernandez-Tajes

    Lund University

    Affiliation as printed

    Department of Clinical Science, Genetic and Molecular Epidemiology, Lund University Diabetes Centre, Helsingborg, Sweden

19. Ian M. Forgie

    University of Dundee · Ninewells Hospital

    Affiliation as printed

    Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, Scotland, UK

20. Mark Haid

    Helmholtz Munich

    Affiliation as printed

    Metabolomics and Proteomics Core, German Research Center for Environmental Health, Helmholtz Zentrum München, Neuherberg, Germany

21. Tue H. Hansen

    University of Copenhagen · Zealand University Hospital Køge · Novo Nordisk Foundation Center for Basic Metabolic Research

    Affiliation as printed

    Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark

    Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Medicine, Zealand University Hospital, Køge, Denmark

22. Angus G. Jones

    University of Exeter

    Affiliation as printed

    Department of Clinical and Biomedical Sciences, University of Exeter College of Medicine & Health, Exeter, UK

23. Tarja Kokkola

    University of Eastern Finland

    Affiliation as printed

    Internal Medicine, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland

24. Sebastian Kalamajski

    Lund University

    Affiliation as printed

    Department of Clinical Science, Genetic and Molecular Epidemiology, Lund University Diabetes Centre, Helsingborg, Sweden

25. Anubha Mahajan

    Centre for Human Genetics · University of Oxford

    Affiliation as printed

    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK

26. T McDonald

    Royal Devon & Exeter NHS Foundation Trust

    Affiliation as printed

    Blood Sciences, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK

27. Donna McEvoy

    Royal Victoria Infirmary

    Affiliation as printed

    Diabetes Research Network, Royal Victoria Infirmary, Newcastle upon Tyne, UK

28. Mirthe Muilwijk

    Amsterdam Public Health · Amsterdam University Medical Centers

    Affiliation as printed

    Amsterdam UMC, Epidemiology and Data Science, Amsterdam, the Netherlands; Amsterdam Public Health, Health Behaviors & Chronic Diseases, Amsterdam, the Netherlands

29. Konstantinos D. Tsirigos

    Novo Nordisk Foundation · Technical University of Denmark

    Affiliation as printed

    Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark

30. Jagadish Vangipurapu

    University of Eastern Finland

    Affiliation as printed

    Internal Medicine, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland; A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland

31. Sabine van Oort

    Amsterdam Public Health · Amsterdam UMC Location Vrije Universiteit Amsterdam

    Affiliation as printed

    Department of General Practice, Amsterdam UMC- location Vumc, Amsterdam Public Health Research Institute, Amsterdam, the Netherlands

32. Henrik Vestergaard

    University of Copenhagen · Novo Nordisk Foundation Center for Basic Metabolic Research · Steno Diabetes Center Copenhagen

    Affiliation as printed

    Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Steno Diabetes Center, Copenhagen, Denmark

33. Jerzy Adamski

    University of Ljubljana · National University of Singapore · Helmholtz Munich

    Affiliation as printed

    Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia

34. Joline W. Beulens

    Amsterdam University Medical Centers

    Affiliation as printed

    Amsterdam UMC, Epidemiology and Data Science, Amsterdam, the Netherlands

35. Søren Brunak

    University of Copenhagen · Novo Nordisk Foundation

    Affiliation as printed

    Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark

36. Emmanouil T. Dermitzakis

    University of Geneva

    Affiliation as printed

    Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland

37. Giuseppe N. Giordano

    Lund University

    Affiliation as printed

    Department of Clinical Science, Genetic and Molecular Epidemiology, Lund University Diabetes Centre, Helsingborg, Sweden

38. Ramneek Gupta

    Technical University of Denmark

    Affiliation as printed

    Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark; Disease Intelligence Pte Ltd, Singapore, Singapore

39. T C Bog Hansen

    University of Copenhagen · Zealand University Hospital Køge · Novo Nordisk Foundation Center for Basic Metabolic Research

    Affiliation as printed

    Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark

    Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Medicine, Zealand University Hospital, Køge, Denmark

40. Leen M. ‘t Hart Aachen Department of Biomedical Data Sciences Section Molecular Epidemiology Department of Cell and Chemical Biology

    Leiden University Medical Center · Amsterdam Public Health · Amsterdam University Medical Centers

    Affiliation as printed

    Amsterdam Public Health, Health Behaviors & Chronic Diseases, Amsterdam, the Netherlands

    Amsterdam UMC, Epidemiology and Data Science, Amsterdam, the Netherlands

    Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands

    Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands

41. Andrew Tym Hattersley

    University of Exeter

    Affiliation as printed

    Department of Clinical and Biomedical Sciences, University of Exeter College of Medicine & Health, Exeter, UK

42. Leanne Hodson

    National Institute for Health and Care Research · University of Oxford · NIHR Oxford Biomedical Research Centre · Oxford Centre for Diabetes, Endocrinology and Metabolism

    Affiliation as printed

    The National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre (BRC), OCDEM, Radcliffe Department of Medicine, University of Oxford, Oxford, UK

43. Laakso Ml

    University of Eastern Finland

    Affiliation as printed

    Internal Medicine, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland

44. Ruth J. F. Loos

    University of Copenhagen · Novo Nordisk Foundation Center for Basic Metabolic Research · Icahn School of Medicine at Mount Sinai

    Affiliation as printed

    Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA

45. Jordi Merino

    University of Copenhagen · Novo Nordisk Foundation Center for Basic Metabolic Research

    Affiliation as printed

    Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark

46. Mattias Ohlsson

    Lund University

    Affiliation as printed

    Center for Environmental and Climate Science, Lund University, Lund, Sweden

47. Oluf Borbye Pedersen

    Gentofte Hospital

    Affiliation as printed

    Center for Clinical Metabolic Research, Herlev and Gentofte University Hospital, Copenhagen, Denmark

48. Martin Ridderstråle

    Lund University

    Affiliation as printed

    Department of Clinical Science, Lund University, Malmö, Sweden

49. Hartmut Ruetten

    Boehringer Ingelheim (Germany)

    Affiliation as printed

    Boehringer Ingelheim Pharma GmbH & Co. KG, Ingelheim, Germany

50. Femke Rutters

    Amsterdam Public Health · Amsterdam University Medical Centers

    Affiliation as printed

    Amsterdam UMC, Epidemiology and Data Science, Amsterdam, the Netherlands; Amsterdam Public Health, Health Behaviors & Chronic Diseases, Amsterdam, the Netherlands

51. Jochen M. Schwenk

    Science for Life Laboratory · KTH Royal Institute of Technology

    Affiliation as printed

    Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden

52. Jeremy Tomlinson

    National Institute for Health and Care Research · University of Oxford · NIHR Oxford Biomedical Research Centre · Oxford Centre for Diabetes, Endocrinology and Metabolism

    Affiliation as printed

    The National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre (BRC), OCDEM, Radcliffe Department of Medicine, University of Oxford, Oxford, UK

53. Mark Walker

    Newcastle University

    Affiliation as printed

    Translational and Clinical Research Institute, Faculty of Medical Sciences, University of Newcastle, Newcastle upon Tyne, UK

54. Hanieh Yaghootkar

    University of Southampton

    Affiliation as printed

    School of Electronics and Computer Science, Faculty of Engineering and Physical Science, University of Southampton, Southampton, UK; School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK

55. Fredrik Karpe

    National Institute for Health and Care Research · University of Oxford · NIHR Oxford Biomedical Research Centre · Oxford Centre for Diabetes, Endocrinology and Metabolism

    Affiliation as printed

    The National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre (BRC), OCDEM, Radcliffe Department of Medicine, University of Oxford, Oxford, UK

56. Mark I. McCarthy

    Centre for Human Genetics · University of Oxford

    Affiliation as printed

    Wellcome Centre for Human Genetics, University of Oxford, UK

57. Elizabeth Louise Thomas

    University of Westminster

    Affiliation as printed

    Research Centre for Optimal Health, School of Life Sciences, University of Westminster, London, UK

58. Jimmy D Bell

    University of Westminster

    Affiliation as printed

    Research Centre for Optimal Health, School of Life Sciences, University of Westminster, London, UK

59. Andrea Mari

    National Research Council

    Affiliation as printed

    Institute of Neuroscience, National Research Council, Padova, Italy

60. Imre J. Pavo
    Affiliation as printed

    Eli Lilly Regional Operations Ges.m.b.H., Vienna, Austria

61. Ewan R. Pearson

    University of Dundee · Ninewells Hospital

    Affiliation as printed

    Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, Scotland, UK

62. Ana Viñuela

    University of Dundee · Ninewells Hospital

    Affiliation as printed

    Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, Scotland, UK

63. Paul W. Franks corresponding

    Queen Mary University of London · Lund University

    Affiliation as printed

    Department of Clinical Science, Genetic and Molecular Epidemiology, Lund University Diabetes Centre, Helsingborg, Sweden; Precision Healthcare University Research Institute, Queen Mary University of London, London, UK. Electronic address: paul.franks@med.lu.se