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Pre-defined gene co-expression modules in rheumatoid arthritis transition towards molecular health following anti-TNF

Megan Sutcliffe1, Nisha Nair1,2, James Oliver1,2

  • 1Versus Arthritis Centre for Genetics and Genomics, Division of Musculoskeletal Sciences, The University of Manchester.

Rheumatology (Oxford, England)
|April 4, 2022
PubMed
Abstract

Insights

Researchers validated gene expression changes in rheumatoid arthritis (RA) patients treated with TNF inhibitors (TNFi). While some gene modules shifted towards a disease-free state, these changes were not exclusive to TNFi therapy.

Area of Science:

  • Immunology
  • Genomics
  • Rheumatology

Background:

  • Rheumatoid arthritis (RA) lacks reliable biomarkers to predict treatment response to TNF inhibitors (TNFi).
  • Gene co-expression modules have been previously reported to change in response to TNFi therapy in RA patients.
  • Understanding these molecular changes is crucial for personalized medicine in RA.

Purpose of the Study:

  • To replicate previously reported changes in gene co-expression modules in RA patients treated with TNFi.
  • To determine if observed module expression changes are specific to TNFi therapy.
  • To assess if module expression transitions towards a disease-free state in patients responding to treatment.

Main Methods:

  • Analysis of published whole-blood transcriptomic data from RA patients treated with adalimumab (a TNFi) or methotrexate.
  • Assessment of treatment response using EULAR criteria at 3 or 6 months.
  • Application of linear mixed models to evaluate transitions in module expression towards a disease-free state.

Main Results:

  • Replication of published findings for 25 out of 27 gene co-expression modules in the adalimumab cohort.
  • Six modules transitioned towards a disease-free state by 3 months, independent of clinical response.
  • One module (M3.2), linked to inflammation and TNF biology, correlated with adalimumab response; similar, but less pronounced, patterns were seen with methotrexate.

Conclusions:

  • Independent validation of module expression changes in response to RA therapy.
  • Observed molecular effects are not specific to TNFi, suggesting broader mechanisms.
  • Further research is needed to explore specific modules for molecular classification of therapeutic response in RA.
Keywords:
BiomarkersRATNFibiological therapiesgeneticsinflammationtranscriptomicstreatment response

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