STRAP RNA-seq Data

The STRAP trial (Stratification of Biologic Therapies for RA by Pathobiology) is an open label, randomised controlled clinical trial which aims to test the utility of synovial histopathology and B cell number together with specific molecular signatures as potential biomarkers to guide therapeutic decisions in patients failing DMARD therapy to improve on current response rates and identify patients more likely to respond. Patients were randomised to receive Rituximab, Tocilizumab or anti-TNF therapy (Etanercept) following a baseline synovial biopsy. STRAP is an important clinical trial within MATURA which is an ambitious research project jointly funded by MRC and ARUK to identify and test biomarkers predictive of response to therapy in rheumatoid arthritis (RA), thereby allowing the stratification of patients into groups according to the therapies that are most likely to be effective.

STRAP Publications

• Barton A & Pitzalis C (2017). Stratified medicine in rheumatoid arthritis—the MATURA programme. Rheumatology (Oxford) 56(8): 1247-50. DOI: 10.1093/rheumatology/kew369
• Rivellese F et al (2023). Stratification of biological therapies by pathobiology in biologic-naive patients with rheumatoid arthritis (STRAP and STRAP-EU): two parallel, open-label, biopsy-driven, randomised trials. The Lancet Rheumatology 5(11): E648-E659. DOI: 10.1016/S2665-9913(23)00241-2

Other Resources and Publications

• The PEAC study investigates the pathobiology of early arthritis. A similar website to explore the PEAC data can be found at https://peac.hpc.qmul.ac.uk with associated pulications:
  • Lewis et. al. (2019) Molecular Portraits of Early Rheumatoid Arthritis Identify Clinical and Treatment Response Phenotypes. Cell Reports 2019; 28(9):2455-2470.e5. DOI: 10.1016/j.celrep.2019.07.091 PMID: 31461658
  • Humby, Lewis et al (2019) Synovial cellular and molecular signatures in early rheumatoid arthritis stratify clinical response to csDMARD therapy and predict radiographic progression. Ann Rheum Dis 2019; 78(6): 761-772. PMID: 30878974.
• The R4RA trial is a stratified, biopsy-driven, open-label, phase 4 randomised controlled trial investigating response to Rituximab and Tocilizumab among RA patients. A similar website to explore the R4RA data can be found at https://r4ra.hpc.qmul.ac.uk with associated pulications:
  • Humby F, et al. (2021) Rituximab versus tocilizumab in anti-TNF inadequate responder patients with rheumatoid arthritis (R4RA): 16-week outcomes of a stratified, biopsy-driven, multicentre, open-label, phase 4 randomised controlled trial. The Lancet 397(10271): 305-17. DOI: 10.1016/S0140-6736(20)32341-2 PMID: 33485455
  • Rivellese F, Surace AEA, Goldmann K, Sciacca E, Çubuk C, Giorli G, John CR, Nerviani A, Fossati-Jimack L, Thorborn G, Ahmed M, Prediletto E, Church SE, Hudson BM, Warren SE, McKeigue PM, Humby F, Bombardieri M, Barnes MR, Lewis MJ, Pitzalis C & the R4RA collaborative group (2022) Rituximab versus tocilizumab in rheumatoid arthritis: synovial biopsy-based biomarker analysis of the phase 4 R4RA randomized trial. Nature Medicine 28: 1256-68. DOI: 10.1038/s41591-022-01789-0 PMID: 35589854
• Myles Lewis, Athina Spiliopoulou, Katriona Goldmann (2023). nestedcv: Nested Cross-Validation with 'glmnet' and 'caret'. R package. https://cran.r-project.org/package=nestedcv.
  • Lewis et al (2023) nestedcv: an R package for fast implementation of nested cross-validation with embedded feature selection designed for transcriptomics and high-dimensional data. Bioinformatics Advances 3(1): vbad048. DOI PMID: 37113250

Associated Software

• Myles Lewis, Katriona Goldmann and Elisabetta Sciacca (2021). glmmSeq: General Linear Mixed Models for Gene-Level Differential Expression. R package. https://CRAN.R-project.org/package=glmmSeq
• Katriona Goldmann and Myles Lewis (2021). volcano3D: Interactive Plotting of Three-Way Differential Expression Analysis. R package. https://CRAN.R-project.org/package=volcano3D.

Shiny Website

The shiny website was implemented by Myles Lewis, Katriona Goldmann, Cankut Çubuk, Rachel Lau, Tom Bradford and Vitaly Kukchenkov.

STRAP RNA-seq Data

The STRAP trial (Stratification of Biologic Therapies for RA by Pathobiology) is an open label, randomised controlled clinical trial which aims to test the utility of synovial histopathology and B cell number together with specific molecular signatures as potential biomarkers to guide therapeutic decisions in patients failing DMARD therapy to improve on current response rates and identify patients more likely to respond. Patients were randomised to receive Rituximab, Tocilizumab or anti-TNF therapy (Etanercept) following a baseline synovial biopsy. STRAP is an important clinical trial within MATURA which is an ambitious research project jointly funded by MRC and ARUK to identify and test biomarkers predictive of response to therapy in rheumatoid arthritis (RA), thereby allowing the stratification of patients into groups according to the therapies that are most likely to be effective.

STRAP Publications

• Barton A & Pitzalis C (2017). Stratified medicine in rheumatoid arthritis—the MATURA programme. Rheumatology (Oxford) 56(8): 1247-50. DOI: 10.1093/rheumatology/kew369
• Rivellese F et al (2023). Stratification of biological therapies by pathobiology in biologic-naive patients with rheumatoid arthritis (STRAP and STRAP-EU): two parallel, open-label, biopsy-driven, randomised trials. The Lancet Rheumatology 5(11): E648-E659. DOI: 10.1016/S2665-9913(23)00241-2