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

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

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.
Myles Lewis, Athina Spiliopoulou, Katriona Goldmann (2023). nestedcv: Nested Cross-Validation with 'glmnet' and 'caret'. R package. https://cran.r-project.org/package=nestedcv.

Shiny Website

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

STRAP RNA-seq Data

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

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Etanercept

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Method

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Subset by Randomised Treatment:

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Etanercept

Rituximab

Tocilizumab

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Second biopsy vs response
Second biopsy vs clinicopathology

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3-visit rolling average

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Pearson

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Subset by randomised treatment

All

Etanercept

Rituximab

Tocilizumab

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Paired samples only All samples

Subset by Randomised Treatment:

All

Etanercept

Rituximab

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Subset by 16 week CDAI50 Response:

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Proteomics

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Paired samples only All samples

STRAP RNA-seq Data

STRAP Publications

Other Resources and Publications

Associated Software

Shiny Website

Gene View

Gene Table View

Longitudinal Analysis

Differential Expression

Clinical Data

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Module Table View

Module Maker

Gene-Gene Correlation

Proteome

Proteomics tables

Multi-omic correlation

STRAP RNA-seq Data

STRAP Publications

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