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Deep molecular profiling of synovial biopsies in the STRAP trial identifies signatures predictive of treatment response to biologic therapies in rheumatoid arthritis

The heterogenous nature of rheumatoid arthritis renders the prediction of responsiveness to biological treatments difficult. Here the authors analyze bulk RNA-seq data from the STRAP trial (n = 208) to build a machine-learning model for predicting responses to etanercept, tocilizumab and rituximab with AUCs around 0.75 to potentially assist in therapy planning.

Myles J. Lewis
Cankut Çubuk
Anne Barton
ResearchOpen Access02 Jul 2025
Nature Communications

Volume: 16, P: 1-18
Axl and MerTK regulate synovial inflammation and are modulated by IL-6 inhibition in rheumatoid arthritis

The TAM tyrosine kinases, Axl and MerTK, have been implicated in rheumatoid arthritis (RA). Here, using a synovial tissue bioresource of patients with RA, the authors describe how Axl and MerTK expression and function are linked to synovial histopathology, disease activity, and therapeutic intervention with IL-6 inhibitors.

Alessandra Nerviani
Marie-Astrid Boutet
Costantino Pitzalis
ResearchOpen Access16 Mar 2024
Nature Communications

Volume: 15, P: 1-16
Rituximab versus tocilizumab in rheumatoid arthritis: synovial biopsy-based biomarker analysis of the phase 4 R4RA randomized trial

Biomarker analysis of the phase 4 R4RA trial identifies pretreatment synovial biopsy features selectively associated with response to rituximab or tocilizumab, and leads to the development of models that might predict treatment benefit in patients with rheumatoid arthritis

Felice Rivellese
Anna E. A. Surace
Costantino Pitzalis
ResearchOpen Access19 May 2022
Nature Medicine

Volume: 28, P: 1256-1268
The effects of death and post-mortem cold ischemia on human tissue transcriptomes

RNA levels in post-mortem tissue can differ greatly from those before death. Studying the effect of post-mortem interval on the transcriptome in 36 human tissues, Ferreira et al. find that the response to death is largely tissue-specific and develop a model to predict time since death based on RNA data.

Pedro G. Ferreira
Manuel Muñoz-Aguirre
Roderic Guigó
ResearchOpen Access13 Feb 2018
Nature Communications

Volume: 9, P: 1-15
Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

Resistance to first line treatment is a major hurdle in cancer treatment, that can be overcome with drug combinations. Here, the authors provide a large drug combination screen across cancer cell lines to benchmark crowdsourced methods and to computationally predict drug synergies.

Michael P. Menden
Dennis Wang
Julio Saez-Rodriguez
ResearchOpen Access17 Jun 2019
Nature Communications

Volume: 10, P: 1-17
A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection

The response to respiratory virus exposure can currently not be predicted by pre- or early post-exposure molecular signatures. Here, the authors conduct a community-based analysis of blood gene expression from healthy individuals exposed to respiratory viruses and provide predictive models and biological insight into the physiological response.

Slim Fourati
Aarthi Talla
Solveig K. Sieberts
ResearchOpen Access24 Oct 2018
Nature Communications

Volume: 9, P: 1-11
Differential metabolic activity and discovery of therapeutic targets using summarized metabolic pathway models

Cankut Çubuk
Marta R. Hidalgo
Joaquín Dopazo
Special FeaturesOpen Access01 Mar 2019
npj Systems Biology and Applications

Volume: 5, P: 1-11

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Deep molecular profiling of synovial biopsies in the STRAP trial identifies signatures predictive of treatment response to biologic therapies in rheumatoid arthritis

Axl and MerTK regulate synovial inflammation and are modulated by IL-6 inhibition in rheumatoid arthritis

Rituximab versus tocilizumab in rheumatoid arthritis: synovial biopsy-based biomarker analysis of the phase 4 R4RA randomized trial

The effects of death and post-mortem cold ischemia on human tissue transcriptomes

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection

Differential metabolic activity and discovery of therapeutic targets using summarized metabolic pathway models

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