Multiscale, mechanistic model of Rheumatoid Arthritis to enable decision making in late stage drug development.

IF 3.5 2区 生物学 Q1 MATHEMATICAL & COMPUTATIONAL BIOLOGY NPJ Systems Biology and Applications Pub Date : 2024-11-04 DOI:10.1038/s41540-024-00454-1
Dinesh Bedathuru, Maithreye Rengaswamy, Madhav Channavazzala, Tamara Ray, Prakash Packrisamy, Rukmini Kumar
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Abstract

Rheumatoid Arthritis (RA) is a chronic autoimmune inflammatory disease that affects about 0.1% to 2% of the population worldwide. Despite the development of several novel therapies, there is only limited benefit for many patients. Thus, there is room for new approaches to improve response to therapy, including designing better trials e.g., by identifying subpopulations that can benefit from specific classes of therapy and enabling reverse translation by analyzing completed clinical trials. We have developed an open-source, mechanistic multi-scale model of RA, which captures the interactions of key immune cells and mediators in an inflamed joint. The model consists of a treatment-naive Virtual Population (Vpop) that responds appropriately (i.e. as reported in clinical trials) to standard-of-care treatment options-Methotrexate (MTX) and Adalimumab (ADA, anti-TNF-α) and an MTX inadequate responder sub-population that responds appropriately to Tocilizumab (TCZ, anti-IL-6R) therapy. The clinical read-outs of interest are the American College of Rheumatology score (ACR score) and Disease Activity Score (DAS28-CRP), which is modeled to be dependent on the physiological variables in the model. Further, we have validated the Vpop by predicting the therapy response of TCZ on ADA Non-responders. This paper aims to share our approach, equations, and code to enable community evaluation and greater adoption of mechanistic models in drug development for autoimmune diseases.

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类风湿关节炎的多尺度机理模型,帮助后期药物开发决策。
类风湿性关节炎(RA)是一种慢性自身免疫性炎症疾病,全球约有 0.1% 至 2% 的人患有此病。尽管已开发出多种新型疗法,但对许多患者的疗效有限。因此,我们需要新的方法来改善对疗法的反应,包括设计更好的试验,例如,确定可从特定类别疗法中获益的亚人群,以及通过分析已完成的临床试验实现逆向转化。我们开发了一个开源的多尺度RA机理模型,该模型捕捉了发炎关节中关键免疫细胞和介质的相互作用。该模型包括一个对标准治疗方案--甲氨蝶呤(MTX)和阿达木单抗(ADA,抗肿瘤坏死因子α)--有适当反应(即临床试验报告)的治疗无效虚拟人群(Vpop),以及一个对托珠单抗(TCZ,抗IL-6R)治疗有适当反应的 MTX 无效反应亚人群。我们感兴趣的临床读数是美国风湿病学会评分(ACR 评分)和疾病活动度评分(DAS28-CRP),这些评分在模型中取决于生理变量。此外,我们还通过预测 TCZ 对 ADA 无应答者的治疗反应验证了 Vpop。本文旨在分享我们的方法、方程式和代码,以便在自身免疫性疾病的药物开发中进行社区评估并更多地采用机理模型。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
NPJ Systems Biology and Applications
NPJ Systems Biology and Applications Mathematics-Applied Mathematics
CiteScore
5.80
自引率
0.00%
发文量
46
审稿时长
8 weeks
期刊介绍: npj Systems Biology and Applications is an online Open Access journal dedicated to publishing the premier research that takes a systems-oriented approach. The journal aims to provide a forum for the presentation of articles that help define this nascent field, as well as those that apply the advances to wider fields. We encourage studies that integrate, or aid the integration of, data, analyses and insight from molecules to organisms and broader systems. Important areas of interest include not only fundamental biological systems and drug discovery, but also applications to health, medical practice and implementation, big data, biotechnology, food science, human behaviour, broader biological systems and industrial applications of systems biology. We encourage all approaches, including network biology, application of control theory to biological systems, computational modelling and analysis, comprehensive and/or high-content measurements, theoretical, analytical and computational studies of system-level properties of biological systems and computational/software/data platforms enabling such studies.
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Exploring heterogeneous cell population dynamics in different microenvironments by novel analytical strategy based on images. Network medicine informed multiomics integration identifies drug targets and repurposable medicines for Amyotrophic Lateral Sclerosis. Multi-bioinformatics revealed potential biomarkers and repurposed drugs for gastric adenocarcinoma-related gastric intestinal metaplasia. Multiscale, mechanistic model of Rheumatoid Arthritis to enable decision making in late stage drug development. An integrative network-based approach to identify driving gene communities in chronic obstructive pulmonary disease.
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