Research ArticleSystems Biology

An interspecies translation model implicates integrin signaling in infliximab-resistant inflammatory bowel disease

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Science Signaling  04 Aug 2020:
Vol. 13, Issue 643, eaay3258
DOI: 10.1126/scisignal.aay3258

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Found in translation

An ongoing challenge for the development of new therapeutics is the difficulty in translating findings from preclinical animal models to human subjects, more so when different types of data (proteomics versus transcriptomics) are compared. Brubaker et al. developed a method to project transcriptomic data from patients with inflammatory bowel disease (IBD) into a principal components analysis of mouse proteomics data to investigate resistance to the anti-TNF antibody infliximab. This analysis, which suggested that integrin signaling contributed to resistance, was validated in experiments, showing that inhibiting α1 integrin subunit signaling enhanced the ability of infliximab to suppress proinflammatory cytokine release from immune cells. These data suggest that this approach for comparing model system and patient data might reveal therapeutically relevant targets for other diseases.


Anti–tumor necrosis factor (anti-TNF) therapy resistance is a major clinical challenge in inflammatory bowel disease (IBD), due, in part, to insufficient understanding of disease-site, protein-level mechanisms. Although proteomics data from IBD mouse models exist, data and phenotype discrepancies contribute to confounding translation from preclinical animal models of disease to clinical cohorts. We developed an approach called translatable components regression (TransComp-R) to overcome interspecies and trans-omic discrepancies between mouse models and human subjects. TransComp-R combines mouse proteomic data with patient pretreatment transcriptomic data to identify molecular features discernable in the mouse data that are predictive of patient response to therapy. Interrogating the TransComp-R models revealed activated integrin pathway signaling in patients with anti–TNF-resistant colonic Crohn’s disease (cCD) and ulcerative colitis (UC). As a step toward validation, we performed single-cell RNA sequencing (scRNA-seq) on biopsies from a patient with cCD and analyzed publicly available immune cell proteomics data to characterize the immune and intestinal cell types contributing to anti-TNF resistance. We found that ITGA1 was expressed in T cells and that interactions between these cells and intestinal cell types were associated with resistance to anti-TNF therapy. We experimentally showed that the α1 integrin subunit mediated the effectiveness of anti-TNF therapy in human immune cells. Thus, TransComp-R identified an integrin signaling mechanism with potential therapeutic implications for overcoming anti-TNF therapy resistance. We suggest that TransComp-R is a generalizable framework for addressing species, molecular, and phenotypic discrepancies between model systems and patients to translationally deliver relevant biological insights.

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