Kwak Min Seob, Hwang Chang-Il, Cha Jae Myung, Jeon Jung Won, Yoon Jin Young, Park Su Bee
Department of Internal Medicine, Kyung Hee University Hospital at Gangdong, College of Medicine, Kyung Hee University, Seoul 05278, Republic of Korea.
Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California Davis, Davis, CA 95616, USA.
Int J Mol Sci. 2023 Sep 14;24(18):14099. doi: 10.3390/ijms241814099.
Primary and secondary non-response affects approximately 50% of patients with Crohn's disease treated with anti-tumour necrosis factor (TNF) monoclonal antibodies. To date, very little single cell research exists regarding drug repurposing in Crohn's disease. We aimed to elucidate the cellular phenomena underlying resistance to anti-TNF therapy in patients with Crohn's disease and to identify potential drug candidates for these patients. Single-cell transcriptome analyses were performed using data (GSE134809) from the Gene Expression Omnibus and Library of Integrated Network-Based Cellular Signatures L1000 Project. Data aligned to the Genome Reference Consortium Human Build 38 reference genome using the Cell Ranger software were processed using the Seurat package. To capture significant functional terms, gene ontology functional enrichment analysis was performed on the marker genes. For biological analysis, 93,893 cells were retained (median 20,163 genes). Through marker genes, seven major cell lineages were identified: B-cells, T-cells, natural killer cells, monocytes, endothelial cells, epithelial cells, and tissue stem cells. In the anti-TNF-resistant samples, the top 10 differentially expressed genes were , , , , , , , , , , , , and , which were robustly distributed in all cell lineages, mainly in B-cells. Through molecular function analyses, we found that the biological functions of both monocyte and T-cell groups mainly involved immune-mediated functions. According to multi-cluster drug repurposing prediction, vorinostat is the top drug candidate for patients with anti-TNF-refractory Crohn's disease. Differences in cell populations and immune-related activity within tissues may influence the responsiveness of Crohn's disease to anti-TNF agents. Vorinostat may serve as a promising novel therapy for anti-TNF-resistant Crohn's disease.
原发性和继发性无应答影响了约50%接受抗肿瘤坏死因子（TNF）单克隆抗体治疗的克罗恩病患者。迄今为止，关于克罗恩病药物再利用的单细胞研究非常少。我们旨在阐明克罗恩病患者对抗TNF治疗耐药的细胞现象，并为这些患者确定潜在的候选药物。使用来自基因表达综合数据库（Gene Expression Omnibus）和基于综合网络的细胞特征库L1000项目的数据（GSE134809）进行单细胞转录组分析。使用Cell Ranger软件与基因组参考联盟人类构建38参考基因组比对的数据，使用Seurat软件包进行处理。为了捕获显著的功能术语，对标记基因进行了基因本体功能富集分析。为了进行生物学分析，保留了93,893个细胞（中位数为20,163个基因）。通过标记基因，鉴定出七个主要细胞谱系：B细胞、T细胞、自然杀伤细胞、单核细胞、内皮细胞、上皮细胞和组织干细胞。在抗TNF耐药样本中，前10个差异表达基因是 、 、 、 、 、 、 、 、 、 、 、 ，它们在所有细胞谱系中均有强烈分布，主要在B细胞中。通过分子功能分析，我们发现单核细胞和T细胞组的生物学功能主要涉及免疫介导功能。根据多聚类药物再利用预测，伏立诺他是抗TNF难治性克罗恩病患者的最佳候选药物。组织内细胞群体和免疫相关活性的差异可能会影响克罗恩病对抗TNF药物的反应性。伏立诺他可能是抗TNF耐药克罗恩病一种有前景的新疗法。
