Transcriptomic profiling of collagenous colitis identifies hallmarks of non-destructive inflammatory bowel disease [Whole mucosa]. Transcriptomic profiling of collagenous colitis identifies hallmarks of non-destructive inflammatory bowel disease [Whole mucosa]

Background and Aims: The pathophysiology of the diarrhoea-predominant inflammatory bowel disease collagenous colitis (CC) is poorly described. Our aim was to use RNA sequencing of colonic biopsies from patients with active CC, CC in remission, refractory CC, ulcerative colitis (UC), and controls to gain insight into CC pathophysiology, identify additional genetic signatures linked to CC, and uncover targets for future therapeutic agents. Methods: We performed whole transcriptome sequencing of CC colonic samples from patients before and during treatment with the corticosteroid drug budesonide, steroid-refractory patients, UC and healthy controls (n=9-13). Bulk mucosa and laser-captured microdissected intestinal epithelial cell gene expression was functionally analyzed by gene-set enrichment and gene-set variation analyses to identify statistically significant pathways and cells, respectively, that change in CC. Leading genes and cells were validated using reverse transcription quantitative PCR and/or immunohistochemistry. Finally, we compared CC transcriptome with that from UC samples. Results: We identified an activation of the adaptive immune response to bacteria in active CC compared to that in remission that could be mediated by dendritic cells. However, a unique signature of genes related to the immune response and DNA transcription remain dysregulated after achieving remission. Budesonide-refractory CC patients fail to restore normal gene expression, which results in a transcriptomic profile close to UC. Intestinal epithelial CC cells displayed an impaired cell proliferation and increased antigen presentation. Conclusion: Our study confirmed previous findings from GWAS and immunological studies related to CC pathogenesis and describes novel genes, pathways and cells that might contribute to the pathophysiology of CC, ongoing epithelial damage, and complications associated with CC. Overall design: Whole colonic mucosa mRNA profiles of collagenous colitis (CC), including paired active/untreated CC (auCC) and inactive/budesonide-treated CC (itCC) samples, active/refractory (budesonide non-responding) CC (aRCC), healthy controls (Hc), and ulcerative colitis (UC) samples. >>> Please note that raw data is not provided as Norwegian law does not allow public access to human sequences raw data. <<<

背景与目的：以腹泻为主要表现的炎症性肠病——胶原性结肠炎（collagenous colitis, CC）的病理生理学机制尚未被充分阐明。本研究旨在对活动期CC、缓解期CC、难治性CC、溃疡性结肠炎（ulcerative colitis, UC）患者及健康对照的结肠活检组织进行RNA测序，以深入解析CC的病理生理过程，识别与CC相关的新型遗传特征，并发掘未来潜在的治疗靶点。

方法：我们对接受糖皮质激素布地奈德（budesonide）治疗前及治疗期间的CC患者、激素难治性CC患者、UC患者及健康对照的结肠样本实施了全转录组测序，每组样本量为9~13例。针对整体黏膜组织与激光捕获显微切割获取的肠上皮细胞的基因表达谱，我们分别采用基因集富集分析（gene-set enrichment analysis）与基因集变异分析（gene-set variation analysis）开展功能注释，以筛选胶原性结肠炎中具有统计学意义的通路与细胞亚群。核心差异基因及细胞亚群通过逆转录定量PCR（reverse transcription quantitative PCR）及/或免疫组化（immunohistochemistry）进行验证。最后，我们将CC的转录组特征与UC样本的转录组数据进行了对比分析。

结果：相较于缓解期CC患者，活动期CC患者体内针对细菌的适应性免疫应答被激活，这一过程或由树突状细胞（dendritic cells）介导。但即便患者达到临床缓解，与免疫应答及DNA转录相关的基因仍持续存在表达失调现象。布地奈德难治性CC患者无法恢复正常的基因表达模式，其转录组特征与UC患者高度相似。CC患者的肠上皮细胞表现出细胞增殖受损与抗原呈递功能增强的表型。

结论：本研究验证了既往全基因组关联研究（Genome-Wide Association Study, GWAS）及免疫学研究中关于CC发病机制的相关结论，并揭示了可能参与CC病理生理过程、持续性上皮损伤及CC相关并发症的新型基因、通路与细胞亚群。

整体实验设计：本研究对胶原性结肠炎（CC）患者的全结肠黏膜mRNA表达谱进行了分析，样本类型包括配对的活动期未治疗CC（auCC）与非活动期布地奈德治疗后CC（itCC）样本、活动期难治性（布地奈德无应答）CC（aRCC）样本、健康对照（Hc）及溃疡性结肠炎（UC）样本。

>>> 请注意，原始数据未予公开——依据挪威相关法律，人类序列原始数据不允许公开获取。 <<<