Nonlesional ileal transcriptome in Crohn's disease reveals alterations in immune response and metabolic pathway

Ho-Su Lee; Yoonho Lee; Jiwon Baek; Yongjae Kim; Sojung Park; Seulgi Jung; Jong Geol Lee; In-Jeoung Baek; Kyuwon Kim; Sung Wook Hwang; Jong Lyul Lee; Sang Hyoung Park; Suk-Kyun Yang; Buhm Han; Kyuyoung Song; Yong Sik Yoon; Byong Duk Ye

doi:10.1111/jgh.16816

Nonlesional ileal transcriptome in Crohn's disease reveals alterations in immune response and metabolic pathway

J Gastroenterol Hepatol. 2024 Nov 27. doi: 10.1111/jgh.16816. Online ahead of print.

Authors

Ho-Su Lee^{1

2}, Yoonho Lee¹, Jiwon Baek¹, Yongjae Kim¹, Sojung Park¹, Seulgi Jung¹, Jong Geol Lee³, In-Jeoung Baek³, Kyuwon Kim⁴, Sung Wook Hwang^{2

5}, Jong Lyul Lee^{2

6}, Sang Hyoung Park^{2

5}, Suk-Kyun Yang^{2

5}, Buhm Han⁷, Kyuyoung Song^{1

2}, Yong Sik Yoon^{2

6}, Byong Duk Ye^{2

5}

Affiliations

¹ Department of Biochemistry and Molecular Biology, Asan Medical Center, Brain Korea 21 Project, University of Ulsan College of Medicine, Seoul, Korea.
² Inflammatory Bowel Disease Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
³ Department of Convergence Medicine, University of Ulsan College of Medicine, Seoul, Korea.
⁴ Department of Gastroenterology, Chung-Ang University Hospital, Chung-Ang University College of Medicine, Seoul, Korea.
⁵ Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
⁶ Division of Colon and Rectal Surgery, Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
⁷ Department of Biomedical Sciences, BK21 Plus Biomedical Science Project, Seoul National University College of Medicine, Seoul, Korea.

PMID: 39604213
DOI: 10.1111/jgh.16816

Abstract

Background and aim: We aimed to assess the gene expression profiles of nonlesional small bowels in patients with Crohn's disease (CD) to identify its accompanying molecular alterations.

Methods: We performed RNA sequencing of the uninflamed small bowel tissues obtained from 70 patients with ileal CD and 9 patients with colon cancer (non-CD controls) during bowel resection. Differentially expressed gene (DEG) analyses were performed using DESeq2. Gene set enrichment, correlation, and cell deconvolution analyses were applied to identify modules and functionally enriched transcriptional signatures of CD.

Results: A comparison of CD patients and non-CD controls revealed that of the 372 DEGs, 49 protein-coding genes and 5 long non-coding RNAs overlapped with the inflammatory bowel disease susceptibility loci. The pathways related to immune and inflammatory reactions were upregulated in CD, while metabolic pathways were downregulated in CD. Compared with non-CD controls, CD patients had significantly higher proportions of immune cells, including plasma cells (P = 1.15 × 10^-4), and a lower proportion of epithelial cells (P = 1.12 × 10^-4). Co-upregulated genes (M14 module) and co-downregulated genes (M9 module) were identified in CD patients. The M14 module was enriched in immune-related genes and significantly associated with the responses to anti-tumor necrosis factor (TNF) therapy. The core signature of the M14 module was comprised of six genes and was upregulated in nonresponders to anti-TNF therapy of five independent cohorts (n = 163), indicating acceptable discrimination ability (area under the receiver operating characteristic curve of 75-86%).

Conclusions: The differences in gene expression and cellular composition between CD patients and non-CD controls imply significant molecular alterations, which are associated with the response to anti-TNF treatment.

Keywords: Crohn's disease; RNA sequencing; anti‐tumor necrosis factor agents; gene expression analysis; prediction.

Abstract

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