Hong Sung Noh, Joung Je-Gun, Bae Joon Seol, Lee Chan Soo, Koo Ja Seol, Park Soo Jung, Im Jong Pil, Kim You Sun, Kim Ji Won, Park Woong Yang, Kim Young-Ho
*Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea;†Laboratory of Translational Genomics, Samsung Genome Institute, Samsung Medical Center, Seoul, Korea;‡Department of Internal Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea;§Korea University Ansan Hospital, Korea University College of Medicine, Ansan, Korea;‖Department of Internal Medicine, Yonsei University School of Medicine, Seoul, Korea;¶Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea; and**Department of Internal Medicine, Inje University College of Medicine, Seoul, Korea.
Inflamm Bowel Dis. 2017 Jul;23(7):1098-1108. doi: 10.1097/MIB.0000000000001066.
Aberrant gene expression in the gut mucosa might contribute to the initiation and progression of Crohn's disease (CD). RNA sequencing (RNA-seq) provides precise measurements of expression levels of transcripts and their isoforms. The aim of this study was to use RNA-seq to investigate transcriptomic differences and identify significantly differentially expressed transcripts in inflamed and noninflamed intestinal mucosa of CD patients.
RNA-seq was performed on 13 pairs of inflamed and noninflamed intestinal mucosa from 13 CD patients and on sex-matched normal mucosa of 13 healthy controls. Significantly differentially expressed transcripts were validated by immunohistochemistry, quantitative reverse transcriptase polymerase chain reaction, and enzyme-linked immunosorbent assay.
RNA-seq revealed genome-wide transcriptomic differences between normal mucosa, noninflamed, and inflamed CD mucosa. Among 950 differentially expressed genes, 19 were up- or downregulated (upregulation: ANGPT2, CHN1, CPXM1, CPZ, CXCL1, FCN3, GJC1, HSD11B1, LZTS1, MEOX1, MMP12, PLA1A, SERPINE1, SGIP1, and TRPC4; downregulation: FAM189A1, PDE6A, SLC38A4, and HMGCS2) with statistical significance (p < 0.01 and q < 0.05). Among them, CXCL1 exhibited the highest fold change between groups. Immunohistochemistry for CXCL1 revealed no expression in normal mucosa, slightly increased expression in noninflamed CD mucosa, and highly increased expression in inflamed CD mucosa. Quantitative reverse transcriptase polymerase chain reaction showed that CXCL1 expression was significantly associated with epithelial damage, increased infiltration of polymorphonuclear leukocytes, and submucosal fibrosis. Serum CXCL1 concentration measured by enzyme-linked immunosorbent assay was better correlated with CD activity index (r = 0.660) than with C-reactive protein (r = 0.204).
RNA-seq revealed transcriptomic differences between normal mucosa, noninflamed CD mucosa, and inflamed CD mucosa. Intestinal and serum CXCL1 was substantially increased with CD activity and can be used as a potential biomarker of CD.
肠道黏膜中的异常基因表达可能促使克罗恩病（CD）的发生与发展。RNA测序（RNA-seq）可精确测量转录本及其异构体的表达水平。本研究旨在利用RNA-seq探究CD患者炎症性和非炎症性肠黏膜的转录组差异，并鉴定出显著差异表达的转录本。
对13例CD患者的13对炎症性和非炎症性肠黏膜以及13名健康对照者的性别匹配正常黏膜进行RNA-seq。通过免疫组织化学、定量逆转录聚合酶链反应和酶联免疫吸附测定对显著差异表达的转录本进行验证。
RNA-seq揭示了正常黏膜、非炎症性CD黏膜和炎症性CD黏膜之间全基因组转录组差异。在950个差异表达基因中，有19个基因上调或下调（上调：血管生成素2、CHN1、羧肽酶X1、羧肽酶Z、趋化因子配体1、甘露糖结合凝集素3、缝隙连接蛋白1、11β-羟基类固醇脱氢酶1、肿瘤抑制基因1、MEOX1、基质金属蛋白酶12、磷脂酶A1、丝氨酸蛋白酶抑制剂E1、SGIP1和瞬时受体电位通道蛋白4；下调：家族性189A1、磷酸二酯酶6A、溶质载体家族38成员4和3-羟基-3-甲基戊二酰辅酶A合成酶2），具有统计学意义（p < 0.01且q < 0.05）。其中，趋化因子配体1在各组间的变化倍数最高。趋化因子配体1的免疫组织化学显示，其在正常黏膜中无表达，在非炎症性CD黏膜中表达略有增加，在炎症性CD黏膜中表达高度增加。定量逆转录聚合酶链反应表明，趋化因子配体1的表达与上皮损伤、多形核白细胞浸润增加和黏膜下纤维化显著相关。通过酶联免疫吸附测定测得的血清趋化因子配体1浓度与CD活动指数（r = 0.660）的相关性优于与C反应蛋白（r = 0.204）的相关性。
RNA-seq揭示了正常黏膜、非炎症性CD黏膜和炎症性CD黏膜之间的转录组差异。肠道和血清中的趋化因子配体1随CD活动显著增加，可作为CD的潜在生物标志物。
