结直肠癌组织中差异表达cirRNA的筛选及功能分析
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摘要
目的筛选结直肠癌组织中差异表达的环状RNA(circRNA),并分析其在结直肠癌发生发展中的作用。方法收集9例原发性结直肠癌患者的肿瘤组织及癌旁正常组织标本,根据TNM分期分为A(T_(1～3)N_0M_0)、B(T_(4a～b)N_0M_0)、C(T_(4a～b)N_(1～2)M_0)组。用Affymetrix Clariom D芯片检测、筛选各组差异表达的circRNA并进行聚类分析和表达趋势分析,通过构建共表达调控网络筛选重点差异表达circRNA及其对应的mRNA。利用GO数据库和KEGG数据库分别进行基因功能注释分析和信号通路富集分析,最终筛选功能最显著的基因及其对应circRNA。结果 A组癌组织与癌旁组织比较,circRNA表达降低者有165个、升高239个;B组分别为284个、276个;C组分别为190个、220个。随着结直肠癌病情进展,差异表达circRNA的表达水平呈逐渐下降趋势。选择既符合主流表达变化趋势同时更具有统计学意义的circRNA群与共表达调控网络基因属性评分前10位的circRNA进行交集处理,筛选出8个与结直肠癌进展密切相关的circRNA即hsa_circ_0000007、hsa_circ_0001111、hsa_circ_0006977、hsa_circ_0079656、hsa_circ_0023608、hsa_circ_0024508、hsa_circ_0026694、hsa_circ_0029903。预测8个circRNA相应的mRNA,GO分析及KEGG分析结果显示,被富集的大部分基因及hsa03010通路主要参与核糖体RNA的加工与代谢、RNA的剪切与加工处理等细胞基础功能,其中hsa_circ_0079656相关的HINFP基因主要参与细胞周期中G_1/S期转录过程调控。结论 hsa_circ_0079656在结直肠癌组织中低表达,且随结直肠癌进展表达逐步降低;其可能通过作用于HINFP基因调控细胞周期中G_1/S期的转录过程,进而影响结直肠癌的进展。
Objective To screen out the differentially expressed circular RNA(circRNA) in the colorectal cancer tissues and to analyze their role in the development of colorectal cancer. Methods Cancer tissues and adjacent tissues of 9 patients with primary colorectal cancer at different pathological stages were collected and grouped according to the staging criteria of 2018.V2 NCCN guidelines: group A(T_(1-3)N_0M_0), group B(T_(4 a-b)N_0M_0), and group C(T_(4 a-b)N_(1-2)M_0). Affymetrix Clariom D chip was used to detect and screen the differentially expressed circRNAs in each group, and cluster analysis and expression trend analysis were performed. The co-expression regulation was constructed to screen the differentially expressed circRNA and its corresponding mRNA. GO database and KEGG database were used to annotate gene function and signal pathway, respectively. Finally, the most prominent genes and their corresponding circRNA were screened out. Results Differential circRNA analysis showed that 165 decreased and 239 increased in the circRNA expression of group A, 284 and 276 in the group B, and 190 and 220 in the group C. With the progress of the disease, the expression level of circRNA decreased gradually. Combined with the analysis of co-expression regulation network, we found 8 circRNA closely related to the progress of colorectal cancer: hsa_circ_0000007, hsa_circ_0001111, hsa_circ_0006977, hsa_circ_0079656, hsa_circ_0023608, hsa_circ_0024508, hsa_circ_0026694, and hsa_circ_0029903. For the circRNA screened out above, the corresponding mRNA was predicted. GO analysis and KEGG analysis showed that most of the enriched genes and the hsa03010 pathway were mainly involved in the processing and metabolism of ribosomal RNA, the shear and processing of RNA and other basic cellular functions, among which, hsa_circ_0079656-related HINFP gene was mainly involved in the transcription process regulation of G_1/S phase.Conclusions The expression level of hsa_circ_0079656 decreases gradually with the progression of colorectal cancer. It is possible that HINFP gene may be involved in the regulation of transcription in G_1/S phase, thereby affecting the progression of colorectal cancer.
Objective To screen out the differentially expressed circular RNA(circRNA) in the colorectal cancer tissues and to analyze their role in the development of colorectal cancer. Methods Cancer tissues and adjacent tissues of 9 patients with primary colorectal cancer at different pathological stages were collected and grouped according to the staging criteria of 2018.V2 NCCN guidelines: group A(T_(1-3)N_0M_0), group B(T_(4 a-b)N_0M_0), and group C(T_(4 a-b)N_(1-2)M_0). Affymetrix Clariom D chip was used to detect and screen the differentially expressed circRNAs in each group, and cluster analysis and expression trend analysis were performed. The co-expression regulation was constructed to screen the differentially expressed circRNA and its corresponding mRNA. GO database and KEGG database were used to annotate gene function and signal pathway, respectively. Finally, the most prominent genes and their corresponding circRNA were screened out. Results Differential circRNA analysis showed that 165 decreased and 239 increased in the circRNA expression of group A, 284 and 276 in the group B, and 190 and 220 in the group C. With the progress of the disease, the expression level of circRNA decreased gradually. Combined with the analysis of co-expression regulation network, we found 8 circRNA closely related to the progress of colorectal cancer: hsa_circ_0000007, hsa_circ_0001111, hsa_circ_0006977, hsa_circ_0079656, hsa_circ_0023608, hsa_circ_0024508, hsa_circ_0026694, and hsa_circ_0029903. For the circRNA screened out above, the corresponding mRNA was predicted. GO analysis and KEGG analysis showed that most of the enriched genes and the hsa03010 pathway were mainly involved in the processing and metabolism of ribosomal RNA, the shear and processing of RNA and other basic cellular functions, among which, hsa_circ_0079656-related HINFP gene was mainly involved in the transcription process regulation of G_1/S phase.Conclusions The expression level of hsa_circ_0079656 decreases gradually with the progression of colorectal cancer. It is possible that HINFP gene may be involved in the regulation of transcription in G_1/S phase, thereby affecting the progression of colorectal cancer.
引文
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[12] Jin Y, Yu LL, Zhang B, et al. Circular RNA hsa_circ_0000523 regulates the proliferation and apoptosis of colorectal cancer cells as miRNA sponge[J]. Braz J Med Biol Res 2018,51:e7811.
[13] Zhang C, Zhang C, Lin J, et al. Circular RNA hsa_circ_0091579 serves as a diagnostic and prognostic marker for hepatocellular carcinoma[J]. Cell Physiol Biochem, 2018,51(1):290-300.
[14] Chi BJ, Zhao DM, Liu L, et al. Downregulation of hsa_circ_0000285 serves as a prognostic biomarker for bladder cancer and is involved in cisplatin resistance[J]. Neoplasma, 2018,Sep 16.pii:180318N185.
[15] Chen S, Li T, Zhao Q, et al. Using circular RNA hsa_circ_0000190 as a new biomarker in the diagnosis of gastric cancer[J]. Clin Chim Acta, 2017,466:167-171.
[16] Qin M, Liu G, Huo X, et al. Hsa_circ_0001649:A circular RNA and potential novel biomarker for hepatocellular carcinoma[J]. Cancer Biomarkers, 2016,16(1):161-169.
[2] 钟琼慧,林晋,王小中.circRNA生物学特性及其与肺癌关系的研究进展[J].山东医药,2018,58(40):111-113.
[3] 何存存,吴会超,成绍敏.环状RNAs在消化系恶性肿瘤中的表达生物学功能及临床应用研究进展[J].山东医药,2017,57(40):100-103.
[4] Danan M, Schwartz S, Edelheit S, et al. Transcriptome-widediscovery of circular RNAs in Archaea[J]. Nucleic Acids Res, 2012,40(7):3131-3142.
[5] Morris KV, Mattick JS. The rise of regulatory RNA[J]. Nat Rev Genet, 2014,15(6):423-437.
[6] 袁近松,石蓓.环状RNA与心血管疾病关系的研究进展[J].山东医药,2018,58(6):108-110.
[7] Wang Y, Mo Y, Gong Z, et al. Circular RNAs in human cancer[J]. Mol Cancer, 2017,16(1):25.
[8] Kim H , Kumar P , Menghi F , et al. Abstract 2909: High-precision quantification of clonal evolution during comparative treatments of triple negative breast cancer[J]. Cancer Res, 2017,77(13 Suppl):2909.
[9] Zhang J, Liu H, Hou L, et al. Circular RNA_LARP4 inhibits cell proliferation and invasion of gastric cancer by sponging miR-424-5p and regulating LATS1 expression[J]. Molecular Cancer, 2017,16(1):151.
[10] Han D, Li J, Wang H, et al. Circular RNA MTO1 acts as the sponge of miR-9 to suppress hepatocellular carcinoma progression[J]. Hepatology, 2017,66(4):1151.
[11] Zhang HD, Jiang LH, Hou JC, et al. Circular RNA hsa_circ_0052112 promotes cell migration and invasion by acting as sponge for miR-125a-5p in breast cancer[J]. Biomed Pharmacother, 2018,107:1342-1353.
[12] Jin Y, Yu LL, Zhang B, et al. Circular RNA hsa_circ_0000523 regulates the proliferation and apoptosis of colorectal cancer cells as miRNA sponge[J]. Braz J Med Biol Res 2018,51:e7811.
[13] Zhang C, Zhang C, Lin J, et al. Circular RNA hsa_circ_0091579 serves as a diagnostic and prognostic marker for hepatocellular carcinoma[J]. Cell Physiol Biochem, 2018,51(1):290-300.
[14] Chi BJ, Zhao DM, Liu L, et al. Downregulation of hsa_circ_0000285 serves as a prognostic biomarker for bladder cancer and is involved in cisplatin resistance[J]. Neoplasma, 2018,Sep 16.pii:180318N185.
[15] Chen S, Li T, Zhao Q, et al. Using circular RNA hsa_circ_0000190 as a new biomarker in the diagnosis of gastric cancer[J]. Clin Chim Acta, 2017,466:167-171.
[16] Qin M, Liu G, Huo X, et al. Hsa_circ_0001649:A circular RNA and potential novel biomarker for hepatocellular carcinoma[J]. Cancer Biomarkers, 2016,16(1):161-169.