Differentially expressed lncRNAs and mRNAs identified by NGS analysis in colorectal cancer patients

Long noncoding RNAs (lncRNAs) play an important role in gene regulation, but their impact on the pathogenesis of colorectal cancer and the biological function of cancer cells is unclear. In this study, we used next‐generation sequencing to study the differences in the expression profiles of lncRNAs and mRNAs in colorectal cancer tissues. We analyzed the differentially expressed genes by Gene Ontology/Kyoto Encyclopedia of Genes and Genomes (GO/KEGG) enrichment and predicted new lncRNA functions. Our results revealed that compared with lncRNAs and mRNAs in nontumor colorectal tissues, 1019 lncRNAs (512 upregulated, 507 downregulated) and 3221 mRNAs (1606 upregulated, 1615 downregulated) were differentially expressed in tumor colorectal tissues (fold change >2 and P < 0.05). We validated some of these genes by qPCR. Furthermore, we identified some new lncRNAs differently expressed in colorectal cancer samples from patients in northern China. We confirmed the function of lncRNA‐FIRRE‐201 and SLCO4A1‐AS1‐202 in colorectal cancer cells to provide an experimental basis for studies on their roles in the occurrence and development of colorectal cancer and in the regulation of networks.

[1]  M. Lai,et al.  The integrated pathway of TGFβ/Snail with TNFα/NFκB may facilitate the tumor-stroma interaction in the EMT process and colorectal cancer prognosis , 2017, Scientific Reports.

[2]  Thomas Wetter,et al.  Gene Expression Profiling of Colorectal Tumors and Normal Mucosa by Microarrays Meta-Analysis Using Prediction Analysis of Microarray, Artificial Neural Network, Classification, and Regression Trees , 2014, Disease markers.

[3]  S. Torp,et al.  Activation of REG family proteins in colitis , 2011, Scandinavian journal of gastroenterology.

[4]  Ying Su,et al.  Long non-coding RNAs: New biomarkers for prognosis and diagnosis of colon cancer , 2017, Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine.

[5]  S. Natsugoe,et al.  Noncoding RNA and colorectal cancer: its epigenetic role , 2016, Journal of Human Genetics.

[6]  Hua-long Yu,et al.  Integrated regulatory mechanisms of miRNAs and targeted genes involved in colorectal cancer. , 2015, International journal of clinical and experimental pathology.

[7]  Howard Y. Chang,et al.  Long noncoding RNAs and human disease. , 2011, Trends in cell biology.

[8]  Maite Huarte.  The emerging role of lncRNAs in cancer , 2015, Nature Medicine.

[9]  Bo Li,et al.  The high expression of long non-coding RNA PANDAR indicates a poor prognosis for colorectal cancer and promotes metastasis by EMT pathway , 2016, Journal of Cancer Research and Clinical Oncology.

[10]  Xu Gao,et al.  Long noncoding RNAs: novel players in colorectal cancer. , 2015, Cancer letters.

[11]  I. Csabai,et al.  Genome-wide expression profiling in colorectal cancer focusing on lncRNAs in the adenoma-carcinoma transition , 2019, BMC Cancer.

[12]  L. Du,et al.  Identification of long noncoding RNAs as potential novel diagnosis and prognosis biomarkers in colorectal cancer , 2016, Journal of Cancer Research and Clinical Oncology.

[13]  Sven Diederichs,et al.  The hallmarks of cancer , 2012, RNA biology.

[14]  D. Coppola,et al.  Cell-surface markers for colon adenoma and adenocarcinoma , 2016, Oncotarget.

[15]  D. Gonzalez,et al.  Understanding next generation sequencing in oncology: A guide for oncologists. , 2015, Critical reviews in oncology/hematology.

[16]  Bing Yu,et al.  MicroRNA-143 inhibits colorectal cancer cell proliferation by targeting MMP7. , 2017, Minerva medica.

[17]  Yali Zhang,et al.  Quercetrin from Toona sinensis leaves induces cell cycle arrest and apoptosis via enhancement of oxidative stress in human colorectal cancer SW620 cells , 2017, Oncology reports.

[18]  Hong Zhou,et al.  Down-regulation of long non-coding RNA RP11-708H21.4 is associated with poor prognosis for colorectal cancer and promotes tumorigenesis through regulating AKT/mTOR pathway , 2017, Oncotarget.

[19]  Graham A Colditz,et al.  Physical activity and survival after colorectal cancer diagnosis. , 2006, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[20]  A. Simpson,et al.  MAGE-A3 is highly expressed in a subset of colorectal cancer patients. , 2012, Cancer immunity.

[21]  Y. Park,et al.  Cystatin SN inhibits auranofin-induced cell death by autophagic induction and ROS regulation via glutathione reductase activity in colorectal cancer , 2017, Cell Death & Disease.

[22]  Zhu Jin,et al.  KRT6 interacting with notch1 contributes to progression of renal cell carcinoma, and aliskiren inhibits renal carcinoma cell lines proliferation in vitro. , 2015, International journal of clinical and experimental pathology.

[23]  H. Fan,et al.  LncRNA NEAT1 Impacts Cell Proliferation and Apoptosis of Colorectal Cancer via Regulation of Akt Signaling , 2017, Pathology & Oncology Research.

[24]  S. Motoyama,et al.  Prognostic role of regenerating gene-I in patients with stage-IV head and neck squamous cell carcinoma , 2016, Diagnostic Pathology.

[25]  Qing Zhai,et al.  The Long Non-Coding RNA CRNDE Promotes Colorectal Carcinoma Progression by Competitively Binding miR-217 with TCF7L2 and Enhancing the Wnt/β-Catenin Signaling Pathway , 2017, Cellular Physiology and Biochemistry.

[26]  Jian-jun Peng,et al.  Long non-coding RNA TUG1 promotes colorectal cancer metastasis via EMT pathway , 2016, Oncotarget.

[27]  Yan Shi,et al.  The lncRNA-DLEU2/miR-186-5p/PDK3 axis promotes the progress of glioma cells. , 2019, American journal of translational research.

[28]  Zhen-yu He,et al.  Screening of lymph nodes metastasis associated lncRNAs in colorectal cancer patients. , 2014, World journal of gastroenterology.

[29]  S. Takasawa,et al.  Regenerating gene I regulates interleukin-6 production in squamous esophageal cancer cells. , 2010, Biochemical and biophysical research communications.

[30]  S. Jee,et al.  Gene-gene interaction analysis identifies a new genetic risk factor for colorectal cancer , 2015, Journal of Biomedical Science.

[31]  Michael Primig,et al.  Transcription of Two Long Noncoding RNAs Mediates Mating-Type Control of Gametogenesis in Budding Yeast , 2012, Cell.

[32]  Chien-Feng Li,et al.  Overexpression of Transcobalamin 1 is an Independent Negative Prognosticator in Rectal Cancers Receiving Concurrent Chemoradiotherapy , 2017, Journal of Cancer.