Systematic study of novel lncRNAs in different gastrointestinal cancer cells.
Recently, many lncRNAs were found to be deregulated in various human cancers and play important roles in carcinogenesis.



To investigate the association of lncRNAs to gastrointestinal cancers, 12 cases of esophageal cancer and hepatic cancer, 16 cases of gastric cancer and colorectal cancer and their matched adjacent tissue samples, 12 esophageal cancer cell lines, 7 gastric cancer cell lines, 10 colorectal cancer cell lines, and 11 hepatic cancer cell lines were examined. RNA-seq, bioinformatics pipeline, co-expression network, and gene ontology enrichment analysis were performed.



We have identified 23,169 candidate novel lncRNA transcripts. Comparing with protein coding genes the lncRNAs tend to be shorter and have less exons. Remarkably, we found 15 lncRNAs that were down-regulated in all cancer cell lines among all four types of cancers. In addition, we analyzed the differentially expressed lncRNAs in gastrointestinal cancer cells before and after treatment with 5-Aza. Many lncRNAs were up-regulated after 5-Aza treatment, which suggested that the expression of these lncRNAs may be regulated by DNA methylation. Finally, based on the co-expression network and GO enrichment analysis, we predicted that many novel lncRNAs were involved in pathways like apoptosis, cell cycle, cell adhesion, EMT, epigenetic regulation, DNA damage response signaling, and immune response.



Based on RNA-Seq and bioinformatics analysis, we have identified a significant number of novel lncRNAs, which could be involved in important pathways related to gastrointestinal cancer development. Overall, we provide a rich resource for identifying new biomarkers and studying novel lncRNA regulation pathways in gastrointestinal cancer.
Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, Beijing 100853, China.|These authors contributed equally to this work.
Baoping
B
Cao
MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.|These authors contributed equally to this work.
Nanxi
N
Song
Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, Beijing 100853, China.|College of Medicine, Nankai University, Tianjin 300071, China.
Meiying
M
Zhang
MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
Chao
C
Di
MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
Yang
Y
Yang
Laboratory of Molecular Oncology, Department of Thoracic Surgery II, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing 100142, China.
Youyong
Y
Lu
Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
Runsheng
R
Chen
MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
Zhi John
ZJ
Lu
Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, Beijing 100853, China.
Mingzhou
M
Guo
D017209:Apoptosis / Q000235:genetics; D001374:Azacitidine / Q000494:pharmacology; D014408:Biomarkers, Tumor / Q000235:genetics; D063646:Carcinogenesis / Q000235:genetics*; D002453:Cell Cycle / Q000235:genetics; D045744:Cell Line, Tumor; D019175:DNA Methylation; D015536:Down-Regulation; D044127:Epigenesis, Genetic; D058750:Epithelial-Mesenchymal Transition / Q000235:genetics; D005770:Gastrointestinal Neoplasms / Q000235:genetics*; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D062085:RNA, Long Noncoding / Q000187:drug effects / Q000235:genetics*; D060888:Real-Time Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D015398:Signal Transduction / Q000235:genetics*; D015854:Up-Regulation
D014408:Biomarkers, Tumor; D062085:RNA, Long Noncoding; D001374:Azacitidine