Transcriptome profiling of the cancer, adjacent non-tumor and distant normal tissues from a colorectal cancer patient by deep sequencing.
Colorectal cancer (CRC) is one of the most commonly diagnosed cancers in the world. A genome-wide screening of transcriptome dysregulation between cancer and normal tissue would provide insight into the molecular basis of CRC initiation and progression. Compared with microarray technology, which is commonly used to identify transcriptional changes, the recently developed RNA-seq technique has the ability to detect other abnormal regulations in the cancer transcriptome, such as alternative splicing, novel transcripts or gene fusion. In this study, we performed high-throughput transcriptome sequencing at ~50× coverage on CRC, adjacent non-tumor and distant normal tissue. The results revealed cancer-specific, differentially expressed genes and differential alternative splicing, suggesting that the extracellular matrix and metabolic pathways are activated and the genes related to cell homeostasis are suppressed in CRC. In addition, one tumor-restricted gene fusion, PRTEN-NOTCH2, was also detected and experimentally confirmed. This study reveals some common features in tumor invasion and provides a comprehensive survey of the CRC transcriptome, which provides better insight into the complexity of regulatory changes during tumorigenesis.
Department of Clinical Laboratory, Fujian Provincial Hospital, Fujian Provincial Clinical Medical College, Fujian Medical University, Fuzhou, China. wya_sl@yahoo.com.cn
Yan'an
Y
Wu
Xuetao
X
Wang
Fangbo
F
Wu
Ruolei
R
Huang
Fangqin
F
Xue
Guantao
G
Liang
Min
M
Tao
Pengwei
P
Cai
Yi
Y
Huang
D017398:Alternative Splicing; D051177:Catenins / Q000378:metabolism; D016000:Cluster Analysis; D003106:Colon / Q000378:metabolism*; D015179:Colorectal Neoplasms / Q000235:genetics* / Q000378:metabolism*; D005091:Exons; D005109:Extracellular Matrix / Q000378:metabolism; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008875:Middle Aged; D055264:Mucin-4 / Q000378:metabolism; D010982:Platelet-Derived Growth Factor / Q000378:metabolism; D020033:Protein Isoforms; D051883:Receptor, Notch2 / Q000096:biosynthesis; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D000095002:Delta Catenin
D051177:Catenins; D055264:Mucin-4; C497764:NOTCH2 protein, human; D010982:Platelet-Derived Growth Factor; D020033:Protein Isoforms; D051883:Receptor, Notch2; C075278:platelet-derived growth factor A; D000095002:Delta Catenin