Genome-wide profiling of chemoradiation‑induced changes in alternative splicing in colon cancer cells

Xiong,Wei; Gao,Depei; Li,Yunfeng; Liu,Xin; Dai,Peiling; Qin,Jiyong; Wang,Guanshun; Li,Kangming; Bai,Han; Li,Wenhui

doi:10.3892/or.2016.5022

Genome-wide profiling of chemoradiation‑induced changes in alternative splicing in colon cancer cells

Authors:
- Wei Xiong
- Depei Gao
- Yunfeng Li
- Xin Liu
- Peiling Dai
- Jiyong Qin
- Guanshun Wang
- Kangming Li
- Han Bai
- Wenhui Li
View Affiliations

Affiliations: Department of Radiation Oncology, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650118, P.R. China, Department of Medical Imaging, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650118, P.R. China, Department of Colorectal Surgery, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650118, P.R. China, Cancer Research Institute of Yunnan Province, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650118, P.R. China
Published online on: August 12, 2016 https://doi.org/10.3892/or.2016.5022
Pages: 2142-2150

Metrics: Total Views: 0 (Spandidos Publications: | PMC Statistics: )

Metrics: Total PDF Downloads: 0 (Spandidos Publications: | PMC Statistics: )

Cited By (CrossRef): 0 citations Loading Articles...

Abstract

Alternative splicing is a key mechanism that regulates protein diversity and has been found to be associated with colon cancer progression and metastasis. However, the function of alternative splicing in chemoradiation‑resistant colon cancer remains elusive. In this study, we constructed a chemoradiation‑resistant colon cancer cell line. Through RNA-sequencing of normal and chemoradiation‑resistant colon cancer cells (HCT116), we found 818 genes that were highly expressed in the normal HCT116 cells, whereas 285 genes were highly expressed in the chemoradiation-resistant HCT116 (RCR-HCT116) cells. Gene ontology (GO) analysis showed that genes that were highly expressed in the HCT116 cells were enriched in GO categories related to cell cycle and cell division, whereas genes that were highly expressed in the RCR-HCT116 cells were associated with regulation of system processes and response to wounding. Analysis of alternative splicing events revealed that exon skipping was significantly increased in the chemoradiation‑resistant colon cancer cells. Moreover, we identified 323 alternative splicing events in 293 genes that were significantly different between the two different HCT116 cell types. These alternative splicing‑related genes were clustered functionally into several groups related with DNA replication, such as deoxyribonucleotide metabolic/catabolic processes, response to DNA damage stimulus and helicase activity. These findings enriched our knowledge by elucidating the function of alternative splicing in chemoradiation-resistant colon cancer.

View Figures

View References

1	Leff SE, Rosenfeld MG and Evans RM: Complex transcriptional units: Diversity in gene expression by alternative RNA processing. Annu Rev Biochem. 55:1091–1117. 1986. View Article : Google Scholar : PubMed/NCBI
2	Pan Q, Shai O, Lee LJ, Frey BJ and Blencowe BJ: Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet. 40:1413–1415. 2008. View Article : Google Scholar : PubMed/NCBI
3	Black DL: Mechanisms of alternative pre-messenger RNA splicing. Annu Rev Biochem. 72:291–336. 2003. View Article : Google Scholar : PubMed/NCBI
4	Matlin AJ, Clark F and Smith CW: Understanding alternative splicing: Towards a cellular code. Nat Rev Mol Cell Biol. 6:386–398. 2005. View Article : Google Scholar : PubMed/NCBI
5	Sammeth M, Foissac S and Guigó R: A general definition and nomenclature for alternative splicing events. PLOS Comput Biol. 4:e10001472008. View Article : Google Scholar : PubMed/NCBI
6	David CJ and Manley JL: Alternative pre-mRNA splicing regulation in cancer: Pathways and programs unhinged. Genes Dev. 24:2343–2364. 2010. View Article : Google Scholar : PubMed/NCBI
7	Oltean S and Bates DO: Hallmarks of alternative splicing in cancer. Oncogene. 33:5311–5318. 2014. View Article : Google Scholar
8	Kim E, Goren A and Ast G: Insights into the connection between cancer and alternative splicing. Trends Genet. 24:7–10. 2008. View Article : Google Scholar
9	Fackenthal JD and Godley LA: Aberrant RNA splicing and its functional consequences in cancer cells. Dis Model Mech. 1:37–42. 2008. View Article : Google Scholar : PubMed/NCBI
10	Miura K, Fujibuchi W and Unno M: Splice isoforms as therapeutic targets for colorectal cancer. Carcinogenesis. 33:2311–2319. 2012. View Article : Google Scholar : PubMed/NCBI
11	Thorsen K, Sørensen KD, Brems-Eskildsen AS, Modin C, Gaustadnes M, Hein AM, Kruhøffer M, Laurberg S, Borre M, Wang K, et al: Alternative splicing in colon, bladder, and prostate cancer identified by exon array analysis. Mol Cell Proteomics. 7:1214–1224. 2008. View Article : Google Scholar : PubMed/NCBI
12	Mojica W and Hawthorn L: Normal colon epithelium: A dataset for the analysis of gene expression and alternative splicing events in colon disease. BMC Genomics. 11:52010. View Article : Google Scholar : PubMed/NCBI
13	Gardina PJ, Clark TA, Shimada B, Staples MK, Yang Q, Veitch J, Schweitzer A, Awad T, Sugnet C, Dee S, et al: Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array. BMC Genomics. 7:3252006. View Article : Google Scholar : PubMed/NCBI
14	Bisognin A, Pizzini S, Perilli L, Esposito G, Mocellin S, Nitti D, Zanovello P, Bortoluzzi S and Mandruzzato S: An integrative framework identifies alternative splicing events in colorectal cancer development. Mol Oncol. 8:129–141. 2014. View Article : Google Scholar
15	Thorsen K, Mansilla F, Schepeler T, Øster B, Rasmussen MH, Dyrskjøt L, Karni R, Akerman M, Krainer AR, Laurberg S, et al: Alternative splicing of SLC39A14 in colorectal cancer is regulated by the Wnt pathway. Mol Cell Proteomics. 10:M110.0029982011. View Article : Google Scholar :
16	Gantt GA, Chen Y, Dejulius K, Mace AG, Barnholtz-Sloan J and Kalady MF: Gene expression profile is associated with chemo-radiation resistance in rectal cancer. Colorectal Dis. 16:57–66. 2014. View Article : Google Scholar
17	Kim Y, Joo KM, Jin J and Nam DH: Cancer stem cells and their mechanism of chemo-radiation resistance. Int J Stem Cells. 2:109–114. 2009. View Article : Google Scholar : PubMed/NCBI
18	Hiro J, Inoue Y, Toiyama Y, Miki C and Kusunoki M: Mechanism of resistance to chemoradiation in p53 mutant human colon cancer. Int J Oncol. 32:1305–1310. 2008.PubMed/NCBI
19	Trapnell C, Pachter L and Salzberg SL: TopHat: Discovering splice junctions with RNA-Seq. Bioinformatics. 25:1105–1111. 2009. View Article : Google Scholar : PubMed/NCBI
20	Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ and Pachter L: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 28:511–515. 2010. View Article : Google Scholar : PubMed/NCBI
21	Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL and Pachter L: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 7:562–578. 2012. View Article : Google Scholar : PubMed/NCBI
22	Katz Y, Wang ET, Airoldi EM and Burge CB: Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat Methods. 7:1009–1015. 2010. View Article : Google Scholar : PubMed/NCBI
23	Yu G, Li F, Qin Y, Bo X, Wu Y and Wang S: GOSemSim: An R package for measuring semantic similarity among GO terms and gene products. Bioinformatics. 26:976–978. 2010. View Article : Google Scholar : PubMed/NCBI
24	Grosso AR, Martins S and Carmo-Fonseca M: The emerging role of splicing factors in cancer. EMBO Rep. 9:1087–1093. 2008. View Article : Google Scholar : PubMed/NCBI
25	Narla G, DiFeo A, Yao S, Banno A, Hod E, Reeves HL, Qiao RF, Camacho-Vanegas O, Levine A, Kirschenbaum A, et al: Targeted inhibition of the KLF6 splice variant, KLF6 SV1, suppresses prostate cancer cell growth and spread. Cancer Res. 65:5761–5768. 2005. View Article : Google Scholar : PubMed/NCBI
26	Venables JP, Klinck R, Koh C, Gervais-Bird J, Bramard A, Inkel L, Durand M, Couture S, Froehlich U, Lapointe E, et al: Cancer-associated regulation of alternative splicing. Nat Struct Mol Biol. 16:670–676. 2009. View Article : Google Scholar : PubMed/NCBI
27	Wielenga VJ, Heider KH, Offerhaus GJ, Adolf GR, van den Berg FM, Ponta H, Herrlich P and Pals ST: Expression of CD44 variant proteins in human colorectal cancer is related to tumor progression. Cancer Res. 53:4754–4756. 1993.PubMed/NCBI
28	Mulder JW, Kruyt PM, Sewnath M, Oosting J, Seldenrijk CA, Weidema WF, Offerhaus GJ and Pals ST: Colorectal cancer prognosis and expression of exon-v6-containing CD44 proteins. Lancet. 344:1470–1472. 1994. View Article : Google Scholar : PubMed/NCBI
29	Herrlich P, Pals S and Ponta H: CD44 in colon cancer. Eur J Cancer. 31A:1110–1112. 1995. View Article : Google Scholar : PubMed/NCBI
30	Bilchik AJ, Poston G, Curley SA, Strasberg S, Saltz L, Adam R, Nordlinger B, Rougier P and Rosen LS: Neoadjuvant chemotherapy for metastatic colon cancer: A cautionary note. J Clin Oncol. 23:9073–9078. 2005. View Article : Google Scholar : PubMed/NCBI
31	Okonkwo A, Musunuri S, Talamonti M, Benson A III, Small W Jr, Stryker SJ and Rao MS: Molecular markers and prediction of response to chemoradiation in rectal cancer. Oncol. 8:497–500. 2001.