Asian Pacific Journal of Cancer Prevention

Asian Pacific Journal of Cancer Prevention (아시아태평양암예방학회)
권호 표지
DOI QR코드

DOI QR Code

Microarray and Next-Generation Sequencing to Analyse Gastric Cancer

  • Dang, Yuan (Department of Experimental Medicine, Fuzhou General Hospital (Dongfang Hospital)) ;
  • Wang, Ying-Chao (The United Innovation platform of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University) ;
  • Huang, Qiao-Jia (Department of Experimental Medicine, Fuzhou General Hospital (Dongfang Hospital))
  • Published : 2014.10.23
Download PDF
⟨ Previous Next ⟩

Abstract

Gastric cancer is the second after lung cause of cancer-related mortality in the world. Early detection and treatment can lead to a long survival time. Recently microarrays and next generation sequencing (NGS) have become very useful tools of comprehensive research into gastric cancer, facilitating the identification of treatment targets and personalized treatments. However, there are numerous challenges from cancer target discovery to practical clinical benefits. Although there are many biomarkers and target agents, only a minority of patients are tested and treated accordingly. Microarray technology with maturity was established more than 10 years ago, and has been widely used in the study of functional genomics, systems biology, and genomes in medicine. Second generation sequencing technology is more recent, but development is very fast, and it has been applied to the genome, including sequencing and epigenetics and many aspects of functional genomics. Here we review insights gained from these studies regarding the technology of microarray and NGS, how to elucidate the molecular basis of gastric cancer and identify potential therapeutic targets, and how to analyse candidate genes. We also discuss the challenges and future directions of such efforts.

Keywords

References

  1. Abnet CC, Freedman ND, Hu N, et al (2010). A shared susceptibility locus in PLCE1 at 10q23 for gastric adenocarcinoma and esophageal squamous cell carcinoma. Nat Genet, 42, 764-7. https://doi.org/10.1038/ng.649
  2. Bhan A, Hussain I, Ansari KI, et al (2014). Bisphenol-A and diethylstilbestrol exposure induces the expression of breast cancer associated long noncoding RNA HOTAIR in vitro and in vivo. J Steroid Biochem Mol Biol, 141, 160-70. https://doi.org/10.1016/j.jsbmb.2014.02.002
  3. Cao WJ, Wu HL, He BS, et al (2013). Analysis of long noncoding RNA expression profiles in gastric cancer. World J Gastroenterol, 19, 3658-64. https://doi.org/10.3748/wjg.v19.i23.3658
  4. Cui J, Chen Y, Chou WC, et al (2011). An integrated transcriptomic and computational analysis for biomarker identification in gastric cancer. Nucleic Acids Res, 39, 1197-207. https://doi.org/10.1093/nar/gkq960
  5. Furuta K, Arao T, Sakai K, et al (2012). Integrated analysis of whole genome exon array and array-comparative genomic hybridization in gastric and colorectal cancer cells. Cancer Sci , 103, 221-7. https://doi.org/10.1111/j.1349-7006.2011.02132.x
  6. Hajjari M, Behmanesh M, Sadeghizadeh M, et al (2013). Upregulation of HOTAIR long non-coding RNA in human gastric adenocarcinoma tissues. Med Oncol, 30, 670. https://doi.org/10.1007/s12032-013-0670-0
  7. He X, Bao W, Li X, et al (2014). The long non-coding RNA HOTAIR is upregulated in endometrial carcinoma and correlates with poor prognosis. Int J Mol Med, 33, 325-32.
  8. Huang L, Liao LM, Liu AW, et al (2014). Overexpression of long noncoding RNA HOTAIR predicts a poor prognosis in patients with cervical cancer. Arch Gynecol Obstet, 290, 717-23. https://doi.org/10.1007/s00404-014-3236-2
  9. Jin G, Ma H, Wu C, et al (2012). Genetic variants at 6p21.1 and 7p15.3 are associated with risk of multiple cancers in Han Chinese. Am J Hum Genet, 91, 928-34. https://doi.org/10.1016/j.ajhg.2012.09.009
  10. Kahvejian A, Quackenbush J, Thompson JF (2008). What would you do if you could sequence everything? Nat Biotechnol, 26, 1125-33. https://doi.org/10.1038/nbt1494
  11. Kamangar F, Dores GM, Anderson WF (2006). Patterns of cancer incidence, mortality, and prevalence across five continents: defining priorities to reduce cancer disparities in different geographic regions of the world. J Clin Oncol, 24, 2137-50. https://doi.org/10.1200/JCO.2005.05.2308
  12. Kang G, Hwang WC, Do IG, et al (2013). Exome sequencing identifies early gastric carcinoma as an early stage of advanced gastric cancer. PLoS One, 8, 82770. https://doi.org/10.1371/journal.pone.0082770
  13. Kim HP, Cho GA, Han SW, et al (2013). Novel fusion transcripts in human gastric cancer revealed by transcriptome analysis. Oncogene. [Epub ahead of print]
  14. Kim YH, Liang H, Liu X, et al (2012). AMPKalpha modulation in cancer progression: multilayer integrative analysis of the whole transcriptome in Asian gastric cancer. Cancer Res, 72, 2512-21. https://doi.org/10.1158/0008-5472.CAN-11-3870
  15. Lee J, van Hummelen P, Go C, et al (2012). High-throughput mutation profiling identifies frequent somatic mutations in advanced gastric adenocarcinoma. PLoS One, 7, 38892. https://doi.org/10.1371/journal.pone.0038892
  16. Li SC, Liao YL, Ho MR, et al (2012). miRNA arm selection and isomiR distribution in gastric cancer. BMC Genomics, 13, 13. https://doi.org/10.1186/1471-2164-13-13
  17. Liu SP, Yang JX, Cao DY, Shen K (2013). Identification of differentially expressed long non-coding RNAs in human ovarian cancer cells with different metastatic potentials. Cancer Biol Med, 10, 138-41.
  18. Luo D, Gao Y, Wang S, et al (2011). Genetic variation in PLCE1 is associated with gastric cancer survival in a Chinese population. J Gastroenterol, 46, 1260-6. https://doi.org/10.1007/s00535-011-0445-3
  19. Nacu S, Yuan W, Kan, et al (2011). Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples. BMC Med Genomics, 4, 11. https://doi.org/10.1186/1755-8794-4-11
  20. Nowell PC. 1962. The minute chromosome (Phl) in chronic granulocytic leukemia. Blut, 8, 65-6. https://doi.org/10.1007/BF01630378
  21. Ono H, Motoi N, Nagano H, et al (2014). Long noncoding RNA HOTAIR is relevant to cellular proliferation, invasiveness, and clinical relapse in small-cell lung cancer. Cancer Med, 3, 632-42. https://doi.org/10.1002/cam4.220
  22. Palanisamy N, Ateeq B, Kalyana-Sundaram S, et al (2010). Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma. Nat Med, 16, 793-8. https://doi.org/10.1038/nm.2166
  23. Park SM, Park SJ, Kim HJ, et al (2013). A known expressed sequence tag, BM742401, is a potent lincRNA inhibiting cancer metastasis. Exp Mol Med, 45, 31. https://doi.org/10.1038/emm.2013.59
  24. Qiao HP, Gao WS, Huo JX, Yang ZS (2013). Long non-coding RNA GAS5 functions as a tumor suppressor in renal cell carcinoma. Asian Pac J Cancer Prev, 14, 1077-82. https://doi.org/10.7314/APJCP.2013.14.2.1077
  25. Ribeiro-dos-Santos A, Khayat AS, Silva A, et al (2010). Ultra-deep sequencing reveals the microRNA expression pattern of the human stomach. PLoS One, 5, 13205. https://doi.org/10.1371/journal.pone.0013205
  26. Roukos DH (2009). Genome-wide association studies and aggressive surgery toward individualized prevention, and improved local control and overall survival for gastric cancer. Ann Surg Oncol, 16, 795-8. https://doi.org/10.1245/s10434-009-0317-8
  27. Sakamoto CH, Yoshimura K, et al (2008). Genetic variation in PSCA is associated with susceptibility to diffuse-type gastric cancer. Nat Genet, 40, 730-40. https://doi.org/10.1038/ng.152
  28. Shi Y, Hu Z , Wu C, et al (2011). A genome-wide association study identifies new susceptibility loci for non-cardia gastric cancer at 3q13.31 and 5p13.1. Nat Genet, 43, 1215-8. https://doi.org/10.1038/ng.978
  29. Song H, Sun W, Ye G, et al (2013). Long non-coding RNA expression profile in human gastric cancer and its clinical significances. J Transl Med, 11, 225. https://doi.org/10.1186/1479-5876-11-225
  30. Sun M, Jin FY, Xia R, et al (2014a). Decreased expression of long noncoding RNA GAS5 indicates a poor prognosis and promotes cell proliferation in gastric cancer. BMC Cancer, 14, 319. https://doi.org/10.1186/1471-2407-14-319
  31. Sun M, Xia R, Jin F, et al (2014b). Downregulated long noncoding RNA MEG3 is associated with poor prognosis and promotes cell proliferation in gastric cancer. Tumour Biol, 35, 1065-73. https://doi.org/10.1007/s13277-013-1142-z
  32. Tomlins SA, Rhodes DR, Perner S, et al (2005). Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science, 310, 644-8. https://doi.org/10.1126/science.1117679
  33. Ueda T, Volinia S, Okumura H, et al (2010). Relation between microRNA expression and progression and prognosis of gastric cancer: a microRNA expression analysis. Lancet Oncol, 11, 136-46. https://doi.org/10.1016/S1470-2045(09)70343-2
  34. Vega F, Medeiros LJ, et al (2003). Chromosomal translocations involved in non-Hodgkin lymphomas. Arch Pathol Lab Med, 127, 1148-60.
  35. Volinia S, Calin GA, Liu CG, et al (2006). A microRNA expression signature of human solid tumors defines cancer gene targets. Proc Natl Acad Sci USA, 103, 2257-61. https://doi.org/10.1073/pnas.0510565103
  36. Wang K, Kan J, Yuen ST, et al (2011). Exome sequencing identifies frequent mutation of ARID1A in molecular subtypes of gastric cancer. Nat Genet, 43, 1219-23. https://doi.org/10.1038/ng.982
  37. Wang LD, Zhou FY, Li XM, et al (2010). Genome-wide association study of esophageal squamous cell carcinoma in Chinese subjects identifies susceptibility loci at PLCE1 and C20orf54. Nat Genet, 42, 759-63. https://doi.org/10.1038/ng.648
  38. Wang Y, Gao S, Liu G, et al (2014). Microarray expression profile analysis of long non-coding RNAs in human gastric cardiac adenocarcinoma. Cell Physiol Biochem, 33, 1225-38. https://doi.org/10.1159/000358692
  39. Wang Z, Gerstein M, Snyder M, et al (2009). RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet, 10, 57-63. https://doi.org/10.1038/nrg2484
  40. Yamashita K, Sakuramoto S, Nemoto M, et al (2011). Trend in gastric cancer: 35 years of surgical experience in Japan. World J Gastroenterol, 17, 3390-7. https://doi.org/10.3748/wjg.v17.i29.3390
  41. Yang F, Xue X, Zheng L, et al (2014). Long non-coding RNA GHET1 promotes gastric carcinoma cell proliferation by increasing c-Myc mRNA stability. FEBS J, 281, 802-13. https://doi.org/10.1111/febs.12625
  42. Yang XX, Li FX, Zhou CP, et al (2012). Association of genetic polymorphisms at 1q22 but not 10q23 with gastric cancer in a southern Chinese population. Asian Pac J Cancer Prev, 13, 2519-22. https://doi.org/10.7314/APJCP.2012.13.6.2519
  43. Yoon K, Lee S, Han T S, et al (2013). Comprehensive genomeand transcriptome-wide analyses of mutations associated with microsatellite instability in Korean gastric cancers. Genome Res, 23, 1109-17. https://doi.org/10.1101/gr.145706.112
  44. Yun SM, Yoon K, Lee S, et al (2013). PPP1R1B-STARD3 chimeric fusion transcript in human gastric cancer promotes tumorigenesis through activation of PI3K/AKT signaling. Oncogene. [Epub ahead of print]
  45. Zang ZJ, Cutcutache I, Poon SL, et al (2012). Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes. Nat Genet, 44, 570-4. https://doi.org/10.1038/ng.2246
  46. Zang ZJ, Ong CK, Cutcutache I, et al (2011). Genetic and structural variation in the gastric cancer kinome revealed through targeted deep sequencing. Cancer Res, 71, 29-39. https://doi.org/10.1158/0008-5472.CAN-10-1749
  47. Zhao Y, Guo Q, Chen J, et al (2014). Role of long non-coding RNA HULC in cell proliferation, apoptosis and tumor metastasis of gastric cancer: a clinical and in vitro investigation. Oncol Rep, 31, 358-64.
  48. Zhou S, Wang J, Zhang Z, et al (2014). An emerging understanding of long noncoding RNAs in kidney cancer. J Cancer Res Clin Oncol. [Epub ahead of print]
  49. Zhuang M, Gao W, Xu J, et al (2014). The long non-coding RNA H19-derived miR-675 modulates human gastric cancer cell proliferation by targeting tumor suppressor RUNX1. Biochem Biophys Res Commun, 448, 315-22. https://doi.org/10.1016/j.bbrc.2013.12.126

Cited by

  1. CDH1 mutations in gastric cancer patients from northern Brazil identified by Next- Generation Sequencing (NGS) vol.39, pp.2, 2016, https://doi.org/10.1590/1678-4685-gmb-2014-0342
  2. Molecular dysexpression in gastric cancer revealed by integrated analysis of transcriptome data vol.13, pp.5, 2017, https://doi.org/10.3892/ol.2017.5798