Research Article
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Year 2021, Volume 15, Issue 1, 11 - 25, 29.04.2021

Abstract

References

  • Cappell MS. Pathophysiology, clinical presentation, and management of colon cancer. Gastroenterol Clin North Am 2008;37:1–24.
  • Colussi D, Brandi G, Bazzoli F, Ricciardiello L. Molecular pathways involved in colorectal cancer: implications for disease behavior and prevention. Int J Mol Sci 2013;14:16365–85.
  • Hisamuddin IM, Yang VW. Molecular genetics of colorectal cancer: an overview. Curr Colorectal Cancer Rep 2006;2:53–9.
  • Tariq K, Ghias K. Colorectal cancer carcinogenesis: a review of mechanisms. Cancer Biol Med 2016;13:120–35.
  • Ogino S, Odze RD, Kawasaki T, Brahmandam M, Kirkner GJ, Laird PW, Loda M, Fuchs CS. Correlation of pathologic features with CpG island methylator phenotype (CIMP) by quantitative DNA methylation analysis in colorectal carcinoma. Am J Surg Pathol 2006;30:1175–83.
  • Peltomäki P, Lothe RA, Aaltonen LA, Pylkkänen L, Nyström-Lahti M, Seruca R, David L, Holm R, Ryberg D, Haugen A, Brøgger A, Børresen AL, de la Chapelle, A. Microsatellite instability is associated with tumors that characterize the hereditary non-polyposis colorectal carcinoma syndrome. Cancer Res 1993;53:5853–5.
  • Haggar FA, Boushey RP. Colorectal cancer epidemiology: incidence, mortality, survival, and risk factors. Clin Colon Rectal Surg 2009;22:191–7.
  • Meyer B, Are C. Current status and future directions in colorectal cancer. Indian J Surg Oncol 2018;9:440–1.
  • Rawla P, Sunkara T, Barsouk A. Epidemiology of colorectal cancer: incidence, mortality, survival, and risk factors. Prz Gastroenterol 2019;14:89–103.
  • White A, Ironmonger L, Steele RJC, Ormiston-Smith N, Crawford C, Seims A. A review of sex-related differences in colorectal cancer incidence, screening uptake, routes to diagnosis, cancer stage and survival in the UK. BMC Cancer 2018;18:906.
  • Carethers JM. Risk factors for colon location of cancer. Transl Gastroenterol Hepatol 2018;3:76.
  • Church JM. Colon cancer screening update and management of the malignant polyp. Clin Colon Rectal Surg 2005;18:141–9.
  • Li F-Y, Lai M-D. Colorectal cancer, one entity or three. J Zhejiang Univ Sci B 2009;10:219–29.
  • Tamas K, Walenkamp AM, de Vries EG, van Vugt MA, Beets-Tan RG, van Etten B, de Groot DJA, Hospers GAP. Rectal and colon cancer: Not just a different anatomic site. Cancer Treat Rev 2015;41:671–9.
  • Lee L, Erkan A, Alhassan N, Kelly JJ, Nassif GJ, Albert MR, Monson JR. Lower survival after right-sided versus left-sided colon cancers: is an extended lymphadenectomy the answer? Surgical Oncol 2018;27:449–55.
  • Turk S, Turk C, Temirci ES, Malkan UY, Ucar G, Ozguven SV. Assessing the genetic impact of Enterococcus faecalis infection on gastric cell line MKN74. Ann Microbiol 2021;71:Article 8.
  • Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, Yefanov A, Lee H, Zhang N, Robertson CL, Serova N, Davis S, Soboleva A. NCBI GEO: archive for functional genomics data sets-update. Nucleic Acids Res 2013;41:D991–D5.
  • Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 2003;31:e15.
  • de Hoon MJL, Imoto S, Nolan J, Miyano S. Open source clustering software. Bioinformatics 2004;20:1453–4.
  • Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003;13:2498–504.
  • Franz M, Rodriguez H, Lopes C, Zuberi K, Montojo J, Bader GD, Morris Q. GeneMANIA update 2018. Nucleic Acids Res 2018;46: W60–W4.
  • Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature protocols 2009;4(1):44–57.
  • Huang da W, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 2009;37:1–13.
  • Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 2005;102:15545–50.
  • Guinney J, Dienstmann R, Wang X, de Reyniès A, Schlicker A, Soneson C, Marisa L, Roepman P, Nyamundanda G, Angelino P, Bot BM, Morris JS, Simon IM, Gerster S, Fessler E, De Sousa E Melo F, Missiaglia E, Ramay H, Barras D, Homicsko K, Maru D, Manyam GC, Broom B, Boige V, Perez-Villamil B, Laderas T, Salazar R, Gray JW, Hanahan D, Tabernero J, Bernards R, Friend SH, Laurent-Puig P, Medema JP, Sadanandam A, Wessels L, Delorenzi M, Kopetz S, Vermeulen L, Tejpar S. The consensus molecular subtypes of colorectal cancer. Nat Med 2015;21:1350–6.
  • Fodde R. The APC gene in colorectal cancer. Eur J Cancer 2002;38: 867–71.
  • Fodde R, Smits R, Clevers H. APC, signal transduction and genetic instability in colorectal cancer. Nat Rev Cancer 2001;1:55–67.
  • Zhang L, Shay JW. Multiple roles of apc and its therapeutic implications in colorectal cancer. J Natl Cancer Ins 2017;109:djw332.
  • Du W-B, Lin C-H, Chen W-B. High expression of APC is an unfavorable prognostic biomarker in T4 gastric cancer patients. World J Gastroenterol 2019;25:4452–67.
  • Jorissen RN, Christie M, Mouradov D, Sakthianandeswaren A, Li S, Love C, Xu ZZ, Molloy PL, Jones JT, McLaughlin S, Ward RL, Hawkins NJ, Ruszkiewicz AR, Moore J, Burgess AW, Busam D, Zhao Q, Strausberg RL, Lipton L, Desai J, Gibbs P, Sieber OM. Wild-type APC predicts poor prognosis in microsatellite-stable proximal colon cancer. Br J Cancer 2015;113:979–88.
  • Katkoori VR, Suarez-Cuervo C, Shanmugam C, Jhala NC, Callens T, Messiaen L, Posey J 3rd, Bumpers HL, Meleth S, Grizzle WE, Manne U. Bax expression is a candidate prognostic and predictive marker of colorectal cancer. J Gastrointest Oncol 2010;1:76–89.
  • Pryczynicz A, Gryko M, Niewiarowska K, Cepowicz D, Ustymowicz M, Kemona A, Guzinska-Ustymowicz K. Bax protein may influence the invasion of colorectal cancer. World J Gastroenterol 2014;20: 1305–10.
  • Kasela M, Nyström M, Kansikas M. PMS2 expression decrease causes severe problems in mismatch repair. Hum Mutat 2019;40:904–7.
  • Lim DR, Kuk JK, Kim T, Shin EJ. Comparison of oncological outcomes of right-sided colon cancer versus left-sided colon cancer after curative resection: which side is better outcome? Medicine (Baltimore) 2017;96:e8241–e.
  • Nahas SC, Nahas CS, Bustamante-Lopez LA, Pinto RA, Marques CF, Campos FG, Cecconello I. Prognostic factors of surgicallytreated patients with cancer of the right colon: a ten years’ experience of a single universitary institution. Arq Bras Cir Dig 2017;30:103–7.
  • Zhao C, Li S, Zhao M, Zhu H, Zhu X. Prognostic values of DNA mismatch repair genes in ovarian cancer patients treated with platinum-based chemotherapy. Archives Gynecol Obstet 2018;297:153– 9.
  • van Alphen RJ, Wiemer EAC, Burger H, Eskens FALM. The spliceosome as target for anticancer treatment. Br J Cancer 2009;100:228–32.
  • Cervena K, Siskova A, Buchler T, Vodicka P, Vymetalkova V. Methylation-based therapies for colorectal cancer. Cells 2020;9: 1540.
  • Weekley CM, He C. Developing drugs targeting transition metal homeostasis. Curr Opin Chem Biol 2017;37:26–32.

In silico transcriptomic analysis of ascending colon cancer unearths known and novel genes and gene sets regard to characteristic features of colon cancer

Year 2021, Volume 15, Issue 1, 11 - 25, 29.04.2021

Abstract

Objectives: Colon cancer emerges as a serious health problem in both men and women. Cancers in the colon have different genotypes and phenotypes according to the anatomical region. Tumors in ascending colon are usually diagnosed later, but it is more malignant than the descending and transverse colon, and the survival rates of patients are lower than other regions. The purpose of this study was to determine significantly high or low expressed genes in the ascending colon tumors by comparing all genome information obtained from cancer samples of ascending, transverse and descending colon. In concordance with all this information, another aim of the study was to identify the pathways to which the genes obtained from the colon in the large intestine and to determine their relationship with each other and to correlate them with the characteristics of cancer. Methods: Gene expression values for three subtypes of colon cancer as ascending, transverse, and descending were obtained from GEO (Gene Expression Omnibus) (GSE41258). Data included a total of 47 ascending, 18 transverse and 31 descending colon cancer patient samples. Linear regression analysis was performed to determine differentially expressed genes. Gene Cluster 3.0 was used in order to cluster the genes hierarchically. In addition to linear regression and hierarchical clustering, network analysis with multivariable genes was performed in Cytoscape application 3.8.2 using GeneMANIA. GSEA 4.1.0 (Gene Set Enrichment Analysis) was performed to understand the different genes among the specified groups. Results: As a result of these analyses, it was determined that there were 85 genes with high expression and 139 genes with low expression in the ascending colon tumor samples. It has been shown that these genes can differentiate tumor samples in the ascending colon better than tumor samples in other colon regions. Conclusion: Our findings are important for understanding the genome of ascending colon tumors; if these findings are confirmed in vitro and clinically, it may have potential to be revealed that the identified genes also have biomarker properties for tumors in the ascending colon.

References

  • Cappell MS. Pathophysiology, clinical presentation, and management of colon cancer. Gastroenterol Clin North Am 2008;37:1–24.
  • Colussi D, Brandi G, Bazzoli F, Ricciardiello L. Molecular pathways involved in colorectal cancer: implications for disease behavior and prevention. Int J Mol Sci 2013;14:16365–85.
  • Hisamuddin IM, Yang VW. Molecular genetics of colorectal cancer: an overview. Curr Colorectal Cancer Rep 2006;2:53–9.
  • Tariq K, Ghias K. Colorectal cancer carcinogenesis: a review of mechanisms. Cancer Biol Med 2016;13:120–35.
  • Ogino S, Odze RD, Kawasaki T, Brahmandam M, Kirkner GJ, Laird PW, Loda M, Fuchs CS. Correlation of pathologic features with CpG island methylator phenotype (CIMP) by quantitative DNA methylation analysis in colorectal carcinoma. Am J Surg Pathol 2006;30:1175–83.
  • Peltomäki P, Lothe RA, Aaltonen LA, Pylkkänen L, Nyström-Lahti M, Seruca R, David L, Holm R, Ryberg D, Haugen A, Brøgger A, Børresen AL, de la Chapelle, A. Microsatellite instability is associated with tumors that characterize the hereditary non-polyposis colorectal carcinoma syndrome. Cancer Res 1993;53:5853–5.
  • Haggar FA, Boushey RP. Colorectal cancer epidemiology: incidence, mortality, survival, and risk factors. Clin Colon Rectal Surg 2009;22:191–7.
  • Meyer B, Are C. Current status and future directions in colorectal cancer. Indian J Surg Oncol 2018;9:440–1.
  • Rawla P, Sunkara T, Barsouk A. Epidemiology of colorectal cancer: incidence, mortality, survival, and risk factors. Prz Gastroenterol 2019;14:89–103.
  • White A, Ironmonger L, Steele RJC, Ormiston-Smith N, Crawford C, Seims A. A review of sex-related differences in colorectal cancer incidence, screening uptake, routes to diagnosis, cancer stage and survival in the UK. BMC Cancer 2018;18:906.
  • Carethers JM. Risk factors for colon location of cancer. Transl Gastroenterol Hepatol 2018;3:76.
  • Church JM. Colon cancer screening update and management of the malignant polyp. Clin Colon Rectal Surg 2005;18:141–9.
  • Li F-Y, Lai M-D. Colorectal cancer, one entity or three. J Zhejiang Univ Sci B 2009;10:219–29.
  • Tamas K, Walenkamp AM, de Vries EG, van Vugt MA, Beets-Tan RG, van Etten B, de Groot DJA, Hospers GAP. Rectal and colon cancer: Not just a different anatomic site. Cancer Treat Rev 2015;41:671–9.
  • Lee L, Erkan A, Alhassan N, Kelly JJ, Nassif GJ, Albert MR, Monson JR. Lower survival after right-sided versus left-sided colon cancers: is an extended lymphadenectomy the answer? Surgical Oncol 2018;27:449–55.
  • Turk S, Turk C, Temirci ES, Malkan UY, Ucar G, Ozguven SV. Assessing the genetic impact of Enterococcus faecalis infection on gastric cell line MKN74. Ann Microbiol 2021;71:Article 8.
  • Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, Yefanov A, Lee H, Zhang N, Robertson CL, Serova N, Davis S, Soboleva A. NCBI GEO: archive for functional genomics data sets-update. Nucleic Acids Res 2013;41:D991–D5.
  • Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 2003;31:e15.
  • de Hoon MJL, Imoto S, Nolan J, Miyano S. Open source clustering software. Bioinformatics 2004;20:1453–4.
  • Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003;13:2498–504.
  • Franz M, Rodriguez H, Lopes C, Zuberi K, Montojo J, Bader GD, Morris Q. GeneMANIA update 2018. Nucleic Acids Res 2018;46: W60–W4.
  • Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature protocols 2009;4(1):44–57.
  • Huang da W, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 2009;37:1–13.
  • Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 2005;102:15545–50.
  • Guinney J, Dienstmann R, Wang X, de Reyniès A, Schlicker A, Soneson C, Marisa L, Roepman P, Nyamundanda G, Angelino P, Bot BM, Morris JS, Simon IM, Gerster S, Fessler E, De Sousa E Melo F, Missiaglia E, Ramay H, Barras D, Homicsko K, Maru D, Manyam GC, Broom B, Boige V, Perez-Villamil B, Laderas T, Salazar R, Gray JW, Hanahan D, Tabernero J, Bernards R, Friend SH, Laurent-Puig P, Medema JP, Sadanandam A, Wessels L, Delorenzi M, Kopetz S, Vermeulen L, Tejpar S. The consensus molecular subtypes of colorectal cancer. Nat Med 2015;21:1350–6.
  • Fodde R. The APC gene in colorectal cancer. Eur J Cancer 2002;38: 867–71.
  • Fodde R, Smits R, Clevers H. APC, signal transduction and genetic instability in colorectal cancer. Nat Rev Cancer 2001;1:55–67.
  • Zhang L, Shay JW. Multiple roles of apc and its therapeutic implications in colorectal cancer. J Natl Cancer Ins 2017;109:djw332.
  • Du W-B, Lin C-H, Chen W-B. High expression of APC is an unfavorable prognostic biomarker in T4 gastric cancer patients. World J Gastroenterol 2019;25:4452–67.
  • Jorissen RN, Christie M, Mouradov D, Sakthianandeswaren A, Li S, Love C, Xu ZZ, Molloy PL, Jones JT, McLaughlin S, Ward RL, Hawkins NJ, Ruszkiewicz AR, Moore J, Burgess AW, Busam D, Zhao Q, Strausberg RL, Lipton L, Desai J, Gibbs P, Sieber OM. Wild-type APC predicts poor prognosis in microsatellite-stable proximal colon cancer. Br J Cancer 2015;113:979–88.
  • Katkoori VR, Suarez-Cuervo C, Shanmugam C, Jhala NC, Callens T, Messiaen L, Posey J 3rd, Bumpers HL, Meleth S, Grizzle WE, Manne U. Bax expression is a candidate prognostic and predictive marker of colorectal cancer. J Gastrointest Oncol 2010;1:76–89.
  • Pryczynicz A, Gryko M, Niewiarowska K, Cepowicz D, Ustymowicz M, Kemona A, Guzinska-Ustymowicz K. Bax protein may influence the invasion of colorectal cancer. World J Gastroenterol 2014;20: 1305–10.
  • Kasela M, Nyström M, Kansikas M. PMS2 expression decrease causes severe problems in mismatch repair. Hum Mutat 2019;40:904–7.
  • Lim DR, Kuk JK, Kim T, Shin EJ. Comparison of oncological outcomes of right-sided colon cancer versus left-sided colon cancer after curative resection: which side is better outcome? Medicine (Baltimore) 2017;96:e8241–e.
  • Nahas SC, Nahas CS, Bustamante-Lopez LA, Pinto RA, Marques CF, Campos FG, Cecconello I. Prognostic factors of surgicallytreated patients with cancer of the right colon: a ten years’ experience of a single universitary institution. Arq Bras Cir Dig 2017;30:103–7.
  • Zhao C, Li S, Zhao M, Zhu H, Zhu X. Prognostic values of DNA mismatch repair genes in ovarian cancer patients treated with platinum-based chemotherapy. Archives Gynecol Obstet 2018;297:153– 9.
  • van Alphen RJ, Wiemer EAC, Burger H, Eskens FALM. The spliceosome as target for anticancer treatment. Br J Cancer 2009;100:228–32.
  • Cervena K, Siskova A, Buchler T, Vodicka P, Vymetalkova V. Methylation-based therapies for colorectal cancer. Cells 2020;9: 1540.
  • Weekley CM, He C. Developing drugs targeting transition metal homeostasis. Curr Opin Chem Biol 2017;37:26–32.

Details

Primary Language English
Subjects Health Care Sciences and Services
Journal Section Original Articles
Authors

Can TÜRK (Primary Author)
LOKMAN HEKİM ÜNİVERSİTESİ, TIP FAKÜLTESİ
0000-0003-1514-7294
Türkiye

Publication Date April 29, 2021
Published in Issue Year 2021, Volume 15, Issue 1

Cite

Bibtex @research article { anatomy852318, journal = {Anatomy}, issn = {}, eissn = {1308-8459}, address = {}, publisher = {Turkish Society of Anatomy and Clinical Anatomy (TSACA)}, year = {2021}, volume = {15}, pages = {11 - 25}, doi = {}, title = {In silico transcriptomic analysis of ascending colon cancer unearths known and novel genes and gene sets regard to characteristic features of colon cancer}, key = {cite}, author = {Türk, Can} }
APA Türk, C. (2021). In silico transcriptomic analysis of ascending colon cancer unearths known and novel genes and gene sets regard to characteristic features of colon cancer . Anatomy , 15 (1) , 11-25 . Retrieved from https://dergipark.org.tr/en/pub/anatomy/issue/62417/852318
MLA Türk, C. "In silico transcriptomic analysis of ascending colon cancer unearths known and novel genes and gene sets regard to characteristic features of colon cancer" . Anatomy 15 (2021 ): 11-25 <https://dergipark.org.tr/en/pub/anatomy/issue/62417/852318>
Chicago Türk, C. "In silico transcriptomic analysis of ascending colon cancer unearths known and novel genes and gene sets regard to characteristic features of colon cancer". Anatomy 15 (2021 ): 11-25
RIS TY - JOUR T1 - In silico transcriptomic analysis of ascending colon cancer unearths known and novel genes and gene sets regard to characteristic features of colon cancer AU - Can Türk Y1 - 2021 PY - 2021 N1 - DO - T2 - Anatomy JF - Journal JO - JOR SP - 11 EP - 25 VL - 15 IS - 1 SN - -1308-8459 M3 - UR - Y2 - 2021 ER -
EndNote %0 Anatomy In silico transcriptomic analysis of ascending colon cancer unearths known and novel genes and gene sets regard to characteristic features of colon cancer %A Can Türk %T In silico transcriptomic analysis of ascending colon cancer unearths known and novel genes and gene sets regard to characteristic features of colon cancer %D 2021 %J Anatomy %P -1308-8459 %V 15 %N 1 %R %U
ISNAD Türk, Can . "In silico transcriptomic analysis of ascending colon cancer unearths known and novel genes and gene sets regard to characteristic features of colon cancer". Anatomy 15 / 1 (April 2021): 11-25 .
AMA Türk C. In silico transcriptomic analysis of ascending colon cancer unearths known and novel genes and gene sets regard to characteristic features of colon cancer. Anatomy. 2021; 15(1): 11-25.
Vancouver Türk C. In silico transcriptomic analysis of ascending colon cancer unearths known and novel genes and gene sets regard to characteristic features of colon cancer. Anatomy. 2021; 15(1): 11-25.
IEEE C. Türk , "In silico transcriptomic analysis of ascending colon cancer unearths known and novel genes and gene sets regard to characteristic features of colon cancer", Anatomy, vol. 15, no. 1, pp. 11-25, Apr. 2021

Anatomy is the official journal of Turkish Society of Anatomy and Clinical Anatomy (TSACA).