Analysis of TGCA Data Reveals Genetic and Epigenetic Changes and Biological Function of MUC Family Genes in Colorectal Cancer

References

• Ferlay J , SoerjomatarmI, DikshitRet al. Cancer incidence and mortality worldwide: sources, methods and major patterns in GLOBOCAN 2012. Int. J. Cancer136(5), E359–E386 (2015).
   PubMed Web of Science ®Google Scholar
• Fagunwa IO , LoughreyMB, ColemanHG. Alcohol, smoking and the risk of premalignant and malignant colorectal neoplasms. Best Pract. Res. Clin. Gastroenterol.31(5), 561–568 (2017).
   PubMed Web of Science ®Google Scholar
• Boada LD , Henríquez-HernándezLA, LuzardoOP. The impact of red and processed meat consumption on cancer and other health outcomes: epidemiological evidences. Food Chem. Toxicol.92, 236–244 (2016).
   PubMed Web of Science ®Google Scholar
• Brevik A , JoshiAD, CorralR, Onland-MoretNCet al. Polymorphisms in base excision repair genes as colorectal cancer risk factors and modifiers of the effect of diets high in red meat. Cancer Epi. Prev. Biomarkers19(12), 3167–3173 (2010).
   PubMed Web of Science ®Google Scholar
• de Voer RM , van KesselAG, WerenRDet al. Germline mutations in the spindle assembly checkpoint genes BUB1 and BUB3 are risk factors for colorectal cancer. Gastroenterology145(3), 544–547 (2013).
   PubMed Web of Science ®Google Scholar
• Kambara T , SimmsLA, WhitehallVet al. BRAF mutation is associated with DNA methylation in serrated polyps and cancers of the colorectum. Gut53(8), 1137–1144 (2004).
   PubMed Web of Science ®Google Scholar
• Imai Y , YamagishiH, FukudaKet al. Differential mucin phenotypes and their significance in a variation of colorectal carcinoma. World J. Gastroenterol.19(25), 3957 (2013).
   PubMed Web of Science ®Google Scholar
• Boltin D , PeretsTT, VilkinAet al. Mucin function in inflammatory bowel disease: an update. J. Clin. Gastroenterol.47(2), 106–111 (2013).
   PubMed Web of Science ®Google Scholar
• Bhatia R , GautamSK, CannonAet al. Cancer-associated mucins: role in immune modulation and metastasis. Cancer Metast. Rev.38(1–2), 223–236 (2019).
   PubMed Web of Science ®Google Scholar
• Shanmugam C , JhalaNC, KatkooriVRet al. Prognostic value of mucin 4 expression in colorectal adenocarcinomas. Cancer116(15), 3577–3586 (2010).
   PubMed Web of Science ®Google Scholar
• Soliman BG , KaragkounisG, ChurchJMet al. Mucinous histology signifies poor oncologic outcome in young patients with colorectal cancer. Dis. Colon Rectum61(5), 547–553 (2018).
   PubMed Web of Science ®Google Scholar
• Ham SY , KwonT, BakYet al. Mucin 1-mediated chemo-resistance in lung cancer cells. Oocogenesis5(1), e185 (2016).
   PubMedGoogle Scholar
• Takahashi H , JinC, RajabiHet al. MUC1-C activates the TAK1 inflammatory pathway in colon cancer. Oncogene34(40), 5187 (2015).
   PubMed Web of Science ®Google Scholar
• Gupta B , DasP, GhoshSet al. Identification of high-risk aberrant crypt foci and mucin-depleted foci in the human colon with study of colon cancer stem cell markers. Clin. Colorectal Cancer16(3), 204–213 (2017).
   PubMed Web of Science ®Google Scholar
• Lahdaoui F , MessagerM, VincentAet al. Depletion of MUC5B mucin in gastrointestinal cancer cells alters their tumorigenic properties: implication of the Wnt/β-catenin pathway. Biochem. J.474(22), 3733–3746 (2017).
   PubMedGoogle Scholar
• Thériault C , PinardM, ComamalaMet al. MUC16 (CA125) regulates epithelial ovarian cancer cell growth, tumorigenesis and metastasis. Gynecol. Oncol.121(3), 434–443 (2011).
   PubMed Web of Science ®Google Scholar
• Sanchez-Vega F , MinaM, ArmeniaJet al. Oncogenic signaling pathways in the cancer genome atlas. Cell73(2), 321–337 (2018).
   Google Scholar
• Ritchie ME , PhipsonB, WuDet al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res.43(7), e47 (2015).
   PubMed Web of Science ®Google Scholar
• Ha G , ShahS. Distinguishing somatic and germline copy number events in cancer patient DNA hybridized to whole-genome SNP genotyping arrays. Methods Mol. Biol.973, 355–372 (2013).
   PubMedGoogle Scholar
• Hochberg Y , BenjaminiY. More powerful procedures for multiple significance testing. Stat. Med.9(7), 811–818 (1990).
   PubMed Web of Science ®Google Scholar
• Hinoue T , WeisenbergerDJ, LangeCPet al. Genome-scale analysis of aberrant DNA methylation in colorectal cancer. Genome Res.22(2), 271–282 (2012).
   PubMed Web of Science ®Google Scholar
• Langfelder P , HorvathS. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics9(1), 559 (2008).
   PubMed Web of Science ®Google Scholar
• Zhang B , HorvathS. A general framework for weighted gene co-expression network analysis. Stat. Appl. Genet. Mol.4(1), 1–43 (2005).
   Google Scholar
• Johansson ME , HanssonGC. Immunological aspects of intestinal mucus and mucins. Nat. Rev. Immunol.16(10), 639 (2016).
   PubMed Web of Science ®Google Scholar
• Sheng YH , LourieR, LindénSKet al. The MUC13 cell-surface mucin protects against intestinal inflammation by inhibiting epithelial cell apoptosis. Gut60(12), 1661–1670 (2011).
   PubMed Web of Science ®Google Scholar
• Gupta BK , MaherDM, EbelingMCet al. Functions and regulation of MUC13 mucin in colon cancer cells. J. Gastroenterol.49(10), 1378–1391 (2014).
   PubMed Web of Science ®Google Scholar
• van der Sluis M , de KoningBA, de BruijnACet al. Muc2-deficient mice spontaneously develop colitis, indicating that MUC2 is critical for colonic protection. Gastroenterology131(1), 117–129 (2006).
   PubMed Web of Science ®Google Scholar
• Betge J , SchneiderNI, HarbaumLet al. MUC1, MUC2, MUC5AC, and MUC6 in colorectal cancer: expression profiles and clinical significance. Virchows Arch.469(3), 255–265 (2016).
   PubMed Web of Science ®Google Scholar
• Hattrup CL , GendlerSJ. Structure and function of the cell surface (tethered) mucins. Annu. Rev. Physiol.70, 431–457 (2008).
   PubMed Web of Science ®Google Scholar
• Jonckheere N , Van SeuningenI. Integrative analysis of the cancer genome atlas and cancer cell lines encyclopedia large-scale genomic databases: MUC4/MUC16/MUC20 signature is associated with poor survival in human carcinomas. J. Transl. Med.16(1), 259 (2018).
   PubMedGoogle Scholar
• Haridas D , ChakrabortyS, PonnusamyMPet al. Pathobiological implications of MUC16 expression in pancreatic cancer. PLoS ONE6(10), e26839 (2011).
   PubMed Web of Science ®Google Scholar
• Li X , PascheB, ZhangWet al. Association of MUC16 mutation with tumor mutation load and outcomes in patients with gastric cancer. JAMA Oncol.4(12), 1691–1698 (2018).
   PubMed Web of Science ®Google Scholar
• Albrecht H , CarrawayIII KL. MUC1 and MUC4: switching the emphasis from large to small. Cancer Biother. Radiopharm.26(3), 61–271 (2011).
   Web of Science ®Google Scholar
• Shanmugam C , JhalaNC, KatkooriVRet al. Prognostic value of mucin 4 expression in colorectal adenocarcinomas. Cancer116(15), 3577–3586 (2010).
   PubMed Web of Science ®Google Scholar
• Wang W , ChenJ, ZhaoFet al. MiR-150-5p suppresses colorectal cancer cell migration and invasion through targeting MUC4. Asian Pac. J. Cancer Prev.15(15), 6269–6273 (2014).
   PubMedGoogle Scholar
• Peng QL , RenJ, YanXMet al. The g. 243A> G mutation in intron 17 of MUC4 is significantly associated with susceptibility/resistance to ETEC F4ab/ac infection in pigs. Anim. Genet.38(4), 397–400 (2007).
   PubMed Web of Science ®Google Scholar
• Okudaira K , KakarS, CunLet al. MUC2 gene promoter methylation in mucinous and non-mucinous colorectal cancer tissues. Int. J. Oncol.36(4), 765–775 (2010).
   PubMed Web of Science ®Google Scholar
• Tang J , ZhangL, SheXet al. Inhibiting CD164 expression in colon cancer cell line HCT116 leads to reduced cancer cell proliferation, mobility, and metastasis in vitro and in vivo. Cancer Invest.30(5), 380–389 (2012).
   PubMed Web of Science ®Google Scholar
• McManus S , ChababiW, ArsenaultDet al. Dissecting oncogenic RTK pathways in colorectal cancer initiation and progression. Methods Mol. Biol.1765, 27–42 (2018).
   PubMedGoogle Scholar
• Masliah-Planchon J , GarinetS, PasmantE. RAS-MAPK pathway epigenetic activation in cancer: miRNAs in action. Oncotarget7(25), 38892 (2016).
   PubMedGoogle Scholar
• Dubois F , LeroyC, SimonVet al. YES oncogenic activity is specified by its SH4 domain and regulates RAS/MAPK signaling in colon carcinoma cells. Am. J. Cancer Res.5(6), 1972 (2015).
   PubMed Web of Science ®Google Scholar
• Jiang H , WangY, AiMet al. Long noncoding RNA CRNDE stabilized by hnRNPUL2 accelerates cell proliferation and migration in colorectal carcinoma via activating Ras/MAPK signaling pathways. Cell Death Dis.8(6), e2862 (2017).
   PubMedGoogle Scholar
• Yokoyama S , HigashiM, TsutsumidaHet al. TET1-mediated DNA hypomethylation regulates the expression of MUC4 in lung cancer. Genes Cancer8(3–4), 517 (2017).
   PubMedGoogle Scholar
• Cho JS , ParkMH, LeeJSet al. Reduced MUC4 expression is a late event in breast carcinogenesis and is correlated with increased infiltration of immune cells as well as promoter hypermethylation in invasive breast carcinoma. Appl. Immunohisto. Mol. Morphol.23(1), 44–53 (2015).
   Web of Science ®Google Scholar