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Research Article

Five genes identified as prognostic markers for colorectal cancer through the integration of genome-wide association study and expression quantitative trait loci data

ORCID Icon, , , , , & ORCID Icon show all
Received 14 Sep 2023, Accepted 30 Jan 2024, Published online: 21 Feb 2024

References

  • Siegel RL, Miller KD, Goding Sauer A et al. Colorectal cancer statistics. CA Cancer J. Clin. 70(3), 145–164 (2020).
  • Lu Y, Kweon SS, Tanikawa C et al. Large-scale genome-wide association study of east Asians identifies loci associated with risk for colorectal cancer. Gastroenterology 156(5), 1455–1466 (2019).
  • Huyghe JR, Bien SA, Harrison TA et al. Discovery of common and rare genetic risk variants for colorectal cancer. Nat. Genet. 51(1), 76–87 (2019).
  • Guo X, Lin W, Wen W et al. Identifying novel susceptibility genes for colorectal cancer risk from a transcriptome-wide association study of 125,478 subjects. Gastroenterology 160(4), 1164–1178 (2021).
  • Schaid DJ, Chen W, Larson NB. From genome-wide associations to candidate causal variants by statistical fine-mapping. Nat. Rev. Genet. 19(8), 491–504 (2018).
  • Nodzak C. Introductory methods for eQTL analyses. Methods Mol. Biol. 2082, 3–14 (2020).
  • Li L, Zhang X, Zhao H. eQTL. Methods Mol. Biol. 871, 265–279 (2012).
  • Emdin CA, Khera AV, Kathiresan S. Mendelian randomization. JAMA 318(19), 1925–1926 (2017).
  • Bowden J, Holmes MV. Meta-analysis and Mendelian randomization: a review. Res. Synth. Methods 10(4), 486–496 (2019).
  • Wu Y, Zeng J, Zhang F et al. Integrative analysis of omics summary data reveals putative mechanisms underlying complex traits. Nat. Commun. 9(1), 918 (2018).
  • Davey Smith G, Hemani G. Mendelian randomization: genetic anchors for causal inference in epidemiological studies. Hum. Mol. Genet. 23(R1), R89–R98 (2014).
  • Thanassoulis G, O'Donnell CJ. Mendelian randomization: nature's randomized trial in the post-genome era. JAMA 301(22), 2386–2388 (2009).
  • Burgess S, Timpson NJ, Ebrahim S et al. Mendelian randomization: where are we now and where are we going? Int. J. Epidemiol. 44(2), 379–388 (2015).
  • Zhu Z, Zhang F, Hu H et al. Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets. Nat. Genet. 48(5), 481–487 (2016).
  • Ishigaki K, Akiyama M, Kanai M et al. Large-scale genome-wide association study in a Japanese population identifies novel susceptibility loci across different diseases. Nat. Genet. 52(7), 669–679 (2020).
  • Lloyd-Jones LR, Holloway A, McRae A et al. The genetic architecture of gene expression in peripheral blood. Am. J. Hum. Genet. 100(2), 228–237 (2017).
  • GTEx Consortium. The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science 369(6509), 1318–1330 (2020).
  • Zhou Y, Zhou B, Pache L et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat. Commun. 10(1), 1523 (2019).
  • Tang Z, Li C, Kang B et al. GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses. Nucleic Acids Res. 45(W1), W98–W102 (2017).
  • Tomczak K, Czerwińska P, Wiznerowicz M. The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge. Contemp. Oncol. (Pozn.) 19(1A), A68–A77 (2015).
  • Wei J, Huang K, Chen Z et al. Characterization of Glycolysis-Associated Molecules in the Tumor Microenvironment Revealed by Pan-Cancer Tissues and Lung Cancer Single Cell Data. Cancer (Basel). 12(7), 1788 (2020).
  • Bruntz RC, Lindsley CW, Brown HA. Phospholipase D signaling pathways and phosphatidic acid as therapeutic targets in cancer. Pharmacol. Rev. 66(4), 1033–1079 (2014).
  • Wagner N, Wagner KD. The role of PPARs in disease. Cells 9(11), 2367 (2020).
  • Currie E, Schulze A, Zechner R et al. Cellular fatty acid metabolism and cancer. Cell Metab. 18(2), 153–161 (2013).
  • Wan Q, Tang J, Han Y et al. Co-expression modules construction by WGCNA and identify potential prognostic markers of uveal melanoma. Exp. Eye Res. 166, 13–20 (2018).
  • Bousquet M, Nguyen D, Chen C et al. MicroRNA-125b transforms myeloid cell lines by repressing multiple mRNA. Haematologica 97(11), 1713–1721 (2012).
  • Li Y, Wang H, Pan Y et al. Identification of bicalutamide resistance-related genes and prognosis prediction in patients with prostate cancer. Front Endocrinol. (Lausanne) 14, 1125299 (2023).
  • Li F, Chen L, Zheng J et al. Mechanism of Gegen Qinlian decoction regulating ABTB1 expression in colorectal cancer metastasis based on PI3K/AKT/FOXO1 pathway. Biomed. Res. Int. 2022, 8131531 (2022).
  • Huang L, Zhang Y, Li Z et al. MiR-4319 suppresses colorectal cancer progression by targeting ABTB1. United European Gastroenterol. J. 7(4), 517–528 (2019).
  • Simonetti L, Bruque CD, Fernández CS et al. CYP21A2 mutation update: comprehensive analysis of databases and published genetic variants. Hum. Mutat. 39(1), 5–22 (2018).
  • Guo Y, Rehati A, Wu Z et al. A novel function of CYP21A2 in regulating cell migration and invasion via Wnt signaling. Gen. Physiol. Biophys. 39(4), 373–381 (2020).
  • Yuan Z, Li Y, Zhang S et al. Extracellular matrix remodeling in tumor progression and immune escape: from mechanisms to treatments. Mol. Cancer 22(1), 48 (2023).
  • Eble JA, Niland S. The extracellular matrix in tumor progression and metastasis. Clin. Exp. Metastasis 36(3), 171–198 (2019).
  • Tryggvason K, Höyhtyä M, Salo T. Proteolytic degradation of extracellular matrix in tumor invasion. Biochim. Biophys. Acta 907(3), 191–217 (1987).
  • Brabletz T, Kalluri R, Nieto MA et al. EMT in cancer. Nat. Rev. Cancer 18(2), 128–134 (2018).
  • Aiello NM, Kang Y. Context-dependent EMT programs in cancer metastasis. J. Exp. Med. 216(5), 1016–1026 (2019).
  • Gugnoni M, Sancisi V, Gandolfi G et al. Cadherin-6 promotes EMT and cancer metastasis by restraining autophagy. Oncogene 36(5), 667–677 (2017).
  • Cao ZQ, Wang Z, Leng P. Aberrant N-cadherin expression in cancer. Biomed. Pharmacother. 118, 109320 (2019).
  • Ma J, Zhao J, Lu J et al. Cadherin-12 enhances proliferation in colorectal cancer cells and increases progression by promoting EMT. Tumour Biol. 37(7), 9077–9088 (2016).
  • Batlle E, Massagué J. Transforming growth factor-β signaling in immunity and cancer. Immunity 50(4), 924–940 (2019).
  • Jung B, Staudacher JJ, Beauchamp D. Transforming growth factor β superfamily signaling in development of colorectal cancer. Gastroenterology 152(1), 36–52 (2017).
  • Zhong FL, Mamaï O, Sborgi L et al. Germline NLRP1 mutations cause skin inflammatory and cancer susceptibility syndromes via inflammasome activation. Cell 167(1), 187–202.e17 (2016).
  • Bauernfried S, Scherr MJ, Pichlmair A et al. Human NLRP1 is a sensor for double-stranded RNA. Science 371(6528), eabd0811 (2021).
  • Man SM, Kanneganti TD. Regulation of inflammasome activation. Immunol. Rev. 265(1), 6–21 (2015).
  • Barnett KC, Li S, Liang K et al. A 360° view of the inflammasome: mechanisms of activation, cell death, and diseases. Cell 186(11), 2288–2312 (2023).
  • Sharma BR, Kanneganti TD. NLRP3 inflammasome in cancer and metabolic diseases. Nat. Immunol. 22(5), 550–559 (2021).
  • Karki R, Man SM, Kanneganti TD. Inflammasomes and cancer. Cancer Immunol. Res. 5(2), 94–99 (2017).
  • Shen E, Han Y, Cai C et al. Low expression of NLRP1 is associated with a poor prognosis and immune infiltration in lung adenocarcinoma patients. Aging (Albany NY) 13(5), 7570–7588 (2021).
  • Dey Sarkar R, Sinha S, Biswas N. Manipulation of inflammasome: a promising approach towards immunotherapy of lung cancer. Int. Rev. Immunol. 40(3), 171–182 (2021).
  • Sharma BR, Kanneganti TD. Inflammasome signaling in colorectal cancer. Transl. Res. 252, 45–52 (2023).
  • Liu R, Truax AD, Chen L et al. Expression profile of innate immune receptors, NLRs and AIM2, in human colorectal cancer: correlation with cancer stages and inflammasome components. Oncotarget 6(32), 33456–33469 (2015).
  • Kishnani PS, Goldstein J, Austin SL et al. Diagnosis and management of glycogen storage diseases type VI and IX: a clinical practice resource of the American College of Medical Genetics and Genomics (ACMG). Genet. Med. 21(4), 772–789 (2019).
  • Jarrar Y, Zihlif M, Al Bawab AQ et al. Effects of intermittent hypoxia on expression of glucose metabolism genes in MCF7 breast cancer cell line. Curr. Cancer Drug Targets 20(3), 216–222 (2020).
  • Katsuta E, Huyser M, Yan L et al. A prognostic score based on long-term survivor unique transcriptomic signatures predicts patient survival in pancreatic ductal adenocarcinoma. Am. J. Cancer Res. 11(9), 4294–4307 (2021).
  • Peng JM, Lin SH, Yu MC et al. CLIC1 recruits PIP5K1A/C to induce cell-matrix adhesions for tumor metastasis. J. Clin. Invest. 131(1), e133525 (2021).
  • Yu X, Zhang Y, Xiong S et al. Omics analyses of a somatic Trp53R245W/+ breast cancer model identify cooperating driver events activating PI3K/AKT/mTOR signaling. Proc. Natl Acad. Sci. USA 119(45), e2210618119 (2022).
  • Xu W, Wang P, Petri B et al. Integrin-induced PIP5K1C kinase polarization regulates neutrophil polarization, directionality, and in vivo infiltration. Immunity 33(3), 340–350 (2010).

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