399
Views
0
CrossRef citations to date
0
Altmetric
Original Research

Proteomics and phosphoproteomics analysis of tissues for the reoccurrence prediction of colorectal cancer

ORCID Icon, , , , , , & ORCID Icon show all
Pages 263-277 | Received 18 Jan 2022, Accepted 07 Oct 2022, Published online: 05 Nov 2022

References

  • Bray F, Ferlay J, Soerjomataram I, et al. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2018;68(6):394–424.
  • Peltrini R, Sacco M, Luglio G, et al. Local excision following chemoradiotherapy in T2-T3 rectal cancer: current status and critical appraisal. Updates Surg. 2020;72(1):29–37.
  • Fischer J, Walker LC, Robinson BA, et al. Clinical implications of the genetics of sporadic colorectal cancer. ANZ J Surg. 2019;89(10):1224–1229.
  • Reece MM, Chapuis PH, Keshava A, et al. When does curatively treated colorectal cancer recur? An Australian perspective. ANZ J Surg. 2018;88(11):1163–1167.
  • van der Stok EP, Spaander M, Grunhagen DJ, et al. Surveillance after curative treatment for colorectal cancer. Nat Rev Clin Oncol. 2017;14(5):297–315.
  • Walker AS, Johnson EK, Maykel JA, et al. Future directions for the early detection of colorectal cancer recurrence. J Cancer. 2014;5(4):272–280.
  • Bockelman C, Engelmann BE, Kaprio T, et al. Risk of recurrence in patients with colon cancer stage II and III: a systematic review and meta-analysis of recent literature. Acta Oncol. 2015;54(1):5–16.
  • Rebuzzi SE, Pesola G, Martelli V, et al. Adjuvant chemotherapy for stage II colon cancer. Cancers (Basel). 2020;12(9):2584.
  • Kanwar SS, Poolla A, Majumdar AP, et al. Regulation of colon cancer recurrence and development of therapeutic strategies. World J Gastrointest Pathophysiol. 2012;3(1):1–9.
  • Patriarca S, Ferretti S, Zanetti R. TNM classification of malignant tumours - eighth edition: which news? Epidemiol Prev. 2017;41(2):140–143.
  • Ting WC, Chen LM, Pao JB, et al. Common genetic variants in Wnt signaling pathway genes as potential prognostic biomarkers for colorectal cancer. PLoS One. 2013;8(2):e56196.
  • Bupathi M, Wu C. Biomarkers for immune therapy in colorectal cancer: mismatch-repair deficiency and others. J Gastrointest Oncol. 2016;7(5):713–720.
  • Maguire A, Sheahan K. Controversies in the pathological assessment of colorectal cancer. World J Gastroenterol. 2014;20(29):9850–9861.
  • Dekker E, Tanis PJ, Vleugels J, et al. Colorectal cancer. Lancet. 2019;394(10207):1467–1480.
  • Abyadeh M, Meyfour A, Gupta V, et al. Recent advances of functional proteomics in gastrointestinal cancers- a path towards the identification of candidate diagnostic, prognostic, and therapeutic molecular biomarkers. Int J Mol Sci. 2020;21(22):8532.
  • Humphrey SJ, James DE, Mann M. Protein phosphorylation: a major switch mechanism for metabolic regulation. Trends Endocrinol Metab. 2015;26(12):676–687.
  • Surmen MG, Surmen S, Ali A, et al. Phosphoproteomic strategies in cancer research: a minireview. Analyst. 2020;145(22):7125–7149.
  • Singh V, Ram M, Kumar R, et al. Phosphorylation: implications in cancer. Protein J. 2017;36(1):1–6.
  • Chen Y, Wang F, Xu F, et al. Mass spectrometry-based protein quantification. Adv Exp Med Biol. 2016;919:255–279.
  • Di Falco MR. Mass spectrometry-based proteomics. Methods Mol Biol. 2018;1775:93–106.
  • Zhou H, Ye M, Dong J, et al. Robust phosphoproteome enrichment using monodisperse microsphere-based immobilized titanium (IV) ion affinity chromatography. Nat Protoc. 2013;8(3):461–480.
  • Wang Z, Chu H, Yang K, et al. Label-free quantitative proteomics analysis of the sorafenib resistance in hepg2 cells. J Anal Test. 2022;6(3):308–317.
  • Tyanova S, Temu T, Sinitcyn P, et al. The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat Methods. 2016;13(9):731–740.
  • Ruprecht B, Lemeer S. Proteomic analysis of phosphorylation in cancer. Expert Rev Proteomics. 2014;11(3):259–267.
  • Day EK, Sosale NG, Lazzara MJ. Cell signaling regulation by protein phosphorylation: a multivariate, heterogeneous, and context-dependent process. Curr Opin Biotechnol. 2016;40:185–192.
  • Gresko E, Ritterhoff S, Sevilla-Perez J, et al. PML tumor suppressor is regulated by HIPK2-mediated phosphorylation in response to DNA damage. Oncogene. 2009;28(5):698–708.
  • Li Y, Sun R, Zou J, et al. Dual roles of the AMP-activated protein kinase pathway in angiogenesis. Cells-Basel. 2019;8(7):752.
  • Colaert N, Helsens K, Martens L, et al. Improved visualization of protein consensus sequences by iceLogo. Nat Methods. 2009;6(11):786–787.
  • Sudol M, Hunter T. NeW wrinkles for an old domain. Cell. 2000;103(7):1001–1004.
  • Kops O, Zhou XZ, Lu KP. Pin1 modulates the dephosphorylation of the RNA polymerase II C-terminal domain by yeast Fcp1. FEBS Lett. 2002;513(2–3):305–311.
  • Roskoski RJ. ERK1/2 MAP kinases: structure, function, and regulation. Pharmacol Res. 2012;66(2):105–143.
  • Manning BD, Cantley LC. AKT/PKB signaling: navigating downstream. Cell. 2007;129(7):1261–1274.
  • Kramer A, Green J, Pollard JJ, et al. Causal analysis approaches in ingenuity pathway analysis. Bioinformatics. 2014;30(4):523–530.
  • Deng Y, Kurland BF, Wang J, et al. High epidermal growth factor receptor expression in metastatic colorectal cancer lymph nodes may be more prognostic of poor survival than in primary tumor. Am J Clin Oncol. 2009;32(3):245–252.
  • Kaczkowski B, Tanaka Y, Kawaji H, et al. Transcriptome analysis of recurrently deregulated genes across multiple cancers identifies new pan-cancer biomarkers. Cancer Res. 2016;76(2):216–226.
  • Li Y, Du H, Qin Y, et al. Activation of the signal transducers and activators of the transcription 3 pathway in alveolar epithelial cells induces inflammation and adenocarcinomas in mouse lung. Cancer Res. 2007;67(18):8494–8503.
  • Hever A, Roth RB, Hevezi PA, et al. Molecular characterization of human adenomyosis. Mol Hum Reprod. 2006;12(12):737–748.
  • Nomura T. Hidradenitis suppurativa as a potential subtype of autoinflammatory keratinization disease. Front Immunol. 2020;11:847.
  • Fujinaga K. P-TEFb as A promising therapeutic target. Molecules. 2020;25(4):838.
  • Kaur A, Westermarck J. Regulation of protein phosphatase 2A (PP2A) tumor suppressor function by PME-1. Biochem Soc Trans. 2016;44(6):1683–1693.
  • Dacol EC, Wang S, Chen Y, et al. The interaction of SET and protein phosphatase 2A as target for cancer therapy. Biochim Biophys Acta Rev Cancer. 2021;1876(1):188578.
  • Patrao AS, Dias F, Teixeira AL, et al. XPO5 genetic polymorphisms in cancer risk and prognosis. Pharmacogenomics. 2018;19(9):799–808.
  • Zhou W, Li J, Lu X, et al. Derivation and validation of a prognostic model for cancer dependency genes based on CRISPR-Cas9 in gastric adenocarcinoma. Front Oncol. 2021;11:617289.
  • Wang P, Zheng H, Zhang J, et al. Identification of key gene modules and genes in colorectal cancer by co-expression analysis weighted gene co-expression network analysis. Biosci Rep. 2020;40(9):R20202044.
  • Chen R, Zhu J, Dong Y, et al. Suppressor of Ty homolog-5, a novel tumor-specific human telomerase reverse transcriptase promoter-binding protein and activator in colon cancer cells. Oncotarget. 2015;6(32):32841–32855.
  • Ceccarelli DF, Ivantsiv S, Mullin AA, et al. FAM105A/OTULINL is a pseudodeubiquitinase of the OTU-Class that localizes to the ER membrane. Structure. 2019;27(6):1000–1012.
  • Veiga-da-Cunha M, Chevalier N, Stroobant V, et al. Metabolite proofreading in carnosine and homocarnosine synthesis: molecular identification of PM20D2 as beta-alanyl-lysine dipeptidase. J Biol Chem. 2014;289(28):19726–19736.
  • Pawlowski KM, Maciejewski H, Majchrzak K, et al. Five markers useful for the distinction of canine mammary malignancy. BMC Vet Res. 2013;9:138.
  • Naik S, Dothager RS, Marasa J, et al. Vascular endothelial growth factor receptor-1 is synthetic lethal to aberrant {beta}-catenin activation in colon cancer. Clin Cancer Res. 2009;15(24):7529–7537.
  • Ardeljan D, Taylor MS, Ting DT, et al. The human long interspersed element-1 retrotransposon: an emerging biomarker of neoplasia. Clin Chem. 2017;63(4):816–822.
  • Crawford NP, Yang H, Mattaini KR, et al. The metastasis efficiency modifier ribosomal RNA processing 1 homolog B (RRP1B) is a chromatin-associated factor. J Biol Chem. 2009;284(42):28660–28673.
  • McCann TS, Parrish JK, Hsieh J, et al. KDM5A and PHF2 positively control expression of pro-metastatic genes repressed by EWS/Fli1, and promote growth and metastatic properties in Ewing sarcoma. Oncotarget. 2020;11(43):3818–3831.
  • Ma F, Bi L, Yang G, et al. ZNF703 promotes tumor cell proliferation and invasion and predicts poor prognosis in patients with colorectal cancer. Oncol Rep. 2014;32(3):1071–1077.
  • Walter SA, Cutler RJ, Martinez R, et al. Stk10, a new member of the polo-like kinase kinase family highly expressed in hematopoietic tissue. J Biol Chem. 2003;278(20):18221–18228.
  • Zheng X, Xu H, Gong L, et al. Vinculin orchestrates prostate cancer progression by regulating tumor cell invasion, migration, and proliferation. Prostate. 2021;81(6):347–356.
  • Mussazhanova Z, Akazawa Y, Matsuda K, et al. Association between p53-binding protein 1 expression and genomic instability in oncocytic follicular adenoma of the thyroid. Endocr J. 2016;63(5):457–467.
  • Ranjpour M, Wajid S, Jain SK. Elevated expression of sepiapterin reductase, regulator of G protein signaling 1, hypothetical protein CXorf58 homolog, and zinc finger and BTB domain-containing protein 21 isoform X2 is associated with progression of hepatocellular carcinoma. Protoplasma. 2021;258(5):1133–1143.
  • Notas G, Kampa M, Pelekanou V, et al. Whole transcriptome analysis of the ERalpha synthetic fragment P295-T311 (ERalpha17p) identifies specific ERalpha-isoform (ERalpha, ERalpha36)-dependent and -independent actions in breast cancer cells. Mol Oncol. 2013;7(3):595–610.
  • Lawson JS, Field AS, Champion S, et al. Low oestrogen receptor alpha expression in normal breast tissue underlies low breast cancer incidence in Japan. Lancet. 1999;354(9192):1787–1788.
  • Sun Z, Ou C, Liu J, et al. YAP1-induced MALAT1 promotes epithelial-mesenchymal transition and angiogenesis by sponging miR-126-5p in colorectal cancer. Oncogene. 2019;38(14):2627–2644.
  • Foster CT, Gualdrini F, Treisman R. Mutual dependence of the MRTF-SRF and YAP-TEAD pathways in cancer-associated fibroblasts is indirect and mediated by cytoskeletal dynamics. Genes Dev. 2017;31(23–24):2361–2375.
  • De Roock W, De Vriendt V, Normanno N, et al. BRAF, PIK3CA, and PTEN mutations: implications for targeted therapies in metastatic colorectal cancer. Lancet Oncol. 2011;12(6):594–603.
  • Gerritsen ME, Tomlinson JE, Zlot C, et al. Using gene expression profiling to identify the molecular basis of the synergistic actions of hepatocyte growth factor and vascular endothelial growth factor in human endothelial cells. Br J Pharmacol. 2003;140(4):595–610.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.