199
Views
1
CrossRef citations to date
0
Altmetric
Review

Proteogenomic examination of esophageal squamous cell carcinoma (ESCC): new lines of inquiry

, , , , &
Pages 649-662 | Received 31 Aug 2020, Accepted 29 Oct 2020, Published online: 17 Dec 2020

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.
  • Ferlay J, Colombet M, Soerjomataram I, et al. Estimating the global cancer incidence and mortality in 2018: GLOBOCAN sources and methods. Int J Cancer. 2019;144(8):1941–1953.
  • Chang JT, Katzka DA. Gastroesophageal reflux disease, Barrett esophagus, and esophageal adenocarcinoma. Arch Intern Med. 2004;164(14):1482–1488.
  • Nesvizhskii AI. Proteogenomics: concepts, applications and computational strategies. Nat Methods. 2014;11(11):1114–1125.
  • Renuse S, Chaerkady R, Pandey A. Proteogenomics. Proteomics. 2011 Feb;11(4):620–630.
  • Mertins P, Mani DR, Ruggles KV, et al. Proteogenomics connects somatic mutations to signalling in breast cancer. Nature. 2016;534(7605):55–62.
  • Ali HR, Rueda OM, Chin SF, et al. Genome-driven integrated classification of breast cancer validated in over 7,500 samples. Genome Biol. 2014;15(8):431.
  • Talseth-Palmer BA, Scott RJ. Genetic variation and its role in malignancy. Int J Biomed Sci. 2011;7(3):158–171.
  • Pawar H, Kashyap MK, Sahasrabuddhe NA, et al. Quantitative tissue proteomics of esophageal squamous cell carcinoma for novel biomarker discovery. Cancer Biol Ther. 2011;12(6):510–522.
  • Mir SA, Rajagopalan P, Jain AP, et al. LC-MS-based serum metabolomic analysis reveals dysregulation of phosphatidylcholines in esophageal squamous cell carcinoma. J Proteomics. 2015;127(Pt A):96–102.
  • Kashyap MK, Harsha HC, Renuse S, et al. SILAC-based quantitative proteomic approach to identify potential biomarkers from the esophageal squamous cell carcinoma secretome. Cancer Biol Ther. 2010;10(8):796–810.
  • Schwacke J, Millar TP, Hammond CE, et al. Discrimination of normal and esophageal cancer plasma proteomes by MALDI-TOF mass spectrometry. Dig Dis Sci. 2015;60(6):1645–1654.
  • Wang LD, Wang DC, Zheng S, et al. Serum proteomic profiles of the subjects with esophageal precancerous and cancerous lesions from Linzhou, an area with high incidence of esophageal cancer in Henan Province, Northern China. Ai Zheng. 2006;25(5):549–554.
  • Uemura N, Nakanishi Y, Kato H, et al. Antibody-based proteomics for esophageal cancer: identification of proteins in the nuclear factor-kappaB pathway and mitotic checkpoint. Cancer Sci. 2009a;100(9):1612–1622.
  • Qi YJ, He QY, Ma YF, et al. Proteomic identification of malignant transformation-related proteins in esophageal squamous cell carcinoma. J Cell Biochem. 200;104(5):1625–1635.
  • Nishimori T, Tomonaga T, Matsushita K, et al. Proteomic analysis of primary esophageal squamous cell carcinoma reveals downregulation of a cell adhesion protein, periplakin. Proteomics. 2006;6(3):1011–1018.
  • Katoh Y, Katoh M. Comparative integromics on Ephrin family. Oncol Rep. 2006;15(5):1391–1395.
  • Zhang Y. Epidemiology of esophageal cancer. World J Gastroenterol. 2013;19(34):5598–5606.
  • Zhao J, Fan YX, Yang Y, et al. Identification of potential plasma biomarkers for esophageal squamous cell carcinoma by a proteomic method. Int J ClinExpPathol. 2015;8(2):1535–1544.
  • Wang X, Peng Y, Xie M, et al. Identification of extracellular matrix protein 1 as a potential plasma biomarker of ESCC by proteomic analysis using iTRAQ and 2D-LC-MS/MS. Proteomics Clin Appl.. 2017;11(9–10):1600163.
  • Nambu M, Masuda T, Ito S, et al. Leucine-rich alpha-2-glycoprotein 1 in serum is a possible biomarker to predict response to preoperative chemoradiotherapy for esophageal cancer. Biol Pharm Bull. 2019;42(10):1766–1771.
  • Zhai XH, Yu JK, Lin C, et al. Combining proteomics, serum biomarkers and bioinformatics to discriminate between esophageal squamous cell carcinoma and pre-cancerous lesion. J Zhejiang UnivSci B. 2012;13(12):964–971.
  • Xu SY, Liu Z, Ma WJ, et al. New potential biomarkers in the diagnosis of esophageal squamous cell carcinoma. Biomarkers. 2009;14(5):340–346.
  • Liu WL, Zhang G, Wang JY, et al. Proteomics-based identification of autoantibody against CDC25B as a novel serum marker in esophageal squamous cell carcinoma. Biochem Biophys Res Commun. 2008;375(3):440–445.
  • Fujita Y, Nakanishi T, Miyamoto Y, et al. Proteomics-based identification of autoantibody against heat shock protein 70 as a diagnostic marker in esophageal squamous cell carcinoma. Cancer Lett. 2008;263(2):280–290.
  • Fujita Y, Nakanishi T, Hiramatsu M, et al. Proteomics-based approach identifying autoantibody against peroxiredoxin VI as a novel serum marker in esophageal squamous cell carcinoma. Clin Cancer Res. 2006;12(21):6415–6420.
  • An JY, Fan ZM, Zhuang ZH, et al. Proteomic analysis of blood level of proteins before and after operation in patients with esophageal squamous cell carcinoma at high-incidence area in henan province. World J Gastroenterol. 2004;10(22):3365–3368.
  • Ma XL, Yao H, Wang X, et al. ILK predicts the efficacy of chemoradiotherapy and the prognosis of patients with esophageal squamous cell carcinoma. Oncol Lett. 2019;18(4):4114–4125.
  • Qi Y, Chiu JF, Wang L, et al. Comparative proteomic analysis of esophageal squamous cell carcinoma. Proteomics. 2005;5(11):2960–2971.
  • Du XL, Hu H, Lin DC, et al. Proteomic profiling of proteins dysregulted in Chinese esophageal squamous cell carcinoma. J Mol Med (Berl). 2007;85(8):863–875.
  • Hatakeyama H, Kondo T, Fujii K, et al. Protein clusters associated with carcinogenesis, histological differentiation and nodal metastasis in esophageal cancer. Proteomics. 2006;6(23):6300–6316.
  • Ning Z, Zhu X, Jiang Y, et al. Integrin-linked kinase is involved in the proliferation and invasion of esophageal squamous cell carcinoma. J Cancer. 2020;11(2):324–333.
  • Yu SB, Gao Q, Lin WW, et al. Proteomic analysis indicates the importance of TPM3 in esophageal squamous cell carcinoma invasion and metastasis. Mol Med Rep. 2017;15(3):1236–1242.
  • Deng F, Zhou K, Li Q, et al. iTRAQ-based quantitative proteomic analysis of esophageal squamous cell carcinoma. Tumour Biol. 2016;37(2):1909–1918.
  • Xu X, Song C, Chen Z, et al. Downregulation of HuR inhibits the progression of esophageal cancer through interleukin-18. Cancer Res Treat. 2018;50(1):71–87.
  • Mrena J, Wiksten JP, Thiel A, et al. Cyclooxygenase-2 is an independent prognostic factor in gastric cancer and its expression is regulated by the messenger RNA stability factor HuR. Clin Cancer Res. 2005;11(20):7362–7368.
  • Denkert C, Koch I, von Keyserlingk N, et al. Expression of the ELAV-like protein HuR in human colon cancer: association with tumor stage and cyclooxygenase-2. Mod Pathol. 2006;19(9):1261–1269.
  • Heinonen M, Fagerholm R, Aaltonen K, et al. Prognostic role of HuR in hereditary breast cancer. Clin Cancer Res. 2007;13(23):6959–6963.
  • Williams TK, Costantino CL, Bildzukewicz NA, et al. pp32 (ANP32A) expression inhibits pancreatic cancer cell growth and induces gemcitabine resistance by disrupting HuR binding to mRNAs. PLoS One. 2010;5(11):e15455.
  • Romeo C, Weber MC, Zarei M, et al. HuR contributes to TRAIL resistance by restricting death receptor 4 expression in pancreatic cancer cells. Mol Cancer Res. 2016;14(7):599–611.
  • Latorre E, Tebaldi T, Viero G, et al. Downregulation of HuR as a new mechanism of doxorubicin resistance in breast cancer cells. Mol Cancer. 2012;11:13.
  • Zhang J, Zhi C, Zhen F, et al. iTRAQ-based quantitative proteomic analyses of high grade esophageal squamous intraepithelial neoplasia. Proteomics Clin Appl. 2017;11:11–12.
  • Pawar H, Maharudraiah J, Kashyap MK, et al. Downregulation of cornulin in esophageal squamous cell carcinoma. ActaHistochem. 2013;115(2):89–99.
  • Chen K, Li Y, Dai Y, et al. Characterization of tumor suppressive function of cornulin in esophageal squamous cell carcinoma. PLoS One. 2013;8(7):e68838.
  • Hsu PK, Kao HL, Chen HY, et al. Loss of CRNN expression is associated with advanced tumor stage and poor survival in patients with esophageal squamous cell carcinoma. J ThoracCardiovasc Surg. 2014;147(5):1612–1618 e4.
  • Feng JG, Liu Q, Qin X, et al. Clinicopathological pattern and Annexin A2 and Cdc42 status in patients presenting with differentiation and lymphnode metastasis of esophageal squamous cell carcinomas. MolBiol Rep. 2012;39(2):1267–1274.
  • Qi YJ, Wang LD, Jiao XY, et al. Dysregulation of Annexin II expression in esophageal squamous cell cancer and adjacent tissues from a high-incidence area for esophageal cancer in Henan province. Ai Zheng. 2007;26(7):730–736.
  • Singhal R, Carrigan JB, Wei W, et al. MALDI profiles of proteins and lipids for the rapid characterisation of upper GI-tract cancers. J Proteomics. 2013 27;80:207–215.
  • Uemura N, Nakanishi Y, Kato H, et al. Transglutaminase 3 as a prognostic biomarker in esophageal cancer revealed by proteomics. Int J Cancer. 2009b;124(9):2106–2115.
  • Fu L, Qin YR, Xie D, et al. Identification of alpha-actinin 4 and 67 kDalaminin receptor as stage-specific markers in esophageal cancer via proteomic approaches. Cancer. 2007;110(12):2672–2681.
  • Jazii FR, Najafi Z, Malekzadeh R, et al. Identification of squamous cell carcinoma associated proteins by proteomics and loss of beta tropomyosin expression in esophageal cancer. World J Gastroenterol. 2006;12(44):7104–7112.
  • Chen HB, Pan K, Tang MK, et al. Comparative proteomic analysis reveals differentially expressed proteins regulated by a potential tumor promoter, BRE, in human esophageal carcinoma cells. Biochem Cell Biol. 2008;86(4):302–311.
  • Islam F, Gopalan V, Lam AK. Mass spectrometry for biomarkers discovery in esophageal squamous cell carcinoma. Methods Mol Biol. 2020;2129:259–268.
  • Xu F, Zhang S, Liu Z, et al. TEX9 and eIF3b functionally synergize to promote the progression of esophageal squamous cell carcinoma. BMC Cancer. 2019;19(1):875.
  • Moghanibashi M, RastgarJazii F, Soheili ZS, et al. Esophageal cancer alters the expression of nuclear pore complex binding protein Hsc70 and eIF5A-1. FunctIntegr Genomics. 2013;13(2):253–260.
  • Moghanibashi M, Jazii FR, Soheili ZS, et al. Proteomics of a new esophageal cancer cell line established from Persian patient. Gene. 2012;500(1):124–133.
  • Wen J, Zheng B, Hu Y, et al. Comparative proteomic analysis of the esophageal squamous carcinoma cell line EC109 and its multi-drug resistant subline EC109/CDDP. Int J Oncol. 2010;36(1):265–274.
  • Datta KK, Patil S, Patel K, et al. Chronic exposure to chewing tobacco induces metabolic reprogramming and cancer stem cell-like properties in esophageal epithelial cells. Cells. 2019;8(9):949.
  • Tsai ST, Wang PJ, Liou NJ, et al. ICAM1 Is a potential cancer stem cell marker of esophageal squamous cell carcinoma. PLoS One. 2015;10(11):e0142834.
  • Hayashida Y, Honda K, Osaka Y, et al. Possible prediction of chemoradiosensitivity of esophageal cancer by serum protein profiling. Clin Cancer Res. 2005;11(22):8042–8047.
  • Sun Y, Zhai L, Ma S, et al. Down-regulation of RIP3 potentiates cisplatin chemoresistance by triggering HSP90-ERK pathway mediated DNA repair in esophageal squamous cell carcinoma. Cancer Lett. 2018;418:97–108.
  • Li C, Xia G, Jianqing Z, et al. Serum differential protein identification of Xinjiang Kazakh esophageal cancer patients based on the two-dimensional liquid-phase chromatography and LTQ MS. MolBiol Rep. 2014;41(5):2893–2905.
  • Zhang C, Zhang J, Wu Q, et al. Sulforaphene induces apoptosis and inhibits the invasion of esophageal cancer cells through MSK2/CREB/Bcl-2 and cadherin pathway in vivo and in vitro. Cancer Cell Int. 2019;19:342.
  • Yang J, Dou Z, Peng X, et al. Transcriptomics and proteomics analyses of anti-cancer mechanisms of TR35-An active fraction from Xinjiang Bactrian camel milk in esophageal carcinoma cell. ClinNutr. 2019;38(5):2349–2359.
  • Zheng WB, Li YJ, Wang Y, et al. Propafenone suppresses esophageal cancer proliferation through inducing mitochondrial dysfunction. Am J Cancer Res. 2017;7(11):2245–2256.
  • Zhang X, Li X, Zheng L, et al. ANXA1 silencing increases the sensitivity of cancer cells to low-concentration arsenic trioxide treatment by inhibiting ERK MAPK activation. Tumori. 2015;101(4):360–367.
  • Li LY, Zhang K, Jiang H, et al. Quantitative proteomics reveals the downregulation of GRB2 as a prominent node of F806-targeted cell proliferation network. J Proteomics. 2015;117:145–155.
  • Du P, Huang P, Huang X, et al. Comprehensive genomic analysis of oesophageal squamous cell carcinoma reveals clinical relevance. Sci Rep. 2017;7(1):15324.
  • Wang Y, Wang G, Ma Y, et al. FAT1, a direct transcriptional target of E2F1, suppresses cell proliferation, migration and invasion in esophageal squamous cell carcinoma. Chin J Cancer Res. 2019;31(4):609–619.
  • Wang Q, Bai J, Abliz A, et al. An old story retold: loss of G1 control defines a distinct genomic subtype of esophageal squamous cell carcinoma. Genomics Proteomics Bioinformatics. 2015;13(4):258–270.
  • Kashyap MK, Marimuthu A, Kishore CJ, et al. Genomewide mRNA profiling of esophageal squamous cell carcinoma for identification of cancer biomarkers. Cancer Biol Ther. 2009;8(1):36–46.
  • Li Y, Nie CJ, Hu L, et al. Characterization of a novel mechanism of genomic instability involving the SEI1/SET/NM23H1 pathway in esophageal cancers. Cancer Res. 2010;70(14):5695–5705.
  • Tang DJ, Hu L, Xie D, et al. Oncogenic transformation by SEI-1 is associated with chromosomal instability. Cancer Res. 2005;65(15):6504–6508.
  • Chen FF, Zhang SR, Peng H, et al. Integrative genomics analysis of hub genes and their relationship with prognosis and signaling pathways in esophageal squamous cell carcinoma. Mol Med Rep. 2019;20(4):3649–3660.
  • Bhushan A, Singh A, Kapur S, et al. Identification and validation of fibroblast growth factor 12 gene as a novel potential biomarker in esophageal cancer using cancer genomic datasets. OMICS. 2017;21(10):616–631.
  • Im WR, Lee HS, Lee YS, et al. A Regulatory Noncoding RNA, nc886, Suppresses Esophageal Cancer by Inhibiting the AKT Pathway and Cell Cycle Progression. Cells. 2020;9(4):801.
  • Rong H, Chen B, Ma K, et al. Downregulation of lncRNA LINC-PINT participates in the recurrence of esophageal squamous cell carcinoma possibly by interacting miRNA-21. Cancer BiotherRadiopharm. 2020.
  • Luo A, Zhou X, Shi X, et al. Exosome-derived miR-339-5p mediates radiosensitivity by targeting Cdc25A in locally advanced esophageal squamous cell carcinoma. Oncogene. 2019;38(25):4990–5006.
  • Lin WC, Chen LH, Hsieh YC, et al. miR-338-5p inhibits cell proliferation, colony formation, migration and cisplatin resistance in esophageal squamous cancer cells by targeting FERMT2. Carcinogenesis. 2019;40(7):883–892.
  • Shimonosono M, Idichi T, Seki N, et al. Molecular pathogenesis of esophageal squamous cell carcinoma: identification of the antitumor effects of miR1453p on gene regulation. Int J Oncol. 2019;54(2):673–688.
  • Zhang W, Hong R, Li L, et al. The chromosome 11q13.3 amplification associated lymph node metastasis is driven by miR-548k through modulating tumor microenvironment. Mol Cancer. 2018;17(1):125.
  • Peng L, Cheng S, Lin Y, et al. CCGD-ESCC: a comprehensive database for genetic variants associated with esophageal squamous cell carcinoma in chinese population. Genomics Proteomics Bioinformatics. 2018;16(4):262–268.
  • Xu J, Chen Y, Zhang R, et al. Global and targeted metabolomics of esophageal squamous cell carcinoma discovers potential diagnostic and therapeutic biomarkers. Mol Cell Proteomics. 2013;12(5):1306–1318.
  • Esteller M. Cancer epigenomics: DNA methylomes and histone-modification maps. Nat Rev Genet. 2007;8(4):286–298.
  • Zhang K, Li L, Zhu M, et al. Comparative analysis of histone H3 and H4 post-translational modifications of esophageal squamous cell carcinoma with different invasive capabilities. J Proteomics. 2015;112:180–189.
  • Syed N, Barbhuiya MA, Pinto SM, et al. Phosphotyrosine profiling identifies ephrin receptor A2 as a potential therapeutic target in esophageal squamous-cell carcinoma. Proteomics. 2015;15(2–3):374–382.
  • Alix-Panabieres C, Pantel K. Challenges in circulating tumour cell research. Nat Rev Cancer. 2014;14(9):623–631.
  • Bobek V, Matkowski R, Gurlich R, et al. Cultivation of circulating tumor cells in esophageal cancer. Folia HistochemCytobiol. 2014;52(3):171–177.
  • Qiao YY, Lin KX, Zhang Z, et al. Monitoring disease progression and treatment efficacy with circulating tumor cells in esophageal squamous cell carcinoma: A case report. World J Gastroenterol. 2015;21(25):7921–7928.
  • Matsushita D, Uenosono Y, Arigami T, et al. Clinical significance of circulating tumor cells in peripheral blood of patients with esophageal squamous cell carcinoma. Ann SurgOncol. 2015;22(11):3674–3680.
  • Bratlie SO, Edebo A, Casselbrant A, et al. The renin-angiotensin system in Barrett’s esophagus. Scand J Gastroenterol. 2016;51(9):1037–1042.
  • Bratlie SO, Wallenius V, Edebo A, et al. Proteomic approach to the potential role of angiotensin ii in barrett dysplasia. Proteomics Clin Appl. 2019;13(4):e1800102.
  • Wu C, Wang Z, Song X, et al. Joint analysis of three genome-wide association studies of esophageal squamous cell carcinoma in Chinese populations. Nat Genet. 2014 Sep;46(9):1001–1006.
  • Slotta-Huspenina J, Berg D, Bauer K, et al. Evidence of prognostic relevant expression profiles of heat-shock proteins and glucose-regulated proteins in oesophageal adenocarcinomas. PLoS One. 2012;7(7):e41420.
  • Phelan JJ, MacCarthy F, Feighery R, et al. Differential expression of mitochondrial energy metabolism profiles across the metaplasia-dysplasia-adenocarcinoma disease sequence in Barrett’s oesophagus. Cancer Lett. 2014;354(1):122–131.
  • Pohler E, Craig AL, Cotton J, et al. The Barrett’s antigen anterior gradient-2 silences the p53 transcriptional response to DNA damage. Mol Cell Proteomics. 2004;3(6):534–547.
  • Manousopoulou A, Hayden A, Mellone M, et al. Quantitative proteomic profiling of primary cancer-associated fibroblasts in oesophageal adenocarcinoma. Br J Cancer. 2018;118(9):1200–1207.
  • Aichler M, Elsner M, Ludyga N, et al. Clinical response to chemotherapy in oesophageal adenocarcinoma patients is linked to defects in mitochondria. J Pathol. 2013;230(4):410–419.
  • O’Neill JR, Pak HS, Pairo-Castineira E, et al. Quantitative shotgun proteomics unveils candidate novel esophageal adenocarcinoma (EAC)-specific proteins. Mol Cell Proteomics. 2017;16(6):1138–1150.
  • Langer R, Ott K, Specht K, et al. Protein expression profiling in esophageal adenocarcinoma patients indicates association of heat-shock protein 27 expression and chemotherapy response. Clin Cancer Res. 2008;14(24):8279–8287.
  • Zhao J, Chang AC, Li C, et al. Comparative proteomics analysis of Barrett metaplasia and esophageal adenocarcinoma using two-dimensional liquid mass mapping. Mol Cell Proteomics. 2007;6(6):987–999.
  • Zaidi AH, Gopalakrishnan V, Kasi PM, et al. Evaluation of a 4-protein serum biomarker panel-biglycan, annexin-A6, myeloperoxidase, and protein S100-A9 (B-AMP)-for the detection of esophageal adenocarcinoma. Cancer. 2014;120(24):3902–3913.
  • Berndt U, Philipsen L, Bartsch S, et al. Comparative Multi-Epitope-Ligand-Cartography reveals essential immunological alterations in Barrett’s metaplasia and esophageal adenocarcinoma. Mol Cancer. 2010;9:177.
  • Song E, Zhu R, Hammoud ZT, et al. MS/MS quantitation of esophagus disease blood serum glycoproteins by enrichment with hydrazide chemistry and lectin affinity chromatography. J Proteome Res. 2014;13(11):4808–4820.
  • Mayampurath A, Song E, Mathur A, et al. Label-free glycopeptide quantification for biomarker discovery in human sera. J Proteome Res. 2014;13(11):4821–4832.
  • Kelly P, Appleyard V, Murray K, et al. Detection of oesophageal cancer biomarkers by plasma proteomic profiling of human cell line xenografts in response to chemotherapy. Br J Cancer. 2010;103(2):232–238.
  • Zaidi N, Kelly RJ. The management of localized esophageal squamous cell carcinoma: western approach. Chin Clin Oncol. 2017 Oct; 6(5):46.
  • Bandla S, Pennathur A, Luketich JD, et al. Comparative genomics of esophageal adenocarcinoma and squamous cell carcinoma. Ann Thorac Surg. 2012 Apr;93(4):1101–1106.
  • Pooja and Niranjan V. An integrative proteogenomics study to identify peptides and protein coding genes in esophageal squamous cell carcinoma. Curr Topics peptide protein Res. 2019;20:51–66.

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.