Research on the Typical MiRNA and Target Genes in Squamous Cell Carcinoma and Adenocarcinoma of Esophagus Cancer with DNA Microarray

Overview

Journal Pathol Oncol Res

Specialty Oncology

Date 2014 Feb 13

PMID 24519530

Citations 12

Authors

Hong Bin Wang

Zhi Biao Jiang

Min Li

Affiliations

Soon will be listed here.

Abstract

To identify the typically expressed miRNAs in squamous cell carcinoma (SCC) and adenocarcinoma (ADC) of esophagus cancer and their target genes, and explore the related functions and pathways, providing potential biomarkers for esophageal carcinoma diagnosis and treatment. Gene expression profile GSE13937 was downloaded from Gene Expression Omnibus database which includes 152 samples, paired non-cancerous and cancerous, 44 SCC cases and 32 ADC cases; the differentially expressed miRNAs were identified with limma packages in R language after the data were normalized. Selected differentially expressed miRNAs were further analyzed using bioinformatics methods. Firstly, verified targets of miRNAs in two miRNA databases: miRecods and miRTarBase were integrated to select the targets genes of differentially expressed miRNAs. Next, String software was used to construct the target genes interaction network. Finally, function and pathway enrichment analysis of genes in the interaction network was carried out with Gestalt software. Up-regulated hsa-miR-21 and down-regulated hsa-miR-203 were identified by comparing normal and cancer tissue samples, and the targets genes regulated by these two miRNAs were most significantly related to cell cycle function and pathway, especially in the phase of G1/S. The two differentially expressed miRNA: hsa-miR-21 and hsa-miR-203 provide evidence for early diagnosis and treatment of esophageal carcinoma. The functions and pathways of target genes shows that deep understanding of cell cycle G1/S will help to illustrate the relationship between cell cycle regulation and pathogenesis of esophageal cancer.

Citing Articles

Salivary biomarkers: a promising approach for predicting immunotherapy response in head and neck cancers.

Nejat Dehkordi A, Maddahi M, Vafa P, Ebrahimi N, Aref A Clin Transl Oncol. 2024; .

PMID: 39377974 DOI: 10.1007/s12094-024-03742-8.

Circulating microRNA‑423 attenuates the phosphorylation of calcium handling proteins in atrial fibrillation.

Park H, Park H, Park J Mol Med Rep. 2022; 25(5).

PMID: 35348192 PMC: 8985206. DOI: 10.3892/mmr.2022.12702.

RNF168 is highly expressed in esophageal squamous cell carcinoma and contributes to the malignant behaviors in association with the Wnt/β-catenin signaling pathway.

Gou Y, Jin D, He S, Han S, Bai Q Aging (Albany NY). 2021; 13(4):5403-5414.

PMID: 33493132 PMC: 7950303. DOI: 10.18632/aging.202471.

Identification of microRNAs as novel biomarkers for esophageal squamous cell carcinoma: a study based on The Cancer Genome Atlas (TCGA) and bioinformatics.

Li C, Zhang W, Xiang J, Wang X, Li J, Wang J Chin Med J (Engl). 2019; 132(18):2213-2222.

PMID: 31490264 PMC: 6797152. DOI: 10.1097/CM9.0000000000000427.

Sub-pathway based approach to systematically track candidate sub-pathway biomarkers for heart failure.

Han D Exp Ther Med. 2019; 17(4):3162-3168.

PMID: 30936989 PMC: 6434253. DOI: 10.3892/etm.2019.7319.

References

Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R . Missing value estimation methods for DNA microarrays. Bioinformatics. 2001; 17(6):520-5. DOI: 10.1093/bioinformatics/17.6.520. View

Yang M, Liu R, Sheng J, Liao J, Wang Y, Pan E . Differential expression profiles of microRNAs as potential biomarkers for the early diagnosis of esophageal squamous cell carcinoma. Oncol Rep. 2012; 29(1):169-76. DOI: 10.3892/or.2012.2105. View

Lau C, Ng P, Li M, Tsui S, Huang L, Kumta S . p63 regulates cell proliferation and cell cycle progression‑associated genes in stromal cells of giant cell tumor of the bone. Int J Oncol. 2012; 42(2):437-43. PMC: 3583652. DOI: 10.3892/ijo.2012.1727. View

Zhang J, Wang J, Zhao F, Liu Q, Jiang K, Yang G . MicroRNA-21 (miR-21) represses tumor suppressor PTEN and promotes growth and invasion in non-small cell lung cancer (NSCLC). Clin Chim Acta. 2010; 411(11-12):846-52. DOI: 10.1016/j.cca.2010.02.074. View

Zhou Y, Zhang T, Zhao J, Wang X, Jiang T, Gu Z . The adenovirus-mediated transfer of PTEN inhibits the growth of esophageal cancer cells in vitro and in vivo. Biosci Biotechnol Biochem. 2010; 74(4):736-40. DOI: 10.1271/bbb.90787. View

Sonkoly E, Wei T, Pavez Lorie E, Suzuki H, Kato M, Torma H . Protein kinase C-dependent upregulation of miR-203 induces the differentiation of human keratinocytes. J Invest Dermatol. 2009; 130(1):124-34. DOI: 10.1038/jid.2009.294. View

Xiong B, Cheng Y, Ma L, Zhang C . MiR-21 regulates biological behavior through the PTEN/PI-3 K/Akt signaling pathway in human colorectal cancer cells. Int J Oncol. 2012; 42(1):219-28. DOI: 10.3892/ijo.2012.1707. View

Li S, Armstrong C, Bertin N, Ge H, Milstein S, Boxem M . A map of the interactome network of the metazoan C. elegans. Science. 2004; 303(5657):540-3. PMC: 1698949. DOI: 10.1126/science.1091403. View

Mishina T, Dosaka-Akita H, Hommura F, Nishi M, Kojima T, Ogura S . Cyclin E expression, a potential prognostic marker for non-small cell lung cancers. Clin Cancer Res. 2000; 6(1):11-6. View

10.

Zhang B, Pan X, Cobb G, Anderson T . microRNAs as oncogenes and tumor suppressors. Dev Biol. 2006; 302(1):1-12. DOI: 10.1016/j.ydbio.2006.08.028. View

11.

Bian K, Fan J, Zhang X, Yang X, Zhu H, Wang L . MicroRNA-203 leads to G1 phase cell cycle arrest in laryngeal carcinoma cells by directly targeting survivin. FEBS Lett. 2012; 586(6):804-9. DOI: 10.1016/j.febslet.2012.01.050. View

12.

Mathe E, Nguyen G, Bowman E, Zhao Y, Budhu A, Schetter A . MicroRNA expression in squamous cell carcinoma and adenocarcinoma of the esophagus: associations with survival. Clin Cancer Res. 2009; 15(19):6192-200. PMC: 2933109. DOI: 10.1158/1078-0432.CCR-09-1467. View

13.

Nam D, Kim S . Gene-set approach for expression pattern analysis. Brief Bioinform. 2008; 9(3):189-97. DOI: 10.1093/bib/bbn001. View

14.

Zhao Y, Srivastava D . A developmental view of microRNA function. Trends Biochem Sci. 2007; 32(4):189-97. DOI: 10.1016/j.tibs.2007.02.006. View

15.

Yuan T, Cantley L . PI3K pathway alterations in cancer: variations on a theme. Oncogene. 2008; 27(41):5497-510. PMC: 3398461. DOI: 10.1038/onc.2008.245. View

16.

Cunningham J, Vierkant R, Sellers T, Phelan C, Rider D, Liebow M . Cell cycle genes and ovarian cancer susceptibility: a tagSNP analysis. Br J Cancer. 2009; 101(8):1461-8. PMC: 2768434. DOI: 10.1038/sj.bjc.6605284. View

17.

Jemal A, Bray F, Center M, Ferlay J, Ward E, Forman D . Global cancer statistics. CA Cancer J Clin. 2011; 61(2):69-90. DOI: 10.3322/caac.20107. View

18.

Lai E . Micro RNAs are complementary to 3' UTR sequence motifs that mediate negative post-transcriptional regulation. Nat Genet. 2002; 30(4):363-4. DOI: 10.1038/ng865. View

19.

Ye Y, Wang K, Gu J, Yang H, Lin J, Ajani J . Genetic variations in microRNA-related genes are novel susceptibility loci for esophageal cancer risk. Cancer Prev Res (Phila). 2009; 1(6):460-9. PMC: 2768267. DOI: 10.1158/1940-6207.CAPR-08-0135. View

20.

Zhang B, Kirov S, Snoddy J . WebGestalt: an integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res. 2005; 33(Web Server issue):W741-8. PMC: 1160236. DOI: 10.1093/nar/gki475. View