Identification of Co-expression Modules and Pathways Correlated with Osteosarcoma and Its Metastasis

Overview

Journal World J Surg Oncol

Publisher Biomed Central

Specialties General Surgery
Oncology

Date 2019 Mar 10

PMID 30849987

Citations 13

Authors

Jian-Sheng Wang

Yun-Guo Wang

Yong-Sheng Zhong

Xue-Dong Li

Shi-Xin Du

Peng Xie

Gui-Zhou Zheng

Jing-Ming Han

Affiliations

Soon will be listed here.

Abstract

Background: Osteosarcoma is the most common bone tumor that occurs in children.

Methods: To identify co-expression modules and pathways correlated with osteosarcoma and its clinical characteristics, we performed weighted gene co-expression network analysis (WGCNA) on RNA-seq data of osteosarcoma with 52 samples. Then we performed pathway enrichment analysis on genes from significant modules.

Results: A total of 5471 genes were included in WGCNA, and 16 modules were identified. Module-trait analysis identified that a module involved in microtubule bundle formation, drug metabolism-cytochrome P450, and IL-17 signaling pathway was negatively correlated with osteosarcoma and positively correlated with metastasis; a module involved in DNA replication was positively correlated with osteosarcoma; a module involved in cell junction was positively correlated with metastasis; and a module involved in heparin binding negatively correlated with osteosarcoma. Moreover, expression levels in four of the top ten differentially expressed genes were validated in another independent dataset.

Conclusions: Our analysis might provide insight for molecular mechanisms of osteosarcoma.

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References

Tan X, Tamori Y, Egami H, Ishikawa S, Kurizaki T, Takai E . Analysis of invasion-metastasis mechanism in pancreatic cancer: involvement of tight junction transmembrane protein occludin and MEK/ERK signal transduction pathway in cancer cell dissociation. Oncol Rep. 2004; 11(5):993-8. View

Siggelkow H, Schmidt E, Hennies B, Hufner M . Evidence of downregulation of matrix extracellular phosphoglycoprotein during terminal differentiation in human osteoblasts. Bone. 2004; 35(2):570-6. DOI: 10.1016/j.bone.2004.03.033. View

Orimo H, Shimada T . Effects of phosphates on the expression of tissue-nonspecific alkaline phosphatase gene and phosphate-regulating genes in short-term cultures of human osteosarcoma cell lines. Mol Cell Biochem. 2005; 282(1-2):101-8. DOI: 10.1007/s11010-006-1520-6. View

Mensah-Osman E, Thomas D, Tabb M, Larios J, Hughes D, Giordano T . Expression levels and activation of a PXR variant are directly related to drug resistance in osteosarcoma cell lines. Cancer. 2007; 109(5):957-65. PMC: 3125968. DOI: 10.1002/cncr.22479. View

Stiller C . International patterns of cancer incidence in adolescents. Cancer Treat Rev. 2007; 33(7):631-45. DOI: 10.1016/j.ctrv.2007.01.001. View

Langfelder P, Horvath S . WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008; 9:559. PMC: 2631488. DOI: 10.1186/1471-2105-9-559. View

Huang D, Sherman B, Lempicki R . Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009; 4(1):44-57. DOI: 10.1038/nprot.2008.211. View

Lamoureux F, Picarda G, Garrigue-Antar L, Baudhuin M, Trichet V, Vidal A . Glycosaminoglycans as potential regulators of osteoprotegerin therapeutic activity in osteosarcoma. Cancer Res. 2009; 69(2):526-36. DOI: 10.1158/0008-5472.CAN-08-2648. View

Barbieri I, Pensa S, Pannellini T, Quaglino E, Maritano D, Demaria M . Constitutively active Stat3 enhances neu-mediated migration and metastasis in mammary tumors via upregulation of Cten. Cancer Res. 2010; 70(6):2558-67. DOI: 10.1158/0008-5472.CAN-09-2840. View

10.

Anninga J, Gelderblom H, Fiocco M, Kroep J, Taminiau A, Hogendoorn P . Chemotherapeutic adjuvant treatment for osteosarcoma: where do we stand?. Eur J Cancer. 2011; 47(16):2431-45. DOI: 10.1016/j.ejca.2011.05.030. View

11.

Ichikawa J, Cole H, Magnussen R, Mignemi N, Butler M, Holt G . Thrombin induces osteosarcoma growth, a function inhibited by low molecular weight heparin in vitro and in vivo: procoagulant nature of osteosarcoma. Cancer. 2011; 118(9):2494-506. DOI: 10.1002/cncr.26518. View

12.

Yu G, Wang L, Han Y, He Q . clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012; 16(5):284-7. PMC: 3339379. DOI: 10.1089/omi.2011.0118. View

13.

Wang M, Wang L, Ren T, Xu L, Wen Z . IL-17A/IL-17RA interaction promoted metastasis of osteosarcoma cells. Cancer Biol Ther. 2012; 14(2):155-63. PMC: 3571997. DOI: 10.4161/cbt.22955. View

14.

Luetke A, Meyers P, Lewis I, Juergens H . Osteosarcoma treatment - where do we stand? A state of the art review. Cancer Treat Rev. 2013; 40(4):523-32. DOI: 10.1016/j.ctrv.2013.11.006. View

15.

Prideaux M, Wijenayaka A, Kumarasinghe D, Ormsby R, Evdokiou A, Findlay D . SaOS2 Osteosarcoma cells as an in vitro model for studying the transition of human osteoblasts to osteocytes. Calcif Tissue Int. 2014; 95(2):183-93. DOI: 10.1007/s00223-014-9879-y. View

16.

Aceto N, Bardia A, Miyamoto D, Donaldson M, Wittner B, Spencer J . Circulating tumor cell clusters are oligoclonal precursors of breast cancer metastasis. Cell. 2014; 158(5):1110-1122. PMC: 4149753. DOI: 10.1016/j.cell.2014.07.013. View

17.

Guzvic M, Braun B, Ganzer R, Burger M, Nerlich M, Winkler S . Combined genome and transcriptome analysis of single disseminated cancer cells from bone marrow of prostate cancer patients reveals unexpected transcriptomes. Cancer Res. 2014; 74(24):7383-94. DOI: 10.1158/0008-5472.CAN-14-0934. View

18.

Liu M, Zhou K, Cao Y . MCRS1 overexpression, which is specifically inhibited by miR-129*, promotes the epithelial-mesenchymal transition and metastasis in non-small cell lung cancer. Mol Cancer. 2014; 13:245. PMC: 4233086. DOI: 10.1186/1476-4598-13-245. View

19.

. Gene Ontology Consortium: going forward. Nucleic Acids Res. 2014; 43(Database issue):D1049-56. PMC: 4383973. DOI: 10.1093/nar/gku1179. View

20.

Catanzaro J, Sheshadri N, Zong W . SerpinB3/B4: mediators of Ras-driven inflammation and oncogenesis. Cell Cycle. 2014; 13(20):3155-6. PMC: 4613179. DOI: 10.4161/15384101.2014.969991. View