title: Genome-Wide Transcriptome Profiling of the Neoplastic Giant Cell Tumor of Bone Stromal Cells by RNA Sequencing.
abstract: Giant cell tumor of bone (GCTB) is the most common non-malignant primary bone tumor reported in Hong Kong. Failure of treatment in advanced GCTB with aggressive local recurrence remains a clinical challenge. In order to reveal the molecular mechanism underlying the pathogenesis of this tumor, we aimed to examine the transcriptome profiling of the neoplastic stromal cells of GCTB in this study. RNA-sequencing was performed on three GCTB stromal cell samples and one bone marrow-derived MSC sample and 174 differentially expressed genes (DEGs) were identified between these two cell types. The top five up-regulated genes are SPP1, F3, TSPAN12, MMP13, and LGALS3BP and further validated by qPCR and Western Blotting. Knockdown of SPP1 was found to induce RUNX2 and OPG expression in GCTB stromal cells but not the MSCs. Ingenuity pathway analysis (IPA) of the 174 DEGs revealed significant alternations in 23 pathways; variant calling analysis revealed 1915 somatic variants of 384 genes with high or moderate impacts. Interestingly, four canonical pathways were found overlapping in both analyses; from which VEGFA, CSF1, PLAUR, and F3 genes with somatic mutation were found up-regulated in GCTB stromal cells. The STRING diagram showed two main clusters of the DEGs; one cluster of histone genes that are down-regulated in GCTB samples and another related to osteoblast differentiation, angiogenesis, cell cycle progression, and tumor growth. The DEGs and somatic mutations found in our study warrant further investigation and validation, nevertheless, our study add new insights in the search for new therapeutic targets in treating GCTB. J. Cell. Biochem. 118: 1349-1360, 2017. © 2016 Wiley Periodicals, Inc.
authors.affiliation: Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Hong Kong, China.|School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.
authors.forename: Carol P Y
authors.initials: CP
authors.lastname: Lau
authors.affiliation: School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.
authors.forename: Jamie S L
authors.initials: JS
authors.lastname: Kwok
authors.affiliation: Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Hong Kong, China.
authors.forename: Joseph C C
authors.initials: JC
authors.lastname: Tsui
authors.affiliation: Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China.
authors.forename: Lin
authors.initials: L
authors.lastname: Huang
authors.affiliation: School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.|Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China.
authors.forename: Kevin Y
authors.initials: KY
authors.lastname: Yang
authors.affiliation: School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.
authors.forename: Stephen K W
authors.initials: SK
authors.lastname: Tsui
authors.affiliation: Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Hong Kong, China.
authors.forename: Shekhar Madhukar
authors.initials: SM
authors.lastname: Kumta
mesh_terms: D001859:Bone Neoplasms / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D020022:Genetic Predisposition to Disease; D055106:Genome-Wide Association Study; D018212:Giant Cell Tumor of Bone / Q000235:genetics*; D006801:Humans; D009154:Mutation; D017423:Sequence Analysis, RNA / Q000379:methods*
keywords: DIFFERENTIALLY EXPRESSED GENES; GIANT CELL TUMOR OF BONE; OSTEOPONTIN; RNA SEQUENCING; SOMATIC MUTATIONS