title: Integrative functional genomic analysis identifies epigenetically regulated fibromodulin as an essential gene for glioma cell migration.
abstract: An integrative functional genomics study of multiple forms of data are vital for discovering molecular drivers of cancer development and progression. Here, we present an integrated genomic strategy utilizing DNA methylation and transcriptome profile data to discover epigenetically regulated genes implicated in cancer development and invasive progression. More specifically, this analysis identified fibromodulin (FMOD) as a glioblastoma (GBM) upregulated gene because of the loss of promoter methylation. Secreted FMOD promotes glioma cell migration through its ability to induce filamentous actin stress fiber formation. Treatment with cytochalasin D, an actin polymerization inhibitor, significantly reduced the FMOD-induced glioma cell migration. Small interfering RNA and small molecule inhibitor-based studies identified that FMOD-induced glioma cell migration is dependent on integrin-FAK-Src-Rho-ROCK signaling pathway. FMOD lacking C-terminus LRR11 domain (ΔFMOD), which does not bind collagen type I, failed to induce integrin and promote glioma cell migration. Further, FMOD-induced integrin activation and migration was abrogated by a 9-mer wild-type peptide from the FMOD C-terminus. However, the same peptide with mutation in two residues essential for FMOD interaction with collagen type I failed to compete with FMOD, thus signifying the importance of collagen type I-FMOD interaction in integrin activation. Chromatin immunoprecipitation-PCR experiments revealed that transforming growth factor beta-1 (TGF-β1) regulates FMOD expression through epigenetic remodeling of FMOD promoter that involved demethylation and gain of active histone marks with a simultaneous loss of DNMT3A and EZH2 occupancy, but enrichment of Sma- and Mad-related protein-2 (SMAD2) and CBP. FMOD silencing inhibited the TGF-β1-mediated glioma cell migration significantly. In univariate and multivariate Cox regression analysis, both FMOD promoter methylation and transcript levels predicted prognosis in GBM. Thus, this study identified several epigenetically regulated alterations responsible for cancer development and progression. Specifically, we found that secreted FMOD as an important regulator of glioma cell migration downstream of TGF-β1 pathway and forms a potential basis for therapeutic intervention in GBM.
authors.affiliation: Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India.
authors.forename: B
authors.initials: B
authors.lastname: Mondal
authors.affiliation: Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India.
authors.forename: V
authors.initials: V
authors.lastname: Patil
authors.affiliation: Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India.
authors.forename: S D
authors.initials: SD
authors.lastname: Shwetha
authors.affiliation: Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India.
authors.forename: K
authors.initials: K
authors.lastname: Sravani
authors.affiliation: Department of Neurosurgery, Sri Satya Sai Institute of Higher Medical Sciences, Bangalore, India.
authors.forename: A S
authors.initials: AS
authors.lastname: Hegde
authors.affiliation: Department of Neurosurgery, National Institute of Mental Health and Neuro Sciences, Bangalore, India.
authors.forename: A
authors.initials: A
authors.lastname: Arivazhagan
authors.affiliation: Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India.
authors.forename: V
authors.initials: V
authors.lastname: Santosh
authors.affiliation: Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska University Hospital, Göteborg, Sweden.
authors.forename: M
authors.initials: M
authors.lastname: Kanduri
authors.affiliation: Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India.
authors.forename: K
authors.initials: K
authors.lastname: Somasundaram
mesh_terms: D045744:Cell Line, Tumor; D002465:Cell Movement / Q000187:drug effects; D042002:Chromatin Assembly and Disassembly; D024042:Collagen Type I / Q000378:metabolism; D003599:Cytoskeleton / Q000378:metabolism; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D057890:Epigenomics / Q000379:methods; D000071235:Fibromodulin / Q000235:genetics*; D051416:Focal Adhesion Protein-Tyrosine Kinases / Q000378:metabolism; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D020043:Genes, Essential; D055106:Genome-Wide Association Study; D005910:Glioma / Q000235:genetics* / Q000378:metabolism / Q000401:mortality; D006801:Humans; D053208:Kaplan-Meier Estimate; D008954:Models, Biological; D011379:Prognosis; D011401:Promoter Regions, Genetic; D015398:Signal Transduction / Q000187:drug effects; D014158:Transcription, Genetic; D059467:Transcriptome; D053773:Transforming Growth Factor beta1 / Q000378:metabolism; D054460:rho-Associated Kinases / Q000378:metabolism; D019061:src-Family Kinases / Q000378:metabolism
chemical_list: D024042:Collagen Type I; D053773:Transforming Growth Factor beta1; D000071235:Fibromodulin; D051416:Focal Adhesion Protein-Tyrosine Kinases; D019061:src-Family Kinases; D054460:rho-Associated Kinases