title: Multi-Omics Data Integration and Mapping of Altered Kinases to Pathways Reveal Gonadotropin Hormone Signaling in Glioblastoma.
abstract: Glioblastoma multiforme (GBM) is one of the most lethal brain tumors with an inadequately understood pathophysiology. Biomarkers that guide accurate diagnosis and treatment decisions would greatly support precision medicine for GBM. Previous studies of GBM have focused on signaling pathways such as epidermal growth factor receptor (EGFR), platelet-derived growth factor receptors (PDGFRs), notch, wnt, and others, identified with single omics technology platforms (genomics, transcriptomics, or proteomics), but not with their integrated use. In this context, we report here a multi-omics pathway view, expanded through integration of the expression data at transcriptomic and proteomic levels, followed by selection of a functionally related group of proteins such as kinases deregulated in GBM. By using this strategy, we observed a highly significant enrichment of the gonadotropin-releasing hormone (GnRH) signaling pathway that was not deciphered with single omics datasets. The curation of the GnRH pathway with extensive literature analysis brought about a comprehensive annotation of the pathway, which included several additional pathway members that were not previously annotated. A targeted search resulted in identification of additional nonkinase members of the pathway in the GBM multi-omics datasets. We found evidence of GnRH receptor expression in GBM and other cancers. We offer here an updated generic pathway map of GnRH signaling, show its enrichment in the context of GBM, and discuss its plausible cross-connectivity with EGFR, wnt, calcium, and focal adhesion kinase signaling pathways that were earlier shown to be the top deregulated pathways in GBM. In conclusion, this study demonstrates the promise of multi-omics research and analyses to better understand complex cancers and suggests continued efforts and research in this direction in the field of integrative biology.
authors.affiliation: 1 Institute of Bioinformatics , International Tech Park, Bangalore, India .|2 School of Life Sciences, Manipal University , Manipal, India .
authors.forename: Savita
authors.initials: S
authors.lastname: Jayaram
authors.affiliation: 1 Institute of Bioinformatics , International Tech Park, Bangalore, India .|2 School of Life Sciences, Manipal University , Manipal, India .
authors.forename: Manoj Kumar
authors.initials: MK
authors.lastname: Gupta
authors.affiliation: 3 Computational Biology and Bioinformatics, Rajiv Gandhi Center for Biotechnology , Thiruvananthapuram, India .
authors.forename: Rajesh
authors.initials: R
authors.lastname: Raju
authors.affiliation: 4 National Institute of Pathology , ICMR, New Delhi, India .
authors.forename: Poonam
authors.initials: P
authors.lastname: Gautam
authors.affiliation: 1 Institute of Bioinformatics , International Tech Park, Bangalore, India .|5 Mazumdar Shaw Centre for Translational Research , Narayana Hrudayalaya Health City, Bangalore, India .
authors.forename: Ravi
authors.initials: R
authors.lastname: Sirdeshmukh
mesh_terms: D001932:Brain Neoplasms / Q000235:genetics / Q000378:metabolism*; D019295:Computational Biology; D066246:ErbB Receptors / Q000235:genetics / Q000378:metabolism; D023281:Genomics; D005909:Glioblastoma / Q000235:genetics / Q000378:metabolism*; D007987:Gonadotropin-Releasing Hormone / Q000235:genetics / Q000378:metabolism; D006801:Humans; D040901:Proteomics; D017479:Receptors, Platelet-Derived Growth Factor / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction
chemical_list: D007987:Gonadotropin-Releasing Hormone; C512478:EGFR protein, human; D066246:ErbB Receptors; D017479:Receptors, Platelet-Derived Growth Factor
keywords: GnRH; glioblastoma; kinases; multi-omic data integration; multi-omics; proteomics; signaling; systems biology; transcriptomics