title: Functional synergies yet distinct modulators affected by genetic alterations in common human cancers.
abstract: An important general concern in cancer research is how diverse genetic alterations and regulatory pathways can produce common signaling outcomes. In this study, we report the construction of cancer models that combine unique regulation and common signaling. We compared and functionally analyzed sets of genetic alterations, including somatic sequence mutations and copy number changes, in breast, colon, and pancreatic cancer and glioblastoma that had been determined previously by global exon sequencing and SNP (single nucleotide polymorphism) array analyses in multiple patients. The genes affected by the different types of alterations were mostly unique in each cancer type, affected different pathways, and were connected with different transcription factors, ligands, and receptors. In our model, we show that distinct amplifications, deletions, and sequence alterations in each cancer resulted in common signaling pathways and transcription regulation. In functional clustering, the impact of the type of alteration was more pronounced than the impact of the kind of cancer. Several pathways such as TGF-β/SMAD signaling and PI3K (phosphoinositide 3-kinase) signaling were defined as synergistic (affected by different alterations in all four cancer types). Despite large differences at the genetic level, all data sets interacted with a common group of 65 "universal cancer genes" (UCG) comprising a concise network focused on proliferation/apoptosis balance and angiogenesis. Using unique nodal regulators ("overconnected" genes), UCGs, and synergistic pathways, the cancer models that we built could combine common signaling with unique regulation. Our findings provide a novel integrated perspective on the complex signaling and regulatory networks that underlie common human cancers.
authors.affiliation: Thomson Reuters, Healthcare & Life Science, St. Joseph, Michigan 49085, USA.
authors.forename: Marina
authors.initials: M
authors.lastname: Bessarabova
authors.forename: Olga
authors.initials: O
authors.lastname: Pustovalova
authors.forename: Weiwei
authors.initials: W
authors.lastname: Shi
authors.forename: Tatiana
authors.initials: T
authors.lastname: Serebriyskaya
authors.forename: Alex
authors.initials: A
authors.lastname: Ishkin
authors.forename: Kornelia
authors.initials: K
authors.lastname: Polyak
authors.forename: Victor E
authors.initials: VE
authors.lastname: Velculescu
authors.forename: Tatiana
authors.initials: T
authors.lastname: Nikolskaya
authors.forename: Yuri
authors.initials: Y
authors.lastname: Nikolsky
mesh_terms: D017209:Apoptosis; D049109:Cell Proliferation; D016000:Cluster Analysis; D005091:Exons; D017353:Gene Deletion; D015972:Gene Expression Regulation, Neoplastic; D005823:Genetics; D006801:Humans; D008954:Models, Biological; D008957:Models, Genetic; D009154:Mutation; D009369:Neoplasms / Q000235:genetics* / Q000378:metabolism; D019869:Phosphatidylinositol 3-Kinases / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D015398:Signal Transduction
chemical_list: D019869:Phosphatidylinositol 3-Kinases