title: Rare amplicons implicate frequent deregulation of cell fate specification pathways in oral squamous cell carcinoma.
abstract: Genomes of solid tumors are characterized by gains and losses of regions, which may contribute to tumorigenesis by altering gene expression. Often the aberrations are extensive, encompassing whole chromosome arms, which makes identification of candidate genes in these regions difficult. Here, we focused on narrow regions of gene amplification to facilitate identification of genetic pathways important in oral squamous cell carcinoma (SCC) development. We used array comparative genomic hybridization (array CGH) to define minimum common amplified regions and then used expression analysis to identify candidate driver genes in amplicons that spanned <3 Mb. We found genes involved in integrin signaling (TLN1), survival (YAP1, BIRC2), and adhesion and migration (TLN1, LAMA3, MMP7), as well as members of the hedgehog (GLI2) and notch (JAG1, RBPSUH, FJX1) pathways to be amplified and overexpressed. Deregulation of these and other members of the hedgehog and notch pathways (HHIP, SMO, DLL1, NOTCH4) implicates deregulation of developmental and differentiation pathways, cell fate misspecification, in oral SCC development.
authors.affiliation: Cancer Research Institute, University of California San Francisco, Box 0808, San Francisco, CA 94143-0808, USA.
authors.forename: Antoine M
authors.initials: AM
authors.lastname: Snijders
authors.forename: Brian L
authors.initials: BL
authors.lastname: Schmidt
authors.forename: Jane
authors.initials: J
authors.lastname: Fridlyand
authors.forename: Nusi
authors.initials: N
authors.lastname: Dekker
authors.forename: Daniel
authors.initials: D
authors.lastname: Pinkel
authors.forename: Richard C K
authors.initials: RC
authors.lastname: Jordan
authors.forename: Donna G
authors.initials: DG
authors.lastname: Albertson
mesh_terms: D002294:Carcinoma, Squamous Cell / Q000235:genetics*; D002448:Cell Adhesion / Q000235:genetics; D002470:Cell Survival / Q000235:genetics; D002471:Cell Transformation, Neoplastic / Q000235:genetics*; D005784:Gene Amplification; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D009062:Mouth Neoplasms / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D015398:Signal Transduction