DNA copy number aberrations in small-cell lung cancer reveal activation of the focal adhesion pathway

Abstract

Small-cell lung cancer (SCLC) is the most aggressive subtype of lung cancer in its clinical behavior, with a 5-year overall survival as low as 5%. Despite years of research in the field, molecular determinants of SCLC behavior are still poorly understood, and this deficiency has translated into an absence of specific diagnostics and targeted therapeutics. We hypothesized that tumor DNA copy number alterations would allow the identification of molecular pathways involved in SCLC progression. Array comparative genomic hybridization was performed on DNA extracted from 46 formalin-fixed paraffin-embedded SCLC tissue specimens. Genomic profiling of tumor and sex-matched control DNA allowed the identification of 70 regions of copy number gain and 55 regions of copy number loss. Using molecular pathway analysis, we found a strong enrichment in these regions of copy number alterations for 11 genes associated with the focal adhesion pathway. We verified these findings at the genomic, gene expression and protein level. Focal Adhesion Kinase (FAK), one of the central genes represented in this pathway, was commonly expressed in SCLC tumors and constitutively phosphorylated in SCLC cell lines. Those were poorly adherent to most substrates but not to laminin-322. Inhibition of FAK phosphorylation at Tyr397 by a small-molecule inhibitor, PF-573,228, induced a dose-dependent decrease of adhesion and an increase of spreading in SCLC cell lines on laminin-322. Cells that tended to spread also showed a decrease in focal adhesions, as demonstrated by a decreased vinculin expression. These results support the concept that pathway analysis of genes in regions of copy number alterations may uncover molecular mechanisms of disease progression and demonstrate a new role of FAK and associated adhesion pathways in SCLC. Further investigations of FAK at the functional level may lead to a better understanding of SCLC progression and may have therapeutic implications.

Pituitary Adenylate Cyclase-Activating Polypeptide Causes Increased Tyrosine Phosphorylation of Focal Adhesion Kinase and Paxillin

“…FAK is overexpressed in SCLC biopsy specimens and cell lines (Ocak et al 2010). FAK Tyr 397 phosphorylation in SCLC cells was inhibited by 10-μM PF-228 (Roberts et al Fig.…”

Proteomic Profiling Identifies PTK2/FAK as a Driver of Radioresistance in HPV-negative Head and Neck Cancer

“…Although PTK2/FAK copy number gain or amplification is observed in approximately 70% of cases, some work indicates that PTK2/FAK protein expression is not driven by copy number amplification (18,21). However, studies in breast and lung cancer have directly linked PTK2/FAK copy number with both mRNA and protein expression (22,23). In the current study, we provide additional evidence of a direct link between PTK2/FAK amplification and expression in HPV-negative HNSCC.…”

Separate enrichment analysis of pathways for up- and downregulated genes

“…However, considering a KEGG pathway as an activating or inhibiting pathway based only on its enrichment for up-or downregulated genes may be inappropriate [44]. For example, though the focal adhesion pathway was significantly enriched for downregulated genes, it also involved many upregulated genes, and may be activated in tumour cells to facilitate the invasion and migration of tumour cells [45]. Further, as the posttranslational modifications could inhibit or activate the functions of proteins [21,38,44,46], they should be considered in determining the activation or inhibition of a perturbed pathway.…”