Novel Genetic and Epigenetic Features of Lung Tumor Genomes

William W Lockwood, Ian M Wilson, Raj Chari, Bradley P Coe, Timon PH Buys, Cathie Garnis, Calum MacAulay, Stephen Lam, Wan L Lam
British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, B.C, V5Z 1L3, Canada

Background: Lung cancer (LC) is the leading cause of cancer related mortality worldwide. Understanding the molecular mechanisms driving LC tumorigenesis will lead to rational development of therapeutics based on the biology of disease. It is currently believed that several alterations are required for LC initiation. These include genetic changes such as gain/amplification and loss/deletion of chromosome segments, as well as epigenetic changes such as aberrations in DNA methylation patterns. Although previous studies have yielded loci specific surveys of these alterations in LC, no studies to date have simultaneously analyzed alterations at the DNA level on a whole genome scale to fully understand their consequences on disease phenotype.

Objective: To comprehensively characterize the underlying molecular alterations driving LC development using an integrative genomic and epigenomic analysis.

Methods: A whole genome tiling path comparative genomic hybridization (CGH) array was used to generate high resolution copy number (CN) profiles of 161 lung tumors and 11 preinvasive carcinoma in situ (CIS) lesions. Whole genome DNA methylation status was assessed by methylation dependant immunoprecipitation (MeDIP) array CGH. In this method, an antibody specific to methylcytosine is used to enrich for methylated DNA segments which are cohybridized with unenriched DNA to demonstrate DNA methylation levels. Array data was visualized using SeeGH software and subjected to a smoothing algorithm to computationally determine regions of gain and loss and areas of differential methylation.

Results: Numerous specific CN and DNA methylation changes were identified generating complementary genomic and epigenomic profiles of LC genomes. In addition to novel regions of recurrent gain and loss, complex rearrangements with multiple segmental alterations present on the same chromosome arm highlighted the instability of the tumors. Focal high level amplifications were characteristic of advanced tumors whereas whole arm changes were more common in the CIS lesions. Interestingly, LC subtypes were defined by unique patterns of CN and methylation changes, indicating their differential development. Lastly, concerted regions of DNA hypermethylation and segmental loss, as well as hypomethylation and gain signified novel two hit mechanisms for both gene silencing and activation respectively.

Conclusions: The discovery of these novel features may shed light on disease mechanisms and identify new molecular targets for therapy.