Pathways impacted by genomic alterations in pulmonary carcinoid tumors

Pulmonary carcinoid tumors account for up to 5% of all lung malignancies in adults, comprise 30% of all carcinoid malignancies, and are defined histologically as typical carcinoid (TC) and atypical carcinoid (AC) tumors. The role of specific genomic alterations in the pathogenesis of pulmonary carcinoid tumors remains poorly understood. We sought to identify genomic alterations and pathways that are deregulated in these tumors to find novel therapeutic targets for pulmonary carcinoid tumors.We performed integrated genomic analysis of carcinoid tumors comprising whole genome and exome sequencing, mRNA expression profiling and SNP genotyping of specimens from normal lung, typical and atypical carcinoid, and small cell lung carcinoma (SCLC) to fully represent the lung neuroendocrine tumor spectrum. Pathway analysis of of CNV and gene expression data suggested deregulation of the NF-ĸB and MAPK/ERK pathways. This study identified mutated genes affecting cancer relevant pathways and biological processes that could provide opportunities for developing targeted therapies for pulmonary carcinoid tumors. RNA for gene expression analysis was extracted using the RNeasy Mini Kit and TissueLyser (Qiagen) according to the manufacturer's instructions. About 100-200 ng of total RNA were used for whole genome mRNA expression profiling which was performed on 64 human lung samples including 31 typical carcinoid, 11 atypical carcinoid, 12 small cell lung cancers and 9 adjacent normal lung tissues using the Illumina Human WG-6_v2 BeadArray Chip in the Mayo Clinic Advanced Microarray Shared Resource. Gene expression data were loaded into the Beadstudio v3 software (Illumina Inc., San Diego, CA) and data were normalized using the cubic spline method. Data were analyzed with Partek Genomics suite software. The normalized data were subsequently analyzed by principal component analysis (PCA) to determine if any intrinsic clustering or outliers existed within the data set. ANOVA analysis, including Fold Change, p-value and False Discovery Rate (FDR) were performed to compare the following 4 groups 1) Typical carcinoid vs. Atypical carcinoid; 2) Carcinoid vs. Normal tissue; 3) Carcinoid vs. Small cell lung cancer; and 4) Small cell lung cancer vs. Normal tissue. A total of 1181 genes were filtered across all groups using criteria of P<0.001 and |Fold change| >3. There were 683, 416 and 612 genes filtered separately in each of groups 2, 3 and 4.