Background: A better understanding of the development of metastatic disease and the identification of molecular markers for cancer spread would be useful for the design of improved treatment strategies. This study was conducted to identify gene expressions associated with metastatic phenotypes of locally advanced cervical carcinomas and investigate whether gains or losses of these genes could play a role in regulation of the transcripts. Gene expressions and copy number changes were determined in primary tumors from 29 patients with and 19 without diagnosed lymph node metastases by use of cDNA and genomic microarray techniques, respectively.

Absolute tumor DNA copy numbers can currently be achieved only on a single gene basis by using fluorescence in situ hybridization (FISH). We present GeneCount, a method for genome-wide calculation of absolute copy numbers from clinical array comparative genomic hybridization data. The tumor cell fraction is reliably estimated in the model. Data consistent with FISH results are achieved. We demonstrate significant improvements over existing methods for exploring gene dosages and intratumor copy number heterogeneity in cancers.

5049 Background: Lymph node involvement is the first indication of cervical cancer spread and a strong prognostic factor. The aims of the present study were to identify genes associated with lymph node involvement. Methods: The nodal status and tumor volume were determined from MR images in 48 patients with FIGO stage 2a to 4a at the time of diagnosis. cDNA microarray technique was used to identify genes that differed in expression between node positive and negative tumors. Biopsies enriched for carcinoma tissue were co-hybridized with a common reference sample in a dye-swap design. Quantitative real time PCR (qRT PCR) and immunohistochemistry were used to validate microarray results and determine protein expression of selected genes. Results: Pathologic lymph nodes were seen in 29 patients and normal nodes in 19. We identified 16 genes with higher and 15 with lower expression in node positive tumors as compared to the negative ones. QRT PCR data of 4 genes were consistent with these findings. CKS2, MRPS23, MRPL11, LSM3 and PDK2 were upregulated in node positive tumors suggesting high proliferation activity and oxygen consumption. MSN, KLF3 and TBX3 were downregulated. CKS2, MRPS23, MRPL11, PDK2, LSM3, TBX3, KLF3 and MSN were significantly related to progression free survival in univariate analysis. Protein expression, determined for CKS2 and MSN, was significantly correlated to survival, consistent with these results. In multivariate analysis including only gene variables, MRPL11, PDK2 and TBX3 were significant. Including also clinical and MRI variables, tumor volume, KLF3 and TBX3 were significant. NEK1, CSTA, ANX4 and DDOST were upregulated indicating activated DNA damage repair (NEK1) and resistance to apoptosis (CSTA, ANX4, DDOST). NTN4 and HYAL1, which are involved in cell-matrix interactions, were downregulated, suggesting mechanisms for increased cell migration and invasive growth. Conclusions: Our findings are consistent with known phenotypic characteristics of node positive cervical tumors, such as hypoxia and high lactate content. They point to molecular mechanisms for development of hypoxia, deregulation of glucose metabolism, activation of survival strategies and interactions between carcinoma cells and tumor stroma that may promote metastasis formation. No significant financial relationships to disclose.

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