Anti-CDKN3 monoclonal antibody Made to order

Micro-arrays can identify co-expressed genes at large scale. The gene expression analysis does however not show functional relationships between co-expressed genes. To address this problem, we link gene expression data to protein interaction data. For the gene products of coexpressed genes, we identify structural domains by sequence alignment and threading. Next, we use the protein structure interaction PSIMAP to find structurally interacting domains. Finally, we generate structural and sequence alignments of the original gene products and the identified structures and check conservation of the relevant interaction interfaces. From this analysis, we derive potentially relevant protein interactions for the gene expression data. We applied this method to co-expressed genes in pancreatic ductal carcinoma. Our method reveals among others a number of functional clusters related to the proteasome, signalling, ubiquitinisation, serine proteases, immunoglobulin and kinases. We investigate the kinase cluster in detail and reveal an interaction between the cell division control protein CDC2 and the cyclin-dependent kinase inhibitor CDKN3, which is also confirmed by literature. Furthermore, our method reveals new interactions between CDKN3 and the cell division protein kinase CDK7 and between CDKN3 and the serine/threonine-protein kinase CDC2L1.

The cyclin-dependent kinase inhibitor 3 (CDKN3) gene, involved in mitosis, is upregulated in cervical cancer (CC). We investigated CDKN3 mRNA as a survival biomarker and potential therapeutic target for CC. CDKN3 mRNA was measured in 134 CC and 25 controls by quantitative PCR. A 5-year survival study was conducted in 121 of these CC patients. Furthermore, CDKN3-specific siRNAs were used to investigate whether CDKN3 is involved in proliferation, migration, and invasion in CC-derived cell lines (SiHa, CaSki, HeLa). CDKN3 mRNA was on average 6.4-fold higher in tumors than in controls (p = 8 x 10(-6), Mann-Whitney). A total of 68.2% of CC patients over expressing CDKN3 gene (fold change >= 17) died within two years of diagnosis, independent of the clinical stage and HPV type (Hazard Ratio = 5.0, 95% CI: 2.5-10, p = 3.3 x 10(-6), Cox proportional-hazards regression). In contrast, only 19.2% of the patients with lower CDKN3 expression died in the same period. In vitro inactivation of CDKN3 decreased cell proliferation on average 67%, although it had no effect on cell migration and invasion. CDKN3 mRNA may be a good survival biomarker and potential therapeutic target in CC.