The analysis of Fanconi anemia/BRCA pathway genesin laryngeal carcinoma

Summary of Doctoral Thesis/Streszczenie pracy doktorskie

DNA Methylation Profiling of Breast Cancer Cell Lines along the Epithelial Mesenchymal Spectrum—Implications for the Choice of Circulating Tumour DNA Methylation Markers

(1) Background: Epithelial–mesenchymal plasticity (EMP) is a dynamic process whereby epithelial carcinoma cells reversibly acquire morphological and invasive characteristics typical of mesenchymal cells. Identifying the methylation differences between epithelial and mesenchymal states may assist in the identification of optimal DNA methylation biomarkers for the blood-based monitoring of cancer. (2) Methods: Methylation-sensitive high-resolution melting (MS-HRM) was used to examine the promoter methylation status of a panel of established and novel markers in a range of breast cancer cell lines spanning the epithelial–mesenchymal spectrum. Pyrosequencing was used to validate the MS-HRM results. (3) Results: VIM, DKK3, and CRABP1 were methylated in the majority of epithelial breast cancer cell lines, while methylation of GRHL2, MIR200C, and CDH1 was restricted to mesenchymal cell lines. Some markers that have been used to assess minimal residual disease such as AKR1B1 and APC methylation proved to be specific for epithelial breast cell lines. However, RASSF1A, RARβ, TWIST1, and SFRP2 methylation was seen in both epithelial and mesenchymal cell lines, supporting their suitability for a multimarker panel. (4) Conclusions: Profiling DNA methylation shows a distinction between epithelial and mesenchymal phenotypes. Understanding how DNA methylation varies between epithelial and mesenchymal phenotypes may lead to more rational selection of methylation-based biomarkers for circulating tumour DNA analysis

DNA methylation profiling of breast cancer cell lines along the epithelial mesenchymal spectrum - implications for the choice of circulating tumour DNA methylation markers

Epithelial-mesenchymal plasticity (EMP) is a dynamic process whereby epithelial carcinoma cells reversibly acquire morphological and invasive characteristics typical of mesenchymal cells, which facilitates metastasis. Understanding the methylation differences between epithelial and mesenchymal states may assist in the identification of optimal DNA methylation biomarkers for the blood-based monitoring of cancer. Methylation-sensitive high-resolution melting (MS-HRM) was used to examine the promoter methylation status of a panel of established and novel markers in a range of breast cancer cell lines spanning the epithelial-mesenchymal spectrum. Pyrosequencing was used to validate the MS-HRM results. The results indicate an overall distinction in methylation between epithelial and mesenchymal phenotypes. The mesenchymal expression markers VIM, DKK3 and CRABP1 were methylated in the majority of epithelial breast cancer cell lines while methylation of the epithelial expression markers GRHL2, MIR200C and CDH1 was restricted to mesenchymal cell lines. We also examined EMP association of several methylation markers that have been used to assess minimal residual disease. Markers such as AKR1B1 and APC methylation proved to be selective for epithelial breast cell lines, however RASSF1A, RARB, TWIST1 and SFRP2 methylation was seen in both epithelial and mesenchymal cell lines, supporting their suitability for a multi-marker panel

Polymorphisms in base-excision repair and nucleotide-excision repair genes in relation to lung cancer risk

A

Global miRNA Expression Profiling Identifies miR-1290 as Novel Potential oncomiR in Laryngeal Carcinoma.

Laryngeal squamous cell carcinoma (LSCC) is the most common group among head and neck cancers. LSCC is characterized by a high incidence in Europe. With the aim of better understanding its genetic background we performed global miRNA expression profiling of LSCC cell lines and primary specimens. By this approach we identified a cohort of 33 upregulated and 9 downregulated miRNA genes in LSCC as compared to epithelial no tumor controls.Within this group we identified overexpression of the novel miR-1290 gene not reported in the context of LSCC before. Using a combined bioinformatical approach in connection with functional analysis we delineated two putative target genes of miR-1290 namely ITPR2 and MAF which are significantly downregulated in LSCC. They are interesting candidates for tumor suppressor genes as they are implicated in apoptosis and other processes deregulated in cancer.Taken together, we propose miR-1290 as the new oncomiR involved in LSCC pathogenesis. Additionally, we suggest that the oncogenic potential of miR-1290 might be expressed by the involvement in downregulation of its target genes MAF and ITPR2

Expression level of miR-1290 target genes.

<p>A) Changes in expression level of <i>MAF</i>, <i>ITPR2</i> and <i>KIF13B</i> genes in UT-SCC-34 treated by miR-1290 inhibitor (black graph) compared to both UT-SCC-34 treated by negative control (dark gray graph) as well as UT-SCC-34 wild type (gray graph). * fold change in UT-SCC-34 treated by miR-1290 inhibitor compared to UT-SCC-34 treated by negative control. B) Changes in expression level of MAF protein in UT-SCC-34 and UT-SCC-107cell lines treated by miR-1290 inhibitor (black graph) compared to both cells treated by negative control (dark gray graph) as well as wild type cells (gray graph). * fold change in cells treated by miR-1290 inhibitor compared to cells treated by negative control.</p

Expression level of selected miRNA and selection scheme of miR-1290 target genes.

<p>A) Overexpression of miR-1290 and miR-1246 in primary LSCC cases (LNA real-time qPCR). B) Schematic presentation of the selection process of miR-1290 candidate genes. C) Expression level of <i>MAF</i>, <i>ITPR2</i> and <i>RGS5</i> in LSCC cell lines and no tumor controls (Affymetrix U133 plus 2.0) based on [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144924#pone.0144924.ref020" target="_blank">20</a>]. * fold change in LSCC cell lines compared to no tumor controls. D) Expression level of <i>MAF</i> and <i>ITPR2</i> in 22 primary tumor samples compared to 5 no tumor controls.</p