Jessenius Faculty of Medicine
in Martin
Comenius University in Bratislava

Department of Molecular Oncology and Diagnostics

 

Head of department: MSc. Veronika Holubeková, PhD.

 

Laboratory of Molecular Pathology (LMP)

Head of laboratory: MSc. Karin Jašek, PhD.

The Laboratory of Molecular Pathology is based on the collaboration of the Department of Pathological Anatomy JFM CU and UHM and the Department of Molecular Biology JFM CU and UHM, which allowed the implementation of original diagnostic procedures and create detailed molecular-characterized cohorts of patients with gastrointestinal stromal tumors, colorectal cancer and myeloproliferative disease. Important part of the research is the non-invasive detec­tion of specific mutations and analysis of tumor heterogeneity using the digital PCR (Fig. 2). In our laboratory we are using the droplet digital PCR that allows for absolute quantification of target DNA molecules and it is possible to use it for the de­tection of copy number variations (CNV), detection of selected mutations and analysis of gene expression. We are also engaged in the detection of BRAF and KRAS mutations in patients diagnosed with colorectal cancer (CRC) and gastrointestinal stromal tumors (GIST) using droplet digital PCR. Our aim is to map the incidence of KRAS and BRAF mutations in oncological disorders and similarly to explain tumour heterogeneity in patients with CRC and GIST.

Fig. 2. Evaluation of mutation analysis for the detection of point mutation in the gene by droplet digital PCR

 

Laboratory of oncological genomics (LOG)

Head of laboratory: Dip. Biol. Katarína Baluchová, PhD.

Laboratory concentrates on collaboration in clinical oncological research with Department of Pathological Anatomy JFM CU and UHM, Urological Clinic JFM CU and UHM, Clinic of Surgery with Transplantation Center JFM CU and UHM and Clinic of Hematology and Transfusiology JFM CU and UHM. The LOG has initiated genomic analysis of tumour cell lines in order to uncover new aspects of cellular regulation in carcinogenesis and to identify new potential therapeutic targets.

In the following project we are using microsatellite instability (MSI) analysis of tumor tissues and studying the methylator phenotype of colorectal cancer.

In a close collaboration with the Laboratory of Molecular pathology, we are going to implement targeted resequencing as one of the most effective strategies allowing for systematic identification of ge­netic changes such as single nucleotide variants, insertions and deletions, variations in the copy number and large genomic alternations. These analyses allow for detection of specific DNA changes in patient´s samples with massive parallel sequencing of several selected genes, which number can include several dozens to hundreds (Fig.3). The big advantage is the possibility to analyze the most frequent mutations, the most mutated on­cogenes and tumor suppressor genes with the follow up of se­lected and potentially clinically relevant genes. The adjustment of sequencing depth allows for detection of somatic changes with high sensitivity.

Fig. 3. The IonPGM is suitable for the mutational analysis of hotspots and for deep sequencing of selected genes responsible for tumor diseases.

The LOG is also analysing the expression of selected apoptotic and anti-apoptotic miRNAs in patients with chronic lymphocytic leukaemia (CLL). The goal is to detect new microRNAs in the peripheral blood of CLL patients which are overexpressed or downregulated. These observations may be used to develop biomarkers and assist in the prediction, treatment and subsequent prognosis of the disease. Using the microarray technology, it is possible to analyse the expression of all recently described miRNA and the CNV in the tumor DNA as well (Obr. 4).

An important research area of the LOG is also molecular profiling of prostate cancer. Aberrant signalling pathways of the androgen receptor play a key role in the prostate carcinogenesis. In our working group, we are studying potential biomarkers that would eventually lead to an early detection of high-risk patients diagnosed with prostate cancer. Such patients may receive radical treatment that would save, extend or improve their lives.

Fig. 4 Working on Agilent Microarray scanner

 

Laboratory molecular oncogynecology

Head of laboratory: RNDr. Zuzana Danková, PhD.

The research activities of this laboratory are specifically focused on the molecular analyses of the breast, ovarian and cervical cancer. The laboratory follows genetic and epigenetic changes in cancer tissue and analyze genetic predisposition for the specific tumorigenesis. The tissue and nucleic acid samples create the biobank.

The current analyses constitute of the identification of genetic changes in somatic mutations of patients with breast or ovarian cancer by the Illumina´s second generation sequencing platform. The obtained data are compared with results of invasive (paraffin embedded tissue) and noninvasive (peripheral blood) diagnostics methods with the aim to assess the effect of standard adjuvant therapy on the patients gene profile.

The laboratory also screens the high-risk types of human papillomavirus (HPV) by in vitro qualitative detection of E6/E7 mRNA using the APTIMA HPV assay tests. Other analyses assess the quantitative methylation of selected promoter regions by pyrosequencing.

The research is focused also on the methylation detection of the breast cancer samples by High Resolution Melting method. The occurrence and quantity of the methylation, obtained from the paraffin embedded tissues, is correlated with known histopatological parameters of the cancer to assess the reciprocal associations. The differences between the methylation status and early stages of the cancer are also evaluated. The results might contribute to the whole patient’s management of diagnostics and therapy.  

The laboratory is preparing the analyses of the oncogene miRNA regulating the gene expression on the posttranscriptional level, evaluating the impact of these molecules during the diagnostics, carcinogenesis and treatment of the breast cancer.

 

Laboratory of environmental oncology

Head of laboratory: MSc. Andrea Kapinová, PhD.

Laboratory of Environmental Oncology is focused on observing of causes of cancers of the respiratory tract and oral cavity. Research is oriented at individual risk of onset and development of neoplastic disease based on genetic predisposition, and also on the possibility of early non-invasive detection of disease.

 

To the Oncology division are integrating parts of projects exploited on the JLF UK focusing on molecular, clinical and ex­perimental oncology i.e.

  • Center of Translation Medicine,
  • Center of Excellence for Research in Personalised Therapy,
  • Molecular Diagnostics of Cervical Cancer,
  • Competence Center for Research and Development in the Area of Diagnostics and Therapy of Oncological Diseases.