Estimates for 2017 indicate that 20% of cancers globally are gastrointestinal tract (GIT) cancers, with oesophageal cancer being the 8th most common cancer. Oesophageal squamous cell carcinoma (OSCC) occurs in the upper to mid oesophagus and is present at high incidence in developing countries including South Africa. There are no early symptoms, resulting in late diagnosis and poor prognosis. In this study, tumour and blood DNA was obtained from 35 OSCC patients and subjected to whole genome sequencing (WGS). Bioinformatics analysis pipelines were designed to identify the possibility of novel viral insertions, investigating Human Endogenous Retroviruses (HERV's) insertions alongside the presence of somatic mutations in patient samples. The aims being to identify integration of any foreign DNA, to investigate if there is any linkage between HERV insertion and somatic mutations, and to identify any somatic mutations of potential interest in the OSCC cohort. The novel virus investigations however, proved to be inconclusive and there appeared to be no link between HERV insertions and somatic mutations present in the patients. Very significantly, it was determined that numerous somatic mutations were present in the MUC3A gene of the patient cohort, an interesting observation as no such previous association with OSCC has been recorded. MUC3A is a membrane-bound glycoprotein component of mucous gels, and its aberrant expression has been correlated with invasion and metastasis in a variety of other cancers. However, due to the complexity of the particular gene sequence and the known inconsistencies of variant calling performed on complex data sets, these mutations should be viewed with extreme caution as they are likely to be false positives. Analysis of RNA-seq data showed a 4.6 log2 fold increase in MUC3A expression in the tumour samples of these OSCC patients, with a P-adjusted value of 7.05e-06, suggesting highly significant differential gene expression. Functional enrichment analysis further showed that MUC3A was significantly associated with one of the top 5 gene ontologies (extracellular matrix structural constituent) for molecular function ontology class together with a number of collagen (COL) and MMP genes known to play a role in oncogenic progression and membrane stiffness. GSEA and KEGG analysis indicated predominantly chemokine/cytokine pro-inflammatory enriched pathways. Immunohistochemistry staining showed 10 out of 13 of the samples had no detectable levels of MUC3A protein, suggesting that the production of a non-functional truncated protein may lead to the upregulation of MUC3A expression that could possibly play a role in downstream pro-oncogenic signalling.

Although it is not a new method endoscopy has undergone incredible development in recent years. The examination is however very unpleasant for a patient, which is why health care staff should be well trained, particularly for child patients. The aim of the thesis was to map the specifics of nursing care for children undergoing endoscopic examination of the gastrointestinal tract. We approached the whole issue from the point of view of caring staff ? nurses. In the theoretical part we first described the gastrointestinal tract anatomy, endoscopy development and types of endoscopic examination. Then we dealt with the role of a nurse in the care for child patients undergoing these examinations. We formed three goals for the research. Goal 1: To find out how nurses prepare child patients for the individual endoscopic examinations. Goal 2: To verify whether nurses caring about a child patient undergoing gastrointestinal tract endoscopy are specifically trained. Goal 3 served as the output of the work: To elaborate recommendation for nurses preparing child patients for the individual endoscopic examinations. We chose quantitative research for collection of the necessary information. A questionnaire designed for nurses caring for child patients was the data collection technique. The questionnaire was anonymous, distributed at paediatric clinics of faculty hospitals of Moravian region. 104 questionnaires suitable for processing returned from 140 issued. The research has shown that nurses working at the clinics where the research was performed master the correct nursing care for child patients undergoing endoscopic examination of the gastrointestinal tract. Nevertheless the fact that most information is gained upon practical experience, with low emphasis on initial and repeated training of nurses also results from the research. A recommendation was elaborated upon the gathered information in the form of a standard nursing procedure proposal.