Next-generation sequencing data analysis, expression analysis and clinical evaluation of alternative transcripts of genes located on 19q13.2-13.4 in human cancer cells and tissues

Postgraduate Thesis uoadl:2779387 412 Read counter

Unit:
Κατεύθυνση Κλινική Βιοχημεία - Μοριακή Διαγνωστική
Library of the School of Science
Deposit date:
2018-07-30
Year:
2018
Author:
Zisi Zafeiro
Supervisors info:
Σκορίλας Ανδρέας, Καθηγητής Κλινικής Βιοχημείας, Τμήμα Βιολογίας, Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών
Original Title:
Ανάλυση δεδομένων αλληλούχησης νέας γενιάς καθώς και μελέτη της έκφρασης και κλινική αξιολόγηση εναλλακτικών μεταγράφων γονιδίων στο γενετικό τόπο 19q13.2-13.4 σε καρκινικά κύτταρα και ιστούς
Languages:
Greek
Translated title:
Next-generation sequencing data analysis, expression analysis and clinical evaluation of alternative transcripts of genes located on 19q13.2-13.4 in human cancer cells and tissues
Summary:
The CEACAM19 gene (CarcinoEmbryonic Antigen-related Cell Adhesion Molecule 19) is part of the recently discovered CEACAM gene family which belongs to the Immunoglobulin gene Superfamily (IgSF) and codes for a group of highly glycosylated transmebrane glykoproteins. CEACAM19 is located in chromosome 19 and codes for a polypeptide of 300 aminoacids. The protein contains a highly conserved region of a eukaryotic translation initiation factor, eIF-5A, which is metabolically associated with transglutaminase expression and activity. Also, it has been proposed that it plays an important role in cellular development and differentiation. Expression analysis studies in healthy tissues indicate a wide expression of the gene.
Studies of the expression of CEACAM19 in cancer tissues lead to the conclusion that it is overexpressed in a wide range of cancer types. Additionally, in particular cancer types, such as breast and ovarian cancer, the gene’s expression was found to be associated with poor prognosis. These observations indicate the potential clinical use of CEACAM19 as a prognostic and monitoring cancer biomarker.
In the present study, sixteen new transcripts of the human CEACAM19 gene were identified and molecularly cloned using the techniques of nested PCR and Next Generation Sequencing (NGS). Extensive bioinformatic analysis revealed that these new transcripts are products of the alternative splicing mechanism and more specifically it was observed that four alternative splicing events may occur during the maturation of CEACAM19 pre-mRNA. Furthermore, NGS data analysis lead to the discovery of two new exons and the retention of the first intron of the gene. The analysis results were evaluated and confirmed by conducting nested PCR with transcript specific primers. These results were also useful for analyzing the expression profile of CEACAM19.
To conclude, the fact that the gene is expressed in a wide variety of cancer tissues in addition to its association with poor prognosis in certain cancer patients render the study and quantification of the new transcripts necessary in large scale studies, in order to explore their potential use as cancer biomarkers.
Main subject category:
Science
Keywords:
next generation sequencing, alternative splicing, biomarkers, cancer
Index:
Yes
Number of index pages:
3
Contains images:
Yes
Number of references:
105
Number of pages:
114
File:
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Διπλωματική Ζήση Ζαφείρω.pdf
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