Unit:
Κατεύθυνση Κλινική Βιοχημεία - Μοριακή ΔιαγνωστικήLibrary of the School of Science
Supervisors info:
Ανδρέας Σκορίλας, Καθηγητής, Τμήμα Βιολογίας, Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών
Original Title:
Μελέτη και κλινική αξιολόγηση μη κωδικών μορίων RNA (ncRNAs), με χρήση δεδομένων αλληλούχησης επόμενης γενιάς, ως νέοι μοριακοί βιοδείκτες καρκίνου
Translated title:
Investigation and clinical evaluation of small non-coding RNAs (ncRNAs) as new molecular cancer biomarkers, using next generation sequencing data
Summary:
Next generation sequencing is a recent method for sequencing of the genome and reveals uninvestigated parts of it. This analysis is useful for prognosis, diagnosis and therapy of diseases such as cancer. Colorectal cancer is the fourth deadliest type of cancer and the establishment of colorectal cancer biomarkers is vital. Small non-coding RNA molecules, such as tRFs, have been investigated by NGS technology and there is a constant interest on them. tRFs derived from pre-mature or mature tRNA molecule and they regulate expression of genes related to cancer and other pathological states. In the present study NGS experiments for colorectal cancer that are registered in the SRA database were analyzed bioinformatically. After this analysis, we examined 3’tRF-GluTTC expression levels in 113 colorectal cancer samples and 50 adjacent non-cancerous counterparts, due to their significant expression in SRA experiments. After the measurement of RNA concentration of the colorectal cancer samples, polyadenylation by the enzyme E. coli and reverse transcription by the reverse transcriptase M-MLV took place. The expression analysis of 3’tRF-GluTTC was carried out using an in-house developed qPCR methodology based on SYBR green chemistry. SYBR green is a non-specific fluorescent dye. The reference gene in qPCR was SNORD48 and colorectal cancer cell line SW-620 was the calibrator between different qPCR experiments. The confirmation about the unique product of qPCR was took place by electrophoresis in agarose gel. 3’tRF-GluTTC expression levels were found significantly lower in cancer than normal tissue samples, after the biostatistical analysis of the 50 sample pairs. Also, patients with elevated 3’tRF-GluTTC expression levels demonstrated significantly lower overall survival. The same trend was observed in stage Ι/ΙΙ as well as grade II patients. In summary, 3’tRF-GluTTC molecule may be a candidate adverse biomarker in prognosis of colorectal adenocarcinoma.
Main subject category:
Science
Keywords:
non-coding RNA, biomarkers, Next Generation Sequencing, colorectal cancer
Number of references:
297
