Promjena entropije metiloma kao pokazatelj epigenetičke deregulacije uzrokovane stresom ili malignom transformacijom

master's thesis

• Title (english): The change in methylome entropy as an indicator of epigenetic deregulation caused by stress or malignant transformation
• Author: Carmen Rožmanić
• Mentor: Aleksandar Vojta (mentor)
• Committee member: Aleksandar Vojta (predsjednik povjerenstva)
• Committee member: Anamaria Štambuk (član povjerenstva)
• Committee member: Marija Gligora Udovič (član povjerenstva)
• Committee member: Mirjana Pavlica (član povjerenstva)
• Granter: University of Zagreb; Faculty of Science; (Department of Biology); Zagreb
• Defense date and country: 2017-12-19, Croatia
• Scientific / art field, discipline and subdiscipline: NATURAL SCIENCES; Biology

Abstract

Koncept entropije prelazi granice teorijske fizike i može se proširiti na teoriju informacije, gdje je poznat kao Shannonova entropija i služi za kvantifikaciju informacijskog sadržaja poruke. Ovaj pristup može se iskoristiti za kvantitativnu procjenu varijacije metilacije DNA, koja predstavlja važan epigenetički mehanizam. Entropija sadržana u uzorku metilacije DNA (entropija metiloma) korelira sa starošću organizma, a promjene u metilaciji DNA povezane su i s kompleksnim bolestima koje prate starenje, kao što su metaboličke bolesti i rak. Djelovanjem stresa aktiviraju se obrambeni mehanizmi stanice koji su epigenetički uvjetovani. Do sada je pokazano da se epigenetičke promjene uzrokovane starenjem i malignom transformacijom odražavaju na informacijskom sadržaju, odnosno entropiji metiloma. U ovom diplomskom radu odabrani su prikladni setovi podataka iz javne baze podataka GEO, implementirana je metoda za određivanje entropije metiloma, određena je epigenetička dob uzoraka i testirana je hipoteza da su promjene uzrokovane raznim tipovima stresa na staničnoj razini analogne promjenama kod degenerativnih procesa kao što su starenje i maligna transformacija. Dobiveni rezultati nemaju statističku značajnost i ovim istraživanjem nije potvrđena postavljena hipoteza. Odabir setova podataka s većim brojem uzoraka ili određivanje entropije posebno odabranih CpG mjesta koja su specifično vezana uz stres bi moglo u budućim istraživanjima dati statistički značajne rezultate.

Abstract (english)

The concept of entropy exceeds the boundaries of theoretical physics and can be expanded on the theory of information where it is known as Shannon entropy. Shannon entropy is used for quantifying information content of a message. This approach can be used to evaluate the variation in DNA methylation, which represents an important epigenetic mechanism. Entropy of DNA methylation patterns (methylome entropy) correlates with chronological age, and changes in DNA methylation are associated with age-related diseases, such as cancer and metabolic disease. On cellular level, stress activates defensive mechanisms, which are epigenetically conditioned. So far it has been shown that epigenetic changes caused by aging and malignant transformation are reflected on information content, or in other words, on methylation entropy. In this thesis we selected data sets from Gene Expression Omnibus (GEO) database, we implemented the method for calculating methylation entropy, we determined the epigenetic age of selected data and we tested the hypothesis that changes caused by various types of stress on a cellular level are synonymous to changes happening in degenerative processes like aging and malignant transformation. Obtained data doesn’t have statistic value, and this experiment didn’t prove the hypothesis. In further experiments of this type. Choosing data sets with bigger number of samples or determinating entropy of carefully chosen CpG places which are in specific correlation with stress could in future scientific research give statistically significant results.

• Keywords: epigenetika; entropija; metilom; stres
• Keywords (english): epigenetics; entropy; methylome; stress
• Language: croatian
• URN:NBN: urn:nbn:hr:217:399277
• Study programme: Title: Experimental Biology; Study programme type: university; Study level: graduate; Academic / professional title: magistar/magistra eksperimentalne biologije (magistar/magistra eksperimentalne biologije)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Open access
• Created on: 2018-01-30 09:00:29