Computational analyses of transcriptome and DNA methylation data

dc.contributorAalto-yliopistofi
dc.contributorAalto Universityen
dc.contributor.advisorLähdesmäki, Harri, Prof., Aalto University, Department of Computer Science. Finland
dc.contributor.authorMalonzo, Maia
dc.contributor.departmentTietotekniikan laitosfi
dc.contributor.departmentDepartment of Computer Scienceen
dc.contributor.labComputational Systems Biology Groupen
dc.contributor.schoolPerustieteiden korkeakoulufi
dc.contributor.schoolSchool of Scienceen
dc.contributor.supervisorLähdesmäki, Harri, Prof., Aalto University, Department of Computer Science. Finland
dc.date.accessioned2024-04-10T09:00:17Z
dc.date.available2024-04-10T09:00:17Z
dc.date.defence2024-04-25
dc.date.issued2024
dc.description.abstractTranscriptomics and epigenomics, via DNA methylation, both study regulation of gene expression. Transcriptomics cover both expression of coding genes which lead to protein expression as well as non-coding genes, like microRNAs, which regulate gene expression, as well as alternative gene splicing. DNA methylation, on the other hand, is the addition of a methyl group to DNA, mostly cytosine, that can either repress or enhance gene expression. Analysis of the transcriptome and DNA methylome are performed to better understand development of diseases (and identify biomarkers) and biological processes such as stem cell development. In this thesis, we analyzed transcriptome and DNA methylation datasets to better understand aspects of stem cell regulation and diseases (asthma and Alzheimer's disease) as well as developed methods for analyzing DNA methylation data.Transcriptome analysis was performed on stem cells to elucidate the function of a stem cell-specific gene, POLR3G, and to determine the relationship of the microRNA Let-7 and protein LIN28 in human embryonic stem cells. It was shown that POLR3G functions in stem cell maintenance rather than repression of transcription as most of the differentially expressed genes were downregulated, which included both coding and non-coding genes. Let-7 and LIN28 function in a negative feedback loop in mouse embryonic stem cells. Unlike the assumption that Let-7 and LIN28 function in hESC as in mESC, it was found that both are expressed in pluripotent hESC. DNA methylation analysis was performed in two diseases, Alzheimer's disease and asthma, as well as on stem cells. Blood samples from twins discordant for AD were analyzed. A gene associated with cognitive function, ADARB2, was found to be differentially methylated in both blood and brain samples. Analysis of blood samples from children with atopic and non-atopic asthma and controls showed that genes previously associated with the immune response and asthma, SMAD3 and PTGDS, were found to be differentially methylated in children with atopic and non-atopic asthma, respectively. Analysis of karyotypically abnormal stem cells showed that a gene known to protect cells against DNA damage and oxidative stress, CAT, was found to be hypermethylated. Moreover, CAT was also found to be differentially methylated in publicly available cancer cell line data. Cancer shares the property of self-renewal with stem cells.Two methods were developed for analysis of DNA methylation data. LuxRep identifies differentially methylated loci by modelling the biochemistry of bisulfite sequencing (BS-seq) at the level of individual DNA methylation libraries. It was shown that inclusion of libraries with varying bisulfite conversion rates in methylation analysis increases accuracy of differential methylation detection. LuxHMM uses HMM and Bayesian regression to identify differentially methylated regions and was shown to perform competitively against other published methods.en
dc.format.extent80 + app. 96
dc.format.mimetypeapplication/pdfen
dc.identifier.isbn978-952-64-1758-5 (electronic)
dc.identifier.isbn978-952-64-1757-8 (printed)
dc.identifier.issn1799-4942 (electronic)
dc.identifier.issn1799-4934 (printed)
dc.identifier.issn1799-4934 (ISSN-L)
dc.identifier.urihttps://aaltodoc.aalto.fi/handle/123456789/127384
dc.identifier.urnURN:ISBN:978-952-64-1758-5
dc.language.isoenen
dc.opnAutio, Reija, Docent, Dr. (Tech.), Senior Research Fellow, Tampere University, Finland
dc.publisherAalto Universityen
dc.publisherAalto-yliopistofi
dc.relation.haspart[Publication 1]: Riikka J. Lund, Nelly Rahkonen, Maia Malonzo, Leni Kauko, Maheswara Reddy Emani, Virpi Kivinen, Elisa Närvä, Esko Kemppainen, Asta Laiho, Heli Skottman, Outi Hovatta, Omid Rasool, Matti Nykter, Harri Lähdesmäki and Riitta Lahesmaa. RNA Polymerase III Subunit POLR3G regulates specific subsets of polyA+ and smallRNA transcriptomes and splicing in human pluripotent stem cells. Stem Cell Reports, 8, 5, 1442-1454, 2017. Full text in Acris/Aaltodoc: https://urn.fi/URN:NBN:fi:aalto-201812216627. DOI: 10.1016/j.stemcr.2017.04.016
dc.relation.haspart[Publication 2]: Nelly Rahkonen, Aki Stubb, Maia Malonzo, Sanna Edelman, Maheswara Reddy Emani, Elisa Närvä, Harri Lähdesmäki, Hannele Ruohola-Baker, Riitta Lahesmaa and Riikka Lund. Mature Let-7 miRNAs fine tune expression of LIN28B in pluripotent human embryonic stem cells. Stem Cell Research, 17, 3, 498-503, 2016. Full text in Acris/Aaltodoc: https://urn.fi/URN:NBN:fi:aalto-201704283714. DOI: 10.1016/j.scr.2016.09.025
dc.relation.haspart[Publication 3]: Mikko Konki, Maia Malonzo, Ida K. Karlsson, Noora Lindgren, Bishwa Ghimire, Johannes Smolander, Noora M. Scheinin, Miina Ollikainen, Asta Laiho, Laura L. Elo, Tapio Lönnberg, Matias Röyttä, Nancy L. Pedersen, Jaakko Kaprio, Harri Lähdesmäki, Juha O. Rinne and Riikka J. Lund. Peripheral blood DNA methylation differences in twin pairs discordant for Alzheimer’s disease. Clinical epigenetics, 11, 1, 1-12, 2019. Full text in Acris/Aaltodoc: https://urn.fi/URN:NBN:fi:aalto-202001021151. DOI: 10.1186/s13148-019-0729-7
dc.relation.haspart[Publication 4]: Riikka J. Lund, Maria Osmala, Maia Malonzo, Minna Lukkarinen, Annamari Leino, Jussi Salmi, Sanna Vuorikoski, Riitta Turunen, Tytti Vuorinen, Cezmi Akdis, Harri Lähdesmäki, Riitta Lahesmaa and Tuomas Jartti. Atopic asthma after rhinovirus-induced wheezing is associated with DNA methylation change in the SMAD3 gene promoter. Allergy, 73, 8, 1735-1740, 2018. Full text in Acris/Aaltodoc: https://urn.fi/URN:NBN:fi:aalto-201808084473. DOI: 10.1111/all.13473
dc.relation.haspart[Publication 5]: Mikko Konki, Kalyan Pasumarthy, Maia Malonzo, Annele Sainio, Cristina Valensisi, Mirva Söderström, Maheswara Reddy Emani, Aki Stubb, Elisa Närvä, Bishwa Ghimire, Asta Laiho, Hannu Järveläinen, Riitta Lahesmaa, Harri Lähdesmäki, R. David Hawkins, and Riikka J. Lund. Epigenetic silencing of the key antioxidant enzyme Catalase in karyotypically abnormal human pluripotent stem cells. Scientific reports, 6, 1, 1-8, 2016. Full text in Acris/Aaltodoc: https://urn.fi/URN:NBN:fi:aalto-201705114192. DOI: 10.1038/srep22190
dc.relation.haspart[Publication 6]: Maia H. Malonzo, Viivi Halla-aho, Mikko Konki, Riikka J. Lund and Harri Lähdesmäki . LuxRep: a technical replicate-aware method for bisulfite sequencing data analysis. BMC bioinformatics, 23, 1, 1-19, 2022. DOI: 10.1186/s12859-021-04546-1
dc.relation.haspart[Publication 7]: Maia H. Malonzo and Harri Lähdesmäki. LuxHMM: DNA methylation analysis with genome segmentation via hidden Markov model. BMC bioinformatics, 24, 1, 1-14, 2023. DOI: 10.1186/s12859-023-05174-7
dc.relation.ispartofseriesAalto University publication series DOCTORAL THESESen
dc.relation.ispartofseries74/2024
dc.revAutio, Reija, Docent, Dr. (Tech.), Senior Research Fellow, Tampere University, Finland
dc.revHautaniemi, Sampsa, Prof., University of Helsinki, Finland
dc.subject.keywordtranscriptomeen
dc.subject.keywordDNA methylationen
dc.subject.keywordbisulfite sequencingen
dc.subject.otherComputer scienceen
dc.titleComputational analyses of transcriptome and DNA methylation dataen
dc.typeG5 Artikkeliväitöskirjafi
dc.type.dcmitypetexten
dc.type.ontasotDoctoral dissertation (article-based)en
dc.type.ontasotVäitöskirja (artikkeli)fi
local.aalto.acrisexportstatuschecked 2024-04-26_1058
local.aalto.archiveyes
local.aalto.formfolder2024_04_10_klo_08_17
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