{"id":{"repo_id":"helsinki","oai_identifier":"oai:helda.helsinki.fi:10138/576810"},"canonical_url":"https://search.dev.ndltd.org/etd/helsinki/oai:helda.helsinki.fi:10138/576810","repository":{"repo_id":"helsinki","name":"University of Helsinki","base_url":"https://helda.helsinki.fi/server/oai/request"},"display":{"title":"The Role of Epigenetics in Hereditary Colorectal Cancer Tumorigenesis: Validation of Genome-Wide Methylation Array Results through Bisulfite Sequencing","abstract":"Colorectal cancer (CRC) poses a considerable global health challenge, with high mortality rates despite advancements in cancer research. Approximately one in ten CRC cases have a hereditary basis, with Lynch syndrome and Familial adenomatous polyposis standing as the two predominant cancer-predisposing syndromes. These conditions are mainly attributed to specific dominant germline mutations in CRC-related genes. However, as the role of epigenetic modifications, including DNA methylation, has become increasingly recognized in colorectal tumorigenesis, identifying these distinct signatures is paramount in gaining deeper insights into the molecular mechanisms underlying CRC. This thesis, conducted as a part of ongoing research into the DNA methylation profile of Lynch syndrome and Familial adenomatous polyposis-associated colorectal tumors, aimed to validate methylation patterns previously obtained from a genome-wide Illumina Methylation EPIC BeadChip array. The validation was performed by utilizing direct bisulfite sequencing across 12 selected gene regions on CRC cell lines and histologically normal control samples and comparing the methylation status to the EPIC array results. The genomic regions selected for this analysis were chosen based on differential methylation observed with EPIC and literature and were limited to regions that included at least one GCGC site for the HhaI digestion enzyme for future in-house MS-MLPA probe design. The results of this study demonstrate a clear differential methylation pattern of the selected genes, with CRC cell lines generally exhibiting higher methylation levels compared to non-cancerous samples, as expected. Specifically, high concordance between EPIC results and bisulfite sequencing data was observed in the methylation status of ADHFE1, EYA4, ITGA4, FBLIM1, and SEPT9, whose connection to CRC has been also shown in the previous studies. Further investigations of the genes in this study could contribute to a better understanding of epigenetic changes underlying colorectal tumors and hold the potential for developing novel biomarkers for early diagnosis and improved patient prognosis.","abstract_html":"Colorectal cancer (CRC) poses a considerable global health challenge, with high mortality rates despite advancements in cancer research. Approximately one in ten CRC cases have a hereditary basis, with Lynch syndrome and Familial adenomatous polyposis standing as the two predominant cancer-predisposing syndromes. These conditions are mainly attributed to specific dominant germline mutations in CRC-related genes. However, as the role of epigenetic modifications, including DNA methylation, has become increasingly recognized in colorectal tumorigenesis, identifying these distinct signatures is paramount in gaining deeper insights into the molecular mechanisms underlying CRC. This thesis, conducted as a part of ongoing research into the DNA methylation profile of Lynch syndrome and Familial adenomatous polyposis-associated colorectal tumors, aimed to validate methylation patterns previously obtained from a genome-wide Illumina Methylation EPIC BeadChip array. The validation was performed by utilizing direct bisulfite sequencing across 12 selected gene regions on CRC cell lines and histologically normal control samples and comparing the methylation status to the EPIC array results. The genomic regions selected for this analysis were chosen based on differential methylation observed with EPIC and literature and were limited to regions that included at least one GCGC site for the HhaI digestion enzyme for future in-house MS-MLPA probe design. The results of this study demonstrate a clear differential methylation pattern of the selected genes, with CRC cell lines generally exhibiting higher methylation levels compared to non-cancerous samples, as expected. Specifically, high concordance between EPIC results and bisulfite sequencing data was observed in the methylation status of ADHFE1, EYA4, ITGA4, FBLIM1, and SEPT9, whose connection to CRC has been also shown in the previous studies. Further investigations of the genes in this study could contribute to a better understanding of epigenetic changes underlying colorectal tumors and hold the potential for developing novel biomarkers for early diagnosis and improved patient prognosis.","abstract_has_math":false,"creators":["Puustinen, Taru"],"institution":"Helsingin yliopisto","degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":null,"school":null,"contributors":["Helsingin yliopisto, Bio- ja ympäristötieteellinen tiedekunta","University of Helsinki, Faculty of Biological and Environmental Sciences","Helsingfors universitet, Bio- och miljövetenskapliga fakulteten"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2024,"date_issued":"2024","date_published":"2024","updated_at":"2026-07-27T19:56:17Z","subjects":["adenoma","bisulfite sequencing","Colorectal cancer","CIMP","DNA methylation","Familial adenomatous polyposis","hereditary CRC","Lynch syndrome","microsatellite instability"],"languages":["eng"],"rights":[],"rights_urls":[],"identifier_entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["URN:NBN:fi:hulib-202406112671"],"render_values":[{"text":"URN:NBN:fi:hulib-202406112671","href":null,"code":true}]}]},"links":{"outbound_url":"http://hdl.handle.net/10138/576810","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Helsingin yliopisto, Bio- ja ympäristötieteellinen tiedekunta","University of Helsinki, Faculty of Biological and Environmental Sciences","Helsingfors universitet, Bio- och miljövetenskapliga fakulteten"]},{"key":"dc:creator","label":"Author","values":["Puustinen, Taru"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.issued","label":"Date","values":["2024"]},{"key":"dc:publisher","label":"Institution","values":["Helsingin yliopisto","University of Helsinki","Helsingfors universitet"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["adenoma","bisulfite sequencing","Colorectal cancer","CIMP","DNA methylation","Familial adenomatous polyposis","hereditary CRC","Lynch syndrome","microsatellite instability"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language.iso","label":"Language (ISO)","values":["eng"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["URN:NBN:fi:hulib-202406112671","http://hdl.handle.net/10138/576810"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Colorectal cancer (CRC) poses a considerable global health challenge, with high mortality rates despite advancements in cancer research. Approximately one in ten CRC cases have a hereditary basis, with Lynch syndrome and Familial adenomatous polyposis standing as the two predominant cancer-predisposing syndromes. These conditions are mainly attributed to specific dominant germline mutations in CRC-related genes. However, as the role of epigenetic modifications, including DNA methylation, has become increasingly recognized in colorectal tumorigenesis, identifying these distinct signatures is paramount in gaining deeper insights into the molecular mechanisms underlying CRC. This thesis, conducted as a part of ongoing research into the DNA methylation profile of Lynch syndrome and Familial adenomatous polyposis-associated colorectal tumors, aimed to validate methylation patterns previously obtained from a genome-wide Illumina Methylation EPIC BeadChip array. The validation was performed by utilizing direct bisulfite sequencing across 12 selected gene regions on CRC cell lines and histologically normal control samples and comparing the methylation status to the EPIC array results. The genomic regions selected for this analysis were chosen based on differential methylation observed with EPIC and literature and were limited to regions that included at least one GCGC site for the HhaI digestion enzyme for future in-house MS-MLPA probe design. The results of this study demonstrate a clear differential methylation pattern of the selected genes, with CRC cell lines generally exhibiting higher methylation levels compared to non-cancerous samples, as expected. Specifically, high concordance between EPIC results and bisulfite sequencing data was observed in the methylation status of ADHFE1, EYA4, ITGA4, FBLIM1, and SEPT9, whose connection to CRC has been also shown in the previous studies. Further investigations of the genes in this study could contribute to a better understanding of epigenetic changes underlying colorectal tumors and hold the potential for developing novel biomarkers for early diagnosis and improved patient prognosis.","Edistyneestä syöpätutkimuksesta huolimatta suolistosyöpä aiheuttaa merkittävän globaalin terveysuhan korkean kuolleisuuden vuoksi. Noin joka kymmenes tapauksista johtuu perinnöllisistä syövälle altistavista oireyhtymistä, joista kaksi yleisintä ovat Lynchin oireyhtymä ja familiaalinen adenomatoottinen polypoosi. Näissä tapauksissa alttius syövälle on usein peräisin ituradan mutaatioista suolistosyövälle altistavissa geeneissä. Nykyisin myös epigeneettisten muutosten, kuten DNA metylaation rooli suolistosyövässä on yhä paremmin tunnettu. Siksi metylaatio muutosten tunnistaminen on ensisijaisen tärkeää suolistosyövän molekulaarisen taustan selvittämiseksi. Tämä tutkielma on osa laajempaa käynnissä olevaa tutkimusta Lynchin oireyhtymään ja perinnölliseen adenomatoottiseen polypoosiin liittyvien kasvainten metylaatioprofiilista. Pyrkimyksenä oli vahvistaa genomin laajuisen Illumina Methylation EPIC BeadChip -sirun avulla havaittujen metylaatiokuvioiden yhtenäisyys. Tässä tehtävässä hyödynnettiin bisulfiittisekvensointia, jonka avulla metylaatiostatus tutkittiin 12 valitun geenin alueella suolistosyöpä-solulinjoilla ja histologisesti normaaleilla kontrollinäytteillä. Tämän jälkeen sekvensoinnin tuloksia verrattiin EPIC-analyysin tuloksiin. Genomisten alueiden valinta tätä tutkimusta varten perustui EPIC-analyysin osoittamaan poikkeavaan metylaatioon sekä kirjallisuuteen. Toisena valintakriteerinä kunkin alueen tuli myös sisältää vähintään yksi GCGC-kohta HhaI entsyymiä varten tulevan MS-MLPA-koettimien suunnittelun vuoksi. Tämän tutkimuksen tulokset osoittavat, että valittujen geenien metylaatio oli yleisesti korkeampi syöpäsolulinjoilla kontrollinäytteisiin verrattuna, kuten odotettua. Erityisen suuri yhtäläisyys EPIC- ja bisulfiittisekvensointi tulosten välillä havaittiin ADHFE1, EYA4, ITGA4, FBLIM1 ja SEPT9 geenien metylaatiossa, joiden yhteys suolistosyöpään on osoitettu myös aiemmissa tutkimuksissa. Näiden, sekä muiden tutkimuksessa mukana olevien geenien epigeneettisten muutosten roolin ymmärtäminen suolistosyövän edistymisessä voisi tarjota mahdollisuuden löytää uusia biomarkkereita varhaiseen diagnosointiin ja potilaiden ennusteen parantamiseksi."]},{"key":"dc:title","label":"Title","values":["The Role of Epigenetics in Hereditary Colorectal Cancer Tumorigenesis: Validation of Genome-Wide Methylation Array Results through Bisulfite Sequencing"]}]}],"canonical_facts":{"dc:contributor":["Helsingin yliopisto, Bio- ja ympäristötieteellinen tiedekunta","University of Helsinki, Faculty of Biological and Environmental Sciences","Helsingfors universitet, Bio- och miljövetenskapliga fakulteten"],"dc:creator":["Puustinen, Taru"],"dc:date.issued":["2024"],"dc:description.abstract":["Colorectal cancer (CRC) poses a considerable global health challenge, with high mortality rates despite advancements in cancer research. Approximately one in ten CRC cases have a hereditary basis, with Lynch syndrome and Familial adenomatous polyposis standing as the two predominant cancer-predisposing syndromes. These conditions are mainly attributed to specific dominant germline mutations in CRC-related genes. However, as the role of epigenetic modifications, including DNA methylation, has become increasingly recognized in colorectal tumorigenesis, identifying these distinct signatures is paramount in gaining deeper insights into the molecular mechanisms underlying CRC. This thesis, conducted as a part of ongoing research into the DNA methylation profile of Lynch syndrome and Familial adenomatous polyposis-associated colorectal tumors, aimed to validate methylation patterns previously obtained from a genome-wide Illumina Methylation EPIC BeadChip array. The validation was performed by utilizing direct bisulfite sequencing across 12 selected gene regions on CRC cell lines and histologically normal control samples and comparing the methylation status to the EPIC array results. The genomic regions selected for this analysis were chosen based on differential methylation observed with EPIC and literature and were limited to regions that included at least one GCGC site for the HhaI digestion enzyme for future in-house MS-MLPA probe design. The results of this study demonstrate a clear differential methylation pattern of the selected genes, with CRC cell lines generally exhibiting higher methylation levels compared to non-cancerous samples, as expected. Specifically, high concordance between EPIC results and bisulfite sequencing data was observed in the methylation status of ADHFE1, EYA4, ITGA4, FBLIM1, and SEPT9, whose connection to CRC has been also shown in the previous studies. Further investigations of the genes in this study could contribute to a better understanding of epigenetic changes underlying colorectal tumors and hold the potential for developing novel biomarkers for early diagnosis and improved patient prognosis.","Edistyneestä syöpätutkimuksesta huolimatta suolistosyöpä aiheuttaa merkittävän globaalin terveysuhan korkean kuolleisuuden vuoksi. Noin joka kymmenes tapauksista johtuu perinnöllisistä syövälle altistavista oireyhtymistä, joista kaksi yleisintä ovat Lynchin oireyhtymä ja familiaalinen adenomatoottinen polypoosi. Näissä tapauksissa alttius syövälle on usein peräisin ituradan mutaatioista suolistosyövälle altistavissa geeneissä. Nykyisin myös epigeneettisten muutosten, kuten DNA metylaation rooli suolistosyövässä on yhä paremmin tunnettu. Siksi metylaatio muutosten tunnistaminen on ensisijaisen tärkeää suolistosyövän molekulaarisen taustan selvittämiseksi. Tämä tutkielma on osa laajempaa käynnissä olevaa tutkimusta Lynchin oireyhtymään ja perinnölliseen adenomatoottiseen polypoosiin liittyvien kasvainten metylaatioprofiilista. Pyrkimyksenä oli vahvistaa genomin laajuisen Illumina Methylation EPIC BeadChip -sirun avulla havaittujen metylaatiokuvioiden yhtenäisyys. Tässä tehtävässä hyödynnettiin bisulfiittisekvensointia, jonka avulla metylaatiostatus tutkittiin 12 valitun geenin alueella suolistosyöpä-solulinjoilla ja histologisesti normaaleilla kontrollinäytteillä. Tämän jälkeen sekvensoinnin tuloksia verrattiin EPIC-analyysin tuloksiin. Genomisten alueiden valinta tätä tutkimusta varten perustui EPIC-analyysin osoittamaan poikkeavaan metylaatioon sekä kirjallisuuteen. Toisena valintakriteerinä kunkin alueen tuli myös sisältää vähintään yksi GCGC-kohta HhaI entsyymiä varten tulevan MS-MLPA-koettimien suunnittelun vuoksi. Tämän tutkimuksen tulokset osoittavat, että valittujen geenien metylaatio oli yleisesti korkeampi syöpäsolulinjoilla kontrollinäytteisiin verrattuna, kuten odotettua. Erityisen suuri yhtäläisyys EPIC- ja bisulfiittisekvensointi tulosten välillä havaittiin ADHFE1, EYA4, ITGA4, FBLIM1 ja SEPT9 geenien metylaatiossa, joiden yhteys suolistosyöpään on osoitettu myös aiemmissa tutkimuksissa. Näiden, sekä muiden tutkimuksessa mukana olevien geenien epigeneettisten muutosten roolin ymmärtäminen suolistosyövän edistymisessä voisi tarjota mahdollisuuden löytää uusia biomarkkereita varhaiseen diagnosointiin ja potilaiden ennusteen parantamiseksi."],"dc:identifier.uri":["URN:NBN:fi:hulib-202406112671","http://hdl.handle.net/10138/576810"],"dc:language.iso":["eng"],"dc:publisher":["Helsingin yliopisto","University of Helsinki","Helsingfors universitet"],"dc:subject":["adenoma","bisulfite sequencing","Colorectal cancer","CIMP","DNA methylation","Familial adenomatous polyposis","hereditary CRC","Lynch syndrome","microsatellite instability"],"dc:title":["The Role of Epigenetics in Hereditary Colorectal Cancer Tumorigenesis: Validation of Genome-Wide Methylation Array Results through Bisulfite Sequencing"]},"updated_at":"2026-07-27T19:56:17Z"}