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dc.contributor.authorAitken, Sarah Jane
dc.date.accessioned2018-10-29T13:20:32Z
dc.date.available2018-10-29T13:20:32Z
dc.date.issued2018-08-23
dc.date.submitted2018-04-04
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/284403
dc.description.abstractCCCTC-binding factor (CTCF) binds DNA, thereby helping to partition the mammalian genome into discrete structural and regulatory domains. In doing so, it insulates chromatin and fine-tunes gene activation, repression, and silencing. Complete removal of CTCF from mammalian cells causes catastrophic genomic dysregulation, most likely due to widespread collapse of 3D chromatin looping within the nucleus. In contrast, Ctcf hemizygous mice with lifelong reduction in CTCF expression are viable but have an increased incidence of spontaneous multi-lineage malignancies. In addition, CTCF is mutated in many human cancers and is thus implicated as a tumour suppressor gene. This study aimed to interrogate the genome-wide consequences of a reduced genomic concentration of Ctcf and its implications for carcinogenesis. In a genetically engineered mouse model, Ctcf hemizygous cells showed modest but robust changes in almost a thousand sites of genomic CTCF occupancy; these were enriched for lower affinity binding events with weaker evolutionary conservation across the mouse lineage. Furthermore, several hundred genes concentrated in cancer-related pathways were dysregulated due to changes in transcriptional regulation. Global chromatin structure was preserved but some loop interactions were destabilised, often around differentially expressed genes and their enhancers. Importantly, these transcriptional alterations were also seen in human cancers. These findings were then examined in a hepatocyte-specific mouse model of Ctcf hemizygosity with diethylnitrosamine-induced liver tumours. Ctcf hemizygous mice had a subtle liver-specific phenotype, although the overall tumour burden in Ctcf hemizygous and wild-type mice was the same. Using whole genome sequencing, the highly reproducible mutational signature caused by DEN exposure was characterised, revealing that Braf(V637E), orthologous to BRAF(V600E) in humans, was the predominant oncogenic driver in these liver tumours. Taken together, while Ctcf loss is partially physiologically compensated, chronic CTCF depletion dysregulates gene expression by subtly altering transcriptional regulation. This study also represents the first comprehensive genome-wide and histopathological characterisation of this commonly used liver cancer model.
dc.description.sponsorshipWellcome Trust Programme for Clinicians Fellowship (106563/Z/14); EMBO|EuropaBio Fellowship (STF 7538); The Pathological Society of Great Britain & Ireland (SGS 2015/04/04); Cancer Research UK (core award 20412).
dc.language.isoen
dc.rightsAll rights reserved
dc.rightsAll Rights Reserveden
dc.rights.urihttps://www.rioxx.net/licenses/all-rights-reserved/en
dc.subjectCTCF
dc.subjectTranscription
dc.subjectHemizygosity
dc.subjectCancer
dc.subjectChromatin state
dc.subjectChromatin architecture
dc.subjectHepatocellular carcinoma
dc.subjectCarcinogen
dc.subjectWhole genome sequencing
dc.subjectRNA sequencing
dc.subjectMutational signatures
dc.subjectHistopathology
dc.titleThe pathological and genomic impact of CTCF depletion in mammalian model systems
dc.typeThesis
dc.type.qualificationlevelDoctoral
dc.type.qualificationnameDoctor of Philosophy (PhD)
dc.publisher.institutionUniversity of Cambridge
dc.publisher.departmentCancer Research UK Cambridge Institute
dc.date.updated2018-10-28T13:55:02Z
dc.identifier.doi10.17863/CAM.31776
dc.contributor.orcidAitken, Sarah Jane [0000-0002-1897-4140]
dc.publisher.collegeChrist's College
dc.type.qualificationtitlePhD
cam.supervisorOdom, Duncan
cam.supervisor.orcidOdom, Duncan [0000-0001-6201-5599]
cam.thesis.fundingfalse
rioxxterms.freetoread.startdate2019-10-29


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