Genome-Wide DNA Methylation and Gene Expression Profiling of Cancer-Associated Myofibroblasts



Najgebauer, H
(2016) Genome-Wide DNA Methylation and Gene Expression Profiling of Cancer-Associated Myofibroblasts. PhD thesis, University of Liverpool.

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Abstract

In recent years it has become increasingly apparent that tumour development and metastasis are not simply driven by mutations within cancer cells. Factors produced by stromal myofibroblasts play a key role in the development and metastasis of many forms of cancer. However, our knowledge of the range of molecular mechanisms that drive paracrine communication between cancer and stromal cells remains incomplete. Evidence from previous studies show that myofibroblasts derived from gastric tumours (CAMs) not only retain their ability to enhance the proliferation and migration of cancer cells in vitro but also have inherently different gene expression profiles compared to patient-matched adjacent tissue myofibroblasts (ATMs), or normal tissue myofibroblasts (NTMs). In addition, it was shown that CAMs are characterized by global loss of DNA methylation when compared to patient-matched ATMs. Taken together, these observations indicate that epigenetic programming of myofibroblasts within the tumour microenvironment may contribute to their tumour-promoting properties. In this study, genome-wide DNA methylation and gene expression profiling was performed on a collection of primary patient-matched gastric CAM and ATM samples and normal NTM samples in order to identify CAM-specific DNA methylation signatures and to assess the extent to which these genome-wide DNA methylation changes may regulate CAM-specific gene expression profile. The differential methylation analysis identified widespread alterations of DNA methylation in gastric CAMs compared to ATMs and NTMs. In addition, the integrated analysis of DNA methylation and gene expression showed that DNA methylation is involved in epigenetic regulation of biological pathways and processes involved in the tumour–promoting function of gastric CAMs. In particular, promoter DNA hypomethylation emerged as regulatory mechanism for transcriptional activation of genes involved in secretion and transport of molecules while promoter DNA hypermethylation emerged as regulatory mechanism for transcriptional repression of genes involved in pathology of gastrointestinal cancers and regulation of developmental processes. Additionally, given that hypoxic conditions may be common within the tumour microenvironment, we were interested to know what role hypoxia may play in regulating paracrine communication between CAMs and gastric cancer cells. Using cell based assays and a combination of genomic, transcriptomic and proteomic approaches we provided a novel insight into the profile of changes in gene expression and protein secretion that result from exposure of normal (NTMs) or cancer-associated myofibroblasts (CAMs) to hypoxic conditions and identified hypoxia-induced factors that may drive CAM-, ATM- and NTM-specific hypoxic responses, which have differential effects on cancer cell migration and proliferation. Importantly, data from this study show that gastric myofibroblasts purified from different tissue microenvironments (CAMs, ATMs, NTMs) have distinct responses to hypoxia, which most probably stem from differential epigenetic profiles providing, once again, strong evidence that epigenetic programming of CAMs is in part mediated by interactions with cancer cells. However, hypoxia is unlikely to be a driving factor in conferring cancer related changes in DNA methylation profiles of gastric myofibroblasts. Taken together, this study is the first to perform a comparative genome-wide analysis of DNA methylation and gene expression patterns in gastric cancer- associated myofibroblasts. Significantly, widespread epigenomic and transcriptomic alterations were observed in CAMs compared to their patient-matched ATMs, providing potential clues as to the molecular mechanism of cancer mediated stromal cell programming. Finally, CAM-specific DNA methylation patterns identified in this study may prove useful in future clinical practice as biomarkers for improved diagnosis and prognosis of gastric cancer.

Item Type: Thesis (PhD)
Additional Information: hanna.najgebauer@gmail.com
Divisions: Faculty of Health and Life Sciences
Depositing User: Symplectic Admin
Date Deposited: 15 Aug 2016 07:57
Last Modified: 02 Aug 2021 07:10
DOI: 10.17638/03001706
Supervisors:
URI: https://livrepository.liverpool.ac.uk/id/eprint/3001706