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Title: Genome-wide expression profiling of human circulating monocytes and macrophages identifies diagnostic and prognostic signatures for cancer outcomes
Author: Fragkogianni, Stamatina
ISNI:       0000 0004 7223 9766
Awarding Body: University of Edinburgh
Current Institution: University of Edinburgh
Date of Award: 2017
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Background: Breast and endometrial cancers are the most common gynaecological cancers in women in the UK. Early detection of tumours is crucial for improving patient survival rates. In breast cancer, mammography is the most reliable screening method for asymptomatic patients; however, its sensitivity is limited by breast density. Currently, there are no early screening assays for endometrial cancer. Thus, there is an urgent need to identify clinical biomarkers for improved non-invasive diagnosis of breast and endometrial cancer. Macrophages are abundant in the tumour microenvironment and their density has been associated with poor prognosis in breast cancer and decreased survival in endometrial cancer. Monocytes are precursors of macrophages and recent studies have shown an association with pro-tumoral functions. The aim of this study has been to examine the transcriptional profiles of human circulating monocytes and tumour associated macrophages (TAMs) in order to investigate their biological relevance and potential as biomarkers for cancer detection and prognosis. Methods: RNA-sequencing was performed on purified monocytes (22 healthy individuals, 21 breast cancer, 16 endometrial cancer samples), as well as purified normal macrophages, TAMs from breast tissue (4 breast cancer, 4 healthy breast) and endometrium tissue (5 endometrial cancer, 9 healthy endometrium). Results: A shift in the transcriptional profile of monocytes in cancer compared to controls was observed. Given these cancer-associated alterations circulating monocytes from cancer patients were called “Tumour Educated Monocytes” (TEMo). A TEMo-derived 13-gene signature was extracted that detected cancer, yielding an accuracy of 94%, a positive predictive value (PPV) of 92% and a negative predictive value (NPV) of 97%. External validation confirmed the ability of the signature to accurately identify cancer patients with perfect accuracy. Transcriptome profiling of TAMs revealed a significantly altered gene expression profile when compared to normal tissue resident macrophages. Furthermore, comparison of TAMs between breast and endometrial cancer also revealed differences suggesting that different tumour microenvironments induce different gene expression profiles in TAMs. Functional analysis of significant genes in breast cancer revealed similar biological pathways to those of murine studies suggesting that TAMs in humans and mice may have similar functions. A gene list of transmembrane receptors has been extracted by comparing breast cancer TAMs with publicly available datasets that could serve as markers for their identification. Finally, exploratory analysis identified a subset of 49 genes associated with recurrence-free and overall survival in publicly available datasets. Conclusion: To my knowledge this is the first genome-wide profiling study of human circulating monocytes and TAMs in breast and endometrial cancer. It provides evidence that monocytes and TAMs can alter their expression profile in the presence of cancer and, using bioinformatics tools I was able to identify biomarkers for diagnosis and prognosis of breast and endometrial cancer.
Supervisor: Pollard, Jeffrey ; Granneman, Sander Sponsor: Medical Research Council (MRC)
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available
Keywords: tumour-associated macrophages ; circulating monocytes ; Tumour Educated Monocytes ; TEMo ; biomarkers ; breast cancer