Fats, tumours and survival: Investigating the prognostic association of fatty acid oxidation in breast cancer

Over the past 15 years, a number of prognostic and treatment predictive signatures for breast cancer have been reported and utilised in the clinic. These signatures, for most part, are dominated by genes that reflect tumour proliferation, and provide limited insight into the biological pathways that drive tumour growth. Large gene expression datasets from primary tumours and well annotated clinical follow-up data have the potential to identify pathways correlated with treatment response and outcome. Rewiring of cellular metabolism is vital to meet the proliferative demands of tumours. To date, very little is known about how tumour metabolism influences patient outcome. This study sought to identify and characterise the metabolic features of tumours which associate with survival in breast cancer patients. Cox regression and gene set enrichment analyses were performed on gene expression data from 973 breast cancer patients. High expression of a signature comprised of 19 genes involved in fatty acid oxidation (FAO) was correlated with better disease-specific survival. The prognostic performance of this signature was validated using independent datasets from breast and several other cancer types. Analysis of the FAO signature in tumour-normal gene expression data revealed decreased expression in tumours compared to normal counterparts, which was exacerbated in advanced disease, compared to primary tumour tissues. The FAO signature was downregulated in various models of EMT induction in cell and organoid systems, independently of proliferation. Additionally, activation of MAPK and Wnt signalling pathways were observed to downregulate expression of the FAO signature in gene expression datasets from in vitro and in vivo systems. Overexpression of CPT1A in MDA-MB231 breast cancer cells decreased the proliferation and wound healing rates. No significant differences were observed in transwell migration rates, or colony formation in soft agar between basal and CPT1A overexpressing cells. MCF7 breast cancer cells with CPT1A knockdown did not alter proliferation rates or colony formation in soft agar, compared to basal expression control. Modulation of CPT1A expression did not alter oxygen consumption in response to exogenous palmitate. Transcriptome analysis suggested that transcriptional activity of EMT, MAPK and Wnt pathways was increased in MCF7 cells with CPT1A knockdown suggests a trend towards increased transcriptional activity of these pathways in this cell system. In summary, this work suggests that cancer cell proliferation and migration processes decreases the FAO signature expression, which is associated with poor patient prognosis. Alterations in the rate-limiting enzyme of this pathway alters proliferation and migration rates in MDA-MB231 cells, and increases expression of genes corresponding to key oncogenic pathways in MCF7 cells. These findings warrant further investigation of this pathway in breast and other cancer cell types. Understanding of how FAO affects tumour biology could help advance therapies that modulate this pathway

Fats, tumours and survival: Investigating the prognostic association of fatty acid oxidation in breast cancer

Over the past 15 years, a number of prognostic and treatment predictive signatures for breast cancer have been reported and utilised in the clinic. These signatures, for most part, are dominated by genes that reflect tumour proliferation, and provide limited insight into the biological pathways that drive tumour growth. Large gene expression datasets from primary tumours and well annotated clinical follow-up data have the potential to identify pathways correlated with treatment response and outcome. Rewiring of cellular metabolism is vital to meet the proliferative demands of tumours. To date, very little is known about how tumour metabolism influences patient outcome. This study sought to identify and characterise the metabolic features of tumours which associate with survival in breast cancer patients. Cox regression and gene set enrichment analyses were performed on gene expression data from 973 breast cancer patients. High expression of a signature comprised of 19 genes involved in fatty acid oxidation (FAO) was correlated with better disease-specific survival. The prognostic performance of this signature was validated using independent datasets from breast and several other cancer types. Analysis of the FAO signature in tumour-normal gene expression data revealed decreased expression in tumours compared to normal counterparts, which was exacerbated in advanced disease, compared to primary tumour tissues. The FAO signature was downregulated in various models of EMT induction in cell and organoid systems, independently of proliferation. Additionally, activation of MAPK and Wnt signalling pathways were observed to downregulate expression of the FAO signature in gene expression datasets from in vitro and in vivo systems. Overexpression of CPT1A in MDA-MB231 breast cancer cells decreased the proliferation and wound healing rates. No significant differences were observed in transwell migration rates, or colony formation in soft agar between basal and CPT1A overexpressing cells. MCF7 breast cancer cells with CPT1A knockdown did not alter proliferation rates or colony formation in soft agar, compared to basal expression control. Modulation of CPT1A expression did not alter oxygen consumption in response to exogenous palmitate. Transcriptome analysis suggested that transcriptional activity of EMT, MAPK and Wnt pathways was increased in MCF7 cells with CPT1A knockdown suggests a trend towards increased transcriptional activity of these pathways in this cell system. In summary, this work suggests that cancer cell proliferation and migration processes decreases the FAO signature expression, which is associated with poor patient prognosis. Alterations in the rate-limiting enzyme of this pathway alters proliferation and migration rates in MDA-MB231 cells, and increases expression of genes corresponding to key oncogenic pathways in MCF7 cells. These findings warrant further investigation of this pathway in breast and other cancer cell types. Understanding of how FAO affects tumour biology could help advance therapies that modulate this pathway

Fatty acid oxidation is associated with proliferation and prognosis in breast and other cancers

Abstract Background Altered cellular metabolism is a hallmark of cancer but the association between utilisation of particular metabolic pathways in tumours and patient outcome is poorly understood. We sought to investigate the association between fatty acid metabolism and outcome in breast and other cancers. Methods Cox regression analysis and Gene Set Enrichment Analysis (GSEA) of a gene expression dataset from primary breast tumours with well annotated clinical and survival information was used to identify genesets associated with outcome. A geneset representing fatty acid oxidation (FAO) was then examined in other datasets. A doxycycline-inducible breast cancer cell line model overexpressing the rate-limiting enzyme in FAO, carnitine palmitoyl transferase 1A (CPT1A) was generated and analysed to confirm the association between FAO and cancer-associated characteristics in vitro. Results We identified a gene expression signature composed of 19 genes associated with fatty acid oxidation (FAO) that was significantly associated with patient outcome. We validated this observation in eight independent breast cancer datasets, and also observed the FAO signature to be prognostic in other cancer types. Furthermore, the FAO signature expression was significantly downregulated in tumours, compared to normal tissues from a variety of anatomic origins. In breast cancer, the expression of CPT1A was higher in oestrogen receptor (ER)-positive, compared to ER-negative tumours and cell lines. Importantly, overexpression of CPT1A significantly decreased the proliferation and wound healing migration rates of MDA-MB231 breast cancer cells, compared to basal expression control. Conclusions Our findings suggest that FAO is downregulated in multiple tumour types, and activation of this pathway may lower cancer cell proliferation, and is associated with improved outcomes in some cancers

Promoterless Transposon Mutagenesis Drives Solid Cancers via Tumor Suppressor Inactivation

A central challenge in cancer genomics is the systematic identification of single and cooperating tumor suppressor gene mutations driving cellular transformation and tumor progression in the absence of oncogenic driver mutation(s). Multiple in vitro and in vivo gene inactivation screens have enhanced our understanding of the tumor suppressor gene landscape in various cancers. However, these studies are limited to single or combination gene effects, specific organs, or require sensitizing mutations. In this study, we developed and utilized a Sleeping Beauty transposon mutagenesis system that functions only as a gene trap to exclusively inactivate tumor suppressor genes. Using whole body transposon mobilization in wild type mice, we observed that cumulative gene inactivation can drive tumorigenesis of solid cancers. We provide a quantitative landscape of the tumor suppressor genes inactivated in these cancers and show that, despite the absence of oncogenic drivers, these genes converge on key biological pathways and processes associated with cancer hallmarks