Title: Systematic analysis of metabolic change in the earliest pre-neoplastic cell niche for identifying possible targets for early detection and intervention
Funder: Cancer Research UK

Abstract: Background: The earliest stages of cancer development, namely the pre-neoplastic stages when the earliest genetic lesion leads to the occurrence and development of pre-neoplastic cells (PNCs) is a poorly studied area of cancer biology. A detailed characterisation of the earliest PNC development at the cellular and molecular level would provide some clues to pursue new ways for cancer early detection and prevention. We have developed a novel zebrafish model of tumour initiation in which the earliest PNCs can be visualised in vivo and their progression monitored. Our previous studies suggest that host innate immune cells are actively interacting with PNCs and promote their growth at the earliest stages of cancer development. We also know that in order to support the demand for rapid proliferation PNCs alter their metabolism, which leads to the generation of altered metabolites. Some of these altered metabolites that are generated have been shown to have immune modulating functions. We hypothesised that altered metabolites generated by rapidly growing PNCs may modulate host cell function (in particular host innate immune cells) within the PNC growing microenvironment (PNC niche). Identifying altered metabolite profiles may provide for novel targets in cancer early detection and prevention. Aims: Metabolomic profiling of PNC carrying larvae during the time course of PNC development to identify key metabolic pathways/ metabolites that are altered due to the growing PNCs. More specifically to identify metabolic pathways and metabolites that are altered within PNCs themselves in vivo during PNC development. Determine how such altered metabolites might modulate host innate immune cell function and contribute to PNC progression. Methods: We will use methods based on hydrophilic interaction chromatography interfaced with high resolution mass spectrometry to profile metabolomics during the time course of PNC development. We will perform integrated analysis by combining Imaging Mass Spectrometry (MSI) of PNC metabolomics in situ and single cell RNAseq profiling of PNCs sub-populations to fully characterise metabolic alterations within PNCs. We will use lineage (PNC) specific CAS9 based gene inactivation in vivo to interrogate the function of putative target genes during PNC initiation and progression. How the results of this research will be used: This would be the first comprehensive analysis of metabolic changes during the earliest stages of cancer development. The data obtained herein will provide us with potential candidates for further tests in the human for the development of early detection and prevention strategies.

Lay abstract: The earliest stage of cancer development, when a genetic change is oncogenic leading to the development of pre-neoplastic cells (PNCs) is a poorly studied area of cancer biology. A detailed characterisation of the earliest PNC development at the cellular and molecular level would provide some clues to pursue in new ways for early detection and prevention of cancer. We have developed a novel zebrafish model of tumour initiation in which the earliest PNCs can be visualised in vivo and their progression monitored. Our previous studies suggest that host innate immune cells are actively interacting with PNCs and promote their growth at this early stage. We also know that in order to support the demand for rapid proliferation PNCs alter their metabolism, leading to the generation of altered metabolites. Some of these altered metabolites have been shown to have immune modulating functions. We hypothesised that altered metabolites generated by rapidly growing PNCs may modulate host cell function (in particular host innate immune cells) within the PNC growing microenvironment (PNC niche). Identifying altered metabolite profiles may provide for novel targets of early cancer detection and prevention. In this project we will integrate Metabolomic, Imaging Mass Spectrometry (MSI) of PNC niche and single cell RNAseq data from PNCs to characterise the metabolic changes in the PNC and its developing niche. We wish to determine how metabolic changes in PNCs might modulate host innate immune function. This study would be the first comprehensive analysis of metabolic changes during the earliest stages of cancer development. The data obtained herein will provide us with potential candidates for further tests in the human for the development of early detection and prevention strategies.

Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: CANCER AND NEOPLASMS