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Surviving metabolism: acid handling and signalling

Periodic Reporting for period 3 - Survive (Surviving metabolism: acid handling and signalling)

Reporting period: 2020-06-01 to 2021-11-30

Epidemiologically, cancer remains a major cause of mortality in Europe, but one that shows remarkable heterogeneity in terms of its causes, advancement, and prognosis. This complexity makes cancer diagnosis and treatment remarkably difficult to implement successfully. Additionally, the clinical and research communities are working under the pressure of high expectations from the general public, who have made considerable investments into this major health issue. One of the challenges in managing cancer is that it involves genetic instability, which allows malignant cells to adapt to changes. This, in turn, produces a system in which cancer cells compete against each other and against normal cells for space and resources. The outcome of this Darwinian-like selection process is survival of the fittest, invariably leading to tumour growth, metastasis and death. Selection, however, occurs only if cells are exposed to a specific environmental factor, such as a chemical, to which some cells respond with death whilst others thrive. A chemical signature of tumours is acidity, and various models have proposed this to act as a selection pressure, favouring certain phenotypes. Since tumour acidity is ultimately a product of cancer’s metabolic activities, the system establishes a feedback, whereby the acidic products influence cell survival, and hence further production of acid. Manipulating this loop would change the disease trajectory and offer new therapeutic options that may have efficacy in multiple types of cancer, because they address a fundamental change associated with the malignancy. In order to exploit this vulnerability, it is necessary to understand the proteins and genes that underpin acid-resistant and acid-sensitive cell. Next, it is critical to understand what is the source of this acidity, and how it influences cell biology, ranging from gene expression to proliferation. To appreciate how selection works, it is necessary to understand what is the unit that is subject to selection, and how this relates to a cancer cell. Indeed, cancer cells do not exist in isolation in tumours, but interact with one another through conduits and also with the stroma consisting of host cells, such as fibroblasts. The aim of this project is therefore to deliver a more mechanistic understanding of the pH-related phenotype, and identify mechanisms that enable some cells to tolerate acid, and exposed vulnerabilities that could become the basis of new therapies.
We focused our research on colorectal cancer, because the biological resources available for this type of cancer are substantial, and the disease is a major and growing healthcare burden. In this reporting period, we addressed three questions. How do colorectal cancer (CRC) cells differ in terms of their measureable behaviours that relate to pH? What proteins and genes underpin resistance to acidity? Do cancer cells communicate with each other and how does this affect their responses to acidity, in light of selection? To address the first question, we developed an innovative work-flow that allow us to study large panels of cell lines. This involved high-throughput screens for phenotypes such as intracellular pH, metabolic rate and survival, which collectively inform a simplified model of how pH affects key measures of cancer biology. This framework allows us to correlate phenotype with gene expression, which in turn addresses the second question. To complement this, we are performing a screen that identifies genes responsible for conferring acid resistance. Our experiments generate large volumes of new data, which necessitates new tools for curating and analysing such information. To improve standards in the area of pH physiology, we have proposed and disseminated guidelines for better experimental practice, with the aim to improve data quality and reproducibility, which ultimately benefits the public. To address the third aim, we implemented new methods to study how cancer cells communicate. We find that such coupling is more widespread than previously thought, and leads to the exchange of substances, such as metabolites and signals, between cells. Intriguingly, this occurs only in subsets of cancer cells, and can involve multiple proteins. We have proposed that barter between cancer cells can profoundly change mechanisms of selection.
At the end of the project, we aim to produce a comprehensive description of pH-related phenotype in a large panel of cell lines, and relate apparent differences to specific mutations carried by the various cell lines. By establishing and testing this phenotype-genotype correlation, we will identify genes and proteins that confer cells with resistance to low pH. We will determine which genes can be exploited to manipulate the disease trajectory, with the aim of offering new therapeutic options. We will also demonstrate how the tumour stroma is exploited by cancer cells to change their responses to pH. Furthermore, we will characterise the degree to which cancer cells communicate via conduits, and how such exchange of metabolites and signals may compensate for genetic mutations in coupled cells. We will show how this can lead to a blurring of phenotypic differences and thereby re-define how selection operates to seek the fittest cells. Collectively, we will establish how best to target acid handling and signalling to derail cancer progression.