Enhancing multi-omic single cell sequencing to resolve fundamental biological mechanisms in humans and non-human organisms
Lead Research Organisation:
University of Birmingham
Department Name: Cancer Sciences
Abstract
The fields of biology and medicine have been dramatically changed over the past 50 years by our increasing knowledge of how the genetic code of cells which consists of DNA which serves as a template for RNA regulates all aspects of cellular function. As the technologies to study DNA and RNA have improved, our understanding of these processes have led to far-reaching discoveries and technological advances impacting on biotechnology, our understanding of the basic biology of cells and of normal developmental biology of whole organs and organisms. Importantly, they also have provided deep insights into disease processes such as infection, inflammation and cancer with an impact on both the human and the animal world.
Each cell has its own command center which resides in the nucleus in form of DNA and we ideally want to know how each individual cell functions as it is always in contact with a multitude of other cells who impact on its physiology. Therefore, until now, these technologies have been relatively low resolution, because we have only been able to take a sample of multiple cells and analyse them as a group. The effect of what each cell does on the whole organism is the sum of how these cells cooperate and where they are within an organ, and lumping them all together does not give us the information we need to understand fundamental biological processes.
We can now perform analysis of the DNA and RNA changes in each single cell within a group of cells, helping us to understand how these cells work together. Using first generation single cell technology, we now know that within a population of seemingly identical cells in a human, animal or plant cells are in different states at a single point in time. A few years ago, we have established a facility within the University of Birmingham that carries out an analysis of all RNA that is within each single cell which tells us in what state each cell is in. However, technology has rapidly progressed and it is now possible to study multiple features all within one cell, such as the composition and intactness our genetic code, and which proteins these cells contain. We can also link such data with data showing where within an organ single cells are located and can thus draw conclusions of how their surroundings influence their behaviour.
In this proposal we apply for funds to buy the equipment enabling us to establish these novel single cell technologies. We believe that without being able to expand our facility and incorporate these new techniques, we will not be able to participate in globally competitive science and we will not be able to address the most pressing biological questions. This application will enable us to carry out these aims. It will widen our user base and for the first time will make these cutting edge technologies available to multiple users within the Midlands.
Each cell has its own command center which resides in the nucleus in form of DNA and we ideally want to know how each individual cell functions as it is always in contact with a multitude of other cells who impact on its physiology. Therefore, until now, these technologies have been relatively low resolution, because we have only been able to take a sample of multiple cells and analyse them as a group. The effect of what each cell does on the whole organism is the sum of how these cells cooperate and where they are within an organ, and lumping them all together does not give us the information we need to understand fundamental biological processes.
We can now perform analysis of the DNA and RNA changes in each single cell within a group of cells, helping us to understand how these cells work together. Using first generation single cell technology, we now know that within a population of seemingly identical cells in a human, animal or plant cells are in different states at a single point in time. A few years ago, we have established a facility within the University of Birmingham that carries out an analysis of all RNA that is within each single cell which tells us in what state each cell is in. However, technology has rapidly progressed and it is now possible to study multiple features all within one cell, such as the composition and intactness our genetic code, and which proteins these cells contain. We can also link such data with data showing where within an organ single cells are located and can thus draw conclusions of how their surroundings influence their behaviour.
In this proposal we apply for funds to buy the equipment enabling us to establish these novel single cell technologies. We believe that without being able to expand our facility and incorporate these new techniques, we will not be able to participate in globally competitive science and we will not be able to address the most pressing biological questions. This application will enable us to carry out these aims. It will widen our user base and for the first time will make these cutting edge technologies available to multiple users within the Midlands.
Technical Summary
Single cell sequencing has transformed our understanding of fundamental biology in many ways, allowing a high resolution examination of the genotype and phenotype of cells leading to many changes in our understanding of biological processes. The University of Birmingham commissioned a single cell 'omics facility in 2016 which has delivered high volumes of data output across multiple fields, with the data generated contributing to manuscripts in Science, Cell, Nature and Nature Genetics. There is now an opportunity to expand our understanding of single cell processes from RNA to DNA, as well as protein surface markers and spatial relationships. We will enhance our current provision to support the BBSRC research community in the Midlands and beyond, providing access to single cell DNA sequencing (via a MissionBio Tapesrtri instrument) allowing mutational detection and copy number variants to be quantified at the single cell resolution. Provision of the next generation of single cell technology (10X Chromium) will allow us to process high numbers of cells (up to 1M) as well as RNA, surface protein and spatial information, more rapidly and reliably. Our proposal will invest in the future of single cell science to ensure that BBSRC researchers retain access to the cutting edge of single cell investigation.
