Defining regional anatomical variation in cellular composition, transcriptome and epigenome in the human kidney

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The kidneys play a vital role in cleaning the blood and controlling the body's water balance. Unfortunately, their function may be affected by a number of common diseases including infection, diabetes, damage by reduced blood supply and high blood pressure or the toxic effects of some drugs. Kidney failure can be treated with dialysis or transplant, but both (particularly dialysis) are associated with reduced life expectancy. The individual building blocks of the kidneys are called cells, and each kidney has hundreds of millions of cells that work in groups that have a similar function. The interaction of individual cells, and groups of cells, is required for normal organ function. Among the different cell types that reside in the kidney are immune cells, the body's defence system cells. These sentinels stand guard and alert the body to local problems by starting an inflammatory response. They also play an important role in tissue healing and repair. Because of their job of excreting waste and controlling water balance, the kidneys make an unusual and difficult environment for immune cells; some parts of the kidney have a very high salt concentration, so the cells are living in a salt marsh and this can affect their function. At present, we don't fully understand the different types of cells that make up the kidney, how many different of immune cells live there, how they are positioned relative to each other, or whether the extreme environment of some parts of the kidney changes how the cells behave. Answering these questions will help us to determine how cell function goes wrong in kidney diseases and will therefore allow the development of better treatments.Our aim is to make a cell map of the human kidney. We will take two experimental approaches: The first is to take a piece of kidney, mash it up to break up the cell groups so that we can analyse individual cells. Different cells have different functions and identification marks because of differences in which parts of their genetic material (called genes) are translated into proteins. Protein are the molecules that mark a cell and allow it to function. Every cell contains tens of thousands of proteins, giving it a unique signature, but these are hard to measure in a single cell. However, we can measure the molecule that acts as an intermediate between genes and proteins, this is called messenger RNA or mRNA. In the past 10 years, technology has advanced such that we can measure thousands of mRNA molecules in a single cell, this is what we plan to do with the mashed kidney samples that we will take from 6 different regions across the human kidney.Our second experimental approach is to take a piece of kidney and keep it intact so that the relationship of the cells in space is maintained. We will then make slices of the piece of kidney so that they are thin enough to be seen under a microscope. We will use the mRNA information from our first experiment to identify a small number of markers that can be visualised by the microscope using probes that are fluorescently labeled. This will allow us to investigate the position of cells relative to each other and how different cells in both the adult and developing kidney provide support or a 'niche' for immune cells.Making a complete map of cells in the normal kidney will provide a critical reference atlas that will help researchers in the future to understand which cells become abnormal in different kidney diseases and how cell interactions are disrupted in disease. This will provide invaluable information to help identify new treatment targets.