Single cell genomics: thinking small

28th April 2014
By Iain Macaulay

All multicellular life starts from a single cell. As cells divide, mutations can occur, leading to considerable genetic diversity in the daughter cells of the zygote. Even very early in life, a human is already a mosaic of subtly different genomes.  Credit: Tarryn Porter

All multicellular life starts from a single cell. As cells divide, mutations can occur, leading to considerable genetic diversity in the daughter cells of the zygote. Even very early in life, a human is already a mosaic of subtly different genomes. Credit: Tarryn Porter

It takes around 3.72 × 10(13) cells to make up an adult human – that’s about 10 times more than the number of stars in the Milky Way. Yet all of these cells originate from a single progenitor cell, the zygote arising from a fertilised egg. During development, extensive cell division occurs, dramatically increasing cell numbers – but at the same time, the emerging cells are specialising, to perform specific roles within the organism.

To learn more about this fundamental process, scientists have developed a way to sequence the miniscule amounts of genetic material in each individual cell. The implications of this new capability are profound.

With single cell genomics, we can explore in great detail what happens to the genome during the expansive processes of developing and sustaining life. Generating trillions of copies of the original genome in the zygote comes at a cost: with every cell division, there is a probability that a small number of mistakes will be made. This means that even two sister cells, arising from a single cell division, may end up with subtly different genomes.

Over many divisions, genomic differences can accrue, to the point where it is suspected that the genomes contained within different cells of the same individual can have significant heterogeneity – a phenomenon known as somatic variation.

The true extent of somatic variation is currently unknown, although it is known that this process occurs from the very first cell divisions after fertilisation, through to adult life. Most genome sequencing studies to date have taken DNA from thousands or millions of cells, all pooled together, and will therefore not easily capture this kind of variation. However, by sequencing the genomes of many single cells in parallel, we can start to explore the rate at which this variation emerges, and how this rate is affected by external mutagenic factors, such as smoking or sunlight, that can change our DNA.

Studying this process may be a key to understanding the initiating processes of cancer, in which a single renegade cell will acquire a mutation, or series of mutations, that give it a competitive advantage over surrounding cells.

Genetic variation within an organism is thought to involve the slow and subtle acquisition of mutation with each cell division. However, the cell’s transcriptome – the catalogue of genes, expressed as RNA, that contain the information required to create essential proteins – can change rapidly. Changes in the cell’s transcriptome occur as part of the specialisation process, where a cell takes on a special role within the organism, and also in response to external stimuli, such as signals from other cells, hormones and drugs.

As with genomics, much of our current understanding of the transcriptome is based on pools of large numbers of cells, which makes it impossible to truly understand variable gene expression in individual cells. There is also significant interest in developing methods to analyse the regulation of gene expression at the single-cell level.

A typical human cell contains only around six picograms, (six trillionths of a gram), of genomic DNA, and around 20 to 30 picograms of RNA. More material is needed to analyse this DNA and RNA, so before sequencing, it first undergoes a process of amplification. Significant technical advances have been made in these amplification procedures, aiming to maximise the amount of a single cell’s genome or transcriptome that can be sequenced, while minimising the chance of errors being introduced. Currently there are no perfect methods for doing this – but substantial progress continues to be made.

The last year or so has seen an explosion in the application of single cell approaches; as the scale of such studies increases to include hundreds, thousands and, one day, millions of single cells, the true extent of somatic variation and heterogeneity in gene regulation and expression within a single organism will start to emerge.

Iain Macaulay is a Postdoctoral Fellow in Professor Chris Ponting’s and Professor Thierry Voet’s groups in the Single Cell Genomics Centre at the Wellcome Trust Sanger Institute.

References