Decisive discovery: how cells forget their past

Breaking new ground 5. nov 2019 4 min Professor Joshua Brickman, Assistant professor William Hamilton Written by Morten Busch

All cells in our body contain the same genetic material. The difference between cells in the brain and in the heart therefore depends solely on which genes are expressed (turned on). How does a cell’s environment control this? New research sheds light on this process and unveiled a mechanism for how a cell can keep multiple genes in this primed state and then select only a subset to be activated in response to an environmental cue. These discoveries provide insight into the fundamental question of how genes are turned on and off and how a cell is capable of becoming multiple types of specialized cells while always choosing just one destiny. This new knowledge will be crucial for stem cell therapy and potentially also for treating people with cancer.

It is like a very complex railway network. The cells of the human body start from the same depot and ride the same rails, but then they encounter a track switch that determines their initial fate. After several track changes, the cells head in very different directions towards their final destinations, making up the different tissues of the body. Unlike a conventional railway, once they have progressed so far into differentiation, the track back to the original depot disappears and there is no return. For 30 years, the dogma has been that proteins called transcription factors are the engines of gene expression, triggering these changes by switching the genes on and off. However, new research reveals something quite different: that the transcription factors may represent the tracks themselves.

“We previously thought that transcription factors drive the process that determines whether a gene is expressed and subsequently translated into the corresponding protein. Our new results show that transcription factors may be more analogous to being the memory of the cell. As long as the transcription factors are connected to a gene, the gene can be read (turned on), but the external signals received by the cells seem to determine whether the gene is turned on or off. As soon as the transcription factors are gone, the track changes and the cells can no longer return to their point of origin,” explains Josh Brickman, Professor and Group Leader, DanStem, University of Copenhagen.

An enormous protein landscape

The question of how a cell slowly develops from one state to another is key to understanding cell behaviour in multicellular organisms. Stem cell researchers consider this vital, which is why they are constantly trying to refine techniques to develop the human body’s most basic cells into various specific types of cells that can be used, for example, to regenerate damaged tissue. So far, however, investigating the signals required to make cells switch tracks has been extremely difficult, since making all the cells in a dish do the same thing at the same time is very difficult. Although there are single-cell approaches, these do not produce high-resolution data that enables the time-resolved molecular mechanism to be described, enabling the resolution of precise causal events that underlie the turning on and off of genes.

“Studying the transcription of DNA in the cells and thus also learning to understand and regulate the processes have been incredibly difficult. The challenge has been that we have lacked tools to turn the signals on and off throughout a culture of cells, so that we can study the molecular events that underlie changes in gene expression as they occur in otherwise undisturbed culture. In our new study, we have succeeded in developing a system that can be used to switch on the signal path with a single substance and switch it off again with another substance,” explains the first author, William Hamilton, Assistant Professor, DanStem, University of Copenhagen.

The researchers used the new on-off signalling system to precisely determine the sequence of the individual events involved in a gene being turned on and off in stem cells for the first time. The researchers were able to describe how genes are turned on and off and under what circumstances a cell can move down the differentiation track but then elect to return to the starting-point. Understanding how the signal modified proteins in the cell was essential for understanding how genes are turned on and off by a signal, and this involved an important collaboration with protein scientists from the Novo Nordisk Foundation Center for Protein Research, including the group of Jesper Olsen, who measured whether the cell’s proteins are phosphorylated or not in response to the signal, and this was decisive for determining the sequence of events leading to changes in gene expression. The modification of proteins by phosphorylation illustrates how cells respond to external signals and environmental conditions.

“Phosphorylations are like switches for proteins, either activating or inactivating some innate function, but essentially they are how information is transmitted in a cell. The collaboration with the protein researchers enabled us to measure the phosphorylation of thousands of proteins inside the cell in response to the signal. As a result, we could create a very precise and incredibly comprehensive landscape of how the behaviour of proteins in the cell continually changed as the cells changed themselves into different stages of differentiation,” continues Josh Brickman.

New answers to basic scientific questions

These results are surprising. Although the sequence of cell transcription processes could not previously be measured as accurately as in this study, the dogma was that transcription factors comprise the on-off switch that is essential to initiate transcription of the individual gene. This is not so for embryonic stem cells and potentially for other cell types.

“Transcription factors are still a key signal, but they do not drive the process, as previously thought. Once they are there, the gene can be read, and they remain in place for a while after the gene is read. And when they are gone, the window in which the gene can be read can be closed again. You can compare it with the vapour trails you see in the sky when an airplane has passed. They linger for a while but slowly dissipate again,” continues William Hamilton.

This discovery is first and foremost basic knowledge, which changes the basis of most research projects in molecular biology. The new results are especially important for stem cell researchers, because they provide new insight into how cells develop, what pathways remain between the individual developmental stages and when the point of no return is reached. This new knowledge will attract special attention in cancer research.

“In the project, we focused on the fibroblast growth factor (FGF)–extracellular signal–regulated kinase (ERK) signalling pathway, which is a signalling pathway from a receptor on the surface of a cell to DNA inside the cell nucleus. This pathway is dysregulated in many types of cancer, and we therefore hope that many of the data in this study will help to inform aspects of cancer biology by indicating new ways to specifically target this signalling pathway in cancer cells,” concludes Josh Brickman.

Dynamic lineage priming is driven via direct enhancer regulation by ERK” has been published in Nature. Several authors are employed at the Novo Nordisk Foundation Center for Stem Cell Biology, DanStem and the Novo Nordisk Foundation Center for Protein Research, University of Copenhagen. This project also involved an important collaboration with the group of Naama Barkai, Professor, Weizmann Institute for Science, Rehovot, Israel, who provided computational insight into the detection of rapid changes in the on and off state of genes in response to environmental signals. Additional grants from the Independent Research Fund Denmark, the Danish National Research Foundation, the Human Frontier Science Program and the Lundbeck Foundation funded this research.

Josh Brickman has a background in molecular biology and gene regulation. From a PhD focused on transcriptional regulation he trained in developmental...

William obtained his PhD at the Edinburgh University in the labs of Tilo Kunath and Mike Tyers, where he worked on defining factors that regulate MAPK...

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