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In the Expression Dynamics project, researcher Marko Jovanovic studied how dendritic cells – the mammalian immune system’s disease early-warning and first-response cells – react to external stimuli. He received funding from the EU’s Marie Skłodowska-Curie fellowship programme.
Jovanovic’s goal was to understand the gene expression changes that occur and, specifically, how these changes are controlled and regulated.
“My question was: Do we see that certain classes of genes are controlled one way and certain other classes another way, and from this can we gain new insights into the way genes are expressed and regulated in a dynamic system?” Jovanovic says. “Take cancer for instance. If the cancer is already developed and is already doing its damage in a quasi steady state you cannot look back and see what changes have occurred to cause the cancer to appear. You can see the secondary and tertiary effects that occurred later in the disease, but ideally you also want to be able to see the primary effects: what gene expression changes occur at the very beginning, the first events that led to the tumour progression. If we can understand first responses in a dynamic system we can better understand cause and effect.”
Dendritic cells are an ideal model system to study dynamic processes because they undergo a rapid and radical transformation when stimulated, for example as a result of exposure to bacterial molecules.
From a dormant, watchful state, dendritic cells switch within hours to actively attacking a detected pathogen, gathering information about it and travelling to the lymph nodes to activate the adaptive immune system. In the process, the cells change expression of several thousand genes – many of which are only turned on in an activated state.
Clarifying mRNA translation
The Expression Dynamics team explored how the three layers of gene expression – messenger RNA (mRNA) levels, mRNA translation and protein degradation – interact to produce this rapid dynamic response that effectively rewires the cell.
mRNA specifically conveys information about how cells should generate the protein products of gene expression - for example to fight disease. In a sense, mRNA carries the recipe for protein production for the cell, transcribed as a copy from the organism’s cookbook of DNA and translated into a specific set of cooking instructions. The simplified assumption is often that the number of mRNA molecules correlates well with the number of protein products.
In the case of dendritic cells, the researchers indeed found that mRNA level changes are the main driver of final protein levels in the activated state. But to meet the new active state needs of the cell, the expression of other genes and their protein products, such as those responsible for fundamental metabolic processes and energy production, also need to be readjusted. This adaptation of the cell’s ‘housekeeping’ genes, Jovanovic discovered, is driven by mRNA translation and protein stability changes.
The gene transcription regulation process by which instructions are copied and transmitted to the cell is widely researched and understood. But the process of translational regulation, the actual decoding of the copy of the instructions and synthesis of specific proteins under the direction of mRNA, remains a much less researched area, partly due to the difficulty of measuring cell protein levels directly.
“The Expression Dynamics project has made a significant contribution to address that challenge, providing a novel methodology to measure how much each type of regulatory layer of gene expression is contributing to final protein levels within the cell,” Jovanovic says. “Maybe as much as 90 % of gene expression and disease is regulated on the transcriptional level, but if 10 % is due to translational factors it is essential that we also study that,” Jovanovic says.
In a separate project, work completed as part of the Marie Curie fellowship has also contributed to the ongoing development of CRISPR-Cas9, a genome editing tool that is faster and more accurate than previous techniques for editing DNA. This has resulted in a patent for a genome-wide screening method to enable researchers to screen for numerous biological processes in different cell types.
Jovanovic, who conducted the research at the Max-Planck Society in Germany and the Broad Institute of MIT and Harvard in the US, is building on the Expression Dynamics results to study gene expression in other kinds of cells, specifically embryonic stem cell differentiation in neurons.
“There have been hints that mutations in certain RNA binding proteins, important regulators of mRNA translation, disrupt embryonic stem cell differentiation and could be linked to neurodegenerative diseases such as Alzheimer’s and Parkinson’s,” he says.