New insights into the function of the protein kinase DYRK1B, an ERK1/2 target gene

The cells in our body are constantly subjected to changes in their environment and they contain an extensive network of signalling pathways that coordinate appropriate responses. For example, exposure to noxious chemicals will activate signal pathways that allow repair of cellular damage and promote cell survival. In the developing embryo, cells may receive stimuli or cues telling them to divide (so called growth factors) or they may receive cues telling them to cease dividing and undergo 'differentiation', a process in which cells acquire the characteristics of specialized cell types that make up the discrete tissues in our adult bodies such as nerves, blood cells or muscles.
This process of cell division and differentiation is not only important in the developing embryo but also throughout our adult lives in responding to cell and tissue damage. For example, if we tear a muscle, special 'stem cells' in the muscle start to divide and then differentiate into new muscle cells to repair muscle tissue. As we get older this process become less efficient and our capacity to repair and renew tissues is reduced. This accounts for the progressive decline in our ability to recover from injuries that pose little problem to our younger selves.
For cells to respond to growth or damage cues they must activate key growth and repair proteins; this often involves increasing the abundance of these proteins. The genetic information for these proteins is stored in discrete pieces of DNA termed genes, which reside on chromosomes in the nucleus. When a cell receives a growth or damage signal these genes are 'transcribed' into messenger RNA (mRNA) molecules, which are in turn 'translated' into the relevant proteins. This whole complex process is orchestrated by signalling pathways, which control every step. Control is the key word here. If the cells divide too much during the repair response they may become cancerous; if they do not divide enough then muscle repair may be defective.
The signalling pathways controlling cell division and differentiation typically involve cascades of enzymes called protein kinases. These enzymes 'tag' other proteins with a phosphate group (a process called phosphorylation) and this changes the activity, abundance or localisation of the protein. The tagged protein is referred to as the 'substrate' of the protein kinase enzyme. This project concerns a protein kinase called DYRK1B.
DYRK1B is one of a small family of protein kinases that are poorly understood but are believed to be very important. For example, the closely related DYRK1A may be important in Down Syndrome whilst DYRK1B itself may be a cancer-causing gene. Importantly, the abundance of DYRK1B increases substantially during the switch from cell division to cell differentiation. However we are currently ignorant about how DYRK1B controls these processes because we know very few proteins that are DYRK1B substrates (i.e. that are tagged with phosphate by DYRK1B).
We have now identified a group of proteins that are phosphorylated by DYRK1B. These proteins are involved in controlling the abundance of the mRNA molecules that are ultimately translated into growth and repair proteins. In this project we will define how DYRK1B controls these proteins, the importance of this for regulating mRNA abundance and the role that DYRK1B plays in muscle differentiation using cells that can be stimulated to change into muscle in the lab.
The results of this study should tell us more about the normal role of DYRK1B in muscle differentiation, which is important in the elderly where muscle repair can be defective. It may also be relevant in other models of differentiation where DYRK1B may be important including fat cells, which is relevant to the rise in obesity. Finally, the ability of DYRK1B to control cell division may be important in cancer. To help us maximize the impact of our research we will work with other scientists in these area.

Protein kinase signalling pathways coordinate key cell fate decisions such as cell survival, proliferation, differentiation and senescence. DYRK1B is a member of the dual-specificity tyrosine phosphorylation-regulated kinases (DYRKs), a highly conserved family of protein kinases found within the CMGC (CDK, MAPK, GSK and CLK) group of the eukaryote kinome. However, in contrast to the CDKs and MAPKs, the normal biological functions of DYRK1B (and other DYRKs) are poorly understood. DYRK1B is inducibly expressed during myogenesis and adipogenesis and upon inhibition of the ERK1/2 signalling pathway (which causes a G1 cell cycle arrest). However, few substrates of DYRK1B have been defined that might help to place it in a biological context.
We have recently collaborated with AstraZeneca in characterising a new DYRK1B-selective inhibitor, AZ191, and have used this to validate the results of a SILAC experiment to identify new DYRK1B-inducible phosphoproteins. This analysis has identified several proteins involved in mRNA degradation (e.g., Dcp1a & 1b, Edc3 & Pat1b) and translational repression (e.g. 4E-T). For two of these (Dcp1a and 4E-T) we have confirmed that they are indeed DYRK1B substrates. These proteins are all found at discrete foci within the cell called Processing Bodies (PBs); these are sites of mRNA degradation and their abundance increases upon cell stress. We find that DYRK1B co-localises with Dcp1a at processing bodies and inducible DYRK1B expression is sufficient to increase PB abundance in the absence of stress.
We suggest that DYRK1B is a novel regulator of mRNA processing. In addition, we suggest that DYRK1B is part of a signalling pathway controlling mRNA processing during ERK1/2 inhibition (G1 cell cycle arrest) and myogenesis (cell cycle arrest & differentiation). In this proposal we will test these hypotheses, anticipating that we will define a new signalling pathway controlling mRNA processing.

The primary impact will come from the advancement of knowledge in mechanisms of signal transduction, related to cell responses to growth or stress cues (see Academic beneficiaries).
Impacts on industry and other stakeholders:
1. Industry: Major pharmaceutical companies (AstraZeneca, GSK, etc) remain interested in protein kinases as drug targets for a variety of diseases. The DYRKs, like RAF, MEK1/2 and ERK1/2, are readily 'druggable'. Indeed, this basic biology project developed out of a BBSRC CASE PhD with AZ with whom Cook has collaborated for ~9 years. Protein kinase inhibitors are also being used in iPS protocols in stem cell research and regenerative medicine, an area of growing commercial investment. Our research will therefore be relevant to a range of BioPharma companies contributing to UK economic competitiveness.
2. BBSRC: This research maps to Grand Challenge 3 within the BBSRC Delivery Plan: Fundamental bioscience enhancing lives and improving wellbeing. In particular: (i) basic molecular and cellular mechanisms responsible for longevity or premature ageing (e.g. triggers of cellular senescence, damage and repair processes) and (ii) basic molecular science underpinning the translation of knowledge about drug targets into chemical and biological tools and drugs. It also maps to BBSRC Strategic Priority 3: Basic Bioscience Underpinning Health. Relevant areas include: biological mechanisms of ageing and the maintenance of health; new tools in chemical biology, lipidomics and genomics; molecular cell biology, chemical biology and biochemistry to drive the discovery and validation of new drug targets or selective pharmaceuticals. Our 4sU labelling experiments fit with BBSRC's drive towards data driven science and mathematical biology and the project exemplifies the use of Partnerships, with contributions across sectors (Institutes, Universities, Industry).
3. Healthcare and 3rd sector charities: DYRK1B is expressed de novo during myogenesis, where it may promote survival, and during adipogenesis. Understanding myogenesis is important because age-related loss of muscle mass significantly impairs quality of life in the elderly. Similarly, adipocytes are critical regulators of metabolism and are involved in a variety of metabolic diseases including obesity. Sarcopenia in the elderly and obesity/diabetes are placing ever-greater demands on the NHS. Thus understanding how DYRK1B controls myogenesis (or adipogenesis) may contribute to future intervention strategies aimed at these problems. In addition, DYRK1B is expressed following ERK1/2 inhibition (a validated anti-cancer strategy) and is amplified in pancreatic and ovarian cancer (both with poor prognosis and in need of new therapeutic approaches) so our basic biology will be of interest to cancer charities as well as the healthcare professions.
Thus our research will impact through new information on drug targets (ERK1/2 pathway and DYRK1B) relevant to diseases and health deficits of old age
Training: This project will provide further training for key researchers (Ashford & Cook) in new scientific skills in growth areas (proteomics, genomics, bioinformatics). It will build on Ashford's excellent organisational skills, honed in industry, providing training for her future contribution to UK science & economic output.
Science & Society: We will continue to contribute to public STEM (science, technology, engineering and maths) understanding through our public engagement activities. Indeed, Ashford has been a STEM Ambassador throughout her PhD in the Cook lab communicating her knowledge and enthusiasm to the next generation of scientists and informing interested adults through activities such as science exhibitions and science visits to schools and local community groups.