Daan van Aalten and his research group working on carbohydrate signalling in mammalian cells have joined the MRC-PPU.
Daan’s work on the regulation and function of the O-GlcNAc modification and how this impacts on biological processes related to improved understanding and treatment of human neurodegeneration, brings an exciting and critical new area of research to our Unit. In particular there are great untapped opportunities to explore interplay between O-GlcNAc, protein phosphorylation and ubiquitylation.
Daan with his expertise in structural biology also brings to our Unit much needed knowhow in the area of elucidation of protein structures. This will lead to many new exciting collaborations and opportunities.
Find out more about Daan’s current research here.
A team of postgraduate students from the College of Life Sciences at the University of Dundee has won the Scottish round of the Biotechnology Young Entrepreneurs Scheme (YES) qualifying them for the finals in London in December.
Biotechnology YES is an innovative competition developed to raise awareness of the commercialisation of bioscience ideas among postgraduate students and postdoctoral scientists. This is the first time a Scottish team has made it through to the finals.
Team members Anna Kelner and Alexander Von Wilamowitz-Moellendorff (both MRC-PPU) as well as Dun Jack Fu, Alistair Davies and Eleni Karinou, called their virtual company BioVita, which offers large supermarkets the potential to extend the shelf life of fruit in grocery stores by removing a plant growth hormone responsible for ripening. This would save tons of fruit that is wasted by supermarkets and consumers every year.
The team pitched their business plan to a panel of business, finance and academic representatives taking the role of venture capitalists. BioVita is one of two teams from each workshop selected to progress through to the Biotechnology YES Finals in London on 10 December 2012.
Biotechnology YES is organised jointly by the University of Nottingham Institute for Enterprise and Innovation (UNIEI) and the Business and Innovation Unit at Biotechnology and Biological Sciences Research Council (BBSRC).
Protein kinases are one of the pharmaceutical industry's most important classes of drug target. Nineteen protein kinase inhibitors have been approved for clinical use and over 150 more are undergoing clinical trials of which about 25 are in Phase III. A major challenge in this area is to develop a drug that selectively suppresses the activity of one, or at most a few, of the 500 protein kinases encoded by the human genome.
The MRC Protein Phosphorylation Unit (MRC-PPU) at Dundee pioneered analysis of the selectivity of protein kinase inhibitors by setting up the first service to tackle this problem in 1998. This procedure, termed 'kinase profiling' proved to be of great help to the pharmaceutical industry, speeding up the development of specific protein kinase inhibitors with therapeutic potential.
In order to enable academic drug discovery efforts and pharmaceutical companies to access kinase profiling services at an affordable price the MRC-PPU has set up the International Centre for Kinase Profiling to analyse the specificity of protein kinase inhibitors against a panel of nearly 150 protein kinases.
To help the research community select the optimal kinase inhibitors for biological studies and to make researchers aware of the limitations of many widely used kinase inhibitors we have generated a new searchable database of the inhibitor specificities of over 200 of the most commonly used signal transduction inhibitors.
We strongly recommend undertaking kinase profiling of any kinase inhibitor to be used in a biological experiment. It is essential to have a good feel for the specificity of the kinase inhibitor you are working with in order to be able to properly interpret your data.
If you have additional kinase inhibitors you are working with that have not been subject to kinase profiling and would like the International Centre for Kinase Profiling team to profile these for you please contact us at email@example.com and see our website for further details.
Note that the International Centre for Kinase Profiling team also offers lipid kinase profiling against 16 lipid kinases.
Jamie Wilson from the MRC PPU was one of the four joint winners of this year’s poster exhibition by PhD students in College of Life Sciences entering their 3rd year. Jamie, who has trained as a pathologist, is currently a Wellcome Trust Clinical Fellow in John Rouse’s lab. Jamie’s poster described the molecular mechanisms and cellular consequences of the binding of the SLX4 DNA repair complex to telomeres – the ends of chromosomes. Jamie also showed that the mechanisms for localizing the SLX4 scaffold protein, and the DNA repair nucleases with which SLX4 associates, to telomeres are distinct from the mechanisms for localizing the complex at sites of DNA damage. Each poster prize winner received £125 so the beers are on Jamie!
Well done to Gerta Hoxhaj for her successful PhD viva, held on October 5th 2012 on her work on the E3 ubiquitin ligase ZNRF2. (Hoxhaj is pronounced HOJ-EYE with a long O, and “XH” in the Albanian alphabet sounds like “J”).
Gerta is Carol MacKintosh’s 11th student to be awarded a PhD. Her examiners were Chris Proud of the University of Southampton and Hari Hundal of the College of Life Sciences, who reported that Gerta gave a lively performance and the exam was fun. Gerta’s first paper on ZNRF2 was published recently (to read click here), and she plans to undertake postdoctoral research in the USA, after she completes her work on ZNRF2 and submits her latest paper on the regulatory roles of this enzyme.
Research carried out by Kris Clark in the MRC-PPU has identified a major fundamental mechanism controlling immune cell function that suggests a new approach to the development of drugs to treat inflammatory diseases. The article describing this discovery has just been published in the Proceedings of the National Academy of Sciences of the USA.
Macrophages are cells of the immune system that defend the body against infection by bacteria and viruses. However, once these invading pathogens have been destroyed, the inflammatory responses triggered by macrophages have to be stopped, to avoid the development of chronic inflammatory diseases. Macrophages also play key roles in terminating the inflammatory response by switching on the production of so-called anti-inflammatory molecules. Kris discovered that the production of anti-inflammatory molecules by macrophages is prevented by members of the SIK sub-family of protein kinases and that, by turning off the function of SIKs within the cell, he could greatly enhance the production of beneficial anti-inflammatory molecules, like Interleukin 10, while stopping the production of the molecules that promote inflammation. These studies suggest that drugs that switch off SIKs may improve current therapies for treating inflammatory diseases, such as rheumatoid arthritis and psoriasis and programmes have been initiated to try and develop such drugs.
Commenting on his findings, Kris said: "These are very exciting times! This discovery represents the first link between SIKs and inflammation. My immediate future goal is to characterize in more detail the roles that SIKs play in the immune system and how they are affected by compounds that switch off this enzyme. My studies have greatly benefitted from working in the multi-disciplinary and collegial environment that has been built up in the MRC Unit, the Scottish Institute for Cell Signalling and the College of Life Sciences at Dundee where I work. My interactions with the scientists who work here and the advice they have given me has not only been invaluable for this project, but also most enjoyable."
Mutations leading to inappropriate activation of Akt isoforms contribute to proliferation and survival of a significant proportion of human cancers. Akt is activated by phosphorylation of its T-loop residue (Thr308) by the 3-phosphoinositide dependent kinase-1 (PDK1) and its C-terminal hydrophobic-motif (Ser473) by mTOR complex 2 (mTORC2).
A PhD student in Dario Alessi’s lab, Ayaz Najafov, characterised the first selective PDK1 inhibitors such as GSK2334470 recently developed by pharmaceutical companies as potential anti-cancer agents.
However, Ayaz found frustratingly that all structurally diverse PDK1 inhibitors he tested were surprisingly ineffective at suppressing Akt activation under conditions that these compounds effectively suppressed activation of other PDK1 substrates such as S6K, RSK and SGK isoforms.
After considerable research Ayaz discovered that resistance to PDK1 inhibitors results from Akt being efficiently recruited to PDK1 via two alternative mechanisms. The first involves ability of Akt and PDK1 to mutually interact with the PI 3-kinase second messenger PtdIns(3,4,5)P3. The second entails recruitment of PDK1 to Akt after its phosphorylation at Ser473 by mTORC2, via a substrate-docking motif termed the PIF-pocket. Ayaz showed that disruption of either the PtdIns(3,4,5)P3 or the Ser473 phosphorylation/PIF-pocket mechanism, only moderately impacts on Akt activation, but induces marked sensitization to PDK1 inhibitors.
The implications of Ayaz’s findings is that it will be difficult to ablate Thr308 phosphorylation and hence activation of Akt, employing PDK1 or even mTOR inhibitors as single agents. Ayaz’s solution was to combine PDK1 and mTOR inhibitors. Indeed in all cell lines he tested, Ayaz observed that combinations of mTOR and PDK1 inhibitors potently suppresses Thr308 and Ser473 phosphorylation to below-basal levels also inhibiting phosphorylation of Akt substrates. Furthermore, combination of PDK1 and mTOR inhibitors had much greater effects on inhibition of proliferation of all evaluated cancer cell lines, than treatments with either of the inhibitors alone.
Ayaz’s results suggests that combination of PDK1 and mTOR inhibitors might represent a new therapeutic strategy for treatment of cancers that harbour mutations elevating Akt activity. To read Ayaz’s paper click here.
A model of how the two alternative PtdIns(3,4,5)P3-binding and PIF-pocket-dependent mechanisms enable Akt to be efficiently activated and account for resistance to PDK1 inhibitors is shown in the figure above.
Fiona Brown who works in the Division of Signal Transduction Therapy Unit is participating in a very major charity event that is taking place this Saturday called Strictly Come Dance for Insight.
Fiona with her partner Scott Devine have been training intensely for nearly one year for this dance competition thattakes place at Kingennie Country Resort. Fourteen couples are dancing on the night. The dances include Jive, Cha cha, Rumba, Quick Step, Salsa, Tango and Waltz. The judges for this competition are Matthew Cutler, Strictly winner series 5 and Christopher Biggins.
The aim of Strictly is to raise funds for Insight Counseling Service, which is the only free counseling service in Angus and Tayside for people who have been bereaved by suicide, have suicidal thoughts, self harm, have been abused as children, are children that are abused and that only names a few issues. People are referred to Insight by doctors, the judicial system and can self refer but sadly there is a 400 waiting list thus self referrals can not be accepted at the moment until waiting list isclear.
We wish Fiona and her Partner good luck
The Infections and Immunity Board of the UK Medical Research Council (MRC) has awarded a grant of almost £1.5 million to Philip Cohen and his team to carry out research over the next five years on the mechanisms that prevent inflammatory and autoimmune diseases. The award is to follow up significant findings which have identified potential new targets for drugs to treat inflammatory and autoimmune diseases.
Commenting on the award Philip said, “About six years ago I decided to change the field of my research to try and understand how the innate immune system not only defends the human body against infection by bacteria and viruses, but also how the deregulation of this system can lead to chronic inflammatory and autoimmune diseases, such as Arthritis, Asthma, Colitis, Lupus, Psoriasis and Sepsis. I made this decision because I felt that the expertise and approaches that I had developed while working out how insulin regulates the synthesis of glycogen many years ago could be exploited to elucidate a very different biological control system that is also of great medical importance. Getting to grips with the complex field of immunology, with which I was previously unfamiliar, as well as the field of ubiquitylation which is so important in the control of immunity, has been a huge learning experience, and I am still learning! However, over the past few years my decision to enter this field has started to pay off and my team are now making interesting discoveries that promise to significiantly advance our understanding of this area.
It would have been very difficult to change my research to a field in which I had no previous track record had I not been working within an MRC Unit. I would therefore like to thank the MRC for setting up the MRC Protein Phosphorylation Unit at Dundee in 1990 because it is the long term core funding provided to MRC Units that enables the scientists that work in them to tackle ambitious and challenging problems without worrying about where their next research grant will come from,”
The International Centre for Kinase Profiling launched a new lipid kinase profiling service on 1st July 2012. These 17 lipid kinases will compliment the protein kinase profiling panel of 139 enzymes.
The lipid kinase panel includes PI3Kinases, PI4Kinases, DAG Kinases as well as Choline Kinases and Sphingosine Kinases.
Compounds can be screened at a single concentration against the panel of enzymes or analysed as 10 point dose response curves against any panel members of choice.
To date the International Centre for Kinase Profiling has screened compounds on behalf of 91 customers worldwide and we look forward to welcoming additional customers based in the lipid kinase signaling area.
If you would like to profile compounds using the service please check our website http://www.kinase-screen.mrc.ac.ukfor details of panel composition, current charges, sample submission guidelines and screening dates or contact us by e-mailing: firstname.lastname@example.org
At an international conference held at Dundee from Jun 24th-26th to mark Philip Cohen's 21 years as the Director of the MRC Protein Phosphorylation Unit, Philip was presented with an "Outstanding Contributor Award" from the Biochemical Journal by Peter Shepherd, the Editor-in-Chief of the Journal. Peter mentioned that the papers Philip and his research team have published in the Biochemical Journal have accumulated more than 10,000 citations, and this body of work alone has an H-factor of 37 (37 papers cited 37 or more times). The most highly cited paper that introduced the importance of profiling the specificities of protein kinase inhibitors (Davies et al, 2000, Biochem. J. 351, 95-105) has been cited nearly 3000 times and was downloaded from the Biochemical Journal website over 7,600 times in the year 2004 alone. Papers published in the Biochemical Journal by scientists at the University of Dundee have accumulated more than 34,000 citations and Peter said that the continued support for the journal by Dundee scientists had in large part been due to the encouragement provided by Philip as well as by his colleagues in the MRC Protein Phosphorylation Unit.
We are pleased to announce that Vicky Cowling and her research group including PhD Students (Thomas Gonatopoulos-Pournatzis, Michael Aregger, Sianadh Dunn, Anna Kelner, Laura Grasso) and postdoc (Nicola Phillips) will be moving into the MRC PPU on July 18th. Vicky's lab are currently based in the Division of Cell Signalling and Immunology within the College of Life Sciences.
Vicky’s research brings an exciting new research area to our Unit that involves understanding how the mRNA methyl cap in mammals and how this is regulated by protein phosphorylation and ubiquitylation pathways. Vicky’s lab is also focused in understanding how methyl cap formation and function is disregulated in diseases especially in cancers and using this information to come up with new therapeutic strategies. Vicky’s lab is also an integral part of our DSTT research collaboration.
To find our more details on Vicky’s research click here
Saif El-Din Shehata graduated from the University of Dundee with a MSc by Research on Thursday June 21st 2012. He did his MSc in the lab of Professor Kei Sakamoto at the MRC PPU, Kei is now working at the Nestle Institute for Health Science (NIHS), École Polytechnique Fédérale de Lausanne, Switzerland.
Saif and his wife Sherin are moving to Lausanne, Switzerland so he can start a PhD with Kei, he will continue his work on understanding the role and regulation of the PCTAIRE-1 protein kinase.
The transforming growth factor-β (TGFβ) signalling pathway plays critical roles through embryogenesis and in adult tissue homeostasis. Consequently, abnormal TGFβ signalling is associated with numerous human diseases, including immune disorders, fibrosis, cancer progression and metastasis. Reversible ubiquitylation of the TGFβ pathway components play crucial roles in determining balanced cellular responses to TGFβ signals. Much is known about the regulation of the key pathway components by ubiquitylation. However, very little is known about the role of deubiquitylating enzymes (DUBs) in the regulation of the TGFβ pathway.
Mazin Al-Salihi, who is a MRC Career Development Fellow in Gopal Sapkota’s laboratory in the MRC Protein Phosphorylation Unit, has focussed on identifying and characterising novel deubiquitylating enzyme regulators of the TGFβ pathway. A proteomic screen undertaken in Gopal’s laboratory identified USP11 as an interactor of SMAD7, a negative regulator of the TGFβ pathway that recruits E3 ubiquitin ligases to the type I TGFβ receptors. Mazin demonstrated that USP11 enhances TGFβ pathway signalling by binding, deubiquitylating, and stabilising the type I TGFβ receptor, ALK5. He showed that USP11 augments the TGFβ-induced phosphorylation of SMAD2/3 as well as transcriptional responses. Furthermore, he found that only wild type USP11, but not a DUB dead mutant that still binds ALK5, is capable of eliciting such responses. Mazin’s findings thus imply a central role for the reversible ubiquitylation balance mediated by the SMAD7-E3 and SMAD7-USP11 complexes on ALK5 stability and consequently TGFβ pathway signalling.
Epithelial to mesenchymal transition (EMT) is a process whereby epithelial cells undergo profound changes in shape and behaviour to become mesenchymal cells. EMT is a fundamental process during embryogenesis and organogenesis conferring enhanced cellular plasticity. While the precise roles of EMT in cancer progression are still unclear, EMT may confer malignant traits such as motility, stemness, invasiveness, and survival in cancer cells. TGFβ is a potent inducer of EMT. By reducing USP11 expression, thus inhibiting TGFβ signalling, TGFβ-induced EMT is inhibited in a cellular model. These findings open an exciting new avenue for drug discovery by targeting USP11 for the inhibition of the TGFβ pathway in cancer.
Lina Herhaus, a PhD student in Gopal’s laboratory, also contributed to this research.
Al-Salihi, M. A., Herhaus, L., Macartney, T. and Sapkota, G. P. (2012) USP11
augments TGFβ signalling by deubiquitylating ALK5. Open Biology 2: 120063
A review describing the regulation of the TGFβ pathway by reversible ubiquitylation was also published recently.
Al-Salihi, M. A., Herhaus, L. and Sapkota, G. P. (2012) Regulation of the TGFß Pathway by Reversible Ubiquitylation. Open Biology 2: 120082.
A new affinity tag for the purification of recombinant proteins termed the ‘Dac-tag’ has been developed by Axel Knebel who is the head of the Protein Production and Assay Development team at SCILLS. Together with the MRC and SCILLS cloning teams Axel has perfected the Dac-tag especially for the purification of recombinant proteins from insect cells. Using this methodology Axel and his team have been able to obtain incredibly pure preparations of enzymes from insect cells much better than could be achieved with other tags such as His, maltose binding and GST. We anticipate that the Dac-tag will become the frontline choice for the future purification of proteins from insect cells.
The Dac-tag is based on a fragment of penicillin binding protein 5, which binds in a pseudo reversible manner to ampicillin Sepharose. In order to obtain a pure protein of interest, the Dag-tag is cloned to the N or C-terminal end of the protein. Because of the properties of the Dac-tag, this fusion protein can then be readily isolated in a highly purified manner using ampicillin Sepharose, which is very selective for penicillin binding proteins. The Dac-tag has the advantage that it is monomeric and does not rely on Cysteine chemistry or metal affinity, so it is ideal for purification of proteins in the Ubiquitin arena.
The paper describing the development and use of the Dac Tag is now published: ‘The Dac-tag, an affinity tag based on penicillin binding protein 5.‘ in Analytical Biochemistry: Methods of the Life Sciences in press. Click here to access the paper.
Eeva Sommer, a PhD student in Dario Alessi’s lab, working on the role of SGK in cancer, recently got married. What was most impressive was that Eeva was still in the lab on the Friday, the day before the wedding and back in the lab again on Monday.
We wish Eeva and Morgan every happiness for the future.
Since Philip Cohen arrived in Dundee in 1971, as well as becoming one of the world’s mostly highly cited biochemists and a leader in his field, he has been a major driving force in putting Dundee on the map in scientific terms. Not only did he establish the MRC Protein Phosphorylation Unit, the award-winning Division of Signal Transduction Therapy (DSTT) and the Scottish Institute for Cell Signalling (SCILLS) but he also played major roles in setting up the Wellcome Trust Biocentre and the Sir James Black Centre.
In April 2012 Philip stood down as Director of the MRC Protein Phosphorylation Unit to concentrate full-time on his lab’s research. At this point it was 21 years since Philip became Director of the MRC-PPU and just over 40 years since he arrived in Dundee. We are planning a special Symposium to celebrate Philip’s extraordinary research achievements during this time.
This event will take place from 24th to 26th June 2012 at the West Park Conference centre in Dundee. As well as the numerous talks by friends, colleagues and collaborators of Philip’s, the highlights of the meeting include Sunday night talks by Nobel Laureates Tim Hunt and Eddy Fischer. Full details of the meeting can be found here.
As you will see we have organized the scientific sessions into the main themes of Philip's research interests over the years. In the final talk of the meeting Philip will reflect on the past 21 years and speak about his future research plans. We hope this will be a memorable event to reflect Philip’s extraordinary achievements.
David Komander, ex-PhD student of Dario Alessi and Daan van Aalten (now working as a group leader at the LMB in Cambridge), and Sonja Flott, ex-PhD student of John Rouse (now working in Abcam in Cambridge) have had a new baby, Emma C. Komander.
Both Emma and Sonja are doing very well and David is “a very happy daddy”.
Congratulations also to David for being awarded a recent Lister Research Prize for his work in dissecting the biological roles of new ubiquitylation pathways.
Mutations in the protein kinase PINK1 were discovered in 2004 in patients with early-onset Parkinson’s disease. PINK1 is unique among all protein kinases since it contains an N-terminal mitochondrial targeting motif and its catalytic domain is also unusual as it possesses three unique insertions between the beta strands that make up the typical fold of the N-lobe of protein kinases. Despite intensive research the substrate for PINK1 remained unknown.
Chandana Kondapalli, a PhD student co-supervised by Miratul Muqit and Dario Alessi, set out to discover the substrate of PINK1. When Chandana embarked on her studies, she found that recombinant PINK1 when expressed in mammalian cells was inactive which limited the ability to use traditional biochemical approaches to identify substrates. In a separate project, another PhD student in the lab, Helen Woodroof had discovered that insect orthologues of PINK1 were constitutively active as judged by their ability to phosphorylate generic substrates. Chandana decided to test whether insect PINK1 could phosphorylate 15 proteins encoded by PD-associated genes as well as proteins reported to bind PINK1. Excitingly she found that PINK1 could only phosphorylate one of these proteins namely the RING E3 ligase Parkin, which is commonly mutated in early-onset Parkinson’s disease. Chandana next mapped the phosphorylation site to a highly conserved residue within the Ubl domain of Parkin at Serine 65 (Ser65).
A major question was how phosphorylation at Ser65 by PINK1 affected Parkin function. A recent study by Helen Walden’s group in London had suggested that Parkin was inactive when expressed in vitro suggesting that it required to be activated. Another PhD student in the lab, Agne Kazlauskaite, sought to test the hypothesis that PINK1 phosphorylation at Ser65 may activate Parkin. Before Agne could perform her experiments, Axel Knebel and Clare Johnson, based in the SCILLS Protein Production Unit, first generated milligram amounts of highly purified Parkin using a method adapted from the Walden lab. Agne then developed an assay whereby she could test Parkin activity in vitro following phosphorylation by PINK1. Remarkably Agne found that Parkin was active only when it was phosphorylated by wild-type but not a kinase-inactive version of PINK1. Furthermore, a Ser65Ala mutant of Parkin could not be activated by PINK1 suggesting that Ser65 phosphorylation was indeed required for Parkin activation.
In further experiments, Chandana was able to show that human PINK1 is normally inactive in cells but that it can become active following mitochondrial depolarisation. Under these conditions she could confirm that human PINK1 can phosphorylate Parkin at Ser65 using mass spectrometry and a phosphospecific antibody against this site. She also mapped a PINK1 autophosphorylation site by mass spectrometry at residue Threonine 257 (Thr257) and confirmed this using a phosphospecific antibody against Thr257. A major hurdle in studying PINK1 in cells has been the detection of endogenous levels of PINK1. However, Ning Zhang, a post-doc in the lab, was able to detect endogenous levels of PINK1 following mitochondrial depolarisation and importantly showed that endogenous PINK1 could phosphorylate Parkin at Ser65.
Chandana’s findings suggest that Parkin is a bona fide PINK1 substrate and indicate that monitoring phosphorylation of Parkin at Ser65 and/or PINK1 at Thr257 represent the first biomarkers for examining the activity of the PINK1-Parkin signalling pathway in vivo. The next major challenge in the field is to identify physiological substrates of Parkin but this research also suggests that small molecule activators of Parkin that mimic the effect of PINK1 phosphorylation may confer therapeutic benefit for Parkinson’s disease.
To read a copy of Chandana’s paper published in Open Biology, click here.
Congratulations to Laura Pearce, an ex-PhD student in Dario Alessi’s lab, who is currently a Sir Henry Wellcome Postdoctoral Fellow in Sadaf Farooqi’s laboratory at the Metabolic Research Laboratories, University of Cambridge. Laura has received a certificate from the Biochemical Journal as her paper describing the first S6K inhibitor is the most read article published in the Biochemical Journal’s ChemBio section in the last 3 years. The inhibitor PF-4708671 is now being used by hundreds of labs worldwide to investigate the roles of S6K in regulating many biological and disease processes.
To read a copy of Laura’s paper please click here.
For the past 14 years the MRC Protein Phosphorylation Unit has been helping the pharmaceutical industry to initiate and accelerate that the development of drugs that target kinases and phosphatases in a unique collaboration, called the Division of Signal Transduction Therapy (DSTT). Founded in 1998, expanded in 2003 and renewed for a second time in 2008, it is widely regarded as a model for how academia and industry can interact productively and was awarded a Queen’s Anniversary Prize for Higher Education in 2006.
The Unit is now delighted to announce the renewal of the collaboration for a further four years from July 1st 2012. The new field of the collaboration will be “kinases and the ubiquitin system” and will include Programme Leaders from the Protein Ubiquitylation Unit of the Scottish Institute for Cell Signalling at Dundee (SCILLS) as well as the MRC Protein Phosphorylation Unit. The collaboration is being funded by six of the world’s leading pharmaceutical companies -- AstraZeneca, Boehringer Ingelheim, GlaxoSmithKline, Janssen Pharmaceutica NV, Merck-Serono (the Pharmaceutical division of Merck KGaA) and Pfizer. They will provide core support of £14.4 million over the period July 1st 2012 – June 30th 2016 for research on the causes of many diseases including cancer, arthritis, Lupus, hypertension and Parkinsonism.
Kinase drug discovery accounts for about 30% of the R&D budget of the pharmaceutical industry and over 50% of global cancer drug discovery. The ubiquitin system is an emerging area of drug discovery in which Dundee has recently developed great strengths through the recruitment of Professor Hay in 2005 and the founding of the SCILLS in 2008.
Professor Sir Philip Cohen, co-founder of the DSTT with Professor Peter Downes, said, “Collaborations between academic laboratories and the pharmaceutical industry typically last a few years. Therefore to maintain and expand support for the DSTT from 1998 until at least 2016 is unprecedented and remarkable. It shows how valuable the collaboration has been for the pharmaceutical industry.”
From July 2012, the New Director will be Professor Dario Alessi with Sir Philip and Professor Ronald Hay acting at Deputy Directors. Commenting on the renewal of the agreement, Professor Alessi said, “I am delighted that the agreement has been renewed, as this offers further potential for us to translate our recent research findings and ideas into new drug therapies for the treatment of many diseases.”
On behalf of the pharmaceutical companies, Dr Malcolm Skingle CBE, of GlaxoSmithKline and Chairman of the Programme Management Group, said, “This has been a very successful collaboration over the past 14 years and we are delighted to see it continue. This project has shown the benefits that can come from pharmaceutical companies working hand-in-hand with top flight research at the University of Dundee.”
Professor Sir John Savill, Chief Executive of the Medical Research Council, said, “The DSTT collaboration is a unique and highly effective partnership that allows academic researchers to collaborate with leading pharmaceutical companies to maximise the translation of basic research towards clinical benefit. We are proud to continue our support of a project that is greatly accelerating pharmaceutical drug discovery programmes for major diseases.”
Minister for Universities and Science, David Willetts, said, “Collaboration between the life sciences industry and academia is vital for the development of new treatments and leverages significant private funding into our research base. This investment will continue the excellent work taking place at the University of Dundee on major global diseases, helping to bring benefits for patients and the economy.”
Representatives of Parkinson’s UK and the J. Macdonald Menzies Charitable Trust, as well as Parkinson’s patients, visited the MRC Protein Phosphorylation Unit (MRC-PPU) on May 3rd to hear about exciting research developments on Parkinson’s disease at the MRC-PPU. Over the last few years the MRC-PPU have received generous funding from Parkinson’s UK to support PhD student Chandana Kondapalli (jointly supervised by Miratul Muqit and Dario Alessi) and more recently the J. Macdonald Menzies Charitable Trust to support Agne Kazlauskaite (supervised by Dario Alessi).
The visitors had an opportunity to hear Chandana and Agne present their latest research findings on the PINK1 and parkin proteins whose genes are mutated in patients with familial Parkinsonism. The presentations were interspersed with many probing questions and helpful suggestions from the visiting delegation. This was followed by a lively discussion on future directions of research. The visit ended with a tour of the labs in which the visitors were able to see firsthand the state-of-the-art facilities housed within the MRC-PPU, including the new mass spectrometry suite.
The event was co-hosted with Anton Gartner from the Wellcome Trust Centre for Gene Regulation and Expression whose group uses the model organism C. elegans to better understand Parkinson’s.
On the 23rd of March three staff from the MRC-PPU visited the Dundee University Nursery to have a fun half day of experimenting. Nicola Wood, Vicky McGuire and Gail Gilmour, assisted by Nursery staff, helped the children get hands-on with some messy, colorful and hopefully thought provoking projects.
A color table was set up showing the kids which colors are in their Smarties, and the immiscible properties of everyday substances like milk and oil. There was exercise a plenty at the body table to demonstrate the function of the heart, and skeleton pictures alongside. Messy gloop and bicarbonate of soda fizzing lava seemed to be a firm favorite with the kids before they moved on to looking at some items collected from the garden under the microscope, kindly donated for the day by Dr Alan Prescott. The visit was then rounded off with the ooohs, aahhs and general excitement produced by the dry ice volcanoes.
As a result of the visit quite a few of the children have promised to become scientists when they grow up, so hopefully they'll be working with us in the not too distant future!!
Many congratulations to Ayaz, a PhD student in Dario Alessi’s lab, for his award of the CLS Innovator of the Year Prize for the development of the ProteinGuru program that greatly facilitates the analysis of complex mass spectrometry data. Ayaz was nominated for this award by Paola delos Heros and other postdocs and PhD students in Dario’s lab.
Ayaz developed this program in his spare time with his brother Jamil Najafov, an undergraduate student studying Computer Science at Gazi University in Turkey. The purpose of ProteinGURU is to facilitate the analysis of complex mass spectrometry data. It rapidly removes all common general contaminants from the data sets leaving only the proteins that are likely to be genuine hits. It also provides lots of valuable information on domain structure, disease links and known functions of genuine hits. Another hugely useful feature of ProteinGuru is that it enables the rapid analyse the data from 3 or 4 mass spectrometry sets of data to search for differences between the data. For example, if you are comparing wild type versus knockout and/or drug treatment samples, the programme enables the researcher to rapidly pinpoint hits that are effected by knockout and/or drug treatment.
ProteinGURU is being widely used in the MRC Protein Phosphorylation Unit and is freely available to anyone worldwide to use without restriction: http://www.proteinguru.com/
Ayaz will be presented with his award by the cancer genetics pioneer, Robert Weinberg, of the Whitehead Institute in Boston on April 13th when he delivers the College of Life Sciences annual Adam Neville Lecture. Ayaz plans to share the £250 prize with his brother.
Ayaz said “I am greatly honoured to have received the Innovator of the Year award from the College of Life Sciences at this early stage of my career. It’s a great pleasure to be able to contribute to the research of my colleagues and beyond. I hope ProteinGURU will be used by more researchers around the world. I wouldn’t have been able to do this without my brother Jamil, and he deserves half of the prize.” Dario would like to stress that Ayaz undertook this work completely independently with no involvement of his PhD supervisor. In fact Dario recollects that he suggested to Ayaz that he concentrates on his main project understanding how PDK1 inhibitors operate rather than “messing around writing computer programs”. This emphasizes the importance of PhD students not always following the advise of their PhD supervisors, if they wish to become successful.
To look at the ProteinGURU programme please click here.
The EMBO Journal Cover Contest, initiated by the editors of the journal in 2003, highlights the creative potential of the authors and readers of The EMBO Journal, and showcases the beauty they find in the scientific and non-scientific world around them. The March 21st issue of EMBO Journal features a beautiful photo taken by Ivan Muñoz from John Rouse’s lab. The photo is a portrait of a puffin on the Isle of May taken during the breeding season when puffins feed their chicks with fish, in this case sand eels. The photo, submitted to last year's EMBO Journal Cover Contest, was one of the pictures selected from "more than 3,000 submissions representing the entire spectrum of scientific and nonscientific nature imagery". Well done Ivan!
The Isle of May is an outstandingly attractive island, which lies at the entrance of the Firth of Forth. This important National Nature Reserve, which is owned and run byScottish Nattural Heritage, has incredible wildlife, including puffins, guillemot, razorbill, shag, and eiderduck. Dolphins, porpoise and whale are often spotted in summer time. Fancy a visit? The Isle of May is easy to get can be reached easily by ferry which leaves from Anstruther, a 40 min drive from Dundee.
The British Biochemical Society has chosen Dr Kristopher Clark in the MRC Protein Phosphorylation Unit (MRC-PPU) at the University of Dundee to receive an Early Career Development Award in 2013.
These prizes are presented annually to four young scientists for work carried out in the United Kingdom in recognition of the impact of their research. Only scientists who have been awarded their PhD degrees within the last five years are eligible.
Each awardee will present their Medal Lecture at a Biochemical Society conference in 2013, when they will also receive an honorarium of £1000 and the medal. The lecture will be published in the Biochemical Society Transactions..
The Biochemical Society expects that “the successful candidates will have produced international quality research outputs, and be able to demonstrate ambitions and aspirations consistent with the potential to achieve world-leading status.”
Dr Clark was selected by Theme Panel V, which covers the field of Signal Transduction. This topic represents a major aspect of current biochemical research.
Over the past two years, Dr Clark has identified how the immune system defends the body against infection by bacteria and viruses without overproducing substances called “cytokines”, which are a major cause of lupus, psoriasis and arthritis. His research has also identified ways in which improved drugs to treat these autoimmune diseases might be developed.
Commenting on his award, Dr Clark said, “I am thrilled to have won this award from the Biochemical Society. It is a great honor to have my research recognised by my peers in this way. Dundee has provided me with a great opportunity and stimulating environment to address key questions in the innate immune system and my research would not have been possible without the support of many people within the College of Life Sciences. I now look forward to presenting my Medal Lecture next year.”
Born and brought up in Montreal, Canada, Dr Clark studied in Canada, Australia and then the Netherlands from where he obtained his Ph.D. degree from the Radboud University Nijmegen in 2007. In March 2006 he was awarded a Short-Term Fellowship from the Federation of European Biochemical Societies to enable him to spend a month in the MRC Protein Phosphorylation Unit and it was this visit that led him to join Philip Cohen’s laboratory in May 2007 after being awarded a Long-Term Fellowship by the European Molecular Biology Organisation.
Sir Philip Cohen, Director of the MRC-PPU, said “I am really delighted that the Biochemical Society has chosen Kris for one of their young investigator awards. He has made two major breakthroughs that have significantly increased our understanding of how the innate immune system is kept in check to prevent the onset of autoimmune diseases. One of these has yet to be published and will make a big impact when it is. About six years ago I changed my field of research to tackle the challenging problem of how the innate immune system is regulated. Kris’s contributions have been instrumental in gaining rapid national and international recognition for this relatively new research programme.”
This is the second time that a scientist who has worked in the MRC Protein Phosphorylation Unit has received the Biochemical Society's Early Career Development Award. David Komander, who carried out his PhD under the joint supervision of Dario Alessi of the MRC-PPU and Daan van Aalten of the College of Life Sciences at Dundee, and is now a Principal Investigator at the MRC Laboratory for Molecular Biology, Cambridge, UK, received the award in 2009.
Thanks to the generosity of the family of Abbie Clark, Sjoerd van Helvert, a visiting intern student from HAN University of Applied Sciences in the Netherlands, is to benefit from the proceeds of a collection made at Abbie’s funeral.
Abbie worked at the University for 11 years, including 8 as a technician at the College of Life Sciences (CLS) before retiring in the summer of 2010. Sadly, Abbie passed away in July 2011. Abbie was a major supporter of research in the MRC Protein Phosphorylation Unit (MRC-PPU). Through Camperdown Lodge, he raised thousands of pounds to fund summer placements at CLS for research students from around the world. In recognition of his fundraising passion, Abbie’s family decided to hold a collection for this cause at his funeral. His wife, Charlotte, son Kevin, and daughter Caroline presented the proceeds of this collection totalling £500 plus £250 from a further collection, to Professor Dario Alessi, from the MRC-PPU.
Sjoerd, who started on 1 February 2012, will be establishing and testing new research tools in Dr Satpal Virdee’s laboratory in the Scottish Institute for Cell Signalling. The technology should enable the detection of interacting partners of critical biomolecules which are otherwise difficult to detect by other methods. Identifying who these biomolecules “talk” to will allow us to piece together communication pathways in cells and how faults in these pathways give rise to diseases such as cancer.
Sjoerd is one of a number of intern students to benefit from an agreement the HAN University of Applied Sciences has with the MRC-PPU which offers an opportunity for undergraduate students to study overseas for a term to gain experience at another institution.
Dario Alessi said “Abbie was a very popular member of staff at the College of Life Sciences, and he helped raise a lot of money for the MRC-PPU, which we are very grateful for. I would also like to thank Charlotte, Kevin and Caroline for carrying on Abbie’s fundraising work. Everyone here is humbled by this gesture and as Abbie’s previous fundraising was used to support the cost of bringing research students to the UK we decided that this donation would be used for the same purpose. His work enabled three students to come to Dundee and get their first flavour of research and also gain expertise and knowledge in diabetes research. Importantly, the majority of these students have since gone on to complete successful PhDs and are still working in sciences. Without the funds that Abbie and the Camperdown Lodge raised these students may not have had an opportunity to undertake a scientific research project and potentially might not be where they are now. We wish Sjoerd the best of luck with his research project in Satpal’s laboratory and I hope that he makes a significant discovery but above all gains a major interest and experience in undertaking scientific research that will help him in his future career. Towards the end of his project Sjoerd will have to give a talk at the Camperdown Lodge to let Abbie’s family and friends know what he has been doing with the precious research funds that they raised!”
Mutations in the gene encoding the protein kinase LRRK2 (leucine rich repeat kinase 2) cause autosomal dominant Parkinson’s disease [1, 2]. The most common mutation replaces glycine 2019 with a serine within the magnesium-binding DFG motif of the kinase domain thereby increasing LRRK2 kinase activity 3-fold [3, 4]. This indicates that inhibitors of LRRK2 kinase activity might be of therapeutic benefit for the treatment of Parkinson’s disease and has stimulated much activity in this field of research.
Recent work has revealed that LRRK2 interacts with14-3-3 phospho-binding adaptor isoforms that is mediated by phosphorylation of Ser910 and Ser935 located prior to the leucine rich repeat domain mediates . Interestingly, 14-3-3 binding has been linked to Parkinson’s disease as Ser910 as well as Ser935 and interaction with the 14-3-3 is inhibited by five of the six validated LRRK2 pathogenic mutations (R1441C, R1441G, R1441H, Y1699C and I2020T) [5, 6].
Intriguingly, treatment of cell and animal models with structurally unrelated LRRK2 kinase inhibitors also results in dephosphorylation of Ser910 and Ser935 that is accompanied by loss of 14-3-3 binding [7, 8]. The kinase(s) and phosphatase(s) that act on Ser910, Ser935, Ser955 and Ser973 are unknown, but the evidence points towards these residues not comprising autophosphorylation sites .
Nic Dzamko a Postdoc in Dario Alessi’s lab who is now a CJ Martin Fellow at the Neuroscience Research Institute in Sydney Australia generated and characterised state of the art hugely sensitive and specific Total and Ser910 and Ser935 phospho specific antibodies in close collaboration with the Michael J Fox foundation for Parkinson’s Research in New York (http://www.michaeljfox.org/), one of the world greatest and most innovative supporters of medical research in the area of understanding and treating Parkinson’s disease. These antibodies enable for the first time the assessment of LRRK2 phosphorylation state by immunoblot analysis in very small amounts of cell extract (<20 micrograms). We expect that these will be usable in ELISA and Immunohistochemical applications as well.
We hope that these reagents will have tremendous benefit in helping the pharmaceutical industry as well as academic researchers assess the efficacy of LRRK2 inhibitors that are being developed. We also think that they will also help in further understanding the link between 14-3-3 binding to LRRK2 and Parkinson’s Disease.
To learn more about these antibodies and to order these please click here for total antibody; click here for the Phospho935 antibody and click here for the phosphSer910 antibody.
We would like to thank the Michael J Fox foundation and especially Sonal Das an associate Director of the Foundation for their support for this project.
1 Zimprich, A., Biskup, S., Leitner, P., Lichtner, P., Farrer, M., Lincoln, S., Kachergus, J., Hulihan, M., Uitti, R. J., Calne, D. B., Stoessl, A. J., Pfeiffer, R. F., Patenge, N., Carbajal, I. C., Vieregge, P., Asmus, F., Muller-Myhsok, B., Dickson, D. W., Meitinger, T., Strom, T. M., Wszolek, Z. K. and Gasser, T. (2004) Mutations in LRRK2 cause autosomal-dominant parkinsonism with pleomorphic pathology. Neuron. 44, 601-607
2 Paisan-Ruiz, C., Jain, S., Evans, E. W., Gilks, W. P., Simon, J., van der Brug, M., Lopez de Munain, A., Aparicio, S., Gil, A. M., Khan, N., Johnson, J., Martinez, J. R., Nicholl, D., Carrera, I. M., Pena, A. S., de Silva, R., Lees, A., Marti-Masso, J. F., Perez-Tur, J., Wood, N. W. and Singleton, A. B. (2004) Cloning of the gene containing mutations that cause PARK8-linked Parkinson's disease. Neuron. 44, 595-600
3 West, A. B., Moore, D. J., Biskup, S., Bugayenko, A., Smith, W. W., Ross, C. A., Dawson, V. L. and Dawson, T. M. (2005) Parkinson's disease-associated mutations in leucine-rich repeat kinase 2 augment kinase activity. Proc Natl Acad Sci U S A. 102, 16842-16847
4 Jaleel, M., McBride, A., Lizcano, J. M., Deak, M., Toth, R., Morrice, N. A. and Alessi, D. R. (2005) Identification of the sucrose non-fermenting related kinase SNRK, as a novel LKB1 substrate. FEBS Lett. 579, 1417-1423
5 Nichols, R. J., Dzamko, N., Morrice, N. A., Campbell, D. G., Deak, M., Ordureau, A., Macartney, T., Tong, Y., Shen, J., Prescott, A. R. and Alessi, D. R. (2010) 14-3-3 binding to LRRK2 is disrupted by multiple Parkinson's disease-associated mutations and regulates cytoplasmic localization. Biochem J. 430, 393-404
6 Li, X., Wang, Q. J., Pan, N., Lee, S., Zhao, Y., Chait, B. T. and Yue, Z. (2011) Phosphorylation-dependent 14-3-3 binding to LRRK2 is impaired by common mutations of familial Parkinson's disease. PLoS One. 6, e17153
7 Dzamko, N., Deak, M., Hentati, F., Reith, A. D., Prescott, A. R., Alessi, D. R. and Nichols, R. J. (2010
) Inhibition of LRRK2 kinase activity leads to dephosphorylation of Ser(910)/Ser(935), disruption of 14-3-3 binding and altered cytoplasmic localization. Biochem J. 430, 405-413
8 Deng, X., Dzamko, N., Prescott, A., Davies, P., Liu, Q., Yang, Q., Lee, J. D., Patricelli, M. P., Nomanbhoy, T. K., Alessi, D. R. and Gray, N. S. (2011) Characterization of a selective inhibitor of the Parkinson's disease kinase LRRK2. Nat Chem Biol. 7, 203-205
Kei Sakamoto, a Programme Leader in the MRC Protein Phosphorylation Unit will become the Head of a new Division of Diabetes Research at the Nestle Institute of Health Sciences in Lausanne Switzerland. Kei, who has also been appointed to a Professorship at the Swiss Federal Institute of Technology, will take up his new post on March 1st 2012. Six members of Kei’s research team will be moving with him to Lausanne and Kei will make nine more appointments over the next couple of years. In Lausanne, Kei will continue to elucidate the molecular mechanisms that control glucose and energy homeostasis with the aim of identifying novel drug targets aimed at treating metabolic disorders such as type 2 diabetes.
Commenting on Kei’s new appointment, Sir Philip Cohen, the Director of the MRC Protein Phosphorylation Unit said:- “Kei has done a great job for our Unit during the eight years that he has been with us. In addition to carrying out ground-breaking research of his own and important collaborative projects with other members of the Unit, he was also instrumental in setting up the Unit’s state-of-the-art Molecular Physiology Laboratory. The huge promotion that Kei has now received is therefore very well deserved and we all wish him every success for the future.
Commenting on his new appointment Kei said:- “I would particularly like to thank Professor Dario Alessi and Sir Philip Cohen for their tremendous support during my research career in Dundee, which was absolutely essential for me to become an independent and established investigator. The MRC Protein Phosphorylation Unit provides such an extraordinary stimulating, interactive and outstanding research environment with the state-of-art facilities, but I have decided to take on a new challenge and will make every effort to achieve breakthroughs in basic and translational research at the Nestle Institute in Lausanne.”
The Nestlé Institute of Health Sciences is based on the campus of the Swiss Federal Institute of Technology in Lausanne and part of Nestlé’s global Research & Development network. It is fully funded by Nestlé, who will contribute 500 million Swiss francs to its development over the next 10 years. The mission of the Institute is "To create and deliver world class excellence in biomedical research to better understand human health and ageing as influenced by genetics, metabolism and environment with the goal of translating this knowledge into personalized science-based nutrition". In Lausanne, Kei will continue to elucidate the molecular mechanisms that control glucose and energy homeostasis with the aim of identifying novel drug targets for the treatment of metabolic disorders such as type 2 diabetes
The January 1st 2012 issue of the Biochemical Journal features three articles by Programme Leaders in the MRC Protein Phosphorylation Unit, which run consecutively from pages 325 – 357 of Volume 441 of the journal. In the first article Dario Alessi's lab report advances in understanding how the protein kinases SPAK and OSR1 regulate the sodium/potassium co-transporter 1 and the protein kinase WNK to regulate blood pressure (Thastrup et al, BJ, 441: 325-337), while in the second Philip Cohen's lab report that the E3 ubiquitin ligase Pellino 1 is activated by two different protein kinases in response to two different inflammatory stimuli (Goh et al, BJ, 441: 339-346). In the third paper, Simon Arthur's lab characterise the cellular actions of a a new pharmacological inhibitor of the Mitogen and Stress-activated Kinases (MSKs) (Naqvi et al, BJ, 441: 347-357).
Congratulations to Dr Kumara Dissanayake from Carol MacKintosh’s group who was awarded the 2011 Howard Elder Prize for his paper on the transcriptional repressor Capicúa [Dissanayake et al Biochem J. 433, 515-525].
Capicúa (Cap-ee-Coo-a) is Catalan for head-and-tail, so named because mutation of the fruit fly version affects early head and tail development. Kumara discovered that the human Capicúa is a missing link that helps explain why oncogenic Ras–Raf signaling stimulates downstream transcription of ETV1 and other genes that are linked to particularly aggressive forms of prostate cancer, melanoma, oligodendroglioma and gastrointestinal stromal tumours. Specifically, Capicúa represses mRNA expression of the PEA3 Ets transcription factors ETV1, ETV4 and ETV5, and this repression is relieved when Capicúa is phosphorylated by the protein kinases ERK and p90RSK that are activated by Raf. Capicúa then binds to the 14-3-3 family of phosphoprotein-binding proteins, which block its binding to DNA.
Kumara found that experimental depletion of Capicúa rendered melanoma cells resistant to the therapeutic effects of drugs that block signaling upstream of ERK. He therefore predicted that the loss of Capicúa might enhance tumourigenesis, and excitingly, mutations in Capicúa were subsequently discovered to contribute to cases of human oligodendroglioma. In addition to its implications for cancer and cancer therapy, Kumara’s study also suggests Capicúa as a nexus that interconnects the signaling networks of growth factor signaling, spinocerebellar ataxias and certain cancers. These findings about Capicúa are the first to emerge from a larger project in which Kumara aims to map the Ras/Raf-regulated 14-3-3-binding phosphoproteome of melanoma comprehensively. Currently, Kumara’s paper is one of the five most downloaded papers published in the Biochemical Journal during 2011.
The Howard Elder Prize was endowed 27 years ago by Dr Alison Burt in memory of her father (Dr Howard Elder, a former medical graduate of the University of Dundee). The prize is awarded annually to the PhD student or postdoctoral researcher in the College of Life Sciences, University of Dundee, deemed to have published the most significant paper in an area related to cancer.
Kumara’s prize maintains the tradition of Howard Elder Prize awardees in the MRC Protein Phosphorylation Unit, with Craig MacKay winning in 2010, Elton Zeqiraj in 2009, and Xu Huang in 2008.
Carol MacKintosh herself received the Brian Cox Senior Investigator Award for Public Engagement at the same event for her contributions over many years to furthering the public understanding of science. These include her activities in the Dundee and Edinburgh International Science Festivals, The Royal Society of Edinburgh Master Classes and the new Science Café in the village of Tayport where her husband Bob has also played a major role in its success.
It has been quite a year for the MacKintosh laboratory since Shuai Chen, a Postdoc in her lab, was awarded the Sir Tim Hunt Prize in August 2011 for the most significant paper in the field of Cell Biology published by a member of the College of Life Sciences.
Congratulations to Jenny van der Wijst, who is currently working as an EMBO Fellow in Dario Alessi’s lab, studying the regulation and function of the unusual TRPM6 and TRPM7 ion channel-protein kinases. Jenny has just been awarded a prize for the best PhD thesis in 2011 of the Nijmegen Centre for Molecular Life Sciences, for her thesis entitled 'New patches in the molecular understanding of renal magnesium handling'.