CURRICULUM VITAE Abdallah K. AL-HAKIM, PhD Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Canada, M5G 1X5 email@example.com; Tel: +1 647 866 6192TRAINING AND EDUCATION2007–2011 Post doctorate, Durocher laboratory Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada2004-2007 PhD, Alessi laboratory MRC Protein Phosphorylation Unit, University of Dundee, UK2000-2002 MSc, Schimmer laboratory Banting & Best Research Institute, University of Toronto, Canada1996-2000 Bachelor of Science (Honors) with high distinction Overall GPA: 3.7/4.0 (A-) Final year GPA: 3.9/4.0 (A+) University of Toronto, CanadaRESEARCH EXPERIENCE2007-2011 Postdoctoral researcher, Samuel Lunenfeld Research Institute, Toronto, CanadaSupervisor: Dr. Dan DurocherDNA DamageTo move toward new cancer treatments, it is critical that we understand the mechanismsthat underpin the body’s defences against mutation or DNA strand breaks. A key projectthat I led was the characterization of a newly discovered, critical component of signallingdownstream of DNA double strand breaks, RNF168 E3 ligase. To understand how thisprotein mediates these important downstream events, I developed a comprehensive plan tocharacterize and elucidate its role in the DNA damage response. Together with mycolleagues we dissected the DNA damage response pathway and established RNF168 as akey regulators of this important pathway. Furthermore, we provided clinical evidence thatmutations in this enzyme are the likely cause of the cellular and developmental phenotypesassociated with RIDDLE syndrome, an immunodeficiency disease. I was also involved infollow-up work to determine the identity of the deubiquitylating enzyme that opposes theactivity of RNF168. Together with Shinichiro Nakada, a postdoctoral fellow in our laboratory,I identified OTUB1 as the deubiquitylating enzyme in this process. We identified a non-canonical function of OTUB1, which rather than acting as a deubiquitylating enzyme,antagonises RNF168-dependent ubiquitylation by binding to and inhibiting the E2 enzyme(UBC13) that cooperates with RNF168. My discovery of these new players of the DNAdamage response was an integral part of publications in the journals Cell and Nature.Importantly, my work has led to identification of two druggable enzyme targets that can beexploited to kill cancer cells that have elevated DNA damage response.Centrosome regulationWorking in the Samuel Lunenfeld Research Institute allowed me to explore furthercollaborations with many of the world-class scientists in different fields of study. To this end,I setup a collaborative project with Pelletier group, a centrosome-focused laboratory, to
study the involvement of UPS (ubiquitin proteasome system) at the centrosome. Togetherwith Laurence Pelletier, I devised a project to characterize the interactome of CP110, a keyregulator of centrosome duplication and its regulation through ubiquitylation is important formaintaining genomic integrity which left unchecked leads to cancer. I employed AP/MStechniques and identified a number of interesting partners that include the E3 ligasesHERC2 and neuralized-like protein NEURL4. Further biological characterization of theseproteins showed them to be localized to the centrosome and their depletion led to formationof abnormal centrosomal structures. I carried out further mass spectrometry analysis ofNEURL4, HERC2 and CEP97 (reported partner for CP110) and determined that two proteincomplexes exist in cells. One complex includes CEP97-CP110-NEURL4 and the other iscomposed of NEURL4-HERC2. My work also demonstrated that HERC2 is the E3 ligasethat ubiquitylates NEURL4, suggesting that this activity is important for regulatingcentrosome architecture. My manuscript for this work was recently accepted for publicationin the journal of molecular and cellular proteomics.Drug developmentMy extensive networking within the institute coupled to my expertise in the area ofubiquitylation made me a sought after target for more collaboration. One such example wasmy involvement with Sicheri group in characterizing CC0651, the small molecule inhibitor ofCDC34. This exciting work, which was recently published in CELL, indicates that it ispossible to develop a highly selective inhibitor of an E2 enzyme and raises the possibility oftargeting other E2s in similar manner. I provided significant contributions to discussion of theproject and to the experimental designs that demonstrated the remarkable specificity of thisinhibitor. I have supplemented my academic research experience with further training in thebusiness development through participation in entrepreneurship courses and venture capitalinvestment courses. Also, I became involved in the local biotechnology community byvolunteering for the Toronto Biotechnology Initiative group.2004-2007 PhD, MRC Protein Phosphorylation Unit, University of Dundee, UKSupervisor: Professor Dario AlessiProject: Characterization of the AMPK-subfamily of protein kinasesI chose to pursue my PhD at the world-renowned MRC protein phosphorylation Unit (PPU).This decision was made with two goals in mind, the first was to gain a better global scientificperspective and be exposed to different management strategies. This international elementhas always been important to me and is reflected in my bilingualism and ability tocommunicate and work with teams around the world. This was also reflected in my extensiveparticipation in team rowing competitions where I represented Canada at the university levelin Europe, Asia and United States. The second was to be exposed to the industry links thatthe PPU had established with a consortium of big pharmaceutical companies (AstraZeneca,Boehringer Ingelheim, GlaxoSmithKline, Merck-Serono and Pfizer). My PhD desertionfocused on studying a novel family of protein kinases that was activated by LKB1 kinase.This was an important project because mutations in LKB1 have linked it to Peutz Jegherssyndrome and it was critical to understand whether these downstream kinases were alsoinvolved in this disease. This was a critical first step to validate these kinase as potentialdrug targets for the treatments of cancer and diabetes.To study this novel family, I was the first in the institute to successfully develop a modifiedversion of the tandem affinity purification strategy. I employed this technique to study the
interacting partners of the twelve AMPK-related kinases. Using mass spectrometry, Iidentified, I identified a number of novel binding partners that interacted with one or more ofthe AMPK subfamily enzymes, including ubiquitin specific protease-9 (USP9) and isoformsof the phospho-protein binding adaptor 14-3-3. I carried out further studies characterized theinteraction between 14-3-3 and the kinases QSK and SIK. I found that the 14-3-3 bounddirectly to the T-loop Thr residue of QSK and SIK, after these were phosphorylated by LKB1This study provided the first example of 14-3-3 binding directly to the T-loop of a proteinkinase and influencing its catalytic activity and cellular localization.The success of my TAP purification strategy made me the go-to-person in the instituteregarding this biochemical technique and I was in a position to offer advice to manycolleagues. Also, my pool of stable cell lines was highly requested by collaborators and Isent these cell lines to many laboratories around the world. I had the opportunity to presentmy findings to the quarterly meetings of the pharmaceutical consortium at the institute. Thisafforded me the opportunity to talk with pharmaceutical representatives and gain aperspective regarding their research targets.During the second half of my PhD, I was interested in studying the crosstalk betweenubiquitylation and phosphorylation mechanisms. This was a novel area at the time but onethat I could foresee becoming an important one for future drug development. I decided tofurther characterize the interaction between USP9 and the AMPK-related kinases NUAK1and MARK4. This was a departure from the focus research area of my institute andtherefore I sought to build a scientific network with the ubiquitylation experts in theUniversity. This was an important step in ensuring rapid progress through this project. Mywork demonstrated that both of these kinases were ubiquitylated in vivo. I showed thatUSP9 catalyses the removal of polyubiquitin chains from wild-type NUAK1. Topologicalanalysis revealed that ubiquitin monomers attached to NUAK1 and MARK4 were linked byLys(29) and/or Lys(33) rather than the more common Lys(48)/Lys(63) linkage chains. I alsoprovided evidence suggesting that polyubiquitylation may inhibit activity of these enzymes.The success of my work in this field allowed me further opportunities to network with thepharmaceutical companies during their visits to the institute and solidified my belief thatprotein ubiquitylation machinery will be an important drug target in the future.2000-2003 MSc, Banting & Best Research Institute, University of Toronto, CanadaSupervisor: Professor Bernard SchimmerProject: Characterization of forskolin resistant Y1 mouse adrenocortical cell linesFour mutant clones independently derived from the Y1 mouse adrenocortical tumour cell linehave adenylyl cyclase (AC) activities that are resistant to forskolin, a direct activator of AC. Icarried out experiments to determine the AC isoform composition of the forskolin-resistantmutants in order to explore the underlying basis for the resistance to forskolin. Asdetermined by Western blot and RT-PCR analysis, the four forskolin-resistant mutants wereall deficient in AC-4; the levels of other AC isoforms (AC-1, AC-3 and AC-5/6) werecomparable to the levels in parent Y1 cells. Transfection of one of the mutant clones with anAC-4 expression vector increased forskolin-stimulated cAMP signalling, and restoredforskolin-induced changes in cell morphology and growth. My work lead to the conclusionthat AC-4 deficiency is a hallmark of the forskolin-resistant phenotype of these mutants andsuggested that AC-4 is an important target of forskolin action in the Y1 adrenal cell line.
PUBLICATIONSManuscripts in press:1. Abdallah K. Al-Hakim, Mikhail Bashkurov, Anne-Claude Gingras, Daniel Durocher andLaurence Pelletier. Interaction proteomics identify NEURL4 and the HECT E3 ligase HERC2as novel modulators of centrosome architecture. Molecular and CellularProteomics mcp.M111.014233. First Published on January 19,2012, doi:10.1074/mcp.M111.0142332. Ceccarelli DF, Tang X, Pelletier B, Orlicky S, Xie W, Plantevin V, Neculai D, Chou YC,Ogunjimi A, Al-Hakim A, Varelas X, Koszela J, Wasney GA, Vedadi M, Dhe-Paganon S,Cox S, Xu S, Lopez-Girona A, Mercurio F, Wrana J, Durocher D, Meloche S, et al.Anallosteric inhibitor of the human cdc34 ubiquitin-conjugating enzyme. Cell. 2011 Jun24;145(7):1075-87. Epub 2011 Jun 163. Al-Hakim A, Escribano-Diaz C, Landry MC, ODonnell L, Panier S, Szilard RK, DurocherD. The ubiquitous role of ubiquitin in the DNA damage response. DNA Repair (Amst). 2010Dec 10;9(12):1229-40. Epub 2010 Nov 4. Review.4. ODonnell L, Panier S, Wildenhain J, Tkach JM, Al-Hakim A, Landry MC, Escribano-DiazC, Szilard RK, Young JT, Munro M, Canny MD, Kolas NK, Zhang W, Harding SM, Ylanko J,Mendez M, Mullin M, Sun T, Habermann B, Datti A, Bristow RG, Gingras AC, et al. TheMMS22L-TONSL complex mediates recovery from replication stress and homologousrecombination. Mol Cell. 2010 Nov 24;40(4):619-31. Epub 2010 Nov 4.5. Nakada S, Tai I, Panier S, Al-Hakim A, Iemura S, Juang YC, ODonnell L, Kumakubo A,Munro M, Sicheri F, Gingras AC, Natsume T, Suda T, Durocher D.Non-canonical inhibitionof DNA damage-dependent ubiquitination by OTUB1. Nature. 2010 Aug 19;466(7309):941-6.6. Stewart GS, Panier S, Townsend K, Al-Hakim AK, Kolas NK, Miller ES, Nakada S,Ylanko J, Olivarius S, Mendez M, Oldreive C, Wildenhain J, Tagliaferro A, Pelletier L,Taubenheim N, Durandy A, Byrd PJ, Stankovic T, Taylor AM, Durocher D.The RIDDLEsyndrome protein mediates a ubiquitin-dependent signaling cascade at sites of DNAdamage. Cell. 2009 Feb 6;136(3):420-34.7. Al-Hakim AK, Zagorska A, Chapman L, Deak M, Peggie M, Alessi DR.Control of AMPK-related kinases by USP9X and atypical Lys(29)/Lys(33)-linked polyubiquitin chains.Biochem J. 2008 Apr 15;411(2):249-60.8. Al-Hakim AK, Göransson O, Deak M, Toth R, Campbell DG, Morrice NA, Prescott AR,Alessi DR.14-3-3 cooperates with LKB1 to regulate the activity and localization of QSK andSIK. J Cell Sci. 2005 Dec 1;118(Pt 23):5661-73.9. Al-Hakim A, Rui X, Tsao J, Albert PR, Schimmer BP.Forskolin-resistant Y1 adrenal cellmutants are deficient in adenylyl cyclase type 4. Mol Cell Endocrinol. 2004 Feb 12;214(1-2):155-65.10. Al-Hakim A, Rui X, Tsao J, Albert PR, Schimmer BP.Expression of adenylyl cyclase-4(AC-4) in Y1 and forskolin-resistant adrenal cells. Mol Cell Endocrinol. 2004 Feb 27;215(1-2):101-8.
AWARDS AND ACHIEVEMENTS2011 Review article “The ubiquitous role of ubiquitin in the DNA damage response” is ranked #2 on a list of 25 hottest articles in Biochemistry, genetics and molecular biology by the journal DNA repair2009-2011 CIHR EIRR21st (Excellence in Radiation Research) post doctoral fellowship ($CA 48,000/yr)2007-2009 TD post-doctoral research fellowship from Toronto Dominion bank of Canada ($CA 40,000/yr)2004-2007 Doctoral Fellowship from Moffat Charity Trust ($CA 25,000/yr)2001-2003 NSERC Fellowship Award from Natural Science and Engineering Research Council of Canada to fund my MSc research project ($CA 17,500/yr)2005 J Cell Sci. (2005) publication was featured in Science STKE as the article of the week in the field of biochemistry2000 Graduate award from the University of Toronto to commence my graduate studies in pharmacology ($CA 1000)1998-2000 Undergraduate fellowship from the University of Toronto in my 3rd and 4th year of undergraduate studies ($CA 1000/year)1997-2000 Golden Key honour Society member, awarded annually to top 15% of students in undergraduate studiesEXPERTISE AND SKILLSManagement and Supervision: Comprehensive experience in managing complex scientificprojects, multiple deadlines and highly collaborative team efforts. Extensive experience insupervising technicians, graduate and undergraduate students.Biochemistry and biophysics: Expression and affinity purification of recombinant proteinsfrom bacterial, insect and mammalian cells, Tandem Affinity Purification (TAP) of proteincomplexes, analysis of protein interactions in vivo and in vitro, BIAcore, immunoprecipitations,protein kinase assays, ubiquitylation/deubiquitylation assays, SDS-PAGE, Westernimmunoblotting, affinity chromatography, HPLC, proteomics approaches for mass spectralidentification of proteins and phosphorylation site mapping.Molecular biology: Standard molecular biology techniques including PCR, RT-PCR, cloningprocedures, DNA/RNA isolation from cells/tissues, FACS cell sorting.Cellular biology and genetics: Mammalian cell culture, transient transfections, generation ofstable cell lines, siRNA, immunofluoresence, confocal microscopy and imaging. Use ofAdenoviral and Retroviral vectors.Bioinformatics: DNA and Protein sequence analysis. Multiple sequence alignment usingClustalW and Tcoffee. Molecular modeling and protein structure analysis. Transcriptomicsand genomic analysis.Web-based tools and social media: Proficient with many forms of social media such asLinkedin, Facebook, twitter and blogging. Familiar with email clients program such as MailChimpand webinar platforms such as Go2Webinar
Languages: Fluent in English and Arabic, basic French.OTHER ACTIVITIES2009-2011 Toronto Biotechnology Initiative (TBI) • Co-organized a Professional Development event attended by > 30 people on ‘Design Thinking’ with keynote speaker Heather Fraser (Director of Designworks™ and Rotman’s Design Initiative) • Active in member recruitment and in attending to members concerns • Co-organizer of the Pub night networking event held each month (between 50- 100 attendees)2010 BioFinance Conference, Toronto, Canada • Member of the volunteer team at the BioFinance conference where I assisted in moderating some of the breakout sessions2010 McMaster University innovation showcase, Hamilton, Canada • Participated as a one of the judges for the posters’ competition2006-2007 Cancer Research UK Fund raising, Dundee, UK • Organized a team of staff, PhD students and post-docs to participate in Dundee’s half-marathon where we raised over $1000 for Cancer Research UK2006 Biotechnology YES Project Competition, Edinburgh, UK • Participated in a team project: (http://www.biotechnologyyes.co.uk/) - project was titled “BIOVERT – a bio-green alternative to automobile exhaust” where we prepared a business plan outlining the project and pitched the idea to a panel of investors. Our project idea was awarded 2nd place overall in Scotland2001-2003 Banting & Best Research Institute’s student representative to the Graduate Students council1994-2004 Competitive Rowing, Hamilton and Toronto, Canada • Committed over 30 hours per week to rowing at Club and University varsity levels • Competed in a number of national and international regattas (Boston, Austin, Pittsburgh, Philadelphia, USA; Milan, Italy; I-Lan, Taiwan)CONTINUING STUDIES2010 Entrepreneurship 101, MaRS discovery district, Toronto, Canada2010 Venture capital strategy course, Rotman School of Management, Toronto, CanadaMEETINGS AND PRESENTATIONS2009 Gordon Research Conference on Mammalian DNA repair-Ventura, California (Poster presentation)2007 Identification and characterization of the interacting proteins of the AMPK- related family of kinases. PhD defence seminar, University of Dundee, Dundee, UK (Oral presentation)2006 Role of protein ubiquitylation in regulating kinase activity of NUAK1 and MARK4 kinases, MRC institute Christmas symposium, St. Andrews, UK (Oral presentation)
2006 LKB1 activated protein kinases are modified by a unique Lys29 and 33 ubiquitin linkage. Planning for Management Committee (PMC) for pharmaceutical collaborations meeting, University of Dundee, Dundee, UK (Oral presentation)2006 FEBS Special Meeting: Cellular Signalling–Dubrovnik, Croatia (Poster presentation)2006 XXXIst Symposium on Hormones and Regulation: Cancer Cell Signalling, Hostellerie du Mont Sainte-Odile, France (Poster presentation)2005 14-3-3 and LKB1 mediate activity and localization of SIK and QSK protein kinases. PMC meeting, University of Dundee, Dundee, UK (Oral presentation)2004 Role of 14-3-3 proteins in regulating the kinase activity of AMPK-related kinases. MRC Institute Christmas symposium, Ayleth, Perthshire, UK (Oral presentation)