
Research Interests
Proteases, One Health, Proteomics, Degradomics, MMPs, Viral proteases, SARS-CoV-2, COVID-19
Research Focus Teams
COVID-19, Rare Diseases
Departments
Oral Biological & Medical Sciences, Centre for Blood Research
Contact
Email: chris.overall@ubc.ca
Office Phone: 604–822–2958
Publications
Lab Website
Professor Christopher Overall is a Full Professor, Distinguished University Scholar and Canada Research Chair Laureate in Protease Proteomics and Systems Biology at the University of British Columbia; an Honorary Professor at Albert-Ludwigs Universität Freiburg, Germany, and a Yonsei Distinguished Scholar of Yonsei University, Seoul, Republic of Korea. He was a Senior Fellow of the Freiburg Institute of Advanced Studies, Albert-Ludwigs Universität Freiburg, Germany (2010–2013) and a Tier 1 Canada Research Chair in Protease Proteomics and Systems Biology (2001–2022). Dr Overall was inducted as a fellow into the Royal Society of Canada (FRASC) Academy of Science in 2018 and the Canadian Academy of Health Sciences (FCAHS) in 2005.
Dr. Overall completed his B.D.S., Honours Science and Master’s degrees at the University of Adelaide, South Australia; his Ph.D. in Biochemistry at the University of Toronto, Canada; and was an MRC Centennial Fellow in his postdoctoral training with Dr. Michael Smith, Nobel Laureate, Biotechnology Laboratory, UBC. He launched his lab at UBC in 1993. On sabbatical in 1997 – 1998, he was a Senior Scientist at British Biotech Pharmaceuticals, Oxford, UK, and in 2004 and 2008, a Senior Scientist at the Expert Protease Platform, Centre for Proteomic Drug Discovery, Novartis Pharma, Basel, Switzerland. He is now a Creative Destruction Lab Scientist at the UBC Sauder School of Business and a consultant for Genentech, Novartis and several Biotechnology companies.
Chris is best known for developing proteomic methodology to discover protease substrates in vivo, thereby establishing the field of degradomics. He has used these techniques to reveal new biological roles for proteases in immunity and disease, most recently in the COVID-19 pandemic by SARS-CoV-2 proteases, developing two new molecular correctors to cure MALT1 protease deficiency in a primary immunodeficiency, and now in One Health Strategies for investigation of viral zoonosis. By generating clinically relevant insights into how proteases dampen disease-fighting defence systems involved in inflammation and immunodeficiency, degradomics has revealed an unexplored layer of complexity in the hierarchy of cell and immune regulation, greatly adding to our understanding of protease function and drug targeting.
He is a highly cited scientist with 316 publications, generating an h-index = 108 from > 41,850 citations—including 68 >100 – 199, 30 >200 – 499, 13 >500 – 999, 3 >1,200 – 1,500, and 1 >1,700, 36 high-impact papers in Nature (2), Science (2), Cell and their daughter journals (32), most as senior PI. He has disseminated his lab findings by > 297 keynote, plenary, and invited talks at international and national conferences, as well as 250 invited seminars at universities, research institutes, and companies. He has mentored 61 graduate students and post-doctoral trainees (40 PDF/14 Ph.D./7 M.Sc.) with great success: 9 of whom have remained in academics as Full Professors (including 2 Department Chairs), 5 are Associate Professors, and 6 are Assistant Professors. Indeed, Chris was awarded the UBC John McNeill Excellence in Health Research Mentorship Award in 2023.
His peers elected Dr. Overall to organize and chair the premier conferences in his field, including the 2003 Matrix Metalloproteinase and 2010 Protease Gordon Research Conferences, and in 2017, he co-chaired the International Proteolysis Society Biannual Meeting. He holds influential roles on the executive of >10 international committees, the most prominent of which was election to the Human Proteome Organization (HUPO) Executive Council and as Chair of the HUPO Chromosome-centric Human Proteome Project (C-HPP). In 2022, he was invited to represent UBC at the G7 Research Summit on One Health. He has received numerous recognitions, e.g., election to the Royal Society of Canada, appointment as a Yonsei Distinguished Scholar (Yonsei University, 2023) and a Distinguished University Scholar of UBC in 2024. He received the UBC 2006 Killam Faculty Research Prize; the 2002 Canadian Institutes of Health Research (CIHR) Researcher of the Year; the Helmholtz Award (2008); International Proteolysis Society Lifetime Achievement Award (2011); Matrix Biology Society of Australia and New Zealand Barry Preston Award (2012); and the IADR Distinguished Scientist Award (2013). His advances in proteomics have been recognized by the Canadian National Proteomics Network Tony Pawson Award (2014); the Proteomass Scientific Society Award (2017); the 2018 Human Proteome Organization (HUPO) Discovery Award in Proteomics Sciences; and the 2022 Helmut Holzer Award. He is a Councilor of the p-Hub Global Proteomics Project, Guangzhou, China (2023 –).
His peers elected Dr. Overall to organize and chair the premier conferences in his field, including the 2003 Matrix Metalloproteinase and 2010 Protease Gordon Research Conferences, and in 2017, he co-chaired the International Proteolysis Society Biannual Meeting. He holds influential roles on the executive of >10 international committees, the most prominent of which was election to the Human Proteome Organization (HUPO) Executive Council and as Chair of the HUPO Chromosome-centric Human Proteome Project (C-HPP). In 2022, he was invited to represent UBC at the G7 Research Summit on One Health. He has received numerous recognitions, e.g., election to the Royal Society of Canada, appointment as a Yonsei Distinguished Scholar (Yonsei University, 2023) and a Distinguished University Scholar of UBC in 2024. He received the UBC 2006 Killam Faculty Research Prize; the 2002 Canadian Institutes of Health Research (CIHR) Researcher of the Year; the Helmholtz Award (2008); International Proteolysis Society Lifetime Achievement Award (2011); Matrix Biology Society of Australia and New Zealand Barry Preston Award (2012); and the IADR Distinguished Scientist Award (2013). His advances in proteomics have been recognized by the Canadian National Proteomics Network Tony Pawson Award (2014); the Proteomass Scientific Society Award (2017); the 2018 Human Proteome Organization (HUPO) Discovery Award in Proteomics Sciences; and the 2022 Helmut Holzer Award. He is a Councilor of 1st p-Hub Global Proteomics Project, Guangzhou, China (2023 – ).
Résumé of Dr. Christopher M. Overall, BDS, BSc (Hons), MDS, PhD, FCAHS, FRSC
Numbers refer to the asterisked 20 Significant publications from his curriculum vitae.
1. General achievements and prior recognition
Professor Overall’s investigations and concepts of proteolytic enzymes and the target substrate proteins they cleave have profoundly changed our understanding of the widespread roles of proteases in health and disease and how they mold proteomes in which they are active. He is best known for two related but distinct scientific achievements. The first is his development of innovative methods for the global discovery of protease substrates in vivo. The most notable are cutting-edge proteomic techniques15-20, which enabled the unbiased identification of protease cleavage sites and protein substrates in vivo for the first time. Thereby, he established the field of degradomics (Nature Reviews Molecular Cell Biology). The second is leveraging his suite of techniques to reveal new and often unexpected biological roles for proteases and their cleaved substrates in normal tissues and their aberrations in disease. His influence has been profound — without exaggeration, his techniques and concepts in proteolysis and proteomics have shaped the field in which he led this new area of investigation. Multiple groups globally now employ his approaches to unveil new roles for proteases and their cleaved substrates in vivo.
As with much of Dr. Overall’s work, his findings have had broad implications for drug targeting and have resolved perplexing results on drug side effects (Nature Reviews Cancer). Thus, he is at the forefront of formulating innovative concepts on drug targeting and the roles of proteolysis in disease and their interplay in controlling cell signalling pathways. His research has resulted in 316 papers, including 36 Nature (2), Science (2), and daughter journal (32) papers, most as senior PI. His papers are highly cited (>41,850 citations), yielding an h-index of 108. He has mentored 40 post-doctoral scientists and graduated 14 Ph.D. and 7 M.Sc. students to achieve their best—9 Full Professors, 5 Associate Professors, and 6 Assistant Professors. Indeed, Chris was awarded the UBC John McNeill Excellence in Health Research Mentorship Award in 2023.
Professor Overall holds influential roles on the executive of >10 international committees, and his peers elected him to organize and chair the premier conferences of his fields: the 2003 MMP and 2010 Protease Gordon Research Conferences and in 2017 he Co-Chaired the International Proteolysis Society (IPS) Meeting. International recognition of Professor Overall’s advances in proteomics and systems biology is reflected by his election in 2015 as Co-Chair and then as Chair (2019 –) of the Human Proteome Organization (HUPO) Chromosome-Centric Human Proteome Project (HPP). The HPP published the high-stringency draft of the human proteome in Nature Communications in 2020: he was the only Canadian author. In 2022, he was invited to represent UBC at the G7 Research Summit on One Health. He is the recipient of numerous recognitions, e.g., election to the Royal Society of Canada; he is a Yonsei Distinguished Scholar of Yonsei University, Korea, an Honorary Professor, Albert-Ludwigs University, Freiburg, DE and at UBC, he is a Distinguished University Scholar and received the 2006 Killam Research Prize. Among his many awards, several stand out, including the Canadian Institutes of Health Research Researcher of the Year (2002), the Helmholtz (2008), IPS Lifetime Achievement (2011), Matrix Biology Society of Australia and New Zealand Barry Preston (2012), and the IADR Distinguished Scientist (2013) Awards. His advances in proteomics have been recognized by the Canadian National Proteomics Network Tony Pawson Award (2014), the Proteomass Scientific Society Award (2017), the 2018 HUPO Discovery Award in Proteomics Sciences, and the 2022 Helmut Holzer Award. He has presented >297 keynote, plenary, and invited talks at international conferences and >250 seminars at universities, institutes, and companies.
2. Degradomics reveals new protein functions in vivo
Only 340/565 human proteases (Nature Reviews Genetics) have known substrates, and from this incomplete knowledge, >200 proteases lack biological roles (Nature Reviews Molecular Cell Biology). This inspired Dr. Overall to invent a suite of approaches14, techniques15-20, and software4,16 to identify protease substrates on a system-wide scale. Recognizing the importance of substrate-binding exosite domains on proteases, he was the first to use these as substrate ‘baits’ in a yeast two-hybrid screen14 (Science)—at a time when protein disulphide cross-linkages were predicted to exclude the yeast two-hybrid approach for extracellular proteins. Dr. Overall showed that this was not a limitation in this yeast system14 with a paradigm shift that MMPs are tissue-protective by orchestrating neutrophil and macrophage leukocyte responses through activation/inactivation of virtually all chemoattractant cytokines known as chemokines10,13,14, and in subsequent research, by multiple cytokines6,8, their binding proteins, and serpin inhibitors11,12.
Defining protease substrate cleavage-site specificity is central to protease characterization, linkage to substrates and drug development. In this way, he pioneered the first peptide library technique to simultaneously identify both the amino (P) and carboxyl (P’) amino acid residues flanking the cleavage site—Proteomic Identification of Cleavage Specificity (PICS)19 (Nature Biotechnology, Nature Protocols). With >14,000 cleavage sites identified by PICS in the protease database MEROPS, its head curator described PICS as “the new gold standard for profiling proteases.” In one application of PICS, he reported >4,300 cleavage sites in the MMP family, leading to structural insight into their active sites. Reported in Nature Communications7, he identified >1000 cleavage sites by an unsuspected metallopeptidase insertion in bacterial flagellin, the monomer of bacterial flagella that propels bacteria through biofilms and tissues. These metalloproteinase-bearing flagellin molecules assemble proteolytically active flagella (~20 µm) in >350 diverse bacterial species, e.g., the pathogen Clostridium haemolyticum.
In conventional proteomics sample preparation for mass spectrometry, 100,000s of trypsin-generated peptides of a proteome dominated by abundant proteins dilute the terminal amino (N) and carboxyl (C) terminal protein ends and protease-generated ‘neo’-termini, rendering these terminal peptides rarely detectable. This is especially problematic for low-abundant transcription factors and signalling proteins like cytokines and antiviral interferons, impairing insight into disease-relevant proteolytic events. Dr. Overall’s technique, Terminal Amino Isotopic Labelling of Substrates (TAILS)18, circumvents these issues in a simple but powerful high-throughput method. TAILS purifies protein N-terminal peptides and cleaved neo-N-terminal peptides using an innovative aldehyde-polymer to simultaneously identify cleavage sites and substrates in native proteomes (Nature Biotechnology; Nature Protocols). Monitoring the end fragments of the cut proteins, also known as terminomics, is a powerful new way to monitor disease activity.
Protein C-termini are difficult to label chemically en route to identification that is also hampered by their absence of C-terminal lysine or arginine residues following trypsin digestion. Dr. Overall discovered a new “trypsin mirror” proteasein Archaea, LysargiNaseTM, to address this15 (Nature Methods). Cutting before lysine or arginine, LysargiNase-digested proteins release C-terminal peptides with an N-terminal lysine or arginine, facilitating detection by shotgun proteomics or by C-terminal peptide enrichment for broad coverage using C-TAILS technique17 (Nature Methods).
To specifically analyze natural and neo-termini, Dr. Overall developed publicly available software: WebPICS, CLIPPER, and the Termini-orientated protein Function INferred Database (TopFIND v4.1)16 (Nature Methods) with >290K termini/>33K cut-sites, receiving >4K hits p.a. PathFINDer and TopFINDer map substrates to protease pathways, which revealed a highly connected protease network in humans12 (PLoS Biology)—so also highlighting the problems in interpreting knockout or overexpression studies, as well as in drug targeting of proteases.
Fundamental to understanding zoonotic virus pathobiology, by a One Health approach in the pandemic, Dr. Overall applied his techniques to discover >300 host cell substrates for the SARS-CoV-2 3CLpro, main protease1 (Cell Reports) and its cleavage site specificity (J Virology). Thereby, he discovered that the cytosolic lectin, galectin-8, is a novel intracellular sensor of SARS-CoV-2 spike protein, but galectin-8 cleavage by SARS-CoV-2 3CLpro defeats autophagic destruction of galectin-8-tagged virus. In expanding the degradome and interactome of 3CLpro 20 (Nature Communications), he revealed mechanisms by which this viral protease bypasses cellular control of signal transduction by interacting with and disrupting protein assemblies in the adherens junction, cytoskeleton and centrosome of infected human lung epithelial cells. Notably, 3CLpro drives the formation of intercellular immune-privileged conduits known as tunnel nanotubes (TNT). Immunolocalization of virions with 3CLpro substrates within TNTs suggests that 3CLpro activity accelerates TNT formation for “stealthy” viral transmission, which impedes the effectiveness of immune recognition and vaccines intended to reduce viral transmission. Recently, he reported the first example of a viral protease, SARS-CoV-2 3CLpro, being secreted with extracellular activity, including inactivation of type III interferons (Cell Reports) 21.
Employing degradomics, Dr. Overall has mechanistically dissected the crosstalk between proteolytic pathways in multiple systems including complement in skin inflammation8 (Science Signaling), lysosomal proteases in pancreatic cancer9 (Cell Reports), MMPs in HIV-Associated Dementia10 (Nature Neuroscience), anti-inflammatory activities of macrophage MMP12 in arthritis11 (Cell Reports) and autoimmunity, e.g., lupus6 (Nature Communications), and MMP12’s unexpected potent antiviral roles5 (Nature Medicine). In this latter work, he made a remarkable discovery that secreted MMP12 is a ‘moonlighting’ protease (Nature Reviews Drug Discovery) that re-enters cells and traffics to the nucleus as a transcription factor regulating ~200 genes. By increasing transcription of IkBa—an inhibitor of the pro-inflammatory NFkB—he found MMP12 was indispensable for IFNa secretion. He further identified multiple substrates of MMP12 whose gene transcription was repressed by nuclear MMP12—thereby demonstrating concerted dual-negative regulation of both protein substrates and their genes—highlighting a mechanism of rapid cellular inhibition and removal of key cellular proteins for antiviral defence.
In related work, Dr. Overall found that macrophage MMP12 first stimulates secretion and then, over time, inactivates anti-viral interferon-a5 (Nature Medicine). Similarly, MMP12 inactivates interferon-g, also by removing the receptor binding site6 (Nature Communications), providing feedback that drives the transition from pro-inflammatory IFN-g-activated macrophages (formerly termed “M1”) to tissue-reparative immunosuppressant (“M2”) macrophages. In discovering new and major roles of MMPs in regulating signalling proteins, his studies reveal deeper complexity in regulating the extracellular matrix and the cell signalling environment than mere degradation.
In a groundbreaking example of clinical application, Professor Overall explored the roles of the intracellular protease MALT1, an essential transducer in lymphocyte antigen receptor signalling and immune activation2 (Nature Communications). He found that independent of proteolytic cleavage, non-proteolytic protein-protein interactions by MALT1 initiate NFkB activation, whereas, at late stages of NFkB signalling, MALT1 cleaves HOIL1 in the Linear Ubiquitin Assembly Complex (LUBAC) to downregulate essential linear ubiquitination of pathway mediators to halt NFkB signalling2. By developing the algorithm GO-2-Substrates, he recently predicted and validated new substrates to double the MALT1 substrate repertoire4; thereby, he upended the concept that MALT1 is solely an enhancer of antigen-driven signalling—with far-reaching consequences for our understanding of immunobiology that has major implications in MALT1 drug targeting for lymphomas. The multidisciplinary team he assembled also reported in Nature Chemical Biology3 the development of a series of potent nanomolar allosteric inhibitors of MALT1 that bind at Trp580. Remarkably, this is the same site as an immunodeficient patient’s MALT1 Trp580Ser mutation, whose markedly diminished levels of the mutant MALT1 led to 50% reduced NFkB signalling and immunodeficiency. In an elegant use of chemical biology, Dr. Overall demonstrated that treatment with this inhibitor stabilized the mutant MALT1, restoring MALT protein levels to normal in the patient’s lymphocytes. Moreover, inhibitor treatment also restored NFkB and JNK signalling in the patient’s B and T lymphocytes and, during treatment pauses, rescued substrate cleavage. Thus, a new low molecular weight pharmacological molecular corrector rescues an enzyme deficiency by substituting for the mutated residue, inspiring therapies to restore enzyme activity to treat similar molecularly defined disorders.
3. Scientific impact
Dr. Overall’s techniques and concepts in proteolysis and proteomics have shaped our understanding of the widespread roles of proteases and triggered a new area of investigation in terminomics/degradomics. In accelerating our appreciation of the unexpected prevalence of precise proteolytic processing in vivo and its effects on protein function, he has been instrumental in transforming our understanding of mechanisms of disease pathogenesis. TAILS has repeatedly demonstrated the unanticipated abundance, from 45–60%, of stable cleaved protein ‘proteoforms’ co-existing with their full-length parent protein in cells and tissues. Given the numerous examples of proteolytically-induced altered functions of bioactive proteins, the pervasive occurrence of truncated proteins in proteomes reveals new levels of control of protein function with profound implications for molecular pathogenesis and patient diagnosis. As presented in six Nature Reviews articles and other reviews and editorials. Dr. Overall’s research and concepts continue to shape the fields of proteomics, proteolytic enzymes, and antiviral and molecular immunology toward a deeper understanding of new drivers of inflammatory, immune, and infectious diseases that are seminal for developing precise diagnostics and new treatments.
Proteomics in a systems biology framework is the primary molecular research approach elevating our ecological and One Health activities. Understanding how a bodily system works requires knowing more than which genes are expressed in each cell: it is crucial to know in what form cellular proteins are expressed, whether they are active or not, and with what other molecules the immune pathway proteins interact, which can only be measured by proteomics. Integration of various ‘omics’ and other phenotypic data to predict specific, testable responses comprises systems biology. We apply systems biology to One Health studies to discover critical differences between the proteins expressed in infected animal vs. human cells, especially host proteins that are cut by viral proteases to enable replication and evasion of innate immunity defences. Leveraging our expertise in proteases, proteomics, degradomics, informatics, structural biology, and drug development, we are identifying viral substrates crucial for immune and vaccine escape and drug resistance of SARS-CoV-2 and disease-causing variants in animal and human cells. We are zeroing in on our novel therapeutic development activities on (a) common vs. unique proteins that promote infection, e.g., proteases, that can be blocked by inhibitor drugs, (b) host cell antiviral protective proteins that can be elevated in amounts by mRNA therapy to increase their effective levels of protection, and (c) host protein substrates that are cut in infection that we will restore to combat the virus using a new class of antivirals, termed “molecular correctors”, as a swath of new antiviral therapies. By understanding fundamental host defence system pathways and their interconnections, our findings will be broadly applicable to multiple viral infectious diseases and those with inflammatory complications, particularly in immunocompromised, unvaccinated, or marginalized populations. Thus, we are preparing for the next outbreak or pandemic using a logical and holistic approach to the problem of pandemics.