- Genentech, Inc., South San Francisco, CA, U.S., Research Fellow in Protein Engineering, 1996-1998.
- Simon Fraser University, Burnaby, BC, PhD in Biochemistry, 1996.
- Simon Fraser University, Burnaby, BC, BSc in Biochemistry, 1990.
- Adjunct Professor, Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University.
MY RESEARCH OVERVIEW (GO TO SCIENTIFIC OVERVIEW)
Manipulating proteins using sophisticated technology to provide further understanding of cellular function and develop better therapies
If cells were computers, DNA would be hardware and proteins would be software. The human genome encodes tens of thousands of proteins, and these are the movers and shakers of life. Some are enzymes that drive chemical reactions, some are building blocks that form cellular architecture, and others are messengers that relay signals within and between cells. In a healthy cell, the complex protein network functions in exquisite balance, but in a diseased state, this balance is disrupted. Because most diseases stem from aberrant protein function, understanding and manipulating natural proteins has become a major goal for therapeutic research.
My interests lie in the field of protein engineering and technologies that explore and shape protein structure and function. My lab uses in vitro evolution to recreate Darwinian selections inside a test tube. We investigate the function of natural proteins and design changes to improve function and reverse the effects of disease. Going further, we can also construct synthetic proteins designed to target proteins inside cells, in much the same way as the immune system produces antibodies to target infectious invaders. With these technologies, we aim to better understand the molecular basis of cellular function and to use this knowledge to develop therapies for cancer, diabetes and other diseases.
I am working closely with other researchers in the Centre, notably the Moffat group, to tackle formidable challenges that would be impossible for any single research group to address. In one building, we have world-class talent that spans the most cutting-edge areas of life science research. The members of the Donnelly Centre were selected for individual talent and for the ability to collaborate, and this is a crucial combination that enables interdisciplinary research that would be difficult to imagine anywhere else.
SCIENTIFIC RESEARCH OVERVIEW
Our lab studies the relationships between protein structure and function, using phage display in conjunction with high-throughput screening and sequencing. By studying the basic principles behind phage display technology, we have greatly improved library diversities and the scaffolds used for protein display. We have applied these advances to the development of synthetic antibody libraries, which we and others are currently using for the development of therapeutic antibodies for unmet medical needs (see project stream 1). We have also extended our phage display, high throughput methodology to the generation of small synthetic proteins that can be used to modulate enzyme function (see project stream 2). In addition, we have been studying peptide-binding modules to gain insight into the biological function of intracellular scaffolding proteins (see project stream 3).
Main streams of projects currently taking place in the lab:
1. Synthetic antibodies
We have optimized the performance of phage display technology by merging high throughput screening and sequencing, and developed highly diverse and functional synthetic antibody libraries to identify antibodies with greater affinity and specificity to given antigens. Moreover, we have developed, in collaboration with Dr. Jason Moffat (Donnelly Centre), a novel cell-based screening method to generate antibodies against cell surface proteins, including those that depend on the membrane environment for proper folding. We are also currently exploring several alternative antibody formats (e.g. diabodies, bi-specific antibodies, VH domains) in order to further improve their applications as diagnostic tools and therapeutic agents.
These developments are culminating in the generation of thousands of therapeutic-grade antibodies to hundreds of disease-related antigens, which are at various stages of clinical development, from initial validation to clinical trials. To support these endeavors, we have established the Toronto Recombinant Antibody Centre (TRAC), a state-of-the-art facility that enables the high throughput generation of synthetic antibodies to virtually any antigen. We have initiated numerous collaborations with cancer and cell biologists to functionally validate antibodies in vivo and ensure that the best candidates are further developed into therapeutics or for other desired applications. We are also developing antibodies targeting diseases other than cancer, including diabetes and obesity, and infectious diseases such as Ebola. In addition, we have collaborations to develop antibodies to improve developing world health practices and the safety of agricultural practices.
These projects are supported by major funding from the Canadian Institutes of Health Research (CIHR), the Ontario Ministry of Research and Innovation (MRI), the Ontario Institute for Cancer Research (OICR), the Canada Foundation for Innovation (CFI), the US National Institutes of Health (NIH), and others. Our antibody development pipeline has spurred intense interest from industrial collaborators both in Canada (e.g. Northern Biologics) and abroad (e.g. Integrated BioTherapeutics , USA and SciGenom, India). We have a long history of successful partnerships with industry and continue to be supported by numerous industrial collaborations, notably a recently established major collaboration with Celgene, Corp.
2. Affinity binders based on small protein scaffolds
Using the methods developed and knowledge gathered in project streams 1 & 3, we are expanding our affinity binder technology to other protein scaffolds and developing novel and general strategies to generate potent and specific inhibitors of specific targets. Notably, after extensively studying the binding determinants for ubiquitin, we developed phage-displayed libraries of ubiquitin variants that we are using to identify inhibitors of all ubiquitin-binding proteins in the ubiquitin-proteasome system, including ubiquitin ligases and deubiquitinases. These inhibitors can be used for structural studies, as intracellular tools for the exploration of cell biology, for target validation, and ultimately, as a source for the development of novel therapeutics. We are also currently applying this concept to other small protein scaffolds. These projects are funded by CIHR, OICR, the Canadian Cancer Society Research Institute (CCSRI), and others, as well as through major industrial collaborations (e.g. Boehringer Ingelheim).
3. Mapping peptide-protein interactions
We have developed rapid combinatorial methods to quantitatively survey binding energetics across protein-binding surfaces using molecular biology and high throughput sequencing. Using these methods, we are systematically analyzing, on a genome-scale level, how intracellular complexes are assembled by peptide-binding modules that recognize small linear protein motifs, to construct maps of intracellular networks. Thus far, we have focused on PDZ, SH3 and WW domains, but we are currently expanding our analyses to other protein domains.
While our discoveries have enormous potential as research reagents, diagnostics, and therapeutics, they will only start having a real impact on Canadians once commercially developed. Therefore, to fill the gap between academic discoveries and commercial development, we have recently launched a new Centre of Excellence supported by the Canadian Government, the Centre for the Commercialization of Antibodies and Biologics (CCAB). The CCAB will provide both business and scientific expertise to rapidly translate academic inventions towards real commercial impact within the health care system and broader impact within the scientific community.
- Selection of recombinant anti-SH3 domain antibodies by high-throughput phage display. Huang H, Economopoulos NO, Liu BA, Uetrecht A, Gu J, Jarvik N, Nadeem V, Pawson T, Moffat J, Miersch S & Sidhu, SS. Protein Sci. 2015 Sep 1.
- A Strategy for Modulation of Enzymes in the Ubiquitin System. Ernst A, Avvakumov G, Tong J, Fan Y, Zhao Y, Alberts P, Persaud A, Walker JR, Neculai AM, Neculai D, Vorobyov A, Garg P, Beatty L, Chan PK, Juang YC, Landry MC, Yeh C, Zeqiraj E, Karamboulas K, Allali-Hassani A, Vedadi M, Tyers M, Moffat J, Sicheri F, Pelletier L, Durocher D, Raught B, Rotin D, Yang J, Moran MF, Dhe-Paganon S & Sidhu SS. Science. 2013 Feb 1;339(6119):590-5.
- CDR-H3 Diversity is Not Required For Antigen Recognition by Synthetic Antibodies. Persson H, Ye W, Wernimont A, Adams JJ, Lam R & Sidhu SS. J Mol Biol. 2013 Feb 22;425(4):803-11.