Feb 25, 2022

Field Spotlight: Functional Genomics and Proteomics

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By Soha Usmani

*Thank you to those who provided and contributed material for this content*  

Many of our faculty conduct ground-breaking research and have made significant breakthroughs in the genomics and proteomics fields. Examples of standout projects and publications include the following:  

The Blencowe lab specializes in studying the regulation of gene expression, primarily focusing on alternative splicing. The group has pioneered the development and application of technologies for the genome-wide quantitative profiling of transcriptomes, RNA interactomes, as well as new CRISPR-based methods for comprehensively elucidating RNA regulatory networks. Their breakthroughs include the discovery of critical roles for alternative splicing in the regulation in neural and embryonic stem cell fate. More recently, the group has discovered and characterized a highly conserved splicing regulatory network comprising neuronal microexons, and has provided evidence that disruption of this network represents a common mechanism underlying autism spectrum disorder. Dr. Blencowe also holds the Banbury Chair in Medical Research and Canada Research Chair in RNA Biology and Genomics. 

The Boone lab uses functional genomics to shed light on genetic, chemical-genetic and protein-protein interactions via the yeast model organism to create a complete network of genes and their products. The group made important enhancements of synthetic genetic array (SGA) strains and methodologies in yeast. For example, they created a computational platform that analyzes large amounts of SGA data to identify genetic interactions and score fitness of specific mutants, which is used by numerous labs globally.  

The Durocher lab aims to understand how genomic integrity is maintained and how cancer cells originate by studying DNA damage and its repair. The group is using various functional genomic approaches to probe genome maintenance mechanisms and in recent years they have used CRISPR/Cas9 screens to build a genetic map of how human cells react to DNA damage. They are also using this technology to uncover genetic vulnerabilities in cancer cells by mapping genetic interactions. For example, they identified that the APE2 nuclease and the CIP2A-TOPBP1 complex are exciting new targets for killing cancer cells that are deficient in the BRCA1 or BRCA2 genes and that the PKMYT1 kinase is essential in cells that have amplification of the cyclin E-coding gene. The group also made insights into the role of a regulatory ubiquitylation pathway in fixing DNA double-stranded breaks that modify histones in the vicinity of break sites. Dr. Durocher also holds the Canada Research Chair in the Molecular Genetics of the DNA Damage Response. 

The Edwards lab employs open science alongside structural and chemical biology methodologies to unearth lesser-studied human protein functions, especially potential drug targets. Dr. Edwards founded the Structural Genomics Consortium and leads six of their labs. Since 2021, his team provided 4500+ structures to the Protein Data Bank.  

The Gingras lab specializes in developing proteomics tools and studying the systems biology of cell proteomes. The group developed several computational proteomics tools such as a LIMS for interaction proteomics MS data called ProHits, software for protein-protein interactions called SAINT and CRAPome and an interactions visualization program called ProHits-viz. They’ve also developed a browser extension for rapid gene product annotation called GIX. The lab also co-developed multiple antibody-based serology assays against COVID-19 and is a member of the COVID-19 Immunity Task Force. They also created an analysis portal software surveying and mapping the living human cell’s proteome called the Human Cell Map. It localizes thousands of cellular proteins across all the organelles. The group utilized organelle markers to tag proteins, which are then detected by mass spectrometry. Dr. Gingras also holds the Canada Research Chair in Functional Proteomics. 

The Greenblatt lab previously studied gene regulation and proteomics in bacteria and yeast and currently studies human gene regulation, with a particular emphasis on the roles of the ~750 C2H2 zinc finger transcription factors (C2H2-ZFPs) in chromosome conformation and transcription initiation and termination, as well as RNA modification, splicing, and 3’-end formation. The group has shown that the C2H2-ZFPs participate in all of these processes, generally by binding to DNA and/or RNA and has characterized protein-protein interactions for these factors. Another recent initiative has been the development of a method to identify human targets for anti-viral drugs, both for the human tumour viruses and those viruses which, like SARS-CoV-2, cause medically significant acute infections

The Hughes lab focuses on identifying, researching and mapping the functional units in the genome, aka the sections recognized by DNA and RNA binding proteins, to see how the cell interprets the genome. One of their previous projects resulted in a computational model which inputs only the sequence preferences of DNA and RNA binding proteins and precisely predicts known gene structures and expression of randomly generated sequences. Other research from the lab found that the increased number of human C2H2 zinc finger proteins and C. elegans nuclear hormone receptors may be driven by retroelements. Dr. Hughes also holds the Canada Research Chair in Decoding Gene Regulation. 

The Kim lab recently engineered antiviral chemical compounds called mirror-image or D-peptides to neutralize the SARS-CoV-2 virus and many of its variants and prevent cell infection. The group developed a software program that synthesized peptides in their D-forms, that would then bind and neutralize its specialized targets, including the SARS-CoV-2 spike protein. The program can easily modify to peptide design, meaning it can target specific variants such as Omicron and other molecular targets in other pathogens, cancer cells and more. Another AI program developed from the lab called ProteinSolver synthesizes proteins from scratch to correspond to a specific geometric shape, similar to the puzzle Sudoku.  

The Maass lab investigates the non-coding genome and seeks to understand how long noncoding RNAs and inter-chromosomal contacts affect gene and genome regulation in development and disease. The lab employs functional genomics and massively parallel reporter assays (MPRA), computational biology, CRISPR methodology, and CRISPR live-cell imaging to study gene regulation and genome organization. The group’s major aim is to decode gene-regulatory non-coding elements in the genome. Dr. Maass is also the Canada Research Chair of Non-coding Disease Mechanisms. 

The Moffat lab specializes in cellular and genetic engineering and studying mammal genotype-phenotype relationships on the genome scale. Recently, they identified 180+ genes facilitating cancer cells avoiding the immune system. The group also co-discovered the first human cell line essential gene set which promotes cell proliferation in culture via RNA interference and CRISPR. The group also led the charge in a project uncovering human cell components involved in the SARS-CoV-2 transmission cycle, applying CRISPR to pick out which human cell proteins are used by the virus to infect and reproduce. Dr. Moffat is also the Canada Research Chair in Functional Genomics of Cancer. 

The Montenegro-Burke lab's primary specialty is metabolomics, specifically mapping out the metabolome’s heterogeneity - including the dark metabolome - in different types of cells, tissues and organisms. Their research aims include mapping out unknown new metabolic pathways by linking enzymes and reactions to specific metabolic molecules and determining their function and impact on biological processes. One publication described how metabolic dysregulation could play a role in inflammatory bowel disease (IBD) and how targeting specific lipid pathways pharmacologically presents a potential therapeutic route. 

The Moran lab utilizes proteomics and functional genomics methods to identify and describe activated proteins in cancers, intracellular signalling in tumours and potential drugs to target these pathways. One of their publications identified somatic mutations and copy number alterations in over 800 genes that could predict early-change non-small cell lung cancer survival or prognosis. Another publication demonstrates an integrated-omic (combining DNA, RNA and proteomics) map for non-small cell lung carcinoma which implicates gene alterations for metabolism proteins being associated with differences in survival.  

The Ramalho-Santos lab studies how the environment influences the epigenome and hyper-transcription in stem cells. Rather than simply turning genes on or off sequentially, embryos sense environmental condition changes and modify their development accordingly. It signifies that diseases and other instances of reduced fitness in humans and other living organisms may have originated from or contributed by environmental exposures during pregnancy and development. It has been demonstrated that developmental stress and other factors during development are transmitted to the germline and next generation. The research group aims to dissect the molecular mechanisms of intergenerational germline transmission of environmental stresses and the impact of environmental factors on epigenetic information transfer throughout generations and mammalian development. Additionally, recent lab research demonstrated substantial gene activity shifts during embryonic growth occur in stem cells among thousands of genes, which was previously unnoticed. This team uncovered that stem cells need these major shifts to rapidly divide and that the embryo needs it to develop and survive. They also identified vital regulatory genes and proteins involved in promoting said gene activity changes.  

The Schramek lab takes advantage of functional genomics approaches to investigate potential personalized cancer therapies that target genotype-specific vulnerabilities. The group generates novel genomics tools such as gene editing in mouse models to annotate hundreds of cancer genes. One of their recent publications discovered 166 lncRNAs associated with survival and as potential pan-cancer non-coding biomarkers. Other studies employed in vivo CRISPR/Cas9 screening in genetically modified mice that can analyze gene function in the skin and oral cavity and identified new tumour suppressor genes involved in head and neck cancers. Dr. Schramek also holds the Canada Research Chair in Functional Cancer Genomics. 

The Sidhu lab specializes in synthetic antibody construction with phage-display technology and protein-protein interactions and is home to the Toronto Recombinant Antibody Centre. The centre synthesized thousands of antibodies against hundreds of human antigens and created ubiquitin variants with phage-display tech to target over 150 proteins in the ubiquitin-proteasome. This pipeline includes developing antibodies against SARS-CoV-2 and hantavirus and inhibitory ubiquitin variants against MERS. The group also engineered a multivalent d-protein to antagonize vascular endothelial growth factor A (VEGF-A), phage-displayed peptide libraries for over 200 wild-type and mutant PDZ domains and peptide inhibitors of the Wnt/beta-catenin pathway and IGF-1.  

The Stagljar lab undertakes proteomics projects to chart out membrane protein-protein interactions (PPI) and how they impact the cell during normal and diseased conditions. The group developed various methodologies to analyze PPIs such as the membrane yeast two-hybrid (MYTH) and mammalian membrane two-hybrid (MaMTH). Ongoing MaMTH projects involve small molecule/drug screening and charting out interactomes for disease-associated PPIs. Recently, they utilized MaMTH screening to map out the interactome of the CFTR protein, whose mutations are linked to cystic fibrosis (CF) and identified around 450 interactors as potential influencers of CF severity and therapeutic targets. Additionally, the group developed a pinprick COVID-19 serological test called SATiN, which utilizes a modified luciferase enzyme and accurately measures antibody concentration in the blood in less than one hour.  

The Taipale lab utilizes functional proteomics and genomics to shed light on the human protein network, or proteome. Recently, the group discovered 200+ transcriptional activators via assaying and screening the human proteome. The group employed the renowned artificial intelligence program AlphaFold to predict interaction interfaces of newly discovered activation domains and verify through mutagenesis experiments. The group also co-led a project which exposed how two similar bacterial toxins from Clostridium difficile and its relative Paeniclostridium sordellii binding unrelated human cell receptors result in different diseases, specifically diarrhea and toxic shock syndrome. Dr. Taipale is also the Canada Research Chair in Functional Proteomics and Proteostasis.  

The Wilson lab specializes in comparative genomics and its role in evolution and disease. Specifically, the group studies: the role of mutations in noncoding DNA in childhood disease, evolution and function of heart gene regulation, the role of topoisomerase II beta enzymes in cancer and development and modelling human-specific genome regions. One of their recent publications characterizes a method called single-cell mapper (scMappr) which utilizes single-cell RNA sequencing to infer the cell type of differentially expressed genes. Dr. Wilson also holds the Canada Research Chair in Comparative Genomics. 

The Youn lab investigates a type of biomolecular condensate, which are membrane-less organelles within cells, called stress granules and their organization, dynamics and functions. These condensates are vital for cellular regulation and response to external conditions such as cellular stress. The lab also studies the impact and role of dysfunctional biomolecular condensates on diseases such as ALS and FTD. Dr. Youn holds a Tier 2 Canada Research Chair in Membraneless Organelle Proteomics.  

The Yuen lab aims to genotype and figure out the function and mechanisms of tandem repeat expansions with genome-wide screens, use WGS analysis for genetic variation in neurological disorders and study genetic modifiers in genetic disorders. Some of the group’s recent discoveries involved conducting whole-genome sequence analyses and discovering new genes and tandem repeats implicated in autism.