Neuronal Development

Neural development, neural degeneration, neural regeneration and the formation of neural networks are all areas under study by members of the Cellular and Molecular Structure and Function group. This work is of central importance to understanding fundamental biological processes, and to generating new approaches for the regeneration of neural tissue after injury or disease. Work in the Van der Kooy lab is aimed at understanding how pluripotent embryonic stem cells lead to neural stem cell development. In the Miller and Kaplan labs, the study of neural development is being approached through an analysis of genes deregulated in autism spectrum disorders. The Kaplan lab also strives to develop molecules to stimulate stem cells to repair the brain and to treat childhood cancers. Neural development is also a central focus of study in the Boulianne lab using Drosophila where neuralized, an E3 ubiquitin ligase involved in the turnover of Notch ligands, has been implicated in cell fate determination. Although the role played by guidance cues in neuronal growth has been well-studied over the years, new work from the Culotti lab reveals that cell growth orthogonal to guidance cue gradients also occurs and identifies receptor mutants that may be locked "in" or "out" of this form of non-canonical guidance. The Lefebvre lab takes a multidisciplinary approach to understand how brain development is influenced by protocadherins, cell surface membrane proteins involved in mediating the formation of neural circuits in the eye and brain. Higher-order neural functions are also being studied by MoGen scientists using various model organisms and techniques. The Okomoto lab employs novel laser optic methods to study learning and memory, and the Zhen lab uses genetics, optogenetics, electrophysiology and computational approaches to study C. elegans locomotion. Taken together, work in this area will shed light on the mechanisms underpinning human disorders in neural development including Alzheimer's disease and autism and facilitate development of new therapeutic strategies.  

Stems Cells, Signalling, Development and Disease

MoGen faculty have made great strides in studying stem cells, embryonic development, cell signalling and the molecular basis of disease in other systems and tissues. Cell polarity and cell shape changes and how these contribute to congenital malformations in diseases like scoliosis and polycystic kidney disease are a key focus of the Ciruna lab, as one example. In the Scott lab, zebra fish is used as a model system to study cardiovascular embryonic development, with the long-term goal of developing approaches to repair damaged heart tissue. Heart and limb development is also being studied in the Hui lab, where the impact of transcriptional regulation is a major focus. The Rossant lab has made seminal discoveries that illuminate control of cell fate decisions in the early mouse embryo. The Kim lab further explores stem cell renewal and differentiation using the gut as a model system. In a novel approach using yeast sporulation as a model, the Meneghini lab seeks to understand how the epigenetic control of gene expression dictates cell differentiation. In the Spence lab, efforts are underway to determine how a novel mode of epigenetic control mediates sex determination in C. elegans. How the cadherins, Fat and Dachsous, modulate tissue growth and organization, and why mutations in the Fat/Dachsous pathway lead to cystic kidney disease and cancer are questions being address in the McNeill lab using Drosophila and mouse models. They recently discovered that mutations in Fat lead to tumor formation by directly modulating mitochondrial function, a novel and unanticipated disease mechanism. Although gene therapy has the potential to have a tremendous impact on the treatment of human disease, gene transfer into stem cells remains a stumbling block. Ongoing work in the Ellis lab is aimed at addressing this challenge, and involves reprogramming somatic cells to generate pluripotent stem cells. Their work has led to models for studying autism, cystic fibrosis and congenital heart disease. Morphogen signalling pathways, such as TGFβ and Wnt, and their interactions with the Hippo signalling pathway are critical in development, and a number of major advances in this area have been made by the Wrana lab. Their work has also revealed the impact of ubiquitin-dependent degradation of target proteins on TGFβ superfamily signalling, with studies focused on Smurf1, an E3-WW-HECT ubiquitin ligase. Cell signalling is also influenced by phosphatidylinositol phosphates (PIPs), and the Brill lab is shedding light on how PIPs and their regulators function in cytokinesis, gametogenesis and organelle biogenesis. 

Genome Stability: DNA Repair and Chromosome Replication and Segregation

Much cellular machinery is devoted to maintaining genome stability. The loss or gain of entire chromosomes or portions of them is linked to aberrant development and is a tumor cell hallmark.  Using frogs, flies and tissue culture systems, the Wilde lab studies cell division and processes that lead to aneuploidy. How chromosomes segregate and plasmids partition in eukaryotes and bacteria, respectively, are a focus of study in the Lavoie and Funnell labs. The perturbation of centrosome biogenesis and function can lead to genome instability, with the identification of centrosome regulators being a key goal of an interdisciplinary collaborative effort involving the Pelletier, Raught and Gingras labs, who together exploit functional genomics, cutting-edge microscopy and mass-spectrometry. DNA repair is an important component of maintaining genome integrity, and an interdisciplinary collaborative effort involving the Durocher and Sicheri labs is shedding light on the role of ubiquitination in recruiting repair enzymes to the sites of double-strand DNA breaks. PML nuclear bodies are important in suppressing oncogenesis in part owing to the role that they play in DNA repair. In a collaborative effort involving the Frappier and Moffat labs, a functional genomic screen has recently identified a number of E3 ubiquitin ligases responsible for degrading PML proteins, with implications for understanding PML body regulation and the relationship with cancer.

Gene Regulation:  RNA, DNA and the Processes that Control Them 

The central dogma in molecular biology - DNA makes RNA makes protein - describes a process that it highly regulated at many levels. The splicing of pre-mRNA to give mature mRNA represents one step at which regulation occurs, and through alternative splicing both protein levels and protein isoforms can be controlled. Exciting new work emerging from the Blencowe lab reveals that the alternative splicing of microexons is tightly controlled in neural tissue and misregulated in autism. The Sicheri lab has shown how the dual-function Ire1 protein serves to promote spliceosome-independent mRNA splicing and gene regulation in response to endoplasmic reticulum (ER) stress. Naked mRNA does not exist in isolation, and efforts to understand how mRNA-protein complexes work to modulate mRNA stability and translatability form the basis of the research ongoing in the Rissland lab. An example of how RNA binding proteins modulate transcripts is provided by recent work from the Miller, Kaplan and Smibert labs who focused on an mRNA complex responsible for maintaining neural cell precursors in a stem cell state. The Greenblatt lab is leading a large-scale effort involving affinity purification, mass spectrometry and second-generation sequencing to characterize the protein-protein, protein-RNA and protein-DNA interactions important in gene regulation. RNA viruses such as HIV-1 rely on the RNA processing machinery of the host cell to process their RNA genomes into viral mRNA, and efforts to target these processes as a means of developing anti-viral agents are ongoing in the Cochrane lab. Over the past few decades a host of "noncoding RNA" molecules with diverse functions have been shown to influence cell differentiation and cell-fate determination. Although many of these small RNAs silence the expression of their target genes, recent work from the Claycomb lab has uncovered a new paradigm in which small RNAs promote gene expression over successive generations, a process called transgenerational epigenetic inheritance. Catalytic RNA molecules provide another example of the diverse roles played by RNA, and the Collins lab has focused on the VS ribozyme, which may ultimately lead to novel approaches to engineering the mitochondrial genome. Metabolomics seeks to fully characterize the complex enzymatic pathways that are involved in converting nutrients into the vast array of molecules found in a living organism, including nucleic acids. The Caudy lab has recently characterized a new metabolic route to the production of ribose a key building block of the DNA templates from which RNA transcripts are generated.

Protein Structure and Function and the Development of Novel Therapeutics

MoGen faculty excel in the computational, structural and biochemical characterization of proteins, work that includes the study of protein folding, protein-protein interactions and the development of novel therapeutics. Intrinsically disordered proteins are now recognized for their ability to mediate diverse and dynamic protein complexes that promote cross-talk between signalling pathways, and work done in the Kay and Forman-Kay labs is beginning to shed light on how they mediate these important roles. Membrane proteins play central roles in signal transduction, ion transport, nutrient uptake and pathogen interactions to mention just a few.  Among these, G protein-coupled receptors (GPCRs) are unique in that they collectively represent approximately one-half of all known drug targets. Using x-ray crystallography and spectroscopic approaches, the Ernst lab uses rhodopsin as a model for understanding how GPCRs mediate signal transduction. Using similar techniques, the Pai lab is studying magnesium ion transport in the bacterial Mg-ion transporter CorA. The Rini lab uses structural and biochemical approaches to study how glycosyltransferases mediate glycoprotein folding and quality control in the eukaryotic ER, and their recent work has also provided novel insights into coronavirus receptor interactions and RNA virus evolution. Antibodies and antibody-drug conjugates represent a tremendously important class of human therapeutics with diverse applications in the treatment of cancer and arthritis. In a large-scale initiative headed by the Sidhu group, protein engineering is being used to design synthetic antibodies against cell surface molecules involved in these diseases as a means of developing novel antibody therapeutics. The Davidson lab uses a multidisciplinary approach to study protein-protein interactions and macromolecular complexes including bacteriophage. They are exploring strategies to harness bacteriophage as an alternative to antibiotics against bacterial pathogens such as Pseudomonas aeruginosa. Using a membrane yeast two-hybrid assay that they have developed, the Stagljar lab seeks to characterize interactions involving ABC transporters, receptor tyrosine kinases and GPCRs as a means of identifying protein targets for the development of novel therapeutic agents. In a complementary approach, the Taipale lab uses functional proteomics to discover novel protein targets of known drugs and ligands. 

Researchers in the Department of Molecular Genetics are leveraging powerful interdisciplinary collaborations to lead the field in the area of Cellular and Molecular Structure and Function.