Gene Regulation and Cell Fate Determination, Organogenesis, and Morphogenesis

The earliest cell fate decisions in the mammalian embryo distinguish the cells that will form extraembryonic tissues from those that give rise to the embryo proper. The laboratory of Janet Rossant uses a combination of genetic analysis and sophisticated embryological manipulation to study early embryogenesis in the mouse. In recent work, the Rossant group and their collaborators showed that two conserved signaling pathways converge on a single transcriptional regulator to specify the first of the extraembryonic lineages.

Early embryogenesis relies heavily on post-transcriptional regulation of gene activity. The laboratories of Howard Lipshitz and Craig Smibert use single-gene and genome-wide approaches to study the regulation of mRNA stability, localization, and translation by RNA-binding proteins and regulatory RNAs in the Drosophila embryo. In recent work, they and their collaborators, including Quaid Morris of MoGen, demonstrated that a single RNA-binding protein called Smaug regulates the stability and translation of a large fraction of the mRNAs in the early embryo. Julie Claycomb's lab explores how gene expression is regulated by endogenous small noncoding RNA pathways. Although these small RNA pathways have generally been thought of as a means of silencing gene expression, members of the Claycomb lab recently discovered that a small RNA pathway in C. elegans epigenetically licenses the transcription of germline genes that are necessary for fertility. Andrew Spence’s lab has produced genetic evidence for maternal epigenetic licensing of the expression of a gene required for determining germ cell sexual fate in C. elegans. Mechanisms of epigenetic inheritance are also the focus of Marc Meneghini’s lab, whose members recently discovered a transgenerational epigenetic phenomenon in the yeast Saccharomyces cerevisiae. S. cerevisiae forms meiotic spores that resist environmental stress, and Prof. Meneghini and his colleagues found that the descendants of these spores exhibit enhanced stress resistance for up to 10 mitotic generations.

Drosophila pupal eye stained for actin (red) and armadillo (green). Image courtesy of Lauren Del Bel and Julie Brill.

Drosophila pupal eye stained for actin (red) and armadillo (green). Image courtesy of Lauren Del Bel and Julie Brill.

As embryogenesis proceeds, transcriptional regulation and signaling gain prominence. The laboratory of C.C. Hui uses mice to study the mechanisms that regulate the activity of Gli family transcription factors, which are required in skeletal and nervous system development, and the roles of the Iroquois family of transcription factors in directing heart and limb development. Ian Scott’s lab investigates cardiovascular development and heart regeneration using zebrafish as a model. Their work has identified a novel signaling pathway that is needed for cardiac progenitor migration and development. Their analysis of zebrafish mutants lacking the function of the ccm3 gene implicated in human cerebral cavernous malformations, a disorder of the vasculature, provided a zebrafish model of the disease. Brent Derry’s lab, in a collaborative effort involving the Zhen and Gingras labs, demonstrated that in C. elegans ccm-3 acts as part of a protein complex that promotes endocytic recycling required for the extension of the tubular excretory canal cell. The Derry and Roy labs are currently collaborating with international partners to screen chemical libraries for compounds that can suppress ccm disease phenotypes in worms. The Cordes lab has provided insight into the mechanisms that regulate vascular branching (angiogenesis) with the discovery that the gumby gene encodes a ubiquitin-specific protease that interacts with members of the Wnt signaling pathway and is required for angiogenesis in mice.

Understanding how cells polarize and rearrange over spatial and temporal scales is another core goal of this Research Field. A major focus of Helen McNeill’s laboratory is how the cell surface proteins Fat and Dachsous, members of the cadherin family, control tissue growth and epithelial planar polarity.  Recent work from the McNeill lab led to the surprising finding that in Drosophila, Fat activity directly regulates mitochondrial function and metabolic state. Lab members also use tissue culture and mouse models to understand why mutations in the Fat/Dachsous pathway lead to cystic kidney disease and cancer. Research in the laboratory of Brian Ciruna aims to determine how polarized changes in cell shape, structure and movement form the vertebrate body during embryonic development and how abnormal cell polarity contributes to congenital malformations and disease including scoliosis, polycystic kidney disease, and tumour metastasis. Recent work from the Ciruna lab demonstrated that zebrafish mutants lacking the activity of a regulator of the Wnt signaling pathway provide the first genetically defined model of idiopathic and congenital scoliosis. The Hopyan lab is defining mechanisms that rearrange cells in three dimensions to generate embryonic structures such as the limb bud and branchial arches in the mouse embryo. Their recent efforts showed how dorsoventrally biased forces acting on the ectoderm of the developing limb orient cell intercalations to give rise to the apical ectodermal ridge. 

Deciphering the regulatory circuitry governing cellular growth and division captivates the attention of numerous MoGen teams. Julie Brill’s lab investigates the functions of phosphatidylinositol phosphates (PIPs), membrane lipids with established roles in cell signaling, in animal development. Using Drosophila, the Brill lab has discovered novel roles for PIPs and their regulators in cytokinesis, gametogenesis and organelle biogenesis. Recent work, for example, showed the PIP-generating enzyme PI4KIIIa to be specifically required for cortical integrity and cell polarity in oogenesis. Cytokinesis is a focus of research in the labs of Bri Lavoie and Andy Wilde. Cell division is an irreversible act, thus cells possess quality control mechanisms to ensure that both chromosome segregation and the re-assembly of the nuclear membrane are complete prior to severing daughter cells.  The Wilde and Lavoie labs have identified a novel quality control pathway that jump-starts cytokinesis following delays in chromosome segregation that have been appropriately resolved by another quality control pathway. Their work suggests that the timing of abscission (cell separation) is determined by a finely tuned balance between opposing quality control pathways at the intracellular bridge.

Stem Cells in Development

MoGen faculty members have been at the forefront of efforts to understand and exploit the remarkable regenerative capacity of stem cells. Embryonic stem cells can give rise to all the tissues of the organism. Powerful methods of gene editing and replacement in mouse embryonic stem cells have been central in achieving our current understanding of mammalian development. Similar approaches using human embryonic stem cells could have enormous potential for treating a wide range of human disease, but the isolation of human embryonic stem cells raises important ethical questions and their use still faces technical challenges. Many adult tissues also contain stem cells that are capable of generating the cell types associated with their tissues of origin and thus have similar therapeutic potential with fewer ethical concerns. The laboratory of Derek Van der Kooy discovered and characterized both retinal stem cells and pancreatic stem cells from both mice and humans. These cells are excellent targets for regenerative medicine strategies to treat diabetes and blindness. The laboratories of David Kaplan and Freda Miller study the roles of stem cells in brain development and investigate how stem cells can be mobilized following injury. They recently demonstrated a role for nerve-derived neural crest derived precursor cells in wound repair in adult skin.

Induced pluripotent stem (iPS) cells provide another alternative to embryonic stem cells. They are produced from differentiated cells, such as skin cells, by introducing genes encoding a set of transcription factors or by specific chemical treatment.  James Ellis uses iPS cells to develop models of Rett syndrome, autism spectrum disorder, cystic fibrosis, and congenital heart disease. Patient-derived iPS cells can be directed to produce the cell types affected in the disease, and the resulting cell populations can be used for more detailed study of the cellular disease phenotype and for identifying drugs that alleviate the phenotype.

Deciphering the molecular mechanisms that control stem cell renewal and differentiation is a focus of multiple MoGen labs. Bret Pearson is interested in the molecular mechanisms underlying the ability of adult stem cells to produce, at the correct place and time, the exact numbers and types of cells required to replace those lost due to tissue turnover or injury. To this end, his lab uses the freshwater planarian, a type of flatworm with a large adult stem cell population and extraordinary regenerative ability, as an in vivo model system to study stem cells and regeneration. He and his colleagues have recently reported that a conserved RNA-binding protein is required both to restrict the stem cell pool and to allow stem cell descendants to differentiate into multiple cell types.  Tae-Hee Kim investigates the mechanisms that regulate stem cell renewal and differentiation using the mouse gut as a model system. His work revealed a permissive chromatin environment around key regulatory genes in gut stem cells that pre-configures the expression of those genes in lineage-specific progenitors.

Cancer

The stem cell paradigm informs our understanding of tumorigenesis and guides efforts to identify treatments for certain types of cancer.  John Dick’s demonstration that only a subset of the cells in several types of leukemia are capable of initiating and sustaining tumour growth provided the foundation for the cancer stem cell hypothesis. His group recently identified hematopoietic stem cells bearing mutations in a DNA methyltransferase gene as the likely precursors of leukemic stem cells in acute myeloid leukemia.  Peter Dirks studies brain cancer in humans and in mouse models using the conceptual framework of stem cell biology.

Cancers may be understood as genetic diseases inasmuch as they result from mutations that disrupt the mechanisms regulating cell proliferation, differentiation, and death. Modern DNA sequencing technology readily provides a catalogue of the mutations present in a particular tumour, and it allows assessment of the genetic heterogeneity of the cells making up the tumour. However, simply cataloguing mutations is not enough, as it does not indicate which mutations are crucial for initiating or sustaining tumour growth and metastasis versus which mutations are merely “passengers” that reflect the genetic instability of the tumour but do not contribute to malignancy.  Daniel Schramek has developed a strategy for efficiently testing candidate genes in mouse embryos to identify those that have a role in tumorigenesis. In one example, he and his colleagues identified the MYH9 gene as a potent tumour suppressor that is required to activate the “guardian of the genome”, p53. Inactivation of MYH9 caused Head and Neck Squamous Cell Carcinoma (HNSCC) in mouse embryos, and mutations in the human gene are associated with several cancers including HNSCC.  Sean Egan designs mouse models of breast cancer and uses them to identify the signaling networks involved in tumorigenesis and metastasis.  Jason Moffatt uses systematic RNA interference with lentiviral vectors in cultured mammalian cells to identify genes and genetic interaction networks that are critical for cancer cell proliferation, and may therefore be suitable targets for therapeutic intervention.

Nervous System Development and Function

Many researchers in MoGen direct their efforts toward understanding the development and function of the most complex products of biology: the brain and the nervous system.  Joe Culotti studies the mechanisms that guide migrating cells and axons to their targets and thus ensure the correct wiring of the nervous system. One such mechanism, involving signaling molecules known as netrins, guides axons along a dorsoventral trajectory. Netrin signaling was discovered by Prof. Culotti and colleagues in the small roundworm C. elegans and later found to serve the same function in the vertebrate spinal cord. The Culotti group has recently found that the activity of the netrin pathway is modulated by a second type of signal known as Wnt to direct migration following a change from a dorsoventral path to an anteroposterior one, providing the first example of cross-talk between the two classes of signal.  Julie LeFebvre studies the mechanisms of neuronal guidance in the mammalian brain with the goals of understanding how precise patterns of connectivity develop, and how disruption of those patterns contributes to childhood brain and behavioural disorders. Correct circuit formation requires that dendrites from the same neuron avoid each other while making specific contacts with other neurons; Prof. Lefebvre’s group has shown that the Slit/Robo signaling pathway, originally identified in fruit flies, is required for self-avoidance of neurons in the mouse cerebellum.

 Understanding mechanisms that underpin diverse neurological and behavioural traits in biology and disease provides another central goal of this Research Field. Mei Zhen and colleagues address the question of how nervous systems generate behavior by exploiting the combined power of genetics, optogenetics and neurophysiology, and the relative simplicity of the C. elegans nervous system. Among their recent findings is that the activity of a particular sodium ion channel is required for persistent neural activity that sustains C. elegans locomotion. Their findings may be relevant to other functions, including learning and memory, which also involve persistent neural activity. The laboratory of Kenichi Okamoto studies the mechanisms of learning and memory in the mammalian brain. Prof. Okamoto and his coworkers use laser microscopy to observe neuronal activity in cell cultures and hippocampal slices, and they have developed optogenetic tools and microscopes for visualizing and manipulating the activity of specific proteins within neurons. Ion channels are the centre of attention in the laboratory of Xi Huang, who studies their contributions to normal brain development and tumorigenesis and investigates the potential of ion channel drugs to treat brain tumours. The Boulianne lab makes use of the fruit fly Drosophila to study nervous system development and function, and to model human diseases such as Alzheimer’s disease.

Models of Disease, and Drug Discovery

Several research groups in MoGen study animal models of human disease to gain insight into mechanisms of pathogenesis, to discover potential targets for therapeutic intervention, and to identify therapeutic agents. Research in the laboratory of Lucy Osborne focuses on neurodevelopmental disorders associated with deletion (Williams syndrome) and duplication (Dup7 syndrome) of chromosome region 7q11.23. The Osborne lab uses mouse models to understand how individual and combinatorial effects of the deletion or duplication of genes in this chromosomal region contribute to cortical development and neuronal defects in these disorders.  Johanna Rommens is interested in human genetic diseases of the exocrine pancreas, including cystic fibrosis and Shwachman-Diamond syndrome. Members of the Rommens laboratory use population studies and mouse models to investigate the mechanisms underlying development and presentation of exocrine pancreatic failure.  Monica Justice is an expert in mouse genetics and developing mouse models of human disease. One current avenue of investigation in the Justice laboratory involves screening for genetic suppressors in a mouse model of Rett syndrome so as to identify pathways that can be pharmacologically targeted to treat the disease.

Expansion of simple DNA sequence repeats in certain genes underlies a set of devastating human diseases, including Huntington’s disease and myotonic dystrophy. The laboratory of Christopher Pearson has identified genetic factors that drive repeat expansions and used transgenic mouse models to validate their association with pathogenesis. They are now seeking ways of targeting these factors so as to arrest or reverse expansion and improve clinical outcomes.

Zebrafish provide a powerful model for diverse diseases studied in MoGen labs. The goal of research in the laboratory of James Dowling is to develop therapies for childhood muscle diseases including congenital myopathies and muscular dystrophies. Prof. Dowling and colleagues use zebrafish and mouse models to dissect disease pathogenesis and to screen for drugs capable of ameliorating disease symptoms. For example, they recently reported that a serotonin re-uptake inhibitor, already in clinical use for other reasons, can prevent dystrophic changes in a zebrafish model of Duchenne muscular dystrophy.  Henry Krause has developed the zebrafish as a platform for high-throughput drug discovery in models of diseases such as diabetes, cancer and depression.

 Another model organism at the forefront of MoGen research in drug discovery and disease is the roundworm C. elegans. Peter Roy’s lab uses C. elegans as a model for parasitic nematodes and to develop models of human genetic diseases including neurodegenerative disorders and diseases resulting from defects in muscle excitability. Members of the lab carry out high-throughput screens for molecules that interfere with the growth and development of the worm or alleviate the defects of the disease models. Testing in other model systems, carried out in collaboration with other labs, identifies the most promising drug leads among the active molecules, while the powerful genetics of C. elegans facilitates elucidation of their mechanisms of action.

Equipped with an outstanding breadth of expertise and employing cutting edge technologies in powerful model systems, this ever-growing portion of our Department is clearly poised to make groundbreaking contributions in the years to come.