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​Research Projects

Our lab is interested in understanding the genetic basis of neuronal differentiation using a variety of genetics, genomics, and cell biology methods. To circumvent the extreme complexity of mammalian nervous systems, we are using the nematode Caenorhabditis elegans as a model system to address many fundamental questions in neurobiology. Compared to the human brain that contains ~100 billion neurons, the C. elegans nervous system only contains 302 neurons, of which the anatomy and neuronal connection were mapped. This relative simplicity and the ease of genetic manipulation allow us to make discoveries about the organizing principles of neuronal development. Given the orthology between C. elegans and human genes, our findings also provide insight into the molecular mechanisms underlying nerve cell development in humans. In addition, we are also interested in using C. elegans to model neurodegenerative diseases and to study axonal regeneration.

 

Currently, we are pursuing the following directions. 

 

1. Identifying novel regulators of microtubule (MT) stability during neurite growth and axonal regeneration. 

       Previous studies using the Touch Receptor Neurons (TRNs) in C. elegans have identified several important molecular mechanisms of neurite guidance and extension, such as Dishevelled attenuating Wnt repelling activity (Zheng et al., 2015, PNAS) and GEFs controlling the directional specificity of neurite growth (Zheng et al., 2016, PNAS). More recently, we found that mutations in tubulin genes dramatically affect neurite growth by altering microtubule stabilities (Zheng et al., 2017, MBoC). Those studies have clinical relevance because mutations in human tubulins cause a wide range of neurodevelopmental disorders. Using the TRNs, we are able to model those human mutations and study their impact at cellular levels.  One set of tubulin mutations is particularly interesting because they increase MT stability and causes ectopic neurite growth. We are using these mutants as a sensitized background to discover novel regulators of MT structure and stability.

       Regulation of MTs has also been found to be critical during axonal regeneration. Since TRNs in C. elegans is an important model for axonal regeneration upon laser axotomy, we are also studying the neuroregenerative function of those MT regulators identified in our screen in an effort to discover molecular targets for regeneration.

 

2. Investigate the role of Hox genes in terminal neuronal differentiation.

        Hox genes encode conserved homeodomain transcription factors that control the body plan along the anterior-posterior (A-P) axis in embryos. In addition to their functions in embryogenesis, previous studies using the TRNs found that Hox genes also regulate terminal differentiation of neurons by 1) acting as "transcriptional guarantors" to ensure activation of terminal selectors and robust fate acquisition (Zheng et al., 2015, Cell Rep.) and 2) by acting as "subtype inducers" to induce diversification among the neurons that share the same general cell fate (Zheng et al., 2015, Neuron). Those studies provided important examples for the understanding the role of Hox genes in terminal neuronal differentiation. 

       We are currently mapping the expression of Hox genes in the entire nervous system of C. elegans and exploring their functions in the differentiation of other neurons. The general goal of this project is to understand whether Hox genes act as guarantors in general in gene regulation, what are the Hox target genes during neuronal differentiation, what is the regulatory logic for Hox-mediated subtype diversification along the A-P axis, and how Hox genes and cofactors coordinate their activities. 

3. Systematically mapping cell fate regulators in C. elegans nervous system 

        C. elegans nervous system in adult hermaphrodites contains 302 neurons, which can be categorized into 118 morphologically distinct classes. Cell fate regulators of ~70% of those neuron types were identified (Hobert, 2016, WIREs Dev Biol), making it one of the best understood nerve systems in terms of differentiation. We are in the process of identifying the cell fate determinants for the rest ~35% neuron types using a combination of forward genetic screen, RNAi screen, and one-hybrid DNA/protein interaction screen. The goal is to have a complete map of the factors that regulate the fate specification of every type of neurons in an animal. This systematic approach would provide important insights for our understanding of the organization of a nervous system.

(Image is provide by the courtesy of the Hobert lab)

4. Comparative genomics to study the evolutionary origin of neuronal diversity 

        One fascinating question about the development of the nervous system is how the extraordinary diversity of neuron types is involved. We try to address this question by understanding the genetic mechanisms underlying the generation of new neuron types and the loss of old neuron types. We are conducting comparative genomics and comparative developmental neurobiology studies to understand how the differences in genomic sequence among nematodes contribute to the difference in their nervous systems. Specifically, we are comparing C. elegans with other Caenorhabditis species and P. pacificus for the difference in neuron counts and neuronal fate specification programs. 

        Moreover, we are interested in intraspecies variation in nervous systems and are investigating this question using a collection of C. elegans wild isolates that are extracted from different geographic locations globally.  By employing a series of bioinformatics methods, we are searching for natural variations in the genome of C. elegans that lead to variations in the pattern of neuronal development and then use experimental methods to verify whether strains that carry those genetic variations would indeed develop a nervous system that deviates from that of the classical C. elegans strains. We aim at understanding to what degree the neuronal development program is invariant within the same species.

5. Modeling Alzheimer's disease and Parkison's disease in C. elegans

        We are also interested in using the simple nematode C. elegans to model neurodegenerative diseases, like Alzheimer's disease and Parkinson's disease. The transparency of the animal allows direct visualization of live neurons; the ease to perform genetic manipulation in a controlled experiment allows modeling of the disease condition and identification of genetic components contribute to the disease; the small size and short life cycle of the animal allow large-scale screens to discover compounds that can prevent or slow down neurodegeneration. We are currently working on identifying microbial metabolites that can interfere with AD or PD pathogenesis.

(Imaged adapted from Kim D.K., Lee SJ. (2015) Aging-Related Neurodegenerative Diseases in Caenorhabditis elegans. In: Mori N., Mook-Jung I. (eds) Aging Mechanisms. Springer, Tokyo)