Portrait of Dr Chieh Hsu

Dr Chieh Hsu

Eastern ARC Research Fellow

About

Chieh did his BSc studies in National Taiwan University in 2002. He continued his postgraduate studies in the Molecular Biology Program, University of Goettingen, Germany, and received MSc in Biochemistry mentored by Dr Jobst Landgrebe (2004-2006). He developed strong interest in cell biology and contributed to the early findings in exosome biogenesis during his PhD curriculum in Prof Mikael Simons' lab at the Max-Planck Institute for Experimental Medicine (2006-2010). Later he broadened his research interest into molecular systems biology. He joined Prof Attila Becskei's group in University of Zurich (2010-2011) and University of Basel (Biozentrum, 2011-2015), Switzerland and was awarded the long-term fellowship from Human Frontier Science Program (2011-2014) to study system stability, cellular memory, and stochastic/deterministic factors in transcriptional auto-regulatory circuits.
Chieh joined School of Biosciences as the Eastern ARC Research Fellow in synthetic biology in March 2015. He aims to bridge disciplines for quantitative studies on intracellular membrane trafficking.

ORCID ID:0000-0002-4780-1222

Research interests

We are currently establishing two major synthetic frameworks using the yeast Saccharomyces cerevisiae:
1.Positive feedback loops and protein membrane domains. In eukaryotic cells, organelles exchange materials in membranous vesicles in a process called intracellular membrane trafficking. To ensure proper sorting, a given membrane needs to be identified before assigned to transport machineries. The protein family, small GTPases, establish membrane identity on various organelles and vesicles. They act as the molecular switches and once activated, they are attached to the membrane and recruit the same molecular to the surrounding membranes. To quantitatively understand this complicated process in which diffusion plays a key role, we utilise synthetic model systems to dissect how individual reaction affects the overall kinetics and dynamics.
2. Evolution of switching rate between cell fates. During evolution, positive feedback often emerges in gene regulation and leads to a switch like response that allows activating certain genes only when the environmental stimuli reach a certain threshold. However, such feedback systems can also result in a phenomenon called cellular memory, or hysteresis. In this case, the cellular response to an environmental stimulus depends on whether the cell has been activated before: a previously activated cell stays activated and vice versa. Obviously, cellular memory slows down or even prevents proper response, which can cause adaptation disadvantage. We synthesise gene circuits that reflect such conditions to study how such switching rates affect fitness and how switching rates evolve in a population under rapid and extreme environmental changes.

Publications

Article

  • Jaquet, V., Hsu, C. and Becskei, A. (2017). Measurement of bistability in a multidimensional parameter space. Integrative Biology [Online] 9:167-177. Available at: http://dx.doi.org/10.1039/C6IB00242K.
  • Hsu, C. et al. (2016). Contribution of bistability and noise to cell fate transitions determined by feedback opening. Journal of Molecular Biology [Online]. Available at: http://dx.doi.org/10.1016/j.jmb.2016.07.024.
  • Hsu, C. et al. (2016). Protein dimerization generates bistability in positive feedback loops. Cell reports [Online] 16:1204-1210. Available at: http://dx.doi.org/10.1016/j.celrep.2016.06.072.
    Bistability plays an important role in cellular memory and cell fate determination. A positive feedback loop can generate bistability if it contains ultrasensitive molecular reactions. It is often difficult to detect bistability based on such molecular mechanisms due to its intricate interaction with cellular growth. We constructed transcriptional feedback loops in yeast. To eliminate growth alterations, we reduced the protein levels of the transcription factors by tuning the translation rates over two orders of magnitude with designed RNA stem-loops. We modulated two ultrasensitive reactions, homodimerization and the cooperative binding of the transcription factor to the promoter. Either of them is sufficient to generate bistability on its own and when acting together, a particularly robust bistability emerges. This bistability persists even in the presence of a negative feedback loop. Since protein homodimerization is ubiquitous, it is likely to play a major role in the behavior of regulatory networks.
  • Hsu, C. et al. (2012). Stochastic signalling rewires the interaction map of a multiple feedback network during yeast evolution. Nature communications [Online] 3:Article 682. Available at: http://dx.doi.org/10.1038/ncomms1687.
    During evolution, genetic networks are rewired through strengthening or weakening their interactions to develop new regulatory schemes. In the galactose network, the GAL1/GAL3 paralogues and the GAL2 gene enhance their own expression mediated by the Gal4p transcriptional activator. The wiring strength in these feedback loops is set by the number of Gal4p binding sites. Here we show using synthetic circuits that multiplying the binding sites increases the expression of a gene under the direct control of an activator, but this enhancement is not fed back in the circuit. The feedback loops are rather activated by genes that have frequent stochastic bursts and fast RNA decay rates. In this way, rapid adaptation to galactose can be triggered even by weakly expressed genes. Our results indicate that nonlinear stochastic transcriptional responses enable feedback loops to function autonomously, or contrary to what is dictated by the strength of interactions enclosing the circuit.
  • Prenzel, T. et al. (2011). Estrogen-dependent gene transcription in human breast cancer cells relies upon proteasome-dependent monoubiquitination of histone H2B. Cancer research [Online] 71:5739-5753. Available at: http://dx.doi.org/10.1158/0008-5472.CAN-11-1896.
    The estrogen receptor-? (ER?) determines the phenotype of breast cancers where it serves as a positive prognostic indicator. ER? is a well-established target for breast cancer therapy, but strategies to target its function remain of interest to address therapeutic resistance and further improve treatment. Recent findings indicate that proteasome inhibition can regulate estrogen-induced transcription, but how ER? function might be regulated was uncertain. In this study, we investigated the transcriptome-wide effects of the proteasome inhibitor bortezomib on estrogen-regulated transcription in MCF7 human breast cancer cells and showed that bortezomib caused a specific global decrease in estrogen-induced gene expression. This effect was specific because gene expression induced by the glucocorticoid receptor was unaffected by bortezomib. Surprisingly, we observed no changes in ER? recruitment or assembly of its transcriptional activation complex on ER? target genes. Instead, we found that proteasome inhibition caused a global decrease in histone H2B monoubiquitination (H2Bub1), leading to transcriptional elongation defects on estrogen target genes and to decreased chromatin dynamics overall. In confirming the functional significance of this link, we showed that RNA interference-mediated knockdown of the H2B ubiquitin ligase RNF40 decreased ER?-induced gene transcription. Surprisingly, RNF40 knockdown also supported estrogen-independent cell proliferation and activation of cell survival signaling pathways. Most importantly, we found that H2Bub1 levels decrease during tumor progression. H2Bub1 was abundant in normal mammary epithelium and benign breast tumors but absent in most malignant and metastatic breast cancers. Taken together, our findings show how ER? activity is blunted by bortezomib treatment as a result of reducing the downstream ubiquitin-dependent function of H2Bub1. In supporting a tumor suppressor role for H2Bub1 in breast cancer, our findings offer a rational basis to pursue H2Bub1-based therapies for future management of breast cancer.
  • Hsu, C. et al. (2010). Regulation of exosome secretion by Rab35 and its GTPase-activating proteins TBC1D10A-C. The Journal of cell biology [Online] 189:223-232. Available at: http://dx.doi.org/10.1083/jcb.200911018.
    Oligodendrocytes secrete vesicles into the extracellular space, where they might play a role in neuron-glia communication. These exosomes are small vesicles with a diameter of 50-100 nm that are formed within multivesicular bodies and are released after fusion with the plasma membrane. The intracellular pathways that generate exosomes are poorly defined. Because Rab family guanosine triphosphatases (GTPases) together with their regulators are important membrane trafficking organizers, we investigated which Rab GTPase-activating proteins interfere with exosome release. We find that TBC1D10A-C regulate exosome secretion in a catalytic activity-dependent manner. We show that Rab35 is the target of TBC1D10A-C and that the inhibition of Rab35 function leads to intracellular accumulation of endosomal vesicles and impairs exosome secretion. Rab35 localizes to the surface of oligodendroglia in a GTP-dependent manner, where it increases the density of vesicles, suggesting a function in docking or tethering. These findings provide a basis for understanding the biogenesis and function of exosomes in the central nervous system.
  • Trajkovic, K. et al. (2008). Ceramide triggers budding of exosome vesicles into multivesicular endosomes. Science (New York, N.Y.) [Online] 319:1244-1247. Available at: http://www.sciencemag.org/content/319/5867/1244.
    Intraluminal vesicles of multivesicular endosomes are either sorted for cargo degradation into lysosomes or secreted as exosomes into the extracellular milieu. The mechanisms underlying the sorting of membrane into the different populations of intraluminal vesicles are unknown. Here, we find that cargo is segregated into distinct subdomains on the endosomal membrane and that the transfer of exosome-associated domains into the lumen of the endosome did not depend on the function of the ESCRT (endosomal sorting complex required for transport) machinery, but required the sphingolipid ceramide. Purified exosomes were enriched in ceramide, and the release of exosomes was reduced after the inhibition of neutral sphingomyelinases. These results establish a pathway in intraendosomal membrane transport and exosome formation.
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