Stanford Advisors

All Publications

  • Early enforcement of cell identity by a functional component of the terminally differentiated state. PLoS biology Bahrami-Nejad, Z., Zhang, Z. B., Tholen, S., Sharma, S., Rabiee, A., Zhao, M. L., Kraemer, F. B., Teruel, M. N. 2022; 20 (12): e3001900


    How progenitor cells can attain a distinct differentiated cell identity is a challenging problem given the fluctuating signaling environment in which cells exist and that critical transcription factors are often not unique to a differentiation process. Here, we test the hypothesis that a unique differentiated cell identity can result from a core component of the differentiated state doubling up as a signaling protein that also drives differentiation. Using live single-cell imaging in the adipocyte differentiation system, we show that progenitor fat cells (preadipocytes) can only commit to terminally differentiate after up-regulating FABP4, a lipid buffer that is highly enriched in mature adipocytes. Upon induction of adipogenesis in mouse preadipocyte cells, we show that after a long delay, cells first abruptly start to engage a positive feedback between CEBPA and PPARG before then engaging, after a second delay, a positive feedback between FABP4 and PPARG. These sequential positive feedbacks both need to engage in order to drive PPARG levels past the threshold for irreversible differentiation. In the last step before commitment, PPARG transcriptionally increases FABP4 expression while fatty acid-loaded FABP4 increases PPARG activity. Together, our study suggests a control principle for robust cell identity whereby a core component of the differentiated state also promotes differentiation from its own progenitor state.

    View details for DOI 10.1371/journal.pbio.3001900

    View details for PubMedID 36469503

  • Network design principle for robust oscillatory behaviors with respect to biological noise ELIFE Qiao, L., Zhang, Z., Zhao, W., Wei, P., Zhang, L. 2022; 11


    Oscillatory behaviors, which are ubiquitous in transcriptional regulatory networks, are often subject to inevitable biological noise. Thus, a natural question is how transcriptional regulatory networks can robustly achieve accurate oscillation in the presence of biological noise. Here, we search all two- and three-node transcriptional regulatory network topologies for those robustly capable of accurate oscillation against the parameter variability (extrinsic noise) or stochasticity of chemical reactions (intrinsic noise). We find that, no matter what source of the noise is applied, the topologies containing the repressilator with positive autoregulation show higher robustness of accurate oscillation than those containing the activator-inhibitor oscillator, and additional positive autoregulation enhances the robustness against noise. Nevertheless, the attenuation of different sources of noise is governed by distinct mechanisms: the parameter variability is buffered by the long period, while the stochasticity of chemical reactions is filtered by the high amplitude. Furthermore, we analyze the noise of a synthetic human nuclear factor κB (NF-κB) signaling network by varying three different topologies and verify that the addition of a repressilator to the activator-inhibitor oscillator, which leads to the emergence of high-robustness motif-the repressilator with positive autoregulation-improves the oscillation accuracy in comparison to the topology with only an activator-inhibitor oscillator. These design principles may be applicable to other oscillatory circuits.

    View details for DOI 10.7554/eLife.76188

    View details for Web of Science ID 000932847700001

    View details for PubMedID 36125857

    View details for PubMedCentralID PMC9489215

  • The circadian clock mediates daily bursts of cell differentiation by periodically restricting cell-differentiation commitment. Proceedings of the National Academy of Sciences of the United States of America Zhang, Z. B., Sinha, J., Bahrami-Nejad, Z., Teruel, M. N. 2022; 119 (33): e2204470119


    Most mammalian cells have an intrinsic circadian clock that coordinates metabolic activity with the daily rest and wake cycle. The circadian clock is known to regulate cell differentiation, but how continuous daily oscillations of the internal clock can control a much longer, multiday differentiation process is not known. Here, we simultaneously monitor circadian clock and adipocyte-differentiation progression live in single cells. Strikingly, we find a bursting behavior in the cell population whereby individual preadipocytes commit to differentiate primarily during a 12-h window each day, corresponding to the time of rest. Daily gating occurs because cells irreversibly commit to differentiate within only a few hours, which is much faster than the rest phase and the overall multiday differentiation process. The daily bursts in differentiation commitment result from a differentiation-stimulus driven variable and slow increase in expression of PPARG, the master regulator of adipogenesis, overlaid with circadian boosts in PPARG expression driven by fast, clock-driven PPARG regulators such as CEBPA. Our finding of daily bursts in cell differentiation only during the circadian cycle phase corresponding to evening in humans is broadly relevant, given that most differentiating somatic cells are regulated by the circadian clock. Having a restricted time each day when differentiation occurs may open therapeutic strategies to use timed treatment relative to the clock to promote tissue regeneration.

    View details for DOI 10.1073/pnas.2204470119

    View details for PubMedID 35939672

  • Design of Tunable Oscillatory Dynamics in a Synthetic NF-kappa B Signaling Circuit CELL SYSTEMS Zhang, Z., Wang, Q., Ke, Y., Liu, S., Ju, J., Lim, W. A., Tang, C., Wei, P. 2017; 5 (5): 460-+


    Although oscillatory circuits are prevalent in transcriptional regulation, it is unclear how a circuit's structure and the specific parameters that describe its components determine the shape of its oscillations. Here, we engineer a minimal, inducible human nuclear factor κB (NF-κB)-based system that is composed of NF-κB (RelA) and degradable inhibitor of NF-κB (IκBα), into the yeast, Saccharomyces cerevisiae. We define an oscillation's waveform quantitatively as a function of signal amplitude, rest time, rise time, and decay time; by systematically tuning RelA concentration, the strength of negative feedback, and the degradation rate of IκBα, we demonstrate that peak shape and frequency of oscillations can be controlled in vivo and predicted mathematically. In addition, we show that nested negative feedback loops can be employed to specifically tune the frequency of oscillations while leaving their peak shape unchanged. In total, this work establishes design principles that enable function-guided design of oscillatory signaling controllers in diverse synthetic biology applications.

    View details for DOI 10.1016/j.cels.2017.09.016

    View details for Web of Science ID 000416533900007

    View details for PubMedID 29102361