Biology subjects

Zhao, M. L.

Publications and source records attributed to Zhao, M. L..

9 recordsLinked to original sources

bioRxiv2026

Quantification of cellular contributions to multi-cellular pattern formation

Multi-cellular pattern formation is a key process in organism development, regeneration, and disease. Such multi-cellular patterns include, for instance, cell density and gene expression patterns. Here, we develop a cell-track-based method that quantifies how much individual cellular processes contribute to the emergence of large-scale patterns. These cellular processes include changes in cellular expression levels, cell motion, cell divisions, and apoptosis. We validate our method using synthetic data, before demonstrating it on two sets of experimental data. Our method is purely geometric and does not require any mechanistic assumptions about the underlying pattern-forming processes, making it very generic and robust. It thus enables unbiased, data-driven study of the mechanisms driving pattern formation across a broad class of systems.

biophysics↗

bioRxiv2026

The limits of scaling in aggregation-driven patterning of cell collectives

Robust development requires maintaining correct proportions as overall size varies. What controls and limits this scaling remains poorly understood due to the complex interplay of mechanical and biochemical embryonic factors. Combining confinement of dissociated embryonic presomitic mesoderm cells with imaging and chemical perturbations, we identified cell aggregation as the initial event in de novo posterior pole formation. Using a continuum model based solely on cell-cell attraction, we quantitatively map how the time available for aggregation-driven patterning limits the maximum scalable system size. Small systems allow rapid, robust pattern scaling, whereas coarsening dynamics substantially delay scaled patterns in large systems. Our experiments quantitatively confirm these predicted scaling regimes. Together, our results reveal a developmental time-size tradeoff governing the scaling of aggregation-driven patterns.

biophysics↗

bioRxiv2022

A dynamic HIF1alpha-PPARgamma circuit controls a paradoxical adipocyte regulatory landscape

Hypoxia-induced upregulation of HIF1 triggers adipose tissue dysfunction and insulin resistance in obese patients. HIF1 closely interacts with PPAR{gamma}, the master regulator of adipocyte differentiation and lipid accumulation, but there are conflicting results how this co-regulation controls the excessive lipid accumulation that drives adipocyte dysfunction. Using single-cell imaging and modeling, we find that, surprisingly, HIF1 both promotes and represses lipid accumulation during adipogenesis. We show that the opposing roles of HIF1 are isolated from each other and depend on when HIF1 increases relative to the positive-feedback mediated upregulation of PPAR{gamma} that drives adipocyte differentiation. A theoretical model incorporating our findings resolves conflicting prior results and suggests that three network nodes before and after the isolation step have to be synergistically targeted in therapeutic strategies to revert hypoxia-mediated adipose tissue dysfunction in obesity. TeaserA systems biology approach detangles the effect of hypoxic and adipogenic regulators on lipid accumulation in adipocytes.

systems biology↗

bioRxiv2020

The highly expressed lipid buffer FABP4 enforces adipocyte cell identity by driving the initial cell differentiation process

How progenitor cells can attain a distinct differentiated cell identity is a challenging problem given that critical transcription factors are often not unique to a differentiation process and the fluctuating signaling environment in which cells exist. 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 upregulating FABP4, a lipid buffer that is highly enriched in mature adipocytes. Upon induction of adipogenesis, 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 binds to and 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. HIGHLIGHTSO_LIFatty-acid loaded FABP4 binds to and increases PPARG expression, thereby turning on PPARG positive feedback loops that further increase PPARG expression. C_LIO_LIFABP4 critically controls the second phase of adipogenesis between activation of the feedback loops and reaching the threshold to differentiate. C_LIO_LIOnly a small fraction ([~]10%) of the FABP4 levels typically attained in mature fat cells is needed to commit cells to the differentiated state, thus providing an explanation for why maintenance of the mature adipocyte state is so robust. C_LI

cell biology↗

bioRxiv2019

A memory of RPS25 loss drives resistance phenotypes

In order to maintain cellular protein homeostasis, ribosomes are safeguarded against dysregulation by myriad processes. Many cell types can nonetheless withstand genetic lesions of certain ribosomal protein genes, some of which are linked to diverse cellular phenotypes and human disease. However, the direct and indirect consequences from sustained alterations in ribosomal protein levels are poorly understood. To address this knowledge gap, we studied in vitro and cellular consequences that follow genetic knockout of the ribosomal proteins RPS25 or RACK1 in a human cell line, as both proteins are implicated in direct translational control. Prompted by the unexpected detection of an off-target ribosome alteration in the RPS25 knockout, we closely interrogated cellular phenotypes. We found that multiple RPS25 knockout clones display viral- and toxin-resistance phenotypes that cannot be rescued by functional cDNA expression, suggesting that RPS25 loss elicits a cell state transition. We characterized this state and found that it underlies pleiotropic phenotypes and has a common rewiring of gene expression. Rescuing RPS25 expression by genomic locus repair failed to correct for the phenotypic and expression hysteresis. Our findings illustrate how the elasticity of cells to a ribosome perturbation can drive specific phenotypic outcomes that are indirectly linked to translation.

molecular biology↗

bioRxiv2019

Stochastic and coincident control of terminal cell differentiation and cell cycle exit

Terminal differentiation is essential for the development and maintenance of tissues in all multi-cellular organisms and is associated with a permanent exit from the cell cycle. Failure to permanently exit the cell cycle can result in cancer and disease. However, the molecular mechanisms and timing that coordinates differentiation commitment and cell cycle exit are not yet understood. Here using adipogenesis as a model system to track differentiation commitment in live cells, we show that a rapid switch mechanism engages exclusively in G1 to trigger a simultaneous commitment to differentiate and permanently exit from the cell cycle. We identify a signal integration mechanism whereby the strengths of both mitogen and differentiation stimuli control a molecular competition between cyclin D1 and PPARG-induced expression of the CDK inhibitor p21 which in turn regulates if and when the differentiation switch is triggered and when the proliferative window closes. In this way, the differentiation control system is able to couple mitogen and differentiation stimuli to sustain a long-term balance between terminally differentiating cells and maintaining the progenitor cell pool, a parameter of critical importance for enabling proper development of tissue domains and organs. HIGHLIGHTSO_LIProgenitor cells both commit to terminally differentiate and permanently exit the cell cycle at a precise time in G1 as a result of a competition process that can last over multiple cell cycles. C_LIO_LIPositive-feedback driven expression of PPARG and the parallel induction of p21 triggers a rapid commitment to terminally differentiate and then maintains a postmitotic adipocyte state. C_LIO_LIOpposing mitogen and adipogenic signals are funneled into a molecular competition in G1 phase that controls if and when cells commit to differentiate, which in turn regulates the number of differentiated cells produced while allowing for the maintenance of sufficient progenitor cells. C_LI

cell biology↗

bioRxiv2019

Loss of adipocyte identity through synergistic repression of PPARγ by TGF-β and mechanical stress

Adipocytes convert into myofibroblasts in a TGF-{beta}-dependent mouse model of fibrosis. The molecular steps and timing underlying this conversion are poorly understood, hindering development of antifibrotic therapies. Here we used two single-cell approaches, lineage tracing and live-cell imaging of an adipocyte marker PPAR{gamma}, to track the fate of adipocytes induced to convert by TGF-{beta}. We found that TGF-{beta} alone was not sufficient to activate the TGF-{beta} pathway and to induce myofibroblast conversion in cells with high PPAR{gamma} expression. However, robust conversion was observed when an additional PPAR{gamma}-inhibiting stimulus, mechanical stress applied by increasing adhesion area on a stiff matrix, was applied simultaneously with TGF-{beta}. We show that the PPAR{gamma} downregulation in response to increased adhesion area required both fibronectin and a sufficiently stiff extracellular matrix (ECM) and was partially mediated by Rho. Our results show for the first time the order of the molecular processes driving fat tissue fibrosis and the requirement for signal convergence for the loss of adipocyte identity.

cell biology↗

bioRxiv2018

Transcription factor dynamics reveals a circadian code for fat cell differentiation

Glucocorticoid and other adipogenic hormones are secreted in mammals in circadian oscillations. Loss of this circadian oscillation pattern during stress and disease correlates with increased fat mass and obesity in humans, raising the intriguing question of how hormone secretion dynamics affect the process of adipocyte differentiation. By using live, single-cell imaging of the key adipogenic transcription factors CEBPB and PPARG, endogenously tagged with fluorescent proteins, we show that pulsatile circadian hormone stimuli are rejected by the adipocyte differentiation control system, leading to very low adipocyte differentiation rates. In striking contrast, equally strong persistent signals trigger maximal differentiation. We identify the mechanism of how hormone oscillations are filtered as a combination of slow and fast positive feedback centered on PPARG. Furthermore, we confirm in mice that flattening of daily glucocorticoid oscillations significantly increases the mass of subcutaneous and visceral fat pads. Together, our study provides a molecular mechanism for why stress, Cushings disease, and other conditions for which glucocorticoid secretion loses its pulsatility can lead to obesity. Given the ubiquitous nature of oscillating hormone secretion in mammals, the filtering mechanism we uncovered may represent a general temporal control principle for differentiation.\n\nHIGHLIGHTO_LIWe found that the fraction of differentiated cells is controlled by rhythmic and pulsatile hormone stimulus patterns.\nC_LIO_LITwelve hours is the cutoff point for daily hormone pulse durations below which cells fail to differentiate, arguing for a circadian code for hormone-induced cell differentiation.\nC_LIO_LIIn addition to fast positive feedback such as between PPARG and CEBPA, the adipogenic transcriptional architecture requires added parallel slow positive feedback to mediate temporal filtering of circadian oscillatory inputs\nC_LI

cell biology↗

bioRxiv2018

Expression variation and covariation impair analog and enable binary signaling control

Due to noise in the synthesis and degradation of proteins, the concentrations of individual vertebrate signaling proteins were estimated to vary with a coefficient of variation (CV) of approximately 25% between cells. This high variation enables population-level regulation of cell functions but abolishes accurate single-cell signal transmission. Here we measure cell-to-cell variability of relative protein abundance using quantitative proteomics of individual Xenopus laevis eggs and cultured human cells and show that variation is typically much lower, in the range of 5-15%, compatible with accurate single-cell transmission. Furthermore, we show that MEK and ERK expression covary which improves controllability of the fraction of cells that activate bimodal ERK signaling, arguing that covariation has a role in facilitating population-level control of binary cell-fate decisions. Together, our experimental and model data argues for a control principle whereby low covariation limits signaling noise for accurate control analog single-cell signaling. In contrast, increased covariation widens the stimulus-range over which external inputs can regulate binary cell activation, thereby enabling accurate control of the fraction of activated cells at the population level.

systems biology↗