Jianhua Xing | University of Pittsburgh (original) (raw)

Papers by Jianhua Xing

arXiv: Tissues and Organs, 2018

Repair of ischemic tissue injury by Wnt-mediated self-renewal and myofibroblasts expansion repres... more Repair of ischemic tissue injury by Wnt-mediated self-renewal and myofibroblasts expansion represents a trade-off because myofibroblasts can promote chronic fibrosis. We used a cell interaction network model to analyze the double-edged effect of Wnt-signaling in mouse ischemic kidney disease. The model predicts multistable dynamics that mapped to three distinct outcomes observed in surviving mice as a function of insult severity: full recovery, recovery with residual and chronic fibrosis. Furthermore we predicted and experimentally verified protective effect of preconditioning by mild ischemia at the cost of fibrosis risk. The model allowed for multi-objective optimization to overcome the trade-off between rapid repair and chronification and guided a successful biphasic treatment with Wnt-agonist followed by Wnt-antagonist. The results underscore the importance of non-linear disease dynamics and propose a non-monotonic targeted therapy by phasic blockade and activation of the same t...

Biological systems need robust mechanism to recover from injury. Increasing evidences suggest tha... more Biological systems need robust mechanism to recover from injury. Increasing evidences suggest that incomplete recovery of acute kidney injury (AKI) increases the risk of chronic kidney diseases (CKD), but it remains ambiguous how AKI and CKD, traditionally treated as two distinct pathological entities, are mechanistically related. With different durations of ischemia-reperfusion injury in mice, we identified a unified repair process that leads to perfect or imperfect adaptive response, or maladaptive response and even death depending on injury severity. Our mathematical modeling revealed that these multi-state outcomes result from a trade-off between two functional requirements imposed on the repair system, fast recovery to reduce the risk of immediate organ failure and organism death, and complete resolution to reduce the risk of CKD. Subsequent experiments confirmed this trade-off mechanism, and demonstrated that targeting the temporal dynamics, instead of traditional monotonic me...

Phenotype transition takes place in many biological processes such as differentiation, and unders... more Phenotype transition takes place in many biological processes such as differentiation, and understanding how a cell reprograms its global gene expression profile is a problem of rate theories. A cell phenotype transition accompanies with switching of expression rates of clusters of genes, analogous to domain flipping in an Ising system. Here through analyzing single cell RNA sequencing data in the framework of transition path theory, we set to study how such a genome-wide expression program switching proceeds in three different cell transition processes. For each process after reconstructing a Markov transition model in the cell state space, we formed an ensemble of shortest paths connecting the initial and final cell states, reconstructed a reaction coordinate describing the transition progression, and inferred the gene regulation network (GRN) along the reaction coordinate. In all three processes we observed common pattern that the frustration of gene regulatory network (GRN), def...

arXiv: Molecular Networks, 2012

How do mammalian cells that share the same genome exist in notably distinct phenotypes, exhibitin... more How do mammalian cells that share the same genome exist in notably distinct phenotypes, exhibiting differences in morphology, gene expression patterns, and epigenetic chromatin statuses? Furthermore how do cells of different phenotypes differentiate reproducibly from a single fertilized egg? These fundamental questions are closely related to a deeply rooted paradigm in developmental biology that cell differentiation is irreversible. Yet, recently a growing body of research suggests the possibility of cell reprogramming, which offers the potential for us to convert one type of cell into another. Despite the significance of quantitative understandings of cell reprogramming, theoretical efforts often suffer from the complexity of large circuits maintaining cell phenotypes coupled at many different epigenetic and gene regulation levels. To capture the global architecture of cell phenotypes, we propose an "epigenetic state network" approach that translates the classical concept...

Science Advances, 2020

Live-cell imaging in multidimensional feature space reveals parallel transition paths of epitheli... more Live-cell imaging in multidimensional feature space reveals parallel transition paths of epithelial-to-mesenchymal transition.

ABSTRACTRecent advances in single cell techniques catalyze an emerging field of studying how cell... more ABSTRACTRecent advances in single cell techniques catalyze an emerging field of studying how cells convert from one phenotype to another, in a step-by-step process. Two grand technical challenges, however, impede further development of the field. Fixed cell-based approaches can provide genome-wide snapshots of cell status but have fundamental limits on revealing temporal information, and fluorescence-based live cell imaging approaches provide temporal information but are technically challenging for multiplex long- term imaging. We present a live-cell imaging platform, Multiplex Trajectory Recording and Analysis of Cellular Kinetics, or M-TRACK, that tracks cellular status change through combining endogenous fluorescent labeling that minimizes perturbation to cell physiology and live cell imaging of high-dimensional cell morphological and texture features. To test the functionality of our platform, we used the A549 VIM-RFP EMT reporter line (ATCC® CCL-185EMT) to explore cell phenotyp...

ABSTRACTCRISPR-based gene knock-in at endogenous sites is desirable in multiple fields such as qu... more ABSTRACTCRISPR-based gene knock-in at endogenous sites is desirable in multiple fields such as quantitative studies of signal transduction pathways and gene regulation, synthetic biology, and disease modeling. Contrasting the knock-out procedure, a key step of CRISPR knock-in procedure relies on the homology-directed repairing (HDR) process that requires a donor construct as repair template. Therefore, it is desirable to generate a series of donor DNA constructs efficiently and cost-effectively. In this study, we developed a general Gibson assembly procedure that combines strengths of a Modular Overlap-Directed Assembly with Linkers (MODAL) strategy and a restriction enzyme based hierarchical framework. This procedure also allows fusing sgRNAs to the constructs for enhanced homology-directed repairing efficiency. Experimental tests on multiple constructs achieved from 3-8 folds of increase in assembly efficiency to high yield of constructs that failed to make with conventional Gibso...

PLOS Computational Biology, 2019

Journal of the American Society of Nephrology : JASN, Jan 17, 2018

AKI is a devastating condition with high morbidity and mortality. The pathologic features of AKI ... more AKI is a devastating condition with high morbidity and mortality. The pathologic features of AKI are characterized by tubular injury, inflammation, and vascular impairment. Whether fibroblasts in the renal interstitium have a role in the pathogenesis of AKI is unknown. In this study, we investigated the role of fibroblast-specific β-catenin signaling in dictating the outcome of AKI, using conditional knockout mice in which β-catenin was specifically ablated in fibroblasts (Gli1-β-cat-/-). After ischemia-reperfusion injury (IRI), Gli1-β-cat-/- mice had lower serum creatinine levels and less morphologic injury than Gli1-β-cat+/+ littermate controls. Moreover, we detected fewer apoptotic cells, as well as decreased cytochrome C release; reduced expression of Bax, FasL, and p53; and increased phosphorylation of Akt, in the Gli1-β-cat-/- kidneys. Gli1-β-cat-/- kidneys also exhibited upregulated expression of proliferating cell nuclear antigen and Ki-67, which are markers of cell prolifer...

The detection and transmission of the temporal quality of intracellular and extracellular signals... more The detection and transmission of the temporal quality of intracellular and extracellular signals is an essential cellular mechanism. It remains largely unexplored how cells interpret the duration information of a stimulus. In this paper, through an integrated quantitative and computational approach we demonstrate that crosstalk among multiple TGF-β activated pathways forms a relay from SMAD to GLI1 that initializes and maintains SNAILl expression, respectively. This transaction is smoothed and accelerated by another temporal switch from elevated cytosolic GSK3 enzymatic activity to reduced nuclear GSK3 enzymatic activity. The intertwined network places SNAIL1 as a key integrator of information from TGF-β signaling subsequently distributed through upstream divergent pathways; essentially cells generate a transient or sustained expression of SNAIL1 depending on TGF-β duration. Other signaling pathways may use similar network structure to encode duration information.

FEBS letters, Jan 31, 2016

miRNAs serve as crucial post-transcriptional regulators in a variety of essential cell fate decis... more miRNAs serve as crucial post-transcriptional regulators in a variety of essential cell fate decisions. However, the contribution of the mRNA-miRNA mutual regulation to bistability is not fully understood. Here, we built a set of mathematical models of mRNA-miRNA interactions and systematically analyzed the sensitivity of the response curves under various conditions. Our findings indicate that mRNA-miRNA reciprocal regulation could manifest ultrasensitivity to subserve the generation of bistability when equipped with a positive feedback loop. We also find that the region of bistability is expanded by a stronger competing endogenous mRNA (ceRNA). Interestingly, bistability can be generated without a feedback loop if multiple miRNA binding sites exist on a target mRNA. Thus, we demonstrate the importance of simple mRNA-miRNA reciprocal regulation in cell fate decisions. This article is protected by copyright. All rights reserved.

Proceedings of the National Academy of Sciences, 2016

Multiple-objective optimization is common in biological systems. In the mammalian olfactory syste... more Multiple-objective optimization is common in biological systems. In the mammalian olfactory system, each sensory neuron stochastically expresses only one out of up to thousands of olfactory receptor (OR) gene alleles; at the organism level, the types of expressed ORs need to be maximized. Existing models focus only on monoallele activation, and cannot explain recent observations in mutants, especially the reduced global diversity of expressed ORs in G9a/GLP knockouts. In this work we integrated existing information on OR expression, and constructed a comprehensive model that has all its components based on physical interactions. Analyzing the model reveals an evolutionarily optimized three-layer regulation mechanism, which includes zonal segregation, epigenetic barrier crossing coupled to a negative feedback loop that mechanistically differs from previous theoretical proposals, and a previously unidentified enhancer competition step. This model not only recapitulates monoallelic OR ...

Epigenetic Technological Applications, 2015

Science Signaling, 2014

Experimental and computational analyses identify multiple cell populations during the epithelial-... more Experimental and computational analyses identify multiple cell populations during the epithelial-to-mesenchymal transition.

Protein-Protein Interactions - Computational and Experimental Tools, 2012

arXiv: Tissues and Organs, 2018

arXiv: Molecular Networks, 2012

Science Advances, 2020

PLOS Computational Biology, 2019

Journal of the American Society of Nephrology : JASN, Jan 17, 2018

FEBS letters, Jan 31, 2016

Proceedings of the National Academy of Sciences, 2016

Epigenetic Technological Applications, 2015

Science Signaling, 2014

Protein-Protein Interactions - Computational and Experimental Tools, 2012

CRISPR-based gene knock-in at endogenous sites is desirable in multiple fields such as quantitati... more CRISPR-based gene knock-in at endogenous sites is desirable in multiple fields such as quantitative studies of signal transduction pathways and gene regulation, synthetic biology, and disease modeling. Contrasting the knock-out procedure, a key step of CRISPR knock-in procedure relies on the homology-directed repairing (HDR) process that requires a donor construct as repair template. Therefore, it is desirable to generate a series of donor DNA constructs efficiently and cost-effectively. In this study, we developed a general Gibson assembly procedure that combines strengths of a Modular Overlap-Directed Assembly with Linkers (MODAL) strategy and a restriction enzyme based hierarchical framework. This procedure also allows fusing sgRNAs to the constructs for enhanced homology-directed repairing efficiency. Experimental tests on multiple constructs achieved from 3-8 folds of increase in assembly efficiency to high yield of constructs that failed to make with conventional Gibson assembly. The modularized procedure is simple, fast and cost-effective while making multiple constructs, and a computer package is provided for customized design.

Targeting microenvironmental factors that foster migratory cell phenotypes is a promising strateg... more Targeting microenvironmental factors that foster migratory cell phenotypes is a promising strategy for halting tumor migration. However, lack of mechanistic understanding of the process impedes pharmaceutical drug development. Using a novel 3D microtumor model with tight control over tumor size, we recapitulated tumor size-induced hypoxic microenvironment and emergence of migratory phenotypes in epithelial T47D breast microtumors as well as those of patient-derived primary metastatic breast cancer cells, mesothelioma cells and lung cancer xenograft cells (PDX). The microtumor models from various patient-derived tumor cells and PDX cells revealed upregulation of tumor secretome, matrix metalloproteinase-9 (MMP9), fibronectin (FN), and soluble E-cadherin (sE-CAD) consistent with the clinically reported elevated levels of FN and MMP9 in the patient breast tumors compared to healthy mammary gland. We further showed that the tumor secretome induces migratory phenotype in non-hypoxic, non-migratory small microtumors. Subsequent mathematical model analysis identified a two-stage microtumor progression and migration mechanism, i.e., hypoxia induces migratory phenotype in the early initialization stage, which then becomes self-sustained through positive feedback loop established among the secretome. Both computational and experimental studies showed that inhibition of tumor secretome effectively halts microtumor migration despite tumor heterogeneity, while inhibition of the hypoxia is effective only within a time window and is compromised by tumor-to-tumor variation of the growth dynamics, supporting our notion that hypoxia initiates migratory phenotypes but does not sustain it. In summary, we show that targeting temporal dynamics of evolving microenvironments during tumor progression can halt and bypass major hurdle of tumor heterogeneity.

11 The detection and transmission of the strength and temporal quality of intracellular and 12 ex... more 11 The detection and transmission of the strength and temporal quality of intracellular and 12 extracellullar signals is an essential cellular mechanism. While TGF-β signaling is one of the 13 most thoroughly studied signaling pathways, the mechanisms by which cells translate TGF-β 14 signals remain unclear. In this paper, through an integrated quantitative and computational 15 approach we demonstrate that crosstalk among multiple TGF-β activated pathways forms a relay 16 from SMAD to GLI1 that initializes and maintains SNAILl expression, respectively. This 17 transaction is smoothed and accelerated by another temporal switch from elevated cytosolic 18 GSK3 enzymatic activity to reduced nuclear GSK3 enzymatic activity. This nested relay 19 mechanism places SNAIL1 as a key integrator of information from TGF-β signaling 20 subsequently distributed through divergent pathways; essentially cells generate a transient or 21 peer-reviewed)