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1.  Model Discrimination in Dynamic Molecular Systems: Application to Parotid De-differentiation Network 
Journal of Computational Biology  2013;20(7):524-539.
Abstract
In modern systems biology the modeling of longitudinal data, such as changes in mRNA concentrations, is often of interest. Fully parametric, ordinary differential equations (ODE)-based models are typically developed for the purpose, but their lack of fit in some examples indicates that more flexible Bayesian models may be beneficial, particularly when there are relatively few data points available. However, under such sparse data scenarios it is often difficult to identify the most suitable model. The process of falsifying inappropriate candidate models is called model discrimination. We propose here a formal method of discrimination between competing Bayesian mixture-type longitudinal models that is both sensitive and sufficiently flexible to account for the complex variability of the longitudinal molecular data. The ideas from the field of Bayesian analysis of computer model validation are applied, along with modern Markov Chain Monte Carlo (MCMC) algorithms, in order to derive an appropriate Bayes discriminant rule. We restrict attention to the two-model comparison problem and present the application of the proposed rule to the mRNA data in the de-differentiation network of three mRNA concentrations in mammalian salivary glands as well as to a large synthetic dataset derived from the model used in the recent DREAM6 competition.
doi:10.1089/cmb.2011.0222
PMCID: PMC3704053  PMID: 23829652
parotid dedifferentiation; ODE model; parameter estimation; Bayesian factor
2.  ZEB1 Imposes a Temporary Stage-Dependent Inhibition of Muscle Gene Expression and Differentiation via CtBP-Mediated Transcriptional Repression 
Molecular and Cellular Biology  2013;33(7):1368-1382.
Skeletal muscle development is orchestrated by the myogenic regulatory factor MyoD, whose activity is blocked in myoblasts by proteins preventing its nuclear translocation and/or binding to G/C-centered E-boxes in target genes. Recent evidence indicates that muscle gene expression is also regulated at the cis level by differential affinity for DNA between MyoD and other E-box binding proteins during myogenesis. MyoD binds to G/C-centered E-boxes, enriched in muscle differentiation genes, in myotubes but not in myoblasts. Here, we used cell-based and in vivo Drosophila, Xenopus laevis, and mouse models to show that ZEB1, a G/C-centered E-box binding transcriptional repressor, imposes a temporary stage-dependent inhibition of muscle gene expression and differentiation via CtBP-mediated transcriptional repression. We found that, contrary to MyoD, ZEB1 binds to G/C-centered E-boxes in muscle differentiation genes at the myoblast stage but not in myotubes. Its knockdown results in precocious expression of muscle differentiation genes and acceleration of myotube formation. Inhibition of muscle genes by ZEB1 occurs via transcriptional repression and involves recruitment of the CtBP corepressor. Lastly, we show that the pattern of gene expression associated with muscle differentiation is accelerated in ZEB1−/− mouse embryos. These results set ZEB1 as an important regulator of the temporal pattern of gene expression controlling muscle differentiation.
doi:10.1128/MCB.01259-12
PMCID: PMC3624276  PMID: 23339872
3.  Cell-Specific Phosphorylation of Zfhep Transcription Factor 
Zinc finger homeodomain enhancer-binding protein (Zfhep/Zfhx1a) is a transcription factor essential for immune system development, skeletal patterning, and life. Regulation of the interleukin 2 gene in T cells has been suggested to depend on post-translational processing of Zfhep, however, no modifications of Zfhep are known. Here we demonstrate that Zfhep is present in both hyperphosphorylated and hypophosphorylated forms. Western analysis demonstrates two forms of Zfhep with different mobilities. Differences in phosphorylation are sufficient to explain the difference in mobilities. Zfhep is primarily phosphorylated on Ser and Thr residues since PP2A dephosphorylates the slower mobility band. Treatment of nuclear extract with O-GlcNAcase did not detect O-linked sugar. Importantly, post-translational processing is cell-specific. Doublets of Zfhep were detected in five cell lines, whereas 6 cell lines contain only, or predominantly, non-phosphorylated Zfhep, and Saos-2 cells contain predominantly the phosphorylated form. These data provide the first demonstration that Zfhep is post-translationally modified.
PMCID: PMC3682420  PMID: 12163027
ZEB; deltaEF1; AREB6; Zfhx1a; phosphatase 2A; vomitoxin; COS; C2C12; CHO
4.  Expression of Zfhep/δEF1 protein in palate, neural progenitors, and differentiated neurons 
Gene expression patterns : GEP  2003;3(6):709-717.
Zfhep/δEF1 is essential for embryonic development. We have investigated the expression pattern of Zfhep protein during mouse embryogenesis. We show expression of Zfhep in the mesenchyme of the palatal shelves, establishing concordance of expression with the reported cleft palate of the δEF1-null mice. Zfhep protein is strongly expressed in proliferating progenitors of the nervous system. In most regions of the brain, post-mitotic cells stop expressing Zfhep when they migrate out of the ventricular zone and differentiate. However, in the hindbrain, Zfhep protein is also highly expressed in post-mitotic migratory neuronal cells of the precerebellar extramural stream that arise from the neuroepithelium adjacent to the lower rhombic lip. Also, Zfhep is expressed as cells migrate from a narrow region of the pons ventricular zone towards the trigeminal nucleus. Co-expression with Islet1 shows that Zfhep is expressed in motor neurons of the trigeminal nucleus of the pons, but not in the inferior olive motor neurons at E12.5. Therefore, Zfhep is strongly expressed in a tightly regulated pattern in proliferating neural stem cells and a subset of neurons. Zfhep protein is also strongly expressed in trigeminal ganglia, and is moderately expressed in other cranial ganglia. In vitro studies have implicated Zfhep as a repressor of myogenesis, however, we find that Zfhep protein expression increases during muscle differentiation.
PMCID: PMC3682426  PMID: 14643678
AREB6; brain nuclei; cleft; cleft palate; cranial ganglia; delta EF-1; ganglion; heart; hindbrain; medulla; muscle; myogenesis; migration; neurogenesis; neurogenin; pons; pontine nucleus; precerebellar; rhombic lip; trigeminal; ventricular zone; ZEB; Zfhx1a
5.  Combination of a Zinc Finger and Homeodomain Required for Protein-Interaction 
Molecular biology reports  2003;30(4):199-206.
The Zinc Finger Homeodomain Enhancer-binding Protein (Zfhep) is involved in skeletal patterning, immune cell, muscle, and brain development, and is necessary for life. Zfhep contains a single central homeodomain (HD) adjacent to an isolated zinc finger, the function of which is unknown. The placement of a zinc finger so close to a homeodomain is novel in nature. The aim of this work was to characterize the Zfhep homeodomain (HD) or the zinc finger homeodomain (ZHD), with respect to DNA-binding and protein-protein interactions. Glutathione-S-transferase (GST) fusion proteins containing either just the HD or both the zinc finger and HD (ZHD) were expressed in E. coli. The GST fusion protein affinity-binding assay demonstrated that Zfhep ZHD interacts specifically with the POU domain of the Oct-1 transcription factor. The adjacent zinc finger is required since Zfhep HD alone does not interact with Oct-1 POU domain. Furthermore, ZHD does not bind to the POU homeodomain lacking the POU specific region. These results demonstrate that the Zfhep zinc finger homeodomain motif functions as a protein-binding domain in vitro, and suggests that Zfhep may modulate the activity of POU domain transcription factors. However, neither the Zfhep ZHD nor the HD bound DNA in EMSA or selected a DNA-binding site from a pool of random oligonucleotides. This is the first demonstration of a function for the HD region of Zfhep, which is the first case of a bi-partite domain requiring both a zinc finger and a HD for binding to protein.
PMCID: PMC3675762  PMID: 14672405
AREB6; Oct-1; POU domain; Zfhep; ZEB; deltaEF1
6.  Zeb1 Represses Mitf and Regulates Pigment Synthesis, Cell Proliferation and Epithelial Morphology 
PURPOSE
Epithelial-mesenchymal transition (EMT) is important in fibrotic responses, formation of cancer stem cells and acquisition of a metastatic phenotype. Zeb1 represses epithelial specification genes to enforce epithelial-mesenchymal phenotypic boundaries during development, and it is one of several E-box-binding repressors whose overexpression triggers EMT. Our purpose was to investigate the potential role for Zeb1 in the EMT leading to dedifferentiation of retinal pigment epithelial (RPE) cells.
METHODS
Real time PCR was used to examine mRNA expression during RPE dedifferentiation in primary cultures of RPE cells from Zeb1(+/−) mice and following knockdown of Zeb1 by lentivirus shRNA. Chromatin Immunoprecipitation was used to detect Zeb1 a gene promoters in vivo.
RESULTS
Zeb1 is overexpressed during RPE dedifferentiation. Heterozygous mutation or shRNA knockdown to prevent this overexpression eliminates the onset of proliferation and the EMT which characterizes RPE dedifferentiation. One role of Zeb1 in this process is to bind directly to the Mitf promoter and repress its transcription. We link Zeb1 expression to cell-cell contact, and demonstrate that forcing dedifferentiated RPE cells to adopt cell-cell only contacts via sphere formation reverses overexpression of Zeb1 and reprograms RPE cells back to a normal phenotype.
CONCLUSION
Overexpression of the EMT transcription factor Zeb1 has an important role in RPE dedifferentiation via its regulation of Mitf and other epithelial specification genes. Expression of Zeb1, and in turn RPE dedifferentiation, is linked to cell-cell contact, and these contacts can be utilized to diminish Zeb1 expression and reprogram dedifferentiated RPE cells.
doi:10.1167/iovs.08-2911
PMCID: PMC3648851  PMID: 19515996
7.  A NOTCH3-mediated squamous cell differentiation program limits expansion of EMT competent cells that express the ZEB transcription factors 
Cancer research  2011;71(21):6836-6847.
Zinc finger E-box binding (ZEB) proteins ZEB1 and ZEB2 are transcription factors essential in transforming growth factor (TGF)-β-mediated senescence, epithelial to mesenchymal transition (EMT) and cancer stem cell function. ZEBs are negatively regulated by members of the miR-200 microRNA family, but precisely how tumor cells expressing ZEBs emerge during invasive growth remains unknown. Here we report that NOTCH3-mediated signaling prevents expansion of a unique subset of ZEB-expressing cells. ZEB expression was associated with the lack of cellular capability of undergoing NOTCH3-mediated squamous differentiation in human esophageal cells. Genetic inhibition of the Notch-mediated transcriptional activity by dominant-negative Mastermind-like1 (DNMAML1) prevented squamous differentiation and induction of Notch target genes including NOTCH3. Moreover, DNMAML1 enriched EMT competent cells exhibited robust upregulation of ZEBs, downregulation of the miR-200 family, and enhanced anchorage independent growth and tumor formation in nude mice. RNA interference (RNAi) experiments suggested the involvement of ZEBs in anchorage independent colony formation, invasion and TGF-β-mediated EMT. Invasive growth and impaired squamous differentiation was recapitulated upon Notch inhibition by DNMAML1 in organotypic 3D culture, a form of human tissue engineering. Together, our findings indicate that NOTCH3 is a key factor limiting the expansion of ZEB-expressing cells, providing novel mechanistic insights into the role of Notch signaling in the cell fate regulation and disease progression of squamous esophageal cancers.
doi:10.1158/0008-5472.CAN-11-0846
PMCID: PMC3206139  PMID: 21890822
Notch; EMT; squamous cell differentiation; ZEB1; miR-200
8.  Cell Type–Specific Transcriptome Analysis Reveals a Major Role for Zeb1 and miR-200b in Mouse Inner Ear Morphogenesis 
PLoS Genetics  2011;7(9):e1002309.
Cellular heterogeneity hinders the extraction of functionally significant results and inference of regulatory networks from wide-scale expression profiles of complex mammalian organs. The mammalian inner ear consists of the auditory and vestibular systems that are each composed of hair cells, supporting cells, neurons, mesenchymal cells, other epithelial cells, and blood vessels. We developed a novel protocol to sort auditory and vestibular tissues of newborn mouse inner ears into their major cellular components. Transcriptome profiling of the sorted cells identified cell type–specific expression clusters. Computational analysis detected transcription factors and microRNAs that play key roles in determining cell identity in the inner ear. Specifically, our analysis revealed the role of the Zeb1/miR-200b pathway in establishing epithelial and mesenchymal identity in the inner ear. Furthermore, we detected a misregulation of the ZEB1 pathway in the inner ear of Twirler mice, which manifest, among other phenotypes, malformations of the auditory and vestibular labyrinth. The association of misregulation of the ZEB1/miR-200b pathway with auditory and vestibular defects in the Twirler mutant mice uncovers a novel mechanism underlying deafness and balance disorders. Our approach can be employed to decipher additional complex regulatory networks underlying other hearing and balance mouse mutants.
Author Summary
The mammalian inner ear is a highly complex sensory organ, and mutations in more than 100 genes underlie hereditary human non-syndromic hearing loss. Nevertheless, little is known about the signaling cascades downstream of deafness genes. Genome-wide expression profiling is an invaluable tool for gaining systems-level understanding of biological processes. We developed and validated a simple and novel protocol to isolate sensory epithelial cells, neurons, blood vessels, and mesenchyme of auditory and vestibular epithelia from newborn wild-type mice. Our protocol is based on flow cytometry to sort and capture cells labeled with commercially available antibodies to endogenously expressed cluster of differentiation (CD) antigens. Using this strategy, we identified Zeb1 and miR200b as regulators of epithelial and mesenchymal identity in the mouse inner ear, and we further identified the signaling pathway disrupted by the Zeb1 mutation in the Twirler mouse mutant. We also show the utility of this approach for characterizing compartment-specific genes and protein–protein networks. Implementation of this isolation strategy to study other mouse mutants with hearing and balance phenotypes could overcome many of the obstacles to understanding the function of deafness genes.
doi:10.1371/journal.pgen.1002309
PMCID: PMC3183091  PMID: 21980309
9.  Mesenchymal cell re-modeling during mouse secondary palate re-orientation 
The formation of mammalian secondary palate requires a series of developmental events such as growth, elevation and fusion. Despite recent advances in the field of palate development, the process of palate elevation remains poorly understood. The current consensus on palate elevation is that the distal end of the vertical palatal shelf corresponds to the medial edge of the elevated horizontal palatal shelf. We provide evidence suggesting that the prospective medial edge of the vertical palate is located toward the interior side (the side adjacent to the tongue), instead of the distal end, of the vertical palatal shelf and that the horizontal palatal axis is generated through palatal outgrowth from the side of the vertical palatal shelf rather than rotating the pre-existing vertical axis orthogonally. Since palate elevation represents a classical example of embryonic tissue re-orientation, our findings here may also shed light on the process of tissue re-orientation in general.
doi:10.1002/dvdy.22339
PMCID: PMC2919369  PMID: 20549719
palate development; palate elevation; tissue re-orientation
10.  The ZFHX1A Gene Is Differentially Autoregulated By Its Isoforms 
The Zfhx1a gene expresses two different isoforms; the full length Zfhx1a-1 and a truncated isoform termed Zfhx1a-2 lacking the first exon. Deletion analysis of the Zfhx1a-1 promoter localized cell-specific repressors, and a proximal G-string that is critically required for transactivation. Transfection of Zfhx1a-1 cDNA, but not Zfhx1a -2, downregulates Zfhx1a-1 promoter activity. Mutation of an E2-box disrupted the binding of both Zfhx1a isoforms. Consistent with this, transfected Zfhx1a-1 does not regulate the transcriptional activity of the E-box mutated Zfhx1a-1 promoter. Competitive EMSAs and transfection assays show that Zfhx1a-2 can function as a dominant negative isoform since it is able to compete and displace Zfhx1a-1 from its binding site and overcome Zfhx1a-1 induced repression of the Zfhx1a-1 promoter in cells. Hence, the Zfhx1a-1 gene is autoregulated in part by negative feedback on its own promoter which is, in turn, modified by the availability of the negative dominant isoform Zfhx1a-2.
doi:10.1016/j.bbrc.2007.06.088
PMCID: PMC2770808  PMID: 17610840
Zfhep/ZEB1/δEF1; autoregulation; gene regulation; promoter characterization
11.  Analysis of Zfhx1a mutant mice reveals palatal shelf contact independent medial edge epithelial differentiation during palate fusion 
Cell and tissue research  2008;333(1):29-38.
Cleft palate is a common birth defect that involves disruptions in multiple developmental steps such as growth, differentiation, elevation and fusion. Medial edge epithelial (MEE) differentiation is essential for palate fusion. An important question is that the MEE differentiation during fusion is induced by palate shelf contact or is programmed intrinsically by the palate shelf itself. Here, we report that the loss of Zfhx1a function in mice leads to a cleft palate phenotype that is mainly due to a delay in palate elevation. Zfhx1a encodes a transcription regulatory protein that modulates several signaling pathways including those activated by members of the TGF-β superfamily. Loss of Zfhx1a function in mice leads to a complete cleft palate with 100% penetrance. Zfhx1a mutant palatal shelves display normal cell differentiation and proliferation and are able to fuse in an in vitro culture system. The only defect detected was a 24–48 hour delay in palatal shelf elevation. Using the Zfhx1a mutant as a model, we studied the relationship between medial edge epithelial differentiation and palate contact/adhesion. We found that down regulation of Jag2 expression in the medial edge epithelial cells, a key differentiation event establishing palate fusion competence is independent of palate contact/adhesion. Moreover, the expression of several key factors essential for fusion, such as TGF-β3 and MMP13, are also down regulated at stage E16.5 in a contact independent manner, suggesting that differentiation of the medial edge epithelium is largely programmed through an intrinsic mechanism within the palate shelf.
doi:10.1007/s00441-008-0612-x
PMCID: PMC2516965  PMID: 18470539
mouse secondary palate; Zfhx1a mutant mice; palate elevation; MEE differentiation; cleft palate
12.  Zeb1 Mutant Mice as a Model of Posterior Corneal Dystrophy 
Purpose
The zinc finger transcription factor, Zeb1, binds to E-box like sequences and is important for maintaining repression of epithelial specification genes in vivo. Overexpression of Zeb1 in cancer triggers epithelial-mesenchymal transition, which facilitates metastasis. Mutation of ZEB1 in humans is linked to posterior polymorphous corneal dystrophy (PPCD), where an epithelial transition of the corneal endothelium is associated with abnormal endothelial proliferation. The purpose of this study is to determine whether Zeb1 null or heterozygous mice may provide an animal model for PPCD.
Methods
Corneal morphology, protein and mRNA expression and cell proliferation were compared in wild-type and Zeb1 gene knockout mice by immunostaining, real time PCR and BrdU incorporation. mRNA expression in isolated embryo fibroblasts derived from wild-type, Zeb1 heterozygous and null mice was analyzed by real time PCR
Results
Zeb1 null mice late in gestation show ectopic expression of epithelial genes in the corneal endothelium and keratocytes, including the basement membrane component, COL4A3, which is ectopically expressed by the corneal endothelium in PPCD. These embryos also show abnormal corneal endothelial and keratocyte proliferation, corneal thickening, and corneolenticular and iridocorneal adhesions. Adult Zeb1 heterozygous mice exhibit these same corneal defects. The ectopic expression of epithelial genes extended to embryonic fibroblasts derived from Zeb1 heterozygous and null mice, suggesting that Zeb1 may have a more general role in suppression of an epithelial phenotype.
Conclusions
We conclude that Zeb1 heterozygous and null mice show features of PPCD, and thus should provide an animal model for genetic dissection of pathways contributing to the disease.
doi:10.1167/iovs.07-0789
PMCID: PMC2504018  PMID: 18436818
13.  ZEB1 Links Epithelial-Mesenchymal Transition and Cellular Senescence 
Development (Cambridge, England)  2008;135(3):579-588.
Overexpression of zinc finger E-box binding homeobox transcription factor 1 (ZEB1) in cancer leads to epithelial-to-mesenchymal transition (EMT) and increased metastasis. As opposed to overexpression, we show that mutation of the ZEB1 gene in mice causes a mesenchymal-epithelial transition in gene expression characterized by ectopic expression of epithelial genes such as E-cadherin and loss of expression of mesenchymal genes such as vimentin. And in contrast to rapid proliferation in cancer cells where ZEB1 is overexpressed, this mesenchymal-epithelial transition in mutant mice is associated with diminished proliferation of progenitor cells at sites of development defects including the forming palate, skeleton and CNS. ZEB1 gene dosage-dependent deregulation of epithelial and mesenchymal genes extends to mouse embryonic fibroblasts (MEFs), and mutant MEFs also display diminished replicative capacity in culture, leading to premature senescence. Replicative senescence in MEFs is classically triggered by products of the INK4a gene. However, this INK4a pathway is not activated during senescence of ZEB1 gene mutant MEFs. Instead, there is ectopic expression of two other cell cycle inhibitory cyclin dependent kinase inhibitors, p15INK4b and p21CDKN1a. And, we demonstrated that this ectopic expression of p15INK4b extends in vivo to sites of diminished progenitor cell proliferation and developmental defects in ZEB1 gene null mice.
doi:10.1242/dev.007047
PMCID: PMC2507753  PMID: 18192284
14.  ISOPROTERENOL INCREASES SORTING OF PAROTID GLAND CARGO PROTEINS TO THE BASOLATERAL PATHWAY 
Exocrine cells have an essential function of sorting secreted proteins into the correct secretory pathway. A clear understanding of sorting in salivary glands would contribute to the correct targeting of therapeutic transgenes. The present work investigated whether there is a change in the relative proportions of basic PRP and acidic PRPs in secretory granules in response to chronic isoproterenol treatment, and whether this alters the sorting of endogenous cargo proteins. Immunoblotting of secretory granules from rat parotids found a large increase of basic PRP over acidic PRPs in response to chronic isoproterenol treatment. Pulse chase experiments demonstrated that isoproterenol also decreased regulated secretion of newly synthesized secretory proteins, including PRPs, amylase and parotid secretory protein. This decreased efficiency of the apical regulated pathway may be mediated by alkalization of the secretory granules since it was reversed by treatment with mild acid. We also investigated changes in secretion through the basolateral (endocrine) pathways. A significant increase in parotid secretory protein and salivary amylase was detected in sera of isoproterenol-treated animals suggesting increased routing of the regulated secretory proteins to the basolateral pathway. These studies demonstrate that shifts of endogenous proteins can modulate regulated secretion and sorting of cargo proteins.
doi:10.1152/ajpcell.00081.2007
PMCID: PMC2084485  PMID: 17537806
amylase; parotid secretory protein; polarized secretion; parotid gland; sorting

Results 1-14 (14)