A simple molecular model of neurulation

Transcription Factor Motifs Associated with Anterior Insula Gene Expression Underlying Mood Disorder Phenotypes

Mood disorders represent a major cause of morbidity and mortality worldwide but the brain-related molecular pathophysiology in mood disorders remains largely undefined. Because the anterior insula is reduced in volume in patients with mood disorders, RNA was extracted from the anterior insula postmortem anterior insula of mood disorder samples and compared with unaffected controls for RNA-sequencing identification of differentially expressed genes (DEGs) in (a) bipolar disorder (BD; n = 37) versus (vs.) controls (n = 33), and (b) major depressive disorder (MDD n = 30) vs. controls, and (c) low vs. high axis I comorbidity (a measure of cumulative psychiatric disease burden). Given the regulatory role of transcription factors (TFs) in gene expression via specific-DNA-binding domains (motifs), we used JASPAR TF binding database to identify TF-motifs. We found that DEGs in BD vs. controls, MDD vs. controls, and high vs. low axis I comorbidity were associated with TF-motifs that are known to regulate expression of toll-like receptor genes, cellular homeostatic-control genes, and genes involved in embryonic, cellular/organ, and brain development. Robust imaging-guided transcriptomics by using meta-analytic imaging results to guide independent postmortem dissection for RNA-sequencing was applied by targeting the gray matter volume reduction in the anterior insula in mood disorders, to guide independent postmortem identification of TF motifs regulating DEG. Our findings of TF-motifs that regulate the expression of immune, cellular homeostatic-control, and developmental genes provide novel information about the hierarchical relationship between gene regulatory networks, the TFs that control them, and proximate underlying neuroanatomical phenotypes in mood disorders.

A strategy for designing allosteric modulators of transcription factor dimerization

Transcription factors in the bHLH family are potentially relevant for tumor growth. Activation requires homodimerization or heterodimerization. Thus, the dimerization step is a likely significant drug target. The oligodendrocyte transcription factor 2 (OLIG2) is overexpressed in gliomas. Here, we developed a fluorescence cross-correlation spectroscopy protocol to examine 10 compounds selected using a pharmacophore-based computational strategy targeting OLIG2 dimerization. We showed that the potency to interact with OLIG2 dimerization in live cells correlates with carcinostatic efficacy. The data indicate a promising approach toward drug development targeting transcription factor overactivity and protein–protein interaction more generally.

Transcription factors (TFs) are fundamental in the regulation of gene expression in the development and differentiation of cells. They may act as oncogenes and when overexpressed in tumors become plausible targets for the design of antitumor agents. Homodimerization or heterodimerization of TFs are required for DNA binding and the association interface between subunits, for the design of allosteric modulators, appears as a privileged structure for the pharmacophore-based computational strategy. Based on this strategy, a set of compounds were earlier identified as potential suppressors of OLIG2 dimerization and found to inhibit tumor growth in a mouse glioblastoma cell line and in a whole-animal study. To investigate whether the antitumor activity is due to the predicted mechanism of action, we undertook a study of OLIG2 dimerization using fluorescence cross-correlation spectroscopy (FCCS) of live HEK cells transfected with 2 spectrally different OLIG2 clones. The selected compounds showed an effect with potency, which correlated with the earlier observed antitumor activity. The OLIG2 proteins showed change in diffusion time under compound treatment in line with dissociation from DNA. The data suggest a general approach of drug discovery based on the design of allosteric modulators of protein–protein interaction.

Model to Link Cell Shape and Polarity with Organogenesis

How do flat sheets of cells form gut and neural tubes? Across systems, several mechanisms are at play: cells wedge, form actomyosin cables, or intercalate. As a result, the cell sheet bends, and the tube elongates. It is unclear to what extent each mechanism can drive tube formation on its own. To address this question, we computationally probe if one mechanism, either cell wedging or intercalation, may suffice for the entire sheet-to-tube transition. Using a physical model with epithelial cells represented by polarized point particles, we show that either cell intercalation or wedging alone can be sufficient and that each can both bend the sheet and extend the tube. When working in parallel, the two mechanisms increase the robustness of the tube formation. The successful simulations of the key features in Drosophila salivary gland budding, sea urchin gastrulation, and mammalian neurulation support the generality of our results.

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Cell wedging and intercalation are modeled using a polarized point-particle approach

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Cell intercalation is sufficient for tube budding

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Tube budding is more robust when intercalation is complemented by wedging

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Wedging and differential proliferation are sufficient for mammalian neurulation

Climbing Brain Levels of Organisation from Genes to Consciousness

Given the tremendous complexity of brain organisation, here I propose a strategy that dynamically links stages of brain organisation from genes to consciousness, at four privileged structural levels: genes; transcription factors (TFs)-gene networks; synaptic epigenesis; and long-range connectivity. These structures are viewed as nested and reciprocally inter-regulated, with a hierarchical organisation that proceeds on different timescales during the course of evolution and development. Interlevel bridging mechanisms include intrinsic variation-selection mechanisms, which offer a community of bottom-up and top-down models linking genes to consciousness in a stepwise manner.

Interplay between Numb and Notch in epithelial cancers: role for dual oxidase maturation factor

Numb and Notch signalling pathways are vitally important in cell fate and differentiation. The outcome of these signalling processes is determined by a delicate balance between opposing effects of Notch and Numb. Imbalance in Numb/Notch regulation was implicated in aberrant differentiation programme and epithelial cancer progression and metastasis. Recent identification of Numb-interacting protein (NIP), which is also known as dual oxidase maturation factor, and was shown to associate with Numb and DUOX and promote their translocation, sheds a new light on how Numb/Notch network may be coordinated in epithelial cancers. Here, a possible link between Numb, Notch and Dual oxidase maturation factor is examined.

Tube formation in Drosophila egg chambers

The reorganization of epithelial sheets into tubes is a fundamental process in the formation of many organs, such as the lungs, kidneys, gut, and neural tube. This process involves the patterning of distinct cell types and the coordination of those cells during the shape changes and rearrangements that produce the tube. A better understanding of the cellular and genetic mechanisms that regulate tube formation is necessary for tissue engineers to develop functional organs in vitro. The Drosophila egg chamber has emerged as an outstanding model for studying tubulogenesis. Synthesis of the dorsal respiratory appendages by the follicular epithelium resembles primary neurulation in vertebrates. This review summarizes work on the patterning and morphogenesis of the dorsal-appendage tubes and highlights key areas where mathematical modeling could contribute to our understanding of these processes.

Simulated morphogenesis of developmental folds due to proliferative pressure

We present a simulation that models individual cells as spherical particles that can migrate, interact, divide and differentiate. We simulate the evolution of a progenitor layer of cells that reproduce, leading either to more progenitors or to differentiated daughters. We find that this simplified model produces spontaneous folds whose lengths depend linearly on the ratio of rates of production of progenitors to differentiated daughters. We also find that folds grow approximately exponentially in time, and that larger folds can be placed via patterning events that perturb the positions of selected progenitor cells early in the developmental process.

On multiscale approaches to three-dimensional modelling of morphogenesis

In this paper we present the foundation of a unified, object-oriented, three-dimensional biomodelling environment, which allows us to integrate multiple submodels at scales from subcellular to those of tissues and organs. Our current implementation combines a modified discrete model from statistical mechanics, the Cellular Potts Model, with a continuum reaction-diffusion model and a state automaton with well-defined conditions for cell differentiation transitions to model genetic regulation. This environment allows us to rapidly and compactly create computational models of a class of complex-developmental phenomena. To illustrate model development, we simulate a simplified version of the formation of the skeletal pattern in a growing embryonic vertebrate limb.

Establishment and maintenance of planar epithelial cell polarity by asymmetric cadherin bridges: A computer model

Animal scales, hairs, feathers, and cilia are oriented due to cell polarization in the epithelial plane. Genes involved have been identified, but the signal and mechanism remain unknown. In Drosophila wing polarization, the action of a gradient of Frizzled activity is widely assumed; and cell-cell signalling by cadherins such as Flamingo surely plays a major role. We present a computer model where reading the Frizzled gradient occurs through biased, feedback-reinforced formation of Flamingo-based asymmetric intercellular complexes. Through these complexes neighboring cells are able to compare their Frizzled activity levels. Our computations are highly noise-resistant and reproduce both wild-type and all known mutant wing phenotypes; other phenotypes are predicted. The model puts stringent limits on a Frizzled activation signal, which should exhibit unusual properties: (1) the extracellular Frizzled signalling gradient should be counterdirectional--decreasing from proximal (P) to distal (D), whereas during polarization, the intracellular Frizzled gradient builds up from P to D; (2) the external gradient should be relatively weak and short-lived, lest it prevent inversion of intracellular Frizzled. These features, largely independent of model details, may provide useful clues for future experimental efforts.

An analytical study of the number of steady states in gene regulatory networks

Herein, I proposed a model for gene networks and studied the steady states in the dynamics both by numerical and analytical methods. In this model, mRNA and protein levels change continuously with time; each gene alters transcriptional regulation depending on the concentration of transcription factors. The dynamical behavior of continuous model is quite complex and different from that of the discrete model, the Boolean network. Large portion of steady states of this model can be classified into three types. The rough structure of gene interactions, which corresponds to Boolean function, is sufficient to predict the expression level of each gene in these types of steady states. I also determined the expected numbers of two major types of steady states observed in a randomly generated gene network. The results obtained from these formulae contradict previously accepted belief. The results are that neither gene number nor connectivity between genes increases the expected number of steady states in a random gene network. The number of steady states is very small. The number of self-regulatory genes, however, effectively increases the number of steady states in a network. These results imply that increases in gene number may not be the direct driving force for the evolution of a variety of different cell types within organisms. Instead, the number of self-regulatory genes may significantly increase cellular diversity.

Noise, delays, robustness, canalization and all that

A biological system such as a developing embryo can withstand many perturbations. What is the basis of this robustness both against noise and mutation? Recent advances in modeling may throw new light on this old problem. First, recent theoretical and experimental work clearly demonstrates the importance of noise and time delays for the proper functioning of genetic networks: noise and delays are simply part of the normal operating constraints. By contrast, sweeping statements have been made recently about a so-called 'robustness' of biological processes, based on work that neglects noise and delays completely. I submit that studying the stability of complex biological systems with such omissions is an unnecessary, inadequate and potentially disastrous simplification. I review the existing alternatives and propose using them to construct a modeling framework that overcomes all serious limitations.

Towards a cellular and molecular understanding of neurulation

Neurulation occurs during the early embryogenesis of chordates, and it results in the formation of the neural tube, a dorsal hollow nerve cord that constitutes the rudiment of the entire adult central nervous system. The goal of studies on neurulation is to understand its tissue, cellular and molecular basis, as well as how neurulation is perturbed during the formation of neural tube defects. The tissue basis of neurulation consists of a series of coordinated morphogenetic movements within the primitive streak (e.g., regression of Hensen's node) and nascent primary germ layers formed during gastrulation. Signaling occurs between Hensen's node and the nascent ectoderm, initiating neurulation by inducing the neural plate (i.e., actually, by suppressing development of the epidermal ectoderm). Tissue movements subsequently result in shaping and bending of the neural plate and closure of the neural groove. The cellular basis of the tissue movements of neurulation consists of changes in the behavior of the constituent cells; namely, changes in cell number, position, shape, size and adhesion. Neurulation, like any morphogenetic event, occurs within the milieu of generic biophysical determinants of form present in all living tissues. Such forces govern and to some degree control morphogenesis in a tissue-autonomous manner. The molecular basis of neurulation remains largely unknown, but we suggest that neurulation genes have evolved to work in concert with such determinants, so that appropriate changes occur in the behaviors of the correct populations of cells at the correct time, maximizing the efficiency of neurulation and leading to heritable species- and axial-differences in this process. In this article, we review the tissue and cellular basis of neurulation and provide strategies to determine its molecular basis. We expect that such strategies will lead to the identification in the near future of critical neurulation genes, genes that when mutated perturb neurulation in a highly specific and predictable fashion and cause neurulation defects, thereby contributing to the formation of neural tube defects.

Sensory system evolution at the origin of craniates

The multiple events at the transition from non-craniate invertebrate ancestors to craniates included the gain and/or elaboration of migratory neural crest and neurogenic placodes. These tissues give rise to the peripherally located, bipolar neurons of all non-visual sensory systems. The brain was also elaborated at or about this same time. Were the peripheral and central events simultaneous or sequential? A serial transformation hypothesis postulates that paired eyes and an enlarged brain evolved before the elaboration of migratory neural crest placodal sensory systems. Circumstantial evidence for this scenario is derived from the independent occurrence of the combination of large, paired eyes plus a large, elaborated brain in at least three taxa (cephalochordates, arthropods and craniates) and partly from the exclusivity of the diencephalon for visual system-related distal sensory components versus the restricted distribution of migratory neural crest-placodal sensory systems to the remaining parts of the neuraxis. This scenario accounts for the similarity of all central sensory system pathways due to the primary establishment of descending visual pathways via the diencephalon and midbrain tectum to brainstem motor regions and the subsequent exploitation of the same central beachhead by the migratory neural crest-placodal systems as a template for their organization.

Control of neurulation by the nucleosome assembly protein-1-like 2

Neurulation is a complex process of histogenesis involving the precise temporal and spatial organization of gene expression. Genes influencing neurulation include proneural genes determining primary cell fate, neurogenic genes involved in lateral inhibition pathways and genes controlling the frequency of mitotic events. This is reflected in the aetiology and genetics of human and mouse neural tube defects, which are of both multifactorial and multigenic origin. The X-linked gene Nap1l2, specifically expressed in neurons, encodes a protein that is highly similar to the nucleosome assembly (NAP) and SET proteins. We inactivated Nap1l2 in mice by gene targeting, leading to embryonic lethality from mid-gestation onwards. Surviving mutant chimaeric embryos showed extensive surface ectoderm defects as well as the presence of open neural tubes and exposed brains similar to those observed in human spina bifida and anencephaly. These defects correlated with an overproduction of neuronal precursor cells. Protein expression studies showed that the Nap1l2 protein binds to condensing chromatin during S phase and in apoptotic cells, but remained cytoplasmic during G1 phase. Nap1l2 therefore likely represents a class of tissue-specific factors interacting with chromatin to regulate neuronal cell proliferation.

Chordate evolution and the origin of craniates: an old brain in a new head

The earliest craniates achieved a unique condition among bilaterally symmetrical animals: they possessed enlarged, elaborated brains with paired sense organs and unique derivatives of neural crest and placodal tissues, including peripheral sensory ganglia, visceral arches, and head skeleton. The craniate sister taxon, cephalochordates, has rostral portions of the neuraxis that are homologous to some of the major divisions of craniate brains. Moreover, recent data indicate that many genes involved in patterning the nervous system are common to all bilaterally symmetrical animals and have been inherited from a common ancestor. Craniates, thus, have an "old" brain in a new head, due to re-expression of these anciently acquired genes. The transition to the craniate brain from a cephalochordate-like ancestral form may have involved a mediolateral shift in expression of the genes that specify nervous system development from various parts of the ectoderm. It is suggested here that the transition was sequential. The first step involved the presence of paired, lateral eyes, elaboration of the alar plate, and enhancement of the descending visual pathway to brainstem motor centers. Subsequently, this central visual pathway served as a template for the additional sensory systems that were elaborated and/or augmented with the "bloom" of migratory neural crest and placodes. This model accounts for the marked uniformity of pattern across central sensory pathways and for the lack of any neural crest-placode cranial nerve for either the diencephalon or mesencephalon. Anat Rec (New Anat) 261:111-125, 2000.

Evolving mechanisms of morphogenesis: on the interplay between differential adhesion and cell differentiation

Differential cell adhesion, mediated by e.g. integrin and cadherins/catenines, plays an important role in morphogenesis and it has been shown that there is intimate cross-talk between their expression and modification, and inter-cellular signalling, cell differentiation, cell growth and apoptosis. In this paper, we introduce and use a formal model to explore the morphogenetic potential of the interplay between these processes. We demonstrate the formation of interesting morphologies. Initiated by cell differentiation, differential cell adhesion leads to a long transient of cell migrations, e.g. engulfing and intercalation of cells and cell layers. This transient can be sustained dynamically by further cell differentiation, and by cell growth/division and cell death which are triggered by the (also long range) forces (stretching and squeezing) generated by the cell adhesion. We study the interrelation between modes of cell differentiation and modes of morphogenesis. We use an evolutionary process to zoom in on gene-regulation networks which lead to cell differentiation. Morphogenesis is not selected for but appears as a side-effect. The evolutionary dynamics shows the hallmarks of evolution on a rugged landscape, including long neutral paths. We show that a combinatorially large set of morphologies occurs in the vicinity of a neutral path which sustains cell differentiation. Thus, an almost linear molecular phylogeny gives rise to mosaic evolution on the morphological level.

Morphogen propagation and action: towards molecular models

Theoretical views on morphogen gradients have altered dramatically with the massive arrival of molecular data regarding the establishment of graded concentrations in the embryo, and the finely tuned reading by cells of these concentration levels. I review these new perspectives, and analyze in detail two models, one pertaining to the propagation of activin in Xenopus embryos, the other to the interpretation of retinoic acid levels into transcription patterns by nuclear receptors. The unifying threads that seem to emerge are the combinatorial uses of receptor subtypes, cooperativity and autocatalysis (positive feedback) to achieve specificity and reliability.