MorphoGraphX 2.0: Providing context for biological image analysis with positional information

Positional information is a central concept in developmental biology. In developing organs, positional information can be idealized as a local coordinate system that arises from morphogen gradients controlled by organizers at key locations. This offers a plausible mechanism for the integration of the molecular networks operating in individual cells into the spatially-coordinated multicellular responses necessary for the organization of emergent forms. Understanding how positional cues guide morphogenesis requires the quantification of gene expression and growth dynamics in the context of their underlying coordinate systems. Here we present recent advances in the MorphoGraphX software (Barbier de Reuille et al. eLife 2015;4:e05864) that implement a generalized framework to annotate developing organs with local coordinate systems. These coordinate systems introduce an organ-centric spatial context to microscopy data, allowing gene expression and growth to be quantified and compared in the context of the positional information thought to control them.

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Dynamic positioning and precision of bistable gene expression boundaries through diffusion and morphogen decay

10.1101/2020.12.17.423202 ◽

2020 ◽

Author(s):

Melinda Liu Perkins

Keyword(s):

Gene Expression ◽

Mathematical Theory ◽

Initial Conditions ◽

Propagation Speed ◽

Positional Information ◽

Future Research ◽

Toggle Switch ◽

Embryonic Patterning ◽

Cell Coupling ◽

Morphogen Gradients

1AbstractTraditional models for how morphogen gradients guide embryonic patterning fail to account for experimental observations of temporal refinement in gene expression domains. Dynamic positional information has recently emerged as a framework to address this shortcoming. Here, we explore two central aspects of dynamic positional information—the precision and placement of gene expression boundaries—in bistable genetic networks driven by morphogen gradients. First, we hypothesize that temporal morphogen decay may increase the precision of a boundary by compensating for variation in initial conditions that would otherwise lead neighboring cells with identical inputs to diverge to separate steady states. Second, we explore how diffusion of gene products may play a key role in placing gene expression boundaries. Using an existing model for Hb patterning in embryonic fruit flies, we show that diffusion permits boundaries to act as near-traveling wavefronts with local propagation speed determined by morphogen concentration. We then harness our understanding of near-traveling fronts to propose a method for achieving accurate steady-state boundary placement independent of initial conditions. Our work posits functional roles for temporally varying inputs and cell-to-cell coupling in the regulation and interpretation of dynamic positional information, illustrating that mathematical theory should serve to clarify not just our quantitative, but also our intuitive understanding of patterning processes.2Author SummaryIn many developmental systems, cells interpret spatial gradients of chemical morphogens to produce gene expression boundaries in exact positions. The simplest mathematical models for “positional information” rely on threshold detection, but such models are not robust to variations in the morphogen gradient or initial protein concentrations. Furthermore, these models fail to account for experimental results showing dynamic shifts in boundary placement and increased boundary precision over time. Here, we propose two theoretical mechanisms for enhancing boundary precision and placement using a bistable toggle switch. Distinct from existing research in “dynamic positional information”, this work posits a functional role for temporal decay in morphogen concentration and for diffusion of gene expression products, the latter of which is often omitted in quantitative models. We suggest that future research into dynamic positional information would benefit from perspectives that link local (cellular) and global (patterning) behaviors, as well as from mathematical theory that builds our intuitive understanding alongside more data-driven approaches.

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Interpretation of morphogen gradients by a synthetic bistable circuit

Nature Communications ◽

10.1038/s41467-020-19098-w ◽

2020 ◽

Vol 11 (1) ◽

Cited By ~ 1

Author(s):

Paul K. Grant ◽

Gregory Szep ◽

Om Patange ◽

Jacob Halatek ◽

Valerie Coppard ◽

...

Keyword(s):

Gene Expression ◽

Computational Models ◽

Positional Information ◽

Spatial Average ◽

Spatial Patterning ◽

Mutual Inhibition ◽

E Coli ◽

Morphogen Gradients ◽

Stable Domains

Abstract During development, cells gain positional information through the interpretation of dynamic morphogen gradients. A proposed mechanism for interpreting opposing morphogen gradients is mutual inhibition of downstream transcription factors, but isolating the role of this specific motif within a natural network remains a challenge. Here, we engineer a synthetic morphogen-induced mutual inhibition circuit in E. coli populations and show that mutual inhibition alone is sufficient to produce stable domains of gene expression in response to dynamic morphogen gradients, provided the spatial average of the morphogens falls within the region of bistability at the single cell level. When we add sender devices, the resulting patterning circuit produces theoretically predicted self-organised gene expression domains in response to a single gradient. We develop computational models of our synthetic circuits parameterised to timecourse fluorescence data, providing both a theoretical and experimental framework for engineering morphogen-induced spatial patterning in cell populations.

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Implications of diffusion and time-varying morphogen gradients for the dynamic positioning and precision of bistable gene expression boundaries

PLoS Computational Biology ◽

10.1371/journal.pcbi.1008589 ◽

2021 ◽

Vol 17 (6) ◽

pp. e1008589

Author(s):

Melinda Liu Perkins

Keyword(s):

Gene Expression ◽

Initial Conditions ◽

Positional Information ◽

Fruit Fly ◽

Time Varying ◽

Gene Products ◽

Embryonic Patterning ◽

Morphogen Gradients ◽

Pde Model ◽

Gradient Evolution

The earliest models for how morphogen gradients guide embryonic patterning failed to account for experimental observations of temporal refinement in gene expression domains. Following theoretical and experimental work in this area, dynamic positional information has emerged as a conceptual framework to discuss how cells process spatiotemporal inputs into downstream patterns. Here, we show that diffusion determines the mathematical means by which bistable gene expression boundaries shift over time, and therefore how cells interpret positional information conferred from morphogen concentration. First, we introduce a metric for assessing reproducibility in boundary placement or precision in systems where gene products do not diffuse, but where morphogen concentrations are permitted to change in time. We show that the dynamics of the gradient affect the sensitivity of the final pattern to variation in initial conditions, with slower gradients reducing the sensitivity. Second, we allow gene products to diffuse and consider gene expression boundaries as propagating wavefronts with velocity modulated by local morphogen concentration. We harness this perspective to approximate a PDE model as an ODE that captures the position of the boundary in time, and demonstrate the approach with a preexisting model for Hunchback patterning in fruit fly embryos. We then propose a design that employs antiparallel morphogen gradients to achieve accurate boundary placement that is robust to scaling. Throughout our work we draw attention to tradeoffs among initial conditions, boundary positioning, and the relative timescales of network and gradient evolution. We conclude by suggesting that mathematical theory should serve to clarify not just our quantitative, but also our intuitive understanding of patterning processes.

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Competing Endogenous RNAs in Cervical Carcinogenesis: A New Layer of Complexity

Processes ◽

10.3390/pr9060991 ◽

2021 ◽

Vol 9 (6) ◽

pp. 991

Author(s):

Fernanda Costa Brandão Berti ◽

Sara Cristina Lobo-Alves ◽

Camila de Freitas Oliveira-Toré ◽

Amanda Salviano-Silva ◽

Karen Brajão de Oliveira ◽

...

Keyword(s):

Gene Expression ◽

Fine Tuning ◽

Molecular Networks ◽

Cervical Carcinogenesis ◽

Molecular Changes ◽

Cellular Processes ◽

Target Mrnas ◽

Competing Endogenous Rnas ◽

Cervical Cells ◽

Post Transcriptional Regulation

MicroRNAs (miRNAs) regulate gene expression by binding to complementary sequences within target mRNAs. Apart from working ‘solo’, miRNAs may interact in important molecular networks such as competing endogenous RNA (ceRNA) axes. By competing for a limited pool of miRNAs, transcripts such as long noncoding RNAs (lncRNAs) and mRNAs can regulate each other, fine-tuning gene expression. Several ceRNA networks led by different lncRNAs—described here as lncRNA-mediated ceRNAs—seem to play essential roles in cervical cancer (CC). By conducting an extensive search, we summarized networks involved in CC, highlighting the major impacts of such dynamic molecular changes over multiple cellular processes. Through the sponging of distinct miRNAs, some lncRNAs as HOTAIR, MALAT1, NEAT1, OIP5-AS1, and XIST trigger crucial molecular changes, ultimately increasing cell proliferation, migration, invasion, and inhibiting apoptosis. Likewise, several lncRNAs seem to be a sponge for important tumor-suppressive miRNAs (as miR-140-5p, miR-143-3p, miR-148a-3p, and miR-206), impairing such molecules from exerting a negative post-transcriptional regulation over target mRNAs. Curiously, some of the involved mRNAs code for important proteins such as PTEN, ROCK1, and MAPK1, known to modulate cell growth, proliferation, apoptosis, and adhesion in CC. Overall, we highlight important lncRNA-mediated functional interactions occurring in cervical cells and their closely related impact on cervical carcinogenesis.

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Abstract P625: Non-coding Rna Regulation Of Gene Expression In Angiotensin Ii-induced Vascular Damage

Hypertension ◽

10.1161/hyp.66.suppl_1.p625 ◽

2015 ◽

Vol 66 (suppl_1) ◽

Author(s):

Kugeng Huo ◽

Tlili Barhoumi ◽

Júlio C Fraulob-Aquino ◽

Chantal Richer ◽

Mathieu Lajoie ◽

...

Keyword(s):

Gene Expression ◽

Differential Expression Analysis ◽

Regulation Of Gene Expression ◽

Vascular Damage ◽

Mesenteric Arteries ◽

Functional Enrichment ◽

Molecular Networks ◽

Mirna Cluster ◽

Ang Ii ◽

Illumina Hiseq

Introduction: Non-coding RNAs (ncRNAs), including long ncRNAs (lncRNAs) and microRNAs (miRs), account for ~98% of the transcribed RNAs. They have been shown to play a role in cardiovascular disease. Vascular damage is an early manifestation and a cause of end-organ damage in hypertension. However, it is unknown whether ncRNAs are involved in the development of vascular injury in hypertension. We hypothesize that ncRNA regulation participates in mechanisms of vascular remodeling and plays an important role in the pathophysiology of hypertension. Methods and Results: Ten-week old male C57BL/6 mice were infused or not with angiotensin (Ang) II for 14 days. Systolic blood pressure (BP) determined by telemetry was increased by Ang II infusion compared to control (146±8 vs 113±5 mmHg, P<0.001). Total RNA was extracted from mesenteric arteries for total and small RNA deep sequencing using Illumina HiSeq-2500. Sequences were aligned to the mm10 genome with STAR, annotated and counted using HTSeq-count or miRDeep2. Differential expression analysis was done in R. Differentially expressed (DE) mRNAs (550 up & 266 down), lncRNAs (7 up & 42 down), miRs (23 up & 12 down) were identified in the Ang II-treated group (1.5 fold change, q<0.05). Targetscan was used to predict interactions between DE miRs and the inversely correlated DE mRNAs or DE lncRNAs. MEME Suite was used to predict DE transcription factor binding sites in the promoter region of genes encoding DE mRNAs, lncRNAs and miRs. Cytoscape was used to construct molecular networks integrating the above interactions and the gene expression profile and to perform functional enrichment analysis, which revealed enrichment of extracellular matrix and developmental processes in DE miR-targeting DE mRNAs (q<1E-20). Ten DE miRNAs whose expression levels correlated (P<0.05) with BP were identified, 9 of which are located in a single miRNA cluster that is conserved in humans. Conclusions: We have identified a conserved miRNA cluster that may play a pivotal role in the regulation of vascular damage in hypertension. A sub-network of genes that participates in the interaction between the miRNA cluster and other BP-correlated RNAs was selected for future investigation to identify therapeutic targets.

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Abstract 290: Proliferation of Cardiac Fibroblasts Defines Early Stages of Genetic Dilated Cardiomyopathy and Precedes Myocardial Metabolic Derangement

Circulation Research ◽

10.1161/res.115.suppl_1.290 ◽

2014 ◽

Vol 115 (suppl_1) ◽

Author(s):

Michael A Burke ◽

Stephen Chang ◽

Danos C Christodoulou ◽

Joshua M Gorham ◽

Hiroko Wakimoto ◽

...

Keyword(s):

Gene Expression ◽

Cardiac Fibroblasts ◽

Expression Patterns ◽

Molecular Networks ◽

Peroxisome Proliferator ◽

Metabolic Derangement ◽

Peroxisome Proliferator Activated Receptor ◽

Cell Remodeling ◽

Ppar Signaling ◽

Myocyte Proliferation

The complex molecular networks underpinning DCM remain poorly understood. To study distinct pathways and networks in the longitudinal development of DCM we performed RNAseq on LV tissue from mice carrying a human DCM mutation in phospholamban (PLN R9C/+ ) before phenotype onset (pre-DCM), with DCM, and during overt heart failure (HF), and also on isolated myocytes and non-myocytes from DCM hearts. PLN R9C/+ mice show progressive fibrosis (20% vs. 1% control, p=6x10 −33 ; n=3) associated with proliferation of cardiac non-myocytes (33% increase over control, p=6x10 −4 ; n=3). Consistent with this, cardiac non-myocytes have upregulated gene expression and pathways, while these are generally downregulated in myocytes. Non-myocytes were enriched in fibrosis, inflammation, and cell remodeling pathways, from pre-DCM to HF. In contrast, myocytes were enriched for metabolic pathways only with overt DCM and HF. Myocytes showed profound derangement of oxidative phosphorylation with DCM (p=2.5x10 −41 ; 44% (53/120) of pathway genes downregulated), suggesting mitochondrial dysfunction. Additionally, we detected probable inhibition of peroxisome proliferator-activated receptor (PPAR) signaling by diminished expression of pathway genes (Figure). DCM and hypertrophic remodeling was compared using RNAseq of a mouse model of HCM; similar patterns of fibrosis with myocyte metabolic dysregulation were evident despite unique differential gene expression patterns between models. DCM caused by PLN R9C/+ is associated with early non-myocyte proliferation and later myocyte metabolic derangement possibly governed by altered PPAR signaling, and is common to DCM and HCM.

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Spatiotemporal control of gene expression boundaries using a feedforward loop

10.1101/806620 ◽

2019 ◽

Author(s):

Prasad U. Bandodkar ◽

Hadel Al Asafen ◽

Gregory T. Reeves

Keyword(s):

Gene Expression ◽

Biological Networks ◽

Target Gene ◽

Network Motif ◽

Control Of Gene Expression ◽

Intermediate Node ◽

Morphogen Gradients ◽

Spatially Distributed ◽

Spatiotemporal Behavior ◽

Spatiotemporal Control

AbstractA feed forward loop (FFL) is commonly observed in several biological networks. The FFL network motif has been mostly been studied with respect to variation of the input signal in time, with only a few studies of FFL activity in a spatially distributed system such as morphogen-mediated tissue patterning. However, most morphogen gradients also evolve in time. We studied the spatiotemporal behavior of a coherent FFL in two contexts: (1) a generic, oscillating morphogen gradient and (2) the dorsal-ventral patterning of the early Drosophila embryo by a gradient of the NF-κB homolog Dorsal with its early target Twist. In both models, we found features in the dynamics of the intermediate node – phase difference and noise filtering – that were largely independent of the parameterization of the models, and thus were functions of the structure of the FFL itself. In the Dorsal gradient model, we also found that the dynamics of Dorsal require maternal pioneering factor Zelda for proper target gene expression.

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Cell-to-cell heterogeneity in Escherichia coli stress response originates from pulsatile expression and growth

10.1101/2020.09.14.297101 ◽

2020 ◽

Author(s):

Nadia M. V. Sampaio ◽

Caroline M. Blassick ◽

Jean-Baptiste Lugagne ◽

Mary J. Dunlop

Keyword(s):

Gene Expression ◽

Escherichia Coli ◽

Stress Response ◽

Single Cell ◽

Phenotypic Variability ◽

Growth Dynamics ◽

Time Lapse ◽

Cell Heterogeneity ◽

Temporal Expression ◽

Functional Consequences

AbstractCell-to-cell heterogeneity in gene expression and growth can have critical functional consequences, such as determining whether individual bacteria survive or die following stress. Although phenotypic variability is well documented, the dynamics that underlie it are often unknown. This information is critical because dramatically different outcomes can arise from gradual versus rapid changes in expression and growth. Using single-cell time-lapse microscopy, we measured the temporal expression of a suite of stress response reporters in Escherichia coli, while simultaneously monitoring growth rate. In conditions without stress, we found widespread examples of pulsatile expression. Single-cell growth rates were often anti-correlated with gene expression, with changes in growth preceding changes in expression. These pulsatile dynamics have functional consequences, which we demonstrate by measuring survival after challenging cells with the antibiotic ciprofloxacin. Our results suggest that pulsatile expression and growth dynamics are common in stress response networks and can have direct consequences for survival.

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Genes that control dorsoventral polarity affect gene expression along the anteroposterior axis of the Drosophila embryo

Development ◽

10.1242/dev.99.3.327 ◽

1987 ◽

Vol 99 (3) ◽

pp. 327-332 ◽

Cited By ~ 1

Author(s):

S.B. Carroll ◽

G.M. Winslow ◽

V.J. Twombly ◽

M.P. Scott

Keyword(s):

Gene Expression ◽

Cell Fate ◽

Maternal Effect ◽

Positional Information ◽

Drosophila Embryo ◽

Dorsoventral Polarity ◽

Anteroposterior Axis ◽

Positional Marker ◽

Control Pattern ◽

The Relationship

At least 13 genes control the establishment of dorsoventral polarity in the Drosophila embryo and more than 30 genes control the anteroposterior pattern of body segments. Each group of genes is thought to control pattern formation along one body axis, independently of the other group. We have used the expression of the fushi tarazu (ftz) segmentation gene as a positional marker to investigate the relationship between the dorsoventral and anteroposterior axes. The ftz gene is normally expressed in seven transverse stripes. Changes in the striped pattern in embryos mutant for other genes (or progeny of females homozygous for maternal-effect mutations) can reveal alterations of cell fate resulting from such mutations. We show that in the absence of any of ten maternal-effect dorsoventral polarity gene functions, the characteristic stripes of ftz protein are altered. Normally there is a difference between ftz stripe spacing on the dorsal and ventral sides of the embryo; in dorsalized mutant embryos the ftz stripes appear to be altered so that dorsal-type spacing occurs on all sides of the embryo. These results indicate that cells respond to dorsoventral positional information in establishing early patterns of gene expression along the anteroposterior axis and that there may be more significant interactions between the different axes of positional information than previously determined.

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Dioxin Disrupts Dynamic DNA Methylation Patterns in Genes That Govern Cardiomyocyte Maturation

Toxicological Sciences ◽

10.1093/toxsci/kfaa153 ◽

2020 ◽

Vol 178 (2) ◽

pp. 325-337

Author(s):

Matthew de Gannes ◽

Chia-I Ko ◽

Xiang Zhang ◽

Jacek Biesiada ◽

Liang Niu ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Heart Development ◽

Expression Patterns ◽

Embryonic Stem Cell Line ◽

Molecular Networks ◽

Unknown Etiology ◽

Postnatal Maturation ◽

Complex Interactions ◽

And Function

Abstract Congenital heart disease (CHD), the leading birth defect worldwide, has a largely unknown etiology, likely to result from complex interactions between genetic and environmental factors during heart development, at a time when the heart adapts to diverse physiological and pathophysiological conditions. Crucial among these is the regulation of cardiomyocyte development and postnatal maturation, governed by dynamic changes in DNA methylation. Previous work from our laboratory has shown that exposure to the environmental toxicant tetrachlorodibenzo-p-dioxin (TCDD) disrupts several molecular networks responsible for heart development and function. To test the hypothesis that the disruption caused by TCDD in the heart results from changes in DNA methylation and gene expression patterns of cardiomyocytes, we established a stable mouse embryonic stem cell line expressing a puromycin resistance selectable marker under control of the cardiomyocyte-specific Nkx2-5 promoter. Differentiation of these cells in the presence of puromycin induces the expression of a large suite of cardiomyocyte-specific markers. To assess the consequences of TCDD treatment on gene expression and DNA methylation in these cardiomyocytes, we subjected them to transcriptome and methylome analyses in the presence of TCDD. Unlike control cardiomyocytes maintained in vehicle, the TCDD-treated cardiomyocytes showed extensive gene expression changes, with a significant correlation between differential RNA expression and DNA methylation in 111 genes, many of which are key elements of pathways that regulate cardiovascular development and function. Our findings provide an important clue toward the elucidation of the complex interactions between genetic and epigenetic mechanisms after developmental TCDD exposure that may contribute to CHD.

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