Growth Regulatory Network Research Articles

Inference of Dynamic Growth Regulatory Network in Cancer Using High-Throughput Transcriptomic Data.

Growth is regulated by gene expression variation at different developmental stages of biological processes such as cell differentiation, disease progression, or drug response. In cancer, a stage-specific regulatory model constructed to infer the dynamic expression changes in genes contributing to tissue growth or proliferation is referred as a dynamic growth regulatory network (dGRN). Over the past decade, gene expression data has been widely used for reconstructing dGRN by computing correlations between the differentially expressed genes (DEGs). A wide variety of pipelines are available to construct the GRNs using DEGs and the choice of a particular method or tool depends on the nature of the study. In this protocol, we have outlined a step-by-step guide for the analysis of DEGs using RNA-Seq data, beginning from data acquisition, pre-processing, mapping to reference genome, and construction of a correlation-based co-expression network to further downstream analysis. We have also outlined the steps for the inclusion of publicly available interaction/regulation information into the dGRN followed by relevant topological inferences. This tutorial has been designed in a way that early researchers can refer to for an easy and comprehensive glimpse of methodologies used in the inference of dGRN using transcriptomics data.

MtTGA1 Transcription Factor Enhances Salt Tolerance through Hormonal Regulation and Antioxidant Enzyme Activity in Medicago truncatula

The TGACG motif-binding factor1 (TGA1) transcription factor, in which belongs to the bZIP transcription factor family and has vast application potential in plant growth and development. Here, we cloned the gene of the MtTGA1 transcription factor from Medicago truncatula. The MtTGA1 promoter region contains a diverse range of photoregulatory and hormonal regulatory elements. The expression profile of MtTGA1 indicated its highest expression in the root. Additionally, the expression level of MtTGA1 was significantly upregulated after SA and BR treatments and showed a downward trend after GA and ABA treatments. To explore the potential function of MtTGA1, we treated the transgenic plants with salt treatment for 15 days, and the results showed that transgenic plants demonstrated significantly longer root lengths and heightened activities of antioxidant enzymes such as ascorbic acid catalase (APX), peroxidase (POD), catalase (CAT), and superoxide dismutase (SOD) in their roots and leaves. The levels of endogenous hormones, including ABA and BR were improved in transgenic plants, with a marked change in the morphology of their leaf cells. Transcriptome analysis identified a total of 193 differentially expressed genes, which were significantly enriched in the pathways of “Brassinosteroid biosynthesis”, “Ascorbate and aldarate metabolism”, and “Plant hormone signal transduction”. Furthermore, MtTGA1 was found to interact with the SPX domain-containing protein 1 (SPX1) in Medicago truncatula. In conclusion, these results are beneficial for further studies about the plant growth and development regulatory network mediated by the TGA1 transcription factor family.

DMyc-dependent upregulation of CD98 amino acid transporters is required for Drosophila brain tumor growth

Tumor cells have an increased demand for nutrients to sustain their growth, but how these increased metabolic needs are ensured or how this influences tumor formation and progression remains unclear. To unravel tumor metabolic dependencies, particularly from extracellular metabolites, we have analyzed the role of plasma membrane metabolic transporters in Drosophila brain tumors. Using a well-established neural stem cell-derived tumor model, caused by brat knockdown, we have found that 13 plasma membrane metabolic transporters, including amino acid, carbohydrate and monocarboxylate transporters, are upregulated in tumors and are required for tumor growth. We identified CD98hc and several of the light chains with which it can form heterodimeric amino acid transporters, as crucial players in brat RNAi (bratIR) tumor progression. Knockdown of these components of CD98 heterodimers caused a dramatic reduction in tumor growth. Our data also reveal that the oncogene dMyc is required and sufficient for the upregulation of CD98 transporter subunits in these tumors. Furthermore, tumor-upregulated dmyc and CD98 transporters orchestrate the overactivation of the growth-promoting signaling pathway TOR, forming a core growth regulatory network to support brat IR tumor progression. Our findings highlight the important link between oncogenes, metabolism, and signaling pathways in the regulation of tumor growth and allow for a better understanding of the mechanisms necessary for tumor progression.

DANCR Induces Cisplatin Resistance of Triple-Negative Breast Cancer by KLF5/p27 Signaling

An increasing body of evidence suggests that long noncoding RNAs play critical roles in human cancer. Breast cancer is a heterogeneous disease and the potential involvement of long noncoding RNAs in breast cancer remains poorly understood. Herein, the study identified a long noncoding RNA, DANCR, which promotes cisplatin chemoresistance in triple-negative breast cancer (TNBC) cells. Mechanistically, binding of DANCR to Krüppel-like factor 5 (KLF5) induced acetylation of KLF5 at lysine 369 (K369), and DANCR knockdown resulted in down-regulation of KLF5 protein levels. Furthermore, DANCR/KLF5 signaling pathway induced hypersensitivity to cisplatin in chemoresistant patients by inhibiting p27 transcription. In summary, this study reinforced the potential presence of a growth regulatory network in TNBC cells, and documented a DANCR/KLF5/p27 signaling pathway mediating cisplatin chemoresistance in TNBC.

On the Construction of Growth Models via Symmetric Copulas and Stochastic Differential Equations

By nature, growth regulatory networks in biology are dynamic and stochastic, and feedback regulates their growth function at different ages. In this study, we carried out a stochastic modeling of growth networks and demonstrated this method using three mixed effect four-parameter Gompertz-type diffusion processes and a combination thereof using the conditional normal copula function. Using the conditional normal copula, newly derived univariate distributions can be combined into trivariate and bivariate distributions, and their corresponding conditional bivariate and univariate distributions. The link between the predictor variable and the remaining one or two explanatory variables can be formalized using copula-type densities and a numerical integration procedure. In this study, for parameter estimation, we used a semiparametric maximum pseudo-likelihood estimator procedure, which was characterized by a two-step technique, namely, separately estimating the parameters of the marginal distributions and the parameters of the copula. The results were illustrated using two observed longitudinal datasets, the first of which included the age, diameter, and potentially available area of 39,437 trees (48 stands), while the second included the age, diameter, potentially available area, and height of 8604 trees (47 stands) covering uneven mixed-species (pine, spruce, and birch) stands. All results were implemented using the MAPLE symbolic algebra system.

BBX21 reduces abscisic acid sensitivity, mesophyll conductance and chloroplast electron transport capacity to increase photosynthesis and water use efficiency in potato plants cultivated under moderated drought.

The B-box (BBX) proteins are zinc-finger transcription factors with a key role in growth and developmental regulatory networks mediated by light. AtBBX21 overexpressing (BBX21-OE) potato (Solanum tuberosum) plants, cultivated in optimal water conditions, have a higher photosynthesis rate and stomatal conductance without penalty in water use efficiency (WUE) and with a higher tuber yield. In this work, we cultivated potato plants in two water regimes: 100 and 35% field capacity of water restriction that imposed leaf water potentials between -0.3 and -1.2 MPa for vegetative and tuber growth during 14 or 28 days, respectively. We found that 42-day-old plants of BBX21-OE were more tolerant to water restriction with higher levels of chlorophylls and tuber yield than wild-type spunta (WT) plants. In addition, the BBX21-OE lines showed higher photosynthesis rates and WUE under water restriction during the morning. Mechanistically, we found that BBX21-OE lines were more tolerant to moderated drought by enhancing mesophyll conductance (gm ) and maximum capacity of electron transport (Jmax ), and by reducing abscisic acid (ABA) sensitivity in plant tissues. By RNA-seq analysis, we found 204 genes whose expression decreased by drought in WT plants and expressed independently of the water condition in BBX21-OE lines as SAP12, MYB73, EGYP1, TIP2-1 and DREB2A, and expressions were confirmed by quantitative polymerase chain reaction. These results suggest that BBX21 interplays with the ABA and growth signaling networks, improving the photosynthetic behavior in suboptimal water conditions with an increase in potato tuber yield.

Integrated analysis of miRNA and mRNA transcriptomic reveals antler growth regulatory network.

The growth of antler is driven by endochondral ossification in the growth center of the apical region. Antler grows faster than cancer tissues, but it can be stably regulated and regenerated periodically. To elucidate the molecular mechanisms of how antler grows rapidly without carcinogenesis, in this study, we used RNA-seq technology to evaluate the changes of miRNA and mRNA profiles in antler at four different developmental stages, including 15, 60, 90, and 110days. We identified a total of 55004 unigenes and 246 miRNAs of which, 10182, 13258, 10740 differentially expressed (DE) unigenes and 35, 53, 27 DE miRNAs were identified in 60-day vs. 15-day, 90-day vs. 60-day, and 110-day vs. 90-day. GO and KEGG pathway analysis indicated that DE unigenes and DE miRNA were mainly associated with chondrogenesis, osteogenesis and inhibition of oncogenesis, that were closely related to antler growth. The interaction networks of mRNA-mRNA and miRNA-mRNA related to chondrogenesis, osteogenesis and inhibition of oncogenesis of antler were constructed. The results indicated that mRNAs (COL2A1, SOX9, WWP2, FGFR1, SPARC, LOX, etc.) and miRNAs (miR-145, miR-199a-3p, miR-140, miR-199a-5p, etc.) might have key roles in chondrogenesis and osteogenesis of antler. As well as mRNA (TP53, Tpm3 and ATP1A1, etc.) and miRNA (miR-106a, miR-145, miR-1260b and miR-2898, etc.) might play important roles in inhibiting the carcinogenesis of antler. In summary, we constructed the mRNA-mRNA and miRNA-mRNA regulatory networks related to chondrogenesis, osteogenesis and inhibition of oncogenesis of antler, and identified key candidate mRNAs and miRNAs among them. Further developments and validations may provide a reference for in-depth analysis of the molecular mechanism of antler growth without carcinogenesis.

The Elongator complex regulates hypocotyl growth in darkness and during photomorphogenesis.

The Elongator complex (hereafter Elongator) promotes RNA polymerase II-mediated transcript elongation through epigenetic activities such as histone acetylation. Elongator regulates growth, development, immune response and sensitivity to drought and abscisic acid. We demonstrate that elo mutants exhibit defective hypocotyl elongation but have a normal apical hook in darkness and are hyposensitive to light during photomorphogenesis. These elo phenotypes are supported by transcriptome changes, including downregulation of circadian clock components, positive regulators of skoto- or photomorphogenesis, hormonal pathways and cell wall biogenesis-related factors. The downregulated genes LHY, HFR1 and HYH are selectively targeted by Elongator for histone H3K14 acetylation in darkness. The role of Elongator in early seedling development in darkness and light is supported by hypocotyl phenotypes of mutants defective in components of the gene network regulated by Elongator, and by double mutants between elo and mutants in light or darkness signaling components. A model is proposed in which Elongator represses the plant immune response and promotes hypocotyl elongation and photomorphogenesis via transcriptional control of positive photomorphogenesis regulators and a growth-regulatory network that converges on genes involved in cell wall biogenesis and hormone signaling.This article has an associated First Person interview with the first author of the paper.

Abstract 5552: Differential proteomic responses of luminal-A and basal-like breast cancer cell lines during growth inhibition induced by co-culture with agarose encapsulated murine renal adenocarcinoma (RENCA) cells

Abstract The existence of a tumor growth regulatory network that is conserved across tumor types and species has been hypothesized. Our evidence for this regulatory network is derived from studies demonstrating tumor growth inhibition by agarose encapsulated cancer cells (cancer macrobeads). The ability of encapsulated, thus growth restricted cells, to inhibit freely growing cancer cells has been shown when the encapsulated cells are murine (RENCA) or human (e.g., J82). Clinical trials are underway (NCT01053013, NCT02046174). We have shown that RENCA macrobeads release >10 known tumor inhibitory proteins targeting several signaling pathways including Akt/PI3. To better understand the mechanism(s) of growth inhibition, we used a systems biology approach to identify protein profiles and interactions from macrobead-treated human breast carcinoma cell lines that are either mildly aggressive (MCF7) or highly aggressive (MDA-MB231 [MDA]). Target cells were co-cultured with RENCA macrobeads or left untreated for 5 days. Lysates of target cells were prepared in Laemmli buffer, frozen, and sent for MS/MS. Samples were run in duplicate, protein intensities normalized, and the treated/untreated ratio log10 transformed to get a normal distribution. Protein profiles were analyzed using Key Pathway Analysis (KPA) and Metacore software. Growth inhibition by RENCA macrobeads was confirmed (MCF7 25%; MDA 57%). KPA of MCF7 proteins showed upregulation of ubiquitin pathways involved in degradation of misfolded proteins. Stress induced apoptosis and DNA damage (which correlates with the growth inhibition) were the top 2 pathways upregulated using Pathway and Process Enrichment analysis. This is in line with a strong epigenetic gene deregulation (Metacore). Transcription Factor and Network analyses show upregulation of CREB, A2MR and ATF3 networks. Also, Regulated Network analysis suggests a role for A2MR or RAGE in the inhibition of proliferation and increased apoptosis. Macrobead-treated MDA cells showed no significant changes using KPA. Pathway, Network and Process enrichment (Metacore) showed 5 of the top 10 upregulated processes were associated with cytoskeleton remodeling. Cell cycle and protein folding processes were also upregulated. Transcription factors associated with this response were similar to that of MCF7. RAGE again appears in many of the pathways as indicated by Network and Regulated Network analysis. The protein response to RENCA macrobeads differs for these 2 cell lines. Proteins related to apoptosis are upregulated in the MCF7 cells whereas MDA have a preference for cytoskeleton remodeling. These data support the hypothesis that distinctive tumors may respond differently to RENCA macrobead exposure at both an epigenetic and protein level, nonetheless resulting in growth inhibition. Citation Format: Melissa A. Laramore, Peter James, Prithy C. Martis, Atira Dudley, Lawrence S. Gazda, Carl A. Borrebaeck, Barry H. Smith. Differential proteomic responses of luminal-A and basal-like breast cancer cell lines during growth inhibition induced by co-culture with agarose encapsulated murine renal adenocarcinoma (RENCA) cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5552. doi:10.1158/1538-7445.AM2017-5552

A Drosophila RNAi library modulates Hippo pathway-dependent tissue growth.

Libraries of transgenic Drosophila melanogaster carrying RNA interference (RNAi) constructs have been used extensively to perform large-scale functional genetic screens in vivo. For example, RNAi screens have facilitated the discovery of multiple components of the Hippo pathway, an evolutionarily conserved growth-regulatory network. Here we investigate an important technical limitation with the widely used VDRC KK RNAi collection. We find that approximately 25% of VDRC KK RNAi lines cause false-positive enhancement of the Hippo pathway, owing to ectopic expression of the Tiptop transcription factor. Of relevance to the broader Drosophila community, ectopic tiptop (tio) expression can also cause organ malformations and mask phenotypes such as organ overgrowth. To enhance the use of the VDRC KK RNAi library, we have generated a D. melanogaster strain that will allow researchers to test, in a single cross, whether their genetic screen of interest will be affected by ectopic tio expression.

Combined Large-Scale Phenotyping and Transcriptomics in Maize Reveals a Robust Growth Regulatory Network.

Leaves are vital organs for biomass and seed production because of their role in the generation of metabolic energy and organic compounds. A better understanding of the molecular networks underlying leaf development is crucial to sustain global requirements for food and renewable energy. Here, we combined transcriptome profiling of proliferative leaf tissue with in-depth phenotyping of the fourth leaf at later stages of development in 197 recombinant inbred lines of two different maize (Zea mays) populations. Previously, correlation analysis in a classical biparental mapping population identified 1,740 genes correlated with at least one of 14 traits. Here, we extended these results with data from a multiparent advanced generation intercross population. As expected, the phenotypic variability was found to be larger in the latter population than in the biparental population, although general conclusions on the correlations among the traits are comparable. Data integration from the two diverse populations allowed us to identify a set of 226 genes that are robustly associated with diverse leaf traits. This set of genes is enriched for transcriptional regulators and genes involved in protein synthesis and cell wall metabolism. In order to investigate the molecular network context of the candidate gene set, we integrated our data with publicly available functional genomics data and identified a growth regulatory network of 185 genes. Our results illustrate the power of combining in-depth phenotyping with transcriptomics in mapping populations to dissect the genetic control of complex traits and present a set of candidate genes for use in biomass improvement.

Plant Growth Beyond Limits.

Growth processes, governed by complex genetic networks in a coordinated manner, are determining factors for numerous crop traits. Many components of these networks, described in Arabidopsis and to a lesser extent in crops, enhance organ growth when perturbed. However, translating our understanding of plant growth into crop improvement has been very limited. We argue here that this lack of success is due to the fact that modifying the expression of single genes in a complex growth regulatory network might be buffered by other components of the network. We discuss the observation that simultaneous perturbations of multiple genes have more pronounced effects, and present novel perspectives to use knowledge of growth regulatory networks to enhance crop yield in a targeted manner.

Gibberellins - a multifaceted hormone in plant growth regulatory network.

Plants tend to acclimatize to unfavourable environs by integrating growth and development to environmentally activated signals. Phytohormones strongly regulate convergent developmental and stress adaptive procedures and synchronize cellular reaction to the exogenous and endogenous conditions within the adaptive signaling networks. Gibberellins (GA), a group of tetracyclic diterpenoids, being vital regulators of plant growth, are accountable for regulating several aspects of growth and development of higher plants. If the element of reproduction is considered as an absolute requisite then for a majority of the higher plants GA signaling is simply indispensable. Latest reports have revealed unique conflicting roles of GA and other phytohormones in amalgamating growth and development in plants through environmental signaling. Numerous physiological researches have detailed substantial crosstalk between GA and other hormones like abscisic acid, auxin, cytokinin, and jasmonic acid. In this review, a number of explanations and clarifications for this discrepancy are explored based on the crosstalk among GA and other phytohormones.

Molecular systems governing leaf growth: from genes to networks.

Arabidopsis leaf growth consists of a complex sequence of interconnected events involving cell division and cell expansion, and requiring multiple levels of genetic regulation. With classical genetics, numerous leaf growth regulators have been identified, but the picture is far from complete. With the recent advances made in quantitative phenotyping, the study of the quantitative, dynamic, and multifactorial features of leaf growth is now facilitated. The use of high-throughput phenotyping technologies to study large numbers of natural accessions or mutants, or to screen for the effects of large sets of chemicals will allow for further identification of the additional players that constitute the leaf growth regulatory networks. Only a tight co-ordination between these numerous molecular players can support the formation of a functional organ. The connections between the components of the network and their dynamics can be further disentangled through gene-stacking approaches and ultimately through mathematical modelling. In this review, we describe these different approaches that should help to obtain a holistic image of the molecular regulation of organ growth which is of high interest in view of the increasing needs for plant-derived products.

Establishment and Drug Sensitivity, Gene Expression and Epigenetic Characterization of a Pediatric Leukemia Cell Line (POETIC1) with Primary Resistance to Decitabine

Introduction: Epigenetic alterations leading to the silencing of key tumor suppressor genes by promoter hypermethylation have been implicated in the pathogenesis of a number of malignancies, including MDS and AML. Currently, the prototypical DNA methyltransferase inhibitor 5-aza-2′-deoxycytidine (decitabine) has been studied in a number of diverse protocols as an anti-leukemic agent. However, the pattern of non-responsiveness to decitabine appears to be complex and multifactorial with some patients showing primary resistance whereas others develop resistance following initial responsiveness. To further understand the molecular mechanisms that define growth regulatory networks in pediatric AML, we have established and performed initial characterization using primary blasts that showed increased cell survival and proliferation in the presence of decitabine.Methods: Bone marrow leukemic blasts from a relapsed pediatric AML patient, who received only conventional chemotherapy, were obtained following local REB approval and informed parental consent. Upon in vitro culture to identify effective therapeutic agents, enhanced cell survival was noted in wells containing decitabine (1uM) compared to untreated cells. This cell population was further expanded in higher concentrations of decitabine that tolerated concentrations higher than 10 uM. These cells were then clonally expanded, and the resulting cell line designated POETIC1, was screened in growth inhibition assays against a panel of 142 pharmaceutical pipe-line agents that target known growth regulatory pathways and signaling molecules. The original primary leukemic cells and normal lymphocytes were used as control. Gene expression analyses were carried out using humanHT-12 v4 Expression BeadChip whole-genome expression arrays, normalized and analyzed using the Illumina BeadStudio Software. The distribution and plasticity, and quantity of DNA methylation were studied using the Illumina Infinium Human Methylation BeadChip Assay.Results: POETIC1 cells showed a differential drug sensitivity in approximately 20% of the agents tested. This includes enhanced susceptibility to agents that interfere with cell cycle regulation such as aurora kinase inhibitors, PLK, HDAC inhibitors and agents that targeted mTOR and proteasome activities. Transcriptome profiling revealed that 399 genes were down-regulated and 977 were up-regulated in the leukemia cells, compared to normal controls. POETIC 1 cells had significantly up-regulated DNA repair, cell cycle, oxidative phosphorylation and many other pro-survival pathways. Pathway analysis revealed that up-regulated genes belonged to cell cycle control and pro-survival signalling pathways including genes encoding for cyclins A and B, Cdc 7, Cdc 20 among others. They also had down-regulated genes relating to apoptosis, endocytosis and cell differentiation pathways. Global DNA methylome analysis revealed profound genome-wide deregulation of DNA methylation in POETIC 1 cells with a large number of genes were differentially methylated, including those involved in the control of cell cycle, oxidative phosphorylation, apoptosis and DNA repair pathways.Discussion: Our findings indicate aberrant cell cycle and metabolic pathways in leukemia cells with primary resistance to decitabine. The POETIC1 cell line, provides a critical experimental tool to investigate the role of epigenetic alterations in leukemogenesis as well as the molecular and physiological mechanisms that define primary resistance to methyltransferase inhibitors and facilitate the identification of novel therapeutic agents for refractory disease in future clinical studies. DisclosuresNo relevant conflicts of interest to declare.

IMP1 loss promotes enhanced recovery from acute colitis (899.3)

Background: mRNA‐binding proteins, including Mushashi1, Lin28b, and Igf2 mRNA‐binding protein 1 (IMP1), are newly recognized regulators of intestinal epithelial homeostasis via their effects on post‐transcriptional regulation of mRNAs comprising critical growth regulatory networks. Imp1‐null mice exhibit severe morphologic defects in the intestinal epithelium, yet the specific mechanisms of IMP1 in normal intestinal homeostasis and response to injury remain to be elucidated. We hypothesize that Imp1 modulates intestinal epithelial cell proliferation in response to acute inflammation.Methods: We generated mice with intestinal epithelial‐specific loss of Imp1 (VillinCre;Imp1flox/flox mice), treated with dextran sodium sulfate (DSS) and measured indices during recovery, as well as IL‐6 and IL‐1β, canonical pro‐inflammatory cytokines. Actively proliferating cells were evaluated using Ki67 staining.Results: Untreated VillinCre;Imp1floxed mice exhibit increased Ki67+ cells in the extra‐proliferative zone compared to controls. Upon DSS treatment followed by 2 days of recovery, VillinCre;Imp1flox/flox mice display decreased histological disease scores and lower cytokine expression compared to controls.Conclusions: VillinCre;Imp1flox/flox mice have enhanced recovery following DSS and a decreased immune response. Mislocalization of actively proliferating cells may be advantageous in this context, providing a novel link of IMP1 to intestinal epithelial regeneration.Grant Funding Source: Supported by: F32 DK093207‐01 (KEH), HHMI MRFP (ETL), NIH RO1 DK056645 (KEH, AKR), NIH UO1 DK085551

Gibberellins and DELLAs: central nodes in growth regulatory networks

Gibberellins (GAs) are growth-promoting phytohormones that were crucial in breeding improved semi-dwarf varieties during the green revolution. However, the molecular basis for GA-induced growth stimulation is poorly understood. In this review, we use light-regulated hypocotyl elongation as a case study, combined with a meta-analysis of available transcriptome data, to discuss the role of GAs as central nodes in networks connecting environmental inputs to growth. These networks are highly tissue-specific, with dynamic and rapid regulation that mostly occurs at the protein level, directly affecting the activity and transcription of effectors. New systems biology approaches addressing the role of GAs in growth should take these properties into account, combining tissue-specific interactomics, transcriptomics and modeling, to provide essential knowledge to fuel a second green revolution.

My body is a cage: mechanisms and modulation of plant cell growth

388 I. 388 II. 389 III. 389 IV. 390 V. 391 VI. 393 VII. 394 VIII. 398 399 References 399 SUMMARY: The wall surrounding plant cells provides protection from abiotic and biotic stresses, and support through the action of turgor pressure. However, the presence of this strong elastic wall also prevents cell movement and resists cell growth. This growth can be likened to extending a house from the inside, using extremely high pressures to push out the walls. Plants must increase cell volume in order to explore their environment, acquire nutrients and reproduce. Cell wall material must stretch and flow in a controlled manner and, concomitantly, new cell wall material must be deposited at the correct rate and site to prevent wall and cell rupture. In this review, we examine biomechanics, cell wall structure and growth regulatory networks to provide a 'big picture' of plant cell growth.

Mapping the human phosphatome on growth pathways.

Large-scale siRNA screenings allow linking the function of poorly characterized genes to phenotypic readouts. According to this strategy, genes are associated with a function of interest if the alteration of their expression perturbs the phenotypic readouts. However, given the intricacy of the cell regulatory network, the mapping procedure is low resolution and the resulting models provide little mechanistic insights. We have developed a new strategy that combines multiparametric analysis of cell perturbation with logic modeling to achieve a more detailed functional mapping of human genes onto complex pathways. A literature-derived optimized model is used to infer the cell activation state following upregulation or downregulation of the model entities. By matching this signature with the experimental profile obtained in the high-throughput siRNA screening it is possible to infer the target of each protein, thus defining its 'entry point' in the network. By this novel approach, 41 phosphatases that affect key growth pathways were identified and mapped onto a human epithelial cell-specific growth model, thus providing insights into the mechanisms underlying their function.

The Hippo pathway and apico–basal cell polarity

The establishment and maintenance of apico-basal cell polarity is a pre-requisite for the formation of a functioning epithelial tissue. Many lines of evidence suggest that cell polarity perturbations favour cancer formation, even though the mechanistic basis for this link remains unclear. Studies in Drosophila have uncovered complex interactions between the conserved Hpo (Hippo) tumour suppressor pathway and apico-basal polarity determinants. The Hpo pathway is a crucial growth regulatory network whose inactivation in Drosophila epithelial tissues induces massive overproliferation. Its core consists of a phosphorylation cascade (comprising the kinases Hpo and Warts) that mediates the inactivation of the pro-growth transcriptional co-activator Yki [Yorkie; YAP (Yes-associated protein) in mammals]. Several apically located proteins, such as Merlin, Expanded or Kibra, have been identified as upstream regulators of the Hpo pathway, leading to the notion that an apical multi-molecular complex modulates core kinase activity and promotes Yki/YAP inactivation. In the present review, we explore the links between apico-basal polarity and Hpo signalling. We focus on the regulation of Yki/YAP by apical proteins, but also on how the Hpo pathway might in turn influence apical domain size as part of a regulatory feedback loop.