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Kosikova T, Philp D. Exploring the emergence of complexity using synthetic replicators. Chem Soc Rev 2018; 46:7274-7305. [PMID: 29099123 DOI: 10.1039/c7cs00123a] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A significant number of synthetic systems capable of replicating themselves or entities that are complementary to themselves have appeared in the last 30 years. Building on an understanding of the operation of synthetic replicators in isolation, this field has progressed to examples where catalytic relationships between replicators within the same network and the extant reaction conditions play a role in driving phenomena at the level of the whole system. Systems chemistry has played a pivotal role in the attempts to understand the origin of biological complexity by exploiting the power of synthetic chemistry, in conjunction with the molecular recognition toolkit pioneered by the field of supramolecular chemistry, thereby permitting the bottom-up engineering of increasingly complex reaction networks from simple building blocks. This review describes the advances facilitated by the systems chemistry approach in relating the expression of complex and emergent behaviour in networks of replicators with the connectivity and catalytic relationships inherent within them. These systems, examined within well-stirred batch reactors, represent conceptual and practical frameworks that can then be translated to conditions that permit replicating systems to overcome the fundamental limits imposed on selection processes in networks operating under closed conditions. This shift away from traditional spatially homogeneous reactors towards dynamic and non-equilibrium conditions, such as those provided by reaction-diffusion reaction formats, constitutes a key change that mimics environments within cellular systems, which possess obvious compartmentalisation and inhomogeneity.
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Affiliation(s)
- Tamara Kosikova
- School of Chemistry and EaStCHEM, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK.
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52
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Zhang XY, Trame MN, Lesko LJ, Schmidt S. Sobol Sensitivity Analysis: A Tool to Guide the Development and Evaluation of Systems Pharmacology Models. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2018; 4:69-79. [PMID: 27548289 PMCID: PMC5006244 DOI: 10.1002/psp4.6] [Citation(s) in RCA: 139] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 10/18/2014] [Indexed: 02/06/2023]
Abstract
A systems pharmacology model typically integrates pharmacokinetic, biochemical network, and systems biology concepts into a unifying approach. It typically consists of a large number of parameters and reaction species that are interlinked based upon the underlying (patho)physiology and the mechanism of drug action. The more complex these models are, the greater the challenge of reliably identifying and estimating respective model parameters. Global sensitivity analysis provides an innovative tool that can meet this challenge. CPT Pharmacometrics Syst. Pharmacol. (2015) 4, 69-79; doi:10.1002/psp4.6; published online 25 February 2015.
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Affiliation(s)
- X-Y Zhang
- Department of Pharmaceutics, Center for Pharmacometrics and Systems Pharmacology, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - M N Trame
- Department of Pharmaceutics, Center for Pharmacometrics and Systems Pharmacology, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - L J Lesko
- Department of Pharmaceutics, Center for Pharmacometrics and Systems Pharmacology, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - S Schmidt
- Department of Pharmaceutics, Center for Pharmacometrics and Systems Pharmacology, College of Pharmacy, University of Florida, Orlando, Florida, USA
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Rogers KW, Lord ND, Gagnon JA, Pauli A, Zimmerman S, Aksel DC, Reyon D, Tsai SQ, Joung JK, Schier AF. Nodal patterning without Lefty inhibitory feedback is functional but fragile. eLife 2017; 6. [PMID: 29215332 PMCID: PMC5720593 DOI: 10.7554/elife.28785] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 11/07/2017] [Indexed: 12/12/2022] Open
Abstract
Developmental signaling pathways often activate their own inhibitors. Such inhibitory feedback has been suggested to restrict the spatial and temporal extent of signaling or mitigate signaling fluctuations, but these models are difficult to rigorously test. Here, we determine whether the ability of the mesendoderm inducer Nodal to activate its inhibitor Lefty is required for development. We find that zebrafish lefty mutants exhibit excess Nodal signaling and increased specification of mesendoderm, resulting in embryonic lethality. Strikingly, development can be fully restored without feedback: Lethal patterning defects in lefty mutants can be rescued by ectopic expression of lefty far from its normal expression domain or by spatially and temporally uniform exposure to a Nodal inhibitor drug. While drug-treated mutants are less tolerant of mild perturbations to Nodal signaling levels than wild type embryos, they can develop into healthy adults. These results indicate that patterning without inhibitory feedback is functional but fragile. During animal development, a single fertilized cell gives rise to different tissues and organs. This ‘patterning’ process depends on signaling molecules that instruct cells in different positions in the embryo to acquire different identities. To avoid mistakes during patterning, each cell must receive the correct amount of signal at the appropriate time. In a process called ‘inhibitory feedback’, a signaling molecule instructs cells to produce molecules that block its own signaling. Although inhibitory feedback is widely used during patterning in organisms ranging from sea urchins to mammals, its exact purpose is often not clear. In part this is because feedback is challenging to experimentally manipulate. Removing the inhibitor disrupts feedback, but also increases signaling. Since the effects of broken feedback and increased signaling are intertwined, any resulting developmental defects do not provide information about what feedback specifically does. In order to examine the role of feedback, it is therefore necessary to disconnect the production of the inhibitor from the signaling process. In developing embryos, a well-known signaling molecule called Nodal instructs cells to become specific types – for example, a heart or gut cell. Nodal also promotes the production of its inhibitor, Lefty. To understand how this feedback system works, Rogers, Lord et al. first removed Lefty from zebrafish embryos. These embryos had excessive levels of Nodal signaling, did not develop correctly, and could not survive. Bathing the embryos in a drug that inhibits Nodal reduced excess signaling and allowed them to develop successfully. In these drug-treated embryos, inhibitor production is disconnected from the signaling process, allowing the role of feedback to be examined. Drug-treated embryos were less able to tolerate fluctuations in Nodal signaling than normal zebrafish embryos, which could compensate for such disturbances by adjusting Lefty levels. Overall, it appears that inhibitory feedback in this patterning system is important to compensate for alterations in Nodal signaling, but is not essential for development. Understanding the role of inhibitory feedback will be useful for efforts to grow tissues and organs in the laboratory for clinical use. The results presented by Rogers, Lord et al. also suggest the possibility that drug treatments could be developed to help correct birth defects in the womb.
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Affiliation(s)
- Katherine W Rogers
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Nathan D Lord
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - James A Gagnon
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Andrea Pauli
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Steven Zimmerman
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Deniz C Aksel
- Program in Biophysics, Harvard Medical School, Boston, United States
| | - Deepak Reyon
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, United States.,Department of Pathology, Harvard Medical School, Boston, United States.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, United States
| | - Shengdar Q Tsai
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, United States.,Department of Pathology, Harvard Medical School, Boston, United States.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, United States
| | - J Keith Joung
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, United States.,Department of Pathology, Harvard Medical School, Boston, United States.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, United States
| | - Alexander F Schier
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States.,Broad Institute of MIT and Harvard University, Cambridge, United States.,Center for Brain Science, Harvard University, Cambridge, United States.,Harvard Stem Cell Institute, Harvard University, Cambridge, United States.,Center for Systems Biology, Harvard University, Cambridge, United States
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54
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Ligerot Y, de Saint Germain A, Waldie T, Troadec C, Citerne S, Kadakia N, Pillot JP, Prigge M, Aubert G, Bendahmane A, Leyser O, Estelle M, Debellé F, Rameau C. The pea branching RMS2 gene encodes the PsAFB4/5 auxin receptor and is involved in an auxin-strigolactone regulation loop. PLoS Genet 2017; 13:e1007089. [PMID: 29220348 PMCID: PMC5738142 DOI: 10.1371/journal.pgen.1007089] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 12/20/2017] [Accepted: 10/30/2017] [Indexed: 12/31/2022] Open
Abstract
Strigolactones (SLs) are well known for their role in repressing shoot branching. In pea, increased transcript levels of SL biosynthesis genes are observed in stems of highly branched SL deficient (ramosus1 (rms1) and rms5) and SL response (rms3 and rms4) mutants indicative of negative feedback control. In contrast, the highly branched rms2 mutant has reduced transcript levels of SL biosynthesis genes. Grafting studies and hormone quantification led to a model where RMS2 mediates a shoot-to-root feedback signal that regulates both SL biosynthesis gene transcript levels and xylem sap levels of cytokinin exported from roots. Here we cloned RMS2 using synteny with Medicago truncatula and demonstrated that it encodes a putative auxin receptor of the AFB4/5 clade. Phenotypes similar to rms2 were found in Arabidopsis afb4/5 mutants, including increased shoot branching, low expression of SL biosynthesis genes and high auxin levels in stems. Moreover, afb4/5 and rms2 display a specific resistance to the herbicide picloram. Yeast-two-hybrid experiments supported the hypothesis that the RMS2 protein functions as an auxin receptor. SL root feeding using hydroponics repressed auxin levels in stems and down-regulated transcript levels of auxin biosynthesis genes within one hour. This auxin down-regulation was also observed in plants treated with the polar auxin transport inhibitor NPA. Together these data suggest a homeostatic feedback loop in which auxin up-regulates SL synthesis in an RMS2-dependent manner and SL down-regulates auxin synthesis in an RMS3 and RMS4-dependent manner.
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Affiliation(s)
- Yasmine Ligerot
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
- Université Paris-Sud, Université Paris-Saclay, Orsay, France
| | | | - Tanya Waldie
- Sainsbury Laboratory Cambridge University, Bateman Street, Cambridge, United Kingdom
| | - Christelle Troadec
- Institute of Plant Sciences Paris-Saclay, INRA, CNRS, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Orsay, France
| | - Sylvie Citerne
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Nikita Kadakia
- Howard Hughes Medical Institute and Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Jean-Paul Pillot
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Michael Prigge
- Howard Hughes Medical Institute and Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Grégoire Aubert
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris-Saclay, INRA, CNRS, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Orsay, France
| | - Ottoline Leyser
- Sainsbury Laboratory Cambridge University, Bateman Street, Cambridge, United Kingdom
| | - Mark Estelle
- Howard Hughes Medical Institute and Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Frédéric Debellé
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Catherine Rameau
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
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55
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Oide S, Inui M. Trehalose acts as a uridine 5'-diphosphoglucose-competitive inhibitor of trehalose 6-phosphate synthase in Corynebacterium glutamicum. FEBS J 2017; 284:4298-4313. [PMID: 29076621 DOI: 10.1111/febs.14309] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 10/06/2017] [Accepted: 10/24/2017] [Indexed: 12/30/2022]
Abstract
Trehalose is a compatible solute widely distributed in nature. The most prevalent pathway for its synthesis starts from condensation of glucose 6-phosphate (Glc6P) and uridine 5'-diphosphoglucose (UDP-Glc) catalyzed by trehalose 6-phosphate synthase (TPS). A previous laboratory evolution experiment with the bacterium Corynebacterium glutamicum generated strains adapted to supraoptimal temperatures, and the R328H substitution of the TPS encoded by otsA was shown to be associated with thermotolerance acquired by the evolved strains. In this study, we found that the OtsA:R328H substitution promotes both intra- and extracellular trehalose accumulation and demonstrated that build-up of intracellular trehalose accounts for the OtsAR328H -dependent thermotolerance, using the mycobacterial trehalose-specific transporter. Counterintuitively, characterization of the recombinant OtsA proteins revealed that the mutation downshifts the temperature optimum of OtsA. A search for the molecular basis of OtsAR328H -dependent enhancement of trehalose synthesis led to the unexpected findings that trehalose is an effective inhibitor of OtsA and that OtsAR328H is highly tolerant to the trehalose-mediated inhibition. The only available report on such feedback regulation of TPS is for the silk moth from over 50 years ago [Murphy TA and Wyatt GR (1965) J Biol Chem 240, 1500-1508]. While trehalose acts as a Glc6P-competitive inhibitor in the silk moth, the disaccharide was found to inhibit OtsA in a UDP-Glc-competitive manner in C. glutamicum, suggesting independent origins of the negative feedback regulations found for the two species. We showed that overexpression of the wild-type OtsA counteracts the trehalose-dependent regulation and restores the evolved strain-like phenotype to the isogenic wild-type otsA revertant, demonstrating that thermotolerance conferred by OtsAR328H is attributable to its feedback-resistant property.
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Affiliation(s)
- Shinichi Oide
- Research Institute of Innovative Technology for the Earth, Kizugawa, Japan
| | - Masayuki Inui
- Research Institute of Innovative Technology for the Earth, Kizugawa, Japan.,Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Japan
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56
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Chen BS, Wu WS. Underlying Principles of Natural Selection in Network Evolution: Systems Biology Approach. Evol Bioinform Online 2017. [DOI: 10.1177/117693430700300010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Systems biology is a rapidly expanding field that integrates diverse areas of science such as physics, engineering, computer science, mathematics, and biology toward the goal of elucidating the underlying principles of hierarchical metabolic and regulatory systems in the cell, and ultimately leading to predictive understanding of cellular response to perturbations. Because post-genomics research is taking place throughout the tree of life, comparative approaches offer a way for combining data from many organisms to shed light on the evolution and function of biological networks from the gene to the organismal level. Therefore, systems biology can build on decades of theoretical work in evolutionary biology, and at the same time evolutionary biology can use the systems biology approach to go in new uncharted directions. In this study, we present a review of how the post-genomics era is adopting comparative approaches and dynamic system methods to understand the underlying design principles of network evolution and to shape the nascent field of evolutionary systems biology. Finally, the application of evolutionary systems biology to robust biological network designs is also discussed from the synthetic biology perspective.
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Affiliation(s)
- Bor-Sen Chen
- Lab of Control and Systems Biology, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Wei-Sheng Wu
- Lab of Control and Systems Biology, National Tsing Hua University, Hsinchu, 300, Taiwan
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57
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Chen BS, Wu WS, Wu WS, Li WH. On the Adaptive Design Rules of Biochemical Networks in Evolution. Evol Bioinform Online 2017. [DOI: 10.1177/117693430700300009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Biochemical networks are the backbones of physiological systems of organisms. Therefore, a biochemical network should be sufficiently robust (not sensitive) to tolerate genetic mutations and environmental changes in the evolutionary process. In this study, based on the robustness and sensitivity criteria of biochemical networks, the adaptive design rules are developed for natural selection in the evolutionary process. This will provide insights into the robust adaptive mechanism of biochemical networks in the evolutionary process. We find that if a mutated biochemical network satisfies the robustness and sensitivity criteria of natural selection, there is a high probability for the biochemical network to prevail during natural selection in the evolutionary process. Since there are various mutated biochemical networks that can satisfy these criteria but have some differences in phenotype, the biochemical networks increase their diversities in the evolutionary process. The robustness of a biochemical network enables co-option so that new phenotypes can be generated in evolution. The proposed robust adaptive design rules of natural selection gain much insight into the evolutionary mechanism and provide a systematic robust biochemical circuit design method of biochemical networks for biotechnological and therapeutic purposes in the future.
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Affiliation(s)
- Bor-Sen Chen
- Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Wan-Shian Wu
- Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Wei-Sheng Wu
- Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Wen-Hsiung Li
- Department of Evolution and Ecology, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, U.S.A
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
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58
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Mathematical comparison of memory functions between mutual activation and repression networks in a stochastic environment. J Theor Biol 2017; 427:28-40. [PMID: 28587744 DOI: 10.1016/j.jtbi.2017.05.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 05/31/2017] [Accepted: 05/31/2017] [Indexed: 11/23/2022]
Abstract
Biological memory is a ubiquitous function that can generate a sustained response to a transient inductive stimulus. To better understand this function, we must consider the mechanisms by which different structures of genetic networks achieve memory. Here, we investigated two competitive gene regulatory network models: the regulated mutual activation network (MAN) and the regulated mutual repression network (MRN). Stochasticity deteriorated the persistence of memory of both the MAN and the MRN. Mathematical comparison by simulation and theoretical analysis identified functional differences in the stochastic memory between the competitive models: specifically, the MAN provided much more robust, persistent memory than the MRN. The stochastic persistent memory pattern of the MAN can be adjusted by changing the binding strength of the activators, whereas the MRN required highly cooperative and strong binding repressors for robust memory.
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59
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Ji L, Jiang B, Jiang X, Charlat O, Chen A, Mickanin C, Bauer A, Xu W, Yan X, Cong F. The SIAH E3 ubiquitin ligases promote Wnt/β-catenin signaling through mediating Wnt-induced Axin degradation. Genes Dev 2017; 31:904-915. [PMID: 28546513 PMCID: PMC5458757 DOI: 10.1101/gad.300053.117] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 05/08/2017] [Indexed: 11/25/2022]
Abstract
In this study, Ji et al. identify SIAH1/2 (SIAH) as the E3 ligase mediating Wnt-induced Axin degradation. Their results suggest that Wnt-induced dissociation of the Axin/GSK3 complex allows SIAH to interact with Axin and promote its degradation, which represents an important feed-forward mechanism to achieve sustained Wnt/β-catenin signaling. The Wnt/β-catenin signaling pathway plays essential roles in embryonic development and adult tissue homeostasis. Axin is a concentration-limiting factor responsible for the formation of the β-catenin destruction complex. Wnt signaling itself promotes the degradation of Axin. However, the underlying molecular mechanism and biological relevance of this targeting of Axin have not been elucidated. Here, we identify SIAH1/2 (SIAH) as the E3 ligase mediating Wnt-induced Axin degradation. SIAH proteins promote the ubiquitination and proteasomal degradation of Axin through interacting with a VxP motif in the GSK3-binding domain of Axin, and this function of SIAH is counteracted by GSK3 binding to Axin. Structural analysis reveals that the Axin segment responsible for SIAH binding is also involved in GSK3 binding but adopts distinct conformations in Axin/SIAH and Axin/GSK3 complexes. Knockout of SIAH1 blocks Wnt-induced Axin ubiquitination and attenuates Wnt-induced β-catenin stabilization. Our data suggest that Wnt-induced dissociation of the Axin/GSK3 complex allows SIAH to interact with Axin not associated with GSK3 and promote its degradation and that SIAH-mediated Axin degradation represents an important feed-forward mechanism to achieve sustained Wnt/β-catenin signaling.
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Affiliation(s)
- Lei Ji
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Bo Jiang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaomo Jiang
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Olga Charlat
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Amy Chen
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Craig Mickanin
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Andreas Bauer
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Wenqing Xu
- Department of Biological Structure, University of Washington, Seattle, Washington 98195, USA
| | - Xiaoxue Yan
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Feng Cong
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
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60
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Ceylan H, Giltinan J, Kozielski K, Sitti M. Mobile microrobots for bioengineering applications. LAB ON A CHIP 2017; 17:1705-1724. [PMID: 28480466 DOI: 10.1039/c7lc00064b] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Untethered micron-scale mobile robots can navigate and non-invasively perform specific tasks inside unprecedented and hard-to-reach inner human body sites and inside enclosed organ-on-a-chip microfluidic devices with live cells. They are aimed to operate robustly and safely in complex physiological environments where they will have a transforming impact in bioengineering and healthcare. Research along this line has already demonstrated significant progress, increasing attention, and high promise over the past several years. The first-generation microrobots, which could deliver therapeutics and other cargo to targeted specific body sites, have just been started to be tested inside small animals toward clinical use. Here, we review frontline advances in design, fabrication, and testing of untethered mobile microrobots for bioengineering applications. We convey the most impactful and recent strategies in actuation, mobility, sensing, and other functional capabilities of mobile microrobots, and discuss their potential advantages and drawbacks to operate inside complex, enclosed and physiologically relevant environments. We lastly draw an outlook to provide directions in the veins of more sophisticated designs and applications, considering biodegradability, immunogenicity, mobility, sensing, and possible medical interventions in complex microenvironments.
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Affiliation(s)
- Hakan Ceylan
- Physical Intelligence Department, Max Planck Institute for Intelligent Systems, 70569 Stuttgart, Germany.
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61
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Sawanth SK, Gopinath G, Sambrani N, Arunkumar KP. The autoregulatory loop: A common mechanism of regulation of key sex determining genes in insects. J Biosci 2017; 41:283-94. [PMID: 27240989 DOI: 10.1007/s12038-016-9609-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sex determination in most insects is structured as a gene cascade, wherein a primary signal is passed through a series of sex-determining genes, culminating in a downstream double-switch known as doublesex that decides the sexual fate of the embryo. From the literature available on sex determination cascades, it becomes apparent that sex determination mechanisms have evolved rapidly. The primary signal that provides the cue to determine the sex of the embryo varies remarkably, not only among taxa, but also within taxa. Furthermore, the upstream key gene in the cascade also varies between species and even among closely related species. The order Insecta alone provides examples of astoundingly complex diversity of upstream key genes in sex determination mechanisms. Besides, unlike key upstream genes, the downstream double-switch gene is alternatively spliced to form functional sex-specific isoforms. This sex-specific splicing is conserved across insect taxa. The genes involved in the sex determination cascade such as Sex-lethal (Sxl) in Drosophila melanogaster, transformer (tra) in many other dipterans, coleopterans and hymenopterans, Feminizer (fem) in Apis mellifera, and IGF-II mRNA-binding protein (Bmimp) in Bombyx mori are reported to be regulated by an autoregulatory positive feedback loop. In this review, by taking examples from various insects, we propose the hypothesis that autoregulatory loop mechanisms of sex determination might be a general strategy. We also discuss the possible reasons for the evolution of autoregulatory loops in sex determination cascades and their impact on binary developmental choices.
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Affiliation(s)
- Suresh Kumar Sawanth
- Centre of Excellence for Genetics and Genomics of Silkmoths, Laboratory of Molecular Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500 001, India
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62
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Jensch A, Thomaseth C, Radde NE. Sampling-based Bayesian approaches reveal the importance of quasi-bistable behavior in cellular decision processes on the example of the MAPK signaling pathway in PC-12 cell lines. BMC SYSTEMS BIOLOGY 2017; 11:11. [PMID: 28122551 PMCID: PMC5267478 DOI: 10.1186/s12918-017-0392-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 01/06/2017] [Indexed: 12/21/2022]
Abstract
BACKGROUND Positive and negative feedback loops are ubiquitous motifs in biochemical signaling pathways. The mitogen-activated protein kinase (MAPK) pathway module is part of many distinct signaling networks and comprises several of these motifs, whose functioning depends on the cell line at hand and on the particular context. The maintainance of specificity of the response of the MAPK module to distinct stimuli has become a key paradigm especially in PC-12 cells, where the same module leads to different cell fates, depending on the stimulating growth factor. This cell fate is regulated by differences in the ERK (MAPK) activation profile, which shows a transient response upon stimulation with EGF, while the response is sustained in case of NGF. This behavior was explained by different effective network topologies. It is widely believed that this sustained response requires a bistable system. RESULTS In this study we present a sampling-based Bayesian model analysis on a dataset, in which PC-12 cells have been stimulated with different growth factors. This is combined with novel analysis methods to investigate the role of feedback interconnections to shape ERK response. Results strongly suggest that, besides bistability, an additional effect called quasi-bistability can contribute to explain the observed responses of the system to different stimuli. Quasi-bistability is the ability of a monostable system to maintain two distinct states over a long time period upon a transient signal, which is also related to positive feedback, but cannot be detected by standard steady state analysis methods. CONCLUSIONS Although applied on a specific example, our framework is generic enough to be also relevant for other regulatory network modeling studies that comprise positive feedback to explain cellular decision making processes. Overall, this study advices to focus not only on steady states, but also to take transient behavior into account in the analysis.
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Affiliation(s)
- Antje Jensch
- Institute for Systems Theory and Automatic Control, University of Stuttgart, Pfaffenwaldring 9, Stuttgart, 70569, Germany
| | - Caterina Thomaseth
- Institute for Systems Theory and Automatic Control, University of Stuttgart, Pfaffenwaldring 9, Stuttgart, 70569, Germany
| | - Nicole E Radde
- Institute for Systems Theory and Automatic Control, University of Stuttgart, Pfaffenwaldring 9, Stuttgart, 70569, Germany.
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63
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Abstract
A negative feedback loop that relies on the coordination-coupled deprotonation (CCD) of a hydrazone switch has been developed. Above a particular threshold of zinc(II), CCD releases enough protons to the environment to trigger a cascade of reactions that yield an imine. This imine sequesters the excess of zinc(II) from the hydrazone switch, hence lowering the effective amount of protons, and switching the cascade reactions "OFF", thus establishing the negative feedback loop.
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Affiliation(s)
- Susnata Pramanik
- Department of Chemistry, Dartmouth College , Hanover, New Hampshire 03755, United States
| | - Ivan Aprahamian
- Department of Chemistry, Dartmouth College , Hanover, New Hampshire 03755, United States
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64
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Doriguzzi A, Salhi J, Sutterlüty-Fall H. Sprouty4 mRNA variants and protein expressions in breast and lung-derived cells. Oncol Lett 2016; 12:4161-4166. [PMID: 27895786 DOI: 10.3892/ol.2016.5216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 07/22/2016] [Indexed: 01/20/2023] Open
Abstract
Sprouty proteins are modulators of mitogen-induced signalling processes and are therefore hypothesized to affect malignant diseases. As a member of the Sprouty family, Sprouty4 has been previously shown to function as a tumour suppressor in lung and breast cancer. The present study analysed the expression of two known Sprouty4 splice variants in cells established from malignant and normal lung and breast tissues using semi-quantitative reverse transcription-polymerase chain reaction and immunoblotting. The results indicated that the expression of the two messenger RNA (mRNA) variants was reduced in the cells derived from malignant tissue in comparison to the normal counterparts. Although the expression of the two splice variants were associated in both tissue types, on average, the relative expression of the longer variant was slightly increased in malignant cells compared with normal tissues. Notably, the protein levels reflected the expression observed at the mRNA level only in breast-derived cells. Contrarily, with regards to the measured mRNA levels, Sprouty4 protein was disproportional augmented in lung cells known to harbour the mutated K-Ras gene.
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Affiliation(s)
- Angelina Doriguzzi
- Institute of Cancer Research, Comprehensive Cancer Center, Department of Medicine I, Medical University of Vienna, A-1090 Vienna, Austria
| | - Jihen Salhi
- Institute of Cancer Research, Comprehensive Cancer Center, Department of Medicine I, Medical University of Vienna, A-1090 Vienna, Austria
| | - Hedwig Sutterlüty-Fall
- Institute of Cancer Research, Comprehensive Cancer Center, Department of Medicine I, Medical University of Vienna, A-1090 Vienna, Austria
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65
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Tape CJ. Systems Biology Analysis of Heterocellular Signaling. Trends Biotechnol 2016; 34:627-637. [DOI: 10.1016/j.tibtech.2016.02.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 02/26/2016] [Accepted: 02/29/2016] [Indexed: 10/22/2022]
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66
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Saadatpour A, Albert R. A comparative study of qualitative and quantitative dynamic models of biological regulatory networks. ACTA ACUST UNITED AC 2016. [DOI: 10.1140/epjnbp/s40366-016-0031-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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67
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Di Camillo B, Carlon A, Eduati F, Toffolo GM. A rule-based model of insulin signalling pathway. BMC SYSTEMS BIOLOGY 2016; 10:38. [PMID: 27245161 PMCID: PMC4888568 DOI: 10.1186/s12918-016-0281-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 05/12/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUND The insulin signalling pathway (ISP) is an important biochemical pathway, which regulates some fundamental biological functions such as glucose and lipid metabolism, protein synthesis, cell proliferation, cell differentiation and apoptosis. In the last years, different mathematical models based on ordinary differential equations have been proposed in the literature to describe specific features of the ISP, thus providing a description of the behaviour of the system and its emerging properties. However, protein-protein interactions potentially generate a multiplicity of distinct chemical species, an issue referred to as "combinatorial complexity", which results in defining a high number of state variables equal to the number of possible protein modifications. This often leads to complex, error prone and difficult to handle model definitions. RESULTS In this work, we present a comprehensive model of the ISP, which integrates three models previously available in the literature by using the rule-based modelling (RBM) approach. RBM allows for a simple description of a number of signalling pathway characteristics, such as the phosphorylation of signalling proteins at multiple sites with different effects, the simultaneous interaction of many molecules of the signalling pathways with several binding partners, and the information about subcellular localization where reactions take place. Thanks to its modularity, it also allows an easy integration of different pathways. After RBM specification, we simulated the dynamic behaviour of the ISP model and validated it using experimental data. We the examined the predicted profiles of all the active species and clustered them in four clusters according to their dynamic behaviour. Finally, we used parametric sensitivity analysis to show the role of negative feedback loops in controlling the robustness of the system. CONCLUSIONS The presented ISP model is a powerful tool for data simulation and can be used in combination with experimental approaches to guide the experimental design. The model is available at http://sysbiobig.dei.unipd.it/ was submitted to Biomodels Database ( https://www.ebi.ac.uk/biomodels-main/ # MODEL 1604100005).
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Affiliation(s)
- Barbara Di Camillo
- Department of Information Engineering, University of Padova, Via Gradenigo 6A, Padova, 35131, Italy
| | - Azzurra Carlon
- Department of Information Engineering, University of Padova, Via Gradenigo 6A, Padova, 35131, Italy.,Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Florence, Italy
| | - Federica Eduati
- Department of Information Engineering, University of Padova, Via Gradenigo 6A, Padova, 35131, Italy.,European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK
| | - Gianna Maria Toffolo
- Department of Information Engineering, University of Padova, Via Gradenigo 6A, Padova, 35131, Italy.
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68
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Regulation of FGF signaling: Recent insights from studying positive and negative modulators. Semin Cell Dev Biol 2016; 53:101-14. [DOI: 10.1016/j.semcdb.2016.01.023] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 01/19/2016] [Indexed: 11/19/2022]
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69
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Konstorum A, Hillen T, Lowengrub J. Feedback Regulation in a Cancer Stem Cell Model can Cause an Allee Effect. Bull Math Biol 2016; 78:754-785. [PMID: 27113934 DOI: 10.1007/s11538-016-0161-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 03/15/2016] [Indexed: 12/24/2022]
Abstract
The exact mechanisms of spontaneous tumor remission or complete response to treatment are phenomena in oncology that are not completely understood. We use a concept from ecology, the Allee effect, to help explain tumor extinction in a model of tumor growth that incorporates feedback regulation of stem cell dynamics, which occurs in many tumor types where certain signaling molecules, such as Wnts, are upregulated. Due to feedback and the Allee effect, a tumor may become extinct spontaneously or after therapy even when the entire tumor has not been eradicated by the end of therapy. We quantify the Allee effect using an 'Allee index' that approximates the area of the basin of attraction for tumor extinction. We show that effectiveness of combination therapy in cancer treatment may occur due to the increased probability that the system will be in the Allee region after combination treatment versus monotherapy. We identify therapies that can attenuate stem cell self-renewal, alter the Allee region and increase its size. We also show that decreased response of tumor cells to growth inhibitors can reduce the size of the Allee region and increase stem cell densities, which may help to explain why this phenomenon is a hallmark of cancer.
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Affiliation(s)
- Anna Konstorum
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA.
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA.
- Center for Quantitative Medicine, University of Connecticut Health Center, Farmington, CT, USA.
| | - Thomas Hillen
- Centre for Mathematical Biology, University of Alberta, Edmonton, AB, Canada
| | - John Lowengrub
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA.
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA.
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, USA.
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70
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Beller M, Blanke S, Brentrup D, Jäckle H. Identification and expression of Ima, a novel Ral-interacting Drosophila protein. Mech Dev 2016; 119 Suppl 1:S253-60. [PMID: 14516694 DOI: 10.1016/s0925-4773(03)00125-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We report the identification of Ima, a novel Drosophila MAGUK-like protein, which contains two WW and four PDZ protein interaction domains and interacts with the small GTPase dRal in the yeast two-hybrid system and pull-down assays. The gene is expressed in distinct spatiotemporal patterns throughout embryonic development. Overexpression of Ima interferes with normal Drosophila development, indicating that the gene functions in a tissue specific manner.
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Affiliation(s)
- Mathias Beller
- Abteilung Molekulare Entwicklungsbiologie, Max-Planck-Institut für biophysikalische Chemie, Am Fassberg, 37077 Göttingen, Germany
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71
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Li S, Zhu X, Liu B, Wang G, Ao P. Endogenous molecular network reveals two mechanisms of heterogeneity within gastric cancer. Oncotarget 2016; 6:13607-27. [PMID: 25962957 PMCID: PMC4537037 DOI: 10.18632/oncotarget.3633] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 04/10/2015] [Indexed: 12/20/2022] Open
Abstract
Intratumor heterogeneity is a common phenomenon and impedes cancer therapy and research. Gastric cancer (GC) cells have generally been classified into two heterogeneous cellular phenotypes, the gastric and intestinal types, yet the mechanisms of maintaining two phenotypes and controlling phenotypic transition are largely unknown. A qualitative systematic framework, the endogenous molecular network hypothesis, has recently been proposed to understand cancer genesis and progression. Here, a minimal network corresponding to such framework was found for GC and was quantified via a stochastic nonlinear dynamical system. We then further extended the framework to address the important question of intratumor heterogeneity quantitatively. The working network characterized main known features of normal gastric epithelial and GC cell phenotypes. Our results demonstrated that four positive feedback loops in the network are critical for GC cell phenotypes. Moreover, two mechanisms that contribute to GC cell heterogeneity were identified: particular positive feedback loops are responsible for the maintenance of intestinal and gastric phenotypes; GC cell progression routes that were revealed by the dynamical behaviors of individual key components are heterogeneous. In this work, we constructed an endogenous molecular network of GC that can be expanded in the future and would broaden the known mechanisms of intratumor heterogeneity.
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Affiliation(s)
- Site Li
- Shanghai Center for Systems Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | | | - Bingya Liu
- Shanghai Center for Systems Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.,Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Gaowei Wang
- Shanghai Center for Systems Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ping Ao
- Shanghai Center for Systems Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.,State Key Laboratory for Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China.,Department of Physics, Shanghai Jiao Tong University, Shanghai 200240, China
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72
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Molecular basis for cytokine biomarkers of complex 3D microtissue physiology in vitro. Drug Discov Today 2016; 21:950-61. [PMID: 27021792 DOI: 10.1016/j.drudis.2016.03.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 02/05/2016] [Accepted: 03/16/2016] [Indexed: 11/24/2022]
Abstract
'Physiologically more-relevant' claims are readily made for cells cultured on any surface or in a scaffold that provides loosely defined 3D geometry. A set of tools to measure culture '3D-ness' more accurately are needed. Such tools should find applications in fields ranging from high-throughput identification of substrates for tissue engineering and regenerative medicine to cell-based screening of drug candidates. Until now, these fields have not provided a consensus for the most promising place to initiate the search. Here, we review recent advances in transcriptomic, proteomic, inflammation and oncology-related pathways, as well as functional studies that strongly point to cytokines as the most likely compounds to form the missing consensus.
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73
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Abelin JG, Patel J, Lu X, Feeney CM, Fagbami L, Creech AL, Hu R, Lam D, Davison D, Pino L, Qiao JW, Kuhn E, Officer A, Li J, Abbatiello S, Subramanian A, Sidman R, Snyder E, Carr SA, Jaffe JD. Reduced-representation Phosphosignatures Measured by Quantitative Targeted MS Capture Cellular States and Enable Large-scale Comparison of Drug-induced Phenotypes. Mol Cell Proteomics 2016; 15:1622-41. [PMID: 26912667 DOI: 10.1074/mcp.m116.058354] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Indexed: 12/11/2022] Open
Abstract
Profiling post-translational modifications represents an alternative dimension to gene expression data in characterizing cellular processes. Many cellular responses to drugs are mediated by changes in cellular phosphosignaling. We sought to develop a common platform on which phosphosignaling responses could be profiled across thousands of samples, and created a targeted MS assay that profiles a reduced-representation set of phosphopeptides that we show to be strong indicators of responses to chemical perturbagens.To develop the assay, we investigated the coordinate regulation of phosphosites in samples derived from three cell lines treated with 26 different bioactive small molecules. Phosphopeptide analytes were selected from these discovery studies by clustering and picking 1 to 2 proxy members from each cluster. A quantitative, targeted parallel reaction monitoring assay was developed to directly measure 96 reduced-representation probes. Sample processing for proteolytic digestion, protein quantification, peptide desalting, and phosphopeptide enrichment have been fully automated, making possible the simultaneous processing of 96 samples in only 3 days, with a plate phosphopeptide enrichment variance of 12%. This highly reproducible process allowed ∼95% of the reduced-representation phosphopeptide probes to be detected in ∼200 samples.The performance of the assay was evaluated by measuring the probes in new samples generated under treatment conditions from discovery experiments, recapitulating the observations of deeper experiments using a fraction of the analytical effort. We measured these probes in new experiments varying the treatments, cell types, and timepoints to demonstrate generalizability. We demonstrated that the assay is sensitive to disruptions in common signaling pathways (e.g. MAPK, PI3K/mTOR, and CDK). The high-throughput, reduced-representation phosphoproteomics assay provides a platform for the comparison of perturbations across a range of biological conditions, suitable for profiling thousands of samples. We believe the assay will prove highly useful for classification of known and novel drug and genetic mechanisms through comparison of phosphoproteomic signatures.
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Affiliation(s)
- Jennifer G Abelin
- From the ‡Broad Institute of MIT and Harvard, 415 Main St. Cambridge, Massachusetts 02142
| | - Jinal Patel
- From the ‡Broad Institute of MIT and Harvard, 415 Main St. Cambridge, Massachusetts 02142
| | - Xiaodong Lu
- From the ‡Broad Institute of MIT and Harvard, 415 Main St. Cambridge, Massachusetts 02142
| | - Caitlin M Feeney
- From the ‡Broad Institute of MIT and Harvard, 415 Main St. Cambridge, Massachusetts 02142
| | - Lola Fagbami
- From the ‡Broad Institute of MIT and Harvard, 415 Main St. Cambridge, Massachusetts 02142
| | - Amanda L Creech
- From the ‡Broad Institute of MIT and Harvard, 415 Main St. Cambridge, Massachusetts 02142
| | - Roger Hu
- From the ‡Broad Institute of MIT and Harvard, 415 Main St. Cambridge, Massachusetts 02142
| | - Daniel Lam
- From the ‡Broad Institute of MIT and Harvard, 415 Main St. Cambridge, Massachusetts 02142
| | - Desiree Davison
- From the ‡Broad Institute of MIT and Harvard, 415 Main St. Cambridge, Massachusetts 02142
| | - Lindsay Pino
- From the ‡Broad Institute of MIT and Harvard, 415 Main St. Cambridge, Massachusetts 02142
| | - Jana W Qiao
- From the ‡Broad Institute of MIT and Harvard, 415 Main St. Cambridge, Massachusetts 02142
| | - Eric Kuhn
- From the ‡Broad Institute of MIT and Harvard, 415 Main St. Cambridge, Massachusetts 02142
| | - Adam Officer
- From the ‡Broad Institute of MIT and Harvard, 415 Main St. Cambridge, Massachusetts 02142
| | - Jianxue Li
- §Beth-Israel Deaconess Medical Center, Boston, Massachusetts, 02215
| | - Susan Abbatiello
- From the ‡Broad Institute of MIT and Harvard, 415 Main St. Cambridge, Massachusetts 02142
| | - Aravind Subramanian
- From the ‡Broad Institute of MIT and Harvard, 415 Main St. Cambridge, Massachusetts 02142
| | - Richard Sidman
- §Beth-Israel Deaconess Medical Center, Boston, Massachusetts, 02215
| | - Evan Snyder
- ¶Sanford-Burhnam Research Institute, La Jolla, California 92037
| | - Steven A Carr
- From the ‡Broad Institute of MIT and Harvard, 415 Main St. Cambridge, Massachusetts 02142
| | - Jacob D Jaffe
- From the ‡Broad Institute of MIT and Harvard, 415 Main St. Cambridge, Massachusetts 02142;
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74
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Schikora-Tamarit MÀ, Toscano-Ochoa C, Domingo Espinós J, Espinar L, Carey LB. A synthetic gene circuit for measuring autoregulatory feedback control. Integr Biol (Camb) 2016; 8:546-55. [PMID: 26728081 DOI: 10.1039/c5ib00230c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Autoregulatory feedback loops occur in the regulation of molecules ranging from ATP to MAP kinases to zinc. Negative feedback loops can increase a system's robustness, while positive feedback loops can mediate transitions between cell states. Recent genome-wide experimental and computational studies predict hundreds of novel feedback loops. However, not all physical interactions are regulatory, and many experimental methods cannot detect self-interactions. Our understanding of regulatory feedback loops is therefore hampered by the lack of high-throughput methods to experimentally quantify the presence, strength and temporal dynamics of autoregulatory feedback loops. Here we present a mathematical and experimental framework for high-throughput quantification of feedback regulation and apply it to RNA binding proteins (RBPs) in yeast. Our method is able to determine the existence of both direct and indirect positive and negative feedback loops, and to quantify the strength of these loops. We experimentally validate our model using two RBPs which lack native feedback loops and by the introduction of synthetic feedback loops. We find that RBP Puf3 does not natively participate in any direct or indirect feedback regulation, but that replacing the native 3'UTR with that of COX17 generates an auto-regulatory negative feedback loop which reduces gene expression noise. Likewise, RBP Pub1 does not natively participate in any feedback loops, but a synthetic positive feedback loop involving Pub1 results in increased expression noise. Our results demonstrate a synthetic experimental system for quantifying the existence and strength of feedback loops using a combination of high-throughput experiments and mathematical modeling. This system will be of great use in measuring auto-regulatory feedback by RNA binding proteins, a regulatory motif that is difficult to quantify using existing high-throughput methods.
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Affiliation(s)
- Miquel Àngel Schikora-Tamarit
- Experimental and Health Sciences, Universitat Pompeu Fabra, 88 Dr. Aiguader, UPF, PRBB, 3rd floor reception, Barcelona, Barcelona, Spain.
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75
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Haney S, Reya T, Bazhenov M. Delayed Onset of Symptoms Through Feedback Interference in Chronic Cancers. CONVERGENT SCIENCE PHYSICAL ONCOLOGY 2016; 2. [PMID: 29744132 DOI: 10.1088/2057-1739/2/4/045002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In many cancers, such as Chronic Myelogenous Leukemia (CML), pancreatic, and colorectal cancer, long delays exist between the initiation of the disease and the onset of debilitating symptoms. The early stages of these diseases present manageable symptoms and, in the case of CML, highly effective treatment options. Progression to the more aggressive stages of the diseases limits effective treatment and significantly exacerbates patient prognosis. The mechanisms causing delay and disease progression are largely unknown. The later stages of these diseases are characterized by excessive build up of primitive cell types, indicating a disruption in the normal cell differentiation process that is commonly regulated through feedback from differentiated types. In this study, we propose a mechanism where mutated primitive cells produce a feedback interference signal that desensitizes them to a normal homeostatic feedback. Using a mathematical model, we show that this mechanism can account for the long delay period between occurrence of genetic changes and symptomatic onset characterized by fast growth of cancerous cell population. Finally, we explore novel concepts for potential treatment of chronic cancers.
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Affiliation(s)
- Seth Haney
- Department of Medicine, University of California, San Diego, La Jolla, CA
| | - Tannishtha Reya
- Department of Pharmacology, University of California, San Diego, La Jolla, CA
| | - Maxim Bazhenov
- Department of Medicine, University of California, San Diego, La Jolla, CA
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76
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Kolar K, Wischhusen HM, Müller K, Karlsson M, Weber W, Zurbriggen MD. A synthetic mammalian network to compute population borders based on engineered reciprocal cell-cell communication. BMC SYSTEMS BIOLOGY 2015; 9:97. [PMID: 26714638 PMCID: PMC4696150 DOI: 10.1186/s12918-015-0252-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 12/15/2015] [Indexed: 02/05/2023]
Abstract
Background Multicellular organisms depend on the exchange of information between specialized cells. This communication is often difficult to decipher in its native context, but synthetic biology provides tools to engineer well-defined systems that allow the convenient study and manipulation of intercellular communication networks. Results Here, we present the first mammalian synthetic network for reciprocal cell-cell communication to compute the border between a sender/receiver and a processing cell population. The two populations communicate via L-tryptophan and interleukin-4 to highlight the population border by the production of a fluorescent protein. The sharpness of that visualized edge can be adjusted by modulating key parameters of the network. Conclusions We anticipate that this network will on the one hand be a useful tool to gain deeper insights into the mechanisms of tissue formation in nature and will on the other hand contribute to our ability to engineer artificial tissues. Electronic supplementary material The online version of this article (doi:10.1186/s12918-015-0252-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katja Kolar
- Faculty of Biology, University of Freiburg, DE-79104, Freiburg, Germany
| | - Hanna M Wischhusen
- Faculty of Biology, University of Freiburg, DE-79104, Freiburg, Germany.,Present address: DMK GmbH, Head of Quality Assurance, DE-26939, Ovelgönne, Germany
| | - Konrad Müller
- Faculty of Biology, University of Freiburg, DE-79104, Freiburg, Germany.,Present address: Novartis Pharma AG, Biologics Process R&D, CH-4002, Basel, Switzerland
| | - Maria Karlsson
- Faculty of Biology, University of Freiburg, DE-79104, Freiburg, Germany.,Present address: Respiratory, Inflammation and Autoimmunity (RIA) iMED, AstraZeneca, SE-431 83, Mölndal, Sweden
| | - Wilfried Weber
- Faculty of Biology, University of Freiburg, DE-79104, Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, DE-79104, Freiburg, Germany
| | - Matias D Zurbriggen
- Faculty of Biology, University of Freiburg, DE-79104, Freiburg, Germany. .,Present address: Institute of Synthetic Biology and Cluster of Excellence on Plant Science (CEPLAS), University of Düsseldorf, DE-40225, Düsseldorf, Germany.
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77
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On the Calculation of System Entropy in Nonlinear Stochastic Biological Networks. ENTROPY 2015. [DOI: 10.3390/e17106801] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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78
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Hazar M, Kim Y, Song J, LeDuc PR, Davidson LA, Messner WC. 3D bio-etching of a complex composite-like embryonic tissue. LAB ON A CHIP 2015; 15:3293-9. [PMID: 26138309 PMCID: PMC4519418 DOI: 10.1039/c5lc00530b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Morphogenesis involves a complex series of cell signaling, migration and differentiation events that are coordinated as tissues self-assemble during embryonic development. Collective cell movements such as those that occur during morphogenesis have typically been studied in 2D with single layers of cultured cells adhering to rigid substrates such as glass or plastic. In vivo, the intricacies of the 3D microenvironment and complex 3D responses are pivotal in the formation of functional tissues. To study such processes as collective cell movements within 3D multilayered tissues, we developed a microfluidic technique capable of producing complex 3D laminar multicellular structures. We call this technique "3D tissue-etching" because it is analogous to techniques used in the microelectromechanics (MEMS) field where complex 3D structures are built by successively removing material from a monolithic solid through subtractive manufacturing. We use a custom-designed microfluidic control system to deliver a range of tissue etching reagents (detergents, chelators, proteases, etc.) to specific regions of multilayered tissues. These tissues were previously isolated by microsurgical excision from embryos of the African claw-toed frog, Xenopus laevis. The ability to shape the 3D form of multicellular tissues and to control 3D stimulation will have a high impact on tissue engineering and regeneration applications in bioengineering and medicine as well as provide significant improvements in the synthesis of highly complex 3D integrated multicellular biosystems.
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Affiliation(s)
- Melis Hazar
- Department of Mechanical Engineering, Carnegie Mellon University, 5000 Forbes Ave., Pittsburgh, PA, 15213, USA
| | - YongTae Kim
- Department of Mechanical Engineering, Georgia Institute of Technology, North avenue NW, Atlanta, GA, 30332 USA
| | - Jiho Song
- Department of Mechanical Engineering, Carnegie Mellon University, 5000 Forbes Ave., Pittsburgh, PA, 15213, USA
| | - Philip R. LeDuc
- Departments of Bioengineering and Developmental Biology, University of Pittsburgh, 3501 Fifth Avenue, 5059-BST3, Pittsburgh, PA, 15260, USA. ; Fax: +1-412-383-5819; Tel: +1-412-383-5820
| | - Lance A. Davidson
- Departments of Mechanical and Biomedical Engineering, and Biological Sciences, Carnegie Mellon University, 5000 Forbes Ave., 420 Scaife Hall, Pittsburgh, PA, 15213, USA. ; Fax: +1-412-268-3348; Tel: +1-412-268-2504
| | - William C. Messner
- Department of Mechanical Engineering, Tufts University, 419 Boston avenue, Medford, MA 02155 USA
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79
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Burow M, Atwell S, Francisco M, Kerwin RE, Halkier BA, Kliebenstein DJ. The Glucosinolate Biosynthetic Gene AOP2 Mediates Feed-back Regulation of Jasmonic Acid Signaling in Arabidopsis. MOLECULAR PLANT 2015; 8:1201-12. [PMID: 25758208 DOI: 10.1016/j.molp.2015.03.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 03/01/2015] [Accepted: 03/02/2015] [Indexed: 05/02/2023]
Abstract
Survival in changing and challenging environments requires an organism to efficiently obtain and use its resources. Due to their sessile nature, it is particularly critical for plants to dynamically optimize their metabolism. In plant primary metabolism, metabolic fine-tuning involves feed-back mechanisms whereby the output of a pathway controls its input to generate a precise and robust response to environmental changes. By contrast, few studies have addressed the potential for feed-back regulation of secondary metabolism. In Arabidopsis, accumulation of the defense compounds glucosinolates has previously been linked to genetic variation in the glucosinolate biosynthetic gene AOP2. AOP2 expression can increase the transcript levels of two known regulators (MYB28 and MYB29) of the pathway, suggesting that AOP2 plays a role in positive feed-back regulation controlling glucosinolate biosynthesis. We generated mutants affecting AOP2, MYB28/29, or both. Transcriptome analysis of these mutants identified a so far unrecognized link between AOP2 and jasmonic acid (JA) signaling independent of MYB28 and MYB29. Thus, AOP2 is part of a regulatory feed-back loop linking glucosinolate biosynthesis and JA signaling and thereby allows the glucosinolate pathway to influence JA sensitivity. The discovery of this regulatory feed-back loop provides insight into how plants optimize the use of resources for defensive metabolites.
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Affiliation(s)
- Meike Burow
- DynaMo Center of Excellence, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark.
| | - Susanna Atwell
- Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA
| | - Marta Francisco
- Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA; Misión Biológica de Galicia, (MBG-CSIC), PO Box 28, 36080 Pontevedra, Spain
| | - Rachel E Kerwin
- Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA
| | - Barbara A Halkier
- DynaMo Center of Excellence, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Daniel J Kliebenstein
- DynaMo Center of Excellence, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA
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80
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Lo WC, Zhou S, Wan FYM, Lander AD, Nie Q. Robust and precise morphogen-mediated patterning: trade-offs, constraints and mechanisms. J R Soc Interface 2015; 12:20141041. [PMID: 25551154 DOI: 10.1098/rsif.2014.1041] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The patterning of many developing tissues is organized by morphogens. Genetic and environmental perturbations of gene expression, protein synthesis and ligand binding are among the sources of unreliability that limit the accuracy and precision of morphogen-mediated patterning. While it has been found that the robustness of morphogen gradients to the perturbation of morphogen synthesis can be enhanced by particular mechanisms, how such mechanisms affect robustness to other perturbations, such as to receptor synthesis for the same morphogen, has been little explored. Here, we investigate the interplay between the robustness of patterning to the changes in receptor synthesis and morphogen synthesis and to the effects of cell-to-cell variability. Our analysis elucidates the trade-offs and constraints that arise as a result of achieving these three performance objectives simultaneously in the context of simple, steady-state morphogen gradients formed by diffusion and receptor-mediated uptake. Analysis of the interdependence between length scales of patterning and these performance objectives reveals several potential mechanisms for mitigating such trade-offs and constraints. One involves downregulation of receptor synthesis in the morphogen source, while another involves the presence of non-signalling cell-surface morphogen-binding molecules. Both of these mechanisms occur in Drosophila wing discs during their patterning. We computationally elucidate how these mechanisms improve the robustness and precision of morphogen-mediated patterning.
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81
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Kakugawa S, Langton PF, Zebisch M, Howell S, Chang TH, Liu Y, Feizi T, Bineva G, O’Reilly N, Snijders AP, Jones EY, Vincent JP. Notum deacylates Wnt proteins to suppress signalling activity. Nature 2015; 519:187-192. [PMID: 25731175 PMCID: PMC4376489 DOI: 10.1038/nature14259] [Citation(s) in RCA: 306] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 01/26/2015] [Indexed: 01/23/2023]
Abstract
Signalling by Wnt proteins is finely balanced to ensure normal development and tissue homeostasis while avoiding diseases such as cancer. This is achieved in part by Notum, a highly conserved secreted feedback antagonist. Notum has been thought to act as a phospholipase, shedding glypicans and associated Wnt proteins from the cell surface. However, this view fails to explain specificity, as glypicans bind many extracellular ligands. Here we provide genetic evidence in Drosophila that Notum requires glypicans to suppress Wnt signalling, but does not cleave their glycophosphatidylinositol anchor. Structural analyses reveal glycosaminoglycan binding sites on Notum, which probably help Notum to co-localize with Wnt proteins. They also identify, at the active site of human and Drosophila Notum, a large hydrophobic pocket that accommodates palmitoleate. Kinetic and mass spectrometric analyses of human proteins show that Notum is a carboxylesterase that removes an essential palmitoleate moiety from Wnt proteins and thus constitutes the first known extracellular protein deacylase.
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Affiliation(s)
- Satoshi Kakugawa
- MRC’s National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Paul F. Langton
- MRC’s National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Matthias Zebisch
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Steve Howell
- MRC’s National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Tao-Hsin Chang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Yan Liu
- Glycosciences Laboratory, Imperial College London, Department of Medicine Du Cane Road, London, W12 0NN UK
| | - Ten Feizi
- Glycosciences Laboratory, Imperial College London, Department of Medicine Du Cane Road, London, W12 0NN UK
| | - Ganka Bineva
- Cancer Research UK, London Research Institute, 44 Lincoln’s Inn Fields, London WC2A 3LY, UK
| | - Nicola O’Reilly
- Cancer Research UK, London Research Institute, 44 Lincoln’s Inn Fields, London WC2A 3LY, UK
| | - Ambrosius P. Snijders
- Cancer Research UK, Clare Hall Laboratories, Blanche Lane, South Mimms, Potters Bar, Hertfordshire. EN6 3LD, UK
| | - E. Yvonne Jones
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Jean-Paul Vincent
- MRC’s National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
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82
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Gu W, Monteiro R, Zuo J, Simões FC, Martella A, Andrieu-Soler C, Grosveld F, Sauka-Spengler T, Patient R. A novel TGFβ modulator that uncouples R-Smad/I-Smad-mediated negative feedback from R-Smad/ligand-driven positive feedback. PLoS Biol 2015; 13:e1002051. [PMID: 25665164 PMCID: PMC4321984 DOI: 10.1371/journal.pbio.1002051] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/17/2014] [Indexed: 01/17/2023] Open
Abstract
As some of the most widely utilised intercellular signalling molecules, transforming growth factor β (TGFβ) superfamily members play critical roles in normal development and become disrupted in human disease. Establishing appropriate levels of TGFβ signalling involves positive and negative feedback, which are coupled and driven by the same signal transduction components (R-Smad transcription factor complexes), but whether and how the regulation of the two can be distinguished are unknown. Genome-wide comparison of published ChIP-seq datasets suggests that LIM domain binding proteins (Ldbs) co-localise with R-Smads at a substantial subset of R-Smad target genes including the locus of inhibitory Smad7 (I-Smad7), which mediates negative feedback for TGFβ signalling. We present evidence suggesting that zebrafish Ldb2a binds and directly activates the I-Smad7 gene, whereas it binds and represses the ligand gene, Squint (Sqt), which drives positive feedback. Thus, the fine tuning of TGFβ signalling derives from positive and negative control by Ldb2a. Expression of ldb2a is itself activated by TGFβ signals, suggesting potential feed-forward loops that might delay the negative input of Ldb2a to the positive feedback, as well as the positive input of Ldb2a to the negative feedback. In this way, precise gene expression control by Ldb2a enables an initial build-up of signalling via a fully active positive feedback in the absence of buffering by the negative feedback. In Ldb2a-deficient zebrafish embryos, homeostasis of TGFβ signalling is perturbed and signalling is stably enhanced, giving rise to excess mesoderm and endoderm, an effect that can be rescued by reducing signalling by the TGFβ family members, Nodal and BMP. Thus, Ldb2a is critical to the homeostatic control of TGFβ signalling and thereby embryonic patterning.
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Affiliation(s)
- Wenchao Gu
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Rui Monteiro
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- BHF Centre of Research Excellence, Oxford, United Kingdom
| | - Jie Zuo
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Filipa Costa Simões
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Andrea Martella
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Charlotte Andrieu-Soler
- INSERM U872, Université René Descartes Sorbonne Paris Cité, Team 17, Centre de Recherche des Cordeliers, Paris, France
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Tatjana Sauka-Spengler
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Roger Patient
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- BHF Centre of Research Excellence, Oxford, United Kingdom
- * E-mail:
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83
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Loying P, Manhas J, Sen S, Bose B. Autoregulation and heterogeneity in expression of human Cripto-1. PLoS One 2015; 10:e0116748. [PMID: 25658584 PMCID: PMC4319928 DOI: 10.1371/journal.pone.0116748] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 12/12/2014] [Indexed: 11/18/2022] Open
Abstract
Cripto-1 (CR-1) is involved in various processes in embryonic development and cancer. Multiple pathways regulate CR-1 expression. Our present work demonstrates a possible positive feedback circuit where CR-1 induces its own expression. Using U-87 MG cells treated with exogenous CR-1, we show that such induction involves ALK4/SMAD2/3 pathway. Stochasticity in gene expression gives rise to heterogeneity in expression in genetically identical cells. Positive feedback increases such heterogeneity and often gives rise to two subpopulations of cells, having higher and lower expression of a gene. Using flow cytometry, we show that U-87 MG cells have a minuscule subpopulation with detectable expression of CR-1. Induction of CR-1 expression, by exogenous CR-1, increases the size of this CR-1 positive subpopulation. However, even at very high dose, most of the cells remain CR-1 negative. We show that population behavior of CR-1 induction has a signature similar to bimodal expression expected in a transcriptional circuit with positive feedback. We further show that treatment of U-87 MG cells with CR-1 leads to higher expression of drug efflux protein MDR-1 in the CR-1 positive subpopulation, indicating correlated induction of these two proteins. Positive feedback driven heterogeneity in expression of CR-1 may play crucial role in phenotypic diversification of cancer cells.
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Affiliation(s)
- Pojul Loying
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati, India
| | - Janvie Manhas
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Sudip Sen
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Biplab Bose
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati, India
- * E-mail:
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84
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Mathematical model of flagella gene expression dynamics in Salmonella enterica serovar typhimurium. SYSTEMS AND SYNTHETIC BIOLOGY 2015; 9:19-31. [PMID: 25972986 DOI: 10.1007/s11693-015-9160-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 10/11/2014] [Accepted: 01/21/2015] [Indexed: 01/11/2023]
Abstract
Flagellar assembly in Salmonella is controlled by an intricate genetic and biochemical network. This network comprises of a number of inter-connected feedback loops, which control the assembly process dynamically. Critical among these are the FliA-FlgM feedback, FliZ-mediated positive feedback, and FliT-mediated negative feedback. In this work, we develop a mathematical model to track the dynamics of flagellar gene expression in Salmonella. Analysis of our model demonstrates that the network is wired to not only control the transition of the cell from a non-flagellated to a flagellated state, but to also control dynamics of gene expression during cell division. Further, we predict that FliZ encoded in the flagellar regulon acts as a critical secretion-dependent molecular link between flagella and Salmonella Pathogenicity Island 1 gene expression. Sensitivity analysis of the model demonstrates that the flagellar regulatory network architecture is extremely robust to mutations.
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85
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Long Y, Scheres B, Blilou I. The logic of communication: roles for mobile transcription factors in plants. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:1133-44. [PMID: 25635110 DOI: 10.1093/jxb/eru548] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Mobile transcription factors play many roles in plant development. Here, we compare the use of mobile transcription factors as signals with some canonical signal transduction processes in prokaryotes and eukaryotes. After an initial survey, we focus on the SHORT-ROOT pathway in Arabidopsis roots to show that, despite the simplicity of the concept of mobile transcription factor signalling, many lines of evidence reveal a surprising complexity in control mechanisms linked to this process. We argue that these controls bestow precision, robustness, and versatility on mobile transcription factor signalling.
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Affiliation(s)
- Yuchen Long
- Plant Developmental Biology, Plant Sciences, Wageningen University and Research Centre, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
| | - Ben Scheres
- Plant Developmental Biology, Plant Sciences, Wageningen University and Research Centre, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
| | - Ikram Blilou
- Plant Developmental Biology, Plant Sciences, Wageningen University and Research Centre, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands.
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86
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Ségaliny AI, Tellez-Gabriel M, Heymann MF, Heymann D. Receptor tyrosine kinases: Characterisation, mechanism of action and therapeutic interests for bone cancers. J Bone Oncol 2015; 4:1-12. [PMID: 26579483 PMCID: PMC4620971 DOI: 10.1016/j.jbo.2015.01.001] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 01/18/2015] [Indexed: 01/13/2023] Open
Abstract
Bone cancers are characterised by the development of tumour cells in bone sites, associated with a dysregulation of their environment. In the last two decades, numerous therapeutic strategies have been developed to target the cancer cells or tumour niche. As the crosstalk between these two entities is tightly controlled by the release of polypeptide mediators activating signalling pathways through several receptor tyrosine kinases (RTKs), RTK inhibitors have been designed. These inhibitors have shown exciting clinical impacts, such as imatinib mesylate, which has become a reference treatment for chronic myeloid leukaemia and gastrointestinal tumours. The present review gives an overview of the main molecular and functional characteristics of RTKs, and focuses on the clinical applications that are envisaged and already assessed for the treatment of bone sarcomas and bone metastases.
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Affiliation(s)
- Aude I Ségaliny
- INSERM, UMR 957, Equipe LIGUE Nationale Contre le Cancer 2012, Nantes 44035, France ; Université de Nantes, Nantes atlantique universités, Pathophysiology of Bone Resorption and Therapy of Primary Bone Tumours, Nantes, France
| | - Marta Tellez-Gabriel
- INSERM, UMR 957, Equipe LIGUE Nationale Contre le Cancer 2012, Nantes 44035, France ; Université de Nantes, Nantes atlantique universités, Pathophysiology of Bone Resorption and Therapy of Primary Bone Tumours, Nantes, France
| | - Marie-Françoise Heymann
- INSERM, UMR 957, Equipe LIGUE Nationale Contre le Cancer 2012, Nantes 44035, France ; Université de Nantes, Nantes atlantique universités, Pathophysiology of Bone Resorption and Therapy of Primary Bone Tumours, Nantes, France ; CHU de Nantes, France
| | - Dominique Heymann
- INSERM, UMR 957, Equipe LIGUE Nationale Contre le Cancer 2012, Nantes 44035, France ; Université de Nantes, Nantes atlantique universités, Pathophysiology of Bone Resorption and Therapy of Primary Bone Tumours, Nantes, France ; CHU de Nantes, France
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87
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Eldar E, Niv Y. Interaction between emotional state and learning underlies mood instability. Nat Commun 2015; 6:6149. [PMID: 25608088 PMCID: PMC5338993 DOI: 10.1038/ncomms7149] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Accepted: 12/14/2014] [Indexed: 11/09/2022] Open
Abstract
Intuitively, good and bad outcomes affect our emotional state, but whether the emotional state feeds back onto the perception of outcomes remains unknown. Here, we use behaviour and functional neuroimaging of human participants to investigate this bidirectional interaction, by comparing the evaluation of slot machines played before and after an emotion-impacting wheel-of-fortune draw. Results indicate that self-reported mood instability is associated with a positive-feedback effect of emotional state on the perception of outcomes. We then use theoretical simulations to demonstrate that such positive feedback would result in mood destabilization. Taken together, our results suggest that the interaction between emotional state and learning may play a significant role in the emergence of mood instability.
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Affiliation(s)
- Eran Eldar
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey 08544, USA
| | - Yael Niv
- 1] Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey 08544, USA [2] Psychology Department, Princeton University, Princeton, New Jersey 08544, USA
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88
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Siegal ML, Leu JY. On the Nature and Evolutionary Impact of Phenotypic Robustness Mechanisms. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2014; 45:496-517. [PMID: 26034410 PMCID: PMC4448758 DOI: 10.1146/annurev-ecolsys-120213-091705] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Biologists have long observed that physiological and developmental processes are insensitive, or robust, to many genetic and environmental perturbations. A complete understanding of the evolutionary causes and consequences of this robustness is lacking. Recent progress has been made in uncovering the regulatory mechanisms that underlie environmental robustness in particular. Less is known about robustness to the effects of mutations, and indeed the evolution of mutational robustness remains a controversial topic. The controversy has spread to related topics, in particular the evolutionary relevance of cryptic genetic variation. This review aims to synthesize current understanding of robustness mechanisms and to cut through the controversy by shedding light on what is and is not known about mutational robustness. Some studies have confused mutational robustness with non-additive interactions between mutations (epistasis). We conclude that a profitable way forward is to focus investigations (and rhetoric) less on mutational robustness and more on epistasis.
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Affiliation(s)
- Mark L Siegal
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003;
| | - Jun-Yi Leu
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan 11529;
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89
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Lauriola M, Enuka Y, Zeisel A, D'Uva G, Roth L, Sharon-Sevilla M, Lindzen M, Sharma K, Nevo N, Feldman M, Carvalho S, Cohen-Dvashi H, Kedmi M, Ben-Chetrit N, Chen A, Solmi R, Wiemann S, Schmitt F, Domany E, Yarden Y. Diurnal suppression of EGFR signalling by glucocorticoids and implications for tumour progression and treatment. Nat Commun 2014; 5:5073. [PMID: 25278152 PMCID: PMC4205848 DOI: 10.1038/ncomms6073] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 08/25/2014] [Indexed: 02/07/2023] Open
Abstract
Signal transduction by receptor tyrosine kinases (RTKs) and nuclear receptors for steroid hormones is essential for body homeostasis, but the cross-talk between these receptor families is poorly understood. We observed that glucocorticoids inhibit signalling downstream of EGFR, an RTK. The underlying mechanism entails suppression of EGFR's positive feedback loops and simultaneous triggering of negative feedback loops that normally restrain EGFR. Our studies in mice reveal that the regulation of EGFR's feedback loops by glucocorticoids translates to circadian control of EGFR signalling: EGFR signals are suppressed by high glucocorticoids during the active phase (night-time in rodents), while EGFR signals are enhanced during the resting phase. Consistent with this pattern, treatment of animals bearing EGFR-driven tumours with a specific kinase inhibitor was more effective if administered during the resting phase of the day, when glucocorticoids are low. These findings support a circadian clock-based paradigm in cancer therapy.
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Affiliation(s)
- Mattia Lauriola
- 1] Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel [2] Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine, Bologna University, Bologna 40138, Italy
| | - Yehoshua Enuka
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Amit Zeisel
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gabriele D'Uva
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Lee Roth
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Michal Sharon-Sevilla
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Moshit Lindzen
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Kirti Sharma
- Division of Molecular Genome Analysis, German Cancer Research Centre (DKFZ), 69120 Heidelberg, Germany
| | - Nava Nevo
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Morris Feldman
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Silvia Carvalho
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Hadas Cohen-Dvashi
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Merav Kedmi
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Nir Ben-Chetrit
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Alon Chen
- Department of Neurobiology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rossella Solmi
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine, Bologna University, Bologna 40138, Italy
| | - Stefan Wiemann
- Division of Molecular Genome Analysis, German Cancer Research Centre (DKFZ), 69120 Heidelberg, Germany
| | - Fernando Schmitt
- 1] Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada M5S 1A8 [2] Department of Pathology, University Health Network, Toronto, Ontario, Canada M5G 2C4 [3] IPATIMUP, University of Porto, Porto 4200-465, Portugal
| | - Eytan Domany
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yosef Yarden
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
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90
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Fu Y, Lin H, Wisitpitthaya S, Blessing WA, Aye Y. A fluorimetric readout reporting the kinetics of nucleotide-induced human ribonucleotide reductase oligomerization. Chembiochem 2014; 15:2598-2604. [PMID: 25256246 DOI: 10.1002/cbic.201402368] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Indexed: 11/11/2022]
Abstract
Human ribonucleotide reductase (hRNR) is a target of nucleotide chemotherapeutics in clinical use. The nucleotide-induced oligomeric regulation of hRNR subunit α is increasingly being recognized as an innate and drug-relevant mechanism for enzyme activity modulation. In the presence of negative feedback inhibitor dATP and leukemia drug clofarabine nucleotides, hRNR-α assembles into catalytically inert hexameric complexes, whereas nucleotide effectors that govern substrate specificity typically trigger α-dimerization. Currently, both knowledge of and tools to interrogate the oligomeric assembly pathway of RNR in any species in real time are lacking. We therefore developed a fluorimetric assay that reliably reports on oligomeric state changes of α with high sensitivity. The oligomerization-directed fluorescence quenching of hRNR-α, covalently labeled with two fluorophores, allows for direct readout of hRNR dimeric and hexameric states. We applied the newly developed platform to reveal the timescales of α self-assembly, driven by the feedback regulator dATP. This information is currently unavailable, despite the pharmaceutical relevance of hRNR oligomeric regulation.
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Affiliation(s)
- Yuan Fu
- Department of Chemistry and Chemical Biology Cornell University, Ithaca, NY 14853
| | - Hongyu Lin
- Department of Chemistry and Chemical Biology Cornell University, Ithaca, NY 14853
| | | | - William A Blessing
- Department of Chemistry and Chemical Biology Cornell University, Ithaca, NY 14853
| | - Yimon Aye
- Department of Chemistry and Chemical Biology Cornell University, Ithaca, NY 14853.,Department of Biochemistry Weill Cornell Medical College, New York, NY, 10065
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91
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Mei Y, Bian C, Li J, Du Z, Zhou H, Yang Z, Zhao RCH. miR-21 modulates the ERK-MAPK signaling pathway by regulating SPRY2 expression during human mesenchymal stem cell differentiation. J Cell Biochem 2014; 114:1374-84. [PMID: 23239100 DOI: 10.1002/jcb.24479] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 12/05/2012] [Indexed: 12/21/2022]
Abstract
The ERK-MAPK signaling pathway plays a pivotal role during mesenchymal stem cell (MSC) differentiation. Studies have demonstrated that ERK-MAPK promotes adipogenesis and osteogenesis through the phosphorylation of differentiation-associated transcription factors and that it is the only active signaling in all three lineages (adipogenic, chondrogenic, and osteogenic) during MSC differentiation. Recent studies pointed to the significant roles of microRNA-21 (miR-21) during several physiological and pathological processes, especially stem cell fate determination. The miR-21 expression pattern is also correlated with ERK-MAPK activity. Here, we found that miR-21 expression is elevated and associated with an increased differentiation potential in MSCs during adipogenesis and osteogenesis. The overexpression of miR-21 elevated the expression level of the differentiation-associated genes PPARγ and Cbfa-1 during MSC differentiation, whereas miR-21 knockdown reduced the expression level of both genes. The ERK-MAPK signaling pathway activity had an increasing tendency to respond to miR-21 upregulation and a decreasing tendency to respond to miR-21 down-regulation during the first 4 days of adipogenesis and osteogenesis. Our data indicate that miR-21 modulated ERK-MAPK signaling activity by repressing SPRY2 expression, a known regulator of the receptor tyrosine kinase (RTK) signaling pathway, to affect the duration and magnitude of ERK-MAPK activity. The ERK-MAPK signaling pathway was regulated by Sprouty2 (SPRY2) expression via a miR-21-mediated mechanism during MSC differentiation.
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Affiliation(s)
- Yang Mei
- Center of Excellence in Tissue Engineering, Department of Cell Biology, Institute of Basic Medical Sciences, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
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92
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Kushner T, Simonyan A, Wan FYM. A New Approach to Feedback for Robust Signaling Gradients. STUDIES IN APPLIED MATHEMATICS (CAMBRIDGE, MASS.) 2014; 133:18-51. [PMID: 25214676 PMCID: PMC4157771 DOI: 10.1111/sapm.12041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The patterning of many developing tissues is orchestrated by gradients of morphogens through a variety of elaborate regulatory interactions. Such interactions are thought to make gradients robust, that is, resistant to changes induced by genetic or environmental perturbations; but just how this might be done is a major unanswered question. Recently extensive numerical simulations suggest that robustness of signaling gradients cannot be attained by negative feedback (of the Hill's function type) on signaling receptors but can be achieved through binding with nonsignaling receptors (or nonreceptors for short) such as heparan sulfate proteoglycans with the resulting complexes degrading after endocytosis. These were followed by a number of analytical and numerical studies in support of the aforementioned observations. However, evidence of feedback regulating signaling gradients has been reported in literature. The present paper undertakes a different approach to the role of feedback in robust signaling gradients. The overall goal of the project is to investigate the effectiveness of feedback mechanisms on ligand synthesis, receptor synthesis, nonreceptor synthesis, and other regulatory processes in the morphogen gradient system. As a first step, we embark herein a proof-of-concept examination of a new spatially uniform feedback process that is distinctly different from the conventional spatially nonuniform Hill function approach.
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Affiliation(s)
- T Kushner
- ST. OLAF COLLEGE, UNIVERSITY OF CALIFORNIA AT IRVINE
| | - A Simonyan
- ST. OLAF COLLEGE, UNIVERSITY OF CALIFORNIA AT IRVINE
| | - F Y M Wan
- ST. OLAF COLLEGE, UNIVERSITY OF CALIFORNIA AT IRVINE
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93
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Yuan D, Ran Y, Liu Q, Zhang Y, Li H, Li P, Zhu D. Enhancement of the HIF-1α/15-LO/15-HETE axis promotes hypoxia-induced endothelial proliferation in preeclamptic pregnancy. PLoS One 2014; 9:e96510. [PMID: 24796548 PMCID: PMC4010521 DOI: 10.1371/journal.pone.0096510] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 04/08/2014] [Indexed: 11/28/2022] Open
Abstract
Preeclampsia (PE) is an extremely serious condition in pregnant women and the leading cause of maternal and fetal morbidity and mortality. Despite active research, the etiological factors of this disorder remain elusive. The increased release of 15-hydroxyeicosatetraenoic acid (15-HETE) in the placenta of preeclamptic patients has been studied, but its exact role in PE pathogenesis remains unknown. Mounting evidence shows that PE is associated with placental hypoxia, impaired placental angiogenesis, and endothelial dysfunction. In this study, we confirmed the upregulated expression of hypoxia-inducible factor 1α (HIF-1α) and 15-lipoxygenase-1/2 (15-LO-1/2) in patients with PE. Production of the arachidonic acid metabolite, 15-HETE, also increased in the preeclamptic placenta, which suggests enhanced activation of the HIF-1α–15-LO–15-HETE axis. Furthermore, this study is the first to show that the umbilical cord of preeclamptic women contains significantly higher serum concentrations of 15-HETE than that of healthy pregnant women. The results also show that expression of 15-LO-1/2 is upregulated in both human umbilical vein endothelial cells (HUVECs) collected from preeclamptic women and in those cultured under hypoxic conditions. Exogenous 15-HETE promotes the migration of HUVECs and in vitro tube formation and promotes cell cycle progression from the G0/G1 phase to the G2/M + S phase, whereas the 15-LO inhibitor, NDGA, suppresses these effects. The HIF-1α/15-LO/15-HETE pathway is therefore significantly associated within the pathology of PE.
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Affiliation(s)
- Dandan Yuan
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yajuan Ran
- Department of Biopharmaceutical Sciences, College of Pharmacy, Harbin Medical University (Daqing), Daqing, China
| | - Qian Liu
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yanhua Zhang
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Huiying Li
- Department of Obstetrics and Gynecology, Hongqi Hospital of Mudanjiang Medical College, Mudanjiang, China
| | - Peiling Li
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
- * E-mail: (PL); (DZ)
| | - Daling Zhu
- Department of Biopharmaceutical Sciences, College of Pharmacy, Harbin Medical University (Daqing), Daqing, China
- * E-mail: (PL); (DZ)
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94
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Onishi H, Katano M. Hedgehog signaling pathway as a new therapeutic target in pancreatic cancer. World J Gastroenterol 2014; 20:2335-2342. [PMID: 24605030 PMCID: PMC3942836 DOI: 10.3748/wjg.v20.i9.2335] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 12/11/2013] [Accepted: 01/08/2014] [Indexed: 02/06/2023] Open
Abstract
Pancreatic cancer is one of the most aggressive and difficult cancers to treat. Despite numerous research efforts, limited success has been achieved in the therapeutic management of patients with this disease. In the current review, we focus on one component of morphogenesis signaling, Hedgehog (Hh), with the aim of developing novel, effective therapies for the treatment of pancreatic cancer. Hh signaling contributes to the induction of a malignant phenotype in pancreatic cancer and is responsible for maintaining pancreatic cancer stem cells. In addition, we propose a novel concept linking Hh signaling and tumor hypoxic conditions, and discuss the effects of Hh inhibitors in clinical trials. The Hh signaling pathway may represent a potential therapeutic target for patients with refractory pancreatic cancer.
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95
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Abstract
While emotion is a central component of human health and well-being, traditional approaches to understanding its biological function have been wanting. A dynamic systems model, however, broadly redefines and recasts emotion as a primary sensory system-perhaps the first sensory system to have emerged, serving the ancient autopoietic function of "self-regulation." Drawing upon molecular biology and revelations from the field of epigenetics, the model suggests that human emotional perceptions provide an ongoing stream of "self-relevant" sensory information concerning optimally adaptive states between the organism and its immediate environment, along with coupled behavioral corrections that honor a universal self-regulatory logic, one still encoded within cellular signaling and immune functions. Exemplified by the fundamental molecular circuitry of sensorimotor control in the E coli bacterium, the model suggests that the hedonic (affective) categories emerge directly from positive and negative feedback processes, their good/bad binary appraisals relating to dual self-regulatory behavioral regimes-evolutionary purposes, through which organisms actively participate in natural selection, and through which humans can interpret optimal or deficit states of balanced being and becoming. The self-regulatory sensory paradigm transcends anthropomorphism, unites divergent theoretical perspectives and isolated bodies of literature, while challenging time-honored assumptions. While suppressive regulatory strategies abound, it suggests that emotions are better understood as regulating us, providing a service crucial to all semantic language, learning systems, evaluative decision-making, and fundamental to optimal physical, mental, and social health.
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Affiliation(s)
- Katherine T Peil
- College of Professional Studies, Northeastern University, Boston, Massachusetts; Harvard Divinity School, Cambridge, Massachusetts, United States
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96
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San-Bento R, Farcot E, Galletti R, Creff A, Ingram G. Epidermal identity is maintained by cell-cell communication via a universally active feedback loop in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 77:46-58. [PMID: 24147836 DOI: 10.1111/tpj.12360] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 09/20/2013] [Accepted: 10/16/2013] [Indexed: 05/05/2023]
Abstract
The transcription factors ARABIDOPSIS THALIANA MERISTEM L1 (ATML1) and PROTODERMAL FACTOR2 (PDF2) are indispensable for epidermal cell-fate specification in Arabidopsis embryos. However, the mechanisms of regulation of these genes, particularly their relationship with cell-cell signalling pathways, although the subject of considerable speculation, remain unclear. Here we demonstrate that the receptor kinase ARABIDOPSIS CRINKLY4 (ACR4) positively affects the expression of ATML1 and PDF2 in seedlings. In contrast, ATML1- and PDF2-containing complexes directly and negatively affect both their own expression and that of ACR4. By modelling the resulting feedback loop, we demonstrate a network structure that is capable of maintaining robust epidermal cell identity post-germination. We show that a second seed-specific signalling pathway involving the subtilase ABNORMAL LEAFSHAPE1 (ALE1) and the receptor kinases GASSHO1 (GSO1) and GASSHO2 (GSO2) acts in parallel to the epidermal loop to control embryonic surface formation via an ATML1/PDF2-independent pathway. Genetic interactions between components of this linear pathway and the epidermal loop suggest that an intact embryo surface is necessary for initiation and/or stabilization of the epidermal loop, specifically during early embryogenesis.
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Affiliation(s)
- Rita San-Bento
- Laboratoire Reproduction et Développement des Plantes, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon Cedex 07, France; Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3JR, UK
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97
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Ramos AI, Barolo S. Low-affinity transcription factor binding sites shape morphogen responses and enhancer evolution. Philos Trans R Soc Lond B Biol Sci 2013; 368:20130018. [PMID: 24218631 DOI: 10.1098/rstb.2013.0018] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In the era of functional genomics, the role of transcription factor (TF)-DNA binding affinity is of increasing interest: for example, it has recently been proposed that low-affinity genomic binding events, though frequent, are functionally irrelevant. Here, we investigate the role of binding site affinity in the transcriptional interpretation of Hedgehog (Hh) morphogen gradients. We noted that enhancers of several Hh-responsive Drosophila genes have low predicted affinity for Ci, the Gli family TF that transduces Hh signalling in the fly. Contrary to our initial hypothesis, improving the affinity of Ci/Gli sites in enhancers of dpp, wingless and stripe, by transplanting optimal sites from the patched gene, did not result in ectopic responses to Hh signalling. Instead, we found that these enhancers require low-affinity binding sites for normal activation in regions of relatively low signalling. When Ci/Gli sites in these enhancers were altered to improve their binding affinity, we observed patterning defects in the transcriptional response that are consistent with a switch from Ci-mediated activation to Ci-mediated repression. Synthetic transgenic reporters containing isolated Ci/Gli sites confirmed this finding in imaginal discs. We propose that the requirement for gene activation by Ci in the regions of low-to-moderate Hh signalling results in evolutionary pressure favouring weak binding sites in enhancers of certain Hh target genes.
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Affiliation(s)
- Andrea I Ramos
- Department of Cell and Developmental Biology and Program in Cellular and Molecular Biology, University of Michigan Medical School, , Ann Arbor, MI 48109, USA
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98
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Tian R. Exploring intercellular signaling by proteomic approaches. Proteomics 2013; 14:498-512. [DOI: 10.1002/pmic.201300259] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Revised: 08/15/2013] [Accepted: 08/28/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Ruijun Tian
- Lunenfeld-Tanenbaum Research Institute; Mount Sinai Hospital; Toronto ON Canada
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99
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Holtz AM, Peterson KA, Nishi Y, Morin S, Song JY, Charron F, McMahon AP, Allen BL. Essential role for ligand-dependent feedback antagonism of vertebrate hedgehog signaling by PTCH1, PTCH2 and HHIP1 during neural patterning. Development 2013; 140:3423-34. [PMID: 23900540 DOI: 10.1242/dev.095083] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Hedgehog (HH) signaling is essential for vertebrate and invertebrate embryogenesis. In Drosophila, feedback upregulation of the HH receptor Patched (PTC; PTCH in vertebrates), is required to restrict HH signaling during development. By contrast, PTCH1 upregulation is dispensable for early HH-dependent patterning in mice. Unique to vertebrates are two additional HH-binding antagonists that are induced by HH signaling, HHIP1 and the PTCH1 homologue PTCH2. Although HHIP1 functions semi-redundantly with PTCH1 to restrict HH signaling in the developing nervous system, a role for PTCH2 remains unresolved. Data presented here define a novel role for PTCH2 as a ciliary localized HH pathway antagonist. While PTCH2 is dispensable for normal ventral neural patterning, combined removal of PTCH2- and PTCH1-feedback antagonism produces a significant expansion of HH-dependent ventral neural progenitors. Strikingly, complete loss of PTCH2-, HHIP1- and PTCH1-feedback inhibition results in ectopic specification of ventral cell fates throughout the neural tube, reflecting constitutive HH pathway activation. Overall, these data reveal an essential role for ligand-dependent feedback inhibition of vertebrate HH signaling governed collectively by PTCH1, PTCH2 and HHIP1.
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Affiliation(s)
- Alexander M Holtz
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
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100
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Chen M, Wang L, Liu CC, Nie Q. Noise attenuation in the ON and OFF states of biological switches. ACS Synth Biol 2013; 2:587-93. [PMID: 23768065 PMCID: PMC3805451 DOI: 10.1021/sb400044g] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Indexed: 11/28/2022]
Abstract
Biological switches must sense changes in signal concentration and at the same time buffer against signal noise. While many studies have focused on the response of switching systems to noise in the ON state, how systems buffer noise at both ON and OFF states is poorly understood. Through analytical and computational approaches, we find that switching systems require different dynamics at the OFF state than at the ON state in order to have good noise buffering capability. Specifically, we introduce a quantity called the input-associated Signed Activation Time (iSAT) that concisely captures an intrinsic temporal property at either the ON or OFF state. We discover a trade-off between achieving good noise buffering in the ON versus the OFF states: a large iSAT corresponds to noise amplification in the OFF state in contrast to noise buffering in the ON state. To search for biological circuits that can buffer noise in both ON and OFF states, we systematically analyze all three-node circuits and identify mutual activation as a central motif. We also study connections among signal sensitivity, iSAT, and noise amplification. We find that a large iSAT at the ON state maintains signaling sensitivity while minimizing noise propagation. Taken together, the analysis of iSATs helps reveal the noise properties of biological networks and should aid in the design of robust switches that can both repress noise at the OFF state and maintain a reliable ON state.
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Affiliation(s)
- Meng Chen
- Department
of Mathematics and Department of Biomedical Engineering, University
of California at Irvine, Irvine, California 92697, United
States
| | - Liming Wang
- Department of Mathematics, California State University, Los Angeles, California
90032, United States
| | - Chang C. Liu
- Department
of Mathematics and Department of Biomedical Engineering, University
of California at Irvine, Irvine, California 92697, United
States
| | - Qing Nie
- Department
of Mathematics and Department of Biomedical Engineering, University
of California at Irvine, Irvine, California 92697, United
States
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