1
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Bell I, Khan H, Stutt N, Horn M, Hydzik T, Lum W, Rea V, Clapham E, Hoeg L, Van Raay TJ. Nkd1 functions downstream of Axin2 to attenuate Wnt signaling. Mol Biol Cell 2024; 35:ar93. [PMID: 38656801 PMCID: PMC11244159 DOI: 10.1091/mbc.e24-02-0059-t] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/10/2024] [Accepted: 04/19/2024] [Indexed: 04/26/2024] Open
Abstract
Wnt signaling is a crucial developmental pathway involved in early development as well as stem-cell maintenance in adults and its misregulation leads to numerous diseases. Thus, understanding the regulation of this pathway becomes vitally important. Axin2 and Nkd1 are widely utilized negative feedback regulators in Wnt signaling where Axin2 functions to destabilize cytoplasmic β-catenin, and Nkd1 functions to inhibit the nuclear localization of β-catenin. Here, we set out to further understand how Axin2 and Nkd1 regulate Wnt signaling by creating axin2gh1/gh1, nkd1gh2/gh2 single mutants and axin2gh1/gh1;nkd1gh2/gh2 double mutant zebrafish using sgRNA/Cas9. All three Wnt regulator mutants were viable and had impaired heart looping, neuromast migration defects, and behavior abnormalities in common, but there were no signs of synergy in the axin2gh1/gh1;nkd1gh2/gh2 double mutants. Further, Wnt target gene expression by qRT-PCR and RNA-seq, and protein expression by mass spectrometry demonstrated that the double axin2gh1/gh1;nkd1gh2/gh2 mutant resembled the nkd1gh2/gh2 phenotype demonstrating that Nkd1 functions downstream of Axin2. In support of this, the data further demonstrates that Axin2 uniquely alters the properties of β-catenin-dependent transcription having novel readouts of Wnt activity compared with nkd1gh2/gh2 or the axin2gh1/gh1;nkd1gh2/gh2 double mutant. We also investigated the sensitivity of the Wnt regulator mutants to exacerbated Wnt signaling, where the single mutants displayed characteristic heightened Wnt sensitivity, resulting in an eyeless phenotype. Surprisingly, this phenotype was rescued in the double mutant, where we speculate that cross-talk between Wnt/β-catenin and Wnt/Planar Cell Polarity pathways could lead to altered Wnt signaling in some scenarios. Collectively, the data emphasizes both the commonality and the complexity in the feedback regulation of Wnt signaling.
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Affiliation(s)
- Ian Bell
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G 2W1 Ontario, Canada
| | - Haider Khan
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G 2W1 Ontario, Canada
| | - Nathan Stutt
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Matthew Horn
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G 2W1 Ontario, Canada
| | - Teesha Hydzik
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G 2W1 Ontario, Canada
| | - Whitney Lum
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G 2W1 Ontario, Canada
| | - Victoria Rea
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G 2W1 Ontario, Canada
| | - Emma Clapham
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G 2W1 Ontario, Canada
| | - Lisa Hoeg
- Department of Bioinformatics, University of Guelph, Guelph, Ontario, N1G 2W1 Canada
| | - Terence J. Van Raay
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G 2W1 Ontario, Canada
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2
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Gaddelapati SC, George S, Moola A, Sengodan K, Palli SR. N(alpha)-acetyltransferase 40-mediated histone acetylation plays an important role in ecdysone regulation of metamorphosis in the red flour beetle, Tribolium castaneum. Commun Biol 2024; 7:521. [PMID: 38702540 PMCID: PMC11068786 DOI: 10.1038/s42003-024-06212-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 04/18/2024] [Indexed: 05/06/2024] Open
Abstract
Histone acetylation, a crucial epigenetic modification, is governed by histone acetyltransferases (HATs), that regulate many biological processes. Functions of HATs in insects are not well understood. We identified 27 HATs and determined their functions using RNA interference (RNAi) in the model insect, Tribolium castaneum. Among HATs studied, N-alpha-acetyltransferase 40 (NAA40) knockdown caused a severe phenotype of arrested larval development. The steroid hormone, ecdysone induced NAA40 expression through its receptor, EcR (ecdysone receptor). Interestingly, ecdysone-induced NAA40 regulates EcR expression. NAA40 acetylates histone H4 protein, associated with the promoters of ecdysone response genes: EcR, E74, E75, and HR3, and causes an increase in their expression. In the absence of ecdysone and NAA40, histone H4 methylation by arginine methyltransferase 1 (ART1) suppressed the above genes. However, elevated ecdysone levels at the end of the larval period induced NAA40, promoting histone H4 acetylation and increasing the expression of ecdysone response genes. NAA40 is also required for EcR, and steroid-receptor co-activator (SRC) mediated induction of E74, E75, and HR3. These findings highlight the key role of ecdysone-induced NAA40-mediated histone acetylation in the regulation of metamorphosis.
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Affiliation(s)
- Sharath Chandra Gaddelapati
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Smitha George
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA
| | - Anilkumar Moola
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA
| | - Karthi Sengodan
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA
| | - Subba Reddy Palli
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA.
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3
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Jiang XM, Xin QL, Liu K, Peng XF, Han S, Zhang LY, Liu W, Xiao GF, Li H, Zhang LK. Regulation of the WNT-CTNNB1 signaling pathway by severe fever with thrombocytopenia syndrome virus in a cap-snatching manner. mBio 2023; 14:e0168823. [PMID: 37882780 PMCID: PMC10746258 DOI: 10.1128/mbio.01688-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/14/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE One of the conserved mechanisms at the stage of genome transcription of segmented negative-strand RNA viruses (sNSVs) is the cap-snatching process, which is vital for sNSVs transcription and provides drugable targets for the development of antivirals. However, the specificity of RNAs snatched by sNSV is still unclear. By transcriptomics analysis of whole blood samples from SFTS patients, we found WNT-CTNNB1 signaling pathway was regulated according to the course of the disease. We then demonstrated that L protein of severe fever with thrombocytopenia syndrome virus (SFTSV) could interact with mRNAs of WNT-CTNNB1 signaling pathway-related gene, thus affecting WNT-CTNNB1 signaling pathway through its cap-snatching activity. Activation of WNT-CTNNB1 signaling pathway enhanced SFTSV replication, while inhibition of this pathway decreased SFTSV replication in vitro and in vivo. These findings suggest that WNT-associated genes may be the substrate for SFTSV "cap-snatching", and indicate a conserved sNSVs replication mechanism involving WNT-CTNNB1 signaling.
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Affiliation(s)
- Xia-Ming Jiang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qi-Lin Xin
- University of Lyon, INRAE, EPHE, IVPC, Lyon, France
| | - Kai Liu
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, China
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Xue-Fang Peng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Shuo Han
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ling-Yu Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Wei Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Geng-Fu Xiao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hao Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lei-Ke Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
- Hubei Jiangxia Laboratory, Wuhan, China
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4
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Vinchhi R, Yelpure C, Balachandran M, Matange N. Pervasive gene deregulation underlies adaptation and maladaptation in trimethoprim-resistant E. coli. mBio 2023; 14:e0211923. [PMID: 38032208 PMCID: PMC10746255 DOI: 10.1128/mbio.02119-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
IMPORTANCE Bacteria employ a number of mechanisms to adapt to antibiotics. Mutations in transcriptional regulators alter the expression levels of genes that can change the susceptibility of bacteria to antibiotics. Two-component signaling proteins are a major class of signaling molecule used by bacteria to regulate transcription. In previous work, we found that mutations in MgrB, a feedback regulator of the PhoQP two-component system, conferred trimethoprim tolerance to Escherichia coli. Here, we elucidate how mutations in MgrB have a domino-like effect on the gene regulatory network of E. coli. As a result, pervasive perturbation of gene regulation ensues. Depending on the environmental context, this pervasive deregulation is either adaptive or maladaptive. Our study sheds light on how deregulation of gene expression can be beneficial for bacteria when challenged with antibiotics, and why regulators like MgrB may have evolved in the first place.
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Affiliation(s)
- Rhea Vinchhi
- Department of Biology, Indian Institute of Science Education and Research, Pashan, Pune, India
| | - Chetna Yelpure
- Department of Biology, Indian Institute of Science Education and Research, Pashan, Pune, India
| | - Manasvi Balachandran
- Department of Biology, Indian Institute of Science Education and Research, Pashan, Pune, India
| | - Nishad Matange
- Department of Biology, Indian Institute of Science Education and Research, Pashan, Pune, India
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5
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Martin RA, Tate AT. Pleiotropy promotes the evolution of inducible immune responses in a model of host-pathogen coevolution. PLoS Comput Biol 2023; 19:e1010445. [PMID: 37022993 PMCID: PMC10079112 DOI: 10.1371/journal.pcbi.1010445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 02/23/2023] [Indexed: 04/07/2023] Open
Abstract
Components of immune systems face significant selective pressure to efficiently use organismal resources, mitigate infection, and resist parasitic manipulation. A theoretically optimal immune defense balances investment in constitutive and inducible immune components depending on the kinds of parasites encountered, but genetic and dynamic constraints can force deviation away from theoretical optima. One such potential constraint is pleiotropy, the phenomenon where a single gene affects multiple phenotypes. Although pleiotropy can prevent or dramatically slow adaptive evolution, it is prevalent in the signaling networks that compose metazoan immune systems. We hypothesized that pleiotropy is maintained in immune signaling networks despite slowed adaptive evolution because it provides some other advantage, such as forcing network evolution to compensate in ways that increase host fitness during infection. To study the effects of pleiotropy on the evolution of immune signaling networks, we used an agent-based modeling approach to evolve a population of host immune systems infected by simultaneously co-evolving parasites. Four kinds of pleiotropic restrictions on evolvability were incorporated into the networks, and their evolutionary outcomes were compared to, and competed against, non-pleiotropic networks. As the networks evolved, we tracked several metrics of immune network complexity, relative investment in inducible and constitutive defenses, and features associated with the winners and losers of competitive simulations. Our results suggest non-pleiotropic networks evolve to deploy highly constitutive immune responses regardless of parasite prevalence, but some implementations of pleiotropy favor the evolution of highly inducible immunity. These inducible pleiotropic networks are no less fit than non-pleiotropic networks and can out-compete non-pleiotropic networks in competitive simulations. These provide a theoretical explanation for the prevalence of pleiotropic genes in immune systems and highlight a mechanism that could facilitate the evolution of inducible immune responses.
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Affiliation(s)
- Reese A. Martin
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Ann T. Tate
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, United States of America
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6
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Grillo E, Ravelli C, Colleluori G, D'Agostino F, Domenichini M, Giordano A, Mitola S. Role of gremlin-1 in the pathophysiology of the adipose tissues. Cytokine Growth Factor Rev 2023; 69:51-60. [PMID: 36155165 DOI: 10.1016/j.cytogfr.2022.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/12/2022] [Indexed: 02/07/2023]
Abstract
Gremlin-1 is a secreted bone morphogenetic protein (BMP) antagonist playing a pivotal role in the regulation of tissue formation and embryonic development. Since its first identification in 1997, gremlin-1 has been shown to be a multifunctional factor involved in wound healing, inflammation, cancer and tissue fibrosis. Among others, the activity of gremlin-1 is mediated by its interaction with BMPs or with membrane receptors such as the vascular endothelial growth factor receptor 2 (VEGFR2) or heparan sulfate proteoglycans (HSPGs). Growing evidence has highlighted a central role of gremlin-1 in the homeostasis of the adipose tissue (AT). Of note, gremlin-1 is involved in AT dysfunction during type 2 diabetes, obesity and non-alcoholic fatty liver disease (NAFLD) metabolic disorders. In this review we discuss recent findings on gremlin-1 involvement in AT biology, with particular attention to its role in metabolic diseases, to highlight its potential as a prognostic marker and therapeutic target.
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Affiliation(s)
- Elisabetta Grillo
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy.
| | - Cosetta Ravelli
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Georgia Colleluori
- Department of Experimental and Clinical Medicine, Marche Polytechnic University, Via Tronto 10/A, 60020 Ancona, Italy
| | - Francesco D'Agostino
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Mattia Domenichini
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Antonio Giordano
- Department of Experimental and Clinical Medicine, Marche Polytechnic University, Via Tronto 10/A, 60020 Ancona, Italy
| | - Stefania Mitola
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
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7
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Jäkel AC, Aufinger L, Simmel FC. Steady-State Operation of a Cell-Free Genetic Band-Detection Circuit. ACS Synth Biol 2022; 11:3273-3284. [PMID: 36095299 DOI: 10.1021/acssynbio.2c00195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Pattern formation processes play a decisive role during embryogenesis and involve the precise spatial and temporal orchestration of intricate gene regulatory processes. Synthetic gene circuits modeled after their biological counterparts can be used to investigate such processes under well-controlled conditions and may, in the future, be utilized for autonomous position determination in synthetic biological materials. Here, we investigated a three-node feed-forward gene regulatory circuit in vitro that generates three distinct fluorescent outputs in response to varying concentrations of a single externally supplied morphogen. The circuit acts as a band detector for the morphogen concentration and, in a spatial context, could serve as a stripe-forming gene circuit. We simulated the behavior of the genetic circuit in the presence of a morphogen gradient using a system of ordinary differential equations and determined optimal parameters for stripe-pattern formation using an evolutionary algorithm. To analyze the subcircuits of the system, we conducted cell-free characterization experiments and finally tested the whole genetic circuit in nanoliter-scale microfluidic flow reactors that provided a continuous supply of cell extract and metabolites and allowed removal of degradation products. To make use of the widely employed promoters PLlacO-1 and PLtetO-1 in our design, we removed LacI from our bacterial cell extract by genome engineering Escherichia coli using a pORTMAGE workflow. Our results show that the band-detector works as designed when operated out of equilibrium within the flow reactors. On the other hand, subcircuits of the system and the whole circuit fail to generate the desired gene expression response when operated in a closed reactor. Our work thus underlines the importance of out-of-equilibrium operation of complex gene circuits, which cannot settle to a steady-state expression pattern within the finite lifetime of a cell-free expression system.
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Affiliation(s)
- Anna C Jäkel
- Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching D-85748, Germany
| | - Lukas Aufinger
- Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching D-85748, Germany
| | - Friedrich C Simmel
- Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching D-85748, Germany
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8
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Segarra-Fas A, Espejo-Serrano C, Bustos F, Zhou H, Wang F, Toth R, Macartney T, Bach I, Nardocci G, Findlay GM. An RNF12-USP26 amplification loop drives germ cell specification and is disrupted by disease-associated mutations. Sci Signal 2022; 15:eabm5995. [PMID: 35857630 PMCID: PMC7613676 DOI: 10.1126/scisignal.abm5995] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The E3 ubiquitin ligase RNF12 plays essential roles during development, and the gene encoding it, RLIM, is mutated in the X-linked human developmental disorder Tonne-Kalscheuer syndrome (TOKAS). Substrates of RNF12 include transcriptional regulators such as the pluripotency-associated transcriptional repressor REX1. Using global quantitative proteomics in male mouse embryonic stem cells, we identified the deubiquitylase USP26 as a putative downstream target of RNF12 activity. RNF12 relieved REX1-mediated repression of Usp26, leading to an increase in USP26 abundance and the formation of RNF12-USP26 complexes. Interaction with USP26 prevented RNF12 autoubiquitylation and proteasomal degradation, thereby establishing a transcriptional feed-forward loop that amplified RNF12-dependent derepression of REX1 targets. We showed that the RNF12-USP26 axis operated specifically in mouse testes and was required for the expression of gametogenesis genes and for germ cell differentiation in vitro. Furthermore, this RNF12-USP26 axis was disrupted by RLIM and USP26 variants found in TOKAS and infertility patients, respectively. This work reveals synergy within the ubiquitylation cycle that controls a key developmental process in gametogenesis and that is disrupted in human genetic disorders.
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Affiliation(s)
- Anna Segarra-Fas
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, The University of Dundee, Dundee DD1 5EH, UK
| | - Carmen Espejo-Serrano
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, The University of Dundee, Dundee DD1 5EH, UK
| | - Francisco Bustos
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, The University of Dundee, Dundee DD1 5EH, UK
| | - Houjiang Zhou
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, The University of Dundee, Dundee DD1 5EH, UK
| | - Feng Wang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Rachel Toth
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, The University of Dundee, Dundee DD1 5EH, UK
| | - Thomas Macartney
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, The University of Dundee, Dundee DD1 5EH, UK
| | - Ingolf Bach
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Gino Nardocci
- School of Medicine, Faculty of Medicine, Universidad de los Andes, Santiago, Chile
- Program in Molecular Biology and Bioinformatics, Center for Biomedical Research and Innovation (CIIB), Universidad de los Andes, Santiago, Chile
- IMPACT, Center of Interventional Medicine for Precision and Advanced Cellular Therapy, Santiago, Chile
| | - Greg M. Findlay
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, The University of Dundee, Dundee DD1 5EH, UK
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9
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Karoui H, Patwal PS, Pavan Kumar BVVS, Martin N. Chemical Communication in Artificial Cells: Basic Concepts, Design and Challenges. Front Mol Biosci 2022; 9:880525. [PMID: 35720123 PMCID: PMC9199989 DOI: 10.3389/fmolb.2022.880525] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/12/2022] [Indexed: 11/13/2022] Open
Abstract
In the past decade, the focus of bottom-up synthetic biology has shifted from the design of complex artificial cell architectures to the design of interactions between artificial cells mediated by physical and chemical cues. Engineering communication between artificial cells is crucial for the realization of coordinated dynamic behaviours in artificial cell populations, which would have implications for biotechnology, advanced colloidal materials and regenerative medicine. In this review, we focus our discussion on molecular communication between artificial cells. We cover basic concepts such as the importance of compartmentalization, the metabolic machinery driving signaling across cell boundaries and the different modes of communication used. The various studies in artificial cell signaling have been classified based on the distance between sender and receiver cells, just like in biology into autocrine, juxtacrine, paracrine and endocrine signaling. Emerging tools available for the design of dynamic and adaptive signaling are highlighted and some recent advances of signaling-enabled collective behaviours, such as quorum sensing, travelling pulses and predator-prey behaviour, are also discussed.
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Affiliation(s)
- Hedi Karoui
- Univ. Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR 5031, Pessac, France
| | - Pankaj Singh Patwal
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, India
| | - B. V. V. S. Pavan Kumar
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, India
- *Correspondence: B. V. V. S. Pavan Kumar, ; Nicolas Martin,
| | - Nicolas Martin
- Univ. Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR 5031, Pessac, France
- *Correspondence: B. V. V. S. Pavan Kumar, ; Nicolas Martin,
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10
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Sahoo A, Pechmann S. Functional network motifs defined through integration of protein-protein and genetic interactions. PeerJ 2022; 10:e13016. [PMID: 35223214 PMCID: PMC8877332 DOI: 10.7717/peerj.13016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/06/2022] [Indexed: 01/11/2023] Open
Abstract
Cells are enticingly complex systems. The identification of feedback regulation is critically important for understanding this complexity. Network motifs defined as small graphlets that occur more frequently than expected by chance have revolutionized our understanding of feedback circuits in cellular networks. However, with their definition solely based on statistical over-representation, network motifs often lack biological context, which limits their usefulness. Here, we define functional network motifs (FNMs) through the systematic integration of genetic interaction data that directly inform on functional relationships between genes and encoded proteins. Occurring two orders of magnitude less frequently than conventional network motifs, we found FNMs significantly enriched in genes known to be functionally related. Moreover, our comprehensive analyses of FNMs in yeast showed that they are powerful at capturing both known and putative novel regulatory interactions, thus suggesting a promising strategy towards the systematic identification of feedback regulation in biological networks. Many FNMs appeared as excellent candidates for the prioritization of follow-up biochemical characterization, which is a recurring bottleneck in the targeting of complex diseases. More generally, our work highlights a fruitful avenue for integrating and harnessing genomic network data.
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Affiliation(s)
- Amruta Sahoo
- Département de Biochimie, Université de Montréal, Montréal, QC, Canada
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11
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Li Z, Ballance W, Joy M, Patel S, Hwang J, Kong H, Saif TA. Adaptive biohybrid pumping machine with flow loop feedback. Biofabrication 2022; 14. [PMID: 35045402 DOI: 10.1088/1758-5090/ac4d19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 01/19/2022] [Indexed: 11/11/2022]
Abstract
Tissue-engineered living machines is an emerging discipline that employs complex interactions between living cells and engineered scaffolds to self-assemble biohybrid systems for diverse scientific research and technological applications. Here, we report an adaptive, autonomous biohybrid pumping machine with flow loop feedback powered by engineered living muscles. The tissue is made from skeletal muscle cells (C2C12) and collagen /Matrigel matrix, which self-assembles into a ring that compresses a soft tube connected at both ends to a rigid fluidic platform. The muscle ring contracts in a cyclic fashion autonomously, squeezing the tube forming an impedance pump. The resulting flow is circulated back to the muscle ring forming a feedback loop, which allows the pump to respond to the cues received from the flow it generates and adaptively manage its pumping performances based on the feedback. The developed biohybrid pumping system may have broad utility and impact in health, medicine and bioengineering.
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Affiliation(s)
- Zhengwei Li
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, 1206 W Green St, Urbana, Urbana, Illinois, 61801-2946, UNITED STATES
| | - William Ballance
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 1206 W Green St, Urbana, Urbana, 61801-3028, UNITED STATES
| | - Md Joy
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, 1206 W Green St, Urbana, Illinois, 61801, UNITED STATES
| | - Shrey Patel
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1206 W Green St, Urbana, Urbana, 61801-3028, UNITED STATES
| | - Joanne Hwang
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 1206 W Green St, Urbana, Urbana, 61801-3028, UNITED STATES
| | - Hyunjoon Kong
- Department of Chemical and Biomolecular Engineering, University of Illinois - Urbana-Champaign, 600 S Mathew Street, 108 RAL, Urbana, IL 61801, USA, Urbana, Illinois, 61801, UNITED STATES
| | - Taher A Saif
- Mechanical Science and Engineering, University of Illinois - Urbana-Champaign, Mechanical Eng. Building, 1206 West Green Street, Urbana, IL 61801, USA, Urbana, 61801, UNITED STATES
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12
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Das S, Das T, Das P, Das D. Controlling the lifetime of cucurbit[8]uril based self-abolishing nanozymes. Chem Sci 2022; 13:4050-4057. [PMID: 35440999 PMCID: PMC8985584 DOI: 10.1039/d1sc07203j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 02/14/2022] [Indexed: 11/21/2022] Open
Abstract
Nature has evolved a unique mechanism of self-regulatory feedback loops that help in maintiaing an internal cellular environment conducive to growth, healing and metabolism. In biology, enzymes display feedback controlled...
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Affiliation(s)
- Saurav Das
- Department of Chemistry, Indian Institute of Technology Guwahati Assam 781039 India
| | - Tanushree Das
- Department of Chemistry, Indian Institute of Technology Guwahati Assam 781039 India
| | - Priyam Das
- Department of Chemistry, Indian Institute of Technology Guwahati Assam 781039 India
| | - Debapratim Das
- Department of Chemistry, Indian Institute of Technology Guwahati Assam 781039 India
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13
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Signalling dynamics in embryonic development. Biochem J 2021; 478:4045-4070. [PMID: 34871368 PMCID: PMC8718268 DOI: 10.1042/bcj20210043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/10/2021] [Accepted: 11/15/2021] [Indexed: 02/08/2023]
Abstract
In multicellular organisms, cellular behaviour is tightly regulated to allow proper embryonic development and maintenance of adult tissue. A critical component in this control is the communication between cells via signalling pathways, as errors in intercellular communication can induce developmental defects or diseases such as cancer. It has become clear over the last years that signalling is not static but varies in activity over time. Feedback mechanisms present in every signalling pathway lead to diverse dynamic phenotypes, such as transient activation, signal ramping or oscillations, occurring in a cell type- and stage-dependent manner. In cells, such dynamics can exert various functions that allow organisms to develop in a robust and reproducible way. Here, we focus on Erk, Wnt and Notch signalling pathways, which are dynamic in several tissue types and organisms, including the periodic segmentation of vertebrate embryos, and are often dysregulated in cancer. We will discuss how biochemical processes influence their dynamics and how these impact on cellular behaviour within multicellular systems.
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14
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Kamptner AZM, Mayer CE, Sutterlüty H. Sprouty3, but Not Sprouty1, Expression Is Beneficial for the Malignant Potential of Osteosarcoma Cells. Int J Mol Sci 2021; 22:ijms222111944. [PMID: 34769378 PMCID: PMC8585105 DOI: 10.3390/ijms222111944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/21/2021] [Accepted: 10/31/2021] [Indexed: 11/16/2022] Open
Abstract
Sprouty proteins are widely accepted modulators of receptor tyrosine kinase-associated pathways and fulfill diversified roles in cancerogenesis dependent on the originating cells. In this study we detected a high expression of Sprouty3 in osteosarcoma-derived cells and addressed the question of whether Sprouty3 and Sprouty1 influence the malignant phenotype of this bone tumor entity. By using adenoviruses, the Sprouty proteins were expressed in two different cell lines and their influence on cellular behavior was assessed. Growth curve analyses and Scratch assays revealed that Sprouty3 accelerates cell proliferation and migration. Additionally, more colonies were grown in Soft agar if the cells express Sprouty3. In parallel, Sprouty1 had no significant effect on the measured endpoints of the study in osteosarcoma-derived cells. The promotion of the tumorigenic capacities in the presence of Sprouty3 coincided with an increased activation of signaling as measured by evaluating the phosphorylation of extracellular signal-regulated kinases (ERKs). Ectopic expression of a mutated Sprouty3 protein, in which the tyrosine necessary for its activation was substituted, resulted in inhibited migration of the treated cells. Our findings identify Sprouty3 as a candidate for a tumor promoter in osteosarcoma.
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15
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Abstract
Active matter comprises self-driven units, such as bacteria and synthetic microswimmers, that can spontaneously form complex patterns and assemble into functional microdevices. These processes are possible thanks to the out-of-equilibrium nature of active-matter systems, fueled by a one-way free-energy flow from the environment into the system. Here, we take the next step in the evolution of active matter by realizing a two-way coupling between active particles and their environment, where active particles act back on the environment giving rise to the formation of superstructures. In experiments and simulations we observe that, under light-illumination, colloidal particles and their near-critical environment create mutually-coupled co-evolving structures. These structures unify in the form of active superstructures featuring a droplet shape and a colloidal engine inducing self-propulsion. We call them active droploids-a portmanteau of droplet and colloids. Our results provide a pathway to create active superstructures through environmental feedback.
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16
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Biological feedback control-Respect the loops. Cell Syst 2021; 12:477-487. [PMID: 34139160 DOI: 10.1016/j.cels.2021.05.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 05/07/2021] [Indexed: 11/21/2022]
Abstract
We, and all organisms, are an evolutionary masterpiece of multiscale feedback control. Feedback loops enable our cells to grow and then stop at the right size, to divide and self-repair, and to respond with agility to their changing environment. Individual cells engage in long range extracellular feedback with other cells, ensuring continued homeostasis of our tissues and organs. Many long ranging feedback loops regulate vital physiological variables. Here, I will argue that focused efforts to understand the properties and constraints of biological feedback control networks should be central to the quest of understanding life. I will also propose many pressing challenges in this field and review conceptual frameworks that might be consequential for addressing them.
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17
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Lord ND, Carte AN, Abitua PB, Schier AF. The pattern of nodal morphogen signaling is shaped by co-receptor expression. eLife 2021; 10:e54894. [PMID: 34036935 PMCID: PMC8266389 DOI: 10.7554/elife.54894] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 05/26/2021] [Indexed: 12/13/2022] Open
Abstract
Embryos must communicate instructions to their constituent cells over long distances. These instructions are often encoded in the concentration of signals called morphogens. In the textbook view, morphogen molecules diffuse from a localized source to form a concentration gradient, and target cells adopt fates by measuring the local morphogen concentration. However, natural patterning systems often incorporate numerous co-factors and extensive signaling feedback, suggesting that embryos require additional mechanisms to generate signaling patterns. Here, we examine the mechanisms of signaling pattern formation for the mesendoderm inducer Nodal during zebrafish embryogenesis. We find that Nodal signaling activity spans a normal range in the absence of signaling feedback and relay, suggesting that diffusion is sufficient for Nodal gradient formation. We further show that the range of endogenous Nodal ligands is set by the EGF-CFC co-receptor Oep: in the absence of Oep, Nodal activity spreads to form a nearly uniform distribution throughout the embryo. In turn, increasing Oep levels sensitizes cells to Nodal ligands. We recapitulate these experimental results with a computational model in which Oep regulates the diffusive spread of Nodal ligands by setting the rate of capture by target cells. This model predicts, and we confirm in vivo, the surprising observation that a failure to replenish Oep transforms the Nodal signaling gradient into a travelling wave. These results reveal that patterns of Nodal morphogen signaling are shaped by co-receptor-mediated restriction of ligand spread and sensitization of responding cells.
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Affiliation(s)
- Nathan D Lord
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
| | - Adam N Carte
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
- Systems, Synthetic, and Quantitative Biology PhD Program, Harvard UniversityCambridgeUnited States
- Biozentrum, University of BaselBaselSwitzerland
| | - Philip B Abitua
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
| | - Alexander F Schier
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
- Biozentrum, University of BaselBaselSwitzerland
- Allen Discovery Center for Cell Lineage Tracing, University of WashingtonSeattleUnited States
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18
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Zhou J, Ramanathan R, Wong WF. Synthesis of the Dynamical Properties of Feedback Loops in Bio-Pathways. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:1217-1226. [PMID: 31443044 DOI: 10.1109/tcbb.2019.2936200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Feedback loops regulate various biological functions such as oscillations, bistability, and robustness. They play a significant role in developmental signalling and failure of feedback can lead to disease. Systematic analysis of feedback loops could be useful in understanding their properties and biological effects. We propose here a method to automatically analyze feedback loops in bio-pathways and synthesize temporal logic properties which describe their dynamics. Starting with an ordinary differential equations (ODEs) based model of a bio-pathway, for a chosen feedback loop present in the pathway, we use a convolutional neural network to classify the behaviours of the key components of the feedback according to templates specified in bounded linear temporal logic (BLTL). Once a template has been identified, we instantiate the symbolic variables appearing in the template and synthesize properties using a parameter estimation procedure based on sequential hypothesis testing. We have applied this framework to a number of bio-pathway models and validated that the synthesized properties faithfully describe the behaviours of the feedback loops.
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19
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Ilyas AMO, Alam MK, Musah JD, Saw LO, Venkatesh S, Yeung CC, Yang M, Vellaisamy ALR, Lau C. Development of a carboxyl-terminated indium tin oxide electrode for improving cell adhesion and facilitating low noise, real-time impedance measurements. Am J Physiol Cell Physiol 2021; 320:C974-C986. [PMID: 33689477 DOI: 10.1152/ajpcell.00537.2020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The working electrode's surface property is crucial to cell adhesion and signal collection in electric cell-substrate impedance sensing (ECIS). To date, the indium tin oxide (ITO)-based working electrode is of interest in ECIS study due to its high transparency and biocompatibility. Of great concern is the impedance signal loss, distortion, and data interpretation conflict profoundly created by the movement of multiple cells during ECIS study. Here, a carboxyl-terminated ITO substrate was prepared by stepwise surface amino silanization, with N-hydroxy succinimide (NHS) and 1-ethyl-3-(3-dimethyl aminopropyl) carbodiimide hydrochloride (EDC) treatment, respectively. We investigated the stepwise changes in the property of the treated ITO, cell-substrate adhesion, collective cell mobility, and time course of change in absolute impedance from multiple Chinese hamster ovary (CHO) cells [(Δt-Δ|Z|)CELLS]. The carboxyl-terminated ITO substrate with a surface roughness of 6.37 nm shows enhanced conductivity, 75% visible light transparency, improved cell adherence, reduced collective cell migration speed by approximately twofold, and diminished signal distortion in the [(Δt-Δ|Z|)CELLS]. Thus, our study provides an ITO surface-treatment strategy to reduce multiple cell movement effects and to obtain essential cell information from the ECIS study of multiple cells through undistorted (Δt-Δ|Z|)CELLS.
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Affiliation(s)
- A M Olabisi Ilyas
- Department of Physics, City University of Hong Kong, Kowloon, Special Administrative Region of China.,Department of Physics, Federal University Oye-Ekiti, Oye-Ekiti, Nigeria
| | - Md Kowsar Alam
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Special Administrative Region of China.,Department of Physics, University of Chittagong, Chittagong, Bangladesh
| | - Jamal-Deen Musah
- State Key Laboratory of Terahertz and Millimeter Waves, Department of Material Science and Engineering, City University of Hong Kong, Kowloon, Special Administrative Region of China
| | - Lin Oo Saw
- State Key Laboratory of Terahertz and Millimeter Waves, Department of Material Science and Engineering, City University of Hong Kong, Kowloon, Special Administrative Region of China
| | - Shishir Venkatesh
- State Key Laboratory of Terahertz and Millimeter Waves, Department of Material Science and Engineering, City University of Hong Kong, Kowloon, Special Administrative Region of China
| | - Chi-Chung Yeung
- Department of Chemistry, City University of Hong Kong, Kowloon, Special Administrative Region of China
| | - Mengsu Yang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Special Administrative Region of China
| | - A L R Vellaisamy
- James Watt School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Condon Lau
- Department of Physics, City University of Hong Kong, Kowloon, Special Administrative Region of China
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20
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LncRNA TINCR favors tumorigenesis via STAT3-TINCR-EGFR-feedback loop by recruiting DNMT1 and acting as a competing endogenous RNA in human breast cancer. Cell Death Dis 2021; 12:83. [PMID: 33446634 PMCID: PMC7809450 DOI: 10.1038/s41419-020-03188-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 10/20/2020] [Accepted: 10/23/2020] [Indexed: 12/18/2022]
Abstract
The long noncoding RNA (lncRNA) TINCR has recently been found to be associated with the progression of human malignancies, but the molecular mechanism of TINCR action remains elusive, particularly in breast cancer. The oncogenic role of TINCR was examined in vitro and in vivo in breast cancer. Next, the interaction between TINCR, DNMT1, and miR-503-5p methylation was explored. Moreover, the mechanism by which TINCR enhances EGFR expression and downstream signaling via an RNA–RNA interaction was comprehensively investigated. Furthermore, upstream transcriptional regulation of TINCR expression by STAT3 was examined by performing chromatin immunoprecipitation. Finally, feedback signaling in the STAT3–TINCR–EGFR downstream cascade was also investigated. TINCR is upregulated in human breast cancer tissues, and TINCR knockdown suppresses tumorigenesis in vitro and in vivo. Mechanistically, TINCR recruits DNMT1 to the miR-503-5p locus promoter, which increases the methylation and suppresses the transcriptional expression of miR-503-5p. Furthermore, TINCR also functions as a competing endogenous RNA to upregulate EGFR expression by sponging miR-503-5p. In addition, TINCR stimulates JAK2–STAT3 signaling downstream from EGFR, and STAT3 reciprocally enhances the transcriptional expression of TINCR. Our findings broaden the current understanding of the diverse manners in which TINCR functions in cancer biology. The newly identified STAT3–TINCR–EGFR-feedback loop could serve as a potential therapeutic target for human cancer.
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21
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Reconstitution of Morphogen Signaling Gradients in Cultured Cells. Methods Mol Biol 2020. [PMID: 33340353 DOI: 10.1007/978-1-0716-1174-6_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Development of multicellular organisms depends on the proper establishment of signaling information in space and time. Secreted molecules called morphogens form concentration gradients in space and provide positional information to differentiating cells within the organism. Although the key molecular components of morphogen pathways have been identified, how the architectures and key parameters of morphogen pathways control the properties of signaling gradients, such as their size, speed, and robustness to perturbations, remains challenging to study in developing embryos. Reconstituting morphogen gradients in cell culture provides an alternative approach to address this question. Here we describe the methodology for reconstituting Sonic Hedgehog (SHH) signaling gradients in mouse fibroblast cells. The protocol includes the design of morphogen sending and receiving cell lines, the setup of radial and linear gradients, the quantitative time-lapse imaging, and the data analysis. Similar approaches could potentially be applied to other cell-cell communication pathways.
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22
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Kobayashi PE, Lainetti PF, Leis-Filho AF, Delella FK, Carvalho M, Cury SS, Carvalho RF, Fonseca-Alves CE, Laufer-Amorim R. Transcriptome of Two Canine Prostate Cancer Cells Treated With Toceranib Phosphate Reveals Distinct Antitumor Profiles Associated With the PDGFR Pathway. Front Vet Sci 2020; 7:561212. [PMID: 33324695 PMCID: PMC7726326 DOI: 10.3389/fvets.2020.561212] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 10/30/2020] [Indexed: 01/17/2023] Open
Abstract
Canine prostate cancer (PC) presents a poor antitumor response, usually late diagnosis and prognosis. Toceranib phosphate (TP) is a nonspecific inhibitor of receptor tyrosine kinases (RTKs), including vascular endothelial growth factor receptor (VEGFR), platelet-derived growth factor receptor (PDGFR), and c-KIT. This study aimed to evaluate VEGFR2, PDGFR-β, and c-KIT protein expression in two established canine PC cell lines (PC1 and PC2) and the transcriptome profile of the cells after treatment with TP. Immunofluorescence (IF) analysis revealed VEGFR2 and PDGFR-β protein expression and the absence of c-KIT protein expression in both cell lines. After TP treatment, only the viability of PC1 cells decreased in a dose-dependent manner. Transcriptome and enrichment analyses of treated PC1 cells revealed 181 upregulated genes, which were related to decreased angiogenesis and cell proliferation. In addition, we found upregulated PDGFR-A, PDGFR-β, and PDGF-D expression in PC1 cells, and the upregulation of PDGFR-β was also observed in treated PC1 cells by qPCR. PC2 cells had fewer protein-protein interactions (PPIs), with 18 upregulated and 22 downregulated genes; the upregulated genes were involved in the regulation of parallel pathways and mechanisms related to proliferation, which could be associated with the resistance observed after treatment. The canine PC1 cell line but not the PC2 cell line showed decreased viability after treatment with TP, although both cell lines expressed PDGFR and VEGFR receptors. Further studies could explain the mechanism of resistance in PC2 cells and provide a basis for personalized treatment for dogs with PC.
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Affiliation(s)
- Priscila E Kobayashi
- Department of Veterinary Clinic, School of Veterinary Medicine and Animal Science, São Paulo State University-UNESP, Botucatu, Brazil
| | - Patrícia F Lainetti
- Department of Veterinary Surgery and Anesthesiology, School of Veterinary Medicine and Animal Science, São Paulo State University-UNESP, Botucatu, Brazil
| | - Antonio F Leis-Filho
- Department of Veterinary Clinic, School of Veterinary Medicine and Animal Science, São Paulo State University-UNESP, Botucatu, Brazil
| | - Flávia K Delella
- Department of Morphology, Institute of Biosciences, São Paulo State University-UNESP, Botucatu, Brazil
| | - Marcio Carvalho
- Department of Veterinary Clinic, School of Veterinary Medicine and Animal Science, São Paulo State University-UNESP, Botucatu, Brazil
| | - Sarah Santiloni Cury
- Department of Morphology, Institute of Biosciences, São Paulo State University-UNESP, Botucatu, Brazil
| | - Robson Francisco Carvalho
- Department of Morphology, Institute of Biosciences, São Paulo State University-UNESP, Botucatu, Brazil
| | - Carlos E Fonseca-Alves
- Department of Veterinary Surgery and Anesthesiology, School of Veterinary Medicine and Animal Science, São Paulo State University-UNESP, Botucatu, Brazil.,Institute of Health Sciences, Paulista University-UNIP, Bauru, Brazil
| | - Renée Laufer-Amorim
- Department of Veterinary Clinic, School of Veterinary Medicine and Animal Science, São Paulo State University-UNESP, Botucatu, Brazil
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23
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Yang S, Pieters PA, Joesaar A, Bögels BWA, Brouwers R, Myrgorodska I, Mann S, de Greef TFA. Light-Activated Signaling in DNA-Encoded Sender-Receiver Architectures. ACS NANO 2020; 14:15992-16002. [PMID: 33078948 PMCID: PMC7690052 DOI: 10.1021/acsnano.0c07537] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 10/14/2020] [Indexed: 05/22/2023]
Abstract
Collective decision making by living cells is facilitated by exchange of diffusible signals where sender cells release a chemical signal that is interpreted by receiver cells. A variety of nonliving artificial cell models have been developed in recent years that mimic various aspects of diffusion-based intercellular communication. However, localized secretion of diffusive signals from individual protocells, which is critical for mimicking biological sender-receiver systems, has remained challenging to control precisely. Here, we engineer light-responsive, DNA-encoded sender-receiver architectures, where protein-polymer microcapsules act as cell mimics and molecular communication occurs through diffusive DNA signals. We prepare spatial distributions of sender and receiver protocells using a microfluidic trapping array and set up a signaling gradient from a single sender cell using light, which activates surrounding receivers through DNA strand displacement. Our systematic analysis reveals how the effective signal range of a single sender is determined by various factors including the density and permeability of receivers, extracellular signal degradation, signal consumption, and catalytic regeneration. In addition, we construct a three-population configuration where two sender cells are embedded in a dense array of receivers that implement Boolean logic and investigate spatial integration of nonidentical input cues. The results offer a means for studying diffusion-based sender-receiver topologies and present a strategy to achieve the congruence of reaction-diffusion and positional information in chemical communication systems that have the potential to reconstitute collective cellular patterns.
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Affiliation(s)
- Shuo Yang
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Computational
Biology Group, Department of Biomedical Engineering and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
| | - Pascal A. Pieters
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Computational
Biology Group, Department of Biomedical Engineering and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
| | - Alex Joesaar
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Computational
Biology Group, Department of Biomedical Engineering and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
| | - Bas W. A. Bögels
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Computational
Biology Group, Department of Biomedical Engineering and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
| | - Rens Brouwers
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Computational
Biology Group, Department of Biomedical Engineering and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
| | - Iuliia Myrgorodska
- Centre
for Protolife Research and Max Planck Bristol Centre for Minimal Biology,
School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Stephen Mann
- Centre
for Protolife Research and Max Planck Bristol Centre for Minimal Biology,
School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Tom F. A. de Greef
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Computational
Biology Group, Department of Biomedical Engineering and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 MB, The Netherlands
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24
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From protocells to prototissues: a materials chemistry approach. Biochem Soc Trans 2020; 48:2579-2589. [DOI: 10.1042/bst20200310] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/29/2020] [Accepted: 10/05/2020] [Indexed: 12/16/2022]
Abstract
Prototissues comprise free-standing 3D networks of interconnected protocell consortia that communicate and display synergistic functions. Significantly, they can be constructed from functional molecules and materials, providing unprecedented opportunities to design tissue-like architectures that can do more than simply mimic living tissues. They could function under extreme conditions and exhibit a wide range of mechanical properties and bio-inspired metabolic functions. In this perspective, I will start by describing recent advancements in the design and synthetic construction of prototissues. I will then discuss the next challenges and the future impact of this emerging research field, which is destined to find applications in the most diverse areas of science and technology, from biomedical science to environmental science, and soft robotics.
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25
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Gammons MV, Renko M, Flack JE, Mieszczanek J, Bienz M. Feedback control of Wnt signaling based on ultrastable histidine cluster co-aggregation between Naked/NKD and Axin. eLife 2020; 9:e59879. [PMID: 33025907 PMCID: PMC7581431 DOI: 10.7554/elife.59879] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/06/2020] [Indexed: 12/20/2022] Open
Abstract
Feedback control is a universal feature of cell signaling pathways. Naked/NKD is a widely conserved feedback regulator of Wnt signaling which controls animal development and tissue homeostasis. Naked/NKD destabilizes Dishevelled, which assembles Wnt signalosomes to inhibit the β-catenin destruction complex via recruitment of Axin. Here, we discover that the molecular mechanism underlying Naked/NKD function relies on its assembly into ultra-stable decameric core aggregates via its conserved C-terminal histidine cluster (HisC). HisC aggregation is facilitated by Dishevelled and depends on accumulation of Naked/NKD during prolonged Wnt stimulation. Naked/NKD HisC cores co-aggregate with a conserved histidine cluster within Axin, to destabilize it along with Dishevelled, possibly via the autophagy receptor p62, which binds to HisC aggregates. Consistent with this, attenuated Wnt responses are observed in CRISPR-engineered flies and human epithelial cells whose Naked/NKD HisC has been deleted. Thus, HisC aggregation by Naked/NKD provides context-dependent feedback control of prolonged Wnt responses.
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Affiliation(s)
- Melissa V Gammons
- MRC Laboratory of Molecular Biology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Miha Renko
- MRC Laboratory of Molecular Biology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Joshua E Flack
- MRC Laboratory of Molecular Biology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Juliusz Mieszczanek
- MRC Laboratory of Molecular Biology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Mariann Bienz
- MRC Laboratory of Molecular Biology, Cambridge Biomedical CampusCambridgeUnited Kingdom
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26
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Müller-McNicoll M, Rossbach O, Hui J, Medenbach J. Auto-regulatory feedback by RNA-binding proteins. J Mol Cell Biol 2020; 11:930-939. [PMID: 31152582 PMCID: PMC6884704 DOI: 10.1093/jmcb/mjz043] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/25/2019] [Accepted: 04/23/2019] [Indexed: 12/19/2022] Open
Abstract
RNA-binding proteins (RBPs) are key regulators in post-transcriptional control of gene expression. Mutations that alter their activity or abundance have been implicated in numerous diseases such as neurodegenerative disorders and various types of cancer. This highlights the importance of RBP proteostasis and the necessity to tightly control the expression levels and activities of RBPs. In many cases, RBPs engage in an auto-regulatory feedback by directly binding to and influencing the fate of their own mRNAs, exerting control over their own expression. For this feedback control, RBPs employ a variety of mechanisms operating at all levels of post-transcriptional regulation of gene expression. Here we review RBP-mediated autogenous feedback regulation that either serves to maintain protein abundance within a physiological range (by negative feedback) or generates binary, genetic on/off switches important for e.g. cell fate decisions (by positive feedback).
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Affiliation(s)
- Michaela Müller-McNicoll
- Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Max-von-Laue-Strasse 13, D-60438 Frankfurt am Main, Germany
| | - Oliver Rossbach
- Institute of Biochemistry, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 17, D-35392 Giessen, Germany
| | - Jingyi Hui
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jan Medenbach
- Institute of Biochemistry I, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
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27
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Tang S, Zhao Y, He X, Zhu J, Chen S, Wen J, Deng Y. Identification of NOVA family proteins as novel β-catenin RNA-binding proteins that promote epithelial-mesenchymal transition. RNA Biol 2020; 17:881-891. [PMID: 32101070 PMCID: PMC7549617 DOI: 10.1080/15476286.2020.1734372] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 02/19/2020] [Accepted: 02/20/2020] [Indexed: 12/27/2022] Open
Abstract
The NOVA (neuro-oncological ventral antigen) protein family, composed of two paralogs, NOVA1 and NOVA2, consists of RNA-binding proteins involving in processes such as alternative splicing and transport of some target mRNAs. The function of NOVA has been well studied, and increasing evidence has shown that NOVA proteins may be important contributors to carcinogenesis. However, the molecular mechanisms underlying the roles of NOVA proteins in carcinogenesis remain to be determined. Here, we have identified both NOVA1 and NOVA2 as novel β-catenin RNA-binding proteins. The NOVA1/NOVA2 heterodimer positively regulates β-catenin expression by enhancing β-catenin mRNA stability. Furthermore, we demonstrated that NOVA1 and NOVA2 promote epithelial-mesenchymal transition via β-catenin in breast cancer cells, as NOVA-induced upregulation of epithelial and mesenchymal marker expression was attenuated by restoring β-catenin expression. Our results advance the current understanding of β-catenin post-transcriptional regulation and shed light on the role of NOVA proteins in cancer, suggesting that NOVA proteins are potential therapeutic targets in breast cancer.
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Affiliation(s)
- Shulin Tang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yurong Zhao
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Xirong He
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jiahui Zhu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Shuang Chen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jikai Wen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yiqun Deng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
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28
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Understanding MAPK Signaling Pathways in Apoptosis. Int J Mol Sci 2020; 21:ijms21072346. [PMID: 32231094 PMCID: PMC7177758 DOI: 10.3390/ijms21072346] [Citation(s) in RCA: 555] [Impact Index Per Article: 138.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/10/2020] [Accepted: 03/25/2020] [Indexed: 02/07/2023] Open
Abstract
MAPK (mitogen-activated protein kinase) signaling pathways regulate a variety of biological processes through multiple cellular mechanisms. In most of these processes, such as apoptosis, MAPKs have a dual role since they can act as activators or inhibitors, depending on the cell type and the stimulus. In this review, we present the main pro- and anti-apoptotic mechanisms regulated by MAPKs, as well as the crosstalk observed between some MAPKs. We also describe the basic signaling properties of MAPKs (ultrasensitivity, hysteresis, digital response), and the presence of different positive feedback loops in apoptosis. We provide a simple guide to predict MAPKs’ behavior, based on the intensity and duration of the stimulus. Finally, we consider the role of MAPKs in osmostress-induced apoptosis by using Xenopus oocytes as a cell model. As we will see, apoptosis is plagued with multiple positive feedback loops. We hope this review will help to understand how MAPK signaling pathways engage irreversible cellular decisions.
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29
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Lander AD, Nie Q, Sanchez-Tapia C, Simonyan A, Wan FYM. Regulatory feedback on receptor and non-receptor synthesis for robust signaling. Dev Dyn 2020; 249:383-409. [PMID: 32034817 DOI: 10.1002/dvdy.160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 01/16/2020] [Indexed: 12/22/2022] Open
Abstract
Elaborate regulatory feedback processes are thought to make biological development robust, that is, resistant to changes induced by genetic or environmental perturbations. How this might be done is still not completely understood. Previous numerical simulations on reaction-diffusion models of Dpp gradients in Drosophila wing imaginal disc have showed that feedback (of the Hill function type) on (signaling) receptors and/or non-(signaling) receptors are of limited effectiveness in promoting robustness. Spatial nonuniformity of the feedback processes has also been shown theoretically to lead to serious shape distortion and a principal cause for ineffectiveness. Through mathematical modeling and analysis, the present article shows that spatially uniform nonlocal feedback mechanisms typically modify gradient shape through a shape parameter (that does not change with location). This in turn enables us to uncover new multi-feedback instrument for effective promotion of robust signaling gradients.
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Affiliation(s)
- Arthur D Lander
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California.,Center for Complex Biological Systems (CCBS), University of California Irvine, Irvine, California
| | - Qing Nie
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California.,Center for Complex Biological Systems (CCBS), University of California Irvine, Irvine, California.,Department of Mathematics, University of California Irvine, Irvine, California.,NSF-Simon Center for Multiscale Cell Fate (CMCF), University of California Irvine, Irvine, California
| | | | - Aghavni Simonyan
- Department of Mathematics, University of California Irvine, Irvine, California.,Geffen Academy, UCLA, Los Angeles, California
| | - Frederic Y M Wan
- Department of Mathematics, University of California Irvine, Irvine, California
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30
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Liu SB, Wang XS, Yue J, Yang L, Li XH, Hu LN, Lu JS, Song Q, Zhang K, Yang Q, Zhang MM, Bernabucci M, Zhao MG, Zhuo M. Cyclic AMP-dependent positive feedback signaling pathways in the cortex contributes to visceral pain. J Neurochem 2020; 153:252-263. [PMID: 31665810 DOI: 10.1111/jnc.14903] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/01/2019] [Accepted: 10/12/2019] [Indexed: 01/02/2023]
Abstract
Cortical areas including the anterior cingulate cortex (ACC) play critical roles in different types of chronic pain. Most of previous studies focus on the sensory inputs from somatic areas, and less information about plastic changes in the cortex for visceral pain. In this study, chronic visceral pain animal model was established by injection with zymosan into the colon of adult male C57/BL6 mice. Whole cell patch-clamp recording, behavioral tests, western blot, and Cannulation and ACC microinjection were employed to explore the role of adenylyl cyclase 1 (AC1) in the ACC of C57/BL6 and AC1 knock out mice. Integrative approaches were used to investigate possible changes of neuronal AC1 in the ACC after the injury. We found that AC1, a key enzyme for pain-related cortical plasticity, was significantly increased in the ACC in an animal model of irritable bowel syndrome. Inhibiting AC1 activity by a selective AC1 inhibitor NB001 significantly reduced the up-regulation of AC1 protein in the ACC. Furthermore, we found that AC1 is required for NMDA GluN2B receptor up-regulation and increases of NMDA receptor-mediated currents. These results suggest that AC1 may form a positive regulation in the cortex during chronic visceral pain. Our findings demonstrate that the up-regulation of AC1 protein in the cortex may underlie the pathology of chronic visceral pain; and inhibiting AC1 activity may be beneficial for the treatment of visceral pain.
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Affiliation(s)
- Shui-Bing Liu
- Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi'an, China.,Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, China.,Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Xin-Shang Wang
- Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi'an, China.,Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, China
| | - Jiao Yue
- Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi'an, China.,Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, China
| | - Le Yang
- Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi'an, China.,Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, China
| | - Xu-Hui Li
- Center for Neuron and Disease, Frontier Institutes of Life Science and of Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Li-Ning Hu
- Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi'an, China.,Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, China
| | - Jing-Shan Lu
- Center for Neuron and Disease, Frontier Institutes of Life Science and of Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Qian Song
- Center for Neuron and Disease, Frontier Institutes of Life Science and of Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Kun Zhang
- Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi'an, China.,Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, China
| | - Qi Yang
- Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi'an, China.,Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, China
| | - Ming-Ming Zhang
- Department of Anatomy, Histology, Embryology & K. K. Leung Brain Research Centre, Fourth Military Medical University, Xi'an, China
| | - Matteo Bernabucci
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Ming-Gao Zhao
- Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi'an, China.,Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, China
| | - Min Zhuo
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.,Center for Neuron and Disease, Frontier Institutes of Life Science and of Science and Technology, Xi'an Jiaotong University, Xi'an, China
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31
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Hasan ABMSU, Kurata H, Pechmann S. Improvement of the memory function of a mutual repression network in a stochastic environment by negative autoregulation. BMC Bioinformatics 2019; 20:734. [PMID: 31881978 PMCID: PMC6935196 DOI: 10.1186/s12859-019-3315-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 12/12/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cellular memory is a ubiquitous function of biological systems. By generating a sustained response to a transient inductive stimulus, often due to bistability, memory is central to the robust control of many important biological processes. However, our understanding of the origins of cellular memory remains incomplete. Stochastic fluctuations that are inherent to most biological systems have been shown to hamper memory function. Yet, how stochasticity changes the behavior of genetic circuits is generally not clear from a deterministic analysis of the network alone. Here, we apply deterministic rate equations, stochastic simulations, and theoretical analyses of Fokker-Planck equations to investigate how intrinsic noise affects the memory function in a mutual repression network. RESULTS We find that the addition of negative autoregulation improves the persistence of memory in a small gene regulatory network by reducing stochastic fluctuations. Our theoretical analyses reveal that this improved memory function stems from an increased stability of the steady states of the system. Moreover, we show how the tuning of critical network parameters can further enhance memory. CONCLUSIONS Our work illuminates the power of stochastic and theoretical approaches to understanding biological circuits, and the importance of considering stochasticity when designing synthetic circuits with memory function.
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Affiliation(s)
- A B M Shamim Ul Hasan
- Department of Biochemistry, Université de Montréal, 2900 Edouard Montpetit Blvd, Montreal, QC, H3T 1J4, Canada.,The Biomedical Informatics R&D Center, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
| | - Hiroyuki Kurata
- The Biomedical Informatics R&D Center, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan.
| | - Sebastian Pechmann
- Department of Biochemistry, Université de Montréal, 2900 Edouard Montpetit Blvd, Montreal, QC, H3T 1J4, Canada.
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32
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VÁZQUEZ-JIMÉNEZ AARÓN, SANTILLÁN MOISÉS, RODRÍGUEZ-GONZÁLEZ JESÚS. CHARACTERIZATION OF INTRINSIC AND EXTRINSIC NOISE EFFECTS IN POSITIVELY REGULATED GENES. J BIOL SYST 2019. [DOI: 10.1142/s0218339019500165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Gene regulation is fundamental for cell survival. This regulation must be both robust to noise and sensitive enough to external stimuli to elicit the proper responses. In this work, we study, through stochastic numerical simulations, how a gene regulatory network with a positive feedback loop responds to environmental changes in the presence of intrinsic and extrinsic noises. Noise effects were characterized by measuring the statistical differences between two protein time series resulting from identical systems subject to the same source of extrinsic noise. A robust analysis was implemented by modifying the kinetic system parameters. We found that the common source of time-varying extrinsic fluctuations leads to a correlation in the systems it affects. The correlation and the extrinsic and intrinsic noise components are modulated by the update period and noise intensity parameters. Our results suggest that noise perception is controlled through the parameters associated with the response time: degradation rates and promoter dissociation constant.
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Affiliation(s)
- AARÓN VÁZQUEZ-JIMÉNEZ
- Centro de Investigación y Estudios Avanzados del IPN, Unidad Monterrey, Vía del Conocimiento 201, Parque PIIT, CP 66600 Apodaca NL, México
| | - MOISÉS SANTILLÁN
- Centro de Investigación y Estudios Avanzados del IPN, Unidad Monterrey, Vía del Conocimiento 201, Parque PIIT, CP 66600 Apodaca NL, México
| | - JESÚS RODRÍGUEZ-GONZÁLEZ
- Centro de Investigación y Estudios Avanzados del IPN, Unidad Monterrey, Vía del Conocimiento 201, Parque PIIT, CP 66600 Apodaca NL, México
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33
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Moschall R, Rass M, Rossbach O, Lehmann G, Kullmann L, Eichner N, Strauss D, Meister G, Schneuwly S, Krahn MP, Medenbach J. Drosophila Sister-of-Sex-lethal reinforces a male-specific gene expression pattern by controlling Sex-lethal alternative splicing. Nucleic Acids Res 2019; 47:2276-2288. [PMID: 30590805 PMCID: PMC6411925 DOI: 10.1093/nar/gky1284] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/04/2018] [Accepted: 12/14/2018] [Indexed: 01/14/2023] Open
Abstract
In Drosophila, female development is governed by a single RNA-binding protein, Sex-lethal (Sxl), that controls the expression of key factors involved in dosage compensation, germline homeostasis and the establishment of female morphology and behaviour. Sxl expression in female flies is maintained by an auto-regulatory, positive feedback loop with Sxl controlling splicing of its own mRNA. Until now, it remained unclear how males prevent accidental triggering of the Sxl expression cascade and protect themselves against runaway protein production. Here, we identify the protein Sister-of-Sex-lethal (Ssx) as an inhibitor of Sxl auto-regulatory splicing. Sxl and Ssx have a comparable RNA-binding specificity and compete for binding to RNA regulatory elements present in the Sxl transcript. In cultured Drosophila cells, Sxl-induced changes to alternative splicing can be reverted by the expression of Ssx. Moreover, in adult male flies ablation of the ssx gene results in a low level of productive Sxl mRNA splicing and Sxl protein production in isolated, clonal cell populations. In sum, this demonstrates that Ssx safeguards male animals against Sxl protein production to reinforce a stable, male-specific gene expression pattern.
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Affiliation(s)
- Rebecca Moschall
- Institute of Biochemistry I, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
| | - Mathias Rass
- Institute of Zoology, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
| | - Oliver Rossbach
- Institute of Biochemistry, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 17, D-35392 Giessen, Germany
| | - Gerhard Lehmann
- Institute of Biochemistry I, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
| | - Lars Kullmann
- Institute for Molecular and Cellular Anatomy, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
| | - Norbert Eichner
- Institute of Biochemistry I, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
| | - Daniela Strauss
- Institute of Biochemistry I, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
| | - Gunter Meister
- Institute of Biochemistry I, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
| | - Stephan Schneuwly
- Institute of Zoology, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
| | - Michael P Krahn
- Institute for Molecular and Cellular Anatomy, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany.,Medical Clinic D, University of Muenster, Domagkstrasse 3, D-48149 Muenster, Germany
| | - Jan Medenbach
- Institute of Biochemistry I, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
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34
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Rogan PK. Multigene signatures of responses to chemotherapy derived by biochemically-inspired machine learning. Mol Genet Metab 2019; 128:45-52. [PMID: 31451418 DOI: 10.1016/j.ymgme.2019.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 08/09/2019] [Accepted: 08/16/2019] [Indexed: 01/08/2023]
Abstract
Pharmacogenomic responses to chemotherapy drugs can be modeled by supervised machine learning of expression and copy number of relevant gene combinations. Such biochemical evidence can form the basis of derived gene signatures using cell line data, which can subsequently be examined in patients that have been treated with the same drugs. These gene signatures typically contain elements of multiple biochemical pathways which together comprise multiple origins of drug resistance or sensitivity. The signatures can capture variation in these responses to the same drug among different patients.
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Affiliation(s)
- Peter K Rogan
- Departments of Biochemistry, Oncology, and Computer Science, University of Western Ontario, London, ON N6A 2C1, UK.
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35
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Yurt MZ, Cakmak Y, Tekin G, Karakurt S, Erbas-Cakmak S. Autoinhibitory Feedback Control over Photodynamic Action. ACS OMEGA 2019; 4:12293-12299. [PMID: 31460346 PMCID: PMC6681998 DOI: 10.1021/acsomega.9b01410] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/05/2019] [Indexed: 06/10/2023]
Abstract
In biology, the activity of enzymes is usually regulated by feedback loops, which enables direct communication between enzymes and the state of the cell. In a similar manner, with the intention to have automated activity regulation, the therapeutic effect of a photosensitizer (BOD1) is shown to be reduced through a negative feedback loop initiated by the photosensitizer. Photodynamic action produces cytotoxic 1O2 and this reactive oxygen species reacts with ascorbate, generating H2O2. Peroxide-mediated oxidation of the photosensitizer auxiliary group leads to the formation of inactive BOD2 from the parent photosensitizer. BOD1 is shown to accumulate in mitochondria, and cell viability is shown to decrease significantly with BOD1 compared to the loop end product, BOD2. Photoinduced enhancement of fluorescence indicates the formation of inactive BOD2 under cellular conditions, and enhanced fluorescence acts as a reporter for the activity of the photosensitizer. We present the first example of PDT autoinactivation, and such a feedback control mechanism would enable a decrease in post-therapy side effects.
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Affiliation(s)
- Mediha
Nur Zafer Yurt
- Institute of Science, Biotechnology
Graduate Program, Research and Development
Center for Diagnostic Kits, Department of Bioengineering, and Department of Molecular Biology
and Genetics, Konya Food and Agriculture
University, Konya 42080, Turkey
| | - Yusuf Cakmak
- Institute of Science, Biotechnology
Graduate Program, Research and Development
Center for Diagnostic Kits, Department of Bioengineering, and Department of Molecular Biology
and Genetics, Konya Food and Agriculture
University, Konya 42080, Turkey
| | - Gülsüm Tekin
- Department
of Biochemistry, Selçuk University, Konya 42030, Turkey
| | - Serdar Karakurt
- Department
of Biochemistry, Selçuk University, Konya 42030, Turkey
| | - Sundus Erbas-Cakmak
- Institute of Science, Biotechnology
Graduate Program, Research and Development
Center for Diagnostic Kits, Department of Bioengineering, and Department of Molecular Biology
and Genetics, Konya Food and Agriculture
University, Konya 42080, Turkey
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36
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Tewary M, Shakiba N, Zandstra PW. Stem cell bioengineering: building from stem cell biology. Nat Rev Genet 2019; 19:595-614. [PMID: 30089805 DOI: 10.1038/s41576-018-0040-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
New fundamental discoveries in stem cell biology have yielded potentially transformative regenerative therapeutics. However, widespread implementation of stem-cell-derived therapeutics remains sporadic. Barriers that impede the development of these therapeutics can be linked to our incomplete understanding of how the regulatory networks that encode stem cell fate govern the development of the complex tissues and organs that are ultimately required for restorative function. Bioengineering tools, strategies and design principles represent core components of the stem cell bioengineering toolbox. Applied to the different layers of complexity present in stem-cell-derived systems - from gene regulatory networks in single stem cells to the systemic interactions of stem-cell-derived organs and tissues - stem cell bioengineering can address existing challenges and advance regenerative medicine and cellular therapies.
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Affiliation(s)
- Mukul Tewary
- Institute of Biomaterials and Biomedical Engineering (IBBME) and The Donnelly Centre for Cellular and Biomolecular Research (CCBR), University of Toronto, Toronto, Ontario, Canada.,Collaborative Program in Developmental Biology, University of Toronto, Toronto, Ontario, Canada
| | - Nika Shakiba
- Institute of Biomaterials and Biomedical Engineering (IBBME) and The Donnelly Centre for Cellular and Biomolecular Research (CCBR), University of Toronto, Toronto, Ontario, Canada
| | - Peter W Zandstra
- Institute of Biomaterials and Biomedical Engineering (IBBME) and The Donnelly Centre for Cellular and Biomolecular Research (CCBR), University of Toronto, Toronto, Ontario, Canada. .,Collaborative Program in Developmental Biology, University of Toronto, Toronto, Ontario, Canada. .,Michael Smith Laboratories and School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada.
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37
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Morley CD, Ellison ST, Bhattacharjee T, O'Bryan CS, Zhang Y, Smith KF, Kabb CP, Sebastian M, Moore GL, Schulze KD, Niemi S, Sawyer WG, Tran DD, Mitchell DA, Sumerlin BS, Flores CT, Angelini TE. Quantitative characterization of 3D bioprinted structural elements under cell generated forces. Nat Commun 2019; 10:3029. [PMID: 31292444 PMCID: PMC6620298 DOI: 10.1038/s41467-019-10919-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 06/03/2019] [Indexed: 12/31/2022] Open
Abstract
With improving biofabrication technology, 3D bioprinted constructs increasingly resemble real tissues. However, the fundamental principles describing how cell-generated forces within these constructs drive deformations, mechanical instabilities, and structural failures have not been established, even for basic biofabricated building blocks. Here we investigate mechanical behaviours of 3D printed microbeams made from living cells and extracellular matrix, bioprinting these simple structural elements into a 3D culture medium made from packed microgels, creating a mechanically controlled environment that allows the beams to evolve under cell-generated forces. By varying the properties of the beams and the surrounding microgel medium, we explore the mechanical behaviours exhibited by these structures. We observe buckling, axial contraction, failure, and total static stability, and we develop mechanical models of cell-ECM microbeam mechanics. We envision these models and their generalizations to other fundamental 3D shapes to facilitate the predictable design of biofabricated structures using simple building blocks in the future.
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Affiliation(s)
- Cameron D Morley
- University of Florida, Herbert Wertheim College of Engineering, Department of Mechanical and Aerospace Engineering, Gainesville, FL, 32611, USA
| | - S Tori Ellison
- University of Florida, Herbert Wertheim College of Engineering, Department of Materials Science and Engineering, Gainesville, FL, 32611, USA
| | - Tapomoy Bhattacharjee
- Princeton University, Department of Chemical and Biological Engineering, Princeton, NJ, 08540, USA
| | - Christopher S O'Bryan
- University of Florida, Herbert Wertheim College of Engineering, Department of Mechanical and Aerospace Engineering, Gainesville, FL, 32611, USA
| | - Yifan Zhang
- University of Florida, Herbert Wertheim College of Engineering, Department of Mechanical and Aerospace Engineering, Gainesville, FL, 32611, USA
| | - Kourtney F Smith
- University of Florida, Herbert Wertheim College of Engineering, Department of Materials Science and Engineering, Gainesville, FL, 32611, USA
| | - Christopher P Kabb
- University of Florida, George and Josephine Butler Polymer Research Laboratory, Center for Macromolecular Science and Engineering, Department of Chemistry, Gainesville, FL, 32611, USA
| | - Mathew Sebastian
- Division of Neuro-Oncology, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, University of Florida, Gainesville, FL, 32611, USA
| | - Ginger L Moore
- University of Florida, Brain Tumor Immunotherapy Program, Preston A. Wells Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, Gainesville, FL, 32611, USA
| | - Kyle D Schulze
- Auburn University, Department of Mechanical Engineering, Auburn, AL, 36849, USA
| | - Sean Niemi
- University of Florida, Herbert Wertheim College of Engineering, Department of Mechanical and Aerospace Engineering, Gainesville, FL, 32611, USA
| | - W Gregory Sawyer
- University of Florida, Herbert Wertheim College of Engineering, Department of Mechanical and Aerospace Engineering, Gainesville, FL, 32611, USA
- University of Florida, Herbert Wertheim College of Engineering, Department of Materials Science and Engineering, Gainesville, FL, 32611, USA
| | - David D Tran
- Division of Neuro-Oncology, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, University of Florida, Gainesville, FL, 32611, USA
| | - Duane A Mitchell
- University of Florida, Brain Tumor Immunotherapy Program, Preston A. Wells Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, Gainesville, FL, 32611, USA
| | - Brent S Sumerlin
- University of Florida, George and Josephine Butler Polymer Research Laboratory, Center for Macromolecular Science and Engineering, Department of Chemistry, Gainesville, FL, 32611, USA
| | - Catherine T Flores
- University of Florida, Brain Tumor Immunotherapy Program, Preston A. Wells Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, Gainesville, FL, 32611, USA
| | - Thomas E Angelini
- University of Florida, Herbert Wertheim College of Engineering, Department of Mechanical and Aerospace Engineering, Gainesville, FL, 32611, USA.
- University of Florida, Herbert Wertheim College of Engineering, Department of Materials Science and Engineering, Gainesville, FL, 32611, USA.
- University of Florida, Herbert Wertheim College of Engineering, J. Crayton Pruitt Family Department of Biomedical Engineering, Gainesville, FL, 32611, USA.
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Abstract
A handful of core intercellular signaling pathways play pivotal roles in a broad variety of developmental processes. It has remained puzzling how so few pathways can provide the precision and specificity of cell-cell communication required for multicellular development. Solving this requires us to quantitatively understand how developmentally relevant signaling information is actively sensed, transformed and spatially distributed by signaling pathways. Recently, single cell analysis and cell-based reconstitution, among other approaches, have begun to reveal the 'communication codes' through which information is represented in the identities, concentrations, combinations and dynamics of extracellular ligands. They have also revealed how signaling pathways decipher these features and control the spatial distribution of signaling in multicellular contexts. Here, we review recent work reporting the discovery and analysis of communication codes and discuss their implications for diverse developmental processes.
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Affiliation(s)
- Pulin Li
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Howard Hughes Medical Institute, Pasadena, CA 91125, USA
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39
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Page DJ, Thuret R, Venkatraman L, Takahashi T, Bentley K, Herbert SP. Positive Feedback Defines the Timing, Magnitude, and Robustness of Angiogenesis. Cell Rep 2019; 27:3139-3151.e5. [PMID: 31189101 PMCID: PMC6581738 DOI: 10.1016/j.celrep.2019.05.052] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 04/01/2019] [Accepted: 05/15/2019] [Indexed: 12/20/2022] Open
Abstract
Angiogenesis is driven by the coordinated collective branching of specialized leading "tip" and trailing "stalk" endothelial cells (ECs). While Notch-regulated negative feedback suppresses excessive tip selection, roles for positive feedback in EC identity decisions remain unexplored. Here, by integrating computational modeling with in vivo experimentation, we reveal that positive feedback critically modulates the magnitude, timing, and robustness of angiogenic responses. In silico modeling predicts that positive-feedback-mediated amplification of VEGF signaling generates an ultrasensitive bistable switch that underpins quick and robust tip-stalk decisions. In agreement, we define a positive-feedback loop exhibiting these properties in vivo, whereby Vegf-induced expression of the atypical tetraspanin, tm4sf18, amplifies Vegf signaling to dictate the speed and robustness of EC selection for angiogenesis. Consequently, tm4sf18 mutant zebrafish select fewer motile ECs and exhibit stunted hypocellular vessels with unstable tip identity that is severely perturbed by even subtle Vegfr attenuation. Hence, positive feedback spatiotemporally shapes the angiogenic switch to ultimately modulate vascular network topology.
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Affiliation(s)
- Donna J Page
- Faculty of Biology, Medicine and Health, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK; School of Healthcare Science, Manchester Metropolitan University, Manchester M1 5GD, UK
| | - Raphael Thuret
- Faculty of Biology, Medicine and Health, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Lakshmi Venkatraman
- Biomedical Engineering Department, Boston University, 610 Commonwealth Avenue, Boston, MA 02215, USA; Immunology, Genetics and Pathology Department, University of Uppsala, 751 85 Uppsala, Sweden
| | - Tokiharu Takahashi
- Faculty of Biology, Medicine and Health, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Katie Bentley
- Biomedical Engineering Department, Boston University, 610 Commonwealth Avenue, Boston, MA 02215, USA; Immunology, Genetics and Pathology Department, University of Uppsala, 751 85 Uppsala, Sweden; Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Cellular Adaptive Behaviour Lab, The Francis Crick Institute, Midland Road, London NW1 1AT, UK; Department of Informatics, Faculty of Natural and Mathematical Sciences, King's College London, Strand Campus, London WC2B 4BG, UK.
| | - Shane P Herbert
- Faculty of Biology, Medicine and Health, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK.
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40
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Healy CP, Deans TL. Genetic circuits to engineer tissues with alternative functions. J Biol Eng 2019; 13:39. [PMID: 31073328 PMCID: PMC6500048 DOI: 10.1186/s13036-019-0170-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 04/17/2019] [Indexed: 12/23/2022] Open
Abstract
Persistent and complex problems arising with respect to human physiology and pathology have led to intense investigation into therapies and tools that permit more targeted outcomes and biomimetic responses to pathological conditions. A primary goal in mammalian synthetic biology is to build genetic circuits that exert fine control over cell behavior for next-generation biomedical applications. In pursuit of this, synthetic biologists have engineered cells endowed with genetic circuits with sensor that are capable of reacting to a variety of stimuli and responding with targeted behavior. Here, we highlight how synthetic biology approaches are being used to program cells with novel functions for therapeutic applications, and how they can be used in stem cells to improve differentiation outcomes. These approaches open the possibilities for engineering synthetic tissues for employing personalized medicine and to develop next-generation biomedical therapies.
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Affiliation(s)
- C P Healy
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112 USA
| | - T L Deans
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112 USA
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41
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Joesaar A, Yang S, Bögels B, van der Linden A, Pieters P, Kumar BVVSP, Dalchau N, Phillips A, Mann S, de Greef TFA. DNA-based communication in populations of synthetic protocells. NATURE NANOTECHNOLOGY 2019; 14:369-378. [PMID: 30833694 PMCID: PMC6451639 DOI: 10.1038/s41565-019-0399-9] [Citation(s) in RCA: 193] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 01/22/2019] [Indexed: 05/20/2023]
Abstract
Developing molecular communication platforms based on orthogonal communication channels is a crucial step towards engineering artificial multicellular systems. Here, we present a general and scalable platform entitled 'biomolecular implementation of protocellular communication' (BIO-PC) to engineer distributed multichannel molecular communication between populations of non-lipid semipermeable microcapsules. Our method leverages the modularity and scalability of enzyme-free DNA strand-displacement circuits to develop protocellular consortia that can sense, process and respond to DNA-based messages. We engineer a rich variety of biochemical communication devices capable of cascaded amplification, bidirectional communication and distributed computational operations. Encapsulating DNA strand-displacement circuits further allows their use in concentrated serum where non-compartmentalized DNA circuits cannot operate. BIO-PC enables reliable execution of distributed DNA-based molecular programs in biologically relevant environments and opens new directions in DNA computing and minimal cell technology.
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Affiliation(s)
- Alex Joesaar
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Shuo Yang
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Bas Bögels
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Ardjan van der Linden
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Pascal Pieters
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - B V V S Pavan Kumar
- Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | | | | | - Stephen Mann
- Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | - Tom F A de Greef
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
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42
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Dixit S, Sharma A, Prasad A, Shrimali MD. Dynamics of nonlinear oscillator with transient feedback. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/s40435-019-00534-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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43
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Sheng Z, Wang C, Ren F, Liu Y, Zhu B. Molecular mechanism of endocrine-disruptive effects induced by Bisphenol A: The role of transmembrane G-protein estrogen receptor 1 and integrin αvβ3. J Environ Sci (China) 2019; 75:1-13. [PMID: 30473274 DOI: 10.1016/j.jes.2018.05.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 05/07/2018] [Accepted: 05/08/2018] [Indexed: 06/09/2023]
Abstract
Bisphenol A (BPA) is one of the highest volume industrial products worldwide and has been widely used to make various products as the intermediates of polycarbonate plastics and epoxy resins. Inevitably, general population has been widely exposed to BPA due to extensive use of BPA-containing products. BPA has similar chemical structure with the natural estrogen and has been shown to induce a variety of estrogen-like endocrine effects on organism in vivo or in vitro. High doses of BPA tend to act as antagonist of estrogen receptors (ERs) by directly regulating the genomic transcription. However, BPA at environmentally relevant low-dose always disrupt the biological function via a non-genomic manner mediated by membrane receptors, rather than ERs. Although some studies had investigated the non-genomic effects of low-dose BPA, the exact molecular mechanism still remains unclear. Recently, we found that membrane G protein-coupled estrogen receptor 1 and integrin αvβ3 and its relative signal pathways participate in the induction of male germ cell proliferation and thyroid transcription disruption by the low-dose BPA. A profound understanding for the mechanism of action of the environmentally relevant BPA exposure not only contributes to objectively evaluate and predict the potential influence to human health, but also provides theoretical basis and methodological support for assessing health effects trigged by other estrogen-like environmental endocrine disruptors. Based mainly on our recent findings, this review outlines the research progress of molecular mechanism on endocrine disrupting effects of environmental low-dose BPA, existing problems and some consideration for future studies.
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Affiliation(s)
- Zhiguo Sheng
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Cong Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Furong Ren
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yuxiang Liu
- College of Chemistry and Chemical Engineering, Xinjiang Normal University, Urumqi 830054, China
| | - Benzhan Zhu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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44
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Rahman A, Tiwari A, Narula J, Hickling T. Importance of Feedback and Feedforward Loops to Adaptive Immune Response Modeling. CPT Pharmacometrics Syst Pharmacol 2018; 7:621-628. [PMID: 30198637 PMCID: PMC6202469 DOI: 10.1002/psp4.12352] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 08/15/2018] [Indexed: 12/15/2022] Open
Abstract
The human adaptive immune system is a very complex network of different types of cells, cytokines, and signaling molecules. This complex network makes it difficult to understand the system level regulations. To properly explain the immune system, it is necessary to explicitly investigate the presence of different feedback and feedforward loops (FFLs) and their crosstalks. Considering that these loops increase the complexity of the system, the mathematical modeling has been proved to be an important tool to explain such complex biological systems. This review focuses on these regulatory loops and discusses their importance on systems modeling of the immune system.
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45
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Pandey SK, Lee HW, Kim MJ, Cho C, Oh E, Kim J. LBD18 uses a dual mode of a positive feedback loop to regulate ARF expression and transcriptional activity in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:233-251. [PMID: 29681137 DOI: 10.1111/tpj.13945] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 04/02/2018] [Accepted: 04/05/2018] [Indexed: 05/10/2023]
Abstract
A hierarchy of transcriptional regulators controlling lateral root formation in Arabidopsis thaliana has been identified, including the AUXIN RESPONSE FACTOR 7 (ARF7)/ARF19-LATERAL ORGAN BOUNDARIES DOMAIN 16 (LBD16)/LBD18 transcriptional network; however, their feedback regulation mechanisms are not known. Here we show that LBD18 controls ARF activity using the dual mode of a positive feedback loop. We showed that ARF7 and ARF19 directly bind AuxRE in the LBD18 promoter. A variety of molecular and biochemical experiments demonstrated that LBD18 binds a specific DNA motif in the ARF19 promoter to regulate its expression in vivo as well as in vitro. LBD18 interacts with ARFs including ARF7 and ARF19 via the Phox and Bem1 domain of ARF to enhance the transcriptional activity of ARF7 on AuxRE, and competes with auxin/indole-3-acetic acid (IAA) repressors for ARF binding, overriding the negative feedback loop exerted by Aux/IAA repressors. Taken together, these results show that LBD18 and ARFs form a double positive feedback loop, and that LBD18 uses the dual mode of a positive feedback loop by binding directly to the ARF19 promoter and through the protein-protein interactions with ARF7 and ARF19. This novel mechanism of feedback loops may constitute a robust feedback mechanism that ensures continued lateral root growth in response to auxin in Arabidopsis.
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Affiliation(s)
- Shashank K Pandey
- Department of Bioenergy Science and Technology, Chonnam National University, Buk-Gu, Gwangju, 500-757, Korea
| | - Han Woo Lee
- Department of Bioenergy Science and Technology, Chonnam National University, Buk-Gu, Gwangju, 500-757, Korea
| | - Min-Jung Kim
- Department of Bioenergy Science and Technology, Chonnam National University, Buk-Gu, Gwangju, 500-757, Korea
| | - Chuloh Cho
- Department of Bioenergy Science and Technology, Chonnam National University, Buk-Gu, Gwangju, 500-757, Korea
| | - Eunkyoo Oh
- Department of Bioenergy Science and Technology, Chonnam National University, Buk-Gu, Gwangju, 500-757, Korea
| | - Jungmook Kim
- Department of Bioenergy Science and Technology, Chonnam National University, Buk-Gu, Gwangju, 500-757, Korea
- Kumho Life Science Laboratory, Chonnam National University, Buk-Gu, Gwangju, 500-757, Korea
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46
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The role of the EGFR signaling pathway in stem cell differentiation during planarian regeneration and homeostasis. Semin Cell Dev Biol 2018; 87:45-57. [PMID: 29775660 DOI: 10.1016/j.semcdb.2018.05.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 05/07/2018] [Accepted: 05/14/2018] [Indexed: 12/25/2022]
Abstract
Cell signaling is essential for cells to adequately respond to their environment. One of the most evolutionarily conserved signaling pathways is that of the epidermal growth factor receptor (EGFR). Transmembrane receptors with intracellular tyrosine kinase activity are activated by the binding of their corresponding ligands. This in turn activates a wide variety of intracellular cascades and induces the up- or downregulation of target genes, leading to a specific cellular response. Freshwater planarians are an excellent model in which to study the role of cell signaling in the context of stem-cell based regeneration. Owing to the presence of a population of pluripotent stem cells called neoblasts, these animals can regenerate the entire organism from a tiny piece of the body. Here, we review the current state of knowledge of the planarian EGFR pathway. We describe the main components of the pathway and their functions in other animals, and focus in particular on receptors and ligands identified in the planarian Schmidtea mediterranea. Moreover, we summarize current data on the function of some of these components during planarian regeneration and homeostasis. We hypothesize that the EGFR pathway may act as a key regulator of the terminal differentiation of distinct populations of lineage-committed progenitors.
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47
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Marcou Q, Carmi-Levy I, Trichot C, Soumelis V, Mora T, Walczak AM. A model for the integration of conflicting exogenous and endogenous signals by dendritic cells. Phys Biol 2018; 15:056001. [PMID: 29360100 DOI: 10.1088/1478-3975/aaaa0a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Cells of the immune system are confronted with opposing pro- and anti-inflammatory signals. Dendritic cells (DC) integrate these cues to make informed decisions whether to initiate an immune response. Confronted with exogenous microbial stimuli, DC endogenously produce both anti- (IL-10) and pro-inflammatory (TNFα) cues whose joint integration controls the cell's final decision. Backed by experimental measurements we present a theoretical model to quantitatively describe the integration mode of these opposing signals. We propose a two step integration model that modulates the effect of the two types of signals: an initial bottleneck integrates both signals (IL-10 and TNFα), the output of which is later modulated by the anti-inflammatory signal. We show that the anti-inflammatory IL-10 signaling is long ranged, as opposed to the short-ranged pro-inflammatory TNFα signaling. The model suggests that the population averaging and modulation of the pro-inflammatory response by the anti-inflammatory signal is a safety guard against excessive immune responses.
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Affiliation(s)
- Quentin Marcou
- Laboratoire de physique théorique, CNRS, UPMC and École normale supérieure, 75005 Paris, France. Equal contribution
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48
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Jiang J, Tang S, Xia J, Wen J, Chen S, Shu X, Huen MSY, Deng Y. C9orf140, a novel Axin1-interacting protein, mediates the negative feedback loop of Wnt/β-catenin signaling. Oncogene 2018; 37:2992-3005. [PMID: 29531269 PMCID: PMC5978805 DOI: 10.1038/s41388-018-0166-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 01/11/2018] [Accepted: 01/12/2018] [Indexed: 12/16/2022]
Abstract
Wnt/β-catenin signaling activity is maintained in homeostasis by an expanding list of molecular determinants. However, the molecular components and the regulatory mechanisms involved in its fine-tuning remain to be determined. Here, we identified C9orf140, a tumor-specific protein, as a novel Axin1-interacting protein by tandem-affinity purification and mass spectrometry. We further showed that C9orf140 is a negative regulator of Wnt/β-catenin signaling in cultured cells as well as in zebrafish embryos. It functions upstream of β-catenin, outcompetes PP2A for binding to Axin1, influences the balance between phosphorylation and de-phosphorylation of β-catenin, and ultimately compromises Wnt3A-induced β-catenin accumulation. Interestingly, Wnt-induced C9orf140 expression via β-catenin. We propose that C9orf140 mediates a negative feedback loop of Wnt/β-catenin signaling by interacting with Axin1. Our results advance the current understanding of the exquisite control of Wnt/β-catenin signaling cascade, and provide evidence of the new role of C9orf140.
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Affiliation(s)
- Jun Jiang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Shulin Tang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Jianhong Xia
- Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, 510530, China
| | - Jikai Wen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Shuang Chen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Xiaodong Shu
- Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, 510530, China
| | - Michael S Y Huen
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Yiqun Deng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China.
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49
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Developmentally inspired programming of adult human mesenchymal stromal cells toward stable chondrogenesis. Proc Natl Acad Sci U S A 2018; 115:4625-4630. [PMID: 29666250 DOI: 10.1073/pnas.1720658115] [Citation(s) in RCA: 45] [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
It is generally accepted that adult human bone marrow-derived mesenchymal stromal cells (hMSCs) are default committed toward osteogenesis. Even when induced to chondrogenesis, hMSCs typically form hypertrophic cartilage that undergoes endochondral ossification. Because embryonic mesenchyme is obviously competent to generate phenotypically stable cartilage, it is questioned whether there is a correspondence between mesenchymal progenitor compartments during development and in adulthood. Here we tested whether forcing specific early events of articular cartilage development can program hMSC fate toward stable chondrogenesis. Inspired by recent findings that spatial restriction of bone morphogenetic protein (BMP) signaling guides embryonic progenitors toward articular cartilage formation, we hypothesized that selective inhibition of BMP drives the phenotypic stability of hMSC-derived chondrocytes. Two BMP type I receptor-biased kinase inhibitors were screened in a microfluidic platform for their time- and dose-dependent effect on hMSC chondrogenesis. The different receptor selectivity profile of tested compounds allowed demonstration that transient blockade of both ALK2 and ALK3 receptors, while permissive to hMSC cartilage formation, is necessary and sufficient to maintain a stable chondrocyte phenotype. Remarkably, even upon compound removal, hMSCs were no longer competent to undergo hypertrophy in vitro and endochondral ossification in vivo, indicating the onset of a constitutive change. Our findings demonstrate that adult hMSCs effectively share properties of embryonic mesenchyme in the formation of transient but also of stable cartilage. This opens potential pharmacological strategies to articular cartilage regeneration and more broadly indicates the relevance of developmentally inspired protocols to control the fate of adult progenitor cell systems.
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50
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Li P, Markson JS, Wang S, Chen S, Vachharajani V, Elowitz MB. Morphogen gradient reconstitution reveals Hedgehog pathway design principles. Science 2018; 360:543-548. [PMID: 29622726 DOI: 10.1126/science.aao0645] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 03/22/2018] [Indexed: 12/30/2022]
Abstract
In developing tissues, cells estimate their spatial position by sensing graded concentrations of diffusible signaling proteins called morphogens. Morphogen-sensing pathways exhibit diverse molecular architectures, whose roles in controlling patterning dynamics and precision have been unclear. In this work, combining cell-based in vitro gradient reconstitution, genetic rewiring, and mathematical modeling, we systematically analyzed the distinctive architectural features of the Sonic Hedgehog pathway. We found that the combination of double-negative regulatory logic and negative feedback through the PTCH receptor accelerates gradient formation and improves robustness to variation in the morphogen production rate compared with alternative designs. The ability to isolate morphogen patterning from concurrent developmental processes and to compare the patterning behaviors of alternative, rewired pathway architectures offers a powerful way to understand and engineer multicellular patterning.
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Affiliation(s)
- Pulin Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Joseph S Markson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Sheng Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Siheng Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Vipul Vachharajani
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA. .,Howard Hughes Medical Institute and Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA
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