1
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Baek S, Ha HS, Park JS, Cho MJ, Kim HS, Yu SE, Chung S, Kim C, Kim J, Lee JY, Lee Y, Kim H, Nam Y, Cho S, Lee K, Yoon JK, Choi JS, Han DH, Sung HJ. Chip collection of hepatocellular carcinoma based on O 2 heterogeneity from patient tissue. Nat Commun 2024; 15:5117. [PMID: 38879551 PMCID: PMC11180182 DOI: 10.1038/s41467-024-49386-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 06/04/2024] [Indexed: 06/19/2024] Open
Abstract
Hepatocellular carcinoma frequently recurs after surgery, necessitating personalized clinical approaches based on tumor avatar models. However, location-dependent oxygen concentrations resulting from the dual hepatic vascular supply drive the inherent heterogeneity of the tumor microenvironment, which presents challenges in developing an avatar model. In this study, tissue samples from 12 patients with hepatocellular carcinoma are cultured directly on a chip and separated based on preference of oxygen concentration. Establishing a dual gradient system with drug perfusion perpendicular to the oxygen gradient enables the simultaneous separation of cells and evaluation of drug responsiveness. The results are further cross-validated by implanting the chips into mice at various oxygen levels using a patient-derived xenograft model. Hepatocellular carcinoma cells exposed to hypoxia exhibit invasive and recurrent characteristics that mirror clinical outcomes. This chip provides valuable insights into treatment prognosis by identifying the dominant hepatocellular carcinoma type in each patient, potentially guiding personalized therapeutic interventions.
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Affiliation(s)
- Sewoom Baek
- Department of Brain Korea 21 FOUR Project for Medical Science, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
- Department of Medical Engineering, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Hyun-Su Ha
- Department of Medical Engineering, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
- Division of Cardiology, Severance Cardiovascular Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Jeong Su Park
- Department of Severance Biomedical Science Institute, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Min Jeong Cho
- Department of Clinical Pharmacology & Therapeutics, Catholic University of Korea, Seoul St. Mary's Hospital, 222, BanpoDaero, Seocho-gu, Seoul, 06591, Republic of Korea
| | - Hye-Seon Kim
- Department of Medical Engineering, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
- Department of Anesthesiology, Perioperative, and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Seung Eun Yu
- Department of Medical Engineering, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Seyong Chung
- Department of Medical Engineering, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Chansik Kim
- Department of Brain Korea 21 FOUR Project for Medical Science, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
- Department of Medical Engineering, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Jueun Kim
- Department of Brain Korea 21 FOUR Project for Medical Science, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
- Department of Medical Engineering, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Ji Youn Lee
- Department of Brain Korea 21 FOUR Project for Medical Science, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
- Department of Medical Engineering, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Yerin Lee
- Department of Medical Engineering, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Hyunjae Kim
- Department of Medical Engineering, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Yujin Nam
- Department of Medical Engineering, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Sungwoo Cho
- Department of Medical Engineering, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Kyubae Lee
- Department of Biomedical Materials, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon, 35365, Republic of Korea
| | - Ja Kyung Yoon
- Department of Radiology, Severance Hospital, Research Institute of Radiological Science, Center for Clinical Imaging Data Science, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Jin Sub Choi
- Department of Surgery, Division of Hepato-biliary and Pancreatic Surgery, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Dai Hoon Han
- Department of Surgery, Division of Hepato-biliary and Pancreatic Surgery, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
| | - Hak-Joon Sung
- Department of Brain Korea 21 FOUR Project for Medical Science, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
- Department of Medical Engineering, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
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2
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Kim HS, Ha HS, Kim DH, Son DH, Baek S, Park J, Lee CH, Park S, Yoon HJ, Yu SE, Kang JI, Park KM, Shin YM, Lee JB, Sung HJ. O 2 variant chip to simulate site-specific skeletogenesis from hypoxic bone marrow. SCIENCE ADVANCES 2023; 9:eadd4210. [PMID: 36947623 PMCID: PMC10032601 DOI: 10.1126/sciadv.add4210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
The stemness of bone marrow mesenchymal stem cells (BMSCs) is maintained by hypoxia. The oxygen level increases from vessel-free cartilage to hypoxic bone marrow and, furthermore, to vascularized bone, which might direct the chondrogenesis to osteogenesis and regenerate the skeletal system. Hence, oxygen was diffused from relatively low to high levels throughout a three-dimensional chip. When we cultured BMSCs in the chip and implanted them into the rabbit defect models of low-oxygen cartilage and high-oxygen calvaria bone, (i) the low oxygen level (base) promoted stemness and chondrogenesis of BMSCs with robust antioxidative potential; (ii) the middle level (two times ≥ low) pushed BMSCs to quiescence; and (iii) the high level (four times ≥ low) promoted osteogenesis by disturbing the redox balance and stemness. Last, endochondral or intramembranous osteogenesis upon transition from low to high oxygen in vivo suggests a developmental mechanism-driven solution to promote chondrogenesis to osteogenesis in the skeletal system by regulating the oxygen environment.
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Affiliation(s)
- Hye-Seon Kim
- Department of Medical Engineering, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Hyun-Su Ha
- Department of Medical Engineering, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Dae-Hyun Kim
- Department of Veterinary Surgery, College of Veterinary Medicine, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Deok Hyeon Son
- Department of Medical Engineering, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Sewoom Baek
- Department of Medical Engineering, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jeongeun Park
- Department of Medical Engineering, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Chan Hee Lee
- Department of Medical Engineering, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Suji Park
- Department of Medical Engineering, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Hyo-Jin Yoon
- Department of Medical Engineering, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Seung Eun Yu
- Department of Medical Engineering, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jeon Il Kang
- Department of Bioengineering and Nano-Bioengineering, College of Life sciences and Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
| | - Kyung Min Park
- Department of Bioengineering and Nano-Bioengineering, College of Life sciences and Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
- Research Center for Biomaterials and Process Development, Incheon National University, Incheon 22012, Republic of Korea
| | - Young Min Shin
- Department of Medical Engineering, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jung Bok Lee
- Department of Biological Sciences, Sookmyung Women’s University, Seoul 04310, Republic of Korea
- Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea
| | - Hak-Joon Sung
- Department of Medical Engineering, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
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3
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Seo D, Kim D, Seo S, Park J, Kim T. Analyses of Pore-Size-Dependent Ionic Transport in Nanopores in the Presence of Concentration and Temperature Gradients. ACS APPLIED MATERIALS & INTERFACES 2023; 15:2409-2418. [PMID: 36562122 DOI: 10.1021/acsami.2c17925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Mass transport through nanopores occurs in various natural systems, including the human body. For example, ion transport across nerve cell membranes plays a significant role in neural signal transmission, which can be significantly affected by the electrolyte and temperature conditions. To better understand and control the underlying nanoscopic transport, it is necessary to develop multiphysical transport models as well as validate them using enhanced experimental methods for facile nanopore fabrication and precise nanoscale transport characterization. Here, we report a nanopore-integrated microfluidic platform to characterize ion transport in the presence of electrolyte and temperature gradients; we employ our previous self-assembled particle membrane (SAPM)-integrated microfluidic platform to produce various nanopores with different pore sizes. Subsequently, we quantify pore-size-dependent ionic transport by measuring the short circuit current (SCC) and open circuit voltage (OCV) across various nanopores by manipulating the electrolyte and temperature gradients. We establish three simple theoretical models that heavily depend on pore size, electrolyte concentration, and temperature and subsequently validate them with the experimental results. Finally, we anticipate that the results of this study would help clarify ion transport phenomena at low-temperature conditions, not only providing a fundamental understanding but also enabling practical applications of cryo-anesthesia in the near future.
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Affiliation(s)
- Dongwoo Seo
- Department of Mechanical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan44919, Republic of Korea
| | - Dongjun Kim
- Department of Mechanical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan44919, Republic of Korea
| | - Sangjin Seo
- Department of Mechanical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan44919, Republic of Korea
| | - Jungyul Park
- Department of Mechanical Engineering, Sogang University, Sinsudong, Mapogu, Seoul04107, Republic of Korea
| | - Taesung Kim
- Department of Mechanical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan44919, Republic of Korea
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4
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Copeland J, Wilson K, Simoes-Costa M. Micromanaging pattern formation: miRNA regulation of signaling systems in vertebrate development. FEBS J 2022; 289:5166-5175. [PMID: 34310060 DOI: 10.1111/febs.16139] [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: 03/23/2021] [Revised: 06/14/2021] [Accepted: 07/23/2021] [Indexed: 11/29/2022]
Abstract
Early embryogenesis requires the establishment of fields of progenitor cells with distinct molecular signatures. A balance of intrinsic and extrinsic cues determines the boundaries of embryonic territories and pushes progenitor cells toward different fates. This process involves multiple layers of regulation, including signaling systems, transcriptional networks, and post-transcriptional control. In recent years, microRNAs (miRNAs) have emerged as undisputed regulators of developmental processes. Here, we discuss how miRNAs regulate pattern formation during vertebrate embryogenesis. We survey how miRNAs modulate the activity of signaling pathways to optimize transcriptional responses in embryonic cells. We also examine how localized RNA interference can generate spatial complexity during early development. Unraveling the complex crosstalk between miRNAs, signaling systems and cell fate decisions will be crucial for our understanding of developmental outcomes and disease.
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Affiliation(s)
- Jacqueline Copeland
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Kayla Wilson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Marcos Simoes-Costa
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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5
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Evenbratt H, Andreasson L, Bicknell V, Brittberg M, Mobini R, Simonsson S. Insights into the present and future of cartilage regeneration and joint repair. CELL REGENERATION (LONDON, ENGLAND) 2022; 11:3. [PMID: 35106664 PMCID: PMC8807792 DOI: 10.1186/s13619-021-00104-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 12/06/2021] [Indexed: 12/23/2022]
Abstract
Knee osteoarthritis is the most common joint disease. It causes pain and suffering for affected patients and is the source of major economic costs for healthcare systems. Despite ongoing research, there is a lack of knowledge regarding disease mechanisms, biomarkers, and possible cures. Current treatments do not fulfill patients' long-term needs, and it often requires invasive surgical procedures with subsequent long periods of rehabilitation. Researchers and companies worldwide are working to find a suitable cell source to engineer or regenerate a functional and healthy articular cartilage tissue to implant in the damaged area. Potential cell sources to accomplish this goal include embryonic stem cells, mesenchymal stem cells, or induced pluripotent stem cells. The differentiation of stem cells into different tissue types is complex, and a suitable concentration range of specific growth factors is vital. The cellular microenvironment during early embryonic development provides crucial information regarding concentrations of signaling molecules and morphogen gradients as these are essential inducers for tissue development. Thus, morphogen gradients implemented in developmental protocols aimed to engineer functional cartilage tissue can potentially generate cells comparable to those within native cartilage. In this review, we have summarized the problems with current treatments, potential cell sources for cell therapy, reviewed the progress of new treatments within the regenerative cartilage field, and highlighted the importance of cell quality, characterization assays, and chemically defined protocols.
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Affiliation(s)
| | - L. Andreasson
- Cline Scientific AB, SE-431 53 Mölndal, Sweden
- Institute of Biomedicine at Sahlgrenska Academy, Department of Clinical Chemistry and Transfusion Medicine, University of Gothenburg, SE-413 45 Gothenburg, Sweden
| | - V. Bicknell
- Cline Scientific AB, SE-431 53 Mölndal, Sweden
| | - M. Brittberg
- Cartilage Research Unit, University of Gothenburg, Region Halland Orthopaedics, Kungsbacka Hospital, S-434 80 Kungsbacka, Sweden
| | - R. Mobini
- Cline Scientific AB, SE-431 53 Mölndal, Sweden
| | - S. Simonsson
- Institute of Biomedicine at Sahlgrenska Academy, Department of Clinical Chemistry and Transfusion Medicine, University of Gothenburg, SE-413 45 Gothenburg, Sweden
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6
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Carvalho AM, Soares da Costa D, Reis RL, Pashkuleva I. Influence of Hyaluronan Density on the Behavior of Breast Cancer Cells with Different CD44 Expression. Adv Healthc Mater 2022; 11:e2101309. [PMID: 34694735 DOI: 10.1002/adhm.202101309] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/18/2021] [Indexed: 11/10/2022]
Abstract
Molecular gradients are common in biosystems and play an essential role in physiological and pathological processes. During carcinogenesis, for example, hyaluronan (HA) homeostasis is dysregulated by cancer cells and the altered synthesis and degradation processes result in the formation of HA gradients within the tumor microenvironment. Herein, a platform is developed to study the biological role of HA gradient in breast cancer cells. Cells with different aggressiveness and expression of CD44-the main HA receptor usually overexpressed in breast cancers, are selected for this study. The developed platform is compatible with several imaging modalities and allows assessment of cell density, morphology, CD44 expression, and cell motility in a function of HA density. Using high-throughput analysis, it is shown that cells that do not express CD44 do not change along the gradient, while CD44 positive cells respond differently to the HA gradient depending on the level of CD44 expression and HA density. This different response is associated with the activation of different signaling pathways by the CD44-HA interactions.
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Affiliation(s)
- Ana M. Carvalho
- 3B's Research Group ‐ Biomaterials Biodegradable and Biomimetics Avepark ‐ Parque de Ciência e Tecnologia Zona Industrial da Gandra Barco 4805‐017 Portugal
- ICVS/3B's ‐ PT Government Associate Laboratory University of Minho Braga/Guimarães Portugal
| | - Diana Soares da Costa
- 3B's Research Group ‐ Biomaterials Biodegradable and Biomimetics Avepark ‐ Parque de Ciência e Tecnologia Zona Industrial da Gandra Barco 4805‐017 Portugal
- ICVS/3B's ‐ PT Government Associate Laboratory University of Minho Braga/Guimarães Portugal
| | - Rui L. Reis
- 3B's Research Group ‐ Biomaterials Biodegradable and Biomimetics Avepark ‐ Parque de Ciência e Tecnologia Zona Industrial da Gandra Barco 4805‐017 Portugal
- ICVS/3B's ‐ PT Government Associate Laboratory University of Minho Braga/Guimarães Portugal
| | - Iva Pashkuleva
- 3B's Research Group ‐ Biomaterials Biodegradable and Biomimetics Avepark ‐ Parque de Ciência e Tecnologia Zona Industrial da Gandra Barco 4805‐017 Portugal
- ICVS/3B's ‐ PT Government Associate Laboratory University of Minho Braga/Guimarães Portugal
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7
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Andreasson L, Evenbratt H, Mobini R, Simonsson S. Differentiation of induced pluripotent stem cells into definitive endoderm on Activin A-functionalized gradient surfaces. J Biotechnol 2020; 325:173-178. [PMID: 33147515 DOI: 10.1016/j.jbiotec.2020.10.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 01/06/2023]
Abstract
Activin A plays a central role in the differentiation of stem cells into definitive endoderm, the first step in embryonic development and function development in many organ systems. The aims of this study were to induce controlled and fine-tuned cell differentiation using a gradient nanotechnology and compare this with a classic protocol and to investigate how induced pluripotent stem cells differentiated depending on the gradual increase of Activin A. The density difference was tested by attaching Activin A to a gold nanoparticle gradient for high-precision density continuity. Cells expressed the definitive endoderm markers SRY-box transcription factor 17 and transcription factor GATA-4 to different extents along the gradient, indicating a density-dependent cell response to Activin A. In both the gradient and the classic differentiation setups, the protein expression increased from days 1 to 5, but a significant increase already on day 3 was found only in the gradient-based setup. By utilizing the gradient technology to present the right amount of active biomolecules to cells in vitro, we were able to find an optimal setting for differentiation into definitive endoderm. The use of gradient surfaces for differentiation allows for improvements, such as efficiency and faster differentiation, compared with a classic protocol.
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Affiliation(s)
- Linnea Andreasson
- Cline Scientific AB, Mölndal SE-431 53, Sweden; Institute of Biomedicine at Sahlgrenska Academy, Department of Clinical Chemistry and Transfusion Medicine, University of Gothenburg, Gothenburg SE-413 45, Sweden.
| | | | - Reza Mobini
- Cline Scientific AB, Mölndal SE-431 53, Sweden.
| | - Stina Simonsson
- Institute of Biomedicine at Sahlgrenska Academy, Department of Clinical Chemistry and Transfusion Medicine, University of Gothenburg, Gothenburg SE-413 45, Sweden.
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8
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Williams I, Lee S, Apriceno A, Sear RP, Battaglia G. Diffusioosmotic and convective flows induced by a nonelectrolyte concentration gradient. Proc Natl Acad Sci U S A 2020; 117:25263-25271. [PMID: 32989158 PMCID: PMC7568292 DOI: 10.1073/pnas.2009072117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Glucose is an important energy source in our bodies, and its consumption results in gradients over length scales ranging from the subcellular to entire organs. Concentration gradients can drive material transport through both diffusioosmosis and convection. Convection arises because concentration gradients are mass density gradients. Diffusioosmosis is fluid flow induced by the interaction between a solute and a solid surface. A concentration gradient parallel to a surface creates an osmotic pressure gradient near the surface, resulting in flow. Diffusioosmosis is well understood for electrolyte solutes, but is more poorly characterized for nonelectrolytes such as glucose. We measure fluid flow in glucose gradients formed in a millimeter-long thin channel and find that increasing the gradient causes a crossover from diffusioosmosis-dominated to convection-dominated flow. We cannot explain this with established theories of these phenomena which predict that both scale linearly. In our system, the convection speed is linear in the gradient, but the diffusioosmotic speed has a much weaker concentration dependence and is large even for dilute solutions. We develop existing models and show that a strong surface-solute interaction, a heterogeneous surface, and accounting for a concentration-dependent solution viscosity can explain our data. This demonstrates how sensitive nonelectrolyte diffusioosmosis is to surface and solution properties and to surface-solute interactions. A comprehensive understanding of this sensitivity is required to understand transport in biological systems on length scales from micrometers to millimeters where surfaces are invariably complex and heterogeneous.
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Affiliation(s)
- Ian Williams
- Institute for Bioengineering of Catalonia, The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain;
- Department of Chemistry, University College London, London WC1H 0AJ, United Kingdom
| | - Sangyoon Lee
- Department of Chemistry, University College London, London WC1H 0AJ, United Kingdom
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Azzurra Apriceno
- Institute for Bioengineering of Catalonia, The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Department of Chemistry, University College London, London WC1H 0AJ, United Kingdom
| | - Richard P Sear
- Department of Physics, University of Surrey, Guildford GU2 7XH, United Kingdom
| | - Giuseppe Battaglia
- Institute for Bioengineering of Catalonia, The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Department of Chemistry, University College London, London WC1H 0AJ, United Kingdom
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9
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Andreasson L, Evenbratt H, Simonsson S. GDF5 induces TBX3 in a concentration dependent manner - on a gold nanoparticle gradient. Heliyon 2020; 6:e04133. [PMID: 32551383 PMCID: PMC7292926 DOI: 10.1016/j.heliyon.2020.e04133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/03/2019] [Accepted: 06/01/2020] [Indexed: 11/19/2022] Open
Abstract
Organs and tissues, such as cartilage and limbs, are formed during development through an orchestration of growth factors that function as morphogens. Examples of growth factors include growth differentiation factor 5 (GDF5) and transforming growth factors beta 1 and 3 (TGFβ-1 and TGFβ-3) which can specify creation of more than one cell type after forming a concentration gradient in vivo. Here, we studied the impact of morphogen gradients during differentiation of induced pluripotent stem cells (iPSCs) into the chondrocyte lineage. Cell budding zones, consisting of condensed cell aggregates, were observed only in gradients of GDF5. T-box transcription factor 3 (TBX3) was detected specifically in the budding zones (ranging from 500-1,500 particles/μm2) of nuclei and cell vesicles. A homogenous density of GDF5 of 900 particles/μm2 on a surface induced budding and expression of TBX3 after five days in iPSCs. Therefore, we conclude that a gradient of GDF5, as well as the specific homogenous density of GDF5, support the induction of TBX3 in iPCSs. Moreover, differentiation of iPSCs first on GDF5 gradient or homogenous surfaces for five days and then in a three-dimensional structure for five weeks resulted in pellets that expressed TBX3.
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Affiliation(s)
- L. Andreasson
- Cline Scientific AB, Mölndal, SE-431 53, Sweden
- Institute of Biomedicine at Sahlgrenska Academy, Department of Clinical Chemistry and Transfusion Medicine, University of Gothenburg, Gothenburg, SE-413 45, Sweden
| | | | - S. Simonsson
- Institute of Biomedicine at Sahlgrenska Academy, Department of Clinical Chemistry and Transfusion Medicine, University of Gothenburg, Gothenburg, SE-413 45, Sweden
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10
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Shen S, Zhang X, Zhang F, Wang D, Long D, Niu Y. Three-gradient constructions in a flow-rate insensitive microfluidic system for drug screening towards personalized treatment. Talanta 2020; 208:120477. [DOI: 10.1016/j.talanta.2019.120477] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/12/2019] [Accepted: 10/15/2019] [Indexed: 12/16/2022]
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11
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Macedo TJS, Santos JMS, Bezerra MÉS, Menezes VG, Gouveia BB, Barbosa LMR, Lins TLBG, Monte APO, Barberino RS, Batista AM, Barros VRP, Wischral A, Queiroz MAA, Araújo GGL, Matos MHT. Immunolocalization of leptin and its receptor in the sheep ovary and in vitro effect of leptin on follicular development and oocyte maturation. Mol Cell Endocrinol 2019; 495:110506. [PMID: 31295510 DOI: 10.1016/j.mce.2019.110506] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 06/22/2019] [Accepted: 07/06/2019] [Indexed: 01/10/2023]
Abstract
The aims of the study were to characterize leptin and it is receptor (LEPR) proteins immunoexpression in ovine ovaries and to evaluate the effects of leptin on development of secondary follicles cultured in vitro. The ovaries were collected and fixed for immunohistochemical analysis. Additional pairs of ovaries were collected and secondary follicles were isolated and cultured, for 18 days, in α-MEM+ alone or supplemented with 10 or 25 ng/mL of leptin. The antrum formation and fully grown oocytes rates were higher in 25 ng/mL leptin than all treatments. GSH levels and mitochondrial activity were higher in 10 or 25 ng/mL leptin than α-MEM+. 25 ng/mL leptin showed a higher percentage of MII than the α-MEM+. In conclusion, leptin and its receptor are expressed in ovine ovaries and 25 ng/mL leptin promoted higher in vitro maturation rates by improving follicular development, GSH levels and mitochondrial activity of ovine oocytes compared to control medium.
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Affiliation(s)
- Taís Jobard S Macedo
- Nucleus of Biotechnology Applied to Ovarian Follicle Development, Federal University of São Francisco Valley, Petrolina, PE, Brazil
| | - Jamile Maiara S Santos
- Nucleus of Biotechnology Applied to Ovarian Follicle Development, Federal University of São Francisco Valley, Petrolina, PE, Brazil
| | - Maria Éllida S Bezerra
- Nucleus of Biotechnology Applied to Ovarian Follicle Development, Federal University of São Francisco Valley, Petrolina, PE, Brazil
| | - Vanúzia G Menezes
- Nucleus of Biotechnology Applied to Ovarian Follicle Development, Federal University of São Francisco Valley, Petrolina, PE, Brazil
| | - Bruna B Gouveia
- Nucleus of Biotechnology Applied to Ovarian Follicle Development, Federal University of São Francisco Valley, Petrolina, PE, Brazil
| | - Lara Mariane R Barbosa
- Nucleus of Biotechnology Applied to Ovarian Follicle Development, Federal University of São Francisco Valley, Petrolina, PE, Brazil
| | - Thae Lane Barbosa G Lins
- Nucleus of Biotechnology Applied to Ovarian Follicle Development, Federal University of São Francisco Valley, Petrolina, PE, Brazil
| | - Alane Pains O Monte
- Nucleus of Biotechnology Applied to Ovarian Follicle Development, Federal University of São Francisco Valley, Petrolina, PE, Brazil
| | - Ricássio S Barberino
- Nucleus of Biotechnology Applied to Ovarian Follicle Development, Federal University of São Francisco Valley, Petrolina, PE, Brazil
| | - André M Batista
- Laboratory of Animal Reproduction, Federal Rural University of Pernambuco, Recife, PE, Brazil
| | - Vanessa Raquel P Barros
- Nucleus of Biotechnology Applied to Ovarian Follicle Development, Federal University of São Francisco Valley, Petrolina, PE, Brazil
| | - Aurea Wischral
- Laboratory of Animal Reproduction, Federal Rural University of Pernambuco, Recife, PE, Brazil
| | - Mário Adriano A Queiroz
- Laboratory of Bromatology and Animal Nutrition, Federal University of São Francisco Valley, Petrolina, PE, Brazil
| | | | - Maria Helena T Matos
- Nucleus of Biotechnology Applied to Ovarian Follicle Development, Federal University of São Francisco Valley, Petrolina, PE, Brazil.
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12
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Johnson HE, Toettcher JE. Signaling Dynamics Control Cell Fate in the Early Drosophila Embryo. Dev Cell 2019; 48:361-370.e3. [PMID: 30753836 DOI: 10.1016/j.devcel.2019.01.009] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 11/27/2018] [Accepted: 01/04/2019] [Indexed: 12/12/2022]
Abstract
The Erk mitogen-activated protein kinase plays diverse roles in animal development. Its widespread reuse raises a conundrum: when a single kinase like Erk is activated, how does a developing cell know which fate to adopt? We combine optogenetic control with genetic perturbations to dissect Erk-dependent fates in the early Drosophila embryo. We find that Erk activity is sufficient to "posteriorize" 88% of the embryo, inducing gut endoderm-like gene expression and morphogenetic movements in all cells within this region. Gut endoderm fate adoption requires at least 1 h of signaling, whereas a 30-min Erk pulse specifies a distinct ectodermal cell type, intermediate neuroblasts. We find that the endoderm-ectoderm cell fate switch is controlled by the cumulative load of Erk activity, not the duration of a single pulse. The fly embryo thus harbors a classic example of dynamic control, where the temporal profile of Erk signaling selects between distinct physiological outcomes.
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Affiliation(s)
- Heath E Johnson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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13
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Wang S, Gao F, Zhao Y, Liu N, Tan T, Wang X. Two-Dimensional CeO 2/RGO Composite-Modified Separator for Lithium/Sulfur Batteries. NANOSCALE RESEARCH LETTERS 2018; 13:377. [PMID: 30470930 PMCID: PMC6251799 DOI: 10.1186/s11671-018-2798-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 11/13/2018] [Indexed: 05/26/2023]
Abstract
In this work, a modified separator coated with a functional layer of reduced graphene oxide (RGO) anchored by cerium oxide (CeO2) nanoparticles was developed. The superior conductivity of RGO and chemical immobilization of high-ordered sulfur-related species (mainly Li2Sn 4 ≤ n ≤ 8) of CeO2 yielded batteries with enhanced characteristics. A remarkable original capacity of 1136 mAh g-1 was obtained at 0.1 C with capacity retention ratio of 75.7% after 100 charge/discharge cycles. Overall, these data indicate that the separator with CeO2/RGO composite is promising to suppress the shuttling of polysulfides for better utilization of the active material.
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Affiliation(s)
- Suyu Wang
- School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300130 China
| | - Fan Gao
- School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300130 China
| | - Yan Zhao
- School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300130 China
| | - Ning Liu
- School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300130 China
| | - Taizhe Tan
- Synergy Innovation Institute of GDUT, Heyuan, 517000 China
| | - Xin Wang
- International Academy of Optoelectronics at Zhaoqing, South China Normal University, Guangzhou, Guangdong Province China
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14
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Strasen J, Sarma U, Jentsch M, Bohn S, Sheng C, Horbelt D, Knaus P, Legewie S, Loewer A. Cell-specific responses to the cytokine TGFβ are determined by variability in protein levels. Mol Syst Biol 2018; 14:e7733. [PMID: 29371237 PMCID: PMC5787704 DOI: 10.15252/msb.20177733] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The cytokine TGFβ provides important information during embryonic development, adult tissue homeostasis, and regeneration. Alterations in the cellular response to TGFβ are involved in severe human diseases. To understand how cells encode the extracellular input and transmit its information to elicit appropriate responses, we acquired quantitative time-resolved measurements of pathway activation at the single-cell level. We established dynamic time warping to quantitatively compare signaling dynamics of thousands of individual cells and described heterogeneous single-cell responses by mathematical modeling. Our combined experimental and theoretical study revealed that the response to a given dose of TGFβ is determined cell specifically by the levels of defined signaling proteins. This heterogeneity in signaling protein expression leads to decomposition of cells into classes with qualitatively distinct signaling dynamics and phenotypic outcome. Negative feedback regulators promote heterogeneous signaling, as a SMAD7 knock-out specifically affected the signal duration in a subpopulation of cells. Taken together, we propose a quantitative framework that allows predicting and testing sources of cellular signaling heterogeneity.
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Affiliation(s)
- Jette Strasen
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center in the Helmholtz Association, Berlin, Germany
| | - Uddipan Sarma
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Marcel Jentsch
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center in the Helmholtz Association, Berlin, Germany.,Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Stefan Bohn
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Caibin Sheng
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center in the Helmholtz Association, Berlin, Germany.,Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Daniel Horbelt
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Petra Knaus
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | | | - Alexander Loewer
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center in the Helmholtz Association, Berlin, Germany .,Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
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15
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Surkova SY, Golubkova EV, Mamon LA, Samsonova MG. Morphogenetic networks which determine the spatial expression of zygotic genes in early Drosophila embryo. Russ J Dev Biol 2016. [DOI: 10.1134/s1062360416040093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Sandler JE, Stathopoulos A. Stepwise Progression of Embryonic Patterning. Trends Genet 2016; 32:432-443. [PMID: 27230753 DOI: 10.1016/j.tig.2016.04.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 04/20/2016] [Accepted: 04/21/2016] [Indexed: 01/23/2023]
Abstract
It is long established that the graded distribution of Dorsal transcription factor influences spatial domains of gene expression along the dorsoventral (DV) axis of Drosophila melanogaster embryos. However, the more recent realization that Dorsal levels also change with time raises the question of whether these dynamics are instructive. An overview of DV axis patterning is provided, focusing on new insights identified through quantitative analysis of temporal changes in Dorsal target gene expression from one nuclear cycle to the next ('steps'). Possible roles for the stepwise progression of this patterning program are discussed including (i) tight temporal regulation of signaling pathway activation, (ii) control of gene expression cohorts, and (iii) ensuring the irreversibility of the patterning and cell fate specification process.
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Affiliation(s)
- Jeremy E Sandler
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Angelike Stathopoulos
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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17
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Dubrulle J, Jordan BM, Akhmetova L, Farrell JA, Kim SH, Solnica-Krezel L, Schier AF. Response to Nodal morphogen gradient is determined by the kinetics of target gene induction. eLife 2015; 4. [PMID: 25869585 PMCID: PMC4395910 DOI: 10.7554/elife.05042] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 03/02/2015] [Indexed: 12/24/2022] Open
Abstract
Morphogen gradients expose cells to different signal concentrations and induce target genes with different ranges of expression. To determine how the Nodal morphogen gradient induces distinct gene expression patterns during zebrafish embryogenesis, we measured the activation dynamics of the signal transducer Smad2 and the expression kinetics of long- and short-range target genes. We found that threshold models based on ligand concentration are insufficient to predict the response of target genes. Instead, morphogen interpretation is shaped by the kinetics of target gene induction: the higher the rate of transcription and the earlier the onset of induction, the greater the spatial range of expression. Thus, the timing and magnitude of target gene expression can be used to modulate the range of expression and diversify the response to morphogen gradients. DOI:http://dx.doi.org/10.7554/eLife.05042.001 How a cell can tell where it is in a developing embryo has fascinated scientists for decades. The pioneering computer scientist and mathematical biologist Alan Turing was the first person to coin the term ‘morphogen’ to describe a protein that provides information about locations in the body. A morphogen is released from a group of cells (called the ‘source’) and as it moves away its activity (called the ‘signal’) declines gradually. Cells sense this signal gradient and use it to detect their position with respect to the source. Nodal is an important morphogen and is required to establish the correct identity of cells in the embryo; for example, it helps determine which cells should become a brain or heart or gut cell and so on. The zebrafish is a widely used model to study animal development, in part because its embryos are transparent; this allows cells and proteins to be easily observed under a microscope. When Nodal acts on cells, another protein called Smad2 becomes activated, moves into the cell's nucleus, and then binds to specific genes. This triggers the expression of these genes, which are first copied into mRNA molecules via a process known as transcription and are then translated into proteins. The protein products of these targeted genes control cell identity and movement. Several models have been proposed to explain how different concentrations of Nodal switch on the expression of different target genes; that is to say, to explain how a cell interprets the Nodal gradient. Dubrulle et al. have now measured factors that underlie how this gradient is interpreted. Individual cells in zebrafish embryos were tracked under a microscope, and Smad2 activation and gene expression were assessed. Dubrulle et al. found that, in contradiction to previous models, the amount of Nodal present on its own was insufficient to predict the target gene response. Instead, their analysis suggests that the size of each target gene's response depends on its rate of transcription and how quickly it is first expressed in response to Nodal. These findings of Dubrulle et al. suggest that timing and transcription rate are important in determining the appropriate response to Nodal. Further work will be now needed to find out whether similar mechanisms regulate other processes that rely on the activity of morphogens. DOI:http://dx.doi.org/10.7554/eLife.05042.002
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Affiliation(s)
- Julien Dubrulle
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Benjamin M Jordan
- Department of Mathematics, College of Science and Engineering, University of Minnesota, Minneapolis, United States
| | - Laila Akhmetova
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Jeffrey A Farrell
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Seok-Hyung Kim
- Division of Medicine, Medical University of South Carolina, Charleston, United States
| | - Lilianna Solnica-Krezel
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, United States
| | - Alexander F Schier
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
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18
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Rossi G, Messina G. Comparative myogenesis in teleosts and mammals. Cell Mol Life Sci 2014; 71:3081-99. [PMID: 24664432 PMCID: PMC4111864 DOI: 10.1007/s00018-014-1604-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 02/17/2014] [Accepted: 03/06/2014] [Indexed: 01/02/2023]
Abstract
Skeletal myogenesis has been and is currently under extensive study in both mammals and teleosts, with the latter providing a good model for skeletal myogenesis because of their flexible and conserved genome. Parallel investigations of muscle studies using both these models have strongly accelerated the advances in the field. However, when transferring the knowledge from one model to the other, it is important to take into account both their similarities and differences. The main difficulties in comparing mammals and teleosts arise from their different temporal development. Conserved aspects can be seen for muscle developmental origin and segmentation, and for the presence of multiple myogenic waves. Among the divergences, many fish have an indeterminate growth capacity throughout their entire life span, which is absent in mammals, thus implying different post-natal growth mechanisms. This review covers the current state of the art on myogenesis, with a focus on the most conserved and divergent aspects between mammals and teleosts.
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Affiliation(s)
- Giuliana Rossi
- Department of Biosciences, University of Milan, 20133, Milan, Italy
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19
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Abstract
This review looks at potential developments in medical devices which may be based upon nanofeaturing implant and tissue engineering scaffolds, and describes the basic science upon which such expectations are based.
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Affiliation(s)
- Adam Curtis
- Centre for Cell Engineering, University of Glasgow, Glasgow G12 8QQ, Scotland, UK.
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20
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Christ GJ, Saul JM, Furth ME, Andersson KE. The pharmacology of regenerative medicine. Pharmacol Rev 2013; 65:1091-133. [PMID: 23818131 DOI: 10.1124/pr.112.007393] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Regenerative medicine is a rapidly evolving multidisciplinary, translational research enterprise whose explicit purpose is to advance technologies for the repair and replacement of damaged cells, tissues, and organs. Scientific progress in the field has been steady and expectations for its robust clinical application continue to rise. The major thesis of this review is that the pharmacological sciences will contribute critically to the accelerated translational progress and clinical utility of regenerative medicine technologies. In 2007, we coined the phrase "regenerative pharmacology" to describe the enormous possibilities that could occur at the interface between pharmacology, regenerative medicine, and tissue engineering. The operational definition of regenerative pharmacology is "the application of pharmacological sciences to accelerate, optimize, and characterize (either in vitro or in vivo) the development, maturation, and function of bioengineered and regenerating tissues." As such, regenerative pharmacology seeks to cure disease through restoration of tissue/organ function. This strategy is distinct from standard pharmacotherapy, which is often limited to the amelioration of symptoms. Our goal here is to get pharmacologists more involved in this field of research by exposing them to the tools, opportunities, challenges, and interdisciplinary expertise that will be required to ensure awareness and galvanize involvement. To this end, we illustrate ways in which the pharmacological sciences can drive future innovations in regenerative medicine and tissue engineering and thus help to revolutionize the discovery of curative therapeutics. Hopefully, the broad foundational knowledge provided herein will spark sustained conversations among experts in diverse fields of scientific research to the benefit of all.
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Affiliation(s)
- George J Christ
- Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA.
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21
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Schmiedel JM, Axmann IM, Legewie S. Multi-target regulation by small RNAs synchronizes gene expression thresholds and may enhance ultrasensitive behavior. PLoS One 2012; 7:e42296. [PMID: 22927924 PMCID: PMC3424230 DOI: 10.1371/journal.pone.0042296] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 07/02/2012] [Indexed: 01/05/2023] Open
Abstract
Cells respond to external cues by precisely coordinating multiple molecular events. Co-regulation may be established by the so-called single-input module (SIM), where a common regulator controls multiple targets. Using mathematical modeling, we compared the ability of SIM architectures to precisely coordinate protein levels despite environmental fluctuations and uncertainties in parameter values. We find that post-transcriptional co-regulation as exemplified by bacterial small RNAs (sRNAs) is particularly robust: sRNA-mediated regulation establishes highly synchronous gene expression thresholds for all mRNA targets without a need for fine-tuning of kinetic parameters. Our analyses reveal that the non-catalytic nature of sRNA action is essential for robust gene expression synchronization, and that sRNA sequestration effects underlie coupling of multiple mRNA pools. This principle also operates in the temporal regime, implying that sRNAs could robustly coordinate the kinetics of mRNA induction as well. Moreover, we observe that multi-target regulation by a small RNA can strongly enhance ultrasensitivity in mRNA expression when compared to the single-target case. Our findings may explain why bacterial small RNAs frequently coordinate all-or-none responses to cellular stress.
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Affiliation(s)
| | - Ilka Maria Axmann
- Institute for Theoretical Biology, Charité-Universitätsmedizin, Berlin, Berlin, Germany
| | - Stefan Legewie
- Institute of Molecular Biology, Mainz, Rheinland-Pfalz, Germany
- * E-mail:
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22
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Chen H, Xu Z, Mei C, Yu D, Small S. A system of repressor gradients spatially organizes the boundaries of Bicoid-dependent target genes. Cell 2012; 149:618-29. [PMID: 22541432 DOI: 10.1016/j.cell.2012.03.018] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Revised: 02/24/2012] [Accepted: 03/16/2012] [Indexed: 12/19/2022]
Abstract
The homeodomain (HD) protein Bicoid (Bcd) is thought to function as a gradient morphogen that positions boundaries of target genes via threshold-dependent activation mechanisms. Here, we analyze 66 Bcd-dependent regulatory elements and show that their boundaries are positioned primarily by repressive gradients that antagonize Bcd-mediated activation. A major repressor is the pair-rule protein Runt (Run), which is expressed in an opposing gradient and is necessary and sufficient for limiting Bcd-dependent activation. Evidence is presented that Run functions with the maternal repressor Capicua and the gap protein Kruppel as the principal components of a repression system that correctly orders boundaries throughout the anterior half of the embryo. These results put conceptual limits on the Bcd morphogen hypothesis and demonstrate how the Bcd gradient functions within the gene network that patterns the embryo.
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Affiliation(s)
- Hongtao Chen
- Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
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23
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Baker SG. Paradoxes in Carcinogenesis Should Spur New Avenues of Research: An Historical Perspective. ACTA ACUST UNITED AC 2012. [DOI: 10.1089/dst.2012.0011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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24
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Abstract
The strength and duration of intracellular signalling pathway activation is a key determinant of the biological outcome of cells in response to extracellular cues. This has been particularly elucidated for the Ras/Raf/MEK [mitogen-activated growth factor/ERK (extracellular-signal-regulated kinase) kinase]/ERK signalling pathway with a number of studies in fibroblasts showing that sustained ERK signalling is a requirement for S-phase entry, whereas transient ERK signalling does not have this capability. A major unanswered question, however, is how a cell can sustain ERK activation, particularly when ERK-specific phosphatases are transcriptionally up-regulated by the pathway itself. A major point of ERK regulation is at the level of Raf, and, to sustain ERK activation in the presence of ERK phosphatases, sustained Raf activation is a requirement. Three Raf proteins exist in mammals, and the activity of all three is induced following growth factor stimulation of cells, but only B-Raf activity is maintained at later time points. This observation points to B-Raf as a regulator of sustained ERK activation. In the present review, we consider evidence for a link between B-Raf and sustained ERK activation, focusing on a potential role for the subcellular localization of B-Raf in this key physiological event.
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25
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Bentzinger CF, Wang YX, Rudnicki MA. Building muscle: molecular regulation of myogenesis. Cold Spring Harb Perspect Biol 2012; 4:4/2/a008342. [PMID: 22300977 DOI: 10.1101/cshperspect.a008342] [Citation(s) in RCA: 737] [Impact Index Per Article: 61.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The genesis of skeletal muscle during embryonic development and postnatal life serves as a paradigm for stem and progenitor cell maintenance, lineage specification, and terminal differentiation. An elaborate interplay of extrinsic and intrinsic regulatory mechanisms controls myogenesis at all stages of development. Many aspects of adult myogenesis resemble or reiterate embryonic morphogenetic episodes, and related signaling mechanisms control the genetic networks that determine cell fate during these processes. An integrative view of all aspects of myogenesis is imperative for a comprehensive understanding of muscle formation. This article provides a holistic overview of the different stages and modes of myogenesis with an emphasis on the underlying signals, molecular switches, and genetic networks.
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Affiliation(s)
- C Florian Bentzinger
- The Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Health Research Institute, Ottawa, Ontario, Canada
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26
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Nahmad M, Lander AD. Spatiotemporal mechanisms of morphogen gradient interpretation. Curr Opin Genet Dev 2011; 21:726-31. [PMID: 22033220 DOI: 10.1016/j.gde.2011.10.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Accepted: 10/04/2011] [Indexed: 02/07/2023]
Abstract
Few mechanistic ideas from the pre-molecular era of biology have had as enduring an impact as the morphogen concept. In the classical view, cells in developing embryos obtain positional information by measuring morphogen concentrations and comparing them with fixed concentration thresholds; as a result, graded morphogen distributions map into discrete spatial arrangements of gene expression. Recent studies on Hedgehog and other morphogens suggest that establishing patterns of gene expression may be less a function of absolute morphogen concentrations, than of the dynamics of signal transduction, gene expression, and gradient formation. The data point away from any universal model of morphogen interpretation and suggest that organisms use multiple mechanisms for reading out developmental signals in order to accomplish specific patterning goals.
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Affiliation(s)
- Marcos Nahmad
- Department of Developmental and Cell Biology and Center for Complex Biological Systems, University of California, Irvine, CA 92697-2300, USA
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27
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Nahmad M. Steady-state invariant genetics: probing the role of morphogen gradient dynamics in developmental patterning. J R Soc Interface 2011; 8:1429-39. [PMID: 21421746 DOI: 10.1098/rsif.2010.0738] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Morphogen-mediated patterning is the predominant mechanism by which positional information is established during animal development. In the classical view, the interpretation of positional signals depends on the equilibrium distribution of a morphogen, regardless of the dynamics of gradient formation. The problem of whether or not morphogen dynamics contribute to developmental patterning has not been explored in detail, partly because genetic experiments, which selectively affect signalling dynamics while maintaining unchanged the steady-state morphogen profile, are difficult to design and interpret. Here, I present a modelling-based approach to identify genetic mutations in developmental patterning that may affect the transient, but leave invariant the steady-state signalling gradient. As a case study, this approach is used to explore the dynamic properties of Hedgehog (Hh) signalling in the developing wing of the fruitfly, Drosophila melanogaster. This analysis provides insights into how different properties of the Hh gradient dynamics, such as the duration of exposure to the signal or the maximum width of the transient gradient, can be genetically perturbed without affecting the steady-state distribution of the Hh concentration profile. I propose that this method can be used as an experimental design tool to investigate the role of transient morphogen gradients in developmental patterning and discuss the generality of these ideas in other problems.
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Affiliation(s)
- Marcos Nahmad
- Department of Control and Dynamical Systems and Division of Biology, California Institute of Technology, 1200 East California Boulevard MC-114-96, Pasadena, CA 91125, USA.
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28
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Nahmad M, Stathopoulos A. Establishing positional information through gradient dynamics: a lesson from the Hedgehog signaling pathway. Fly (Austin) 2010; 4:273-7. [PMID: 20699656 DOI: 10.4161/fly.4.4.12677] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A long standing question in developmental biology is how morphogen gradients establish positional information during development. Although the existence of gradients and their role in developmental patterning is no longer in doubt, the ability of cells to respond to different morphogen concentrations has been controversial. In the Drosophila wing disc, Hedgehog (Hh) forms a concentration gradient along the anterior-posterior axis and establishes at least three different gene expression patterns. In a recent study, we challenged the prevailing idea that Hh establishes positional information in a dose-dependent manner and proposed a model in which dynamics of the gradient, resulting from the Hh gene network architecture, determines pattern formation in the wing disc. In this Extra View, we discuss further the methodology used in this study, highlight differences between this and other models of developmental patterning, and also present some questions that remain to be answered in this system.
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Affiliation(s)
- Marcos Nahmad
- Department of Control and Dynamical Systems, California Institute of Technology, Pasadena, CA, USA
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29
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Rbpj cell autonomous regulation of retinal ganglion cell and cone photoreceptor fates in the mouse retina. J Neurosci 2009; 29:12865-77. [PMID: 19828801 DOI: 10.1523/jneurosci.3382-09.2009] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Vertebrate retinal progenitor cells (RPCs) are pluripotent, but pass through competence states that progressively restrict their developmental potential (Cepko et al., 1996; Livesey and Cepko, 2001; Cayouette et al., 2006). In the rodent eye, seven retinal cell classes differentiate in overlapping waves, with RGCs, cone photoreceptors, horizontals, and amacrines forming predominantly before birth, and rod photoreceptors, bipolars, and Müller glia differentiating postnatally. Both intrinsic and extrinsic factors regulate each retinal cell type (for review, see Livesey and Cepko, 2001). Here, we conditionally deleted the transcription factor Rbpj, a critical integrator of multiple Notch signals (Jarriault et al., 1995; Honjo, 1996; Kato et al., 1997; Han et al., 2002), during prenatal mouse retinal neurogenesis. Removal of Rbpj caused reduced proliferation, premature neuronal differentiation, apoptosis, and profound mispatterning. To determine the cell autonomous requirements for Rbpj during RGC and cone formation, we marked Cre-generated retinal lineages with GFP expression, which showed that Rbpj autonomously promotes RPC mitotic activity, and suppresses RGC and cone fates. In addition, the progressive loss of Rbpj-/- RPCs resulted in a diminished progenitor pool available for rod photoreceptor formation. This circumstance, along with the overproduction of Rbpj-/- cones, revealed that photoreceptor development is under homeostatic regulation. Finally, to understand how the Notch pathway regulates the simultaneous formation of multiple cell types, we compared the RGC and cone phenotypes of Rbpj to Notch1 (Jadhav et al., 2006b; Yaron et al., 2006), Notch3, and Hes1 mutants. We found particular combinations of Notch pathway genes regulate the development of each retinal cell type.
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Nahmad M, Stathopoulos A. Dynamic interpretation of hedgehog signaling in the Drosophila wing disc. PLoS Biol 2009; 7:e1000202. [PMID: 19787036 PMCID: PMC2744877 DOI: 10.1371/journal.pbio.1000202] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2009] [Accepted: 08/13/2009] [Indexed: 11/19/2022] Open
Abstract
Morphogens are classically defined as molecules that control patterning by acting at a distance to regulate gene expression in a concentration-dependent manner. In the Drosophila wing imaginal disc, secreted Hedgehog (Hh) forms an extracellular gradient that organizes patterning along the anterior-posterior axis and specifies at least three different domains of gene expression. Although the prevailing view is that Hh functions in the Drosophila wing disc as a classical morphogen, a direct correspondence between the borders of these patterns and Hh concentration thresholds has not been demonstrated. Here, we provide evidence that the interpretation of Hh signaling depends on the history of exposure to Hh and propose that a single concentration threshold is sufficient to support multiple outputs. Using mathematical modeling, we predict that at steady state, only two domains can be defined in response to Hh, suggesting that the boundaries of two or more gene expression patterns cannot be specified by a static Hh gradient. Computer simulations suggest that a spatial "overshoot" of the Hh gradient occurs, i.e., a transient state in which the Hh profile is expanded compared to the Hh steady-state gradient. Through a temporal examination of Hh target gene expression, we observe that the patterns initially expand anteriorly and then refine, providing in vivo evidence for the overshoot. The Hh gene network architecture suggests this overshoot results from the Hh-dependent up-regulation of the receptor, Patched (Ptc). In fact, when the network structure was altered such that the ptc gene is no longer up-regulated in response to Hh-signaling activation, we found that the patterns of gene expression, which have distinct borders in wild-type discs, now overlap. Our results support a model in which Hh gradient dynamics, resulting from Ptc up-regulation, play an instructional role in the establishment of patterns of gene expression.
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Affiliation(s)
- Marcos Nahmad
- Department of Control and Dynamical Systems, California Institute of Technology, Pasadena, California, United States of America
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Angelike Stathopoulos
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
- * E-mail:
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Piddini E, Vincent JP. Interpretation of the wingless gradient requires signaling-induced self-inhibition. Cell 2009; 136:296-307. [PMID: 19167331 DOI: 10.1016/j.cell.2008.11.036] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2008] [Revised: 09/24/2008] [Accepted: 11/21/2008] [Indexed: 11/30/2022]
Abstract
In a classical view of development, a cell can acquire positional information by reading the local concentration of a morphogen independently of its neighbors. Accordingly, in Drosophila, the morphogen Wingless produced in the wing's prospective distal region activates target genes in a dose-dependent fashion to organize the proximodistal pattern. Here, we show that, in parallel, Wingless triggers two nonautonomous inhibitory programs that play an important role in the establishment of positional information. Cells flanking the source of Wingless produce a negative signal (encoded by notum) that inhibits Wingless signaling in nearby cells. Additionally, in response to Wingless, all prospective wing cells produce an unidentified signal that dampens target gene expression in surrounding cells. Thus, cells influence each other's response to Wingless through at least two modes of lateral inhibition. Without lateral inhibition, some cells acquire ectopic fates. Lateral inhibition may be a general mechanism behind the interpretation of morphogen gradients.
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Affiliation(s)
- Eugenia Piddini
- MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
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The Hedgehog, TGF-β/BMP and Wnt Families of Morphogens in Axon Guidance. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2008; 621:116-33. [DOI: 10.1007/978-0-387-76715-4_9] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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33
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mef2 activity levels differentially affect gene expression during Drosophila muscle development. Proc Natl Acad Sci U S A 2008; 105:918-23. [PMID: 18198273 DOI: 10.1073/pnas.0711255105] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Cell differentiation is controlled by key transcription factors, and a major question is how they orchestrate cell-type-specific genetic programs. Muscle differentiation is a well studied paradigm in which the conserved Mef2 transcription factor plays a pivotal role. Recent genomic studies have identified a large number of mef2-regulated target genes with distinct temporal expression profiles during Drosophila myogenesis. However, the question remains as to how a single transcription factor can control such diverse patterns of gene expression. In this study we used a strategy combining genomics and developmental genetics to address this issue in vivo during Drosophila muscle development. We found that groups of mef2-regulated genes respond differently to changes in mef2 activity levels: some require higher levels for their expression than others. Furthermore, this differential requirement correlates with when the gene is first expressed during the muscle differentiation program. Genes that require higher levels are activated later. These results implicate mef2 in the temporal regulation of muscle gene expression, and, consistent with this, we show that changes in mef2 activity levels can alter the start of gene expression in a predictable manner. Together these results indicate that Mef2 is not an all-or-none regulator; rather, its action is more subtle, and levels of its activity are important in the differential expression of muscle genes. This suggests a route by which mef2 can orchestrate the muscle differentiation program and contribute to the stringent regulation of gene expression during myogenesis.
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34
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TGFbeta-SMAD signal transduction: molecular specificity and functional flexibility. Nat Rev Mol Cell Biol 2007; 8:970-82. [PMID: 18000526 DOI: 10.1038/nrm2297] [Citation(s) in RCA: 971] [Impact Index Per Article: 57.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Ligands of the transforming growth factor-beta (TGFbeta) superfamily of growth factors initiate signal transduction through a bewildering complexity of ligand-receptor interactions. Signalling then converges to nuclear accumulation of transcriptionally active SMAD complexes and gives rise to a plethora of specific functional responses in both embryos and adult organisms. Current research is focused on the mechanisms that regulate SMAD activity to evoke cell-type-specific and context-dependent transcriptional programmes. An equally important challenge is understanding the functional role of signal strength and duration. How are these quantitative aspects of the extracellular signal regulated? How are they then sensed and interpreted, and how do they affect responses?
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Kopan R, Cheng HT, Surendran K. Molecular insights into segmentation along the proximal-distal axis of the nephron. J Am Soc Nephrol 2007; 18:2014-20. [PMID: 17568016 PMCID: PMC2375141 DOI: 10.1681/asn.2007040453] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The structure of a mammalian kidney is parsed into large collections of polarized nephrons, and each segment is home to a diverse community of cells that specialize in renal endocrine and excretory functions. Early developmental lengthening and diversification of nephron segments along a proximal--distal axis initiate all subsequent facets of tubular growth and function. Morphogenic cues and biochemical interactions that are critical to this process are starting to emerge. The underlying principles of regional cell signaling and transcriptional control organizing early segmentation are the subject of this review.
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Affiliation(s)
- Raphael Kopan
- Department of Molecular Biology, Washington University School of Medicine, St Louis, MO 63110, USA.
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36
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Abstract
Morphogenetic fields organize tissue morphology in the embryo. By analogy, morphostatic fields maintain normal cell behaviour and normal tissue microarchitecture in the adult. The most prominent feature of cancer is the disruption of tissue microarchitecture. Cancer occurs much more frequently when morphostatic influences fail (metaplasia) or at the junction of two different morphostatic fields. This Review will describe what we know about morphostats and morphostasis, discuss the evidence for the role of disruption of morphostasis in malignancy, and address some testable hypotheses.
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Affiliation(s)
- John D Potter
- Fred Hutchinson Cancer Research Center, P.O. Box 19024, M4-B814, Seattle, Washington 98109-1024, USA.
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37
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Hufnagel L, Teleman AA, Rouault H, Cohen SM, Shraiman BI. On the mechanism of wing size determination in fly development. Proc Natl Acad Sci U S A 2007; 104:3835-40. [PMID: 17360439 PMCID: PMC1820670 DOI: 10.1073/pnas.0607134104] [Citation(s) in RCA: 255] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
A fundamental and unresolved problem in animal development is the question of how a growing tissue knows when it has achieved its correct final size. A widely held view suggests that this process is controlled by morphogen gradients, which adapt to tissue size and become flatter as tissue grows, leading eventually to growth arrest. Here, we present evidence that the decapentaplegic (Dpp) morphogen distribution in the developing Drosophila wing imaginal disk does not adapt to disk size. We measure the distribution of a functional Dpp-GFP transgene and the Dpp signal transduced by phospho-Mad and show that the characteristic length scale of the Dpp profile remains approximately constant during growth. This finding suggests an alternative scenario of size determination, where disk size is determined relative to the fixed morphogen distribution by a certain threshold level of morphogen required for growth. We propose that when disk boundary reaches the threshold the arrest of cell proliferation throughout the disk is induced by mechanical stress in the tissue. Mechanical stress is expected to arise from the nonuniformity of morphogen distribution that drives growth. This stress, through a negative feedback on growth, can compensate for the nonuniformity of morphogen, achieving uniform growth with the rate that vanishes when disk boundary reaches the threshold. The mechanism is demonstrated through computer simulations of a tissue growth model that identifies the key assumptions and testable predictions. This analysis provides an alternative hypothesis for the size determination process. Novel experimental approaches will be needed to test this model.
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Affiliation(s)
- Lars Hufnagel
- *Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106
| | - Aurelio A. Teleman
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany; and
| | - Hervé Rouault
- Laboratoire de Physique Statistique, Ecole Normale Superieure, 24 Rue Lhomond, Paris Cedex 5, France
| | - Stephen M. Cohen
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany; and
| | - Boris I. Shraiman
- *Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106
- To whom correspondence should be addressed. E-mail:
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38
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Jones PF, Sleeman BD. Angiogenesis - understanding the mathematical challenge. Angiogenesis 2006; 9:127-38. [PMID: 17051342 DOI: 10.1007/s10456-006-9039-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2006] [Accepted: 06/27/2006] [Indexed: 11/24/2022]
Abstract
Biological mathematics is based on the development of mathematical descriptions of biological systems and behaviour. We are interested in developing mathematical models of capillary sprouting, and have adopted a novel approach to our modelling, in that the mathematics is based on the biochemistry underpinning cell behaviour. By considering the crucial steps of the angiogenic process, and through an understanding of the biochemistry involved, we successfully developed a preliminary model of angiogenesis. More importantly, our approach is applicable to many other areas of biological research. As mathematics remains a mystery to the majority of life scientists, we have aimed to describe our mathematical modelling strategy in biological terms. The assumptions and simplifications that form the basis of the modelling are explained, pinpointing the manner in which the different biological processes are linked via the mathematics. Examples of simulations using the mathematical model are shown, highlighting the success of our approach.
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Affiliation(s)
- Pamela F Jones
- Leeds Institute of Molecular Medicine, University of Leeds, JIF Building, St. James's University Hospital, Leeds LS9 7TF, UK.
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39
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Esser AT, Smith KC, Weaver JC, Levin M. Mathematical model of morphogen electrophoresis through gap junctions. Dev Dyn 2006; 235:2144-59. [PMID: 16786594 DOI: 10.1002/dvdy.20870] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Gap junctional communication is important for embryonic morphogenesis. However, the factors regulating the spatial properties of small molecule signal flows through gap junctions remain poorly understood. Recent data on gap junctions, ion transporters, and serotonin during left-right patterning suggest a specific model: the net unidirectional transfer of small molecules through long-range gap junctional paths driven by an electrophoretic mechanism. However, this concept has only been discussed qualitatively, and it is not known whether such a mechanism can actually establish a gradient within physiological constraints. We review the existing functional data and develop a mathematical model of the flow of serotonin through the early Xenopus embryo under an electrophoretic force generated by ion pumps. Through computer simulation of this process using realistic parameters, we explored quantitatively the dynamics of morphogen movement through gap junctions, confirming the plausibility of the proposed electrophoretic mechanism, which generates a considerable gradient in the available time frame. The model made several testable predictions and revealed properties of robustness, cellular gradients of serotonin, and the dependence of the gradient on several developmental constants. This work quantitatively supports the plausibility of electrophoretic control of morphogen movement through gap junctions during early left-right patterning. This conceptual framework for modeling gap junctional signaling -- an epigenetic patterning mechanism of wide relevance in biological regulation -- suggests numerous experimental approaches in other patterning systems.
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Affiliation(s)
- Axel T Esser
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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40
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Diambra L, Costa LDF. Pattern formation in a gene network model with boundary shape dependence. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2006; 73:031917. [PMID: 16605568 DOI: 10.1103/physreve.73.031917] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2005] [Revised: 10/03/2005] [Indexed: 05/08/2023]
Abstract
A fundamental task in developmental biology is to identify the mechanisms which drive morphogenesis. Traditionally pattern formation have been modeled mainly using Turing-type mechanisms, where complex patterns arise by symmetry breaking. However, there is a growing experimental evidence that the influence of signals derived from surrounding tissues can contribute to the patterning processes. In this paper, we show that the interplay between the shape of surrounding tissues and a hierarchically organized gene regulatory network can be able to induce stable complex patterns. The rise of these patterns depends strongly on the shape of the surrounding tissues.
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Affiliation(s)
- Luis Diambra
- Institute of Physics at São Carlos, University of São Paulo, Caixa Postal 369, cep 13560-970, São Carlos, SP, Brazil.
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41
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Abstract
Embryonic stem (ES) cells have provided a valid model to understand early events of mammalian lineage specification and differentiation, leading to important insights into the mechanisms that control embryogenesis at the molecular and cellular levels. Furthermore, ES cells have recently evoked great scientific interest as ideal candidates for the generation of tissues for transplantation therapies. In this respect, particular attention has been paid to the molecules and signaling pathways triggering ES cell differentiation. The EGF-CFC Cripto protein is a key regulator of ES cells fate. The cripto gene is expressed both in ES cells and during the early phases of embryo development, while, in the adult, it is reactivated in a wide range of epithelial cancers. This review will discuss recent findings on the molecular basis of Cripto signaling in ES cell differentiation, providing an intriguing link between stem cell and tumor biology.
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Affiliation(s)
- Gabriella Minchiotti
- Institute of Genetics and Biophysics A Buzzati-Traverso, CNR, Via Pietro Castellino 111, 80131 Naples, Italy.
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42
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Charron F, Tessier-Lavigne M. Novel brain wiring functions for classical morphogens: a role as graded positional cues in axon guidance. Development 2005; 132:2251-62. [PMID: 15857918 DOI: 10.1242/dev.01830] [Citation(s) in RCA: 181] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
During embryonic development, morphogens act as graded positional cues to dictate cell fate specification and tissue patterning. Recent findings indicate that morphogen gradients also serve to guide axonal pathfinding during development of the nervous system. These findings challenge our previous notions about morphogens and axon guidance molecules, and suggest that these proteins, rather than having sharply divergent functions, act more globally to provide graded positional information that can be interpreted by responding cells either to specify cell fate or to direct axonal pathfinding. This review presents the roles identified for members of three prominent morphogen families – the Hedgehog, Wnt and TGFβ/BMP families– in axon guidance, and discusses potential implications for the molecular mechanisms underlying their guidance functions.
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Affiliation(s)
- Frédéric Charron
- Department of Biological Sciences, Stanford University, 371 Serra Mall, Stanford, California 94305, USA
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43
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Abstract
How developmental signaling proteins traverse tissue during animal development, through or around tightly packed cells, remains an incompletely resolved mystery. Signaling protein movement is regulated to create gradients, control amounts, impose barriers, or provide direction. Signaling can be controlled by the rate of signal production, modification, active transport, trapping along the path, or by the properties of the receptor apparatus. Signals may move by diffusion outside cells, attached to migrating cells, attached to carrier molecules, through cells by transcytosis, along cell extensions, or in released membrane packets. Recent findings about the movement of Hedgehog, Wingless (Wnt), and TGF-beta signaling proteins have helped to clarify the molecular mechanisms used to ensure that developmental signals carry only good news.
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Affiliation(s)
- Alan Jian Zhu
- Department of Developmental Biology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305-5439, USA
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44
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Keshamouni VG, Reddy RC, Arenberg DA, Joel B, Thannickal VJ, Kalemkerian GP, Standiford TJ. Peroxisome proliferator-activated receptor-γ activation inhibits tumor progression in non-small-cell lung cancer. Oncogene 2004; 23:100-8. [PMID: 14712215 DOI: 10.1038/sj.onc.1206885] [Citation(s) in RCA: 158] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The peroxisome proliferator-activated receptor-gamma (PPAR-gamma) is a member of the nuclear hormone receptor superfamily of ligand-activated transcription factors and a crucial regulator of cellular differentiation. Differentiation-inducing and antiproliferative effects of PPAR-gamma suggest that PPAR-gamma agonists might be useful as effective anticancer agents. Few studies have examined the efficacy of these agonists in animal models of tumorigenesis, and their mechanism(s) of action are still not clear. Our studies indicate higher PPAR-gamma expression in primary tumors from non-small-cell lung cancer (NSCLC) patients when compared to normal surrounding tissue. The expression of PPAR-gamma was also observed in several NSCLC lines. The treatment of lung adenocarcinoma cells (A549) with troglitazone (Tro), a PPAR-gamma ligand, enhanced PPAR-gamma transcriptional activity and induced a dose-dependent inhibition of A549 cell growth. The observed growth arrest was predominantly due to the inhibition of cell proliferation without significant induction of apoptosis. Cell cycle analysis of Tro-treated cells revealed a cell cycle arrest at G(0)/G(1) with concomitant downregulation of G(0)/G(1) cyclins D and E. In addition, Tro treatment stimulated sustained Erk1/2 activation in A549 cells, suggesting the activation of a differentiation-inducing pathway. Furthermore, treatment of A549 tumor-bearing SCID mice with Tro or Pio inhibited primary tumor growth by 66.7% and significantly inhibited the number of spontaneous lung metastatic lesions. Collectively, our data demonstrate that activation of PPAR-gamma impedes lung tumor progression and suggest that PPAR-gamma ligands may serve as potential therapeutic agents for NSCLC.
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Affiliation(s)
- Venkateshwar G Keshamouni
- Division of Pulmonary and Critical Care Medicine, University of Michigan Medical Center, 6301 MSRB III, 1150 W. Medical Center Drive, Ann Arbor, MI 48109, USA
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45
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Takei Y, Ozawa Y, Sato M, Watanabe A, Tabata T. ThreeDrosophilaEXT genes shape morphogen gradients through synthesis of heparan sulfate proteoglycans. Development 2004; 131:73-82. [PMID: 14645127 DOI: 10.1242/dev.00913] [Citation(s) in RCA: 216] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The signaling molecules Hedgehog (Hh), Decapentaplegic (Dpp) and Wingless(Wg) function as morphogens and organize wing patterning in Drosophila. In the screen for mutations that alter the morphogen activity, we identified novel mutants of two Drosophila genes, sister of tout-velu (sotv) and brother of tout-velu(botv), and new alleles of toutvelu (ttv). The encoded proteins of these genes belong to an EXT family of proteins that have or are closely related to glycosyltransferase activities required for biosynthesis of heparan sulfate proteoglycans (HSPGs). Mutation in any of these genes impaired biosynthesis of HSPGs in vivo, indicating that, despite their structural similarity, they are not redundant in the HSPG biosynthesis. Protein levels and signaling activities of Hh, Dpp and Wg were reduced in the cells mutant for any of these EXT genes to a various degree, Wg signaling being the least sensitive. Moreover, all three morphogens were accumulated in the front of EXT mutant cells, suggesting that these morphogens require HSPGs to move efficiently. In contrast to previous reports that ttv is involved exclusively in Hh signaling, we found that ttv mutations also affected Dpp and Wg. These data led us to conclude that each of three EXT genes studied contribute to Hh, Dpp and Wg morphogen signaling. We propose that HSPGs facilitate the spreading of morphogens and therefore, function to generate morphogen concentration gradients.
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Affiliation(s)
- Yuki Takei
- Institute of Molecular and Cellular Biosciences, University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-0032, Japan
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46
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Müller B, Hartmann B, Pyrowolakis G, Affolter M, Basler K. Conversion of an extracellular Dpp/BMP morphogen gradient into an inverse transcriptional gradient. Cell 2003; 113:221-33. [PMID: 12705870 DOI: 10.1016/s0092-8674(03)00241-1] [Citation(s) in RCA: 144] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Morphogen gradients control body pattern by differentially regulating cellular behavior. Here, we analyze the molecular events underlying the primary response to the Dpp/BMP morphogen in Drosophila. Throughout development, Dpp transduction causes the graded transcriptional downregulation of the brinker (brk) gene. We first provide significance for the brk expression gradient by showing that different Brk levels repress distinct combinations of wing genes expressed at different distances from Dpp-secreting cells. We then dissect the brk regulatory region and identify two separable elements with opposite properties, a constitutive enhancer and a Dpp morphogen-regulated silencer. Furthermore, we present genetic and biochemical evidence that the brk silencer serves as a direct target for a protein complex consisting of the Smad homologs Mad/Medea and the zinc finger protein Schnurri. Together, our results provide the molecular framework for a mechanism by which the extracellular Dpp/BMP morphogen establishes a finely tuned, graded read-out of transcriptional repression.
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Affiliation(s)
- Bruno Müller
- Institut für Molekularbiologie, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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47
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Müller F, Rohrer H. Molecular control of ciliary neuron development: BMPs and downstream transcriptional control in the parasympathetic lineage. Development 2002; 129:5707-17. [PMID: 12421710 DOI: 10.1242/dev.00165] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The generation of noradrenergic sympathetic neurons is controlled by BMPs and the downstream transcription factors Mash1, Phox2b, Phox2a and dHand. We examined the role of these signals in developing cholinergic parasympathetic neurons. The expression of Mash1 (Cash1), Phox2b and Phox2a in the chick ciliary ganglion is followed by the sequential expression of panneuronal, noradrenergic and cholinergic marker genes. BMPs are expressed at the site where ciliary ganglia form and are essential and sufficient for ciliary neuron development. Unlike sympathetic neurons, ciliary neurons do not express dHand; noradrenergic gene expression is eventually lost but can be maintained by ectopic dHand expression. Together, these results demonstrate a common BMP dependence of sympathetic neurons and parasympathetic ciliary neurons and implicate dHand in the maintenance of noradrenergic gene expression in the autonomic nervous system.
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Affiliation(s)
- Frank Müller
- Max-Planck-Institut für Hirnforschung, Abteilung Neurochemie, Deutschordenstrasse 46, 60528 Frankfurt/Main, Germany
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48
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Green J. Morphogen gradients, positional information, and Xenopus: interplay of theory and experiment. Dev Dyn 2002; 225:392-408. [PMID: 12454918 DOI: 10.1002/dvdy.10170] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The idea of morphogen gradients has long been an important one in developmental biology. Studies with amphibians and with Xenopus in particular have made significant contributions to demonstrating the existence, identity, and mechanisms of action of morphogens. Mesoderm induction and patterning by activin, nodals, bone morphogenetic proteins, and fibroblast growth factors have been analyzed thoroughly and reveal recurrent and combinatorial roles for these protein growth factor morphogens and their antagonists. The dynamics of nodal-type signaling and the intersection of VegT and beta-catenin intracellular gradients reveal detailed steps in early long-range patterning. Interpretation of gradients requires sophisticated mechanisms for sharpening thresholds, and the activin-Xbra-Gsc system provides an example of this. The understanding of growth factor signal transduction has elucidated growth factor morphogen action and provided tools for dissecting their direct long-range action and distribution. The physical mechanisms of morphogen gradient establishment are the focus of new interest at both the experimental and theoretical level. General themes and emerging trends in morphogen gradient studies are discussed.
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Affiliation(s)
- Jeremy Green
- Dana Farber Cancer Institute, Harvard Medical School Department of Genetics, Boston, Massachusetts 02115, USA.
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49
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Bennett D, Alphey L. PP1 binds Sara and negatively regulates Dpp signaling in Drosophila melanogaster. Nat Genet 2002; 31:419-23. [PMID: 12134149 DOI: 10.1038/ng938] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In signaling involving the transforming growth factor-beta (TGF-beta) superfamily of proteins, ligand binding brings the constitutively active type II receptor kinase into close proximity to its substrate, the type I receptor kinase, which it then activates by phosphorylation. The type I receptor kinase in turn phosphorylates one of the Smad family of transcription factors, which translocates to the nucleus and regulates gene expression. Smads are recruited to the receptor complex by an anchor protein, SARA (Smad anchor for receptor activation). Although several protein kinases in this pathway were known, including the receptors themselves, the relevant phosphatases had not previously been identified. Here we report the isolation of a Drosophila melanogaster homolog of SARA (Sara) in a screen for proteins that bind the catalytic subunit of type 1 serine/threonine protein phosphatase (PP1c). We identified a PP1c-binding motif in Sara, disruption of which reduced the ability of Sara to bind PP1c. Expression of this non-PP1c-binding mutant resulted in hyperphosphorylation of the type I receptor and stimulated expression of a target of TGF-beta signaling. Reducing PP1c activity enhanced the increase in the basal level of expression of genes responsive to Dpp (Decapentaplegic) caused by ectopic expression of the type II receptor Punt. Together these data suggest that PP1c is targeted to Dpp receptor complexes by Sara, where it acts as a negative regulator of Dpp signaling by affecting the phosphorylation state of the type I receptor.
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Affiliation(s)
- Daimark Bennett
- Department of Zoology, Oxford University, South Parks Road, Oxford OX1 3PS, UK
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50
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Murphy LO, Smith S, Chen RH, Fingar DC, Blenis J. Molecular interpretation of ERK signal duration by immediate early gene products. Nat Cell Biol 2002; 4:556-64. [PMID: 12134156 DOI: 10.1038/ncb822] [Citation(s) in RCA: 721] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The duration of intracellular signalling is associated with distinct biological responses, but how cells interpret differences in signal duration are unknown. We show that the immediate early gene product c-Fos functions as a sensor for ERK1 (extracellular-signal-regulated kinase 1) and ERK2 signal duration. When ERK activation is transient, its activity declines before the c-Fos protein accumulates, and under these conditions c-Fos is unstable. However, when ERK signalling is sustained, c-Fos is phosphorylated by still-active ERK and RSK (90K-ribosomal S6 kinase). Carboxy-terminal phosphorylation stabilizes c-Fos and primes additional phosphorylation by exposing a docking site for ERK, termed the FXFP (DEF) domain. Mutating the DEF domain disrupts the c-Fos sensor and c-Fos-mediated signalling. Other immediate early gene products that control cell cycle progression, neuronal differentiation and circadium rhythms also contain putative DEF domains, indicating that multiple sensors exist for sustained ERK signalling. Together, our data identify a general mechanism by which cells can interpret differences in ERK activation kinetics.
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Affiliation(s)
- Leon O Murphy
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
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