1
|
Kawecki NS, Chen KK, Smith CS, Xie Q, Cohen JM, Rowat AC. Scalable Processes for Culturing Meat Using Edible Scaffolds. Annu Rev Food Sci Technol 2024; 15:241-264. [PMID: 38211941 DOI: 10.1146/annurev-food-072023-034451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
There is increasing consumer demand for alternative animal protein products that are delicious and sustainably produced to address concerns about the impacts of mass-produced meat on human and planetary health. Cultured meat has the potential to provide a source of nutritious dietary protein that both is palatable and has reduced environmental impact. However, strategies to support the production of cultured meats at the scale required for food consumption will be critical. In this review, we discuss the current challenges and opportunities of using edible scaffolds for scaling up the production of cultured meat. We provide an overview of different types of edible scaffolds, scaffold fabrication techniques, and common scaffold materials. Finally, we highlight potential advantages of using edible scaffolds to advance cultured meat production by accelerating cell growth and differentiation, providing structure to build complex 3D tissues, and enhancing the nutritional and sensory properties of cultured meat.
Collapse
Affiliation(s)
- N Stephanie Kawecki
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California, USA;
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California, USA
| | - Kathleen K Chen
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California, USA;
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, USA
| | - Corinne S Smith
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California, USA;
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California, USA
| | - Qingwen Xie
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California, USA;
| | - Julian M Cohen
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California, USA;
| | - Amy C Rowat
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California, USA
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California, USA
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California, USA;
- Broad Stem Cell Center, University of California, Los Angeles, Los Angeles, California, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California, USA
| |
Collapse
|
2
|
Loffet EA, Durel JF, Nerurkar NL. Evo-Devo Mechanobiology: The Missing Link. Integr Comp Biol 2023; 63:1455-1473. [PMID: 37193661 DOI: 10.1093/icb/icad033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/18/2023] Open
Abstract
While the modern framework of evolutionary development (evo-devo) has been decidedly genetic, historic analyses have also considered the importance of mechanics in the evolution of form. With the aid of recent technological advancements in both quantifying and perturbing changes in the molecular and mechanical effectors of organismal shape, how molecular and genetic cues regulate the biophysical aspects of morphogenesis is becoming increasingly well studied. As a result, this is an opportune time to consider how the tissue-scale mechanics that underlie morphogenesis are acted upon through evolution to establish morphological diversity. Such a focus will enable a field of evo-devo mechanobiology that will serve to better elucidate the opaque relations between genes and forms by articulating intermediary physical mechanisms. Here, we review how the evolution of shape is measured and related to genetics, how recent strides have been made in the dissection of developmental tissue mechanics, and how we expect these areas to coalesce in evo-devo studies in the future.
Collapse
Affiliation(s)
- Elise A Loffet
- Department of Biomedical Engineering, Columbia University, 351 Engineering Terrace, 1210 Amsterdam Avenue, New York, NY 10027, USA
| | - John F Durel
- Department of Biomedical Engineering, Columbia University, 351 Engineering Terrace, 1210 Amsterdam Avenue, New York, NY 10027, USA
| | - Nandan L Nerurkar
- Department of Biomedical Engineering, Columbia University, 351 Engineering Terrace, 1210 Amsterdam Avenue, New York, NY 10027, USA
| |
Collapse
|
3
|
Amezquita J, Desbois M, Opperman KJ, Pak JS, Christensen EL, Nguyen NT, Diaz-Garcia K, Borgen MA, Grill B. Axon development is regulated at genetic and proteomic interfaces between the integrin adhesome and the RPM-1 ubiquitin ligase signaling hub. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.15.566604. [PMID: 38014183 PMCID: PMC10680716 DOI: 10.1101/2023.11.15.566604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Integrin signaling plays important roles in development and disease. An adhesion signaling network called the integrin adhesome has been principally defined using bioinformatics and proteomics. To date, the adhesome has not been studied using integrated proteomic and genetic approaches. Here, proteomic studies in C. elegans identified physical associations between the RPM-1 ubiquitin ligase signaling hub and numerous adhesome components including Talin, Kindlin and beta-integrin. C. elegans RPM-1 is orthologous to human MYCBP2, a prominent player in nervous system development associated with a neurodevelopmental disorder. Using neuron-specific, CRISPR loss-of-function strategies, we show that core adhesome components affect axon development and interact genetically with RPM-1. Mechanistically, Talin opposes RPM-1 in a functional 'tug-of-war' on growth cones that is required for accurate axon termination. Thus, our findings orthogonally validate the adhesome via multi-component genetic and physical interfaces with a key neuronal signaling hub and identify new links between the adhesome and brain disorders.
Collapse
|
4
|
A review on regulation of cell cycle by extracellular matrix. Int J Biol Macromol 2023; 232:123426. [PMID: 36708893 DOI: 10.1016/j.ijbiomac.2023.123426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/12/2023] [Accepted: 01/21/2023] [Indexed: 01/26/2023]
Abstract
The extracellular matrix (ECM) is a network of structural proteins, glycoproteins and proteoglycans that assists independent cells in aggregating and forming highly organized functional structures. ECM serves numerous purposes and is an essential component of tissue structure and functions. Initially, the role of ECM was considered to be confined to passive functions like providing mechanical strength and structural identity to tissues, serving as barriers and platforms for cells. The doors to understanding ECM's proper role in tissue functioning opened with the discovery of cellular receptors, integrins to which ECM components binds and influences cellular activities. Understanding and utilizing ECM's potential to control cellular function has become a topic of much interest in recent decades, providing different outlooks to study processes involved in developmental programs, wound healing and tumour progression. On another front, the regulatory mechanisms operating to prevent errors in the cell cycle have been topics of a titanic amount of studies. This is expected as many diseases, most infamously cancer, are associated with defects in their functioning. This review focuses on how ECM, through different methods, influences the progression of the somatic cell cycle and provides deeper insights into molecular mechanisms of functional communication between adhesion complex, signalling pathways and cell cycle machinery.
Collapse
|
5
|
Integrin receptor trafficking in health and disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 196:271-302. [PMID: 36813362 DOI: 10.1016/bs.pmbts.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Integrins are a family of 24 different heterodimers that are indispensable for multicellular life. Cell polarity, adhesion and migration are controlled by integrins delivered to the cell surface which in turn is regulated by the exo- and endocytic trafficking of integrins. The deep integration between trafficking and cell signaling determines the spatial and temporal output from any biochemical cue. Integrin trafficking plays a key role in development and many pathological conditions, especially cancer. Several novel regulators of integrin traffic have been discovered in recent times, including a novel class of integrin carrying vesicles, the intracellular nanovesicles (INVs). The tight regulation of trafficking pathways by cell signaling, where kinases phosphorylate key small GTPases in the trafficking pathway enable coordination of cell response to the extracellular milieu. Integrin heterodimer expression and trafficking differ in different tissues and contexts. In this Chapter, we discuss recent studies on integrin trafficking and its contribution to normal physiological and pathophysiological states.
Collapse
|
6
|
SIN-3 functions through multi-protein interaction to regulate apoptosis, autophagy, and longevity in Caenorhabditis elegans. Sci Rep 2022; 12:10560. [PMID: 35732652 PMCID: PMC9217932 DOI: 10.1038/s41598-022-13864-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/09/2022] [Indexed: 11/08/2022] Open
Abstract
SIN3/HDAC is a multi-protein complex that acts as a regulatory unit and functions as a co-repressor/co-activator and a general transcription factor. SIN3 acts as a scaffold in the complex, binding directly to HDAC1/2 and other proteins and plays crucial roles in regulating apoptosis, differentiation, cell proliferation, development, and cell cycle. However, its exact mechanism of action remains elusive. Using the Caenorhabditis elegans (C. elegans) model, we can surpass the challenges posed by the functional redundancy of SIN3 isoforms. In this regard, we have previously demonstrated the role of SIN-3 in uncoupling autophagy and longevity in C. elegans. In order to understand the mechanism of action of SIN3 in these processes, we carried out a comparative analysis of the SIN3 protein interactome from model organisms of different phyla. We identified conserved, expanded, and contracted gene classes. The C. elegans SIN-3 interactome -revealed the presence of well-known proteins, such as DAF-16, SIR-2.1, SGK-1, and AKT-1/2, involved in autophagy, apoptosis, and longevity. Overall, our analyses propose potential mechanisms by which SIN3 participates in multiple biological processes and their conservation across species and identifies candidate genes for further experimental analysis.
Collapse
|
7
|
Mijanović L, Weber I. Adhesion of Dictyostelium Amoebae to Surfaces: A Brief History of Attachments. Front Cell Dev Biol 2022; 10:910736. [PMID: 35721508 PMCID: PMC9197732 DOI: 10.3389/fcell.2022.910736] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/13/2022] [Indexed: 12/23/2022] Open
Abstract
Dictyostelium amoebae adhere to extracellular material using similar mechanisms to metazoan cells. Notably, the cellular anchorage loci in Amoebozoa and Metazoa are both arranged in the form of discrete spots and incorporate a similar repertoire of intracellular proteins assembled into multicomponent complexes located on the inner side of the plasma membrane. Surprisingly, however, Dictyostelium lacks integrins, the canonical transmembrane heterodimeric receptors that dominantly mediate adhesion of cells to the extracellular matrix in multicellular animals. In this review article, we summarize the current knowledge about the cell-substratum adhesion in Dictyostelium, present an inventory of the involved proteins, and draw parallels with the situation in animal cells. The emerging picture indicates that, while retaining the basic molecular architecture common to their animal relatives, the adhesion complexes in free-living amoeboid cells have evolved to enable less specific interactions with diverse materials encountered in their natural habitat in the deciduous forest soil. Dissection of molecular mechanisms that underlay short lifetime of the cell-substratum attachments and high turnover rate of the adhesion complexes in Dictyostelium should provide insight into a similarly modified adhesion phenotype that accompanies the mesenchymal-amoeboid transition in tumor metastasis.
Collapse
Affiliation(s)
- Lucija Mijanović
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Igor Weber
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| |
Collapse
|
8
|
Functional Remodeling of the Contractile Smooth Muscle Cell Cortex, a Provocative Concept, Supported by Direct Visualization of Cortical Remodeling. BIOLOGY 2022; 11:biology11050662. [PMID: 35625390 PMCID: PMC9138025 DOI: 10.3390/biology11050662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/06/2022] [Accepted: 04/24/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary As a key element of the smooth muscle cell contractile apparatus, the actin cytoskeleton participates in the development of force by acting as a molecular track for the myosin cross bridge motor. At the same time, the actin cytoskeleton must transmit the force developed during contraction to the extracellular matrix and, thus, to neighboring cells. This propagation of force to the cell periphery and beyond is initiated in part on specifically localized cellular cortical actin filaments also involved in mechano-chemical transduction. During the contractile process itself and in response to extracellular structural and chemical alterations, the smooth muscle actin cytoskeletal remodels. This indicates that the cytoskeleton is a dynamic cellular organelle that adapts to the changes in cell shape and chemical cues. Current evidence connecting contractile function and mechano-transduction mechanisms to the plasticity of the vascular smooth muscle actin cytoskeleton is reviewed; we then describe new evidence for cytoskeletal remodeling in vascular smooth muscle cells. Here, using immunoelectron microscopy, we visualize the actin binding proteins filamin A, zyxin and talin in these cells and show that they participate in the cortical cell cytoskeletal alteration, thus supporting the premise that smooth muscle cell remodeling occurs during contraction. Abstract Considerable controversy has surrounded the functional anatomy of the cytoskeleton of the contractile vascular smooth muscle cell. Recent studies have suggested a dynamic nature of the cortical cytoskeleton of these cells, but direct proof has been lacking. Here, we review past studies in this area suggesting a plasticity of smooth muscle cells. We also present images testing these suggestions by using the technique of immunoelectron microscopy of metal replicas to directly visualize the cortical actin cytoskeleton of the contractile smooth muscle cell along with interactions by representative cytoskeletal binding proteins. We find the cortical cytoskeletal matrix to be a branched, interconnected network of linear actin bundles. Here, the focal adhesion proteins talin and zyxin were localized with nanometer accuracy. Talin is reported in past studies to span the integrin–cytoplasm distance in fibroblasts and zyxin is known to be an adaptor protein between alpha-actinin and VASP. In response to activation of signal transduction with the alpha-agonist phenylephrine, we found that no movement of talin was detectable but that the zyxin-zyxin spacing was statistically significantly decreased in the smooth muscle cells examined. Contractile smooth muscle is often assumed to have a fixed cytoskeletal structure. Thus, the results included here are important in that they directly support the concept at the electron microscopic level that the focal adhesion of the contractile smooth muscle cell has a dynamic nature and that the protein–protein interfaces showing plasticity are protein-specific.
Collapse
|
9
|
Hegewisch-Solloa E, Seo S, Mundy-Bosse BL, Mishra A, Waldman EH, Maurrasse S, Grunstein E, Connors TJ, Freud AG, Mace EM. Differential Integrin Adhesome Expression Defines Human NK Cell Residency and Developmental Stage. THE JOURNAL OF IMMUNOLOGY 2021; 207:950-965. [PMID: 34282002 DOI: 10.4049/jimmunol.2100162] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 06/03/2021] [Indexed: 11/19/2022]
Abstract
NK cells are innate immune cells that reside within tissue and circulate in peripheral blood. They interact with a variety of microenvironments, yet how NK cells engage with these varied microenvironments is not well documented. The adhesome represents a molecular network of defined and predicted integrin-mediated signaling interactions. In this study, we define the integrin adhesome expression profile of NK cells from human tonsil, peripheral blood, and those derived from human hematopoietic precursors through stromal cell coculture systems. We report that the site of cell isolation and NK cell developmental stage dictate differences in expression of adhesome associated genes and proteins. Furthermore, we define differences in cortical actin content associated with differential expression of actin regulating proteins, suggesting that differences in adhesome expression are associated with differences in cortical actin homeostasis. These data provide understanding of the diversity of human NK cell populations and how they engage with their microenvironment.
Collapse
Affiliation(s)
- Everardo Hegewisch-Solloa
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Seungmae Seo
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Bethany L Mundy-Bosse
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH.,Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, OH
| | - Anjali Mishra
- Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, OH.,Division of Dermatology, Department of Internal Medicine, The Ohio State University, Columbus, OH
| | - Erik H Waldman
- Department of Otolaryngology-Head and Neck Surgery, Columbia University Medical Center, New York, NY
| | - Sarah Maurrasse
- Department of Otolaryngology-Head and Neck Surgery, Columbia University Medical Center, New York, NY
| | - Eli Grunstein
- Department of Otolaryngology-Head and Neck Surgery, Columbia University Medical Center, New York, NY
| | - Thomas J Connors
- Division of Pediatric Critical Care and Hospital Medicine, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY; and
| | - Aharon G Freud
- Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, OH.,Department of Pathology, The Ohio State University, Columbus, OH
| | - Emily M Mace
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY;
| |
Collapse
|
10
|
Subramanian K, Petzold H, Seelbinder B, Hersemann L, Nüsslein I, Kreysing M. Optical plasticity of mammalian cells. JOURNAL OF BIOPHOTONICS 2021; 14:e202000457. [PMID: 33345429 DOI: 10.1002/jbio.202000457] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
Transparency is widespread in nature, ranging from transparent insect wings to ocular tissues that enable you to read this text, and transparent marine vertebrates. And yet, cells and tissue models in biology are usually strongly light scattering and optically opaque, precluding deep optical microscopy. Here we describe the directed evolution of cultured mammalian cells toward increased transparency. We find that mutations greatly diversify the optical phenotype of Chinese Hamster Ovary cells, a cultured mammalian cell line. Furthermore, only three rounds of high-throughput optical selection and competitive growth are required to yield fit cells with greatly improved transparency. Based on 15 monoclonal cell lines derived from this directed evolution experiment, we find that the evolved transparency frequently goes along with a reduction of nuclear granularity and physiological shifts in gene expression profiles. In the future this optical plasticity of mammalian cells may facilitate genetic clearance of living tissues for in vivo microscopy.
Collapse
Affiliation(s)
- Kaushikaram Subramanian
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | - Heike Petzold
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Benjamin Seelbinder
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | - Lena Hersemann
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | - Ina Nüsslein
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Moritz Kreysing
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
- Cluster of Excellence, PoL | Physics of Life, Biotechnology Center of the TU Dresden, Dresden, Germany
| |
Collapse
|
11
|
Adonin L, Drozdov A, Barlev NA. Sea Urchin as a Universal Model for Studies of Gene Networks. Front Genet 2021; 11:627259. [PMID: 33552139 PMCID: PMC7854572 DOI: 10.3389/fgene.2020.627259] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 12/10/2020] [Indexed: 01/06/2023] Open
Abstract
The purple sea urchin Strongylocentrotus purpuratus has been used for over 150 years as a model organism in developmental biology. Using this model species, scientists have been able to describe, in detail, the mechanisms of cell cycle control and cell adhesion, fertilization, calcium signaling, cell differentiation, and death. Massive parallel sequencing of the sea urchin genome enabled the deciphering of the main components of gene regulatory networks during the activation of embryonic signaling pathways. This knowledge helped to extrapolate aberrations in somatic cells that may lead to diseases, including cancer in humans. Furthermore, since many, if not all, developmental signaling pathways were shown to be controlled by non-coding RNAs (ncRNAs), the sea urchin organism represents an attractive experimental model. In this review, we discuss the main discoveries in the genetics, genomics, and transcriptomics of sea urchins during embryogenesis with the main focus on the role of ncRNAs. This information may be useful for comparative studies between different organisms, and may help identify new regulatory networks controlled by ncRNAs.
Collapse
Affiliation(s)
- Leonid Adonin
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, Tyumen, Russia.,Orekhovich Institute of Biomedical Chemistry, Moscow, Russia
| | - Anatoliy Drozdov
- Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Nickolai A Barlev
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Orekhovich Institute of Biomedical Chemistry, Moscow, Russia.,Institute of Cytology, Russian Academy of Sciences, Saint-Petersburg, Russia
| |
Collapse
|
12
|
Lv Z, Qiu L, Wang W, Liu Z, Liu Q, Wang L, Song L. The Members of the Highly Diverse Crassostrea gigas Integrin Family Cooperate for the Generation of Various Immune Responses. Front Immunol 2020; 11:1420. [PMID: 32793197 PMCID: PMC7390872 DOI: 10.3389/fimmu.2020.01420] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 06/02/2020] [Indexed: 12/25/2022] Open
Abstract
Studies on invertebrate immune receptors can provide insights into characteristics specific to innate immune system. Here, eight α and three β integrins are identified from an invertebrate, the Pacific oyster Crassostrea gigas, and their possible immune functions are studied. Oyster α/β integrins exhibit a higher degree of sequence and structural variability than the members from Homo sapiens and Drosophila melanogaster. The analysis reveals that oyster RGD- and laminin-binding receptor homologs are present in the phylogenetic tree of α integrins, but the other six oyster α integrins mainly form a species-specific branch; meanwhile, oyster β integrins are clustered with insect β integrins but distinct from a member from the mollusk Biomphalaria glabrata. Although phylogenetically lacking the important α integrin branches of LDV-binding, PS3-type, and αI-containing integrins, oyster integrins can bind to most ECM ligands, including RGDCP, LDVCP, GFOGERCP, and laminin protein in a distinct binding pattern. Besides, oyster integrins are distributed in different hemocyte subpopulations, while only specific integrins are selectively involved in hemocyte phagocytosis, migration, and encapsulation, and some of them participate in more than one immune response in a sophisticated pattern. Especially, oyster β integrins are arranged in the core to mediate complex immune responses, unlike the counterparts in humans that mainly depend on αI-containing integrins to incite immune reactions. This study represents the first comprehensive attempt to reveal the structural and evolutionary features of the integrin family and their involvement in cellular immune responses in the non-model invertebrate C. gigas and sheds light on the characteristics specific to the innate immune system in the integrin family.
Collapse
Affiliation(s)
- Zhao Lv
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Limei Qiu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Weilin Wang
- Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China.,Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, China
| | - Zhaoqun Liu
- Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China.,Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, China
| | - Qing Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Lingling Wang
- Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China.,Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, China
| | - Linsheng Song
- Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China.,Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, China
| |
Collapse
|
13
|
Kang KB, Lawrence BD, Gao XR, Luo Y, Zhou Q, Liu A, Guaiquil VH, Rosenblatt MI. Micro- and Nanoscale Topographies on Silk Regulate Gene Expression of Human Corneal Epithelial Cells. Invest Ophthalmol Vis Sci 2017; 58:6388-6398. [PMID: 29260198 PMCID: PMC5736325 DOI: 10.1167/iovs.17-22213] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Purpose Corneal basement membrane has topographical features that provide biophysical cues to direct cell adherence, migration, and proliferation. In this study, we hypothesize that varying topographic pitch created on silk films can alter epithelial cell morphology, adhesion, and the genetic expression involved in cytoskeletal dynamics-related pathways. Methods Silicon wafers with parallel ridge widths of 2000, 1000, and 800 nm were produced and used to pattern silk films via soft lithography. Human corneal epithelial cells were cultured onto silk. After 72 hours of incubation, images were taken to study cell morphology and alignment. Cytoskeletal structures were studied by immunofluorescent staining. RNA was collected from cultured cells to perform RNA-Seq transcriptome analysis using the Illumina Hiseq 2500 sequencing system. Differentially expressed genes were identified using DNAstar Qseq then verified using quantitative real-time PCR. These genes were used to perform pathway analyses using Ingenuity Pathways Analysis. Results Primary human corneal epithelial cell alignment to the surface pattern was the greatest on 1000-nm features. Fluorescent microscopy of f-actin staining showed cell cytoskeleton alignment either in parallel (2000 nm) or perpendicular (1000 and 800 nm) to the long feature axis. Z-stack projection of vinculin staining indicated increased focal adhesion formation localized on the cellular basal surface. RNA-seq analysis revealed differentially expressed genes involved in actin organization, integrin signaling, and focal adhesion kinase signaling (−log (P)>5). Conclusions Patterned silk film substrates may serve as a scaffold and provide biophysical cues to corneal epithelial cells that change their gene expression, alter cellular adherence, morphology, and may offer a promising customizable material for use in ocular surface repair.
Collapse
Affiliation(s)
- Kai B Kang
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, University of Illinois at Chicago, Chicago, Illinois, United States
| | - Brian D Lawrence
- Department of Ophthalmology, Weill Cornell Medical College, New York, New York, United States
| | - X Raymond Gao
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, University of Illinois at Chicago, Chicago, Illinois, United States
| | - Yuncin Luo
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, University of Illinois at Chicago, Chicago, Illinois, United States
| | - Qiang Zhou
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, University of Illinois at Chicago, Chicago, Illinois, United States
| | - Aihong Liu
- Department of Ophthalmology, Weill Cornell Medical College, New York, New York, United States
| | - Victor H Guaiquil
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, University of Illinois at Chicago, Chicago, Illinois, United States
| | - Mark I Rosenblatt
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, University of Illinois at Chicago, Chicago, Illinois, United States
| |
Collapse
|
14
|
Wasik AA, Schiller HB. Functional proteomics of cellular mechanosensing mechanisms. Semin Cell Dev Biol 2017; 71:118-128. [DOI: 10.1016/j.semcdb.2017.06.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 06/23/2017] [Accepted: 06/25/2017] [Indexed: 10/19/2022]
|
15
|
Calkins S, Youssef NH. Insights into the Utility of the Focal Adhesion Scaffolding Proteins in the Anaerobic Fungus Orpinomyces sp. C1A. PLoS One 2016; 11:e0163553. [PMID: 27685796 PMCID: PMC5042518 DOI: 10.1371/journal.pone.0163553] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 09/11/2016] [Indexed: 12/30/2022] Open
Abstract
Focal adhesions (FAs) are large eukaryotic multiprotein complexes that are present in all metazoan cells and function as stable sites of tight adhesion between the extracellular matrix (ECM) and the cell's cytoskeleton. FAs consist of anchor membrane protein (integrins), scaffolding proteins (e.g. α-actinin, talin, paxillin, and vinculin), signaling proteins of the IPP complex (e.g. integrin-linked kinase, α-parvin, and PINCH), and signaling kinases (e.g. focal adhesion kinase (FAK) and Src kinase). While genes encoding complete focal adhesion machineries are present in genomes of all multicellular Metazoa; incomplete machineries were identified in the genomes of multiple non-metazoan unicellular Holozoa, basal fungal lineages, and amoebozoan representatives. Since a complete FA machinery is required for functioning, the putative role, if any, of these incomplete FA machineries is currently unclear. We sought to examine the expression patterns of FA-associated genes in the anaerobic basal fungal isolate Orpinomyces sp. strain C1A under different growth conditions and at different developmental stages. Strain C1A lacks clear homologues of integrin, and the two signaling kinases FAK and Src, but encodes for all scaffolding proteins, and the IPP complex proteins. We developed a protocol for synchronizing growth of C1A cultures, allowing for the collection and mRNA extraction from flagellated spores, encysted germinating spores, active zoosporangia, and late inactive sporangia of strain C1A. We demonstrate that the genes encoding the FA scaffolding proteins α-actinin, talin, paxillin, and vinculin are indeed transcribed under all growth conditions, and at all developmental stages of growth. Further, analysis of the observed transcriptional patterns suggests the putative involvement of these components in alternative non-adhesion-specific functions, such as hyphal tip growth during germination and flagellar assembly during zoosporogenesis. Based on these results, we propose putative alternative functions for such proteins in the anaerobic gut fungi. Our results highlight the presumed diverse functionalities of FA scaffolding proteins in basal fungi.
Collapse
Affiliation(s)
- Shelby Calkins
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, United States of America
| | - Noha H. Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, United States of America
| |
Collapse
|
16
|
Abstract
The complexity of cell-matrix adhesion convolves its roles in the development and functioning of multicellular organisms and their evolutionary tinkering. Cell-matrix adhesion is mediated by sites along the plasma membrane that anchor the actin cytoskeleton to the matrix via a large number of proteins, collectively called the integrin adhesome. Fundamental challenges for understanding how cell-matrix adhesion sites assemble and function arise from their multi-functionality, rapid dynamics, large number of components and molecular diversity. Systems biology faces these challenges in its strive to understand how the integrin adhesome gives rise to functional adhesion sites. Synthetic biology enables engineering intracellular modules and circuits with properties of interest. In this review I discuss some of the fundamental questions in systems biology of cell-matrix adhesion and how synthetic biology can help addressing them.
Collapse
Affiliation(s)
- Eli Zamir
- a Department of Systemic Cell Biology , Max Planck Institute of Molecular Physiology , Dortmund , Germany
| |
Collapse
|
17
|
Proteome Based Construction of the Lymphocyte Function-Associated Antigen 1 (LFA-1) Interactome in Human Dendritic Cells. PLoS One 2016; 11:e0149637. [PMID: 26889827 PMCID: PMC4758637 DOI: 10.1371/journal.pone.0149637] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 02/03/2016] [Indexed: 12/21/2022] Open
Abstract
The β2-integrin lymphocyte function-associated antigen 1 (LFA-1) plays an important role in the migration, adhesion and intercellular communication of dendritic cells (DCs). During the differentiation of human DCs from monocyte precursors, LFA-1 ligand binding capacity is completely lost, even though its expression levels were remained constant. Yet LFA-1-mediated adhesive capacity on DCs can be regained by exposing DCs to the chemokine CCL21, suggesting a high degree of regulation of LFA-1 activity during the course of DC differentiation. The molecular mechanisms underlying this regulation of LFA-1 function in DCs, however, remain elusive. To get more insight we attempted to identify specific LFA-1 binding partners that may play a role in regulating LFA-1 activity in DCs. We used highly sensitive label free quantitative mass-spectrometry to identify proteins co-immunoprecipitated (co-IP) with LFA-1 from ex vivo generated DCs. Among the potential binding partners we identified not only established components of integrin signalling pathways and cytoskeletal proteins, but also several novel LFA-1 binding partners including CD13, galectin-3, thrombospondin-1 and CD44. Further comparison to the LFA-1 interaction partners in monocytes indicated that DC differentiation was accompanied by an overall increase in LFA-1 associated proteins, in particular cytoskeletal, signalling and plasma membrane (PM) proteins. The here presented LFA-1 interactome composed of 78 proteins thus represents a valuable resource of potential regulators of LFA-1 function during the DC lifecycle.
Collapse
|
18
|
Dergai M, Iershov A, Novokhatska O, Pankivskyi S, Rynditch A. Evolutionary Changes on the Way to Clathrin-Mediated Endocytosis in Animals. Genome Biol Evol 2016; 8:588-606. [PMID: 26872775 PMCID: PMC4824007 DOI: 10.1093/gbe/evw028] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Endocytic pathways constitute an evolutionarily ancient system that significantly contributed to the eukaryotic cell architecture and to the diversity of cell type-specific functions and signaling cascades, in particular of metazoans. Here we used comparative proteomic studies to analyze the universal internalization route in eukaryotes, clathrin-mediated endocytosis (CME), to address the issues of how this system evolved and what are its specific features. Among 35 proteins crucially required for animal CME, we identified a subset of 22 proteins common to major eukaryotic branches and 13 gradually acquired during evolution. Based on exploration of structure-function relationship between conserved homologs in sister, distantly related and early diverged branches, we identified novel features acquired during evolution of endocytic proteins on the way to animals: Elaborated way of cargo recruitment by multiple sorting proteins, structural changes in the core endocytic complex AP2, the emergence of the Fer/Cip4 homology domain-only protein/epidermal growth factor receptor substrate 15/intersectin functional complex as an additional interaction hub and activator of AP2, as well as changes in late endocytic stages due to recruitment of dynamin/sorting nexin 9 complex and involvement of the actin polymerization machinery. The evolutionary reconstruction showed the basis of the CME process and its subsequent step-by-step development. Documented changes imply more precise regulation of the pathway, as well as CME specialization for the uptake of specific cargoes and cell type-specific functions.
Collapse
Affiliation(s)
- Mykola Dergai
- Department of Functional Genomics, Institute of Molecular Biology and Genetics, NASU, Kyiv, Ukraine
| | - Anton Iershov
- Department of Biosynthesis of Nucleic Acids, Institute of Molecular Biology and Genetics, NASU, Kyiv, Ukraine
| | - Olga Novokhatska
- Department of Functional Genomics, Institute of Molecular Biology and Genetics, NASU, Kyiv, Ukraine
| | - Serhii Pankivskyi
- Department of Functional Genomics, Institute of Molecular Biology and Genetics, NASU, Kyiv, Ukraine
| | - Alla Rynditch
- Department of Functional Genomics, Institute of Molecular Biology and Genetics, NASU, Kyiv, Ukraine
| |
Collapse
|
19
|
Saphirstein RJ, Gao YZ, Lin QQ, Morgan KG. Cortical actin regulation modulates vascular contractility and compliance in veins. J Physiol 2015; 593:3929-41. [PMID: 26096914 DOI: 10.1113/jp270845] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 06/16/2015] [Indexed: 12/31/2022] Open
Abstract
Most cardiovascular research focuses on arterial mechanisms of disease, largely ignoring venous mechanisms. Here we examine ex vivo venous stiffness, spanning tissue to molecular levels, using biomechanics and magnetic microneedle technology, and show for the first time that venous stiffness is regulated by a molecular actin switch within the vascular smooth muscle cell in the wall of the vein. This switch connects the contractile apparatus within the cell to adhesion structures and facilitates stiffening of the vessel wall, regulating blood flow return to the heart. These studies also demonstrate that passive stiffness, the component of total stiffness not attributable to vascular smooth muscle activation, is severalfold lower in venous tissue than in arterial tissue. We show here that the activity of the smooth muscle cells plays a dominant role in determining total venous stiffness and regulating venous return. The literature on arterial mechanics is extensive, but far less is known about mechanisms controlling mechanical properties of veins. We use here a multi-scale approach to identify subcellular sources of venous stiffness. Portal vein tissue displays a severalfold decrease in passive stiffness compared to aortic tissues. The α-adrenergic agonist phenylephrine (PE) increased tissue stress and stiffness, both attenuated by cytochalasin D (CytoD) and PP2, inhibitors of actin polymerization and Src activity, respectively. We quantify, for the first time, cortical cellular stiffness in freshly isolated contractile vascular smooth muscle cells using magnetic microneedle technology. Cortical stiffness is significantly increased by PE and CytoD inhibits this increase but, surprisingly, PP2 does not. No detectable change in focal adhesion size, measured by immunofluorescence of FAK and zyxin, accompanies the PE-induced changes in cortical stiffness. Probing with phospho-specific antibodies confirmed activation of FAK/Src and ERK pathways and caldesmon phosphorylation. Thus, venous tissue stiffness is regulated both at the level of the smooth muscle cell cortex, via cortical actin polymerization, and by downstream smooth muscle effectors of Src/ERK signalling pathways. These findings identify novel potential molecular targets for the modulation of venous capacitance and venous return in health and disease.
Collapse
Affiliation(s)
| | - Yuan Z Gao
- Department of Health Sciences, Boston University, Boston, MA, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Qian Qian Lin
- Department of Health Sciences, Boston University, Boston, MA, USA
| | | |
Collapse
|
20
|
Robertson J, Jacquemet G, Byron A, Jones MC, Warwood S, Selley JN, Knight D, Humphries JD, Humphries MJ. Defining the phospho-adhesome through the phosphoproteomic analysis of integrin signalling. Nat Commun 2015; 6:6265. [PMID: 25677187 PMCID: PMC4338609 DOI: 10.1038/ncomms7265] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 01/09/2015] [Indexed: 01/09/2023] Open
Abstract
Cell–extracellular matrix (ECM) adhesion is a fundamental requirement for multicellular existence due to roles in positioning, proliferation and differentiation. Phosphorylation plays a major role in adhesion signalling; however, a full understanding of the phosphorylation events that occur at sites of adhesion is lacking. Here we report a proteomic and phosphoproteomic analysis of adhesion complexes isolated from cells spread on fibronectin. We identify 1,174 proteins, 499 of which are phosphorylated (1,109 phosphorylation sites), including both well-characterized and novel adhesion-regulated phosphorylation events. Immunoblotting suggests that two classes of phosphorylated residues are found at adhesion sites—those induced by adhesion and those constitutively phosphorylated but recruited in response to adhesion. Kinase prediction analysis identifies novel kinases with putative roles in adhesion signalling including CDK1, inhibition of which reduces adhesion complex formation. This phospho-adhesome data set constitutes a valuable resource to improve our understanding of the signalling mechanisms through which cell–ECM interactions control cell behaviour. Protein phosphorylation is known to play an important role in cell adhesion signalling. Robertson et al. present a proteomic resource mapping the phosphorylation states of proteins isolated from adhesion complexes and, taking advantage of this data set, show that the cell cycle kinase CDK1 may influence cell adhesion.
Collapse
Affiliation(s)
- Joseph Robertson
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Guillaume Jacquemet
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Adam Byron
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Matthew C Jones
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Stacey Warwood
- Biological Mass Spectrometry Core Facility, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Julian N Selley
- Biological Mass Spectrometry Core Facility, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - David Knight
- Biological Mass Spectrometry Core Facility, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Jonathan D Humphries
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Martin J Humphries
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| |
Collapse
|
21
|
Abstract
Vertebrate adherens junctions mediate cell–cell adhesion via a “classical” cadherin–catenin “core” complex, which is associated with and regulated by a functional network of proteins, collectively named the cadherin adhesome (“cadhesome”). The most basal metazoans have been shown to conserve the cadherin–catenin “core”, but little is known about the evolution of the cadhesome. Using a bioinformatics approach based on both sequence and structural analysis, we have traced the evolution of this larger network in 26 organisms, from the uni-cellular ancestors of metazoans, through basal metazoans, to vertebrates. Surprisingly, we show that approximately 70% of the cadhesome, including proteins with similarity to the catenins, predate metazoans. We found that the transition to multicellularity was accompanied by the appearance of a small number of adaptor proteins, and we show how these proteins may have helped to integrate pre-metazoan sub-networks via PDZ domain–peptide interactions. Finally, we found the increase in network complexity in higher metazoans to have been driven primarily by expansion of paralogs. In summary, our analysis helps to explain how the complex protein network associated with cadherin at adherens junctions first came together in the first metazoan and how it evolved into the even more complex mammalian cadhesome.
Collapse
Affiliation(s)
- Paul S Murray
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA Center of Computational Biology and Bioinformatics, Department of Systems Biology, Columbia University, Irving Cancer Research Center, New York, NY 10032, USA
| | - Ronen Zaidel-Bar
- Mechanobiology Institute Singapore, National University of Singapore, Singapore 117411 Department of Biomedical Engineering, National University of Singapore, Singapore 117575
| |
Collapse
|
22
|
Chen X, Chalfie M. Modulation of C. elegans touch sensitivity is integrated at multiple levels. J Neurosci 2014; 34:6522-36. [PMID: 24806678 PMCID: PMC4012311 DOI: 10.1523/jneurosci.0022-14.2014] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 03/11/2014] [Accepted: 03/31/2014] [Indexed: 01/20/2023] Open
Abstract
Sensory systems can adapt to different environmental signals. Here we identify four conditions that modulate anterior touch sensitivity in Caenorhabditis elegans after several hours and demonstrate that such sensory modulation is integrated at multiple levels to produce a single output. Prolonged vibration involving integrin signaling directly sensitizes the touch receptor neurons (TRNs). In contrast, hypoxia, the dauer state, and high salt reduce touch sensitivity by preventing the release of long-range neuroregulators, including two insulin-like proteins. Integration of these latter inputs occurs at upstream neurohormonal cells and at the insulin signaling cascade within the TRNs. These signals and those from integrin signaling converge to modulate touch sensitivity by regulating AKT kinases and DAF-16/FOXO. Thus, activation of either the integrin or insulin pathways can compensate for defects in the other pathway. This modulatory system integrates conflicting signals from different modalities, and adapts touch sensitivity to both mechanical and non-mechanical conditions.
Collapse
Affiliation(s)
- Xiaoyin Chen
- Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Martin Chalfie
- Department of Biological Sciences, Columbia University, New York, New York 10027
| |
Collapse
|
23
|
Zanivan S, Maione F, Hein MY, Hernández-Fernaud JR, Ostasiewicz P, Giraudo E, Mann M. SILAC-based proteomics of human primary endothelial cell morphogenesis unveils tumor angiogenic markers. Mol Cell Proteomics 2013; 12:3599-611. [PMID: 23979707 PMCID: PMC3861710 DOI: 10.1074/mcp.m113.031344] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 07/21/2013] [Indexed: 02/04/2023] Open
Abstract
Proteomics has been successfully used for cell culture on dishes, but more complex cellular systems have proven to be challenging and so far poorly approached with proteomics. Because of the complexity of the angiogenic program, we still do not have a complete understanding of the molecular mechanisms involved in this process, and there have been no in depth quantitative proteomic studies. Plating endothelial cells on matrigel recapitulates aspects of vessel growth, and here we investigate this mechanism by using a spike-in SILAC quantitative proteomic approach. By comparing proteomic changes in primary human endothelial cells morphogenesis on matrigel to general adhesion mechanisms in cells spreading on culture dish, we pinpoint pathways and proteins modulated by endothelial cells. The cell-extracellular matrix adhesion proteome depends on the adhesion substrate, and a detailed proteomic profile of the extracellular matrix secreted by endothelial cells identified CLEC14A as a matrix component, which binds to MMRN2. We verify deregulated levels of these proteins during tumor angiogenesis in models of multistage carcinogenesis. This is the most in depth quantitative proteomic study of endothelial cell morphogenesis, which shows the potential of applying high accuracy quantitative proteomics to in vitro models of vessel growth to shed new light on mechanisms that accompany pathological angiogenesis. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD000359.
Collapse
MESH Headings
- Animals
- Antigens, Surface/genetics
- Antigens, Surface/metabolism
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carbon Isotopes
- Cell Adhesion
- Cell Adhesion Molecules/genetics
- Cell Adhesion Molecules/metabolism
- Cell Differentiation
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Collagen/chemistry
- Drug Combinations
- Extracellular Matrix/chemistry
- Extracellular Matrix/genetics
- Extracellular Matrix/metabolism
- Gene Expression Regulation, Neoplastic
- Human Umbilical Vein Endothelial Cells/metabolism
- Human Umbilical Vein Endothelial Cells/pathology
- Humans
- Isotope Labeling
- Laminin/chemistry
- Lectins, C-Type/genetics
- Lectins, C-Type/metabolism
- Mass Spectrometry
- Membrane Glycoproteins/genetics
- Membrane Glycoproteins/metabolism
- Mice
- Morphogenesis/genetics
- Neovascularization, Pathologic
- Primary Cell Culture
- Protein Binding
- Proteoglycans/chemistry
- Proteomics
- Signal Transduction
Collapse
Affiliation(s)
- Sara Zanivan
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
- §The Beatson Institute for Cancer Research, Glasgow G61 1BD, United Kingdom
| | - Federica Maione
- ¶Laboratory of Transgenic Mouse Models, Institute for Cancer Research at Candiolo (IRCC), 10060 Candiolo, Italy
- ‖Department of Science and Drug Technology, University of Torino, 10125, Torino, Italy
| | - Marco Y. Hein
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | | | - Pawel Ostasiewicz
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
- **Department of Pathology, Wroclaw Medical University, 50-368, Wroclaw, Poland
| | - Enrico Giraudo
- ¶Laboratory of Transgenic Mouse Models, Institute for Cancer Research at Candiolo (IRCC), 10060 Candiolo, Italy
- ‖Department of Science and Drug Technology, University of Torino, 10125, Torino, Italy
| | - Matthias Mann
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
- ‡‡The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
24
|
Schiller HB, Fässler R. Mechanosensitivity and compositional dynamics of cell-matrix adhesions. EMBO Rep 2013; 14:509-19. [PMID: 23681438 DOI: 10.1038/embor.2013.49] [Citation(s) in RCA: 202] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 03/21/2013] [Indexed: 12/27/2022] Open
Abstract
Cells perceive information about the biochemical and biophysical properties of their tissue microenvironment through integrin-mediated cell-matrix adhesions, which connect the cytoskeleton with the extracellular matrix and thereby allow cohesion and long-range mechanical connections within tissues. The formation of cell-matrix adhesions and integrin signalling involves the dynamic recruitment and assembly of an inventory of proteins, collectively termed the 'adhesome', at the adhesive site. The recruitment of some adhesome proteins, most notably the Lin11-, Isl1- and Mec3-domain-containing proteins, depends on mechanical tension generated by myosin II-mediated contractile forces exerted on cell-matrix adhesions. When exposed to force, mechanosensitive adhesome proteins can change their conformation or expose cryptic-binding sites leading to the recruitment of proteins, rearrangement of the cytoskeleton, reinforcement of the adhesive site and signal transduction. Biophysical methods and proteomics revealed force ranges within the adhesome and cytoskeleton, and also force-dependent changes in adhesome composition. In this review, we provide an overview of the compositional dynamics of cell-matrix adhesions, discuss the most prevalent functional domains in adhesome proteins and review literature and concepts about mechanosensing mechanisms that operate at the adhesion site.
Collapse
Affiliation(s)
- Herbert B Schiller
- Department of Molecular Medicine, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | | |
Collapse
|
25
|
|
26
|
Cervero P, Himmel M, Krüger M, Linder S. Proteomic analysis of podosome fractions from macrophages reveals similarities to spreading initiation centres. Eur J Cell Biol 2012; 91:908-22. [DOI: 10.1016/j.ejcb.2012.05.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 05/10/2012] [Accepted: 05/11/2012] [Indexed: 12/24/2022] Open
|
27
|
Fibronectin stimulates migration through lipid raft dependent NHE-1 activation in mouse embryonic stem cells: involvement of RhoA, Ca(2+)/CaM, and ERK. Biochim Biophys Acta Gen Subj 2012; 1820:1618-27. [PMID: 22683701 DOI: 10.1016/j.bbagen.2012.05.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Revised: 05/25/2012] [Accepted: 05/30/2012] [Indexed: 02/04/2023]
Abstract
BACKGROUND Extracellular matrix (ECM) components and intracellular pH (pH(i)) may serve as regulators of cell migration in various cell types. METHODS The Oris migration assay was used to assess the effect of fibronectin (FN) on cell motility. The Na(+)/H(+) exchanger (NHE)-1 activity was evaluated by measuring pH(i) and [(22)Na(+)] uptake. To examine activated signaling molecules, western blot analysis and immunoprecipitation was performed. RESULTS ECM components (FN, laminin, fibrinogen, and collagen type I) increased [(22)Na(+)] uptake, pH(i), and cell migration. In addition, FN-induced increase of cell migration was inhibited by NHE-1 inhibitor amiloride or NHE-1-specific siRNA. FN selectively increased the mRNA and protein expression of NHE-1, but not that of NHE-2 or NHE-3. FN binds integrin β1 and subsequently stimulates caveolin-1 phosphorylation and Ca(2+) influx. Then, NHE-1 is phosphorylated by RhoA and Rho kinases, and Ca(2+)/calmodulin (CaM) signaling elicits complex formation with NHE-1, which is enriched in lipid raft/caveolae microdomains of the plasma membrane. Activation of NHE-1 continuously induces an increase of [(22)Na(+)] uptake and pH(i). Finally, NHE-1-dependent extracellular signal-regulated kinase (ERK) 1/2 phosphorylation enhanced matrix metalloproteinase-2 (MMP-2) and filamentous-actin (F-actin) expression, partially contributing to the regulation of embryonic stem cells (ESCs) migration. CONCLUSIONS FN stimulated mESCs migration and proliferation through NHE-1 activation, which were mediated by lipid raft-associated caveolin-1, RhoA/ROCK, and Ca(2+)/CaM signaling pathways. GENERAL SIGNIFICANCE The precise role of NHE in the modulation of ECM-related physiological functions such as proliferation and migration remains poorly understood. Thus, this study analyzed the relationship between FN and NHE in regulating the migration of mouse ESCs and their related signaling pathways.
Collapse
|
28
|
Turnover of focal adhesions and cancer cell migration. Int J Cell Biol 2012; 2012:310616. [PMID: 22319531 PMCID: PMC3272802 DOI: 10.1155/2012/310616] [Citation(s) in RCA: 175] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 10/23/2011] [Indexed: 12/22/2022] Open
Abstract
Cells are usually surrounded by the extracellular matrix (ECM), and adhesion of the cells to the ECM is a key step in their migration through tissues. Integrins are important receptors for the ECM and form structures called focal adhesions (FAs). Formation and disassembly of FAs are regulated dynamically during cell migration. Adhesion to the ECM has been studied mainly using cells cultured on an ECM-coated substratum, where the rate of cell migration is determined by the turnover of FAs. However, the molecular events underlying the disassembly of FAs are less well understood. We have recently identified both a new regulator of this disassembly process and its interaction partners. Here, we summarize our understanding of FA disassembly by focusing on the proteins implicated in this process.
Collapse
|
29
|
Abstract
All cells exist within the context of a three-dimensional microenvironment in which they are exposed to mechanical and physical cues. These cues can be disrupted through perturbations to mechanotransduction, from the nanoscale-level to the tissue-level, which compromises tensional homeostasis to promote pathologies such as cardiovascular disease and cancer. The mechanisms of such perturbations suggest that a complex interplay exists between the extracellular microenvironment and cellular function. Furthermore, sustained disruptions in tensional homeostasis can be caused by alterations in the extracellular matrix, allowing it to serve as a mechanically based memory-storage device that can perpetuate a disease or restore normal tissue behaviour.
Collapse
|
30
|
Spassov DS, Wong CH, Moasser MM. Trask phosphorylation defines the reverse mode of a phosphotyrosine signaling switch that underlies cell anchorage state. Cell Cycle 2011; 10:1225-32. [PMID: 21490433 DOI: 10.4161/cc.10.8.15343] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Phosphotyrosine signaling in anchored epithelial cells constitutes a spacially ordained signaling program that largely functions to promote integrin-linked focal adhesion complexes, serving to secure cell anchorage to matrix and as a bidirectional signaling hub that coordinates the physical state of the cell and its environment with cellular functions including proliferation and survival. Cells release their adhesions during processes such as mitosis, migration, or tumorigenesis, but the fate of signaling through tyrosine phosphorylation in unanchored cells remains poorly understood. In an examination of epithelial cells in the unanchored state, we find abundant phosphotyrosine signaling, largely recommitted to an anti-adhesive function mediated through the Src family phosphorylation of their transmembrane substrate Trask/CDCP1/gp140. Src-Trask phosphorylation inhibits integrin clustering and focal adhesion assembly and signaling, defining an active phosphotyrosine signaling program underlying the unanchored state. Src-Trask signaling and Src-focal adhesion signaling inactivate each other, constituting two opposing modes of phosphotyrosine signaling that define a switch underline cell anchorage state. Src kinases are prominent drivers of both signaling modes, identifying their position at the helm of adhesion signaling capable of specifying anchorage state through substrate selection. These experimental studies along with concurring phylogenetic evidence suggest that phosphorylation on tyrosine is a signaling function fundamentally linked with the regulation of integrins.
Collapse
Affiliation(s)
- Danislav S Spassov
- Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA
| | | | | |
Collapse
|
31
|
Valdembri D, Sandri C, Santambrogio M, Serini G. Regulation of integrins by conformation and traffic: it takes two to tango. MOLECULAR BIOSYSTEMS 2011; 7:2539-46. [DOI: 10.1039/c1mb05066d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
32
|
Marg S, Winkler U, Sestu M, Himmel M, Schönherr M, Bär J, Mann A, Moser M, Mierke CT, Rottner K, Blessing M, Hirrlinger J, Ziegler WH. The vinculin-DeltaIn20/21 mouse: characteristics of a constitutive, actin-binding deficient splice variant of vinculin. PLoS One 2010; 5:e11530. [PMID: 20644727 PMCID: PMC2904371 DOI: 10.1371/journal.pone.0011530] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Accepted: 06/17/2010] [Indexed: 01/13/2023] Open
Abstract
Background The cytoskeletal adaptor protein vinculin plays a fundamental role in cell contact regulation and affects central aspects of cell motility, which are essential to both embryonal development and tissue homeostasis. Functional regulation of this evolutionarily conserved and ubiquitously expressed protein is dominated by a high-affinity, autoinhibitory head-to-tail interaction that spatially restricts ligand interactions to cell adhesion sites and, furthermore, limits the residency time of vinculin at these sites. To date, no mutants of the vinculin protein have been characterized in animal models. Methodology/Principal Findings Here, we investigate vinculin-ΔEx20, a splice variant of the protein lacking the 68 amino acids encoded by exon 20 of the vinculin gene VCL. Vinculin-ΔEx20 was found to be expressed alongside with wild type protein in a knock-in mouse model with a deletion of introns 20 and 21 (VCL-ΔIn20/21 allele) and shows defective head-to-tail interaction. Homozygous VCL-ΔIn20/21 embryos die around embryonal day E12.5 showing cranial neural tube defects and exencephaly. In mouse embryonic fibroblasts and upon ectopic expression, vinculin-ΔEx20 reveals characteristics of constitutive head binding activity. Interestingly, the impact of vinculin-ΔEx20 on cell contact induction and stabilization, a hallmark of the vinculin head domain, is only moderate, thus allowing invasion and motility of cells in three-dimensional collagen matrices. Lacking both F-actin interaction sites of the tail, the vinculin-ΔEx20 variant unveils vinculin's dynamic binding to cell adhesions independent of a cytoskeletal association, and thus differs from head-to-tail binding deficient mutants such as vinculin-T12, in which activated F-actin binding locks the protein variant to cell contact sites. Conclusions/Significance Vinculin-ΔEx20 is an active variant supporting adhesion site stabilization without an enhanced mechanical coupling. Its presence in a transgenic animal reveals the potential of splice variants in the vinculin gene to alter vinculin function in vivo. Correct control of vinculin is necessary for embryonic development.
Collapse
Affiliation(s)
- Susanna Marg
- Faculty of Medicine, Interdisciplinary Centre for Clinical Research (IZKF) Leipzig, University of Leipzig, Leipzig, Germany
| | - Ulrike Winkler
- Faculty of Medicine, Interdisciplinary Centre for Clinical Research (IZKF) Leipzig, University of Leipzig, Leipzig, Germany
- Faculty of Medicine, Carl-Ludwig-Institute for Physiology, University of Leipzig, Leipzig, Germany
| | - Marcello Sestu
- Faculty of Medicine, Interdisciplinary Centre for Clinical Research (IZKF) Leipzig, University of Leipzig, Leipzig, Germany
| | - Mirko Himmel
- Faculty of Medicine, Interdisciplinary Centre for Clinical Research (IZKF) Leipzig, University of Leipzig, Leipzig, Germany
| | - Madeleine Schönherr
- Faculty of Medicine, Interdisciplinary Centre for Clinical Research (IZKF) Leipzig, University of Leipzig, Leipzig, Germany
| | - Janina Bär
- Faculty of Medicine, Interdisciplinary Centre for Clinical Research (IZKF) Leipzig, University of Leipzig, Leipzig, Germany
| | - Amrit Mann
- Faculty of Veterinary Medicine, Centre for Biotechnology and Biomedicine, University of Leipzig, Leipzig, Germany
| | - Markus Moser
- Department of Molecular Medicine, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Claudia T. Mierke
- Centre for Medical Physics and Technology, Friedrich-Alexander-University of Erlangen-Nuremberg, Erlangen, Germany
| | - Klemens Rottner
- Cytoskeleton Dynamics Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Manfred Blessing
- Faculty of Veterinary Medicine, Centre for Biotechnology and Biomedicine, University of Leipzig, Leipzig, Germany
| | - Johannes Hirrlinger
- Faculty of Medicine, Interdisciplinary Centre for Clinical Research (IZKF) Leipzig, University of Leipzig, Leipzig, Germany
- Faculty of Medicine, Carl-Ludwig-Institute for Physiology, University of Leipzig, Leipzig, Germany
| | - Wolfgang H. Ziegler
- Faculty of Medicine, Interdisciplinary Centre for Clinical Research (IZKF) Leipzig, University of Leipzig, Leipzig, Germany
- Department of Nephrology, Hannover Medical School, Hannover, Germany
- * E-mail:
| |
Collapse
|
33
|
Ancient origin of the integrin-mediated adhesion and signaling machinery. Proc Natl Acad Sci U S A 2010; 107:10142-7. [PMID: 20479219 DOI: 10.1073/pnas.1002257107] [Citation(s) in RCA: 198] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The evolution of animals (metazoans) from their unicellular ancestors required the emergence of novel mechanisms for cell adhesion and cell-cell communication. One of the most important cell adhesion mechanisms for metazoan development is integrin-mediated adhesion and signaling. The integrin adhesion complex mediates critical interactions between cells and the extracellular matrix, modulating several aspects of cell physiology. To date this machinery has been considered strictly metazoan specific. Here we report the results of a comparative genomic analysis of the integrin adhesion machinery, using genomic data from several unicellular relatives of Metazoa and Fungi. Unexpectedly, we found that core components of the integrin adhesion complex are encoded in the genome of the apusozoan protist Amastigomonas sp., and therefore their origins predate the divergence of Opisthokonta, the clade that includes metazoans and fungi. Furthermore, our analyses suggest that key components of this apparatus have been lost independently in fungi and choanoflagellates. Our data highlight the fact that many of the key genes that had formerly been cited as crucial for metazoan origins have a much earlier origin. This underscores the importance of gene cooption in the unicellular-to-multicellular transition that led to the emergence of the Metazoa.
Collapse
|