1
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Amran A, Pigatto L, Farley J, Godini R, Pocock R, Gopal S. The matrisome landscape controlling in vivo germ cell fates. Nat Commun 2024; 15:4200. [PMID: 38760342 PMCID: PMC11101451 DOI: 10.1038/s41467-024-48283-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 04/26/2024] [Indexed: 05/19/2024] Open
Abstract
The developmental fate of cells is regulated by intrinsic factors and the extracellular environment. The extracellular matrix (matrisome) delivers chemical and mechanical cues that can modify cellular development. However, comprehensive understanding of how matrisome factors control cells in vivo is lacking. Here we show that specific matrisome factors act individually and collectively to control germ cell development. Surveying development of undifferentiated germline stem cells through to mature oocytes in the Caenorhabditis elegans germ line enabled holistic functional analysis of 443 conserved matrisome-coding genes. Using high-content imaging, 3D reconstruction, and cell behavior analysis, we identify 321 matrisome genes that impact germ cell development, the majority of which (>80%) are undescribed. Our analysis identifies key matrisome networks acting autonomously and non-autonomously to coordinate germ cell behavior. Further, our results demonstrate that germ cell development requires continual remodeling of the matrisome landscape. Together, this study provides a comprehensive platform for deciphering how extracellular signaling controls cellular development and anticipate this will establish new opportunities for manipulating cell fates.
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Affiliation(s)
- Aqilah Amran
- Department of Experimental Medical Science, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
- Lund Cancer Center, Lund University, Lund, Sweden
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute. Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia
| | - Lara Pigatto
- Department of Experimental Medical Science, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
- Lund Cancer Center, Lund University, Lund, Sweden
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute. Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia
| | - Johanna Farley
- Department of Experimental Medical Science, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
- Lund Cancer Center, Lund University, Lund, Sweden
| | - Rasoul Godini
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute. Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia
| | - Roger Pocock
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute. Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia.
| | - Sandeep Gopal
- Department of Experimental Medical Science, Lund University, Lund, Sweden.
- Lund Stem Cell Center, Lund University, Lund, Sweden.
- Lund Cancer Center, Lund University, Lund, Sweden.
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute. Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia.
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2
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Coraggio F, Bhushan M, Roumeliotis S, Caroti F, Bevilacqua C, Prevedel R, Rapti G. Age-progressive interplay of HSP-proteostasis, ECM-cell junctions and biomechanics ensures C. elegans astroglial architecture. Nat Commun 2024; 15:2861. [PMID: 38570505 PMCID: PMC10991496 DOI: 10.1038/s41467-024-46827-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 03/12/2024] [Indexed: 04/05/2024] Open
Abstract
Tissue integrity is sensitive to temperature, tension, age, and is sustained throughout life by adaptive cell-autonomous or extrinsic mechanisms. Safeguarding the remarkably-complex architectures of neurons and glia ensures age-dependent integrity of functional circuits. Here, we report mechanisms sustaining the integrity of C. elegans CEPsh astrocyte-like glia. We combine large-scale genetics with manipulation of genes, cells, and their environment, quantitative imaging of cellular/ subcellular features, tissue material properties and extracellular matrix (ECM). We identify mutants with age-progressive, environment-dependent defects in glial architecture, consequent disruption of neuronal architecture, and abnormal aging. Functional loss of epithelial Hsp70/Hsc70-cochaperone BAG2 causes ECM disruption, altered tissue biomechanics, and hypersensitivity of glia to environmental temperature and mechanics. Glial-cell junctions ensure epithelia-ECM-CEPsh glia association. Modifying glial junctions or ECM mechanics safeguards glial integrity against disrupted BAG2-proteostasis. Overall, we present a finely-regulated interplay of proteostasis-ECM and cell junctions with conserved components that ensures age-progressive robustness of glial architecture.
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Affiliation(s)
- Francesca Coraggio
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mahak Bhushan
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Spyridon Roumeliotis
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Francesca Caroti
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Carlo Bevilacqua
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Robert Prevedel
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, Rome, Italy
- Interdisciplinary Center of Neurosciences, Heidelberg University, Heidelberg, Germany
- German Center for Lung Research (DZL), Heidelberg, Germany
| | - Georgia Rapti
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, Rome, Italy.
- Interdisciplinary Center of Neurosciences, Heidelberg University, Heidelberg, Germany.
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3
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Schön JL, Groß VE, Post WB, Daum A, Matúš D, Pilz J, Schnorr R, Horn S, Bäumers M, Weidtkamp-Peters S, Hughes S, Schöneberg T, Prömel S. The adhesion GPCR and PCP component flamingo (FMI-1) alters body size and regulates the composition of the extracellular matrix. Matrix Biol 2024; 128:1-10. [PMID: 38378098 DOI: 10.1016/j.matbio.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 02/02/2024] [Accepted: 02/16/2024] [Indexed: 02/22/2024]
Abstract
The extracellular matrix (ECM) is a network of macromolecules that presents a vital scaffold for cells and enables multiple ways of cellular communication. Thus, it is essential for many physiological processes such as development, tissue morphogenesis, homeostasis, the shape and partially the size of the body and its organs. To ensure these, the composition of the ECM is tissue-specific and highly dynamic. ECM homeostasis is therefore tightly controlled by several mechanisms. Here, we show that FMI-1, the homolog of the Adhesion GPCR Flamingo/CELSR/ADGRC in the nematode Caenorhabditis elegans, modulates the composition of the ECM by controlling the production both of ECM molecules such as collagens and also of ECM modifying enzymes. Thereby, FMI-1 affects the morphology and functionality of the nematode´s cuticle, which is mainly composed of ECM, and also modulates the body size. Mechanistic analyses highlight the fact that FMI-1 exerts its function from neurons non-cell autonomously (trans) solely via its extracellular N terminus. Our data support a model, by which the activity of the receptor, which has a well-described role in the planar cell polarity (PCP) pathway, involves the PCP molecule VANG-1, but seems to be independent of the DBL-1/BMP pathway.
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Affiliation(s)
- Johanna Lena Schön
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany; Department of Dermatology, Venereology and Allergology, Leipzig University Medical Center, Leipzig University, Leipzig, Germany
| | - Victoria Elisabeth Groß
- Institute of Cell Biology, Department of Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Willem Berend Post
- Institute of Cell Biology, Department of Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Alexandra Daum
- Institute of Cell Biology, Department of Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Daniel Matúš
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany; Department of Molecular and Cellular Physiology, Stanford University, Stanford, USA
| | - Johanna Pilz
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Rene Schnorr
- Institute of Cell Biology, Department of Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Susanne Horn
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Miriam Bäumers
- Center for Advanced Imaging, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | - Samantha Hughes
- A-LIFE, Section Environmental Health and Toxicology, Free University Amsterdam, Amsterdam, the Netherlands
| | - Torsten Schöneberg
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany; School of Medicine, University of Global Health Equity, Kigali, Rwanda
| | - Simone Prömel
- Institute of Cell Biology, Department of Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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4
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Dhakal A, Salim C, Skelly M, Amichan Y, Lamm AT, Hundley HA. ADARs regulate cuticle collagen expression and promote survival to pathogen infection. BMC Biol 2024; 22:37. [PMID: 38360623 PMCID: PMC10870475 DOI: 10.1186/s12915-024-01840-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 02/02/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND In all organisms, the innate immune system defends against pathogens through basal expression of molecules that provide critical barriers to invasion and inducible expression of effectors that combat infection. The adenosine deaminase that act on RNA (ADAR) family of RNA-binding proteins has been reported to influence innate immunity in metazoans. However, studies on the susceptibility of ADAR mutant animals to infection are largely lacking. RESULTS Here, by analyzing adr-1 and adr-2 null mutants in well-established slow-killing assays, we find that both Caenorhabditis elegans ADARs are important for organismal survival to gram-negative and gram-positive bacteria, all of which are pathogenic to humans. Furthermore, our high-throughput sequencing and genetic analysis reveal that ADR-1 and ADR-2 function in the same pathway to regulate collagen expression. Consistent with this finding, our scanning electron microscopy studies indicate adr-1;adr-2 mutant animals also have altered cuticle morphology prior to pathogen exposure. CONCLUSIONS Our data uncover a critical role of the C. elegans ADAR family of RNA-binding proteins in promoting cuticular collagen expression, which represents a new post-transcriptional regulatory node that influences the extracellular matrix. In addition, we provide the first evidence that ADAR mutant animals have altered susceptibility to infection with several opportunistic human pathogens, suggesting a broader role of ADARs in altering physical barriers to infection to influence innate immunity.
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Affiliation(s)
- Alfa Dhakal
- Cell, Molecular and Cancer Biology Graduate Program, Indiana University School of Medicine-Bloomington, Bloomington, IN, 47405, USA
| | - Chinnu Salim
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Mary Skelly
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Yarden Amichan
- Faculty of Biology, Technion Institute of Technology, Haifa, Israel
| | - Ayelet T Lamm
- Faculty of Biology, Technion Institute of Technology, Haifa, Israel
| | - Heather A Hundley
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA.
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5
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Teuscher AC, Statzer C, Goyala A, Domenig SA, Schoen I, Hess M, Hofer AM, Fossati A, Vogel V, Goksel O, Aebersold R, Ewald CY. Longevity interventions modulate mechanotransduction and extracellular matrix homeostasis in C. elegans. Nat Commun 2024; 15:276. [PMID: 38177158 PMCID: PMC10766642 DOI: 10.1038/s41467-023-44409-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 12/12/2023] [Indexed: 01/06/2024] Open
Abstract
Dysfunctional extracellular matrices (ECM) contribute to aging and disease. Repairing dysfunctional ECM could potentially prevent age-related pathologies. Interventions promoting longevity also impact ECM gene expression. However, the role of ECM composition changes in healthy aging remains unclear. Here we perform proteomics and in-vivo monitoring to systematically investigate ECM composition (matreotype) during aging in C. elegans revealing three distinct collagen dynamics. Longevity interventions slow age-related collagen stiffening and prolong the expression of collagens that are turned over. These prolonged collagen dynamics are mediated by a mechanical feedback loop of hemidesmosome-containing structures that span from the exoskeletal ECM through the hypodermis, basement membrane ECM, to the muscles, coupling mechanical forces to adjust ECM gene expression and longevity via the transcriptional co-activator YAP-1 across tissues. Our results provide in-vivo evidence that coordinated ECM remodeling through mechanotransduction is required and sufficient to promote longevity, offering potential avenues for interventions targeting ECM dynamics.
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Affiliation(s)
- Alina C Teuscher
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, Schwerzenbach, CH-8603, Switzerland
| | - Cyril Statzer
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, Schwerzenbach, CH-8603, Switzerland
| | - Anita Goyala
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, Schwerzenbach, CH-8603, Switzerland
| | - Seraina A Domenig
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, Schwerzenbach, CH-8603, Switzerland
| | - Ingmar Schoen
- School of Pharmacy and Biomolecular Sciences, Irish Centre for Vascular Biology, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Laboratory of Applied Mechanobiology, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, Zurich, Switzerland
| | - Max Hess
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, Schwerzenbach, CH-8603, Switzerland
| | - Alexander M Hofer
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, Schwerzenbach, CH-8603, Switzerland
| | - Andrea Fossati
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, 94158, CA, USA
| | - Viola Vogel
- Laboratory of Applied Mechanobiology, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, Zurich, Switzerland
| | - Orcun Goksel
- Department of Information Technology and Electrical Engineering, ETH Zürich, Zürich, Switzerland
- Department of Information Technology, Uppsala University, Uppsala, Sweden
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland
| | - Collin Y Ewald
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, Schwerzenbach, CH-8603, Switzerland.
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6
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Adams JRG, Pooranachithra M, Jyo EM, Zheng SL, Goncharov A, Crew JR, Kramer JM, Jin Y, Ernst AM, Chisholm AD. Nanoscale patterning of collagens in C. elegans apical extracellular matrix. Nat Commun 2023; 14:7506. [PMID: 37980413 PMCID: PMC10657453 DOI: 10.1038/s41467-023-43058-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 10/30/2023] [Indexed: 11/20/2023] Open
Abstract
Apical extracellular matrices (aECMs) are complex extracellular compartments that form important interfaces between animals and their environment. In the adult C. elegans cuticle, layers are connected by regularly spaced columnar structures known as struts. Defects in struts result in swelling of the fluid-filled medial cuticle layer ('blistering', Bli). Here we show that three cuticle collagens BLI-1, BLI-2, and BLI-6, play key roles in struts. BLI-1 and BLI-2 are essential for strut formation whereas activating mutations in BLI-6 disrupt strut formation. BLI-1, BLI-2, and BLI-6 precisely colocalize to arrays of puncta in the adult cuticle, corresponding to struts, initially deposited in diffuse stripes adjacent to cuticle furrows. They eventually exhibit tube-like morphology, with the basal ends of BLI-containing struts contact regularly spaced holes in the cuticle. Genetic interaction studies indicate that BLI strut patterning involves interactions with other cuticle components. Our results reveal strut formation as a tractable example of precise aECM patterning at the nanoscale.
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Affiliation(s)
- Jennifer R G Adams
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Murugesan Pooranachithra
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Erin M Jyo
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Sherry Li Zheng
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Alexandr Goncharov
- Department of Neurobiology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jennifer R Crew
- Northwestern University School of Medicine, Department of Cell and Molecular Biology, Chicago, IL, 60611, USA
| | - James M Kramer
- Northwestern University School of Medicine, Department of Cell and Molecular Biology, Chicago, IL, 60611, USA
| | - Yishi Jin
- Department of Neurobiology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Andreas M Ernst
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Andrew D Chisholm
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA.
- Department of Neurobiology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA.
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7
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Woodruff GC, Willis JH, Johnson E, Phillips PC. Widespread changes in gene expression accompany body size evolution in nematodes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564729. [PMID: 37961435 PMCID: PMC10635002 DOI: 10.1101/2023.10.30.564729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Body size is a fundamental trait that drives multiple evolutionary and ecological patterns. Caenorhabditis inopinata is a fig-associated nematode that is exceptionally large relative to other members of the genus, including C. elegans. We previously showed that C. inopinata is large primarily due to postembryonic cell size expansion that occurs during the larval-to-adult transition. Here, we describe gene expression patterns in C. elegans and C. inopinata throughout this developmental period to understand the transcriptional basis of body size change. We performed RNA-seq in both species across the L3, L4, and adult stages. Most genes are differentially expressed across all developmental stages, consistent with C. inopinata's divergent ecology and morphology. We also used a model comparison approach to identify orthologs with divergent dynamics across this developmental period between the two species. This included genes connected to neurons, behavior, stress response, developmental timing, and small RNA/chromatin regulation. Multiple hypodermal collagens were also observed to harbor divergent developmental dynamics across this period, and genes important for molting and body morphology were also detected. Genes associated with TGF-β signaling revealed idiosyncratic and unexpected transcriptional patterns given their role in body size regulation in C. elegans. Widespread transcriptional divergence between these species is unexpected and may be a signature of the ecological and morphological divergence of C. inopinata. Alternatively, transcriptional turnover may be the rule in the Caenorhabditis genus, indicative of widespread developmental system drift among species. This work lays the foundation for future functional genetic studies interrogating the bases of body size evolution in this group.
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Affiliation(s)
- Gavin C Woodruff
- University of Oregon, Eugene, Oregon, USA
- Current institution: University of Oklahoma, Norman, Oklahoma, USA
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8
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Reich H, Savage-Dunn C. Signaling circuits and the apical extracellular matrix in aging: connections identified in the nematode Caenorhabditis elegans. Am J Physiol Cell Physiol 2023; 325:C1201-C1211. [PMID: 37721005 PMCID: PMC10861026 DOI: 10.1152/ajpcell.00195.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/24/2023] [Accepted: 09/11/2023] [Indexed: 09/19/2023]
Abstract
Numerous conserved signaling pathways play critical roles in aging, including insulin/IGF-1, TGF-β, and Wnt pathways. Some of these pathways also play prominent roles in the formation and maintenance of the extracellular matrix. The nematode Caenorhabditis elegans has been an enduringly productive system for the identification of conserved mechanisms of biological aging. Recent studies in C. elegans highlight the regulatory circuits between conserved signaling pathways and the extracellular matrix, revealing a bidirectional relationship between these factors and providing a platform to address how regulation of and by the extracellular matrix can impact lifespan and organismal health during aging. These discoveries provide new opportunities for clinical advances and novel therapeutic strategies.
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Affiliation(s)
- Hannah Reich
- Department of Biology, Queens College, City University of New York, Flushing, New York, United States
| | - Cathy Savage-Dunn
- Department of Biology, Queens College, City University of New York, Flushing, New York, United States
- PhD Program in Biology, The Graduate Center, City University of New York, New York, New York, United States
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9
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Jongsma E, Goyala A, Mateos JM, Ewald CY. Removal of extracellular human amyloid beta aggregates by extracellular proteases in C. elegans. eLife 2023; 12:e83465. [PMID: 37728486 PMCID: PMC10541181 DOI: 10.7554/elife.83465] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 09/19/2023] [Indexed: 09/21/2023] Open
Abstract
The amyloid beta (Aβ) plaques found in Alzheimer's disease (AD) patients' brains contain collagens and are embedded extracellularly. Several collagens have been proposed to influence Aβ aggregate formation, yet their role in clearance is unknown. To investigate the potential role of collagens in forming and clearance of extracellular aggregates in vivo, we created a transgenic Caenorhabditis elegans strain that expresses and secretes human Aβ1-42. This secreted Aβ forms aggregates in two distinct places within the extracellular matrix. In a screen for extracellular human Aβ aggregation regulators, we identified different collagens to ameliorate or potentiate Aβ aggregation. We show that a disintegrin and metalloprotease a disintegrin and metalloprotease 2 (ADM-2), an ortholog of ADAM9, reduces the load of extracellular Aβ aggregates. ADM-2 is required and sufficient to remove the extracellular Aβ aggregates. Thus, we provide in vivo evidence of collagens essential for aggregate formation and metalloprotease participating in extracellular Aβ aggregate removal.
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Affiliation(s)
- Elisabeth Jongsma
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH ZürichSchwerzenbachSwitzerland
| | - Anita Goyala
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH ZürichSchwerzenbachSwitzerland
| | - José Maria Mateos
- Center for Microscopy and Image Analysis, University of ZurichZurichSwitzerland
| | - Collin Yvès Ewald
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH ZürichSchwerzenbachSwitzerland
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10
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Petrov PB, Considine JM, Izzi V, Naba A. Matrisome AnalyzeR - a suite of tools to annotate and quantify ECM molecules in big datasets across organisms. J Cell Sci 2023; 136:jcs261255. [PMID: 37555624 PMCID: PMC10499032 DOI: 10.1242/jcs.261255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 08/01/2023] [Indexed: 08/10/2023] Open
Abstract
The extracellular matrix (ECM) is a complex meshwork of proteins that forms the scaffold of all tissues in multicellular organisms. It plays crucial roles in all aspects of life - from orchestrating cell migration during development, to supporting tissue repair. It also plays critical roles in the etiology or progression of diseases. To study this compartment, we have previously defined the compendium of all genes encoding ECM and ECM-associated proteins for multiple organisms. We termed this compendium the 'matrisome' and further classified matrisome components into different structural or functional categories. This nomenclature is now largely adopted by the research community to annotate '-omics' datasets and has contributed to advance both fundamental and translational ECM research. Here, we report the development of Matrisome AnalyzeR, a suite of tools including a web-based application and an R package. The web application can be used by anyone interested in annotating, classifying and tabulating matrisome molecules in large datasets without requiring programming knowledge. The companion R package is available to more experienced users, interested in processing larger datasets or in additional data visualization options.
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Affiliation(s)
- Petar B. Petrov
- Infotech Institute, University of Oulu, FI-90014 Oulu, Finland
| | - James M. Considine
- Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL 60612, USA
| | - Valerio Izzi
- Faculty of Biochemistry and Molecular Medicine & Faculty of Medicine, BioIM Unit, University of Oulu, FI-90014 Oulu, Finland
- Foundation for the Finnish Cancer Institute, Tukholmankatu 8, Fl-00290 Helsinki, Finland
| | - Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL 60612, USA
- University of Illinois Cancer Center, Chicago, IL 60612, USA
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11
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Birnbaum SK, Cohen JD, Belfi A, Murray JI, Adams JRG, Chisholm AD, Sundaram MV. The proprotein convertase BLI-4 promotes collagen secretion prior to assembly of the Caenorhabditis elegans cuticle. PLoS Genet 2023; 19:e1010944. [PMID: 37721936 PMCID: PMC10538796 DOI: 10.1371/journal.pgen.1010944] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 09/28/2023] [Accepted: 08/30/2023] [Indexed: 09/20/2023] Open
Abstract
Some types of collagens, including transmembrane MACIT collagens and C. elegans cuticle collagens, are N-terminally cleaved at a dibasic site that resembles the consensus for furin or other proprotein convertases of the subtilisin/kexin (PCSK) family. Such cleavage may release transmembrane collagens from the plasma membrane and affect extracellular matrix assembly or structure. However, the functional consequences of such cleavage are unclear and evidence for the role of specific PCSKs is lacking. Here, we used endogenous collagen fusions to fluorescent proteins to visualize the secretion and assembly of the first collagen-based cuticle in C. elegans and then tested the role of the PCSK BLI-4 in these processes. Unexpectedly, we found that cuticle collagens SQT-3 and DPY-17 are secreted into the extraembryonic space several hours before cuticle matrix assembly. Furthermore, this early secretion depends on BLI-4/PCSK; in bli-4 and cleavage-site mutants, SQT-3 and DPY-17 are not efficiently secreted and instead form large intracellular puncta. Their later assembly into cuticle matrix is reduced but not entirely blocked. These data reveal a role for collagen N-terminal processing in intracellular trafficking and the control of matrix assembly in vivo. Our observations also prompt a revision of the classic model for C. elegans cuticle matrix assembly and the pre-cuticle-to-cuticle transition, suggesting that cuticle layer assembly proceeds via a series of regulated steps and not simply by sequential secretion and deposition.
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Affiliation(s)
- Susanna K. Birnbaum
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Jennifer D. Cohen
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Alexandra Belfi
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - John I. Murray
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Jennifer R. G. Adams
- Departments of Neurobiology and Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, San Diego, California, United States of America
| | - Andrew D. Chisholm
- Departments of Neurobiology and Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, San Diego, California, United States of America
| | - Meera V. Sundaram
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
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12
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Vroman R, Hunter RS, Wood MJ, Davis OC, Malfait Z, George DS, Ren D, Tavares-Ferreira D, Price TJ, Miller RJ, Malfait AM, Malfait F, Miller RE, Syx D. Analysis of matrisome expression patterns in murine and human dorsal root ganglia. Front Mol Neurosci 2023; 16:1232447. [PMID: 37664243 PMCID: PMC10471487 DOI: 10.3389/fnmol.2023.1232447] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/27/2023] [Indexed: 09/05/2023] Open
Abstract
The extracellular matrix (ECM) is a dynamic structure of molecules that can be divided into six different categories and are collectively called the matrisome. The ECM plays pivotal roles in physiological processes in many tissues, including the nervous system. Intriguingly, alterations in ECM molecules/pathways are associated with painful human conditions and murine pain models. Nevertheless, mechanistic insight into the interplay of normal or defective ECM and pain is largely lacking. The goal of this study was to integrate bulk, single-cell, and spatial RNA sequencing (RNAseq) datasets to investigate the expression and cellular origin of matrisome genes in male and female murine and human dorsal root ganglia (DRG). Bulk RNAseq showed that about 65% of all matrisome genes were expressed in both murine and human DRG, with proportionally more core matrisome genes (glycoproteins, collagens, and proteoglycans) expressed compared to matrisome-associated genes (ECM-affiliated genes, ECM regulators, and secreted factors). Single cell RNAseq on male murine DRG revealed the cellular origin of matrisome expression. Core matrisome genes, especially collagens, were expressed by fibroblasts whereas matrisome-associated genes were primarily expressed by neurons. Cell-cell communication network analysis with CellChat software predicted an important role for collagen signaling pathways in connecting vascular cell types and nociceptors in murine tissue, which we confirmed by analysis of spatial transcriptomic data from human DRG. RNAscope in situ hybridization and immunohistochemistry demonstrated expression of collagens in fibroblasts surrounding nociceptors in male and female human DRG. Finally, comparing human neuropathic pain samples with non-pain samples also showed differential expression of matrisome genes produced by both fibroblasts and by nociceptors. This study supports the idea that the DRG matrisome may contribute to neuronal signaling in both mouse and human, and that dysregulation of matrisome genes is associated with neuropathic pain.
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Affiliation(s)
- Robin Vroman
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Rahel S. Hunter
- Department of Internal Medicine, Division of Rheumatology, Rush University Medical Center, Chicago, IL, United States
| | - Matthew J. Wood
- Department of Internal Medicine, Division of Rheumatology, Rush University Medical Center, Chicago, IL, United States
| | - Olivia C. Davis
- Department of Neuroscience and Center for Advanced Pain Studies, University of Texas at Dallas, Richardson, TX, United States
| | - Zoë Malfait
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Dale S. George
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Dongjun Ren
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Diana Tavares-Ferreira
- Department of Neuroscience and Center for Advanced Pain Studies, University of Texas at Dallas, Richardson, TX, United States
| | - Theodore J. Price
- Department of Neuroscience and Center for Advanced Pain Studies, University of Texas at Dallas, Richardson, TX, United States
| | - Richard J. Miller
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Anne-Marie Malfait
- Department of Internal Medicine, Division of Rheumatology, Rush University Medical Center, Chicago, IL, United States
| | - Fransiska Malfait
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Rachel E. Miller
- Department of Internal Medicine, Division of Rheumatology, Rush University Medical Center, Chicago, IL, United States
| | - Delfien Syx
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University, Ghent, Belgium
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13
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Birnbaum SK, Cohen JD, Belfi A, Murray JI, Adams JRG, Chisholm AD, Sundaram MV. The proprotein convertase BLI-4 promotes collagen secretion during assembly of the Caenorhabditis elegans cuticle. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.06.542650. [PMID: 37333289 PMCID: PMC10274747 DOI: 10.1101/2023.06.06.542650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Some types of collagens, including transmembrane MACIT collagens and C. elegans cuticle collagens, are N-terminally cleaved at a dibasic site that resembles the consensus for furin or other proprotein convertases of the subtilisin/kexin (PCSK) family. Such cleavage may release transmembrane collagens from the plasma membrane and affect extracellular matrix assembly or structure. However, the functional consequences of such cleavage are unclear and evidence for the role of specific PCSKs is lacking. Here, we used endogenous collagen fusions to fluorescent proteins to visualize the secretion and assembly of the first collagen-based cuticle in C. elegans and then tested the role of the PCSK BLI-4 in these processes. Unexpectedly, we found that cuticle collagens SQT-3 and DPY-17 are secreted into the extraembryonic space several hours before cuticle matrix assembly. Furthermore, this early secretion depends on BLI-4/PCSK; in bli-4 and cleavage-site mutants, SQT-3 and DPY-17 are not efficiently secreted and instead form large intracellular aggregates. Their later assembly into cuticle matrix is reduced but not entirely blocked. These data reveal a role for collagen N-terminal processing in intracellular trafficking and in the spatial and temporal restriction of matrix assembly in vivo . Our observations also prompt a revision of the classic model for C. elegans cuticle matrix assembly and the pre-cuticle-to-cuticle transition, suggesting that cuticle layer assembly proceeds via a series of regulated steps and not simply by sequential secretion and deposition.
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Affiliation(s)
- Susanna K Birnbaum
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia PA
| | - Jennifer D Cohen
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia PA
| | - Alexandra Belfi
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia PA
| | - John I Murray
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia PA
| | - Jennifer R G Adams
- Departments of Neurobiology and Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, San Diego CA
| | - Andrew D Chisholm
- Departments of Neurobiology and Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, San Diego CA
| | - Meera V Sundaram
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia PA
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14
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Statzer C, Park JYC, Ewald CY. Extracellular Matrix Dynamics as an Emerging yet Understudied Hallmark of Aging and Longevity. Aging Dis 2023; 14:670-693. [PMID: 37191434 DOI: 10.14336/ad.2022.1116] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 11/16/2022] [Indexed: 05/17/2023] Open
Abstract
The biomechanical properties of extracellular matrices (ECM) and their consequences for cellular homeostasis have recently emerged as a driver of aging. Here we review the age-dependent deterioration of ECM in the context of our current understanding of the aging processes. We discuss the reciprocal interactions of longevity interventions with ECM remodeling. And the relevance of ECM dynamics captured by the matrisome and the matreotypes associated with health, disease, and longevity. Furthermore, we highlight that many established longevity compounds promote ECM homeostasis. A large body of evidence for the ECM to qualify as a hallmark of aging is emerging, and the data in invertebrates is promising. However, direct experimental proof that activating ECM homeostasis is sufficient to slow aging in mammals is lacking. We conclude that further research is required and anticipate that a conceptual framework for ECM biomechanics and homeostasis will provide new strategies to promote health during aging.
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Affiliation(s)
- Cyril Statzer
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, Schwerzenbach CH-8603, Switzerland
| | - Ji Young Cecilia Park
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, Schwerzenbach CH-8603, Switzerland
| | - Collin Y Ewald
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, Schwerzenbach CH-8603, Switzerland
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15
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Johnson LC, Vo AA, Clancy JC, Myles KM, Pooranachithra M, Aguilera J, Levenson MT, Wohlenberg C, Rechtsteiner A, Ragle JM, Chisholm AD, Ward JD. NHR-23 activity is necessary for C. elegans developmental progression and apical extracellular matrix structure and function. Development 2023; 150:dev201085. [PMID: 37129010 PMCID: PMC10233720 DOI: 10.1242/dev.201085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 04/11/2023] [Indexed: 05/03/2023]
Abstract
Nematode molting is a remarkable process where animals must repeatedly build a new apical extracellular matrix (aECM) beneath a previously built aECM that is subsequently shed. The nuclear hormone receptor NHR-23 (also known as NR1F1) is an important regulator of C. elegans molting. NHR-23 expression oscillates in the epidermal epithelium, and soma-specific NHR-23 depletion causes severe developmental delay and death. Tissue-specific RNAi suggests that nhr-23 acts primarily in seam and hypodermal cells. NHR-23 coordinates the expression of factors involved in molting, lipid transport/metabolism and remodeling of the aECM. NHR-23 depletion causes dampened expression of a nas-37 promoter reporter and a loss of reporter oscillation. The cuticle collagen ROL-6 and zona pellucida protein NOAH-1 display aberrant annular localization and severe disorganization over the seam cells after NHR-23 depletion, while the expression of the adult-specific cuticle collagen BLI-1 is diminished and frequently found in patches. Consistent with these localization defects, the cuticle barrier is severely compromised when NHR-23 is depleted. Together, this work provides insight into how NHR-23 acts in the seam and hypodermal cells to coordinate aECM regeneration during development.
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Affiliation(s)
- Londen C. Johnson
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - An A. Vo
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - John C. Clancy
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Krista M. Myles
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Murugesan Pooranachithra
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Joseph Aguilera
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Max T. Levenson
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Chloe Wohlenberg
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Andreas Rechtsteiner
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - James Matthew Ragle
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Andrew D. Chisholm
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Jordan D. Ward
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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16
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Petrov PB, Considine JM, Izzi V, Naba A. Matrisome AnalyzeR: A suite of tools to annotate and quantify ECM molecules in big datasets across organisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.18.537378. [PMID: 37131773 PMCID: PMC10153148 DOI: 10.1101/2023.04.18.537378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The extracellular matrix (ECM) is a complex meshwork of proteins that forms the scaffold of all tissues in multicellular organisms. It plays critical roles in all aspects of life: from orchestrating cell migration during development, to supporting tissue repair. It also plays critical roles in the etiology or progression of diseases. To study this compartment, we defined the compendium of all genes encoding ECM and ECM-associated proteins for multiple organisms. We termed this compendium the "matrisome" and further classified matrisome components into different structural or functional categories. This nomenclature is now largely adopted by the research community to annotate -omics datasets and has contributed to advance both fundamental and translational ECM research. Here, we report the development of Matrisome AnalyzeR, a suite of tools including a web-based application ( https://sites.google.com/uic.edu/matrisome/tools/matrisome-analyzer ) and an R package ( https://github.com/Matrisome/MatrisomeAnalyzeR ). The web application can be used by anyone interested in annotating, classifying, and tabulating matrisome molecules in large datasets without requiring programming knowledge. The companion R package is available to more experienced users, interested in processing larger datasets or in additional data visualization options. SUMMARY STATEMENT Matrisome AnalyzeR is a suite of tools, including a web-based app and an R package, designed to facilitate the annotation and quantification of extracellular matrix components in big datasets.
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Affiliation(s)
- Petar B. Petrov
- Infotech Institute, University of Oulu, FI-90014 Oulu, Finland
| | - James M. Considine
- Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL 60612, USA
| | - Valerio Izzi
- Faculty of Biochemistry and Molecular Medicine & Faculty of Medicine, BioIM Unit, University of Oulu, FI-90014 Oulu, Finland
- Foundation for the Finnish Cancer Institute, Tukholmankatu 8, Helsinki, Finland
| | - Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL 60612, USA
- University of Illinois Cancer Center, Chicago, IL 60612, USA
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17
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Goyala A, Ewald CY. CRISPR-activated expression of collagen col-120 increases lifespan and heat tolerance. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000730. [PMID: 37122503 PMCID: PMC10133990 DOI: 10.17912/micropub.biology.000730] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 04/05/2023] [Accepted: 04/11/2023] [Indexed: 05/02/2023]
Abstract
Transgenic overexpression of collagen col-120 increases the lifespan of C. elegans . However, whether post-developmental enhancement of collagen expression could also increase the lifespan is unknown. Recently, we described a method to induce the expression of a target gene using catalytically dead Cas9 (dCas9)-engineered C. elegans via ingestion of bacteria expressing a pair of promoter-specific single guide RNAs (sgRNA). Here, we cloned col-120 promoter-specific sgRNA oligo pair into L4440-Biobrick-sgRNA and fed these bacteria to dCas9::VP64 transgenic C. elegans . We observed a similar percentage of lifespan extension by post-developmentally dCas9-induced expression of col-120 , as previously reported through transgenic overexpression of col-120 . Consistent with this result is that induction of another previously shown longevity-promoting collagen, col-10 , also increased lifespan. Furthermore, we found an enhanced resilience to heat stress and increased expression of hsp-16.2 upon dCas9-activated col-120 expression. Together, these results provide an orthogonal method to validate longevity by enhancing col-120 expression and point towards a potential role of collagen enhancement in thermotolerance.
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Affiliation(s)
- Anita Goyala
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, Schwerzenbach CH-8603, Switzerland
| | - Collin Y. Ewald
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, Schwerzenbach CH-8603, Switzerland
- Correspondence to: Collin Y. Ewald (
)
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18
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Yücel D. Ketamine induces apical extracellular matrix modifications in Caenorhabditis elegans. Sci Rep 2022; 12:22122. [PMID: 36543791 PMCID: PMC9772317 DOI: 10.1038/s41598-022-24632-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 11/17/2022] [Indexed: 12/24/2022] Open
Abstract
Ketamine is a widely used anesthetic agent since 1960s and has recently been exploited for its rapid antidepressant action at subanesthetic doses. It has been demonstrated that ketamine induces alterations in extracellular matrix (ECM) in rodent models which in part plays a role in its anti-depressant action. The nematode Caenorhabditis elegans serves as a powerful tool for understanding mechanisms of drug action with its short life cycle, genetic amenability and conserved cellular processes. Further investigation is required particularly in in vivo systems to gain broader understanding of ketamine's actions. In this study, we aimed to decipher ketamine-mediated alterations using C. elegans as a model. We show that ketamine specifically induces apical extracellular matrix modifications (aECM) in the vulva and the cuticle. Ketamine treatment phenocopies neuronal migration and vulval invagination defects of chondroitin mutants despite wild-type like chondroitin staining pattern. Normal vulval expansion and defective vulval eversion phenotypes of ketamine-treated animals are suggestive of alterations in the network of aECM factors which do not impinge on chondroitin. Ketamine ameliorates impaired movement of a group of roller mutants characterised with collagen defects in the cuticle and RNA-seq identifies that 30% of the cuticular collagens are upregulated in response to ketamine. Ketamine alters aECM, neuronal migration and collagen expression in C. elegans. We propose C. elegans as a putative animal model to investigate ketamine-mediated ECM modifications.
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Affiliation(s)
- Duygu Yücel
- grid.411739.90000 0001 2331 2603Genome and Stem Cell Center (GENKOK), Erciyes University, 38039 Melikgazi, Kayseri Turkey
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19
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Further Extension of Lifespan by Unc-43/CaMKII and Egl-8/PLCβ Mutations in Germline-Deficient Caenorhabditis elegans. Cells 2022; 11:cells11223527. [PMID: 36428956 PMCID: PMC9688844 DOI: 10.3390/cells11223527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/30/2022] [Accepted: 11/05/2022] [Indexed: 11/09/2022] Open
Abstract
Reduction of insulin/insulin-like growth factor 1 (IGF1) signaling (IIS) promotes longevity across species. In the nematode Caenorhabditis elegans, ablation of germline stem cells (GSCs) and activity changes of the conserved signaling mediators unc-43/CaMKII (calcium/calmodulin-dependent kinase type II) and egl-8/PLCβ (phospholipase Cβ) also increase lifespan. Like IIS, these pathways depend on the conserved transcription factor daf-16/FOXO for lifespan extension, but how they functionally interact is unknown. Here, we show that altered unc-43/egl-8 activity further increases the lifespan of long-lived GSC-deficient worms, but not of worms that are long-lived due to a strong reduction-of-function mutation in the insulin/IGF1-like receptor daf-2. Additionally, we provide evidence for unc-43 and, to a lesser extent, egl-8 modulating the expression of certain collagen genes, which were reported to be dispensable for longevity of these particular daf-2 mutant worms, but not for other forms of longevity. Together, these results provide new insights into the conditions and potential mechanisms by which CaMKII- and PLCβ-signals modulate C. elegans lifespan.
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20
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Betschart B, Bisoffi M, Alaeddine F. Identification and characterization of epicuticular proteins of nematodes sharing motifs with cuticular proteins of arthropods. PLoS One 2022; 17:e0274751. [PMID: 36301857 PMCID: PMC9612446 DOI: 10.1371/journal.pone.0274751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 09/05/2022] [Indexed: 11/18/2022] Open
Abstract
Specific collagens and insoluble proteins called cuticlins are major constituents of the nematode cuticles. The epicuticle, which forms the outermost electron-dense layer of the cuticle, is composed of another category of insoluble proteins called epicuticlins. It is distinct from the insoluble cuticlins localized in the cortical layer and the fibrous ribbon underneath lateral alae. Our objective was to identify and characterize genes and their encoded proteins forming the epicuticle. The combination between previously obtained laboratory results and recently made available data through the whole-genome shotgun contigs (WGS) and the transcriptome Shotgun Assembly (TSA) sequencing projects of Ascaris suum allowed us to identify the first epicuticlin gene, Asu-epic-1, on the chromosome VI. This gene is formed of exon1 (55 bp) and exon2 (1067 bp), separated by an intron of 1593 bp. Exon 2 is formed of tandem repeats (TR) whose number varies in different cDNA and genomic clones of Asu-epic-1. These variations could be due to slippage of the polymerases during DNA replication and RNA transcription leading to insertions and deletions (Indels). The deduced protein, Asu-EPIC-1, consists of a signal peptide of 20 amino acids followed by 353 amino acids composed of seven TR of 49 or 51 amino acids each. Three highly conserved tyrosine motifs characterize each repeat. The GYR motif is the Pfam motif PF02756 present in several cuticular proteins of arthropods. Asu-EPIC-1 is an intrinsically disordered protein (IDP) containing seven predicted molecular recognition features (MoRFs). This type of protein undergoes a disorder-to-order transition upon binding protein partners. Three epicuticular sequences have been identified in A. suum, Ascaris lumbricoides, and Toxocara canis. Homologous epicuticular proteins were identified in over 50 other nematode species. The potential of this new category of proteins in forming the nematode cuticle through covalent interactions with other cuticular components, particularly with collagens, is discussed. Their localization in the outermost layer of the nematode body and their unique structure render them crucial candidates for biochemical and molecular interaction studies and targets for new biotechnological and biomedical applications.
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Affiliation(s)
- Bruno Betschart
- Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- * E-mail:
| | - Marco Bisoffi
- Chemistry and Biochemistry, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Ferial Alaeddine
- Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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21
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A pan-cancer analysis of matrisome proteins reveals CTHRC1 and a related network as major ECM regulators across cancers. PLoS One 2022; 17:e0270063. [PMID: 36190948 PMCID: PMC9529084 DOI: 10.1371/journal.pone.0270063] [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: 02/04/2022] [Accepted: 06/02/2022] [Indexed: 11/07/2022] Open
Abstract
The extracellular matrix in the tumour microenvironment can regulate cancer cell growth and progression. A pan-cancer analysis of TCGA data from 30 cancer types, identified the top 5% of matrisome genes with amplifications or deletions in their copy number, that affect their expression and cancer survival. A similar analysis of matrisome genes in individual cancers identified CTHRC1 to be significantly altered. CTHRC1, a regulator of collagen synthesis, was identified as the most prominently upregulated matrisome gene of interest across cancers. Differential gene expression analysis identified 19 genes whose expression is increased with CTHRC1. STRING analysis of these genes classified them as ‘extracellular’, involved most prominently in ECM organization and cell adhesion. KEGG analysis showed their involvement in ECM-receptor and growth factor signalling. Cytohubba analysis of these genes revealed 13 hub genes, of which MMP13, POSTN, SFRP4, ADAMTS16 and FNDC1 were significantly altered in their expression with CTHRC1 and seen to affect survival across cancers. This could in part be mediated by their overlapping roles in regulating ECM (collagen or fibronectin) expression and organisation. In breast cancer tumour samples CTHRC1 protein levels are significantly upregulated with POSTN and MMP13, further supporting the need to evaluate their crosstalk in cancers.
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22
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Vidović T, Ewald CY. Longevity-Promoting Pathways and Transcription Factors Respond to and Control Extracellular Matrix Dynamics During Aging and Disease. FRONTIERS IN AGING 2022; 3:935220. [PMID: 35874275 PMCID: PMC9301135 DOI: 10.3389/fragi.2022.935220] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 05/27/2022] [Indexed: 05/28/2023]
Abstract
Aging is one of the largest risk factors for cancer, type 2 diabetes, osteoarthritis, cardiovascular diseases, and other age-related pathologies. Here, we give a detailed description of the interplay of chronic age-related pathologies with the remodeling of the extracellular matrix during disease development and progression. Longevity-promoting signaling pathways slow or prevent age-related diseases. In particular, we focus on the mTOR signaling pathway, sirtuins, and canonical longevity-promoting transcription factors, such as FOXO, NF-κB, and Nrf2. We extend our analysis using chromatin immunoprecipitation (ChIP) sequencing and transcriptomic data and report that many established and emerging longevity-promoting transcription factors, such as CREB1, FOXO1,3, GATA1,2,3,4, HIF1A, JUN, KLF4, MYC, NFE2L2/Nrf2, RELA/NF-κB, REST, STAT3,5A, and TP53/p53, directly regulate many extracellular matrix genes and remodelers. We propose that modulation of these pathways increases lifespan and protects from age-related diseases in part due to their effects on extracellular matrix remodeling. Therefore, to successfully treat age-related diseases, it is necessary to better understand the connection between extracellular matrix components and longevity pathways.
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Affiliation(s)
| | - Collin Y. Ewald
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
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23
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Jayadev R, Morais MRPT, Ellingford JM, Srinivasan S, Naylor RW, Lawless C, Li AS, Ingham JF, Hastie E, Chi Q, Fresquet M, Koudis NM, Thomas HB, O’Keefe RT, Williams E, Adamson A, Stuart HM, Banka S, Smedley D, Sherwood DR, Lennon R. A basement membrane discovery pipeline uncovers network complexity, regulators, and human disease associations. SCIENCE ADVANCES 2022; 8:eabn2265. [PMID: 35584218 PMCID: PMC9116610 DOI: 10.1126/sciadv.abn2265] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 03/22/2022] [Indexed: 05/17/2023]
Abstract
Basement membranes (BMs) are ubiquitous extracellular matrices whose composition remains elusive, limiting our understanding of BM regulation and function. By developing a bioinformatic and in vivo discovery pipeline, we define a network of 222 human proteins and their animal orthologs localized to BMs. Network analysis and screening in C. elegans and zebrafish uncovered BM regulators, including ADAMTS, ROBO, and TGFβ. More than 100 BM network genes associate with human phenotypes, and by screening 63,039 genomes from families with rare disorders, we found loss-of-function variants in LAMA5, MPZL2, and MATN2 and show that they regulate BM composition and function. This cross-disciplinary study establishes the immense complexity of BMs and their impact on in human health.
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Affiliation(s)
- Ranjay Jayadev
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Mychel R. P. T. Morais
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Jamie M. Ellingford
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester M13 9WL, UK
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Sandhya Srinivasan
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Richard W. Naylor
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Craig Lawless
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Anna S. Li
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Jack F. Ingham
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Eric Hastie
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Qiuyi Chi
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Maryline Fresquet
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Nikki-Maria Koudis
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Huw B. Thomas
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Raymond T. O’Keefe
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Emily Williams
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Antony Adamson
- Genome Editing Unit Core Facility, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Helen M. Stuart
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester M13 9WL, UK
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester M13 9WL, UK
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Damian Smedley
- William Harvey Research Institute, Charterhouse Square, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, EC1M 6BQ London, UK
| | - Genomics England Research Consortium
- William Harvey Research Institute, Charterhouse Square, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, EC1M 6BQ London, UK
- Genomics England, London, UK
| | - David R. Sherwood
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Rachel Lennon
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
- Department of Paediatric Nephrology, Royal Manchester Children’s Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9WL, UK
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Abstract
INTRODUCTION The matrisome and adhesome comprise proteins that are found within or are associated with the extracellular matrix (ECM) and adhesion complexes, respectively. Interactions between cells and their microenvironment are mediated by key matrisome and adhesome proteins, which direct fundamental processes, including growth and development. Due to their underlying complexity, it has historically been challenging to undertake mass spectrometry (MS)-based profiling of these proteins. New developments in sample preparative workflows, informatics databases, and MS techniques have enabled in-depth proteomic characterization of the matrisome and adhesome, resulting in a comprehensive understanding of the interactomes, and cellular signaling that occur at the cell-ECM interface. AREA COVERED This review summarizes recent advances in proteomic characterization of the matrisome and adhesome. It focuses on the importance of curated databases and discusses key strengths and limitations of different workflows. EXPERT OPINION MS-based proteomics has shown promise in characterizing the matrisome and topology of adhesome networks in health and disease. Moving forward, it will be important to incorporate integrative analysis to define the bidirectional signaling between the matrisome and adhesome, and adopt new methods for post-translational modification and in vivo analyses to better dissect the critical roles that these proteins play in human pathophysiology.
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Affiliation(s)
- Lukas Krasny
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Paul H Huang
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
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25
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Statzer C, Jongsma E, Liu SX, Dakhovnik A, Wandrey F, Mozharovskyi P, Zülli F, Ewald CY. Youthful and age-related matreotypes predict drugs promoting longevity. Aging Cell 2021; 20:e13441. [PMID: 34346557 PMCID: PMC8441316 DOI: 10.1111/acel.13441] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 06/16/2021] [Accepted: 07/08/2021] [Indexed: 12/19/2022] Open
Abstract
The identification and validation of drugs that promote health during aging ("geroprotectors") are key to the retardation or prevention of chronic age-related diseases. Here, we found that most of the established pro-longevity compounds shown to extend lifespan in model organisms also alter extracellular matrix gene expression (i.e., matrisome) in human cell lines. To harness this observation, we used age-stratified human transcriptomes to define the age-related matreotype, which represents the matrisome gene expression pattern associated with age. Using a "youthful" matreotype, we screened in silico for geroprotective drug candidates. To validate drug candidates, we developed a novel tool using prolonged collagen expression as a non-invasive and in-vivo surrogate marker for Caenorhabditis elegans longevity. With this reporter, we were able to eliminate false-positive drug candidates and determine the appropriate dose for extending the lifespan of C. elegans. We improved drug uptake for one of our predicted compounds, genistein, and reconciled previous contradictory reports of its effects on longevity. We identified and validated new compounds, tretinoin, chondroitin sulfate, and hyaluronic acid, for their ability to restore age-related decline of collagen homeostasis and increase lifespan. Thus, our innovative drug screening approach-employing extracellular matrix homeostasis-facilitates the discovery of pharmacological interventions promoting healthy aging.
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Affiliation(s)
- Cyril Statzer
- Department of Health Sciences and TechnologyInstitute of Translational MedicineEidgenössische Technische Hochschule ZürichSchwerzenbach‐ZürichSwitzerland
| | - Elisabeth Jongsma
- Department of Health Sciences and TechnologyInstitute of Translational MedicineEidgenössische Technische Hochschule ZürichSchwerzenbach‐ZürichSwitzerland
| | - Sean X. Liu
- Department of Health Sciences and TechnologyInstitute of Translational MedicineEidgenössische Technische Hochschule ZürichSchwerzenbach‐ZürichSwitzerland
| | - Alexander Dakhovnik
- Department of Health Sciences and TechnologyInstitute of Translational MedicineEidgenössische Technische Hochschule ZürichSchwerzenbach‐ZürichSwitzerland
| | | | | | - Fred Zülli
- Mibelle Biochemistry, Mibelle AGBuchsSwitzerland
| | - Collin Y. Ewald
- Department of Health Sciences and TechnologyInstitute of Translational MedicineEidgenössische Technische Hochschule ZürichSchwerzenbach‐ZürichSwitzerland
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26
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Hayes AJ, Melrose J. Neural Tissue Homeostasis and Repair Is Regulated via CS and DS Proteoglycan Motifs. Front Cell Dev Biol 2021; 9:696640. [PMID: 34409033 PMCID: PMC8365427 DOI: 10.3389/fcell.2021.696640] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/13/2021] [Indexed: 01/04/2023] Open
Abstract
Chondroitin sulfate (CS) is the most abundant and widely distributed glycosaminoglycan (GAG) in the human body. As a component of proteoglycans (PGs) it has numerous roles in matrix stabilization and cellular regulation. This chapter highlights the roles of CS and CS-PGs in the central and peripheral nervous systems (CNS/PNS). CS has specific cell regulatory roles that control tissue function and homeostasis. The CNS/PNS contains a diverse range of CS-PGs which direct the development of embryonic neural axonal networks, and the responses of neural cell populations in mature tissues to traumatic injury. Following brain trauma and spinal cord injury, a stabilizing CS-PG-rich scar tissue is laid down at the defect site to protect neural tissues, which are amongst the softest tissues of the human body. Unfortunately, the CS concentrated in gliotic scars also inhibits neural outgrowth and functional recovery. CS has well known inhibitory properties over neural behavior, and animal models of CNS/PNS injury have demonstrated that selective degradation of CS using chondroitinase improves neuronal functional recovery. CS-PGs are present diffusely in the CNS but also form denser regions of extracellular matrix termed perineuronal nets which surround neurons. Hyaluronan is immobilized in hyalectan CS-PG aggregates in these perineural structures, which provide neural protection, synapse, and neural plasticity, and have roles in memory and cognitive learning. Despite the generally inhibitory cues delivered by CS-A and CS-C, some CS-PGs containing highly charged CS disaccharides (CS-D, CS-E) or dermatan sulfate (DS) disaccharides that promote neural outgrowth and functional recovery. CS/DS thus has varied cell regulatory properties and structural ECM supportive roles in the CNS/PNS depending on the glycoform present and its location in tissue niches and specific cellular contexts. Studies on the fruit fly, Drosophila melanogaster and the nematode Caenorhabditis elegans have provided insightful information on neural interconnectivity and the role of the ECM and its PGs in neural development and in tissue morphogenesis in a whole organism environment.
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Affiliation(s)
- Anthony J. Hayes
- Bioimaging Research Hub, Cardiff School of Biosciences, Cardiff University, Wales, United Kingdom
| | - James Melrose
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW, Australia
- Raymond Purves Bone and Joint Research Laboratories, Kolling Institute of Medical Research, Royal North Shore Hospital and The Faculty of Medicine and Health, The University of Sydney, St. Leonard’s, NSW, Australia
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27
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Sacher F, Feregrino C, Tschopp P, Ewald CY. Extracellular matrix gene expression signatures as cell type and cell state identifiers. Matrix Biol Plus 2021; 10:100069. [PMID: 34195598 PMCID: PMC8233473 DOI: 10.1016/j.mbplus.2021.100069] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/06/2021] [Accepted: 05/06/2021] [Indexed: 02/07/2023] Open
Abstract
Transcriptomic signatures based on cellular mRNA expression profiles can be used to categorize cell types and states. Yet whether different functional groups of genes perform better or worse in this process remains largely unexplored. Here we test the core matrisome - that is, all genes coding for structural proteins of the extracellular matrix - for its ability to delineate distinct cell types in embryonic single-cell RNA-sequencing (scRNA-seq) data. We show that even though expressed core matrisome genes correspond to less than 2% of an entire cellular transcriptome, their RNA expression levels suffice to recapitulate essential aspects of cell type-specific clustering. Notably, using scRNA-seq data from the embryonic limb, we demonstrate that core matrisome gene expression outperforms random gene subsets of similar sizes and can match and exceed the predictive power of transcription factors. While transcription factor signatures generally perform better in predicting cell types at early stages of chicken and mouse limb development, i.e., when cells are less differentiated, the information content of the core matrisome signature increases in more differentiated cells. Moreover, using cross-species analyses, we show that these cell type-specific signatures are evolutionarily conserved. Our findings suggest that each cell type produces its own unique extracellular matrix, or matreotype, which becomes progressively more refined and cell type-specific as embryonic tissues mature.
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Affiliation(s)
- Fabio Sacher
- Laboratory of Regulatory Evolution, DUW Zoology, University of Basel, Basel CH-4051, Switzerland
| | - Christian Feregrino
- Laboratory of Regulatory Evolution, DUW Zoology, University of Basel, Basel CH-4051, Switzerland
| | - Patrick Tschopp
- Laboratory of Regulatory Evolution, DUW Zoology, University of Basel, Basel CH-4051, Switzerland
| | - Collin Y. Ewald
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, Schwerzenbach CH-8603, Switzerland
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28
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Neill T, Kapoor A, Xie C, Buraschi S, Iozzo RV. A functional outside-in signaling network of proteoglycans and matrix molecules regulating autophagy. Matrix Biol 2021; 100-101:118-149. [PMID: 33838253 PMCID: PMC8355044 DOI: 10.1016/j.matbio.2021.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 02/07/2023]
Abstract
Proteoglycans and selected extracellular matrix constituents are emerging as intrinsic and critical regulators of evolutionarily conversed, intracellular catabolic pathways. Often, these secreted molecules evoke sustained autophagy in a variety of cell types, tissues, and model systems. The unique properties of proteoglycans have ushered in a paradigmatic shift to broaden our understanding of matrix-mediated signaling cascades. The dynamic cellular pathway controlling autophagy is now linked to an equally dynamic and fluid signaling network embedded in a complex meshwork of matrix molecules. A rapidly emerging field of research encompasses multiple matrix-derived candidates, representing a menagerie of soluble matrix constituents including decorin, biglycan, endorepellin, endostatin, collagen VI and plasminogen kringle 5. These matrix constituents are pro-autophagic and simultaneously anti-angiogenic. In contrast, perlecan, laminin α2 chain, and lumican have anti-autophagic functions. Mechanistically, each matrix constituent linked to intracellular catabolic events engages a specific cell surface receptor that often converges on a common core of the autophagic machinery including AMPK, Peg3 and Beclin 1. We consider this matrix-evoked autophagy as non-canonical given that it occurs in an allosteric manner and is independent of nutrient availability or prevailing bioenergetics control. We propose that matrix-regulated autophagy is an important outside-in signaling mechanism for proper tissue homeostasis that could be therapeutically leveraged to combat a variety of diseases.
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Affiliation(s)
- Thomas Neill
- Department of Pathology, Anatomy, and Cell Biology, and the Translational Cellular Oncology Program, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA.
| | - Aastha Kapoor
- Department of Pathology, Anatomy, and Cell Biology, and the Translational Cellular Oncology Program, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Christopher Xie
- Department of Pathology, Anatomy, and Cell Biology, and the Translational Cellular Oncology Program, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Simone Buraschi
- Department of Pathology, Anatomy, and Cell Biology, and the Translational Cellular Oncology Program, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Renato V Iozzo
- Department of Pathology, Anatomy, and Cell Biology, and the Translational Cellular Oncology Program, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA.
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29
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Sandhu A, Badal D, Sheokand R, Tyagi S, Singh V. Specific collagens maintain the cuticle permeability barrier in Caenorhabditis elegans. Genetics 2021; 217:iyaa047. [PMID: 33789349 PMCID: PMC8045729 DOI: 10.1093/genetics/iyaa047] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 12/05/2020] [Indexed: 01/01/2023] Open
Abstract
Collagen-enriched cuticle forms the outermost layer of skin in nematode Caenorhabditis elegans. The nematode's genome encodes 177 collagens, but little is known about their role in maintaining the structure or barrier function of the cuticle. In this study, we found six permeability determining (PD) collagens. Loss of any of these PD collagens-DPY-2, DPY-3, DPY-7, DPY-8, DPY-9, and DPY-10-led to enhanced susceptibility of nematodes to paraquat (PQ) and antihelminthic drugs- levamisole and ivermectin. Upon exposure to PQ, PD collagen mutants accumulated more PQ and incurred more damage and death despite the robust activation of antioxidant machinery. We find that BLMP-1, a zinc finger transcription factor, maintains the barrier function of the cuticle by regulating the expression of PD collagens. We show that the permeability barrier maintained by PD collagens acts in parallel to FOXO transcription factor DAF-16 to enhance survival of insulin-like receptor mutant, daf-2. In all, this study shows that PD collagens regulate cuticle permeability by maintaining the structure of C. elegans cuticle and thus provide protection against exogenous toxins.
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Affiliation(s)
- Anjali Sandhu
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore 560012, India
| | - Divakar Badal
- Center for Biosystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Riya Sheokand
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore 560012, India
| | - Shalini Tyagi
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore 560012, India
| | - Varsha Singh
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore 560012, India
- Center for Biosystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
- Lead contact
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30
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Karamanos NK, Theocharis AD, Piperigkou Z, Manou D, Passi A, Skandalis SS, Vynios DH, Orian-Rousseau V, Ricard-Blum S, Schmelzer CEH, Duca L, Durbeej M, Afratis NA, Troeberg L, Franchi M, Masola V, Onisto M. A guide to the composition and functions of the extracellular matrix. FEBS J 2021; 288:6850-6912. [PMID: 33605520 DOI: 10.1111/febs.15776] [Citation(s) in RCA: 312] [Impact Index Per Article: 104.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/13/2021] [Accepted: 02/18/2021] [Indexed: 12/13/2022]
Abstract
Extracellular matrix (ECM) is a dynamic 3-dimensional network of macromolecules that provides structural support for the cells and tissues. Accumulated knowledge clearly demonstrated over the last decade that ECM plays key regulatory roles since it orchestrates cell signaling, functions, properties and morphology. Extracellularly secreted as well as cell-bound factors are among the major members of the ECM family. Proteins/glycoproteins, such as collagens, elastin, laminins and tenascins, proteoglycans and glycosaminoglycans, hyaluronan, and their cell receptors such as CD44 and integrins, responsible for cell adhesion, comprise a well-organized functional network with significant roles in health and disease. On the other hand, enzymes such as matrix metalloproteinases and specific glycosidases including heparanase and hyaluronidases contribute to matrix remodeling and affect human health. Several cell processes and functions, among them cell proliferation and survival, migration, differentiation, autophagy, angiogenesis, and immunity regulation are affected by certain matrix components. Structural alterations have been also well associated with disease progression. This guide on the composition and functions of the ECM gives a broad overview of the matrisome, the major ECM macromolecules, and their interaction networks within the ECM and with the cell surface, summarizes their main structural features and their roles in tissue organization and cell functions, and emphasizes the importance of specific ECM constituents in disease development and progression as well as the advances in molecular targeting of ECM to design new therapeutic strategies.
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Affiliation(s)
- Nikos K Karamanos
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, Greece.,Foundation for Research and Technology-Hellas (FORTH)/Institute of Chemical Engineering Sciences (ICE-HT), Patras, Greece
| | - Achilleas D Theocharis
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, Greece
| | - Zoi Piperigkou
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, Greece.,Foundation for Research and Technology-Hellas (FORTH)/Institute of Chemical Engineering Sciences (ICE-HT), Patras, Greece
| | - Dimitra Manou
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, Greece
| | - Alberto Passi
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Spyros S Skandalis
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, Greece
| | - Demitrios H Vynios
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, Greece
| | - Véronique Orian-Rousseau
- Karlsruhe Institute of Technology, Institute of Biological and Chemical Systems- Functional Molecular Systems, Eggenstein-Leopoldshafen, Germany
| | - Sylvie Ricard-Blum
- University of Lyon, UMR 5246, ICBMS, Université Lyon 1, CNRS, Villeurbanne Cedex, France
| | - Christian E H Schmelzer
- Fraunhofer Institute for Microstructure of Materials and Systems IMWS, Halle (Saale), Germany.,Institute of Pharmacy, Faculty of Natural Sciences I, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Laurent Duca
- UMR CNRS 7369 Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Team 2: Matrix Aging and Vascular Remodelling, Université de Reims Champagne Ardenne (URCA), UFR Sciences Exactes et Naturelles, Reims, France
| | - Madeleine Durbeej
- Department of Experimental Medical Science, Unit of Muscle Biology, Lund University, Sweden
| | - Nikolaos A Afratis
- Department Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Linda Troeberg
- Norwich Medical School, University of East Anglia, Bob Champion Research and Education Building, Norwich, UK
| | - Marco Franchi
- Department for Life Quality Study, University of Bologna, Rimini, Italy
| | | | - Maurizio Onisto
- Department of Biomedical Sciences, University of Padova, Italy
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31
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Zhang Z, Luo S, Barbosa GO, Bai M, Kornberg TB, Ma DK. The conserved transmembrane protein TMEM-39 coordinates with COPII to promote collagen secretion and regulate ER stress response. PLoS Genet 2021; 17:e1009317. [PMID: 33524011 PMCID: PMC7901769 DOI: 10.1371/journal.pgen.1009317] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 02/23/2021] [Accepted: 12/22/2020] [Indexed: 12/22/2022] Open
Abstract
Dysregulation of collagen production and secretion contributes to aging and tissue fibrosis of major organs. How procollagen proteins in the endoplasmic reticulum (ER) route as specialized cargos for secretion remains to be fully elucidated. Here, we report that TMEM39, an ER-localized transmembrane protein, regulates production and secretory cargo trafficking of procollagen. We identify the C. elegans ortholog TMEM-39 from an unbiased RNAi screen and show that deficiency of tmem-39 leads to striking defects in cuticle collagen production and constitutively high ER stress response. RNAi knockdown of the tmem-39 ortholog in Drosophila causes similar defects in collagen secretion from fat body cells. The cytosolic domain of human TMEM39A binds to Sec23A, a vesicle coat protein that drives collagen secretion and vesicular trafficking. TMEM-39 regulation of collagen secretion is independent of ER stress response and autophagy. We propose that the roles of TMEM-39 in collagen secretion and ER homeostasis are likely evolutionarily conserved. As the most abundant protein in animals, collagen plays diverse roles and its dysregulation impacts aging and many fibrotic disorders. It is important to understand how premature collagen proteins in the ER are processed and secreted, as many other aspects of collagen regulation have been elucidated in mechanistic detail. In this paper, we have characterized a novel conserved family of TMEM39 proteins, including human TMEM39A and C. elegans tmem-39 that regulates ER stress response and collagen secretion. Human TMEM39A directly interacts with SEC23A, a core component of the COPII vesicle coating complex responsible for vesicular cargo secretion to the Golgi apparatus. The function of TMEM-39 proteins in collagen secretion appears highly conserved and independent to the ER stress response and the autophagy pathway. Our results provide insights into functions and mechanisms of TMEM39 proteins in collagen secretion and suggest it as a plausible target for tissue fibrotic diseases.
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Affiliation(s)
- Zhe Zhang
- School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (ZZ); (DKM)
| | - Shuo Luo
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California, United States of America
| | - Guilherme Oliveira Barbosa
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California, United States of America
| | - Meirong Bai
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California, United States of America
| | - Thomas B. Kornberg
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California, United States of America
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Dengke K. Ma
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California, United States of America
- Department of Physiology, University of California San Francisco, San Francisco, California, United States of America
- Innovative Genomics Institute, Berkeley, California, United States of America
- * E-mail: (ZZ); (DKM)
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32
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Li Zheng S, Adams JG, Chisholm AD. Form and function of the apical extracellular matrix: new insights from Caenorhabditis elegans, Drosophila melanogaster, and the vertebrate inner ear. Fac Rev 2020; 9:27. [PMID: 33659959 PMCID: PMC7886070 DOI: 10.12703/r/9-27] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Apical extracellular matrices (aECMs) are the extracellular layers on the apical sides of epithelia. aECMs form the outer layer of the skin in most animals and line the luminal surface of internal tubular epithelia. Compared to the more conserved basal ECMs (basement membranes), aECMs are highly diverse between tissues and between organisms and have been more challenging to understand at mechanistic levels. Studies in several genetic model organisms are revealing new insights into aECM composition, biogenesis, and function and have begun to illuminate common principles and themes of aECM organization. There is emerging evidence that, in addition to mechanical or structural roles, aECMs can participate in reciprocal signaling with associated epithelia and other cell types. Studies are also revealing mechanisms underlying the intricate nanopatterns exhibited by many aECMs. In this review, we highlight recent findings from well-studied model systems, including the external cuticle and ductal aECMs of Caenorhabditis elegans, Drosophila melanogaster, and other insects and the internal aECMs of the vertebrate inner ear.
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Affiliation(s)
- Sherry Li Zheng
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Jennifer Gotenstein Adams
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Andrew D Chisholm
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
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Noble LM, Miah A, Kaur T, Rockman MV. The Ancestral Caenorhabditis elegans Cuticle Suppresses rol-1. G3 (BETHESDA, MD.) 2020; 10:2385-2395. [PMID: 32423919 PMCID: PMC7341120 DOI: 10.1534/g3.120.401336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/09/2020] [Indexed: 12/30/2022]
Abstract
Genetic background commonly modifies the effects of mutations. We discovered that worms mutant for the canonical rol-1 gene, identified by Brenner in 1974, do not roll in the genetic background of the wild strain CB4856. Using linkage mapping, association analysis and gene editing, we determined that N2 carries an insertion in the collagen gene col-182 that acts as a recessive enhancer of rol-1 rolling. From population and comparative genomics, we infer the insertion is derived in N2 and related laboratory lines, likely arising during the domestication of Caenorhabditis elegans, and breaking a conserved protein. The ancestral version of col-182 also modifies the phenotypes of four other classical cuticle mutant alleles, and the effects of natural genetic variation on worm shape and locomotion. These results underscore the importance of genetic background and the serendipity of Brenner's choice of strain.
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Affiliation(s)
- Luke M Noble
- Institut de Biologie, École Normale Supérieure, CNRS 8197, Inserm U1024, PSL Research University, F-75005 Paris, France
| | - Asif Miah
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, 10003
| | - Taniya Kaur
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, 10003
| | - Matthew V Rockman
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, 10003
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Mesbahi H, Pho KB, Tench AJ, Leon Guerrero VL, MacNeil LT. Cuticle Collagen Expression Is Regulated in Response to Environmental Stimuli by the GATA Transcription Factor ELT-3 in Caenorhabditis elegans. Genetics 2020; 215:483-495. [PMID: 32229533 PMCID: PMC7268988 DOI: 10.1534/genetics.120.303125] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 03/23/2020] [Indexed: 12/21/2022] Open
Abstract
The nematode Caenorhabditis elegans is protected from the environment by the cuticle, an extracellular collagen-based matrix that encloses the animal. Over 170 cuticular collagens are predicted in the C. elegans genome, but the role of each individual collagen is unclear. Stage-specific specialization of the cuticle explains the need for some collagens; however, the large number of collagens suggests that specialization of the cuticle may also occur in response to other environmental triggers. Missense mutations in many collagen genes can disrupt cuticle morphology, producing a helically twisted body causing the animal to move in a stereotypical pattern described as rolling. We find that environmental factors, including diet, early developmental arrest, and population density can differentially influence the penetrance of rolling in these mutants. These effects are in part due to changes in collagen gene expression that are mediated by the GATA family transcription factor ELT-3 We propose a model by which ELT-3 regulates collagen gene expression in response to environmental stimuli to promote the assembly of a cuticle specialized to a given environment.
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Affiliation(s)
- Hiva Mesbahi
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8S 4K1
| | - Kim B Pho
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8S 4K1
| | - Andrea J Tench
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8S 4K1
| | - Victoria L Leon Guerrero
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8S 4K1
| | - Lesley T MacNeil
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8S 4K1
- Farncombe Family Digestive Health Research Institute, McMaster University, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada L8S 4K1
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Shao X, Taha IN, Clauser KR, Gao Y(T, Naba A. MatrisomeDB: the ECM-protein knowledge database. Nucleic Acids Res 2020; 48:D1136-D1144. [PMID: 31586405 PMCID: PMC6943062 DOI: 10.1093/nar/gkz849] [Citation(s) in RCA: 161] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 09/13/2019] [Accepted: 09/30/2019] [Indexed: 12/30/2022] Open
Abstract
The extracellular matrix (ECM) is a complex and dynamic meshwork of cross-linked proteins that supports cell polarization and functions and tissue organization and homeostasis. Over the past few decades, mass-spectrometry-based proteomics has emerged as the method of choice to characterize the composition of the ECM of normal and diseased tissues. Here, we present a new release of MatrisomeDB, a searchable collection of curated proteomic data from 17 studies on the ECM of 15 different normal tissue types, six cancer types (different grades of breast cancers, colorectal cancer, melanoma, and insulinoma) and other diseases including vascular defects and lung and liver fibroses. MatrisomeDB (http://www.pepchem.org/matrisomedb) was built by retrieving raw mass spectrometry data files and reprocessing them using the same search parameters and criteria to allow for a more direct comparison between the different studies. The present release of MatrisomeDB includes 847 human and 791 mouse ECM proteoforms and over 350 000 human and 600 000 mouse ECM-derived peptide-to-spectrum matches. For each query, a hierarchically-clustered tissue distribution map, a peptide coverage map, and a list of post-translational modifications identified, are generated. MatrisomeDB is the most complete collection of ECM proteomic data to date and allows the building of a comprehensive ECM atlas.
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Affiliation(s)
- Xinhao Shao
- College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Isra N Taha
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL 60612, USA
| | | | - Yu (Tom) Gao
- College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
- University of Illinois at Chicago Cancer Center, Chicago, IL 60612, USA
| | - Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL 60612, USA
- University of Illinois at Chicago Cancer Center, Chicago, IL 60612, USA
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Ewald CY. The Matrisome during Aging and Longevity: A Systems-Level Approach toward Defining Matreotypes Promoting Healthy Aging. Gerontology 2019; 66:266-274. [PMID: 31838471 PMCID: PMC7214094 DOI: 10.1159/000504295] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/22/2019] [Indexed: 12/12/2022] Open
Abstract
Accumulation of damage is generally considered the cause of aging. Interventions that delay aging mobilize mechanisms that protect and repair cellular components. Consequently, research has been focused on studying the protective and homeostatic mechanisms within cells. However, in humans and other multicellular organisms, cells are surrounded by extracellular matrices (ECMs), which are important for tissue structure, function, and intercellular communication. During aging, components of the ECM become damaged through fragmentation, glycation, crosslinking, and accumulation of protein aggregation, all of which contribute to age-related pathologies. Interestingly, placing senescent cells into a young ECM rejuvenates them. Furthermore, we found that many longevity-assurances pathways reactivate de novo synthesis of ECM proteins during aging. This raises the question of what constitutes a young ECM to reverse aging or maintain health? In order to make inroads to answering this question, I suggest a systems-level approach of quantifying the matrisome or ECM compositions reflecting health, pathology, or phenotype and propose a novel term, the "matreotype," to describe this. The matreotype is defined as the composition and modification of ECM or matrisome proteins associated with or caused by a phenotype, such as longevity, or a distinct and acute physiological state, as observed during aging or disease. Every cell type produces its unique ECM. Intriguingly, cancer-cell types can even be identified based on their unique ECM composition. Thus, the matreotype reflects cellular identity and physiological status. Defined matreotypes could be used as biomarkers or prognostic factors for disease or health status during aging with potential relevance for personalized medicine. Treatment with biologics that alter ECM-to-cell mechanotransduction might be a strategy to reverse age-associated pathologies. An understanding of how to reverse from an old to a young matreotype might point toward novel strategies to rejuvenate cells and help maintain tissue homeostasis to promote health during aging.
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Affiliation(s)
- Collin Yvès Ewald
- ETH Zürich, Department of Health Sciences and Technology, Institute of Translational Medicine, Schwerzenbach, Switzerland,
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Davis MN, Horne-Badovinac S, Naba A. In-silico definition of the Drosophila melanogaster matrisome. Matrix Biol Plus 2019; 4:100015. [PMID: 33543012 PMCID: PMC7852309 DOI: 10.1016/j.mbplus.2019.100015] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/04/2019] [Accepted: 09/05/2019] [Indexed: 01/02/2023] Open
Abstract
The extracellular matrix (ECM) is an assembly of hundreds of proteins that structurally supports the cells it surrounds and biochemically regulates their functions. Drosophila melanogaster has emerged as a powerful model organism to study fundamental mechanisms underlying ECM protein secretion, ECM assembly, and ECM roles in pathophysiological processes. However, as of today, we do not possess a well-defined list of the components forming the ECM of this organism. We previously reported the development of computational pipelines to define the matrisome - the ensemble of genes encoding ECM and ECM-associated proteins - of humans, mice, zebrafish and C. elegans. Using a similar approach, we report here that our pipeline has identified 641 genes constituting the Drosophila matrisome. We further classify these genes into different structural and functional categories, including an expanded way to classify genes encoding proteins forming apical ECMs. We illustrate how having a comprehensive list of Drosophila matrisome proteins can be used to annotate large proteomic datasets and identify unsuspected roles for the ECM in pathophysiological processes. Last, to aid the dissemination and usage of the proposed definition and categorization of the Drosophila matrisome by the scientific community, our list has been made available through three public portals: The Matrisome Project (http://matrisome.org), The FlyBase (https://flybase.org/), and GLAD (https://www.flyrnai.org/tools/glad/web/).
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Affiliation(s)
- Martin N. Davis
- Department of Physiology and Biophysics, University of Illinois at Chicago, 835 S. Wolcott Avenue, Chicago, IL 60612, USA
| | - Sally Horne-Badovinac
- Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA
| | - Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois at Chicago, 835 S. Wolcott Avenue, Chicago, IL 60612, USA
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