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Brock K, Alpha KM, Brennan G, De Jong EP, Luke E, Turner CE. A comparative analysis of paxillin and Hic-5 proximity interactomes. Cytoskeleton (Hoboken) 2024. [PMID: 38801098 DOI: 10.1002/cm.21878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/18/2024] [Accepted: 05/06/2024] [Indexed: 05/29/2024]
Abstract
Focal adhesions serve as structural and signaling hubs, facilitating bidirectional communication at the cell-extracellular matrix interface. Paxillin and the related Hic-5 (TGFβ1i1) are adaptor/scaffold proteins that recruit numerous structural and regulatory proteins to focal adhesions, where they perform both overlapping and discrete functions. In this study, paxillin and Hic-5 were expressed in U2OS osteosarcoma cells as biotin ligase (BioID2) fusion proteins and used as bait proteins for proximity-dependent biotinylation in order to directly compare their respective interactomes. The fusion proteins localized to both focal adhesions and the centrosome, resulting in biotinylation of components of each of these structures. Biotinylated proteins were purified and analyzed by mass spectrometry. The list of proximity interactors for paxillin and Hic-5 comprised numerous shared core focal adhesion proteins that likely contribute to their similar functions in cell adhesion and migration, as well as proteins unique to paxillin and Hic-5 that have been previously localized to focal adhesions, the centrosome, or the nucleus. Western blotting confirmed biotinylation and enrichment of FAK and vinculin, known interactors of Hic-5 and paxillin, as well as several potentially unique proximity interactors of Hic-5 and paxillin, including septin 7 and ponsin, respectively. Further investigation into the functional relationship between the unique interactors and Hic-5 or paxillin may yield novel insights into their distinct roles in cell migration.
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Affiliation(s)
- Katia Brock
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, New York, USA
| | - Kyle M Alpha
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, New York, USA
| | - Grant Brennan
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, New York, USA
| | - Ebbing P De Jong
- Proteomics Core Facility, State University of New York Upstate Medical University, Syracuse, New York, USA
| | - Elizabeth Luke
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, New York, USA
| | - Christopher E Turner
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, New York, USA
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2
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Fu Y, Zhou Y, Wang K, Li Z, Kong W. Extracellular Matrix Interactome in Modulating Vascular Homeostasis and Remodeling. Circ Res 2024; 134:931-949. [PMID: 38547250 DOI: 10.1161/circresaha.123.324055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
The ECM (extracellular matrix) is a major component of the vascular microenvironment that modulates vascular homeostasis. ECM proteins include collagens, elastin, noncollagen glycoproteins, and proteoglycans/glycosaminoglycans. ECM proteins form complex matrix structures, such as the basal lamina and collagen and elastin fibers, through direct interactions or lysyl oxidase-mediated cross-linking. Moreover, ECM proteins directly interact with cell surface receptors or extracellular secreted molecules, exerting matricellular and matricrine modulation, respectively. In addition, extracellular proteases degrade or cleave matrix proteins, thereby contributing to ECM turnover. These interactions constitute the ECM interactome network, which is essential for maintaining vascular homeostasis and preventing pathological vascular remodeling. The current review mainly focuses on endogenous matrix proteins in blood vessels and discusses the interaction of these matrix proteins with other ECM proteins, cell surface receptors, cytokines, complement and coagulation factors, and their potential roles in maintaining vascular homeostasis and preventing pathological remodeling.
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Affiliation(s)
- Yi Fu
- Department of Physiology and Pathophysiology (Y.F., K.W., Z.L., W.K.), School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Yuan Zhou
- Department of Biomedical Informatics (Y.Z.), School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Kai Wang
- Department of Physiology and Pathophysiology (Y.F., K.W., Z.L., W.K.), School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Zhuofan Li
- Department of Physiology and Pathophysiology (Y.F., K.W., Z.L., W.K.), School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Wei Kong
- Department of Physiology and Pathophysiology (Y.F., K.W., Z.L., W.K.), School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
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3
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Bouti P, Klein BJAM, Verkuijlen PJH, Schornagel K, van Alphen FPJ, Taris KKH, van den Biggelaar M, Hoogendijk AJ, van Bruggen R, Kuijpers TW, Matlung HL. SKAP2 acts downstream of CD11b/CD18 and regulates neutrophil effector function. Front Immunol 2024; 15:1344761. [PMID: 38487529 PMCID: PMC10937362 DOI: 10.3389/fimmu.2024.1344761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 02/01/2024] [Indexed: 03/17/2024] Open
Abstract
Background The importance of CD11b/CD18 expression in neutrophil effector functions is well known. Beyond KINDLIN3 and TALIN1, which are involved in the induction of the high-affinity binding CD11b/CD18 conformation, the signaling pathways that orchestrate this response remain incompletely understood. Method We performed an unbiased screening method for protein selection by biotin identification (BioID) and investigated the KINDLIN3 interactome. We used liquid chromatography with tandem mass spectrometry as a powerful analytical tool. Generation of NB4 CD18, KINDLIN3, or SKAP2 knockout neutrophils was achieved using CRISPR-Cas9 technology, and the cells were examined for their effector function using flow cytometry, live cell imaging, microscopy, adhesion, or antibody-dependent cellular cytotoxicity (ADCC). Results Among the 325 proteins significantly enriched, we identified Src kinase-associated phosphoprotein 2 (SKAP2), a protein involved in actin polymerization and integrin-mediated outside-in signaling. CD18 immunoprecipitation in primary or NB4 neutrophils demonstrated the presence of SKAP2 in the CD11b/CD18 complex at a steady state. Under this condition, adhesion to plastic, ICAM-1, or fibronectin was observed in the absence of SKAP2, which could be abrogated by blocking the actin rearrangements with latrunculin B. Upon stimulation of NB4 SKAP2-deficient neutrophils, adhesion to fibronectin was enhanced whereas CD18 clustering was strongly reduced. This response corresponded with significantly impaired CD11b/CD18-dependent NADPH oxidase activity, phagocytosis, and cytotoxicity against tumor cells. Conclusion Our results suggest that SKAP2 has a dual role. It may restrict CD11b/CD18-mediated adhesion only under resting conditions, but its major contribution lies in the regulation of dynamic CD11b/CD18-mediated actin rearrangements and clustering as required for cellular effector functions of human neutrophils.
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Affiliation(s)
- Panagiota Bouti
- Department of Molecular Hematology Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Bart J. A. M. Klein
- Department of Molecular Hematology Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Paul J. H. Verkuijlen
- Department of Molecular Hematology Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Karin Schornagel
- Department of Molecular Hematology Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Floris P. J. van Alphen
- Department of Molecular Hematology Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Kees-Karel H. Taris
- Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, Netherlands
- LaserLaB Amsterdam, Vrije Universiteit, Amsterdam, Netherlands
| | - Maartje van den Biggelaar
- Department of Molecular Hematology Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Arie J. Hoogendijk
- Department of Molecular Hematology Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Robin van Bruggen
- Department of Molecular Hematology Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Taco W. Kuijpers
- Department of Molecular Hematology Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, Netherlands
- Department of Pediatric Immunology and Infectious Diseases, Emma Children’s Hospital, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Hanke L. Matlung
- Department of Molecular Hematology Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, Netherlands
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Newman D, Young LE, Waring T, Brown L, Wolanska KI, MacDonald E, Charles-Orszag A, Goult BT, Caswell PT, Sakuma T, Yamamoto T, Machesky LM, Morgan MR, Zech T. 3D matrix adhesion feedback controls nuclear force coupling to drive invasive cell migration. Cell Rep 2023; 42:113554. [PMID: 38100355 DOI: 10.1016/j.celrep.2023.113554] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 06/23/2023] [Accepted: 11/20/2023] [Indexed: 12/17/2023] Open
Abstract
Cell invasion is a multi-step process, initiated by the acquisition of a migratory phenotype and the ability to move through complex 3D extracellular environments. We determine the composition of cell-matrix adhesion complexes of invasive breast cancer cells in 3D matrices and identify an interaction complex required for invasive migration. βPix and myosin18A (Myo18A) drive polarized recruitment of non-muscle myosin 2A (NM2A) to adhesion complexes at the tips of protrusions. Actomyosin force engagement then displaces the Git1-βPix complex from paxillin, establishing a feedback loop for adhesion maturation. We observe active force transmission to the nucleus during invasive migration that is needed to pull the nucleus forward. The recruitment of NM2A to adhesions creates a non-muscle myosin isoform gradient, which extends from the protrusion to the nucleus. We postulate that this gradient facilitates coupling of cell-matrix interactions at the protrusive cell front with nuclear movement, enabling effective invasive migration and front-rear cell polarity.
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Affiliation(s)
- Daniel Newman
- Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Lorna E Young
- Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Thomas Waring
- Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Louise Brown
- Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Katarzyna I Wolanska
- Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Ewan MacDonald
- Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, UK
| | | | | | - Patrick T Caswell
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology, Medicine, and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Tetsushi Sakuma
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima 739-8526, Japan
| | - Takashi Yamamoto
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima 739-8526, Japan
| | - Laura M Machesky
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, UK; Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow, UK; Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, UK
| | - Mark R Morgan
- Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Tobias Zech
- Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, UK.
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5
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He Q, Sze SK, Ng KS, Koh CG. Paxillin interactome identified by SILAC and label-free approaches coupled to TurboID sheds light on the compositions of focal adhesions in mouse embryonic stem cells. Biochem Biophys Res Commun 2023; 680:73-85. [PMID: 37725837 DOI: 10.1016/j.bbrc.2023.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 08/25/2023] [Accepted: 09/08/2023] [Indexed: 09/21/2023]
Abstract
Self-renewal and differentiation of mouse embryonic stem cells (mESCs) are greatly affected by the extracellular matrix (ECM) environment; the composition and stiffness of which are sensed by the cells via integrin-associated focal adhesions (FAs) which link the cells to the ECM. Although FAs have been studied extensively in differentiated cells, their composition and function in mESCs are not as well elucidated. To gain more detailed knowledge of the molecular compositions of FAs in mESCs, we adopted the proximity-dependent biotinylation (BioID) proteomics approach. Paxillin, a known FA protein (FAP), is fused to the promiscuous biotin ligase TurboID as bait. We employed both SILAC- and label-free (LF)-based quantitative proteomics to strengthen as well as complement individual approach. The mass spectrometry data derived from SILAC and LF identified 38 and 443 proteins, respectively, with 35 overlapping candidates. Fifteen of these shared proteins are known FAPs based on literature-curated adhesome and 7 others are among the reported "meta-adhesome", suggesting the components of FAs are largely conserved between mESCs and differentiated cells. Furthermore, the LF data set contained an additional 18 literature-curated FAPs. Notably, the overlapped proteomics data failed to detect LIM-domain proteins such as zyxin family proteins, which suggests that FAs in mESCs are less mature than differentiated cells. Using the LF approach, we are able to identify PDLIM7, a LIM-domain protein, as a FAP in mESCs. This study illustrates the effectiveness of TurboID in mESCs. Importantly, we found that application of both SILAC and LF methods in combination allowed us to analyze the TurboID proteomics data in an unbiased, stringent and yet comprehensive manner.
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Affiliation(s)
- Qianqian He
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Kai Soon Ng
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Cheng-Gee Koh
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
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6
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Novoseletskaya ES, Evdokimov PV, Efimenko AY. Extracellular matrix-induced signaling pathways in mesenchymal stem/stromal cells. Cell Commun Signal 2023; 21:244. [PMID: 37726815 PMCID: PMC10507829 DOI: 10.1186/s12964-023-01252-8] [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: 06/16/2023] [Accepted: 07/31/2023] [Indexed: 09/21/2023] Open
Abstract
The extracellular matrix (ECM) is a crucial component of the stem cell microenvironment, or stem-cell niches, and contributes to the regulation of cell behavior and fate. Accumulating evidence indicates that different types of stem cells possess a large variety of molecules responsible for interactions with the ECM, mediating specific epigenetic rearrangements and corresponding changes in transcriptome profile. Signals from the ECM are crucial at all stages of ontogenesis, including embryonic and postnatal development, as well as tissue renewal and repair. The ECM could regulate stem cell transition from a quiescent state to readiness to perceive the signals of differentiation induction (competence) and the transition between different stages of differentiation (commitment). Currently, to unveil the complex networks of cellular signaling from the ECM, multiple approaches including screening methods, the analysis of the cell matrixome, and the creation of predictive networks of protein-protein interactions based on experimental data are used. In this review, we consider the existing evidence regarded the contribution of ECM-induced intracellular signaling pathways into the regulation of stem cell differentiation focusing on mesenchymal stem/stromal cells (MSCs) as well-studied type of postnatal stem cells totally depended on signals from ECM. Furthermore, we propose a system biology-based approach for the prediction of ECM-mediated signal transduction pathways in target cells. Video Abstract.
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Affiliation(s)
- Ekaterina Sergeevna Novoseletskaya
- Faculty of Biology, Dayun New Town, Shenzhen MSU-BIT University, 1 International University Park Road, Dayun New Town, Longgang District, Shenzhen, Guangdong Province, P. R. China.
- Institute for Regenerative Medicine, Medical Research and Education Center, Lomonosov Moscow State University, Lomonosov Ave., 27/10, 119991, Moscow, Russia.
| | - Pavel Vladimirovich Evdokimov
- Materials Science Department, Lomonosov Moscow State University, Leninskie Gory, 1, Building 73, 119991, Moscow, Russia
- Chemistry Department, Lomonosov Moscow State University, GSP-1, Leninskiye Gory, 1-3, Moscow, Russia
| | - Anastasia Yurievna Efimenko
- Institute for Regenerative Medicine, Medical Research and Education Center, Lomonosov Moscow State University, Lomonosov Ave., 27/10, 119991, Moscow, Russia
- Faculty of Medicine, Lomonosov Moscow State University, Lomonosov Ave., 27/1, 119991, Moscow, Russia
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7
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Zehrbach NM, Dubois F, Turner CE. Paxillin regulates Rab5-mediated vesicle motility through modulating microtubule acetylation. Mol Biol Cell 2023; 34:ar65. [PMID: 37043310 PMCID: PMC10295489 DOI: 10.1091/mbc.e22-10-0455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 04/13/2023] Open
Abstract
Rab GTPase-mediated vesicle trafficking of cell surface proteins, including integrins, through endocytic and recycling pathways is important in controlling cell-extracellular matrix interactions during cell migration. The focal adhesion adaptor protein, paxillin, plays a central role in regulating adhesion dynamics and was previously shown to promote anterograde vesicle trafficking through modulation of microtubule acetylation via its inhibition of the deacetylase HDAC6. The role of paxillin in retrograde trafficking is unknown. Herein, we identified a role for paxillin in the modulation of the Rab5 GTPase, which is necessary for regulating early endosome dynamics and focal adhesion turnover. Using MDA-MB-231 breast cancer cells and paxillin (-/-) fibroblasts, paxillin was shown to impact Rab5-associated vesicle size and distribution, as well as Rab5 GTPase activity, through its modulation of HDAC6. Using a combination of real-time imaging and particle tracking analysis, paxillin was shown to promote Rab5-associated vesicle motility through inhibition of HDAC6-mediated micro-tubule deacetylation, along with the localization of active integrin to focal adhesions.
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Affiliation(s)
- Nicholas M. Zehrbach
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Fatemeh Dubois
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Christopher E. Turner
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
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8
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Rashid M, Olson EC. Delayed cortical development in mice with a neural specific deletion of β1 integrin. Front Neurosci 2023; 17:1158419. [PMID: 37250402 PMCID: PMC10213249 DOI: 10.3389/fnins.2023.1158419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/24/2023] [Indexed: 05/31/2023] Open
Abstract
The adhesion systems employed by migrating cortical neurons are not well understood. Genetic deletion studies of focal adhesion kinase (FAK) and paxillin in mice suggested that these classical focal adhesion molecules control the morphology and speed of cortical neuron migration, but whether β1 integrins also regulate migration morphology and speed is not known. We hypothesized that a β1 integrin adhesion complex is required for proper neuronal migration and for proper cortical development. To test this, we have specifically deleted β1 integrin from postmitotic migrating and differentiating neurons by crossing conditional β1 integrin floxed mice into the NEX-Cre transgenic line. Similar to our prior findings with conditional paxillin deficiency, we found that both homozygous and heterozygous deletion of β1 integrin causes transient mispositioning of cortical neurons in the developing cortex when analyzed pre- and perinatally. Paxillin and β1 integrin colocalize in the migrating neurons and deletion of paxillin in the migrating neuron causes an overall reduction of the β1 integrin immunofluorescence signal and reduction in the number of activated β1 integrin puncta in the migrating neurons. These findings suggest that these molecules may form a functional complex in migrating neurons. Similarly, there was an overall reduced number of paxillin+ puncta in the β1 integrin deficient neurons, despite the normal distribution of FAK and Cx26, a connexin required for cortical migration. The double knockout of paxillin and β1 integrin produces a cortical malpositioning phenotype similar to the paxillin or β1 integrin single knockouts, as would be expected if paxillin and β1 integrin function on a common pathway. Importantly, an isolation-induced pup vocalization test showed that β1 integrin mutants produced a significantly smaller number of calls compared to their littermate controls when analyzed at postnatal day 4 (P4) and revealed a several days trend in reduced vocalization development compared to controls. The current study establishes a role for β1 integrin in cortical development and suggests that β1 integrin deficiency leads to migration and neurodevelopmental delays.
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Affiliation(s)
- Mamunur Rashid
- Department of Neuroscience and Physiology, State University of New York Upstate Medical University, Syracuse, NY, United States
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, United States
| | - Eric C. Olson
- Department of Neuroscience and Physiology, State University of New York Upstate Medical University, Syracuse, NY, United States
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9
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Geiger B, Boujemaa-Paterski R, Winograd-Katz SE, Balan Venghateri J, Chung WL, Medalia O. The Actin Network Interfacing Diverse Integrin-Mediated Adhesions. Biomolecules 2023; 13:biom13020294. [PMID: 36830665 PMCID: PMC9953007 DOI: 10.3390/biom13020294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 01/29/2023] [Accepted: 01/30/2023] [Indexed: 02/08/2023] Open
Abstract
The interface between the cellular actin network and diverse forms of integrin-mediated cell adhesions displays a unique capacity to serve as accurate chemical and mechanical sensors of the cell's microenvironment. Focal adhesion-like structures of diverse cell types, podosomes in osteoclasts, and invadopodia of invading cancer cells display distinct morphologies and apparent functions. Yet, all three share a similar composition and mode of coupling between a protrusive structure (the lamellipodium, the core actin bundle of the podosome, and the invadopodia protrusion, respectively), and a nearby adhesion site. Cytoskeletal or external forces, applied to the adhesion sites, trigger a cascade of unfolding and activation of key adhesome components (e.g., talin, vinculin, integrin), which in turn, trigger the assembly of adhesion sites and generation of adhesion-mediated signals that affect cell behavior and fate. The structural and molecular mechanisms underlying the dynamic crosstalk between the actin cytoskeleton and the adhesome network are discussed.
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Affiliation(s)
- Benjamin Geiger
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
- Correspondence: (B.G.); (O.M.)
| | - Rajaa Boujemaa-Paterski
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Sabina E. Winograd-Katz
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jubina Balan Venghateri
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Wen-Lu Chung
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Correspondence: (B.G.); (O.M.)
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10
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Kanchanawong P, Calderwood DA. Organization, dynamics and mechanoregulation of integrin-mediated cell-ECM adhesions. Nat Rev Mol Cell Biol 2023; 24:142-161. [PMID: 36168065 PMCID: PMC9892292 DOI: 10.1038/s41580-022-00531-5] [Citation(s) in RCA: 77] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2022] [Indexed: 02/04/2023]
Abstract
The ability of animal cells to sense, adhere to and remodel their local extracellular matrix (ECM) is central to control of cell shape, mechanical responsiveness, motility and signalling, and hence to development, tissue formation, wound healing and the immune response. Cell-ECM interactions occur at various specialized, multi-protein adhesion complexes that serve to physically link the ECM to the cytoskeleton and the intracellular signalling apparatus. This occurs predominantly via clustered transmembrane receptors of the integrin family. Here we review how the interplay of mechanical forces, biochemical signalling and molecular self-organization determines the composition, organization, mechanosensitivity and dynamics of these adhesions. Progress in the identification of core multi-protein modules within the adhesions and characterization of rearrangements of their components in response to force, together with advanced imaging approaches, has improved understanding of adhesion maturation and turnover and the relationships between adhesion structures and functions. Perturbations of adhesion contribute to a broad range of diseases and to age-related dysfunction, thus an improved understanding of their molecular nature may facilitate therapeutic intervention in these conditions.
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Affiliation(s)
- Pakorn Kanchanawong
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore.
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore.
| | - David A Calderwood
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA.
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.
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11
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Atherton P, Konstantinou R, Neo SP, Wang E, Balloi E, Ptushkina M, Bennett H, Clark K, Gunaratne J, Critchley D, Barsukov I, Manser E, Ballestrem C. Tensin3 interaction with talin drives the formation of fibronectin-associated fibrillar adhesions. J Biophys Biochem Cytol 2022; 221:213452. [PMID: 36074065 PMCID: PMC9462884 DOI: 10.1083/jcb.202107022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 05/30/2022] [Accepted: 08/05/2022] [Indexed: 12/11/2022] Open
Abstract
The formation of healthy tissue involves continuous remodeling of the extracellular matrix (ECM). Whilst it is known that this requires integrin-associated cell-ECM adhesion sites (CMAs) and actomyosin-mediated forces, the underlying mechanisms remain unclear. Here, we examine how tensin3 contributes to the formation of fibrillar adhesions (FBs) and fibronectin fibrillogenesis. Using BioID mass spectrometry and a mitochondrial targeting assay, we establish that tensin3 associates with the mechanosensors such as talin and vinculin. We show that the talin R11 rod domain binds directly to a helical motif within the central intrinsically disordered region (IDR) of tensin3, whilst vinculin binds indirectly to tensin3 via talin. Using CRISPR knock-out cells in combination with defined tensin3 mutations, we show (i) that tensin3 is critical for the formation of α5β1-integrin FBs and for fibronectin fibrillogenesis, and (ii) the talin/tensin3 interaction drives this process, with vinculin acting to potentiate it.
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Affiliation(s)
- Paul Atherton
- Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester, UK.,Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Rafaella Konstantinou
- Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester, UK.,sGSK Group, Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
| | - Suat Peng Neo
- Quantitative Proteomics Group, Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
| | - Emily Wang
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Eleonora Balloi
- Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester, UK
| | - Marina Ptushkina
- Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester, UK
| | - Hayley Bennett
- Genome Editing Unit, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Kath Clark
- Department of Biochemistry, University of Leicester, Leicester, UK
| | - Jayantha Gunaratne
- Quantitative Proteomics Group, Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
| | - David Critchley
- Department of Biochemistry, University of Leicester, Leicester, UK
| | - Igor Barsukov
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Edward Manser
- sGSK Group, Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
| | - Christoph Ballestrem
- Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester, UK
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12
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Villari G, Gioelli N, Valdembri D, Serini G. Vesicle choreographies keep up cell-to-extracellular matrix adhesion dynamics in polarized epithelial and endothelial cells. Matrix Biol 2022; 112:62-71. [PMID: 35961423 DOI: 10.1016/j.matbio.2022.08.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/21/2022] [Accepted: 08/08/2022] [Indexed: 12/19/2022]
Abstract
In metazoans, cell adhesion to the extracellular matrix (ECM) drives the development, functioning, and repair of different tissues, organs, and systems. Disruption or dysregulation of cell-to-ECM adhesion promote the initiation and progression of several diseases, such as bleeding, immune disorders and cancer. Integrins are major ECM transmembrane receptors, whose function depends on both allosteric changes and exo-endocytic traffic, which carries them to and from the plasma membrane. In apico-basally polarized cells, asymmetric adhesion to the ECM is maintained by continuous targeting of the plasma membrane by vesicles coming from the trans Golgi network and carrying ECM proteins. Active integrin-bound ECM is indeed endocytosed and replaced by the exocytosis of fresh ECM. Such vesicular traffic is finely driven by the teamwork of microtubules (MTs) and their associated kinesin and dynein motors. Here, we review the main cytoskeletal actors involved in the control of the spatiotemporal distribution of active integrins and their ECM ligands, highlighting the key role of the synchronous (ant)agonistic cooperation between MT motors transporting vesicular cargoes, in the same or in opposite direction, in the regulation of traffic logistics, and the establishment of epithelial and endothelial cell polarity.
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Affiliation(s)
- Giulia Villari
- Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 10060, Candiolo, Torino, Italy; Department of Oncology, University of Torino School of Medicine, 10060, Candiolo, Torino, Italy
| | - Noemi Gioelli
- Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 10060, Candiolo, Torino, Italy; Department of Oncology, University of Torino School of Medicine, 10060, Candiolo, Torino, Italy
| | - Donatella Valdembri
- Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 10060, Candiolo, Torino, Italy; Department of Oncology, University of Torino School of Medicine, 10060, Candiolo, Torino, Italy.
| | - Guido Serini
- Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 10060, Candiolo, Torino, Italy; Department of Oncology, University of Torino School of Medicine, 10060, Candiolo, Torino, Italy.
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13
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Zuidema A, Atherton P, Kreft M, Hoekman L, Bleijerveld OB, Nagaraj N, Chen N, Fässler R, Sonnenberg A. PEAK1 Y635 phosphorylation regulates cell migration through association with Tensin3 and integrins. J Biophys Biochem Cytol 2022; 221:213273. [PMID: 35687021 PMCID: PMC9194829 DOI: 10.1083/jcb.202108027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 03/22/2022] [Accepted: 05/18/2022] [Indexed: 02/03/2023] Open
Abstract
Integrins mediate cell adhesion by connecting the extracellular matrix to the intracellular cytoskeleton and orchestrate signal transduction in response to chemical and mechanical stimuli by interacting with many cytoplasmic proteins. We used BioID to interrogate the interactomes of β1 and β3 integrins in epithelial cells and identified PEAK1 as an interactor of the RGD-binding integrins α5β1, αVβ3, and αVβ5 in focal adhesions. We demonstrate that the interaction between integrins and PEAK1 occurs indirectly through Tensin3, requiring both the membrane-proximal NPxY motif on the integrin β tail and binding of the SH2 domain of Tensin3 to phosphorylated Tyr-635 on PEAK1. Phosphorylation of Tyr-635 is mediated by Src and regulates cell migration. Additionally, we found that Shc1 localizes in focal adhesions in a PEAK1 phosphorylated Tyr-1188-dependent fashion. Besides binding Shc1, PEAK1 also associates with a protein cluster that mediates late EGFR/Shc1 signaling. We propose a model in which PEAK1 binds Tensin3 and Shc1 to converge integrin and growth factor receptor signal transduction.
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Affiliation(s)
- Alba Zuidema
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Paul Atherton
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Maaike Kreft
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Liesbeth Hoekman
- Proteomics Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Onno B. Bleijerveld
- Proteomics Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Nagarjuna Nagaraj
- Mass Spectrometry Core Facility at the Max-Planck Institute of Biochemistry, Planegg, Germany
| | - Nanpeng Chen
- Department of Molecular Medicine, Max-Planck Institute of Biochemistry, Planegg, Germany
| | - Reinhard Fässler
- Department of Molecular Medicine, Max-Planck Institute of Biochemistry, Planegg, Germany
| | - Arnoud Sonnenberg
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands,Correspondence to Arnoud Sonnenberg:
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14
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Humphries JD, Zha J, Burns J, Askari JA, Below CR, Chastney MR, Jones MC, Mironov A, Knight D, O'Reilly DA, Dunne MJ, Garrod DR, Jorgensen C, Humphries MJ. Pancreatic ductal adenocarcinoma cells employ integrin α6β4 to form hemidesmosomes and regulate cell proliferation. Matrix Biol 2022; 110:16-39. [PMID: 35405272 DOI: 10.1016/j.matbio.2022.03.010] [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: 08/16/2021] [Revised: 03/15/2022] [Accepted: 03/31/2022] [Indexed: 12/24/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) has a dismal prognosis due to its aggressive progression, late detection and lack of druggable driver mutations, which often combine to result in unsuitability for surgical intervention. Together with activating mutations of the small GTPase KRas, which are found in over 90% of PDAC tumours, a contributory factor for PDAC tumour progression is formation of a rigid extracellular matrix (ECM) and associated desmoplasia. This response leads to aberrant integrin signalling, and accelerated proliferation and invasion. To identify the integrin adhesion systems that operate in PDAC, we analysed a range of pancreatic ductal epithelial cell models using 2D, 3D and organoid culture systems. Proteomic analysis of isolated integrin receptor complexes from human pancreatic ductal epithelial (HPDE) cells predominantly identified integrin α6β4 and hemidesmosome components, rather than classical focal adhesion components. Electron microscopy, together with immunofluorescence, confirmed the formation of hemidesmosomes by HPDE cells, both in 2D and 3D culture systems. Similar results were obtained for the human PDAC cell line, SUIT-2. Analysis of HPDE cell secreted proteins and cell-derived matrices (CDM) demonstrated that HPDE cells secrete a range of laminin subunits and form a hemidesmosome-specific, laminin 332-enriched ECM. Expression of mutant KRas (G12V) did not affect hemidesmosome composition or formation by HPDE cells. Cell-ECM contacts formed by mouse and human PDAC organoids were also assessed by electron microscopy. Organoids generated from both the PDAC KPC mouse model and human patient-derived PDAC tissue displayed features of acinar-ductal cell polarity, and hemidesmosomes were visible proximal to prominent basement membranes. Furthermore, electron microscopy identified hemidesmosomes in normal human pancreas. Depletion of integrin β4 reduced cell proliferation in both SUIT-2 and HPDE cells, reduced the number of SUIT-2 cells in S-phase, and induced G1 cell cycle arrest, suggesting a requirement for α6β4-mediated adhesion for cell cycle progression and growth. Taken together, these data suggest that laminin-binding adhesion mechanisms in general, and hemidesmosome-mediated adhesion in particular, may be under-appreciated in the context of PDAC. Proteomic data are available via ProteomeXchange with the identifiers PXD027803, PXD027823 and PXD027827.
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Affiliation(s)
- Jonathan D Humphries
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Junzhe Zha
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Jessica Burns
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Janet A Askari
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Christopher R Below
- Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Cheshire SK10 4TG, UK
| | - Megan R Chastney
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Matthew C Jones
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Aleksandr Mironov
- Electron Microscopy Core Facility (RRID: SCR_021147), Faculty of Biology, Medicine & Health, University of Manchester, Manchester M13 9PT, UK
| | - David Knight
- Biological Mass Spectrometry Core Facility (RRID: SCR_020987), Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9PT, UK
| | - Derek A O'Reilly
- Department of Hepatobiliary and Pancreatic Surgery, Manchester Royal Infirmary, Oxford Road, Manchester M13 9WL, UK; Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9PT, UK
| | - Mark J Dunne
- Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9PT, UK
| | - David R Garrod
- Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9PT, UK
| | - Claus Jorgensen
- Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Cheshire SK10 4TG, UK
| | - Martin J Humphries
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK.
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15
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Proximity labeling methods for proteomic analysis of membrane proteins. J Proteomics 2022; 264:104620. [DOI: 10.1016/j.jprot.2022.104620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 11/19/2022]
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16
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Ripamonti M, Wehrle-Haller B, de Curtis I. Paxillin: A Hub for Mechano-Transduction from the β3 Integrin-Talin-Kindlin Axis. Front Cell Dev Biol 2022; 10:852016. [PMID: 35450290 PMCID: PMC9016114 DOI: 10.3389/fcell.2022.852016] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/14/2022] [Indexed: 01/11/2023] Open
Abstract
Focal adhesions are specialized integrin-dependent adhesion complexes, which ensure cell anchoring to the extracellular matrix. Focal adhesions also function as mechano-signaling platforms by perceiving and integrating diverse physical and (bio)chemical cues of their microenvironment, and by transducing them into intracellular signaling for the control of cell behavior. The fundamental biological mechanism of creating intracellular signaling in response to changes in tensional forces appears to be tightly linked to paxillin recruitment and binding to focal adhesions. Interestingly, the tension-dependent nature of the paxillin binding to adhesions, combined with its scaffolding function, suggests a major role of this protein in integrating multiple signals from the microenvironment, and accordingly activating diverse molecular responses. This minireview offers an overview of the molecular bases of the mechano-sensitivity and mechano-signaling capacity of core focal adhesion proteins, and highlights the role of paxillin as a key component of the mechano-transducing machinery based on the interaction of cells to substrates activating the β3 integrin-talin1-kindlin.
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Affiliation(s)
- Marta Ripamonti
- Division of Neuroscience, San Raffaele Scientific Institute and Vita-Salute San Raffaele University, Milano, Italy
| | - Bernhard Wehrle-Haller
- Department of Cell Physiology and Metabolism, University of Geneva, Centre Médical Universitaire, Geneva, Switzerland
| | - Ivan de Curtis
- Division of Neuroscience, San Raffaele Scientific Institute and Vita-Salute San Raffaele University, Milano, Italy
- *Correspondence: Ivan de Curtis,
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17
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Dionne U, Gingras AC. Proximity-Dependent Biotinylation Approaches to Explore the Dynamic Compartmentalized Proteome. Front Mol Biosci 2022; 9:852911. [PMID: 35309513 PMCID: PMC8930824 DOI: 10.3389/fmolb.2022.852911] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/07/2022] [Indexed: 12/12/2022] Open
Abstract
In recent years, proximity-dependent biotinylation approaches, including BioID, APEX, and their derivatives, have been widely used to define the compositions of organelles and other structures in cultured cells and model organisms. The associations between specific proteins and given compartments are regulated by several post-translational modifications (PTMs); however, these effects have not been systematically investigated using proximity proteomics. Here, we discuss the progress made in this field and how proximity-dependent biotinylation strategies could elucidate the contributions of PTMs, such as phosphorylation, to the compartmentalization of proteins.
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Affiliation(s)
- Ugo Dionne
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- *Correspondence: Anne-Claude Gingras,
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18
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Case LB, De Pasquale M, Henry L, Rosen MK. Synergistic phase separation of two pathways promotes integrin clustering and nascent adhesion formation. eLife 2022; 11:e72588. [PMID: 35049497 PMCID: PMC8791637 DOI: 10.7554/elife.72588] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 01/10/2022] [Indexed: 12/14/2022] Open
Abstract
Integrin adhesion complexes (IACs) are integrin-based plasma-membrane-associated compartments where cells sense environmental cues. The physical mechanisms and molecular interactions that mediate initial IAC formation are unclear. We found that both p130Cas ('Cas') and Focal adhesion kinase ('FAK') undergo liquid-liquid phase separation in vitro under physiologic conditions. Cas- and FAK- driven phase separation is sufficient to reconstitute kindlin-dependent integrin clustering in vitro with recombinant mammalian proteins. In vitro condensates and IACs in mouse embryonic fibroblasts (MEFs) exhibit similar sensitivities to environmental perturbations including changes in temperature and pH. Furthermore, mutations that inhibit or enhance phase separation in vitro reduce or increase the number of IACs in MEFs, respectively. Finally, we find that the Cas and FAK pathways act synergistically to promote phase separation, integrin clustering, IAC formation and partitioning of key components in vitro and in cells. We propose that Cas- and FAK-driven phase separation provides an intracellular trigger for integrin clustering and nascent IAC formation.
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Affiliation(s)
- Lindsay B Case
- Department of Biophysics, Howard Hughes Medical Institute, The University of Texas Southwestern Medical CenterDallasUnited States
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Milagros De Pasquale
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Lisa Henry
- Department of Biophysics, Howard Hughes Medical Institute, The University of Texas Southwestern Medical CenterDallasUnited States
| | - Michael K Rosen
- Department of Biophysics, Howard Hughes Medical Institute, The University of Texas Southwestern Medical CenterDallasUnited States
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19
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Christopher JA, Geladaki A, Dawson CS, Vennard OL, Lilley KS. SUBCELLULAR TRANSCRIPTOMICS & PROTEOMICS: A COMPARATIVE METHODS REVIEW. Mol Cell Proteomics 2021; 21:100186. [PMID: 34922010 PMCID: PMC8864473 DOI: 10.1016/j.mcpro.2021.100186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 11/16/2021] [Accepted: 12/13/2021] [Indexed: 12/23/2022] Open
Abstract
The internal environment of cells is molecularly crowded, which requires spatial organization via subcellular compartmentalization. These compartments harbor specific conditions for molecules to perform their biological functions, such as coordination of the cell cycle, cell survival, and growth. This compartmentalization is also not static, with molecules trafficking between these subcellular neighborhoods to carry out their functions. For example, some biomolecules are multifunctional, requiring an environment with differing conditions or interacting partners, and others traffic to export such molecules. Aberrant localization of proteins or RNA species has been linked to many pathological conditions, such as neurological, cancer, and pulmonary diseases. Differential expression studies in transcriptomics and proteomics are relatively common, but the majority have overlooked the importance of subcellular information. In addition, subcellular transcriptomics and proteomics data do not always colocate because of the biochemical processes that occur during and after translation, highlighting the complementary nature of these fields. In this review, we discuss and directly compare the current methods in spatial proteomics and transcriptomics, which include sequencing- and imaging-based strategies, to give the reader an overview of the current tools available. We also discuss current limitations of these strategies as well as future developments in the field of spatial -omics. Subcellular information of protein and RNA give insights into molecular function. This review discusses strategies available to measure subcellular information. Hybridization of methods shows promise for exploring the composition of organelles. Advances are aiding understanding of the organisation and dynamics of cells.
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Affiliation(s)
- Josie A Christopher
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Aikaterini Geladaki
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK; Department of Genetics, University of Cambridge, 20 Downing Place, Cambridge, CB2 3EJ, UK
| | - Charlotte S Dawson
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Owen L Vennard
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK.
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20
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Legerstee K, Houtsmuller AB. A Layered View on Focal Adhesions. BIOLOGY 2021; 10:biology10111189. [PMID: 34827182 PMCID: PMC8614905 DOI: 10.3390/biology10111189] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/06/2021] [Accepted: 11/08/2021] [Indexed: 12/31/2022]
Abstract
Simple Summary The cytoskeleton is a network of protein fibres within cells that provide structure and support intracellular transport. Focal adhesions are protein complexes associated with the outer cell membrane that are found at the ends of specialised actin fibres of this cytoskeleton. They mediate cell adhesion by connecting the cytoskeleton to the extracellular matrix, a protein and sugar network that surrounds cells in tissues. Focal adhesions also translate forces on actin fibres into forces contributing to cell migration. Cell adhesion and migration are crucial to diverse biological processes such as embryonic development, proper functioning of the immune system or the metastasis of cancer cells. Advances in fluorescence microscopy and data analysis methods provided a more detailed understanding of the dynamic ways in which proteins bind and dissociate from focal adhesions and how they are organised within these protein complexes. In this review, we provide an overview of the advances in the current scientific understanding of focal adhesions and summarize relevant imaging techniques. One of the key insights is that focal adhesion proteins are organised into three layers parallel to the cell membrane. We discuss the relevance of this layered nature for the functioning of focal adhesion. Abstract The cytoskeleton provides structure to cells and supports intracellular transport. Actin fibres are crucial to both functions. Focal Adhesions (FAs) are large macromolecular multiprotein assemblies at the ends of specialised actin fibres linking these to the extracellular matrix. FAs translate forces on actin fibres into forces contributing to cell migration. This review will discuss recent insights into FA protein dynamics and their organisation within FAs, made possible by advances in fluorescence imaging techniques and data analysis methods. Over the last decade, evidence has accumulated that FAs are composed of three layers parallel to the plasma membrane. We focus on some of the most frequently investigated proteins, two from each layer, paxillin and FAK (bottom, integrin signalling layer), vinculin and talin (middle, force transduction layer) and zyxin and VASP (top, actin regulatory layer). Finally, we discuss the potential impact of this layered nature on different aspects of FA behaviour.
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21
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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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22
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Baskaran Y, Tay FPL, Ng EYW, Swa CLF, Wee S, Gunaratne J, Manser E. Proximity proteomics identifies PAK4 as a component of Afadin-Nectin junctions. Nat Commun 2021; 12:5315. [PMID: 34493720 PMCID: PMC8423818 DOI: 10.1038/s41467-021-25011-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 07/08/2021] [Indexed: 02/07/2023] Open
Abstract
Human PAK4 is an ubiquitously expressed p21-activated kinase which acts downstream of Cdc42. Since PAK4 is enriched in cell-cell junctions, we probed the local protein environment around the kinase with a view to understanding its location and substrates. We report that U2OS cells expressing PAK4-BirA-GFP identify a subset of 27 PAK4-proximal proteins that are primarily cell-cell junction components. Afadin/AF6 showed the highest relative biotin labelling and links to the nectin family of homophilic junctional proteins. Reciprocally >50% of the PAK4-proximal proteins were identified by Afadin BioID. Co-precipitation experiments failed to identify junctional proteins, emphasizing the advantage of the BioID method. Mechanistically PAK4 depended on Afadin for its junctional localization, which is similar to the situation in Drosophila. A highly ranked PAK4-proximal protein LZTS2 was immuno-localized with Afadin at cell-cell junctions. Though PAK4 and Cdc42 are junctional, BioID analysis did not yield conventional cadherins, indicating their spatial segregation. To identify cellular PAK4 substrates we then assessed rapid changes (12') in phospho-proteome after treatment with two PAK inhibitors. Among the PAK4-proximal junctional proteins seventeen PAK4 sites were identified. We anticipate mammalian group II PAKs are selective for the Afadin/nectin sub-compartment, with a demonstrably distinct localization from tight and cadherin junctions.
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Affiliation(s)
- Yohendran Baskaran
- sGSK Group, Institute of Molecular & Cell Biology, A*STAR, Singapore, Singapore
| | - Felicia Pei-Ling Tay
- FB Laboratory, Institute of Molecular & Cell Biology, A*STAR, Singapore, Singapore
| | - Elsa Yuen Wai Ng
- sGSK Group, Institute of Molecular & Cell Biology, A*STAR, Singapore, Singapore
| | - Claire Lee Foon Swa
- Quantitative Proteomics Group, Institute of Molecular & Cell Biology, Singapore, Singapore
| | - Sheena Wee
- Quantitative Proteomics Group, Institute of Molecular & Cell Biology, Singapore, Singapore
| | - Jayantha Gunaratne
- Quantitative Proteomics Group, Institute of Molecular & Cell Biology, Singapore, Singapore
| | - Edward Manser
- sGSK Group, Institute of Molecular & Cell Biology, A*STAR, Singapore, Singapore.
- Department of Pharmacology, National University of Singapore, Singapore, Singapore.
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23
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Tahir R, Madugundu AK, Udainiya S, Cutler JA, Renuse S, Wang L, Pearson NA, Mitchell CJ, Mahajan N, Pandey A, Wu X. Proximity-Dependent Biotinylation to Elucidate the Interactome of TNK2 Nonreceptor Tyrosine Kinase. J Proteome Res 2021; 20:4566-4577. [PMID: 34428048 DOI: 10.1021/acs.jproteome.1c00551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nonreceptor tyrosine kinases (NRTKs) represent an important class of signaling molecules driving diverse cellular pathways. Aberrant expression and hyperphosphorylation of TNK2, an NRTK, have been implicated in multiple cancers. However, the exact proteins and cellular events that mediate phenotypic changes downstream of TNK2 are unclear. Biological systems that employ proximity-dependent biotinylation methods, such as BioID, are being increasingly used to map protein-protein interactions, as they provide increased sensitivity in discovering interaction partners. In this study, we employed stable isotope labeling with amino acids in cell culture and BioID coupled to the biotinylation site identification technology (BioSITe) method that we recently developed to quantitatively explore the interactome of TNK2. By performing a controlled comparative analysis between full-length TNK2 and its truncated counterpart, we were able to not only identify site-level biotinylation of previously well-established TNK2 binders and substrates including NCK1, NCK2, CTTN, and STAT3, but also discover several novel TNK2 interacting partners. We also performed co-immunoprecipitation and immunofluorescence analysis to validate the interaction between TNK2 and CLINT1, a novel TNK2 interacting protein. Overall, this work reveals the power of the BioSITe method coupled to BioID and highlights several molecules that warrant further exploration to assess their functional significance in TNK2-mediated signaling.
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Affiliation(s)
- Raiha Tahir
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,Ginkgo Bioworks, Boston, Massachusetts 02210, United States
| | - Anil K Madugundu
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India.,Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore 560029, Karnataka, India.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Savita Udainiya
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore 560029, Karnataka, India.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Jevon A Cutler
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,Pre-Doctoral Training Program in Human Genetics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Santosh Renuse
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Li Wang
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Nicole A Pearson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States
| | | | - Nupam Mahajan
- Siteman Cancer Center, Washington University, St. Louis, Missouri 63110, United States
| | - Akhilesh Pandey
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore 560029, Karnataka, India.,Departments of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Xinyan Wu
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States.,Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota 55905, United States
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24
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Rabanal-Ruiz Y, Byron A, Wirth A, Madsen R, Sedlackova L, Hewitt G, Nelson G, Stingele J, Wills JC, Zhang T, Zeug A, Fässler R, Vanhaesebroeck B, Maddocks OD, Ponimaskin E, Carroll B, Korolchuk VI. mTORC1 activity is supported by spatial association with focal adhesions. J Cell Biol 2021; 220:e202004010. [PMID: 33635313 PMCID: PMC7923692 DOI: 10.1083/jcb.202004010] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 11/21/2020] [Accepted: 01/29/2021] [Indexed: 02/07/2023] Open
Abstract
The mammalian target of rapamycin complex 1 (mTORC1) integrates mitogenic and stress signals to control growth and metabolism. Activation of mTORC1 by amino acids and growth factors involves recruitment of the complex to the lysosomal membrane and is further supported by lysosome distribution to the cell periphery. Here, we show that translocation of lysosomes toward the cell periphery brings mTORC1 into proximity with focal adhesions (FAs). We demonstrate that FAs constitute discrete plasma membrane hubs mediating growth factor signaling and amino acid input into the cell. FAs, as well as the translocation of lysosome-bound mTORC1 to their vicinity, contribute to both peripheral and intracellular mTORC1 activity. Conversely, lysosomal distribution to the cell periphery is dispensable for the activation of mTORC1 constitutively targeted to FAs. This study advances our understanding of spatial mTORC1 regulation by demonstrating that the localization of mTORC1 to FAs is both necessary and sufficient for its activation by growth-promoting stimuli.
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Affiliation(s)
- Yoana Rabanal-Ruiz
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Adam Byron
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Alexander Wirth
- Cellular Neurophysiology, Hannover Medical School, Hannover, Germany
| | - Ralitsa Madsen
- UCL Cancer Institute, University College London, London, UK
| | - Lucia Sedlackova
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Graeme Hewitt
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Glyn Nelson
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Julian Stingele
- Gene Center, Ludwig Maximilians University Munich, Munich, Germany
- Department of Biochemistry, Ludwig Maximilians University Munich, Munich, Germany
| | - Jimi C. Wills
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Tong Zhang
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - André Zeug
- Cellular Neurophysiology, Hannover Medical School, Hannover, Germany
| | - Reinhard Fässler
- Department of Molecular Medicine, Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | - Oliver D.K. Maddocks
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Evgeni Ponimaskin
- Cellular Neurophysiology, Hannover Medical School, Hannover, Germany
- Institute of Neuroscience, Lobachevsky State University of Nizhni Novgorod, Nizhny Novgorod, Russia
| | | | - Viktor I. Korolchuk
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
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25
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Christopher JA, Stadler C, Martin CE, Morgenstern M, Pan Y, Betsinger CN, Rattray DG, Mahdessian D, Gingras AC, Warscheid B, Lehtiö J, Cristea IM, Foster LJ, Emili A, Lilley KS. Subcellular proteomics. NATURE REVIEWS. METHODS PRIMERS 2021; 1:32. [PMID: 34549195 PMCID: PMC8451152 DOI: 10.1038/s43586-021-00029-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/15/2021] [Indexed: 12/11/2022]
Abstract
The eukaryotic cell is compartmentalized into subcellular niches, including membrane-bound and membrane-less organelles. Proteins localize to these niches to fulfil their function, enabling discreet biological processes to occur in synchrony. Dynamic movement of proteins between niches is essential for cellular processes such as signalling, growth, proliferation, motility and programmed cell death, and mutations causing aberrant protein localization are associated with a wide range of diseases. Determining the location of proteins in different cell states and cell types and how proteins relocalize following perturbation is important for understanding their functions, related cellular processes and pathologies associated with their mislocalization. In this Primer, we cover the major spatial proteomics methods for determining the location, distribution and abundance of proteins within subcellular structures. These technologies include fluorescent imaging, protein proximity labelling, organelle purification and cell-wide biochemical fractionation. We describe their workflows, data outputs and applications in exploring different cell biological scenarios, and discuss their main limitations. Finally, we describe emerging technologies and identify areas that require technological innovation to allow better characterization of the spatial proteome.
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Affiliation(s)
- Josie A. Christopher
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Charlotte Stadler
- Department of Protein Sciences, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Claire E. Martin
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Marcel Morgenstern
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Yanbo Pan
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Cora N. Betsinger
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - David G. Rattray
- Department of Biochemistry & Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Diana Mahdessian
- Department of Protein Sciences, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Bettina Warscheid
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, Freiburg, Germany
- BIOSS and CIBSS Signaling Research Centers, University of Freiburg, Freiburg, Germany
| | - Janne Lehtiö
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Ileana M. Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Leonard J. Foster
- Department of Biochemistry & Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrew Emili
- Center for Network Systems Biology, Boston University, Boston, MA, USA
| | - Kathryn S. Lilley
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
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26
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Bu W, Levitskaya Z, Tan SM, Gao YG. Emerging evidence for kindlin oligomerization and its role in regulating kindlin function. J Cell Sci 2021; 134:256567. [PMID: 33912917 DOI: 10.1242/jcs.256115] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Integrin-mediated cell-extracellular matrix (ECM) interactions play crucial roles in a broad range of physiological and pathological processes. Kindlins are important positive regulators of integrin activation. The FERM-domain-containing kindlin family comprises three members, kindlin-1, kindlin-2 and kindlin-3 (also known as FERMT1, FERMT2 and FERMT3), which share high sequence similarity (identity >50%), as well as domain organization, but exhibit diverse tissue-specific expression patterns and cellular functions. Given the significance of kindlins, analysis of their atomic structures has been an attractive field for decades. Recently, the structures of kindlin and its β-integrin-bound form have been obtained, which greatly advance our understanding of the molecular functions that involve kindlins. In particular, emerging evidence indicates that oligomerization of kindlins might affect their integrin binding and focal adhesion localization, positively or negatively. In this Review, we presented an update on the recent progress of obtaining kindlin structures, and discuss the implication for integrin activation based on kindlin oligomerization, as well as the possible regulation of this process.
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Affiliation(s)
- Wenting Bu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore637551.,Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China518055
| | - Zarina Levitskaya
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore637551
| | - Suet-Mien Tan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore637551
| | - Yong-Gui Gao
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore637551.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore639798
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27
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Structural and functional analysis of LIM domain-dependent recruitment of paxillin to αvβ3 integrin-positive focal adhesions. Commun Biol 2021; 4:380. [PMID: 33782527 PMCID: PMC8007706 DOI: 10.1038/s42003-021-01886-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 02/11/2021] [Indexed: 02/06/2023] Open
Abstract
The LIM domain-dependent localization of the adapter protein paxillin to β3 integrin-positive focal adhesions (FAs) is not mechanistically understood. Here, by combining molecular biology, photoactivation and FA-isolation experiments, we demonstrate specific contributions of each LIM domain of paxillin and reveal multiple paxillin interactions in adhesion-complexes. Mutation of β3 integrin at a putative paxillin binding site (β3VE/YA) leads to rapidly inward-sliding FAs, correlating with actin retrograde flow and enhanced paxillin dissociation kinetics. Induced mechanical coupling of paxillin to β3VE/YA integrin arrests the FA-sliding, thereby disclosing an essential structural function of paxillin for the maturation of β3 integrin/talin clusters. Moreover, bimolecular fluorescence complementation unveils the spatial orientation of the paxillin LIM-array, juxtaposing the positive LIM4 to the plasma membrane and the β3 integrin-tail, while in vitro binding assays point to LIM1 and/or LIM2 interaction with talin-head domain. These data provide structural insights into the molecular organization of β3 integrin-FAs.
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28
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Ostrowska-Podhorodecka Z, Ding I, Lee W, Tanic J, Abbasi S, Arora PD, Liu RS, Patteson AE, Janmey PA, McCulloch CA. Vimentin tunes cell migration on collagen by controlling β1 integrin activation and clustering. J Cell Sci 2021; 134:jcs.254359. [PMID: 33558312 DOI: 10.1242/jcs.254359] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 01/20/2021] [Indexed: 12/17/2022] Open
Abstract
Vimentin is a structural protein that is required for mesenchymal cell migration and directly interacts with actin, β1 integrin and paxillin. We examined how these interactions enable vimentin to regulate cell migration on collagen. In fibroblasts, depletion of vimentin increased talin-dependent activation of β1 integrin by more than 2-fold. Loss of vimentin was associated with reduction of β1 integrin clustering by 50% and inhibition of paxillin recruitment to focal adhesions by more than 60%, which was restored by vimentin expression. This reduction of paxillin was associated with 65% lower Cdc42 activation, a 60% reduction of cell extension formation and a greater than 35% decrease in cell migration on collagen. The activation of PAK1, a downstream effector of Cdc42, was required for vimentin phosphorylation and filament maturation. We propose that vimentin tunes cell migration through collagen by acting as an adaptor protein for focal adhesion proteins, thereby regulating β1 integrin activation, resulting in well-organized, mature integrin clusters.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
| | - Isabel Ding
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
| | - Wilson Lee
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
| | - Jelena Tanic
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
| | - Sevil Abbasi
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
| | - Pamma D Arora
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
| | - Richard S Liu
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
| | - Alison E Patteson
- Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104-6393, USA.,Physics Department, Syracuse University, Syracuse, NY 13244, USA
| | - Paul A Janmey
- Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104-6393, USA
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29
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Bouti P, Webbers SDS, Fagerholm SC, Alon R, Moser M, Matlung HL, Kuijpers TW. β2 Integrin Signaling Cascade in Neutrophils: More Than a Single Function. Front Immunol 2021; 11:619925. [PMID: 33679708 PMCID: PMC7930317 DOI: 10.3389/fimmu.2020.619925] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/31/2020] [Indexed: 12/13/2022] Open
Abstract
Neutrophils are the most prevalent leukocytes in the human body. They have a pivotal role in the innate immune response against invading bacterial and fungal pathogens, while recent emerging evidence also demonstrates their role in cancer progression and anti-tumor responses. The efficient execution of many neutrophil effector responses requires the presence of β2 integrins, in particular CD11a/CD18 or CD11b/CD18 heterodimers. Although extensively studied at the molecular level, the exact signaling cascades downstream of β2 integrins still remain to be fully elucidated. In this review, we focus mainly on inside-out and outside-in signaling of these two β2 integrin members expressed on neutrophils and describe differences between various neutrophil stimuli with respect to integrin activation, integrin ligand binding, and the pertinent differences between mouse and human studies. Last, we discuss how integrin signaling studies could be used to explore the therapeutic potential of targeting β2 integrins and the intracellular signaling cascade in neutrophils in several, among other, inflammatory conditions in which neutrophil activity should be dampened to mitigate disease.
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Affiliation(s)
- Panagiota Bouti
- Sanquin Research and Landsteiner Laboratory, Department of Blood Cell Research, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Steven D S Webbers
- Sanquin Research and Landsteiner Laboratory, Department of Blood Cell Research, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands.,Department of Pediatric Immunology, Rheumatology and Infectious Disease, Amsterdam University Medical Center (AUMC), Emma Children's Hospital, University of Amsterdam, Amsterdam, Netherlands
| | - Susanna C Fagerholm
- Research Program of Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Ronen Alon
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
| | - Markus Moser
- Institute of Experimental Hematology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Hanke L Matlung
- Sanquin Research and Landsteiner Laboratory, Department of Blood Cell Research, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Taco W Kuijpers
- Sanquin Research and Landsteiner Laboratory, Department of Blood Cell Research, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands.,Department of Pediatric Immunology, Rheumatology and Infectious Disease, Amsterdam University Medical Center (AUMC), Emma Children's Hospital, University of Amsterdam, Amsterdam, Netherlands
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30
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Samoudi M, Kuo CC, Robinson CM, Shams-Ud-Doha K, Schinn SM, Kol S, Weiss L, Petersen Bjorn S, Voldborg BG, Rosa Campos A, Lewis NE. In situ detection of protein interactions for recombinant therapeutic enzymes. Biotechnol Bioeng 2021; 118:890-904. [PMID: 33169829 PMCID: PMC7855575 DOI: 10.1002/bit.27621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 10/20/2020] [Accepted: 10/25/2020] [Indexed: 12/13/2022]
Abstract
Despite their therapeutic potential, many protein drugs remain inaccessible to patients since they are difficult to secrete. Each recombinant protein has unique physicochemical properties and requires different machinery for proper folding, assembly, and posttranslational modifications (PTMs). Here we aimed to identify the machinery supporting recombinant protein secretion by measuring the protein-protein interaction (PPI) networks of four different recombinant proteins (SERPINA1, SERPINC1, SERPING1, and SeAP) with various PTMs and structural motifs using the proximity-dependent biotin identification (BioID) method. We identified PPIs associated with specific features of the secreted proteins using a Bayesian statistical model and found proteins involved in protein folding, disulfide bond formation, and N-glycosylation were positively correlated with the corresponding features of the four model proteins. Among others, oxidative folding enzymes showed the strongest association with disulfide bond formation, supporting their critical roles in proper folding and maintaining the ER stability. Knockdown of disulfide-isomerase PDIA4, a measured interactor with significance for SERPINC1 but not SERPINA1, led to the decreased secretion of SERPINC1, which relies on its extensive disulfide bonds, compared to SERPINA1, which has no disulfide bonds. Proximity-dependent labeling successfully identified the transient interactions supporting synthesis of secreted recombinant proteins and refined our understanding of key molecular mechanisms of the secretory pathway during recombinant protein production.
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Affiliation(s)
- Mojtaba Samoudi
- Dept of Pediatrics, University of California, San Diego
- Novo Nordisk Foundation Center for Biosustainability at UC San Diego
| | - Chih-Chung Kuo
- Novo Nordisk Foundation Center for Biosustainability at UC San Diego
- Dept of Bioengineering, University of California, San Diego
| | - Caressa M. Robinson
- Novo Nordisk Foundation Center for Biosustainability at UC San Diego
- Dept of Bioengineering, University of California, San Diego
| | | | - Song-Min Schinn
- Dept of Pediatrics, University of California, San Diego
- Novo Nordisk Foundation Center for Biosustainability at UC San Diego
| | - Stefan Kol
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark
| | - Linus Weiss
- Dept of Biochemistry, Eberhard Karls University of Tübingen, Germany
| | - Sara Petersen Bjorn
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark
| | - Bjorn G. Voldborg
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark
| | | | - Nathan E. Lewis
- Dept of Pediatrics, University of California, San Diego
- Novo Nordisk Foundation Center for Biosustainability at UC San Diego
- Dept of Bioengineering, University of California, San Diego
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31
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Abstract
The extracellular matrix (ECM) is the noncellular compartment of living organisms and is formed of a complex network of cross-linked proteins, which is collectively known as the matrisome. Apart from providing the structure for an organism, cells interact and thereby communicate with the ECM. Cells interact with their surrounding ECM using cell-surface receptors, such as integrins. Upon integrin engagement with the ECM, cytoskeletal proteins are recruited to integrins and form a molecular protein complex known as the integrin adhesome. Global descriptions of the matrisome and integrin adhesome have been proposed using in silico bioinformatics approaches, as well as through biochemical enrichment of matrisome and adhesome fractions coupled with mass spectrometry-based proteomic analyses, providing inventories of their compositions in different contexts. Here, methods are described for the computational downstream analyses of matrisome and adhesome mass spectrometry datasets that are accessible to wet lab biologists, which include comparing datasets to in silico descriptions, generating interaction networks and performing functional ontological analyses.
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32
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Proximity-Dependent Biotinylation (BioID) of Integrin Interaction Partners. Methods Mol Biol 2020. [PMID: 33215377 DOI: 10.1007/978-1-0716-0962-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/02/2023]
Abstract
Integrins are heterodimeric adhesion receptors that maintain cell-extracellular matrix (ECM) interactions in diverse tissue microenvironments. They mediate cell adhesion and signaling through the assembly of large cytoplasmic multiprotein complexes that focally connect with the cytoskeleton. Integrin adhesion complexes (IAC) are specialized by the type of integrin-ECM contact and are sensitive to mechanical forces. Thus, they encrypt context-dependent information about the microenvironment in their composition. Signals mediated through IACs modulate many aspects of cell behavior, which allows cells to adapt to their surroundings. To gain insights into their function, IACs have been isolated from cultured cells and explored by proteomics. IACs are insoluble by nature and held together by transient/weak interactions, which makes it challenging to isolate intact IACs. Usually all IACs coupled to a specified ECM, which may employ different integrins, are isolated. Here we describe an alternative method based on proximity-dependent biotin identification (BioID), where specific integrin interaction partners are labeled in live cells and isolated without the need to isolate intact IACs.
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33
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Zheng J, Chen X, Yang Y, Tan CSH, Tian R. Mass Spectrometry-Based Protein Complex Profiling in Time and Space. Anal Chem 2020; 93:598-619. [DOI: 10.1021/acs.analchem.0c04332] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jiangnan Zheng
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiong Chen
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yun Yang
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Chris Soon Heng Tan
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ruijun Tian
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
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34
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Pino LK, Rose J, O'Broin A, Shah S, Schilling B. Emerging mass spectrometry-based proteomics methodologies for novel biomedical applications. Biochem Soc Trans 2020; 48:1953-1966. [PMID: 33079175 PMCID: PMC7609030 DOI: 10.1042/bst20191091] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 12/14/2022]
Abstract
Research into the basic biology of human health and disease, as well as translational human research and clinical applications, all benefit from the growing accessibility and versatility of mass spectrometry (MS)-based proteomics. Although once limited in throughput and sensitivity, proteomic studies have quickly grown in scope and scale over the last decade due to significant advances in instrumentation, computational approaches, and bio-sample preparation. Here, we review these latest developments in MS and highlight how these techniques are used to study the mechanisms, diagnosis, and treatment of human diseases. We first describe recent groundbreaking technological advancements for MS-based proteomics, including novel data acquisition techniques and protein quantification approaches. Next, we describe innovations that enable the unprecedented depth of coverage in protein signaling and spatiotemporal protein distributions, including studies of post-translational modifications, protein turnover, and single-cell proteomics. Finally, we explore new workflows to investigate protein complexes and structures, and we present new approaches for protein-protein interaction studies and intact protein or top-down MS. While these approaches are only recently incipient, we anticipate that their use in biomedical MS proteomics research will offer actionable discoveries for the improvement of human health.
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Affiliation(s)
- Lindsay K. Pino
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, U.S.A
| | - Jacob Rose
- Buck Institute for Research on Aging, Novato, CA, U.S.A
| | - Amy O'Broin
- Buck Institute for Research on Aging, Novato, CA, U.S.A
| | - Samah Shah
- Buck Institute for Research on Aging, Novato, CA, U.S.A
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35
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Pedley R, King LE, Mallikarjun V, Wang P, Swift J, Brennan K, Gilmore AP. BioID-based proteomic analysis of the Bid interactome identifies novel proteins involved in cell-cycle-dependent apoptotic priming. Cell Death Dis 2020; 11:872. [PMID: 33067418 PMCID: PMC7567853 DOI: 10.1038/s41419-020-03091-8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 09/24/2020] [Accepted: 09/28/2020] [Indexed: 12/12/2022]
Abstract
Apoptotic priming controls the commitment of cells to apoptosis by determining how close they lie to mitochondrial permeabilisation. Variations in priming are important for how both healthy and cancer cells respond to chemotherapeutic agents, but how it is dynamically coordinated by Bcl-2 proteins remains unclear. The Bcl-2 family protein Bid is phosphorylated when cells enter mitosis, increasing apoptotic priming and sensitivity to antimitotic drugs. Here, we report an unbiased proximity biotinylation (BioID) screen to identify regulators of apoptotic priming in mitosis, using Bid as bait. The screen primarily identified proteins outside of the canonical Bid interactome. Specifically, we found that voltage-dependent anion-selective channel protein 2 (VDAC2) was required for Bid phosphorylation-dependent changes in apoptotic priming during mitosis. These results highlight the importance of the wider Bcl-2 family interactome in regulating the temporal control of apoptotic priming.
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Affiliation(s)
- Robert Pedley
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Louise E King
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Venkatesh Mallikarjun
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Pengbo Wang
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
- Cancer Research UK Manchester Institute, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Joe Swift
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Keith Brennan
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Andrew P Gilmore
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.
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Sun X, Phua DYZ, Axiotakis L, Smith MA, Blankman E, Gong R, Cail RC, Espinosa de Los Reyes S, Beckerle MC, Waterman CM, Alushin GM. Mechanosensing through Direct Binding of Tensed F-Actin by LIM Domains. Dev Cell 2020; 55:468-482.e7. [PMID: 33058779 DOI: 10.1016/j.devcel.2020.09.022] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 08/04/2020] [Accepted: 09/21/2020] [Indexed: 01/21/2023]
Abstract
Mechanical signals transmitted through the cytoplasmic actin cytoskeleton must be relayed to the nucleus to control gene expression. LIM domains are protein-protein interaction modules found in cytoskeletal proteins and transcriptional regulators. Here, we identify three LIM protein families (zyxin, paxillin, and FHL) whose members preferentially localize to the actin cytoskeleton in mechanically stimulated cells through their tandem LIM domains. A minimal actin-myosin reconstitution system reveals that representatives of all three families directly bind F-actin only in the presence of mechanical force. Point mutations at a site conserved in each LIM domain of these proteins disrupt tensed F-actin binding in vitro and cytoskeletal localization in cells, demonstrating a common, avidity-based mechanism. Finally, we find that binding to tensed F-actin in the cytoplasm excludes the cancer-associated transcriptional co-activator FHL2 from the nucleus in stiff microenvironments. This establishes direct force-activated F-actin binding as a mechanosensing mechanism by which cytoskeletal tension can govern nuclear localization.
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Affiliation(s)
- Xiaoyu Sun
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, NY 10065, USA
| | - Donovan Y Z Phua
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, NY 10065, USA
| | - Lucas Axiotakis
- Laboratory of Macromolecular Interactions, Cell Biology and Physiology Center, Division of Intramural Research, National Heart Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Mark A Smith
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Elizabeth Blankman
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Rui Gong
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, NY 10065, USA
| | - Robert C Cail
- Laboratory of Macromolecular Interactions, Cell Biology and Physiology Center, Division of Intramural Research, National Heart Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | | | - Mary C Beckerle
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Clare M Waterman
- Cell and Developmental Biology Center, Division of Intramural Research, National Heart Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Gregory M Alushin
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, NY 10065, USA; Laboratory of Macromolecular Interactions, Cell Biology and Physiology Center, Division of Intramural Research, National Heart Lung and Blood Institute, NIH, Bethesda, MD 20892, USA.
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37
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Chastney MR, Lawless C, Humphries MJ. Multiplexed Proximity Biotinylation Coupled to Mass Spectrometry for Defining Integrin Adhesion Complexes. CURRENT PROTOCOLS IN CELL BIOLOGY 2020; 88:e113. [PMID: 32833344 DOI: 10.1002/cpcb.113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BioID, a proximity biotinylation technique, offers a valuable approach to examine the interactions occurring within protein complexes that complements traditional protein biochemical methods. BioID has various advantages that are beneficial to the study of complexes, including an ability to detect insoluble and transient proteins. We have applied BioID to the study of integrin adhesion complexes (IACs), which are located at the junction between the plasma membrane and actin cytoskeleton. The use of multiple BioID baits enables a complex-wide, spatial annotation of IACs, which in turn facilitates the detection of novel proximal interactors and provides insights into IAC architecture. This article describes the labeling and affinity purification of IAC-proximal proteins and their analysis by label-free quantitative mass spectrometry. The article also outlines steps to identify high-confidence proximity interactors, and to interrogate the topology and functional relevance of proximity interaction networks through bioinformatic analyses. © 2020 The Authors. Basic Protocol 1: Proximity biotinylation of integrin adhesion complex components Basic Protocol 2: Mass spectrometry data processing by MaxQuant and detection of high-confidence proximal interactors Basic Protocol 3: Bioinformatic analysis and data visualization.
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Affiliation(s)
- Megan R Chastney
- Faculty of Biology, Medicine & Health, Wellcome Centre for Cell-Matrix Research, Manchester Academic Health Science Centre, University of Manchester, Michael Smith Building, Oxford Road, Manchester, United Kingdom
| | - Craig Lawless
- Faculty of Biology, Medicine & Health, Wellcome Centre for Cell-Matrix Research, Manchester Academic Health Science Centre, University of Manchester, Michael Smith Building, Oxford Road, Manchester, United Kingdom
| | - Martin J Humphries
- Faculty of Biology, Medicine & Health, Wellcome Centre for Cell-Matrix Research, Manchester Academic Health Science Centre, University of Manchester, Michael Smith Building, Oxford Road, Manchester, United Kingdom
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38
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Te Molder L, Hoekman L, Kreft M, Bleijerveld O, Sonnenberg A. Comparative interactomics analysis reveals potential regulators of α6β4 distribution in keratinocytes. Biol Open 2020; 9:bio.054155. [PMID: 32709696 PMCID: PMC7438003 DOI: 10.1242/bio.054155] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The integrin α6β4 and cytoskeletal adaptor plectin are essential components of type I and type II hemidesmosomes (HDs). We recently identified an alternative type II HD adhesion complex that also contains CD151 and the integrin α3β1. Here, we have taken a BioID proximity labeling approach to define the proximity protein environment for α6β4 in keratinocytes. We identified 37 proteins that interacted with both α6 and β4, while 20 and 78 proteins specifically interacted with the α6 and β4 subunits, respectively. Many of the proximity interactors of α6β4 are components of focal adhesions (FAs) and the cortical microtubule stabilizing complex (CMSC). Though the close association of CMSCs with α6β4 in HDs was confirmed by immunofluorescence analysis, CMSCs have no role in the assembly of HDs. Analysis of the β4 interactome in the presence or absence of CD151 revealed that they are strikingly similar; only 11 different interactors were identified. One of these was the integrin α3β1, which interacted with α6β4 more strongly in the presence of CD151 than in its absence. These findings indicate that CD151 does not significantly contribute to the interactome of α6β4, but suggest a role of CD151 in linking α3β1 and α6β4 together in tetraspanin adhesion structures. Summary: Comparative interactomics analysis reveals close proximity of HDs, FAs and CMSCs, and a role of CD151 in linking α3β1 and α6β4 together in an alternative type II HD-like adhesion complex.
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Affiliation(s)
- Lisa Te Molder
- Division of Cell Biology I, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, The Netherlands
| | - Liesbeth Hoekman
- Mass Spectrometry/Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, The Netherlands
| | - Maaike Kreft
- Division of Cell Biology I, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, The Netherlands
| | - Onno Bleijerveld
- Mass Spectrometry/Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, The Netherlands
| | - Arnoud Sonnenberg
- Division of Cell Biology I, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, The Netherlands
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Chastney MR, Lawless C, Humphries JD, Warwood S, Jones MC, Knight D, Jorgensen C, Humphries MJ. Topological features of integrin adhesion complexes revealed by multiplexed proximity biotinylation. J Cell Biol 2020; 219:e202003038. [PMID: 32585685 PMCID: PMC7401799 DOI: 10.1083/jcb.202003038] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/09/2020] [Accepted: 04/28/2020] [Indexed: 12/16/2022] Open
Abstract
Integrin adhesion complexes (IACs) bridge the extracellular matrix to the actin cytoskeleton and transduce signals in response to both chemical and mechanical cues. The composition, interactions, stoichiometry, and topological organization of proteins within IACs are not fully understood. To address this gap, we used multiplexed proximity biotinylation (BioID) to generate an in situ, proximity-dependent adhesome in mouse pancreatic fibroblasts. Integration of the interactomes of 16 IAC-associated baits revealed a network of 147 proteins with 361 proximity interactions. Candidates with underappreciated roles in adhesion were identified, in addition to established IAC components. Bioinformatic analysis revealed five clusters of IAC baits that link to common groups of prey, and which therefore may represent functional modules. The five clusters, and their spatial associations, are consistent with current models of IAC interaction networks and stratification. This study provides a resource to examine proximal relationships within IACs at a global level.
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Affiliation(s)
- Megan R. Chastney
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Craig Lawless
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Jonathan D. Humphries
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Stacey Warwood
- Biological Mass Spectrometry Core Facility, Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Matthew C. Jones
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - David Knight
- Biological Mass Spectrometry Core Facility, Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Claus Jorgensen
- Cancer Research UK Manchester Institute, Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Alderley Park, Manchester, UK
| | - Martin J. Humphries
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
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Kadry YA, Maisuria EM, Huet-Calderwood C, Calderwood DA. Differences in self-association between kindlin-2 and kindlin-3 are associated with differential integrin binding. J Biol Chem 2020; 295:11161-11173. [PMID: 32546480 DOI: 10.1074/jbc.ra120.013618] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/03/2020] [Indexed: 12/15/2022] Open
Abstract
The integrin family of transmembrane adhesion receptors coordinates complex signaling networks that control the ability of cells to sense and communicate with the extracellular environment. Kindlin proteins are a central cytoplasmic component of these networks, directly binding integrin cytoplasmic domains and mediating interactions with cytoskeletal and signaling proteins. The physiological importance of kindlins is well established, but how the scaffolding functions of kindlins are regulated at the molecular level is still unclear. Here, using a combination of GFP nanotrap association assays, pulldown and integrin-binding assays, and live-cell imaging, we demonstrate that full-length kindlins can oligomerize (self-associate) in mammalian cells, and we propose that this self-association inhibits integrin binding and kindlin localization to focal adhesions. We show that both kindlin-2 and kindlin-3 can self-associate and that kindlin-3 self-association is more robust. Using chimeric mapping, we demonstrate that the F2PH and F3 subdomains are important for kindlin self-association. Through comparative sequence analysis of kindlin-2 and kindlin-3, we identify kindlin-3 point mutations that decrease self-association and enhance integrin binding, affording mutant kindlin-3 the ability to localize to focal adhesions. Our results support the notion that kindlin self-association negatively regulates integrin binding.
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Affiliation(s)
- Yasmin A Kadry
- Department of Pharmacology, Yale University, New Haven, Connecticut, USA
| | - Eesha M Maisuria
- Department of Molecular Biophysics and Biochemistry, Yale College, Yale University, New Haven, Connecticut, USA
| | | | - David A Calderwood
- Department of Pharmacology, Yale University, New Haven, Connecticut, USA .,Department of Cell Biology, Yale University, New Haven, Connecticut, USA
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41
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Cell matrix adhesion in cell migration. Essays Biochem 2020; 63:535-551. [PMID: 31444228 DOI: 10.1042/ebc20190012] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/22/2019] [Accepted: 08/06/2019] [Indexed: 02/06/2023]
Abstract
The ability of cells to migrate is a fundamental physiological process involved in embryonic development, tissue homeostasis, immune surveillance and wound healing. In order for cells to migrate, they must interact with their environment using adhesion receptors, such as integrins, and form specialized adhesion complexes that mediate responses to different extracellular cues. In this review, we discuss the role of integrin adhesion complexes (IACs) in cell migration, highlighting the layers of regulation that are involved, including intracellular signalling cascades, mechanosensing and reciprocal feedback to the extracellular environment. We also discuss the role of IACs in extracellular matrix remodeling and how they impact upon cell migration.
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42
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Samavarchi-Tehrani P, Samson R, Gingras AC. Proximity Dependent Biotinylation: Key Enzymes and Adaptation to Proteomics Approaches. Mol Cell Proteomics 2020; 19:757-773. [PMID: 32127388 PMCID: PMC7196579 DOI: 10.1074/mcp.r120.001941] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/25/2020] [Indexed: 12/12/2022] Open
Abstract
The study of protein subcellular distribution, their assembly into complexes and the set of proteins with which they interact with is essential to our understanding of fundamental biological processes. Complementary to traditional assays, proximity-dependent biotinylation (PDB) approaches coupled with mass spectrometry (such as BioID or APEX) have emerged as powerful techniques to study proximal protein interactions and the subcellular proteome in the context of living cells and organisms. Since their introduction in 2012, PDB approaches have been used in an increasing number of studies and the enzymes themselves have been subjected to intensive optimization. How these enzymes have been optimized and considerations for their use in proteomics experiments are important questions. Here, we review the structural diversity and mechanisms of the two main classes of PDB enzymes: the biotin protein ligases (BioID) and the peroxidases (APEX). We describe the engineering of these enzymes for PDB and review emerging applications, including the development of PDB for coincidence detection (split-PDB). Lastly, we briefly review enzyme selection and experimental design guidelines and reflect on the labeling chemistries and their implication for data interpretation.
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Affiliation(s)
| | - Reuben Samson
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada.
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43
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Kadry YA, Calderwood DA. Chapter 22: Structural and signaling functions of integrins. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2020; 1862:183206. [PMID: 31991120 PMCID: PMC7063833 DOI: 10.1016/j.bbamem.2020.183206] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/21/2020] [Accepted: 01/22/2020] [Indexed: 02/06/2023]
Abstract
The integrin family of transmembrane adhesion receptors is essential for sensing and adhering to the extracellular environment. Integrins are heterodimers composed of non-covalently associated α and β subunits that engage extracellular matrix proteins and couple to intracellular signaling and cytoskeletal complexes. Humans have 24 different integrin heterodimers with differing ligand binding specificities and non-redundant functions. Complex structural rearrangements control the ability of integrins to engage ligands and to activate diverse downstream signaling networks, modulating cell adhesion and dynamics, processes which are crucial for metazoan life and development. Here we review the structural and signaling functions of integrins focusing on recent advances which have enhanced our understanding of how integrins are activated and regulated, and the cytoplasmic signaling networks downstream of integrins.
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Affiliation(s)
- Yasmin A Kadry
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, United States of America
| | - David A Calderwood
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, United States of America; Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, United States of America..
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44
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Conformationally active integrin endocytosis and traffic: why, where, when and how? Biochem Soc Trans 2020; 48:83-93. [PMID: 32065228 PMCID: PMC7054750 DOI: 10.1042/bst20190309] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/16/2020] [Accepted: 01/28/2020] [Indexed: 12/30/2022]
Abstract
Spatiotemporal control of integrin-mediated cell adhesion to the extracellular matrix (ECM) is critical for physiological and pathological events in multicellular organisms, such as embryonic development, angiogenesis, platelet aggregation, leukocytes extravasation, and cancer cell metastatic dissemination. Regulation of integrin adhesive function and signaling relies on the modulation of both conformation and traffic. Indeed, integrins exist in a dynamic equilibrium between a bent/closed (inactive) and an extended/open (active) conformation, respectively endowed with low and high affinity for ECM ligands. Increasing evidence proves that, differently to what hypothesized in the past, detachment from the ECM and conformational inactivation are not mandatory for integrin to get endocytosed and trafficked. Specific transmembrane and cytosolic proteins involved in the control of ECM proteolytic fragment-bound active integrin internalization and recycling exist. In the complex masterplan that governs cell behavior, active integrin traffic is key to the turnover of ECM polymers and adhesion sites, the polarized secretion of endogenous ECM proteins and modifying enzymes, the propagation of motility and survival endosomal signals, and the control of cell metabolism.
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45
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Abstract
The endothelium physically separates blood from surrounding tissue and yet allows for the regulated passage of nutrients, waste, and leukocytes into and out of the circulation. Trans-endothelium flux occurs across endothelial cells (transcellular) and between endothelial cells (paracellular). Paracellular endothelial barrier function depends on the regulation of cell-cell junctions. Interestingly, a functional relationship between cell-cell junctions and cell-matrix adhesions has long been appreciated but the molecular mechanisms underpinning this relationship are not fully understood. Here we review the evidence that supports the notion that cell-matrix interactions contribute to the regulation of cell-cell junctions, focusing primarily on the important adherens junction protein VE-cadherin. In particular, we will discuss recent insights gained into how integrin signaling impacts VE-cadherin stability in adherens junctions and endothelial barrier function.
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Affiliation(s)
- Fadi E Pulous
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center (FEP, BGP) and Cancer Biology Graduate Program (FEP), Emory University School of Medicine, Atlanta, GA, USA
| | - Brian G Petrich
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center (FEP, BGP) and Cancer Biology Graduate Program (FEP), Emory University School of Medicine, Atlanta, GA, USA
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46
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Santin YG. Uncovering the In Vivo Proxisome Using Proximity‐Tagging Methods. Bioessays 2019; 41:e1900131. [DOI: 10.1002/bies.201900131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/04/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Yoann G. Santin
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie de la MéditerranéeAix‐Marseille Université – CNRS UMR7255 31 Chemin Joseph Aiguier, CS70071, 13402 Marseille Cedex 09 France
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47
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Chen C, Manso AM, Ross RS. Talin and Kindlin as Integrin-Activating Proteins: Focus on the Heart. Pediatr Cardiol 2019; 40:1401-1409. [PMID: 31367953 PMCID: PMC7590617 DOI: 10.1007/s00246-019-02167-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 07/18/2019] [Indexed: 01/11/2023]
Abstract
Integrin receptors enable cells to sense and respond to their chemical and physical environment. As a class of membrane receptors, they provide a dynamic, tightly regulated link between the extracellular matrix or cellular counter-receptors and intracellular cytoskeletal and signaling networks. They enable transmission of mechanical force across the plasma membrane, and particularly for cardiomyocytes, may sense the mechanical load placed on cells. Talins and Kindlins are two families of FERM-domain proteins which bind the cytoplasmic tail of integrins, recruit cytoskeletal and signaling proteins involved in mechano-transduction, and those which synergize to activate integrins, allowing the integrins to physically change and bind to extracellular ligands. In this review, we will discuss the roles of talin and kindlin, particularly as integrin activators, with a focus on cardiac myocytes.
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Affiliation(s)
- Chao Chen
- Department of Medicine/Cardiology, UCSD School of Medicine, La Jolla, CA, 92093, USA
- Department of Medicine/Cardiology, Veterans Administration Healthcare, San Diego, CA, 92161, USA
| | - Ana Maria Manso
- Department of Medicine/Cardiology, UCSD School of Medicine, La Jolla, CA, 92093, USA
- Department of Medicine/Cardiology, Veterans Administration Healthcare, San Diego, CA, 92161, USA
| | - Robert S Ross
- Department of Medicine/Cardiology, UCSD School of Medicine, La Jolla, CA, 92093, USA.
- Department of Medicine/Cardiology, Veterans Administration Healthcare, San Diego, CA, 92161, USA.
- University of California, San Diego, Biomedical Research Facility 2, Room 2A-17, 9500 Gilman Drive #0613-C, La Jolla, CA, 92093-0613, USA.
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48
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Lock JG, Baschieri F, Jones MC, Humphries JD, Montagnac G, Strömblad S, Humphries MJ. Clathrin-containing adhesion complexes. J Cell Biol 2019; 218:2086-2095. [PMID: 31208994 PMCID: PMC6605790 DOI: 10.1083/jcb.201811160] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/28/2019] [Accepted: 05/29/2019] [Indexed: 12/27/2022] Open
Abstract
An understanding of the mechanisms whereby cell adhesion complexes (ACs) relay signals bidirectionally across the plasma membrane is necessary to interpret the role of adhesion in regulating migration, differentiation, and growth. A range of AC types has been defined, but to date all have similar compositions and are dependent on a connection to the actin cytoskeleton. Recently, a new class of AC has been reported that normally lacks association with both the cytoskeleton and integrin-associated adhesome components, but is rich in components of the clathrin-mediated endocytosis machinery. The characterization of this new type of adhesion structure, which is emphasized by mitotic cells and cells in long-term culture, identifies a hitherto underappreciated link between the adhesion machinery and clathrin structures at the plasma membrane. While this discovery has implications for how ACs are assembled and disassembled, it raises many other issues. Consequently, to increase awareness within the field, and stimulate research, we explore a number of the most significant questions below.
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Affiliation(s)
- John G Lock
- Department of Pathology, School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Francesco Baschieri
- Institut National de la Santé et de la Recherche Médicale U1170, Gustave Roussy Institute, Université Paris-Saclay, Villejuif, France
| | - Matthew C Jones
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Jonathan D Humphries
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Guillaume Montagnac
- Institut National de la Santé et de la Recherche Médicale U1170, Gustave Roussy Institute, Université Paris-Saclay, Villejuif, France
| | - Staffan Strömblad
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Martin J Humphries
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
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49
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Hennigan RF, Fletcher JS, Guard S, Ratner N. Proximity biotinylation identifies a set of conformation-specific interactions between Merlin and cell junction proteins. Sci Signal 2019; 12:12/578/eaau8749. [PMID: 31015291 DOI: 10.1126/scisignal.aau8749] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Neurofibromatosis type 2 is an inherited, neoplastic disease associated with schwannomas, meningiomas, and ependymomas and that is caused by inactivation of the tumor suppressor gene NF2 The NF2 gene product, Merlin, has no intrinsic catalytic activity; its tumor suppressor function is mediated through the proteins with which it interacts. We used proximity biotinylation followed by mass spectrometry and direct binding assays to identify proteins that associated with wild-type and various mutant forms of Merlin in immortalized Schwann cells. We defined a set of 52 proteins in close proximity to wild-type Merlin. Most of the Merlin-proximal proteins were components of cell junctional signaling complexes, suggesting that additional potential interaction partners may exist in adherens junctions, tight junctions, and focal adhesions. With mutant forms of Merlin that cannot bind to phosphatidylinositol 4,5-bisphosphate (PIP2) or that constitutively adopt a closed conformation, we confirmed a critical role for PIP2 binding in Merlin function and identified a large cohort of proteins that specifically interacted with Merlin in the closed conformation. Among these proteins, we identified a previously unreported Merlin-binding protein, apoptosis-stimulated p53 protein 2 (ASPP2, also called Tp53bp2), that bound to closed-conformation Merlin predominately through the FERM domain. Our results demonstrate that Merlin is a component of cell junctional mechanosensing complexes and defines a specific set of proteins through which it acts.
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Affiliation(s)
- Robert F Hennigan
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA.
| | - Jonathan S Fletcher
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | - Steven Guard
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Nancy Ratner
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
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Humphries JD, Chastney MR, Askari JA, Humphries MJ. Signal transduction via integrin adhesion complexes. Curr Opin Cell Biol 2019; 56:14-21. [PMID: 30195153 DOI: 10.1016/j.ceb.2018.08.004] [Citation(s) in RCA: 171] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/13/2018] [Accepted: 08/14/2018] [Indexed: 12/19/2022]
Abstract
Integrin adhesion complexes (IACs) have evolved over millions of years to integrate metazoan cells physically with their microenvironment. It is presumed that the simultaneous interaction of thousands of integrin receptors to binding sites in anisotropic extracellular matrix (ECM) networks enables cells to assemble a topological description of the chemical and mechanical properties of their surroundings. This information is then converted into intracellular signals that influence cell positioning, differentiation and growth, but may also influence other fundamental processes, such as protein synthesis and energy regulation. In this way, changes in the microenvironment can influence all aspects of cell phenotype. Current concepts envisage cell fate decisions being controlled by the integrated signalling output of myriad receptor clusters, but the mechanisms are not understood. Analyses of the adhesome, the complement of proteins attracted to the vicinity of IACs, are now providing insights into some of the primordial links connecting these processes. This article reviews recent advances in our understanding of the composition of IACs, the mechanisms used to transduce signals through these junctions, and the links between IACs and cell phenotype.
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Affiliation(s)
- Jonathan D Humphries
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9PT, UK
| | - Megan R Chastney
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9PT, UK
| | - Janet A Askari
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9PT, UK
| | - Martin J Humphries
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9PT, UK.
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