1
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Hollis JA, Chan MC, Malik HS, Campbell MG. Evolutionary origin and structural ligand mimicry by the inserted domain of alpha-integrin proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.05.565221. [PMID: 37986796 PMCID: PMC10659397 DOI: 10.1101/2023.11.05.565221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Heterodimeric integrin proteins transmit signals through conformational changes upon ligand binding between their alpha (α) and beta (β) subunits. Early in chordate evolution, some α subunits acquired an "inserted" (I) domain, which expanded their ligand binding capacity but simultaneously obstructed the ancestral ligand-binding pocket. While this would seemingly impede conventional ligand-mediated integrin activation, it was proposed that the I domain itself could serve both as a ligand replacement and an activation trigger. Here, we provide compelling evidence in support of this longstanding hypothesis using high-resolution cryo-electron microscopy structures of two distinct integrin complexes: the ligand-free and E-cadherin-bound states of the αEβ7 integrin with the I domain, as well as the α4β7 integrin lacking the I domain in both a ligand-free state and bound to MadCAM-1. We trace the evolutionary origin of the I domain to an ancestral collagen-collagen interaction domain. Our analyses illuminate how the I domain intrinsically mimics an extrinsic ligand, enabling integrins to undergo the canonical allosteric cascade of conformational activation and dramatically expanding the range of cellular communication mechanisms in vertebrates.
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Affiliation(s)
- Jeremy A. Hollis
- Division of Basic Sciences, Fred Hutchinson Cancer Center; Seattle, WA 98109, USA
- Graduate Program in Molecular and Cellular Biology, University of Washington; Seattle, WA 98195, USA
| | - Matthew C. Chan
- Division of Basic Sciences, Fred Hutchinson Cancer Center; Seattle, WA 98109, USA
| | - Harmit S. Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Center; Seattle, WA 98109, USA
- Howard Hughes Medical Institute; Seattle, WA 98109, USA
| | - Melody G. Campbell
- Division of Basic Sciences, Fred Hutchinson Cancer Center; Seattle, WA 98109, USA
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2
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Totoki Y, Saito-Adachi M, Shiraishi Y, Komura D, Nakamura H, Suzuki A, Tatsuno K, Rokutan H, Hama N, Yamamoto S, Ono H, Arai Y, Hosoda F, Katoh H, Chiba K, Iida N, Nagae G, Ueda H, Shihang C, Sekine S, Abe H, Nomura S, Matsuura T, Sakai E, Ohshima T, Rino Y, Yeoh KG, So J, Sanghvi K, Soong R, Fukagawa A, Yachida S, Kato M, Seto Y, Ushiku T, Nakajima A, Katai H, Tan P, Ishikawa S, Aburatani H, Shibata T. Multiancestry genomic and transcriptomic analysis of gastric cancer. Nat Genet 2023; 55:581-594. [PMID: 36914835 DOI: 10.1038/s41588-023-01333-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/06/2023] [Indexed: 03/16/2023]
Abstract
Gastric cancer is among the most common malignancies worldwide, characterized by geographical, epidemiological and histological heterogeneity. Here, we report an extensive, multiancestral landscape of driver events in gastric cancer, involving 1,335 cases. Seventy-seven significantly mutated genes (SMGs) were identified, including ARHGAP5 and TRIM49C. We also identified subtype-specific drivers, including PIGR and SOX9, which were enriched in the diffuse subtype of the disease. SMGs also varied according to Epstein-Barr virus infection status and ancestry. Non-protein-truncating CDH1 mutations, which are characterized by in-frame splicing alterations, targeted localized extracellular domains and uniquely occurred in sporadic diffuse-type cases. In patients with gastric cancer with East Asian ancestry, our data suggested a link between alcohol consumption or metabolism and the development of RHOA mutations. Moreover, mutations with potential roles in immune evasion were identified. Overall, these data provide comprehensive insights into the molecular landscape of gastric cancer across various subtypes and ancestries.
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Affiliation(s)
- Yasushi Totoki
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Mihoko Saito-Adachi
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yuichi Shiraishi
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Daisuke Komura
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiromi Nakamura
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Akihiro Suzuki
- Department of Gastroenterology and Hepatology, Yokohama City University Graduate School of Medicine, Kanagawa, Japan.,Genome Science and Medicine Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Kenji Tatsuno
- Genome Science and Medicine Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Hirofumi Rokutan
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Natsuko Hama
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Shogo Yamamoto
- Genome Science and Medicine Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Hanako Ono
- Division of Bioinformatics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yasuhito Arai
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Fumie Hosoda
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Hiroto Katoh
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kenichi Chiba
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Naoko Iida
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Genta Nagae
- Genome Science and Medicine Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Hiroki Ueda
- Biological Data Science, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Chen Shihang
- Genome Science and Medicine Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Shigeki Sekine
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan
| | - Hiroyuki Abe
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Sachiyo Nomura
- Department of Gastrointestinal Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tetsuya Matsuura
- Department of Gastroenterology and Hepatology, Yokohama City University Graduate School of Medicine, Kanagawa, Japan
| | - Eiji Sakai
- Department of Gastroenterology and Hepatology, Yokohama City University Graduate School of Medicine, Kanagawa, Japan
| | - Takashi Ohshima
- Department of Gastrointestinal Surgery, Kanagawa Cancer Center, Kanagawa, Japan
| | - Yasushi Rino
- Department of Surgery, Yokohama City University Graduate School of Medicine, Kanagawa, Japan
| | - Khay Guan Yeoh
- Dept of Medicine, National University of Singapore, Singapore, Singapore
| | - Jimmy So
- Dept of Surgery, National University of Singapore, Singapore, Singapore
| | - Kaushal Sanghvi
- Dept of Surgery, Tan Tock Seng Hospital, Singapore, Singapore
| | - Richie Soong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Akihiko Fukagawa
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Shinichi Yachida
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan.,Division of Genomic Medicine, National Cancer Center Research Institute, Tokyo, Japan
| | - Mamoru Kato
- Division of Bioinformatics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yasuyuki Seto
- Department of Gastrointestinal Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Atsushi Nakajima
- Department of Gastroenterology and Hepatology, Yokohama City University Graduate School of Medicine, Kanagawa, Japan
| | - Hitoshi Katai
- Department of Gastric Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Patrick Tan
- Cancer and Stem Cell Biology, Duke-NUS Medical School Singapore, Singapore, Singapore.,Epigenomic and Epitranscriptomic Regulation, Genome Institute of Singapore, Singapore, Singapore
| | - Shumpei Ishikawa
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Aburatani
- Genome Science and Medicine Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan. .,Laboratory of Molecular Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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3
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Vasile F, Lavore F, Gazzola S, Vettraino C, Parisini E, Piarulli U, Belvisi L, Civera M. A combined fragment-based virtual screening and STD-NMR approach for the identification of E-cadherin ligands. Front Chem 2022; 10:946087. [PMID: 36059878 PMCID: PMC9437437 DOI: 10.3389/fchem.2022.946087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 07/22/2022] [Indexed: 12/02/2022] Open
Abstract
Cadherins promote cell-cell adhesion by forming homophilic interactions via their N-terminal extracellular domains. Hence, they have broad-ranging physiological effects on tissue organization and homeostasis. When dysregulated, cadherins contribute to different aspects of cancer progression and metastasis; therefore, targeting the cadherin adhesive interface with small-molecule antagonists is expected to have potential therapeutic and diagnostic value. Here, we used molecular docking simulations to evaluate the propensity of three different libraries of commercially available drug-like fragments (nearly 18,000 compounds) to accommodate into the Trp2 binding pocket of E-cadherin, a crucial site for the orchestration of the protein’s dimerization mechanism. Top-ranked fragments featuring five different aromatic chemotypes were expanded by means of a similarity search on the PubChem database (Tanimoto index >90%). Of this set, seven fragments containing an aromatic scaffold linked to an aliphatic chain bearing at least one amine group were finally selected for further analysis. Ligand-based NMR data (Saturation Transfer Difference, STD) and molecular dynamics simulations suggest that these fragments can bind E-cadherin mostly through their aromatic moiety, while their aliphatic portions may also diversely engage with the mobile regions of the binding site. A tetrahydro-β-carboline scaffold functionalized with an ethylamine emerged as the most promising fragment.
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Affiliation(s)
- Francesca Vasile
- Department of Chemistry, Università Degli Studi di Milano, Milan, Italy
| | - Francesca Lavore
- Department of Chemistry, Università Degli Studi di Milano, Milan, Italy
| | - Silvia Gazzola
- Department of Science and High Technology, Università Degli Studi Dell’Insubria, Como, Italy
| | - Chiara Vettraino
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia @Polimi, Milan, Italy
| | - Emilio Parisini
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia @Polimi, Milan, Italy
- Latvian Institute of Organic Synthesis, Riga, Latvia
- Department of Chemistry “Giacomo Ciamician”, Università Degli Studi di Bologna, Bologna, Italy
| | - Umberto Piarulli
- Department of Science and High Technology, Università Degli Studi Dell’Insubria, Como, Italy
| | - Laura Belvisi
- Department of Chemistry, Università Degli Studi di Milano, Milan, Italy
| | - Monica Civera
- Department of Chemistry, Università Degli Studi di Milano, Milan, Italy
- *Correspondence: Monica Civera,
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4
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Tomassetti A. Editorial to the Special Issue “Activations of Cadherin Signaling in Cancer”. Int J Mol Sci 2022; 23:ijms23137022. [PMID: 35806026 PMCID: PMC9266632 DOI: 10.3390/ijms23137022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 06/15/2022] [Indexed: 02/01/2023] Open
Abstract
The major object of this Editorial is to briefly put into context the processes, occurring during tumor onset and progression, and the biological mechanisms mediated by cadherins described in the review and research articles included in the Special Issue entitled "Activations of Cadherin Signaling in Cancer" [...].
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Affiliation(s)
- Antonella Tomassetti
- Unit of Molecular Therapies, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milan, Italy
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5
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Mendoza C, Nagidi SH, Collett K, Mckell J, Mizrachi D. Calcium regulates the interplay between the tight junction and epithelial adherens junction at the plasma membrane. FEBS Lett 2022; 596:219-231. [PMID: 34882783 DOI: 10.1002/1873-3468.14252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/05/2021] [Accepted: 12/05/2021] [Indexed: 01/15/2023]
Abstract
The apical junctional complex (AJC) is a membrane protein ultrastructure that regulates cell adhesion and homeostasis. The tight junction (TJ) and the adherens junction (AJ) are substructures of the AJC. The interplay between TJ and AJ membrane proteins to assemble the AJC remains unclear. We employed synthetic biology strategies to express the basic membrane elements of a simple AJC-the adhesive extracellular domains of junctional adhesion molecule A (JAM-A), epithelial cadherin, claudin 1, and occludin-to study their interactions. Our results suggest that calcium concentration fluctuations and JAM-A, acting as an interface molecule between the TJ and AJ, orchestrate their interplay. Calcium affects the secondary structure, oligomerization, and binding affinity of homotypic and heterotypic interactions of TJ and AJ components, thus acting as a molecular switch influencing AJC dynamics.
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Affiliation(s)
- Christopher Mendoza
- Department of Physiology and Developmental Biology, College of Life Sciences, Brigham Young University, Provo, UT, USA
| | - Sai Harsha Nagidi
- Department of Molecular Microbiology, College of Life Sciences, Brigham Young University, Provo, UT, USA
| | - Kjetil Collett
- Department of Physiology and Developmental Biology, College of Life Sciences, Brigham Young University, Provo, UT, USA
| | - Jacob Mckell
- Department of Physiology and Developmental Biology, College of Life Sciences, Brigham Young University, Provo, UT, USA
| | - Dario Mizrachi
- Department of Physiology and Developmental Biology, College of Life Sciences, Brigham Young University, Provo, UT, USA
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6
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Lee M, Ni N, Tang H, Li Y, Wei W, Kakinen A, Wan X, Davis TP, Song Y, Leong DT, Ding F, Ke PC. A Framework of Paracellular Transport via Nanoparticles-Induced Endothelial Leakiness. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2102519. [PMID: 34495564 PMCID: PMC8564447 DOI: 10.1002/advs.202102519] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/21/2021] [Indexed: 05/29/2023]
Abstract
Nanomaterial-induced endothelial leakiness (NanoEL) is an interfacial phenomenon denoting the paracellular transport of nanoparticles that is pertinent to nanotoxicology, nanomedicine and biomedical engineering. While the NanoEL phenomenon is complementary to the enhanced permeability and retention effect in terms of their common applicability to delineating the permeability and behavior of nanoparticles in tumoral environments, these two effects significantly differ in scope, origin, and manifestation. In the current study, the descriptors are fully examined of the NanoEL phenomenon elicited by generic citrate-coated gold nanoparticles (AuNPs) of changing size and concentration, from microscopic gap formation and actin reorganization down to molecular signaling pathways and nanoscale interactions of AuNPs with VE-cadherin and its intra/extracellular cofactors. Employing synergistic in silico methodologies, for the first time the molecular and statistical mechanics of cadherin pair disruption, especially in response to AuNPs of the smallest size and highest concentration are revealed. This study marks a major advancement toward establishing a comprehensive NanoEL framework for complementing the understanding of the transcytotic pathway and for guiding the design and application of future nanomedicines harnessing the myriad functions of the mammalian vasculature.
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Affiliation(s)
- Myeongsang Lee
- Department of Physics and AstronomyClemson UniversityClemsonSC29634USA
| | - Nengyi Ni
- National University of SingaporeDepartment of Chemical and Biomolecular Engineering4 Engineering Drive 4Singapore117585Singapore
| | - Huayuan Tang
- Department of Physics and AstronomyClemson UniversityClemsonSC29634USA
| | - Yuhuan Li
- Liver Cancer InstituteZhongshan HospitalKey Laboratory of Carcinogenesis and Cancer InvasionMinistry of EducationFudan UniversityShanghai200032China
- Drug DeliveryDisposition and DynamicsMonash Institute of Pharmaceutical SciencesMonash University381 Royal ParadeParkvilleVIC3052Australia
| | - Wei Wei
- Key Laboratory of Luminescence Analysis and Molecular SensingMinistry of EducationCollege of Pharmaceutical SciencesSouthwest University2 Tiansheng Rd, Beibei DistrictChongqing400715China
| | - Aleksandr Kakinen
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandBrisbaneQld4072Australia
| | - Xulin Wan
- Key Laboratory of Luminescence Analysis and Molecular SensingMinistry of EducationCollege of Pharmaceutical SciencesSouthwest University2 Tiansheng Rd, Beibei DistrictChongqing400715China
| | - Thomas P. Davis
- Drug DeliveryDisposition and DynamicsMonash Institute of Pharmaceutical SciencesMonash University381 Royal ParadeParkvilleVIC3052Australia
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandBrisbaneQld4072Australia
| | - Yang Song
- Key Laboratory of Luminescence Analysis and Molecular SensingMinistry of EducationCollege of Pharmaceutical SciencesSouthwest University2 Tiansheng Rd, Beibei DistrictChongqing400715China
- State Key Laboratory of Environmental Chemistry and EcotoxicologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
| | - David Tai Leong
- National University of SingaporeDepartment of Chemical and Biomolecular Engineering4 Engineering Drive 4Singapore117585Singapore
| | - Feng Ding
- Department of Physics and AstronomyClemson UniversityClemsonSC29634USA
| | - Pu Chun Ke
- Drug DeliveryDisposition and DynamicsMonash Institute of Pharmaceutical SciencesMonash University381 Royal ParadeParkvilleVIC3052Australia
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandBrisbaneQld4072Australia
- The GBA National Institute for Nanotechnology Innovation136 Kaiyuan AvenueGuangzhou510700China
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7
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Desaulniers D, Vasseur P, Jacobs A, Aguila MC, Ertych N, Jacobs MN. Integration of Epigenetic Mechanisms into Non-Genotoxic Carcinogenicity Hazard Assessment: Focus on DNA Methylation and Histone Modifications. Int J Mol Sci 2021; 22:10969. [PMID: 34681626 PMCID: PMC8535778 DOI: 10.3390/ijms222010969] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetics involves a series of mechanisms that entail histone and DNA covalent modifications and non-coding RNAs, and that collectively contribute to programing cell functions and differentiation. Epigenetic anomalies and DNA mutations are co-drivers of cellular dysfunctions, including carcinogenesis. Alterations of the epigenetic system occur in cancers whether the initial carcinogenic events are from genotoxic (GTxC) or non-genotoxic (NGTxC) carcinogens. NGTxC are not inherently DNA reactive, they do not have a unifying mode of action and as yet there are no regulatory test guidelines addressing mechanisms of NGTxC. To fil this gap, the Test Guideline Programme of the Organisation for Economic Cooperation and Development is developing a framework for an integrated approach for the testing and assessment (IATA) of NGTxC and is considering assays that address key events of cancer hallmarks. Here, with the intent of better understanding the applicability of epigenetic assays in chemical carcinogenicity assessment, we focus on DNA methylation and histone modifications and review: (1) epigenetic mechanisms contributing to carcinogenesis, (2) epigenetic mechanisms altered following exposure to arsenic, nickel, or phenobarbital in order to identify common carcinogen-specific mechanisms, (3) characteristics of a series of epigenetic assay types, and (4) epigenetic assay validation needs in the context of chemical hazard assessment. As a key component of numerous NGTxC mechanisms of action, epigenetic assays included in IATA assay combinations can contribute to improved chemical carcinogen identification for the better protection of public health.
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Affiliation(s)
- Daniel Desaulniers
- Environmental Health Sciences and Research Bureau, Hazard Identification Division, Health Canada, AL:2203B, Ottawa, ON K1A 0K9, Canada
| | - Paule Vasseur
- CNRS, LIEC, Université de Lorraine, 57070 Metz, France;
| | - Abigail Jacobs
- Independent at the Time of Publication, Previously US Food and Drug Administration, Rockville, MD 20852, USA;
| | - M. Cecilia Aguila
- Toxicology Team, Division of Human Food Safety, Center for Veterinary Medicine, US Food and Drug Administration, Department of Health and Human Services, Rockville, MD 20852, USA;
| | - Norman Ertych
- German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany;
| | - Miriam N. Jacobs
- Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton OX11 0RQ, UK;
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8
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Regulation of cadherin dimerization by chemical fragments as a trigger to inhibit cell adhesion. Commun Biol 2021; 4:1041. [PMID: 34493804 PMCID: PMC8423723 DOI: 10.1038/s42003-021-02575-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 08/20/2021] [Indexed: 02/07/2023] Open
Abstract
Many cadherin family proteins are associated with diseases such as cancer. Since cell adhesion requires homodimerization of cadherin molecules, a small-molecule regulator of dimerization would have therapeutic potential. Herein, we describe identification of a P-cadherin-specific chemical fragment that inhibits P-cadherin-mediated cell adhesion. Although the identified molecule is a fragment compound, it binds to a cavity of P-cadherin that has not previously been targeted, indirectly prevents formation of hydrogen bonds necessary for formation of an intermediate called the X dimer and thus modulates the process of X dimerization. Our findings will impact on a strategy for regulation of protein-protein interactions and stepwise assembly of protein complexes using small molecules.
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9
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Fan X, Jin S, Li Y, Khadaroo PA, Dai Y, He L, Zhou D, Lin H. Genetic And Epigenetic Regulation Of E-Cadherin Signaling In Human Hepatocellular Carcinoma. Cancer Manag Res 2019; 11:8947-8963. [PMID: 31802937 PMCID: PMC6801489 DOI: 10.2147/cmar.s225606] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 09/27/2019] [Indexed: 12/24/2022] Open
Abstract
E-cadherin is well known as a growth and invasion suppressor and belongs to the large cadherin family. Loss of E-cadherin is widely known as the hallmark of epithelial-to-mesenchymal transition (EMT) with the involvement of transcription factors such as Snail, Slug, Twist and Zeb1/2. Tumor cells undergoing EMT could migrate to distant sites and become metastases. Recently, numerous studies have revealed how the expression of E-cadherin is regulated by different kinds of genetic and epigenetic alteration, which are implicated in several crucial transcription factors and pathways. E-cadherin signaling plays an important role in hepatocellular carcinoma (HCC) initiation and progression considering the highly mutated frequency of CTNNB1 (27%). Combining the data from The Cancer Genome Atlas (TCGA) database and previous studies, we have summarized the roles of gene mutations, chromosome instability, DNA methylation, histone modifications and non-coding RNA in E-cadherin in HCC. In this review, we discuss the current understanding of the relationship between these modifications and HCC. Perspectives on E-cadherin-related research in HCC are provided.
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Affiliation(s)
- Xiaoxiao Fan
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Shengxi Jin
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China.,School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Yirun Li
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Parikshit Asutosh Khadaroo
- School of Medicine, Zhejiang University, Hangzhou, People's Republic of China.,School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Yili Dai
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China.,School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Lifeng He
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Daizhan Zhou
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Hui Lin
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
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10
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Dalle Vedove A, Falchi F, Donini S, Dobric A, Germain S, Di Martino GP, Prosdocimi T, Vettraino C, Torretta A, Cavalli A, Rigot V, André F, Parisini E. Structure-Based Virtual Screening Allows the Identification of Efficient Modulators of E-Cadherin-Mediated Cell-Cell Adhesion. Int J Mol Sci 2019; 20:ijms20143404. [PMID: 31373305 PMCID: PMC6678102 DOI: 10.3390/ijms20143404] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 07/06/2019] [Accepted: 07/08/2019] [Indexed: 12/13/2022] Open
Abstract
Cadherins are a large family of transmembrane calcium-dependent cell adhesion proteins that orchestrate adherens junction formation and are crucially involved in tissue morphogenesis. Due to their important role in cancer development and metastasis, cadherins can be considered attractive targets for drug discovery. A recent crystal structure of the complex of a cadherin extracellular portion and a small molecule inhibitor allowed the identification of a druggable interface, thus providing a viable strategy for the design of cadherin dimerization modulators. Here, we report on a structure-based virtual screening approach that led to the identification of efficient and selective modulators of E-cadherin-mediated cell–cell adhesion. Of all the putative inhibitors that were identified and experimentally tested by cell adhesion assays using human pancreatic tumor BxPC-3 cells expressing both E-cadherin and P-cadherin, two compounds turned out to be effective in inhibiting stable cell–cell adhesion at micromolar concentrations. Moreover, at the same concentrations, one of them also showed anti-invasive properties in cell invasion assays. These results will allow further development of novel and selective cadherin-mediated cell–cell adhesion modulators for the treatment of a variety of cadherin-expressing solid tumors and for improving the efficiency of drug delivery across biological barriers.
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Affiliation(s)
- Andrea Dalle Vedove
- Center for Nano Science and Technology @PoliMi, Istituto Italiano di Tecnologia, Via Pascoli 70/3, 20133 Milano, Italy
| | - Federico Falchi
- Computational Sciences, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40121 Bologna, Italy
| | - Stefano Donini
- Center for Nano Science and Technology @PoliMi, Istituto Italiano di Tecnologia, Via Pascoli 70/3, 20133 Milano, Italy
| | - Aurelie Dobric
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, 13273 Marseille CEDEX 09, France
| | - Sebastien Germain
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, 13273 Marseille CEDEX 09, France
| | - Giovanni Paolo Di Martino
- Computational Sciences, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40121 Bologna, Italy
| | - Tommaso Prosdocimi
- Center for Nano Science and Technology @PoliMi, Istituto Italiano di Tecnologia, Via Pascoli 70/3, 20133 Milano, Italy
| | - Chiara Vettraino
- Center for Nano Science and Technology @PoliMi, Istituto Italiano di Tecnologia, Via Pascoli 70/3, 20133 Milano, Italy
| | - Archimede Torretta
- Center for Nano Science and Technology @PoliMi, Istituto Italiano di Tecnologia, Via Pascoli 70/3, 20133 Milano, Italy
| | - Andrea Cavalli
- Computational Sciences, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40121 Bologna, Italy
| | - Veronique Rigot
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, 13273 Marseille CEDEX 09, France
| | - Frederic André
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, 13273 Marseille CEDEX 09, France
| | - Emilio Parisini
- Center for Nano Science and Technology @PoliMi, Istituto Italiano di Tecnologia, Via Pascoli 70/3, 20133 Milano, Italy.
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11
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Civera M, Vasile F, Potenza D, Colombo C, Parente S, Vettraino C, Prosdocimi T, Parisini E, Belvisi L. Exploring E-cadherin-peptidomimetics interaction using NMR and computational studies. PLoS Comput Biol 2019; 15:e1007041. [PMID: 31158220 PMCID: PMC6564044 DOI: 10.1371/journal.pcbi.1007041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 06/13/2019] [Accepted: 04/22/2019] [Indexed: 02/02/2023] Open
Abstract
Cadherins are homophilic cell-cell adhesion molecules whose aberrant expression has often been shown to correlate with different stages of tumor progression. In this work, we investigate the interaction of two peptidomimetic ligands with the extracellular portion of human E-cadherin using a combination of NMR and computational techniques. Both ligands have been previously developed as mimics of the tetrapeptide sequence Asp1-Trp2-Val3-Ile4 of the cadherin adhesion arm, and have been shown to inhibit E-cadherin-mediated adhesion in epithelial ovarian cancer cells with millimolar potency. To sample a set of possible interactions of these ligands with the E-cadherin extracellular portion, STD-NMR experiments in the presence of two slightly different constructs, the wild type E-cadherin-EC1-EC2 fragment and the truncated E-cadherin-(Val3)-EC1-EC2 fragment, were carried out at three temperatures. Depending on the protein construct, a different binding epitope of the ligand and also a different temperature effect on STD signals were observed, both suggesting an involvement of the Asp1-Trp2 protein sequence among all the possible binding events. To interpret the experimental results at the atomic level and to probe the role of the cadherin adhesion arm in the dynamic interaction with the peptidomimetic ligand, a computational protocol based on docking calculations and molecular dynamics simulations was applied. In agreement with NMR data, the simulations at different temperatures unveil high variability/dynamism in ligand-cadherin binding, thus explaining the differences in ligand binding epitopes. In particular, the modulation of the signals seems to be dependent on the protein flexibility, especially at the level of the adhesive arm, which appears to participate in the interaction with the ligand. Overall, these results will help the design of novel cadherin inhibitors that might prevent the swap dimer formation by targeting both the Trp2 binding pocket and the adhesive arm residues. Classical cadherins are the main adhesive proteins at the intercellular junctions and play an essential role in tissue morphogenesis and homeostasis. A large number of studies have shown that cadherin aberrant expression and/or dysregulation often correlate with pathological processes, such as tumor development and progression. Notwithstanding the emerging role played by cadherins in a number of solid tumors, the rational design of small inhibitors targeting these proteins is still in its infancy, likely due to the challenges posed by the development of small drug-like molecules that modulate protein-protein interactions and to the structural complexity of the various cadherin dimerization interfaces that constantly form and disappear as the protein moves along its highly dynamic and reversible homo-dimerization trajectory. In this work, we study the interaction of two small molecules with the extracellular portion of human E-cadherin using a combination of spectroscopic and computational techniques. The availability of molecules interfering in the cadherin homophilic interactions could provide a useful tool for the investigation of cadherin function in tumors, and potentially pave the way to the development of novel alternative diagnostic and therapeutic interventions in cadherin-expressing solid tumors.
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Affiliation(s)
- Monica Civera
- Dipartimento di Chimica, Università degli Studi di Milano, Milan, Italy
- Istituto di Scienze e Tecnologie Molecolari (ISTM), Consiglio Nazionale delle Ricerche, Milan, Italy
- * E-mail: (MC); (FV)
| | - Francesca Vasile
- Dipartimento di Chimica, Università degli Studi di Milano, Milan, Italy
- Istituto di Scienze e Tecnologie Molecolari (ISTM), Consiglio Nazionale delle Ricerche, Milan, Italy
- * E-mail: (MC); (FV)
| | - Donatella Potenza
- Dipartimento di Chimica, Università degli Studi di Milano, Milan, Italy
| | - Cinzia Colombo
- Dipartimento di Chimica, Università degli Studi di Milano, Milan, Italy
| | - Sara Parente
- Dipartimento di Scienza e Alta Tecnologia, Università degli Studi dell'Insubria, Como, Italy
| | - Chiara Vettraino
- Center for Nano Science and Technology @PoliMi, Istituto Italiano di Tecnologia, Milan, Italy
| | - Tommaso Prosdocimi
- Center for Nano Science and Technology @PoliMi, Istituto Italiano di Tecnologia, Milan, Italy
| | - Emilio Parisini
- Center for Nano Science and Technology @PoliMi, Istituto Italiano di Tecnologia, Milan, Italy
| | - Laura Belvisi
- Dipartimento di Chimica, Università degli Studi di Milano, Milan, Italy
- Istituto di Scienze e Tecnologie Molecolari (ISTM), Consiglio Nazionale delle Ricerche, Milan, Italy
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12
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Rea K, Roggiani F, De Cecco L, Raspagliesi F, Carcangiu ML, Nair-Menon J, Bagnoli M, Bortolomai I, Mezzanzanica D, Canevari S, Kourtidis A, Anastasiadis PZ, Tomassetti A. Simultaneous E-cadherin and PLEKHA7 expression negatively affects E-cadherin/EGFR mediated ovarian cancer cell growth. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2018; 37:146. [PMID: 29996940 PMCID: PMC6042237 DOI: 10.1186/s13046-018-0796-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 06/14/2018] [Indexed: 12/19/2022]
Abstract
Background The disruption of E-cadherin-mediated adhesion is considered an important driver of tumor progression. Nevertheless, numerous studies have demonstrated that E-cadherin promotes growth- or invasion-related signaling, contrary to the prevailing notion. During tumor progression, epithelial ovarian cancer (EOC) maintains E-cadherin expression and can positively affect EOC cell growth by contributing to PI3K/AKT activation. In polarized epithelia PLEKHA7, a regulator of the zonula adherens integrity, impinges E-cadherin functionality, but its role in EOCs has been never studied. Methods Ex-vivo EOC cells and cell lines were used to study E-cadherin contribution to growth and EGFR activation. The expression of the proteins involved was assessed by real time RT-PCR, immunohistochemistry and western blotting. Cells growth and drug susceptibility was monitored in different 3-dimensional (3D) systems. Recombinant lentivirus-mediated gene expression, western blotting, immunoprecipitation and confocal microscopy were applied to investigate the biological impact of PLEKHA7 on E-cadherin behaviour. The clinical impact of PLEKHA7 was determined in publicly available datasets. Results We show that E-cadherin expression contributes to growth of EOC cells and forms a complex with EGFR thus positively affecting ligand-dependent EGFR/CDK5 signaling. Accordingly, 3D cultures of E-cadherin-expressing EOC cells are sensitive to the CDK5 inhibitor roscovitine combined with cisplatin. We determined that PLEKHA7 overexpression reduces the formation of E-cadherin-EGFR complex, EGFR activation and cell tumorigenicity. Clinically, PLEKHA7 mRNA is statistically decreased in high grade EOCs respect to low malignant potential and low grade EOCs and correlates with better EOC patient outcome. Conclusions These data represent a significant step towards untangling the role of E-cadherin in EOCs by assessing its positive effects on EGFR/CDK5 signaling and its contribution to cell growth. Hence, the inhibition of this signaling using a CDK5 inhibitor exerts a synergistic effect with cisplatin prompting on the design of new therapeutic strategies to inhibit growth of EOC cells. We assessed for the first time in EOC cells that PLEKHA7 induces changes in the asset of E-cadherin-containing cell-cell contacts thus inhibiting E-cadherin/EGFR crosstalk and leading to a less aggressive tumor phenotype. Accordingly, PLEKHA7 levels are lower in high grade EOC patient tumors and EOC patients with better outcomes display higher PLEKHA7 levels. Electronic supplementary material The online version of this article (10.1186/s13046-018-0796-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katia Rea
- Unit of Molecular Therapies, Department of Research, Via Amadeo 42, 20133, Milan, Italy
| | - Francesca Roggiani
- Unit of Molecular Therapies, Department of Research, Via Amadeo 42, 20133, Milan, Italy
| | - Loris De Cecco
- Genomics, Department of Applied Research and Technology Development, Via Amadeo 42, 20133, Milan, Italy
| | | | - Maria Luisa Carcangiu
- Unit of Anatomic Pathology I, Deparment of Anatomic Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133, Milan, Italy
| | - Joyce Nair-Menon
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC, 29425, USA
| | - Marina Bagnoli
- Unit of Molecular Therapies, Department of Research, Via Amadeo 42, 20133, Milan, Italy
| | - Ileana Bortolomai
- Unit of Molecular Therapies, Department of Research, Via Amadeo 42, 20133, Milan, Italy.,Present address: Telethon Institute for Gene Therapy (SR-TIGET), Division of Regenerative Medicine, Stem Cells and gene Therapy, IRCCS San Raffaele Scientific Institute, Via Olgettina 60, 20132, Milan, Italy.,Department of Cancer Biology, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Delia Mezzanzanica
- Unit of Molecular Therapies, Department of Research, Via Amadeo 42, 20133, Milan, Italy
| | - Silvana Canevari
- Unit of Molecular Therapies, Department of Research, Via Amadeo 42, 20133, Milan, Italy
| | - Antonis Kourtidis
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC, 29425, USA
| | - Panos Z Anastasiadis
- Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Antonella Tomassetti
- Unit of Molecular Therapies, Department of Research, Via Amadeo 42, 20133, Milan, Italy.
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13
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Senoo A, Nagatoishi S, Moberg A, Babol LN, Mitani T, Tashima T, Kudo S, Tsumoto K. Inhibition of homophilic dimerization and disruption of cell adhesion by P-cadherin-specific small molecules from SPR-based assays. Chem Commun (Camb) 2018; 54:5350-5353. [DOI: 10.1039/c8cc01964a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Our SPR-based screening identified a compound which was able to inhibit cell adhesion mediated by homophilic dimerization of P-cadherin.
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Affiliation(s)
- Akinobu Senoo
- Department of Chemistry and Biotechnology
- School of Engineering
- The University of Tokyo
- Tokyo 113-8656
- Japan
| | - Satoru Nagatoishi
- Department of Chemistry and Biotechnology
- School of Engineering
- The University of Tokyo
- Tokyo 113-8656
- Japan
| | - Anna Moberg
- GE Healthcare Bio-sciences AB
- SE-751 84 Uppsala
- Sweden
| | | | - Tomoya Mitani
- Life Science Division
- GE Healthcare Japan
- Tokyo 169-0073
- Japan
| | - Takumi Tashima
- Department of Chemistry and Biotechnology
- School of Engineering
- The University of Tokyo
- Tokyo 113-8656
- Japan
| | - Shota Kudo
- Department of Chemistry and Biotechnology
- School of Engineering
- The University of Tokyo
- Tokyo 113-8656
- Japan
| | - Kouhei Tsumoto
- Department of Chemistry and Biotechnology
- School of Engineering
- The University of Tokyo
- Tokyo 113-8656
- Japan
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14
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Xia J, Cheng Y, Zhang H, Li R, Hu Y, Liu B. The role of adhesions between homologous cancer cells in tumor progression and targeted therapy. Expert Rev Anticancer Ther 2017; 17:517-526. [DOI: 10.1080/14737140.2017.1322511] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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15
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Roggiani F, Mezzanzanica D, Rea K, Tomassetti A. Guidance of Signaling Activations by Cadherins and Integrins in Epithelial Ovarian Cancer Cells. Int J Mol Sci 2016; 17:ijms17091387. [PMID: 27563880 PMCID: PMC5037667 DOI: 10.3390/ijms17091387] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 08/11/2016] [Accepted: 08/13/2016] [Indexed: 12/12/2022] Open
Abstract
Epithelial ovarian cancer (EOC) is the deadliest tumor among gynecological cancer in the industrialized countries. The EOC incidence and mortality have remained unchanged over the last 30 years, despite the progress in diagnosis and treatment. In order to develop novel and more effective therapeutic approaches, the molecular mechanisms involved in EOC progression have been thoroughly investigated in the last few decades. At the late stage, peritoneal metastases originate from the attachment of small clusters of cancer cells that shed from the primary site and carried by the ascites adhere to the abdominal peritoneum or omentum. This behavior suggests that cell–cell or cell–matrix adhesion mechanisms regulate EOC growth and dissemination. Complex downstream signalings, which might be influenced by functional cross-talk between adhesion molecules and co-expressed and activated signaling proteins, can affect the proliferation/survival and the migration/invasion of EOC cells. This review aimed to define the impact of the mechanisms of cell–cell, through cadherins, and cell–extracellular matrix adhesion, through integrins, on the signaling cascades induced by membrane receptors and cytoplasmic proteins known to have a role in the proliferation, migration and invasion of EOC cells. Finally, some novel approaches using peptidomimetic ligands to cadherin and integrins are summarized.
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Affiliation(s)
- Francesca Roggiani
- Unit of Molecular Therapies, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, Milan 20133, Italy.
| | - Delia Mezzanzanica
- Unit of Molecular Therapies, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, Milan 20133, Italy.
| | - Katia Rea
- Unit of Molecular Therapies, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, Milan 20133, Italy.
| | - Antonella Tomassetti
- Unit of Molecular Therapies, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, Milan 20133, Italy.
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