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Camponeschi C, Righino B, Pirolli D, Semeraro A, Ria F, De Rosa MC. Prediction of CD44 Structure by Deep Learning-Based Protein Modeling. Biomolecules 2023; 13:1047. [PMID: 37509083 PMCID: PMC10376988 DOI: 10.3390/biom13071047] [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: 05/29/2023] [Revised: 06/19/2023] [Accepted: 06/24/2023] [Indexed: 07/30/2023] Open
Abstract
CD44 is a cell surface glycoprotein transmembrane receptor that is involved in cell-cell and cell-matrix interactions. It crucially associates with several molecules composing the extracellular matrix, the main one of which is hyaluronic acid. It is ubiquitously expressed in various types of cells and is involved in the regulation of important signaling pathways, thus playing a key role in several physiological and pathological processes. Structural information about CD44 is, therefore, fundamental for understanding the mechanism of action of this receptor and developing effective treatments against its aberrant expression and dysregulation frequently associated with pathological conditions. To date, only the structure of the hyaluronan-binding domain (HABD) of CD44 has been experimentally determined. To elucidate the nature of CD44s, the most frequently expressed isoform, we employed the recently developed deep-learning-based tools D-I-TASSER, AlphaFold2, and RoseTTAFold for an initial structural prediction of the full-length receptor, accompanied by molecular dynamics simulations on the most promising model. All three approaches correctly predicted the HABD, with AlphaFold2 outperforming D-I-TASSER and RoseTTAFold in the structural comparison with the crystallographic HABD structure and confidence in predicting the transmembrane helix. Low confidence regions were also predicted, which largely corresponded to the disordered regions of CD44s. These regions allow the receptor to perform its unconventional activity.
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Affiliation(s)
- Chiara Camponeschi
- Institute of Chemical Sciences and Technologies ''Giulio Natta'' (SCITEC)-CNR, 00168 Rome, Italy
| | - Benedetta Righino
- Institute of Chemical Sciences and Technologies ''Giulio Natta'' (SCITEC)-CNR, 00168 Rome, Italy
| | - Davide Pirolli
- Institute of Chemical Sciences and Technologies ''Giulio Natta'' (SCITEC)-CNR, 00168 Rome, Italy
| | - Alessandro Semeraro
- Department of Chemistry and Technology of Drugs, Sapienza University of Rome, 00185 Rome, Italy
| | - Francesco Ria
- Department of Translational Medicine and Surgery, Section of General Pathology, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Maria Cristina De Rosa
- Institute of Chemical Sciences and Technologies ''Giulio Natta'' (SCITEC)-CNR, 00168 Rome, Italy
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Moliterni C, Tredicine M, Pistilli A, Falcicchia R, Bartolini D, Stabile AM, Rende M, Ria F, Di Sante G. In Vitro and Ex Vivo Methodologies for T-Cell Trafficking Through Blood-Brain Barrier After TLR Activation. Methods Mol Biol 2023; 2700:199-219. [PMID: 37603183 DOI: 10.1007/978-1-0716-3366-3_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
This chapter describes ex vivo isolation of human T cells and of naïve splenocytes respectively collected from multiple sclerosis patients and healthy controls and experimental autoimmune encephalomyelitis-affected mice. After the magnetic sorting of naïve and activated T helper lymphocytes, we provide details about the cell cultures to measure the interaction with extracellular matrix proteins using standard cell invasion or hand-made in vitro assays, upon different stimuli, through Toll-like receptor(s) ligands, T-cell activators, and cell adhesion molecules modulators. Finally, we describe the methods to harvest and recover T cells to evaluate the properties associated with their trafficking ability.
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Affiliation(s)
- Camilla Moliterni
- Department of Translational Medicine and Surgery, Section of General Pathology, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Biology and Biotechnology Charles Darwin, University of Rome Sapienza, Rome, Italy
| | - Maria Tredicine
- Department of Translational Medicine and Surgery, Section of General Pathology, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Alessandra Pistilli
- Department of Medicine and Surgery, Section of Human Anatomy, University of Perugia, Perugia, Italy
| | - Renato Falcicchia
- Department of Translational Medicine and Surgery, Section of General Pathology, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Desirée Bartolini
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Anna Maria Stabile
- Department of Medicine and Surgery, Section of Human Anatomy, University of Perugia, Perugia, Italy
| | - Mario Rende
- Department of Medicine and Surgery, Section of Human Anatomy, University of Perugia, Perugia, Italy
| | - Francesco Ria
- Department of Translational Medicine and Surgery, Section of General Pathology, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Gabriele Di Sante
- Department of Medicine and Surgery, Section of Human Anatomy, University of Perugia, Perugia, Italy.
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Tredicine M, Camponeschi C, Pirolli D, Lucchini M, Valentini M, Geloso MC, Mirabella M, Fidaleo M, Righino B, Moliterni C, Giorda E, Rende M, De Rosa MC, Foti M, Constantin G, Ria F, Di Sante G. A TLR/CD44 axis regulates T cell trafficking in experimental and human multiple sclerosis. iScience 2022; 25:103763. [PMID: 35128357 PMCID: PMC8804271 DOI: 10.1016/j.isci.2022.103763] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/28/2021] [Accepted: 01/07/2022] [Indexed: 12/14/2022] Open
Abstract
In the pathogenesis of autoimmune disorders, the modulation of leukocytes' trafficking plays a central role, still poorly understood. Here, we focused on the effect of TLR2 ligands in trafficking of T helper cells through reshuffling of CD44 isoforms repertoire. Concurrently, strain background and TLR2 haplotype affected Wnt/β-catenin signaling pathway and expression of splicing factors. During EAE, mCD44 v9- v 10 was specifically enriched in the forebrain and showed an increased ability to bind stably to osteopontin. Similarly, we observed that hCD44 v7 was highly enriched in cells of cerebrospinal fluid from MS patients with active lesions. Moreover, TLRs engagement modulated the composition of CD44 variants also in human T helper cells, supporting the hypothesis that pathogens or commensals, through TLRs, in turn modulate the repertoire of CD44 isoforms, thereby controlling the distribution of lesions in the CNS. The interference with this mechanism(s) represents a potential tool for prevention and treatment of autoimmune relapses and exacerbations.
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Affiliation(s)
- Maria Tredicine
- Department of Translational Medicine and Surgery, Section of General Pathology, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Rome, Italy
| | - Chiara Camponeschi
- Department of Translational Medicine and Surgery, Section of General Pathology, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Rome, Italy
| | - Davide Pirolli
- Institute of Chemical Sciences and Technologies “Giulio Natta” (SCITEC) -CNR, Largo Francesco Vito 1,00168 Rome, Italy
| | - Matteo Lucchini
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli1-8,00168 Rome, Italy
- Centro di ricerca per la Sclerosi Multipla (CERSM), Università Cattolica del Sacro Cuore, Largo Francesco Vito 1,00168 Rome, Italy
| | - Mariagrazia Valentini
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli1-8,00168 Rome, Italy
| | - Maria Concetta Geloso
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli1-8,00168 Rome, Italy
- Department of Neuroscience, Section of Human Anatomy, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1,00168 Rome, Italy
| | - Massimiliano Mirabella
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli1-8,00168 Rome, Italy
- Centro di ricerca per la Sclerosi Multipla (CERSM), Università Cattolica del Sacro Cuore, Largo Francesco Vito 1,00168 Rome, Italy
| | - Marco Fidaleo
- Department of Biology and Biotechnology Charles Darwin, University of Rome Sapienza,00185 Rome, Italy
| | - Benedetta Righino
- Institute of Chemical Sciences and Technologies “Giulio Natta” (SCITEC) -CNR, Largo Francesco Vito 1,00168 Rome, Italy
| | - Camilla Moliterni
- Department of Biology and Biotechnology Charles Darwin, University of Rome Sapienza,00185 Rome, Italy
| | - Ezio Giorda
- Core Facilities di Ricerca, Ospedale Pediatrico Bambino Gesù Roma – IRCCS, V.le Ferdinando Baldelli,40,00146 Roma, Italy
| | - Mario Rende
- Department of Medicine and Surgery, Section of Human, Clinic and Forensic Anatomy, University of Perugia, Piazza L. Severi, 06132 Perugia, Italy
| | - Maria Cristina De Rosa
- Institute of Chemical Sciences and Technologies “Giulio Natta” (SCITEC) -CNR, Largo Francesco Vito 1,00168 Rome, Italy
| | - Maria Foti
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Gabriela Constantin
- Department of Medicine, Section of General Pathology, University of Verona, Strada le Grazie 8,37134 Verona, Italy
| | - Francesco Ria
- Department of Translational Medicine and Surgery, Section of General Pathology, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli1-8,00168 Rome, Italy
| | - Gabriele Di Sante
- Department of Translational Medicine and Surgery, Section of General Pathology, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Rome, Italy
- Department of Medicine and Surgery, Section of Human, Clinic and Forensic Anatomy, University of Perugia, Piazza L. Severi, 06132 Perugia, Italy
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Mayr L, Pirker C, Lötsch D, Van Schoonhoven S, Windhager R, Englinger B, Berger W, Kubista B. CD44 drives aggressiveness and chemoresistance of a metastatic human osteosarcoma xenograft model. Oncotarget 2017; 8:114095-114108. [PMID: 29371972 PMCID: PMC5768389 DOI: 10.18632/oncotarget.23125] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 11/28/2017] [Indexed: 12/15/2022] Open
Abstract
Background Osteosarcoma is the most common primary malignant bone tumor with a 5 year survival rate of up to 70%. However, patients with metastatic disease have still a very poor prognosis. Osteosarcoma metastasis models are essential to develop novel treatment strategies for advanced disease. Methods Based on a serial transplantation approach, we have established a U-2 OS osteosarcoma xenograft model with increased metastatic potential and compared it to other metastatic osteosarcoma models from international sources. Subclones with differing invasive potential were compared for genomic gains and losses as well as gene expression changes by several bioinformatic approaches. Based on the acquired results, the effects of a shRNA-mediated CD44 mRNA knockdown on migration, invasion and chemosensitivity were evaluated. Results The CD44 gene was part of an amplified region at chromosome 11p found in both U-2 OS subclones with enhanced metastatic potential but not in parental U-2 OS cells, corresponding with distinct CD44 overexpression. Accordingly, shRNA-mediated CD44 knockdown significantly attenuated osteosarcoma cell migration, invasion, and viability especially in the metastatic subclones of U-2 OS and Saos-2 cells. Metastatic subclones generally were hypersensitive against the integrin inhibitor cilengitide paralleled by alterations in integrin expression pattern following CD44 knock-down. Additionally, attenuation of CD44 expression sensitized these cell models against osteosarcoma chemotherapy with doxorubicin but not methotrexate and cisplatin. Conclusions The osteosarcoma xenograft models with increased metastatic potential developed in this study can be useful for identification of mechanisms driving metastasis and resistance towards clinically used and novel therapeutic regimens.
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Affiliation(s)
- Lisa Mayr
- Institute of Cancer Research and Comprehensive Cancer Center, Department of Medicine I, Medical University Vienna, 1090 Vienna, Austria
| | - Christine Pirker
- Institute of Cancer Research and Comprehensive Cancer Center, Department of Medicine I, Medical University Vienna, 1090 Vienna, Austria
| | - Daniela Lötsch
- Institute of Cancer Research and Comprehensive Cancer Center, Department of Medicine I, Medical University Vienna, 1090 Vienna, Austria
| | - Sushilla Van Schoonhoven
- Institute of Cancer Research and Comprehensive Cancer Center, Department of Medicine I, Medical University Vienna, 1090 Vienna, Austria
| | - Reinhard Windhager
- Department of Orthopaedics, Medical University Vienna, 1090 Vienna, Austria
| | - Bernhard Englinger
- Institute of Cancer Research and Comprehensive Cancer Center, Department of Medicine I, Medical University Vienna, 1090 Vienna, Austria
| | - Walter Berger
- Institute of Cancer Research and Comprehensive Cancer Center, Department of Medicine I, Medical University Vienna, 1090 Vienna, Austria
| | - Bernd Kubista
- Department of Orthopaedics, Medical University Vienna, 1090 Vienna, Austria
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Kim CH, Kim YD, Choi EK, Kim HR, Na BR, Im SH, Jun CD. Nuclear Speckle-related Protein 70 Binds to Serine/Arginine-rich Splicing Factors 1 and 2 via an Arginine/Serine-like Region and Counteracts Their Alternative Splicing Activity. J Biol Chem 2016; 291:6169-81. [PMID: 26797131 DOI: 10.1074/jbc.m115.689414] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Indexed: 11/06/2022] Open
Abstract
Nuclear speckles are subnuclear storage sites containing pre-mRNA splicing machinery. Proteins assembled in nuclear speckles are known to modulate transcription and pre-mRNA processing. We have previously identified nuclear speckle-related protein 70 (NSrp70) as a novel serine/arginine (SR)-related protein that co-localizes with classical SR proteins such as serine/arginine-rich splicing factor 1 (SRSF1 or ASF/SF2) and SRSF2 (SC35). NSrp70 mediates alternative splice site selection, targeting several pre-mRNAs, including CD44 exon v5. Here we demonstrated that NSrp70 interacts physically with two SR proteins, SRSF1 and SRSF2, and reverses their splicing activity in terms of CD44 exon v5 as exon exclusion. The NSrp70 RS-like region was subdivided into three areas. Deletion of the first arginine/serine-rich-like region (RS1) completely abrogated binding to the SR proteins and to target mRNA and also failed to induce splicing of CD44 exon v5, suggesting that RS1 is critical for NSrp70 functioning. Interestingly, RS1 deletion also resulted in the loss of NSrp70 and SR protein speckle positioning, implying a potential scaffolding role for NSrp70 in nuclear speckles. NSrp70 contains an N-terminal coiled-coil domain that is critical not only for self-oligomerization but also for splicing activity. Consistently, deletion of the coiled-coil domain resulted in indefinite formation of nuclear speckles. Collectively, these results demonstrate that NSrp70 acts as a new molecular counterpart for alternative splicing of target RNA, counteracting SRSF1 and SRSF2 splicing activity.
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Affiliation(s)
- Chang-Hyun Kim
- From the School of Life Sciences, Immune Synapse Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea
| | - Young-Dae Kim
- the Stem Cell Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseng-gu, Daejeon 3414, Korea, and
| | - Eun-Kyung Choi
- From the School of Life Sciences, Immune Synapse Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea
| | - Hye-Ran Kim
- From the School of Life Sciences, Immune Synapse Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea
| | - Bo-Ra Na
- From the School of Life Sciences, Immune Synapse Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea
| | - Sin-Hyeog Im
- the Academy of Immunology and Microbiology, Institute for Basic Science, and Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Chang-Duk Jun
- From the School of Life Sciences, Immune Synapse Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea,
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