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Yuda GPWC, Hanif N, Hermawan A. Computational Screening Using a Combination of Ligand-Based Machine Learning and Molecular Docking Methods for the Repurposing of Antivirals Targeting the SARS-CoV-2 Main Protease. Daru 2024; 32:47-65. [PMID: 37907683 PMCID: PMC11087449 DOI: 10.1007/s40199-023-00484-w] [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: 02/21/2023] [Accepted: 09/20/2023] [Indexed: 11/02/2023] Open
Abstract
BACKGROUND COVID-19 is an infectious disease caused by SARS-CoV-2, a close relative of SARS-CoV. Several studies have searched for COVID-19 therapies. The topics of these works ranged from vaccine discovery to natural products targeting the SARS-CoV-2 main protease (Mpro), a potential therapeutic target due to its essential role in replication and conserved sequences. However, published research on this target is limited, presenting an opportunity for drug discovery and development. METHOD This study aims to repurpose 10692 drugs in DrugBank by using ligand-based virtual screening (LBVS) machine learning (ML) with Konstanz Information Miner (KNIME) to seek potential therapeutics based on Mpro inhibitors. The top candidate compounds, the native ligand (GC-376) of the Mpro inhibitor, and the positive control boceprevir were then subjected to absorption, distribution, metabolism, excretion, and toxicity (ADMET) characterization, drug-likeness prediction, and molecular docking (MD). Protein-protein interaction (PPI) network analysis was added to provide accurate information about the Mpro regulatory network. RESULTS This study identified 3,166 compound candidates inhibiting Mpro. The random forest (RF) molecular access system ML model provided the highest confidence score of 0.95 (bromo-7-nitroindazole) and identified the top 22 candidate compounds. Subjecting the 22 candidate compounds, the native ligand GC-376, and boceprevir to further ADMET property characterization and drug-likeness predictions revealed that one compound had two violations of Lipinski's rule. Additional MD results showed that only five compounds had more negative binding energies than the native ligand (- 12.25 kcal/mol). Among these compounds, CCX-140 exhibited the lowest score of - 13.64 kcal/mol. Through literature analysis, six compound classes with potential activity for Mpro were discovered. They included benzopyrazole, azole, pyrazolopyrimidine, carboxylic acids and derivatives, benzene and substituted derivatives, and diazine. Four pathologies were also discovered on the basis of the Mpro PPI network. CONCLUSION Results demonstrated the efficiency of LBVS combined with MD. This combined strategy provided positive evidence showing that the top screened drugs, including CCX-140, which had the lowest MD score, can be reasonably advanced to the in vitro phase. This combined method may accelerate the discovery of therapies for novel or orphan diseases from existing drugs.
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Affiliation(s)
- Gusti Putu Wahyunanda Crista Yuda
- Laboratory of Macromolecular Engineering, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Gadjah Mada Sekip Utara II, 55281, Yogyakarta, Indonesia
| | - Naufa Hanif
- Master Student of Pharmaceutical Sciences, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Hacettepe University, Ankara, 06100, Turkey
| | - Adam Hermawan
- Laboratory of Macromolecular Engineering, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Gadjah Mada Sekip Utara II, 55281, Yogyakarta, Indonesia.
- Laboratory of Advanced Pharmaceutical Sciences. APSLC Building, Faculty of Pharmacy, Universitas Gadjah Mada Sekip Utara II, 55281, Yogyakarta, Indonesia.
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Chang H, Chen H, Ma T, Ma K, Li Y, Suo L, Liang X, Jia K, Ma J, Li J, Sun D. Multi-omics pan-cancer study of SPTBN2 and its value as a potential therapeutic target in pancreatic cancer. Sci Rep 2024; 14:9764. [PMID: 38684762 PMCID: PMC11059406 DOI: 10.1038/s41598-024-60780-6] [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: 02/07/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024] Open
Abstract
SPTBN2 is a protein-coding gene that is closely related to the development of malignant tumors. However, its prognostic value and biological function in pan-cancer, especially pancreatic cancer (PAAD), have not been reported. In the present study, a novel exploration of the value and potential mechanism of SPTBN2 in PAAD was conducted using multi-omics in the background of pan-cancer. Via various database analysis, up-regulated expression of SPTBN2 was detected in most of the tumor tissues examined. Overexpression of SPTBN2 in PAAD and kidney renal clear cell cancer patients potentially affected overall survival, disease-specific survival, and progression-free interval. In PAAD, SPTBN2 can be used as an independent factor affecting prognosis. Mutations and amplification of SPTBN2 were detected, with abnormal methylation of SPTBN2 affecting its expression and the survival outcome of PAAD patients. Immunoassay results demonstrate that SPTBN2 was a potential biomarker for predicting therapeutic response in PAAD, and may influence the immunotherapy efficacy of PAAD by regulating levels of CD8 + T cells and neutrophil infiltration. Results from an enrichment analysis indicated that SPTBN2 may regulate the development of PAAD via immune pathways. Thus, SPTBN2 is a potential prognostic biomarker and immunotherapy target based on its crucial role in the development of PAAD.
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Affiliation(s)
- Hongliang Chang
- Division of Cholelithiasis Minimally Invasive Surgery, Department of General Surgery, Affiliated Zhongshan Hospital of Dalian University, Dalian, 116001, China
| | - Hong Chen
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, No. 467 Zhongshan Road, Dalian, 116021, China
| | - Taiheng Ma
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, No. 467 Zhongshan Road, Dalian, 116021, China
| | - Kexin Ma
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, No. 467 Zhongshan Road, Dalian, 116021, China
| | - Yi Li
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, No. 467 Zhongshan Road, Dalian, 116021, China
| | - Lida Suo
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, No. 467 Zhongshan Road, Dalian, 116021, China
| | - Xiangnan Liang
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, No. 467 Zhongshan Road, Dalian, 116021, China
| | - Kunyu Jia
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, No. 467 Zhongshan Road, Dalian, 116021, China
| | - Jiahong Ma
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, No. 467 Zhongshan Road, Dalian, 116021, China
| | - Jing Li
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, No. 467 Zhongshan Road, Dalian, 116021, China
| | - Deguang Sun
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, No. 467 Zhongshan Road, Dalian, 116021, China.
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3
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Atang AE, Keller AR, Denha SA, Avery AW. Increased Actin Binding Is a Shared Molecular Consequence of Numerous SCA5 Mutations in β-III-Spectrin. Cells 2023; 12:2100. [PMID: 37626910 PMCID: PMC10453832 DOI: 10.3390/cells12162100] [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: 06/13/2023] [Revised: 07/28/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Spinocerebellar ataxia type 5 (SCA5) is a neurodegenerative disease caused by mutations in the SPTBN2 gene encoding the cytoskeletal protein β-III-spectrin. Previously, we demonstrated that a L253P missense mutation, localizing to the β-III-spectrin actin-binding domain (ABD), causes increased actin-binding affinity. Here we investigate the molecular consequences of nine additional ABD-localized, SCA5 missense mutations: V58M, K61E, T62I, K65E, F160C, D255G, T271I, Y272H, and H278R. We show that all of the mutations, similar to L253P, are positioned at or near the interface of the two calponin homology subdomains (CH1 and CH2) comprising the ABD. Using biochemical and biophysical approaches, we demonstrate that the mutant ABD proteins can attain a well-folded state. However, thermal denaturation studies show that all nine mutations are destabilizing, suggesting a structural disruption at the CH1-CH2 interface. Importantly, all nine mutations cause increased actin binding. The mutant actin-binding affinities vary greatly, and none of the nine mutations increase actin-binding affinity as much as L253P. ABD mutations causing high-affinity actin binding, with the notable exception of L253P, appear to be associated with an early age of symptom onset. Altogether, the data indicate that increased actin-binding affinity is a shared molecular consequence of numerous SCA5 mutations, which has important therapeutic implications.
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Affiliation(s)
| | | | | | - Adam W. Avery
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA
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4
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Cunha P, Petit E, Coutelier M, Coarelli G, Mariotti C, Faber J, Van Gaalen J, Damasio J, Fleszar Z, Tosi M, Rocca C, De Michele G, Minnerop M, Ewenczyk C, Santorelli FM, Heinzmann A, Bird T, Amprosi M, Indelicato E, Benussi A, Charles P, Stendel C, Romano S, Scarlato M, Le Ber I, Bassi MT, Serrano M, Schmitz-Hübsch T, Doss S, Van Velzen GAJ, Thomas Q, Trabacca A, Ortigoza-Escobar JD, D'Arrigo S, Timmann D, Pantaleoni C, Martinuzzi A, Besse-Pinot E, Marsili L, Cioffi E, Nicita F, Giorgetti A, Moroni I, Romaniello R, Casali C, Ponger P, Casari G, De Bot ST, Ristori G, Blumkin L, Borroni B, Goizet C, Marelli C, Boesch S, Anheim M, Filla A, Houlden H, Bertini E, Klopstock T, Synofzik M, Riant F, Zanni G, Magri S, Di Bella D, Nanetti L, Sequeiros J, Oliveira J, Van de Warrenburg B, Schöls L, Taroni F, Brice A, Durr A. Extreme phenotypic heterogeneity in non-expansion spinocerebellar ataxias. Am J Hum Genet 2023; 110:1098-1109. [PMID: 37301203 PMCID: PMC10357418 DOI: 10.1016/j.ajhg.2023.05.009] [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: 03/26/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
Although the best-known spinocerebellar ataxias (SCAs) are triplet repeat diseases, many SCAs are not caused by repeat expansions. The rarity of individual non-expansion SCAs, however, has made it difficult to discern genotype-phenotype correlations. We therefore screened individuals who had been found to bear variants in a non-expansion SCA-associated gene through genetic testing, and after we eliminated genetic groups that had fewer than 30 subjects, there were 756 subjects bearing single-nucleotide variants or deletions in one of seven genes: CACNA1A (239 subjects), PRKCG (175), AFG3L2 (101), ITPR1 (91), STUB1 (77), SPTBN2 (39), or KCNC3 (34). We compared age at onset, disease features, and progression by gene and variant. There were no features that reliably distinguished one of these SCAs from another, and several genes-CACNA1A, ITPR1, SPTBN2, and KCNC3-were associated with both adult-onset and infantile-onset forms of disease, which also differed in presentation. Nevertheless, progression was overall very slow, and STUB1-associated disease was the fastest. Several variants in CACNA1A showed particularly wide ranges in age at onset: one variant produced anything from infantile developmental delay to ataxia onset at 64 years of age within the same family. For CACNA1A, ITPR1, and SPTBN2, the type of variant and charge change on the protein greatly affected the phenotype, defying pathogenicity prediction algorithms. Even with next-generation sequencing, accurate diagnosis requires dialogue between the clinician and the geneticist.
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Affiliation(s)
- Paulina Cunha
- Sorbonne Université, Paris Brain Institute (ICM), Pitié-Salpêtrière Hospital, AP-HP, INSERM, CNRS, University Hospital Pitié-Salpêtrière, CS21414, 75646 PARIS Cedex 13, France
| | - Emilien Petit
- Sorbonne Université, Paris Brain Institute (ICM), Pitié-Salpêtrière Hospital, AP-HP, INSERM, CNRS, University Hospital Pitié-Salpêtrière, CS21414, 75646 PARIS Cedex 13, France
| | - Marie Coutelier
- Sorbonne Université, Paris Brain Institute (ICM), Pitié-Salpêtrière Hospital, AP-HP, INSERM, CNRS, University Hospital Pitié-Salpêtrière, CS21414, 75646 PARIS Cedex 13, France
| | - Giulia Coarelli
- Sorbonne Université, Paris Brain Institute (ICM), Pitié-Salpêtrière Hospital, AP-HP, INSERM, CNRS, University Hospital Pitié-Salpêtrière, CS21414, 75646 PARIS Cedex 13, France
| | - Caterina Mariotti
- Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Jennifer Faber
- German Center for Neurodegenerative Disease (DZNE), 53127 Bonn, Germany; Department of Neurology, University Hospital of Bonn, 53111 Bonn, Germany
| | - Judith Van Gaalen
- Department of Neurology, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
| | - Joana Damasio
- Neurology Department, Hospital de Santo António, Centro Hospitalar Universitário de Santo António, 4099-001 Porto, Portugal; CGPP, IBMC-Institute for Molecular and Cell Biology & UnIGENe, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Zofia Fleszar
- German Center for Neurodegenerative Disease (DZNE), 72076 Tübingen, Germany; Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research & Center of Neurology, University of Tübingen, 72076 Tübingen, Germany
| | - Michele Tosi
- Unit of Neuromuscular and Neurodegenerative Disorders, Bambino Gesu' Children's Research Hospital, IRCCS, 00165 Rome, Italy
| | - Clarissa Rocca
- Department of Neuromuscular Diseases, UCL Queen's Square Institute of Neurology, Queen's Square House, Queen's Square, WC1N 3BG London, UK
| | - Giovanna De Michele
- Department of Neuroscience and Reproductive and Odontostomatological Sciences, University of Naples Federico II, 80131 Naples, Italy
| | - Martina Minnerop
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, 52428 Jülich, Germany; Institute of Clinical Neuroscience and Medical Psychology and Department of Neurology, Center for Movement Disorders and Neuromodulation, Medical Faculty & University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Claire Ewenczyk
- Sorbonne Université, Paris Brain Institute (ICM), Pitié-Salpêtrière Hospital, AP-HP, INSERM, CNRS, University Hospital Pitié-Salpêtrière, CS21414, 75646 PARIS Cedex 13, France
| | - Filippo M Santorelli
- Molecular Medicine & Neurogenetics, IRCCS Fondazione Stella Maris, 56128 Calambrone, Italy
| | - Anna Heinzmann
- Sorbonne Université, Paris Brain Institute (ICM), Pitié-Salpêtrière Hospital, AP-HP, INSERM, CNRS, University Hospital Pitié-Salpêtrière, CS21414, 75646 PARIS Cedex 13, France
| | - Thomas Bird
- University of Washington, Seattle, WA 98195, USA
| | - Matthias Amprosi
- Center for Rare Movement Disorders, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Elisabetta Indelicato
- Center for Rare Movement Disorders, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Alberto Benussi
- Centre for Neurodegenerative Disorders, Department of Clinical and Experimental Sciences, University of Brescia, 25121 Brescia, Italy
| | - Perrine Charles
- Sorbonne Université, Paris Brain Institute (ICM), Pitié-Salpêtrière Hospital, AP-HP, INSERM, CNRS, University Hospital Pitié-Salpêtrière, CS21414, 75646 PARIS Cedex 13, France
| | - Claudia Stendel
- German Center for Neurodegenerative Disease (DZNE), München, Germany; Department of Neurology, Friedrich-Baur Institute, University Hospital of Ludwig-Maximilians-University, Munich Cluster for Systems Neurology (SyNergy), 80336 Munich, Germany
| | - Silvia Romano
- Neurosciences, Mental Health, and Sensory Organs (NESMOS) Department, S. Andrea Hospital, Sapienza University of Rome, 00189 Rome, Italy
| | - Marina Scarlato
- San Raffaele Hospital and Vita-Salute San Raffaele University, Milan, Italy
| | - Isabelle Le Ber
- Sorbonne Université, Paris Brain Institute (ICM), Pitié-Salpêtrière Hospital, AP-HP, INSERM, CNRS, University Hospital Pitié-Salpêtrière, CS21414, 75646 PARIS Cedex 13, France
| | - Maria Teresa Bassi
- Scientific Institute I.R.C.C.S. Eugenio Medea, 23842 Bosisio Parini, Italy
| | - Mercedes Serrano
- Pediatric Neurology Department, Sant Joan de Déu Hospital, 08950 Barcelona, Spain
| | - Tanja Schmitz-Hübsch
- Department of Neurology and Experimental Neurology, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Sarah Doss
- Department of Neurology and Experimental Neurology, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Gijs A J Van Velzen
- Department of Neurology, Leiden University Medical Center, 2333 Leiden, the Netherlands
| | - Quentin Thomas
- Department of Clinical Genetics, Dijon University Hospital, 21000 Dijon, France
| | - Antonio Trabacca
- Scientific Institute I.R.C.C.S. Eugenio Medea, 23842 Bosisio Parini, Italy
| | | | - Stefano D'Arrigo
- Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Dagmar Timmann
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), Essen University Hospital, University of Duisburg-Essen, 45147 Essen, Germany
| | - Chiara Pantaleoni
- Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Andrea Martinuzzi
- Scientific Institute I.R.C.C.S. Eugenio Medea, 23842 Bosisio Parini, Italy
| | - Elsa Besse-Pinot
- Department of Neurology, Clermont-Ferrand University Hospital, 63000 Clermont-Ferrand, France
| | - Luca Marsili
- Gardner Family Center for Parkinson's Disease and Movement Disorders, Department of Neurology, University of Cincinnati, Cincinnati, OH 45219, USA
| | - Ettore Cioffi
- Sapienza University of Rome, Department of Medico-Surgical Sciences and Biotechnologies, Polo Pontino, 04100 Latina, Italy
| | - Francesco Nicita
- Unit of Neuromuscular and Neurodegenerative Disorders, Bambino Gesu' Children's Research Hospital, IRCCS, 00165 Rome, Italy
| | - Alejandro Giorgetti
- Computational Biomedicine, Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany; Department of Biotechnology, Università degli Studi di Verona, 37134 Verona, Italy
| | - Isabella Moroni
- Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Romina Romaniello
- Scientific Institute I.R.C.C.S. Eugenio Medea, 23842 Bosisio Parini, Italy
| | - Carlo Casali
- Sapienza University of Rome, Department of Medico-Surgical Sciences and Biotechnologies, Polo Pontino, 04100 Latina, Italy
| | - Penina Ponger
- Neurology Department, Tel-Aviv Sourasky Medical Center, 6329302 Tel-Aviv, Israel; Sackler School of Medicine, Tel-Aviv University, 6997801 Tel-Aviv, Israel
| | - Giorgio Casari
- San Raffaele Hospital and Vita-Salute San Raffaele University, Milan, Italy
| | - Susanne T De Bot
- Department of Neurology, Leiden University Medical Center, 2333 Leiden, the Netherlands
| | - Giovanni Ristori
- Neurosciences, Mental Health, and Sensory Organs (NESMOS) Department, S. Andrea Hospital, Sapienza University of Rome, 00189 Rome, Italy
| | - Lubov Blumkin
- Sackler School of Medicine, Tel-Aviv University, 6997801 Tel-Aviv, Israel; Pediatric Movement Disorders Clinic, Pediatric Neurology Unit, Wolfson Medical Center, 5822012 Holon, Israel
| | - Barbara Borroni
- Centre for Neurodegenerative Disorders, Department of Clinical and Experimental Sciences, University of Brescia, 25121 Brescia, Italy
| | - Cyril Goizet
- University Bordeaux, Equipe « Neurogénétique Translationnelle - NRGEN », INCIA CNRS UMR5287 Université Bordeaux and Centre de Reference Maladies Rares « Neurogénétique », Service de Génétique Médicale, Bordeaux University Hospital (CHU Bordeaux), 33000 Bordeaux, France
| | - Cecilia Marelli
- MMDN, University Montpellier, EPHE, INSERM and Expert Center for Neurogenetic Diseases, CHU, 34095 Montpellier, France
| | - Sylvia Boesch
- Center for Rare Movement Disorders, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Mathieu Anheim
- Department of Neurology, Strasbourg University Hospital, 67098 Strasbourg, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM-U964; CNRS-UMR7104; University of Strasbourg, 67400 Illkirch-Graffenstaden, France
| | - Alessandro Filla
- Department of Neuroscience and Reproductive and Odontostomatological Sciences, University of Naples Federico II, 80131 Naples, Italy
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen's Square Institute of Neurology, Queen's Square House, Queen's Square, WC1N 3BG London, UK
| | - Enrico Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, Bambino Gesu' Children's Research Hospital, IRCCS, 00165 Rome, Italy
| | - Thomas Klopstock
- German Center for Neurodegenerative Disease (DZNE), München, Germany; Department of Neurology, Friedrich-Baur Institute, University Hospital of Ludwig-Maximilians-University, Munich Cluster for Systems Neurology (SyNergy), 80336 Munich, Germany
| | - Matthis Synofzik
- German Center for Neurodegenerative Disease (DZNE), 72076 Tübingen, Germany; Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research & Center of Neurology, University of Tübingen, 72076 Tübingen, Germany
| | - Florence Riant
- Department of Neurovascular Molecular Genetics, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Louis, 75010 Paris, France
| | - Ginevra Zanni
- Unit of Neuromuscular and Neurodegenerative Disorders, Bambino Gesu' Children's Research Hospital, IRCCS, 00165 Rome, Italy
| | - Stefania Magri
- Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Daniela Di Bella
- Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Lorenzo Nanetti
- Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Jorge Sequeiros
- CGPP, IBMC-Institute for Molecular and Cell Biology & UnIGENe, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Jorge Oliveira
- CGPP, IBMC-Institute for Molecular and Cell Biology & UnIGENe, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Bart Van de Warrenburg
- Department of Neurology, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
| | - Ludger Schöls
- German Center for Neurodegenerative Disease (DZNE), 72076 Tübingen, Germany; Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research & Center of Neurology, University of Tübingen, 72076 Tübingen, Germany
| | - Franco Taroni
- Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Alexis Brice
- Sorbonne Université, Paris Brain Institute (ICM), Pitié-Salpêtrière Hospital, AP-HP, INSERM, CNRS, University Hospital Pitié-Salpêtrière, CS21414, 75646 PARIS Cedex 13, France
| | - Alexandra Durr
- Sorbonne Université, Paris Brain Institute (ICM), Pitié-Salpêtrière Hospital, AP-HP, INSERM, CNRS, University Hospital Pitié-Salpêtrière, CS21414, 75646 PARIS Cedex 13, France.
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Atang AE, Keller AR, Denha SA, Avery AW. Increased actin binding is a shared molecular consequence of numerous spinocerebellar ataxia mutations in β-III-spectrin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.20.529285. [PMID: 36865188 PMCID: PMC9980045 DOI: 10.1101/2023.02.20.529285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Spinocerebellar ataxia type 5 (SCA5) is a neurodegenerative disease caused by mutations in the SPTBN2 gene encoding the cytoskeletal protein β-III-spectrin. Previously, we demonstrated that a L253P missense mutation, localizing to the β-III-spectrin actin-binding domain (ABD), causes increased actin-binding affinity. Here we investigate the molecular consequences of nine additional ABD-localized, SCA5 missense mutations: V58M, K61E, T62I, K65E, F160C, D255G, T271I, Y272H, and H278R. We show that all of the mutations, similar to L253P, are positioned at or near the interface of the two calponin homology subdomains (CH1 and CH2) comprising the ABD. Using biochemical and biophysical approaches, we demonstrate that the mutant ABD proteins can attain a well-folded state. However, thermal denaturation studies show that all nine mutations are destabilizing, suggesting a structural disruption at the CH1-CH2 interface. Importantly, all nine mutations cause increased actin binding. The mutant actin-binding affinities vary greatly, and none of the nine mutations increase actin-binding affinity as much as L253P. ABD mutations causing high-affinity actin binding, with the notable exception of L253P, appear to be associated with early age of symptom onset. Altogether, the data indicate increased actin-binding affinity is a shared molecular consequence of numerous SCA5 mutations, which has important therapeutic implications.
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Affiliation(s)
| | - Amanda R. Keller
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA
| | - Sarah A. Denha
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA
| | - Adam W. Avery
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA
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Lorenzo DN, Edwards RJ, Slavutsky AL. Spectrins: molecular organizers and targets of neurological disorders. Nat Rev Neurosci 2023; 24:195-212. [PMID: 36697767 PMCID: PMC10598481 DOI: 10.1038/s41583-022-00674-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2022] [Indexed: 01/26/2023]
Abstract
Spectrins are cytoskeletal proteins that are expressed ubiquitously in the mammalian nervous system. Pathogenic variants in SPTAN1, SPTBN1, SPTBN2 and SPTBN4, four of the six genes encoding neuronal spectrins, cause neurological disorders. Despite their structural similarity and shared role as molecular organizers at the cell membrane, spectrins vary in expression, subcellular localization and specialization in neurons, and this variation partly underlies non-overlapping disease presentations across spectrinopathies. Here, we summarize recent progress in discerning the local and long-range organization and diverse functions of neuronal spectrins. We provide an overview of functional studies using mouse models, which, together with growing human genetic and clinical data, are helping to illuminate the aetiology of neurological spectrinopathies. These approaches are all critical on the path to plausible therapeutic solutions.
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Affiliation(s)
- Damaris N Lorenzo
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Reginald J Edwards
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Anastasia L Slavutsky
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Ghorbani F, de Boer EN, Benjamins-Stok M, Verschuuren-Bemelmans CC, Knapper J, de Boer-Bergsma J, de Vries JJ, Sikkema-Raddatz B, Verbeek DS, Westers H, van Diemen CC. Copy Number Variant Analysis of Spinocerebellar Ataxia Genes in a Cohort of Dutch Patients With Cerebellar Ataxia. Neurol Genet 2023; 9:e200050. [PMID: 38058854 PMCID: PMC10696507 DOI: 10.1212/nxg.0000000000200050] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/27/2022] [Indexed: 12/08/2023]
Abstract
Background and Objectives The spinocerebellar ataxias (SCAs) are a genetically heterogeneous group of neurodegenerative disorders generally caused by single nucleotide variants (SNVs) or indels in coding regions or by repeat expansions in coding and noncoding regions of SCA genes. Copy number variants (CNVs) have now also been reported for 3 genes-ITPR1, FGF14, and SPTBN2-but not all SCA genes have been screened for CNVs as the underlying cause of the disease in patients. In this study, we aim to assess the prevalence of CNVs encompassing 36 known SCA genes. Methods A cohort of patients with cerebellar ataxia who were referred to the University Medical Center Groningen for SCA genetic diagnostics was selected for this study. Genome-wide single nucleotide polymorphism (SNP) genotyping was performed using the Infinium Global Screening Array. Following data processing, genotyping data were uploaded into NxClinical software to perform CNV analysis per patient and to visualize identified CNVs in 36 genes with allocated SCA symbols. The clinical relevance of detected CNVs was determined using evidence from studies based on PubMed literature searches for similar CNVs and phenotypic features. Results Of the 338 patients with cerebellar ataxia, we identified putative clinically relevant CNV deletions in 3 patients: an identical deletion encompassing ITPR1 in 2 patients, who turned out to be related, and a deletion involving PPP2R2B in another patient. Although the CNV deletion in ITPR1 was clearly the underlying cause of SCA15 in the 2 related patients, the clinical significance of the deletion in PPP2R2B remained unknown. Discussion We showed that CNVs detectable with the limited resolution of SNP array are a very rare cause of SCA. Nevertheless, we suggest adding CNV analysis alongside SNV analysis to SCA gene diagnostics using next-generation sequencing approaches, at least for ITPR1, to improve the genetic diagnostics for patients.
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Affiliation(s)
- Fatemeh Ghorbani
- From the Department of Genetics (F.G., E.N.d.B., M.B.-S., C.C.V.-B., J.K., J.d.B.-B., B.S.-R., D.S.V., H.W., C.C.v.D.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; and Department of Neurology (J.J.d.V.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Eddy N de Boer
- From the Department of Genetics (F.G., E.N.d.B., M.B.-S., C.C.V.-B., J.K., J.d.B.-B., B.S.-R., D.S.V., H.W., C.C.v.D.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; and Department of Neurology (J.J.d.V.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Marloes Benjamins-Stok
- From the Department of Genetics (F.G., E.N.d.B., M.B.-S., C.C.V.-B., J.K., J.d.B.-B., B.S.-R., D.S.V., H.W., C.C.v.D.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; and Department of Neurology (J.J.d.V.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Corien C Verschuuren-Bemelmans
- From the Department of Genetics (F.G., E.N.d.B., M.B.-S., C.C.V.-B., J.K., J.d.B.-B., B.S.-R., D.S.V., H.W., C.C.v.D.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; and Department of Neurology (J.J.d.V.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Jurjen Knapper
- From the Department of Genetics (F.G., E.N.d.B., M.B.-S., C.C.V.-B., J.K., J.d.B.-B., B.S.-R., D.S.V., H.W., C.C.v.D.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; and Department of Neurology (J.J.d.V.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Jelkje de Boer-Bergsma
- From the Department of Genetics (F.G., E.N.d.B., M.B.-S., C.C.V.-B., J.K., J.d.B.-B., B.S.-R., D.S.V., H.W., C.C.v.D.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; and Department of Neurology (J.J.d.V.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Jeroen J de Vries
- From the Department of Genetics (F.G., E.N.d.B., M.B.-S., C.C.V.-B., J.K., J.d.B.-B., B.S.-R., D.S.V., H.W., C.C.v.D.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; and Department of Neurology (J.J.d.V.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Birgit Sikkema-Raddatz
- From the Department of Genetics (F.G., E.N.d.B., M.B.-S., C.C.V.-B., J.K., J.d.B.-B., B.S.-R., D.S.V., H.W., C.C.v.D.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; and Department of Neurology (J.J.d.V.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Dineke S Verbeek
- From the Department of Genetics (F.G., E.N.d.B., M.B.-S., C.C.V.-B., J.K., J.d.B.-B., B.S.-R., D.S.V., H.W., C.C.v.D.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; and Department of Neurology (J.J.d.V.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Helga Westers
- From the Department of Genetics (F.G., E.N.d.B., M.B.-S., C.C.V.-B., J.K., J.d.B.-B., B.S.-R., D.S.V., H.W., C.C.v.D.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; and Department of Neurology (J.J.d.V.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Cleo C van Diemen
- From the Department of Genetics (F.G., E.N.d.B., M.B.-S., C.C.V.-B., J.K., J.d.B.-B., B.S.-R., D.S.V., H.W., C.C.v.D.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; and Department of Neurology (J.J.d.V.), University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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Vo Ngoc LDT, Osei R, Dohr K, Olsen C, Seneca S, Gheldof A. EDIR: exome database of interspersed repeats. Bioinformatics 2022; 39:6858440. [PMID: 36453866 PMCID: PMC9805566 DOI: 10.1093/bioinformatics/btac771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 11/12/2022] [Accepted: 11/30/2022] [Indexed: 12/03/2022] Open
Abstract
MOTIVATION Intragenic exonic deletions are known to contribute to genetic diseases and are often flanked by regions of homology. RESULTS In order to get a more clear view of these interspersed repeats encompassing a coding sequence, we have developed EDIR (Exome Database of Interspersed Repeats) which contains the positions of these structures within the human exome. EDIR has been calculated by an inductive strategy, rather than by a brute force approach and can be queried through an R/Bioconductor package or a web interface allowing the per-gene rapid extraction of homology-flanked sequences throughout the exome. AVAILABILITY AND IMPLEMENTATION The code used to compile EDIR can be found at https://github.com/lauravongoc/EDIR. The full dataset of EDIR can be queried via an Rshiny application at http://193.70.34.71:3857/edir/. The R package for querying EDIR is called 'EDIRquery' and is available on Bioconductor. The full EDIR dataset can be downloaded from https://osf.io/m3gvx/ or http://193.70.34.71/EDIR.tar.gz. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Laura D T Vo Ngoc
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Clinical Sciences, Research Group Reproduction and Genetics, Centre for Medical Genetics, Brussels 1090, Belgium
| | - Randy Osei
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Clinical Sciences, Research Group Reproduction and Genetics, Centre for Medical Genetics, Brussels 1090, Belgium
| | - Katrin Dohr
- Department of Paediatrics and Adolescent Medicine, Research Unit of Analytical Mass Spectrometry, Cell Biology and Biochemistry of Inborn Errors of Metabolism, Graz 8010, Austria
| | - Catharina Olsen
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Clinical Sciences, Research Group Reproduction and Genetics, Centre for Medical Genetics, Brussels 1090, Belgium,Brussels Interuniversity Genomics High Throughput Core (BRIGHTcore), VUB-ULB, Brussels 1090, Belgium,Interuniversity Institute of Bioinformatics in Brussels (IB)2, VUB-ULB, Brussels 1050, Belgium
| | - Sara Seneca
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Clinical Sciences, Research Group Reproduction and Genetics, Centre for Medical Genetics, Brussels 1090, Belgium
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Benevides ML, França M. Expanding the Landscape of Spinocerebellar Ataxia Type 5. Neuropediatrics 2022; 53:358-360. [PMID: 35545114 DOI: 10.1055/a-1849-8128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Spinocerebellar ataxia type 5 (SCA5) is a rare subtype of SCA that usually affects adults. It has been recently reported in children in Europe, North America, and China. This study aims to describe clinical, radiological, and genetic data of a child presenting with SCA5, caused by a heterozygous likely pathogenic missense variant in SPTBN2 (NM_006946.3: c.1052G > C, p.Arg351Pro). According to databases and a review of the literature, this is one of few cases of SCA5 from Latin America. Expanding the landscape of SCA5 is relevant to the differential diagnosis of ataxic cerebral palsy and the autosomal recessive cerebellar ataxias.
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Affiliation(s)
- Maria Luiza Benevides
- Child Neurology Service, Neurology Department, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Marcondes França
- Department of Neurology, Neuromuscular Diseases, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
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SPTBN2 Promotes the Progression of Thyroid Cancer by Accelerating G1/S Transition and Inhibiting Apoptosis. DISEASE MARKERS 2022; 2022:2562595. [PMID: 35968508 PMCID: PMC9365581 DOI: 10.1155/2022/2562595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/10/2022] [Accepted: 07/16/2022] [Indexed: 11/17/2022]
Abstract
Background. Thyroid carcinoma (TC) is an increasingly common malignancy of endocrine organs, and its most frequently encountered histotype is papillary thyroid cancer (PTC). Identifying new potential gene alterations is important for completely elucidating the mechanism of PTC initiation and progression. Thus, we performed whole transcriptome sequence analysis (RNA-seq) on 79 PTC tissue samples and paired adjacent nontumor tissue samples to study the molecular mechanism of TC tumorigenesis and progression further. The results of RNA-seq analysis showed that spectrin beta, nonerythrocytic 2 (SPTBN2), was markedly overexpressed in PTC tissues relative to that in the paired nontumor tissues. Additionally, the analysis results for 502 PTC samples and 58 nontumor thyroid samples from The Cancer Genome Atlas dataset were consistent with our RNA-seq results. However, the molecular mechanisms and function of SPTBN2 in TC progression remain unknown. Methods. We examined SPTBN2 gene expression in 48 papillary thyroid tumor tissues and paired adjacent normal thyroid tissues by using qRT-PCR. SPTBN2 expression in the TC cell lines was silenced by small interfering RNA. Then, the transfected TC cells were used to investigate the in vitro function of SPTBN2. Result. The expression of SPTBN2 was significantly upregulated in our RNA-seq cohort, our local validated cohort, and TCGA RNA-seq cohort. The results of the in vitro experiment revealed that in TC cell lines, SPTBN2 downregulation considerably suppressed tumor cell proliferation, the cell cycle, migration, colony formation, and invasion and induced cell apoptosis. Furthermore, the protein levels of CCNE2, CDK2, CDK4, and Bcl-2 were downregulated, and those of P21, Bax, cleaved caspase-8, and cleaved caspase-3 had increased in transfected TC cells relative to in control TC cells. Conclusion. The downregulation of SPTBN2 caused apoptosis and retarded G1/S cell cycle transition in TC cells. Thus, SPTBN2 may be a good candidate gene for TC diagnosis and therapy.
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Li S, Liu T, Li K, Bai X, Xi K, Chai X, Mi L, Li J. Spectrins and human diseases. Transl Res 2022; 243:78-88. [PMID: 34979321 DOI: 10.1016/j.trsl.2021.12.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 11/18/2022]
Abstract
Spectrin, as one of the major components of a plasma membrane-associated cytoskeleton, is a cytoskeletal protein composed of the modular structure of α and β subunits. The spectrin-based skeleton is essential for preserving the integrity and mechanical characteristics of the cell membrane. Moreover, spectrin regulates a variety of cell processes including cell apoptosis, cell adhesion, cell spreading, and cell cycle. Dysfunction of spectrins is implicated in various human diseases including hemolytic anemia, neurodegenerative diseases, ataxia, heart diseases, and cancers. Here, we briefly discuss spectrins function as well as the clinical manifestations and currently known molecular mechanisms of human diseases related to spectrins, highlighting that strategies for targeting regulation of spectrins function may provide new avenues for therapeutic intervention for these diseases.
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Affiliation(s)
- Shan Li
- The First School of Clinical Medicine, Lanzhou University, Gansu, China
| | - Ting Liu
- The First School of Clinical Medicine, Lanzhou University, Gansu, China
| | - Kejing Li
- The First School of Clinical Medicine, Lanzhou University, Gansu, China
| | - Xinyi Bai
- The First School of Clinical Medicine, Lanzhou University, Gansu, China
| | - Kewang Xi
- The First School of Clinical Medicine, Lanzhou University, Gansu, China
| | - Xiaojing Chai
- Central Laboratory, The First Hospital of Lanzhou University, Gansu, China
| | - Leyuan Mi
- The First School of Clinical Medicine, Lanzhou University, Gansu, China; Clinical Laboratory Center, Gansu Provincial Maternity and Child Care Hospital, Gansu, China
| | - Juan Li
- Gansu Key Laboratory of Genetic Study of Hematopathy, The First Hospital of Lanzhou University, Gansu, China; Central Laboratory, The First Hospital of Lanzhou University, Gansu, China.
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12
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Wu C, Dong B, Huang L, Liu Y, Ye G, Li S, Qi Y. SPTBN2, a New Biomarker of Lung Adenocarcinoma. Front Oncol 2021; 11:754290. [PMID: 34745988 PMCID: PMC8563792 DOI: 10.3389/fonc.2021.754290] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/27/2021] [Indexed: 12/25/2022] Open
Abstract
Objectives The roles played by β-III-spectrin, also known as spectrin beta, non-erythrocytic 2 (SPTBN2), in the occurrence and development of lung adenocarcinoma (LUAD) have not been previously examined. Our study aimed to reveal the relationship between the SPTBN2 expression and LUAD. Materials and Methods Twenty pairs of LUAD tissues and adjacent tissues were collected from patients diagnosed and treated at the Thoracic Surgery Department of The First Affiliated Hospital of Zhengzhou University from July 2019 to September 2020. RNA sequencing (RNA-seq) analysis determined that the expression of SPTBN2 was higher in LUAD samples than in adjacent normal tissues. The expression levels of SPTBN2 were examined in various databases, including the Cancer Cell Line Encyclopedia (CCLE), Gene Expression Omnibus (GEO), and Human Protein Atlas (HPA). The Search Tool for the Retrieval of Interacting Genes (STRING) online website was used to examine protein–protein interactions involving SPTBN2, and the results were visualized by Cytoscape software. The Molecular Complex Detection (MCODE) plug-in for Cytoscape software was used to identify functional modules of the obtained protein–protein interaction (PPI) network. Gene enrichment analysis was performed, and survival analysis was conducted using the Kaplan–Meier plotter. The online prediction website TargetScan was used to predict SPTBN2-targeted miRNA sequences by searching for SPTBN2 sequences. Finally, we verified the expression of SPTBN2 in the obtained tissue samples using real-time fluorescence quantitative polymerase chain reaction (RT-qPCR). The human lung cancer cell lines A549 and H1299 were selected for the transfection of small interfering RNA (siRNA) targeting SPTBN2 (si-SPTBN2), and the knockdown efficiency was evaluated by RT-qPCR. The cellular proliferation, migration, and invasion capacities of A549 and H1299 cells were determined using the cell counting kit-8 (CCK-8) proliferation assay; the wound-healing assay and the Transwell migration assay; and the Matrigel invasion assay, respectively. Results The expression of SPTBN2 in non–small cell lung cancer (NSCLC) ranked 13th among cancer cell lines based on the CCLE database. At the mRNA and protein levels, the expression levels of SPTBN2 were higher in LUAD tissues than in normal lung tissues. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that proteins related to SPTBN2 were enriched in apoptotic and phagosomal pathways. Kaplan–Meier survival analysis revealed that SPTBN2 expression was significantly related to the prognosis of patients with LUAD. The TargetScan database verified that miR-16 was a negative regulator of SPTBN2 mRNA expression. The results of the CCK-8 cell proliferation assay revealed that SPTBN2 knockdown significantly inhibited the cell proliferation abilities of A549 and H1299 cells. The wound-healing assay indicated that SPTBN2 knockdown resulted in reduced migration after 48 h compared with the control group. The Transwell migration and invasion test revealed that the migration and invasion abilities were greatly decreased by SPTBN2 knockdown compared with control conditions. Conclusion We uncovered a novel gene, SPTBN2, that was significantly upregulated in LUAD tissues relative to normal tissue expression. SPTBN2 is highly expressed in LUAD, positively correlated with poor prognosis, and can promote the proliferation, migration, and invasion of LUAD cells.
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Affiliation(s)
- Chunli Wu
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Henan, China
| | - Bo Dong
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Henan, China
| | - Lan Huang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Henan, China
| | - Yafei Liu
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Henan, China
| | - Guanchao Ye
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Henan, China
| | - Shihao Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Henan, China
| | - Yu Qi
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Henan, China
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