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Scimone C, Donato L, Alibrandi S, Conti A, Bortolotti C, Germanò A, Alafaci C, Vinci SL, D'Angelo R, Sidoti A. Methylome analysis of endothelial cells suggests new insights on sporadic brain arteriovenous malformation. Heliyon 2024; 10:e35126. [PMID: 39170526 PMCID: PMC11336478 DOI: 10.1016/j.heliyon.2024.e35126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Accepted: 07/23/2024] [Indexed: 08/23/2024] Open
Abstract
Arteriovenous malformation of the brain (bAVM) is a vascular phenotype related to brain defective angiogenesis. Involved vessels show impaired expression of vascular differentiation markers resulting in the arteriolar to venule direct shunt. In order to clarify aberrant gene expression occurring in bAVM, here we describe results obtained by methylome analysis performed on endothelial cells (ECs) isolated from bAVM specimens, compared to human cerebral microvascular ECs. Results were validated by quantitative methylation-specific PCR and quantitative realtime-PCR. Differential methylation events occur in genes already linked to bAVM onset, as RBPJ and KRAS. However, among differentially methylated genes, we identified EPHB1 and several other loci involved in EC adhesion as well as in EC/vascular smooth muscle cell (VSMC) crosstalk, suggesting that only endothelial dysfunction might not be sufficient to trigger the bAVM phenotype. Moreover, aberrant methylation pattern was reported for many lncRNA genes targeting transcription factors expressed during neurovascular development. Among these, the YBX1 that was recently shown to target the arteridin coding gene. Finally, in addition to the conventional CpG methylation, we further considered the role of impaired CHG methylation, mainly occurring in brain at embryo stage. We showed as differentially CHG methylated genes are clustered in pathways related to EC homeostasis, as well as to VSMC-EC crosstalk, suggesting as impairment of this interaction plays a prominent role in loss of vascular differentiation, in bAVM phenotype.
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Affiliation(s)
- Concetta Scimone
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Via Consolare Valeria 1, 98125, Messina, Italy
- Department of Biomolecular Strategies, Genetics, Cutting-edge Therapies, I.E.ME.S.T., Via Michele Miraglia 20, Palermo, 90139, Italy
| | - Luigi Donato
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Via Consolare Valeria 1, 98125, Messina, Italy
- Department of Biomolecular Strategies, Genetics, Cutting-edge Therapies, I.E.ME.S.T., Via Michele Miraglia 20, Palermo, 90139, Italy
| | - Simona Alibrandi
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Via Consolare Valeria 1, 98125, Messina, Italy
- Department of Biomolecular Strategies, Genetics, Cutting-edge Therapies, I.E.ME.S.T., Via Michele Miraglia 20, Palermo, 90139, Italy
| | - Alfredo Conti
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, Bologna, Via Altura 3, 40123, Bologna, Italy
- Department of Biomedical and NeuroMotor Sciences (DiBiNeM), Alma Mater Studiorum – University of Bologna, Bologna, Italy
| | - Carlo Bortolotti
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, Bologna, Via Altura 3, 40123, Bologna, Italy
| | - Antonino Germanò
- Neurosurgery Unit, Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Via Consolare Valeria 1, 98125, Messina, Italy
| | - Concetta Alafaci
- Neurosurgery Unit, Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Via Consolare Valeria 1, 98125, Messina, Italy
| | - Sergio Lucio Vinci
- Neuroradiology Unit, Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Rosalia D'Angelo
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Via Consolare Valeria 1, 98125, Messina, Italy
- Department of Biomolecular Strategies, Genetics, Cutting-edge Therapies, I.E.ME.S.T., Via Michele Miraglia 20, Palermo, 90139, Italy
| | - Antonina Sidoti
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Via Consolare Valeria 1, 98125, Messina, Italy
- Department of Biomolecular Strategies, Genetics, Cutting-edge Therapies, I.E.ME.S.T., Via Michele Miraglia 20, Palermo, 90139, Italy
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Phillips AT, Boumil EF, Venkatesan A, Tilstra-Smith C, Castro N, Knox BE, Henty-Ridilla JL, Bernstein AM. The formin DAAM1 regulates the deubiquitinase activity of USP10 and integrin homeostasis. Eur J Cell Biol 2023; 102:151347. [PMID: 37562219 PMCID: PMC10839120 DOI: 10.1016/j.ejcb.2023.151347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 08/12/2023] Open
Abstract
The differentiation of fibroblasts into pathological myofibroblasts during wound healing is characterized by increased cell surface expression of αv-integrins. Our previous studies found that the deubiquitinase (DUB) USP10 removes ubiquitin from αv-integrins, leading to cell surface integrin accumulation, subsequent TGFβ1 activation, and pathological myofibroblast differentiation. In this study, a yeast two-hybrid screen revealed a novel binding partner for USP10, the formin, DAAM1. We found that DAAM1 binds to and inhibits USP10's DUB activity through the FH2 domain of DAAM1 independent of its actin functions. The USP10/DAAM1 interaction was also supported by proximity ligation assay (PLA) in primary human corneal fibroblasts. Treatment with TGFβ1 significantly increased USP10 and DAAM1 protein expression, PLA signal, and co-localization to actin stress fibers. DAAM1 siRNA knockdown significantly reduced co-precipitation of USP10 and DAAM1 on purified actin stress fibers, and β1- and β5-integrin ubiquitination. This resulted in increased αv-, β1-, and β5-integrin total protein levels, αv-integrin recycling, and extracellular fibronectin (FN) deposition. Together, our data demonstrate that DAAM1 inhibits USP10's DUB activity on integrins subsequently regulating cell surface αv-integrin localization and FN accumulation.
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Affiliation(s)
- Andrew T Phillips
- SUNY Upstate Medical University, Department of Ophthalmology and Visual Sciences, 750 East Adams Street, Syracuse, NY 13210, USA
| | - Edward F Boumil
- SUNY Upstate Medical University, Department of Ophthalmology and Visual Sciences, 750 East Adams Street, Syracuse, NY 13210, USA
| | - Arunkumar Venkatesan
- SUNY Upstate Medical University, Department of Ophthalmology and Visual Sciences, 750 East Adams Street, Syracuse, NY 13210, USA
| | - Christine Tilstra-Smith
- SUNY Upstate Medical University, Department of Ophthalmology and Visual Sciences, 750 East Adams Street, Syracuse, NY 13210, USA
| | - Nileyma Castro
- SUNY Upstate Medical University, Department of Ophthalmology and Visual Sciences, 750 East Adams Street, Syracuse, NY 13210, USA; New York VA Health Care, Syracuse VA Medical Center, 800 Irving Ave, Syracuse 13210, USA
| | - Barry E Knox
- SUNY Upstate Medical University, Department of Ophthalmology and Visual Sciences, 750 East Adams Street, Syracuse, NY 13210, USA; SUNY Upstate Medical University, Biochemistry and Molecular Biology, 750 East Adams Street, Syracuse, NY 13210, USA
| | - Jessica L Henty-Ridilla
- SUNY Upstate Medical University, Biochemistry and Molecular Biology, 750 East Adams Street, Syracuse, NY 13210, USA
| | - Audrey M Bernstein
- SUNY Upstate Medical University, Department of Ophthalmology and Visual Sciences, 750 East Adams Street, Syracuse, NY 13210, USA; SUNY Upstate Medical University, Biochemistry and Molecular Biology, 750 East Adams Street, Syracuse, NY 13210, USA; New York VA Health Care, Syracuse VA Medical Center, 800 Irving Ave, Syracuse 13210, USA.
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Qiu X, Lin J, Liang B, Chen Y, Liu G, Zheng J. Identification of Hub Genes and MicroRNAs Associated With Idiopathic Pulmonary Arterial Hypertension by Integrated Bioinformatics Analyses. Front Genet 2021; 12:667406. [PMID: 33995494 PMCID: PMC8117102 DOI: 10.3389/fgene.2021.636934] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/22/2021] [Indexed: 01/04/2023] Open
Abstract
Objective The aim of this study is the identification of hub genes associated with idiopathic pulmonary arterial hypertension (IPAH). Materials and Methods GSE15197 gene expression data was downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified by screening IPAH patients and controls. The 5,000 genes with the greatest variances were analyzed using a weighted gene co-expression network analysis (WGCNA). Modules with the strongest correlation with IPAH were chosen, followed by a functional enrichment analysis. Protein–protein interaction (PPI) networks were constructed to identify hub gene candidates using calculated degrees. Real hub genes were found from the overlap of DEGs and candidate hub genes. microRNAs (miRNAs) targeting real hub genes were found by screening miRNet 2.0. The most important IPAH miRNAs were identified. Results There were 4,395 DEGs identified. WGCNA indicated that green and brown modules associated most strongly with IPAH. Functional enrichment analysis showed that green and brown module genes were mainly involved in protein digestion and absorption and proteoglycans in cancer, respectively. The top ten candidate hub genes in green and brown modules were identified, respectively. After overlapping with DEGs, 11 real hub genes were identified: EP300, MMP2, CDH2, CDK2, GNG10, ALB, SMC2, DHX15, CUL3, BTBD1, and LTN1. These genes were expressed with significant differences in IPAH versus controls, indicating a high diagnostic ability. The miRNA–gene network showed that hsa-mir-1-3p could associate with IPAH. Conclusion EP300, MMP2, CDH2, CDK2, GNG10, ALB, SMC2, DHX15, CUL3, BTBD1, and LTN1 may play essential roles in IPAH. Predicted miRNA hsa-mir-1-3p could regulate gene expression in IPAH. Such hub genes may contribute to the pathology and progression in IPAH, providing potential diagnostic and therapeutic opportunities for IPAH patients.
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Affiliation(s)
- Xue Qiu
- Department of Cardiology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jinyan Lin
- The First Clinical Medical School, Guangxi Medical University, Nanning, China
| | - Bixiao Liang
- The First Clinical Medical School, Guangxi Medical University, Nanning, China
| | - Yanbing Chen
- The First Clinical Medical School, Guangxi Medical University, Nanning, China
| | - Guoqun Liu
- The First Clinical Medical School, Guangxi Medical University, Nanning, China
| | - Jing Zheng
- Department of Cardiology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
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Noncanonical Wnt planar cell polarity signaling in lung development and disease. Biochem Soc Trans 2020; 48:231-243. [PMID: 32096543 DOI: 10.1042/bst20190597] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/24/2020] [Accepted: 01/28/2020] [Indexed: 02/06/2023]
Abstract
The planar cell polarity (PCP) signaling pathway is a potent developmental regulator of directional cell behaviors such as migration, asymmetric division and morphological polarization that are critical for shaping the body axis and the complex three-dimensional architecture of tissues and organs. PCP is considered a noncanonical Wnt pathway due to the involvement of Wnt ligands and Frizzled family receptors in the absence of the beta-catenin driven gene expression observed in the canonical Wnt cascade. At the heart of the PCP mechanism are protein complexes capable of generating molecular asymmetries within cells along a tissue-wide axis that are translated into polarized actin and microtubule cytoskeletal dynamics. PCP has emerged as an important regulator of developmental, homeostatic and disease processes in the respiratory system. It acts along other signaling pathways to create the elaborately branched structure of the lung by controlling the directional protrusive movements of cells during branching morphogenesis. PCP operates in the airway epithelium to establish and maintain the orientation of respiratory cilia along the airway axis for anatomically directed mucociliary clearance. It also regulates the establishment of the pulmonary vasculature. In adult tissues, PCP dysfunction has been linked to a variety of chronic lung diseases such as cystic fibrosis, chronic obstructive pulmonary disease, and idiopathic pulmonary arterial hypertension, stemming chiefly from the breakdown of proper tissue structure and function and aberrant cell migration during regenerative wound healing. A better understanding of these (impaired) PCP mechanisms is needed to fully harness the therapeutic opportunities of targeting PCP in chronic lung diseases.
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