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Pileggi S, Colombo EA, Ancona S, Quadri R, Bernardelli C, Colapietro P, Taiana M, Fontana L, Miozzo M, Lesma E, Sirchia SM. Dysfunction in IGF2R Pathway and Associated Perturbations in Autophagy and WNT Processes in Beckwith-Wiedemann Syndrome Cell Lines. Int J Mol Sci 2024; 25:3586. [PMID: 38612397 PMCID: PMC11011696 DOI: 10.3390/ijms25073586] [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: 01/31/2024] [Revised: 03/08/2024] [Accepted: 03/18/2024] [Indexed: 04/14/2024] Open
Abstract
Beckwith-Wiedemann Syndrome (BWS) is an imprinting disorder characterized by overgrowth, stemming from various genetic and epigenetic changes. This study delves into the role of IGF2 upregulation in BWS, focusing on insulin-like growth factor pathways, which are poorly known in this syndrome. We examined the IGF2R, the primary receptor of IGF2, WNT, and autophagy/lysosomal pathways in BWS patient-derived lymphoblastoid cell lines, showing different genetic and epigenetic defects. The findings reveal a decreased expression and mislocalization of IGF2R protein, suggesting receptor dysfunction. Additionally, our results point to a dysregulation in the AKT/GSK-3/mTOR pathway, along with imbalances in autophagy and the WNT pathway. In conclusion, BWS cells, regardless of the genetic/epigenetic profiles, are characterized by alteration of the IGF2R pathway that is associated with the perturbation of the autophagy and lysosome processes. These alterations seem to be a key point of the molecular pathogenesis of BWS and potentially contribute to BWS's characteristic overgrowth and cancer susceptibility. Our study also uncovers alterations in the WNT pathway across all BWS cell lines, consistent with its role in growth regulation and cancer development.
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Affiliation(s)
- Silvana Pileggi
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milan, Italy; (S.P.)
| | - Elisa A. Colombo
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milan, Italy; (S.P.)
| | - Silvia Ancona
- Pharmacology, Department of Health Sciences, Università degli Studi di Milano, 20142 Milan, Italy (E.L.)
| | - Roberto Quadri
- Department of Biosciences, Università degli Studi di Milano, 20133 Milan, Italy
| | - Clara Bernardelli
- Pharmacology, Department of Health Sciences, Università degli Studi di Milano, 20142 Milan, Italy (E.L.)
| | - Patrizia Colapietro
- Medical Genetics, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, 20122 Milan, Italy
| | - Michela Taiana
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, 20122 Milan, Italy
| | - Laura Fontana
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milan, Italy; (S.P.)
- Unit of Medical Genetics, ASST Santi Paolo e Carlo, 20142 Milan, Italy
| | - Monica Miozzo
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milan, Italy; (S.P.)
- Unit of Medical Genetics, ASST Santi Paolo e Carlo, 20142 Milan, Italy
| | - Elena Lesma
- Pharmacology, Department of Health Sciences, Università degli Studi di Milano, 20142 Milan, Italy (E.L.)
| | - Silvia M. Sirchia
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milan, Italy; (S.P.)
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Vetchinova AS, Kapkaeva MR, Ivanov MV, Kutukova KA, Mudzhiri NM, Frumkina LE, Brydun AV, Sukhorukov VS, Illarioshkin SN. Mitochondrial Dysfunction in Dopaminergic Neurons Derived from Patients with LRRK2- and SNCA-Associated Genetic Forms of Parkinson's Disease. Curr Issues Mol Biol 2023; 45:8395-8411. [PMID: 37886972 PMCID: PMC10605424 DOI: 10.3390/cimb45100529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/24/2023] [Accepted: 10/11/2023] [Indexed: 10/28/2023] Open
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease. Some cases of PD may be caused by genetic factors, among which mutations in the LRRK2 and SNCA genes play an important role. To develop effective neuroprotective strategies for PD, it is important to diagnose the disease at the earliest stages of the neurodegenerative process. Therefore, the detection of diagnostic and prognostic markers of Parkinson's disease (PD) is an urgent medical need. Advances in induced pluripotent stem cell (iPSC) culture technology provide new opportunities for the search for new biomarkers of PD and its modeling in vitro. In our work, we used a new technology for multiplex profiling of gene expression using barcoding on the Nanostring platform to assess the activity of mitochondrial genes on iPSC-derived cultures of dopaminergic neurons obtained from patients with LRRK2- and SNCA-associated genetic forms PD and a healthy donor. Electron microscopy revealed ultrastructural changes in mitochondria in both LRRK2 and SNCA mutant cells, whereas mitochondria in cells from a healthy donor were normal. In a culture with the SNCA gene mutation, the ratio of the area occupied by mitochondria to the total area of the cytoplasm was significantly lower than in the control and in the line with the LRRK2 gene mutation. Transcriptome analysis of 105 mitochondria proteome genes using the Nanostring platform revealed differences between the diseased and normal cells in the activity of genes involved in respiratory complex function, the tricarboxylic acid cycle, ATP production, mitochondria-endoplasmic reticulum interaction, mitophagy, regulation of calcium concentration, and mitochondrial DNA replication.
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Affiliation(s)
- Anna S. Vetchinova
- Laboratory of Neurobiology and Tissue Engineering, Brain Science Institute, Research Center of Neurology, Moscow 125367, Russia
| | - Marina R. Kapkaeva
- Laboratory of Neurobiology and Tissue Engineering, Brain Science Institute, Research Center of Neurology, Moscow 125367, Russia
| | - Mikhail V. Ivanov
- Laboratory of Neuromorphology, Brain Science Institute, Research Center of Neurology, Moscow 125367, Russia (N.M.M.)
| | - Kristina A. Kutukova
- Laboratory of Neuromorphology, Brain Science Institute, Research Center of Neurology, Moscow 125367, Russia (N.M.M.)
| | - Natalia M. Mudzhiri
- Laboratory of Neuromorphology, Brain Science Institute, Research Center of Neurology, Moscow 125367, Russia (N.M.M.)
| | - Lydia E. Frumkina
- Laboratory of Neuromorphology, Brain Science Institute, Research Center of Neurology, Moscow 125367, Russia (N.M.M.)
| | - Anatoly V. Brydun
- Laboratory of Neuromorphology, Brain Science Institute, Research Center of Neurology, Moscow 125367, Russia (N.M.M.)
| | - Vladimir S. Sukhorukov
- Laboratory of Neuromorphology, Brain Science Institute, Research Center of Neurology, Moscow 125367, Russia (N.M.M.)
| | - Sergey N. Illarioshkin
- Laboratory of Neurobiology and Tissue Engineering, Brain Science Institute, Research Center of Neurology, Moscow 125367, Russia
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Bilinska A, Pszczola M, Stachowiak M, Stachecka J, Garbacz F, Aksoy MO, Szczerbal I. Droplet Digital PCR Quantification of Selected Intracellular and Extracellular microRNAs Reveals Changes in Their Expression Pattern during Porcine In Vitro Adipogenesis. Genes (Basel) 2023; 14:genes14030683. [PMID: 36980955 PMCID: PMC10047974 DOI: 10.3390/genes14030683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/27/2023] [Accepted: 03/08/2023] [Indexed: 03/12/2023] Open
Abstract
Extracellular miRNAs have attracted considerable interest because of their role in intercellular communication, as well as because of their potential use as diagnostic and prognostic biomarkers for many diseases. It has been shown that miRNAs secreted by adipose tissue can contribute to the pathophysiology of obesity. Detailed knowledge of the expression of intracellular and extracellular microRNAs in adipocytes is thus urgently required. The system of in vitro differentiation of mesenchymal stem cells (MSCs) into adipocytes offers a good model for such an analysis. The aim of this study was to quantify eight intracellular and extracellular miRNAs (miR-21a, miR-26b, miR-30a, miR-92a, miR-146a, miR-148a, miR-199, and miR-383a) during porcine in vitro adipogenesis using droplet digital PCR (ddPCR), a highly sensitive method. It was found that only some miRNAs associated with the inflammatory process (miR-21a, miR-92a) were highly expressed in differentiated adipocytes and were also secreted by cells. All miRNAs associated with adipocyte differentiation were highly abundant in both the studied cells and in the cell culture medium. Those miRNAs showed a characteristic expression profile with upregulation during differentiation.
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Das R, Jakubowski MA, Spildener J, Cheng YW. Identification of Novel MET Exon 14 Skipping Variants in Non-Small Cell Lung Cancer Patients: A Prototype Workflow Involving in Silico Prediction and RT-PCR. Cancers (Basel) 2022; 14:cancers14194814. [PMID: 36230737 PMCID: PMC9563401 DOI: 10.3390/cancers14194814] [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: 06/30/2022] [Revised: 09/11/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
Background and aims: The MET exon 14 skipping (METex14) is an oncogenic driver mutation that provides a therapeutic opportunity in non-small cell lung cancer (NSCLCs) patients. This event often results from sequence changes at the MET canonical splicing sites. We characterize two novel non-canonical splicing site variants of MET that produce METex14. Materials and Methods: Two variants were identified in three advanced-stage NSCLC patients in a next-generation sequencing panel. The potential impact on splicing was predicted using in silico tools. METex14 mutation was confirmed using reverse transcription (RT)-PCR and a Sanger sequencing analysis on RNA extracted from stained cytology smears. Results: The interrogated MET (RefSeq ID NM_000245.3) variants include a single nucleotide substitution, c.3028+3A>T, in intron 14 and a deletion mutation, c.3012_3028del, in exon 14. The in silico prediction analysis exhibited reduced splicing strength in both variants compared with the MET normal transcript. The RT-PCR and subsequent Sanger sequencing analyses confirmed METex14 skipping in all three patients carrying these variants. Conclusion: This study reveals two non-canonical MET splice variants that cause exon 14 skipping, concurrently also proposes a clinical workflow for the classification of such non-canonical splicing site variants detected by routine DNA-based NGS test. It shows the usefulness of in silico prediction to identify potential METex14 driver mutation and exemplifies the opportunity of routine cytology slides for RNA-based testing.
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Affiliation(s)
| | | | | | - Yu-Wei Cheng
- Correspondence: ; Tel.: +1-216-445-0757; Fax: +1-216-445-0681
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Pileggi S, La Vecchia M, Colombo EA, Fontana L, Colapietro P, Rovina D, Morotti A, Tabano S, Porta G, Alcalay M, Gervasini C, Miozzo M, Sirchia SM. Cohesin Mutations Induce Chromatin Conformation Perturbation of the H19/ IGF2 Imprinted Region and Gene Expression Dysregulation in Cornelia de Lange Syndrome Cell Lines. Biomolecules 2021; 11:1622. [PMID: 34827619 PMCID: PMC8615450 DOI: 10.3390/biom11111622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 02/07/2023] Open
Abstract
Traditionally, Cornelia de Lange Syndrome (CdLS) is considered a cohesinopathy caused by constitutive mutations in cohesin complex genes. Cohesin is a major regulator of chromatin architecture, including the formation of chromatin loops at the imprinted IGF2/H19 domain. We used 3C analysis on lymphoblastoid cells from CdLS patients carrying mutations in NIPBL and SMC1A genes to explore 3D chromatin structure of the IGF2/H19 locus and evaluate the influence of cohesin alterations in chromatin architecture. We also assessed quantitative expression of imprinted loci and WNT pathway genes, together with DMR methylation status of the imprinted genes. A general impairment of chromatin architecture and the emergence of new interactions were found. Moreover, imprinting alterations also involved the expression and methylation levels of imprinted genes, suggesting an association among cohesin genetic defects, chromatin architecture impairment, and imprinting network alteration. The WNT pathway resulted dysregulated: canonical WNT, cell cycle, and WNT signal negative regulation were the most significantly affected subpathways. Among the deregulated pathway nodes, the key node of the frizzled receptors was repressed. Our study provides new evidence that mutations in genes of the cohesin complex have effects on the chromatin architecture and epigenetic stability of genes commonly regulated by high order chromatin structure.
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Affiliation(s)
- Silvana Pileggi
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
| | - Marta La Vecchia
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
| | - Elisa Adele Colombo
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
| | - Laura Fontana
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
- Unit of Medical Genetics, ASST Santi Paolo e Carlo, 20142 Milano, Italy
| | - Patrizia Colapietro
- Department of Pathophysiology and Transplantation, Medical Genetics, Università degli Studi di Milano, 20122 Milan, Italy; (P.C.); (S.T.)
| | - Davide Rovina
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
| | - Annamaria Morotti
- Research Laboratories Coordination Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milano, Italy;
| | - Silvia Tabano
- Department of Pathophysiology and Transplantation, Medical Genetics, Università degli Studi di Milano, 20122 Milan, Italy; (P.C.); (S.T.)
- Laboratory of Medical Genetics, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Giovanni Porta
- Centro di Medicina Genomica, Department of Medicine and Surgery, Università degli Studi dell’Insubria, 21100 Varese, Italy;
| | - Myriam Alcalay
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, 20139 Milan, Italy;
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Cristina Gervasini
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
| | - Monica Miozzo
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
- Unit of Medical Genetics, ASST Santi Paolo e Carlo, 20142 Milano, Italy
| | - Silvia Maria Sirchia
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
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Suteau V, Seegers V, Munier M, Ben Boubaker R, Reyes C, Gentien D, Wery M, Croué A, Illouz F, Hamy A, Rodien P, Briet C. G Protein-coupled Receptors in Radioiodine-refractory Thyroid Cancer in the Era of Precision Medicine. J Clin Endocrinol Metab 2021; 106:2221-2232. [PMID: 34000025 DOI: 10.1210/clinem/dgab343] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Indexed: 12/11/2022]
Abstract
CONTEXT Radioiodine-refractory thyroid cancers have poor outcomes and limited therapeutic options (tyrosine kinase inhibitors) due to transient efficacy and toxicity of treatments. Therefore, combinatorial treatments with new therapeutic approaches are needed. Many studies link G protein-coupled receptors (GPCRs) to cancer cell biology. OBJECTIVE To perform a specific atlas of GPCR expression in progressive and refractory thyroid cancer to identify potential targets among GPCRs aiming at drug repositioning. METHODS We analyzed samples from tumor and normal thyroid tissues from 17 patients with refractory thyroid cancer (12 papillary thyroid cancers [PTCs] and 5 follicular thyroid cancers [FTCs]). We assessed GPCR mRNA expression using NanoString technology with a custom panel of 371 GPCRs. The data were compared with public repositories and pharmacological databases to identify eligible drugs. The analysis of prognostic value of genes was also performed with TCGA datasets. RESULTS With our transcriptomic analysis, 4 receptors were found to be downregulated in FTC (VIPR1, ADGRL2/LPHN2, ADGRA3, and ADGRV1). In PTC, 24 receptors were deregulated, 7 of which were also identified by bioinformatics analyses of publicly available datasets on primary thyroid cancers (VIPR1, ADORA1, GPRC5B, P2RY8, GABBR2, CYSLTR2, and LPAR5). Among all the differentially expressed genes, 22 GPCRs are the target of approved drugs and some GPCRs are also associated with prognostic factors. DISCUSSION For the first time, we performed GPCR mRNA expression profiling in progressive and refractory thyroid cancers. These findings provide an opportunity to identify potential therapeutic targets for drug repositioning and precision medicine in radioiodine-refractory thyroid cancer.
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Affiliation(s)
- Valentine Suteau
- Département d'Endocrinologie-diabétologie nutrition, CHU Angers, Angers, France
- Faculty of Health, University of Angers (CHU Angers), Inserm 1083, CNRS 6015, MITOVASC, SFR ICAT, Angers, France
| | - Valérie Seegers
- Institut de Cancérologie de l'Ouest, Service de Biométrie, Angers, France
| | - Mathilde Munier
- Département d'Endocrinologie-diabétologie nutrition, CHU Angers, Angers, France
- Faculty of Health, University of Angers (CHU Angers), Inserm 1083, CNRS 6015, MITOVASC, SFR ICAT, Angers, France
- Centre de référence des maladies rares de la Thyroïde et des Récepteurs Hormonaux, Endo-ERN centre for rare endocrine diseases, Angers, France
| | - Rym Ben Boubaker
- Faculty of Health, University of Angers (CHU Angers), Inserm 1083, CNRS 6015, MITOVASC, SFR ICAT, Angers, France
| | - Cécile Reyes
- Institut Curie, Plateforme Génomique, Paris, France
| | | | - Méline Wery
- Faculty of Health, University of Angers (CHU Angers), SFR ICAT, Angers, France
| | - Anne Croué
- Département de Pathologie Cellulaire et Tissulaire, CHU Angers, Angers, France
| | - Frédéric Illouz
- Département d'Endocrinologie-diabétologie nutrition, CHU Angers, Angers, France
- Centre de référence des maladies rares de la Thyroïde et des Récepteurs Hormonaux, Endo-ERN centre for rare endocrine diseases, Angers, France
- Centre de compétence TUTHYREF, TUTHYREF Network, Angers, France
| | - Antoine Hamy
- Service de chirurgie viscérale, CHU d'Angers, Angers, France
| | - Patrice Rodien
- Département d'Endocrinologie-diabétologie nutrition, CHU Angers, Angers, France
- Faculty of Health, University of Angers (CHU Angers), Inserm 1083, CNRS 6015, MITOVASC, SFR ICAT, Angers, France
- Centre de référence des maladies rares de la Thyroïde et des Récepteurs Hormonaux, Endo-ERN centre for rare endocrine diseases, Angers, France
- Centre de compétence TUTHYREF, TUTHYREF Network, Angers, France
| | - Claire Briet
- Département d'Endocrinologie-diabétologie nutrition, CHU Angers, Angers, France
- Faculty of Health, University of Angers (CHU Angers), Inserm 1083, CNRS 6015, MITOVASC, SFR ICAT, Angers, France
- Centre de référence des maladies rares de la Thyroïde et des Récepteurs Hormonaux, Endo-ERN centre for rare endocrine diseases, Angers, France
- Centre de compétence TUTHYREF, TUTHYREF Network, Angers, France
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