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Olazagoitia-Garmendia A, Rojas-Márquez H, Romero MDM, Ruiz P, Agirre-Lizaso A, Chen Y, Perugorria MJ, Herrero L, Serra D, Luo C, Bujanda L, He C, Castellanos-Rubio A. Inhibition of YTHDF1 by salvianolic acid overcomes gluten-induced intestinal inflammation. Gut 2023:gutjnl-2023-330459. [PMID: 37907258 DOI: 10.1136/gutjnl-2023-330459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/11/2023] [Indexed: 11/02/2023]
Affiliation(s)
- Ane Olazagoitia-Garmendia
- Department of Biochemistry and Molecular Biology, University of the Basque Country, UPV/EHU, Leioa, Spain
- Biobizkaia Health Research Institute, Barakaldo, Spain
| | - Henar Rojas-Márquez
- Biobizkaia Health Research Institute, Barakaldo, Spain
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Maria Del Mar Romero
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Pamela Ruiz
- Research Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU), University of the Basque Country, UPV/EHU, Plentzia, Spain
- BCTA Research Group, Department of Zoology and Animal Cell Biology, University of the Basque Country, UPV-EHU, Leioa, Spain
| | - Aloña Agirre-Lizaso
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, Donostia-san Sebastian, Spain
| | - Yantao Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, Beijing, Beijing, China
| | - Maria Jesus Perugorria
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, Donostia-san Sebastian, Spain
- Department of Medicine, Faculty of Medicine and Nursing, University of the Basque Country, UPV/EHU, Leioa, Spain
- Centro de Investigación Biomédica en Red enfermedades hepaticas y digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Laura Herrero
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Dolors Serra
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Cheng Luo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, Beijing, Beijing, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China
| | - Luis Bujanda
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, Donostia-san Sebastian, Spain
- Department of Medicine, Faculty of Medicine and Nursing, University of the Basque Country, UPV/EHU, Leioa, Spain
- Centro de Investigación Biomédica en Red enfermedades hepaticas y digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
- Howard Hughes Medical Institute, Chicago, Illinois, USA
| | - Ainara Castellanos-Rubio
- Biobizkaia Health Research Institute, Barakaldo, Spain
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, UPV/EHU, Leioa, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
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Olazagoitia-Garmendia A, Senovilla-Ganzo R, García-Moreno F, Castellanos-Rubio A. Functional evolutionary convergence of long noncoding RNAs involved in embryonic development. Commun Biol 2023; 6:908. [PMID: 37670146 PMCID: PMC10480150 DOI: 10.1038/s42003-023-05278-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 08/24/2023] [Indexed: 09/07/2023] Open
Abstract
Long noncoding RNAs have been identified in most vertebrates, but the functional characterization of these molecules is challenging, mainly due to the lack of linear sequence homology between species. In this work, we aimed to find functional evolutionary convergent lncRNAs involved in development by screening of k-mer content (nonlinear similarity) and secondary structure-based approaches combining in silico, in vitro and in vivo validation analysis. From the Madagascar gecko genes, we have found a non-orthologous lncRNA with a similar k-mer content and structurally concordant with the human lncRNA EVX1AS. Analysis of function-related characteristics together with locus-specific targeting of human EVX1AS and gecko EVX1AS-like (i.e., CRISPR Display) in human neuroepithelial cells and chicken mesencephalon have confirmed that gecko EVX1AS-like lncRNA mimics human EVX1AS function and induces EVX1 expression independently of the target species. Our data shows functional convergence of non-homologous lncRNAs and presents a useful approach for the definition and manipulation of lncRNA function within different model organisms.
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Affiliation(s)
- Ane Olazagoitia-Garmendia
- University of the Basque Country, UPV-EHU, Leioa, Spain
- Biobizkaia Health Research Institute, Barakaldo, Spain
| | | | - Fernando García-Moreno
- University of the Basque Country, UPV-EHU, Leioa, Spain
- Achucarro Basque Center for Neuroscience, Leioa, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Ainara Castellanos-Rubio
- University of the Basque Country, UPV-EHU, Leioa, Spain.
- Biobizkaia Health Research Institute, Barakaldo, Spain.
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
- CIBERDEM/CIBERER, Madrid, Spain.
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3
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González-Moro I, Rojas-Márquez H, Sebastian-delaCruz M, Mentxaka-Salgado J, Olazagoitia-Garmendia A, Mendoza LM, Lluch A, Fantuzzi F, Lambert C, Ares Blanco J, Marselli L, Marchetti P, Cnop M, Delgado E, Fernández-Real JM, Ortega FJ, Castellanos-Rubio A, Santin I. A long non-coding RNA that harbors a SNP associated with type 2 diabetes regulates the expression of TGM2 gene in pancreatic beta cells. Front Endocrinol (Lausanne) 2023; 14:1101934. [PMID: 36824360 PMCID: PMC9941620 DOI: 10.3389/fendo.2023.1101934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/24/2023] [Indexed: 02/10/2023] Open
Abstract
INTRODUCTION Most of the disease-associated single nucleotide polymorphisms (SNPs) lie in non- coding regions of the human genome. Many of these variants have been predicted to impact the expression and function of long non-coding RNAs (lncRNA), but the contribution of these molecules to the development of complex diseases remains to be clarified. METHODS Here, we performed a genetic association study between a SNP located in a lncRNA known as LncTGM2 and the risk of developing type 2 diabetes (T2D), and analyzed its implication in disease pathogenesis at pancreatic beta cell level. Genetic association study was performed on human samples linking the rs2076380 polymorphism with T2D and glycemic traits. The pancreatic beta cell line EndoC-bH1 was employed for functional studies based on LncTGM2 silencing and overexpression experiments. Human pancreatic islets were used for eQTL analysis. RESULTS We have identified a genetic association between LncTGM2 and T2D risk. Functional characterization of the LncTGM2 revealed its implication in the transcriptional regulation of TGM2, coding for a transglutaminase. The T2Dassociated risk allele in LncTGM2 disrupts the secondary structure of this lncRNA, affecting its stability and the expression of TGM2 in pancreatic beta cells. Diminished LncTGM2 in human beta cells impairs glucose-stimulated insulin release. CONCLUSIONS These findings provide novel information on the molecular mechanisms by which T2D-associated SNPs in lncRNAs may contribute to disease, paving the way for the development of new therapies based on the modulation of lncRNAs.
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Affiliation(s)
- Itziar González-Moro
- Department of Biochemistry and Molecular Biology, University of the Basque Country UPV/EHU, Leioa, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Henar Rojas-Márquez
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, Leioa, Spain
| | - Maialen Sebastian-delaCruz
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, Leioa, Spain
| | - Jon Mentxaka-Salgado
- Department of Biochemistry and Molecular Biology, University of the Basque Country UPV/EHU, Leioa, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Ane Olazagoitia-Garmendia
- Department of Biochemistry and Molecular Biology, University of the Basque Country UPV/EHU, Leioa, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, Leioa, Spain
| | - Luis Manuel Mendoza
- Department of Biochemistry and Molecular Biology, University of the Basque Country UPV/EHU, Leioa, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Aina Lluch
- Institut d’Investigació Biomèdica de Girona, Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
| | - Federica Fantuzzi
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels, Belgium
| | - Carmen Lambert
- Health Research Institute of the Principality of Asturias (ISPA), Oviedo, Spain
- University of Barcelona, Barcelona, Spain
| | - Jessica Ares Blanco
- Health Research Institute of the Principality of Asturias (ISPA), Oviedo, Spain
- Endocrinology and Nutrition Department, Central University Hospital of Asturias (HUCA), Oviedo, Spain
- Department of Medicine, University of Oviedo, Oviedo, Spain
| | - Lorella Marselli
- Department of Clinical and Experimental Medicine, Cisanello University Hospital, Pisa, Italy
| | - Piero Marchetti
- Department of Clinical and Experimental Medicine, Cisanello University Hospital, Pisa, Italy
| | - Miriam Cnop
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels, Belgium
- Division of Endocrinology, Erasmus Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Elías Delgado
- Health Research Institute of the Principality of Asturias (ISPA), Oviedo, Spain
- Endocrinology and Nutrition Department, Central University Hospital of Asturias (HUCA), Oviedo, Spain
- Department of Medicine, University of Oviedo, Oviedo, Spain
- Spanish Biomedical Research Network in Rare Diseases (CIBERER), Madrid, Spain
| | - José Manuel Fernández-Real
- Institut d’Investigació Biomèdica de Girona, Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
- Department of Medical Sciences, School of Medicine, University of Girona, Oviedo, Spain
| | - Francisco José Ortega
- Institut d’Investigació Biomèdica de Girona, Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
| | - Ainara Castellanos-Rubio
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, Leioa, Spain
- Diabetes and Associated Metabolic Diseases Networking Biomedical Research Centre, Madrid, Spain
- Ikerbasque - Basque Foundation for Science, Bilbao, Spain
- *Correspondence: Izortze Santin, ; Ainara Castellanos-Rubio,
| | - Izortze Santin
- Department of Biochemistry and Molecular Biology, University of the Basque Country UPV/EHU, Leioa, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Diabetes and Associated Metabolic Diseases Networking Biomedical Research Centre, Madrid, Spain
- *Correspondence: Izortze Santin, ; Ainara Castellanos-Rubio,
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Mendoza-Gomez LM, Sebastian-delaCruz M, Olazagoitia-Garmendia A, González-Moro I, Rojas-Márquez H, Mentxaka J, Santin I, Castellanos-Rubio A. Preparation of pepsin trypsin digested gliadin for stimulation experiments. Methods Cell Biol 2022; 179:195-201. [PMID: 37625875 DOI: 10.1016/bs.mcb.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Celiac disease (CD) is a complex immune disorder of the intestine that developes in genetically susceptible individuals. CD develops as an intolerance to ingested gluten proteins (gliadins, secalins, hordeins and avenins), being gliadin one of the most immunogenic. Here we present a protocol for the preparation of digested gliadin for laboratory use, a fundamental axis for in vitro and in vivo stimulation studies related to celiac disease research. The importance of a scrupulous handling of materials, products and laboratory instruments to achieve a lipopolysaccharide free gliadin is explained and emphasized. Therefore, in the present chapter, a step-by-step set-up of the protocol for pepsin trypsin gliadin digestion is explained.
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Affiliation(s)
- Luis Manuel Mendoza-Gomez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Maialen Sebastian-delaCruz
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, UPV/EHU, Leioa, Spain; Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Ane Olazagoitia-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, UPV/EHU, Leioa, Spain; Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Itziar González-Moro
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, UPV/EHU, Leioa, Spain; Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Henar Rojas-Márquez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, UPV/EHU, Leioa, Spain; Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Jon Mentxaka
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, UPV/EHU, Leioa, Spain; Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Izortze Santin
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, UPV/EHU, Leioa, Spain; Biocruces Bizkaia Health Research Institute, Barakaldo, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
| | - Ainara Castellanos-Rubio
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, UPV/EHU, Leioa, Spain; Biocruces Bizkaia Health Research Institute, Barakaldo, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain.
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5
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Olazagoitia-Garmendia A. Pepsin-trypsin digested gliadin treatment in intestinal cells. Methods Cell Biol 2022; 179:1-11. [PMID: 37625867 DOI: 10.1016/bs.mcb.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Celiac disease (CD) is an intestinal autoimmune disorder developed in genetically susceptible individuals upon gluten ingestion. Gliadin is known to be the most immunogenic gluten component, which can activate the host immune response represented by NFkB activation and release of proinflammatory cytokines as IL8. However, many aspects of the involvement of gliadin in CD pathophysiology is not well understood yet. Lack of a CD animal model increases difficulty elucidating key steps in CD development, what increases the importance of in vitro experiments. Here we present a protocol for in vitro pepsin-trypsin digested gliadin (PTG) treatment for long term studies in HCT116 intestinal cell line.
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Affiliation(s)
- Ane Olazagoitia-Garmendia
- University of the Basque Country, UPV/EHU, Leioa, Spain; Biocruces Bizkaia, Health Research Institute, Barakaldo, Spain.
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6
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Olazagoitia-Garmendia A, Zhang L, Mera P, Godbout JK, Sebastian-DelaCruz M, Garcia-Santisteban I, Mendoza LM, Huerta A, Irastorza I, Bhagat G, Green PH, Herrero L, Serra D, Rodriguez JA, Verdu EF, He C, Bilbao JR, Castellanos-Rubio A. Gluten-induced RNA methylation changes regulate intestinal inflammation via allele-specific XPO1 translation in epithelial cells. Gut 2022; 71:68-76. [PMID: 33526437 PMCID: PMC8666699 DOI: 10.1136/gutjnl-2020-322566] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 12/23/2020] [Accepted: 01/17/2021] [Indexed: 12/16/2022]
Abstract
OBJECTIVES Coeliac disease (CD) is a complex autoimmune disorder that develops in genetically susceptible individuals. Dietary gluten triggers an immune response for which the only available treatment so far is a strict, lifelong gluten free diet. Human leucocyte antigen (HLA) genes and several non-HLA regions have been associated with the genetic susceptibility to CD, but their role in the pathogenesis of the disease is still essentially unknown, making it complicated to develop much needed non-dietary treatments. Here, we describe the functional involvement of a CD-associated single-nucleotide polymorphism (SNP) located in the 5'UTR of XPO1 in the inflammatory environment characteristic of the coeliac intestinal epithelium. DESIGN The function of the CD-associated SNP was investigated using an intestinal cell line heterozygous for the SNP, N6-methyladenosine (m6A)-related knock-out and HLA-DQ2 mice, and human samples from patients with CD. RESULTS Individuals harbouring the risk allele had higher m6A methylation in the 5'UTR of XPO1 RNA, rendering greater XPO1 protein amounts that led to downstream nuclear factor kappa B (NFkB) activity and subsequent inflammation. Furthermore, gluten exposure increased overall m6A methylation in humans as well as in in vitro and in vivo models. CONCLUSION We identify a novel m6A-XPO1-NFkB pathway that is activated in CD patients. The findings will prompt the development of new therapeutic approaches directed at m6A proteins and XPO1, a target under evaluation for the treatment of intestinal disorders.
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Affiliation(s)
- Ane Olazagoitia-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), Leioa, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Linda Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois, USA
| | - Paula Mera
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Julie K Godbout
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Maialen Sebastian-DelaCruz
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), Leioa, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Iraia Garcia-Santisteban
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), Leioa, Spain
| | - Luis Manuel Mendoza
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), Leioa, Spain
| | - Alain Huerta
- Enfermedades Digestivas, Hospital de Galdakao-Usansolo, Galdacano, Spain
| | - Iñaki Irastorza
- Department of Pediatrics, University of the Basque Country (UPV-EHU), Leioa, Spain
| | - Govind Bhagat
- Celiac Disease Center, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Peter H Green
- Celiac Disease Center, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Laura Herrero
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Dolors Serra
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Jose Antonio Rodriguez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), Leioa, Spain
| | - Elena F Verdu
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois, USA
| | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), Leioa, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
| | - Ainara Castellanos-Rubio
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), Leioa, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
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7
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Sebastian-delaCruz M, Olazagoitia-Garmendia A, Huerta Madrigal A, Garcia-Etxebarria K, Mendoza L, Fernandez-Jimenez N, Garcia Casales Z, de la Calle Navarro E, Calvo A, Legarda M, Tutau C, Irastorza I, Bujanda L, Bilbao J, Castellanos-Rubio A. A Novel Noninvasive Method Based on Salivary Inflammatory Biomarkers for the Screening of Celiac Disease. Cell Mol Gastroenterol Hepatol 2021; 12:1511-1513.e2. [PMID: 34062280 PMCID: PMC8531944 DOI: 10.1016/j.jcmgh.2021.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/18/2021] [Accepted: 05/24/2021] [Indexed: 12/10/2022]
Affiliation(s)
- M. Sebastian-delaCruz
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain,Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - A. Olazagoitia-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain,Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | | | - K. Garcia-Etxebarria
- Biodonostia, Gastrointestinal Genetics Group, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, San Sebastian, Spain
| | - L.M. Mendoza
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - N. Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain,Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | | | | | - A.E. Calvo
- Hospital de Txagorritxu, Vitoria-Gasteiz, Spain
| | - M. Legarda
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain,Department of Pediatrics, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - C. Tutau
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain,Department of Pediatrics, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - I. Irastorza
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain,Department of Pediatrics, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - L. Bujanda
- Department of Gastroenterology, Biodonostia Health Research Institute, Universidad del País Vasco, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, San Sebastian, Spain
| | - J.R. Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain,Biocruces Bizkaia Health Research Institute, Barakaldo, Spain,Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas, Instituto de Salud Carlos III, Madrid, Spain
| | - A. Castellanos-Rubio
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain,Biocruces Bizkaia Health Research Institute, Barakaldo, Spain,Department of Gastroenterology, Biodonostia Health Research Institute, Universidad del País Vasco, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, San Sebastian, Spain,Ikerbasque, Basque Foundation for Science, Bilbao, Spain,Corresponding author: Ainara Castellanos-Rubio, PhD, Department of Genetics, Physical Anthropology and Animal Physiology Maria Goyri building, Lab 1.11 University of the Basque Country (UPV/EHU) Leioa, 48940, Spain
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8
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Castellanos-Rubio I, Arriortua O, Marcano L, Rodrigo I, Iglesias-Rojas D, Barón A, Olazagoitia-Garmendia A, Olivi L, Plazaola F, Fdez-Gubieda ML, Castellanos-Rubio A, Garitaonandia JS, Orue I, Insausti M. Shaping Up Zn-Doped Magnetite Nanoparticles from Mono- and Bimetallic Oleates: The Impact of Zn Content, Fe Vacancies, and Morphology on Magnetic Hyperthermia Performance. Chem Mater 2021; 33:3139-3154. [PMID: 34556898 PMCID: PMC8451613 DOI: 10.1021/acs.chemmater.0c04794] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 04/02/2021] [Indexed: 05/15/2023]
Abstract
The currently existing magnetic hyperthermia treatments usually need to employ very large doses of magnetic nanoparticles (MNPs) and/or excessively high excitation conditions (H × f > 1010 A/m s) to reach the therapeutic temperature range that triggers cancer cell death. To make this anticancer therapy truly minimally invasive, it is crucial the development of improved chemical routes that give rise to monodisperse MNPs with high saturation magnetization and negligible dipolar interactions. Herein, we present an innovative chemical route to synthesize Zn-doped magnetite NPs based on the thermolysis of two kinds of organometallic precursors: (i) a mixture of two monometallic oleates (FeOl + ZnOl), and (ii) a bimetallic iron-zinc oleate (Fe3-y Zn y Ol). These approaches have allowed tailoring the size (10-50 nm), morphology (spherical, cubic, and cuboctahedral), and zinc content (Zn x Fe3-x O4, 0.05 < x < 0.25) of MNPs with high saturation magnetization (≥90 Am2/kg at RT). The oxidation state and the local symmetry of Zn2+ and Fe2+/3+ cations have been investigated by means of X-ray absorption near-edge structure (XANES) spectroscopy, while the Fe center distribution and vacancies within the ferrite lattice have been examined in detail through Mössbauer spectroscopy, which has led to an accurate determination of the stoichiometry in each sample. To achieve good biocompatibility and colloidal stability in physiological conditions, the Zn x Fe3-x O4 NPs have been coated with high-molecular-weight poly(ethylene glycol) (PEG). The magnetothermal efficiency of Zn x Fe3-x O4@PEG samples has been systematically analyzed in terms of composition, size, and morphology, making use of the latest-generation AC magnetometer that is able to reach 90 mT. The heating capacity of Zn0.06Fe2.9 4O4 cuboctahedrons of 25 nm reaches a maximum value of 3652 W/g (at 40 kA/m and 605 kHz), but most importantly, they reach a highly satisfactory value (600 W/g) under strict safety excitation conditions (at 36 kA/m and 125 kHz). Additionally, the excellent heating power of the system is kept identical both immobilized in agar and in the cellular environment, proving the great potential and reliability of this platform for magnetic hyperthermia therapies.
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Affiliation(s)
- Idoia Castellanos-Rubio
- Dpto.
Electricidad y Electrónica, Facultad de Ciencia y Tecnología, UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Oihane Arriortua
- Dpto.
Química Inorgánica, Facultad de Ciencia y Tecnología, UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Lourdes Marcano
- Dpto.
Electricidad y Electrónica, Facultad de Ciencia y Tecnología, UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Spain
- Helmholtz-Zentrum
Berlin für Materialien und Energie, Albert-Einstein-Str.15, 12489 Berlin, Germany
| | - Irati Rodrigo
- Dpto.
Electricidad y Electrónica, Facultad de Ciencia y Tecnología, UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Spain
- BC
Materials, Basque Center for Materials, Applications and Nanostructures, Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Daniela Iglesias-Rojas
- Dpto.
Química Inorgánica, Facultad de Ciencia y Tecnología, UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Ander Barón
- Dpto.
Química Inorgánica, Facultad de Ciencia y Tecnología, UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Ane Olazagoitia-Garmendia
- Dpto.
Genética, Antropología Física y Fisiología
Animal, Facultad de Medicina, UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Spain
- Biocruces
Bizkaia Health Research Institute, Cruces Plaza, 48903 Barakaldo, Spain
| | - Luca Olivi
- Elettra
Synchrotron Trieste, 34149 Basovizza, Italy
| | - Fernando Plazaola
- Dpto.
Electricidad y Electrónica, Facultad de Ciencia y Tecnología, UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Spain
| | - M. Luisa Fdez-Gubieda
- Dpto.
Electricidad y Electrónica, Facultad de Ciencia y Tecnología, UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Spain
- BC
Materials, Basque Center for Materials, Applications and Nanostructures, Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Ainara Castellanos-Rubio
- Dpto.
Genética, Antropología Física y Fisiología
Animal, Facultad de Medicina, UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Spain
- Biocruces
Bizkaia Health Research Institute, Cruces Plaza, 48903 Barakaldo, Spain
- Biomedical
Research Center in Diabetes Network and Associated Metabolic Diseases, 28029 Madrid, Spain
- IKERBASQUE
Basque Foundation for Science, 48013 Bilbao, Spain
| | - José S. Garitaonandia
- Dpto.
Física Aplicada II, Facultad de Ciencia y Tecnología, UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Iñaki Orue
- SGIker,
Servicios Generales de Investigación, UPV/EHU, Barrio Sarriena
s/n, 48940 Leioa, Spain
| | - Maite Insausti
- Dpto.
Química Inorgánica, Facultad de Ciencia y Tecnología, UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Spain
- BC
Materials, Basque Center for Materials, Applications and Nanostructures, Barrio Sarriena s/n, 48940 Leioa, Spain
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9
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Sebastian-delaCruz M, Gonzalez-Moro I, Olazagoitia-Garmendia A, Castellanos-Rubio A, Santin I. The Role of lncRNAs in Gene Expression Regulation through mRNA Stabilization. Noncoding RNA 2021; 7:ncrna7010003. [PMID: 33466464 PMCID: PMC7839045 DOI: 10.3390/ncrna7010003] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 12/12/2022] Open
Abstract
mRNA stability influences gene expression and translation in almost all living organisms, and the levels of mRNA molecules in the cell are determined by a balance between production and decay. Maintaining an accurate balance is crucial for the correct function of a wide variety of biological processes and to maintain an appropriate cellular homeostasis. Long non-coding RNAs (lncRNAs) have been shown to participate in the regulation of gene expression through different molecular mechanisms, including mRNA stabilization. In this review we provide an overview on the molecular mechanisms by which lncRNAs modulate mRNA stability and decay. We focus on how lncRNAs interact with RNA binding proteins and microRNAs to avoid mRNA degradation, and also on how lncRNAs modulate epitranscriptomic marks that directly impact on mRNA stability.
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Affiliation(s)
- Maialen Sebastian-delaCruz
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, 48940 Leioa, Spain; (M.S.-d.); (A.O.-G.); (A.C.-R.)
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
| | - Itziar Gonzalez-Moro
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
| | - Ane Olazagoitia-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, 48940 Leioa, Spain; (M.S.-d.); (A.O.-G.); (A.C.-R.)
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
| | - Ainara Castellanos-Rubio
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, 48940 Leioa, Spain; (M.S.-d.); (A.O.-G.); (A.C.-R.)
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
- Ikerbasque, Basque Foundation for Science, 48009 Bilbao, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Izortze Santin
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-94-601-32-09
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10
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Abstract
Technological advances in high-throughput sequencing in combination with antibody enrichment and/or induced nucleotide-specific chemical modifications have accelerated the mapping of epitranscriptomic modifications. However, site-specific detection and quantification of m6A are still technically challenging. Here, we describe a simple RT-QPCR-based approach for the relative quantification of candidate m6A regions that takes advantage of the diminished capacity of BstI enzyme to retrotranscribe m6A residues.
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Affiliation(s)
- Ane Olazagoitia-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), Leioa, Spain.,BioCruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Ainara Castellanos-Rubio
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), Leioa, Spain. .,BioCruces Bizkaia Health Research Institute, Barakaldo, Spain. .,Ikerbasque, Basque Foundation for Science, Bilbao, Spain. .,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain.
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11
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Sebastian-delaCruz M, Olazagoitia-Garmendia A, Gonzalez-Moro I, Santin I, Garcia-Etxebarria K, Castellanos-Rubio A. Implication of m6A mRNA Methylation in Susceptibility to Inflammatory Bowel Disease. Epigenomes 2020; 4:16. [PMID: 34968289 PMCID: PMC8594712 DOI: 10.3390/epigenomes4030016] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/21/2020] [Accepted: 07/28/2020] [Indexed: 01/08/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic inflammatory condition of the gastrointestinal tract that develops due to the interaction between genetic and environmental factors. More than 160 loci have been associated with IBD, but the functional implication of many of the associated genes remains unclear. N6-Methyladenosine (m6A) is the most abundant internal modification in mRNA. m6A methylation regulates many aspects of mRNA metabolism, playing important roles in the development of several pathologies. Interestingly, SNPs located near or within m6A motifs have been proposed as possible contributors to disease pathogenesis. We hypothesized that certain IBD-associated SNPs could regulate the function of genes involved in IBD development via m6A-dependent mechanisms. We used online available GWAS, m6A and transcriptome data to find differentially expressed genes that harbored m6A-SNPs associated with IBD. Our analysis resulted in five candidate genes corresponding to two of the major IBD subtypes: UBE2L3 and SLC22A4 for Crohn's Disease and TCF19, C6orf47 and SNAPC4 for Ulcerative Colitis. Further analysis using in silico predictions and co-expression analyses in combination with in vitro functional studies showed that our candidate genes seem to be regulated by m6A-dependent mechanisms. These findings provide the first indication of the implication of RNA methylation events in IBD pathogenesis.
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Affiliation(s)
- Maialen Sebastian-delaCruz
- Department of Genetics, Physical Anthropology and Animal Fisiology, University of the Basque Country, 48940 Leioa, Spain; (M.S.-d.); (A.O.-G.)
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (I.G.-M.); (I.S.)
| | - Ane Olazagoitia-Garmendia
- Department of Genetics, Physical Anthropology and Animal Fisiology, University of the Basque Country, 48940 Leioa, Spain; (M.S.-d.); (A.O.-G.)
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (I.G.-M.); (I.S.)
| | - Itziar Gonzalez-Moro
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (I.G.-M.); (I.S.)
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
| | - Izortze Santin
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (I.G.-M.); (I.S.)
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
- CIBER (Centro de Investigación Biomédica en Red) de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | | | - Ainara Castellanos-Rubio
- Department of Genetics, Physical Anthropology and Animal Fisiology, University of the Basque Country, 48940 Leioa, Spain; (M.S.-d.); (A.O.-G.)
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (I.G.-M.); (I.S.)
- CIBER (Centro de Investigación Biomédica en Red) de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
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12
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Castellanos-Rubio I, Rodrigo I, Olazagoitia-Garmendia A, Arriortua O, Gil de Muro I, Garitaonandia JS, Bilbao JR, Fdez-Gubieda ML, Plazaola F, Orue I, Castellanos-Rubio A, Insausti M. Highly Reproducible Hyperthermia Response in Water, Agar, and Cellular Environment by Discretely PEGylated Magnetite Nanoparticles. ACS Appl Mater Interfaces 2020; 12:27917-27929. [PMID: 32464047 PMCID: PMC8489799 DOI: 10.1021/acsami.0c03222] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Local heat generation from magnetic nanoparticles (MNPs) exposed to alternating magnetic fields can revolutionize cancer treatment. However, the application of MNPs as anticancer agents is limited by serious drawbacks. Foremost among these are the fast uptake and biodegradation of MNPs by cells and the unpredictable magnetic behavior of the MNPs when they accumulate within or around cells and tissues. In fact, several studies have reported that the heating power of MNPs is severely reduced in the cellular environment, probably due to a combination of increased viscosity and strong NP agglomeration. Herein, we present an optimized protocol to coat magnetite (Fe3O4) NPs larger than 20 nm (FM-NPs) with high molecular weight PEG molecules that avoid collective coatings, prevent the formation of large clusters of NPs and keep constant their high heating performance in environments with very different ionic strengths and viscosities (distilled water, physiological solutions, agar and cell culture media). The great reproducibility and reliability of the heating capacity of this FM-NP@PEG system in such different environments has been confirmed by AC magnetometry and by more conventional calorimetric measurements. The explanation of this behavior has been shown to lie in preserving as much as possible the magnetic single domain-type behavior of nearly isolated NPs. In vitro endocytosis experiments in a colon cancer-derived cell line indicate that FM-NP@PEG formulations with PEGs of higher molecular weight (20 kDa) are more resistant to endocytosis than formulations with smaller PEGs (5 kDa), showing quite large uptake mean-life (τ > 5 h) in comparison with other NP systems. The in vitro magnetic hyperthermia was performed at 21 mT and 650 kHz during 1 h in a pre-endocytosis stage and complete cell death was achieved 48 h posthyperthermia. These optimal FM-NP@PEG formulations with high resistance to endocytosis and predictable magnetic response will aid the progress and accuracy of the emerging era of theranostics.
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Affiliation(s)
- Idoia Castellanos-Rubio
- Departamento de Química Inorgánica, Facultad de Ciencia y Tecnología, UPV/EHU, Barrio Sarriena s/n, 48940, Leioa, Spain
- Department of Electricidad
y Electrónica, Facultad de Ciencia
y Tecnología, UPV/EHU, Barrio
Sarriena s/n, 48940, Leioa, Spain
- (I.C.-R.)
| | - Irati Rodrigo
- Department of Electricidad
y Electrónica, Facultad de Ciencia
y Tecnología, UPV/EHU, Barrio
Sarriena s/n, 48940, Leioa, Spain
- BC Materials, Basque Center for Materials, Applications, and Nanostructures, Barrio Sarriena s/n, 48940, Leioa, Spain
| | - Ane Olazagoitia-Garmendia
- Departamento de
Genética, Antropología Física y Fisiología
Animal, Facultad de Medicina y Enfermería, Barrio Sarriena s/n, 48940, Leioa, Spain
- Biocruces Bizkaia
Health Research Institute, Cruces Plaza, 48903, Barakaldo, Spain
| | - Oihane Arriortua
- Departamento de Química Inorgánica, Facultad de Ciencia y Tecnología, UPV/EHU, Barrio Sarriena s/n, 48940, Leioa, Spain
| | - Izaskun Gil de Muro
- Departamento de Química Inorgánica, Facultad de Ciencia y Tecnología, UPV/EHU, Barrio Sarriena s/n, 48940, Leioa, Spain
| | - José S. Garitaonandia
- Departamento de Física
Aplicada II, Facultad de Ciencia y Tecnología,
UPV/EHU, Barrio Sarriena s/n, 48940, Leioa, Spain
| | - Jose Ramón Bilbao
- Departamento de
Genética, Antropología Física y Fisiología
Animal, Facultad de Medicina y Enfermería, Barrio Sarriena s/n, 48940, Leioa, Spain
- Biocruces Bizkaia
Health Research Institute, Cruces Plaza, 48903, Barakaldo, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic
Diseases (CIBERDEM), 28029 Madrid, Spain
| | - M. Luisa Fdez-Gubieda
- Department of Electricidad
y Electrónica, Facultad de Ciencia
y Tecnología, UPV/EHU, Barrio
Sarriena s/n, 48940, Leioa, Spain
| | - Fernando Plazaola
- Department of Electricidad
y Electrónica, Facultad de Ciencia
y Tecnología, UPV/EHU, Barrio
Sarriena s/n, 48940, Leioa, Spain
| | - Iñaki Orue
- SGIker, Servicios
Generales de Investigación, UPV/EHU, Barrio Sarriena s/n, 48940, Leioa, Spain
| | - Ainara Castellanos-Rubio
- Departamento de
Genética, Antropología Física y Fisiología
Animal, Facultad de Medicina y Enfermería, Barrio Sarriena s/n, 48940, Leioa, Spain
- Biocruces Bizkaia
Health Research Institute, Cruces Plaza, 48903, Barakaldo, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic
Diseases (CIBERDEM), 28029 Madrid, Spain
- IKERBASQUE Basque Foundation for Science, 48013, Bilbao, Spain
| | - Maite Insausti
- Departamento de Química Inorgánica, Facultad de Ciencia y Tecnología, UPV/EHU, Barrio Sarriena s/n, 48940, Leioa, Spain
- BC Materials, Basque Center for Materials, Applications, and Nanostructures, Barrio Sarriena s/n, 48940, Leioa, Spain
- (M.I.)
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13
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Aldaregia J, Errarte P, Olazagoitia-Garmendia A, Gimeno M, Uriz JJ, Gershon TR, Garcia I, Matheu A. Erbb4 Is Required for Cerebellar Developmentand Malignant Phenotype of Medulloblastoma. Cancers (Basel) 2020; 12:cancers12040997. [PMID: 32316671 PMCID: PMC7226104 DOI: 10.3390/cancers12040997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 04/10/2020] [Indexed: 11/18/2022] Open
Abstract
Medulloblastoma is the most common and malignant pediatric brain tumor in childhood. It originates from dysregulation of cerebellar development, due to an excessive proliferation of cerebellar granule neuron precursor cells (CGNPs). The underlying molecular mechanisms, except for the role of SHH and WNT pathways, remain largely unknown. ERBB4 is a tyrosine kinase receptor whose activity in cancer is tissue dependent. In this study, we characterized the role of ERBB4 during cerebellum development and medulloblastoma progression paying particular interests to its role in CGNPs and medulloblastoma stem cells (MBSCs). Our results show that ERBB4 is expressed in the CGNPs during cerebellum development where it plays a critical role in migration, apoptosis and differentiation. Similarly, it is enriched in the population of MBSCs, where also controls those critical processes, as well as self-renewal and tumor initiation for medulloblastoma progression. These results are translated to clinical samples where high levels of ERBB4 correlate with poor outcome in Group 4 and all medulloblastomas groups. Transcriptomic analysis identified critical processes and pathways altered in cells with knock-down of ERBB4. These results highlight the impact and underlying mechanisms of ERBB4 in critical processes during cerebellum development and medulloblastoma.
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Affiliation(s)
- Juncal Aldaregia
- Cellular Oncology group, Biodonostia Health Research Institute, Dr. Beguiristain s/n, 20014 San Sebastian, Spain; (J.A.); (P.E.); (A.O.-G.); (M.G.)
| | - Peio Errarte
- Cellular Oncology group, Biodonostia Health Research Institute, Dr. Beguiristain s/n, 20014 San Sebastian, Spain; (J.A.); (P.E.); (A.O.-G.); (M.G.)
| | - Ane Olazagoitia-Garmendia
- Cellular Oncology group, Biodonostia Health Research Institute, Dr. Beguiristain s/n, 20014 San Sebastian, Spain; (J.A.); (P.E.); (A.O.-G.); (M.G.)
| | - Marian Gimeno
- Cellular Oncology group, Biodonostia Health Research Institute, Dr. Beguiristain s/n, 20014 San Sebastian, Spain; (J.A.); (P.E.); (A.O.-G.); (M.G.)
| | | | - Timothy R. Gershon
- Department of Neurology, University of North Carolina School of Medicine, Chapel Hill, NC 27516, USA;
| | - Idoia Garcia
- Cellular Oncology group, Biodonostia Health Research Institute, Dr. Beguiristain s/n, 20014 San Sebastian, Spain; (J.A.); (P.E.); (A.O.-G.); (M.G.)
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
- Correspondence: (I.G.); (A.M.); Tel.: +34-943006073 (I.G. & A.M.)
| | - Ander Matheu
- Cellular Oncology group, Biodonostia Health Research Institute, Dr. Beguiristain s/n, 20014 San Sebastian, Spain; (J.A.); (P.E.); (A.O.-G.); (M.G.)
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
- CIBERfes, Carlos III Institute, 28029 Madrid, Spain
- Correspondence: (I.G.); (A.M.); Tel.: +34-943006073 (I.G. & A.M.)
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14
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Jauregi-Miguel A, Santin I, Garcia-Etxebarria K, Olazagoitia-Garmendia A, Romero-Garmendia I, Sebastian-delaCruz M, Irastorza I, Castellanos-Rubio A, Bilbao JR. MAGI2 Gene Region and Celiac Disease. Front Nutr 2019; 6:187. [PMID: 31921880 PMCID: PMC6930898 DOI: 10.3389/fnut.2019.00187] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 12/03/2019] [Indexed: 12/13/2022] Open
Abstract
Celiac disease (CD) patients present a loss of intestinal barrier function due to structural alterations in the tight junction (TJ) network, the most apical unions between epithelial cells. The association of TJ-related gene variants points to an implication of this network in disease susceptibility. This work aims to characterize the functional implication of TJ-related, disease-associated loci in CD pathogenesis. We performed an association study of 8 TJ-related gene variants in a cohort of 270 CD and 91 non-CD controls. The expression level of transcripts located in the associated SNP region was analyzed by RT-PCR in several human tissues and in duodenal biopsies of celiac patients and non-CD controls. (si)RNA-driven silencing combined with gliadin in the Caco2 intestinal cell line was used to analyze the implication of transcripts from the associated region in the regulation of TJ genes. We replicated the association of rs6962966*A variant [p = 0.0029; OR = 1.88 (95%1.24–2.87)], located in an intron of TJ-related MAGI2 coding gene and upstream of RP4-587D13.2 transcript, bioinformatically classified as a long non-coding RNA (lncRNA). The expression of both genes is correlated and constitutively downregulated in CD intestine. Silencing of lncRNA decreases the levels of MAGI2 protein. At the same time, silencing of MAGI2 affects the expression of several TJ-related genes. The associated region is functionally altered in disease, probably affecting CD-related TJ genes.
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Affiliation(s)
- Amaia Jauregi-Miguel
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute, University of the Basque Country (Universidad del País Vasco/Euskal Herriko Unibertsitatea), Leioa, Spain
| | - Izortze Santin
- Department of Biochemistry and Molecular Biology, Biocruces-Bizkaia Health Research Institute, University of the Basque Country (Universidad del País Vasco/Euskal Herriko Unibertsitatea), Leioa, Spain.,CIBER in Diabetes and Associated Metabolic Diseases, Madrid, Spain
| | - Koldo Garcia-Etxebarria
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute, University of the Basque Country (Universidad del País Vasco/Euskal Herriko Unibertsitatea), Leioa, Spain
| | - Ane Olazagoitia-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute, University of the Basque Country (Universidad del País Vasco/Euskal Herriko Unibertsitatea), Leioa, Spain
| | - Irati Romero-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute, University of the Basque Country (Universidad del País Vasco/Euskal Herriko Unibertsitatea), Leioa, Spain
| | - Maialen Sebastian-delaCruz
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute, University of the Basque Country (Universidad del País Vasco/Euskal Herriko Unibertsitatea), Leioa, Spain
| | - Iñaki Irastorza
- Department of Pediatrics, Biocruces-Bizkaia Health Research Institute, Cruces University Hospital, University of the Basque Country (Universidad del País Vasco/Euskal Herriko Unibertsitatea), Barakaldo, Spain
| | | | - Ainara Castellanos-Rubio
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute, University of the Basque Country (Universidad del País Vasco/Euskal Herriko Unibertsitatea), Leioa, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Jose Ramón Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute, University of the Basque Country (Universidad del País Vasco/Euskal Herriko Unibertsitatea), Leioa, Spain.,CIBER in Diabetes and Associated Metabolic Diseases, Madrid, Spain
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15
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Castellanos-Rubio A, Santin I, Olazagoitia-Garmendia A, Romero-Garmendia I, Jauregi-Miguel A, Legarda M, Bilbao JR. A novel RT-QPCR-based assay for the relative quantification of residue specific m6A RNA methylation. Sci Rep 2019; 9:4220. [PMID: 30862814 PMCID: PMC6414506 DOI: 10.1038/s41598-019-40018-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 02/06/2019] [Indexed: 11/25/2022] Open
Abstract
N6-methyladenosine (m6A) is the most common and abundant RNA modification. Recent studies have shown its importance in the regulation of several biological processes, including the immune response, and different approaches have been developed in order to map and quantify m6A marks. However, site specific detection of m6A methylation has been technically challenging, and existing protocols are long and tedious and often involve next-generation sequencing. Here, we describe a simple RT-QPCR based approach for the relative quantification of candidate m6A regions that takes advantage of the diminished capacity of BstI enzyme to retrotranscribe m6A residues. Using this technique, we have been able to confirm the recently described m6A methylation in the 3′UTR of SOCS1 and SOCS3 transcripts. Moreover, using the method presented here, we have also observed alterations in the relative levels of m6A in specific motifs of SOCS genes in celiac disease patients and in pancreatic β-cells exposed to inflammatory stimuli.
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Affiliation(s)
- Ainara Castellanos-Rubio
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Spain. .,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain. .,Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain.
| | - Izortze Santin
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV-EHU), Endocrinology and Diabetes Research Group, Biocruces-Bizkaia Health Research Institute, Leioa, Spain.,Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
| | - Ane Olazagoitia-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Spain
| | - Irati Romero-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Spain
| | - Amaia Jauregi-Miguel
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Spain
| | - Maria Legarda
- Pediatric Gastroenterology Unit, Cruces University Hospital, University of the Basque Country (UPV-EHU), Barakaldo, Spain
| | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), Biocruces-Bizkaia Health Research Institute, Leioa, Spain. .,Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain.
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16
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Dos Santos RS, Marroqui L, Velayos T, Olazagoitia-Garmendia A, Jauregi-Miguel A, Castellanos-Rubio A, Eizirik DL, Castaño L, Santin I. DEXI, a candidate gene for type 1 diabetes, modulates rat and human pancreatic beta cell inflammation via regulation of the type I IFN/STAT signalling pathway. Diabetologia 2019; 62:459-472. [PMID: 30478640 DOI: 10.1007/s00125-018-4782-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 10/29/2018] [Indexed: 01/09/2023]
Abstract
AIMS/HYPOTHESIS The initial stages of type 1 diabetes are characterised by an aberrant islet inflammation that is in part regulated by the interaction between type 1 diabetes susceptibility genes and environmental factors. Chromosome 16p13 is associated with type 1 diabetes and CLEC16A is thought to be the aetiological gene in the region. Recent gene expression analysis has, however, indicated that SNPs in CLEC16A modulate the expression of a neighbouring gene with unknown function named DEXI, encoding dexamethasone-induced protein (DEXI). We therefore evaluated the role of DEXI in beta cell responses to 'danger signals' and determined the mechanisms involved. METHODS Functional studies based on silencing or overexpression of DEXI were performed in rat and human pancreatic beta cells. Beta cell inflammation and apoptosis, driven by a synthetic viral double-stranded RNA, were evaluated by real-time PCR, western blotting and luciferase assays. RESULTS DEXI-silenced beta cells exposed to a synthetic double-stranded RNA (polyinosinic:polycytidylic acid [PIC], a by-product of viral replication) showed reduced activation of signal transducer and activator of transcription (STAT) 1 and lower production of proinflammatory chemokines that was preceded by a reduction in IFNβ levels. Exposure to PIC increased chromatin-bound DEXI and IFNβ promoter activity. This effect on IFNβ promoter was inhibited in DEXI-silenced beta cells, suggesting that DEXI is implicated in the regulation of IFNβ transcription. In a mirror image of knockdown experiments, DEXI overexpression led to increased levels of STAT1 and proinflammatory chemokines. CONCLUSIONS/INTERPRETATION These observations support DEXI as the aetiological gene in the type 1 diabetes-associated 16p13 genomic region, and provide the first indication of a link between this candidate gene and the regulation of local antiviral immune responses in beta cells. Moreover, our results provide initial information on the function of DEXI.
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Affiliation(s)
- Reinaldo S Dos Santos
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Instituto de Biología Molecular y Celular (IBMC), and Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universitas Miguel Hernández, Elche, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
| | - Laura Marroqui
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Instituto de Biología Molecular y Celular (IBMC), and Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universitas Miguel Hernández, Elche, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
| | - Teresa Velayos
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Department of Pediatrics, University of the Basque Country, Leioa, Spain
| | - Ane Olazagoitia-Garmendia
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Department of Genetics, Physical Anthropology and Animal Fisiology, University of the Basque Country, Leioa, Spain
| | - Amaia Jauregi-Miguel
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Department of Genetics, Physical Anthropology and Animal Fisiology, University of the Basque Country, Leioa, Spain
| | - Ainara Castellanos-Rubio
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Department of Genetics, Physical Anthropology and Animal Fisiology, University of the Basque Country, Leioa, Spain
| | - Decio L Eizirik
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Luis Castaño
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Department of Pediatrics, University of the Basque Country, Leioa, Spain
- CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Izortze Santin
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain.
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain.
- CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.
- Department of Biochemistry and Molecular Biology, University of the Basque Country, Barrio Sarriena, S/N, 48940, Leioa, Bizkaia, Spain.
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17
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Olazagoitia-Garmendia A, Santin I, Castellanos-Rubio A. Functional implication of celiac disease associated lncRNAs in disease pathogenesis. Comput Biol Med 2018; 102:369-375. [DOI: 10.1016/j.compbiomed.2018.08.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/09/2018] [Accepted: 08/09/2018] [Indexed: 12/11/2022]
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