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Vilas A, Briso-Montiano Á, Segovia-Falquina C, Martín-Martínez A, Soriano-Sexto A, Gallego D, Ruiz-Montés V, Gámez A, Pérez B. HepG2 PMM2-CDG knockout model: A versatile platform for variant and therapeutic evaluation. Mol Genet Metab 2024; 143:108538. [PMID: 39096554 DOI: 10.1016/j.ymgme.2024.108538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 06/28/2024] [Accepted: 07/15/2024] [Indexed: 08/05/2024]
Abstract
Phosphomannomutase 2 deficiency (PMM2-CDG), the most frequent congenital disorder of glycosylation, is an autosomal recessive disease caused by biallelic pathogenic variants in the PMM2 gene. There is no cure for this multisystemic syndrome. Some of the therapeutic approaches that are currently in development include mannose-1-phosphate replacement therapy, drug repurposing, and the use of small chemical molecules to correct folding defects. Preclinical models are needed to evaluate the efficacy of treatments to overcome the high lethality of the available animal model. In addition, the number of variants with unknown significance is increasing in clinical settings. This study presents the generation of a cellular disease model by knocking out the PMM2 gene in the hepatoma HepG2 cell line using CRISPR-Cas9 gene editing. The HepG2 knockout model accurately replicates the PMM2-CDG phenotype, exhibiting a complete absence of PMM2 protein and mRNA, a 90% decrease in PMM enzymatic activity, and altered ICAM-1, LAMP1 and A1AT glycoprotein patterns. The evaluation of PMM2 disease-causing variants validates the model's utility for studying new PMM2 clinical variants, providing insights for diagnosis and potentially for evaluating therapies. A CRISPR-Cas9-generated HepG2 knockout model accurately recapitulates the PMM2-CDG phenotype, providing a valuable tool for assessing disease-causing variants and advancing therapeutic strategies.
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Affiliation(s)
- Alicia Vilas
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain; U746 - CIBER de Enfermedades Raras (CIBERER), Madrid, Spain; Instituto de Investigación Sanitaria IdiPAZ, Madrid, Spain
| | - Álvaro Briso-Montiano
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain; U746 - CIBER de Enfermedades Raras (CIBERER), Madrid, Spain; Instituto de Investigación Sanitaria IdiPAZ, Madrid, Spain
| | - Cristina Segovia-Falquina
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain; U746 - CIBER de Enfermedades Raras (CIBERER), Madrid, Spain; Instituto de Investigación Sanitaria IdiPAZ, Madrid, Spain
| | - Arturo Martín-Martínez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain; U746 - CIBER de Enfermedades Raras (CIBERER), Madrid, Spain; Instituto de Investigación Sanitaria IdiPAZ, Madrid, Spain
| | - Alejandro Soriano-Sexto
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain; U746 - CIBER de Enfermedades Raras (CIBERER), Madrid, Spain; Instituto de Investigación Sanitaria IdiPAZ, Madrid, Spain
| | - Diana Gallego
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain; U746 - CIBER de Enfermedades Raras (CIBERER), Madrid, Spain; Instituto de Investigación Sanitaria IdiPAZ, Madrid, Spain
| | - Vera Ruiz-Montés
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain; U746 - CIBER de Enfermedades Raras (CIBERER), Madrid, Spain; Instituto de Investigación Sanitaria IdiPAZ, Madrid, Spain
| | - Alejandra Gámez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain; U746 - CIBER de Enfermedades Raras (CIBERER), Madrid, Spain; Instituto de Investigación Sanitaria IdiPAZ, Madrid, Spain
| | - Belén Pérez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain; U746 - CIBER de Enfermedades Raras (CIBERER), Madrid, Spain; Instituto de Investigación Sanitaria IdiPAZ, Madrid, Spain.
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Morales-Romero B, Muñoz-Pujol G, Artuch R, García-Cazorla A, O'Callaghan M, Sykut-Cegielska J, Campistol J, Moreno-Lozano PJ, Oud MM, Wevers RA, Lefeber DJ, Esteve-Codina A, Yepez VA, Gagneur J, Wortmann SB, Prokisch H, Ribes A, García-Villoria J, Tort F. Genome and RNA sequencing were essential to reveal cryptic intronic variants associated to defective ATP6AP1 mRNA processing. Mol Genet Metab 2024; 142:108511. [PMID: 38878498 DOI: 10.1016/j.ymgme.2024.108511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 07/05/2024]
Abstract
The diagnosis of Mendelian disorders has notably advanced with integration of whole exome and genome sequencing (WES and WGS) in clinical practice. However, challenges in variant interpretation and uncovered variants by WES still leave a substantial percentage of patients undiagnosed. In this context, integrating RNA sequencing (RNA-seq) improves diagnostic workflows, particularly for WES inconclusive cases. Additionally, functional studies are often necessary to elucidate the impact of prioritized variants on gene expression and protein function. Our study focused on three unrelated male patients (P1-P3) with ATP6AP1-CDG (congenital disorder of glycosylation), presenting with intellectual disability and varying degrees of hepatopathy, glycosylation defects, and an initially inconclusive diagnosis through WES. Subsequent RNA-seq was pivotal in identifying the underlying genetic causes in P1 and P2, detecting ATP6AP1 underexpression and aberrant splicing. Molecular studies in fibroblasts confirmed these findings and identified the rare intronic variants c.289-233C > T and c.289-289G > A in P1 and P2, respectively. Trio-WGS also revealed the variant c.289-289G > A in P3, which was a de novo change in both patients. Functional assays expressing the mutant alleles in HAP1 cells demonstrated the pathogenic impact of these variants by reproducing the splicing alterations observed in patients. Our study underscores the role of RNA-seq and WGS in enhancing diagnostic rates for genetic diseases such as CDG, providing new insights into ATP6AP1-CDG molecular bases by identifying the first two deep intronic variants in this X-linked gene. Additionally, our study highlights the need to integrate RNA-seq and WGS, followed by functional validation, in routine diagnostics for a comprehensive evaluation of patients with an unidentified molecular etiology.
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Affiliation(s)
- Blai Morales-Romero
- Section of Inborn Errors of Metabolism-IBC, Biochemistry and Molecular Genetics Department, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, ISCIII, Barcelona, Spain.
| | - Gerard Muñoz-Pujol
- Section of Inborn Errors of Metabolism-IBC, Biochemistry and Molecular Genetics Department, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, ISCIII, Barcelona, Spain.
| | - Rafael Artuch
- Clinical Biochemistry Department, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, CIBERER, Esplugues de Llobregat, Barcelona, Spain.
| | - Angels García-Cazorla
- Neurology Department, Hospital Sant Joan de Déu, Institut de Recerca Hospital Sant Joan de Déu, CIBERER and MetabERN, Esplugues de Llobregat, Barcelona, Spain.
| | - Mar O'Callaghan
- Neurology Department, Hospital Sant Joan de Déu, Institut de Recerca Hospital Sant Joan de Déu, CIBERER and MetabERN, Esplugues de Llobregat, Barcelona, Spain.
| | - Jolanta Sykut-Cegielska
- Department of Inborn Errors of Metabolism and Pediatrics, Institute of Mother and Child, Warsaw, Poland
| | - Jaume Campistol
- Neurology Department, Hospital Sant Joan de Déu, Institut de Recerca Hospital Sant Joan de Déu, CIBERER and MetabERN, Esplugues de Llobregat, Barcelona, Spain.
| | - Pedro Juan Moreno-Lozano
- Inherited Metabolic Diseases and Muscle Disorders' Research Group, Department of Internal Medicine, Hospital Clinic de Barcelona, IDIBAPS, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain.
| | - Machteld M Oud
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Ron A Wevers
- Department of Human Genetics, Translational Metabolic Laboratory (TML), Radboud University Medical Center, Nijmegen, the Netherlands; United for Metabolic Diseases, The Netherlands.
| | - Dirk J Lefeber
- Department of Human Genetics, Translational Metabolic Laboratory (TML), Radboud University Medical Center, Nijmegen, the Netherlands; Department of Neurology, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Anna Esteve-Codina
- Centro Nacional de Análisis Genómico (CNAG), Parc Científic de Barcelona, Barcelona, Spain.
| | - Vicente A Yepez
- Institute of Human Genetics, School of Medicine, Technical University of Munich, 81675 Munich, Germany; TUM School of Computation, Information and Technology, Technical University of Munich, 85748 Garching, Germany.
| | - Julien Gagneur
- Institute of Human Genetics, School of Medicine, Technical University of Munich, 81675 Munich, Germany; TUM School of Computation, Information and Technology, Technical University of Munich, 85748 Garching, Germany.
| | - Saskia B Wortmann
- University Children's Hospital Salzburg, Paracelsus Medical University, Salzburg, Austria; Amalia Children's Hospital, Department of Pediatrics, Radboudumc, Nijmegen, the Netherlands.
| | - Holger Prokisch
- Institute of Human Genetics, School of Medicine, Technical University of Munich, 81675 Munich, Germany; Institute of Neurogenomics, Helmholtz Zentrum München, 85764 Neuherberg, Germany.
| | - Antonia Ribes
- Section of Inborn Errors of Metabolism-IBC, Biochemistry and Molecular Genetics Department, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, ISCIII, Barcelona, Spain.
| | - Judit García-Villoria
- Section of Inborn Errors of Metabolism-IBC, Biochemistry and Molecular Genetics Department, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, ISCIII, Barcelona, Spain.
| | - Frederic Tort
- Section of Inborn Errors of Metabolism-IBC, Biochemistry and Molecular Genetics Department, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, ISCIII, Barcelona, Spain.
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Gallego D, Serrano M, Cordoba-Caballero J, Gámez A, Seoane P, Perkins JR, Ranea JAG, Pérez B. Transcriptomic analysis identifies dysregulated pathways and therapeutic targets in PMM2-CDG. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167163. [PMID: 38599261 DOI: 10.1016/j.bbadis.2024.167163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/15/2024] [Accepted: 04/04/2024] [Indexed: 04/12/2024]
Abstract
PMM2-CDG (MIM # 212065), the most common congenital disorder of glycosylation, is caused by the deficiency of phosphomannomutase 2 (PMM2). It is a multisystemic disease of variable severity that particularly affects the nervous system; however, its molecular pathophysiology remains poorly understood. Currently, there is no effective treatment. We performed an RNA-seq based transcriptomic study using patient-derived fibroblasts to gain insight into the mechanisms underlying the clinical symptomatology and to identify druggable targets. Systems biology methods were used to identify cellular pathways potentially affected by PMM2 deficiency, including Senescence, Bone regulation, Cell adhesion and Extracellular Matrix (ECM) and Response to cytokines. Functional validation assays using patients' fibroblasts revealed defects related to cell proliferation, cell cycle, the composition of the ECM and cell migration, and showed a potential role of the inflammatory response in the pathophysiology of the disease. Furthermore, treatment with a previously described pharmacological chaperone reverted the differential expression of some of the dysregulated genes. The results presented from transcriptomic data might serve as a platform for identifying therapeutic targets for PMM2-CDG, as well as for monitoring the effectiveness of therapeutic strategies, including pharmacological candidates and mannose-1-P, drug repurposing.
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Affiliation(s)
- Diana Gallego
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, U746- CIBER de Enfermedades Raras (CIBERER), Instituto de Investigación Sanitaria IdiPAZ, 28049 Madrid, Spain
| | - Mercedes Serrano
- Pediatric Neurology Department, Hospital Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; U-703 Centre for Biomedical Research on Rare Diseases (CIBER-ER), Instituto de Salud Carlos III, Spain
| | - Jose Cordoba-Caballero
- Department of Molecular Biology and Biochemistry, University of Málaga, Málaga, Spain; U-741, CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Alejandra Gámez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, U746- CIBER de Enfermedades Raras (CIBERER), Instituto de Investigación Sanitaria IdiPAZ, 28049 Madrid, Spain
| | - Pedro Seoane
- Department of Molecular Biology and Biochemistry, University of Málaga, Málaga, Spain; U-741, CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - James R Perkins
- Department of Molecular Biology and Biochemistry, University of Málaga, Málaga, Spain; U-741, CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; The Biomedical Research Institute of Málaga (IBIMA), Málaga, Spain; Spanish National Bioinformatics Institute (INB/ELIXIR-ES), Madrid, Spain
| | - Juan A G Ranea
- Department of Molecular Biology and Biochemistry, University of Málaga, Málaga, Spain; U-741, CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; The Biomedical Research Institute of Málaga (IBIMA), Málaga, Spain; Spanish National Bioinformatics Institute (INB/ELIXIR-ES), Madrid, Spain.
| | - Belén Pérez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, U746- CIBER de Enfermedades Raras (CIBERER), Instituto de Investigación Sanitaria IdiPAZ, 28049 Madrid, Spain.
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4
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Flook M, Rojano E, Gallego-Martinez A, Escalera-Balsera A, Perez-Carpena P, Moleon MDC, Gonzalez-Aguado R, Rivero de Jesus V, Domínguez-Durán E, Frejo L, G Ranea JA, Lopez-Escamez JA. Cytokine profiling and transcriptomics in mononuclear cells define immune variants in Meniere Disease. Genes Immun 2024; 25:124-131. [PMID: 38396174 PMCID: PMC11023934 DOI: 10.1038/s41435-024-00260-z] [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: 09/22/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024]
Abstract
Meniere Disease (MD) is a chronic inner ear disorder characterized by vertigo attacks, sensorineural hearing loss, tinnitus, and aural fullness. Extensive evidence supporting the inflammatory etiology of MD has been found, therefore, by using transcriptome analysis, we aim to describe the inflammatory variants of MD. We performed Bulk RNAseq on 45 patients with definite MD and 15 healthy controls. MD patients were classified according to their basal levels of IL-1β into 2 groups: high and low. Differentially expression analysis was performed using the ExpHunter Suite, and cell type proportion was evaluated using the estimation algorithms xCell, ABIS, and CIBERSORTx. MD patients showed 15 differentially expressed genes (DEG) compared to controls. The top DEGs include IGHG1 (p = 1.64 × 10-6) and IGLV3-21 (p = 6.28 × 10-3), supporting a role in the adaptative immune response. Cytokine profiling defines a subgroup of patients with high levels of IL-1β with up-regulation of IL6 (p = 7.65 × 10-8) and INHBA (p = 3.39 × 10-7) genes. Transcriptomic data from peripheral blood mononuclear cells support a proinflammatory subgroup of MD patients with high levels of IL6 and an increase in naïve B-cells, and memory CD8+ T cells.
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Affiliation(s)
- Marisa Flook
- Otology and Neurotology Group CTS495, Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, ibs.GRANADA, Granada, Universidad de Granada, Granada, Spain.
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain.
- UCL Ear Institute, University College London, London, UK.
| | - Elena Rojano
- Department of Molecular Biology and Biochemistry, Faculty of Sciences, University of Malaga, Malaga, Spain
- Institute of Biomedical Research in Malaga (IBIMA-Plataforma BIONAND), Malaga, Spain
| | - Alvaro Gallego-Martinez
- Otology and Neurotology Group CTS495, Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, ibs.GRANADA, Granada, Universidad de Granada, Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain
| | - Alba Escalera-Balsera
- Otology and Neurotology Group CTS495, Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, ibs.GRANADA, Granada, Universidad de Granada, Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain
| | - Patricia Perez-Carpena
- Otology and Neurotology Group CTS495, Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, ibs.GRANADA, Granada, Universidad de Granada, Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain
- Department of Otolaryngology, Instituto de Investigación Biosanitaria, ibs.Granada, Hospital Universitario Virgen de las Nieves, Granada, Spain
| | - M Del Carmen Moleon
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain
- Department of Otolaryngology, Hospital Universitario San Cecilio, Granada, Spain
| | - Rocio Gonzalez-Aguado
- Department of Otorhinolaryngology, Hospital Universitario Marques de Valdecilla, Santander, Spain
| | | | - Emilio Domínguez-Durán
- Unidad de Gestión Clínica de Otorrinolaringología, Hospital Universitario Virgen Macarena, Sevilla, Spain
| | - Lidia Frejo
- Otology and Neurotology Group CTS495, Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, ibs.GRANADA, Granada, Universidad de Granada, Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain
- Meniere Disease Neuroscience Research Program, Faculty of Medicine & Health, School of Medical Sciences, The Kolling Institute, University of Sydney, Sydney, NSW, Australia
| | - Juan A G Ranea
- Department of Molecular Biology and Biochemistry, Faculty of Sciences, University of Malaga, Malaga, Spain
- Institute of Biomedical Research in Malaga (IBIMA-Plataforma BIONAND), Malaga, Spain
- Centro de Investigación Biomedica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 29029, Madrid, Spain
- Spanish National Bioinformatics Institute (INB/ELIXIR-ES), 08034, Barcelona, Spain
| | - Jose Antonio Lopez-Escamez
- Otology and Neurotology Group CTS495, Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, ibs.GRANADA, Granada, Universidad de Granada, Granada, Spain.
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain.
- Meniere Disease Neuroscience Research Program, Faculty of Medicine & Health, School of Medical Sciences, The Kolling Institute, University of Sydney, Sydney, NSW, Australia.
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Tian X, Li J, Chen S. Key anti-freeze genes and pathways of Lanzhou lily (Lilium davidii, var. unicolor) during the seedling stage. PLoS One 2024; 19:e0299259. [PMID: 38512835 PMCID: PMC10956819 DOI: 10.1371/journal.pone.0299259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 02/07/2024] [Indexed: 03/23/2024] Open
Abstract
Temperature is one of the most important environmental factors for plant growth, as low-temperature freezing damage seriously affects the yield and distribution of plants. The Lanzhou lily (Lilium davidii, var. unicolor) is a famous ornamental plant with high ornamental value. Using an Illumina HiSeq transcriptome sequencing platform, sequencing was conducted on Lanzhou lilies exposed to two different temperature conditions: a normal temperature treatment at 20°C (A) and a cold treatment at -4°C (C). After being treated for 24 hours, a total of 5848 differentially expressed genes (DEGs) were identified, including 3478 significantly up regulated genes and 2370 significantly down regulated genes, accounting for 10.27% of the total number of DEGs. Quantitative real-time PCR (QRT-PCR) analysis showed that the expression trends of 10 randomly selected DEGs coincided with the results of high-throughput sequencing. In addition, genes responding to low-temperature stress were analyzed using the interaction regulatory network method. The anti-freeze pathway of Lanzhou lily was found to involve the photosynthetic and metabolic pathways, and the key freezing resistance genes were the OLEO3 gene, 9 CBF family genes, and C2H2 transcription factor c117817_g1 (ZFP). This lays the foundation for revealing the underlying mechanism of the molecular anti-freeze mechanism in Lanzhou lily.
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Affiliation(s)
- Xuehui Tian
- Department of Ecological Environment and Engineering, Yangling Vocational and Technical College, Shaanxi, Yangling, China
| | - Jianning Li
- Gansu Provincial Transportation Planning Survey and Design Institute Limited Liability Company, Lanzhou, Gansu Province, China
| | - Sihui Chen
- Department of Ecological Environment and Engineering, Yangling Vocational and Technical College, Shaanxi, Yangling, China
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Cordoba-Caballero J, Perkins JR, García-Criado F, Gallego D, Navarro-Sánchez A, Moreno-Estellés M, Garcés C, Bonet F, Romá-Mateo C, Toro R, Perez B, Sanz P, Kohl M, Rojano E, Seoane P, Ranea JAG. Exploring miRNA-target gene pair detection in disease with coRmiT. Brief Bioinform 2024; 25:bbae060. [PMID: 38436559 PMCID: PMC10939301 DOI: 10.1093/bib/bbae060] [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: 09/21/2023] [Revised: 12/14/2023] [Accepted: 01/10/2024] [Indexed: 03/05/2024] Open
Abstract
A wide range of approaches can be used to detect micro RNA (miRNA)-target gene pairs (mTPs) from expression data, differing in the ways the gene and miRNA expression profiles are calculated, combined and correlated. However, there is no clear consensus on which is the best approach across all datasets. Here, we have implemented multiple strategies and applied them to three distinct rare disease datasets that comprise smallRNA-Seq and RNA-Seq data obtained from the same samples, obtaining mTPs related to the disease pathology. All datasets were preprocessed using a standardized, freely available computational workflow, DEG_workflow. This workflow includes coRmiT, a method to compare multiple strategies for mTP detection. We used it to investigate the overlap of the detected mTPs with predicted and validated mTPs from 11 different databases. Results show that there is no clear best strategy for mTP detection applicable to all situations. We therefore propose the integration of the results of the different strategies by selecting the one with the highest odds ratio for each miRNA, as the optimal way to integrate the results. We applied this selection-integration method to the datasets and showed it to be robust to changes in the predicted and validated mTP databases. Our findings have important implications for miRNA analysis. coRmiT is implemented as part of the ExpHunterSuite Bioconductor package available from https://bioconductor.org/packages/ExpHunterSuite.
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Affiliation(s)
- Jose Cordoba-Caballero
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur, 31, Málaga, 29010, Spain
- Research Unit, Biomedical Research and Innovation Institute of Cádiz (INiBICA), Puerta del Mar University Hospital, Cádiz, Spain
| | - James R Perkins
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur, 31, Málaga, 29010, Spain
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA-Plataforma BIONAND), C/ Severo Ochoa, 35, Parque Tecnológico de Andalucía (PTA), Campanillas, Málaga, 29590, Spain
| | - Federico García-Criado
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur, 31, Málaga, 29010, Spain
| | - Diana Gallego
- CIBER de Enfermedades Raras (CIBERER), Avda. Monforte de Lemos, 3-5, Pabellón 11, Planta 0, Madrid, 28029, Spain
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, Spain
- Instituto de Investigación Sanitaria IdiPaZ, Madrid, Spain
| | - Alicia Navarro-Sánchez
- CIBER de Enfermedades Raras (CIBERER), Avda. Monforte de Lemos, 3-5, Pabellón 11, Planta 0, Madrid, 28029, Spain
- Departament de Fisiologia, Facultat de Medicina i Odontologia, Universitat de València, Av. Blasco Ibáñez 15, 46010, València, Spain
| | - Mireia Moreno-Estellés
- CIBER de Enfermedades Raras (CIBERER), Avda. Monforte de Lemos, 3-5, Pabellón 11, Planta 0, Madrid, 28029, Spain
- Consejo Superior de Investigaciones Científicas, Instituto de Biomedicina de Valencia, Jaime Roig 11, 46010, Valencia, Spain
| | - Concepción Garcés
- CIBER de Enfermedades Raras (CIBERER), Avda. Monforte de Lemos, 3-5, Pabellón 11, Planta 0, Madrid, 28029, Spain
- Departament de Fisiologia, Facultat de Medicina i Odontologia, Universitat de València, Av. Blasco Ibáñez 15, 46010, València, Spain
| | - Fernando Bonet
- Research Unit, Biomedical Research and Innovation Institute of Cádiz (INiBICA), Puerta del Mar University Hospital, Cádiz, Spain
- Medicine Department, School of Medicine, University of Cádiz, Cádiz, Spain
| | - Carlos Romá-Mateo
- CIBER de Enfermedades Raras (CIBERER), Avda. Monforte de Lemos, 3-5, Pabellón 11, Planta 0, Madrid, 28029, Spain
- Departament de Fisiologia, Facultat de Medicina i Odontologia, Universitat de València, Av. Blasco Ibáñez 15, 46010, València, Spain
- Incliva Biomedical Research Institute, 46010, València, Spain
| | - Rocio Toro
- Research Unit, Biomedical Research and Innovation Institute of Cádiz (INiBICA), Puerta del Mar University Hospital, Cádiz, Spain
- Medicine Department, School of Medicine, University of Cádiz, Cádiz, Spain
| | - Belén Perez
- CIBER de Enfermedades Raras (CIBERER), Avda. Monforte de Lemos, 3-5, Pabellón 11, Planta 0, Madrid, 28029, Spain
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, Spain
- Instituto de Investigación Sanitaria IdiPaZ, Madrid, Spain
| | - Pascual Sanz
- CIBER de Enfermedades Raras (CIBERER), Avda. Monforte de Lemos, 3-5, Pabellón 11, Planta 0, Madrid, 28029, Spain
- Consejo Superior de Investigaciones Científicas, Instituto de Biomedicina de Valencia, Jaime Roig 11, 46010, Valencia, Spain
| | - Matthias Kohl
- Faculty of Medical and Life Sciences, Furtwangen University, Germany
| | - Elena Rojano
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur, 31, Málaga, 29010, Spain
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA-Plataforma BIONAND), C/ Severo Ochoa, 35, Parque Tecnológico de Andalucía (PTA), Campanillas, Málaga, 29590, Spain
| | - Pedro Seoane
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur, 31, Málaga, 29010, Spain
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA-Plataforma BIONAND), C/ Severo Ochoa, 35, Parque Tecnológico de Andalucía (PTA), Campanillas, Málaga, 29590, Spain
- CIBER de Enfermedades Raras (CIBERER), Avda. Monforte de Lemos, 3-5, Pabellón 11, Planta 0, Madrid, 28029, Spain
| | - Juan A G Ranea
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur, 31, Málaga, 29010, Spain
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA-Plataforma BIONAND), C/ Severo Ochoa, 35, Parque Tecnológico de Andalucía (PTA), Campanillas, Málaga, 29590, Spain
- CIBER de Enfermedades Raras (CIBERER), Avda. Monforte de Lemos, 3-5, Pabellón 11, Planta 0, Madrid, 28029, Spain
- Instituto Nacional de Bioinformática (INB/ELIXIR-ES), Instituto de Salud Carlos III (ISCIII), C/ Sinesio Delgado, 4, Madrid, 28029, Spain
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Monterde B, Rojano E, Córdoba-Caballero J, Seoane P, Perkins JR, Medina MÁ, Ranea JAG. Integrating differential expression, co-expression and gene network analysis for the identification of common genes associated with tumor angiogenesis deregulation. J Biomed Inform 2023; 144:104421. [PMID: 37315831 DOI: 10.1016/j.jbi.2023.104421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/16/2023]
Abstract
Angiogenesis is essential for tumor growth and cancer metastasis. Identifying the molecular pathways involved in this process is the first step in the rational design of new therapeutic strategies to improve cancer treatment. In recent years, RNA-seq data analysis has helped to determine the genetic and molecular factors associated with different types of cancer. In this work we performed integrative analysis using RNA-seq data from human umbilical vein endothelial cells (HUVEC) and patients with angiogenesis-dependent diseases to find genes that serve as potential candidates to improve the prognosis of tumor angiogenesis deregulation and understand how this process is orchestrated at the genetic and molecular level. We downloaded four RNA-seq datasets (including cellular models of tumor angiogenesis and ischaemic heart disease) from the Sequence Read Archive. Our integrative analysis includes a first step to determine differentially and co-expressed genes. For this, we used the ExpHunter Suite, an R package that performs differential expression, co-expression and functional analysis of RNA-seq data. We used both differentially and co-expressed genes to explore the human gene interaction network and determine which genes were found in the different datasets that may be key for the angiogenesis deregulation. Finally, we performed drug repositioning analysis to find potential targets related to angiogenesis inhibition. We found that that among the transcriptional alterations identified, SEMA3D and IL33 genes are deregulated in all datasets. Microenvironment remodeling, cell cycle, lipid metabolism and vesicular transport are the main molecular pathways affected. In addition to this, interacting genes are involved in intracellular signaling pathways, especially in immune system and semaphorins, respiratory electron transport and fatty acid metabolism. The methodology presented here can be used for finding common transcriptional alterations in other genetically-based diseases.
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Affiliation(s)
- Beatriz Monterde
- Departamento de Señalización Celular y Molecular, Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-CSIC., C/Albert Einstein, 22, Santander, 39011, Spain
| | - Elena Rojano
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur, 31, Málaga, 29010, Spain; Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA-Plataforma BIONAND), C/ Severo Ochoa, 35, Parque Tecnológico de Andalucía (PTA), Campanillas, Málaga, 29590, Spain
| | - José Córdoba-Caballero
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur, 31, Málaga, 29010, Spain; Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Avda. Ana de Viya, 21, Cádiz, 11009, Spain
| | - Pedro Seoane
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur, 31, Málaga, 29010, Spain; Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA-Plataforma BIONAND), C/ Severo Ochoa, 35, Parque Tecnológico de Andalucía (PTA), Campanillas, Málaga, 29590, Spain; CIBER de Enfermedades Raras (CIBERER), Avda. Monforte de Lemos, 3-5, Pabellón 11, Planta 0, Madrid, 28029, Spain.
| | - James R Perkins
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur, 31, Málaga, 29010, Spain; Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA-Plataforma BIONAND), C/ Severo Ochoa, 35, Parque Tecnológico de Andalucía (PTA), Campanillas, Málaga, 29590, Spain; CIBER de Enfermedades Raras (CIBERER), Avda. Monforte de Lemos, 3-5, Pabellón 11, Planta 0, Madrid, 28029, Spain
| | - Miguel Ángel Medina
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur, 31, Málaga, 29010, Spain; Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA-Plataforma BIONAND), C/ Severo Ochoa, 35, Parque Tecnológico de Andalucía (PTA), Campanillas, Málaga, 29590, Spain; CIBER de Enfermedades Raras (CIBERER), Avda. Monforte de Lemos, 3-5, Pabellón 11, Planta 0, Madrid, 28029, Spain
| | - Juan A G Ranea
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur, 31, Málaga, 29010, Spain; Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA-Plataforma BIONAND), C/ Severo Ochoa, 35, Parque Tecnológico de Andalucía (PTA), Campanillas, Málaga, 29590, Spain; CIBER de Enfermedades Raras (CIBERER), Avda. Monforte de Lemos, 3-5, Pabellón 11, Planta 0, Madrid, 28029, Spain; Spanish National Bioinformatics Institute (INB/ELIXIR-ES), Instituto de Salud Carlos III (ISCIII), C/ Sinesio Delgado, 4, Madrid, 28029, Spain
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8
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Castilla-Vallmanya L, Centeno-Pla M, Serrano M, Franco-Valls H, Martínez-Cabrera R, Prat-Planas A, Rojano E, Ranea JAG, Seoane P, Oliva C, Paredes-Fuentes AJ, Marfany G, Artuch R, Grinberg D, Rabionet R, Balcells S, Urreizti R. Advancing in Schaaf-Yang syndrome pathophysiology: from bedside to subcellular analyses of truncated MAGEL2. J Med Genet 2023; 60:406-415. [PMID: 36243518 PMCID: PMC10086475 DOI: 10.1136/jmg-2022-108690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/27/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND Schaaf-Yang syndrome (SYS) is caused by truncating mutations in MAGEL2, mapping to the Prader-Willi region (15q11-q13), with an observed phenotype partially overlapping that of Prader-Willi syndrome. MAGEL2 plays a role in retrograde transport and protein recycling regulation. Our aim is to contribute to the characterisation of SYS pathophysiology at clinical, genetic and molecular levels. METHODS We performed an extensive phenotypic and mutational revision of previously reported patients with SYS. We analysed the secretion levels of amyloid-β 1-40 peptide (Aβ1-40) and performed targeted metabolomic and transcriptomic profiles in fibroblasts of patients with SYS (n=7) compared with controls (n=11). We also transfected cell lines with vectors encoding wild-type (WT) or mutated MAGEL2 to assess stability and subcellular localisation of the truncated protein. RESULTS Functional studies show significantly decreased levels of secreted Aβ1-40 and intracellular glutamine in SYS fibroblasts compared with WT. We also identified 132 differentially expressed genes, including non-coding RNAs (ncRNAs) such as HOTAIR, and many of them related to developmental processes and mitotic mechanisms. The truncated form of MAGEL2 displayed a stability similar to the WT but it was significantly switched to the nucleus, compared with a mainly cytoplasmic distribution of the WT MAGEL2. Based on the updated knowledge, we offer guidelines for the clinical management of patients with SYS. CONCLUSION A truncated MAGEL2 protein is stable and localises mainly in the nucleus, where it might exert a pathogenic neomorphic effect. Aβ1-40 secretion levels and HOTAIR mRNA levels might be promising biomarkers for SYS. Our findings may improve SYS understanding and clinical management.
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Affiliation(s)
- Laura Castilla-Vallmanya
- Department of Genetics, Microbiology and Statistics, IBUB, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca Sant Joan de Déu, Espluques de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instiuto de Salud Carlos III, Madrid, Spain
| | - Mónica Centeno-Pla
- Department of Genetics, Microbiology and Statistics, IBUB, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca Sant Joan de Déu, Espluques de Llobregat, Barcelona, Spain
- Clinical Biochemistry Department, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Mercedes Serrano
- Institut de Recerca Sant Joan de Déu, Espluques de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instiuto de Salud Carlos III, Madrid, Spain
- Neurology Department, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Héctor Franco-Valls
- Department of Genetics, Microbiology and Statistics, IBUB, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Raúl Martínez-Cabrera
- Department of Genetics, Microbiology and Statistics, IBUB, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Aina Prat-Planas
- Department of Genetics, Microbiology and Statistics, IBUB, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca Sant Joan de Déu, Espluques de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instiuto de Salud Carlos III, Madrid, Spain
| | - Elena Rojano
- Department of Molecular Biology and Biochemistry; Institute of Biomedical Research in Málaga (IBIMA), University of Málaga, Málaga, Spain
| | - Juan A G Ranea
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instiuto de Salud Carlos III, Madrid, Spain
- Department of Molecular Biology and Biochemistry; Institute of Biomedical Research in Málaga (IBIMA), University of Málaga, Málaga, Spain
| | - Pedro Seoane
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instiuto de Salud Carlos III, Madrid, Spain
- Department of Molecular Biology and Biochemistry; Institute of Biomedical Research in Málaga (IBIMA), University of Málaga, Málaga, Spain
| | - Clara Oliva
- Institut de Recerca Sant Joan de Déu, Espluques de Llobregat, Barcelona, Spain
- Clinical Biochemistry Department, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Abraham J Paredes-Fuentes
- Institut de Recerca Sant Joan de Déu, Espluques de Llobregat, Barcelona, Spain
- Clinical Biochemistry Department, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Gemma Marfany
- Department of Genetics, Microbiology and Statistics, IBUB, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca Sant Joan de Déu, Espluques de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instiuto de Salud Carlos III, Madrid, Spain
| | - Rafael Artuch
- Institut de Recerca Sant Joan de Déu, Espluques de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instiuto de Salud Carlos III, Madrid, Spain
- Clinical Biochemistry Department, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Daniel Grinberg
- Department of Genetics, Microbiology and Statistics, IBUB, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca Sant Joan de Déu, Espluques de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instiuto de Salud Carlos III, Madrid, Spain
| | - Raquel Rabionet
- Department of Genetics, Microbiology and Statistics, IBUB, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca Sant Joan de Déu, Espluques de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instiuto de Salud Carlos III, Madrid, Spain
| | - Susanna Balcells
- Department of Genetics, Microbiology and Statistics, IBUB, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca Sant Joan de Déu, Espluques de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instiuto de Salud Carlos III, Madrid, Spain
| | - Roser Urreizti
- Institut de Recerca Sant Joan de Déu, Espluques de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instiuto de Salud Carlos III, Madrid, Spain
- Clinical Biochemistry Department, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
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SpPdp11 Administration in Diet Modified the Transcriptomic Response and Its Microbiota Associated in Mechanically Induced Wound Sparus aurata Skin. Animals (Basel) 2023; 13:ani13020193. [PMID: 36670734 PMCID: PMC9854838 DOI: 10.3390/ani13020193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/22/2022] [Accepted: 12/30/2022] [Indexed: 01/06/2023] Open
Abstract
Skin lesions are a frequent fact associated with intensive conditions affecting farmed fish. Knowing that the use of probiotics can improve fish skin health, SpPdp11 dietary administration has demonstrated beneficial effects for farmed fish, so its potential on the skin needs to be studied more deeply. The wounded specimens that received the diet with SpPdp11 showed a decrease in the abundance of Enterobacteriaceae, Photobacterium and Achromobacter related to bacterial biofilm formation, as well as the overexpression of genes involved in signaling mechanisms (itpr3), cell migration and differentiation (panxa, ttbk1a, smpd3, vamp5); and repression of genes related to cell proliferation (vstm4a, areg), consistent with a more efficient skin healing processes than that observed in the wounded control group. In addition, among the groups of damaged skin with different diets, Achromobacter, f_Ruminococcaceae, p_Bacteroidetes, Fluviicola and Flavobacterium genera with significant differences showed positive correlations with genes related to cell migration and negative correlations with inflammation and cell proliferation and may be the target of future studies.
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10
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Revealing genetic links of Type 2 diabetes that lead to the development of Alzheimer's disease. Heliyon 2022; 9:e12202. [PMID: 36711310 PMCID: PMC9876837 DOI: 10.1016/j.heliyon.2022.e12202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 11/01/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
Background A factor leading to Alzheimer's Disease (AD), portrayed by peripheral insulin resistance, is Type 2 diabetes mellitus (T2D). The likelihood of T2D cases would be at boosted danger in alternating AD cases has severe social consequences. Several genes have been detected via gene expression profiling or different techniques; despite the consideration of the utility of numerous of these genes stays insufficient. Methods This project is designed to uncover the mutual genomics motifs between AD and T2D via non-negative matrix factorization (NMF) of differentially expressed genes (DEGs) of T2D Mellitus of human cortical neurons of the neurovascular unit gene expression data. A rank factorization value is calculated by employing the combination of the NMF model with the unit invariant knee (UIK) point method. The metagenes are further determined by remarking the enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and gene ontology (GO) enrichment tools. In this study, the most highly expressed genes of metagenes are subjected to protein-protein interaction (PPI) network study to discover the most significant biomarkers of T2D Mellitus in the ageing brain. Results We screened the most important shared genes (CDKN1A, COL22A1, EIF4A, GFAP, SLC1A1, and VIM) and essential human molecular pathways that motivate these diseases. The study aimed to validate the most significant hub genes using network-based methods which detected the corresponding relationship between AD and T2D. Conclusions Using in silico tools, the computational pipeline has broadly examined transformed pathways and discovered promising biomarkers and drug targets. We validated the most significant hub genes using network-based methods which detected the corresponding relationship between AD and T2D. These consequences on brain cells hypothetically reserve to diabetic Alzheimer's so-called type 3 diabetes (T3D) and may offer promising methodologies for curative intrusion.
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11
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Nuñez R, Rodriguez MJ, Palomares F, Gomez F, Jabato FM, Cordoba-Caballero J, Seoane P, Losada J, Rojo J, Torres MJ, Perkins JR, Mayorga C. Transcriptional changes in dendritic cells underlying allergen specific induced tolerance in a mouse model. Sci Rep 2022; 12:2797. [PMID: 35181694 PMCID: PMC8857182 DOI: 10.1038/s41598-022-06186-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 01/14/2022] [Indexed: 12/13/2022] Open
Abstract
To investigate food allergy-tolerance mechanisms induced through allergen-specific immunotherapy we used RNA-Sequencing to measure gene expression in lymph-node-derived dendritic cells from Pru p 3-anaphylactic mice after immunotherapy with glycodendropeptides at 2 nM and 5 nM, leading to permanent tolerance and short-term desensitization, respectively. Gene expression was also measured in mice receiving no immunotherapy (anaphylaxis); and in which anaphylaxis could never occur (antigen-only). Compared to anaphylaxis, the antigen-only group showed the greatest number of expression-changes (411), followed by tolerant (186) and desensitized (119). Only 29 genes changed in all groups, including Il12b, Cebpb and Ifngr1. The desensitized group showed enrichment for genes related to chronic inflammatory response, secretory granule, and regulation of interleukin-12 production; the tolerant group showed genes related to cytokine receptor activity and glucocorticoid receptor binding, suggesting distinct pathways for similar outcomes. We identified genes and processes potentially involved in the restoration of long-term tolerance via allergen-specific immunotherapy, representing potential prognostic biomarkers.
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Affiliation(s)
- Rafael Nuñez
- Allergy Research Group, Research Laboratory, Allergy Unit, Hospital Regional Universitario de Málaga-IBIMA, Instituto de Investigación Biomédica de Málaga-IBIMA, 29009, Málaga, Spain
| | - Maria Jose Rodriguez
- Allergy Research Group, Research Laboratory, Allergy Unit, Hospital Regional Universitario de Málaga-IBIMA, Instituto de Investigación Biomédica de Málaga-IBIMA, 29009, Málaga, Spain
| | - Francisca Palomares
- Allergy Research Group, Research Laboratory, Allergy Unit, Hospital Regional Universitario de Málaga-IBIMA, Instituto de Investigación Biomédica de Málaga-IBIMA, 29009, Málaga, Spain
| | - Francisca Gomez
- Allergy Clinical Unit, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - Fernando M Jabato
- Department of Molecular Biology and Biochemistry, University of Malaga, Malaga, Spain
| | | | - Pedro Seoane
- Department of Molecular Biology and Biochemistry, University of Malaga, Malaga, Spain
- CIBER de Enfermedades Raras, Instituto de Salud Carlos III, Madrid, Spain
| | - Jorge Losada
- Laboratory of Carbohydrates, Instituto de Investigaciones Químicas (IIQ), CSIC-Universidad de Sevilla, Sevilla, Spain
| | - Javier Rojo
- Laboratory of Carbohydrates, Instituto de Investigaciones Químicas (IIQ), CSIC-Universidad de Sevilla, Sevilla, Spain
| | - Maria Jose Torres
- Allergy Research Group, Research Laboratory, Allergy Unit, Hospital Regional Universitario de Málaga-IBIMA, Instituto de Investigación Biomédica de Málaga-IBIMA, 29009, Málaga, Spain
- Allergy Clinical Unit, Hospital Regional Universitario de Málaga, Málaga, Spain
- Nanostructures for Diagnosing and Treatment of Allergic Diseases Laboratory, Centro Andaluz de Nanomedicina y Biotecnología-BIONAND, Málaga, Spain
- Medicine Department, Universidad de Málaga-UMA, Málaga, Spain
| | - James Richard Perkins
- Allergy Research Group, Research Laboratory, Allergy Unit, Hospital Regional Universitario de Málaga-IBIMA, Instituto de Investigación Biomédica de Málaga-IBIMA, 29009, Málaga, Spain
- Department of Molecular Biology and Biochemistry, University of Malaga, Malaga, Spain
- CIBER de Enfermedades Raras, Instituto de Salud Carlos III, Madrid, Spain
| | - Cristobalina Mayorga
- Allergy Research Group, Research Laboratory, Allergy Unit, Hospital Regional Universitario de Málaga-IBIMA, Instituto de Investigación Biomédica de Málaga-IBIMA, 29009, Málaga, Spain.
- Allergy Clinical Unit, Hospital Regional Universitario de Málaga, Málaga, Spain.
- Nanostructures for Diagnosing and Treatment of Allergic Diseases Laboratory, Centro Andaluz de Nanomedicina y Biotecnología-BIONAND, Málaga, Spain.
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