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Toro-Domínguez D, Martorell-Marugán J, Martinez-Bueno M, López-Domínguez R, Carnero-Montoro E, Barturen G, Goldman D, Petri M, Carmona-Sáez P, Alarcón-Riquelme ME. Response to the letter 'testing the effectiveness of MyPROSLE in classifying patients with lupus nephritis'. Brief Bioinform 2023; 25:bbad454. [PMID: 38084921 PMCID: PMC10753528 DOI: 10.1093/bib/bbad454] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 11/09/2023] [Accepted: 11/18/2023] [Indexed: 12/18/2023] Open
Affiliation(s)
- Daniel Toro-Domínguez
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración 114, 18016, Granada, Spain
| | - Jordi Martorell-Marugán
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración 114, 18016, Granada, Spain
- Fundación para la Investigación Biosanitaria de Andalucía Oriental-Alejandro Otero (FIBAO), 18012, Granada, Spain
| | - Manuel Martinez-Bueno
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración 114, 18016, Granada, Spain
| | - Raúl López-Domínguez
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración 114, 18016, Granada, Spain
- Department of Statistics, University of Granada, 18071, Granada, Spain
| | - Elena Carnero-Montoro
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración 114, 18016, Granada, Spain
| | - Guillermo Barturen
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración 114, 18016, Granada, Spain
| | - Daniel Goldman
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Michelle Petri
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Pedro Carmona-Sáez
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración 114, 18016, Granada, Spain
- Department of Statistics, University of Granada, 18071, Granada, Spain
| | - Marta E Alarcón-Riquelme
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración 114, 18016, Granada, Spain
- Unit of Inflammatory Diseases, Department of Environmental Medicine, Karolinska Institute, 171 67, Solna, Sweden
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Jimenez-Carretero M, Rodríguez-López J, Ropero-Moreno C, Granada J, Delgado-Martín J, Martinez-Bueno M, Fernandez-Vivas A, Jimenez-Lopez C. Biomimetic magnetic nanoparticles for bacterial magnetic concentration in liquids and qPCR-detection. Food Control 2023. [DOI: 10.1016/j.foodcont.2023.109623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Toro-Domínguez D, Martorell-Marugán J, Martinez-Bueno M, López-Domínguez R, Carnero-Montoro E, Barturen G, Goldman D, Petri M, Carmona-Sáez P, Alarcón-Riquelme ME. Scoring personalized molecular portraits identify Systemic Lupus Erythematosus subtypes and predict individualized drug responses, symptomatology and disease progression. Brief Bioinform 2022; 23:bbac332. [PMID: 35947992 PMCID: PMC9487588 DOI: 10.1093/bib/bbac332] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [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] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 07/04/2022] [Accepted: 07/21/2022] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES Systemic Lupus Erythematosus is a complex autoimmune disease that leads to significant worsening of quality of life and mortality. Flares appear unpredictably during the disease course and therapies used are often only partially effective. These challenges are mainly due to the molecular heterogeneity of the disease, and in this context, personalized medicine-based approaches offer major promise. With this work we intended to advance in that direction by developing MyPROSLE, an omic-based analytical workflow for measuring the molecular portrait of individual patients to support clinicians in their therapeutic decisions. METHODS Immunological gene-modules were used to represent the transcriptome of the patients. A dysregulation score for each gene-module was calculated at the patient level based on averaged z-scores. Almost 6100 Lupus and 750 healthy samples were used to analyze the association among dysregulation scores, clinical manifestations, prognosis, flare and remission events and response to Tabalumab. Machine learning-based classification models were built to predict around 100 different clinical parameters based on personalized dysregulation scores. RESULTS MyPROSLE allows to molecularly summarize patients in 206 gene-modules, clustered into nine main lupus signatures. The combination of these modules revealed highly differentiated pathological mechanisms. We found that the dysregulation of certain gene-modules is strongly associated with specific clinical manifestations, the occurrence of relapses or the presence of long-term remission and drug response. Therefore, MyPROSLE may be used to accurately predict these clinical outcomes. CONCLUSIONS MyPROSLE (https://myprosle.genyo.es) allows molecular characterization of individual Lupus patients and it extracts key molecular information to support more precise therapeutic decisions.
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Affiliation(s)
- Daniel Toro-Domínguez
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración 114, 18016, Granada, Spain
| | - Jordi Martorell-Marugán
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración 114, 18016, Granada, Spain
- Department of Statistics. University of Granada, 18071, Granada, Spain
- Data Science for Health Research Unit. Fondazione Bruno Kessler, 38123, Trento, Italy
| | - Manuel Martinez-Bueno
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración 114, 18016, Granada, Spain
| | - Raúl López-Domínguez
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración 114, 18016, Granada, Spain
- Department of Statistics. University of Granada, 18071, Granada, Spain
| | - Elena Carnero-Montoro
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración 114, 18016, Granada, Spain
| | - Guillermo Barturen
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración 114, 18016, Granada, Spain
| | - Daniel Goldman
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Michelle Petri
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Pedro Carmona-Sáez
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración 114, 18016, Granada, Spain
- Department of Statistics. University of Granada, 18071, Granada, Spain
| | - Marta E Alarcón-Riquelme
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración 114, 18016, Granada, Spain
- Unit of Inflammatory Diseases, Department of Environmental Medicine, Karolinska Institute, 171 67, Solna, Sweden
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Carnero-Montoro E, Barturen G, Povedano E, Kerick M, Martinez-Bueno M, Ballestar E, Martin J, Teruel M, Alarcón-Riquelme ME. Epigenome-Wide Comparative Study Reveals Key Differences Between Mixed Connective Tissue Disease and Related Systemic Autoimmune Diseases. Front Immunol 2019; 10:1880. [PMID: 31440254 PMCID: PMC6693476 DOI: 10.3389/fimmu.2019.01880] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 05/15/2019] [Accepted: 07/24/2019] [Indexed: 11/26/2022] Open
Abstract
Mixed Connective Tissue Disease (MCTD) is a rare complex systemic autoimmune disease (SAD) characterized by the presence of increased levels of anti-U1 ribonucleoprotein autoantibodies and signs and symptoms that resemble other SADs such as systemic sclerosis (SSc), rheumatoid arthritis (RA), and systemic lupus erythematosus (SLE). Due to its low prevalence, this disease has been very poorly studied at the molecular level. We performed for the first time an epigenome-wide association study interrogating DNA methylation data obtained with the Infinium MethylationEPIC array from whole blood samples in 31 patients diagnosed with MCTD and 255 healthy subjects. We observed a pervasive hypomethylation involving 170 genes enriched for immune-related function such as those involved in type I interferon signaling pathways or in negative regulation of viral genome replication. We mostly identified epigenetic signals at genes previously implicated in other SADs, for example MX1, PARP9, DDX60, or IFI44L, for which we also observed that MCTD patients exhibit higher DNA methylation variability compared with controls, suggesting that these sites might be involved in plastic immune responses that are relevant to the disease. Through methylation quantitative trait locus (meQTL) analysis we identified widespread local genetic effects influencing DNA methylation variability at MCTD-associated sites. Interestingly, for IRF7, IFI44 genes, and the HLA region we have evidence that they could be exerting a genetic risk on MCTD mediated through DNA methylation changes. Comparison of MCTD-associated epigenome with patients diagnosed with SLE, or Sjögren's Syndrome, reveals a common interferon-related epigenetic signature, however we find substantial epigenetic differences when compared with patients diagnosed with rheumatoid arthritis and systemic sclerosis. Furthermore, we show that MCTD-associated CpGs are potential epigenetic biomarkers with high diagnostic value. Our study serves to reveal new genes and pathways involved in MCTD, to illustrate the important role of epigenetic modifications in MCTD pathology, in mediating the interaction between different genetic and environmental MCTD risk factors, and as potential biomarkers of SADs.
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Affiliation(s)
- Elena Carnero-Montoro
- GENYO, Center for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Guillermo Barturen
- GENYO, Center for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Elena Povedano
- GENYO, Center for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Martin Kerick
- CSIC-IBPLN, Consejo Superior de Investigaciones Científicas, Instituto de Parasitología y Biomedicina López-Neyra, Granada, Spain
| | - Manuel Martinez-Bueno
- GENYO, Center for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | | | - Esteban Ballestar
- IDIBELL, Bellvitge Biomedical Research Institute L'Hospitalet de Llobregat, Barcelona, Spain
| | - Javier Martin
- CSIC-IBPLN, Consejo Superior de Investigaciones Científicas, Instituto de Parasitología y Biomedicina López-Neyra, Granada, Spain
| | - María Teruel
- GENYO, Center for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Marta E Alarcón-Riquelme
- GENYO, Center for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain.,Institute for Environmental Medicine, Karolinska Institutet, Solna, Sweden
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Frejo L, Requena T, Okawa S, Gallego-Martinez A, Martinez-Bueno M, Aran I, Batuecas-Caletrio A, Benitez-Rosario J, Espinosa-Sanchez JM, Fraile-Rodrigo JJ, García-Arumi AM, González-Aguado R, Marques P, Martin-Sanz E, Perez-Fernandez N, Pérez-Vázquez P, Perez-Garrigues H, Santos-Perez S, Soto-Varela A, Tapia MC, Trinidad-Ruiz G, Del Sol A, Alarcon Riquelme ME, Lopez-Escamez JA. Regulation of Fn14 Receptor and NF-κB Underlies Inflammation in Meniere's Disease. Front Immunol 2017; 8:1739. [PMID: 29326686 PMCID: PMC5733484 DOI: 10.3389/fimmu.2017.01739] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [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: 08/11/2017] [Accepted: 11/23/2017] [Indexed: 12/17/2022] Open
Abstract
Meniere’s disease (MD) is a rare disorder characterized by episodic vertigo, sensorineural hearing loss, tinnitus, and aural fullness. It is associated with a fluid imbalance between the secretion of endolymph in the cochlear duct and its reabsorption into the subarachnoid space, leading to an accumulation of endolymph in the inner ear. Epidemiological evidence, including familial aggregation, indicates a genetic contribution and a consistent association with autoimmune diseases (AD). We conducted a case–control study in two phases using an immune genotyping array in a total of 420 patients with bilateral MD and 1,630 controls. We have identified the first locus, at 6p21.33, suggesting an association with bilateral MD [meta-analysis leading signal rs4947296, OR = 2.089 (1.661–2.627); p = 1.39 × 10−09]. Gene expression profiles of homozygous genotype-selected peripheral blood mononuclear cells (PBMCs) demonstrated that this region is a trans-expression quantitative trait locus (eQTL) in PBMCs. Signaling analysis predicted several tumor necrosis factor-related pathways, the TWEAK/Fn14 pathway being the top candidate (p = 2.42 × 10−11). This pathway is involved in the modulation of inflammation in several human AD, including multiple sclerosis, systemic lupus erythematosus, or rheumatoid arthritis. In vitro studies with genotype-selected lymphoblastoid cells from patients with MD suggest that this trans-eQTL may regulate cellular proliferation in lymphoid cells through the TWEAK/Fn14 pathway by increasing the translation of NF-κB. Taken together; these findings suggest that the carriers of the risk genotype may develop an NF-κB-mediated inflammatory response in MD.
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Affiliation(s)
- Lidia Frejo
- Otology and Neurotology Group CTS495, Department of Genomic Medicine - Centre for Genomics and Oncological Research - Pfizer/Universidad de Granada/Junta de Andalucía (GENYO), Granada, Spain
| | - Teresa Requena
- Otology and Neurotology Group CTS495, Department of Genomic Medicine - Centre for Genomics and Oncological Research - Pfizer/Universidad de Granada/Junta de Andalucía (GENYO), Granada, Spain
| | - Satoshi Okawa
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine (LCSB), Universite du Luxembourg, Belval, Luxembourg
| | - Alvaro Gallego-Martinez
- Otology and Neurotology Group CTS495, Department of Genomic Medicine - Centre for Genomics and Oncological Research - Pfizer/Universidad de Granada/Junta de Andalucía (GENYO), Granada, Spain
| | - Manuel Martinez-Bueno
- Group of Genetics of Complex Diseases, Department of Genomic Medicine - Centre for Genomics and Oncological Research - Pfizer/Universidad de Granada/Junta de Andalucía (GENYO), Granada, Spain
| | - Ismael Aran
- Department of Otolaryngology, Complexo Hospitalario de Pontevedra, Pontevedra, Spain
| | | | - Jesus Benitez-Rosario
- Department of Otolaryngology, Hospital Universitario de Gran Canaria Dr Negrin, Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Juan M Espinosa-Sanchez
- Otology and Neurotology Group CTS495, Department of Genomic Medicine - Centre for Genomics and Oncological Research - Pfizer/Universidad de Granada/Junta de Andalucía (GENYO), Granada, Spain.,Department of Otolaryngology, Instituto de Investigación Biosanitaria ibs.GRANADA, Hospital Universitario Virgen de las Nieves, Granada, Spain
| | | | - Ana María García-Arumi
- Department of Otorhinolaryngology, Hospital Universitario Vall d'Hebron, Barcelona, Spain
| | - Rocío González-Aguado
- Department of Otorhinolaryngology, Hospital Universitario Marqués de Valdecilla, Santander, Cantabria, Spain
| | - Pedro Marques
- Department of Otorhinolaryngology, Centro Hospitalar de S.João, EPE, University of Porto Medical School, Porto, Portugal
| | - Eduardo Martin-Sanz
- Department of Otolaryngology, Hospital Universitario de Getafe, Getafe, Madrid, Spain
| | | | - Paz Pérez-Vázquez
- Department of Otorhinolaryngology, Hospital Universitario de Cabueñes, Gijón, Asturias, Spain
| | | | - Sofía Santos-Perez
- Division of Otoneurology, Department of Otorhinolaryngology, Complexo Hospitalario Universitario, Santiago de Compostela, Spain
| | - Andres Soto-Varela
- Division of Otoneurology, Department of Otorhinolaryngology, Complexo Hospitalario Universitario, Santiago de Compostela, Spain
| | - Maria C Tapia
- Department of Otorhinolaryngology, Instituto Antolí Candela, Madrid, Spain
| | - Gabriel Trinidad-Ruiz
- Division of Otoneurology, Department of Otorhinolaryngology, Complejo Hospitalario Badajoz, Badajoz, Spain
| | - Antonio Del Sol
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine (LCSB), Universite du Luxembourg, Belval, Luxembourg
| | - Marta E Alarcon Riquelme
- Group of Genetics of Complex Diseases, Department of Genomic Medicine - Centre for Genomics and Oncological Research - Pfizer/Universidad de Granada/Junta de Andalucía (GENYO), Granada, Spain.,Unit of Chronic Inflammatory Diseases, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Jose A Lopez-Escamez
- Otology and Neurotology Group CTS495, Department of Genomic Medicine - Centre for Genomics and Oncological Research - Pfizer/Universidad de Granada/Junta de Andalucía (GENYO), Granada, Spain.,Department of Otolaryngology, Instituto de Investigación Biosanitaria ibs.GRANADA, Hospital Universitario Virgen de las Nieves, Granada, Spain.,Luxembourg Centre for System Biomedicine (LCSB), Universite du Luxembourg, Belval, Luxembourg
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Günther C, Kind B, Reijns MAM, Berndt N, Martinez-Bueno M, Wolf C, Tüngler V, Chara O, Lee YA, Hübner N, Lee YA, Bicknell L, Blum S, Krug C, Schmidt F, Krug C, Kretschmer S, Koss S, Astell KR, Ramantani G, Bauerfeind A, Morris DL, Graham DSC, Bubeck D, Leitch A, Ralston SH, Blackburn EA, Gahr M, Witte T, Vyse TJ, Melchers I, Mangold E, Nöthen MM, Aringer M, Kuhn A, Lüthke K, Unger L, Bley A, Lorenzi A, Isaacs JD, Alexopoulou D, Conrad K, Dahl A, Roers A, Alarcon-Riquelme ME, Jackson AP, Lee-Kirsch MA. Defective removal of ribonucleotides from DNA promotes systemic lupus erythematosus. Pediatr Rheumatol Online J 2015. [PMCID: PMC4597412 DOI: 10.1186/1546-0096-13-s1-o86] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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7
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Günther C, Kind B, Reijns MAM, Berndt N, Martinez-Bueno M, Wolf C, Tüngler V, Chara O, Lee YA, Hübner N, Bicknell L, Blum S, Krug C, Schmidt F, Kretschmer S, Koss S, Astell KR, Ramantani G, Bauerfeind A, Morris DL, Cunninghame Graham DS, Bubeck D, Leitch A, Ralston SH, Blackburn EA, Gahr M, Witte T, Vyse TJ, Melchers I, Mangold E, Nöthen MM, Aringer M, Kuhn A, Lüthke K, Unger L, Bley A, Lorenzi A, Isaacs JD, Alexopoulou D, Conrad K, Dahl A, Roers A, Alarcon-Riquelme ME, Jackson AP, Lee-Kirsch MA. Defective removal of ribonucleotides from DNA promotes systemic autoimmunity. J Clin Invest 2014; 125:413-24. [PMID: 25500883 DOI: 10.1172/jci78001] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 10/09/2014] [Indexed: 01/22/2023] Open
Abstract
Genome integrity is continuously challenged by the DNA damage that arises during normal cell metabolism. Biallelic mutations in the genes encoding the genome surveillance enzyme ribonuclease H2 (RNase H2) cause Aicardi-Goutières syndrome (AGS), a pediatric disorder that shares features with the autoimmune disease systemic lupus erythematosus (SLE). Here we determined that heterozygous parents of AGS patients exhibit an intermediate autoimmune phenotype and demonstrated a genetic association between rare RNASEH2 sequence variants and SLE. Evaluation of patient cells revealed that SLE- and AGS-associated mutations impair RNase H2 function and result in accumulation of ribonucleotides in genomic DNA. The ensuing chronic low level of DNA damage triggered a DNA damage response characterized by constitutive p53 phosphorylation and senescence. Patient fibroblasts exhibited constitutive upregulation of IFN-stimulated genes and an enhanced type I IFN response to the immunostimulatory nucleic acid polyinosinic:polycytidylic acid and UV light irradiation, linking RNase H2 deficiency to potentiation of innate immune signaling. Moreover, UV-induced cyclobutane pyrimidine dimer formation was markedly enhanced in ribonucleotide-containing DNA, providing a mechanism for photosensitivity in RNase H2-associated SLE. Collectively, our findings implicate RNase H2 in the pathogenesis of SLE and suggest a role of DNA damage-associated pathways in the initiation of autoimmunity.
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Valverde-Tercedor C, Abadía-Molina F, Martinez-Bueno M, Pineda-Molina E, Chen L, Oestreicher Z, Lower BH, Lower SK, Bazylinski DA, Jimenez-Lopez C. Subcellular localization of the magnetosome protein MamC in the marine magnetotactic bacterium Magnetococcus marinus strain MC-1 using immunoelectron microscopy. Arch Microbiol 2014; 196:481-8. [PMID: 24760293 DOI: 10.1007/s00203-014-0984-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 04/02/2014] [Accepted: 04/09/2014] [Indexed: 02/07/2023]
Abstract
Magnetotactic bacteria are a diverse group of prokaryotes that biomineralize intracellular magnetosomes, composed of magnetic (Fe3O4) crystals each enveloped by a lipid bilayer membrane that contains proteins not found in other parts of the cell. Although partial roles of some of these magnetosome proteins have been determined, the roles of most have not been completely elucidated, particularly in how they regulate the biomineralization process. While studies on the localization of these proteins have been focused solely on Magnetospirillum species, the goal of the present study was to determine, for the first time, the localization of the most abundant putative magnetosome membrane protein, MamC, in Magnetococcus marinus strain MC-1. MamC was expressed in Escherichia coli and purified. Monoclonal antibodies were produced against MamC and immunogold labeling TEM was used to localize MamC in thin sections of cells of M. marinus. Results show that MamC is located only in the magnetosome membrane of Mc. marinus. Based on our findings and the abundance of this protein, it seems likely that it is important in magnetosome biomineralization and might be used in controlling the characteristics of synthetic nanomagnetite.
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Affiliation(s)
- C Valverde-Tercedor
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071, Granada, Spain
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Oparina NY, Delgado-Vega AM, Martinez-Bueno M, Magro-Checa C, Fernández C, Castro RO, Pons-Estel BA, D'Alfonso S, Sebastiani GD, Witte T, Lauwerys BR, Endreffy E, Kovács L, Escudero A, López-Pedrera C, Vasconcelos C, da Silva BM, Frostegård J, Truedsson L, Martin J, Raya E, Ortego-Centeno N, de los Angeles Aguirre M, de Ramón Garrido E, Palma MJC, Alarcon-Riquelme ME, Kozyrev SV. PXKlocus in systemic lupus erythematosus: fine mapping and functional analysis reveals novel susceptibility geneABHD6. Ann Rheum Dis 2014; 74:e14. [DOI: 10.1136/annrheumdis-2013-204909] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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10
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Montalban-Lopez M, Sanchez-Hidalgo M, Valdivia E, Martinez-Bueno M, Maqueda M. Are Bacteriocins Underexploited? NOVEL Applications for OLD Antimicrobials. Curr Pharm Biotechnol 2011; 12:1205-20. [DOI: 10.2174/138920111796117364] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2010] [Accepted: 06/30/2010] [Indexed: 11/22/2022]
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Sanchez-Hidalgo M, M Fernandez-Escamilla A, Martinez-Bueno M, Valdivia E, Serrano L, Maqueda M. Conformational Stability and Activity of Circular Enterocin AS-48 Derivatives. Protein Pept Lett 2010; 17:708-14. [DOI: 10.2174/092986610791190390] [Citation(s) in RCA: 11] [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: 04/10/2009] [Accepted: 11/20/2009] [Indexed: 11/22/2022]
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12
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Sanchez-Hidalgo M, Martinez-Bueno M, Fernandez-Escamilla AM, Valdivia E, Serrano L, Maqueda M. Effect of replacing glutamic residues upon the biological activity and stability of the circular enterocin AS-48. J Antimicrob Chemother 2008. [DOI: 10.1093/jac/dkn254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Martinez-Bueno M, Valdivia E, Martin I, Quirantes R, Maqueda M. Physical mapping of the conjugative plasmid pMB1-1 of Enterococcus faecalis. Lett Appl Microbiol 1998. [DOI: 10.1046/j.1472-765x.1998.00417.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Raze D, Dardenne O, Hallut S, Martinez-Bueno M, Coyette J, Ghuysen JM. The gene encoding the low-affinity penicillin-binding protein 3r in Enterococcus hirae S185R is borne on a plasmid carrying other antibiotic resistance determinants. Antimicrob Agents Chemother 1998; 42:534-9. [PMID: 9517928 PMCID: PMC105494 DOI: 10.1128/aac.42.3.534] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/1997] [Accepted: 11/20/1997] [Indexed: 02/06/2023] Open
Abstract
Two plasmid-derived NcoI DNA fragments of 14 and 4.5 kb, respectively, have been isolated from the multidrug-resistant strain Enterococcus hirae S185R and analyzed. The 14-kb fragment contains two inverted (L and R) IS1216 insertion modules of the ISS1 family. These modules define a Tn5466 transposon-like structure that contains one copy of the methylase-encoding ermAM conferring erythromycin resistance and one copy of the adenylyl-transferase-encoding aadE conferring streptomycin resistance. Immediately on the left side of IS1216L there occurs a copy of pbp3r encoding the low-affinity penicillin-binding protein (PBP) PBP3r, itself preceded by a psr-like gene (psr3r) that controls the synthesis of PBP3r. ermAM, aadE, and the transposase gene (tnp) of IS1216R have the same polarities, and these are opposite those of psr3r, pbp3r, and the tnp gene of IS1216L. The 4.5-kb fragment is a copy of the 4.5-kb sequence at the 5' end of the 14-kb fragment, although it is not a restriction product of the 14-kb fragment. It contains three genes with the same polarity: psr3r, pbp3r, and tnp in an IS1216 element. Because of the very high degree of identity (99%) with the chromosomal psrfm and pbp5fm genes of Enterococcus faecium D63R, it is proposed that both the psr3r and pbp3r genes were transferred from an E.faecium strain and inserted in a plasmid of E. hirae. E. hirae is the first known bacterial species in which a low-affinity PBP-encoding gene has been found to be plasmid borne.
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Affiliation(s)
- D Raze
- Centre d'Ingénierie des Protéines, Institut de Chimie, Université de Liège, Sart Tilman, Belgium
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Samyn B, Martinez-Bueno M, Devreese B, Maqueda M, Gálvez A, Valdivia E, Coyette J, Van Beeumen J. The cyclic structure of the enterococcal peptide antibiotic AS-48. FEBS Lett 1994; 352:87-90. [PMID: 7925951 DOI: 10.1016/0014-5793(94)00925-2] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The complete primary structure of the peptide antibiotic AS-48 produced by Enterococcus faecalis has been determined by chemical degradation analysis. The cyclic nature of this 70 residues containing peptide was demonstrated by plasma desorption mass analysis of the generated peptides and electrospray ionisation mass analysis of the native polypeptide. As far as we know, this is the first example of an antibiotic protein cyclised by a tail-head peptide bond formation and not by branching of the polypeptide side chains.
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Affiliation(s)
- B Samyn
- Department of Biochemistry, Physiology and Microbiology, University Gent, Belgium
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Cordovilla P, Valdivia E, Gonzalez-Segura A, Galvez A, Martinez-Bueno M, Maqueda M. Antagonistic action of the bacterium Bacillus licheniformis M-4 toward the amoeba Naegleria fowleri. J Eukaryot Microbiol 1993; 40:323-8. [PMID: 8508169 DOI: 10.1111/j.1550-7408.1993.tb04923.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Free-living amoebae belonging to the species Naegleria fowleri are known to be the etiological agents for a form of fulminant meningoencephalitis that is generally fatal (primary amoebic meningoencephalitis). In a broad bacterial screening from soil and water we have isolated three strains (M-4, D-13 and A-12) belonging to the species Bacillus licheniformis that have remarkable amoebicidal activity against Naegleria sp. and also against different Gram-positive and Gram-negative bacteria. Physical-chemical characteristics, partial purification and biological activities of a substance produced by the M-4 strain have been investigated. This substance (m-4) is stable at high temperature (up to 100 degrees C) and extremes of pH (2.5-9.5) and also at -20 degrees C for months. Its production is greatly influenced by oxygenation of the cultures and is probably related to the sporulation process of the bacterium. Scanning electron microscope observations reveal that amoebae are lysed after a few minutes contact with m-4.
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Affiliation(s)
- P Cordovilla
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Spain
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Maqueda M, Valdivia E, Martinez-Bueno M, Mascaro ML, Mascaro C. Growth of an Acanthamoeba Isolate on a Gram-Negative Bacterium, Probably Pasteurella haemolytica. J Parasitol 1988. [DOI: 10.2307/3282069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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