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Kumbhare SV, Pedroso I, Ugalde JA, Márquez-Miranda V, Sinha R, Almonacid DE. Drug and gut microbe relationships: Moving beyond antibiotics. Drug Discov Today 2023; 28:103797. [PMID: 37806386 DOI: 10.1016/j.drudis.2023.103797] [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] [Received: 05/17/2023] [Revised: 09/23/2023] [Accepted: 10/04/2023] [Indexed: 10/10/2023]
Abstract
Our understanding of drug-microbe relationships has evolved from viewing microbes as mere drug producers to a dynamic, modifiable system where they can serve as drugs or targets of precision pharmacology. This review highlights recent findings on the gut microbiome, particularly focusing on four aspects of research: (i) drugs for bugs, covering recent strategies for targeting gut pathogens; (ii) bugs as drugs, including probiotics; (iii) drugs from bugs, including postbiotics; and (iv) bugs and drugs, discussing additional types of drug-microbe interactions. This review provides a perspective on future translational research, including efficient companion diagnostics in pharmaceutical interventions.
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Affiliation(s)
| | | | - Juan A Ugalde
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Valeria Márquez-Miranda
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
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Latapiat V, Saez M, Pedroso I, Martin AJM. Corrigendum: Unraveling patient heterogeneity in complex diseases through individualized co-expression networks: a perspective. Front Genet 2023; 14:1286081. [PMID: 37811146 PMCID: PMC10552750 DOI: 10.3389/fgene.2023.1286081] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 10/10/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fgene.2023.1209416.].
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Affiliation(s)
- Verόnica Latapiat
- Programa de Doctorado en Genómica Integrativa, Vicerrectoría de Investigación, Universidad Mayor, Santiago, Chile
- Vicerrectoría de Investigación, Universidad Mayor, Santiago, Chile
- Laboratorio de Redes Biológicas, Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Mauricio Saez
- Centro de Oncología de Precisión, Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Santiago, Chile
- Laboratorio de Investigación en Salud de Precisión, Departamento de Procesos Diagnósticos y Evaluación, Facultad de Ciencias de la Salud, Universidad Católica de Temuco, Temuco, Chile
| | - Inti Pedroso
- Vicerrectoría de Investigación, Universidad Mayor, Santiago, Chile
| | - Alberto J. M. Martin
- Laboratorio de Redes Biológicas, Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Escuela de Ingeniería, Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
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Latapiat V, Saez M, Pedroso I, Martin AJM. Unraveling patient heterogeneity in complex diseases through individualized co-expression networks: a perspective. Front Genet 2023; 14:1209416. [PMID: 37636264 PMCID: PMC10449456 DOI: 10.3389/fgene.2023.1209416] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 07/24/2023] [Indexed: 08/29/2023] Open
Abstract
This perspective highlights the potential of individualized networks as a novel strategy for studying complex diseases through patient stratification, enabling advancements in precision medicine. We emphasize the impact of interpatient heterogeneity resulting from genetic and environmental factors and discuss how individualized networks improve our ability to develop treatments and enhance diagnostics. Integrating system biology, combining multimodal information such as genomic and clinical data has reached a tipping point, allowing the inference of biological networks at a single-individual resolution. This approach generates a specific biological network per sample, representing the individual from which the sample originated. The availability of individualized networks enables applications in personalized medicine, such as identifying malfunctions and selecting tailored treatments. In essence, reliable, individualized networks can expedite research progress in understanding drug response variability by modeling heterogeneity among individuals and enabling the personalized selection of pharmacological targets for treatment. Therefore, developing diverse and cost-effective approaches for generating these networks is crucial for widespread application in clinical services.
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Affiliation(s)
- Verónica Latapiat
- Programa de Doctorado en Genómica Integrativa, Vicerrectoría de Investigación, Universidad Mayor, Santiago, Chile
- Vicerrectoría de Investigación, Universidad Mayor, Santiago, Chile
- Laboratorio de Redes Biológicas, Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Mauricio Saez
- Centro de Oncología de Precisión, Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Santiago, Chile
- Laboratorio de Investigación en Salud de Precisión, Departamento de Procesos Diagnósticos y Evaluación, Facultad de Ciencias de la Salud, Universidad Católica de Temuco, Temuco, Chile
| | - Inti Pedroso
- Vicerrectoría de Investigación, Universidad Mayor, Santiago, Chile
| | - Alberto J. M. Martin
- Laboratorio de Redes Biológicas, Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Escuela de Ingeniería, Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
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Pedroso I, Kumbhare SV, Joshi B, Saravanan SK, Mongad DS, Singh-Rambiritch S, Uday T, Muthukumar KM, Irudayanathan C, Reddy-Sinha C, Dulai PS, Sinha R, Almonacid DE. Mental Health Symptom Reduction Using Digital Therapeutics Care Informed by Genomic SNPs and Gut Microbiome Signatures. J Pers Med 2022; 12:jpm12081237. [PMID: 36013186 PMCID: PMC9409755 DOI: 10.3390/jpm12081237] [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] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/21/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022] Open
Abstract
Neuropsychiatric diseases and obesity are major components of morbidity and health care costs, with genetic, lifestyle, and gut microbiome factors linked to their etiology. Dietary and weight-loss interventions can help improve mental health, but there is conflicting evidence regarding their efficacy; and moreover, there is substantial interindividual heterogeneity that needs to be understood. We aimed to identify genetic and gut microbiome factors that explain interindividual differences in mental health improvement after a dietary and lifestyle intervention for weight loss. We recruited 369 individuals participating in Digbi Health’s personalized digital therapeutics care program and evaluated the association of 23 genetic scores, the abundance of 178 gut microbial genera, and 42 bacterial pathways with mental health. We studied the presence/absence of anxiety or depression, or sleep problems at baseline and improvement on anxiety, depression, and insomnia after losing at least 2% body weight. Participants lost on average 5.4% body weight and >95% reported improving mental health symptom intensity. There were statistically significant correlations between: (a) genetic scores with anxiety or depression at baseline, gut microbial functions with sleep problems at baseline, and (b) genetic scores and gut microbial taxa and functions with anxiety, depression, and insomnia improvement. Our results are concordant with previous findings, including the association between anxiety or depression at baseline with genetic scores for alcohol use disorder and major depressive disorder. As well, our results uncovered new associations in line with previous epidemiological literature. As evident from previous literature, we also observed associations of gut microbial signatures with mental health including short-chain fatty acids and bacterial neurotoxic metabolites specifically with depression. Our results also show that microbiome and genetic factors explain self-reported mental health status and improvement better than demographic variables independently. The genetic and microbiome factors identified in this study provide the basis for designing and personalizing dietary interventions to improve mental health.
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Affiliation(s)
- Inti Pedroso
- Digbi Health, Mountain View, CA 94040, USA; (I.P.); (S.V.K.); (B.J.); (S.K.S.); (S.S.-R.); (T.U.); (K.M.M.); (C.I.); (C.R.-S.); (R.S.)
| | - Shreyas Vivek Kumbhare
- Digbi Health, Mountain View, CA 94040, USA; (I.P.); (S.V.K.); (B.J.); (S.K.S.); (S.S.-R.); (T.U.); (K.M.M.); (C.I.); (C.R.-S.); (R.S.)
| | - Bharat Joshi
- Digbi Health, Mountain View, CA 94040, USA; (I.P.); (S.V.K.); (B.J.); (S.K.S.); (S.S.-R.); (T.U.); (K.M.M.); (C.I.); (C.R.-S.); (R.S.)
| | - Santosh K. Saravanan
- Digbi Health, Mountain View, CA 94040, USA; (I.P.); (S.V.K.); (B.J.); (S.K.S.); (S.S.-R.); (T.U.); (K.M.M.); (C.I.); (C.R.-S.); (R.S.)
| | | | - Simitha Singh-Rambiritch
- Digbi Health, Mountain View, CA 94040, USA; (I.P.); (S.V.K.); (B.J.); (S.K.S.); (S.S.-R.); (T.U.); (K.M.M.); (C.I.); (C.R.-S.); (R.S.)
| | - Tejaswini Uday
- Digbi Health, Mountain View, CA 94040, USA; (I.P.); (S.V.K.); (B.J.); (S.K.S.); (S.S.-R.); (T.U.); (K.M.M.); (C.I.); (C.R.-S.); (R.S.)
| | - Karthik Marimuthu Muthukumar
- Digbi Health, Mountain View, CA 94040, USA; (I.P.); (S.V.K.); (B.J.); (S.K.S.); (S.S.-R.); (T.U.); (K.M.M.); (C.I.); (C.R.-S.); (R.S.)
| | - Carmel Irudayanathan
- Digbi Health, Mountain View, CA 94040, USA; (I.P.); (S.V.K.); (B.J.); (S.K.S.); (S.S.-R.); (T.U.); (K.M.M.); (C.I.); (C.R.-S.); (R.S.)
| | - Chandana Reddy-Sinha
- Digbi Health, Mountain View, CA 94040, USA; (I.P.); (S.V.K.); (B.J.); (S.K.S.); (S.S.-R.); (T.U.); (K.M.M.); (C.I.); (C.R.-S.); (R.S.)
| | - Parambir S. Dulai
- Division of Gastroenterology, Northwestern University, Chicago, IL 60208, USA;
| | - Ranjan Sinha
- Digbi Health, Mountain View, CA 94040, USA; (I.P.); (S.V.K.); (B.J.); (S.K.S.); (S.S.-R.); (T.U.); (K.M.M.); (C.I.); (C.R.-S.); (R.S.)
| | - Daniel Eduardo Almonacid
- Digbi Health, Mountain View, CA 94040, USA; (I.P.); (S.V.K.); (B.J.); (S.K.S.); (S.S.-R.); (T.U.); (K.M.M.); (C.I.); (C.R.-S.); (R.S.)
- Correspondence:
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Strahsburger E, Zapata F, Pedroso I, Fuentes D, Tapia P, Ponce R, Valdes J. Draft genome sequence of Exiguobacterium aurantiacum strain PN47 isolate from saline ponds, known as "Salar del Huasco", located in the Altiplano in the North of Chile. Braz J Microbiol 2018; 49:7-9. [PMID: 28757098 PMCID: PMC5790568 DOI: 10.1016/j.bjm.2017.03.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 02/14/2017] [Accepted: 03/10/2017] [Indexed: 11/24/2022] Open
Abstract
In this report, we present a draft genome of 2,886,173bp of an Exiguobacterium aurantiacum strain PN47 isolate from the sediment of a saline pond named "Salar del Huasco" in the Altiplano in the North of Chile. Strain PN47 encodes adaptive characteristics enabling survival in extreme environmental conditions of high heavy metal and salt concentrations and high alkalinity.
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Affiliation(s)
- Erwin Strahsburger
- Universidad Arturo Prat, Faculty of Renewable Naturals Resources, Molecular Biotechnology Laboratory, Iquique, Chile.
| | - Felipe Zapata
- Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Bio-Computing and Applied Genetics Division, Santiago, Chile
| | - Inti Pedroso
- Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Bio-Computing and Applied Genetics Division, Santiago, Chile
| | - Derie Fuentes
- Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Bio-Computing and Applied Genetics Division, Santiago, Chile
| | - Paz Tapia
- Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Bio-Computing and Applied Genetics Division, Santiago, Chile
| | - Raul Ponce
- Universidad Arturo Prat, Faculty of Renewable Naturals Resources, Molecular Biotechnology Laboratory, Iquique, Chile
| | - Jorge Valdes
- Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Bio-Computing and Applied Genetics Division, Santiago, Chile.
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Manfredini F, Romero AE, Pedroso I, Paccanaro A, Sumner S, Brown MJF. Neurogenomic Signatures of Successes and Failures in Life-History Transitions in a Key Insect Pollinator. Genome Biol Evol 2017; 9:3059-3072. [PMID: 29087523 PMCID: PMC5714134 DOI: 10.1093/gbe/evx220] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [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] [Accepted: 10/25/2017] [Indexed: 12/22/2022] Open
Abstract
Life-history transitions require major reprogramming at the behavioral and physiological level. Mating and reproductive maturation are known to trigger changes in gene transcription in reproductive tissues in a wide range of organisms, but we understand little about the molecular consequences of a failure to mate or become reproductively mature, and it is not clear to what extent these processes trigger neural as well as physiological changes. In this study, we examined the molecular processes underpinning the behavioral changes that accompany the major life-history transitions in a key pollinator, the bumblebee Bombus terrestris. We compared neuro-transcription in queens that succeeded or failed in switching from virgin and immature states, to mated and reproductively mature states. Both successes and failures were associated with distinct molecular profiles, illustrating how development during adulthood triggers distinct molecular profiles within a single caste of a eusocial insect. Failures in both mating and reproductive maturation were explained by a general up-regulation of brain gene transcription. We identified 21 genes that were highly connected in a gene coexpression network analysis: nine genes are involved in neural processes and four are regulators of gene expression. This suggests that negotiating life-history transitions involves significant neural processing and reprogramming, and not just changes in physiology. These findings provide novel insights into basic life-history transitions of an insect. Failure to mate or to become reproductively mature is an overlooked component of variation in natural systems, despite its prevalence in many sexually reproducing organisms, and deserves deeper investigation in the future.
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Affiliation(s)
- Fabio Manfredini
- School of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
- Department of Computer Science, and Centre for Systems and Synthetic Biology, Royal Holloway University of London, Egham, United Kingdom
| | - Alfonso E Romero
- Department of Computer Science, and Centre for Systems and Synthetic Biology, Royal Holloway University of London, Egham, United Kingdom
| | - Inti Pedroso
- Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Santiago, Chile
| | - Alberto Paccanaro
- Department of Computer Science, and Centre for Systems and Synthetic Biology, Royal Holloway University of London, Egham, United Kingdom
| | - Seirian Sumner
- School of Biological Sciences, University of Bristol, United Kingdom
- Present address: Centre for Biodiversity & Environment Research, Department of Genetics, Evolution & Environment, University College London, London, United Kingdom
| | - Mark J F Brown
- School of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
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Spain SL, Pedroso I, Kadeva N, Miller MB, Iacono WG, McGue M, Stergiakouli E, Smith GD, Putallaz M, Lubinski D, Meaburn EL, Plomin R, Simpson MA. A genome-wide analysis of putative functional and exonic variation associated with extremely high intelligence. Mol Psychiatry 2016; 21:1152. [PMID: 26324102 PMCID: PMC7608118 DOI: 10.1038/mp.2015.145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Rucker JJ, Breen G, Pinto D, Pedroso I, Lewis CM, Cohen-Woods S, Uher R, Schosser A, Rivera M, Aitchison KJ, Craddock N, Owen MJ, Jones L, Jones I, Korszun A, Muglia P, Barnes MR, Preisig M, Mors O, Gill M, Maier W, Rice J, Rietschel M, Holsboer F, Farmer AE, Craig IW, Scherer SW, McGuffin P. Genome-wide association analysis of copy number variation in recurrent depressive disorder. Mol Psychiatry 2013; 18:183-9. [PMID: 22042228 PMCID: PMC3939438 DOI: 10.1038/mp.2011.144] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Large, rare copy number variants (CNVs) have been implicated in a variety of psychiatric disorders, but the role of CNVs in recurrent depression is unclear. We performed a genome-wide analysis of large, rare CNVs in 3106 cases of recurrent depression, 459 controls screened for lifetime-absence of psychiatric disorder and 5619 unscreened controls from phase 2 of the Wellcome Trust Case Control Consortium (WTCCC2). We compared the frequency of cases with CNVs against the frequency observed in each control group, analysing CNVs over the whole genome, genic, intergenic, intronic and exonic regions. We found that deletion CNVs were associated with recurrent depression, whereas duplications were not. The effect was significant when comparing cases with WTCCC2 controls (P=7.7 × 10(-6), odds ratio (OR) =1.25 (95% confidence interval (CI) 1.13-1.37)) and to screened controls (P=5.6 × 10(-4), OR=1.52 (95% CI 1.20-1.93). Further analysis showed that CNVs deleting protein coding regions were largely responsible for the association. Within an analysis of regions previously implicated in schizophrenia, we found an overall enrichment of CNVs in our cases when compared with screened controls (P=0.019). We observe an ordered increase of samples with deletion CNVs, with the lowest proportion seen in screened controls, the next highest in unscreened controls and the highest in cases. This may suggest that the absence of deletion CNVs, especially in genes, is associated with resilience to recurrent depression.
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Affiliation(s)
- James J.H. Rucker
- MRC SGDP Centre, Institute of Psychiatry, King’s College London, Denmark Hill, London, UK
| | - Gerome Breen
- MRC SGDP Centre, Institute of Psychiatry, King’s College London, Denmark Hill, London, UK
,National Institute for Health Research Biomedical Research Centre, South London and Maudsley National Health Service Trust and Institute of Psychiatry, King’s College London, London, UK
| | - Dalila Pinto
- The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, MaRS Centre–East Tower, 101 College Street, Toronto, Ontario, Canada
| | - Inti Pedroso
- MRC SGDP Centre, Institute of Psychiatry, King’s College London, Denmark Hill, London, UK
,National Institute for Health Research Biomedical Research Centre, South London and Maudsley National Health Service Trust and Institute of Psychiatry, King’s College London, London, UK
| | - Cathryn M. Lewis
- MRC SGDP Centre, Institute of Psychiatry, King’s College London, Denmark Hill, London, UK
| | - Sarah Cohen-Woods
- MRC SGDP Centre, Institute of Psychiatry, King’s College London, Denmark Hill, London, UK
| | - Rudolf Uher
- MRC SGDP Centre, Institute of Psychiatry, King’s College London, Denmark Hill, London, UK
| | - Alexandra Schosser
- MRC SGDP Centre, Institute of Psychiatry, King’s College London, Denmark Hill, London, UK
,Department of Psychiatry and Psychotherapy, Medical University Vienna, Austria
| | - Margarita Rivera
- MRC SGDP Centre, Institute of Psychiatry, King’s College London, Denmark Hill, London, UK
,CIBERSAM, University of Granada, Section of Psychiatry, Institute of Neurosciences, Biomedical Research Centre (CIBM), Granada, Spain
| | - Katherine J. Aitchison
- MRC SGDP Centre, Institute of Psychiatry, King’s College London, Denmark Hill, London, UK
| | - Nick Craddock
- MRC Centre for Neuropsychiatric Genetics and Genomics, Neuroscience and Mental Health Research Institute, Cardiff University
| | - Michael J. Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Neuroscience and Mental Health Research Institute, Cardiff University
| | - Lisa Jones
- Department of Psychiatry, University of Birmingham, Birmingham, UK
| | - Ian Jones
- MRC Centre for Neuropsychiatric Genetics and Genomics, Neuroscience and Mental Health Research Institute, Cardiff University
| | - Ania Korszun
- Barts and The London Medical School, Queen Mary University of London, London, UK
| | | | | | - Martin Preisig
- Department of Adult Psychiatry, University Hospital of Lausanne, Switzerland
| | - Ole Mors
- Centre of Psychiatric Research, Aarhus University Hospital, Risskov, Denmark
| | - Mike Gill
- Department of Psychiatry, Trinity Centre for Health Sciences, St James’s Hospital, Dublin, Ireland
| | - Wolfgang Maier
- Department of Psychiatry, University of Bonn, Bonn, Germany
| | - John Rice
- Department of Psychiatry, Washington University, St Louis, USA
| | | | | | - Anne E. Farmer
- MRC SGDP Centre, Institute of Psychiatry, King’s College London, Denmark Hill, London, UK
,National Institute for Health Research Biomedical Research Centre, South London and Maudsley National Health Service Trust and Institute of Psychiatry, King’s College London, London, UK
| | - Ian W. Craig
- MRC SGDP Centre, Institute of Psychiatry, King’s College London, Denmark Hill, London, UK
| | - Stephen W. Scherer
- The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, MaRS Centre–East Tower, 101 College Street, Toronto, Ontario, Canada
| | - Peter McGuffin
- MRC SGDP Centre, Institute of Psychiatry, King’s College London, Denmark Hill, London, UK
,National Institute for Health Research Biomedical Research Centre, South London and Maudsley National Health Service Trust and Institute of Psychiatry, King’s College London, London, UK
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Navarrete K, Pedroso I, De Jong S, Stefansson H, Steinberg S, Stefansson K, Ophoff RA, Schalkwyk LC, Collier DA. TCF4 (e2-2; ITF2): a schizophrenia-associated gene with pleiotropic effects on human disease. Am J Med Genet B Neuropsychiatr Genet 2013; 162B:1-16. [PMID: 23129290 DOI: 10.1002/ajmg.b.32109] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 09/27/2012] [Indexed: 12/22/2022]
Abstract
Common SNPs in the transcription factor 4 (TCF4; ITF2, E2-2, SEF-2) gene, which encodes a basic Helix-Loop-Helix (bHLH) transcription factor, are associated with schizophrenia, conferring a small increase in risk. Other common SNPs in the gene are associated with the common eye disorder Fuch's corneal dystrophy, while rare, mostly de novo inactivating mutations cause Pitt-Hopkins syndrome. In this review, we present a systematic bioinformatics and literature review of the genomics, biological function and interactome of TCF4 in the context of schizophrenia. The TCF4 gene is present in all vertebrates, and although protein length varies, there is high conservation of primary sequence, including the DNA binding domain. Humans have a unique leucine-rich nuclear export signal. There are two main isoforms (A and B), as well as complex splicing generating many possible N-terminal amino acid sequences. TCF4 is highly expressed in the brain, where plays a role in neurodevelopment, interacting with class II bHLH transcription factors Math1, HASH1, and neuroD2. The Ca(2+) sensor protein calmodulin interacts with the DNA binding domain of TCF4, inhibiting transcriptional activation. It is also the target of microRNAs, including mir137, which is implicated in schizophrenia. The schizophrenia-associated SNPs are in linkage disequilibrium with common variants within putative DNA regulatory elements, suggesting that regulation of expression may underlie association with schizophrenia. Combined gene co-expression analyses and curated protein-protein interaction data provide a network involving TCF4 and other putative schizophrenia susceptibility genes. These findings suggest new opportunities for understanding the molecular basis of schizophrenia and other mental disorders.
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Affiliation(s)
- Katherinne Navarrete
- Social, Genetic and Developmental Psychiatry Centre, King's College London, Institute of Psychiatry, London, UK
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Pedroso I, Lourdusamy A, Rietschel M, Nöthen MM, Cichon S, McGuffin P, Al-Chalabi A, Barnes MR, Breen G. Common genetic variants and gene-expression changes associated with bipolar disorder are over-represented in brain signaling pathway genes. Biol Psychiatry 2012; 72:311-7. [PMID: 22502986 DOI: 10.1016/j.biopsych.2011.12.031] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 12/13/2011] [Accepted: 12/15/2011] [Indexed: 12/24/2022]
Abstract
BACKGROUND Despite high heritability, the genetic variants influencing bipolar disorder (BD) susceptibility remain largely unknown. Low statistical power to detect the small effect-size alleles believed to underlie much of the genetic risk and possible heterogeneity between cohorts are an increasing concern. Integrative biology approaches might offer advantages over genetic analysis alone by combining different genomic datasets at the higher level of biological processes rather than the level of specific genetic variants or genes. We employed this strategy to identify biological processes involved in BD etiopathology. METHOD Three genome-wide association studies and a brain gene-expression study were combined with the Human Protein Reference Database protein-protein interaction network data. We used bioinformatic analysis to search for biological networks with evidence of association on the basis of enrichment among both genetic and differential-expression associations with BD. RESULTS We identified association with gene networks involved in transmission of nerve impulse, Wnt, and Notch signaling. Three features stand out among these genes: 1) they localized to the human postsynaptic density, which is crucial for neuronal function; 2) their mouse knockouts present altered behavioral phenotypes; and 3) some are known targets of the pharmacological treatments for BD. CONCLUSIONS Genetic and gene-expression associations of BD cluster in discrete regions of the protein-protein interaction network. We found replicated evidence for association for networks involving several interlinked signaling pathways. These genes are promising candidates to generate animal models and pharmacological interventions. Our results demonstrate the potential advantage of integrative biology analyses of BD datasets.
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Affiliation(s)
- Inti Pedroso
- Medical Research Council Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, United Kingdom
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Keers R, Pedroso I, Breen G, Aitchison KJ, Nolan PM, Cichon S, Nöthen MM, Rietschel M, Schalkwyk LC, Fernandes C. Reduced anxiety and depression-like behaviours in the circadian period mutant mouse afterhours. PLoS One 2012; 7:e38263. [PMID: 22719873 PMCID: PMC3376117 DOI: 10.1371/journal.pone.0038263] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 05/04/2012] [Indexed: 01/27/2023] Open
Abstract
Background Disruption of the circadian rhythm is a key feature of bipolar disorder. Variation in genes encoding components of the molecular circadian clock has been associated with increased risk of the disorder in clinical populations. Similarly in animal models, disruption of the circadian clock can result in altered mood and anxiety which resemble features of human mania; including hyperactivity, reduced anxiety and reduced depression-like behaviour. One such mutant, after hours (Afh), an ENU-derived mutant with a mutation in a recently identified circadian clock gene Fbxl3, results in a disturbed (long) circadian rhythm of approximately 27 hours. Methodology Anxiety, exploratory and depression-like behaviours were evaluated in Afh mice using the open-field, elevated plus maze, light-dark box, holeboard and forced swim test. To further validate findings for human mania, polymorphisms in the human homologue of FBXL3, genotyped by three genome wide case control studies, were tested for association with bipolar disorder. Principal Findings Afh mice showed reduced anxiety- and depression-like behaviour in all of the behavioural tests employed, and some evidence of increased locomotor activity in some tests. An analysis of three separate human data sets revealed a gene wide association between variation in FBXL3 and bipolar disorder (P = 0.009). Conclusions Our results are consistent with previous studies of mutants with extended circadian periods and suggest that disruption of FBXL3 is associated with mania-like behaviours in both mice and humans.
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Affiliation(s)
- Robert Keers
- MRC SGDP Centre, Institute of Psychiatry, King’s College London, London, United Kingdom
| | - Inti Pedroso
- MRC SGDP Centre, Institute of Psychiatry, King’s College London, London, United Kingdom
| | - Gerome Breen
- MRC SGDP Centre, Institute of Psychiatry, King’s College London, London, United Kingdom
| | - Kathy J. Aitchison
- MRC SGDP Centre, Institute of Psychiatry, King’s College London, London, United Kingdom
| | - Patrick M. Nolan
- MRC Mammalian Genetics Unit, Harwell, Didcot, Oxfordshire, United Kingdom
| | - Sven Cichon
- Institute of Neuroscience and Medicine (INM-1), Structural and Functional Organization of the Brain, Genomic Imaging, Research Center Juelich, Juelich, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Markus M. Nöthen
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, University of Mannheim, Mannheim, Germany
| | - Leonard C. Schalkwyk
- MRC SGDP Centre, Institute of Psychiatry, King’s College London, London, United Kingdom
| | - Cathy Fernandes
- MRC SGDP Centre, Institute of Psychiatry, King’s College London, London, United Kingdom
- * E-mail:
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Furney SJ, Simmons A, Breen G, Pedroso I, Lunnon K, Proitsi P, Hodges A, Powell J, Wahlund LO, Kloszewska I, Mecocci P, Soininen H, Tsolaki M, Vellas B, Spenger C, Lathrop M, Shen L, Kim S, Saykin AJ, Weiner MW, Lovestone S. Genome-wide association with MRI atrophy measures as a quantitative trait locus for Alzheimer's disease. Mol Psychiatry 2011; 16:1130-8. [PMID: 21116278 PMCID: PMC5980656 DOI: 10.1038/mp.2010.123] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [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: 05/16/2010] [Revised: 09/06/2010] [Accepted: 09/27/2010] [Indexed: 11/08/2022]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder with considerable evidence suggesting an initiation of disease in the entorhinal cortex and hippocampus and spreading thereafter to the rest of the brain. In this study, we combine genetics and imaging data obtained from the Alzheimer's Disease Neuroimaging Initiative and the AddNeuroMed study. To identify genetic susceptibility loci for AD, we conducted a genome-wide study of atrophy in regions associated with neurodegeneration in this condition. We identified one single-nucleotide polymorphism (SNP) with a disease-specific effect associated with entorhinal cortical volume in an intron of the ZNF292 gene (rs1925690; P-value=2.6 × 10(-8); corrected P-value for equivalent number of independent quantitative traits=7.7 × 10(-8)) and an intergenic SNP, flanking the ARPP-21 gene, with an overall effect on entorhinal cortical thickness (rs11129640; P-value=5.6 × 10(-8); corrected P-value=1.7 × 10(-7)). Gene-wide scoring also highlighted PICALM as the most significant gene associated with entorhinal cortical thickness (P-value=6.7 × 10(-6)).
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Affiliation(s)
- SJ Furney
- National Institute for Health Research (NIHR) Biomedical Research Centre for Mental Health, Institute of Psychiatry, King's College London, London, UK
| | - A Simmons
- National Institute for Health Research (NIHR) Biomedical Research Centre for Mental Health, Institute of Psychiatry, King's College London, London, UK
| | - G Breen
- National Institute for Health Research (NIHR) Biomedical Research Centre for Mental Health, Institute of Psychiatry, King's College London, London, UK
| | - I Pedroso
- National Institute for Health Research (NIHR) Biomedical Research Centre for Mental Health, Institute of Psychiatry, King's College London, London, UK
| | - K Lunnon
- National Institute for Health Research (NIHR) Biomedical Research Centre for Mental Health, Institute of Psychiatry, King's College London, London, UK
| | - P Proitsi
- National Institute for Health Research (NIHR) Biomedical Research Centre for Mental Health, Institute of Psychiatry, King's College London, London, UK
| | - A Hodges
- National Institute for Health Research (NIHR) Biomedical Research Centre for Mental Health, Institute of Psychiatry, King's College London, London, UK
| | - J Powell
- National Institute for Health Research (NIHR) Biomedical Research Centre for Mental Health, Institute of Psychiatry, King's College London, London, UK
| | - L-O Wahlund
- Department of Neurobiology, Care Sciences and Society, Section of Clinical Geriatrics, Karolinska Institutet, Karolinska University Hospital, Huddinge, Stockholm, Sweden
| | - I Kloszewska
- Department of Old Age Psychiatry and Psychotic Disorders, Medical University of Lodz, Lodz, Poland
| | - P Mecocci
- Department of Clinical and Experimental Medicine, Section of Gerontology and Geriatrics, University of Perugia, Perugia, Ital
| | - H Soininen
- Department of Neurology, Kuopio University and University Hospital, Kuopio, Finland
| | - M Tsolaki
- Third Department of Neurology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - B Vellas
- Department of Internal and Geriatrics Medicine, Hôpitaux de Toulouse, Toulouse, France
| | - C Spenger
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - M Lathrop
- Centre National de Genotypage, Institut Genomique, Commissariat à l'Énergie Atomique, Evry, France
| | - L Shen
- Department of Radiology and Imaging Sciences, Center for Neuroimaging, Indiana University School of Medicine, Indianapolis, IN, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - S Kim
- Department of Radiology and Imaging Sciences, Center for Neuroimaging, Indiana University School of Medicine, Indianapolis, IN, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - AJ Saykin
- Department of Radiology and Imaging Sciences, Center for Neuroimaging, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - MW Weiner
- Departments of Radiology, Medicine and Psychiatry, University of California San Francisco, San Francisco, CA, USA
| | - S Lovestone
- National Institute for Health Research (NIHR) Biomedical Research Centre for Mental Health, Institute of Psychiatry, King's College London, London, UK
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Abstract
The application of high-throughput genotyping in humans has yielded numerous insights into the genetic basis of human phenotypes and an unprecedented amount of genetic data. Genome-wide association studies (GWAS) have increased in number in recent years, but the variants that have been found have generally explained only a tiny proportion of the estimated genetic contribution to phenotypic variation. This article summarizes the progress made in the development of gene set analysis (GSA) and network analysis for GWAS was a way to identify the underlying molecular processes of human phenotypes. It also highlights some promising findings and indicates future directions that may greatly enhance the analysis and interpretation of GWAS.
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Abstract
The recent application of high throughput genotyping in humans has yielded numerous insights into the genetic basis of human phenotypes and unprecedented amount of genetic variation data. Each genome wide significant finding has explained only a tiny proportion of phenotypic variation, yet genome wide association studies (GWAS) in their entirety can provide unprecedented windows into the molecular genetics of these phenotypes. New methods are emerging to mine modest association signals from these data using information on biological pathways and networks underlying the phenotype variation. These methods promise to enhance the information extracted from GWAS providing grounds for follow up studies of both a genetic and molecular nature.
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Affiliation(s)
- Inti Pedroso
- NIHR Biomedical Research Centre for Mental Health, South London, UK
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15
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Wain LV, Pedroso I, Landers JE, Breen G, Shaw CE, Leigh PN, Brown RH, Tobin MD, Al-Chalabi A. The role of copy number variation in susceptibility to amyotrophic lateral sclerosis: genome-wide association study and comparison with published loci. PLoS One 2009; 4:e8175. [PMID: 19997636 PMCID: PMC2780722 DOI: 10.1371/journal.pone.0008175] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Accepted: 11/12/2009] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The genetic contribution to sporadic amyotrophic lateral sclerosis (ALS) has not been fully elucidated. There are increasing efforts to characterise the role of copy number variants (CNVs) in human diseases; two previous studies concluded that CNVs may influence risk of sporadic ALS, with multiple rare CNVs more important than common CNVs. A little-explored issue surrounding genome-wide CNV association studies is that of post-calling filtering and merging of raw CNV calls. We undertook simulations to define filter thresholds and considered optimal ways of merging overlapping CNV calls for association testing, taking into consideration possibly overlapping or nested, but distinct, CNVs and boundary estimation uncertainty. METHODOLOGY AND PRINCIPAL FINDINGS In this study we screened Illumina 300K SNP genotyping data from 730 ALS cases and 789 controls for copy number variation. Following quality control filters using thresholds defined by simulation, a total of 11321 CNV calls were made across 575 cases and 621 controls. Using region-based and gene-based association analyses, we identified several loci showing nominally significant association. However, the choice of criteria for combining calls for association testing has an impact on the ranking of the results by their significance. Several loci which were previously reported as being associated with ALS were identified here. However, of another 15 genes previously reported as exhibiting ALS-specific copy number variation, only four exhibited copy number variation in this study. Potentially interesting novel loci, including EEF1D, a translation elongation factor involved in the delivery of aminoacyl tRNAs to the ribosome (a process which has previously been implicated in genetic studies of spinal muscular atrophy) were identified but must be treated with caution due to concerns surrounding genomic location and platform suitability. CONCLUSIONS AND SIGNIFICANCE Interpretation of CNV association findings must take into account the effects of filtering and combining CNV calls when based on early genome-wide genotyping platforms and modest study sizes.
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Affiliation(s)
- Louise V. Wain
- Departments of Health Sciences and Genetics, University of Leicester, Leicester, United Kingdom
| | - Inti Pedroso
- MRC Centre for Social, Genetic and Developmental Psychiatry, Institute of Psychiatry, King's College London, London, United Kingdom
- NIHR Biomedical Research Centre for Mental Health, South London and Maudsley NHS Foundation Trust and Institute of Psychiatry, King's College London, London, United Kingdom
| | - John E. Landers
- Day Neuromuscular Research Laboratory, Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Gerome Breen
- MRC Centre for Social, Genetic and Developmental Psychiatry, Institute of Psychiatry, King's College London, London, United Kingdom
- NIHR Biomedical Research Centre for Mental Health, South London and Maudsley NHS Foundation Trust and Institute of Psychiatry, King's College London, London, United Kingdom
| | - Christopher E. Shaw
- MRC Centre for Neurodegeneration Research, Institute of Psychiatry, King's College London, London, United Kingdom
| | - P. Nigel Leigh
- MRC Centre for Neurodegeneration Research, Institute of Psychiatry, King's College London, London, United Kingdom
| | - Robert H. Brown
- Day Neuromuscular Research Laboratory, Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Martin D. Tobin
- Departments of Health Sciences and Genetics, University of Leicester, Leicester, United Kingdom
- * E-mail: (AAC); (MDT)
| | - Ammar Al-Chalabi
- MRC Centre for Neurodegeneration Research, Institute of Psychiatry, King's College London, London, United Kingdom
- * E-mail: (AAC); (MDT)
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16
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Obeso J, Jahanshahi M, Alvarez L, Macias R, Pedroso I, Wilkinson L, Pavon N, Day B, Pinto S, Rodríguez-Oroz M, Tejeiro J, Artieda J, Talelli P, Swayne O, Rodríguez R, Bhatia K, Rodriguez-Diaz M, Lopez G, Guridi J, Rothwell J. What can man do without basal ganglia motor output? The effect of combined unilateral subthalamotomy and pallidotomy in a patient with Parkinson's disease. Exp Neurol 2009; 220:283-92. [DOI: 10.1016/j.expneurol.2009.08.030] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Revised: 08/26/2009] [Accepted: 08/30/2009] [Indexed: 11/27/2022]
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Alvarez L, Macias R, Pavón N, López G, Rodríguez-Oroz MC, Rodríguez R, Alvarez M, Pedroso I, Teijeiro J, Fernández R, Casabona E, Salazar S, Maragoto C, Carballo M, García I, Guridi J, Juncos JL, DeLong MR, Obeso JA. Therapeutic efficacy of unilateral subthalamotomy in Parkinson's disease: results in 89 patients followed for up to 36 months. J Neurol Neurosurg Psychiatry 2009; 80:979-85. [PMID: 19204026 DOI: 10.1136/jnnp.2008.154948] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Stereotactic thermocoagulative lesions of the subthalamic nucleus (STN) have been shown to induce significant motor improvement in patients with Parkinson's disease (PD). PATIENTS AND METHODS 89 patients with PD were treated with unilateral subthalamotomy. 68 patients were available for evaluations after 12 months, 36 at 24 months and 25 at 36 months. RESULTS The Unified Parkinson's Disease Rating Scale (UPDRS) motor scores improved significantly contralaterally to the lesion in the "off" and "on" states throughout the follow-up, except for the "on" state at the last evaluation. Axial features and signs ipsilateral to the lesion progressed steadily throughout the study. Levodopa daily doses were significantly reduced by 45%, 36% and 28% at 12, 24 and 36 months post-surgery. 14 patients (15%) developed postoperative hemichorea-ballism which required pallidotomy in eight. These 14 patients had significantly higher dyskinesia scores (levodopa induced) preoperatively than the entire cohort. CONCLUSION Unilateral subthalamotomy was associated with significant and sustained motor benefit contralateral to the lesion. Further work is needed to ascertain what factors led to severe, persistent chorea-ballism in a subset of patients. Subthalamotomy may be considered an option in circumstances when deep brain stimulation is not viable.
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Affiliation(s)
- L Alvarez
- Movement Disorders, Functional Neurosurgery and Neurophysiology Units, Centro Internacional de Restauración Neurológica (CIREN), La Habana, Cuba
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18
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Valdés J, Pedroso I, Quatrini R, Dodson RJ, Tettelin H, Blake R, Eisen JA, Holmes DS. Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications. BMC Genomics 2008; 9:597. [PMID: 19077236 PMCID: PMC2621215 DOI: 10.1186/1471-2164-9-597] [Citation(s) in RCA: 315] [Impact Index Per Article: 19.7] [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: 06/26/2008] [Accepted: 12/11/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Acidithiobacillus ferrooxidans is a major participant in consortia of microorganisms used for the industrial recovery of copper (bioleaching or biomining). It is a chemolithoautrophic, gamma-proteobacterium using energy from the oxidation of iron- and sulfur-containing minerals for growth. It thrives at extremely low pH (pH 1-2) and fixes both carbon and nitrogen from the atmosphere. It solubilizes copper and other metals from rocks and plays an important role in nutrient and metal biogeochemical cycling in acid environments. The lack of a well-developed system for genetic manipulation has prevented thorough exploration of its physiology. Also, confusion has been caused by prior metabolic models constructed based upon the examination of multiple, and sometimes distantly related, strains of the microorganism. RESULTS The genome of the type strain A. ferrooxidans ATCC 23270 was sequenced and annotated to identify general features and provide a framework for in silico metabolic reconstruction. Earlier models of iron and sulfur oxidation, biofilm formation, quorum sensing, inorganic ion uptake, and amino acid metabolism are confirmed and extended. Initial models are presented for central carbon metabolism, anaerobic metabolism (including sulfur reduction, hydrogen metabolism and nitrogen fixation), stress responses, DNA repair, and metal and toxic compound fluxes. CONCLUSION Bioinformatics analysis provides a valuable platform for gene discovery and functional prediction that helps explain the activity of A. ferrooxidans in industrial bioleaching and its role as a primary producer in acidic environments. An analysis of the genome of the type strain provides a coherent view of its gene content and metabolic potential.
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Affiliation(s)
- Jorge Valdés
- Center for Bioinformatics and Genome Biology, Fundación Ciencia para la Vida, Facultad de Ciencias de la Salud, Universidad Andres Bello, Santiago, Chile.
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Casabona E, Álvarez L, Pedroso I, Bringas Vega M. 251. Stop signal task to evaluate inhibition in Parkinson Disease. Clin Neurophysiol 2008. [DOI: 10.1016/j.clinph.2008.04.267] [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: 11/15/2022]
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Abstract
AlterORF is a searchable database that contains information regarding alternate open reading frames (ORFs) for over 1.5 million genes in 481 prokaryotic genomes. The objective of the database is to provide a platform for improving genome annotation and to serve as an aid for the identification of prokaryotic genes that potentially encode proteins in more than one reading frame. The AlterORF Database can be accessed through a web interface at www.alterorf.cl
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Affiliation(s)
- Inti Pedroso
- Center for Bioinformatics and Genome Biology, Life Science Foundation, MIFAB and Andrés Bello University, Santiago, Chile and Department of Informatics, University of Santiago, Santiago, Chile
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Quatrini R, Lefimil C, Veloso FA, Pedroso I, Holmes DS, Jedlicki E. Bioinformatic prediction and experimental verification of Fur-regulated genes in the extreme acidophile Acidithiobacillus ferrooxidans. Nucleic Acids Res 2007; 35:2153-66. [PMID: 17355989 PMCID: PMC1874648 DOI: 10.1093/nar/gkm068] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2006] [Revised: 01/16/2007] [Accepted: 01/22/2007] [Indexed: 01/12/2023] Open
Abstract
The gamma-proteobacterium Acidithiobacillus ferrooxidans lives in extremely acidic conditions (pH 2) and, unlike most organisms, is confronted with an abundant supply of soluble iron. It is also unusual in that it oxidizes iron as an energy source. Consequently, it faces the challenging dual problems of (i) maintaining intracellular iron homeostasis when confronted with extremely high environmental loads of iron and (ii) of regulating the use of iron both as an energy source and as a metabolic micronutrient. A combined bioinformatic and experimental approach was undertaken to identify Fur regulatory sites in the genome of A. ferrooxidans and to gain insight into the constitution of its Fur regulon. Fur regulatory targets associated with a variety of cellular functions including metal trafficking (e.g. feoPABC, tdr, tonBexbBD, copB, cdf), utilization (e.g. fdx, nif), transcriptional regulation (e.g. phoB, irr, iscR) and redox balance (grx, trx, gst) were identified. Selected predicted Fur regulatory sites were confirmed by FURTA, EMSA and in vitro transcription analyses. This study provides the first model for a Fur-binding site consensus sequence in an acidophilic iron-oxidizing microorganism and lays the foundation for future studies aimed at deepening our understanding of the regulatory networks that control iron uptake, homeostasis and oxidation in extreme acidophiles.
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Affiliation(s)
- Raquel Quatrini
- Center for Bioinformatics and Genome Biology, MIFAB, Life Science Foundation and Andrés Bello University, Santiago, Chile.
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Gómez-Fernández L, Calzada-Sierra DJ, Macías R, Pedroso I. [Juvenile amyotrophic lateral sclerosis. Apropos of a case]. Rev Neurol 1999; 29:49-51. [PMID: 10528312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
INTRODUCTION There are scanty reports on juvenile forms of amyotrophic lateral sclerosis, specially amyotrophic lateral sclerosis and deafness, and it is known as Madras pattern of motor neurone disease. CLINICAL CASE We describe an sporadic case of juvenile amyotrophic lateral sclerosis with deafness in a young person who started with hearing loss at 21 years old, loss of strength in upper limbs and muscular atrophy. He was seen by a neurologist when he was 25 years old, there were evident generalized fasciculation activity in proximal and distal muscles in the four limbs and the tongue, with swallowing troubles, and increased tendon reflexes in lower limbs with abnormal plantar extensor responses. All the paraclinical test were normal, except the electromyogram, showing a classical pattern of lower motor neuron disease, and the auditory brain stem response with absence of the main components of this evoked response, as expression of VIII cranial nerve damage. DISCUSSION Patients like this one were first described in Madras (India), and the evolution of this kind of juvenile form of amyotrophic lateral sclerosis is chronically progressive and relative benign, in relation to the classical form of amyotrophic lateral sclerosis and other forms of motor neurone disease which begin in childhood, adolescence or young adulthood. CONCLUSION Its recognition is very important in order to diminish misleading therapies in these patients.
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Affiliation(s)
- L Gómez-Fernández
- Centro Internacional de Restauración Neurológica, CIREN, La Habana, Cuba.
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Sánchez L, Ayala M, Freyre F, Pedroso I, Bell H, Falcón V, Gavilondo JV. High cytoplasmic expression in E. coli, purification, and in vitro refolding of a single chain Fv antibody fragment against the hepatitis B surface antigen. J Biotechnol 1999; 72:13-20. [PMID: 10406095 DOI: 10.1016/s0168-1656(99)00036-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [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: 01/02/2023]
Abstract
A single-chain Fv (scFv) antibody fragment against the hepatitis B surface antigen (HBsAg) was expressed in Escherichia coli in the form of two independent fusion proteins, with either 60 ('long') or 27 ('short') amino acid N-terminal encoding sequences related to human interleukin-2. Both fusion proteins were expressed insolubly and at high levels in the bacterial cytoplasm (approximately 30% of total bacterial protein in MM294 cells at a laboratory scale). When recombinant cells were cultured in 5-1 fermentors, expression and optical density increased 2- and 4-fold, respectively, compared to a previous periplasmic insoluble version of the same anti HBsAg scFv. After extraction and solubilization in urea, the cytoplasmic scFvs were purified using immobilized metal ion affinity chromatography, followed by DTT treatment, and refolding by dialysis against a basic pH buffer containing EDTA. The refolded scFvs recognized the recombinant HBsAg in ELISA. Results of an ELISA where antigen affinity chromatography repurified scFvs were used as standards, indicated that refolding efficiencies were high: 56.2% for the 'short' fusion scFv, and 50.6% for the 'long' fusion scFv. Corrected final yields of active scFv were 30.3 and 27.3 mg l-1, respectively, for the aforementioned fusion proteins, 5-6 times better than those reported for the periplasmic scFv variant.
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Affiliation(s)
- L Sánchez
- Division of Immunotechnology and Diagnostics, Center for Genetic Engineering and Biotechnology, Havana, Cuba
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Canaán-Haden L, Ayala M, Fernández-de-Cossio ME, Pedroso I, Rodés L, Gavilondo JV. Purification and application of a single-chain Fv antibody fragment specific to hepatitis B virus surface antigen. Biotechniques 1995; 19:606-8, 610, 612 passim. [PMID: 8777055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Immobilized metal affinity chromatography (IMAC) has been recently applied to the purification of of recombinant proteins bearing multi-histidine domains at their N or C terminus. We have now used this procedure for the single-step purification of an anti-Hepatitis B virus surface antigen (HBsAg) single-chain Fv (scFv) antibody fragment. Adjusting the metal ion (Cu+2 or Ni+2) and elution conditions (pH or imidazole), we efficiently separated active scFv forms from inactive molecules. Achieved purity was 93%, with a 20% yield with respect to the scFv content in the initial material. The pure scFv was coupled to CNBr-activated Sepharose 4B and compared the original monoclonal antibody (MAb) CB-Hep.1 in the immunoaffinity purification of a vaccine recombinant HBsAg (r-HBsAg). Results indicate that eluted antigen per mg of coupled ligand was similar for the scFv and the MAb when pure r-HBsAg was used as starting material. Preliminary results with unpurified starting material are also encouraging.
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Affiliation(s)
- L Canaán-Haden
- Division of Immunotechnology and Diagnostics, Center for Genetic Engineering and Biotechnology, La Habana, Cuba
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