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Birkenheuer CH, Baines JD. Aberrant RNA polymerase initiation and processivity on the genome of a herpes simplex virus 1 mutant lacking ICP27. J Virol 2024; 98:e0071224. [PMID: 38780246 PMCID: PMC11237563 DOI: 10.1128/jvi.00712-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
Within the first 15 minutes of infection, herpes simplex virus 1 immediate early proteins repurpose cellular RNA polymerase (Pol II) for viral transcription. An important role of the viral-infected cell protein 27 (ICP27) is to facilitate viral pre-mRNA processing and export viral mRNA to the cytoplasm. Here, we use precision nuclear run-on followed by deep sequencing (PRO-seq) to characterize transcription of a viral ICP27 null mutant. At 1.5 and 3 hours post infection (hpi), we observed increased total levels of Pol II on the mutant viral genome and accumulation of Pol II downstream of poly A sites indicating increased levels of initiation and processivity. By 6 hpi, Pol II accumulation on specific mutant viral genes was higher than that on wild-type virus either at or upstream of poly A signals, depending on the gene. The PRO-seq profile of the ICP27 mutant on late genes at 6 hpi was similar but not identical to that caused by treatment with flavopiridol, a known inhibitor of RNA processivity. This pattern was different from PRO-seq profiles of other α gene mutants and upon inhibition of viral DNA replication with PAA. Together, these results indicate that ICP27 contributes to the repression of aberrant viral transcription at 1.5 and 3 hpi by inhibiting initiation and decreasing RNA processivity. However, ICP27 is needed to enhance processivity on most late genes by 6 hpi in a mechanism distinguishable from its role in viral DNA replication.IMPORTANCEWe developed and validated the use of a processivity index for precision nuclear run-on followed by deep sequencing data. The processivity index calculations confirm infected cell protein 27 (ICP27) induces downstream of transcription termination on certain host genes. The processivity indices and whole gene probe data implicate ICP27 in transient immediate early gene-mediated repression, a process that also requires ICP4, ICP22, and ICP0. The data indicate that ICP27 directly or indirectly regulates RNA polymerase (Pol II) initiation and processivity on specific genes at specific times post infection. These observations support specific and varied roles for ICP27 in regulating Pol II activity on viral genes in addition to its known roles in post transcriptional mRNA processing and export.
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Affiliation(s)
- Claire H. Birkenheuer
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Joel D. Baines
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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2
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Camellato BR, Brosh R, Ashe HJ, Maurano MT, Boeke JD. Synthetic reversed sequences reveal default genomic states. Nature 2024; 628:373-380. [PMID: 38448583 PMCID: PMC11006607 DOI: 10.1038/s41586-024-07128-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 01/29/2024] [Indexed: 03/08/2024]
Abstract
Pervasive transcriptional activity is observed across diverse species. The genomes of extant organisms have undergone billions of years of evolution, making it unclear whether these genomic activities represent effects of selection or 'noise'1-4. Characterizing default genome states could help understand whether pervasive transcriptional activity has biological meaning. Here we addressed this question by introducing a synthetic 101-kb locus into the genomes of Saccharomyces cerevisiae and Mus musculus and characterizing genomic activity. The locus was designed by reversing but not complementing human HPRT1, including its flanking regions, thus retaining basic features of the natural sequence but ablating evolved coding or regulatory information. We observed widespread activity of both reversed and native HPRT1 loci in yeast, despite the lack of evolved yeast promoters. By contrast, the reversed locus displayed no activity at all in mouse embryonic stem cells, and instead exhibited repressive chromatin signatures. The repressive signature was alleviated in a locus variant lacking CpG dinucleotides; nevertheless, this variant was also transcriptionally inactive. These results show that synthetic genomic sequences that lack coding information are active in yeast, but inactive in mouse embryonic stem cells, consistent with a major difference in 'default genomic states' between these two divergent eukaryotic cell types, with implications for understanding pervasive transcription, horizontal transfer of genetic information and the birth of new genes.
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Affiliation(s)
| | - Ran Brosh
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
| | - Hannah J Ashe
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
| | - Matthew T Maurano
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
- Department of Pathology, NYU Langone Health, New York, NY, USA
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA.
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA.
- Department of Biomedical Engineering, NYU Tandon School of Engineering, New York, NY, USA.
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3
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Li S, Poelmans G, van Boekel RLM, Coenen MJH. Genome-wide association study on pharmacological outcomes of musculoskeletal pain in UK Biobank. THE PHARMACOGENOMICS JOURNAL 2023; 23:161-168. [PMID: 37587271 DOI: 10.1038/s41397-023-00314-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 08/18/2023]
Abstract
The pharmacological management of musculoskeletal pain starts with NSAIDs, followed by weak or strong opioids until the pain is under control. However, the treatment outcome is usually unsatisfying due to inter-individual differences. To investigate the genetic component of treatment outcome differences, we performed a genome-wide association study (GWAS) in ~23,000 participants with musculoskeletal pain from the UK Biobank. NSAID vs. opioid users were compared as a reflection of the treatment outcome of NSAIDs. We identified one genome-wide significant hit in chromosome 4 (rs549224715, P = 3.88 × 10-8). Suggestive significant (P < 1 × 10-6) loci were functionally annotated to 18 target genes, including four genes linked to neuropathic pain processes or musculoskeletal development. Pathway and network analyses identified immunity-related processes and a (putative) central role of EGFR. However, this study should be viewed as a first step to elucidate the genetic background of musculoskeletal pain treatment.
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Affiliation(s)
- Song Li
- Department of Human Genetics, Radboud Institute for Health Sciences, Radboud university medical center, Nijmegen, The Netherlands
| | - Geert Poelmans
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Regina L M van Boekel
- Department of Anesthesiology, Pain and Palliative Medicine, Radboud Institute for Health Sciences, Radboud university medical center, Nijmegen, The Netherlands
| | - Marieke J H Coenen
- Department of Human Genetics, Radboud Institute for Health Sciences, Radboud university medical center, Nijmegen, The Netherlands.
- Department of Clinical Chemistry, Erasmus Medical Center, Rotterdam, The Netherlands.
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4
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Merle DA, Sen M, Armento A, Stanton CM, Thee EF, Meester-Smoor MA, Kaiser M, Clark SJ, Klaver CCW, Keane PA, Wright AF, Ehrmann M, Ueffing M. 10q26 - The enigma in age-related macular degeneration. Prog Retin Eye Res 2023; 96:101154. [PMID: 36513584 DOI: 10.1016/j.preteyeres.2022.101154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/21/2022] [Accepted: 12/01/2022] [Indexed: 12/14/2022]
Abstract
Despite comprehensive research efforts over the last decades, the pathomechanisms of age-related macular degeneration (AMD) remain far from being understood. Large-scale genome wide association studies (GWAS) were able to provide a defined set of genetic aberrations which contribute to disease risk, with the strongest contributors mapping to distinct regions on chromosome 1 and 10. While the chromosome 1 locus comprises factors of the complement system with well-known functions, the role of the 10q26-locus in AMD-pathophysiology remains enigmatic. 10q26 harbors a cluster of three functional genes, namely PLEKHA1, ARMS2 and HTRA1, with most of the AMD-associated genetic variants mapping to the latter two genes. High linkage disequilibrium between ARMS2 and HTRA1 has kept association studies from reliably defining the risk-causing gene for long and only very recently the genetic risk region has been narrowed to ARMS2, suggesting that this is the true AMD gene at this locus. However, genetic associations alone do not suffice to prove causality and one or more of the 14 SNPs on this haplotype may be involved in long-range control of gene expression, leaving HTRA1 and PLEKHA1 still suspects in the pathogenic pathway. Both, ARMS2 and HTRA1 have been linked to extracellular matrix homeostasis, yet their exact molecular function as well as their role in AMD pathogenesis remains to be uncovered. The transcriptional regulation of the 10q26 locus adds an additional level of complexity, given, that gene-regulatory as well as epigenetic alterations may influence expression levels from 10q26 in diseased individuals. Here, we provide a comprehensive overview on the 10q26 locus and its three gene products on various levels of biological complexity and discuss current and future research strategies to shed light on one of the remaining enigmatic spots in the AMD landscape.
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Affiliation(s)
- David A Merle
- Institute for Ophthalmic Research, Department for Ophthalmology, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany; Department for Ophthalmology, University Eye Clinic, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany; Department of Ophthalmology, Medical University of Graz, 8036, Graz, Austria.
| | - Merve Sen
- Institute for Ophthalmic Research, Department for Ophthalmology, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany
| | - Angela Armento
- Institute for Ophthalmic Research, Department for Ophthalmology, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany
| | - Chloe M Stanton
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Eric F Thee
- Department of Ophthalmology, Erasmus University Medical Center, 3015GD, Rotterdam, Netherlands; Department of Epidemiology, Erasmus University Medical Center, 3015CE, Rotterdam, Netherlands
| | - Magda A Meester-Smoor
- Department of Ophthalmology, Erasmus University Medical Center, 3015GD, Rotterdam, Netherlands; Department of Epidemiology, Erasmus University Medical Center, 3015CE, Rotterdam, Netherlands
| | - Markus Kaiser
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, 45117, Essen, Germany
| | - Simon J Clark
- Institute for Ophthalmic Research, Department for Ophthalmology, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany; Department for Ophthalmology, University Eye Clinic, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany; Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Caroline C W Klaver
- Department of Ophthalmology, Erasmus University Medical Center, 3015GD, Rotterdam, Netherlands; Department of Epidemiology, Erasmus University Medical Center, 3015CE, Rotterdam, Netherlands; Department of Ophthalmology, Radboudumc, 6525EX, Nijmegen, Netherlands; Institute of Molecular and Clinical Ophthalmology Basel, CH-4031, Basel, Switzerland
| | - Pearse A Keane
- Institute for Health Research, Biomedical Research Centre for Ophthalmology, Moorfields Eye Hospital NHS Foundation Trust, UCL Institute of Ophthalmology, London, EC1V 2PD, UK
| | - Alan F Wright
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Michael Ehrmann
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, 45117, Essen, Germany
| | - Marius Ueffing
- Institute for Ophthalmic Research, Department for Ophthalmology, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany; Department for Ophthalmology, University Eye Clinic, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany.
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5
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Johnson AO, Gonzalez-Villanueva M, Tee KL, Wong TS. An Engineered Constitutive Promoter Set with Broad Activity Range for Cupriavidus necator H16. ACS Synth Biol 2018; 7:1918-1928. [PMID: 29949349 DOI: 10.1021/acssynbio.8b00136] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Well-characterized promoters with variable strength form the foundation of heterologous pathway optimization. It is also a key element that bolsters the success of microbial engineering and facilitates the development of biological tools like biosensors. In comparison to microbial hosts such as Escherichia coli and Saccharomyces cerevisiae, the promoter repertoire of Cupriavidus necator H16 is highly limited. This limited number of characterized promoters poses a significant challenge during the engineering of C. necator H16 for biomanufacturing and biotechnological applications. In this article, we first examined the architecture and genetic elements of the four most widely used constitutive promoters of C. necator H16 (i.e., P phaC1, P rrsC, P j5, and P g25) and established a narrow 6-fold difference in their promoter activities. Next, using these four promoters as starting points and applying a range of genetic modifications (including point mutation, length alteration, incorporation of regulatory genetic element, promoter hybridization, and configuration alteration), we created a library of 42 constitutive promoters, all of which are functional in C. necator H16. Although these promoters are also functional in E. coli, they show different promoter strength and hierarchical rank of promoter activity. Subsequently, the activity of each promoter was individually characterized, using l-arabinose-inducible P BAD promoter as a benchmark. This study has extended the range of constitutive promoter activities to 137-fold, with some promoter variants exceeding the l-arabinose-inducible range of P BAD promoter. Not only has the work enhanced our flexibility in engineering C. necator H16, it presented novel strategies in adjusting promoter activity in C. necator H16 and highlighted similarities and differences in transcriptional activity between this organism and E. coli.
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Affiliation(s)
- Abayomi Oluwanbe Johnson
- Department of Chemical & Biological Engineering and Advanced Biomanufacturing Centre, University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield S1 3JD, United Kingdom
| | - Miriam Gonzalez-Villanueva
- Department of Chemical & Biological Engineering and Advanced Biomanufacturing Centre, University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield S1 3JD, United Kingdom
| | - Kang Lan Tee
- Department of Chemical & Biological Engineering and Advanced Biomanufacturing Centre, University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield S1 3JD, United Kingdom
| | - Tuck Seng Wong
- Department of Chemical & Biological Engineering and Advanced Biomanufacturing Centre, University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield S1 3JD, United Kingdom
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6
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Bralten J, van Hulzen KJ, Martens MB, Galesloot TE, Arias Vasquez A, Kiemeney LA, Buitelaar JK, Muntjewerff JW, Franke B, Poelmans G. Autism spectrum disorders and autistic traits share genetics and biology. Mol Psychiatry 2018; 23:1205-1212. [PMID: 28507316 PMCID: PMC5984081 DOI: 10.1038/mp.2017.98] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 02/06/2017] [Accepted: 03/16/2017] [Indexed: 02/06/2023]
Abstract
Autism spectrum disorders (ASDs) and autistic traits in the general population may share genetic susceptibility factors. In this study, we investigated such potential overlap based on common genetic variants. We developed and validated a self-report questionnaire of autistic traits in adults. We then conducted genome-wide association studies (GWASs) of six trait scores derived from the questionnaire through exploratory factor analysis in 1981 adults from the general population. Using the results from the Psychiatric Genomics Consortium GWAS of ASDs, we observed genetic sharing between ASDs and the autistic traits 'childhood behavior', 'rigidity' and 'attention to detail'. Gene-set analysis subsequently identified 'rigidity' to be significantly associated with a network of ASD gene-encoded proteins that regulates neurite outgrowth. Gene-wide association with the well-established ASD gene MET reached significance. Taken together, our findings provide evidence for an overlapping genetic and biological etiology underlying ASDs and autistic population traits, which suggests that genetic studies in the general population may yield novel ASD genes.
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Affiliation(s)
- J Bralten
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - K J van Hulzen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - M B Martens
- Department of Neuroinformatics, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - T E Galesloot
- Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - A Arias Vasquez
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
- Department of Cognitive Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Psychiatry, Radboud University Medical Center, Nijmegen, The Netherlands
| | - L A Kiemeney
- Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - J K Buitelaar
- Department of Cognitive Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
- Karakter Child and Adolescent Psychiatry University Centre, Nijmegen, The Netherlands
| | - J W Muntjewerff
- Department of Psychiatry, Radboud University Medical Center, Nijmegen, The Netherlands
| | - B Franke
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
- Department of Psychiatry, Radboud University Medical Center, Nijmegen, The Netherlands
| | - G Poelmans
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behaviour, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen, The Netherlands
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7
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Klemann C, Visser J, Van Den Bosch L, Martens G, Poelmans G. Integrated molecular landscape of amyotrophic lateral sclerosis provides insights into disease etiology. Brain Pathol 2018; 28:203-211. [PMID: 28035716 PMCID: PMC8028446 DOI: 10.1111/bpa.12485] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/23/2016] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a severe, progressive and ultimately fatal motor neuron disease caused by a combination of genetic and environmental factors, but its underlying mechanisms are largely unknown. To gain insight into the etiology of ALS, we here conducted genetic network and literature analyses of the top-ranked findings from six genome-wide association studies of sporadic ALS (involving 3589 cases and 8577 controls) as well as genes implicated in ALS etiology through other evidence, including familial ALS candidate gene association studies. We integrated these findings into a molecular landscape of ALS that allowed the identification of three main processes that interact with each other and are crucial to maintain axonal functionality, especially of the long axons of motor neurons, i.e. (1) Rho-GTPase signaling; (2) signaling involving the three regulatory molecules estradiol, folate, and methionine; and (3) ribonucleoprotein granule functioning and axonal transport. Interestingly, estradiol signaling is functionally involved in all three cascades and as such an important mediator of the molecular ALS landscape. Furthermore, epidemiological findings together with an analysis of possible gender effects in our own cohort of sporadic ALS patients indicated that estradiol may be a protective factor, especially for bulbar-onset ALS. Taken together, our molecular landscape of ALS suggests that abnormalities within three interconnected molecular processes involved in the functioning and maintenance of motor neuron axons are important in the etiology of ALS. Moreover, estradiol appears to be an important modulator of the ALS landscape, providing important clues for the development of novel disease-modifying treatments.
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Affiliation(s)
- C.J.H.M. Klemann
- Department of Molecular Animal PhysiologyDonders Institute for Brain, Cognition and Behaviour, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud UniversityNijmegenThe Netherlands
| | - J.E. Visser
- Department of Molecular Animal PhysiologyDonders Institute for Brain, Cognition and Behaviour, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud UniversityNijmegenThe Netherlands
- Department of NeurologyDonders Institute for Brain, Cognition and Behaviour, Radboud University Medical CenterNijmegenThe Netherlands
- Department of NeurologyAmphia HospitalBredaThe Netherlands
| | - L. Van Den Bosch
- Department of NeurosciencesLaboratory of Neurobiology, Experimental Neurology, KU Leuven and VIB, Vesalius Research CenterLeuvenBelgium
| | - G.J.M. Martens
- Department of Molecular Animal PhysiologyDonders Institute for Brain, Cognition and Behaviour, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud UniversityNijmegenThe Netherlands
| | - G. Poelmans
- Department of Molecular Animal PhysiologyDonders Institute for Brain, Cognition and Behaviour, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud UniversityNijmegenThe Netherlands
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
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8
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Klemann CJHM, Martens GJM, Sharma M, Martens MB, Isacson O, Gasser T, Visser JE, Poelmans G. Integrated molecular landscape of Parkinson's disease. NPJ PARKINSONS DISEASE 2017. [PMID: 28649614 PMCID: PMC5460267 DOI: 10.1038/s41531-017-0015-3] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Parkinson’s disease is caused by a complex interplay of genetic and environmental factors. Although a number of independent molecular pathways and processes have been associated with familial Parkinson’s disease, a common mechanism underlying especially sporadic Parkinson’s disease is still largely unknown. In order to gain further insight into the etiology of Parkinson’s disease, we here conducted genetic network and literature analyses to integrate the top-ranked findings from thirteen published genome-wide association studies of Parkinson’s disease (involving 13.094 cases and 47.148 controls) and other genes implicated in (familial) Parkinson’s disease, into a molecular interaction landscape. The molecular Parkinson’s disease landscape harbors four main biological processes—oxidative stress response, endosomal-lysosomal functioning, endoplasmic reticulum stress response, and immune response activation—that interact with each other and regulate dopaminergic neuron function and death, the pathological hallmark of Parkinson’s disease. Interestingly, lipids and lipoproteins are functionally involved in and influenced by all these processes, and affect dopaminergic neuron-specific signaling cascades. Furthermore, we validate the Parkinson’s disease -lipid relationship by genome-wide association studies data-based polygenic risk score analyses that indicate a shared genetic risk between lipid/lipoprotein traits and Parkinson’s disease. Taken together, our findings provide novel insights into the molecular pathways underlying the etiology of (sporadic) Parkinson’s disease and highlight a key role for lipids and lipoproteins in Parkinson’s disease pathogenesis, providing important clues for the development of disease-modifying treatments of Parkinson’s disease. Lipids and lipoproteins play a central role in four key biological processes underlying Parkinson’s disease (PD). Using bioinformatics and other extensive analyses of previously published data, Geert Poelmans, Cornelius Klemann and colleagues in The Netherlands, Germany and the USA have mapped the interactions of proteins that are encoded by genes associated with both familial and sporadic forms of PD. They identify the oxidative stress response, lysosomal function, endoplasmic reticulum stress response and immune response activation as the main mechanisms leading to the death of dopaminergic neurons. Lipid signaling is implicated in all four of these processes and the authors find a link between the levels of particular lipids and lipoproteins and the risk of PD. These findings suggest that compounds that regulate lipid or lipoprotein levels offer a potential new treatment strategy for PD.
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Affiliation(s)
- C J H M Klemann
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behaviour, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen, The Netherlands
| | - G J M Martens
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behaviour, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen, The Netherlands
| | - M Sharma
- Centre for Genetic Epidemiology, Institute for Clinical Epidemiology and Applied Biometry, University of Tübingen, Tübingen, Germany
| | - M B Martens
- Department of Neuroinformatics, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - O Isacson
- Neuroregeneration Research Institute, McLean Hospital/Harvard Medical School, Belmont, MA USA
| | - T Gasser
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research, University of Tübingen, and German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - J E Visser
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behaviour, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen, The Netherlands.,Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Neurology, Amphia Hospital, Breda, The Netherlands
| | - G Poelmans
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behaviour, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen, The Netherlands.,Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
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9
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Kwok J, O'Shea M, Hume DA, Lengeling A. Jmjd6, a JmjC Dioxygenase with Many Interaction Partners and Pleiotropic Functions. Front Genet 2017; 8:32. [PMID: 28360925 PMCID: PMC5352680 DOI: 10.3389/fgene.2017.00032] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/27/2017] [Indexed: 12/20/2022] Open
Abstract
Lysyl hydroxylation and arginyl demethylation are post-translational events that are important for many cellular processes. The jumonji domain containing protein 6 (JMJD6) has been reported to catalyze both lysyl hydroxylation and arginyl demethylation on diverse protein substrates. It also interacts directly with RNA. This review summarizes knowledge of JMJD6 functions that have emerged in the last 15 years and considers how a single Jumonji C (JmjC) domain-containing enzyme can target so many different substrates. New links and synergies between the three main proposed functions of Jmjd6 in histone demethylation, promoter proximal pause release of polymerase II and RNA splicing are discussed. The physiological context of the described molecular functions is considered and recently described novel roles for JMJD6 in cancer and immune biology are reviewed. The increased knowledge of JMJD6 functions has wider implications for our general understanding of the JmjC protein family of which JMJD6 is a member.
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Affiliation(s)
- Janice Kwok
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Edinburgh, UK
| | - Marie O'Shea
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Edinburgh, UK
| | - David A Hume
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Edinburgh, UK
| | - Andreas Lengeling
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Edinburgh, UK
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10
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Najafi H, Soltani BM, Dokanehiifard S, Nasiri S, Mowla SJ. Alternative splicing of the OCC-1 gene generates three splice variants and a novel exonic microRNA, which regulate the Wnt signaling pathway. RNA (NEW YORK, N.Y.) 2017; 23:70-85. [PMID: 27986894 PMCID: PMC5159651 DOI: 10.1261/rna.056317.116] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 10/10/2016] [Indexed: 06/06/2023]
Abstract
The Wnt signaling pathway is hyperactivated in most colorectal cancers (CRC). Finding new regulators of this pathway represents the potential for cancer diagnosis or treatment. OCC-1 was initially reported as an up-regulated gene in colon carcinoma, without knowing its mechanism of action. Here, two novel transcript variants and an exonic microRNA that originated from the OCC-1 gene are reported, showing positive effects on Wnt activity. Up-regulation of the known OCC-1 variant (assigned as OCC-1A/B) was limited to CRC, and its overexpression increased survival of CRC-originated SW480 cells (Wnt+), while resulting in apoptosis of Wnt-suppressed SW480 cells or HeLa cells (Wnt-) detected by PI staining. Immunocytochemistry showed that the OCC-1A/B-encoded peptide was localized to the nucleus, where its overexpression resulted in Wnt signaling up-regulation, detected by TOP/FOPflash assay. The noncoding portion of the OCC-1A/B transcript had a suppressive effect on Wnt activity and had a negative correlation with APPL2 neighboring gene expression. Unlike OCC-1A/B, the novel OCC-1C splice variant had no expression alteration in CRC, and it seemed to encode a smaller peptide with cytoplasmic localization. A 60-nucleotide (nt) fragment containing an AUG start codon is spliced out to produce an OCC-1D noncoding RNA variant. The 60-nt RNA was validated as the precursor of a novel microRNA, which we named miR-ex1 Both OCC-1D and miR-ex1 were coordinately up-regulated in CRC. MiR-ex1 functional analysis revealed that it is targeting the APC2 tumor suppressor gene and is an activator of the Wnt signaling pathway. Overall, the OCC-1 gene is now introduced as a novel Wnt signaling regulator and as a potential therapeutic target.
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Affiliation(s)
- Hadi Najafi
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, 14115-116 Tehran, Iran
| | - Bahram M Soltani
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, 14115-116 Tehran, Iran
| | - Sadat Dokanehiifard
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, 14115-116 Tehran, Iran
| | - Shirzad Nasiri
- Tehran University of Medical Sciences, Shariati Hospital, 1411713135 Tehran, Iran
| | - Seyed Javad Mowla
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, 14115-116 Tehran, Iran
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11
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Naaijen J, Bralten J, Poelmans G, Glennon JC, Franke B, Buitelaar JK. Glutamatergic and GABAergic gene sets in attention-deficit/hyperactivity disorder: association to overlapping traits in ADHD and autism. Transl Psychiatry 2017; 7:e999. [PMID: 28072412 PMCID: PMC5545734 DOI: 10.1038/tp.2016.273] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 11/13/2016] [Accepted: 11/27/2016] [Indexed: 02/02/2023] Open
Abstract
Attention-deficit/hyperactivity disorder (ADHD) and autism spectrum disorders (ASD) often co-occur. Both are highly heritable; however, it has been difficult to discover genetic risk variants. Glutamate and GABA are main excitatory and inhibitory neurotransmitters in the brain; their balance is essential for proper brain development and functioning. In this study we investigated the role of glutamate and GABA genetics in ADHD severity, autism symptom severity and inhibitory performance, based on gene set analysis, an approach to investigate multiple genetic variants simultaneously. Common variants within glutamatergic and GABAergic genes were investigated using the MAGMA software in an ADHD case-only sample (n=931), in which we assessed ASD symptoms and response inhibition on a Stop task. Gene set analysis for ADHD symptom severity, divided into inattention and hyperactivity/impulsivity symptoms, autism symptom severity and inhibition were performed using principal component regression analyses. Subsequently, gene-wide association analyses were performed. The glutamate gene set showed an association with severity of hyperactivity/impulsivity (P=0.009), which was robust to correcting for genome-wide association levels. The GABA gene set showed nominally significant association with inhibition (P=0.04), but this did not survive correction for multiple comparisons. None of single gene or single variant associations was significant on their own. By analyzing multiple genetic variants within candidate gene sets together, we were able to find genetic associations supporting the involvement of excitatory and inhibitory neurotransmitter systems in ADHD and ASD symptom severity in ADHD.
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Affiliation(s)
- J Naaijen
- Department of Cognitive Neuroscience, Donders Institute of Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands,Department of Cognitive Neuroscience, Donders Institute of Brain, Cognition and Behaviour, Radboud University Medical Center, Geert Grooteplein Noord 10 (Huispost 126), Nijmegen 6525 EZ, The Netherlands. E-mail:
| | - J Bralten
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - G Poelmans
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - J C Glennon
- Department of Cognitive Neuroscience, Donders Institute of Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - B Franke
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands,Department of Psychiatry, Radboud University Medical Center, Nijmegen, The Netherlands
| | - J K Buitelaar
- Department of Cognitive Neuroscience, Donders Institute of Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands,Karakter Child and Adolescent Psychiatry University Center, Nijmegen, The Netherlands
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12
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Trypsteen W, Mohammadi P, Van Hecke C, Mestdagh P, Lefever S, Saeys Y, De Bleser P, Vandesompele J, Ciuffi A, Vandekerckhove L, De Spiegelaere W. Differential expression of lncRNAs during the HIV replication cycle: an underestimated layer in the HIV-host interplay. Sci Rep 2016; 6:36111. [PMID: 27782208 PMCID: PMC5080576 DOI: 10.1038/srep36111] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 10/10/2016] [Indexed: 12/21/2022] Open
Abstract
Studying the effects of HIV infection on the host transcriptome has typically focused on protein-coding genes. However, recent advances in the field of RNA sequencing revealed that long non-coding RNAs (lncRNAs) add an extensive additional layer to the cell’s molecular network. Here, we performed transcriptome profiling throughout a primary HIV infection in vitro to investigate lncRNA expression at the different HIV replication cycle processes (reverse transcription, integration and particle production). Subsequently, guilt-by-association, transcription factor and co-expression analysis were performed to infer biological roles for the lncRNAs identified in the HIV-host interplay. Many lncRNAs were suggested to play a role in mechanisms relying on proteasomal and ubiquitination pathways, apoptosis, DNA damage responses and cell cycle regulation. Through transcription factor binding analysis, we found that lncRNAs display a distinct transcriptional regulation profile as compared to protein coding mRNAs, suggesting that mRNAs and lncRNAs are independently modulated. In addition, we identified five differentially expressed lncRNA-mRNA pairs with mRNA involvement in HIV pathogenesis with possible cis regulatory lncRNAs that control nearby mRNA expression and function. Altogether, the present study demonstrates that lncRNAs add a new dimension to the HIV-host interplay and should be further investigated as they may represent targets for controlling HIV replication.
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Affiliation(s)
- Wim Trypsteen
- Department of Internal Medicine, HIV Cure Research Centre, Ghent University, Ghent, Belgium
| | - Pejman Mohammadi
- Institute of Microbiology (IMUL), Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Clarissa Van Hecke
- Department of Internal Medicine, HIV Cure Research Centre, Ghent University, Ghent, Belgium
| | | | | | - Yvan Saeys
- Inflammation Research Center, Flanders Institute of Biotechnology (VIB), Ghent, Belgium.,Department of Biomedical Molecular Biology Ghent University, Ghent, Belgium
| | - Pieter De Bleser
- Inflammation Research Center, Flanders Institute of Biotechnology (VIB), Ghent, Belgium.,Department of Respiratory Medicine, Ghent University, Ghent, Belgium
| | | | - Angela Ciuffi
- Institute of Microbiology (IMUL), Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Linos Vandekerckhove
- Department of Internal Medicine, HIV Cure Research Centre, Ghent University, Ghent, Belgium
| | - Ward De Spiegelaere
- Department of Internal Medicine, HIV Cure Research Centre, Ghent University, Ghent, Belgium.,Department of Morphology, Ghent University, Belgium
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13
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Zhuang X, Lv M, Zhong Z, Zhang L, Jiang R, Chen J. Interplay between intergrin-linked kinase and ribonuclease inhibitor affects growth and metastasis of bladder cancer through signaling ILK pathways. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2016; 35:130. [PMID: 27576342 PMCID: PMC5006283 DOI: 10.1186/s13046-016-0408-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 08/17/2016] [Indexed: 12/29/2022]
Abstract
Background Integrin-linked kinase (ILK) is a multifunctional adaptor protein which is involved with protein signalling within cells to modulate malignant (cancer) cell movement, cell cycle, metastasis and epithelial–mesenchymal transition (EMT). Our previous experiment demonstrated that ILK siRNA inhibited the growth and induced apoptosis of bladder cancer cells as well as increased the expression of Ribonuclease inhibitor (RI), an important cytoplasmic protein with many functions. We also reported that RI overexpression inhibited ILK and phosphorylation of AKT and GSK3β. ILK and RI gene both locate on chromosome 11p15 and the two genes are always at the adjacent position of same chromosome during evolution, which suggest that ILK and RI could have some relationship. However, underlying interacting mechanisms remain unclear between them. Here, we postulate that RI might regulate ILK signaling pathway via interacting with ILK. Methods Co-immunoprecipitation, GST pull-down and co-localization under laser confocal microscope assay were used to determine the interaction between ILK and RI exogenously and endogenously. Furthermore, we further verified that there is a direct binding between the two proteins by fluorescence resonance energy transfer (FRET) in cells. Next, The effects of interplay between ILK and RI on the key target protein expressions of PI3K/AKT/mTOR signaling pathway were determined by western blot, immunohistochemistry and immunofluorescence assay in vivo and in vitro. Finally, the interaction was assessed using nude mice xenograft model. Results We first found that ILK could combine with RI both in vivo and in vitro by GST pull-down, co-immunoprecipitation (Co-IP) and FRET. The protein levels of ILK and RI revealed a significant inverse correlation in vivo and in vitro. Subsequently, The results showed that up-regulating ILK could increase cell proliferation, change cell morphology and regulate cell cycle. We also demonstrated that the overexpression of ILK remarkably promoted EMT and expressions of target molecules of ILK signaling pathways in vitro and in vivo. Finally, we found that ILK overexpression significantly enhanced growth, metastasis and angiogenesis of xenograft tumor; Whereas, RI has a contrary role compared to ILK in vivo and in vitro. Conclusions Our findings, for the first time, directly proved that the interplay between ILK and RI regulated EMT via ILK/PI3K/AKT signaling pathways for bladder cancer, which highlights the possibilities that ILK/RI could be valuable markers together for the therapy and diagnosis of human carcinoma of urinary bladder.
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Affiliation(s)
- Xiang Zhuang
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, 400016, China
| | - Mengxin Lv
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, 400016, China
| | - Zhenyu Zhong
- The First Clinical College, Chongqing Medical University, Chongqing, 400016, China
| | - Luyu Zhang
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, 400016, China
| | - Rong Jiang
- Laboratory of Stem Cells and Tissue Engineering, Chongqing Medical University, Chongqing, China
| | - Junxia Chen
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, 400016, China.
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14
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van de Vondervoort I, Poelmans G, Aschrafi A, Pauls DL, Buitelaar JK, Glennon JC, Franke B. An integrated molecular landscape implicates the regulation of dendritic spine formation through insulin-related signalling in obsessive-compulsive disorder. J Psychiatry Neurosci 2016; 41:280-5. [PMID: 26854754 PMCID: PMC4915937 DOI: 10.1503/jpn.140327] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Obsessive-compulsive disorder (OCD) is a neuropsychiatric disorder with onset in childhood and is characterized by obsessions (recurrent, intrusive, persistent thoughts, impulses and/or ideas that often cause anxiety or distress) and compulsions (ritualized and stereotypic behaviours or mental acts that are often performed to relieve anxiety or distress associated with obsessions). Although OCD is a heritable disorder, its complex molecular etiology is poorly understood. METHODS We combined enrichment analyses and an elaborate literature review of the top-ranked genes emerging from the 2 published genome-wide association studies of OCD and candidate genes implicated through other evidence in order to identify biological processes that, when dysregulated, increase the risk for OCD. RESULTS The resulting molecular protein landscape was enriched for proteins involved in regulating postsynaptic dendritic spine formation - and hence synaptic plasticity - through insulin-dependent molecular signalling cascades. LIMITATIONS This study is a first attempt to integrate molecuar information from different sources in order to identify biological mechanisms underlying OCD etiology. Our findings are constrained by the limited information from hypothesis-free studies and the incompleteness and existing limitations of the OCD literature and the gene function annotations of gene enrichment tools. As this study was solely based on in silico analyses, experimental validation of the provided hypotheses is warranted. CONCLUSION Our work suggests a key role for insulin and insulin-related signalling in OCD etiology and - if confirmed by independent studies - could eventually pave the way for the development of novel OCD treatments.
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Affiliation(s)
| | | | | | | | | | | | - Barbara Franke
- Correspondence to: B. Franke, Department of Human Genetics, Radboud University Medical Center, P.O. Box 9101 (HP 855), 6500 HB Nijmegen, the Netherlands;
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15
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Aebi M, van Donkelaar MMJ, Poelmans G, Buitelaar JK, Sonuga‐Barke EJS, Stringaris A, consortium IMAGE, Faraone SV, Franke B, Steinhausen H, van Hulzen KJE. Gene-set and multivariate genome-wide association analysis of oppositional defiant behavior subtypes in attention-deficit/hyperactivity disorder. Am J Med Genet B Neuropsychiatr Genet 2016; 171:573-88. [PMID: 26184070 PMCID: PMC4715802 DOI: 10.1002/ajmg.b.32346] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 06/29/2015] [Indexed: 12/02/2022]
Abstract
Oppositional defiant disorder (ODD) is a frequent psychiatric disorder seen in children and adolescents with attention-deficit-hyperactivity disorder (ADHD). ODD is also a common antecedent to both affective disorders and aggressive behaviors. Although the heritability of ODD has been estimated to be around 0.60, there has been little research into the molecular genetics of ODD. The present study examined the association of irritable and defiant/vindictive dimensions and categorical subtypes of ODD (based on latent class analyses) with previously described specific polymorphisms (DRD4 exon3 VNTR, 5-HTTLPR, and seven OXTR SNPs) as well as with dopamine, serotonin, and oxytocin genes and pathways in a clinical sample of children and adolescents with ADHD. In addition, we performed a multivariate genome-wide association study (GWAS) of the aforementioned ODD dimensions and subtypes. Apart from adjusting the analyses for age and sex, we controlled for "parental ability to cope with disruptive behavior." None of the hypothesis-driven analyses revealed a significant association with ODD dimensions and subtypes. Inadequate parenting behavior was significantly associated with all ODD dimensions and subtypes, most strongly with defiant/vindictive behaviors. In addition, the GWAS did not result in genome-wide significant findings but bioinformatics and literature analyses revealed that the proteins encoded by 28 of the 53 top-ranked genes functionally interact in a molecular landscape centered around Beta-catenin signaling and involved in the regulation of neurite outgrowth. Our findings provide new insights into the molecular basis of ODD and inform future genetic studies of oppositional behavior. © 2015 The Authors. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Marcel Aebi
- Department of Forensic Psychiatry, Child and Youth Forensic ServiceUniversity Hospital of PsychiatryZurichSwitzerland
- Department of Child and Adolescent PsychiatryUniversity of ZurichZurichSwitzerland
| | - Marjolein M. J. van Donkelaar
- Department of Human GeneticsRadboud University Medical Center, Donders Institute for Brain, Cognition and BehaviourNijmegenThe Netherlands
| | - Geert Poelmans
- Department of Human GeneticsRadboud University Medical Center, Donders Institute for Brain, Cognition and BehaviourNijmegenThe Netherlands
- Department of Cognitive NeuroscienceDonders Institute for Brain, Cognition and Behaviour, Radboud University Medical CenterNijmegenThe Netherlands
- Department of Molecular Animal PhysiologyDonders Institute for Brain, Cognition and Behavior, Radboud Institute for Molecular Life Sciences, Radboud UniversityNijmegenThe Netherlands
| | - Jan K. Buitelaar
- Department of Cognitive NeuroscienceDonders Institute for Brain, Cognition and Behaviour, Radboud University Medical CenterNijmegenThe Netherlands
| | - Edmund J. S. Sonuga‐Barke
- Developmental Brain‐Behaviour LaboratoryDepartment of PsychologyUniversity of SouthamptonSouthamptonUK
- Department of Experimental Clinical and Health PsychologyGhent UniversityGhentBelgium
| | | | - IMAGE consortium
- Department of Forensic Psychiatry, Child and Youth Forensic ServiceUniversity Hospital of PsychiatryZurichSwitzerland
| | - Stephen V. Faraone
- Department of PsychiatrySUNY Upstate Medical UniversitySyracuseNew York
- Departmentof Neuroscience and PhysiologySUNY Upstate Medical UniversitySyracuseNew York
- Department of BiomedicineK.G. Jebsen Centre for Psychiatric DisordersUniversity of BergenBergenNorway
| | - Barbara Franke
- Department of Human GeneticsRadboud University Medical Center, Donders Institute for Brain, Cognition and BehaviourNijmegenThe Netherlands
- Department of PsychiatryDonders Institute for Brain, Cognition and Behaviour, Radboud University Medical CenterNijmegenThe Netherlands
| | - Hans‐Christoph Steinhausen
- Department of Child and Adolescent PsychiatryUniversity of ZurichZurichSwitzerland
- Department of Psychology, Clinical Psychology and EpidemiologyUniversity of BaselBaselSwitzerland
- Research Unit for Child and Adolescent Psychiatry, Psychiatric HospitalAalborg University HospitalAalborgDenmark
| | - Kimm J. E. van Hulzen
- Department of Human GeneticsRadboud University Medical Center, Donders Institute for Brain, Cognition and BehaviourNijmegenThe Netherlands
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16
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Chiaramonte C, Bommarito D, Zambaiti E, Antona V, Li Voti G. Genetic Basis of Posterior Urethral Valves Inheritance. Urology 2016; 95:175-9. [PMID: 27261184 DOI: 10.1016/j.urology.2016.05.043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/18/2016] [Accepted: 05/23/2016] [Indexed: 10/21/2022]
Abstract
OBJECTIVE To highlight genetic pattern of posterior urethral valves (PUVs), we performed a genetic study on 2 siblings affected. PUVs are the most common congenital cause of lower urinary tract obstruction and an important cause of renal failure in infants (50% progress to end-stage renal disease in 10 years). PUVs occur in 1 of 5000-8000 male infants, but real incidence is arduous to determine because of the wide spectrum of possible clinical presentation. A different recurrence rate is reported in African Americans and children with Down syndrome, although usually PUVs are not found in syndromic conditions but constitute an isolated disorder. Although most cases appear to be sporadic, some reports in literature suggest a partial genetic etiology. MATERIALS AND METHODS We report 2 brothers with PUVs. The children's mother was a healthy woman but had a history of urinary tract infections of unknown etiology. We investigated possible familial genetic anomalies using a DNA array comparative genomic hybridization technique. RESULTS We identified 2 partial duplications in the short arm of chromosome 11 recurring in both children and mother. CONCLUSION This finding, not previously reported to our knowledge, adds new data to support the hypothesis of the presence of a hereditary component in the occurrences of PUVs.
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Affiliation(s)
| | | | - Elisa Zambaiti
- Pediatric Surgery Unit, Palermo University, Palermo, Italy
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17
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Li L, Pan XY, Shu J, Jiang R, Zhou YJ, Chen JX. Ribonuclease inhibitor up-regulation inhibits the growth and induces apoptosis in murine melanoma cells through repression of angiogenin and ILK/PI3K/AKT signaling pathway. Biochimie 2014; 103:89-100. [PMID: 24769129 DOI: 10.1016/j.biochi.2014.04.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 04/11/2014] [Indexed: 10/25/2022]
Abstract
Human ribonuclease inhibitor (RI), a cytoplasmic protein, is constructed almost entirely of leucine rich repeats. RI could suppress activities of ribonuclease and angiogenin (ANG) through closely combining with them. ANG is a potent inducer of blood vessel growth and has been implicated in the establishment, growth, and metastasis of tumors. ILK/PI3K/AKT signaling pathway also plays important roles in cell growth, cell-cycle progression, tumor angiogenesis, and cell apoptosis. Our previous experiments demonstrated that RI might effectively inhibit some tumor growth and metastasis. Our recent study showed that ILK siRNA inhibited the growth and induced apoptosis in bladder cancer cells as well as increased RI expression, which suggest a correlation between RI and ILK. However, the exact molecular mechanism of RI in anti-tumor and in the cross-talk of ANG and ILK signaling pathway remains largely unknown. Here we investigated the effects of up-regulating RI on the growth and apoptosis in murine melanoma cells through angiogenin and ILK/PI3K/AKT signaling pathway. We demonstrated that up-regulating RI obviously decreased ANG expression and activity. We also discovered that RI overexpression could remarkably inhibit cell proliferation, regulate cell cycle and induce apoptosis. Furthermore, up-regulation of RI inhibited phosphorylation of ILK downstream signaling targets protein kinase B/Akt, glycogen synthase kinase 3-beta (GSK-3β), and reduced β-catenin expression in vivo and vitro. More importantly, RI significant inhibited the tumor growth and angiogenesis of tumor bearing C57BL/6 mice. In conclusion, our findings, for the first time, suggest that angiogenin and ILK signaling pathway plays a pivotal role in mediating the inhibitory effects of RI on melanoma cells growth. This study identifies that RI may be a useful molecular target for melanoma therapy.
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Affiliation(s)
- Lin Li
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing 400016, PR China
| | - Xiang-Yang Pan
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing 400016, PR China
| | - Jing Shu
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing 400016, PR China
| | - Rong Jiang
- Laboratory of Stem Cells and Tissue Engineering, Chongqing Medical University, Chongqing 400016, PR China
| | - Yu-Jian Zhou
- The Experimental Teaching Center, Chongqing Medical University, Chongqing 400016, PR China
| | - Jun-Xia Chen
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing 400016, PR China.
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18
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Boopathi P, Subudhi AK, Garg S, Middha S, Acharya J, Pakalapati D, Saxena V, Aiyaz M, Chand B, Mugasimangalam RC, Kochar SK, Sirohi P, Kochar DK, Das A. Revealing natural antisense transcripts from Plasmodium vivax isolates: Evidence of genome regulation in complicated malaria. INFECTION GENETICS AND EVOLUTION 2013; 20:428-43. [DOI: 10.1016/j.meegid.2013.09.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 09/24/2013] [Accepted: 09/25/2013] [Indexed: 01/08/2023]
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Abstract
Autism spectrum disorders (ASDs) are highly heritable, and six genome-wide association studies (GWASs) of ASDs have been published to date. In this study, we have integrated the findings from these GWASs with other genetic data to identify enriched genetic networks that are associated with ASDs. We conducted bioinformatics and systematic literature analyses of 200 top-ranked ASD candidate genes from five published GWASs. The sixth GWAS was used for replication and validation of our findings. Further corroborating evidence was obtained through rare genetic variant studies, that is, exome sequencing and copy number variation (CNV) studies, and/or other genetic evidence, including candidate gene association, microRNA and gene expression, gene function and genetic animal studies. We found three signaling networks regulating steroidogenesis, neurite outgrowth and (glutamatergic) synaptic function to be enriched in the data. Most genes from the five GWASs were also implicated--independent of gene size--in ASDs by at least one other line of genomic evidence. Importantly, A-kinase anchor proteins (AKAPs) functionally integrate signaling cascades within and between these networks. The three identified protein networks provide an important contribution to increasing our understanding of the molecular basis of ASDs. In addition, our results point towards the AKAPs as promising targets for developing novel ASD treatments.
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20
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Cooper DN, Ball EV, Mort M. Chromosomal distribution of disease genes in the human genome. Genet Test Mol Biomarkers 2010; 14:441-6. [PMID: 20642358 DOI: 10.1089/gtmb.2010.0081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Genes are nonrandomly distributed in the human genome, both within and between chromosomes. Thus, genes of similar function and common evolutionary origin are often clustered, as are genes with similar expression profiles. We now report that the >2400 genes known to underlie human monogenic inherited disease are non-randomly distributed in the genome over and above the general nonrandomness evident in the distribution of human genes. Further, a subset of 315 inherited disease genes subject to gross deletion was found to exhibit a degree of clustering that was twice that manifested by disease genes in general. The clustering of human disease genes is likely to have important implications for understanding the genotype-phenotype relationship in contiguous gene syndromes as well as those conditions characterized by multigene deletions or complex chromosomal rearrangements.
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Affiliation(s)
- David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, United Kingdom.
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