(LGI) Genes, and Mutational Analysis in Familial Spontaneous Epileptic Cats
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The Conserved DNMT1-Dependent Methylation Regions in Human Cells
Freeman et al. Epigenetics & Chromatin (2020) 13:17 https://doi.org/10.1186/s13072-020-00338-8 Epigenetics & Chromatin RESEARCH Open Access The conserved DNMT1-dependent methylation regions in human cells are vulnerable to neurotoxicant rotenone exposure Dana M. Freeman1 , Dan Lou1, Yanqiang Li1, Suzanne N. Martos1 and Zhibin Wang1,2,3* Abstract Background: Allele-specifc DNA methylation (ASM) describes genomic loci that maintain CpG methylation at only one inherited allele rather than having coordinated methylation across both alleles. The most prominent of these regions are germline ASMs (gASMs) that control the expression of imprinted genes in a parent of origin-dependent manner and are associated with disease. However, our recent report reveals numerous ASMs at non-imprinted genes. These non-germline ASMs are dependent on DNA methyltransferase 1 (DNMT1) and strikingly show the feature of random, switchable monoallelic methylation patterns in the mouse genome. The signifcance of these ASMs to human health has not been explored. Due to their shared allelicity with gASMs, herein, we propose that non-tradi- tional ASMs are sensitive to exposures in association with human disease. Results: We frst explore their conservancy in the human genome. Our data show that our putative non-germline ASMs were in conserved regions of the human genome and located adjacent to genes vital for neuronal develop- ment and maturation. We next tested the hypothesized vulnerability of these regions by exposing human embryonic kidney cell HEK293 with the neurotoxicant rotenone for 24 h. Indeed,14 genes adjacent to our identifed regions were diferentially expressed from RNA-sequencing. We analyzed the base-resolution methylation patterns of the predicted non-germline ASMs at two neurological genes, HCN2 and NEFM, with potential to increase the risk of neurodegenera- tion. -
Identification of Differentially Expressed Genes in Urinary Bladder Cancer by Meta-Analysis by Using a Bioinformatics Tool Sathya Mylsamy1* and K Devaki2
Research Article iMedPub Journals Journal of Clinical & Experimental Nephrology 2019 http://www.imedpub.com/ Vol 5.No.5:95 ISSN 2472-5056 Identification of Differentially Expressed Genes in Urinary Bladder Cancer by Meta-Analysis by Using a Bioinformatics Tool Sathya Mylsamy1* and K Devaki2 1Department of Biochemistry, CMS College of Science and Commerce, Coimbatore, Tamil Nadu, India 2Department of Biochemistry, Karpagam Academy of Higher Education, Coimbatore, Tamil Nadu, India *Corresponding author: Sathya Mylsamy, CMS College of Science and Commerce, Tamil Nadu, India, Tel: (+91)7904349498; E-mail: [email protected] Received date: November 18, 2020 ; Accepted date: December 02, 2020 ; Published date: December 09, 2020 Citation: Mylsamy S, Devaki K (2020) Identification of Differentially Expressed Genes in Urinary Bladder Cancer by Meta-Analysis by using a Bioinformatics Tool. J Clin Exp Nephrol Vol.5 No.5:95. Copyright: © 2020 Mylsamy S, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. understand the mechanism behind the tumor progression and its diagnosis. Abstract Background: Bladder cancer is the ninth most prevalent Keywords: Bladder cancer; GEO; CCNB2; NUSAP1; malignant disease globally, which ranges from mild with low ADAM22; KEGG; Gene ontology mortality rate to extremely high grade tumors associated with high mortality rate. The present study was aimed to identify the key genes associated with bladder cancer Introduction progression and later it may also be used as marker in the diagnosis and prognosis. The bladder is probably one of the few sites in the body where the environmental factors play an undeniable role in Materials and methods: The GSE3167, GSE7476, GSE68928 genesis of cancer [1]. -
Lgi1 (NM 145769) Rat Tagged ORF Clone – RR210565 | Origene
OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for RR210565 Lgi1 (NM_145769) Rat Tagged ORF Clone Product data: Product Type: Expression Plasmids Product Name: Lgi1 (NM_145769) Rat Tagged ORF Clone Tag: Myc-DDK Symbol: Lgi1 Synonyms: MGC105310 Vector: pCMV6-Entry (PS100001) E. coli Selection: Kanamycin (25 ug/mL) Cell Selection: Neomycin This product is to be used for laboratory only. Not for diagnostic or therapeutic use. View online » ©2021 OriGene Technologies, Inc., 9620 Medical Center Drive, Ste 200, Rockville, MD 20850, US 1 / 4 Lgi1 (NM_145769) Rat Tagged ORF Clone – RR210565 ORF Nucleotide >RR210565 representing NM_145769 Sequence: Red=Cloning site Blue=ORF Green=Tags(s) TTTTGTAATACGACTCACTATAGGGCGGCCGGGAATTCGTCGACTGGATCCGGTACCGAGGAGATCTGCC GCCGCGATCGCC ATGGAATCAGAAAGCATCAGAAGGATGGGAAATGCCTGCATTCCCCTGAAAAGAATTGCCTATTTCCTAT GCCTCTTTTCTGTGGTTTTGCTGACTGAGGGGAAGAAACCAGCGAAGCCAAAATGCCCTGCTGTGTGTAC TTGTAGCAAAGATAACGCTTTATGTGAGAATGCGAGATCCATTCCACGCACCGTTCCTCCTGATGTTATC TCACTATCCTTTGTGAGATCTGGTTTTACTGAAATCTCAGAAGGGAGTTTCTTGTTCACACCATCGCTGC AGCTCTTGTTATTCACGTCGAACTCCTTTGATGTGATCAGTGACGATGCTTTTATTGGTCTTCCACACCT AGAATATTTATTCATAGAAAACAACAATATCAAGTCCATTTCAAGACATACTTTCCGGGGACTCAAGTCT CTGATTCACTTGAGTCTTGCAAACAACAATCTCCAGACACTCCCAAAAGACATTTTCAAAGGCCTGGATT CTTTAACAAATGTGGACCTAAGAGGGAACTCATTTAACTGTGACTGTAAACTGAAGTGGCTGGTGGAATG GCTCGGCCACACCAACGCAACCGTGGAAGACATCTACTGCGAAGGACCACCGGAGTATAAGAAACGTAAA -
Product Description P408-A2 ADLTE-LGI1-V02
MRC-Holland ® Product Description version A2-02; Issued 02 December 2020 MLPA Product Description SALSA® MLPA® Probemix P408-A2 ADLTE-LGI1 To be used with the MLPA General Protocol. Version A2. For complete product history see page 7. Catalogue numbers: • P408-025R: SALSA MLPA Probemix P408 ADLTE-LGI1, 25 reactions. • P408-050R: SALSA MLPA Probemix P408 ADLTE-LGI1, 50 reactions. • P408-100R: SALSA MLPA Probemix P408 ADLTE-LGI1, 100 reactions. To be used in combination with a SALSA MLPA reagent kit and Coffalyser.Net data analysis software. MLPA reagent kits are either provided with FAM or Cy5.0 dye-labelled PCR primer, suitable for Applied Biosystems and Beckman/SCIEX capillary sequencers, respectively (see www.mlpa.com). Certificate of Analysis: Information regarding storage conditions, quality tests, and a sample electropherogram from the current sales lot is available at www.mlpa.com. Precautions and warnings: For professional use only. Always consult the most recent product description AND the MLPA General Protocol before use: www.mlpa.com. It is the responsibility of the user to be aware of the latest scientific knowledge of the application before drawing any conclusions from findings generated with this product. General information: The SALSA MLPA Probemix P408 ADLTE-LGI1 is a research use only (RUO) assay for the detection of deletions or duplications in ADAM22, ADGRV1 (was GPR98), KCNA1, KCNA4, KCNAB1, LGI1, and PDYN genes, which are associated with autosomal dominant lateral temporal epilepsy (ADLTE). ADLTE, also known as autosomal dominant partial epilepsy with auditory features (ADPEAF), is a rare familial form of epilepsy likely arising from the lateral temporal lobe of the brain. -
LGI1–ADAM22–MAGUK Configures Transsynaptic Nanoalignment for Synaptic Transmission and Epilepsy Prevention
LGI1–ADAM22–MAGUK configures transsynaptic nanoalignment for synaptic transmission and epilepsy prevention Yuko Fukataa,b,1, Xiumin Chenc,d,1, Satomi Chikenb,e, Yoko Hiranoa,f, Atsushi Yamagatag, Hiroki Inahashia, Makoto Sanboh, Hiromi Sanob,e, Teppei Gotoh, Masumi Hirabayashib,h, Hans-Christian Kornaui,j, Harald Prüssi,k, Atsushi Nambub,e, Shuya Fukail, Roger A. Nicollc,d,2, and Masaki Fukataa,b,2 aDivision of Membrane Physiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Aichi 444-8787, Japan; bDepartment of Physiological Sciences, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Aichi 444-8585, Japan; cDepartment of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158; dDepartment of Physiology, University of California, San Francisco, CA 94158; eDivision of System Neurophysiology, Department of System Neuroscience, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Aichi 444-8585, Japan; fDepartment of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; gLaboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Kanagawa 230-0045, Japan; hCenter for Genetic Analysis of Behavior, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki 444-8787, Japan; iGerman Center for Neurodegenerative Diseases (DZNE), 10117 Berlin, Germany; jNeuroscience Research Center, Cluster NeuroCure, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany; kDepartment of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany; and lDepartment of Chemistry, Graduate School of Science, Kyoto University, 606-8502 Kyoto, Japan Contributed by Roger A. Nicoll, December 1, 2020 (sent for review October 29, 2020; reviewed by David S. -
Quantitative Proteomics Reveals Significant Differences
cells Article Quantitative Proteomics Reveals Significant Differences between Mouse Brain Formations in Expression of Proteins Involved in Neuronal Plasticity during Aging Dominika Drulis-Fajdasz 1,† , Kinga Gostomska-Pampuch 2,3,† , Przemysław Duda 1 , Jacek Roman Wi´sniewski 2 and Dariusz Rakus 1,* 1 Department of Molecular Physiology and Neurobiology, University of Wrocław, Sienkiewicza 21, 50-335 Wrocław, Poland; [email protected] (D.D.-F.); [email protected] (P.D.) 2 Biochemical Proteomics Group, Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; [email protected] (K.G.-P.); [email protected] (J.R.W.) 3 Department of Biochemistry and Immunochemistry, Wrocław Medical University, Chałubi´nskiego10, 50-368 Wrocław, Poland * Correspondence: [email protected] † The authors participated equally. Abstract: Aging is associated with a general decline in cognitive functions, which appears to be due to alterations in the amounts of proteins involved in the regulation of synaptic plasticity. Here, we present a quantitative analysis of proteins involved in neurotransmission in three brain regions, namely, the hippocampus, the cerebral cortex and the cerebellum, in mice aged 1 and 22 months, Citation: Drulis-Fajdasz, D.; using the total protein approach technique. We demonstrate that although the titer of some proteins Gostomska-Pampuch, K.; Duda, P.; involved in neurotransmission and synaptic plasticity is affected by aging in a similar manner Wi´sniewski,J.R.; Rakus, D. Quantitative Proteomics Reveals in all the studied brain formations, in fact, each of the formations represents its own mode of Significant Differences between aging. -
Neurology Genetics
An Official Journal of the American Academy of Neurology Neurology.org/ng • Online ISSN: 2376-7839 Volume 3, Number 4, August 2017 Genetics Functionally pathogenic ExACtly zero or once: Clinical and experimental EARS2 variants in vitro A clinically helpful guide studies of a novel P525R may not manifest a to assessing genetic FUS mutation in amyotrophic phenotype in vivo variants in mild epilepsies lateral sclerosis Table of Contents Neurology.org/ng Online ISSN: 2376-7839 Volume 3, Number 4, August 2017 THE HELIX e171 Autopsy case of the C12orf65 mutation in a patient e175 What does phenotype have to do with it? with signs of mitochondrial dysfunction S.M. Pulst H. Nishihara, M. Omoto, M. Takao, Y. Higuchi, M. Koga, M. Kawai, H. Kawano, E. Ikeda, H. Takashima, and T. Kanda EDITORIAL e173 This variant alters protein function, but is it pathogenic? M. Pandolfo e174 Prevalence of spinocerebellar ataxia 36 in a US Companion article, e162 population J.M. Valera, T. Diaz, L.E. Petty, B. Quintáns, Z. Yáñez, ARTICLES E. Boerwinkle, D. Muzny, D. Akhmedov, R. Berdeaux, e162 Functionally pathogenic EARS2 variants in vitro may M.J. Sobrido, R. Gibbs, J.R. Lupski, D.H. Geschwind, not manifest a phenotype in vivo S. Perlman, J.E. Below, and B.L. Fogel N. McNeill, A. Nasca, A. Reyes, B. Lemoine, B. Cantarel, A. Vanderver, R. Schiffmann, and D. Ghezzi Editorial, e173 e170 Loss-of-function variants of SCN8A in intellectual disability without seizures e163 ExACtly zero or once: A clinically helpful guide to J.L. Wagnon, B.S. Barker, M. -
Prediction of Human Disease Genes by Human-Mouse Conserved Coexpression Analysis
Prediction of Human Disease Genes by Human-Mouse Conserved Coexpression Analysis Ugo Ala1., Rosario Michael Piro1., Elena Grassi1, Christian Damasco1, Lorenzo Silengo1, Martin Oti2, Paolo Provero1*, Ferdinando Di Cunto1* 1 Molecular Biotechnology Center, Department of Genetics, Biology and Biochemistry, University of Turin, Turin, Italy, 2 Department of Human Genetics and Centre for Molecular and Biomolecular Informatics, University Medical Centre Nijmegen, Nijmegen, The Netherlands Abstract Background: Even in the post-genomic era, the identification of candidate genes within loci associated with human genetic diseases is a very demanding task, because the critical region may typically contain hundreds of positional candidates. Since genes implicated in similar phenotypes tend to share very similar expression profiles, high throughput gene expression data may represent a very important resource to identify the best candidates for sequencing. However, so far, gene coexpression has not been used very successfully to prioritize positional candidates. Methodology/Principal Findings: We show that it is possible to reliably identify disease-relevant relationships among genes from massive microarray datasets by concentrating only on genes sharing similar expression profiles in both human and mouse. Moreover, we show systematically that the integration of human-mouse conserved coexpression with a phenotype similarity map allows the efficient identification of disease genes in large genomic regions. Finally, using this approach on 850 OMIM loci characterized by an unknown molecular basis, we propose high-probability candidates for 81 genetic diseases. Conclusion: Our results demonstrate that conserved coexpression, even at the human-mouse phylogenetic distance, represents a very strong criterion to predict disease-relevant relationships among human genes. Citation: Ala U, Piro RM, Grassi E, Damasco C, Silengo L, et al. -
LGI1 Gene Leucine Rich Glioma Inactivated 1
LGI1 gene leucine rich glioma inactivated 1 Normal Function The LGI1 gene provides instructions for making a protein called leucine-rich glioma inactivated 1 (Lgi1) or epitempin. This protein is found primarily in nerve cells (neurons) in the brain, including a part of the brain called the lateral temporal lobe. The temporal lobe of the brain is involved in hearing, speech, memory, and emotion. Although researchers have proposed several functions for epitempin, its precise role in the brain remains uncertain. This protein is probably involved in normal brain development. Some studies have suggested that epitempin plays a role in the normal function of potassium channels in neurons. These channels are embedded in the cell membrane, where they transport charged potassium atoms (potassium ions) out of neurons. Potassium channels are critical for normal electrical signaling in these cells. Other studies have found that epitempin is transported (secreted) out of neurons. The function of this protein outside cells is unclear. Epitempin may also help regulate the communication between neurons. Researchers have determined that epitempin attaches (binds) to a receptor protein called ADAM22 on the surface of neurons. Together, these proteins help control the release of certain brain chemicals called neurotransmitters. These chemicals allow neighboring neurons to communicate with each other, which is how signals are relayed throughout the brain. Health Conditions Related to Genetic Changes Autosomal dominant partial epilepsy with auditory features At least 22 mutations in the LGI1 gene have been identified in people with autosomal dominant partial epilepsy with auditory features (ADPEAF). Some LGI1 mutations change a single protein building block (amino acid) in the epitempin protein, which alters the protein's structure. -
Global Proteomic Analysis of Extracellular Matrix in Mouse And
Edinburgh Research Explorer Global proteomic analysis of extracellular matrix in mouse and human brain highlights relevance to cerebrovascular disease Citation for published version: Pokhilko, A, Brezzo, G, Handunnetthi, L, Heilig, R, Lennon, R, Smith, C, Allan, SM, Granata, A, Sinha, S, Wang, T, Markus, HS, Naba, A, Fischer, R, Van Agtmael, T, Horsburgh, K & Cader, MZ 2021, 'Global proteomic analysis of extracellular matrix in mouse and human brain highlights relevance to cerebrovascular disease', Journal of Cerebral Blood Flow and Metabolism, vol. 41, no. 9, pp. 2423–2438. https://doi.org/10.1177/0271678X211004307 Digital Object Identifier (DOI): 10.1177/0271678X211004307 Link: Link to publication record in Edinburgh Research Explorer Document Version: Publisher's PDF, also known as Version of record Published In: Journal of Cerebral Blood Flow and Metabolism General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 02. Oct. -
Similarity of Molecular Phenotype Between Known Epilepsy Gene LGI1 and Disease Candidate Gene LGI2
Limviphuvadh et al. BMC Biochemistry 2010, 11:39 http://www.biomedcentral.com/1471-2091/11/39 RESEARCH ARTICLE Open Access Similarity of molecular phenotype between known epilepsy gene LGI1 and disease candidate gene LGI2 Vachiranee Limviphuvadh1†, Ling Ling Chua1†, Rabi ’Atul’ Adawiyah Bte Rahim1, Frank Eisenhaber1,2,3, Sebastian Maurer-Stroh1,4, Sharmila Adhikari1* Abstract Background: The LGI2 (leucine-rich, glioma inactivated 2) gene, a prime candidate for partial epilepsy with pericentral spikes, belongs to a family encoding secreted, beta-propeller domain proteins with EPTP/EAR epilepsy- associated repeats. In another family member, LGI1 (leucine-rich, glioma inactivated 1) mutations are responsible for autosomal dominant lateral temporal epilepsy (ADLTE). Because a few LGI1 disease mutations described in the literature cause secretion failure, we experimentally analyzed the secretion efficiency and subcellular localization of several LGI1 and LGI2 mutant proteins corresponding to observed non-synonymous single nucleotide polymorphisms (nsSNPs) affecting the signal peptide, the leucine-rich repeats and the EAR propeller. Results: Mapping of disease-causing mutations in the EAR domain region onto a 3D-structure model shows that many of these mutations co-localize at an evolutionary conserved surface region of the propeller. We find that wild-type LGI2 is secreted to the extracellular medium in glycosylated form similarly to LGI1, whereas several mutant proteins tested in this study are secretion-deficient and accumulate in the endoplasmic reticulum. Interestingly, mutations at structurally homologous positions in the EAR domain have the same effect on secretion in LGI1 and LGI2. Conclusions: This similarity of experimental mislocalization phenotypes for mutations at homologous positions of LGI2 and the established epilepsy gene LGI1 suggests that both genes share a potentially common molecular pathogenesis mechanism that might be the reason for genotypically distinct but phenotypically related forms of epilepsy. -
The Conserved DNMT1 Dependent Methylation Regions in Human Cells Are Vulnerable to Environmental Rotenone
bioRxiv preprint doi: https://doi.org/10.1101/798587; this version posted October 9, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. The conserved DNMT1 dependent methylation regions in human cells are vulnerable to environmental rotenone. Dana M. Freemana, Dan Loua, Yanqiang Lia, Suzanne N. Martosa, Zhibin Wanga* aLaboratory of Environmental Epigenomes, Department of Environmental Health & Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD *To whom correspondence should be addressed: Zhibin Wang, Ph.D., Associate Professor, Laboratory of Environmental Epigenomes, Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD. Phone: (410) 955-7840; Email: [email protected] Abstract Allele-specific DNA methylation (ASM) describes genomic loci that maintain CpG methylation at only one inherited allele rather than having coordinated methylation across both alleles. The most prominent of these regions are germline ASMs (gASMs) that control the expression of imprinted genes in a parent of origin- dependent manner and are associated with disease. However, our recent report reveals numerous ASMs at non-imprinted genes. These non-germline ASMs are dependent on DNA methyltransferase 1 (DNMT1) and strikingly show the feature of random, switchable monoallelic methylation patterns in the mouse genome. The significance of these ASMs to human health has not been explored. Due to their shared allelicity with gASMs, herein, we propose that non-traditional ASMs are sensitive to exposures in association with human disease. We first explore their conservancy in the human genome.