Curriculum Vitae
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A Ph-Eqtl Interaction at the RIT2-SYT4 Parkinson's Disease Risk
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.16.423140; this version posted June 4, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. A pH-eQTL interaction at the RIT2-SYT4 Parkinson’s disease risk locus in the substantia nigra Authors and affiliations: Sejal Patel1*, Derek Howard1, Leon French1,2,3,4* 1. Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada 2. Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada 3. Department of Psychiatry, University of Toronto, Toronto 4. Institute for Medical Science, University of Toronto, Toronto, Canada Abstract Parkinson's disease (PD) causes severe motor and cognitive disabilities that result from the progressive loss of dopamine neurons in the substantia nigra. The rs12456492 variant in the RIT2 gene has been repeatedly associated with increased risk for Parkinson's disease. From a transcriptomic perspective, a meta-analysis found that RIT2 gene expression is correlated with pH in the human brain. To assess these pH associations in relation to PD risk, we examined the two datasets that assayed rs12456492, gene expression, and pH in the postmortem human brain. Using the BrainEAC dataset, we replicate the positive correlation between RIT2 gene expression and pH in the human brain (n=100). Furthermore, we found that the relationship between expression and pH is influenced by rs12456492. -
Modulation of the Alternative Pathway of Complement by Murine Factor H–Related Proteins
The Journal of Immunology Modulation of the Alternative Pathway of Complement by Murine Factor H–Related Proteins Alexandra H. Antonioli,* Janice White,† Frances Crawford,† Brandon Renner,* Kevin J. Marchbank,‡ Jonathan P. Hannan,* Joshua M. Thurman,* Philippa Marrack,†,x,{ and V. Michael Holers* Factor H (FH) is a key alternative pathway regulator that controls complement activation both in the fluid phase and on specific cell surfaces, thus allowing the innate immune response to discriminate between self and foreign pathogens. However, the interrela- tionships between FH and a group of closely related molecules, designated the FH-related (FHR) proteins, are currently not well understood. Whereas some studies have suggested that human FHR proteins possess complement regulatory abilities, recent studies have shown that FHR proteins are potent deregulators. Furthermore, the roles of the FHR proteins have not been explored in any in vivo models of inflammatory disease. In this study, we report the cloning and expression of recombinant mouse FH and three FHR proteins (FHR proteins A–C). Results from functional assays show that FHR-A and FHR-B proteins antagonize the protective function of FH in sheep erythrocyte hemolytic assays and increase cell-surface C3b deposition on a mouse kidney proximal tubular cell line (TEC) and a human retinal pigment epithelial cell line (ARPE-19). We also report apparent KD values for the binding interaction of mouse C3d with mouse FH (3.85 mM), FHR-A (136 nM), FHR-B (546 nM), and FHR-C (1.04 mM), which directly correlate with results from functional assays. Collectively, our work suggests that similar to their human counterparts, a subset of mouse FHR proteins have an important modulatory role in complement activation. -
Investigation of Modifier Genes Within Copy Number Variations in Rett Syndrome
See discussions, stats, and author profiles for this publication at: http://www.researchgate.net/publication/51147767 Investigation of modifier genes within copy number variations in Rett syndrome ARTICLE in JOURNAL OF HUMAN GENETICS · MAY 2011 Impact Factor: 2.53 · DOI: 10.1038/jhg.2011.50 · Source: PubMed CITATIONS DOWNLOADS VIEWS 6 89 134 15 AUTHORS, INCLUDING: Dag H Yasui Maria Antonietta Mencarelli University of California, Davis Azienda Ospedaliera Universitaria Senese 30 PUBLICATIONS 1,674 CITATIONS 58 PUBLICATIONS 962 CITATIONS SEE PROFILE SEE PROFILE Francesca Mari Janine M Lasalle Università degli Studi di Siena University of California, Davis 81 PUBLICATIONS 1,658 CITATIONS 98 PUBLICATIONS 3,525 CITATIONS SEE PROFILE SEE PROFILE Available from: Janine M Lasalle Retrieved on: 22 July 2015 Europe PMC Funders Group Author Manuscript J Hum Genet. Author manuscript; available in PMC 2012 January 01. Published in final edited form as: J Hum Genet. 2011 July ; 56(7): 508–515. doi:10.1038/jhg.2011.50. Europe PMC Funders Author Manuscripts Investigation of modifier genes within copy number variations in Rett syndrome Rosangela Artuso1,*, Filomena Tiziana Papa1,*, Elisa Grillo1, Mafalda Mucciolo1, Dag H. Yasui2, Keith W. Dunaway2, Vittoria Disciglio1, Maria Antonietta Mencarelli1, Marzia Pollazzon1, Michele Zappella3, Giuseppe Hayek4, Francesca Mari1, Alessandra Renieri1, Janine M. LaSalle2, and Francesca Ariani1 1 Medical Genetics Section, Biotechnology Department, University of Siena, Italy 2 Medical Microbiology and Immunology, Genome Center, School of Medicine, University of California, Davis, CA, USA 3 Child Neuropsychiatry, Versilia Hospital, Viareggio, Italy 4 Infantile Neuropsychiatry, Siena General Hospital, Italy Abstract MECP2 mutations are responsible for two different phenotypes in females, classical Rett syndrome and the milder Zappella variant (Z-RTT). -
Complement Factor H Deficiency and Endocapillary Glomerulonephritis Due to Paternal Isodisomy and a Novel Factor H Mutation
Genes and Immunity (2011) 12, 90–99 & 2011 Macmillan Publishers Limited All rights reserved 1466-4879/11 www.nature.com/gene ORIGINAL ARTICLE Complement factor H deficiency and endocapillary glomerulonephritis due to paternal isodisomy and a novel factor H mutation L Schejbel1, IM Schmidt2, M Kirchhoff3, CB Andersen4, HV Marquart1, P Zipfel5 and P Garred1 1Department of Clinical Immunology, Laboratory of Molecular Medicine, Rigshospitalet, Copenhagen, Denmark; 2Department of Pediatrics, Rigshospitalet, Copenhagen, Denmark; 3Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark; 4Department of Pathology, Rigshospitalet, Copenhagen, Denmark and 5Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany Complement factor H (CFH) is a regulator of the alternative complement activation pathway. Mutations in the CFH gene are associated with atypical hemolytic uremic syndrome, membranoproliferative glomerulonephritis type II and C3 glomerulonephritis. Here, we report a 6-month-old CFH-deficient child presenting with endocapillary glomerulonephritis rather than membranoproliferative glomerulonephritis (MPGN) or C3 glomerulonephritis. Sequence analyses showed homozygosity for a novel CFH missense mutation (Pro139Ser) associated with severely decreased CFH plasma concentration (o6%) but normal mRNA splicing and expression. The father was heterozygous carrier of the mutation, but the mother was a non-carrier. Thus, a large deletion in the maternal CFH locus or uniparental isodisomy was suspected. Polymorphic markers across chromosome 1 showed homozygosity for the paternal allele in all markers and a lack of the maternal allele in six informative markers. This combined with a comparative genomic hybridization assay demonstrated paternal isodisomy. Uniparental isodisomy increases the risk of homozygous variations in other genes on the affected chromosome. -
Zbtb16 Regulates Social Cognitive Behaviors and Neocortical
Usui et al. Translational Psychiatry (2021) 11:242 https://doi.org/10.1038/s41398-021-01358-y Translational Psychiatry ARTICLE Open Access Zbtb16 regulates social cognitive behaviors and neocortical development Noriyoshi Usui 1,2,3,4, Stefano Berto5,AmiKonishi1, Makoto Kondo1,4, Genevieve Konopka5,HideoMatsuzaki 2,6,7 and Shoichi Shimada1,2,4 Abstract Zinc finger and BTB domain containing 16 (ZBTB16) play the roles in the neural progenitor cell proliferation and neuronal differentiation during development, however, how the function of ZBTB16 is involved in brain function and behaviors unknown. Here we show the deletion of Zbtb16 in mice leads to social impairment, repetitive behaviors, risk- taking behaviors, and cognitive impairment. To elucidate the mechanism underlying the behavioral phenotypes, we conducted histological analyses and observed impairments in thinning of neocortical layer 6 (L6) and a reduction of TBR1+ neurons in Zbtb16 KO mice. Furthermore, we found increased dendritic spines and microglia, as well as developmental defects in oligodendrocytes and neocortical myelination in the prefrontal cortex (PFC) of Zbtb16 KO mice. Using genomics approaches, we identified the Zbtb16 transcriptome that includes genes involved in neocortical maturation such as neurogenesis and myelination, and both autism spectrum disorder (ASD) and schizophrenia (SCZ) pathobiology. Co-expression networks further identified Zbtb16-correlated modules that are unique to ASD or SCZ, respectively. Our study provides insight into the novel roles of ZBTB16 in behaviors and neocortical development related to the disorders. 1234567890():,; 1234567890():,; 1234567890():,; 1234567890():,; Introduction identified as a causative mutation for skeletal defects, ZBTB16 (PLZF) encodes a transcription factor, which genital hypoplasia, and mental retardation (SGYMR)6,7. -
Identification of Potential Key Genes and Pathway Linked with Sporadic Creutzfeldt-Jakob Disease Based on Integrated Bioinformatics Analyses
medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Identification of potential key genes and pathway linked with sporadic Creutzfeldt-Jakob disease based on integrated bioinformatics analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 , Iranna Kotturshetti 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. 3. Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, Karnataka 562209, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Abstract Sporadic Creutzfeldt-Jakob disease (sCJD) is neurodegenerative disease also called prion disease linked with poor prognosis. The aim of the current study was to illuminate the underlying molecular mechanisms of sCJD. The mRNA microarray dataset GSE124571 was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened. -
Gene Expression Responses to DNA Damage Are Altered in Human Aging and in Werner Syndrome
Oncogene (2005) 24, 5026–5042 & 2005 Nature Publishing Group All rights reserved 0950-9232/05 $30.00 www.nature.com/onc Gene expression responses to DNA damage are altered in human aging and in Werner Syndrome Kasper J Kyng1,2, Alfred May1, Tinna Stevnsner2, Kevin G Becker3, Steen Klvra˚ 4 and Vilhelm A Bohr*,1 1Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, 5600 Nathan Shock Drive, Baltimore, MD 21224, USA; 2Danish Center for Molecular Gerontology, Department of Molecular Biology, University of Aarhus, DK-8000 Aarhus C, Denmark; 3Gene Expression and Genomics Unit, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA; 4Institute for Human Genetics, University of Aarhus, Denmark The accumulation of DNA damage and mutations is syndromes, caused by heritable mutations inactivating considered a major cause of cancer and aging. While it is proteins that sense or repair DNA damage, which known that DNA damage can affect changes in gene accelerate some but not all signs of normal aging (Hasty expression, transcriptional regulation after DNA damage et al., 2003). Age is associated withan increase in is poorly understood. We characterized the expression of susceptibility to various forms of stress, and sporadic 6912 genes in human primary fibroblasts after exposure to reports suggest that an age-related decrease in DNA three different kinds of cellular stress that introduces repair may increase the susceptibility of cells to agents DNA damage: 4-nitroquinoline-1-oxide (4NQO), c-irra- causing DNA damage. Reduced base excision repair has diation, or UV-irradiation. Each type of stress elicited been demonstrated in nuclear extracts from aged human damage specific gene expression changes of up to 10-fold. -
Experimental Eye Research 129 (2014) 93E106
Experimental Eye Research 129 (2014) 93e106 Contents lists available at ScienceDirect Experimental Eye Research journal homepage: www.elsevier.com/locate/yexer Transcriptomic analysis across nasal, temporal, and macular regions of human neural retina and RPE/choroid by RNA-Seq S. Scott Whitmore a, b, Alex H. Wagner a, c, Adam P. DeLuca a, b, Arlene V. Drack a, b, Edwin M. Stone a, b, Budd A. Tucker a, b, Shemin Zeng a, b, Terry A. Braun a, b, c, * Robert F. Mullins a, b, Todd E. Scheetz a, b, c, a Stephen A. Wynn Institute for Vision Research, The University of Iowa, Iowa City, IA, USA b Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, IA, USA c Department of Biomedical Engineering, College of Engineering, The University of Iowa, Iowa City, IA, USA article info abstract Article history: Proper spatial differentiation of retinal cell types is necessary for normal human vision. Many retinal Received 14 September 2014 diseases, such as Best disease and male germ cell associated kinase (MAK)-associated retinitis pigmen- Received in revised form tosa, preferentially affect distinct topographic regions of the retina. While much is known about the 31 October 2014 distribution of cell types in the retina, the distribution of molecular components across the posterior pole Accepted in revised form 4 November 2014 of the eye has not been well-studied. To investigate regional difference in molecular composition of Available online 5 November 2014 ocular tissues, we assessed differential gene expression across the temporal, macular, and nasal retina and retinal pigment epithelium (RPE)/choroid of human eyes using RNA-Seq. -
Mai Muudatuntuu Ti on Man Mini
MAIMUUDATUNTUU US009809854B2 TI ON MAN MINI (12 ) United States Patent ( 10 ) Patent No. : US 9 ,809 ,854 B2 Crow et al. (45 ) Date of Patent : Nov . 7 , 2017 Whitehead et al. (2005 ) Variation in tissue - specific gene expression ( 54 ) BIOMARKERS FOR DISEASE ACTIVITY among natural populations. Genome Biology, 6 :R13 . * AND CLINICAL MANIFESTATIONS Villanueva et al. ( 2011 ) Netting Neutrophils Induce Endothelial SYSTEMIC LUPUS ERYTHEMATOSUS Damage , Infiltrate Tissues, and Expose Immunostimulatory Mol ecules in Systemic Lupus Erythematosus . The Journal of Immunol @(71 ) Applicant: NEW YORK SOCIETY FOR THE ogy , 187 : 538 - 552 . * RUPTURED AND CRIPPLED Bijl et al. (2001 ) Fas expression on peripheral blood lymphocytes in MAINTAINING THE HOSPITAL , systemic lupus erythematosus ( SLE ) : relation to lymphocyte acti vation and disease activity . Lupus, 10 :866 - 872 . * New York , NY (US ) Crow et al . (2003 ) Microarray analysis of gene expression in lupus. Arthritis Research and Therapy , 5 :279 - 287 . * @(72 ) Inventors : Mary K . Crow , New York , NY (US ) ; Baechler et al . ( 2003 ) Interferon - inducible gene expression signa Mikhail Olferiev , Mount Kisco , NY ture in peripheral blood cells of patients with severe lupus . PNAS , (US ) 100 ( 5 ) : 2610 - 2615. * GeneCards database entry for IFIT3 ( obtained from < http : / /www . ( 73 ) Assignee : NEW YORK SOCIETY FOR THE genecards. org /cgi - bin / carddisp .pl ? gene = IFIT3 > on May 26 , 2016 , RUPTURED AND CRIPPLED 15 pages ) . * Navarra et al. (2011 ) Efficacy and safety of belimumab in patients MAINTAINING THE HOSPITAL with active systemic lupus erythematosus : a randomised , placebo FOR SPECIAL SURGERY , New controlled , phase 3 trial . The Lancet , 377 :721 - 731. * York , NY (US ) Abramson et al . ( 1983 ) Arthritis Rheum . -
Mouse Rit2 Knockout Project (CRISPR/Cas9)
https://www.alphaknockout.com Mouse Rit2 Knockout Project (CRISPR/Cas9) Objective: To create a Rit2 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Rit2 gene (NCBI Reference Sequence: NM_009065 ; Ensembl: ENSMUSG00000057455 ) is located on Mouse chromosome 18. 5 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 5 (Transcript: ENSMUST00000153060). Exon 3 will be selected as target site. Cas9 and gRNA will be co-injected into fertilized eggs for KO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Exon 3 starts from about 24.73% of the coding region. Exon 3 covers 11.37% of the coding region. The size of effective KO region: ~74 bp. The KO region does not have any other known gene. Page 1 of 8 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 3 5 Legends Exon of mouse Rit2 Knockout region Page 2 of 8 https://www.alphaknockout.com Overview of the Dot Plot (up) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section upstream of Exon 3 is aligned with itself to determine if there are tandem repeats. No significant tandem repeat is found in the dot plot matrix. So this region is suitable for PCR screening or sequencing analysis. Overview of the Dot Plot (down) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section downstream of Exon 3 is aligned with itself to determine if there are tandem repeats. -
A Hybrid CFHR3-1 Gene Causes Familial C3 Glomerulopathy
BRIEF COMMUNICATION www.jasn.org A Hybrid CFHR3-1 Gene Causes Familial C3 Glomerulopathy †‡ Talat H. Malik,* Peter J. Lavin, Elena Goicoechea de Jorge,* Katherine A. Vernon,* | Kirsten L. Rose,* Mitali P. Patel,* Marcel de Leeuw,§ John J. Neary, Peter J. Conlon,¶ † Michelle P. Winn, and Matthew C. Pickering* *Centre for Complement and Inflammation Research, Imperial College, London, United Kingdom; †Department of Medicine, Duke University Medical Center, Durham, North Carolina; ‡Trinity Health Kidney Centre, Tallaght Hospital, Trinity College, Dublin, Ireland; §Beckman Coulter Genomics, Grenoble, France; |Department of Renal Medicine, Royal Infirmary Edinburgh, Edinburgh, United Kingdom; and ¶Department of Nephrology, Beaumont Hospital, Dublin, Ireland ABSTRACT Controlled activation of the complement system, a key component of innate immunity, that CFHR1 and CFHR3 impair comple- enables destruction of pathogens with minimal damage to host tissue. Complement ment processing within the kidney. This factor H (CFH), which inhibits complement activation, and five CFH-related proteins hypothesis would predict that an increase (CFHR1–5) compose a family of structurally related molecules. Combined deletion of in CFHR1 and CFHR3 copy number would CFHR3 and CFHR1 is common and confers a protective effect in IgA nephropathy. Here, enhance susceptibility to complement- we report an autosomal dominant complement-mediated GN associated with abnormal mediated kidney injury. Here, we report increases in copy number across the CFHR3 and CFHR1 loci. In addition to normal a novel CFHR3–1 hybrid gene located on copies of these genes, affected individuals carry a unique hybrid CFHR3–1 gene. an allele that also contained intact copies In addition to identifying an association between these genetic observations and of the CFHR1 and CFHR3 genes. -
Differential Gene Expression Profile of Human Neutrophils Cultured with Plasmodium Falciparum-Parasitized Title Erythrocytes
Differential Gene Expression Profile of Human Neutrophils Cultured with Plasmodium falciparum-Parasitized Title Erythrocytes Author(s) Terkawi, Mohamad Alaa; Takano, Ryo; Kato, Kentaro Journal of immunology research, 2018, 6709424 Citation https://doi.org/10.1155/2018/6709424 Issue Date 2018-07-05 Doc URL http://hdl.handle.net/2115/71366 Rights(URL) http://creativecommons.org/licenses/by/4.0/ Type article File Information 6709424.pdf Instructions for use Hokkaido University Collection of Scholarly and Academic Papers : HUSCAP Hindawi Journal of Immunology Research Volume 2018, Article ID 6709424, 8 pages https://doi.org/10.1155/2018/6709424 Research Article Differential Gene Expression Profile of Human Neutrophils Cultured with Plasmodium falciparum-Parasitized Erythrocytes 1,2 1 1,3 Mohamad Alaa Terkawi, Ryo Takano, and Kentaro Kato 1National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro, Hokkaido 080-8555, Japan 2Department of Orthopedic Surgery, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Kita-15, Nish-7, Kita-ku, Sapporo 060-8638, Japan 3Research Center for Global Agromedicine, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro, Hokkaido 080-8555, Japan Correspondence should be addressed to Kentaro Kato; [email protected] Received 31 January 2018; Revised 8 May 2018; Accepted 15 May 2018; Published 5 July 2018 Academic Editor: Baohui Xu Copyright © 2018 Mohamad Alaa Terkawi et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Neutrophils (PMNs) are the most abundant cellular component of our innate immune system, where they play central roles in the pathogenesis of and resistance to a broad range of diseases.