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Bartholomäus A, Kolte B, Mustafayeva A, Goebel I, Fuchs S, Benndorf D, Engelmann S, Ignatova Z. smORFer: a modular algorithm to detect small ORFs in prokaryotes. Nucleic Acids Res 2021; 49:e89. [PMID: 34125903 PMCID: PMC8421149 DOI: 10.1093/nar/gkab477] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 04/29/2021] [Accepted: 05/18/2021] [Indexed: 11/15/2022] Open
Abstract
Emerging evidence places small proteins (≤50 amino acids) more centrally in physiological processes. Yet, their functional identification and the systematic genome annotation of their cognate small open-reading frames (smORFs) remains challenging both experimentally and computationally. Ribosome profiling or Ribo-Seq (that is a deep sequencing of ribosome-protected fragments) enables detecting of actively translated open-reading frames (ORFs) and empirical annotation of coding sequences (CDSs) using the in-register translation pattern that is characteristic for genuinely translating ribosomes. Multiple identifiers of ORFs that use the 3-nt periodicity in Ribo-Seq data sets have been successful in eukaryotic smORF annotation. They have difficulties evaluating prokaryotic genomes due to the unique architecture (e.g. polycistronic messages, overlapping ORFs, leaderless translation, non-canonical initiation etc.). Here, we present a new algorithm, smORFer, which performs with high accuracy in prokaryotic organisms in detecting putative smORFs. The unique feature of smORFer is that it uses an integrated approach and considers structural features of the genetic sequence along with in-frame translation and uses Fourier transform to convert these parameters into a measurable score to faithfully select smORFs. The algorithm is executed in a modular way, and dependent on the data available for a particular organism, different modules can be selected for smORF search.
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Affiliation(s)
- Alexander Bartholomäus
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany.,Inst. Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | - Baban Kolte
- Inst. Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | - Ayten Mustafayeva
- Helmholtz Center for Infection Research, Microbial Proteomics, 38124 Braunschweig, Germany.,Inst. Microbiology, TU Braunschweig, Braunschweig, Germany
| | - Ingrid Goebel
- Inst. Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | | | - Dirk Benndorf
- Otto von Guericke University, Bioprocess Engineering, 39106 Magdeburg, Germany.,Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, 39106 Magdeburg, Germany
| | - Susanne Engelmann
- Helmholtz Center for Infection Research, Microbial Proteomics, 38124 Braunschweig, Germany.,Inst. Microbiology, TU Braunschweig, Braunschweig, Germany
| | - Zoya Ignatova
- Inst. Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
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2
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Czech A, Konarev PV, Goebel I, Svergun DI, Wills PR, Ignatova Z. Author Correction: Octa-repeat domain of the mammalian prion protein mRNA forms stable A-helical hairpin structure rather than G-quadruplexes. Sci Rep 2020; 10:4378. [PMID: 32127648 PMCID: PMC7054425 DOI: 10.1038/s41598-020-61336-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Andreas Czech
- Institute of Biochemistry and Molecular Biology University of Hamburg, Hamburg, Germany.
| | - Petr V Konarev
- A. V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russia.,National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Ingrid Goebel
- Institute of Biochemistry and Molecular Biology University of Hamburg, Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Hamburg, Germany
| | - Peter R Wills
- Department of Physics, University of Auckland, Auckland, New Zealand
| | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology University of Hamburg, Hamburg, Germany
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3
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Czech A, Konarev PV, Goebel I, Svergun DI, Wills PR, Ignatova Z. Octa-repeat domain of the mammalian prion protein mRNA forms stable A-helical hairpin structure rather than G-quadruplexes. Sci Rep 2019; 9:2465. [PMID: 30792490 PMCID: PMC6384910 DOI: 10.1038/s41598-019-39213-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 12/19/2018] [Indexed: 12/22/2022] Open
Abstract
Misfolding and aggregation of prion protein (PrP) causes neurodegenerative diseases like Creutzfeldt-Jakob disease (CJD) and scrapie. Besides the consensus that spontaneous conversion of normal cellular PrPC into misfolded and aggregating PrPSc is the central event in prion disease, an alternative hypothesis suggests the generation of pathological PrPSc by rare translational frameshifting events in the octa-repeat domain of the PrP mRNA. Ribosomal frameshifting most commonly relies on a slippery site and an adjacent stable RNA structure to stall translating ribosome. Hence, it is crucial to unravel the secondary structure of the octa-repeat domain of PrP mRNA. Each of the five octa-repeats contains a motif (GGCGGUGGUGGCUGGG) which alone in vitro forms a G-quadruplex. Since the propensity of mRNA to form secondary structure depends on the sequence context, we set to determine the structure of the complete octa-repeat region. We assessed the structure of full-length octa-repeat domain of PrP mRNA using dynamic light scattering (DLS), small angle X-ray scattering (SAXS), circular dichroism (CD) spectroscopy and selective 2'-hydroxyl acylation analysis by primer extension (SHAPE). Our data show that the PrP octa-repeat mRNA forms stable A-helical hairpins with no evidence of G-quadruplex structure even in the presence of G-quadruplex stabilizing agents.
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Affiliation(s)
- Andreas Czech
- Institute of Biochemistry and Molecular Biology University of Hamburg, Hamburg, Germany.
| | - Petr V Konarev
- A. V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russia
- National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Ingrid Goebel
- Institute of Biochemistry and Molecular Biology University of Hamburg, Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Hamburg, Germany
| | - Peter R Wills
- Department of Physics, University of Auckland, Auckland, New Zealand
| | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology University of Hamburg, Hamburg, Germany
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4
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Anders M, Chelysheva I, Goebel I, Trenkner T, Zhou J, Mao Y, Verzini S, Qian SB, Ignatova Z. Dynamic m 6A methylation facilitates mRNA triaging to stress granules. Life Sci Alliance 2018; 1:e201800113. [PMID: 30456371 PMCID: PMC6238392 DOI: 10.26508/lsa.201800113] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 06/25/2018] [Accepted: 06/26/2018] [Indexed: 12/21/2022] Open
Abstract
Reversible post-transcriptional modifications on messenger RNA emerge as prevalent phenomena in RNA metabolism. The most abundant among them is N6-methyladenosine (m6A) which is pivotal for RNA metabolism and function; its role in stress response remains elusive. We have discovered that in response to oxidative stress, transcripts are additionally m6A modified in their 5' vicinity. Distinct from that of the translationally active mRNAs, this methylation pattern provides a selective mechanism for triaging mRNAs from the translatable pool to stress-induced stress granules. These stress-induced newly methylated sites are selectively recognized by the YTH domain family 3 (YTHDF3) "reader" protein, thereby revealing a new role for YTHDF3 in shaping the selectivity of stress response. Our findings describe a previously unappreciated function for RNA m6A modification in oxidative-stress response and expand the breadth of physiological roles of m6A.
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Affiliation(s)
- Maximilian Anders
- Institute for Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, Hamburg, Germany
| | - Irina Chelysheva
- Institute for Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, Hamburg, Germany
| | - Ingrid Goebel
- Institute for Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, Hamburg, Germany
| | - Timo Trenkner
- Institute for Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, Hamburg, Germany
| | - Jun Zhou
- Division of Nutritional Science, Cornell University, Ithaca, NY, USA
| | - Yuanhui Mao
- Division of Nutritional Science, Cornell University, Ithaca, NY, USA
| | - Silvia Verzini
- Institute for Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, Hamburg, Germany
| | - Shu-Bing Qian
- Division of Nutritional Science, Cornell University, Ithaca, NY, USA
| | - Zoya Ignatova
- Institute for Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, Hamburg, Germany
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5
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Lessel D, Wu D, Trujillo C, Ramezani T, Lessel I, Alwasiyah MK, Saha B, Hisama FM, Rading K, Goebel I, Schütz P, Speit G, Högel J, Thiele H, Nürnberg G, Nürnberg P, Hammerschmidt M, Zhu Y, Tong DR, Katz C, Martin GM, Oshima J, Prives C, Kubisch C. Dysfunction of the MDM2/p53 axis is linked to premature aging. J Clin Invest 2017; 127:3598-3608. [PMID: 28846075 DOI: 10.1172/jci92171] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 07/14/2017] [Indexed: 12/20/2022] Open
Abstract
The tumor suppressor p53, a master regulator of the cellular response to stress, is tightly regulated by the E3 ubiquitin ligase MDM2 via an autoregulatory feedback loop. In addition to its well-established role in tumorigenesis, p53 has also been associated with aging in mice. Several mouse models with aberrantly increased p53 activity display signs of premature aging. However, the relationship between dysfunction of the MDM2/p53 axis and human aging remains elusive. Here, we have identified an antiterminating homozygous germline mutation in MDM2 in a patient affected by a segmental progeroid syndrome. We show that this mutation abrogates MDM2 activity, thereby resulting in enhanced levels and stability of p53. Analysis of the patient's primary cells, genome-edited cells, and in vitro and in vivo analyses confirmed the MDM2 mutation's aberrant regulation of p53 activity. Functional data from a zebrafish model further demonstrated that mutant Mdm2 was unable to rescue a p53-induced apoptotic phenotype. Altogether, our findings indicate that mutant MDM2 is a likely driver of the observed segmental form of progeria.
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Affiliation(s)
- Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Danyi Wu
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Carlos Trujillo
- Genetics Unit, Dr. Erfan & Bagedo Hospital, Jeddah, Saudi Arabia
| | - Thomas Ramezani
- Institute of Developmental Biology, University of Cologne, Cologne, Germany
| | - Ivana Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mohammad K Alwasiyah
- Aziziah Maternity and Children's Hospital, Ministry of Health, Jeddah, Saudi Arabia
| | - Bidisha Saha
- Department of Pathology, University of Washington, Seattle, Washington, USA
| | - Fuki M Hisama
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Katrin Rading
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ingrid Goebel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Petra Schütz
- Institute of Human Genetics, University of Ulm, Ulm, Germany
| | - Günter Speit
- Institute of Human Genetics, University of Ulm, Ulm, Germany
| | - Josef Högel
- Institute of Human Genetics, University of Ulm, Ulm, Germany
| | | | | | - Peter Nürnberg
- Cologne Center for Genomics.,Center for Molecular Medicine Cologne, and.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Matthias Hammerschmidt
- Institute of Developmental Biology, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, and.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Yan Zhu
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - David R Tong
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Chen Katz
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - George M Martin
- Department of Pathology, University of Washington, Seattle, Washington, USA.,Molecular Biology Institute, UCLA, Los Angeles, California, USA
| | - Junko Oshima
- Department of Pathology, University of Washington, Seattle, Washington, USA.,Department of Medicine, Chiba University, Chiba, Japan
| | - Carol Prives
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Christian Kubisch
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Institute of Human Genetics, University of Ulm, Ulm, Germany
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6
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Lang-Roth R, Fischer-Krall E, Kornblum C, Nürnberg G, Meschede D, Goebel I, Nürnberg P, Beutner D, Kubisch C, Walger M, Volk AE. AUNA2: A Novel Type of Non-Syndromic Slowly Progressive Auditory Synaptopathy/Auditory Neuropathy with Autosomal-Dominant Inheritance. Audiol Neurootol 2017; 22:30-40. [PMID: 28601886 DOI: 10.1159/000474929] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 03/31/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Auditory synaptopathy/neuropathy (AS/AN) is a heterogeneous disorder, which may be caused by environmental factors like postnatal hyperbilirubinemia or by genetic factors. The genetic forms are subdivided into syndromic and non-syndromic types, and show different inheritance patterns with a strong preponderance of autosomal-recessive forms. To date, only a single locus for non-syndromic autosomal-dominant AS/AN (AUNA1) has been reported in a single family, in which a non-coding DIAPH3 mutation was subsequently described as causative. MATERIALS AND METHODS Here, we report detailed clinical data on a large German AS/AN family with slowly progressive postlingual hearing loss. Affected family members developed their first symptoms in their second decade. Moderate hearing loss in the fourth decade then progressed to profound hearing impairment in older family members. Comprehensive audiological and neurological tests were performed in the affected family members. Genetic testing comprised linkage analyses with polymorphic markers and a genome-wide linkage analysis using the Affymetrix GeneChip® Human Mapping 250K. RESULTS AND CONCLUSION We identified a large family with autosomal-dominant AS/AN. By means of linkage analyses, the AUNA1 locus was excluded, and putatively linked regions on chromosomal bands 12q24 and 13q34 were identified as likely carrying the second locus for autosomal-dominant AS/AN (AUNA2). AUNA2 is associated with a slowly progressive postlingual hearing loss without any evidence for additional symptoms in other organ systems.
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Affiliation(s)
- Ruth Lang-Roth
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Cologne, Cologne, Germany
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7
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Daud S, Kakar N, Goebel I, Hashmi AS, Yaqub T, Nürnberg G, Nürnberg P, Morris-Rosendahl DJ, Wasim M, Volk AE, Kubisch C, Ahmad J, Borck G. Identification of two novel ALS2 mutations in infantile-onset ascending hereditary spastic paraplegia. Amyotroph Lateral Scler Frontotemporal Degener 2016; 17:260-5. [PMID: 26751646 DOI: 10.3109/21678421.2015.1125501] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Biallelic mutations of ALS2 cause a clinical spectrum of overlapping autosomal recessive neurodegenerative disorders: infantile-onset ascending hereditary spastic paralysis (IAHSP), juvenile primary lateral sclerosis (JPLS), and juvenile amyotrophic lateral sclerosis (ALS2). We report on eleven individuals affected with IAHSP from two consanguineous Pakistani families. A combination of linkage analysis with homozygosity mapping and targeted sequencing identified two novel ALS2 mutations, a c.194T > C (p.Phe65Ser) missense substitution located in the first RCC-like domain of ALS2/alsin and a c.2998delA (p.Ile1000*) nonsense mutation. This study of extended families including a total of eleven affected individuals suggests that a given ALS2 mutation may lead to a phenotype with remarkable intrafamilial clinical homogeneity.
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Affiliation(s)
- Shakeela Daud
- a Institute of Biochemistry and Biotechnology (IBBt), UVAS , Lahore , Pakistan
| | - Naseebullah Kakar
- b Institute of Human Genetics, University of Ulm , Ulm , Germany .,c International Graduate School in Molecular Medicine Ulm, University of Ulm , Ulm , Germany .,d Department of Biotechnology and Informatics , BUITEMS , Quetta , Pakistan
| | - Ingrid Goebel
- b Institute of Human Genetics, University of Ulm , Ulm , Germany .,e Institute of Human Genetics, University Medical Center Hamburg-Eppendorf , Hamburg , Germany
| | - Abu Saeed Hashmi
- a Institute of Biochemistry and Biotechnology (IBBt), UVAS , Lahore , Pakistan
| | - Tahir Yaqub
- a Institute of Biochemistry and Biotechnology (IBBt), UVAS , Lahore , Pakistan .,f Department of Microbiology , UVAS , Lahore , Pakistan
| | - Gudrun Nürnberg
- g Cologne Center for Genomics (CCG), University of Cologne , Cologne , Germany
| | - Peter Nürnberg
- g Cologne Center for Genomics (CCG), University of Cologne , Cologne , Germany .,h Center for Molecular Medicine Cologne (CMMC), University of Cologne , Cologne , Germany .,i Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne , Cologne , Germany
| | - Deborah J Morris-Rosendahl
- j Clinical Genetics and Genomics, Royal Brompton Hospital , London , United Kingdom .,k National Heart and Lung Institute, Imperial College London , London , United Kingdom
| | - Muhammad Wasim
- a Institute of Biochemistry and Biotechnology (IBBt), UVAS , Lahore , Pakistan
| | - Alexander E Volk
- b Institute of Human Genetics, University of Ulm , Ulm , Germany .,e Institute of Human Genetics, University Medical Center Hamburg-Eppendorf , Hamburg , Germany
| | - Christian Kubisch
- b Institute of Human Genetics, University of Ulm , Ulm , Germany .,e Institute of Human Genetics, University Medical Center Hamburg-Eppendorf , Hamburg , Germany
| | - Jamil Ahmad
- d Department of Biotechnology and Informatics , BUITEMS , Quetta , Pakistan
| | - Guntram Borck
- b Institute of Human Genetics, University of Ulm , Ulm , Germany
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8
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Hübers A, Just W, Rosenbohm A, Müller K, Marroquin N, Goebel I, Högel J, Thiele H, Altmüller J, Nürnberg P, Weishaupt JH, Kubisch C, Ludolph AC, Volk AE. De novo FUS mutations are the most frequent genetic cause in early-onset German ALS patients. Neurobiol Aging 2015; 36:3117.e1-3117.e6. [PMID: 26362943 DOI: 10.1016/j.neurobiolaging.2015.08.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 07/15/2015] [Accepted: 08/08/2015] [Indexed: 01/27/2023]
Abstract
In amyotrophic lateral sclerosis (ALS) patients with known genetic cause, mutations in chromosome 9 open reading frame 72 (C9orf72) and superoxide dismutase 1 (SOD1) account for most familial and late-onset sporadic cases, whereas mutations in fused in sarcoma (FUS) can be identified in just around 5% of familial and 1% of overall sporadic cases. There are only few reports on de novo FUS mutations in juvenile ALS patients. To date, no systematic evaluation on the frequency of de novo FUS mutations in early-onset ALS patients has been conducted. Here, we screened a cohort of 14 early-onset sporadic ALS patients (onset age <35 years) to determine the frequency of mutations in C9orf72, SOD1, and FUS in this defined patient cohort. All patients were recruited prospectively by a single center in a period of 38 months. No mutations were detected in SOD1 or C9orf72; however, we identified 6 individuals (43%) carrying a heterozygous FUS mutation including 1 mutation that has not been described earlier (c.1504delG [p.Asp502Thrfs*27]). Genetic testing of parents was possible in 5 families and revealed that the mutations in these patients arose de novo. Three of the 6 identified patients presented with initial bulbar symptoms. Our study identifies FUS mutations as the most frequent genetic cause in early-onset ALS. Genetic testing of FUS thus seems indicated in sporadic early-onset ALS patients especially if showing predominant bulbar symptoms and an aggressive disease course.
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Affiliation(s)
- Annemarie Hübers
- Department of Neurology, University Hospital of Ulm, Ulm, Germany.
| | - Walter Just
- Institute of Human Genetics, University of Ulm, Ulm, Germany
| | - Angela Rosenbohm
- Department of Neurology, University Hospital of Ulm, Ulm, Germany
| | - Kathrin Müller
- Department of Neurology, University Hospital of Ulm, Ulm, Germany
| | | | - Ingrid Goebel
- Institute of Human Genetics, University of Ulm, Ulm, Germany; Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Josef Högel
- Institute of Human Genetics, University of Ulm, Ulm, Germany
| | - Holger Thiele
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany; Institute of Human Genetics, University of Cologne, Cologne, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | | | - Christian Kubisch
- Institute of Human Genetics, University of Ulm, Ulm, Germany; Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Albert C Ludolph
- Department of Neurology, University Hospital of Ulm, Ulm, Germany
| | - Alexander E Volk
- Institute of Human Genetics, University of Ulm, Ulm, Germany; Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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9
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Fischer AG, Endrass T, Goebel I, Reuter M, Montag C, Kubisch C, Ullsperger M. Interactive effects of citalopram and serotonin transporter genotype on neural correlates of response inhibition and attentional orienting. Neuroimage 2015; 116:59-67. [PMID: 25957993 DOI: 10.1016/j.neuroimage.2015.04.064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 03/25/2015] [Accepted: 04/28/2015] [Indexed: 01/09/2023] Open
Abstract
The brain's serotonergic (5-HT) system has been implicated in controlling impulsive behavior and attentional orienting and linked to impulse control and anxiety related disorders. However, interactions between genotypical variation and responses to serotonergic drugs impede both treatment efficacy and neuroscientific research. We examine behavioral and electrophysiological responses to acute intravenous administration of a selective serotonin reuptake inhibitor (SSRI) while controlling for major genetic differences regarding 5-HT transporter (5-HTT) genotypes. Out of a genotyped sample of healthy Caucasian subjects (n=878) two extreme-groups regarding 5-HTT genotypes were selected (n=32). A homozygous high-expressing group based on tri-allelic 5-HTTLPR and rs25532 (LAC/LAC=LL) was compared to homozygous S allele carriers (SS). Both groups were administered a low dose of citalopram (10mg) intravenously in a double blind crossover fashion and performed a novelty NoGo paradigm while high density EEG was recorded. Interactions between drug and genotype were seen on both behavioral and neurophysiological levels. Reaction slowing following inhibitory events was decreased by the administration of citalopram in the LL but not SS group. This was accompanied by decreases in the amplitude of the inhibitory N2 EEG component and the P3b in the LL group, which was not seen in the SS group. SS subjects showed an increase in P3a amplitudes following SSRI administration to any type of deviant stimulus possibly reflecting increased attentional capture. The acute SSRI response on inhibitory processes and attentional orienting interacts with genotypes regulating 5-HTT gene expression. SS subjects may show increased attentional side effects reflected in increases in P3a amplitudes which could contribute to treatment discontinuation. Inhibitory processes and their neural correlates are affected only in LL subjects. These findings may indicate an underlying mechanism that could relate genotypical differences to altered side effect profiles and drug responses and are compatible with a non-monotonic relationship between 5-HT levels and optimal functioning.
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Affiliation(s)
- Adrian G Fischer
- Otto-von-Guericke University, Institute of Psychology II, Magdeburg, Germany; Max Planck Institute for Neurological Research, Cologne, Germany.
| | - Tanja Endrass
- Otto-von-Guericke University, Institute of Psychology II, Magdeburg, Germany
| | - Ingrid Goebel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Reuter
- Department of Psychology, University of Bonn, Bonn, Germany
| | | | - Christian Kubisch
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Markus Ullsperger
- Otto-von-Guericke University, Institute of Psychology II, Magdeburg, Germany; Max Planck Institute for Neurological Research, Cologne, Germany; Radboud University, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, Netherlands; Center for Behavioral Brain Sciences, Magdeburg, Germany
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10
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Reiter R, Brosch S, Goebel I, Ludwig KU, Pickhard A, Högel J, Schlömer G, Mangold E, Kubisch C, Borck G. A post GWAS association study of SNPs associated with cleft lip with or without cleft palate in submucous cleft palate. Am J Med Genet A 2015; 167A:670-3. [DOI: 10.1002/ajmg.a.36891] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 10/30/2014] [Indexed: 12/19/2022]
Affiliation(s)
- Rudolf Reiter
- Section of Phoniatrics and Pedaudiology; Department of Otolaryngology - Head and Neck Surgery; University of Ulm; Ulm Germany
| | - Sibylle Brosch
- Section of Phoniatrics and Pedaudiology; Department of Otolaryngology - Head and Neck Surgery; University of Ulm; Ulm Germany
| | - Ingrid Goebel
- Institute of Human Genetics; University of Ulm; Ulm Germany
- Institute of Human Genetics; University Medical Center Hamburg-Eppendorf; Hamburg Germany
| | - Kerstin U. Ludwig
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Department of Genomics; Life and Brain Center; University of Bonn; Bonn Germany
| | - Anja Pickhard
- Department of Otolaryngology - Head and Neck Surgery; Technical University Munich; Munich Germany
| | - Josef Högel
- Institute of Human Genetics; University of Ulm; Ulm Germany
| | - Guido Schlömer
- Department of Cranio-Maxillo-Facial Surgery; University of Ulm; Ulm Germany
| | | | - Christian Kubisch
- Institute of Human Genetics; University of Ulm; Ulm Germany
- Institute of Human Genetics; University Medical Center Hamburg-Eppendorf; Hamburg Germany
| | - Guntram Borck
- Institute of Human Genetics; University of Ulm; Ulm Germany
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Kakar N, Goebel I, Daud S, Nürnberg G, Agha N, Ahmad A, Nürnberg P, Kubisch C, Ahmad J, Borck G. A homozygous splice site mutation in TRAPPC9 causes intellectual disability and microcephaly. Eur J Med Genet 2012; 55:727-31. [PMID: 22989526 DOI: 10.1016/j.ejmg.2012.08.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 08/21/2012] [Indexed: 10/27/2022]
Abstract
Autosomal recessive intellectual disability is believed to be particularly prevalent in highly consanguineous populations and genetic isolates and may account for a quarter of all non-syndromic cases. Mutations in more than 50 genes have been reported to be involved in autosomal recessive intellectual disability, including TRAPPC9 (MIM 611966), mutations of which have been identified in six families from different geographical origins. We performed a clinical and molecular genetic study of a consanguineous Pakistani family segregating intellectual disability and microcephaly. SNP-array-based homozygosity mapping revealed suggestive linkage to four genomic regions including one on chromosome 8 that contained TRAPPC9. We detected a homozygous TRAPPC9 splice donor site mutation (c.1024+1G>T) that cosegregated with intellectual disability in the family and led to skipping of exon 3 and exons 3 and 4 in blood-derived patient RNA. We have thus identified a novel splice site mutation leading to exon skipping and premature termination of TRAPPC9 translation. These data further suggest that TRAPPC9 mutations -unlike mutations in the vast majority of the known intellectual disability-associated genes- constitute a more frequent cause of autosomal-recessive cognitive deficits, especially when microcephaly is also present.
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Affiliation(s)
- Naseebullah Kakar
- Department of Biotechnology and Informatics, BUITEMS, Quetta, Pakistan
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12
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Anttila V, Stefansson H, Kallela M, Todt U, Terwindt GM, Calafato MS, Nyholt DR, Dimas AS, Freilinger T, Müller-Myhsok B, Artto V, Inouye M, Alakurtti K, Kaunisto MA, Hämäläinen E, de Vries B, Stam AH, Weller CM, Heinze A, Heinze-Kuhn K, Goebel I, Borck G, Göbel H, Steinberg S, Wolf C, Björnsson A, Gudmundsson G, Kirchmann M, Hauge A, Werge T, Schoenen J, Eriksson JG, Hagen K, Stovner L, Wichmann HE, Meitinger T, Alexander M, Moebus S, Schreiber S, Aulchenko YS, Breteler MMB, Uitterlinden AG, Hofman A, van Duijn CM, Tikka-Kleemola P, Vepsäläinen S, Lucae S, Tozzi F, Muglia P, Barrett J, Kaprio J, Färkkilä M, Peltonen L, Stefansson K, Zwart JA, Ferrari MD, Olesen J, Daly M, Wessman M, van den Maagdenberg AMJM, Dichgans M, Kubisch C, Dermitzakis ET, Frants RR, Palotie A. Genome-wide association study of migraine implicates a common susceptibility variant on 8q22.1. Nat Genet 2010; 42:869-73. [PMID: 20802479 PMCID: PMC2948563 DOI: 10.1038/ng.652] [Citation(s) in RCA: 273] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Accepted: 07/02/2010] [Indexed: 11/17/2022]
Abstract
Migraine is a common episodic neurological disorder, typically presenting with recurrent attacks of severe headache and autonomic dysfunction. Apart from rare monogenic subtypes, no genetic or molecular markers for migraine have been convincingly established. We identified the minor allele of rs1835740 on chromosome 8q22.1 to be associated with migraine (p=5.12 × 10−9, OR 1.23 [1.150-1.324]) in a genome-wide association study of 2,748 migraineurs from three European headache clinics and 10,747 population-matched controls. The association was replicated in 3,202 cases and 40,062 controls for an overall meta-analysis p-value of 1.60 × 10−11 (OR 1.18 [1.127 – 1.244]). rs1835740 is located between the astrocyte elevated gene 1 (MTDH/AEG-1) and plasma glutamate carboxypeptidase (PGCP). In an expression quantitative trait study in lymphoblastoid cell lines transcript levels of the MTDH/AEG-1 were found to have a significant correlation to rs1835740. Our data establish rs1835740 as the first genetic risk factor for migraine.
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Affiliation(s)
- Verneri Anttila
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK.
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Sajjad N, Goebel I, Kakar N, Cheema AM, Kubisch C, Ahmad J. A novel HSF4 gene mutation (p.R405X) causing autosomal recessive congenital cataracts in a large consanguineous family from Pakistan. BMC Med Genet 2008; 9:99. [PMID: 19014451 PMCID: PMC2592245 DOI: 10.1186/1471-2350-9-99] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2008] [Accepted: 11/11/2008] [Indexed: 11/10/2022]
Abstract
Background Hereditary cataracts are most frequently inherited as autosomal dominant traits, but can also be inherited in an autosomal recessive or X-linked fashion. To date, 12 loci for autosomal recessive cataracts have been mapped including a locus on chromosome 16q22 containing the disease-causing gene HSF4 (Genbank accession number NM_001040667). Here, we describe a family from Pakistan with the first nonsense mutation in HSF4 thus expanding the mutational spectrum of this heat shock transcription factor gene. Methods A large consanguineous Pakistani family with autosomal recessive cataracts was collected from Quetta. Genetic linkage analysis was performed for the common known autosomal recessive cataracts loci and linkage to a locus containing HSF4 (OMIM 602438) was found. All exons and adjacent splice sites of the heat shock transcription factor 4 gene (HSF4) were sequenced. A mutation-specific restriction enzyme digest (HphI) was performed for all family members and unrelated controls. Results The disease phenotype perfectly co-segregated with markers flanking the known cataract gene HSF4, whereas other autosomal recessive loci were excluded. A maximum two-point LOD score with a Zmax = 5.6 at θ = 0 was obtained for D16S421. Direct sequencing of HSF4 revealed the nucleotide exchange c.1213C > T in this family predicting an arginine to stop codon exchange (p.R405X). Conclusion We identified the first nonsense mutation (p.R405X) in exon 11 of HSF4 in a large consanguineous Pakistani family with autosomal recessive cataract.
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Affiliation(s)
- Naheed Sajjad
- Faculty of Biotechnology and Informatics, BUITEMS, Quetta, Pakistan.
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Netzer C, Freudenberg J, Toliat MR, Heinze A, Heinze-Kuhn K, Thiele H, Goebel I, Nürnberg P, Ptácek LJ, Göbel H, Todt U, Kubisch C. Genetic association studies of the chromosome 15 GABA-A receptor cluster in migraine with aura. Am J Med Genet B Neuropsychiatr Genet 2008; 147B:37-41. [PMID: 17680603 DOI: 10.1002/ajmg.b.30560] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Recently, a novel susceptibility locus for migraine with aura (MA) on chromosome 15q containing three GABA-A receptor subunits has been identified by linkage analysis in several large pedigrees. To further study the role of this locus in MA etiology we genotyped 56 SNPs capturing the known common haplotype variations of these three candidate genes in a sample comprising 270 MA patients and 273 matched controls. In a single marker analysis, four SNPs displayed nominally significant (P < 0.05) association with MA. However, after permutation-based correction for the number of tests performed, the P-values of these SNPs were non-significant. Furthermore, a replication study of two of these SNPs in a second independent sample of 379 MA patients and 379 controls did not result in a significant finding. We also compared haplotype estimates based on case-control genotypes. Again we could not demonstrate a significant association with the phenotype after correction for multiple testing. In summary, we found no convincing evidence for an involvement of common SNPs at the GABA-A receptor cluster on 15q11-q12 in the pathophysiology of MA.
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Affiliation(s)
- Christian Netzer
- Institute of Human Genetics, University of Cologne, Cologne, Germany
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Todt U, Freudenberg J, Goebel I, Heinze A, Heinze-Kuhn K, Rietschel M, Göbel H, Kubisch C. Variation of the serotonin transporter gene SLC6A4 in the susceptibility to migraine with aura. Neurology 2006; 67:1707-9. [PMID: 17101915 DOI: 10.1212/01.wnl.0000242883.96822.93] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
To replicate a reported association between migraine with aura (MA) and a promoter polymorphism in the serotonin transporter gene (SLC6A4), we performed a case-control study in a large German sample comprising 472 patients with MA and 506 controls. Neither this polymorphism nor a systematic analysis with single nucleotide polymorphisms capturing the main haplotype diversity of the SLC6A4 locus provided evidence for a contribution of SLC6A4 to the predisposition of complex inherited MA.
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Affiliation(s)
- U Todt
- Institute of Human Genetics, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
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Todt U, Freudenberg J, Goebel I, Netzer C, Heinze A, Heinze-Kuhn K, Göbel H, Kubisch C. MTHFR C677T polymorphism and migraine with aura. Ann Neurol 2006; 60:621-622. [PMID: 16800002 DOI: 10.1002/ana.20911] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Ramirez A, Heimbach A, Gründemann J, Stiller B, Hampshire D, Cid LP, Goebel I, Mubaidin AF, Wriekat AL, Roeper J, Al-Din A, Hillmer AM, Karsak M, Liss B, Woods CG, Behrens MI, Kubisch C. Hereditary parkinsonism with dementia is caused by mutations in ATP13A2, encoding a lysosomal type 5 P-type ATPase. Nat Genet 2006; 38:1184-91. [PMID: 16964263 DOI: 10.1038/ng1884] [Citation(s) in RCA: 826] [Impact Index Per Article: 45.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2006] [Accepted: 08/18/2006] [Indexed: 11/09/2022]
Abstract
Neurodegenerative disorders such as Parkinson and Alzheimer disease cause motor and cognitive dysfunction and belong to a heterogeneous group of common and disabling disorders. Although the complex molecular pathophysiology of neurodegeneration is largely unknown, major advances have been achieved by elucidating the genetic defects underlying mendelian forms of these diseases. This has led to the discovery of common pathophysiological pathways such as enhanced oxidative stress, protein misfolding and aggregation and dysfunction of the ubiquitin-proteasome system. Here, we describe loss-of-function mutations in a previously uncharacterized, predominantly neuronal P-type ATPase gene, ATP13A2, underlying an autosomal recessive form of early-onset parkinsonism with pyramidal degeneration and dementia (PARK9, Kufor-Rakeb syndrome). Whereas the wild-type protein was located in the lysosome of transiently transfected cells, the unstable truncated mutants were retained in the endoplasmic reticulum and degraded by the proteasome. Our findings link a class of proteins with unknown function and substrate specificity to the protein networks implicated in neurodegeneration and parkinsonism.
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Affiliation(s)
- Alfredo Ramirez
- Institute of Human Genetics, University of Cologne, 50931 Cologne, Germany
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Todt U, Dichgans M, Jurkat-Rott K, Heinze A, Zifarelli G, Koenderink JB, Goebel I, Zumbroich V, Stiller A, Ramirez A, Friedrich T, Göbel H, Kubisch C. Rare missense variants in ATP1A2 in families with clustering of common forms of migraine. Hum Mutat 2006; 26:315-21. [PMID: 16110494 DOI: 10.1002/humu.20229] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Migraine is a recurrent neurovascular disease. Its two most common forms-migraine without aura (MO) and migraine with aura (MA)-both show familial clustering and a complex pattern of inheritance. Familial hemiplegic migraine (FHM) is a rare monogenic subform caused by mutations in the calcium channel gene CACNA1A or the Na(+)/K(+)-ATPase gene ATP1A2. An involvement of FHM genes in the pathogenesis of common forms of migraine is not proven. We therefore systematically screened ATP1A2 in families with several members affected by MA and/or MO. We identified two novel missense alterations [c.520G>A (p.E174 K) and c.1544G>A (p.C515Y)] in two out of 45 families, which were not found in 520 control chromosomes. Functional studies of these variants in Xenopus oocytes by two-electrode voltage clamp measurements and radiochemical determination of ATPase activity showed that C515Y leads to a complete loss of function comparable with the effect of FHM-mutations whereas for E174 K no functional alteration could be found in the in vitro assays. In conclusion we propose that rare variants in ATP1A2 are involved in the susceptibility to common forms of migraine, because of 1) the absence of alterations in controls, 2) the particular pattern of segregation in both families, 3) the high conservation of mutated residues in Na(+)/K(+)-ATPases, 4) the functional effect of C515Y, and 5) the involvement of ATP1A2 in a monogenic form of migraine.
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Affiliation(s)
- Unda Todt
- Institut für Humangenetik, Universitätsklinikum Bonn, Bonn, Germany
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Netzer C, Todt U, Heinze A, Freudenberg J, Zumbroich V, Becker T, Goebel I, Ohlraun S, Goebel H, Kubisch C. Haplotype-based systematic association studies of ATP1A2 in migraine with aura. Am J Med Genet B Neuropsychiatr Genet 2006; 141B:257-60. [PMID: 16508935 DOI: 10.1002/ajmg.b.30283] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mutations in ATP1A2 cause familial hemiplegic migraine (FHM) type 2, a rare monogenic form of migraine with aura (MA). Moreover, rare ATP1A2 missense variants are found in familial clustering of common forms of migraine in single pedigrees. To determine whether also common ATP1A2 polymorphisms contribute to MA pathogenesis, we performed systematic case-control association studies in 284 MA cases and 241 control individuals. By direct sequencing of the 23 coding exons and adjacent intronic regions in 45 MA patients, 16 polymorphisms (12 SNPs, 3 small indels, 1 microsatellite marker) were identified. The sequencing results were used to estimate seven common ATP1A2 haplotypes (with a frequency >5%) covering about 97% of total haplotype diversity for this region. Subsequently, six haplotype-tagging SNPs/polymorphisms were genotyped in 95 individuals with a family history of MA, in 189 individuals with sporadic MA, and in a gender-matched control sample. A haplotype analysis was performed using the program FAMHAP. No significant differences in the ATP1A2 haplotype distribution could be detected between MA patients (or patient subgroups) and the control group. In a single-marker analysis the allele and genotype frequencies of ATP1A2 polymorphisms between cases and controls were compared. Neither the six ht-SNPs nor a single allele of the microsatellite marker were significantly associated with MA. In summary, we found no evidence for a common contribution of ATP1A2 to the pathogenesis of complex inherited MA.
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Affiliation(s)
- Christian Netzer
- Institute of Human Genetics, University of Cologne, Cologne, Germany
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Ramírez A, Faupel J, Goebel I, Stiller A, Beyer S, Stöckle C, Hasan C, Bode U, Kornak U, Kubisch C. Identification of a novel mutation in the coding region of the grey-lethal geneOSTM1in human malignant infantile osteopetrosis. Hum Mutat 2004; 23:471-6. [PMID: 15108279 DOI: 10.1002/humu.20028] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Autosomal recessive malignant infantile osteopetrosis (ARO) is characterized by severe osteosclerosis, pathologic fractures, hepatosplenomegaly, and pancytopenia. The pathophysiological basis is inadequate bone resorption due to osteoclast dysfunction. In the majority of cases, mutations in either of two human genes cause this fatal disorder: TCIRG1, encoding a subunit of the osteoclast H(+)-ATPase, and the voltage-gated chloride channel gene CLCN7. We excluded both genes in a small inbred family with malignant infantile osteopetrosis and undertook linkage analysis of several candidate loci that are involved in murine osteopetrosis. A region spanning more than 20 cM between the markers D6S1717 and D6S1608 on chromosome 6q21 was found to be homozygous in the affected child. This locus is syntenic to the genomic region harboring the gene for the osteopetrotic mutant mouse grey-lethal (gl). Recently, mutations in a novel gene of unknown function were described in the grey-lethal mouse and in one human patient. Mutation screening of the grey-lethal gene (OSTM1), revealed a homozygous 2-bp deletion in exon 2 (c.415_416delAG) in the affected child. No mutations could be found in six independent ARO patients who had tested negative for mutations in TCIRG1 and CLCN7. In summary, we describe the identification of a novel mutation in the coding sequence of the human grey-lethal gene, which is the second OSTM1 mutation found in human ARO, confirming the involvement of this gene in the pathogenesis of this severe bone disease.
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Schmitz C, Goebel I, Wagner S, Vomberg A, Klinner U. Competition between n-alkane-assimilating yeasts and bacteria during colonization of sandy soil microcosms. Appl Microbiol Biotechnol 2000; 54:126-32. [PMID: 10952016 DOI: 10.1007/s002530000348] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
An n-alkane-assimilating strain of Candida tropicalis was selected in sandy soil inoculated with microorganisms from contaminated sites. Competition experiments with n-alkane utilizers from different strain collections confirmed that yeasts overgrow bacteria in sandy soil. Acidification of the soil is one of the colonization factors useful for the yeasts. It can be counteracted by addition of bentonite, a clay mineral with high ion exchange capacity, but not, however, by kaolin. Strains of different yeast species showed different levels of competitiveness. Strains of Arxula adeninivorans, Candida maltosa, and Yarrowia lipolytica overgrew strains of C. tropicalis, C. shehatae or Pichia stipitis. Two strains of C. maltosa and Y. lipolytica coexisted during several serial transfers under microcosm conditions.
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Affiliation(s)
- C Schmitz
- Lehr- und Forschungsgebiet Angewandte Mikrobiologie, Institute für Biologie IV (Mikrobiolgie), RWTH Aachen, Germany
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