99901
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Tao S, Zhou T, Saelao P, Wang Y, Zhu Y, Li T, Zhou H, Wang J. Intrauterine Growth Restriction Alters the Genome-Wide DNA Methylation Profiles in Small Intestine, Liver and Longissimus Dorsi Muscle of Newborn Piglets. Curr Protein Pept Sci 2019; 20:713-726. [PMID: 30678618 DOI: 10.2174/1389203720666190124165243] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 12/30/2018] [Accepted: 01/01/2019] [Indexed: 01/20/2023]
Abstract
Intrauterine growth restriction (IUGR) remains a major problem in swine production since the associated low birth weight leads to high rates of pre-weaning morbidity and mortality, and permanent retardation of growth and development. The underlying regulatory mechanisms from the aspects of epigenetic modification has received widespread attention. Studies explore the changes in genome wide methylation in small intestine (SI), liver and longissimus dorsi muscle (LDM) between IUGR and normal birth weight (NBW) newborn piglets using a methylated DNA immunoprecipitation-sequencing (MeDIP-Seq) approach. The data demonstrated that methylated peaks were prominently distributed in distal intergenic regions and the quantities of peaks in IUGR piglets were more than that of NBW piglets. IUGR piglets had relatively high methylated level in promoters, introns and coding exons in all the three tissues. Through KEGG pathway analysis of differentially methylated genes found that 33, 54 and 5 differentially methylated genes in small intestine, liver and longissimus dorsi muscle between NBW and IUGR piglets, respectively, which are related to development and differentiation, carbohydrate and energy metabolism, lipid metabolism, protein turnover, immune response, detoxification, oxidative stress and apoptosis pathway. The objective of this review is to assess the impact of differentially methylation status on developmental delay, metabolic disorders and immune deficiency of IUGR piglets.
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Affiliation(s)
- Shiyu Tao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Tianjiao Zhou
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Perot Saelao
- Department of Animal Science, University of California, Davis, CA 95616, United States
| | - Ying Wang
- Department of Animal Science, University of California, Davis, CA 95616, United States
| | - Yuhua Zhu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Tiantian Li
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, CA 95616, United States
| | - Junjun Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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99902
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Leone P, Galluccio M, Quarta S, Anoz-Carbonell E, Medina M, Indiveri C, Barile M. Mutation of Aspartate 238 in FAD Synthase Isoform 6 Increases the Specific Activity by Weakening the FAD Binding. Int J Mol Sci 2019; 20:ijms20246203. [PMID: 31835305 PMCID: PMC6941110 DOI: 10.3390/ijms20246203] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/04/2019] [Accepted: 12/06/2019] [Indexed: 02/07/2023] Open
Abstract
FAD synthase (FADS, or FMN:ATP adenylyl transferase) coded by the FLAD1 gene is the last enzyme in the pathway of FAD synthesis. The mitochondrial isoform 1 and the cytosolic isoform 2 are characterized by the following two domains: the C-terminal PAPS domain (FADSy) performing FAD synthesis and pyrophosphorolysis; the N-terminal molybdopterin-binding domain (FADHy) performing a Co++/K+-dependent FAD hydrolysis. Mutations in FLAD1 gene are responsible for riboflavin responsive and non-responsive multiple acyl-CoA dehydrogenases and combined respiratory chain deficiency. In patients harboring frameshift mutations, a shorter isoform (hFADS6) containing the sole FADSy domain is produced representing an emergency protein. With the aim to ameliorate its function we planned to obtain an engineered more efficient hFADS6. Thus, the D238A mutant, resembling the D181A FMNAT “supermutant” of C. glabrata, was overproduced and purified. Kinetic analysis of this enzyme highlighted a general increase of Km, while the kcat was two-fold higher than that of WT. The data suggest that the FAD synthesis rate can be increased. Additional modifications could be performed to further improve the synthesis of FAD. These results correlate with previous data produced in our laboratory, and point towards the following proposals (i) FAD release is the rate limiting step of the catalytic cycle and (ii) ATP and FMN binding sites are synergistically connected.
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Affiliation(s)
- Piero Leone
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, via Orabona 4–, 70126 Bari, Italy; (P.L.); (S.Q.)
- Department of Biology, Ecology and Earth Sciences (DiBEST), Unit of Biochemistry and Molecular Biotechnology, University of Calabria, via P. Bucci 4c, 87036 Arcavacata di Rende, Italy; (M.G.); (C.I.)
| | - Michele Galluccio
- Department of Biology, Ecology and Earth Sciences (DiBEST), Unit of Biochemistry and Molecular Biotechnology, University of Calabria, via P. Bucci 4c, 87036 Arcavacata di Rende, Italy; (M.G.); (C.I.)
| | - Stefano Quarta
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, via Orabona 4–, 70126 Bari, Italy; (P.L.); (S.Q.)
| | - Ernesto Anoz-Carbonell
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, 50009 Zaragoza, Spain; (E.A.-C.); (M.M.)
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, 50009 Zaragoza, Spain; (E.A.-C.); (M.M.)
| | - Cesare Indiveri
- Department of Biology, Ecology and Earth Sciences (DiBEST), Unit of Biochemistry and Molecular Biotechnology, University of Calabria, via P. Bucci 4c, 87036 Arcavacata di Rende, Italy; (M.G.); (C.I.)
| | - Maria Barile
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, via Orabona 4–, 70126 Bari, Italy; (P.L.); (S.Q.)
- Correspondence:
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99903
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Manicka S, Levin M. Modeling somatic computation with non-neural bioelectric networks. Sci Rep 2019; 9:18612. [PMID: 31819119 PMCID: PMC6901451 DOI: 10.1038/s41598-019-54859-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 11/13/2019] [Indexed: 02/08/2023] Open
Abstract
The field of basal cognition seeks to understand how adaptive, context-specific behavior occurs in non-neural biological systems. Embryogenesis and regeneration require plasticity in many tissue types to achieve structural and functional goals in diverse circumstances. Thus, advances in both evolutionary cell biology and regenerative medicine require an understanding of how non-neural tissues could process information. Neurons evolved from ancient cell types that used bioelectric signaling to perform computation. However, it has not been shown whether or how non-neural bioelectric cell networks can support computation. We generalize connectionist methods to non-neural tissue architectures, showing that a minimal non-neural Bio-Electric Network (BEN) model that utilizes the general principles of bioelectricity (electrodiffusion and gating) can compute. We characterize BEN behaviors ranging from elementary logic gates to pattern detectors, using both fixed and transient inputs to recapitulate various biological scenarios. We characterize the mechanisms of such networks using dynamical-systems and information-theory tools, demonstrating that logic can manifest in bidirectional, continuous, and relatively slow bioelectrical systems, complementing conventional neural-centric architectures. Our results reveal a variety of non-neural decision-making processes as manifestations of general cellular biophysical mechanisms and suggest novel bioengineering approaches to construct functional tissues for regenerative medicine and synthetic biology as well as new machine learning architectures.
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Affiliation(s)
- Santosh Manicka
- Allen Discovery Center, 200 College Ave., Tufts University, Medford, MA, 02155, USA
| | - Michael Levin
- Allen Discovery Center, 200 College Ave., Tufts University, Medford, MA, 02155, USA.
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99904
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Nguyen L, Montrasio F, Pattamatta A, Tusi SK, Bardhi O, Meyer KD, Hayes L, Nakamura K, Banez-Coronel M, Coyne A, Guo S, Laboissonniere LA, Gu Y, Narayanan S, Smith B, Nitsch RM, Kankel MW, Rushe M, Rothstein J, Zu T, Grimm J, Ranum LPW. Antibody Therapy Targeting RAN Proteins Rescues C9 ALS/FTD Phenotypes in C9orf72 Mouse Model. Neuron 2019; 105:645-662.e11. [PMID: 31831332 DOI: 10.1016/j.neuron.2019.11.007] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/10/2019] [Accepted: 11/05/2019] [Indexed: 10/25/2022]
Abstract
The intronic C9orf72 G4C2 expansion, the most common genetic cause of ALS and FTD, produces sense- and antisense-expansion RNAs and six dipeptide repeat-associated, non-ATG (RAN) proteins, but their roles in disease are unclear. We generated high-affinity human antibodies targeting GA or GP RAN proteins. These antibodies cross the blood-brain barrier and co-localize with intracellular RAN aggregates in C9-ALS/FTD BAC mice. In cells, α-GA1 interacts with TRIM21, and α-GA1 treatment reduced GA levels, increased GA turnover, and decreased RAN toxicity and co-aggregation of proteasome and autophagy proteins to GA aggregates. In C9-BAC mice, α-GA1 reduced GA as well as GP and GR proteins, improved behavioral deficits, decreased neuroinflammation and neurodegeneration, and increased survival. Glycosylation of the Fc region of α-GA1 is important for cell entry and efficacy. These data demonstrate that RAN proteins drive C9-ALS/FTD in C9-BAC transgenic mice and establish a novel therapeutic approach for C9orf72 ALS/FTD and other RAN-protein diseases.
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Affiliation(s)
- Lien Nguyen
- Center for NeuroGenetics, Department of Molecular Genetics and Microbiology, Genetics Institute, McKnight Brain Institute, Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL 32610, USA
| | | | - Amrutha Pattamatta
- Center for NeuroGenetics, Department of Molecular Genetics and Microbiology, Genetics Institute, McKnight Brain Institute, Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL 32610, USA
| | - Solaleh Khoramian Tusi
- Center for NeuroGenetics, Department of Molecular Genetics and Microbiology, Genetics Institute, McKnight Brain Institute, Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL 32610, USA
| | - Olgert Bardhi
- Center for NeuroGenetics, Department of Molecular Genetics and Microbiology, Genetics Institute, McKnight Brain Institute, Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL 32610, USA
| | - Kevin D Meyer
- Neurimmune AG, 8952 Schlieren, Switzerland; Institute for Regenerative Medicine-IREM, University of Zurich, 8952 Schlieren, Switzerland
| | - Lindsey Hayes
- Department of Neurology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Katsuya Nakamura
- Center for NeuroGenetics, Department of Molecular Genetics and Microbiology, Genetics Institute, McKnight Brain Institute, Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL 32610, USA
| | - Monica Banez-Coronel
- Center for NeuroGenetics, Department of Molecular Genetics and Microbiology, Genetics Institute, McKnight Brain Institute, Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL 32610, USA
| | - Alyssa Coyne
- Department of Neurology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Shu Guo
- Center for NeuroGenetics, Department of Molecular Genetics and Microbiology, Genetics Institute, McKnight Brain Institute, Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL 32610, USA
| | - Lauren A Laboissonniere
- Center for NeuroGenetics, Department of Molecular Genetics and Microbiology, Genetics Institute, McKnight Brain Institute, Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL 32610, USA
| | - Yuanzheng Gu
- Neuromuscular and Movement Disorders, Biogen, Cambridge, MA 02142, USA
| | | | - Benjamin Smith
- Neuromuscular and Movement Disorders, Biogen, Cambridge, MA 02142, USA
| | - Roger M Nitsch
- Neurimmune AG, 8952 Schlieren, Switzerland; Institute for Regenerative Medicine-IREM, University of Zurich, 8952 Schlieren, Switzerland
| | - Mark W Kankel
- Neuromuscular and Movement Disorders, Biogen, Cambridge, MA 02142, USA
| | - Mia Rushe
- Neuromuscular and Movement Disorders, Biogen, Cambridge, MA 02142, USA
| | - Jeffrey Rothstein
- Department of Neurology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Tao Zu
- Center for NeuroGenetics, Department of Molecular Genetics and Microbiology, Genetics Institute, McKnight Brain Institute, Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL 32610, USA
| | - Jan Grimm
- Neurimmune AG, 8952 Schlieren, Switzerland
| | - Laura P W Ranum
- Center for NeuroGenetics, Department of Molecular Genetics and Microbiology, Genetics Institute, McKnight Brain Institute, Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL 32610, USA.
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99905
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Distinct patterns of complex rearrangements and a mutational signature of microhomeology are frequently observed in PLP1 copy number gain structural variants. Genome Med 2019; 11:80. [PMID: 31818324 PMCID: PMC6902434 DOI: 10.1186/s13073-019-0676-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 10/10/2019] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND We investigated the features of the genomic rearrangements in a cohort of 50 male individuals with proteolipid protein 1 (PLP1) copy number gain events who were ascertained with Pelizaeus-Merzbacher disease (PMD; MIM: 312080). We then compared our new data to previous structural variant mutagenesis studies involving the Xq22 region of the human genome. The aggregate data from 159 sequenced join-points (discontinuous sequences in the reference genome that are joined during the rearrangement process) were studied. Analysis of these data from 150 individuals enabled the spectrum and relative distribution of the underlying genomic mutational signatures to be delineated. METHODS Genomic rearrangements in PMD individuals with PLP1 copy number gain events were investigated by high-density customized array or clinical chromosomal microarray analysis and breakpoint junction sequence analysis. RESULTS High-density customized array showed that the majority of cases (33/50; ~ 66%) present with single duplications, although complex genomic rearrangements (CGRs) are also frequent (17/50; ~ 34%). Breakpoint mapping to nucleotide resolution revealed further previously unknown structural and sequence complexities, even in single duplications. Meta-analysis of all studied rearrangements that occur at the PLP1 locus showed that single duplications were found in ~ 54% of individuals and that, among all CGR cases, triplication flanked by duplications is the most frequent CGR array CGH pattern observed. Importantly, in ~ 32% of join-points, there is evidence for a mutational signature of microhomeology (highly similar yet imperfect sequence matches). CONCLUSIONS These data reveal a high frequency of CGRs at the PLP1 locus and support the assertion that replication-based mechanisms are prominent contributors to the formation of CGRs at Xq22. We propose that microhomeology can facilitate template switching, by stabilizing strand annealing of the primer using W-C base complementarity, and is a mutational signature for replicative repair.
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99906
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Liu W, Yan H, Zhou D, Cai X, Zhang Y, Li S, Li H, Li S, Zhou DS, Li X, Zhang C, Sun Y, Dai JP, Zhong J, Yao YG, Luo XJ, Fang Y, Zhang D, Ma Y, Yue W, Li M, Xiao X. The depression GWAS risk allele predicts smaller cerebellar gray matter volume and reduced SIRT1 mRNA expression in Chinese population. Transl Psychiatry 2019; 9:333. [PMID: 31819045 PMCID: PMC6901563 DOI: 10.1038/s41398-019-0675-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 11/19/2019] [Accepted: 11/27/2019] [Indexed: 12/28/2022] Open
Abstract
Major depressive disorder (MDD) is recognized as a primary cause of disability worldwide, and effective management of this illness has been a great challenge. While genetic component is supposed to play pivotal roles in MDD pathogenesis, the genetic and phenotypic heterogeneity of the illness has hampered the discovery of its genetic determinants. In this study, in an independent Han Chinese sample (1824 MDD cases and 3031 controls), we conducted replication analyses of two genetic loci highlighted in a previous Chinese MDD genome-wide association study (GWAS), and confirmed the significant association of a single nucleotide polymorphism (SNP) rs12415800 near SIRT1. Subsequently, using hypothesis-free whole-brain analysis in two independent Han Chinese imaging samples, we found that individuals carrying the MDD risk allele of rs12415800 exhibited aberrant gray matter volume in the left posterior cerebellar lobe compared with those carrying the non-risk allele. Besides, in independent Han Chinese postmortem brain and peripheral blood samples, the MDD risk allele of rs12415800 predicted lower SIRT1 mRNA levels, which was consistent with the reduced expression of this gene in MDD patients compared with healthy subjects. These results provide further evidence for the involvement of SIRT1 in MDD, and suggest that this gene might participate in the illness via affecting the development of cerebellum, a brain region that is potentially underestimated in previous MDD studies.
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Affiliation(s)
- Weipeng Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Hao Yan
- Peking University Sixth Hospital/Institute of Mental Health, Beijing, China
- NHC Key Laboratory of Mental Health (Peking University) and National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Danyang Zhou
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xin Cai
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yuyanan Zhang
- Peking University Sixth Hospital/Institute of Mental Health, Beijing, China
- NHC Key Laboratory of Mental Health (Peking University) and National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Shiyi Li
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China
| | - Huijuan Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Shiwu Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Dong-Sheng Zhou
- Department of Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang, China
| | - Xingxing Li
- Department of Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang, China
| | - Chen Zhang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Sun
- Wuhan Institute for Neuroscience and Neuroengineering, South-Central University for Nationalities, Wuhan, Hubei, China
- Chinese Brain Bank Center, Wuhan, Hubei, China
| | - Jia-Pei Dai
- Wuhan Institute for Neuroscience and Neuroengineering, South-Central University for Nationalities, Wuhan, Hubei, China
- Chinese Brain Bank Center, Wuhan, Hubei, China
| | - Jingmei Zhong
- Psychiatry Department, The first people's hospital of Yunnan province, Kunming, Yunnan, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
- CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, China
| | - Xiong-Jian Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yiru Fang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Dai Zhang
- Peking University Sixth Hospital/Institute of Mental Health, Beijing, China
- NHC Key Laboratory of Mental Health (Peking University) and National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
- Peking-Tsinghua Joint Center for Life Sciences and PKU IDG/McGovern Institute for Brain Research, Peking University, Beijing, China
| | - Yina Ma
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China
| | - Weihua Yue
- Peking University Sixth Hospital/Institute of Mental Health, Beijing, China.
- NHC Key Laboratory of Mental Health (Peking University) and National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China.
- Peking-Tsinghua Joint Center for Life Sciences and PKU IDG/McGovern Institute for Brain Research, Peking University, Beijing, China.
| | - Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China.
- CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
| | - Xiao Xiao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
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99907
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Statistical methods for testing X chromosome variant associations: application to sex-specific characteristics of bipolar disorder. Biol Sex Differ 2019; 10:57. [PMID: 31818333 PMCID: PMC6902568 DOI: 10.1186/s13293-019-0272-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/21/2019] [Indexed: 11/17/2022] Open
Abstract
Background Bipolar disorder (BD) affects both sexes, but important sex differences exist with respect to its symptoms and comorbidities. For example, rapid cycling (RC) is more prevalent in females, and alcohol use disorder (AUD) is more prevalent in males. We hypothesize that X chromosome variants may be associated with sex-specific characteristics of BD. Few studies have explored the role of the X chromosome in BD, which is complicated by X chromosome inactivation (XCI). This process achieves “dosage compensation” for many X chromosome genes by silencing one of the two copies in females, and most statistical methods either ignore that XCI occurs or falsely assume that one copy is inactivated at all loci. We introduce new statistical methods that do not make these assumptions. Methods We investigated this hypothesis in 1001 BD patients from the Genetic Association Information Network (GAIN) and 957 BD patients from the Mayo Clinic Bipolar Disorder Biobank. We examined the association of over 14,000 X chromosome single nucleotide polymorphisms (SNPs) with sex-associated BD traits using two statistical approaches that account for whether a SNP may be undergoing or escaping XCI. In the “XCI-informed approach,” we fit a sex-adjusted logistic regression model assuming additive genetic effects where we coded the SNP either assuming one copy is expressed or two copies are expressed based on prior knowledge about which regions are inactivated. In the “XCI-robust approach,” we fit a logistic regression model with sex, SNP, and SNP-sex interaction effects that is flexible to whether the region is inactivated or escaping XCI. Results Using the “XCI-informed approach,” which considers only the main effect of SNP and does not allow the SNP effect to differ by sex, no significant associations were identified for any of the phenotypes. Using the “XCI-robust approach,” intergenic SNP rs5932307 was associated with BD (P = 8.3 × 10−8), with a stronger effect in females (odds ratio in males (ORM) = 1.13, odds ratio in females for a change of two allele copies (ORW2) = 3.86). Conclusion X chromosome association studies should employ methods which account for its unique biology. Future work is needed to validate the identified associations with BD, to formally assess the performance of both approaches under different true genetic architectures, and to apply these approaches to study sex differences in other conditions.
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99908
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Gong S, Wang X, Meng F, Cui L, Yi Q, Zhao Q, Cang X, Cai Z, Mo JQ, Liang Y, Guan MX. Overexpression of mitochondrial histidyl-tRNA synthetase restores mitochondrial dysfunction caused by a deafness-associated tRNA His mutation. J Biol Chem 2019; 295:940-954. [PMID: 31819004 DOI: 10.1074/jbc.ra119.010998] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/27/2019] [Indexed: 01/19/2023] Open
Abstract
The deafness-associated m.12201T>C mutation affects the A5-U68 base-pairing within the acceptor stem of mitochondrial tRNAHis The primary defect in this mutation is an alteration in tRNAHis aminoacylation. Here, we further investigate the molecular mechanism of the deafness-associated tRNAHis 12201T>C mutation and test whether the overexpression of the human mitochondrial histidyl-tRNA synthetase gene (HARS2) in cytoplasmic hybrid (cybrid) cells carrying the m.12201T>C mutation reverses mitochondrial dysfunctions. Using molecular dynamics simulations, we demonstrate that the m.12201T>C mutation perturbs the tRNAHis structure and function, supported by decreased melting temperature, conformational changes, and instability of mutated tRNA. We show that the m.12201T>C mutation-induced alteration of aminoacylation tRNAHis causes mitochondrial translational defects and respiratory deficiency. We found that the transfer of HARS2 into the cybrids carrying the m.12201T>C mutation raises the levels of aminoacylated tRNAHis from 56.3 to 75.0% but does not change the aminoacylation of other tRNAs. Strikingly, HARS2 overexpression increased the steady-state levels of tRNAHis and of noncognate tRNAs, including tRNAAla, tRNAGln, tRNAGlu, tRNALeu(UUR), tRNALys, and tRNAMet, in cells bearing the m.12201T>C mutation. This improved tRNA metabolism elevated the efficiency of mitochondrial translation, activities of oxidative phosphorylation complexes, and respiration capacity. Furthermore, HARS2 overexpression markedly increased mitochondrial ATP levels and membrane potential and reduced production of reactive oxygen species in cells carrying the m.12201T>C mutation. These results indicate that HARS2 overexpression corrects the mitochondrial dysfunction caused by the tRNAHis mutation. These findings provide critical insights into the pathophysiology of mitochondrial disease and represent a step toward improved therapeutic interventions for mitochondrial disorders.
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Affiliation(s)
- Shasha Gong
- Taizhou University Hospital, Taizhou University, Taizhou, Zhejiang 318000, China.,Institute of Genetics, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xiaoqiong Wang
- Department of Otolaryngology, Taizhou Municipal Hospital, Taizhou, Zhejiang 318000, China.,Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Feilong Meng
- Institute of Genetics, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Division of Medical Genetics and Genomics, the Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Limei Cui
- Institute of Genetics, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Qiuzi Yi
- Institute of Genetics, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Qiong Zhao
- Institute of Genetics, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xiaohui Cang
- Institute of Genetics, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zhiyi Cai
- Department of Otolaryngology, Taizhou Municipal Hospital, Taizhou, Zhejiang 318000, China
| | - Jun Qin Mo
- Department of Pathology, Rady Children's Hospital, University of California School of Medicine, San Diego, California 92123
| | - Yong Liang
- Taizhou University Hospital, Taizhou University, Taizhou, Zhejiang 318000, China
| | - Min-Xin Guan
- Institute of Genetics, Zhejiang University, Hangzhou, Zhejiang 310058, China .,Division of Medical Genetics and Genomics, the Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Key Laboratory of Reproductive Genetics, Ministry of Education of PRC, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Joint Institute of Genetics and Genomic Medicine between Zhejiang University and University of Toronto, Hangzhou, Zhejiang 310058, China
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99909
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Lauhasurayotin S, Cuvelier GD, Klaassen RJ, Fernandez CV, Pastore YD, Abish S, Rayar M, Steele M, Jardine L, Breakey VR, Brossard J, Sinha R, Silva M, Goodyear L, Lipton JH, Michon B, Corriveau-Bourque C, Sung L, Shabanova I, Li H, Zlateska B, Dhanraj S, Cada M, Scherer SW, Dror Y. Reanalysing genomic data by normalized coverage values uncovers CNVs in bone marrow failure gene panels. NPJ Genom Med 2019; 4:30. [PMID: 31839986 PMCID: PMC6901453 DOI: 10.1038/s41525-019-0104-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 10/04/2019] [Indexed: 11/09/2022] Open
Abstract
Inherited bone marrow failure syndromes (IBMFSs) are genetically heterogeneous disorders with cytopenia. Many IBMFSs also feature physical malformations and an increased risk of cancer. Point mutations can be identified in about half of patients. Copy number variation (CNVs) have been reported; however, the frequency and spectrum of CNVs are unknown. Unfortunately, current genome-wide methods have major limitations since they may miss small CNVs or may have low sensitivity due to low read depths. Herein, we aimed to determine whether reanalysis of NGS panel data by normalized coverage value could identify CNVs and characterize them. To address this aim, DNA from IBMFS patients was analyzed by a NGS panel assay of known IBMFS genes. After analysis for point mutations, heterozygous and homozygous CNVs were searched by normalized read coverage ratios and specific thresholds. Of the 258 tested patients, 91 were found to have pathogenic point variants. NGS sample data from 165 patients without pathogenic point mutations were re-analyzed for CNVs; 10 patients were found to have deletions. Diamond Blackfan anemia genes most commonly exhibited heterozygous deletions, and included RPS19, RPL11, and RPL5. A diagnosis of GATA2-related disorder was made in a patient with myelodysplastic syndrome who was found to have a heterozygous GATA2 deletion. Importantly, homozygous FANCA deletion were detected in a patient who could not be previously assigned a specific syndromic diagnosis. Lastly, we identified compound heterozygousity for deletions and pathogenic point variants in RBM8A and PARN genes. All deletions were validated by orthogonal methods. We conclude that careful analysis of normalized coverage values can detect CNVs in NGS panels and should be considered as a standard practice prior to do further investigations.
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Affiliation(s)
- Supanun Lauhasurayotin
- 1Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON Canada.,2Marrow Failure and Myelodysplasia Program, Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON Canada
| | - Geoff D Cuvelier
- 3Pediatric Hematology-Oncology-Bone Marrow Transplantation, University of Manitoba, Cancer Care Manitoba, Winnipeg, MB Canada
| | - Robert J Klaassen
- 4Department of Pediatrics, Children's Hospital of Eastern Ontario, Ottawa, ON Canada
| | | | | | - Sharon Abish
- 7Pediatric Hematology Oncology, Montreal Children's Hospital, Montreal, QC Canada
| | - Meera Rayar
- 8Division of Hematology/Oncology, UBC & B.C. Children's Hospital, Vancouver, BC Canada
| | | | - Lawrence Jardine
- 10Children's Hospital, London Health Sciences Centre, London, ON Canada
| | - Vicky R Breakey
- 11Department of Pediatrics, McMaster University, Hamilton, ON Canada
| | - Josee Brossard
- 12Centre hospitalier universitaire, Sherbrooke, QC Canada
| | - Roona Sinha
- 13Royal University Hospital, Saskatoon, SK Canada
| | | | - Lisa Goodyear
- 15Pediatric Hematology/Oncology, Janeway Child Health Centre, St. John's, NF Canada
| | - Jeffrey H Lipton
- 16Allogeneic Blood and Marrow Transplant Program, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON Canada
| | - Bruno Michon
- 17Centre Hospitalier Universitaire de Quebec, Sainte-Foy, QC Canada
| | | | - Lillian Sung
- 19Population Health Sciences, Research Institute, Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON Canada
| | - Iren Shabanova
- 1Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON Canada
| | - Hongbing Li
- 1Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON Canada
| | - Bozana Zlateska
- 1Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON Canada
| | - Santhosh Dhanraj
- 1Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON Canada.,20Institute of Medical Science, University of Toronto, Toronto, ON Canada
| | - Michaela Cada
- 2Marrow Failure and Myelodysplasia Program, Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON Canada
| | - Stephen W Scherer
- 1Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON Canada.,21McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
| | - Yigal Dror
- 1Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON Canada.,2Marrow Failure and Myelodysplasia Program, Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON Canada.,20Institute of Medical Science, University of Toronto, Toronto, ON Canada
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99910
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Memme JM, Erlich AT, Phukan G, Hood DA. Exercise and mitochondrial health. J Physiol 2019; 599:803-817. [PMID: 31674658 DOI: 10.1113/jp278853] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 10/28/2019] [Indexed: 12/12/2022] Open
Abstract
Mitochondrial health is an important mediator of cellular function across a range of tissues, and as a result contributes to whole-body vitality in health and disease. Our understanding of the regulation and function of these organelles is of great interest to scientists and clinicians across many disciplines within our healthcare system. Skeletal muscle is a useful model tissue for the study of mitochondrial adaptations because of its mass and contribution to whole body metabolism. The remarkable plasticity of mitochondria allows them to adjust their volume, structure and capacity under conditions such as exercise, which is useful or improving metabolic health in individuals with various diseases and/or advancing age. Mitochondria exist within muscle as a functional reticulum which is maintained by dynamic processes of biogenesis and fusion, and is balanced by opposing processes of fission and mitophagy. The sophisticated coordination of these events is incompletely understood, but is imperative for organelle function and essential for the maintenance of an interconnected organelle network that is finely tuned to the metabolic needs of the cell. Further elucidation of the mechanisms of mitochondrial turnover in muscle could offer potential therapeutic targets for the advancement of health and longevity among our ageing populations. As well, investigating exercise modalities that are both convenient and capable of inducing robust mitochondrial adaptations are useful in fostering more widespread global adherence. To this point, exercise remains the most potent behavioural therapeutic approach for the improvement of mitochondrial health, not only in muscle, but potentially also in other tissues.
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Affiliation(s)
- Jonathan M Memme
- Muscle Health Research Centre, York University, Toronto, Ontario, Canada, M3J 1P3.,School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada, M3J 1P3
| | - Avigail T Erlich
- Muscle Health Research Centre, York University, Toronto, Ontario, Canada, M3J 1P3.,School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada, M3J 1P3
| | - Geetika Phukan
- Muscle Health Research Centre, York University, Toronto, Ontario, Canada, M3J 1P3.,School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada, M3J 1P3
| | - David A Hood
- Muscle Health Research Centre, York University, Toronto, Ontario, Canada, M3J 1P3.,School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada, M3J 1P3
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99911
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Suzuki M, Katayama S, Yamamoto M. Two effects of GATA2 enhancer repositioning by 3q chromosomal rearrangements. IUBMB Life 2019; 72:159-169. [PMID: 31820561 DOI: 10.1002/iub.2191] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/09/2019] [Indexed: 01/15/2023]
Abstract
Chromosomal inversion and translocation between 3q21 and 3q26 [inv (3)(q21.3q26.2) and t(3;3)(q21.3;q26.2), respectively] give rise to acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS), which have poor prognoses. The chromosomal rearrangements reposition a GATA2 distal hematopoietic enhancer from the original 3q21 locus to the EVI1 (also known as MECOM) locus on 3q26. Therefore, the GATA2 enhancer from one of two GATA2 alleles drives EVI1 gene expression in hematopoietic stem and progenitor cells, which promotes the accumulation of abnormal progenitors and induces leukemogenesis. On the other hand, one allele of the GATA2 gene loses its enhancer, which results in reduced GATA2 expression. The GATA2 gene encodes a transcription factor critical for the generation and maintenance of hematopoietic stem and progenitor cells. GATA2 haploinsufficiency has been known to cause immunodeficiency and myeloid leukemia. Notably, reduced GATA2 expression suppresses the differentiation but promotes the proliferation of EVI1-expressing leukemic cells, which accelerates EVI1-driven leukemogenesis. A series of studies have shown that the GATA2 enhancer repositioning caused by the chromosomal rearrangements between 3q21 and 3q26 provokes misexpression of both the EVI1 and GATA2 genes and that these two effects coordinately elicit high-risk leukemia.
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Affiliation(s)
- Mikiko Suzuki
- Center for Radioisotope Sciences, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Saori Katayama
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan.,Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Masayuki Yamamoto
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan.,Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
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99912
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Papúchová H, Meissner TB, Li Q, Strominger JL, Tilburgs T. The Dual Role of HLA-C in Tolerance and Immunity at the Maternal-Fetal Interface. Front Immunol 2019; 10:2730. [PMID: 31921098 PMCID: PMC6913657 DOI: 10.3389/fimmu.2019.02730] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 11/07/2019] [Indexed: 12/20/2022] Open
Abstract
To establish a healthy pregnancy, maternal immune cells must tolerate fetal allo-antigens and remain competent to respond to infections both systemically and in placental tissues. Extravillous trophoblasts (EVT) are the most invasive cells of extra-embryonic origin to invade uterine tissues and express polymorphic Human Leucocyte Antigen-C (HLA-C) of both maternal and paternal origin. Thus, HLA-C is a key molecule that can elicit allogeneic immune responses by maternal T and NK cells and for which maternal-fetal immune tolerance needs to be established. HLA-C is also the only classical MHC molecule expressed by EVT that can present a wide variety of peptides to maternal memory T cells and establish protective immunity. The expression of paternal HLA-C by EVT provides a target for maternal NK and T cells, whereas HLA-C expression levels may influence how this response is shaped. This dual function of HLA-C requires tight transcriptional regulation of its expression to balance induction of tolerance and immunity. Here, we critically review new insights into: (i) the mechanisms controlling expression of HLA-C by EVT, (ii) the mechanisms by which decidual NK cells, effector T cells and regulatory T cells recognize HLA-C allo-antigens, and (iii) immune recognition of pathogen derived antigens in context of HLA-C.
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Affiliation(s)
- Henrieta Papúchová
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, United States
| | - Torsten B Meissner
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, United States.,Department of Surgery, Beth Israel Deaconess Medical Center, Boston, MA, United States
| | - Qin Li
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, United States
| | - Jack L Strominger
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, United States
| | - Tamara Tilburgs
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, United States.,Division of Immunobiology, Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
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99913
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Boison D, Yegutkin GG. Adenosine Metabolism: Emerging Concepts for Cancer Therapy. Cancer Cell 2019; 36:582-596. [PMID: 31821783 PMCID: PMC7224341 DOI: 10.1016/j.ccell.2019.10.007] [Citation(s) in RCA: 184] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/23/2019] [Accepted: 10/18/2019] [Indexed: 12/20/2022]
Abstract
Adenosine is a key metabolic and immune-checkpoint regulator implicated in the tumor escape from the host immune system. Major gaps in knowledge that impede the development of effective adenosine-based therapeutics include: (1) lack of consideration of redundant pathways controlling ATP and adenosine levels; (2) lack of distinction between receptor-dependent and -independent effects of adenosine, and (3) focus on extracellular adenosine without consideration of intracellular metabolism and compartmentalization. In light of current clinical trials, we provide an overview of adenosine metabolism and point out the need for a more careful evaluation of the entire purinome in emerging cancer therapies.
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Affiliation(s)
- Detlev Boison
- Department of Neurosurgery, Robert Wood Johnson & New Jersey Medical Schools, Rutgers University, Piscataway, NJ 08854, USA; Rutgers Brain Health Institute, Piscataway, NJ 08854, USA.
| | - Gennady G Yegutkin
- MediCity Research Laboratory, University of Turku, Tykistökatu 6A, Turku, 20520, Finland.
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99914
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Chen W, McKenna A, Schreiber J, Haeussler M, Yin Y, Agarwal V, Noble WS, Shendure J. Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair. Nucleic Acids Res 2019; 47:7989-8003. [PMID: 31165867 PMCID: PMC6735782 DOI: 10.1093/nar/gkz487] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 04/23/2019] [Accepted: 05/23/2019] [Indexed: 12/22/2022] Open
Abstract
Non-homologous end-joining (NHEJ) plays an important role in double-strand break (DSB) repair of DNA. Recent studies have shown that the error patterns of NHEJ are strongly biased by sequence context, but these studies were based on relatively few templates. To investigate this more thoroughly, we systematically profiled ∼1.16 million independent mutational events resulting from CRISPR/Cas9-mediated cleavage and NHEJ-mediated DSB repair of 6872 synthetic target sequences, introduced into a human cell line via lentiviral infection. We find that: (i) insertions are dominated by 1 bp events templated by sequence immediately upstream of the cleavage site, (ii) deletions are predominantly associated with microhomology and (iii) targets exhibit variable but reproducible diversity with respect to the number and relative frequency of the mutational outcomes to which they give rise. From these data, we trained a model that uses local sequence context to predict the distribution of mutational outcomes. Exploiting the bias of NHEJ outcomes towards microhomology mediated events, we demonstrate the programming of deletion patterns by introducing microhomology to specific locations in the vicinity of the DSB site. We anticipate that our results will inform investigations of DSB repair mechanisms as well as the design of CRISPR/Cas9 experiments for diverse applications including genome-wide screens, gene therapy, lineage tracing and molecular recording.
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Affiliation(s)
- Wei Chen
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98195, USA.,Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Aaron McKenna
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Jacob Schreiber
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA
| | - Maximilian Haeussler
- Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA
| | - Yi Yin
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Vikram Agarwal
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.,Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.,Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA.,Howard Hughes Medical Institute, Seattle, WA 98195, USA.,Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98195, USA
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99915
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Gudbjartsson DF, Thorgeirsson G, Sulem P, Helgadottir A, Gylfason A, Saemundsdottir J, Bjornsson E, Norddahl GL, Jonasdottir A, Jonasdottir A, Eggertsson HP, Gretarsdottir S, Thorleifsson G, Indridason OS, Palsson R, Jonasson F, Jonsdottir I, Eyjolfsson GI, Sigurdardottir O, Olafsson I, Danielsen R, Matthiasson SE, Kristmundsdottir S, Halldorsson BV, Hreidarsson AB, Valdimarsson EM, Gudnason T, Benediktsson R, Steinthorsdottir V, Thorsteinsdottir U, Holm H, Stefansson K. Lipoprotein(a) Concentration and Risks of Cardiovascular Disease and Diabetes. J Am Coll Cardiol 2019; 74:2982-2994. [PMID: 31865966 DOI: 10.1016/j.jacc.2019.10.019] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 09/05/2019] [Accepted: 10/06/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND Lipoprotein(a) [Lp(a)] is a causal risk factor for cardiovascular diseases that has no established therapy. The attribute of Lp(a) that affects cardiovascular risk is not established. Low levels of Lp(a) have been associated with type 2 diabetes (T2D). OBJECTIVES This study investigated whether cardiovascular risk is conferred by Lp(a) molar concentration or apolipoprotein(a) [apo(a)] size, and whether the relationship between Lp(a) and T2D risk is causal. METHODS This was a case-control study of 143,087 Icelanders with genetic information, including 17,715 with coronary artery disease (CAD) and 8,734 with T2D. This study used measured and genetically imputed Lp(a) molar concentration, kringle IV type 2 (KIV-2) repeats (which determine apo(a) size), and a splice variant in LPA associated with small apo(a) but low Lp(a) molar concentration to disentangle the relationship between Lp(a) and cardiovascular risk. Loss-of-function homozygotes and other subjects genetically predicted to have low Lp(a) levels were evaluated to assess the relationship between Lp(a) and T2D. RESULTS Lp(a) molar concentration was associated dose-dependently with CAD risk, peripheral artery disease, aortic valve stenosis, heart failure, and lifespan. Lp(a) molar concentration fully explained the Lp(a) association with CAD, and there was no residual association with apo(a) size. Homozygous carriers of loss-of-function mutations had little or no Lp(a) and increased the risk of T2D. CONCLUSIONS Molar concentration is the attribute of Lp(a) that affects risk of cardiovascular diseases. Low Lp(a) concentration (bottom 10%) increases T2D risk. Pharmacologic reduction of Lp(a) concentration in the 20% of individuals with the greatest concentration down to the population median is predicted to decrease CAD risk without increasing T2D risk.
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Affiliation(s)
- Daniel F Gudbjartsson
- deCODE genetics/Amgen, Reykjavik, Iceland; School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Gudmundur Thorgeirsson
- deCODE genetics/Amgen, Reykjavik, Iceland; Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Division of Cardiology and Cardiovascular Research Center, Internal Medicine Services, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland
| | | | | | | | | | - Eythor Bjornsson
- deCODE genetics/Amgen, Reykjavik, Iceland; Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | - Hannes P Eggertsson
- deCODE genetics/Amgen, Reykjavik, Iceland; School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | - Olafur S Indridason
- Division of Nephrology, Internal Medicine Services, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland
| | - Runolfur Palsson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Division of Nephrology, Internal Medicine Services, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland
| | - Fridbert Jonasson
- deCODE genetics/Amgen, Reykjavik, Iceland; Department of Ophthalmology, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland
| | - Ingileif Jonsdottir
- deCODE genetics/Amgen, Reykjavik, Iceland; Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Department of Immunology, Landspitali, The National University Hospital of Iceland
| | | | | | - Isleifur Olafsson
- Department of Clinical Biochemistry, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland
| | - Ragnar Danielsen
- Division of Cardiology and Cardiovascular Research Center, Internal Medicine Services, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland
| | | | - Snaedis Kristmundsdottir
- deCODE genetics/Amgen, Reykjavik, Iceland; School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
| | - Bjarni V Halldorsson
- deCODE genetics/Amgen, Reykjavik, Iceland; School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
| | - Astradur B Hreidarsson
- Division of Endocrinology and Metabolic Medicine, Internal Medicine Services, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland
| | - Einar M Valdimarsson
- Department of Neurology, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland
| | - Thorarinn Gudnason
- Division of Cardiology and Cardiovascular Research Center, Internal Medicine Services, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland
| | - Rafn Benediktsson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Division of Endocrinology and Metabolic Medicine, Internal Medicine Services, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland
| | | | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen, Reykjavik, Iceland; Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Hilma Holm
- deCODE genetics/Amgen, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE genetics/Amgen, Reykjavik, Iceland; Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
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99916
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Ginanneschi F, D’Amore A, Barghigiani M, Tessa A, Rossi A, Santorelli FM. SPG8 mutations in Italian families: clinical data and literature review. Neurol Sci 2019; 41:699-703. [DOI: 10.1007/s10072-019-04180-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 11/25/2019] [Indexed: 01/03/2023]
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99917
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Abstract
Metals are essential components in all forms of life required for the function of nearly half of all enzymes and are critically involved in virtually all fundamental biological processes. Especially, the transition metals iron (Fe), zinc (Zn), manganese (Mn), nickel (Ni), copper (Cu) and cobalt (Co) are crucial micronutrients known to play vital roles in metabolism as well due to their unique redox properties. Metals carry out three major functions within metalloproteins: to provide structural support, to serve as enzymatic cofactors, and to mediate electron transportation. Metal ions are also involved in the immune system from metal allergies to nutritional immunity. Within the past decade, much attention has been drawn to the roles of metal ions in the immune system, since increasing evidence has mounted to suggest that metals are critically implicated in regulating both the innate immune sensing of and the host defense against invading pathogens. The importance of ions in immunity is also evidenced by the identification of various immunodeficiencies in patients with mutations in ion channels and transporters. In addition, cancer immunotherapy has recently been conclusively demonstrated to be effective and important for future tumor treatment, although only a small percentage of cancer patients respond to immunotherapy because of inadequate immune activation. Importantly, metal ion-activated immunotherapy is becoming an effective and potential way in tumor therapy for better clinical application. Nevertheless, we are still in a primary stage of discovering the diverse immunological functions of ions and mechanistically understanding the roles of these ions in immune regulation. This review summarizes recent advances in the understanding of metal-controlled immunity. Particular emphasis is put on the mechanisms of innate immune stimulation and T cell activation by the essential metal ions like calcium (Ca2+), zinc (Zn2+), manganese (Mn2+), iron (Fe2+/Fe3+), and potassium (K+), followed by a few unessential metals, in order to draw a general diagram of metalloimmunology.
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Affiliation(s)
- Chenguang Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Rui Zhang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Xiaoming Wei
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Mengze Lv
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Zhengfan Jiang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
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99918
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Broussard A, Florwick A, Desbiens C, Nischan N, Robertson C, Guan Z, Kohler JJ, Wells L, Boyce M. Human UDP-galactose 4'-epimerase (GALE) is required for cell-surface glycome structure and function. J Biol Chem 2019; 295:1225-1239. [PMID: 31819007 DOI: 10.1074/jbc.ra119.009271] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 11/23/2019] [Indexed: 12/27/2022] Open
Abstract
Glycan biosynthesis relies on nucleotide sugars (NSs), abundant metabolites that serve as monosaccharide donors for glycosyltransferases. In vivo, signal-dependent fluctuations in NS levels are required to maintain normal cell physiology and are dysregulated in disease. However, how mammalian cells regulate NS levels and pathway flux remains largely uncharacterized. To address this knowledge gap, here we examined UDP-galactose 4'-epimerase (GALE), which interconverts two pairs of essential NSs. Using immunoblotting, flow cytometry, and LC-MS-based glycolipid and glycan profiling, we found that CRISPR/Cas9-mediated GALE deletion in human cells triggers major imbalances in NSs and dramatic changes in glycolipids and glycoproteins, including a subset of integrins and the cell-surface death receptor FS-7-associated surface antigen. In particular, we observed substantial decreases in total sialic acid, galactose, and GalNAc levels in glycans. These changes also directly impacted cell signaling, as GALE -/- cells exhibited FS-7-associated surface antigen ligand-induced apoptosis. Our results reveal a role of GALE-mediated NS regulation in death receptor signaling and may have implications for the molecular etiology of illnesses characterized by NS imbalances, including galactosemia and metabolic syndrome.
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Affiliation(s)
- Alex Broussard
- Department of Biochemistry, Duke University, Durham, North Carolina 27710
| | - Alyssa Florwick
- Department of Biochemistry, Duke University, Durham, North Carolina 27710
| | - Chelsea Desbiens
- Department of Chemistry, University of Georgia, Athens, Georgia 30602
| | - Nicole Nischan
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Corrina Robertson
- Department of Biochemistry, Duke University, Durham, North Carolina 27710
| | - Ziqiang Guan
- Department of Biochemistry, Duke University, Durham, North Carolina 27710
| | - Jennifer J Kohler
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Lance Wells
- Department of Chemistry, University of Georgia, Athens, Georgia 30602.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Michael Boyce
- Department of Biochemistry, Duke University, Durham, North Carolina 27710
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99919
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Stürner KH, Siembab I, Schön G, Stellmann JP, Heidari N, Fehse B, Heesen C, Eiermann TH, Martin R, Binder TM. Is multiple sclerosis progression associated with the HLA-DR15 haplotype? Mult Scler J Exp Transl Clin 2019; 5:2055217319894615. [PMID: 31839982 PMCID: PMC6902395 DOI: 10.1177/2055217319894615] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 11/04/2019] [Accepted: 11/09/2019] [Indexed: 11/17/2022] Open
Abstract
Background The prevalence of multiple sclerosis is associated with the major histocompatibility complex class II DR15 haplotype HLA-DRB1*15:01∼HLA-DRB5*01:01. Objective To assess whether multiple sclerosis progression is associated with the main susceptibility haplotype HLA-DRB1*15:01∼HLA-DRB5*01:01. Methods Patients (n = 1230) and healthy controls (n = 2110) were genotyped for HLA-DRB1 and HLA-DRB5. The baseline Expanded Disability Status Scale (EDSS) score was determined and patients were followed for at least 3 years. Results After follow-up of the consecutive cohort 349 patients were classified as having clinical isolated syndrome and 881 patients as having multiple sclerosis. The susceptibility allele HLA-DRB1*15:01 was more frequent in clinical isolated syndrome (odds ratio 1.56) and multiple sclerosis (odds ratio 3.17) compared to controls. HLA- DRB1*15:01 was the only enriched HLA-DRB1 allele in multiple sclerosis patients. Comparison of clinical characteristics between HLA-DRB1*15:01∼HLA-DRB5*01:01 negative and positive patients with multiple sclerosis showed that baseline EDSS score, disease duration and frequency of the category secondary progressive multiple sclerosis with relapse were increased in the HLA-DRB1*15:01∼HLA-DRB5*01:01 positive group. Conclusion The study confirmed HLA-DRB1*15:01 and HLA-DRB5*01:01 as the main susceptibility alleles and showed weak indirect evidence for a role in progression of the disease.
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Affiliation(s)
- Klarissa Hanja Stürner
- Institute for Neuroimmunology and Clinical MS Research, University Medical Center Hamburg-Eppendorf, Germany
| | - Inessa Siembab
- Institute for Neuroimmunology and Clinical MS Research, University Medical Center Hamburg-Eppendorf, Germany
| | - Gerhard Schön
- Department of Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, Germany
| | - Jan-Patrick Stellmann
- Institute for Neuroimmunology and Clinical MS Research, University Medical Center Hamburg-Eppendorf, Germany
| | - Nika Heidari
- Institute for Neuroimmunology and Clinical MS Research, University Medical Center Hamburg-Eppendorf, Germany
| | - Boris Fehse
- Research Department Cell and Gene Therapy, University Medical Center Hamburg-Eppendorf, Germany
| | - Christoph Heesen
- Institute for Neuroimmunology and Clinical MS Research, University Medical Center Hamburg-Eppendorf, Germany
| | - Thomas H Eiermann
- HLA Laboratory, University Medical Center Hamburg-Eppendorf, Germany
| | - Roland Martin
- Institute for Neuroimmunology and Clinical MS Research, University Medical Center Hamburg-Eppendorf, Germany
| | - Thomas Mc Binder
- HLA Laboratory, University Medical Center Hamburg-Eppendorf, Germany
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99920
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Teixeira MAL, Vieira PE, Pleijel F, Sampieri BR, Ravara A, Costa FO, Nygren A. Molecular and morphometric analyses identify new lineages within a large
Eumida
(Annelida) species complex. ZOOL SCR 2019. [DOI: 10.1111/zsc.12397] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Marcos A. L. Teixeira
- Departamento de Biologia CBMA Centre of Molecular and Environmental Biology Universidade do Minho Braga Portugal
- Institute of Science and Innovation for Bio‐Sustainability (IB‐S) Universidade do Minho Braga Portugal
| | - Pedro E. Vieira
- Departamento de Biologia CBMA Centre of Molecular and Environmental Biology Universidade do Minho Braga Portugal
- Institute of Science and Innovation for Bio‐Sustainability (IB‐S) Universidade do Minho Braga Portugal
| | - Fredrik Pleijel
- Institutionen for marina vetenskaper Göteborgs Universitet Tjärnö Strömstad Sweden
| | - Bruno R. Sampieri
- Departamento de Biologia CBMA Centre of Molecular and Environmental Biology Universidade do Minho Braga Portugal
- Institute of Science and Innovation for Bio‐Sustainability (IB‐S) Universidade do Minho Braga Portugal
- Museu de Zoologia Instituto de Biologia Universidade Estadual de Campinas – IB/UNICAMP Campinas Brazil
| | - Ascensão Ravara
- Departamento de Biologia CESAM – Centro de Estudos do Ambiente e do Mar Universidade de Aveiro Aveiro Portugal
| | - Filipe O. Costa
- Departamento de Biologia CBMA Centre of Molecular and Environmental Biology Universidade do Minho Braga Portugal
- Institute of Science and Innovation for Bio‐Sustainability (IB‐S) Universidade do Minho Braga Portugal
| | - Arne Nygren
- Institutionen for marina vetenskaper Göteborgs Universitet Tjärnö Strömstad Sweden
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99921
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Morgenthaler AB, Kinney WR, Ebmeier CC, Walsh CM, Snyder DJ, Cooper VS, Old WM, Copley SD. Mutations that improve efficiency of a weak-link enzyme are rare compared to adaptive mutations elsewhere in the genome. eLife 2019; 8:53535. [PMID: 31815667 PMCID: PMC6941894 DOI: 10.7554/elife.53535] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 12/02/2019] [Indexed: 11/13/2022] Open
Abstract
New enzymes often evolve by gene amplification and divergence. Previous experimental studies have followed the evolutionary trajectory of an amplified gene, but have not considered mutations elsewhere in the genome when fitness is limited by an evolving gene. We have evolved a strain of Escherichia coli in which a secondary promiscuous activity has been recruited to serve an essential function. The gene encoding the ‘weak-link’ enzyme amplified in all eight populations, but mutations improving the newly needed activity occurred in only one. Most adaptive mutations occurred elsewhere in the genome. Some mutations increase expression of the enzyme upstream of the weak-link enzyme, pushing material through the dysfunctional metabolic pathway. Others enhance production of a co-substrate for a downstream enzyme, thereby pulling material through the pathway. Most of these latter mutations are detrimental in wild-type E. coli, and thus would require reversion or compensation once a sufficient new activity has evolved.
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Affiliation(s)
- Andrew B Morgenthaler
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, United States.,Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, United States
| | - Wallis R Kinney
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, United States.,Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, United States
| | - Christopher C Ebmeier
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, United States
| | - Corinne M Walsh
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, United States.,Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, United States
| | - Daniel J Snyder
- Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, United States
| | - Vaughn S Cooper
- Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, United States
| | - William M Old
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, United States
| | - Shelley D Copley
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, United States.,Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, United States
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99922
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Lehmann D, Tuppen HAL, Campbell GE, Alston CL, Lawless C, Rosa HS, Rocha MC, Reeve AK, Nicholls TJ, Deschauer M, Zierz S, Taylor RW, Turnbull DM, Vincent AE. Understanding mitochondrial DNA maintenance disorders at the single muscle fibre level. Nucleic Acids Res 2019; 47:7430-7443. [PMID: 31147703 PMCID: PMC6698645 DOI: 10.1093/nar/gkz472] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/12/2019] [Accepted: 05/16/2019] [Indexed: 01/07/2023] Open
Abstract
Clonal expansion of mitochondrial DNA (mtDNA) deletions is an important pathological mechanism in adults with mtDNA maintenance disorders, leading to a mosaic mitochondrial respiratory chain deficiency in skeletal muscle. This study had two aims: (i) to determine if different Mendelian mtDNA maintenance disorders showed similar pattern of mtDNA deletions and respiratory chain deficiency and (ii) to investigate the correlation between the mitochondrial genetic defect and corresponding respiratory chain deficiency. We performed a quantitative analysis of respiratory chain deficiency, at a single cell level, in a cohort of patients with mutations in mtDNA maintenance genes. Using the same tissue section, we performed laser microdissection and single cell genetic analysis to investigate the relationship between mtDNA deletion characteristics and the respiratory chain deficiency. The pattern of respiratory chain deficiency is similar with different genetic defects. We demonstrate a clear correlation between the level of mtDNA deletion and extent of respiratory chain deficiency within a single cell. Long-range and single molecule PCR shows the presence of multiple mtDNA deletions in approximately one-third of all muscle fibres. We did not detect evidence of a replicative advantage for smaller mtDNA molecules in the majority of fibres, but further analysis is needed to provide conclusive evidence.
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Affiliation(s)
- Diana Lehmann
- Department of Neurology, University of Ulm, 89075, Ulm, Germany.,Department of Neurology, University of Halle-Wittenberg, 06120, Halle/Saale, Germany
| | - Helen A L Tuppen
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Georgia E Campbell
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Charlotte L Alston
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.,NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE2 4HH, UK
| | - Conor Lawless
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Hannah S Rosa
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Mariana C Rocha
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Amy K Reeve
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.,Centre for Ageing and Vitality, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Thomas J Nicholls
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Marcus Deschauer
- Department of Neurology, Technical University Munich, 81675, Munich, Germany
| | - Stephan Zierz
- Department of Neurology, University of Halle-Wittenberg, 06120, Halle/Saale, Germany
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.,NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE2 4HH, UK
| | - Doug M Turnbull
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.,Centre for Ageing and Vitality, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Amy E Vincent
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.,Centre for Ageing and Vitality, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
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99923
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Ratnakumar A, Zimmerman SE, Jordan BA, Mar JC. Estrogen activates Alzheimer's disease genes. ALZHEIMERS & DEMENTIA-TRANSLATIONAL RESEARCH & CLINICAL INTERVENTIONS 2019; 5:906-917. [PMID: 31890855 PMCID: PMC6926344 DOI: 10.1016/j.trci.2019.09.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Introduction Women are at increased risk for Alzheimer's disease (AD), but the reason why remains unknown. One hypothesis is that low estrogen levels at menopause increases vulnerability to AD, but this remains unproven. Methods We compared neuronal genes upregulated by estrogen in ovariectomized female rhesus macaques with a database of >17,000 diverse gene sets and applied a rare variant burden test to exome sequencing data from 1208 female AD patients with the age of onset < 75 years and 2162 female AD controls. Results We found a striking overlap between genes upregulated by estrogen in macaques and genes downregulated in the human postmortem AD brain, and we found that estrogen upregulates the APOE gene and that progesterone acts antagonistically to estrogen genome-wide. We also found that female patients with AD have excess rare mutations in the early menopause gene MCM8. Discussion We show with genomic data that the menopausal loss of estrogen could underlie the increased risk for AD in women.
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Affiliation(s)
- Abhirami Ratnakumar
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Samuel E Zimmerman
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Bryen A Jordan
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA.,Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jessica C Mar
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, USA.,Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, Australia
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99924
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Kalaskar VK, Alur RP, Li LK, Thomas JW, Sergeev YV, Blain D, Hufnagel RB, Cogliati T, Brooks BP. High-throughput custom capture sequencing identifies novel mutations in coloboma-associated genes: Mutation in DNA-binding domain of retinoic acid receptor beta affects nuclear localization causing ocular coloboma. Hum Mutat 2019; 41:678-695. [PMID: 31816153 PMCID: PMC7027867 DOI: 10.1002/humu.23954] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 10/04/2019] [Accepted: 11/09/2019] [Indexed: 12/11/2022]
Abstract
Uveal coloboma is a potentially blinding congenital ocular malformation caused by the failure of optic fissure closure during the fifth week of human gestation. We performed custom capture high‐throughput screening of 38 known coloboma‐associated genes in 66 families. Suspected causative novel variants were identified in TFAP2A and CHD7, as well as two previously reported variants of uncertain significance in RARB and BMP7. The variant in RARB, unlike previously reported disease mutations in the ligand‐binding domain, was a missense change in the highly conserved DNA‐binding domain predicted to affect the protein's DNA‐binding ability. In vitro studies revealed lower steady‐state protein levels, reduced transcriptional activity, and incomplete nuclear localization of the mutant RARB protein compared with wild‐type. Zebrafish studies showed that human RARB messenger RNA partially reduced the ocular phenotype caused by morpholino knockdown of rarga gene, a zebrafish homolog of human RARB. Our study indicates that sequence alterations in known coloboma genes account for a small percentage of coloboma cases and that mutations in the RARB DNA‐binding domain could result in human disease.
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Affiliation(s)
- Vijay K Kalaskar
- Pediatric, Developmental & Genetic Ophthalmology Section, Ophthalmic Genetics and Visual Function Branch (OGVFB), National Eye Institute (NEI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Ramakrishna P Alur
- Pediatric, Developmental & Genetic Ophthalmology Section, Ophthalmic Genetics and Visual Function Branch (OGVFB), National Eye Institute (NEI), National Institutes of Health (NIH), Bethesda, Maryland
| | - LeeAnn K Li
- Pediatric, Developmental & Genetic Ophthalmology Section, Ophthalmic Genetics and Visual Function Branch (OGVFB), National Eye Institute (NEI), National Institutes of Health (NIH), Bethesda, Maryland
| | - James W Thomas
- National Institutes of Health Intramural Sequencing Center, National Human Genome Research Institute, NIH, Bethesda, Maryland
| | - Yuri V Sergeev
- Protein Biochemistry and Molecular Modeling Group, OGVFB, NEI, NIH, Bethesda, Maryland
| | - Delphine Blain
- Ophthalmic Clinical Genetics Section, OGVFB, NEI, NIH, Bethesda, Maryland
| | - Robert B Hufnagel
- Medical Genetics and Ophthalmic Genomics Unit, OGVFB, NEI, NIH, Bethesda, Maryland
| | - Tiziana Cogliati
- Pediatric, Developmental & Genetic Ophthalmology Section, Ophthalmic Genetics and Visual Function Branch (OGVFB), National Eye Institute (NEI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Brian P Brooks
- Pediatric, Developmental & Genetic Ophthalmology Section, Ophthalmic Genetics and Visual Function Branch (OGVFB), National Eye Institute (NEI), National Institutes of Health (NIH), Bethesda, Maryland.,Ophthalmic Clinical Genetics Section, OGVFB, NEI, NIH, Bethesda, Maryland
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99925
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Okamoto Y, Tomioka M, Ogasawara F, Nagaiwa K, Kimura Y, Kioka N, Ueda K. C-terminal of ABCA1 separately regulates cholesterol floppase activity and cholesterol efflux activity. Biosci Biotechnol Biochem 2019; 84:764-773. [PMID: 31814539 DOI: 10.1080/09168451.2019.1700775] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
ATP-Binding Cassette A1 (ABCA1) is a key lipid transporter for cholesterol homeostasis. We recently reported that ABCA1 not only exports excess cholesterol in an apoA-I dependent manner, but that it also flops cholesterol from the inner to the outer leaflet of the plasma membrane. However, the relationship between these two activities of ABCA1 is still unclear. In this study, we analyzed the subcellular localization of ABCA1 by using a newly generated monoclonal antibody against its extracellular domain and the functions of eleven chimera proteins, in which the C-terminal domain of ABCA1 was replaced with those of the other ABCA subfamily members. We identified two motifs important for the functions of ABCA1. Three periodically repeated leucine residues were necessary for the cholesterol floppase activity but not the cholesterol efflux activity, while a VFVNFA motif was essential for both activities of ABCA1. These results suggest that the C-terminal of ABCA1 separately regulates the cholesterol floppase activity and the cholesterol efflux activity.
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Affiliation(s)
- Yusuke Okamoto
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Maiko Tomioka
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Fumihiko Ogasawara
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto, Japan
| | - Kota Nagaiwa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yasuhisa Kimura
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Noriyuki Kioka
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.,Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto, Japan
| | - Kazumitsu Ueda
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto, Japan
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99926
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Comparison between Adult Patients with Sickle Cell Disease of Sub-Saharan African Origin Born in Metropolitan France and in Sub-Saharan Africa. J Clin Med 2019; 8:jcm8122173. [PMID: 31835320 PMCID: PMC6947353 DOI: 10.3390/jcm8122173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 02/02/2023] Open
Abstract
Sickle cell disease (SCD) prevalence has increased rapidly in Europe as a result of an increase in the life expectancy of these patients and the arrival of SCD migrants from Africa. The aim of our study was to compare the phenotypes of adult patients born in Sub-Saharan Africa (SSA) who migrated to France with those of patients with the same origin who were born in France. This single-center observational study compared the demographic, clinical and biological characteristics of SCD adult patients of SSA origin who were born in France or SSA. Data were collected from computerized medical charts. Groups were compared using multivariate logistic regression with adjustment for age, gender and type of SCD. Of the 323 SCD patients followed in our center, 235 were enrolled, including 111 patients born in France and 124 patients born in SSA. SCD genotypes were balanced between groups. Patients born in Africa were older (median age 32.1 (24.4-39) vs. 25.6 (22.1-30.5) years, p < 0.001) and more often women (n = 75 (60.5%) vs. 48 (43.2%), p = 0.008). The median age at arrival in France was 18 years (13-23). The median height was lower among patients born in SSA (169 (163-175) vs. 174.5 cm (168-179), p < 0.001). Over their lifetimes, patients born in France had more acute chest syndromes (median number 2 (1-4) vs. 1 (0-3), p = 0.002), with the first episode occurring earlier (19 (11.6-22.3) vs. 24 (18.4-29.5) years, p < 0.007), and were admitted to intensive care units more often (53.3% vs. 34.9%, p = 0.006). This difference was more pronounced in the SS/Sβ0 population. Conversely, patients born in SSA had more skin ulcers (19.4% vs. 6.3%, p = 0.03). No significant differences were found in social and occupational insertion or other complications between the two groups. Patients born in SSA had a less severe disease phenotype regardless of their age than those born in France. This difference could be related to a survival bias occurring in Africa during childhood and migration to Europe that selected the least severe phenotypes.
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99927
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Hao S, Salzo J, Hao M, Ferreri NR. Regulation of NKCC2B by TNF-α in response to salt restriction. Am J Physiol Renal Physiol 2019; 318:F273-F282. [PMID: 31813248 DOI: 10.1152/ajprenal.00388.2019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We have previously shown that TNF-α produced by renal epithelial cells inhibits Na+-K+-2Cl- cotransporter (NKCC2) activity as part of a mechanism that attenuates increases in blood pressure in response to high NaCl intake. As the role of TNF-α in the kidney is still being defined, the effects of low salt intake on TNF-α and NKCC2B expression were determined. Mice given a low-salt (0.02% NaCl) diet (LSD) for 7 days exhibited a 62 ± 7.4% decrease in TNF-α mRNA accumulation in the renal cortex. Mice that ingested the LSD also exhibited an ~63% increase in phosphorylated NKCC2 expression in the cortical thick ascending limb of Henle's loop and a concomitant threefold increase in NKCC2B mRNA abundance without a concurrent change in NKCC2A mRNA accumulation. NKCC2B mRNA levels increased fivefold in mice that ingested the LSD and also received an intrarenal injection of a lentivirus construct that specifically silenced TNF-α in the kidney (U6-TNF-ex4) compared with mice injected with control lentivirus. Administration of a single intrarenal injection of murine recombinant TNF-α (5 ng/g body wt) attenuated the increases of NKCC2B mRNA by ~50% and inhibited the increase in phosphorylated NKCC2 by ~54% in the renal cortex of mice given the LSD for 7 days. Renal silencing of TNF-α decreased urine volume and NaCl excretion in mice given the LSD, effects that were reversed when NKCC2B was silenced in the kidney. Collectively, these findings demonstrate that downregulation of renal TNF-α production in response to low-salt conditions contributes to the regulation of NaCl reabsorption via an NKCC2B-dependent mechanism.
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Affiliation(s)
- Shoujin Hao
- Department of Pharmacology, New York Medical College, Valhalla, New York
| | - Joseph Salzo
- Department of Pharmacology, New York Medical College, Valhalla, New York
| | - Mary Hao
- Department of Pharmacology, New York Medical College, Valhalla, New York
| | - Nicholas R Ferreri
- Department of Pharmacology, New York Medical College, Valhalla, New York
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99928
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Inferring trait-specific similarity among individuals from molecular markers and phenotypes with Bayesian regression. Theor Popul Biol 2019; 132:47-59. [PMID: 31830483 DOI: 10.1016/j.tpb.2019.11.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 12/20/2022]
Abstract
Modeling covariance structure based on genetic similarity between pairs of relatives plays an important role in evolutionary, quantitative and statistical genetics. Historically, genetic similarity between individuals has been quantified from pedigrees via the probability that randomly chosen homologous alleles between individuals are identical by descent (IBD). At present, however, many genetic analyses rely on molecular markers, with realized measures of genomic similarity replacing IBD-based expected similarities. Animal and plant breeders, for example, now employ marker-based genomic relationship matrices between individuals in prediction models and in estimation of genome-based heritability coefficients. Phenotypes convey information about genetic similarity as well. For instance, if phenotypic values are at least partially the result of the action of quantitative trait loci, one would expect the former to inform about the latter, as in genome-wide association studies. Statistically, a non-trivial conditional distribution of unknown genetic similarities, given phenotypes, is to be expected. A Bayesian formalism is presented here that applies to whole-genome regression methods where some genetic similarity matrix, e.g., a genomic relationship matrix, can be defined. Our Bayesian approach, based on phenotypes and markers, converts prior (markers only) expected similarity into trait-specific posterior similarity. A simulation illustrates situations under which effective Bayesian learning from phenotypes occurs. Pinus and wheat data sets were used to demonstrate applicability of the concept in practice. The methodology applies to a wide class of Bayesian linear regression models, it extends to the multiple-trait domain, and can also be used to develop phenotype-guided similarity kernels in prediction problems.
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99929
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Goel D, Un Nisa K, Reza MI, Rahman Z, Aamer S. Aberrant DNA Methylation Pattern may Enhance Susceptibility to Migraine: A Novel Perspective. CNS & NEUROLOGICAL DISORDERS-DRUG TARGETS 2019; 18:504-515. [DOI: 10.2174/1871527318666190809162631] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 06/04/2019] [Accepted: 07/27/2019] [Indexed: 12/17/2022]
Abstract
In today’s world, migraine is one of the most frequent disorders with an estimated world prevalence of 14.7% characterized by attacks of a severe headache making people enfeebled and imposing a big socioeconomic burden. The pathophysiology of a migraine is not completely understood however there are pieces of evidence that epigenetics performs a primary role in the pathophysiology of migraine. Here, in this review, we highlight current evidence for an epigenetic link with migraine in particular DNA methylation of numerous genes involved in migraine pathogenesis. Outcomes of various studies have explained the function of DNA methylation of a several migraine related genes such as RAMP1, CALCA, NOS1, ESR1, MTHFR and NR4A3 in migraine pathogenesis. Mentioned data suggested there exist a strong association of DNA methylation of migraine-related genes in migraine. Although we now have a general understanding of the role of epigenetic modifications of a numerous migraine associated genes in migraine pathogenesis, there are many areas of active research are of key relevance to medicine. Future studies into the complexities of epigenetic modifications will bring a new understanding of the mechanisms of migraine processes and open novel approaches towards therapeutic intervention.
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Affiliation(s)
- Divya Goel
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education & Research, Guwahati, India
| | - Kaiser Un Nisa
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education & Research, SAS Nagar, India
| | - Mohammad Irshad Reza
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education & Research, SAS Nagar, India
| | - Ziaur Rahman
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education & Research, SAS Nagar, India
| | - Shaikh Aamer
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education & Research, SAS Nagar, India
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99930
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Plantier V, Sanchez-Brualla I, Dingu N, Brocard C, Liabeuf S, Gackière F, Brocard F. Calpain fosters the hyperexcitability of motoneurons after spinal cord injury and leads to spasticity. eLife 2019; 8:e51404. [PMID: 31815668 PMCID: PMC6927741 DOI: 10.7554/elife.51404] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 12/08/2019] [Indexed: 12/12/2022] Open
Abstract
Up-regulation of the persistent sodium current (INaP) and down-regulation of the potassium/chloride extruder KCC2 lead to spasticity after spinal cord injury (SCI). We here identified calpain as the driver of the up- and down-regulation of INaP and KCC2, respectively, in neonatal rat lumbar motoneurons. Few days after SCI, neonatal rats developed behavioral signs of spasticity with the emergence of both hyperreflexia and abnormal involuntary muscle contractions on hindlimbs. At the same time, in vitro isolated lumbar spinal cords became hyperreflexive and displayed numerous spontaneous motor outputs. Calpain-I expression paralleled with a proteolysis of voltage-gated sodium (Nav) channels and KCC2. Acute inhibition of calpains reduced this proteolysis, restored the motoneuronal expression of Nav and KCC2, normalized INaP and KCC2 function, and curtailed spasticity. In sum, by up- and down-regulating INaP and KCC2, the calpain-mediated proteolysis of Nav and KCC2 drives the hyperexcitability of motoneurons which leads to spasticity after SCI.
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Affiliation(s)
- Vanessa Plantier
- Institut de Neurosciences de la Timone (UMR7289), Aix-Marseille Université and CNRSMarseilleFrance
| | - Irene Sanchez-Brualla
- Institut de Neurosciences de la Timone (UMR7289), Aix-Marseille Université and CNRSMarseilleFrance
| | - Nejada Dingu
- Institut de Neurosciences de la Timone (UMR7289), Aix-Marseille Université and CNRSMarseilleFrance
| | - Cécile Brocard
- Institut de Neurosciences de la Timone (UMR7289), Aix-Marseille Université and CNRSMarseilleFrance
| | - Sylvie Liabeuf
- Institut de Neurosciences de la Timone (UMR7289), Aix-Marseille Université and CNRSMarseilleFrance
| | - Florian Gackière
- Institut de Neurosciences de la Timone (UMR7289), Aix-Marseille Université and CNRSMarseilleFrance
| | - Frédéric Brocard
- Institut de Neurosciences de la Timone (UMR7289), Aix-Marseille Université and CNRSMarseilleFrance
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99931
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Gail MH, Altman DG, Cadarette SM, Collins G, Evans SJ, Sekula P, Williamson E, Woodward M. Design choices for observational studies of the effect of exposure on disease incidence. BMJ Open 2019; 9:e031031. [PMID: 31822541 PMCID: PMC6924819 DOI: 10.1136/bmjopen-2019-031031] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 08/30/2019] [Accepted: 11/07/2019] [Indexed: 11/03/2022] Open
Abstract
The purpose of this paper is to help readers choose an appropriate observational study design for measuring an association between an exposure and disease incidence. We discuss cohort studies, sub-samples from cohorts (case-cohort and nested case-control designs), and population-based or hospital-based case-control studies. Appropriate study design is the foundation of a scientifically valid observational study. Mistakes in design are often irremediable. Key steps are understanding the scientific aims of the study and what is required to achieve them. Some designs will not yield the information required to realise the aims. The choice of design also depends on the availability of source populations and resources. Choosing an appropriate design requires balancing the pros and cons of various designs in view of study aims and practical constraints. We compare various cohort and case-control designs to estimate the effect of an exposure on disease incidence and mention how certain design features can reduce threats to study validity.
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Affiliation(s)
- Mitchell H Gail
- Biostatistics Branch, National Cancer Institute, Rockville, Maryland, USA
| | - Douglas G Altman
- Nuffield Department of Orthopaedics, Centre for Statistics in Medicine, Oxford, UK
| | - Suzanne M Cadarette
- Faculty of Pharmacy and School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Gary Collins
- Centre for Statistics in Medicine, University of Oxford, Oxford, UK
| | - Stephen Jw Evans
- Medical Statistics Unit, London School of Hygiene and Tropical Medicine, London, UK
| | - Peggy Sekula
- Institute of Genetic Epidemiology and Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
| | - Elizabeth Williamson
- Department of Medical Statistics, London School of Hygiene and Tropical Medicine, London, UK
| | - Mark Woodward
- The George Institute for Global Health, Oxford University UK and University of New South Wales, Sydney, New South Wales, Australia
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99932
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Genetic Disorders Associated with Metal Metabolism. Cells 2019; 8:cells8121598. [PMID: 31835360 PMCID: PMC6952812 DOI: 10.3390/cells8121598] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 12/12/2022] Open
Abstract
Genetic disorders associated with metal metabolism form a large group of disorders and mostly result from defects in the proteins/enzymes involved in nutrient metabolism and energy production. These defects can affect different metabolic pathways and cause mild to severe disorders related to metal metabolism. Some disorders have moderate to severe clinical consequences. In severe cases, these elements accumulate in different tissues and organs, particularly the brain. As they are toxic and interfere with normal biological functions, the severity of the disorder increases. However, the human body requires a very small amount of these elements, and a deficiency of or increase in these elements can cause different genetic disorders to occur. Some of the metals discussed in the present review are copper, iron, manganese, zinc, and selenium. These elements may play a key role in the pathology and physiology of the nervous system.
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99933
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Pang H, Zong Z, Hao L, Cao Q. ABO blood group influences risk of venous thromboembolism and myocardial infarction. J Thromb Thrombolysis 2019; 50:430-438. [DOI: 10.1007/s11239-019-02012-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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99934
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CRISPR/Cas9-based targeted genome editing for correction of recessive dystrophic epidermolysis bullosa using iPS cells. Proc Natl Acad Sci U S A 2019; 116:26846-26852. [PMID: 31818947 DOI: 10.1073/pnas.1907081116] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Recessive dystrophic epidermolysis bullosa (RDEB) is a severe inherited skin disorder caused by mutations in the COL7A1 gene encoding type VII collagen (C7). The spectrum of severity depends on the type of mutation in the COL7A1 gene. C7 is the major constituent of anchoring fibrils (AFs) at the basement membrane zone (BMZ). Patients with RDEB lack functional C7 and have severely impaired dermal-epidermal stability, resulting in extensive blistering and open wounds on the skin that greatly affect the patient's quality of life. There are currently no therapies approved for the treatment of RDEB. Here, we demonstrated the correction of mutations in exon 19 (c.2470insG) and exon 32 (c.3948insT) in the COL7A1 gene through homology-directed repair (HDR). We used the clustered regulatory interspaced short palindromic repeats (CRISPR) Cas9-gRNAs system to modify induced pluripotent stem cells (iPSCs) derived from patients with RDEB in both the heterozygous and homozygous states. Three-dimensional human skin equivalents (HSEs) were generated from gene-corrected iPSCs, differentiated into keratinocytes (KCs) and fibroblasts (FBs), and grafted onto immunodeficient mice, which showed normal expression of C7 at the BMZ as well as restored AFs 2 mo postgrafting. Safety assessment for potential off-target Cas9 cleavage activity did not reveal any unintended nuclease activity. Our findings represent a crucial advance for clinical applications of innovative autologous stem cell-based therapies for RDEB.
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99935
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Kim JH, Hwang J, Jung JH, Lee HJ, Lee DY, Kim SH. Molecular networks of FOXP family: dual biologic functions, interplay with other molecules and clinical implications in cancer progression. Mol Cancer 2019; 18:180. [PMID: 31815635 PMCID: PMC6900861 DOI: 10.1186/s12943-019-1110-3] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 11/25/2019] [Indexed: 02/06/2023] Open
Abstract
Though Forkhead box P (FOXP) transcription factors comprising of FOXP1, FOXP2, FOXP3 and FOXP4 are involved in the embryonic development, immune disorders and cancer progression, the underlying function of FOXP3 targeting CD4 + CD25+ regulatory T (Treg) cells and the dual roles of FOXP proteins as an oncogene or a tumor suppressor are unclear and controversial in cancers to date. Thus, the present review highlighted research history, dual roles of FOXP proteins as a tumor suppressor or an oncogene, their molecular networks with other proteins and noncoding RNAs, cellular immunotherapy targeting FOXP3, and clinical implications in cancer progression.
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Affiliation(s)
- Ju-Ha Kim
- Cancer Molecular Target Herbal Research Lab, College of Korean Medicine, Kyung Hee university, 1 Hoegi-dong, Dongdaemun-gu, Seoul, 02447, Republic of Korea
| | - Jisung Hwang
- Cancer Molecular Target Herbal Research Lab, College of Korean Medicine, Kyung Hee university, 1 Hoegi-dong, Dongdaemun-gu, Seoul, 02447, Republic of Korea
| | - Ji Hoon Jung
- Cancer Molecular Target Herbal Research Lab, College of Korean Medicine, Kyung Hee university, 1 Hoegi-dong, Dongdaemun-gu, Seoul, 02447, Republic of Korea
| | - Hyo-Jung Lee
- Cancer Molecular Target Herbal Research Lab, College of Korean Medicine, Kyung Hee university, 1 Hoegi-dong, Dongdaemun-gu, Seoul, 02447, Republic of Korea
| | - Dae Young Lee
- Department of Herbal Crop Research, Rural Development Administration, National Institute of Horticultural and Herbal Science, Eumseong, 27709, Republic of Korea
| | - Sung-Hoon Kim
- Cancer Molecular Target Herbal Research Lab, College of Korean Medicine, Kyung Hee university, 1 Hoegi-dong, Dongdaemun-gu, Seoul, 02447, Republic of Korea.
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99936
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Tilot AK, Vino A, Kucera KS, Carmichael DA, van den Heuvel L, den Hoed J, Sidoroff-Dorso AV, Campbell A, Porteous DJ, St Pourcain B, van Leeuwen TM, Ward J, Rouw R, Simner J, Fisher SE. Investigating genetic links between grapheme-colour synaesthesia and neuropsychiatric traits. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190026. [PMID: 31630655 PMCID: PMC6834005 DOI: 10.1098/rstb.2019.0026] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2019] [Indexed: 12/22/2022] Open
Abstract
Synaesthesia is a neurological phenomenon affecting perception, where triggering stimuli (e.g. letters and numbers) elicit unusual secondary sensory experiences (e.g. colours). Family-based studies point to a role for genetic factors in the development of this trait. However, the contributions of common genomic variation to synaesthesia have not yet been investigated. Here, we present the SynGenes cohort, the largest genotyped collection of unrelated people with grapheme-colour synaesthesia (n = 723). Synaesthesia has been associated with a range of other neuropsychological traits, including enhanced memory and mental imagery, as well as greater sensory sensitivity. Motivated by the prior literature on putative trait overlaps, we investigated polygenic scores derived from published genome-wide scans of schizophrenia and autism spectrum disorder (ASD), comparing our SynGenes cohort to 2181 non-synaesthetic controls. We found a very slight association between schizophrenia polygenic scores and synaesthesia (Nagelkerke's R2 = 0.0047, empirical p = 0.0027) and no significant association for scores related to ASD (Nagelkerke's R2 = 0.00092, empirical p = 0.54) or body mass index (R2 = 0.00058, empirical p = 0.60), included as a negative control. As sample sizes for studying common genomic variation continue to increase, genetic investigations of the kind reported here may yield novel insights into the shared biology between synaesthesia and other traits, to complement findings from neuropsychology and brain imaging. This article is part of a discussion meeting issue 'Bridging senses: novel insights from synaesthesia'.
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Affiliation(s)
- Amanda K. Tilot
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, The Netherlands
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA 90033, USA
| | - Arianna Vino
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, The Netherlands
| | - Katerina S. Kucera
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, The Netherlands
| | - Duncan A. Carmichael
- School of Applied Sciences, Edinburgh Napier University, Sighthill Court, Edinburgh EH11 4BN, UK
| | - Loes van den Heuvel
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, The Netherlands
| | - Joery den Hoed
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, The Netherlands
| | | | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh EH16 4UX, UK
| | - David J. Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Beate St Pourcain
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, The Netherlands
| | - Tessa M. van Leeuwen
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6500 HE Nijmegen, The Netherlands
| | - Jamie Ward
- School of Psychology, University of Sussex, Brighton BN1 9RH, UK
| | - Romke Rouw
- Department of Psychology, University of Amsterdam, 1018 WT Amsterdam, The Netherlands
| | - Julia Simner
- School of Psychology, University of Sussex, Brighton BN1 9RH, UK
| | - Simon E. Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6500 HE Nijmegen, The Netherlands
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99937
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Sun QY, Xu Q, Tian Y, Hu ZM, Qin LX, Yang JX, Huang W, Xue J, Li JC, Zeng S, Wang Y, Min HX, Chen XY, Wang JP, Xie B, Liang F, Zhang HN, Wang CY, Lei LF, Yan XX, Xu HW, Duan RH, Xia K, Liu JY, Jiang H, Shen L, Guo JF, Tang BS. Expansion of GGC repeat in the human-specific NOTCH2NLC gene is associated with essential tremor. Brain 2019; 143:222-233. [PMID: 31819945 DOI: 10.1093/brain/awz372] [Citation(s) in RCA: 138] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 09/06/2019] [Accepted: 10/04/2019] [Indexed: 12/22/2022] Open
Abstract
Abstract
Essential tremor is one of the most common movement disorders. Despite its high prevalence and heritability, the genetic aetiology of essential tremor remains elusive. Up to now, only a few genes/loci have been identified, but these genes have not been replicated in other essential tremor families or cohorts. Here we report a genetic study in a cohort of 197 Chinese pedigrees clinically diagnosed with essential tremor. Using a comprehensive strategy combining linkage analysis, whole-exome sequencing, long-read whole-genome sequencing, repeat-primed polymerase chain reaction and GC-rich polymerase chain reaction, we identified an abnormal GGC repeat expansion in the 5′ region of the NOTCH2NLC gene that co-segregated with disease in 11 essential tremor families (5.58%) from our cohort. Clinically, probands that had an abnormal GGC repeat expansion were found to have more severe tremor phenotypes, lower activities of daily living ability. Obvious genetic anticipation was also detected in these 11 essential tremor-positive families. These results indicate that abnormal GGC repeat expansion in the 5′ region of NOTCH2NLC gene is associated with essential tremor, and provide strong evidence that essential tremor is a family of diseases with high clinical and genetic heterogeneities.
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Affiliation(s)
- Qi-Ying Sun
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qian Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yun Tian
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zheng-Mao Hu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
| | - Li-Xia Qin
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jin-Xia Yang
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wen Huang
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Jin Xue
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Jin-Chen Li
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Sheng Zeng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ying Wang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | | | - Xiao-Yu Chen
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jun-Pu Wang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bin Xie
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Fan Liang
- GrandOmics Biosciences, Beijing, China
| | - Hai-Nan Zhang
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Chun-Yu Wang
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Li-Fang Lei
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xin-Xiang Yan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hong-Wei Xu
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ran-Hui Duan
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
| | - Kun Xia
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
| | - Jing-Yu Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Center for Human Genome Research, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Hong Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China
| | - Lu Shen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ji-Feng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bei-Sha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China
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99938
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Gong HB, Wu XJ, Pu XM, Kang XJ. Association of Interleukin-23R Gene Polymorphisms with Behcet’s Disease Susceptibility: A Meta-Analysis of Case-control Studies. Immunol Invest 2019; 49:648-661. [PMID: 31814470 DOI: 10.1080/08820139.2019.1698600] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Hai-Bo Gong
- Department of Dermatology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, China
| | - Xiu-Juan Wu
- Department of Dermatology, Shanghai Xuhui Central Hospital, Shanghai, China
| | - Xiong-Ming Pu
- Department of Dermatology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, China
| | - Xiao-Jing Kang
- Department of Dermatology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, China
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99939
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Abstract
Aortic aneurysms are a common vascular disease in Western populations that can involve virtually any portion of the aorta. Abdominal aortic aneurysms are much more common than thoracic aortic aneurysms and combined they account for >25 000 deaths in the United States annually. Although thoracic and abdominal aortic aneurysms share some common characteristics, including the gross anatomic appearance, alterations in extracellular matrix, and loss of smooth muscle cells, they are distinct diseases. In recent years, advances in genetic analysis, robust molecular tools, and increased availability of animal models have greatly enhanced our knowledge of the pathophysiology of aortic aneurysms. This review examines the various proposed cellular mechanisms responsible for aortic aneurysm formation and identifies opportunities for future studies.
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Affiliation(s)
- Raymundo Alain Quintana
- From the Division of Cardiology, Department of Medicine (R.A.Q., W.R.T.), Emory University School of Medicine, Atlanta, GA
| | - W Robert Taylor
- From the Division of Cardiology, Department of Medicine (R.A.Q., W.R.T.), Emory University School of Medicine, Atlanta, GA.,Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology (W.R.T.), Emory University School of Medicine, Atlanta, GA.,Division of Cardiology, Atlanta VA Medical Center, Decatur, GA (W.R.T.)
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99940
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Schwartzman DJ, Bor D, Rothen N, Seth AK. Neurophenomenology of induced and natural synaesthesia. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190030. [PMID: 31630656 PMCID: PMC6834010 DOI: 10.1098/rstb.2019.0030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2019] [Indexed: 12/15/2022] Open
Abstract
People with synaesthesia have additional perceptual experiences, which are automatically and consistently triggered by specific inducing stimuli. Synaesthesia therefore offers a unique window into the neurocognitive mechanisms underlying conscious perception. A long-standing question in synaesthesia research is whether it is possible to artificially induce non-synaesthetic individuals to have synaesthesia-like experiences. Although synaesthesia is widely considered a congenital condition, increasing evidence points to the potential of a variety of approaches to induce synaesthesia-like experiences, even in adulthood. Here, we summarize a range of methods for artificially inducing synaesthesia-like experiences, comparing the resulting experiences to the key hallmarks of natural synaesthesia which include consistency, automaticity and a lack of 'perceptual presence'. We conclude that a number of aspects of synaesthesia can be artificially induced in non-synaesthetes. These data suggest the involvement of developmental and/or learning components in the acquisition of synaesthesia, and they extend previous reports of perceptual plasticity leading to dramatic changes in perceptual phenomenology in adults. This article is part of a discussion meeting issue 'Bridging senses: novel insights from synaesthesia'.
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Affiliation(s)
- David J. Schwartzman
- Sackler Centre for Consciousness Science, University of Sussex, Brighton BN1 9QJ, UK
- Department of Informatics, University of Sussex, Brighton BN1 9QJ, UK
| | - Daniel Bor
- Department of Psychology, University of Cambridge, Downing Street, Cambridge CB2 3EB, UK
| | - Nicolas Rothen
- Sackler Centre for Consciousness Science, University of Sussex, Brighton BN1 9QJ, UK
- Faculty of Psychology, Swiss Distance University Institute, 3900 Brig, Switzerland
| | - Anil K. Seth
- Sackler Centre for Consciousness Science, University of Sussex, Brighton BN1 9QJ, UK
- Department of Informatics, University of Sussex, Brighton BN1 9QJ, UK
- Azrieli Programme on Brain, Mind, and Consciousness, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
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99941
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Yohe S, Sivasankar M, Ghosh A, Ghosh A, Holle J, Murugan S, Gupta R, Schimmenti LA, Vedam R, Thyagarajan B. Prevalence of mutations in inherited retinal diseases: A comparison between the United States and India. Mol Genet Genomic Med 2019; 8:e1081. [PMID: 31816670 PMCID: PMC7005662 DOI: 10.1002/mgg3.1081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 10/14/2019] [Accepted: 10/30/2019] [Indexed: 11/26/2022] Open
Abstract
Background Studies evaluating next‐generation sequencing (NGS) for retinal disorders may not reflect clinical practice. We report results of retrospective analysis of patients referred for clinical testing at two institutions (US and India). Methods This retrospective study of 131 patients who underwent clinically validated targeted NGS or exome sequencing for a wide variety of clinical phenotypes categorized results into a definitive, indeterminate, or negative molecular diagnosis. Results A definitive molecular diagnosis (52%) was more common in the India cohort (62% vs. 39%, p = .009), while an indeterminate molecular diagnosis occurred only in the US cohort (12%). In the US cohort, a lower diagnostic rate in Hispanic, non‐Caucasians (23%) was seen compared to Caucasians (57%). The India cohort had a high rate of homozygous variants (61%) and different frequency of genes involved compared to the US cohort. Conclusion Despite inherent limitations in clinical testing, the diagnostic rate across the two cohorts (52%) was similar to the 50%–65% diagnostic rate in the literature. However, the diagnostic rate was lower in the US cohort and appears partly explained by racial background. The high rate of consanguinity in the Indian population is reflected in the high rate of homozygosity for pathogenic mutations and may have implications for population level screening and genetic counseling. Clinical laboratories may note diagnostic rates that differ from the literature, due to factors such as heterogeneity in racial background or consanguinity rates in the populations being tested. This information may be useful for post‐test counseling.
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Affiliation(s)
- Sophia Yohe
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | | | | | | | - Jennifer Holle
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | | | | | - Lisa A Schimmenti
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | | | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
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99942
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Abstract
The genetic correlation describes the genetic relationship between two traits and can contribute to a better understanding of the shared biological pathways and/or the causality relationships between them. The rarity of large family cohorts with recorded instances of two traits, particularly disease traits, has made it difficult to estimate genetic correlations using traditional epidemiological approaches. However, advances in genomic methodologies, such as genome-wide association studies, and widespread sharing of data now allow genetic correlations to be estimated for virtually any trait pair. Here, we review the definition, estimation, interpretation and uses of genetic correlations, with a focus on applications to human disease.
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99943
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Donadon I, Bussani E, Riccardi F, Licastro D, Romano G, Pianigiani G, Pinotti M, Konstantinova P, Evers M, Lin S, Rüegg MA, Pagani F. Rescue of spinal muscular atrophy mouse models with AAV9-Exon-specific U1 snRNA. Nucleic Acids Res 2019; 47:7618-7632. [PMID: 31127278 PMCID: PMC6698663 DOI: 10.1093/nar/gkz469] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 05/10/2019] [Accepted: 05/16/2019] [Indexed: 12/12/2022] Open
Abstract
Spinal Muscular Atrophy results from loss-of-function mutations in SMN1 but correcting aberrant splicing of SMN2 offers hope of a cure. However, current splice therapy requires repeated infusions and is expensive. We previously rescued SMA mice by promoting the inclusion of a defective exon in SMN2 with germline expression of Exon-Specific U1 snRNAs (ExspeU1). Here we tested viral delivery of SMN2 ExspeU1s encoded by adeno-associated virus AAV9. Strikingly the virus increased SMN2 exon 7 inclusion and SMN protein levels and rescued the phenotype of mild and severe SMA mice. In the severe mouse, the treatment improved the neuromuscular function and increased the life span from 10 to 219 days. ExspeU1 expression persisted for 1 month and was effective at around one five-hundredth of the concentration of the endogenous U1snRNA. RNA-seq analysis revealed our potential drug rescues aberrant SMA expression and splicing profiles, which are mostly related to DNA damage, cell-cycle control and acute phase response. Vastly overexpressing ExspeU1 more than 100-fold above the therapeutic level in human cells did not significantly alter global gene expression or splicing. These results indicate that AAV-mediated delivery of a modified U1snRNP particle may be a novel therapeutic option against SMA.
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Affiliation(s)
- Irving Donadon
- Human Molecular Genetics, International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy
| | - Erica Bussani
- Human Molecular Genetics, International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy
| | - Federico Riccardi
- Human Molecular Genetics, International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy
| | - Danilo Licastro
- CBM S.c.r.l., Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Giulia Romano
- Human Molecular Genetics, International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy
| | - Giulia Pianigiani
- Human Molecular Genetics, International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy
| | - Mirko Pinotti
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Pavlina Konstantinova
- Department of Research & Development, uniQure biopharma B.V., Amsterdam, The Netherlands
| | - Melvin Evers
- Department of Research & Development, uniQure biopharma B.V., Amsterdam, The Netherlands
| | - Shuo Lin
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
| | - Markus A Rüegg
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
| | - Franco Pagani
- Human Molecular Genetics, International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy
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99944
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Dubois EL, Guitton-Sert L, Béliveau M, Parmar K, Chagraoui J, Vignard J, Pauty J, Caron MC, Coulombe Y, Buisson R, Jacquet K, Gamblin C, Gao Y, Laprise P, Lebel M, Sauvageau G, D d'Andrea A, Masson JY. A Fanci knockout mouse model reveals common and distinct functions for FANCI and FANCD2. Nucleic Acids Res 2019; 47:7532-7547. [PMID: 31219578 PMCID: PMC6698648 DOI: 10.1093/nar/gkz514] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 05/22/2019] [Accepted: 06/05/2019] [Indexed: 12/12/2022] Open
Abstract
Fanconi Anemia (FA) clinical phenotypes are heterogenous and rely on a mutation in one of the 22 FANC genes (FANCA-W) involved in a common interstrand DNA crosslink-repair pathway. A critical step in the activation of FA pathway is the monoubiquitination of FANCD2 and its binding partner FANCI. To better address the clinical phenotype associated with FANCI and the epistatic relationship with FANCD2, we created the first conditional inactivation model for FANCI in mouse. Fanci −/− mice displayed typical FA features such as delayed development in utero, microphtalmia, cellular sensitivity to mitomycin C, occasional limb abnormalities and hematological deficiencies. Interestingly, the deletion of Fanci leads to a strong meiotic phenotype and severe hypogonadism. FANCI was localized in spermatocytes and spermatids and in the nucleus of oocytes. Both FANCI and FANCD2 proteins co-localized with RPA along meiotic chromosomes, albeit at different levels. Consistent with a role in meiotic recombination, FANCI interacted with RAD51 and stimulated D-loop formation, unlike FANCD2. The double knockout Fanci−/− Fancd2−/− also showed epistatic relationship for hematological defects while being not epistatic with respect to generating viable mice in crosses of double heterozygotes. Collectively, this study highlights common and distinct functions of FANCI and FANCD2 during mouse development, meiotic recombination and hematopoiesis.
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Affiliation(s)
- Emilie L Dubois
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - Laure Guitton-Sert
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - Mariline Béliveau
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - Kalindi Parmar
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jalila Chagraoui
- Laboratory of Molecular Genetics of Hematopoietic Stem Cells, Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, H3C 3J7, Canada
| | - Julien Vignard
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - Joris Pauty
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - Marie-Christine Caron
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - Yan Coulombe
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - Rémi Buisson
- Department of Biological Chemistry, University of California, Irvine, CA 92697, USA
| | - Karine Jacquet
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - Clémence Gamblin
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - Yuandi Gao
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - Patrick Laprise
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - Michel Lebel
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - Guy Sauvageau
- Department of Biological Chemistry, University of California, Irvine, CA 92697, USA
| | - Alan D d'Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jean-Yves Masson
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada.,FRQS chair in genome stability
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99945
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Woo Y, Kim SJ, Suh BK, Kwak Y, Jung HJ, Nhung TTM, Mun DJ, Hong JH, Noh SJ, Kim S, Lee A, Baek ST, Nguyen MD, Choe Y, Park SK. Sequential phosphorylation of NDEL1 by the DYRK2-GSK3β complex is critical for neuronal morphogenesis. eLife 2019; 8:e50850. [PMID: 31815665 PMCID: PMC6927744 DOI: 10.7554/elife.50850] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 12/08/2019] [Indexed: 12/20/2022] Open
Abstract
Neuronal morphogenesis requires multiple regulatory pathways to appropriately determine axonal and dendritic structures, thereby to enable the functional neural connectivity. Yet, however, the precise mechanisms and components that regulate neuronal morphogenesis are still largely unknown. Here, we newly identified the sequential phosphorylation of NDEL1 critical for neuronal morphogenesis through the human kinome screening and phospho-proteomics analysis of NDEL1 from mouse brain lysate. DYRK2 phosphorylates NDEL1 S336 to prime the phosphorylation of NDEL1 S332 by GSK3β. TARA, an interaction partner of NDEL1, scaffolds DYRK2 and GSK3β to form a tripartite complex and enhances NDEL1 S336/S332 phosphorylation. This dual phosphorylation increases the filamentous actin dynamics. Ultimately, the phosphorylation enhances both axonal and dendritic outgrowth and promotes their arborization. Together, our findings suggest the NDEL1 phosphorylation at S336/S332 by the TARA-DYRK2-GSK3β complex as a novel regulatory mechanism underlying neuronal morphogenesis.
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Affiliation(s)
- Youngsik Woo
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
| | - Soo Jeong Kim
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
| | - Bo Kyoung Suh
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
| | - Yongdo Kwak
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
| | - Hyun-Jin Jung
- Korea Brain Research InstituteDaeguRepublic of Korea
| | - Truong Thi My Nhung
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
| | - Dong Jin Mun
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
| | - Ji-Ho Hong
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
| | - Su-Jin Noh
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
| | - Seunghyun Kim
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
| | - Ahryoung Lee
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
| | - Seung Tae Baek
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
| | - Minh Dang Nguyen
- Hotchkiss Brain Institute, Cumming School of MedicineUniversity of CalgaryCalgaryCanada
- Department of Clinical Neurosciences, Cumming School of MedicineUniversity of CalgaryCalgaryCanada
- Department of Cell Biology and Anatomy, Cumming School of MedicineUniversity of CalgaryCalgaryCanada
- Department of Biochemistry and Molecular Biology, Cumming School of MedicineUniversity of CalgaryCalgaryCanada
| | | | - Sang Ki Park
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
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99946
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Su J, Fu H, Xie B, Lu W, Li W, Wei Y, Zhang Q, Wei S, Chen Q, Lu Y, Jiang T, Luo J, Qin Z. Prenatal diagnosis of cri-du-chat syndrome by SNP array: report of twelve cases and review of the literature. Mol Cytogenet 2019; 12:49. [PMID: 31827621 PMCID: PMC6902614 DOI: 10.1186/s13039-019-0462-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 11/27/2019] [Indexed: 04/28/2023] Open
Abstract
Background Cri-du-chat syndrome (CdCS; OMIM#123450) is a classic contiguous gene syndrome caused by chromosome 5p terminal deletion (5p-), which characterized by a high-pitched cat-like cry, developmental delay, severe psychomotor, mental retardation, and dysmorphic features in infancy. Prenatal diagnosis of CdCS is difficult due to the non-specific ultrasound features. And reports using array analysis are rare. This study presented the first retrospective analysis of prenatal series of CdCS fetuses diagnosed by single nucleotide polymorphism (SNP) array in China. Case presentation A total of 35,233 pregnant women were enrolled from Jan 2014 to April 2019 in our center, there are twelve 5p- cases with abnormal sonographic signs revealed by SNP array, giving an incidence of 0.034% (12/35,233). Clinical information and molecular basis included: maternal demographics, indications for invasive testing, sonographic findings and SNP array results. Among all the 5p- cases revealed, nine cases were diagnosed by both karyotyping and SNP array, three cases were detected only by SNP array. Half of our cases (6/12) had an isolated 5p terminal deletion, which sizes ranged from 9.0 Mb to 30 Mb. The other half of cases (6/12) characterized by unbalanced translocation, with sex ratio 7:5 (female: male), when combine the clinical features observed from this study and available literature, the most frequent anomaly observed in prenatal ultrasound examination of CdCS was cerebral abnormalities, accounted for 44.4% (16/36) of the existing cases. Features that are less consistent included: choroid plexus cyst (13.8%, 5/36), single umbilical artery (13.3%, 4/30), ventricular septal defect (11.1%, 4/36), hydrops fetalis (8.3%, 3/36), ascites (8.3%, 3/36), increased NT/NF (8.3%, 3/36), absent/severely hypoplastic nasal bone (5.5%, 2/36), in order. Conclusion Prenatal findings such as cerebral abnormalities, absent/hypoplastic nasal bone, hydrops fetalis, ascites or encephalocele may act as suggestive signs of CdCS or other microdeletion/duplication syndromes. Combining typical karyotyping with chromosomal microarray analysis (CMA) is a definitive method for a precise diagnosis of CdCS and provides more accurate results in order to offer genetic counseling to families which need to deal with cryptic aberrations.
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Affiliation(s)
- Jiasun Su
- 1Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Guangxi Birth Defects Prevention and Control Institute, No.59, Xiangzhu Road, Nanning, China
| | - Huayu Fu
- 2Department of Genetic Counseling, Guangxi Maternal and Child Health Hospital, No.225, Xinyang Road, Nanning, China
| | - Bobo Xie
- 1Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Guangxi Birth Defects Prevention and Control Institute, No.59, Xiangzhu Road, Nanning, China
| | - Weiliang Lu
- 1Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Guangxi Birth Defects Prevention and Control Institute, No.59, Xiangzhu Road, Nanning, China
| | - Wei Li
- 1Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Guangxi Birth Defects Prevention and Control Institute, No.59, Xiangzhu Road, Nanning, China
| | - Yuan Wei
- 1Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Guangxi Birth Defects Prevention and Control Institute, No.59, Xiangzhu Road, Nanning, China
| | - Qiang Zhang
- 1Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Guangxi Birth Defects Prevention and Control Institute, No.59, Xiangzhu Road, Nanning, China
| | - Shengkai Wei
- 1Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Guangxi Birth Defects Prevention and Control Institute, No.59, Xiangzhu Road, Nanning, China
| | - Qiuli Chen
- 1Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Guangxi Birth Defects Prevention and Control Institute, No.59, Xiangzhu Road, Nanning, China
| | - Yingchi Lu
- 1Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Guangxi Birth Defects Prevention and Control Institute, No.59, Xiangzhu Road, Nanning, China
| | - Tingting Jiang
- 1Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Guangxi Birth Defects Prevention and Control Institute, No.59, Xiangzhu Road, Nanning, China
| | - Jingsi Luo
- 1Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Guangxi Birth Defects Prevention and Control Institute, No.59, Xiangzhu Road, Nanning, China
| | - Zailong Qin
- 1Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Guangxi Birth Defects Prevention and Control Institute, No.59, Xiangzhu Road, Nanning, China
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99947
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Shohayeb B, Ho U, Yeap YY, Parton RG, Millard SS, Xu Z, Piper M, Ng DCH. The association of microcephaly protein WDR62 with CPAP/IFT88 is required for cilia formation and neocortical development. Hum Mol Genet 2019; 29:248-263. [DOI: 10.1093/hmg/ddz281] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 02/07/2023] Open
Abstract
Abstract
WDR62 mutations that result in protein loss, truncation or single amino-acid substitutions are causative for human microcephaly, indicating critical roles in cell expansion required for brain development. WDR62 missense mutations that retain protein expression represent partial loss-of-function mutants that may therefore provide specific insights into radial glial cell processes critical for brain growth. Here we utilized CRISPR/Cas9 approaches to generate three strains of WDR62 mutant mice; WDR62 V66M/V66M and WDR62R439H/R439H mice recapitulate conserved missense mutations found in humans with microcephaly, with the third strain being a null allele (WDR62stop/stop). Each of these mutations resulted in embryonic lethality to varying degrees and gross morphological defects consistent with ciliopathies (dwarfism, anophthalmia and microcephaly). We find that WDR62 mutant proteins (V66M and R439H) localize to the basal body but fail to recruit CPAP. As a consequence, we observe deficient recruitment of IFT88, a protein that is required for cilia formation. This underpins the maintenance of radial glia as WDR62 mutations caused premature differentiation of radial glia resulting in reduced generation of neurons and cortical thinning. These findings highlight the important role of the primary cilium in neocortical expansion and implicate ciliary dysfunction as underlying the pathology of MCPH2 patients.
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Affiliation(s)
- Belal Shohayeb
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, St Lucia 4072, Australia
| | - Uda Ho
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, St Lucia 4072, Australia
| | - Yvonne Y Yeap
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, St Lucia 4072, Australia
| | - Robert G Parton
- Institute for Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia
- Centre for Microscopy and Microanalysis, The University of Queensland, St Lucia 4072, Australia
| | - S Sean Millard
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, St Lucia 4072, Australia
| | - Zhiheng Xu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Michael Piper
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, St Lucia 4072, Australia
| | - Dominic C H Ng
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, St Lucia 4072, Australia
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99948
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McDermott MI, Wang Y, Wakelam MJO, Bankaitis VA. Mammalian phospholipase D: Function, and therapeutics. Prog Lipid Res 2019; 78:101018. [PMID: 31830503 DOI: 10.1016/j.plipres.2019.101018] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 10/08/2019] [Accepted: 10/14/2019] [Indexed: 01/23/2023]
Abstract
Despite being discovered over 60 years ago, the precise role of phospholipase D (PLD) is still being elucidated. PLD enzymes catalyze the hydrolysis of the phosphodiester bond of glycerophospholipids producing phosphatidic acid and the free headgroup. PLD family members are found in organisms ranging from viruses, and bacteria to plants, and mammals. They display a range of substrate specificities, are regulated by a diverse range of molecules, and have been implicated in a broad range of cellular processes including receptor signaling, cytoskeletal regulation and membrane trafficking. Recent technological advances including: the development of PLD knockout mice, isoform-specific antibodies, and specific inhibitors are finally permitting a thorough analysis of the in vivo role of mammalian PLDs. These studies are facilitating increased recognition of PLD's role in disease states including cancers and Alzheimer's disease, offering potential as a target for therapeutic intervention.
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Affiliation(s)
- M I McDermott
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843-1114, United States of America.
| | - Y Wang
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843-1114, United States of America; Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, United States of America
| | - M J O Wakelam
- Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - V A Bankaitis
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843-1114, United States of America; Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, United States of America; Department of Chemistry, Texas A&M University, College Station, Texas 77840, United States of America
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99949
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Page DJ, Miossec MJ, Williams SG, Monaghan RM, Fotiou E, Cordell HJ, Sutcliffe L, Topf A, Bourgey M, Bourque G, Eveleigh R, Dunwoodie SL, Winlaw DS, Bhattacharya S, Breckpot J, Devriendt K, Gewillig M, Brook JD, Setchfield KJ, Bu'Lock FA, O'Sullivan J, Stuart G, Bezzina CR, Mulder BJM, Postma AV, Bentham JR, Baron M, Bhaskar SS, Black GC, Newman WG, Hentges KE, Lathrop GM, Santibanez-Koref M, Keavney BD. Whole Exome Sequencing Reveals the Major Genetic Contributors to Nonsyndromic Tetralogy of Fallot. Circ Res 2019; 124:553-563. [PMID: 30582441 DOI: 10.1161/circresaha.118.313250] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
RATIONALE Familial recurrence studies provide strong evidence for a genetic component to the predisposition to sporadic, nonsyndromic Tetralogy of Fallot (TOF), the most common cyanotic congenital heart disease phenotype. Rare genetic variants have been identified as important contributors to the risk of congenital heart disease, but relatively small numbers of TOF cases have been studied to date. OBJECTIVE We used whole exome sequencing to assess the prevalence of unique, deleterious variants in the largest cohort of nonsyndromic TOF patients reported to date. METHODS AND RESULTS Eight hundred twenty-nine TOF patients underwent whole exome sequencing. The presence of unique, deleterious variants was determined; defined by their absence in the Genome Aggregation Database and a scaled combined annotation-dependent depletion score of ≥20. The clustering of variants in 2 genes, NOTCH1 and FLT4, surpassed thresholds for genome-wide significance (assigned as P<5×10-8) after correction for multiple comparisons. NOTCH1 was most frequently found to harbor unique, deleterious variants. Thirty-one changes were observed in 37 probands (4.5%; 95% CI, 3.2%-6.1%) and included 7 loss-of-function variants 22 missense variants and 2 in-frame indels. Sanger sequencing of the unaffected parents of 7 cases identified 5 de novo variants. Three NOTCH1 variants (p.G200R, p.C607Y, and p.N1875S) were subjected to functional evaluation, and 2 showed a reduction in Jagged1-induced NOTCH signaling. FLT4 variants were found in 2.4% (95% CI, 1.6%-3.8%) of TOF patients, with 21 patients harboring 22 unique, deleterious variants. The variants identified were distinct to those that cause the congenital lymphoedema syndrome Milroy disease. In addition to NOTCH1, FLT4 and the well-established TOF gene, TBX1, we identified potential association with variants in several other candidates, including RYR1, ZFPM1, CAMTA2, DLX6, and PCM1. CONCLUSIONS The NOTCH1 locus is the most frequent site of genetic variants predisposing to nonsyndromic TOF, followed by FLT4. Together, variants in these genes are found in almost 7% of TOF patients.
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Affiliation(s)
- Donna J Page
- From the Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, Manchester Academic Health Science Centre, University of Manchester, United Kingdom (D.J.P., S.G.W., R.M.M., E.F., B.D.K.)
| | - Matthieu J Miossec
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom (M.J.M., H.J.C., L.S., A.T., M.S.-K.).,Center for Bioinformatics and Integrative Biology, Faculty of Biological Sciences, Universidad Andrés Bello, Santiago, Chile (M.J.M.)
| | - Simon G Williams
- From the Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, Manchester Academic Health Science Centre, University of Manchester, United Kingdom (D.J.P., S.G.W., R.M.M., E.F., B.D.K.)
| | - Richard M Monaghan
- From the Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, Manchester Academic Health Science Centre, University of Manchester, United Kingdom (D.J.P., S.G.W., R.M.M., E.F., B.D.K.)
| | - Elisavet Fotiou
- From the Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, Manchester Academic Health Science Centre, University of Manchester, United Kingdom (D.J.P., S.G.W., R.M.M., E.F., B.D.K.)
| | - Heather J Cordell
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom (M.J.M., H.J.C., L.S., A.T., M.S.-K.)
| | | | - Ana Topf
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom (M.J.M., H.J.C., L.S., A.T., M.S.-K.)
| | - Mathieu Bourgey
- Canadian Centre for Computational Genomics, Montréal, QC, Canada (M.B.).,McGill Genome Center, Montréal, QC, Canada (M.B., G.B., R.E., G.M.L.)
| | - Guillaume Bourque
- McGill Genome Center, Montréal, QC, Canada (M.B., G.B., R.E., G.M.L.)
| | - Robert Eveleigh
- McGill Genome Center, Montréal, QC, Canada (M.B., G.B., R.E., G.M.L.)
| | - Sally L Dunwoodie
- Chain Reaction Program in Congenital Heart Disease Research, Victor Chang Cardiac Research Institute, Sydney, NSW, Australia (S.L.D.).,Faculties of Medicine and Science, University of New South Wales, Sydney (S.L.D.).,Heart Centre for Children, The Children's Hospital at Westmead, Sydney, NSW (S.L.D.)
| | - David S Winlaw
- School of Child and Adolescent Health, Sydney Medical School, University of Sydney (D.S.W.).,Victor Chang Cardiac Research Institute, NSW, Australia (D.S.W.).,RDM Cardiovascular Medicine, Wellcome Centre for Human Genetics, University of Oxford (D.S.W., S.B.)
| | - Shoumo Bhattacharya
- RDM Cardiovascular Medicine, Wellcome Centre for Human Genetics, University of Oxford (D.S.W., S.B.).,Center for Human Genetics, Catholic University Leuven, Belgium (S.B., J.B., K.D.)
| | - Jeroen Breckpot
- Center for Human Genetics, Catholic University Leuven, Belgium (S.B., J.B., K.D.).,Pediatric and Congenital Cardiology, UZ Leuven (J.B., M.G.)
| | - Koenraad Devriendt
- Center for Human Genetics, Catholic University Leuven, Belgium (S.B., J.B., K.D.)
| | - Marc Gewillig
- Pediatric and Congenital Cardiology, UZ Leuven (J.B., M.G.)
| | - J David Brook
- School of Life Sciences, University of Nottingham, Queen's Medical Centre (J.D.B., K.J.S.)
| | - Kerry J Setchfield
- School of Life Sciences, University of Nottingham, Queen's Medical Centre (J.D.B., K.J.S.)
| | - Frances A Bu'Lock
- Congenital and Paediatric Cardiology, East Midlands Congenital Heart Centre and University of Leicester, Glenfield Hospital (F.A.B.)
| | - John O'Sullivan
- Adult Congenital and Paediatric Cardiac Unit, Freeman Hospital, Newcastle upon Tyne (J.O.)
| | - Graham Stuart
- University Hospitals Bristol NHS Foundation Trust, Bristol (G.S.)
| | - Connie R Bezzina
- Heart Center, Department of Clinical and Experimental Cardiology (C.R.B.), Academic Medical Center, Amsterdam, the Netherlands
| | - Barbara J M Mulder
- Department of Medical Biology (B.J.M.M.), Academic Medical Center, Amsterdam, the Netherlands
| | - Alex V Postma
- Department of Clinical Genetics (A.V.P.), Academic Medical Center, Amsterdam, the Netherlands
| | - James R Bentham
- Department of Paediatric Cardiology, Yorkshire Heart Centre, Leeds (J.R.B.)
| | - Martin Baron
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester (M.B.)
| | - Sanjeev S Bhaskar
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Oxford, Manchester (S.S.B., G.C.B.)
| | - Graeme C Black
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Oxford, Manchester (S.S.B., G.C.B.)
| | - William G Newman
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford (W.G.N.); and Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, UK
| | | | - G Mark Lathrop
- McGill Genome Center, Montréal, QC, Canada (M.B., G.B., R.E., G.M.L.)
| | - Mauro Santibanez-Koref
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom (M.J.M., H.J.C., L.S., A.T., M.S.-K.)
| | - Bernard D Keavney
- From the Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, Manchester Academic Health Science Centre, University of Manchester, United Kingdom (D.J.P., S.G.W., R.M.M., E.F., B.D.K.)
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99950
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Abstract
BACKGROUND/OBJECTIVE Familial Mediterranean fever (FMF) is an autosomal recessive disease, characterized by recurrent, self-limited attacks of fever with serositis. Various diseases were reported to be associated with FMF. The aim of this study was to investigate the frequency and characteristics of sacroiliitis in children with FMF. METHODS Files of FMF patients who had been seen in 2 reference hospitals in Ankara were retrospectively evaluated. Patients with FMF and concomitant sacroiliitis were included to the study. All patients had magnetic resonance imaging evidence of sacroiliitis. RESULTS Among 650 FMF patients, 17 (11 females, 6 males; mean age, 13.32 ± 4.24 years) (2.6%) of them were found to have sacroiliitis. Familial Mediterranean fever diagnosis was done prior to sacroiliitis diagnosis in 11 patients (65%) and concurrently or afterward in 6 patients (35%). Ten patients had isolated sacroiliitis, and 7 had associated diseases (5 enthesitis-related arthritis, 1 psoriatic arthritis, and 1 ulcerative colitis). Arthritis (59%), arthralgia (77%), leg pain (71%), heel pain (41%), and enthesitis (29%) were common complaints. Sacroiliac tenderness was detected in 77%, and M694V mutation in almost 90% of the patients. All patients received colchicine therapy. Additionally, 14 of them were treated with nonsteroidal anti-inflammatory drugs, 10 were on sulfasalazine treatment, and 7 of them were on biological agents. CONCLUSIONS Sacroiliitis can be seen in patients with FMF during childhood, and M694V mutation seems to be a susceptibility factor for its development. Inflammatory low-back pain and leg and heel pain could suggest sacroiliitis.
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