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Leroy T. Re-evaluating the driving force behind mutations. eLife 2023; 12:e89706. [PMID: 37819030 PMCID: PMC10567108 DOI: 10.7554/elife.89706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023] Open
Abstract
Experiments on tropical trees suggest that new mutations in plants are driven by age rather than number of cell divisions during growth.
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Affiliation(s)
- Thibault Leroy
- GenPhySE, INRAE, INP, ENVT, Université de ToulouseAuzeville-TolosaneFrance
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2
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Abstract
Idiopathic short stature (ISS) is a term used to describe a selection of short children for whom no precise aetiology has been identified. Molecular investigations have made notable discoveries in children with ISS, thus removing them from this category. However, many, if not the majority of children referred with short stature, are designated ISS. Our interest in defects of GH action, i.e. GH resistance, has led to a study of children with mild GH resistance, who we believe can be mis-categorised as ISS leading to potential inappropriate management. Approval of ISS by the FDA for hGH therapy has resulted in many short children receiving this treatment. The results are extremely variable. It is therefore important to correctly assess and investigate all ISS subjects in order to identify those with mild but unequivocal GH resistance, as in cases of PAPP-A2 deficiency. The correct identification of GH resistance defects will direct therapy towards rhIGF-I rather than rhGH. This example illustrates the importance of recognition of GH resistance among the very large number patients referred with short stature who are labelled as 'ISS'.
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Affiliation(s)
- Martin O. Savage
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine & Dentistry, Queen Mary University of London, London, United Kingdom
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3
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Moreira JD, Gopal DM, Kotton DN, Fetterman JL. Gaining Insight into Mitochondrial Genetic Variation and Downstream Pathophysiology: What Can i(PSCs) Do? Genes (Basel) 2021; 12:1668. [PMID: 34828274 PMCID: PMC8624338 DOI: 10.3390/genes12111668] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 12/14/2022] Open
Abstract
Mitochondria are specialized organelles involved in energy production that have retained their own genome throughout evolutionary history. The mitochondrial genome (mtDNA) is maternally inherited and requires coordinated regulation with nuclear genes to produce functional enzyme complexes that drive energy production. Each mitochondrion contains 5-10 copies of mtDNA and consequently, each cell has several hundreds to thousands of mtDNAs. Due to the presence of multiple copies of mtDNA in a mitochondrion, mtDNAs with different variants may co-exist, a condition called heteroplasmy. Heteroplasmic variants can be clonally expanded, even in post-mitotic cells, as replication of mtDNA is not tied to the cell-division cycle. Heteroplasmic variants can also segregate during germ cell formation, underlying the inheritance of some mitochondrial mutations. Moreover, the uneven segregation of heteroplasmic variants is thought to underlie the heterogeneity of mitochondrial variation across adult tissues and resultant differences in the clinical presentation of mitochondrial disease. Until recently, however, the mechanisms mediating the relation between mitochondrial genetic variation and disease remained a mystery, largely due to difficulties in modeling human mitochondrial genetic variation and diseases. The advent of induced pluripotent stem cells (iPSCs) and targeted gene editing of the nuclear, and more recently mitochondrial, genomes now provides the ability to dissect how genetic variation in mitochondrial genes alter cellular function across a variety of human tissue types. This review will examine the origins of mitochondrial heteroplasmic variation and propagation, and the tools used to model mitochondrial genetic diseases. Additionally, we discuss how iPSC technologies represent an opportunity to advance our understanding of human mitochondrial genetics in disease.
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Affiliation(s)
- Jesse D. Moreira
- Evans Department of Medicine and the Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA 02118, USA; (J.D.M.); (D.M.G.)
| | - Deepa M. Gopal
- Evans Department of Medicine and the Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA 02118, USA; (J.D.M.); (D.M.G.)
- Cardiovascular Medicine Section, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Darrell N. Kotton
- Boston Medical Center, Center for Regenerative Medicine of Boston University, Boston, MA 02118, USA;
- The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Jessica L. Fetterman
- Evans Department of Medicine and the Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA 02118, USA; (J.D.M.); (D.M.G.)
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4
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Koschak A, Fernandez-Quintero ML, Heigl T, Ruzza M, Seitter H, Zanetti L. Cav1.4 dysfunction and congenital stationary night blindness type 2. Pflugers Arch 2021; 473:1437-1454. [PMID: 34212239 PMCID: PMC8370969 DOI: 10.1007/s00424-021-02570-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/14/2021] [Accepted: 04/18/2021] [Indexed: 12/04/2022]
Abstract
Cav1.4 L-type Ca2+ channels are predominantly expressed in retinal neurons, particularly at the photoreceptor terminals where they mediate sustained Ca2+ entry needed for continuous neurotransmitter release at their ribbon synapses. Cav1.4 channel gating properties are controlled by accessory subunits, associated regulatory proteins, and also alternative splicing. In humans, mutations in the CACNA1F gene encoding for Cav1.4 channels are associated with X-linked retinal disorders such as congenital stationary night blindness type 2. Mutations in the Cav1.4 protein result in a spectrum of altered functional channel activity. Several mouse models broadened our understanding of the role of Cav1.4 channels not only as Ca2+ source at retinal synapses but also as synaptic organizers. In this review, we highlight different structural and functional phenotypes of Cav1.4 mutations that might also occur in patients with congenital stationary night blindness type 2. A further important yet mostly neglected aspect that we discuss is the influence of alternative splicing on channel dysfunction. We conclude that currently available functional phenotyping strategies should be refined and summarize potential specific therapeutic options for patients carrying Cav1.4 mutations. Importantly, the development of new therapeutic approaches will permit a deeper understanding of not only the disease pathophysiology but also the physiological function of Cav1.4 channels in the retina.
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MESH Headings
- 3-Pyridinecarboxylic acid, 1,4-dihydro-2,6-dimethyl-5-nitro-4-(2-(trifluoromethyl)phenyl)-, Methyl ester/pharmacology
- Animals
- Calcium Channel Agonists/pharmacology
- Calcium Channels, L-Type/genetics
- Calcium Channels, L-Type/metabolism
- Eye Diseases, Hereditary/genetics
- Eye Diseases, Hereditary/metabolism
- Genetic Diseases, X-Linked/genetics
- Genetic Diseases, X-Linked/metabolism
- Humans
- Mutation/physiology
- Myopia/genetics
- Myopia/metabolism
- Night Blindness/genetics
- Night Blindness/metabolism
- Retina/drug effects
- Retina/metabolism
- Synapses/drug effects
- Synapses/genetics
- Synapses/metabolism
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Affiliation(s)
- Alexandra Koschak
- Institute of Pharmacy, Pharmacology and Toxicology, Center for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82/III, 6020, Innsbruck, Austria.
| | - Monica L Fernandez-Quintero
- Institute of General, Inorganic and Theoretical Chemistry, Center for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82/III, 6020, Innsbruck, Austria
| | - Thomas Heigl
- Institute of Pharmacy, Pharmacology and Toxicology, Center for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82/III, 6020, Innsbruck, Austria
| | - Marco Ruzza
- Institute of Pharmacy, Pharmacology and Toxicology, Center for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82/III, 6020, Innsbruck, Austria
| | - Hartwig Seitter
- Institute of Pharmacy, Pharmacology and Toxicology, Center for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82/III, 6020, Innsbruck, Austria
| | - Lucia Zanetti
- Institute of Pharmacy, Pharmacology and Toxicology, Center for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82/III, 6020, Innsbruck, Austria
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5
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Xu DD, Li GQ, Wu ZS, Liu XQ, Yang XX, Wang JH. Bioinformatics analysis and identification of genes and molecular pathways involved in Parkinson's disease in patients with mutations in the glucocerebrosidase gene. Neuroreport 2021; 32:918-924. [PMID: 34132705 PMCID: PMC8253507 DOI: 10.1097/wnr.0000000000001685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 02/09/2021] [Indexed: 11/25/2022]
Abstract
Glucocerebrosidase (GBA) mutations occur frequently in Parkinson's disease (PD) patients. This study aims to identify potential crucial genes and pathways associated with GBA mutations in patients with PD and to further analyze new molecular mechanisms related to the occurrence of gene mutations from the perspective of bioinformatics. Gene expression profiles of datasets GSE53424 and GSE99142 were acquired from the Gene Expression Ominibus database. Differentially expressed genes (DEGs) were detected, using the 'limma' package in R, comparing IDI-PD 1 (idiopathic PD patients) and GBA-PD 1 [PD patients with heterozygous GBA mutations (GBA N370S)] group samples. The functions of top modules were assessed using the DAVID, whereas gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed. Protein-protein interaction networks were assembled with Cytoscape software and separated into subnetworks using the Molecular Complex Detection Algorithm. Data from GSE53424 and GSE99142 were also extracted to verify our findings. There were 283 DEGs identified in PD patients heterozygous for GBA mutations. Module analysis revealed that GBA mutations in PD patients were associated with significant pathways, including Calcium signaling pathway, Rap1 signaling pathway and Cytokine-cytokine receptor interaction. Hub genes of the two modules were corticotropin-releasing hormone (CRH) and Melatonin receptor 1B (MTNR1B). The expression of CRH was downregulated, whereas that of MTNR1B was upregulated in PD patients with GBA mutations. The expression of CRH and MTNR1B has diagnostic value for PD patients with heterozygous GBA mutations. Novel DEGs and pathways identified herein might provide new insights into the underlying molecular mechanisms of heterozygous GBA mutations in PD patients.
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Affiliation(s)
- Dan-Dan Xu
- Department of Neurology, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, Fujian 362000, China
| | - Guo-Qian Li
- Department of Neurology, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, Fujian 362000, China
| | - Zhi-Sheng Wu
- Department of Neurology, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, Fujian 362000, China
| | - Xiao-Qiang Liu
- Department of Neurology, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, Fujian 362000, China
| | - Xiao-Xia Yang
- Department of Neurology, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, Fujian 362000, China
| | - Jie-Hua Wang
- Department of Neurology, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, Fujian 362000, China
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6
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Kosillo P, Bateup HS. Dopaminergic Dysregulation in Syndromic Autism Spectrum Disorders: Insights From Genetic Mouse Models. Front Neural Circuits 2021; 15:700968. [PMID: 34366796 PMCID: PMC8343025 DOI: 10.3389/fncir.2021.700968] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/21/2021] [Indexed: 12/12/2022] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder defined by altered social interaction and communication, and repetitive, restricted, inflexible behaviors. Approximately 1.5-2% of the general population meet the diagnostic criteria for ASD and several brain regions including the cortex, amygdala, cerebellum and basal ganglia have been implicated in ASD pathophysiology. The midbrain dopamine system is an important modulator of cellular and synaptic function in multiple ASD-implicated brain regions via anatomically and functionally distinct dopaminergic projections. The dopamine hypothesis of ASD postulates that dysregulation of dopaminergic projection pathways could contribute to the behavioral manifestations of ASD, including altered reward value of social stimuli, changes in sensorimotor processing, and motor stereotypies. In this review, we examine the support for the idea that cell-autonomous changes in dopaminergic function are a core component of ASD pathophysiology. We discuss the human literature supporting the involvement of altered dopamine signaling in ASD including genetic, brain imaging and pharmacologic studies. We then focus on genetic mouse models of syndromic neurodevelopmental disorders in which single gene mutations lead to increased risk for ASD. We highlight studies that have directly examined dopamine neuron number, morphology, physiology, or output in these models. Overall, we find considerable support for the idea that the dopamine system may be dysregulated in syndromic ASDs; however, there does not appear to be a consistent signature and some models show increased dopaminergic function, while others have deficient dopamine signaling. We conclude that dopamine dysregulation is common in syndromic forms of ASD but that the specific changes may be unique to each genetic disorder and may not account for the full spectrum of ASD-related manifestations.
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Affiliation(s)
- Polina Kosillo
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Helen S. Bateup
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, United States
- Chan Zuckerberg Biohub, San Francisco, CA, United States
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7
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Jing L, Cheng S, Pan Y, Liu Q, Yang W, Li S, Li XJ. Accumulation of Endogenous Mutant Huntingtin in Astrocytes Exacerbates Neuropathology of Huntington Disease in Mice. Mol Neurobiol 2021; 58:5112-5126. [PMID: 34250577 DOI: 10.1007/s12035-021-02451-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 06/10/2021] [Indexed: 01/16/2023]
Abstract
Selective neuronal accumulation of misfolded proteins is a key step toward neurodegeneration in a wide range of neurodegenerative diseases, including Huntington's (HD) diseases. Our recent studies suggest that Hsp70-binding protein 1 (HspBP1), an Hsp70/CHIP inhibitor that reduces protein folding, is highly expressed in neuronal cells and accounts for the accumulation of the HD protein huntingtin (HTT) in neuronal cells. To further determine the role of HspBP1 in regulation of mutant protein accumulation, we investigated whether increasing expression of HspBP1 in glial cells can also induce the accumulation of endogenous mutant HTT in glial cells and yield non-cell-autonomous toxic effects. We performed stereotaxic injection of AAV to selectively express HspBP1 in astrocytes in the brains of HD140Q knock-in (KI) mice that express mutant HTT ubiquitously but do not display obvious neurodegeneration. However, HspBP1 expression in HD140Q astrocytes led to the increased accumulation of endogenous mutant HTT and robust neuronal loss in the striatum of HD140Q KI mice. In transgenic HD mice that selectively express mutant HTT in astrocytes, increased accumulation of mutant HTT in astrocytes via HspBP1 expression did not elicit neurodegeneration but could exacerbate neurological symptoms. Consistently, suppressing the expression of endogenous HspBp1 in the striatum of HD140Q KI mice via CRISPR/Cas9 led to a significant reduction of mutant HTT accumulation. Our findings suggest that although endogenous mutant HTT in astrocytes can exacerbate neurological symptoms, it mediates neurodegeneration only when mutant HTT is also accumulated in neuronal cells.
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Affiliation(s)
- Liang Jing
- Department of Emergency, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hunan, China
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Siying Cheng
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Yongcheng Pan
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Qiong Liu
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Weili Yang
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Shihua Li
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Xiao-Jiang Li
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China.
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8
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Kłopotowski K, Czyżewska MM, Mozrzymas JW. Glycine substitution of α1F64 residue at the loop D of GABA A receptor impairs gating - Implications for importance of binding site-channel gate linker rigidity. Biochem Pharmacol 2021; 192:114668. [PMID: 34216603 DOI: 10.1016/j.bcp.2021.114668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/27/2021] [Accepted: 06/28/2021] [Indexed: 12/29/2022]
Abstract
GABAA receptors (GABAARs) play a crucial role in mediating inhibition in adult mammalian brains. In the recent years, an impressive progress in revealing the static structure of GABAARs was achieved but the molecular mechanisms underlying their conformational transitions remain elusive. Phenylalanine 64 (α1F64) is located at the loop D of the orthosteric binding site of GABAAR and was found to directly interact with GABA molecule. Mutations of α1F64 were demonstrated to affect not only binding but also some gating properties. Loop D is a rigid β strand which seems to be particularly suitable to convey activatory signaling from the ligand binding site (LBS) to the gate at the channel pore. To test this scenario, we have investigated the substitution of α1F64 with glycine, the smallest amino acid, widely recognized as a rigidity "reducer" of protein structures. To this end, we assessed the impact of the α1F64G mutation in the α1β2γ2L type of GABAARs on gating properties by analyzing both macroscopic responses to rapid agonist applications and single-channel currents. We found that this substitution dramatically altered all gating features of the receptor (opening/closing, preactivation and desensitization) which contrasts with markedly weaker effects of previously considered substitutions (α1F64L and α1F64A). In particular, α1F64G mutation practically abolished the desensitization process. At the same time, the α1F64G mutant maintained gating integrity manifested as single-channel activity in the form of clusters. We conclude that rigidity of the loop D plays a crucial role in conveying the activation signal from the LBS to the channel gate.
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Affiliation(s)
- Karol Kłopotowski
- Wroclaw Medical University, Department of Biophysics and Neuroscience, Chalubinskiego 3A, Wroclaw, Dolnośląskie PL 50-368, +48 71 784 15 51, Poland.
| | - Marta M Czyżewska
- Wroclaw Medical University, Department of Biophysics and Neuroscience, Chalubinskiego 3A, Wroclaw, Dolnośląskie PL 50-368, +48 71 784 15 51, Poland
| | - Jerzy W Mozrzymas
- Wroclaw Medical University, Department of Biophysics and Neuroscience, Chalubinskiego 3A, Wroclaw, Dolnośląskie PL 50-368, +48 71 784 15 51, Poland.
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Raj K, Akundi RS. Mutant Ataxin-3-Containing Aggregates (MATAGGs) in Spinocerebellar Ataxia Type 3: Dynamics of the Disorder. Mol Neurobiol 2021; 58:3095-3118. [PMID: 33629274 DOI: 10.1007/s12035-021-02314-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 01/25/2021] [Indexed: 11/25/2022]
Abstract
Spinocerebellar ataxia type 3 (SCA3) is the most common type of SCA worldwide caused by abnormal polyglutamine expansion in the coding region of the ataxin-3 gene. Ataxin-3 is a multi-faceted protein involved in various cellular processes such as deubiquitination, cytoskeletal organisation, and transcriptional regulation. The presence of an expanded poly(Q) stretch leads to altered processing and misfolding of the protein culminating in the production of insoluble protein aggregates in the cell. Various post-translational modifications affect ataxin-3 fibrillation and aggregation. This review provides an exhaustive assessment of the various pathogenic mechanisms undertaken by the mutant ataxin-3-containing aggregates (MATAGGs) for disease induction and neurodegeneration. This includes in-depth discussion on MATAGG dynamics including their formation, role in neuronal pathogenesis, and the debate over the toxic v/s protective nature of the MATAGGs in disease progression. Additionally, the currently available therapeutic strategies against SCA3 have been reviewed. The shift in the focus of such strategies, from targeting the steps that lead to or reduce aggregate formation to targeting the expression of mutant ataxin-3 itself via RNA-based therapeutics, has also been presented. We also discuss the intriguing promise that various growth and neurotrophic factors, especially the insulin pathway, hold in the modulation of SCA3 progression. These emerging areas show the newer directions through which SCA3 can be targeted including various preclinical and clinical trials. All these advances made in the last three decades since the discovery of the ataxin-3 gene have been critically reviewed here.
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Affiliation(s)
- Kritika Raj
- Neuroinflammation Research Lab, Faculty of Life Sciences and Biotechnology, South Asian University, Chanakyapuri, New Delhi, 110021, India
| | - Ravi Shankar Akundi
- Neuroinflammation Research Lab, Faculty of Life Sciences and Biotechnology, South Asian University, Chanakyapuri, New Delhi, 110021, India.
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Liu X, Hu Q, Wang W, Ma H, Pu J, Cui J, Gong T, Wu Y, Lu W, Huang J. A protein-fragment complementation assay reveals that celastrol and gambogic acid suppress ERα mutants in breast cancer. Biochem Pharmacol 2021; 188:114583. [PMID: 33915156 DOI: 10.1016/j.bcp.2021.114583] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/05/2021] [Accepted: 04/22/2021] [Indexed: 01/14/2023]
Abstract
Somatic gain-of-function mutations within estrogen receptor alpha (ERα) are highly associated with hormone therapy resistance in breast cancer. However, current understanding of abnormal activity of ERα mutants and their relevant targeted intervention is still very limited. Herein, we developed a new, real-time, and reliably Gaussia luciferase-based protein-fragment complementation assay (GLPCA) for evaluating ERα mutants activities. We found that, compared with ER WT, ERα mutants (Y537S/N and D538G) exhibit high ligand-independent activity, suggesting the gain-of-function phenotype of these ERα mutants. Notably, Y537S, the most common ERα mutant type, has the highest intrinsic activation. We then collected and screened a natural product library for potential ERα antagonists via GLPCA and identified celastrol and gambogic acid as new antagonists of the ERα Y537S mutant. Moreover, interactions between these two compounds and the ERα Y537S mutant were confirmed by molecular docking and cellular thermal shift assay. Importantly, we further demonstrated that celastrol and gambogic acid exhibit synergistic antiproliferative and pro-apoptotic effects when combined with an approved CDK4/6 inhibitor abemaciclib in breast cancer cells expressing ERα Y537S. In summary, GLPCA provides a powerful platform for exploring innovative functional biology and drug discovery of antagonists targeting ERα mutants.
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Affiliation(s)
- Xi Liu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Qian Hu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Wanyan Wang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Hui Ma
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Jiaqian Pu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Jiayan Cui
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Ting Gong
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yu Wu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Weiqiang Lu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.
| | - Jin Huang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.
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11
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Edwards DM, Røyrvik EC, Chustecki JM, Giannakis K, Glastad RC, Radzvilavicius AL, Johnston IG. Avoiding organelle mutational meltdown across eukaryotes with or without a germline bottleneck. PLoS Biol 2021; 19:e3001153. [PMID: 33891583 PMCID: PMC8064548 DOI: 10.1371/journal.pbio.3001153] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/23/2021] [Indexed: 11/25/2022] Open
Abstract
Mitochondrial DNA (mtDNA) and plastid DNA (ptDNA) encode vital bioenergetic apparatus, and mutations in these organelle DNA (oDNA) molecules can be devastating. In the germline of several animals, a genetic “bottleneck” increases cell-to-cell variance in mtDNA heteroplasmy, allowing purifying selection to act to maintain low proportions of mutant mtDNA. However, most eukaryotes do not sequester a germline early in development, and even the animal bottleneck remains poorly understood. How then do eukaryotic organelles avoid Muller’s ratchet—the gradual buildup of deleterious oDNA mutations? Here, we construct a comprehensive and predictive genetic model, quantitatively describing how different mechanisms segregate and decrease oDNA damage across eukaryotes. We apply this comprehensive theory to characterise the animal bottleneck with recent single-cell observations in diverse mouse models. Further, we show that gene conversion is a particularly powerful mechanism to increase beneficial cell-to-cell variance without depleting oDNA copy number, explaining the benefit of observed oDNA recombination in diverse organisms which do not sequester animal-like germlines (for example, sponges, corals, fungi, and plants). Genomic, transcriptomic, and structural datasets across eukaryotes support this mechanism for generating beneficial variance without a germline bottleneck. This framework explains puzzling oDNA differences across taxa, suggesting how Muller’s ratchet is avoided in different eukaryotes. A comprehensive model for mitochondrial and plasmid DNA segregation, supported by with genomic, transcriptomic, and single-cell data, shows how the attritional effects of Muller’s ratchet can be avoided in the organelles of diverse eukaryotes.
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Affiliation(s)
| | | | | | | | | | | | - Iain G. Johnston
- Department of Mathematics, University of Bergen, Norway
- Computational Biology Unit, University of Bergen, Norway
- * E-mail:
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12
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Downs AM, Fan X, Kadakia RF, Donsante Y, Jinnah HA, Hess EJ. Cell-intrinsic effects of TorsinA(ΔE) disrupt dopamine release in a mouse model of TOR1A dystonia. Neurobiol Dis 2021; 155:105369. [PMID: 33894367 DOI: 10.1016/j.nbd.2021.105369] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/29/2021] [Accepted: 04/19/2021] [Indexed: 11/19/2022] Open
Abstract
TOR1A-associated dystonia, otherwise known as DYT1 dystonia, is an inherited dystonia caused by a three base-pair deletion in the TOR1A gene (TOR1AΔE). Although the mechanisms underlying the dystonic movements are largely unknown, abnormalities in striatal dopamine and acetylcholine neurotransmission are consistently implicated whereby dopamine release is reduced while cholinergic tone is increased. Because striatal cholinergic neurotransmission mediates dopamine release, it is not known if the dopamine release deficit is mediated indirectly by abnormal acetylcholine neurotransmission or if Tor1a(ΔE) acts directly within dopaminergic neurons to attenuate release. To dissect the microcircuit that governs the deficit in dopamine release, we conditionally expressed Tor1a(ΔE) in either dopamine neurons or cholinergic interneurons in mice and assessed striatal dopamine release using ex vivo fast scan cyclic voltammetry or dopamine efflux using in vivo microdialysis. Conditional expression of Tor1a(ΔE) in cholinergic neurons did not affect striatal dopamine release. In contrast, conditional expression of Tor1a(ΔE) in dopamine neurons reduced dopamine release to 50% of normal, which is comparable to the deficit in Tor1a+/ΔE knockin mice that express the mutation ubiquitously. Despite the deficit in dopamine release, we found that the Tor1a(ΔE) mutation does not cause obvious nerve terminal dysfunction as other presynaptic mechanisms, including electrical excitability, vesicle recycling/refilling, Ca2+ signaling, D2 dopamine autoreceptor function and GABAB receptor function, are intact. Although the mechanistic link between Tor1a(ΔE) and dopamine release is unclear, these results clearly demonstrate that the defect in dopamine release is caused by the action of the Tor1a(ΔE) mutation within dopamine neurons.
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Affiliation(s)
- Anthony M Downs
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, 101 Woodruff Circle, WMB 6304, Atlanta, GA 30322, USA
| | - Xueliang Fan
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, 101 Woodruff Circle, WMB 6304, Atlanta, GA 30322, USA
| | - Radhika F Kadakia
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, 101 Woodruff Circle, WMB 6304, Atlanta, GA 30322, USA
| | - Yuping Donsante
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, 101 Woodruff Circle, WMB 6304, Atlanta, GA 30322, USA
| | - H A Jinnah
- Department of Neurology, Emory University School of Medicine, 101 Woodruff Circle, WMB 6304, Atlanta, GA 30322, USA; Department of Human Genetics, Emory University School of Medicine, 101 Woodruff Circle, WMB 6300, Atlanta, GA 30322, USA; Department of Pediatrics, Emory University School of Medicine, 101 Woodruff Circle, WMB 6300, Atlanta, GA 30322, USA
| | - Ellen J Hess
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, 101 Woodruff Circle, WMB 6304, Atlanta, GA 30322, USA; Department of Neurology, Emory University School of Medicine, 101 Woodruff Circle, WMB 6304, Atlanta, GA 30322, USA.
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13
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Wang H, Wang W, Chen X, Shi H, Shi Y, Ding G. Screening and Functional Analysis of TPO Gene Mutations in a Cohort of Chinese Patients With Congenital Hypothyroidism. Front Endocrinol (Lausanne) 2021; 12:774941. [PMID: 35002963 PMCID: PMC8729100 DOI: 10.3389/fendo.2021.774941] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/24/2021] [Indexed: 01/18/2023] Open
Abstract
BACKGROUNDS As a crucial enzyme in thyroid hormone synthesis, the genetic defective thyroid peroxidase (TPO) was one of the main genetic factors leading to congenital hypothyroidism (CH). METHODS Mutations in the TPO gene were screened and identified in 219 patients with CH from northwest China by using high-throughput sequencing and bioinformatics analysis. The biological function of detected variants was studied by in vitro experiments and homology modeling. RESULTS Nineteen rare variants, including seven novel ones, were detected in 17 of 219 patients (7.8%). Most cases were detected with one single heterozygous variant, and only two patients were detected with multiple variants, i.e., compounds for (1) IVS7-1G>A, p.Ala443Val, and p.Arg769Trp and (2) p.Asn592Ser and p.Asn798Lys. The biological function of the four missense mutations (i.e., p.Ala443Val, p.Arg769Trp, p.Asn592Ser, and p.Asn798Lys) they carried were further studied. Experimental data showed that these four mutations did not affect the protein expression level of the TPO gene but remarkably reduced the peroxidase activity toward guaiacol oxidation, retaining 8-32% of activity of the wild-type protein. The comparison of the predicted 3-D structures of wild-type and mutant TPO proteins showed that these four amino acid substitutions changed the non-covalent interactions of studied residues that might alter the structure and function of the TPO protein. CONCLUSION This study was the first to analyze the TPO mutation spectrum of patients with CH in northwest China. Our data indicated that the TPO mutation was not a common reason to cause CH in China. The functional data may help to clarify the structure-function relationship of the TPO protein and provide further evidence for the elucidation of the genetic etiology of CH.
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Affiliation(s)
- Huijjuan Wang
- The National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi’an, China
- *Correspondence: Huijjuan Wang, ; Guifeng Ding,
| | - Wenxia Wang
- The National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi’an, China
| | - Xi Chen
- Pediatrics, Urumqi Maternal and Child Health Care Hospital, Urumqi, China
| | - Hailong Shi
- College of Basic Medicine, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Yinmin Shi
- The National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi’an, China
| | - Guifeng Ding
- Obstetrics and Gynecology Department, Urumqi Maternal and Child Health Care Hospital, Urumqi, China
- *Correspondence: Huijjuan Wang, ; Guifeng Ding,
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14
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de Ruiter RD, Smilde BJ, Pals G, Bravenboer N, Knaus P, Schoenmaker T, Botman E, Sánchez-Duffhues G, Pacifici M, Pignolo RJ, Shore EM, van Egmond M, Van Oosterwyck H, Kaplan FS, Hsiao EC, Yu PB, Bocciardi R, De Cunto CL, Longo Ribeiro Delai P, de Vries TJ, Hilderbrandt S, Jaspers RT, Keen R, Koolwijk P, Morhart R, Netelenbos JC, Rustemeyer T, Scott C, Stockklausner C, ten Dijke P, Triffit J, Ventura F, Ravazzolo R, Micha D, Eekhoff EMW. Fibrodysplasia Ossificans Progressiva: What Have We Achieved and Where Are We Now? Follow-up to the 2015 Lorentz Workshop. Front Endocrinol (Lausanne) 2021; 12:732728. [PMID: 34858325 PMCID: PMC8631510 DOI: 10.3389/fendo.2021.732728] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/22/2021] [Indexed: 11/20/2022] Open
Abstract
Fibrodysplasia ossificans progressiva (FOP) is an ultra-rare progressive genetic disease effecting one in a million individuals. During their life, patients with FOP progressively develop bone in the soft tissues resulting in increasing immobility and early death. A mutation in the ACVR1 gene was identified as the causative mutation of FOP in 2006. After this, the pathophysiology of FOP has been further elucidated through the efforts of research groups worldwide. In 2015, a workshop was held to gather these groups and discuss the new challenges in FOP research. Here we present an overview and update on these topics.
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Affiliation(s)
- Ruben D. de Ruiter
- Department of Internal Medicine, Section Endocrinology, Amsterdam University Medical Center (Amsterdam UMC), Vrije Universiteit Amsterdam, Amsterdam Movement Sciences, Amsterdam, Netherlands
- *Correspondence: Ruben D. de Ruiter, ; Elisabeth M. W. Eekhoff,
| | - Bernard J. Smilde
- Department of Internal Medicine, Section Endocrinology, Amsterdam University Medical Center (Amsterdam UMC), Vrije Universiteit Amsterdam, Amsterdam Movement Sciences, Amsterdam, Netherlands
| | - Gerard Pals
- Department of Clinical Genetics and Bone Histomorphology, Amsterdam University Medical Center (Amsterdam UMC), Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Nathalie Bravenboer
- Department of Clinical Chemistry, Amsterdam University Medical Center (Amsterdam UMC), Vrije Universiteit Amsterdam, Amsterdam Movement Sciences, Amsterdam, Netherlands
| | - Petra Knaus
- Freie Universität Berlin, Institute for Chemistry and Biochemistry, Berlin, Germany
| | - Ton Schoenmaker
- Department of Periodontology, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and Vrije Universiteit, Amsterdam, Netherlands
| | - Esmée Botman
- Department of Internal Medicine, Section Endocrinology, Amsterdam University Medical Center (Amsterdam UMC), Vrije Universiteit Amsterdam, Amsterdam Movement Sciences, Amsterdam, Netherlands
| | | | - Maurizio Pacifici
- Translational Research Program in Pediatric Orthopaedics, Abramson Research Center, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | | | - Eileen M. Shore
- Department of Orthopaedic Surgery and Genetics, and the Center for Research in FOP and Related Disorders, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Marjolein van Egmond
- Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, Amsterdam University Medical Center (Amsterdam UMC), Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Hans Van Oosterwyck
- Division of Biomechanics, Department of Mechanical Engineering, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
- Prometheus division of skeletal tissue engineering, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Frederick S. Kaplan
- Department of Orthopaedic Surgery and Medicine, Center for Research in FOP and Related Disorders, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Edward C. Hsiao
- Department of Endocrinology and Metabolism, and the Institute for Human Genetics, Department of Medicine, University of California, San Francisco, CA, United States
| | - Paul B. Yu
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Renata Bocciardi
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), Università degli Studi di Genova, Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Carmen Laura De Cunto
- Rheumatology Section, Department of Pediatrics, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | | | - Teun J. de Vries
- Department of Periodontology, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and Vrije Universiteit, Amsterdam, Netherlands
| | - Susanne Hilderbrandt
- Freie Universität Berlin, Institute for Chemistry and Biochemistry, Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies, Charité Medical University of Berlin, Berlin, Germany
| | - Richard T. Jaspers
- Laboratory for Myology, Faculty of Behavioural and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam Movement Sciences, Amsterdam, Netherlands
| | - Richard Keen
- Centre for Metabolic Bone Disease, Royal National Orthopaedic Hospital, Stanmore, United Kingdom
| | - Peter Koolwijk
- Department of Physiology, Amsterdam University Medical Center (Amsterdam UMC), Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Rolf Morhart
- Department of Pediatrics, Garmisch-Partenkichen Medical Center, Garmisch-Partenkirchen, Germany
| | - Jan C. Netelenbos
- Department of Internal Medicine, Section Endocrinology, Amsterdam University Medical Center (Amsterdam UMC), Vrije Universiteit Amsterdam, Amsterdam Movement Sciences, Amsterdam, Netherlands
| | - Thomas Rustemeyer
- Department of Dermatology, Amsterdam University Medical Center (AmsterdamUMC), Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Christiaan Scott
- Division of Paediatric Rheumatology, Departmet of Paediatrics and Child Heath, Red Cross War Memorial Children’s Hospital, University of Cape Town, Cape Town, South Africa
| | - Clemens Stockklausner
- Laboratory for Myology, Faculty of Behavioural and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam Movement Sciences, Amsterdam, Netherlands
| | - Peter ten Dijke
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - James Triffit
- Botnar Research Centre, University of Oxford, Oxford, United Kingdom
| | - Francesc Ventura
- Departamento de Cièncias Fisiológicas, Facultad de Medicina y Ciencias de la Salud, Universitat de Barcelona, Barcelona, Spain
| | - Roberto Ravazzolo
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), Università degli Studi di Genova, Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Dimitra Micha
- Department of Clinical Genetics and Bone Histomorphology, Amsterdam University Medical Center (Amsterdam UMC), Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Elisabeth M. W. Eekhoff
- Department of Internal Medicine, Section Endocrinology, Amsterdam University Medical Center (Amsterdam UMC), Vrije Universiteit Amsterdam, Amsterdam Movement Sciences, Amsterdam, Netherlands
- *Correspondence: Ruben D. de Ruiter, ; Elisabeth M. W. Eekhoff,
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15
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Abstract
Asthenozoospermia (AZS), defined by reduced motility or absent sperm motility, is one of the main causes of male infertility. This condition may be divided into isolated AZS in the absence of other symptoms and syndromic AZS, which is characterized by several concurrent clinical symptoms. Sperm motility depends on fully functional flagellum, energy availability, and the crosstalk of several signaling pathways; therefore, mutations in genes involved in flagellar assembly and motile regulation can cause AZS. Thus, it is crucial to understand the genetic causes and mechanisms contributing to AZS. In this review, we summarize the current knowledge about the particular genes and mechanisms involved in intact flagellum, energy availability, and signaling transduction that could cause human AZS and discuss the respective gene defects known to be responsible for these abnormalities. Additionally, we discuss intracytoplasmic sperm injection outcomes and offspring health where available in these cases.
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Affiliation(s)
- Chaofeng Tu
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China; Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China; College of Life Science, Hunan Normal University, Changsha, China
| | - Weili Wang
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Tongyao Hu
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Guangxiu Lu
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Ge Lin
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China; Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Yue-Qiu Tan
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China; Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China; College of Life Science, Hunan Normal University, Changsha, China.
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16
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Robert J. [Genomic instability, the engine of oncogenesis]. Bull Cancer 2020; 108:38-40. [PMID: 33187684 DOI: 10.1016/j.bulcan.2020.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 10/18/2020] [Indexed: 11/17/2022]
Affiliation(s)
- Jacques Robert
- Université de Bordeaux, Inserm unité 1218, Bordeaux, France.
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17
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Schmutzer M, Wagner A. Gene expression noise can promote the fixation of beneficial mutations in fluctuating environments. PLoS Comput Biol 2020; 16:e1007727. [PMID: 33104710 PMCID: PMC7644098 DOI: 10.1371/journal.pcbi.1007727] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 11/05/2020] [Accepted: 09/15/2020] [Indexed: 02/03/2023] Open
Abstract
Nongenetic phenotypic variation can either speed up or slow down adaptive evolution. We show that it can speed up evolution in environments where available carbon and energy sources change over time. To this end, we use an experimentally validated model of Escherichia coli growth on two alternative carbon sources, glucose and acetate. On the superior carbon source (glucose), all cells achieve high growth rates, while on the inferior carbon source (acetate) only a small fraction of the population manages to initiate growth. Consequently, populations experience a bottleneck when the environment changes from the superior to the inferior carbon source. Growth on the inferior carbon source depends on a circuit under the control of a transcription factor that is repressed in the presence of the superior carbon source. We show that noise in the expression of this transcription factor can increase the probability that cells start growing on the inferior carbon source. In doing so, it can decrease the severity of the bottleneck and increase mean population fitness whenever this fitness is low. A modest amount of noise can also enhance the fitness effects of a beneficial allele that increases the fraction of a population initiating growth on acetate. Additionally, noise can protect this allele from extinction, accelerate its spread, and increase its likelihood of going to fixation. Central to the adaptation-enhancing principle we identify is the ability of noise to mitigate population bottlenecks, particularly in environments that fluctuate periodically. Because such bottlenecks are frequent in fluctuating environments, and because periodically fluctuating environments themselves are common, this principle may apply to a broad range of environments and organisms.
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Affiliation(s)
- Michael Schmutzer
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Santa Fe Institute, Santa Fe, New Mexico, USA
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18
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Cano AV, Payne JL. Mutation bias interacts with composition bias to influence adaptive evolution. PLoS Comput Biol 2020; 16:e1008296. [PMID: 32986712 PMCID: PMC7571706 DOI: 10.1371/journal.pcbi.1008296] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 10/19/2020] [Accepted: 08/30/2020] [Indexed: 11/19/2022] Open
Abstract
Mutation is a biased stochastic process, with some types of mutations occurring more frequently than others. Previous work has used synthetic genotype-phenotype landscapes to study how such mutation bias affects adaptive evolution. Here, we consider 746 empirical genotype-phenotype landscapes, each of which describes the binding affinity of target DNA sequences to a transcription factor, to study the influence of mutation bias on adaptive evolution of increased binding affinity. By using empirical genotype-phenotype landscapes, we need to make only few assumptions about landscape topography and about the DNA sequences that each landscape contains. The latter is particularly important because the set of sequences that a landscape contains determines the types of mutations that can occur along a mutational path to an adaptive peak. That is, landscapes can exhibit a composition bias—a statistical enrichment of a particular type of mutation relative to a null expectation, throughout an entire landscape or along particular mutational paths—that is independent of any bias in the mutation process. Our results reveal the way in which composition bias interacts with biases in the mutation process under different population genetic conditions, and how such interaction impacts fundamental properties of adaptive evolution, such as its predictability, as well as the evolution of genetic diversity and mutational robustness. Mutation is often depicted as a random process due its unpredictable nature. However, such randomness does not imply uniformly distributed outcomes, because some DNA sequence changes happen more frequently than others. Mutation bias can be an orienting factor in adaptive evolution, influencing the mutational trajectories populations follow toward higher-fitness genotypes. Because these trajectories are typically just a small subset of all possible mutational trajectories, they can exhibit composition bias—an enrichment of a particular kind of DNA sequence change, such as transition or transversion mutations. Here, we use empirical data from eukaryotic transcriptional regulation to study how mutation bias and composition bias interact to influence adaptive evolution.
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Affiliation(s)
- Alejandro V. Cano
- Institute of Integrative Biology, ETH, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Joshua L. Payne
- Institute of Integrative Biology, ETH, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- * E-mail:
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19
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Abstract
Cells adjust their metabolism in response to mutations, but how this reprogramming depends on the genetic context is not well known. Specifically, the absence of individual enzymes can affect reprogramming, and thus the impact of mutations in cell growth. Here, we examine this issue with an in silico model of Saccharomyces cerevisiae's metabolism. By quantifying the variability in the growth rate of 10000 different mutant metabolisms that accumulated changes in their reaction fluxes, in the presence, or absence, of a specific enzyme, we distinguish a subset of modifier genes serving as buffers or potentiators of variability. We notice that the most potent modifiers refer to the glycolysis pathway and that, more broadly, they show strong pleiotropy and epistasis. Moreover, the evidence that this subset depends on the specific growing condition strengthens its systemic underpinning, a feature only observed before in a toy model of a gene-regulatory network. Some of these enzymes also modulate the effect that biochemical noise and environmental fluctuations produce in growth. Thus, the reorganization of metabolism induced by mutations has not only direct physiological implications but also transforms the influence that other mutations have on growth. This is a general result with implications in the development of cancer therapies based on metabolic inhibitors.
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Affiliation(s)
- Juan F. Poyatos
- Logic of Genomic Systems Lab (CNB-CSIC), Madrid, Spain
- Center for Genomics and Systems Biology (NYU), New York, United States of America
- * E-mail:
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20
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Batjargal K, Tajima T, Jimbo EF, Yamagata T. Effect of 4-phenylbutyrate and valproate on dominant mutations of WFS1 gene in Wolfram syndrome. J Endocrinol Invest 2020; 43:1317-1325. [PMID: 32219690 DOI: 10.1007/s40618-020-01228-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 03/17/2020] [Indexed: 02/08/2023]
Abstract
PURPOSE Wolfram syndrome (WS) is a rare disorder caused by mutations in WFS1 that is characterized by diabetes mellitus, optic atrophy, sensorineural deafness, diabetes insipidus, and neurodegeneration. This disease is usually inherited as an autosomal recessive trait, but an autosomal dominant form has been reported. WFS1 encodes a transmembrane protein, which is a maintenance component of endoplasmic homeostasis. These dominant mutations were thought to increase endoplasmic reticulum (ER) stress. Recent studies suggest that 4-phenylbutyrate (PBA) and valproate (VPA) reduce ER stress. The objective of this study was to analyze the effect of PBA and VPA on dominant WFS1 mutants in vitro. METHODS We determined whether dominant WFS1 mutants (p.His313Tyr, p.Trp314Arg, p.Asp325_Ile328del, p.Glu809Lys, and p.Glu864Lys) have the dominant negative effect using a luciferase assay of ER stress response element marker as ER stress. Moreover, the rescue of cell apoptosis induced by dominant WFS1 mutants following treatment with PBA or VPA was determined by quantitative real-time PCR of C/EBP homologous protein (CHOP) mRNA expression. RESULTS These mutants showed the dominant negative effect on the wild-type WFS1. In addition, the levels of ER stress and CHOP mRNA were significantly elevated by all dominant WFS1 mutants. After treatment with PBA or VPA, ER stress and cell apoptosis were reduced in each mutant. CONCLUSIONS PBA and VPA could reduce the ER stress and cell apoptosis caused by dominant WFS1 mutants.
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Affiliation(s)
- K Batjargal
- Department of Pediatrics, Graduate School of Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi, 329-0498, Japan.
- Department of Pediatrics, School of Medicine, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia.
| | - T Tajima
- Department of Pediatrics, Graduate School of Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi, 329-0498, Japan
| | - E F Jimbo
- Department of Pediatrics, Graduate School of Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi, 329-0498, Japan
| | - T Yamagata
- Department of Pediatrics, Graduate School of Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi, 329-0498, Japan
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21
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Flores SK, Deng Y, Cheng Z, Zhang X, Tao S, Saliba A, Chu I, Burnichon N, Gimenez-Roqueplo AP, Wang E, Aguiar RCT, Dahia PLM. Functional Characterization of TMEM127 Variants Reveals Novel Insights into Its Membrane Topology and Trafficking. J Clin Endocrinol Metab 2020; 105:dgaa396. [PMID: 32575117 PMCID: PMC7414969 DOI: 10.1210/clinem/dgaa396] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/17/2020] [Indexed: 02/08/2023]
Abstract
CONTEXT TMEM127 is a poorly known tumor suppressor gene associated with pheochromocytomas, paragangliomas, and renal carcinomas. Our incomplete understanding of TMEM127 function has limited our ability to predict variant pathogenicity. PURPOSE To better understand the function of the transmembrane protein TMEM127 we undertook cellular and molecular evaluation of patient-derived germline variants. DESIGN Subcellular localization and steady-state levels of tumor-associated, transiently expressed TMEM127 variants were compared to the wild-type protein using immunofluorescence and immunoblot analysis, respectively, in cells genetically modified to lack endogenous TMEM127. Membrane topology and endocytic mechanisms were also assessed. RESULTS We identified 3 subgroups of mutations and determined that 71% of the variants studied are pathogenic or likely pathogenic through loss of membrane-binding ability, stability, and/or internalization capability. Investigation into an N-terminal cluster of missense variants uncovered a previously unrecognized transmembrane domain, indicating that TMEM127 is a 4- transmembrane, not a 3-transmembrane domain-containing protein. Additionally, a C-terminal variant with predominant plasma membrane localization revealed an atypical, extended acidic, dileucine-based motif required for TMEM127 internalization through clathrin-mediated endocytosis. CONCLUSION We characterized the functional deficits of several germline TMEM127 variants and identified novel structure-function features of TMEM127. These findings will assist in determining pathogenicity of TMEM127 variants and will help guide future studies investigating the cellular role of TMEM127.
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Affiliation(s)
- Shahida K Flores
- Division of Hematology and Medical Oncology, Department of Medicine, UT Health San Antonio
| | - Yilun Deng
- Division of Hematology and Medical Oncology, Department of Medicine, UT Health San Antonio
| | - Ziming Cheng
- Division of Hematology and Medical Oncology, Department of Medicine, UT Health San Antonio
| | - Xingyu Zhang
- Division of Hematology and Medical Oncology, Department of Medicine, UT Health San Antonio
- Central South University Xiangya School of Medicine, Changsha, Hunan, China
| | - Sifan Tao
- Division of Hematology and Medical Oncology, Department of Medicine, UT Health San Antonio
- Central South University Xiangya School of Medicine, Changsha, Hunan, China
| | - Afaf Saliba
- Division of Hematology and Medical Oncology, Department of Medicine, UT Health San Antonio
| | - Irene Chu
- Division of Hematology and Medical Oncology, Department of Medicine, UT Health San Antonio
| | - Nelly Burnichon
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Européen Georges Pompidou, Genetics Department, Paris, France
- Université de Paris, PARCC, INSERM, Equipe Labellisée par la Ligue contre le Cancer, Paris, France
| | - Anne-Paule Gimenez-Roqueplo
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Européen Georges Pompidou, Genetics Department, Paris, France
- Université de Paris, PARCC, INSERM, Equipe Labellisée par la Ligue contre le Cancer, Paris, France
| | - Exing Wang
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, Texas
| | - Ricardo C T Aguiar
- Division of Hematology and Medical Oncology, Department of Medicine, UT Health San Antonio
- Mays Cancer Center, UT Health San Antonio, San Antonio, Texas
- South Texas Veterans Health Care System, Audie Murphy VA Hospital, San Antonio, Texas
| | - Patricia L M Dahia
- Division of Hematology and Medical Oncology, Department of Medicine, UT Health San Antonio
- Mays Cancer Center, UT Health San Antonio, San Antonio, Texas
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22
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He Q, Gu L, Lin Q, Ma Y, Liu C, Pei X, Li PA, Yang Y. The Immp2l Mutation Causes Ovarian Aging Through ROS-Wnt/β-Catenin-Estrogen Pathway: Preventive Effect of Melatonin. Endocrinology 2020; 161:5870341. [PMID: 32652035 DOI: 10.1210/endocr/bqaa119] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 07/09/2020] [Indexed: 02/07/2023]
Abstract
Mitochondria play important roles in ovarian follicle development. Mitochondrial dysfunction, including mitochondrial gene deficiency, impairs ovarian development. Here, we explored the role and mechanism of mitochondrial inner membrane gene Immp2l in ovarian follicle growth and development. Our results revealed that female Immp2l-/- mice were infertile, whereas Immp2l+/- mice were normal. Body and ovarian weights were reduced in the female Immp2l-/- mice, ovarian follicle growth and development were stunted in the secondary follicle stage. Although a few ovarian follicles were ovulated, the oocytes were not fertilized because of mitochondrial dysfunction. Increased oxidative stress, decreased estrogen levels, and altered genes expression of Wnt/β-catenin and steroid hormone synthesis pathways were observed in 28-day-old Immp2l-/- mice. The Immp2l mutation accelerated ovarian aging process, as no ovarian follicles were detected by age 5 months in Immp2l-/- mice. All the aforementioned changes in the Immp2l-/- mice were reversed by administration of antioxidant melatonin to the Immp2l-/- mice. Furthermore, our in vitro study using Immp2l knockdown granulosa cells confirmed that the Immp2l downregulation induced granulosa cell aging by enhancing reactive oxygen species (ROS) levels, suppressing Wnt16, increasing β-catenin, and decreasing steroid hormone synthesis gene cyp19a1 and estrogen levels, accompanied by an increase in the aging phenotype of granulosa cells. Melatonin treatment delayed granulosa cell aging progression. Taken together, Immp2l causes ovarian aging through the ROS-Wnt/β-catenin-estrogen (cyp19a1) pathway, which can be reversed by melatonin treatment.
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Affiliation(s)
- Qing He
- Key Laboratory of Fertility Preservation and Maintenance, Ministry of Education, Key Laboratory of Reproduction and Genetics in Ningxia, Department of Histology and Embryology, Department of Pathology, Ningxia Key Laboratory of Cerebrocranial Diseases, Incubation Base of National Key Laboratory, Department of Center for Reproductive Medicine, General Hospital, Ningxia Medical University, Yinchuan, Ningxia, P.R. China
| | - Lifang Gu
- Key Laboratory of Fertility Preservation and Maintenance, Ministry of Education, Key Laboratory of Reproduction and Genetics in Ningxia, Department of Histology and Embryology, Department of Pathology, Ningxia Key Laboratory of Cerebrocranial Diseases, Incubation Base of National Key Laboratory, Department of Center for Reproductive Medicine, General Hospital, Ningxia Medical University, Yinchuan, Ningxia, P.R. China
| | - Qingyin Lin
- Key Laboratory of Fertility Preservation and Maintenance, Ministry of Education, Key Laboratory of Reproduction and Genetics in Ningxia, Department of Histology and Embryology, Department of Pathology, Ningxia Key Laboratory of Cerebrocranial Diseases, Incubation Base of National Key Laboratory, Department of Center for Reproductive Medicine, General Hospital, Ningxia Medical University, Yinchuan, Ningxia, P.R. China
| | - Yi Ma
- Key Laboratory of Fertility Preservation and Maintenance, Ministry of Education, Key Laboratory of Reproduction and Genetics in Ningxia, Department of Histology and Embryology, Department of Pathology, Ningxia Key Laboratory of Cerebrocranial Diseases, Incubation Base of National Key Laboratory, Department of Center for Reproductive Medicine, General Hospital, Ningxia Medical University, Yinchuan, Ningxia, P.R. China
| | - Chunlian Liu
- Key Laboratory of Fertility Preservation and Maintenance, Ministry of Education, Key Laboratory of Reproduction and Genetics in Ningxia, Department of Histology and Embryology, Department of Pathology, Ningxia Key Laboratory of Cerebrocranial Diseases, Incubation Base of National Key Laboratory, Department of Center for Reproductive Medicine, General Hospital, Ningxia Medical University, Yinchuan, Ningxia, P.R. China
| | - Xiuying Pei
- Key Laboratory of Fertility Preservation and Maintenance, Ministry of Education, Key Laboratory of Reproduction and Genetics in Ningxia, Department of Histology and Embryology, Department of Pathology, Ningxia Key Laboratory of Cerebrocranial Diseases, Incubation Base of National Key Laboratory, Department of Center for Reproductive Medicine, General Hospital, Ningxia Medical University, Yinchuan, Ningxia, P.R. China
| | - P Andy Li
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technological Enterprise (BRITE), College of Health and Sciences, North Carolina Central University, Durham, North Carolina
| | - Yanzhou Yang
- Key Laboratory of Fertility Preservation and Maintenance, Ministry of Education, Key Laboratory of Reproduction and Genetics in Ningxia, Department of Histology and Embryology, Department of Pathology, Ningxia Key Laboratory of Cerebrocranial Diseases, Incubation Base of National Key Laboratory, Department of Center for Reproductive Medicine, General Hospital, Ningxia Medical University, Yinchuan, Ningxia, P.R. China
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23
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Splichal I, Rychlik I, Splichalova I, Karasova D, Splichalova A. Toll-Like Receptor 4 Signaling in the Ileum and Colon of Gnotobiotic Piglets Infected with Salmonella Typhimurium or Its Isogenic ∆ rfa Mutants. Toxins (Basel) 2020; 12:toxins12090545. [PMID: 32842482 PMCID: PMC7551901 DOI: 10.3390/toxins12090545] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/16/2020] [Accepted: 08/20/2020] [Indexed: 02/06/2023] Open
Abstract
Salmonella Typhimurium is a Gram-negative bacterium that causes enterocolitis in humans and pigs. Lipopolysaccharide (LPS) is a component of the outer leaflet of Gram-negative bacteria that provokes endotoxin shock. LPS can be synthesized completely or incompletely and creates S (smooth) or R (rough) chemotypes. Toll-like receptors (TLR) 2, 4, and 9 initiate an inflammatory reaction to combat bacterial infections. We associated/challenged one-week-old gnotobiotic piglets with wild-type S. Typhimurium with S chemotype or its isogenic ∆rfa mutants with R chemotype LPS. The wild-type S. Typhimurium induced TLR2 and TLR4 mRNA expression but not TLR9 mRNA expression in the ileum and colon of one-week-old gnotobiotic piglets 24 h after challenge. The TLR2 and TLR4 stimulatory effects of the S. Typhimurium ∆rfa mutants were related to the completeness of their LPS chain. The transcription of IL-12/23 p40, IFN-γ, and IL-6 in the intestine and the intestinal and plasmatic levels of IL-12/23 p40 and IL-6 but not IFN-γ were related to the activation of TLR2 and TLR4 signaling pathways. The avirulent S. Typhimurium ∆rfa mutants are potentially useful for modulation of the TLR2 and TLR4 signaling pathways to protect the immunocompromised gnotobiotic piglets against subsequent infection with the virulent S. Typhimurium.
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Affiliation(s)
- Igor Splichal
- Laboratory of Gnotobiology, Institute of Microbiology, Czech Academy of Sciences, 549 22 Novy Hradek, Czech Republic;
| | - Ivan Rychlik
- Department of Immunology, Veterinary Research Institute, 621 00 Brno, Czech Republic; (I.R.); (D.K.)
| | - Iva Splichalova
- Laboratory of Immunobiology, Institute of Molecular Genetics, Czech Academy of Sciences, 142 20 Prague 4-Krc, Czech Republic;
| | - Daniela Karasova
- Department of Immunology, Veterinary Research Institute, 621 00 Brno, Czech Republic; (I.R.); (D.K.)
| | - Alla Splichalova
- Laboratory of Gnotobiology, Institute of Microbiology, Czech Academy of Sciences, 549 22 Novy Hradek, Czech Republic;
- Correspondence: ; Tel.: +420-491-418-539
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24
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Pons BJ, Loiseau N, Hashim S, Tadrist S, Mirey G, Vignard J. Functional Study of Haemophilus ducreyi Cytolethal Distending Toxin Subunit B. Toxins (Basel) 2020; 12:toxins12090530. [PMID: 32825080 PMCID: PMC7551728 DOI: 10.3390/toxins12090530] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/13/2020] [Accepted: 08/17/2020] [Indexed: 12/17/2022] Open
Abstract
The Cytolethal Distending Toxin (CDT) is produced by many Gram-negative pathogenic bacteria responsible for major foodborne diseases worldwide. CDT induces DNA damage and cell cycle arrest in host-cells, eventually leading to senescence or apoptosis. According to structural and sequence comparison, the catalytic subunit CdtB is suggested to possess both nuclease and phosphatase activities, carried by a single catalytic site. However, the impact of each activity on cell-host toxicity is yet to be characterized. Here, we analyze the consequences of cell exposure to different CDT mutated on key CdtB residues, focusing on cell viability, cell cycle defects, and DNA damage induction. A first class of mutant, devoid of any activity, targets putative catalytic (H160A), metal binding (D273R), and DNA binding residues (R117A-R144A-N201A). The second class of mutants (A163R, F156-T158, and the newly identified G114T), which gathers mutations on residues potentially involved in lipid substrate binding, has only partially lost its toxic effects. However, their defects are alleviated when CdtB is artificially introduced inside cells, except for the F156-T158 double mutant that is defective in nuclear addressing. Therefore, our data reveal that CDT toxicity is mainly correlated to CdtB nuclease activity, whereas phosphatase activity may probably be involved in CdtB intracellular trafficking.
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Affiliation(s)
| | | | | | | | - Gladys Mirey
- Correspondence: (G.M.); (J.V.); Tel.: +33-582-066-338 (G.M.)
| | - Julien Vignard
- Correspondence: (G.M.); (J.V.); Tel.: +33-582-066-338 (G.M.)
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25
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Abstract
The evolutionarily conserved p53 protein and its cellular pathways mediate tumour suppression through an informed, regulated and integrated set of responses to environmental perturbations resulting in either cellular death or the maintenance of cellular homeostasis. The p53 and MDM2 proteins form a central hub in this pathway that receives stressful inputs via MDM2 and respond via p53 by informing and altering a great many other pathways and functions in the cell. The MDM2-p53 hub is one of the hubs most highly connected to other signalling pathways in the cell, and this may be why TP53 is the most commonly mutated gene in human cancers. Initial or truncal TP53 gene mutations (the first mutations in a stem cell) are selected for early in cancer development inectodermal and mesodermal-derived tissue-specific stem and progenitor cells and then, following additional mutations, produce tumours from those tissue types. In endodermal-derived tissue-specific stem or progenitor cells, TP53 mutations are functionally selected as late mutations transitioning the mutated cell into a malignant tumour. The order in which oncogenes or tumour suppressor genes are functionally selected for in a stem cell impacts the timing and development of a tumour.
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Affiliation(s)
- Arnold J Levine
- Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ, USA.
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26
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Newell-Stamper BL, Huibregtse BM, Boardman JD, Domingue BW. A mutation associated with stress resistance in mice is associated with human grip strength and mortality. Biodemography Soc Biol 2020; 65:245-256. [PMID: 32727277 DOI: 10.1080/19485565.2020.1744425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Hand grip strength (GS) is a valid and reliable predictor of future morbidity and mortality and is considered a useful indicator of aging. In this paper, we use results from the genetic analysis in animal studies to evaluate associations for GS, frailty, and subsequent mortality among humans. Specifically, we use data from the Health and Retirement Survey (HRS) to investigate the association between three polymorphisms in a candidate frailty gene (Tiam1) and GS. Results suggest that the A allele in rs724561 significantly reduces GS among older adults in the US (b = -0.340; p < .006) and is significantly associated with self-reported weakness (b = 0.221; p = .036). This same polymorphism was weakly associated (one-tailed) with an increased risk of mortality (b = 1.091; p < .093) and adjustments for GS rendered this association statistically non-significant (b = 1.048; p < .361). Overall, our results provide tentative evidence that the Tiam1 gene may be associated with frailty development, but we encourage further studies.
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Affiliation(s)
- Breanne L Newell-Stamper
- Department of Integrative Physiology, University of Colorado at Boulder , Boulder, Colorado, USA
- Institute for Behavioral Genetics, University of Colorado at Boulder , Boulder, Colorado, USA
| | - Brooke M Huibregtse
- Institute for Behavioral Genetics, University of Colorado at Boulder , Boulder, Colorado, USA
| | - Jason D Boardman
- Department of Integrative Physiology, University of Colorado at Boulder , Boulder, Colorado, USA
- Institute for Behavioral Genetics, University of Colorado at Boulder , Boulder, Colorado, USA
- Department of Sociology, University of Colorado at Boulder , Boulder, Colorado, USA
| | - Benjamin W Domingue
- Graduate School of Education, Stanford University , Stanford, California, USA
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27
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Abstract
Haematopoiesis is governed by haematopoietic stem cells (HSCs) that produce all lineages of blood and immune cells. The maintenance of blood homeostasis requires a dynamic response of HSCs to stress, and dysregulation of these adaptive-response mechanisms underlies the development of myeloid leukaemia. Leukaemogenesis often occurs in a stepwise manner, with genetic and epigenetic changes accumulating in pre-leukaemic HSCs prior to the emergence of leukaemic stem cells (LSCs) and the development of acute myeloid leukaemia. Clinical data have revealed the existence of age-related clonal haematopoiesis, or the asymptomatic clonal expansion of mutated blood cells in the elderly, and this phenomenon is connected to susceptibility to leukaemic transformation. Here we describe how selection for specific mutations that increase HSC competitive fitness, in conjunction with additional endogenous and environmental changes, drives leukaemic transformation. We review the ways in which LSCs take advantage of normal HSC properties to promote survival and expansion, thus underlying disease recurrence and resistance to conventional therapies, and we detail our current understanding of leukaemic 'stemness' regulation. Overall, we link the cellular and molecular mechanisms regulating HSC behaviour with the functional dysregulation of these mechanisms in myeloid leukaemia and discuss opportunities for targeting LSC-specific mechanisms for the prevention or cure of malignant diseases.
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Affiliation(s)
- Masayuki Yamashita
- Columbia Stem Cell Initiative, Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, USA
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Paul V Dellorusso
- Columbia Stem Cell Initiative, Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Oakley C Olson
- Columbia Stem Cell Initiative, Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Emmanuelle Passegué
- Columbia Stem Cell Initiative, Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, USA.
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28
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Abstract
The ATP-sensitive potassium channel (KATP channel) couples blood levels of glucose to insulin secretion from pancreatic β-cells. KATP channel closure triggers a cascade of events that results in insulin release. Metabolically generated changes in the intracellular concentrations of adenosine nucleotides are integral to this regulation, with ATP and ADP closing the channel and MgATP and MgADP increasing channel activity. Activating mutations in the genes encoding either of the two types of KATP channel subunit (Kir6.2 and SUR1) result in neonatal diabetes mellitus, whereas loss-of-function mutations cause hyperinsulinaemic hypoglycaemia of infancy. Sulfonylurea and glinide drugs, which bind to SUR1, close the channel through a pathway independent of ATP and are now the primary therapy for neonatal diabetes mellitus caused by mutations in the genes encoding KATP channel subunits. Insight into the molecular details of drug and nucleotide regulation of channel activity has been illuminated by cryo-electron microscopy structures that reveal the atomic-level organization of the KATP channel complex. Here we review how these structures aid our understanding of how the various mutations in the genes encoding Kir6.2 (KCNJ11) and SUR1 (ABCC8) lead to a reduction in ATP inhibition and thereby neonatal diabetes mellitus. We also provide an update on known mutations and sulfonylurea therapy in neonatal diabetes mellitus.
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Affiliation(s)
- Tanadet Pipatpolkai
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Samuel Usher
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, Oxford, UK
- School of Life Sciences, University of Warwick, Coventry, UK
- Department of Chemistry, University of Warwick, Coventry, UK
| | - Frances M Ashcroft
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.
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29
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Kiss E, Abdelwahab EHMM, Steib A, Papp E, Torok Z, Jakab L, Smuk G, Sarosi V, Pongracz JE. Cisplatin treatment induced interleukin 6 and 8 production alters lung adenocarcinoma cell migration in an oncogenic mutation dependent manner. Respir Res 2020; 21:120. [PMID: 32434541 PMCID: PMC7238555 DOI: 10.1186/s12931-020-01389-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 05/08/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The predominant metastatic site of lung cancer (LC) is the brain. Although outdated, conventional cisplatin treatment is still the main therapeutic approach for patients with advanced non-small cell lung cancer (NSCLC), since targeted therapy that offers better tumor control is not always possible. In the present study brain metastasis associated cytokine expression was investigated in primary NSCLC adenocarcinoma (AC) tissues with known oncogenic mutations in the presence or absence of platina based and tyrosine kinase inhibitor (TKI) drugs. METHODS Primary lung tumor samples were isolated, DNA was sequenced and then the samples were grouped based on mutation. Experiments were also performed using KRAS mutant A549 and EGFR mutant PC-9 cells. Drug response was analyzed in three dimensional (3D) tissue cultures. We assessed drug response and IL-6 and IL-8 cytokine expression in relation to cellular invasion using ATP dependent cell viability, qRT-PCR analysis, cytokine bead array, and migration assay. RESULTS In 3D co-cultures, primary NSCLC derived cells harboring EGFR mutation responded better to erlotinib treatment than KRAS mutant or KRAS/EGFR wild type (WT) cancer cells. In contrast, under the same culture conditions KRAS/EGFR WT or KRAS mutant cancer cells are more sensitive to cisplatin than EGFR mutant cells. Drug response and pro-inflammatory cytokine production varied depending on the driver mutations. Cisplatin but not erlotinib increased both IL-6 and IL-8 secretion and only IL-6 increased cellular migration and proliferation. CONCLUSION In vitro assays are available to determine the response to planned therapeutic approach of lung cancer subtypes. The sequence of administration of therapeutic drugs determines cytokine production and therefore therapeutic response.
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Affiliation(s)
- Edit Kiss
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, University of Pecs, 2 Rokus Str, Pecs, Hungary
- Humeltis Ltd, 20 Ifjusag Str, Pecs, Hungary
- Szentagothai Research Centre, University of Pecs, 20 Ifjusag Str, Pecs, Hungary
| | - El Husseiny Mohamed Mahmud Abdelwahab
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, University of Pecs, 2 Rokus Str, Pecs, Hungary
- Szentagothai Research Centre, University of Pecs, 20 Ifjusag Str, Pecs, Hungary
| | | | - Emoke Papp
- Department of Internal Medicine, Medical School and Clinical Centre, University of Pecs, 13 Ifjusag Str, Pecs, Hungary
| | - Zsofia Torok
- Department of Internal Medicine, Medical School and Clinical Centre, University of Pecs, 13 Ifjusag Str, Pecs, Hungary
| | - Laszlo Jakab
- Department of Surgery, Medical School and Clinical Centre, University of Pecs, 13 Ifjusag Str, Pecs, Hungary
| | - Gabor Smuk
- Department of Pathology, Medical School and Clinical Centre, University of Pecs, 13 Ifjusag Str, Pecs, Hungary
| | - Veronika Sarosi
- Department of Internal Medicine, Medical School and Clinical Centre, University of Pecs, 13 Ifjusag Str, Pecs, Hungary
| | - Judit Erzsebet Pongracz
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, University of Pecs, 2 Rokus Str, Pecs, Hungary
- Humeltis Ltd, 20 Ifjusag Str, Pecs, Hungary
- Szentagothai Research Centre, University of Pecs, 20 Ifjusag Str, Pecs, Hungary
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30
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Bianchi JJ, Zhao X, Mays JC, Davoli T. Not all cancers are created equal: Tissue specificity in cancer genes and pathways. Curr Opin Cell Biol 2020; 63:135-143. [PMID: 32092639 PMCID: PMC7247947 DOI: 10.1016/j.ceb.2020.01.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 01/02/2020] [Accepted: 01/07/2020] [Indexed: 12/22/2022]
Abstract
Tumors arise through waves of genetic alterations and clonal expansion that allow tumor cells to acquire cancer hallmarks, such as genome instability and immune evasion. Recent genomic analyses showed that the vast majority of cancer driver genes are mutated in a tissue-dependent manner, that is, are altered in some cancers but not others. Often the tumor type also affects the likelihood of therapy response. What is the origin of tissue specificity in cancer? Recent studies suggest that both cell-intrinsic and cell-extrinsic factors play a role. On one hand, cell type-specific wiring of the cell signaling network determines the outcome of cancer driver gene mutations. On the other hand, the tumor cells' exposure to tissue-specific microenvironments (e.g. immune cells) also contributes to shape the tissue specificity of driver genes and of therapy response. In the future, a more complete understanding of tissue specificity in cancer may inform methods to better predict and improve therapeutic outcomes.
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Affiliation(s)
- Joy J Bianchi
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, 10016, USA
| | - Xin Zhao
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, 10016, USA
| | - Joseph C Mays
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, 10016, USA
| | - Teresa Davoli
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, 10016, USA.
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31
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Nishikido A, Okamura T, Nakajima Y, Ishida E, Miyamoto T, Toki AK, Matsumoto S, Yoshino S, Horiguchi K, Saito T, Yamada E, Ozawa A, Shimoda Y, Oyama T, Yamada M. Regulation of the KCNJ5 gene by SF-1 in the adrenal cortex: Complete genomic organization and promoter function. Mol Cell Endocrinol 2020; 501:110657. [PMID: 31751625 DOI: 10.1016/j.mce.2019.110657] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 11/07/2019] [Accepted: 11/16/2019] [Indexed: 11/18/2022]
Abstract
Activating mutations in the KCNJ5 gene are responsible for the significant number of aldosterone-producing adenomas. To elucidate the molecular mechanisms underlying KCNJ5 expression, we characterized the entire human KCNJ5 gene. The gene spanned approximately 29.8 kb and contained three exons and two introns. The strongest expression of KCNJ5 mRNA was observed in the adrenal gland. The promoter region contained a putative binding site for SF-1 at -1782 bp. A construct containing -2444 bp of the promoter region exhibited the strongest promoter activity in adrenal H295R cells, and the introduction of a mutation in the SF-1 binding site almost completely abolished promoter activity. Furthermore, deletion mutation, EMSA, and knockdown analyses revealed that SF-1 bound to this element and was functional. Immunochemistry showed that KCNJ5 was predominantly expressed in the zona glomerulosa, while SF-1 was ubiquitously expressed in the adrenal cortex. These results demonstrated that SF-1 mediates the expression of human KCNJ5 in the adrenal cortex.
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Affiliation(s)
- Ayaka Nishikido
- Department of Internal Medicine, Division of Endocrinology and Metabolism, Gunma University Graduate School of Medicine, Maebashi, 371-8511, Japan
| | - Takashi Okamura
- Department of Internal Medicine, Division of Endocrinology and Metabolism, Gunma University Graduate School of Medicine, Maebashi, 371-8511, Japan
| | - Yasuyo Nakajima
- Department of Internal Medicine, Division of Endocrinology and Metabolism, Gunma University Graduate School of Medicine, Maebashi, 371-8511, Japan
| | - Emi Ishida
- Department of Internal Medicine, Division of Endocrinology and Metabolism, Gunma University Graduate School of Medicine, Maebashi, 371-8511, Japan
| | - Tomoko Miyamoto
- Department of Internal Medicine, Division of Endocrinology and Metabolism, Gunma University Graduate School of Medicine, Maebashi, 371-8511, Japan
| | - Akiko-Katano Toki
- Department of Internal Medicine, Division of Endocrinology and Metabolism, Gunma University Graduate School of Medicine, Maebashi, 371-8511, Japan
| | - Shunichi Matsumoto
- Department of Internal Medicine, Division of Endocrinology and Metabolism, Gunma University Graduate School of Medicine, Maebashi, 371-8511, Japan
| | - Satoshi Yoshino
- Department of Internal Medicine, Division of Endocrinology and Metabolism, Gunma University Graduate School of Medicine, Maebashi, 371-8511, Japan
| | - Kazuhiko Horiguchi
- Department of Internal Medicine, Division of Endocrinology and Metabolism, Gunma University Graduate School of Medicine, Maebashi, 371-8511, Japan
| | - Tsugumichi Saito
- Department of Internal Medicine, Division of Endocrinology and Metabolism, Gunma University Graduate School of Medicine, Maebashi, 371-8511, Japan
| | - Eijiro Yamada
- Department of Internal Medicine, Division of Endocrinology and Metabolism, Gunma University Graduate School of Medicine, Maebashi, 371-8511, Japan
| | - Atsushi Ozawa
- Department of Internal Medicine, Division of Endocrinology and Metabolism, Gunma University Graduate School of Medicine, Maebashi, 371-8511, Japan
| | - Yuki Shimoda
- Department of Diagnostic Pathology, Gunma University Graduate School of Medicine, Maebashi, 371-8511, Japan
| | - Tetsunari Oyama
- Department of Diagnostic Pathology, Gunma University Graduate School of Medicine, Maebashi, 371-8511, Japan
| | - Masanobu Yamada
- Department of Internal Medicine, Division of Endocrinology and Metabolism, Gunma University Graduate School of Medicine, Maebashi, 371-8511, Japan.
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32
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Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Limits on amplifiers of natural selection under death-Birth updating. PLoS Comput Biol 2020; 16:e1007494. [PMID: 31951609 PMCID: PMC6968837 DOI: 10.1371/journal.pcbi.1007494] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 10/18/2019] [Indexed: 12/29/2022] Open
Abstract
The fixation probability of a single mutant invading a population of residents is among the most widely-studied quantities in evolutionary dynamics. Amplifiers of natural selection are population structures that increase the fixation probability of advantageous mutants, compared to well-mixed populations. Extensive studies have shown that many amplifiers exist for the Birth-death Moran process, some of them substantially increasing the fixation probability or even guaranteeing fixation in the limit of large population size. On the other hand, no amplifiers are known for the death-Birth Moran process, and computer-assisted exhaustive searches have failed to discover amplification. In this work we resolve this disparity, by showing that any amplification under death-Birth updating is necessarily bounded and transient. Our boundedness result states that even if a population structure does amplify selection, the resulting fixation probability is close to that of the well-mixed population. Our transience result states that for any population structure there exists a threshold r⋆ such that the population structure ceases to amplify selection if the mutant fitness advantage r is larger than r⋆. Finally, we also extend the above results to δ-death-Birth updating, which is a combination of Birth-death and death-Birth updating. On the positive side, we identify population structures that maintain amplification for a wide range of values r and δ. These results demonstrate that amplification of natural selection depends on the specific mechanisms of the evolutionary process. Extensive literature exists on amplifiers of natural selection for the Birth-death Moran process, but no amplifiers are known for the death-Birth Moran process. Here we show that if amplifiers exist under death-Birth updating, they must be bounded and transient. Boundedness implies weak amplification, and transience implies amplification for only a limited range of the mutant fitness advantage. These results demonstrate that amplification depends on the specific mechanisms of the evolutionary process.
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Affiliation(s)
| | | | | | - Martin A. Nowak
- Program for Evolutionary Dynamics, Department of Organismic and Evolutionary Biology, Department of Mathematics, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail:
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Stankiewicz TR, Pena C, Bouchard RJ, Linseman DA. Dysregulation of Rac or Rho elicits death of motor neurons and activation of these GTPases is altered in the G93A mutant hSOD1 mouse model of amyotrophic lateral sclerosis. Neurobiol Dis 2020; 136:104743. [PMID: 31931138 DOI: 10.1016/j.nbd.2020.104743] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 12/18/2019] [Accepted: 01/08/2020] [Indexed: 12/11/2022] Open
Abstract
Rho GTPases play a central role in neuronal survival; however, the antagonistic relationship between Rac and Rho in the regulation of motor neuron survival remains poorly defined. In the current study, we demonstrate that treatment with NSC23766, a selective inhibitor of the Rac-specific guanine nucleotide exchange factors, Tiam1 and Trio, is sufficient to induce the death of embryonic stem cell (ESC)-derived motor neurons. The mode of cell death is primarily apoptotic and is characterized by caspase-3 activation, de-phosphorylation of ERK5 and AKT, and nuclear translocation of the BH3-only protein Bad. As opposed to the inhibition of Rac, motor neuron cell death is also induced by constitutive activation of Rho, via a mechanism that depends on Rho kinase (ROCK) activity. Investigation of Rac and Rho in the G93A mutant, human Cu, Zn-superoxide dismutase (hSOD1) mouse model of amyotrophic lateral sclerosis (ALS), revealed that active Rac1-GTP is markedly decreased in spinal cord motor neurons of transgenic mice at disease onset and end-stage, when compared to age-matched wild type (WT) littermates. Furthermore, although there is no significant change in active RhoA-GTP, total RhoB displays a striking redistribution from motor neuron nuclei in WT mouse spinal cord to motor neuron axons in end-stage G93A mutant hSOD1 mice. Collectively, these data suggest that the intricate balance between pro-survival Rac signaling and pro-apoptotic Rho/ROCK signaling is critical for motor neuron survival and therefore, disruption in the balance of their activities and/or localization may contribute to the death of motor neurons in ALS.
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Affiliation(s)
- Trisha R Stankiewicz
- University of Denver, Department of Biological Sciences, Denver, CO 80208, United States
| | - Claudia Pena
- University of Denver, Department of Biological Sciences, Denver, CO 80208, United States
| | - Ron J Bouchard
- Research Service, Veterans Affairs Medical Center, Denver, CO, 80220, United States
| | - Daniel A Linseman
- University of Denver, Department of Biological Sciences, Eleanor Roosevelt Institute, and Knoebel Institute for Healthy Aging, 2155 E. Wesley Ave., Denver, CO, 80208, United States.
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Veeragoni SR, Lange B, Serrano M, Nawrath C, Bauer S, Schäffner AR, Thordal-Christensen H, Durner J, Gaupels F. Mutant Muddle: Some Arabidopsis eds5 Mutant Lines Have a Previously Unnoticed Second-Site Mutation in FAH1. Plant Physiol 2020; 182:460-462. [PMID: 31685644 PMCID: PMC6945866 DOI: 10.1104/pp.19.01125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 10/24/2019] [Indexed: 05/26/2023]
Abstract
Some of the salicylic acid-deficient Arabidopsis eds5 mutants have an unnoticed fah1-2 background mutation, which could cause salicylic acid- and EDS5-independent mutant phenotypes.
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Affiliation(s)
- Sravani Ram Veeragoni
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
| | - Birgit Lange
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
| | - Mario Serrano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62209 Cuernavaca, Morelos, México
| | - Christiane Nawrath
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Sibylle Bauer
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
| | - Anton Rudolf Schäffner
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
| | - Hans Thordal-Christensen
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, DK-1871 Frederiksberg, Denmark
| | - Jörg Durner
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- Biochemical Plant Pathology, Technische Universität München, D-85354 Freising, Germany
| | - Frank Gaupels
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
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Benson E, Lolaico M, Tarasov Y, Gådin A, Högberg B. Evolutionary Refinement of DNA Nanostructures Using Coarse-Grained Molecular Dynamics Simulations. ACS Nano 2019; 13:12591-12598. [PMID: 31613092 PMCID: PMC7613751 DOI: 10.1021/acsnano.9b03473] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
In the past decade, DNA nanostructures have made the leap from small assemblies of a handful of oligonucleotides to megadalton objects assembled from hundreds or thousands of component DNA strands. Most DNA designs today are either lattice based with simple and reliable design tools or lattice free with a larger shape space but more challenging design and lower rigidity. In parallel with the development of DNA nanostructures, software packages for the simulation of nucleic acids have seen rapid development allowing for the simulation of the dynamics of full DNA nanostructure assemblies. Here, we implement an unsupervised software based on the coarse-grained molecular dynamics package oxDNA to simulate DNA origami structures and evaluate their rigidity. From this, the software autonomously produces mutant structures by adding or removing base pairs or modifying the positions of internal supports. These mutant structures are iteratively generated and evaluated by simulation to create an in silico evolution toward more rigid DNA nanostructures.
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Tischer A, Antelo G, Coltro G, Finke CM, Gonsalves W, Pardanani A, Ketterling R, Mangaonkar A, Gangat N, Tefferi A, Patnaik MM, Lasho TL. Functional evaluation of isocitrate dehydrogenase 1 and 2 variants of unclear significance in chronic myeloid neoplasms. Leuk Res 2019; 87:106264. [PMID: 31706195 DOI: 10.1016/j.leukres.2019.106264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 10/21/2019] [Indexed: 11/19/2022]
Affiliation(s)
- Alexander Tischer
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Guadalupe Antelo
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Giacomo Coltro
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Christy M Finke
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Wilson Gonsalves
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Animesh Pardanani
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Rhett Ketterling
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Abhishek Mangaonkar
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Naseema Gangat
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ayalew Tefferi
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Mrinal M Patnaik
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Terra L Lasho
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, USA.
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Abstract
The effective therapeutic treatment and the disease-modifying therapy for spinocerebellar ataxia type 2 (SCA2) (a progressive hereditary disease caused by an expansion of polyglutamine in the ataxin-2 protein) is not available yet. At present, only symptomatic treatment and methods of palliative care are prescribed to the patients. Many attempts were made to study the physiological, molecular, and biochemical changes in SCA2 patients and in a variety of the model systems to find new therapeutic targets for SCA2 treatment. A better understanding of the uncovered molecular mechanisms of the disease allowed the scientific community to develop strategies of potential therapy and helped to create some promising therapeutic approaches for SCA2 treatment. Recent progress in this field will be discussed in this review article.
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Affiliation(s)
- Polina A Egorova
- Laboratory of Molecular Neurodegeneration, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, 195251, Russia
| | - Ilya B Bezprozvanny
- Laboratory of Molecular Neurodegeneration, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, 195251, Russia.
- Department of Physiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, ND12.200, Dallas, Texas, 75390, USA.
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Abstract
Spinocerebellar ataxia type 31 (SCA31) is one of the autosomal-dominant neurodegenerative disorders that shows progressive cerebellar ataxia as a cardinal symptom. This disease is caused by a 2.5- to 3.8-kb-long complex pentanucleotide repeat containing (TGGAA)n, (TAGAA)n, (TAAAA)n, and (TAAAATAGAA)n in an intron of the gene called BEAN1 (brain expressed, associated with Nedd4). By comparing various pentanucleotide repeats in this particular locus among control Japanese and Caucasian populations, it was found that (TGGAA)n was the only sequence segregating with SCA31, strongly suggesting the pathogenicity of (TGGAA)n. The complex repeat also lies in an intron of another gene, TK2 (thymidine kinase 2), which is transcribed in the opposite direction, indicating that the complex repeat is bi-directionally transcribed as noncoding repeats. In SCA31 human brains, (UGGAA)n, the BEAN1 transcript of SCA31 mutation was found to form abnormal RNA structures called RNA foci in cerebellar Purkinje cell nuclei. Subsequent RNA pulldown analysis disclosed that (UGGAA)n binds to RNA-binding proteins TDP-43, FUS, and hnRNP A2/B1. In fact, TDP-43 was found to co-localize with RNA foci in human SCA31 Purkinje cells. To dissect the pathogenesis of (UGGAA)n in SCA31, we generated transgenic fly models of SCA31 by overexpressing SCA31 complex pentanucleotide repeats in Drosophila. We found that the toxicity of (UGGAA)n is length- and expression level-dependent, and it was dampened by co-expressing TDP-43, FUS, and hnRNP A2/B1. Further investigation revealed that TDP-43 ameliorates (UGGAA)n toxicity by directly fixing the abnormal structure of (UGGAA)n. This led us to propose that TDP-43 acts as an RNA chaperone against toxic (UGGAA)n. Further research on the role of RNA-binding proteins as RNA chaperones may provide a novel therapeutic strategy for SCA31.
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Affiliation(s)
- Kinya Ishikawa
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.
- The Center for Personalized Medicine for Healthy Aging, Tokyo Medical and Dental University, Tokyo, Japan.
| | - Yoshitaka Nagai
- Department of Neurotherapeutics, Osaka University Graduate School of Medicine, Osaka, Japan
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
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Clarke SL, Thompson LR, Dandekar E, Srinivasan A, Montgomery MR. Distinct TP53 Mutation Subtypes Differentially Influence Cellular Iron Metabolism. Nutrients 2019; 11:nu11092144. [PMID: 31500291 PMCID: PMC6769808 DOI: 10.3390/nu11092144] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/02/2019] [Accepted: 09/05/2019] [Indexed: 01/31/2023] Open
Abstract
The most commonly mutated gene in all human cancers is the tumor suppressor gene TP53; however, in addition to the loss of tumor suppressor functions, mutations in TP53 can also promote cancer progression by altering cellular iron acquisition and metabolism. The primary objective of this work was to determine how TP53 mutation status influences the molecular control of iron homeostasis. The effect of TP53 mutation type on cellular iron homeostasis was examined using cell lines with inducible versions of either wild-type TP53 or a representative mutated TP53 gene from exemplary "hotspot" mutations in the DNA binding domain (R248, R273, and R175) as well as H193Y. The introduction of distinct TP53 mutation types alone was sufficient to disrupt cellular iron metabolism. These effects were mediated, at least in part, due to differences in the responsiveness of iron regulatory proteins (IRPs) to cellular iron availability. IRPs are considered the master regulators of intracellular iron homeostasis because they coordinate the expression of iron storage (ferritin) and iron uptake (transferrin receptor) genes. In response to changes in iron availability, cells harboring either a wild-type TP53 or R273H TP53 mutation displayed canonical IRP-mediated responses, but neither IRP1 RNA binding activity nor IRP2 protein levels were affected by changes in iron status in cells harboring the R175H mutation type. However, all mutation types exhibited robust changes in ferritin and transferrin receptor protein expression in response to iron loading and iron chelation, respectively. These findings suggest a novel, IRP-independent mode of iron regulation in cells expressing distinct TP53 mutations. As TP53 is mutated in nearly half of all human cancers, and iron is necessary for cancer cell growth and proliferation, the studies have implications for a wide range of clinically important cancers.
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Affiliation(s)
- Stephen L Clarke
- Department of Nutritional Sciences, Oklahoma State University, Stillwater, OK 74074, USA.
| | - Laurie R Thompson
- Department of Nutritional Sciences, Oklahoma State University, Stillwater, OK 74074, USA.
| | - Eshan Dandekar
- Department of Nutritional Sciences, Oklahoma State University, Stillwater, OK 74074, USA.
| | - Aishwarya Srinivasan
- Department of Nutritional Sciences, Oklahoma State University, Stillwater, OK 74074, USA.
| | - McKale R Montgomery
- Department of Nutritional Sciences, Oklahoma State University, Stillwater, OK 74074, USA.
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Raimondi F, Inoue A, Kadji FMN, Shuai N, Gonzalez JC, Singh G, de la Vega AA, Sotillo R, Fischer B, Aoki J, Gutkind JS, Russell RB. Rare, functional, somatic variants in gene families linked to cancer genes: GPCR signaling as a paradigm. Oncogene 2019; 38:6491-6506. [PMID: 31337866 PMCID: PMC6756116 DOI: 10.1038/s41388-019-0895-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 03/04/2019] [Accepted: 04/08/2019] [Indexed: 12/26/2022]
Abstract
Oncodriver genes are usually identified when mutations recur in multiple tumours. Different drivers often converge in the activation or repression of key cancer-relevant pathways. However, as many pathways contain multiple members of the same gene family, individual mutations might be overlooked, as each family member would necessarily have a lower mutation frequency and thus not identified as significant in any one-gene-at-a-time analysis. Here, we looked for mutated, functional sequence positions in gene families that were mutually exclusive (in patients) with another gene in the same pathway, which identified both known and new candidate oncodrivers. For instance, many inactivating mutations in multiple G-protein (particularly Gi/o) coupled receptors, are mutually exclusive with Gαs oncogenic activating mutations, both of which ultimately enhance cAMP signalling. By integrating transcriptomics and interaction data, we show that the Gs pathway is upregulated in multiple cancer types, even those lacking known GNAS activating mutations. This suggests that cancer cells may develop alternative strategies to activate adenylate cyclase signalling in multiple cancer types. Our study provides a mechanistic interpretation for several rare somatic mutations in multi-gene oncodrivers, and offers possible explanations for known and potential off-label cancer treatments, suggesting new therapeutic opportunities.
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Affiliation(s)
- Francesco Raimondi
- BioQuant, Heidelberg University, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany.
- Heidelberg University Biochemistry Centre (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany.
| | - Asuka Inoue
- Graduate School of Pharmaceutical Science, Tohoku University, Sendai, 980-8578, Miyagi, Japan
- Advanced Research & Development Programs for Medical Innovation (PRIME), Japan Agency for Medical Research and Development (AMED), Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Francois M N Kadji
- Graduate School of Pharmaceutical Science, Tohoku University, Sendai, 980-8578, Miyagi, Japan
- Advanced Research & Development Programs for Medical Innovation (PRIME), Japan Agency for Medical Research and Development (AMED), Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Ni Shuai
- Computational Genome Biology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Juan-Carlos Gonzalez
- BioQuant, Heidelberg University, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany
- Heidelberg University Biochemistry Centre (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Gurdeep Singh
- BioQuant, Heidelberg University, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany
- Heidelberg University Biochemistry Centre (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Alicia Alonso de la Vega
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), 69120, Heidelberg, Germany
| | - Rocio Sotillo
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), 69120, Heidelberg, Germany
| | - Bernd Fischer
- Computational Genome Biology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Junken Aoki
- Graduate School of Pharmaceutical Science, Tohoku University, Sendai, 980-8578, Miyagi, Japan
- Advanced Research & Development Programs for Medical Innovation (PRIME), Japan Agency for Medical Research and Development (AMED), Chiyoda-ku, Tokyo, 100-0004, Japan
| | - J Silvio Gutkind
- Moores Cancer Center, University of San Diego, San Diego, La Jolla, CA 92093, USA
| | - Robert B Russell
- BioQuant, Heidelberg University, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany.
- Heidelberg University Biochemistry Centre (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany.
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Foster CJ, Gopalakrishnan S, Antoniewicz MR, Maranas CD. From Escherichia coli mutant 13C labeling data to a core kinetic model: A kinetic model parameterization pipeline. PLoS Comput Biol 2019; 15:e1007319. [PMID: 31504032 PMCID: PMC6759195 DOI: 10.1371/journal.pcbi.1007319] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 09/24/2019] [Accepted: 08/02/2019] [Indexed: 12/02/2022] Open
Abstract
Kinetic models of metabolic networks offer the promise of quantitative phenotype prediction. The mechanistic characterization of enzyme catalyzed reactions allows for tracing the effect of perturbations in metabolite concentrations and reaction fluxes in response to genetic and environmental perturbation that are beyond the scope of stoichiometric models. In this study, we develop a two-step computational pipeline for the rapid parameterization of kinetic models of metabolic networks using a curated metabolic model and available 13C-labeling distributions under multiple genetic and environmental perturbations. The first step involves the elucidation of all intracellular fluxes in a core model of E. coli containing 74 reactions and 61 metabolites using 13C-Metabolic Flux Analysis (13C-MFA). Here, fluxes corresponding to the mid-exponential growth phase are elucidated for seven single gene deletion mutants from upper glycolysis, pentose phosphate pathway and the Entner-Doudoroff pathway. The computed flux ranges are then used to parameterize the same (i.e., k-ecoli74) core kinetic model for E. coli with 55 substrate-level regulations using the newly developed K-FIT parameterization algorithm. The K-FIT algorithm employs a combination of equation decomposition and iterative solution techniques to evaluate steady-state fluxes in response to genetic perturbations. k-ecoli74 predicted 86% of flux values for strains used during fitting within a single standard deviation of 13C-MFA estimated values. By performing both tasks using the same network, errors associated with lack of congruity between the two networks are avoided, allowing for seamless integration of data with model building. Product yield predictions and comparison with previously developed kinetic models indicate shifts in flux ranges and the presence or absence of mutant strains delivering flux towards pathways of interest from training data significantly impact predictive capabilities. Using this workflow, the impact of completeness of fluxomic datasets and the importance of specific genetic perturbations on uncertainties in kinetic parameter estimation are evaluated.
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Affiliation(s)
- Charles J. Foster
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Saratram Gopalakrishnan
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Maciek R. Antoniewicz
- Department of Chemical and Biomolecular Engineering, University of Delaware. Newark, Delaware, United States of America
| | - Costas D. Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, United States of America
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Abstract
Engineering polymerases to synthesize artificial genetic polymers with unique backbone structures is limited by a general lack of understanding about the structural determinants that govern substrate specificity. Here, we report a high-throughput microfluidic-based approach for mapping sequence-function relationships that combines droplet-based optical polymerase sorting with deep mutational scanning. We applied this strategy to map the finger subdomain of a replicative DNA polymerase isolated from Thermococcus kodakarensis (Kod). The enrichment profile provides an unbiased view of the ability of each mutant to synthesize threose nucleic acid, which was used as a model non-natural genetic polymer. From a single round of sorting, we discovered two cases of positive epistasis and demonstrate the near inversion of substrate specificity from a double mutant variant. This effort indicates that polymerase specificity may be governed by a small number of highly specific residues that can be elucidated by deep mutational scanning without the need for iterative rounds of directed evolution.
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Affiliation(s)
- Ali Nikoomanzar
- Departments of Pharmaceutical Sciences, Chemistry, and Molecular Biology and Biochemistry , University of California , Irvine , California 92697-3958 , United States
| | - Derek Vallejo
- Departments of Pharmaceutical Sciences, Chemistry, and Molecular Biology and Biochemistry , University of California , Irvine , California 92697-3958 , United States
| | - John C Chaput
- Departments of Pharmaceutical Sciences, Chemistry, and Molecular Biology and Biochemistry , University of California , Irvine , California 92697-3958 , United States
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Abstract
Classically, phenotype is what is observed, and genotype is the genetic makeup. Statistical studies aim to project phenotypic likelihoods of genotypic patterns. The traditional genotype-to-phenotype theory embraces the view that the encoded protein shape together with gene expression level largely determines the resulting phenotypic trait. Here, we point out that the molecular biology revolution at the turn of the century explained that the gene encodes not one but ensembles of conformations, which in turn spell all possible gene-associated phenotypes. The significance of a dynamic ensemble view is in understanding the linkage between genetic change and the gained observable physical or biochemical characteristics. Thus, despite the transformative shift in our understanding of the basis of protein structure and function, the literature still commonly relates to the classical genotype–phenotype paradigm. This is important because an ensemble view clarifies how even seemingly small genetic alterations can lead to pleiotropic traits in adaptive evolution and in disease, why cellular pathways can be modified in monogenic and polygenic traits, and how the environment may tweak protein function.
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Affiliation(s)
- Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- * E-mail:
| | - Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
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44
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Chen K, Chen S, Xu J, Yu Y, Liu Z, Tan A, Huang Y. Maelstrom regulates spermatogenesis of the silkworm, Bombyx mori. Insect Biochem Mol Biol 2019; 109:43-51. [PMID: 30970276 DOI: 10.1016/j.ibmb.2019.03.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 03/03/2019] [Accepted: 03/28/2019] [Indexed: 06/09/2023]
Abstract
The spermatogenesis of animal is essential for the reproduction and a very large number of genes participate in this procession. The Maelstrom (Mael) is identified essential for spermatogenesis in both Drosophila and mouse, though the mechanisms appear to differ. It was initially found that Mael gene is necessary for axis specification of oocytes in Drosophila, and recent studies suggested that Mael participates in the piRNA pathway. In this study, we obtained Bombyx mori Mael mutants by using a binary transgenic CRISPR/Cas9 system and analyzed the function of Mael in B. mori, a model lepidopteran insect. The results showed that BmMael is not necessary for piRNA pathway in the ovary of silkworm, whereas it might be essential for transposon elements (TEs) repression in testis. The BmMael mutation resulted in male sterility, and further analysis established that BmMael was essential for spermatogenesis. The spermatogenesis defects occurred in the elongation stage and resulted in nuclei concentration arrest. RNA-seq and qRT-PCR analyses demonstrated that spermatogenesis defects were associated with tight junctions and apoptosis. We also found that BmMael was not involved in the silkworm sex determination pathway. Our data provide insights into the biological function of BmMael in male spermatogenesis and might be useful for developing novel methods to control lepidopteron pests.
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Affiliation(s)
- Kai Chen
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuqing Chen
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun Xu
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Ye Yu
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zulian Liu
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Anjiang Tan
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yongping Huang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
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Chernyuk D, Zernov N, Kabirova M, Bezprozvanny I, Popugaeva E. Antagonist of neuronal store-operated calcium entry exerts beneficial effects in neurons expressing PSEN1ΔE9 mutant linked to familial Alzheimer disease. Neuroscience 2019; 410:118-127. [PMID: 31055008 DOI: 10.1016/j.neuroscience.2019.04.043] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 04/16/2019] [Accepted: 04/17/2019] [Indexed: 12/13/2022]
Abstract
Alzheimer's disease (AD) is the neurodegenerative disorder with no cure. Recent studies suggest that dysregulated postsynaptic store-operated calcium entry (nSOCE) may underlie mushroom spine loss that is related to AD pathology. In the present study we observed that PSEN1ΔE9 familial AD (FAD) mutation causes mushroom spine loss in hippocampal neuronal cultures. We also demonstrated that amplitude of TRPC6-mediated nSOCE is increased in PSEN1ΔE9-expressing neurons and we suggested that inhibition of nSOCE may help to rescue synaptic defects in this model. We further established that nSOCE antagonist EVP4593 decreases PSEN1ΔE9-mediated nSOCE upregulation and rescues mushroom spines in PSEN1ΔE9-expressing neurons. Obtained results further highlight the connection between dysregulation of endoplasmic reticulum calcium signaling and synaptic loss in AD and suggest that calcium signaling modulators may have a therapeutic value for treatment of memory loss in AD.
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Affiliation(s)
- Daria Chernyuk
- Peter the Great St. Petersburg Polytechnic University, Department of Medical Physics, Laboratory of Molecular Neurodegeneration, St Petersburg, Russia
| | - Nikita Zernov
- Peter the Great St. Petersburg Polytechnic University, Department of Medical Physics, Laboratory of Molecular Neurodegeneration, St Petersburg, Russia
| | - Marina Kabirova
- Peter the Great St. Petersburg Polytechnic University, Department of Medical Physics, Laboratory of Molecular Neurodegeneration, St Petersburg, Russia
| | - Ilya Bezprozvanny
- Peter the Great St. Petersburg Polytechnic University, Department of Medical Physics, Laboratory of Molecular Neurodegeneration, St Petersburg, Russia; UT Southwestern Medical Center, Department of Physiology, Dallas, USA.
| | - Elena Popugaeva
- Peter the Great St. Petersburg Polytechnic University, Department of Medical Physics, Laboratory of Molecular Neurodegeneration, St Petersburg, Russia.
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Brown AL, Li M, Goncearenco A, Panchenko AR. Finding driver mutations in cancer: Elucidating the role of background mutational processes. PLoS Comput Biol 2019; 15:e1006981. [PMID: 31034466 PMCID: PMC6508748 DOI: 10.1371/journal.pcbi.1006981] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 05/09/2019] [Accepted: 03/28/2019] [Indexed: 01/22/2023] Open
Abstract
Identifying driver mutations in cancer is notoriously difficult. To date, recurrence of a mutation in patients remains one of the most reliable markers of mutation driver status. However, some mutations are more likely to occur than others due to differences in background mutation rates arising from various forms of infidelity of DNA replication and repair machinery, endogenous, and exogenous mutagens. We calculated nucleotide and codon mutability to study the contribution of background processes in shaping the observed mutational spectrum in cancer. We developed and tested probabilistic pan-cancer and cancer-specific models that adjust the number of mutation recurrences in patients by background mutability in order to find mutations which may be under selection in cancer. We showed that mutations with higher mutability values had higher observed recurrence frequency, especially in tumor suppressor genes. This trend was prominent for nonsense and silent mutations or mutations with neutral functional impact. In oncogenes, however, highly recurring mutations were characterized by relatively low mutability, resulting in an inversed U-shaped trend. Mutations not yet observed in any tumor had relatively low mutability values, indicating that background mutability might limit mutation occurrence. We compiled a dataset of missense mutations from 58 genes with experimentally validated functional and transforming impacts from various studies. We found that mutability of driver mutations was lower than that of passengers and consequently adjusting mutation recurrence frequency by mutability significantly improved ranking of mutations and driver mutation prediction. Even though no training on existing data was involved, our approach performed similarly or better to the state-of-the-art methods.
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Affiliation(s)
- Anna-Leigh Brown
- National Center for Biotechnology Information, NLM, NIH, Bethesda, MD, United States of America
| | - Minghui Li
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Alexander Goncearenco
- National Center for Biotechnology Information, NLM, NIH, Bethesda, MD, United States of America
| | - Anna R. Panchenko
- National Center for Biotechnology Information, NLM, NIH, Bethesda, MD, United States of America
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Dayan-Alon O, Kanner BI. Internal gate mutants of the GABA transporter GAT1 are capable of substrate exchange. Neuropharmacology 2019; 161:107534. [PMID: 30790582 DOI: 10.1016/j.neuropharm.2019.02.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 02/10/2019] [Accepted: 02/12/2019] [Indexed: 11/17/2022]
Abstract
GAT1 is a member of the neurotransmitter:sodium: symporter family and mediates transport of GABA together with sodium and chloride in an electrogenic process enabling efficient synaptic transmission. Biochemical and modelling studies based on the structure of the bacterial homologue LeuT are consistent with a transport mechanism whereby the binding pocket is alternately accessible to either side of the membrane. This is achieved by the sequential opening and closing of extracellular and intracellular gates. The amino acid residues participating in the formation of these gates are highly conserved within the neurotransmitter:sodium: symporter family. Net flux requires that the gating mechanism is operative regardless if the binding pocket is loaded with substrate or empty. On the other hand, exchange of labelled for non-labelled substrate across the membrane only requires gating in the presence of substrate. To address the question if the gating requirements of the substrate-bound and empty transporters are similar or different, we analyzed the impact of mutation of intra- and extra-cellular gate residues on net GABA influx and on exchange by liposomes inlaid with the mutant transporters. Whereas net flux by all four internal gate mutants tested was severely abrogated, each exhibited significant levels of exchange. In contrast, two external gate mutants were impaired in both processes. Our results indicate that perturbation of the internal gate of GAT1 selectively impairs the gating mechanism of the empty transporter. This article is part of the issue entitled 'Special Issue on Neurotransmitter Transporters'.
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Affiliation(s)
- Oshrat Dayan-Alon
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University Hadassah Medical School, Jerusalem, 91120, Israel
| | - Baruch I Kanner
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University Hadassah Medical School, Jerusalem, 91120, Israel.
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Pacentine IV, Nicolson T. Subunits of the mechano-electrical transduction channel, Tmc1/2b, require Tmie to localize in zebrafish sensory hair cells. PLoS Genet 2019; 15:e1007635. [PMID: 30726219 PMCID: PMC6380590 DOI: 10.1371/journal.pgen.1007635] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 02/19/2019] [Accepted: 01/03/2019] [Indexed: 12/26/2022] Open
Abstract
Mutations in transmembrane inner ear (TMIE) cause deafness in humans; previous studies suggest involvement in the mechano-electrical transduction (MET) complex in sensory hair cells, but TMIE’s precise role is unclear. In tmie zebrafish mutants, we observed that GFP-tagged Tmc1 and Tmc2b, which are subunits of the MET channel, fail to target to the hair bundle. In contrast, overexpression of Tmie strongly enhances the targeting of Tmc1-GFP and Tmc2b-GFP to stereocilia. To identify the motifs of Tmie underlying the regulation of the Tmcs, we systematically deleted or replaced peptide segments. We then assessed localization and functional rescue of each mutated/chimeric form of Tmie in tmie mutants. We determined that the first putative helix was dispensable and identified a novel critical region of Tmie, the extracellular region and transmembrane domain, which is required for both mechanosensitivity and Tmc2b-GFP expression in bundles. Collectively, our results suggest that Tmie’s role in sensory hair cells is to target and stabilize Tmc channel subunits to the site of MET. Hair cells mediate hearing and balance through the activity of a mechanosensitive channel in the cell membrane. The transmembrane inner ear (TMIE) protein is an essential component of the protein complex that gates this so-called mechanotransduction channel. While it is known that loss of TMIE results in deafness, the function of TMIE within the complex is unclear. Using zebrafish as a deafness model, Pacentine and Nicolson demonstrate that Tmie is required for the localization of the channel subunits, transmembrane channel-like (Tmc) proteins Tmc1/2b. They then evaluate thirteen unique versions of Tmie, each containing mutations in different domains of Tmie. This analysis reveals that specific mutated versions of Tmie reduce hair cell activity, and that these same dysfunctional versions also cause reduced Tmc expression at the normal site of the channel. These findings link hair cell activity with the levels of Tmc in the bundle, reinforcing the notion that the Tmcs are the pore-forming subunits of the mechanotransduction channel. The authors conclude that Tmie, through distinct regions, is involved in both trafficking and stabilizing the channels at the site of mechanotransduction.
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Affiliation(s)
- Itallia V. Pacentine
- Oregon Hearing Research Center and Vollum Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Teresa Nicolson
- Oregon Hearing Research Center and Vollum Institute, Oregon Health & Science University, Portland, Oregon, United States of America
- * E-mail:
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Islamaj Dogan R, Kim S, Chatr-Aryamontri A, Wei CH, Comeau DC, Antunes R, Matos S, Chen Q, Elangovan A, Panyam NC, Verspoor K, Liu H, Wang Y, Liu Z, Altinel B, Hüsünbeyi ZM, Özgür A, Fergadis A, Wang CK, Dai HJ, Tran T, Kavuluru R, Luo L, Steppi A, Zhang J, Qu J, Lu Z. Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine. Database (Oxford) 2019; 2019:5303240. [PMID: 30689846 PMCID: PMC6348314 DOI: 10.1093/database/bay147] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 12/19/2018] [Indexed: 12/16/2022]
Abstract
The Precision Medicine Initiative is a multicenter effort aiming at formulating personalized treatments leveraging on individual patient data (clinical, genome sequence and functional genomic data) together with the information in large knowledge bases (KBs) that integrate genome annotation, disease association studies, electronic health records and other data types. The biomedical literature provides a rich foundation for populating these KBs, reporting genetic and molecular interactions that provide the scaffold for the cellular regulatory systems and detailing the influence of genetic variants in these interactions. The goal of BioCreative VI Precision Medicine Track was to extract this particular type of information and was organized in two tasks: (i) document triage task, focused on identifying scientific literature containing experimentally verified protein-protein interactions (PPIs) affected by genetic mutations and (ii) relation extraction task, focused on extracting the affected interactions (protein pairs). To assist system developers and task participants, a large-scale corpus of PubMed documents was manually annotated for this task. Ten teams worldwide contributed 22 distinct text-mining models for the document triage task, and six teams worldwide contributed 14 different text-mining systems for the relation extraction task. When comparing the text-mining system predictions with human annotations, for the triage task, the best F-score was 69.06%, the best precision was 62.89%, the best recall was 98.0% and the best average precision was 72.5%. For the relation extraction task, when taking homologous genes into account, the best F-score was 37.73%, the best precision was 46.5% and the best recall was 54.1%. Submitted systems explored a wide range of methods, from traditional rule-based, statistical and machine learning systems to state-of-the-art deep learning methods. Given the level of participation and the individual team results we find the precision medicine track to be successful in engaging the text-mining research community. In the meantime, the track produced a manually annotated corpus of 5509 PubMed documents developed by BioGRID curators and relevant for precision medicine. The data set is freely available to the community, and the specific interactions have been integrated into the BioGRID data set. In addition, this challenge provided the first results of automatically identifying PubMed articles that describe PPI affected by mutations, as well as extracting the affected relations from those articles. Still, much progress is needed for computer-assisted precision medicine text mining to become mainstream. Future work should focus on addressing the remaining technical challenges and incorporating the practical benefits of text-mining tools into real-world precision medicine information-related curation.
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Affiliation(s)
- Rezarta Islamaj Dogan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Sun Kim
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | - Chih-Hsuan Wei
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Donald C Comeau
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Rui Antunes
- Department of Electronics, Telecommunications and Informatics (DETI)/Institute of Electronics and Informatics Engineering of Aveiro (IEETA), University of Aveiro, Aveiro, Portugal
| | - Sérgio Matos
- Department of Electronics, Telecommunications and Informatics (DETI)/Institute of Electronics and Informatics Engineering of Aveiro (IEETA), University of Aveiro, Aveiro, Portugal
| | - Qingyu Chen
- School of Computing and Information Systems, The University of Melbourne, Melbourne, VIC, Australia
| | - Aparna Elangovan
- School of Computing and Information Systems, The University of Melbourne, Melbourne, VIC, Australia
| | - Nagesh C Panyam
- School of Computing and Information Systems, The University of Melbourne, Melbourne, VIC, Australia
| | - Karin Verspoor
- School of Computing and Information Systems, The University of Melbourne, Melbourne, VIC, Australia
| | - Hongfang Liu
- Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
| | - Yanshan Wang
- Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
| | - Zhuang Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian, China
| | - Berna Altinel
- Department of Computer Engineering, Marmara University, Istanbul, Turkey
| | | | | | - Aris Fergadis
- School of Electrical and Computer Engineering, National Technical University of Athens, Zografou, Athens, Greece
| | - Chen-Kai Wang
- Graduate Institute of Biomedical Informatics, Taipei Medical University, Taipei, Taiwan
| | - Hong-Jie Dai
- Department of Electrical Engineering, National Kaousiung University of Science and Technology, Kaohsiung, Taiwan
| | - Tung Tran
- Department of Computer Science, University of Kentucky, Lexington, KY, USA
| | - Ramakanth Kavuluru
- Division of Biomedical Informatics, Department of Internal Medicine, University of Kentucky, Lexington, KY, USA
| | - Ling Luo
- College of Computer Science and Technology, Dalian University of Technology, Dalian, China
| | - Albert Steppi
- Department of Statistics, Florida State University, Florida, USA
| | - Jinfeng Zhang
- Department of Statistics, Florida State University, Florida, USA
| | - Jinchan Qu
- Department of Statistics, Florida State University, Florida, USA
| | - Zhiyong Lu
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
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50
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Zhang P, Lee Y, Wei X, Wu J, Liu Q, Wan S. Enhanced production of tanshinone IIA in endophytic fungi Emericella foeniculicola by genome shuffling. Pharm Biol 2018; 56:357-362. [PMID: 30266071 PMCID: PMC6171462 DOI: 10.1080/13880209.2018.1481108] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 03/14/2018] [Accepted: 05/16/2018] [Indexed: 06/08/2023]
Abstract
CONTEXT Tanshinone IIA, commercially produced from Salvia miltiorrhiza Bunge (C.Y.Wu) (Labiatae), has various biological benefits. Currently, this compound is mainly extracted from plants. However, because of the long growth cycle and the unstable quality of plants, the market demands can barely be satisfied. OBJECTIVE The genomic shuffling technology is applied to screen the high-yield tanshinone IIA strain, which could be used to replace the plant S. miltiorrhiza for the production of tanshinone IIA. The change in the production of tanshinone IIA is clarified by comparing it with the original strain. MATERIALS AND METHODS Tanshinone IIA was extracted from Strains cells, which was prepared through 0.5 mL protoplast samples by using hypertonic solution I from two different strains. Then, it was analyzed by high-performance liquid chromatography at 30 °C and UV 270 nm. Total DNA from the strains was extracted for RAPD amplification and electrophoresis to isolate the product. RESULTS In this study, a high-yield tanshinone IIA strain F-3.4 was screened and the yield of tanshinone IIA was increased by 387.56 ± 0.02 mg/g, 11.07 times higher than that of the original strain TR21. DISCUSSION This study shows that the genetic basis of high-yield strains is achieved through genome shuffling, which proves that genome shuffling can shorten the breeding cycle and improve the mutagenesis efficiency in obtaining the strains with good traits and it is a useful method for the molecular breeding of industrial strains.
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Affiliation(s)
- Pengyu Zhang
- College of Life Sciences, Shaanxi Normal University, Chang’an Campus, Xi’an, Shaanxi, China
| | - Yiting Lee
- College of Life Sciences, Shaanxi Normal University, Chang’an Campus, Xi’an, Shaanxi, China
| | - Xiying Wei
- College of Life Sciences, Shaanxi Normal University, Chang’an Campus, Xi’an, Shaanxi, China
| | - Jinlan Wu
- College of Life Sciences, Shaanxi Normal University, Chang’an Campus, Xi’an, Shaanxi, China
| | - Qingmei Liu
- College of Life Sciences, Shaanxi Normal University, Chang’an Campus, Xi’an, Shaanxi, China
| | - Shanning Wan
- College of Life Sciences, Shaanxi Normal University, Chang’an Campus, Xi’an, Shaanxi, China
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