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Xu DC, Sas-Nowosielska H, Donahue G, Huang H, Pourshafie N, Good CR, Berger SL. Histone acetylation in an Alzheimer's disease cell model promotes homeostatic amyloid-reducing pathways. Acta Neuropathol Commun 2024; 12:3. [PMID: 38167174 PMCID: PMC10759377 DOI: 10.1186/s40478-023-01696-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 11/21/2023] [Indexed: 01/05/2024] Open
Abstract
Alzheimer's Disease (AD) is a disorder characterized by cognitive decline, neurodegeneration, and accumulation of amyloid plaques and tau neurofibrillary tangles in the brain. Dysregulation of epigenetic histone modifications may lead to expression of transcriptional programs that play a role either in protecting against disease genesis or in worsening of disease pathology. One such histone modification, acetylation of histone H3 lysine residue 27 (H3K27ac), is primarily localized to genomic enhancer regions and promotes active gene transcription. We previously discovered H3K27ac to be more abundant in AD patient brain tissue compared to the brains of age-matched non-demented controls. In this study, we use iPSC-neurons derived from familial AD patients with an amyloid precursor protein (APP) duplication (APPDup neurons) as a model to study the functional effect of lowering CBP/P300 enzymes that catalyze H3K27ac. We found that homeostatic amyloid-reducing genes were upregulated in the APPDup neurons compared to non-demented controls. We lowered CBP/P300 to reduce H3K27ac, which led to decreased expression of numerous of these homeostatic amyloid-reducing genes, along with increased extracellular secretion of a toxic amyloid-β species, Aβ(1-42). Our findings suggest that epigenomic histone acetylation, including H3K27ac, drives expression of compensatory genetic programs in response to AD-associated insults, specifically those resulting from APP duplication, and thus may play a role in mitigating AD pathology in neurons.
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Affiliation(s)
- Daniel C Xu
- Department of Cell and Developmental Biology, Perelman School of Medicine Philadelphia, Penn Institute of Epigenetics, Philadelphia, PA, 19104, USA
| | - Hanna Sas-Nowosielska
- Department of Cell and Developmental Biology, Perelman School of Medicine Philadelphia, Penn Institute of Epigenetics, Philadelphia, PA, 19104, USA
| | - Greg Donahue
- Department of Cell and Developmental Biology, Perelman School of Medicine Philadelphia, Penn Institute of Epigenetics, Philadelphia, PA, 19104, USA
| | - Hua Huang
- Department of Cell and Developmental Biology, Perelman School of Medicine Philadelphia, Penn Institute of Epigenetics, Philadelphia, PA, 19104, USA
| | - Naemeh Pourshafie
- Department of Cell and Developmental Biology, Perelman School of Medicine Philadelphia, Penn Institute of Epigenetics, Philadelphia, PA, 19104, USA
| | - Charly R Good
- Department of Cell and Developmental Biology, Perelman School of Medicine Philadelphia, Penn Institute of Epigenetics, Philadelphia, PA, 19104, USA
| | - Shelley L Berger
- Department of Cell and Developmental Biology, Perelman School of Medicine Philadelphia, Penn Institute of Epigenetics, Philadelphia, PA, 19104, USA.
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2
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Dorogova NV, Fedorova SA, Bolobolova EU, Baricheva EM. The misregulation of mitochondria-associated genes caused by GAGA-factor lack promotes autophagic germ cell death in Drosophila testes. Genetica 2023; 151:349-355. [PMID: 37819589 DOI: 10.1007/s10709-023-00197-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 10/01/2023] [Indexed: 10/13/2023]
Abstract
The Drosophila GAGA-factor encoded by the Trithorax-like (Trl) gene is DNA-binding protein with unusually wide range of applications in diverse cell contexts. In Drosophila spermatogenesis, reduced GAGA expression caused by Trl mutations induces mass autophagy leading to germ cell death. In this work, we investigated the contribution of mitochondrial abnormalities to autophagic germ cell death in Trl gene mutants. Using a cytological approach, in combination with an analysis of high-throughput RNA sequencing (RNA-seq) data, we demonstrated that the GAGA deficiency led to considerable defects in mitochondrial ultrastructure, by causing misregulation of GAGA target genes encoding essential components of mitochondrial molecular machinery. Mitochondrial anomalies induced excessive production of reactive oxygen species and their release into the cytoplasm, thereby provoking oxidative stress. Changes in transcription levels of some GAGA-independent genes in the Trl mutants indicated that testis cells experience ATP deficiency and metabolic aberrations, that may trigger extensive autophagy progressing to cell death.
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Affiliation(s)
- Natalia V Dorogova
- Department of Cell Biology, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (ICG SB RAS), Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russian Federation.
| | - Svetlana A Fedorova
- Department of Cell Biology, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (ICG SB RAS), Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russian Federation
| | - Elena U Bolobolova
- Department of Cell Biology, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (ICG SB RAS), Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russian Federation
| | - Elina M Baricheva
- Department of Cell Biology, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (ICG SB RAS), Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russian Federation
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3
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Russell SL, Castillo JR, Sullivan WT. Wolbachia endosymbionts manipulate the self-renewal and differentiation of germline stem cells to reinforce fertility of their fruit fly host. PLoS Biol 2023; 21:e3002335. [PMID: 37874788 PMCID: PMC10597519 DOI: 10.1371/journal.pbio.3002335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 09/14/2023] [Indexed: 10/26/2023] Open
Abstract
The alphaproteobacterium Wolbachia pipientis infects arthropod and nematode species worldwide, making it a key target for host biological control. Wolbachia-driven host reproductive manipulations, such as cytoplasmic incompatibility (CI), are credited for catapulting these intracellular bacteria to high frequencies in host populations. Positive, perhaps mutualistic, reproductive manipulations also increase infection frequencies, but are not well understood. Here, we identify molecular and cellular mechanisms by which Wolbachia influences the molecularly distinct processes of germline stem cell (GSC) self-renewal and differentiation. We demonstrate that wMel infection rescues the fertility of flies lacking the translational regulator mei-P26 and is sufficient to sustain infertile homozygous mei-P26-knockdown stocks indefinitely. Cytology revealed that wMel mitigates the impact of mei-P26 loss through restoring proper pMad, Bam, Sxl, and Orb expression. In Oregon R files with wild-type fertility, wMel infection elevates lifetime egg hatch rates. Exploring these phenotypes through dual-RNAseq quantification of eukaryotic and bacterial transcripts revealed that wMel infection rescues and offsets many gene expression changes induced by mei-P26 loss at the mRNA level. Overall, we show that wMel infection beneficially reinforces host fertility at mRNA, protein, and phenotypic levels, and these mechanisms may promote the emergence of mutualism and the breakdown of host reproductive manipulations.
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Affiliation(s)
- Shelbi L. Russell
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Jennie Ruelas Castillo
- Division of Infectious Diseases, Department of Medicine, The Johns Hopkins Hospital, Baltimore, Maryland, United States of America
| | - William T. Sullivan
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
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4
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Papaspyropoulos A, Hazapis O, Altulea A, Polyzou A, Verginis P, Evangelou K, Fousteri M, Papantonis A, Demaria M, Gorgoulis V. Decoding of translation-regulating entities reveals heterogeneous translation deficiency patterns in cellular senescence. Aging Cell 2023; 22:e13893. [PMID: 37547972 PMCID: PMC10497830 DOI: 10.1111/acel.13893] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/04/2023] [Indexed: 08/08/2023] Open
Abstract
Cellular senescence constitutes a generally irreversible proliferation barrier, accompanied by macromolecular damage and metabolic rewiring. Several senescence types have been identified based on the initiating stimulus, such as replicative (RS), stress-induced (SIS) and oncogene-induced senescence (OIS). These senescence subtypes are heterogeneous and often develop subset-specific phenotypes. Reduced protein synthesis is considered a senescence hallmark, but whether this trait pertains to various senescence subtypes and if distinct molecular mechanisms are involved remain largely unknown. Here, we analyze large published or experimentally produced RNA-seq and Ribo-seq datasets to determine whether major translation-regulating entities such as ribosome stalling, the presence of uORFs/dORFs and IRES elements may differentially contribute to translation deficiency in senescence subsets. We show that translation-regulating mechanisms may not be directly relevant to RS, however uORFs are significantly enriched in SIS. Interestingly, ribosome stalling, uORF/dORF patterns and IRES elements comprise predominant mechanisms upon OIS, strongly correlating with Notch pathway activation. Our study provides for the first time evidence that major translation dysregulation mechanisms/patterns occur during cellular senescence, but at different rates depending on the stimulus type. The degree at which those mechanisms accumulate directly correlates with translation deficiency levels. Our thorough analysis contributes to elucidating crucial and so far unknown differences in the translation machinery between senescence subsets.
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Affiliation(s)
- Angelos Papaspyropoulos
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of MedicineNational Kapodistrian University of Athens (NKUA)AthensGreece
- Biomedical Research FoundationAcademy of AthensAthensGreece
| | - Orsalia Hazapis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of MedicineNational Kapodistrian University of Athens (NKUA)AthensGreece
| | - Abdullah Altulea
- European Research Institute for the Biology of Ageing (ERIBA)University Medical Center GroningenGroningenThe Netherlands
| | - Aikaterini Polyzou
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of MedicineNational Kapodistrian University of Athens (NKUA)AthensGreece
| | | | - Konstantinos Evangelou
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of MedicineNational Kapodistrian University of Athens (NKUA)AthensGreece
| | - Maria Fousteri
- Institute for Fundamental Biomedical ResearchBiomedical Sciences Research Center “Alexander Fleming”VariGreece
| | - Argyris Papantonis
- Institute of PathologyUniversity Medical Center GöttingenGöttingenGermany
- Center for Molecular Medicine CologneUniversity of CologneCologneGermany
| | - Marco Demaria
- European Research Institute for the Biology of Ageing (ERIBA)University Medical Center GroningenGroningenThe Netherlands
| | - Vassilis Gorgoulis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of MedicineNational Kapodistrian University of Athens (NKUA)AthensGreece
- Biomedical Research FoundationAcademy of AthensAthensGreece
- Clinical Molecular PathologyMedical School, University of DundeeDundeeUK
- Molecular and Clinical Cancer Sciences, Manchester Cancer Research Centre, Manchester Academic Health Sciences CentreUniversity of ManchesterManchesterUK
- Center for New Biotechnologies and Precision MedicineMedical School, National and Kapodistrian University of AthensAthensGreece
- Faculty of Health and Medical SciencesUniversity of SurreySurreyUK
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5
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Zhao H, Moberg KH, Veraksa A. Hippo pathway and Bonus control developmental cell fate decisions in the Drosophila eye. Dev Cell 2023; 58:416-434.e12. [PMID: 36868234 PMCID: PMC10023510 DOI: 10.1016/j.devcel.2023.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 08/10/2022] [Accepted: 02/06/2023] [Indexed: 03/05/2023]
Abstract
The canonical function of the Hippo signaling pathway is the regulation of organ growth. How this pathway controls cell-fate determination is less well understood. Here, we identify a function of the Hippo pathway in cell-fate decisions in the developing Drosophila eye, exerted through the interaction of Yorkie (Yki) with the transcriptional regulator Bonus (Bon), an ortholog of mammalian transcriptional intermediary factor 1/tripartite motif (TIF1/TRIM) family proteins. Instead of controlling tissue growth, Yki and Bon promote epidermal and antennal fates at the expense of the eye fate. Proteomic, transcriptomic, and genetic analyses reveal that Yki and Bon control these cell-fate decisions by recruiting transcriptional and post-transcriptional co-regulators and by repressing Notch target genes and activating epidermal differentiation genes. Our work expands the range of functions and regulatory mechanisms under Hippo pathway control.
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Affiliation(s)
- Heya Zhao
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Kenneth H Moberg
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Alexey Veraksa
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA.
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6
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Secretory Phospholipases A2, from Snakebite Envenoming to a Myriad of Inflammation Associated Human Diseases-What Is the Secret of Their Activity? Int J Mol Sci 2023; 24:ijms24021579. [PMID: 36675102 PMCID: PMC9863470 DOI: 10.3390/ijms24021579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/05/2023] [Accepted: 01/11/2023] [Indexed: 01/15/2023] Open
Abstract
Secreted phospholipases of type A2 (sPLA2s) are proteins of 14-16 kDa present in mammals in different forms and at different body sites. They are involved in lipid transformation processes, and consequently in various immune, inflammatory, and metabolic processes. sPLA2s are also major components of snake venoms, endowed with various toxic and pharmacological properties. The activity of sPLA2s is not limited to the enzymatic one but, through interaction with different types of molecules, they exert other activities that are still little known and explored, both outside and inside the cells, as they can be endocytosed. The aim of this review is to analyze three features of sPLA2s, yet under-explored, knowledge of which could be crucial to understanding the activity of these proteins. The first feature is their disulphide bridge pattern, which has always been considered immutable and necessary for their stability, but which might instead be modulable. The second characteristic is their ability to undergo various post-translational modifications that would control their interaction with other molecules. The third feature is their ability to participate in active molecular condensates both on the surface and within the cell. Finally, the implications of these features in the design of anti-inflammatory drugs are discussed.
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7
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Karam CS, Williams BL, Morozova I, Yuan Q, Panarsky R, Zhang Y, Hodgkinson CA, Goldman D, Kalachikov S, Javitch JA. Functional Genomic Analysis of Amphetamine Sensitivity in Drosophila. Front Psychiatry 2022; 13:831597. [PMID: 35250674 PMCID: PMC8894854 DOI: 10.3389/fpsyt.2022.831597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/24/2022] [Indexed: 11/14/2022] Open
Abstract
Abuse of psychostimulants, including amphetamines (AMPHs), is a major public health problem with profound psychiatric, medical, and psychosocial complications. The actions of these drugs at the dopamine transporter (DAT) play a critical role in their therapeutic efficacy as well as their liability for abuse and dependence. To date, however, the mechanisms that mediate these actions are not well-understood, and therapeutic interventions for AMPH abuse have been limited. Drug exposure can induce broad changes in gene expression that can contribute to neuroplasticity and effect long-lasting changes in neuronal function. Identifying genes and gene pathways perturbed by drug exposure is essential to our understanding of the molecular basis of drug addiction. In this study, we used Drosophila as a model to examine AMPH-induced transcriptional changes that are DAT-dependent, as those would be the most relevant to the stimulatory effects of the drug. Using this approach, we found genes involved in the control of mRNA translation to be significantly upregulated in response to AMPH in a DAT-dependent manner. To further prioritize genes for validation, we explored functional convergence between these genes and genes we identified in a genome-wide association study of AMPH sensitivity using the Drosophila Genetic Reference Panel. We validated a number of these genes by showing that they act specifically in dopamine neurons to mediate the behavioral effects of AMPH. Taken together, our data establish Drosophila as a powerful model that enables the integration of behavioral, genomic and transcriptomic data, followed by rapid gene validation, to investigate the molecular underpinnings of psychostimulant action.
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Affiliation(s)
- Caline S Karam
- Department of Psychiatry, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, United States.,Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY, United States
| | - Brenna L Williams
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY, United States
| | - Irina Morozova
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, United States.,Department of Chemical Engineering, Columbia University, New York, NY, United States
| | - Qiaoping Yuan
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, Bethesda, MD, United States
| | - Rony Panarsky
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, Bethesda, MD, United States
| | - Yuchao Zhang
- Department of Psychiatry, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, United States.,Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY, United States
| | - Colin A Hodgkinson
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, Bethesda, MD, United States
| | - David Goldman
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, Bethesda, MD, United States
| | - Sergey Kalachikov
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, United States.,Department of Chemical Engineering, Columbia University, New York, NY, United States
| | - Jonathan A Javitch
- Department of Psychiatry, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, United States.,Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY, United States.,Department of Molecular Pharmacology and Therapeutics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, United States
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8
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Abstract
Since 1992, FlyBase has provided a freely available online database of information about the model organism Drosophila melanogaster. Data in FlyBase is curated manually from research papers as well as computationally from a variety of relevant sources, to serve as an information hub that enables and accelerates research discovery. This chapter aims to give users new to the database an overview of the layout and types of data available, as well as introducing some tools with which to access the data. More experienced users will find useful information about recent improvements and descriptions to enable more efficient navigation of the database.
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Affiliation(s)
| | - Aoife Larkin
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Jim Thurmond
- Department of Biology, Indiana University, Bloomington, IN, USA
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9
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Coats T, Bean D, Vatopoulou T, Vijayavalli D, El‐Bashir R, Panopoulou A, Wood H, Wimalachandra M, Coppell J, Medd P, Furtado M, Tucker D, Kulasakeraraj A, Pawade J, Dobson R, Ireland R. An open-source, expert-designed decision tree application to support accurate diagnosis of myeloid malignancies. EJHAEM 2021; 2:261-265. [PMID: 35845286 PMCID: PMC9175663 DOI: 10.1002/jha2.182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 03/01/2021] [Indexed: 11/08/2022]
Abstract
Accurate, reproducible diagnoses can be difficult to make in haemato-oncology due to multi-parameter clinical data, complex diagnostic criteria and time-pressured environments. We have designed a decision tree application (DTA) that reflects WHO diagnostic criteria to support accurate diagnoses of myeloid malignancies. The DTA returned the correct diagnoses in 94% of clinical cases tested. The DTA maintained a high level of accuracy in a second validation using artificially generated clinical cases. Optimisations have been made to the DTA based on the validations, and the revised version is now publicly available for use at http://bit.do/ADAtool.
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Affiliation(s)
- Thomas Coats
- Department of HaematologyRoyal Devon and Exeter NHS Foundation TrustExeterUK
| | - Daniel Bean
- Biostatistics and Health InformaticsKing's College LondonLondonUK
- Health Data Research UK LondonUniversity College LondonLondonUK
| | - Theodora Vatopoulou
- Department of HaematologySt George's University Hospitals NHS Foundation TrustLondonUK
| | - Dhanapal Vijayavalli
- Department of HaematologyMedway NHS Foundation TrustKentUK
- Department of Haematological MedicineKing's College Hospital NHS Foundation TrustLondonUK
| | | | - Aikaterini Panopoulou
- Department of HaematologyDarent Valley HospitalKentUK
- Department of HaematologyRoyal Marsden NHS Foundation TrustLondonUK
| | - Henry Wood
- Department of Haematological MedicineKing's College Hospital NHS Foundation TrustLondonUK
| | | | - Jason Coppell
- Department of HaematologyRoyal Devon and Exeter NHS Foundation TrustExeterUK
| | - Patrick Medd
- Department of HaematologyDerriford HospitalPlymouthUK
| | | | - David Tucker
- Department of HaematologyRoyal Cornwall NHS TrustTruroUK
| | - Austin Kulasakeraraj
- Department of Haematological MedicineKing's College Hospital NHS Foundation TrustLondonUK
| | - Joya Pawade
- Department of PathologyNorth Bristol NHS TrustBristolUK
| | - Richard Dobson
- Biostatistics and Health InformaticsKing's College LondonLondonUK
- Health Data Research UK LondonUniversity College LondonLondonUK
| | - Robin Ireland
- Department of Haematological MedicineKing's College Hospital NHS Foundation TrustLondonUK
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10
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D’Agostino D, Liò P, Aldinucci M, Merelli I. Advantages of using graph databases to explore chromatin conformation capture experiments. BMC Bioinformatics 2021; 22:43. [PMID: 33902433 PMCID: PMC8073886 DOI: 10.1186/s12859-020-03937-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 12/15/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND High-throughput sequencing Chromosome Conformation Capture (Hi-C) allows the study of DNA interactions and 3D chromosome folding at the genome-wide scale. Usually, these data are represented as matrices describing the binary contacts among the different chromosome regions. On the other hand, a graph-based representation can be advantageous to describe the complex topology achieved by the DNA in the nucleus of eukaryotic cells. METHODS Here we discuss the use of a graph database for storing and analysing data achieved by performing Hi-C experiments. The main issue is the size of the produced data and, working with a graph-based representation, the consequent necessity of adequately managing a large number of edges (contacts) connecting nodes (genes), which represents the sources of information. For this, currently available graph visualisation tools and libraries fall short with Hi-C data. The use of graph databases, instead, supports both the analysis and the visualisation of the spatial pattern present in Hi-C data, in particular for comparing different experiments or for re-mapping omics data in a space-aware context efficiently. In particular, the possibility of describing graphs through statistical indicators and, even more, the capability of correlating them through statistical distributions allows highlighting similarities and differences among different Hi-C experiments, in different cell conditions or different cell types. RESULTS These concepts have been implemented in NeoHiC, an open-source and user-friendly web application for the progressive visualisation and analysis of Hi-C networks based on the use of the Neo4j graph database (version 3.5). CONCLUSION With the accumulation of more experiments, the tool will provide invaluable support to compare neighbours of genes across experiments and conditions, helping in highlighting changes in functional domains and identifying new co-organised genomic compartments.
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Affiliation(s)
- Daniele D’Agostino
- Institute of Electronics, Computer and Telecommunication Engineering, National Research Council of Italy, Genoa, Italy
| | - Pietro Liò
- Computer Laboratory, University of Cambridge, Cambridge, UK
| | - Marco Aldinucci
- Computer Science Department, University of Turin, Turin, Italy
| | - Ivan Merelli
- Institute for Biomedical Technologies, National Research Council of Italy, Segrate, MI Italy
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11
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Oughtred R, Rust J, Chang C, Breitkreutz B, Stark C, Willems A, Boucher L, Leung G, Kolas N, Zhang F, Dolma S, Coulombe‐Huntington J, Chatr‐aryamontri A, Dolinski K, Tyers M. The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions. Protein Sci 2021; 30:187-200. [PMID: 33070389 PMCID: PMC7737760 DOI: 10.1002/pro.3978] [Citation(s) in RCA: 632] [Impact Index Per Article: 210.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/09/2020] [Accepted: 10/13/2020] [Indexed: 02/06/2023]
Abstract
The BioGRID (Biological General Repository for Interaction Datasets, thebiogrid.org) is an open-access database resource that houses manually curated protein and genetic interactions from multiple species including yeast, worm, fly, mouse, and human. The ~1.93 million curated interactions in BioGRID can be used to build complex networks to facilitate biomedical discoveries, particularly as related to human health and disease. All BioGRID content is curated from primary experimental evidence in the biomedical literature, and includes both focused low-throughput studies and large high-throughput datasets. BioGRID also captures protein post-translational modifications and protein or gene interactions with bioactive small molecules including many known drugs. A built-in network visualization tool combines all annotations and allows users to generate network graphs of protein, genetic and chemical interactions. In addition to general curation across species, BioGRID undertakes themed curation projects in specific aspects of cellular regulation, for example the ubiquitin-proteasome system, as well as specific disease areas, such as for the SARS-CoV-2 virus that causes COVID-19 severe acute respiratory syndrome. A recent extension of BioGRID, named the Open Repository of CRISPR Screens (ORCS, orcs.thebiogrid.org), captures single mutant phenotypes and genetic interactions from published high throughput genome-wide CRISPR/Cas9-based genetic screens. BioGRID-ORCS contains datasets for over 1,042 CRISPR screens carried out to date in human, mouse and fly cell lines. The biomedical research community can freely access all BioGRID data through the web interface, standardized file downloads, or via model organism databases and partner meta-databases.
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Affiliation(s)
- Rose Oughtred
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonNew JerseyUSA
| | - Jennifer Rust
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonNew JerseyUSA
| | - Christie Chang
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonNew JerseyUSA
| | | | - Chris Stark
- The Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoOntarioCanada
| | - Andrew Willems
- The Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoOntarioCanada
| | - Lorrie Boucher
- The Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoOntarioCanada
| | - Genie Leung
- The Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoOntarioCanada
| | - Nadine Kolas
- The Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoOntarioCanada
| | - Frederick Zhang
- Arthur and Sonia Labatt Brain Tumor Research Center and Developmental and Stem Cell BiologyThe Hospital for Sick ChildrenTorontoOntarioCanada
| | - Sonam Dolma
- Arthur and Sonia Labatt Brain Tumor Research Center and Developmental and Stem Cell BiologyThe Hospital for Sick ChildrenTorontoOntarioCanada
| | | | | | - Kara Dolinski
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonNew JerseyUSA
| | - Mike Tyers
- The Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoOntarioCanada
- Institute for Research in Immunology and CancerUniversité de MontréalQuebecCanada
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12
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Identification of Genes Involved in the Differentiation of R7y and R7p Photoreceptor Cells in Drosophila. G3-GENES GENOMES GENETICS 2020; 10:3949-3958. [PMID: 32972998 PMCID: PMC7642934 DOI: 10.1534/g3.120.401370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The R7 and R8 photoreceptor cells of the Drosophila compound eye mediate color vision. Throughout the majority of the eye, these cells occur in two principal types of ommatidia. Approximately 35% of ommatidia are of the pale type and express Rh3 in R7 cells and Rh5 in R8 cells. The remaining 65% are of the yellow type and express Rh4 in R7 cells and Rh6 in R8 cells. The specification of an R8 cell in a pale or yellow ommatidium depends on the fate of the adjacent R7 cell. However, pale and yellow R7 cells are specified by a stochastic process that requires the genes spineless, tango and klumpfuss. To identify additional genes involved in this process we performed genetic screens using a collection of 480 P{EP} transposon insertion strains. We identified genes in gain of function and loss of function screens that significantly altered the percentage of Rh3 expressing R7 cells (Rh3%) from wild-type. 36 strains resulted in altered Rh3% in the gain of function screen where the P{EP} insertion strains were crossed to a sevEP-GAL4 driver line. 53 strains resulted in altered Rh3% in the heterozygous loss of function screen. 4 strains showed effects that differed between the two screens, suggesting that the effect found in the gain of function screen was either larger than, or potentially masked by, the P{EP} insertion alone. Analyses of homozygotes validated many of the candidates identified. These results suggest that R7 cell fate specification is sensitive to perturbations in mRNA transcription, splicing and localization, growth inhibition, post-translational protein modification, cleavage and secretion, hedgehog signaling, ubiquitin protease activity, GTPase activation, actin and cytoskeletal regulation, and Ser/Thr kinase activity, among other diverse signaling and cell biological processes.
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13
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de Lima JM, Morand GB, Macedo CCS, Diesel L, Hier MP, Mlynarek A, Kowalski LP, Maschietto M, Alaoui-Jamali MA, da Silva SD. NDRG1 deficiency is associated with regional metastasis in oral cancer by inducing epithelial-mesenchymal transition. Carcinogenesis 2020; 41:769-777. [PMID: 32112078 DOI: 10.1093/carcin/bgaa017] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 01/13/2020] [Accepted: 02/24/2020] [Indexed: 12/17/2022] Open
Abstract
Regional metastasis is the single most important prognostic factor in oral squamous cell carcinoma (OSCC). Abnormal expression of N-myc downstream-regulated genes (NDRGs) has been identified to occur in several tumor types and to predict poor prognosis. In OSCC, the clinical significance of deregulated NDRG expression has not been fully established. In this study, NDRG1 relevance was assessed at gene and protein levels in 100 OSCC patients followed up by at least 10 years. Survival outcome was analyzed using a multivariable analysis. Tumor progression and metastasis was investigated in preclinical model using oral cancer cell lines (HSC3 and SCC25) treated with epidermal growth factor (EGF) and orthotopic mouse model of metastatic murine OSCC (AT84). We identified NDRG1 expression levels to be significantly lower in patients with metastatic tumors compared with patients with local disease only (P = 0.001). NDRG1 expression was associated with MMP-2, -9, -10 (P = 0.022, P = 0.002, P = 0.042, respectively) and BCL2 (P = 0.035). NDRG1 lower expression was able to predict recurrence and metastasis (log-rank test, P = 0.001). In multivariable analysis, the expression of NDRG1 was an independent prognostic factor (Cox regression, P = 0.013). In invasive OSCC cells, NDRG1 expression is diminished in response to EGF and this was associated with a potent induction of epithelial-mesenchymal transition phenotype. This result was further confirmed in an orthotopic OSCC mouse model. Together, this data support that NDRG1 downregulation is a potential predictor of metastasis and approaches aimed at NDRG1 signaling rescue can serve as potential therapeutic strategy to prevent oral cancer progression to metastasis.
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Affiliation(s)
- Jefferson Muniz de Lima
- Department of Otolaryngology Head and Neck Surgery, Sir Mortimer B. Davis-Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Grégoire B Morand
- Department of Otolaryngology Head and Neck Surgery, Sir Mortimer B. Davis-Jewish General Hospital, McGill University, Montreal, QC, Canada.,Segal Cancer Centre and Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Departments of Medicine, Oncology, and Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC, Canada.,Department of Otorhinolaryngology - Head and Neck Surgery, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Carolina Carneiro Soares Macedo
- Department of Otolaryngology Head and Neck Surgery, Sir Mortimer B. Davis-Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Luciana Diesel
- Department of Otolaryngology Head and Neck Surgery, Sir Mortimer B. Davis-Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Michael P Hier
- Department of Otolaryngology Head and Neck Surgery, Sir Mortimer B. Davis-Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Alex Mlynarek
- Department of Otolaryngology Head and Neck Surgery, Sir Mortimer B. Davis-Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Luiz P Kowalski
- AC Camargo Cancer Center and National Institute of Science and Technology on Oncogenomics (INCITO), Sao Paulo, Sao Paulo, Brazil
| | | | - Moulay A Alaoui-Jamali
- Department of Otolaryngology Head and Neck Surgery, Sir Mortimer B. Davis-Jewish General Hospital, McGill University, Montreal, QC, Canada.,Segal Cancer Centre and Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Departments of Medicine, Oncology, and Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Sabrina Daniela da Silva
- Department of Otolaryngology Head and Neck Surgery, Sir Mortimer B. Davis-Jewish General Hospital, McGill University, Montreal, QC, Canada.,Segal Cancer Centre and Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Departments of Medicine, Oncology, and Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC, Canada
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14
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Zhang X, Bandyopadhyay S, Araujo LP, Tong K, Flores J, Laubitz D, Zhao Y, Yap G, Wang J, Zou Q, Ferraris R, Zhang L, Hu W, Bonder EM, Kiela PR, Coffey R, Verzi MP, Ivanov II, Gao N. Elevating EGFR-MAPK program by a nonconventional Cdc42 enhances intestinal epithelial survival and regeneration. JCI Insight 2020; 5:135923. [PMID: 32686657 PMCID: PMC7455142 DOI: 10.1172/jci.insight.135923] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 07/09/2020] [Indexed: 01/05/2023] Open
Abstract
The regulatory mechanisms enabling the intestinal epithelium to maintain a high degree of regenerative capacity during mucosal injury remain unclear. Ex vivo survival and clonogenicity of intestinal stem cells (ISCs) strictly required growth response mediated by cell division control 42 (Cdc42) and Cdc42-deficient enteroids to undergo rapid apoptosis. Mechanistically, Cdc42 engaging with EGFR was required for EGF-stimulated, receptor-mediated endocytosis and sufficient to promote MAPK signaling. Proteomics and kinase analysis revealed that a physiologically, but nonconventionally, spliced Cdc42 variant 2 (V2) exhibited stronger MAPK-activating capability. Human CDC42-V2 is transcriptionally elevated in some colon tumor tissues. Accordingly, mice engineered to overexpress Cdc42-V2 in intestinal epithelium showed elevated MAPK signaling, enhanced regeneration, and reduced mucosal damage in response to irradiation. Overproducing Cdc42-V2 specifically in mouse ISCs enhanced intestinal regeneration following injury. Thus, the intrinsic Cdc42-MAPK program is required for intestinal epithelial regeneration, and elevating this signaling cascade is capable of initiating protection from genotoxic injury.
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Affiliation(s)
- Xiao Zhang
- Department of Biological Sciences, Division of Life Sciences, School of Arts and Sciences, Rutgers University, Newark, New Jersey, USA
| | - Sheila Bandyopadhyay
- Department of Biological Sciences, Division of Life Sciences, School of Arts and Sciences, Rutgers University, Newark, New Jersey, USA
| | - Leandro Pires Araujo
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Kevin Tong
- Department of Genetics, Division of Life Sciences, School of Arts and Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Juan Flores
- Department of Biological Sciences, Division of Life Sciences, School of Arts and Sciences, Rutgers University, Newark, New Jersey, USA
| | - Daniel Laubitz
- Department of Pediatrics, University of Arizona, Tucson, Arizona, USA
| | - Yanlin Zhao
- Center for Immunity and Inflammation, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - George Yap
- Center for Immunity and Inflammation, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Jingren Wang
- Department of Mechanical and Aerospace Engineering, School of Engineering, Rutgers University, Piscataway, New Jersey, USA
| | - Qingze Zou
- Department of Mechanical and Aerospace Engineering, School of Engineering, Rutgers University, Piscataway, New Jersey, USA
| | - Ronaldo Ferraris
- Department of Pharmacology, Physiology and Neuroscience, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Lanjing Zhang
- Department of Biological Sciences, Division of Life Sciences, School of Arts and Sciences, Rutgers University, Newark, New Jersey, USA
- Department of Pathology, University Medical Center of Princeton, Plainsboro, New Jersey, USA
| | - Wenwei Hu
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Edward M Bonder
- Department of Biological Sciences, Division of Life Sciences, School of Arts and Sciences, Rutgers University, Newark, New Jersey, USA
| | - Pawel R Kiela
- Department of Pediatrics, University of Arizona, Tucson, Arizona, USA
| | - Robert Coffey
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, and Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Michael P Verzi
- Department of Genetics, Division of Life Sciences, School of Arts and Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Ivaylo I Ivanov
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Nan Gao
- Department of Biological Sciences, Division of Life Sciences, School of Arts and Sciences, Rutgers University, Newark, New Jersey, USA
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
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15
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Benslimane Y, Bertomeu T, Coulombe-Huntington J, McQuaid M, Sánchez-Osuna M, Papadopoli D, Avizonis D, Russo MDST, Huard C, Topisirovic I, Wurtele H, Tyers M, Harrington L. Genome-Wide Screens Reveal that Resveratrol Induces Replicative Stress in Human Cells. Mol Cell 2020; 79:846-856.e8. [PMID: 32755594 DOI: 10.1016/j.molcel.2020.07.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 05/12/2020] [Accepted: 07/07/2020] [Indexed: 12/26/2022]
Abstract
Resveratrol is a natural product associated with wide-ranging effects in animal and cellular models, including lifespan extension. To identify the genetic target of resveratrol in human cells, we conducted genome-wide CRISPR-Cas9 screens to pinpoint genes that confer sensitivity or resistance to resveratrol. An extensive network of DNA damage response and replicative stress genes exhibited genetic interactions with resveratrol and its analog pterostilbene. These genetic profiles showed similarity to the response to hydroxyurea, an inhibitor of ribonucleotide reductase that causes replicative stress. Resveratrol, pterostilbene, and hydroxyurea caused similar depletion of nucleotide pools, inhibition of replication fork progression, and induction of replicative stress. The ability of resveratrol to inhibit cell proliferation and S phase transit was independent of the histone deacetylase sirtuin 1, which has been implicated in lifespan extension by resveratrol. These results establish that a primary impact of resveratrol on human cell proliferation is the induction of low-level replicative stress.
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Affiliation(s)
- Yahya Benslimane
- Institute for Research in Immunology and Cancer, Université de Montréal, PO Box 6128, Downtown Station, Montréal, QC H3C 3J7, Canada
| | - Thierry Bertomeu
- Institute for Research in Immunology and Cancer, Université de Montréal, PO Box 6128, Downtown Station, Montréal, QC H3C 3J7, Canada
| | - Jasmin Coulombe-Huntington
- Institute for Research in Immunology and Cancer, Université de Montréal, PO Box 6128, Downtown Station, Montréal, QC H3C 3J7, Canada
| | - Mary McQuaid
- Centre de recherche de l'Hôpital Maisonneuve-Rosemont, 5415 boulevard de l'Assomption, Montréal, QC H1T 2M4, Canada
| | - María Sánchez-Osuna
- Institute for Research in Immunology and Cancer, Université de Montréal, PO Box 6128, Downtown Station, Montréal, QC H3C 3J7, Canada
| | - David Papadopoli
- Gerald Bronfman Department of Oncology, Departments of Biochemistry and Experimental Medicine and Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montréal, QC H3T 1E2, Canada
| | - Daina Avizonis
- Goodman Cancer Research Center, Metabolomics Core Facility, 1160 Pine Avenue West, Room 418, Montréal, QC H3A 1A3, Canada
| | - Mariana De Sa Tavares Russo
- Goodman Cancer Research Center, Metabolomics Core Facility, 1160 Pine Avenue West, Room 418, Montréal, QC H3A 1A3, Canada
| | - Caroline Huard
- Institute for Research in Immunology and Cancer, Université de Montréal, PO Box 6128, Downtown Station, Montréal, QC H3C 3J7, Canada
| | - Ivan Topisirovic
- Gerald Bronfman Department of Oncology, Departments of Biochemistry and Experimental Medicine and Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montréal, QC H3T 1E2, Canada
| | - Hugo Wurtele
- Centre de recherche de l'Hôpital Maisonneuve-Rosemont, 5415 boulevard de l'Assomption, Montréal, QC H1T 2M4, Canada
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, Université de Montréal, PO Box 6128, Downtown Station, Montréal, QC H3C 3J7, Canada
| | - Lea Harrington
- Institute for Research in Immunology and Cancer, Université de Montréal, PO Box 6128, Downtown Station, Montréal, QC H3C 3J7, Canada.
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16
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Blanck M, Budnik-Zawilska MB, Lenger SR, McGonigle JE, Martin GR, le Sage C, Lawo S, Pemberton HN, Tiwana GS, Sorrell DA, Cross BC. A Flexible, Pooled CRISPR Library for Drug Development Screens. CRISPR J 2020; 3:211-222. [PMID: 33054419 PMCID: PMC7567641 DOI: 10.1089/crispr.2019.0066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Functional genomic screening with CRISPR has provided a powerful and precise new way to interrogate the phenotypic consequences of gene manipulation in high-throughput, unbiased analyses. However, some experimental paradigms prove especially challenging and require carefully and appropriately adapted screening approaches. In particular, negative selection (or sensitivity) screening, often the most experimentally desirable modality of screening, has remained a challenge in drug discovery. Here we assess whether our new, modular genome-wide pooled CRISPR library can improve negative selection CRISPR screening and add utility throughout the drug development pipeline. Our pooled library is split into three parts, allowing it to be scaled to accommodate the experimental challenges encountered during drug development, such as target identification using unlimited cell numbers compared with target identification studies for cell populations where cell numbers are limiting. To test our new library, we chose to look for drug-gene interactions using a well-described small molecule inhibitor targeting poly(ADP-ribose) polymerase 1 (PARP1), and in particular to identify genes which sensitise cells to this drug. We simulate hit identification and performance using each library partition and support these findings through orthogonal drug combination cell panel screening. We also compare our data with a recently published CRISPR sensitivity dataset obtained using the same PARP1 inhibitor. Overall, our data indicate that generating a comprehensive CRISPR knockout screening library where the number of guides can be scaled to suit the biological question being addressed allows a library to have multiple uses throughout the drug development pipeline, and that initial validation of hits can be achieved through high-throughput cell panels screens where clinical grade chemical or biological matter exist.
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Affiliation(s)
| | | | | | | | | | | | - Steffen Lawo
- Max Planck Institute for Biology of Ageing, Cologne, Germany
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17
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Lock A, Rutherford K, Harris MA, Hayles J, Oliver SG, Bähler J, Wood V. PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information. Nucleic Acids Res 2020; 47:D821-D827. [PMID: 30321395 PMCID: PMC6324063 DOI: 10.1093/nar/gky961] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 10/11/2018] [Indexed: 12/16/2022] Open
Abstract
PomBase (www.pombase.org), the model organism database for the fission yeast Schizosaccharomyces pombe, has undergone a complete redevelopment, resulting in a more fully integrated, better-performing service. The new infrastructure supports daily data updates as well as fast, efficient querying and smoother navigation within and between pages. New pages for publications and genotypes provide routes to all data curated from a single source and to all phenotypes associated with a specific genotype, respectively. For ontology-based annotations, improved displays balance comprehensive data coverage with ease of use. The default view now uses ontology structure to provide a concise, non-redundant summary that can be expanded to reveal underlying details and metadata. The phenotype annotation display also offers filtering options to allow users to focus on specific areas of interest. An instance of the JBrowse genome browser has been integrated, facilitating loading of and intuitive access to, genome-scale datasets. Taken together, the new data and pages, along with improvements in annotation display and querying, allow users to probe connections among different types of data to form a comprehensive view of fission yeast biology. The new PomBase implementation also provides a rich set of modular, reusable tools that can be deployed to create new, or enhance existing, organism-specific databases.
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Affiliation(s)
- Antonia Lock
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Kim Rutherford
- Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Midori A Harris
- Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Jacqueline Hayles
- Cell Cycle Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Stephen G Oliver
- Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Jürg Bähler
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Valerie Wood
- Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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18
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Behdani E, Ghaderi-Zefrehei M, Rafeie F, Bakhtiarizadeh MR, Roshanfeker H, Fayazi J. RNA-Seq Bayesian Network Exploration of Immune System in Bovine. IRANIAN JOURNAL OF BIOTECHNOLOGY 2020; 17:e1748. [PMID: 32195281 PMCID: PMC7080973 DOI: 10.29252/ijb.1748] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Background: The stress is one of main factors effects on production system. Several factors (both genetic and environmental elements) regulate immune response to stress. Objectives: In order to determine the major immune system regulatory genes underlying stress responses, a learning Bayesian network approach for those regulatory
genes was applied to RNA-Seq data from a bovine leukocyte model system. Material and Methods: The transcriptome dataset GSE37447 was used from GEO and a Bayesian network on differentially expressed genes was learned to investigate the gene regulatory network. Results: Applying the method produced a strongly interconnected network with four genes (TERF2IP, PDCD10, DDX10 and CENPE) acting as nodes,
suggesting these genes may be important in the transcriptome regulation program of stress response. Of these genes TERF2IP has been
shown previously to regulate gene expression, act as a regulator of the nuclear factor-kappa B (NF-κB) signalling, and to activate
expression of NF-κB target genes; PDCD10 encodes a conserved protein associated with cell apoptosis; DDX10 encodes a DEAD box protein
and is believed to be associated with cellular growth and division; and CENPE involves unstable spindle microtubule capture at kinetochores.
Together these genes are involved in DNA damage of apoptosis, RNA splicing, DNA repairing, and regulating cell division in the bovine genome.
The topology of the learned Bayesian gene network indicated that the genes had a minimal interrelationship with each other.
This type of structure, using the publically available computational tool, was also observed on human orthologous genes of the differentially expressed genes. Conclusions: Overall, the results might be used in transcriptomic-assisted selection and design of new drug targets to treat stress-related problems in bovines.
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Affiliation(s)
- Elham Behdani
- Department of Animal Science, Faculty of Animal and Food Science, Khuzestan Agricultural Sciences and Natural Resources University, Mollasani, Khuzestan, Iran
| | | | - Farjad Rafeie
- Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | | | - Hedayatollah Roshanfeker
- Department of Animal Science, Faculty of Animal and Food Science, Khuzestan Agricultural Sciences and Natural Resources University, Mollasani, Khuzestan, Iran
| | - Jamal Fayazi
- Department of Animal Science, Faculty of Animal and Food Science, Khuzestan Agricultural Sciences and Natural Resources University, Mollasani, Khuzestan, Iran
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19
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Feuillette S, Charbonnier C, Frebourg T, Campion D, Lecourtois M. A Connected Network of Interacting Proteins Is Involved in Human-Tau Toxicity in Drosophila. Front Neurosci 2020; 14:68. [PMID: 32116515 PMCID: PMC7026268 DOI: 10.3389/fnins.2020.00068] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/17/2020] [Indexed: 12/13/2022] Open
Abstract
Tauopathies are neurodegenerative diseases characterized by the presence of aggregates of abnormally phosphorylated Tau. Deciphering the pathophysiological mechanisms that lead from the alteration of Tau biology to neuronal death depends on the identification of Tau cellular partners. Combining genetic and transcriptomic analyses in Drosophila, we identified 77 new modulators of human Tau-induced toxicity, bringing to 301 the number of Tau genetic interactors identified so far in flies. Network analysis showed that 229 of these genetic modulators constitute a connected network. The addition of 77 new genes strengthened the network structure, increased the intergenic connectivity and brought up key hubs with high connectivities, namely Src64B/FYN, Src42A/FRK, kuz/ADAM10, heph/PTBP1, scrib/SCRIB, and Cam/CALM3. Interestingly, we established for the first time a genetic link between Tau-induced toxicity and ADAM10, a recognized Alzheimer Disease protective factor. In addition, our data support the importance of the presynaptic compartment in mediating Tau toxicity.
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Affiliation(s)
- Sébastien Feuillette
- UNIROUEN, Inserm U1245, CNR-MAJ, F 76000, Department of Genetics, Normandy Center for Genomic and Personalized Medicine, Rouen University Hospital, Normandie Université, Rouen, France
| | - Camille Charbonnier
- UNIROUEN, Inserm U1245, CNR-MAJ, F 76000, Department of Genetics, Normandy Center for Genomic and Personalized Medicine, Rouen University Hospital, Normandie Université, Rouen, France
| | - Thierry Frebourg
- UNIROUEN, Inserm U1245, CNR-MAJ, F 76000, Department of Genetics, Normandy Center for Genomic and Personalized Medicine, Rouen University Hospital, Normandie Université, Rouen, France
| | - Dominique Campion
- UNIROUEN, Inserm U1245, CNR-MAJ, F 76000, Department of Genetics, Normandy Center for Genomic and Personalized Medicine, Rouen University Hospital, Normandie Université, Rouen, France.,Centre Hospitalier du Rouvray, Sotteville-lès-Rouen, France
| | - Magalie Lecourtois
- UNIROUEN, Inserm U1245, CNR-MAJ, F 76000, Department of Genetics, Normandy Center for Genomic and Personalized Medicine, Rouen University Hospital, Normandie Université, Rouen, France
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20
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Kwon SY, Massey K, Watson MA, Hussain T, Volpe G, Buckley CD, Nicolaou A, Badenhorst P. Oxidised metabolites of the omega-6 fatty acid linoleic acid activate dFOXO. Life Sci Alliance 2020; 3:3/2/e201900356. [PMID: 31992650 PMCID: PMC6988086 DOI: 10.26508/lsa.201900356] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 12/20/2019] [Accepted: 12/23/2019] [Indexed: 01/04/2023] Open
Abstract
Obesity-induced inflammation, or meta-inflammation, plays key roles in metabolic syndrome and is a significant risk factor in diabetes and cardiovascular disease. To investigate causal links between obesity, meta-inflammation, and insulin signaling we established a Drosophila model to determine how elevated dietary fat and changes in the levels and balance of saturated fatty acids (SFAs) and polyunsaturated fatty acids (PUFAs) influence inflammation. We observe negligible effect of saturated fatty acid on inflammation but marked enhancement or suppression by omega-6 and omega-3 PUFAs, respectively. Using combined lipidomic and genetic analysis, we show omega-6 PUFA enhances meta-inflammation by producing linoleic acid-derived lipid mediator 9-hydroxy-octadecadienoic acid (9-HODE). Transcriptome analysis reveals 9-HODE functions by regulating FOXO family transcription factors. We show 9-HODE activates JNK, triggering FOXO nuclear localisation and chromatin binding. FOXO TFs are important transducers of the insulin signaling pathway that are normally down-regulated by insulin. By activating FOXO, 9-HODE could antagonise insulin signaling providing a molecular conduit linking changes in dietary fatty acid balance, meta-inflammation, and insulin resistance.
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Affiliation(s)
- So Yeon Kwon
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, UK
| | - Karen Massey
- Bradford School of Pharmacy, University of Bradford, Bradford, UK
| | - Mark A Watson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, UK
| | - Tayab Hussain
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, UK
| | - Giacomo Volpe
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, UK
| | - Christopher D Buckley
- Institute of Inflammation and Ageing, Centre for Translational Inflammation Research, Queen Elizabeth Hospital, Edgbaston, UK.,Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Anna Nicolaou
- Bradford School of Pharmacy, University of Bradford, Bradford, UK.,Laboratory for Lipidomics and Lipid Biology, Division of Pharmacy and Optometry, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, Manchester, UK
| | - Paul Badenhorst
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, UK
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21
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Skipper KA, Hollensen AK, Antoniou MN, Mikkelsen JG. Sustained transgene expression from sleeping beauty DNA transposons containing a core fragment of the HNRPA2B1-CBX3 ubiquitous chromatin opening element (UCOE). BMC Biotechnol 2019; 19:75. [PMID: 31706316 PMCID: PMC6842454 DOI: 10.1186/s12896-019-0570-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 10/15/2019] [Indexed: 12/22/2022] Open
Abstract
Background DNA transposon-based vectors are effective nonviral tools for gene therapy and genetic engineering of cells. However, promoter DNA methylation and a near-random integration profile, which can result in transgene integration into heterochromatin, renders such vectors vulnerable to transcriptional repression. Therefore, to secure persistent transgene expression it may be necessary to protect transposon-embedded transgenes with anti-transcriptional silencing elements. Results We compare four different protective strategies in CHO-K1 cells. Our findings show robust protection from silencing of transgene cassettes mediated by the ubiquitous chromatin-opening element (UCOE) derived from the HNRPA2B1-CBX3 locus. Using a bioinformatic approach, we define a shorter HNRPA2B1-CBX3 UCOE core fragment and demonstrate that this can robustly maintain transgene expression after extended passaging of CHO-K1 cells carrying DNA transposon vectors equipped with this protective feature. Conclusions Our findings contribute to the understanding of the mechanism of HNRPA2B1-CBX3 UCOE-based transgene protection and support the use of a correctly oriented core fragment of this UCOE for DNA transposon vector-based production of recombinant proteins in CHO-K1 cells.
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Affiliation(s)
| | - Anne Kruse Hollensen
- Department of Biomedicine, HEALTH, Aarhus University, DK- 8000, Aarhus C, Denmark.,Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Michael N Antoniou
- Gene Expression and Therapy Group, King's College London, Faculty of Life Sciences & Medicine, Department of Medical and Molecular Genetics, 8th Floor Tower Wing, Guy's Hospital, London, SE1 9RT, UK
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22
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Cavallari T, Arima LY, Ferrasa A, Moysés SJ, Tetu Moysés S, Hirochi Herai R, Iani Werneck R. Dental caries: Genetic and protein interactions. Arch Oral Biol 2019; 108:104522. [PMID: 31476523 DOI: 10.1016/j.archoralbio.2019.104522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 07/09/2019] [Accepted: 08/11/2019] [Indexed: 10/26/2022]
Abstract
OBJECTIVE To present a genetic and protein interaction analysis associated with dental caries. MATERIAL AND METHODS The first step was to conduct a systematic literature review (SLR) through an electronic database search. Case-controls that reported associations between genes and dental caries were the main type of study design used as inclusion criteria, retrieved from the PubMed and the Virtual Health Library databases, comprising the chronological range from 1982 to 2017. The SLR was guided by PRISMA protocol and the methodological quality of the studies was established through Newcastle-Ottawa Scale (NOS). In the second step, the String Protein Interaction (SPI) approach was used to analyze protein interaction (by esyN software) and also the Ingenuity Pathway Analysis (IPA) to check biological pathways associated with dental caries genes. RESULTS A total of 51 articles were included to perform this SLR, describing a number of 27 genes associated with dental caries development. At the genetic level, 23 genes have at least one other gene with which they interact. The genes TUFT1, VDR, TFIP11, LTF, HLA-DRB1, MMP2, MMP3 and MUC5B were shown to be connected in interactive networks by at least 10 other genes. CONCLUSION It is essential to apprehend the multifactorial pattern of inheritance in human disease. This study presents pathways which may be directly correlated with several dental caries phenotype and this contributes to a better understanding of this disease, opening up a wider range of biotechnology options for its effective control in the future.
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Affiliation(s)
- Tayla Cavallari
- Graduate Program in Dentistry, Dentistry Department, School of Life Sciences, Pontifícia Universidade Católica do Paraná, Rua Imaculada Conceição 1155, Curitiba, Paraná, Brazil, 80215-901.
| | - Letícia Yumi Arima
- Graduate Program in Dentistry, Dentistry Department, School of Life Sciences, Pontifícia Universidade Católica do Paraná, Rua Imaculada Conceição 1155, Curitiba, Paraná, Brazil, 80215-901.
| | - Adriano Ferrasa
- Graduate Program in Health Sciences (PPGCS), School of Medicine, Pontifícia Universidade Católica do Paraná (PUCPR), Rua Imaculada Conceição 1155, Curitiba, Paraná, Brazil, 80215-901; Informatics Department, Universidade Estadual de Ponta Grossa (UEPG), Paraná, Brazil, 84030-900.
| | - Samuel Jorge Moysés
- Graduate Program in Dentistry, Dentistry Department, School of Life Sciences, Pontifícia Universidade Católica do Paraná, Rua Imaculada Conceição 1155, Curitiba, Paraná, Brazil, 80215-901.
| | - Simone Tetu Moysés
- Graduate Program in Dentistry, Dentistry Department, School of Life Sciences, Pontifícia Universidade Católica do Paraná, Rua Imaculada Conceição 1155, Curitiba, Paraná, Brazil, 80215-901.
| | - Roberto Hirochi Herai
- Graduate Program in Health Sciences (PPGCS), School of Medicine, Pontifícia Universidade Católica do Paraná (PUCPR), Rua Imaculada Conceição 1155, Curitiba, Paraná, Brazil, 80215-901; Research Division, Lico Kaesemodel Institute, Paraná, Brazil, 80240-000.
| | - Renata Iani Werneck
- Graduate Program in Dentistry, Dentistry Department, School of Life Sciences, Pontifícia Universidade Católica do Paraná, Rua Imaculada Conceição 1155, Curitiba, Paraná, Brazil, 80215-901.
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23
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Lee YY, Mok MT, Kang W, Yang W, Tang W, Wu F, Xu L, Yan M, Yu Z, Lee SD, Tong JHM, Cheung YS, Lai PBS, Yu DY, Wang Q, Wong GLH, Chan AM, Yip KY, To KF, Cheng ASL. Loss of tumor suppressor IGFBP4 drives epigenetic reprogramming in hepatic carcinogenesis. Nucleic Acids Res 2019; 46:8832-8847. [PMID: 29992318 PMCID: PMC6158508 DOI: 10.1093/nar/gky589] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 06/19/2018] [Indexed: 12/13/2022] Open
Abstract
Genomic sequencing of hepatocellular carcinoma (HCC) uncovers a paucity of actionable mutations, underscoring the necessity to exploit epigenetic vulnerabilities for therapeutics. In HCC, EZH2-mediated H3K27me3 represents a major oncogenic chromatin modification, but how it modulates the therapeutic vulnerability of signaling pathways remains unknown. Here, we show EZH2 acts antagonistically to AKT signaling in maintaining H3K27 methylome through epigenetic silencing of IGFBP4. ChIP-seq revealed enrichment of Ezh2/H3K27me3 at silenced loci in HBx-transgenic mouse-derived HCCs, including Igfbp4 whose down-regulation significantly correlated with EZH2 overexpression and poor survivals of HCC patients. Functional characterizations demonstrated potent growth- and invasion-suppressive functions of IGFBP4, which was associated with transcriptomic alterations leading to deregulation of multiple signaling pathways. Mechanistically, IGFBP4 stimulated AKT/EZH2 phosphorylation to abrogate H3K27me3-mediated silencing, forming a reciprocal feedback loop that suppressed core transcription factor networks (FOXA1/HNF1A/HNF4A/KLF9/NR1H4) for normal liver homeostasis. Consequently, the in vivo tumorigenicity of IGFBP4-silenced HCC cells was vulnerable to pharmacological inhibition of EZH2, but not AKT. Our study unveils chromatin regulation of a novel liver tumor suppressor IGFBP4, which constitutes an AKT-EZH2 reciprocal loop in driving H3K27me3-mediated epigenetic reprogramming. Defining the aberrant chromatin landscape of HCC sheds light into the mechanistic basis of effective EZH2-targeted inhibition.
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Affiliation(s)
- Ying-Ying Lee
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Myth Ts Mok
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Wei Kang
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, China
| | - Weiqin Yang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Wenshu Tang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Feng Wu
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, China
| | - Liangliang Xu
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Mingfei Yan
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Zhuo Yu
- Department of Liver Disease, Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Sau-Dan Lee
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, China
| | - Joanna H M Tong
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yue-Sun Cheung
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Paul B S Lai
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Dae-Yeul Yu
- Disease Model Research Laboratory, Aging Intervention Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Qianben Wang
- Department of Pathology and Duke Cancer Institute, Duke University School of Medicine, Durham, NC, USA
| | - Grace L H Wong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Andrew M Chan
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kevin Y Yip
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, China
| | - Ka-Fai To
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, China.,Li Ka Shing Institute of Health Science, Sir Y.K. Pao Cancer Center, State Key Laboratory in Oncology in South China, The Chinese University of Hong Kong, Hong Kong, China.,State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China
| | - Alfred S L Cheng
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.,State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China
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24
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Nurse P, Hayles J. Using genetics to understand biology. Heredity (Edinb) 2019; 123:4-13. [PMID: 31189902 PMCID: PMC6781147 DOI: 10.1038/s41437-019-0209-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/25/2019] [Accepted: 03/06/2019] [Indexed: 12/16/2022] Open
Affiliation(s)
- Paul Nurse
- The Francis Crick Institute, 1, Midland Road, London, NW1 1AT, UK
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25
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Aqaqe N, Yassin M, Yassin AA, Ershaid N, Katz-Even C, Zipin-Roitman A, Kugler E, Lechman ER, Gan OI, Mitchell A, Dick JE, Izraeli S, Milyavsky M. An ERG Enhancer-Based Reporter Identifies Leukemia Cells with Elevated Leukemogenic Potential Driven by ERG-USP9X Feed-Forward Regulation. Cancer Res 2019; 79:3862-3876. [PMID: 31175119 DOI: 10.1158/0008-5472.can-18-3215] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 03/21/2019] [Accepted: 06/04/2019] [Indexed: 11/16/2022]
Abstract
Acute leukemia is a rapidly progressing blood cancer with low survival rates. Unfavorable prognosis is attributed to insufficiently characterized subpopulations of leukemia stem cells (LSC) that drive chemoresistance and leukemia relapse. Here we utilized a genetic reporter that assesses stemness to enrich and functionally characterize LSCs. We observed heterogeneous activity of the ERG+85 enhancer-based fluorescent reporter in human leukemias. Cells with high reporter activity (tagBFPHigh) exhibited elevated expression of stemness and chemoresistance genes and demonstrated increased clonogenicity and resistance to chemo- and radiotherapy as compared with their tagBFPNeg counterparts. The tagBFPHigh fraction was capable of regenerating the original cellular heterogeneity and demonstrated increased invasive ability. Moreover, the tagBFPHigh fraction was enriched for leukemia-initiating cells in a xenograft assay. We identified the ubiquitin hydrolase USP9X as a novel ERG transcriptional target that sustains ERG+85-positive cells by controlling ERG ubiquitination. Therapeutic targeting of USP9X led to preferential inhibition of the ERG-dependent leukemias. Collectively, these results characterize human leukemia cell functional heterogeneity and suggest that targeting ERG via USP9X inhibition may be a potential treatment strategy in patients with leukemia. SIGNIFICANCE: This study couples a novel experimental tool with state-of-the-art approaches to delineate molecular mechanisms underlying stem cell-related characteristics in leukemia cells.
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Affiliation(s)
- Nasma Aqaqe
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Muhammad Yassin
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Abed Alkader Yassin
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nour Ershaid
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chen Katz-Even
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Adi Zipin-Roitman
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eitan Kugler
- Department of Pediatric Hemato-Oncology, Schneider Children Medical Center Petah-Tikva, Israel.,The Gene Development and Environment Pediatric Research Institute, Pediatric Hemato-Oncology, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Department of Molecular Human Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eric R Lechman
- Princess Margaret Cancer Centre, University Health Network and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Olga I Gan
- Princess Margaret Cancer Centre, University Health Network and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Amanda Mitchell
- Princess Margaret Cancer Centre, University Health Network and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Shai Izraeli
- Department of Pediatric Hemato-Oncology, Schneider Children Medical Center Petah-Tikva, Israel.,The Gene Development and Environment Pediatric Research Institute, Pediatric Hemato-Oncology, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Department of Molecular Human Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Michael Milyavsky
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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26
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NetR and AttR, Two New Bioinformatic Tools to Integrate Diverse Datasets into Cytoscape Network and Attribute Files. Genes (Basel) 2019; 10:genes10060423. [PMID: 31159440 PMCID: PMC6628208 DOI: 10.3390/genes10060423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/25/2019] [Accepted: 05/27/2019] [Indexed: 11/17/2022] Open
Abstract
High-throughput technologies have allowed researchers to obtain genome-wide data from a wide array of experimental model systems. Unfortunately, however, new data generation tends to significantly outpace data re-utilization, and most high throughput datasets are only rarely used in subsequent studies or to generate new hypotheses to be tested experimentally. The reasons behind such data underutilization include a widespread lack of programming expertise among experimentalist biologists to carry out the necessary file reformatting that is often necessary to integrate published data from disparate sources. We have developed two programs (NetR and AttR), which allow experimental biologists with little to no programming background to integrate publicly available datasets into files that can be later visualized with Cytoscape to display hypothetical networks that result from combining individual datasets, as well as a series of published attributes related to the genes or proteins in the network. NetR also allows users to import protein and genetic interaction data from InterMine, which can further enrich a network model based on curated information. We expect that NetR/AttR will allow experimental biologists to mine a largely unexploited wealth of data in their fields and facilitate their integration into hypothetical models to be tested experimentally.
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27
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Cantwell H, Nurse P. A systematic genetic screen identifies essential factors involved in nuclear size control. PLoS Genet 2019; 15:e1007929. [PMID: 30759079 PMCID: PMC6391033 DOI: 10.1371/journal.pgen.1007929] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 02/26/2019] [Accepted: 01/02/2019] [Indexed: 12/15/2022] Open
Abstract
Nuclear size correlates with cell size, but the mechanism by which this scaling is achieved is not known. Here we screen fission yeast gene deletion mutants to identify essential factors involved in this process. Our screen has identified 25 essential factors that alter nuclear size, and our analysis has implicated RNA processing and LINC complexes in nuclear size control. This study has revealed lower and more extreme higher nuclear size phenotypes and has identified global cellular processes and specific structural nuclear components important for nuclear size control. As cells grow and divide, the size of the nucleus is generally maintained as a fixed proportion of cell size. The mechanism by which this nuclear/cytoplasmic ratio is maintained is unclear. Previous studies have suggested that essential gene products may be important for nuclear size control. Therefore, we have exploited the genetic tractability of fission yeast to carry out a systematic genetic screen of deleted essential genes to identify those with aberrant nuclear size phenotypes. Our study has revealed 25 novel genes that influence nuclear size and our bioinformatic analyses have implicated both RNA processing and protein complexes connecting nuclear chromatin to the cytoskeleton in nuclear size control. Our work sheds light on the biological processes that contribute to nuclear size control in fission yeast contributing to our mechanistic understanding of nuclear scaling, a biological phenomenon that is conserved through evolution.
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Affiliation(s)
- Helena Cantwell
- Cell Cycle Laboratory, The Francis Crick Institute, London, United Kingdom
- * E-mail:
| | - Paul Nurse
- Cell Cycle Laboratory, The Francis Crick Institute, London, United Kingdom
- Laboratory of Yeast Genetics and Cell Biology, Rockefeller University, New York, United States of America
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28
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Li N, van Unen V, Abdelaal T, Guo N, Kasatskaya SA, Ladell K, McLaren JE, Egorov ES, Izraelson M, Chuva de Sousa Lopes SM, Höllt T, Britanova OV, Eggermont J, de Miranda NFCC, Chudakov DM, Price DA, Lelieveldt BPF, Koning F. Memory CD4 + T cells are generated in the human fetal intestine. Nat Immunol 2019; 20:301-312. [PMID: 30664737 PMCID: PMC6420108 DOI: 10.1038/s41590-018-0294-9] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 12/04/2018] [Indexed: 12/31/2022]
Abstract
The fetus is thought to be protected from exposure to foreign antigens,
yet CD45RO+ T cells reside in the fetal intestine. Here we combined
functional assays with mass cytometry, single-cell RNA-sequencing and
high-throughput T cell antigen receptor (TCR) sequencing to characterize the
CD4+ T cell compartment in the human fetal intestine. We
identified 22 CD4+ T cell clusters, including naive-like,
regulatory-like and memory-like subpopulations, which were confirmed and further
characterized at the transcriptional level. Memory-like CD4+ T cells
had high expression of Ki-67, indicative of cell division, and CD5, a surrogate
marker of TCR avidity, and produced the cytokines IFN-γ and IL-2. Pathway
analysis revealed a differentiation trajectory associated with cellular
activation and proinflammatory effector functions, and TCR repertoire analysis
indicated clonal expansions, distinct repertoire characteristics and
interconnections between subpopulations of memory-like CD4+ T cells.
Imaging-mass cytometry indicated that memory-like CD4+ T cells
colocalized with antigen-presenting cells. Collectively, these results provide
evidence for the generation of memory-like CD4+ T cells in the human
fetal intestine that is consistent with exposure to foreign antigens.
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Affiliation(s)
- Na Li
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Vincent van Unen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Tamim Abdelaal
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, the Netherlands.,Department of Pattern Recognition and Bioinformatics Group, Delft University of Technology, Delft, the Netherlands
| | - Nannan Guo
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Sofya A Kasatskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Centre for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Kristin Ladell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - James E McLaren
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Evgeny S Egorov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Mark Izraelson
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | - Thomas Höllt
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, the Netherlands.,Computer Graphics and Visualization Group, Delft University of Technology, Delft, the Netherlands
| | - Olga V Britanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Jeroen Eggermont
- Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Dmitriy M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Centre for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Molecular Technologies, Pirogov Russian National Research Medical University, Moscow, Russia.,MiLaboratory LLC, Skolkovo Innovation Centre, Moscow, Russia.,Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK.,Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, UK
| | - Boudewijn P F Lelieveldt
- Department of Pattern Recognition and Bioinformatics Group, Delft University of Technology, Delft, the Netherlands.,Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Frits Koning
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands.
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29
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30
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Solovev I, Dobrovolskaya E, Shaposhnikov M, Sheptyakov M, Moskalev A. Neuron-specific overexpression of core clock genes improves stress-resistance and extends lifespan of Drosophila melanogaster. Exp Gerontol 2018; 117:61-71. [PMID: 30415070 DOI: 10.1016/j.exger.2018.11.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 10/31/2018] [Accepted: 11/07/2018] [Indexed: 10/27/2022]
Abstract
Gene expression is much altered in aging. We observed age-dependent decline of core clock genes' expression in the whole body of the fruit fly. We hypothesized that inducible overexpression of clock genes (cry, per, tim, cyc and Clk) in the nervous system can improve healthspan of D. melanogaster. We studied the lifespan of transgenic Drosophila and showed life extension for cry, per, cyc and tim genes. It was also the significant positive changes in the stress-resistance of flies overexpressing core clock genes in conditions of hyperthermia, hyperoxia, starvation and persistent lighting. The overexpression of per and cry restore circadian rhythms of locomotor activity. The results presented support the hypotheses that the compensation of circadian oscillator genes expression can improve the healthspan in Drosophila melanogaster.
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Affiliation(s)
- Ilya Solovev
- Laboratory of Molecular Radiobiology and Gerontology, Institute of Biology of Komi Science Center of Ural Division of Russian Academy of Sciences, Syktyvkar, Russia; Department of Ecology, Syktyvkar State University, Syktyvkar, Russia
| | - Eugenia Dobrovolskaya
- Laboratory of Molecular Radiobiology and Gerontology, Institute of Biology of Komi Science Center of Ural Division of Russian Academy of Sciences, Syktyvkar, Russia
| | - Mikhail Shaposhnikov
- Laboratory of Molecular Radiobiology and Gerontology, Institute of Biology of Komi Science Center of Ural Division of Russian Academy of Sciences, Syktyvkar, Russia
| | - Maksim Sheptyakov
- Laboratory of Genetics of Aging and Longevity, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Alexey Moskalev
- Laboratory of Molecular Radiobiology and Gerontology, Institute of Biology of Komi Science Center of Ural Division of Russian Academy of Sciences, Syktyvkar, Russia; Department of Ecology, Syktyvkar State University, Syktyvkar, Russia; Laboratory of Genetics of Aging and Longevity, Moscow Institute of Physics and Technology, Dolgoprudny, Russia; Laboratory of Post-Genomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
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31
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Lacher SE, Levings DC, Freeman S, Slattery M. Identification of a functional antioxidant response element at the HIF1A locus. Redox Biol 2018; 19:401-411. [PMID: 30241031 PMCID: PMC6146589 DOI: 10.1016/j.redox.2018.08.014] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/21/2018] [Accepted: 08/22/2018] [Indexed: 12/12/2022] Open
Abstract
Reactive oxygen species (ROS), which are a byproduct of oxidative metabolism, serve as signaling molecules in a number of physiological settings. However, if their levels are not tightly maintained, excess ROS lead to potentially cytotoxic oxidative stress. Accordingly, several transcriptional regulatory networks have evolved to include components that are highly ROS-responsive. Depending on the context, these regulatory networks can leverage ROS to respond to nutrient conditions, metabolism, or other physiological signals, or to respond to oxidative stress. However, ROS signaling is complex, so regulatory interactions between various ROS-responsive transcription factors are still being mapped out. Here we show that the transcription factor NRF2, a key regulator of the adaptive response to oxidative stress, directly regulates expression of HIF1A, which encodes HIF1α, a key transcriptional regulator of the adaptive response to hypoxia. We used an integrative genomics approach to identify HIF1A as a ROS-responsive transcript and we found an NRF2-bound antioxidant response element (ARE) approximately 30 kilobases upstream of HIF1A. This ARE sequence is deeply conserved, and we verified that it is directly bound and activated by NRF2. In addition, we found that HIF1A is upregulated in breast and bladder tumors with high NRF2 activity. Taken together, our results demonstrate that NRF2 targets a functional ARE at the HIF1A locus, and reveal a direct regulatory connection between two important oxygen responsive transcription factors.
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Affiliation(s)
- Sarah E Lacher
- Department of Biomedical Sciences, University of Minnesota Medical School, 1035 University Drive, SMed 255, Duluth, MN 55812, United States
| | - Daniel C Levings
- Department of Biomedical Sciences, University of Minnesota Medical School, 1035 University Drive, SMed 255, Duluth, MN 55812, United States
| | - Samuel Freeman
- Department of Biomedical Sciences, University of Minnesota Medical School, 1035 University Drive, SMed 255, Duluth, MN 55812, United States
| | - Matthew Slattery
- Department of Biomedical Sciences, University of Minnesota Medical School, 1035 University Drive, SMed 255, Duluth, MN 55812, United States.
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32
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Machine learning identifies interacting genetic variants contributing to breast cancer risk: A case study in Finnish cases and controls. Sci Rep 2018; 8:13149. [PMID: 30177847 PMCID: PMC6120908 DOI: 10.1038/s41598-018-31573-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 08/22/2018] [Indexed: 01/01/2023] Open
Abstract
We propose an effective machine learning approach to identify group of interacting single nucleotide polymorphisms (SNPs), which contribute most to the breast cancer (BC) risk by assuming dependencies among BCAC iCOGS SNPs. We adopt a gradient tree boosting method followed by an adaptive iterative SNP search to capture complex non-linear SNP-SNP interactions and consequently, obtain group of interacting SNPs with high BC risk-predictive potential. We also propose a support vector machine formed by the identified SNPs to classify BC cases and controls. Our approach achieves mean average precision (mAP) of 72.66, 67.24 and 69.25 in discriminating BC cases and controls in KBCP, OBCS and merged KBCP-OBCS sample sets, respectively. These results are better than the mAP of 70.08, 63.61 and 66.41 obtained by using a polygenic risk score model derived from 51 known BC-associated SNPs, respectively, in KBCP, OBCS and merged KBCP-OBCS sample sets. BC subtype analysis further reveals that the 200 identified KBCP SNPs from the proposed method performs favorably in classifying estrogen receptor positive (ER+) and negative (ER-) BC cases both in KBCP and OBCS data. Further, a biological analysis of the identified SNPs reveals genes related to important BC-related mechanisms, estrogen metabolism and apoptosis.
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Chromatin That Guides Dosage Compensation Is Modulated by the siRNA Pathway in Drosophila melanogaster. Genetics 2018; 209:1085-1097. [PMID: 29921620 PMCID: PMC6063223 DOI: 10.1534/genetics.118.301173] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 06/15/2018] [Indexed: 12/03/2022] Open
Abstract
A family of X-linked repetitive elements enhances dosage compensation of nearby genes in male flies. Here, Deshpande and Meller show that chromatin around these repeats is modified in a siRNA-dependent manner. Proteins that interact with the siRNA effector... Many heterogametic organisms adjust sex chromosome expression to accommodate differences in gene dosage. This requires selective recruitment of regulatory factors to the modulated chromosome. How these factors are localized to a chromosome with requisite accuracy is poorly understood. Drosophila melanogaster males increase expression from their single X chromosome. Identification of this chromosome involves cooperation between different classes of X-identity elements. The chromatin entry sites (CES) recruit a chromatin-modifying complex that spreads into nearby genes and increases expression. In addition, a family of satellite repeats that is enriched on the X chromosome, the 1.688X repeats, promotes recruitment of the complex to nearby genes. The 1.688X repeats and CES are dissimilar, and appear to operate through different mechanisms. Interestingly, the siRNA pathway and siRNA from a 1.688X repeat also promote X recognition. We postulate that siRNA-dependent modification of 1.688X chromatin contributes to recognition of nearby genes. In accord with this, we found enrichment of the siRNA effector Argonaute2 (Ago2) at some 1.688X repeats. Mutations in several proteins that physically interact with Ago2, including the histone methyltransferase Su(var)3-9, enhance the lethality of males with defective X recognition. Su(var)3-9 deposits H3K9me2 on some 1.688X repeats, and this mark is disrupted upon ectopic expression of 1.688X siRNA. Furthermore, integration of 1.688X DNA on an autosome induces local H3K9me2 deposition, but enhances expression of nearby genes in a siRNA-dependent manner. Our findings are consistent with a model in which siRNA-directed modification of 1.688X chromatin contributes to recognition of the male X chromosome for dosage compensation.
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Pan X, Wang B, Yuan T, Zhang M, Kent KC, Guo LW. Analysis of Combined Transcriptomes Identifies Gene Modules that Differentially Respond to Pathogenic Stimulation of Vascular Smooth Muscle and Endothelial Cells. Sci Rep 2018; 8:395. [PMID: 29321689 PMCID: PMC5762668 DOI: 10.1038/s41598-017-18675-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 12/15/2017] [Indexed: 12/22/2022] Open
Abstract
Smooth muscle cells (SMCs) and endothelial cells (ECs) are vital cell types composing the vascular medial wall and the atheroprotective inner lining, respectively. Current treatments for cardiovascular disease inhibit SMC hyperplasia but compromise EC integrity, predisposing patients to thrombosis. Therapeutics targeting SMCs without collateral damage to ECs are highly desirable. However, differential (SMC versus EC) disease-associated regulations remain poorly defined. We conducted RNA-seq experiments to investigate SMC-versus-EC differential transcriptomic dynamics, following treatment of human primary SMCs and ECs with TNFα or IL-1β, both established inducers of SMC hyperplasia and EC dysfunction. As revealed by combined SMC/EC transcriptomes, after TNFα or IL-1β induction, 174 and 213 genes respectively showed greater up-regulation in SMCs than in ECs (SMC-enriched), while 117 and 138 genes showed greater up-regulation in ECs over SMCs (EC-enriched). Analysis of gene interaction networks identified central genes shared in the two SMC-enriched gene sets, and a distinct group of central genes common in the two EC-enriched gene sets. Significantly, four gene modules (subnetworks) were identified from these central genes, including SMC-enriched JUN and FYN modules and EC-enriched SMAD3 and XPO1 modules. These modules may inform potential intervention targets for selective blockage of SMC hyperplasia without endothelial damage.
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Affiliation(s)
- Xiaokang Pan
- Department of Surgery, Wisconsin Institute for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53705, USA.,James Molecular Laboratory, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43240, USA
| | - Bowen Wang
- Department of Surgery, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Tiezheng Yuan
- Department of Surgery, Wisconsin Institute for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53705, USA
| | - Mengxue Zhang
- Department of Surgery, Wisconsin Institute for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53705, USA.,Department of Surgery and Department of Physiology & Cell Biology, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - K Craig Kent
- Department of Surgery, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Lian-Wang Guo
- Department of Surgery, Wisconsin Institute for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53705, USA. .,Department of Surgery and Department of Physiology & Cell Biology, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA.
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Zhou S, Luoma SE, St. Armour GE, Thakkar E, Mackay TFC, Anholt RRH. A Drosophila model for toxicogenomics: Genetic variation in susceptibility to heavy metal exposure. PLoS Genet 2017; 13:e1006907. [PMID: 28732062 PMCID: PMC5544243 DOI: 10.1371/journal.pgen.1006907] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 08/04/2017] [Accepted: 07/06/2017] [Indexed: 12/20/2022] Open
Abstract
The genetic factors that give rise to variation in susceptibility to environmental toxins remain largely unexplored. Studies on genetic variation in susceptibility to environmental toxins are challenging in human populations, due to the variety of clinical symptoms and difficulty in determining which symptoms causally result from toxic exposure; uncontrolled environments, often with exposure to multiple toxicants; and difficulty in relating phenotypic effect size to toxic dose, especially when symptoms become manifest with a substantial time lag. Drosophila melanogaster is a powerful model that enables genome-wide studies for the identification of allelic variants that contribute to variation in susceptibility to environmental toxins, since the genetic background, environmental rearing conditions and toxic exposure can be precisely controlled. Here, we used extreme QTL mapping in an outbred population derived from the D. melanogaster Genetic Reference Panel to identify alleles associated with resistance to lead and/or cadmium, two ubiquitous environmental toxins that present serious health risks. We identified single nucleotide polymorphisms (SNPs) associated with variation in resistance to both heavy metals as well as SNPs associated with resistance specific to each of them. The effects of these SNPs were largely sex-specific. We applied mutational and RNAi analyses to 33 candidate genes and functionally validated 28 of them. We constructed networks of candidate genes as blueprints for orthologous networks of human genes. The latter not only provided functional contexts for known human targets of heavy metal toxicity, but also implicated novel candidate susceptibility genes. These studies validate Drosophila as a translational toxicogenomics gene discovery system. Although physiological effects of environmental toxins are well documented, we know little about the genetic factors that determine individual variation in susceptibility to toxins. Such information is difficult to obtain in human populations due to heterogeneity in genetic background and environmental exposure, and the diversity of symptoms and time lag with which they appear after toxic exposure. Here, we show that the fruit fly, Drosophila, can serve as a powerful genetic model system to elucidate the genetic underpinnings that contribute to individual variation in resistance to toxicity, using lead and cadmium exposure as an experimental paradigm. We identified genes that harbor genetic variants that contribute to individual variation in resistance to heavy metal exposure. Furthermore, we constructed genetic networks on which we could superimpose human counterparts of Drosophila genes. We were able to place human genes previously implicated in heavy metal toxicity in biological context and identify novel targets for heavy metal toxicity. Thus, we demonstrate that based on evolutionary conservation of fundamental biological processes, we can use Drosophila as a powerful translational model for toxicogenomics studies.
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Affiliation(s)
- Shanshan Zhou
- Program in Genetics, W. M. Keck Center for Behavioral Biology, and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Sarah E. Luoma
- Program in Genetics, W. M. Keck Center for Behavioral Biology, and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Genevieve E. St. Armour
- Program in Genetics, W. M. Keck Center for Behavioral Biology, and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Esha Thakkar
- Enloe Magnet High School, Raleigh, North Carolina, United States of America
| | - Trudy F. C. Mackay
- Program in Genetics, W. M. Keck Center for Behavioral Biology, and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Robert R. H. Anholt
- Program in Genetics, W. M. Keck Center for Behavioral Biology, and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail:
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Improving the detection of pathways in genome-wide association studies by combined effects of SNPs from Linkage Disequilibrium blocks. Sci Rep 2017; 7:3512. [PMID: 28615668 PMCID: PMC5471232 DOI: 10.1038/s41598-017-03826-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 05/05/2017] [Indexed: 01/31/2023] Open
Abstract
Genome-wide association studies (GWAS) have successfully identified single variants associated with diseases. To increase the power of GWAS, gene-based and pathway-based tests are commonly employed to detect more risk factors. However, the gene- and pathway-based association tests may be biased towards genes or pathways containing a large number of single-nucleotide polymorphisms (SNPs) with small P-values caused by high linkage disequilibrium (LD) correlations. To address such bias, numerous pathway-based methods have been developed. Here we propose a novel method, DGAT-path, to divide all SNPs assigned to genes in each pathway into LD blocks, and to sum the chi-square statistics of LD blocks for assessing the significance of the pathway by permutation tests. The method was proven robust with the type I error rate >1.6 times lower than other methods. Meanwhile, the method displays a higher power and is not biased by the pathway size. The applications to the GWAS summary statistics for schizophrenia and breast cancer indicate that the detected top pathways contain more genes close to associated SNPs than other methods. As a result, the method identified 17 and 12 significant pathways containing 20 and 21 novel associated genes, respectively for two diseases. The method is available online by http://sparks-lab.org/server/DGAT-path.
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McMillan KJ, Gallon M, Jellett AP, Clairfeuille T, Tilley FC, McGough I, Danson CM, Heesom KJ, Wilkinson KA, Collins BM, Cullen PJ. Atypical parkinsonism-associated retromer mutant alters endosomal sorting of specific cargo proteins. J Cell Biol 2017; 214:389-99. [PMID: 27528657 PMCID: PMC4987296 DOI: 10.1083/jcb.201604057] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 07/22/2016] [Indexed: 01/12/2023] Open
Abstract
Mutations in the retromer complex, which is involved in sorting integral membrane proteins from endosomes to cellular compartments, are associated with atypical parkinsonism, but how these mutations affect retromer function remains unclear. Through a quantitative proteomic analysis of the retromer interactome, McMillan et al. reveal a new mechanism for perturbed endosomal sorting in parkinsonism. The retromer complex acts as a scaffold for endosomal protein complexes that sort integral membrane proteins to various cellular destinations. The retromer complex is a heterotrimer of VPS29, VPS35, and VPS26. Two of these paralogues, VPS26A and VPS26B, are expressed in humans. Retromer dysfunction is associated with neurodegenerative disease, and recently, three VPS26A mutations (p.K93E, p.M112V, and p.K297X) were discovered to be associated with atypical parkinsonism. Here, we apply quantitative proteomics to provide a detailed description of the retromer interactome. By establishing a comparative proteomic methodology, we identify how this interactome is perturbed in atypical parkinsonism-associated VPS26A mutants. In particular, we describe a selective defect in the association of VPS26A (p.K297X) with the SNX27 cargo adaptor. By showing how a retromer mutant leads to altered endosomal sorting of specific PDZ ligand–containing cargo proteins, we reveal a new mechanism for perturbed endosomal cargo sorting in atypical parkinsonism.
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Affiliation(s)
- Kirsty J McMillan
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, England, UK
| | - Matthew Gallon
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, England, UK
| | - Adam P Jellett
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, England, UK
| | - Thomas Clairfeuille
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Frances C Tilley
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, England, UK
| | - Ian McGough
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, England, UK
| | - Chris M Danson
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, England, UK
| | - Kate J Heesom
- Proteomics Facility, School of Biochemistry, University of Bristol, Bristol BS8 1TD, England, UK
| | - Kevin A Wilkinson
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, England, UK
| | - Brett M Collins
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Peter J Cullen
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, England, UK
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Bingsohn L, Knorr E, Billion A, Narva KE, Vilcinskas A. Knockdown of genes in the Toll pathway reveals new lethal RNA interference targets for insect pest control. INSECT MOLECULAR BIOLOGY 2017; 26:92-102. [PMID: 27862545 DOI: 10.1111/imb.12273] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
RNA interference (RNAi) is a promising alternative strategy for ecologically friendly pest management. However, the identification of RNAi candidate genes is challenging owing to the absence of laboratory strains and the seasonality of most pest species. Tribolium castaneum is a well-established model, with a strong and robust RNAi response, which can be used as a high-throughput screening platform to identify potential RNAi target genes. Recently, the cactus gene was identified as a sensitive RNAi target for pest control. To explore whether the spectrum of promising RNAi targets can be expanded beyond those found by random large-scale screening, to encompass others identified using targeted knowledge-based approaches, we constructed a Cactus interaction network. We tested nine genes in this network and found that the delivery of double-stranded RNA corresponding to fusilli and cactin showed lethal effects. The silencing of cactin resulted in 100% lethality at every developmental stage from the larva to the adult. The knockdown of pelle, Dorsal-related immunity factor and short gastrulation reduced or even prevented egg hatching in the next generation. The combination of such targets with lethal and parental RNAi effects can now be tested against different pest species in field studies.
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Affiliation(s)
- L Bingsohn
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| | - E Knorr
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| | - A Billion
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| | - K E Narva
- Dow AgroSciences, Indianapolis, IN, USA
| | - A Vilcinskas
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- Institute for Insect Biotechnology, Giessen, Germany
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39
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Gene-based analyses reveal novel genetic overlap and allelic heterogeneity across five major psychiatric disorders. Hum Genet 2016; 136:263-274. [DOI: 10.1007/s00439-016-1755-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 12/22/2016] [Indexed: 10/20/2022]
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Abstract
We have carried out a haploinsufficiency (HI) screen in fission yeast using heterozygous deletion diploid mutants of a genome-wide set of cell cycle genes to identify genes encoding products whose level determines the rate of progression through the cell cycle. Cell size at division was used as a measure of advancement or delay of the G2-M transition of rod-shaped fission yeast cells. We found that 13 mutants were significantly longer or shorter (greater than 10%) than control cells at cell division. These included mutants of the cdc2, cdc25, wee1 and pom1 genes, which have previously been shown to play a role in the timing of entry into mitosis, and which validate this approach. Seven of these genes are involved in regulation of the G2-M transition, 5 for nuclear transport and one for nucleotide metabolism. In addition we identified 4 more genes that were 8–10% longer or shorter than the control that also had roles in regulation of the G2-M transition or in nuclear transport. The genes identified here are all conserved in human cells, suggesting that this dataset will be useful as a basis for further studies to identify rate-limiting steps for progression through the cell cycle in other eukaryotes.
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Identification of S-phase DNA damage-response targets in fission yeast reveals conservation of damage-response networks. Proc Natl Acad Sci U S A 2016; 113:E3676-85. [PMID: 27298342 DOI: 10.1073/pnas.1525620113] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The cellular response to DNA damage during S-phase regulates a complicated network of processes, including cell-cycle progression, gene expression, DNA replication kinetics, and DNA repair. In fission yeast, this S-phase DNA damage response (DDR) is coordinated by two protein kinases: Rad3, the ortholog of mammalian ATR, and Cds1, the ortholog of mammalian Chk2. Although several critical downstream targets of Rad3 and Cds1 have been identified, most of their presumed targets are unknown, including the targets responsible for regulating replication kinetics and coordinating replication and repair. To characterize targets of the S-phase DDR, we identified proteins phosphorylated in response to methyl methanesulfonate (MMS)-induced S-phase DNA damage in wild-type, rad3∆, and cds1∆ cells by proteome-wide mass spectrometry. We found a broad range of S-phase-specific DDR targets involved in gene expression, stress response, regulation of mitosis and cytokinesis, and DNA replication and repair. These targets are highly enriched for proteins required for viability in response to MMS, indicating their biological significance. Furthermore, the regulation of these proteins is similar in fission and budding yeast, across 300 My of evolution, demonstrating a deep conservation of S-phase DDR targets and suggesting that these targets may be critical for maintaining genome stability in response to S-phase DNA damage across eukaryotes.
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Profiling DNA damage-induced phosphorylation in budding yeast reveals diverse signaling networks. Proc Natl Acad Sci U S A 2016; 113:E3667-75. [PMID: 27298372 DOI: 10.1073/pnas.1602827113] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The DNA damage response (DDR) is regulated by a protein kinase signaling cascade that orchestrates DNA repair and other processes. Identifying the substrate effectors of these kinases is critical for understanding the underlying physiology and mechanism of the response. We have used quantitative mass spectrometry to profile DDR-dependent phosphorylation in budding yeast and genetically explored the dependency of these phosphorylation events on the DDR kinases MEC1, RAD53, CHK1, and DUN1. Based on these screens, a database containing many novel DDR-regulated phosphorylation events has been established. Phosphorylation of many of these proteins has been validated by quantitative peptide phospho-immunoprecipitation and examined for functional relevance to the DDR through large-scale analysis of sensitivity to DNA damage in yeast deletion strains. We reveal a link between DDR signaling and the metabolic pathways of inositol phosphate and phosphatidyl inositol synthesis, which are required for resistance to DNA damage. We also uncover links between the DDR and TOR signaling as well as translation regulation. Taken together, these data shed new light on the organization of DDR signaling in budding yeast.
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Abstract
For nearly 25 years, FlyBase (flybase.org) has provided a freely available online database of biological information about Drosophila species, focusing on the model organism D. melanogaster. The need for a centralized, integrated view of Drosophila research has never been greater as advances in genomic, proteomic, and high-throughput technologies add to the quantity and diversity of available data and resources.FlyBase has taken several approaches to respond to these changes in the research landscape. Novel report pages have been generated for new reagent types and physical interaction data; Drosophila models of human disease are now represented and showcased in dedicated Human Disease Model Reports; other integrated reports have been established that bring together related genes, datasets, or reagents; Gene Reports have been revised to improve access to new data types and to highlight functional data; links to external sites have been organized and expanded; and new tools have been developed to display and interrogate all these data, including improved batch processing and bulk file availability. In addition, several new community initiatives have served to enhance interactions between researchers and FlyBase, resulting in direct user contributions and improved feedback.This chapter provides an overview of the data content, organization, and available tools within FlyBase, focusing on recent improvements. We hope it serves as a guide for our diverse user base, enabling efficient and effective exploration of the database and thereby accelerating research discoveries.
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Affiliation(s)
- Steven J. Marygold
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Madeline A. Crosby
- The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Joshua L. Goodman
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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Hoffman CS, Wood V, Fantes PA. An Ancient Yeast for Young Geneticists: A Primer on the Schizosaccharomyces pombe Model System. Genetics 2015; 201:403-23. [PMID: 26447128 PMCID: PMC4596657 DOI: 10.1534/genetics.115.181503] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The fission yeast Schizosaccharomyces pombe is an important model organism for the study of eukaryotic molecular and cellular biology. Studies of S. pombe, together with studies of its distant cousin, Saccharomyces cerevisiae, have led to the discovery of genes involved in fundamental mechanisms of transcription, translation, DNA replication, cell cycle control, and signal transduction, to name but a few processes. However, since the divergence of the two species approximately 350 million years ago, S. pombe appears to have evolved less rapidly than S. cerevisiae so that it retains more characteristics of the common ancient yeast ancestor, causing it to share more features with metazoan cells. This Primer introduces S. pombe by describing the yeast itself, providing a brief description of the origins of fission yeast research, and illustrating some genetic and bioinformatics tools used to study protein function in fission yeast. In addition, a section on some key differences between S. pombe and S. cerevisiae is included for readers with some familiarity with budding yeast research but who may have an interest in developing research projects using S. pombe.
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Affiliation(s)
- Charles S Hoffman
- Biology Department, Boston College, Chestnut Hill, Massachusetts 02467
| | - Valerie Wood
- Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, CB2 1GA Cambridge, United Kingdom
| | - Peter A Fantes
- School of Biological Sciences, College of Science and Engineering, University of Edinburgh EH9 3JR Edinburgh, United Kingdom
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