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Yang J, Zhang Y, Zhao J, Gao Y, Liu Z, Zhang P, Fan R, Xing S, Zhou X. Target gene selection for RNAi-based biopesticides against the hawthorn spider mite, Amphitetranychus viennensis (Acari: Tetranychidae). PEST MANAGEMENT SCIENCE 2023; 79:2482-2492. [PMID: 36866409 DOI: 10.1002/ps.7437] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 01/27/2023] [Accepted: 03/02/2023] [Indexed: 06/02/2023]
Abstract
BACKGROUND Recently, RNA interference (RNAi)-based biopesticide, a species-specific pest control alternative, has been deregulated and commercialized in the US and Canada. The hawthorn spider mite, Amphitetranychus viennensis Zacher, is a major pest for rosaceous plants, which has been controlled primarily by synthetic pesticides. To address the emerging resistance issues in A. viennensis, we initiated a project to develop RNAi-based biopesticides. RESULTS In this study, we (i) developed a dietary RNAi system for A. viennensis using leaf disc, (ii) assessed the suitability of multiple control genes to distinguish sequence-specific silencing from non-specific effects within this RNAi system, and (iii) screened for the target gene candidates. As a result, β-Glucuronidase (GUS), an enzyme derived from E. coli and a broadly used reporter for plants is the appropriate control for A. viennensis RNAi, while green fluorescent protein (GFP), is not suitable due to its significantly higher mortality than the other controls. For target gene screening, suppression was confirmed for all the candidates, including two housekeeping genes (Vacuolar-type H + -ATPase subunit A (V-ATPase A) and Glyceraldehyde 3-phosphate dehydrogenase, (GAPDH)), and three genes associated with development (ATP-dependent RNA Helicase DDX3Y (Belle), CREB-binding protein (CBP), and Farnesoic acid O-methyltransferase (FaMet)). Knocking down of V-ATPase A resulted in the highest mortality (~ 90%) and reduced fecundity (over 90%) than other candidates. As for the genes associated with development, suppression of Belle and CBP, led to approximately 65% mortality, as well as 86% and 40% reduction in fecundity, respectively. Silencing of FaMet, however, had negligible biological impacts on A. viennensis. CONCLUSION The combined efforts not only establish an effective dsRNA delivery method, but also provide potential target genes for RNAi-based biopesticides against A. viennensis, a devastating invasive pest for fruit trees and woody ornamental plants throughout Asia and Europe. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Jing Yang
- College of Plant Protection, Shanxi Agricultural University/Shanxi Key Laboratory of Integrated Pest Management in Agriculture, Taiyuan, China
| | - Yuying Zhang
- College of Plant Protection, Shanxi Agricultural University/Shanxi Key Laboratory of Integrated Pest Management in Agriculture, Taiyuan, China
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Jin Zhao
- Research Institute of Applied Biology, Shanxi University, Taiyuan, China
| | - Yue Gao
- College of Plant Protection, Shanxi Agricultural University/Shanxi Key Laboratory of Integrated Pest Management in Agriculture, Taiyuan, China
| | - Zhongfang Liu
- College of Plant Protection, Shanxi Agricultural University/Shanxi Key Laboratory of Integrated Pest Management in Agriculture, Taiyuan, China
| | - Pengjiu Zhang
- College of Plant Protection, Shanxi Agricultural University/Shanxi Key Laboratory of Integrated Pest Management in Agriculture, Taiyuan, China
| | - Renjun Fan
- College of Plant Protection, Shanxi Agricultural University/Shanxi Key Laboratory of Integrated Pest Management in Agriculture, Taiyuan, China
| | - Shuping Xing
- Research Institute of Applied Biology, Shanxi University, Taiyuan, China
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington, KY, USA
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2
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Batdorj E, AlOgayil N, Zhuang QKW, Galvez JH, Bauermeister K, Nagata K, Kimura T, Ward MA, Taketo T, Bourque G, Naumova AK. Genetic variation in the Y chromosome and sex-biased DNA methylation in somatic cells in the mouse. Mamm Genome 2023; 34:44-55. [PMID: 36454369 PMCID: PMC9947081 DOI: 10.1007/s00335-022-09970-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/22/2022] [Indexed: 12/05/2022]
Abstract
Several lines of evidence suggest that the presence of the Y chromosome influences DNA methylation of autosomal loci. To better understand the impact of the Y chromosome on autosomal DNA methylation patterns and its contribution to sex bias in methylation, we identified Y chromosome dependent differentially methylated regions (yDMRs) using whole-genome bisulfite sequencing methylation data from livers of mice with different combinations of sex-chromosome complement and gonadal sex. Nearly 90% of the autosomal yDMRs mapped to transposable elements (TEs) and most of them had lower methylation in XY compared to XX or XO mice. Follow-up analyses of four reporter autosomal yDMRs showed that Y-dependent methylation levels were consistent across most somatic tissues but varied in strains with different origins of the Y chromosome, suggesting that genetic variation in the Y chromosome influenced methylation levels of autosomal regions. Mice lacking the q-arm of the Y chromosome (B6.NPYq-2) as well as mice with a loss-of-function mutation in Kdm5d showed no differences in methylation levels compared to wild type mice. In conclusion, the Y-linked modifier of TE methylation is likely to reside on the short arm of Y chromosome and further studies are required to identify this gene.
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Affiliation(s)
- Enkhjin Batdorj
- Department of Human Genetics, McGill University, Montréal, QC, H3A 1C7, Canada
| | - Najla AlOgayil
- Department of Human Genetics, McGill University, Montréal, QC, H3A 1C7, Canada
| | - Qinwei Kim-Wee Zhuang
- Department of Human Genetics, McGill University, Montréal, QC, H3A 1C7, Canada
- Canadian Centre for Computational Genomics, Montréal, QC, H3A 0G1, Canada
| | - Jose Hector Galvez
- Canadian Centre for Computational Genomics, Montréal, QC, H3A 0G1, Canada
| | - Klara Bauermeister
- Department of Human Genetics, McGill University, Montréal, QC, H3A 1C7, Canada
| | - Kei Nagata
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-Ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Tohru Kimura
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-Ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Monika A Ward
- Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii, 1960 East-West Road, HonoluluHonolulu, HIHI, 96822, USA
| | - Teruko Taketo
- The Research Institute of the McGill University Health Centre, Montréal, QC, H4A 3J1, Canada
- Department of Surgery, McGill University, Montréal, QC, H4A 3J1, Canada
- Department of Obstetrics and Gynecology, McGill University, Montréal, QC, H4A 3J1, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montréal, QC, H3A 1C7, Canada
- Canadian Centre for Computational Genomics, Montréal, QC, H3A 0G1, Canada
| | - Anna K Naumova
- Department of Human Genetics, McGill University, Montréal, QC, H3A 1C7, Canada.
- The Research Institute of the McGill University Health Centre, Montréal, QC, H4A 3J1, Canada.
- Department of Obstetrics and Gynecology, McGill University, Montréal, QC, H4A 3J1, Canada.
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3
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McGlacken-Byrne SM, Del Valle I, Le Quesne Stabej P, Bellutti L, Garcia-Alonso L, Ocaka LA, Ishida M, Suntharalingham JP, Gagunashvili A, Ogunbiyi OK, Mistry T, Buonocore F, Crespo B, Moreno N, Niola P, Brooks T, Brain CE, Dattani MT, Kelberman D, Vento-Tormo R, Lagos CF, Livera G, Conway GS, Achermann JC. Pathogenic variants in the human m6A reader YTHDC2 are associated with primary ovarian insufficiency. JCI Insight 2022; 7:154671. [PMID: 35138268 PMCID: PMC8983136 DOI: 10.1172/jci.insight.154671] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 01/26/2022] [Indexed: 11/17/2022] Open
Abstract
Primary ovarian insufficiency (POI) affects 1% of women and carries significant medical and psychosocial sequelae. Approximately 10% of POI has a defined genetic cause, with most implicated genes relating to biological processes involved in early fetal ovary development and function. Recently, Ythdc2, an RNA helicase and N6-methyladenosine (m6a) reader, has emerged as a novel regulator of meiosis in mice. Here, we describe homozygous pathogenic variants in YTHDC2 in three women with early-onset POI from two families: c. 2567C>G, p.P856R in the helicase-associated (HA2) domain; and c.1129G>T, p.E377*. We demonstrate that YTHDC2 is expressed in the developing human fetal ovary and is upregulated in meiotic germ cells, together with related meiosis-associated factors. The p.P856R variant results in a less flexible protein that likely disrupts downstream conformational kinetics of the HA2 domain, whereas the p.E377* variant truncates the helicase core. Taken together, our results reveal that YTHDC2 is a key new regulator of meiosis in humans and pathogenic variants within this gene are associated with POI.
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Affiliation(s)
- Sinead M McGlacken-Byrne
- Genetics and Genomics Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Ignacio Del Valle
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Polona Le Quesne Stabej
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Laura Bellutti
- Laboratory of Development of the Gonads, UMR E008, Université de Paris, Université Paris Saclay, CEA, Fontenay aux Roses, France
| | - Luz Garcia-Alonso
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Louise A Ocaka
- GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Miho Ishida
- Genetics and Genomics Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Jenifer P Suntharalingham
- Genetics and Genomics Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Andrey Gagunashvili
- GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Olumide K Ogunbiyi
- Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Talisa Mistry
- Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Federica Buonocore
- Genetics and Genomics Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | | | - Berta Crespo
- Developmental Biology and Cancer, UCL Great Ormond Street Institute of Child health, London, United Kingdom
| | - Nadjeda Moreno
- Developmental Biology and Cancer, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Paola Niola
- UCL Genomics, Zayed Centre for Research, London, United Kingdom
| | - Tony Brooks
- UCL Genomics, Zayed Centre for Research, London, United Kingdom
| | - Caroline E Brain
- Department of Paediatric Endocrinology, Great Ormond Street Hospital, London, United Kingdom
| | - Mehul T Dattani
- Genetics and Genomics Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Daniel Kelberman
- GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Carlos F Lagos
- Chemical Biology & Drug Discovery Lab, Escuela de Química y Farmacia, Universidad San Sebastián, Santiago, Chile
| | - Gabriel Livera
- Laboratory of Development of the Gonads, UMR E008, Université de Paris, Université Paris Saclay, CEA, Fontenay aux Roses, France
| | - Gerard S Conway
- Institute for Women's Health, University College London, London, United Kingdom
| | - John C Achermann
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
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4
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Cheng W, Wang S, Zhang Z, Morgens DW, Hayes LR, Lee S, Portz B, Xie Y, Nguyen BV, Haney MS, Yan S, Dong D, Coyne AN, Yang J, Xian F, Cleveland DW, Qiu Z, Rothstein JD, Shorter J, Gao FB, Bassik MC, Sun S. CRISPR-Cas9 Screens Identify the RNA Helicase DDX3X as a Repressor of C9ORF72 (GGGGCC)n Repeat-Associated Non-AUG Translation. Neuron 2019; 104:885-898.e8. [PMID: 31587919 DOI: 10.1016/j.neuron.2019.09.003] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 06/16/2019] [Accepted: 09/04/2019] [Indexed: 12/14/2022]
Abstract
Hexanucleotide GGGGCC repeat expansion in C9ORF72 is the most prevalent genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). One pathogenic mechanism is the aberrant accumulation of dipeptide repeat (DPR) proteins produced by the unconventional translation of expanded RNA repeats. Here, we performed genome-wide CRISPR-Cas9 screens for modifiers of DPR protein production in human cells. We found that DDX3X, an RNA helicase, suppresses the repeat-associated non-AUG translation of GGGGCC repeats. DDX3X directly binds to (GGGGCC)n RNAs but not antisense (CCCCGG)n RNAs. Its helicase activity is essential for the translation repression. Reduction of DDX3X increases DPR levels in C9ORF72-ALS/FTD patient cells and enhances (GGGGCC)n-mediated toxicity in Drosophila. Elevating DDX3X expression is sufficient to decrease DPR levels, rescue nucleocytoplasmic transport abnormalities, and improve survival of patient iPSC-differentiated neurons. This work identifies genetic modifiers of DPR protein production and provides potential therapeutic targets for C9ORF72-ALS/FTD.
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Affiliation(s)
- Weiwei Cheng
- Department of Pathology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shaopeng Wang
- Department of Pathology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Zhe Zhang
- Department of Pathology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - David W Morgens
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lindsey R Hayes
- Brain Science Institute and Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Soojin Lee
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Bede Portz
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yongzhi Xie
- Department of Pathology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Baotram V Nguyen
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael S Haney
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shirui Yan
- Department of Pathology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daoyuan Dong
- Department of Pathology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Alyssa N Coyne
- Brain Science Institute and Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Junhua Yang
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Fengfan Xian
- Department of Pathology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Don W Cleveland
- Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Zhaozhu Qiu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jeffrey D Rothstein
- Brain Science Institute and Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Fen-Biao Gao
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Michael C Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shuying Sun
- Department of Pathology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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5
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Cusumano P, Damulewicz M, Carbognin E, Caccin L, Puricella A, Specchia V, Bozzetti MP, Costa R, Mazzotta GM. The RNA Helicase BELLE Is Involved in Circadian Rhythmicity and in Transposons Regulation in Drosophila melanogaster. Front Physiol 2019; 10:133. [PMID: 30842743 PMCID: PMC6392097 DOI: 10.3389/fphys.2019.00133] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/04/2019] [Indexed: 02/05/2023] Open
Abstract
Circadian clocks control and synchronize biological rhythms of several behavioral and physiological phenomena in most, if not all, organisms. Rhythm generation relies on molecular auto-regulatory oscillations of interlocked transcriptional-translational feedback loops. Rhythmic clock-gene expression is at the base of rhythmic protein accumulation, though post-transcriptional and post-translational mechanisms have evolved to adjust and consolidate the proper pace of the clock. In Drosophila, BELLE, a conserved DEAD-box RNA helicase playing important roles in reproductive capacity, is involved in the small RNA-mediated regulation associated to the piRNA pathway. Here, we report that BELLE is implicated in the circadian rhythmicity and in the regulation of endogenous transposable elements (TEs) in both nervous system and gonads. We suggest that BELLE acts as important element in the piRNA-mediated regulation of the TEs and raise the hypothesis that this specific regulation could represent another level of post-transcriptional control adopted by the clock to ensure the proper rhythmicity.
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Affiliation(s)
- Paola Cusumano
- Department of Biology, University of Padua, Padua, Italy
| | - Milena Damulewicz
- Department of Cell Biology and Imaging, Jagiellonian University, Kraków, Poland
| | | | - Laura Caccin
- Department of Biology, University of Padua, Padua, Italy
| | - Antonietta Puricella
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Valeria Specchia
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Maria Pia Bozzetti
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Rodolfo Costa
- Department of Biology, University of Padua, Padua, Italy
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6
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Olesnicky EC, Antonacci S, Popitsch N, Lybecker MC, Titus MB, Valadez R, Derkach PG, Marean A, Miller K, Mathai SK, Killian DJ. Shep interacts with posttranscriptional regulators to control dendrite morphogenesis in sensory neurons. Dev Biol 2018; 444:116-128. [PMID: 30352216 DOI: 10.1016/j.ydbio.2018.09.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 08/20/2018] [Accepted: 09/09/2018] [Indexed: 10/28/2022]
Abstract
RNA binding proteins (RBPs) mediate posttranscriptional gene regulatory events throughout development. During neurogenesis, many RBPs are required for proper dendrite morphogenesis within Drosophila sensory neurons. Despite their fundamental role in neuronal morphogenesis, little is known about the molecular mechanisms in which most RBPs participate during neurogenesis. In Drosophila, alan shepard (shep) encodes a highly conserved RBP that regulates dendrite morphogenesis in sensory neurons. Moreover, the C. elegans ortholog sup-26 has also been implicated in sensory neuron dendrite morphogenesis. Nonetheless, the molecular mechanism by which Shep/SUP-26 regulate dendrite development is not understood. Here we show that Shep interacts with the RBPs Trailer Hitch (Tral), Ypsilon schachtel (Yps), Belle (Bel), and Poly(A)-Binding Protein (PABP), to direct dendrite morphogenesis in Drosophila sensory neurons. Moreover, we identify a conserved set of Shep/SUP-26 target RNAs that include regulators of cell signaling, posttranscriptional gene regulators, and known regulators of dendrite development.
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Affiliation(s)
- Eugenia C Olesnicky
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, United States.
| | - Simona Antonacci
- Department of Molecular Biology, Colorado College, Colorado Springs, CO 80903, United States
| | - Niko Popitsch
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, A-1090 Vienna, Austria
| | - Meghan C Lybecker
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, United States
| | - M Brandon Titus
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, United States
| | - Racquel Valadez
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, United States
| | - Paul G Derkach
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, United States
| | - Amber Marean
- Department of Molecular Biology, Colorado College, Colorado Springs, CO 80903, United States
| | - Katherine Miller
- Department of Molecular Biology, Colorado College, Colorado Springs, CO 80903, United States
| | - Samuel K Mathai
- Department of Molecular Biology, Colorado College, Colorado Springs, CO 80903, United States
| | - Darrell J Killian
- Department of Molecular Biology, Colorado College, Colorado Springs, CO 80903, United States
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7
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Shu Z, Huang YC, Palmer WH, Tamori Y, Xie G, Wang H, Liu N, Deng WM. Systematic analysis reveals tumor-enhancing and -suppressing microRNAs in Drosophila epithelial tumors. Oncotarget 2017; 8:108825-108839. [PMID: 29312571 PMCID: PMC5752484 DOI: 10.18632/oncotarget.22226] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 10/13/2017] [Indexed: 12/19/2022] Open
Abstract
Despite their emergence as an important class of noncoding RNAs involved in cancer cell transformation, invasion, and migration, the precise role of microRNAs (miRNAs) in tumorigenesis remains elusive. To gain insights into how miRNAs contribute to primary tumor formation, we conducted an RNA sequencing (RNA-Seq) analysis of Drosophila wing disc epithelial tumors induced by knockdown of a neoplastic tumor-suppressor gene (nTSG) lethal giant larvae (lgl), combined with overexpression of an active form of oncogene Ras (RasV12 ), and identified 51 mature miRNAs that changed significantly in tumorous discs. Followed by in vivo tumor enhancer and suppressor screens in sensitized genetic backgrounds, we identified 10 tumor-enhancing (TE) miRNAs and 11 tumor-suppressing (TS) miRNAs that contributed to the nTSG defect-induced tumorigenesis. Among these, four TE and three TS miRNAs have human homologs. From this study, we also identified 29 miRNAs that individually had no obvious role in enhancing or alleviating tumorigenesis despite their changed expression levels in nTSG tumors. This systematic analysis, which includes both RNA-Seq and in vivo functional studies, helps to categorize miRNAs into different groups based on their expression profile and functional relevance in epithelial tumorigenesis, whereas the evolutionarily conserved TE and TS miRNAs provide potential therapeutic targets for epithelial tumor treatment.
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Affiliation(s)
- Zhiqiang Shu
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Yi-Chun Huang
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - William H Palmer
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA.,Current/Present address: Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Yoichiro Tamori
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA.,Current/Present address: Structural Biology Center, National Institute of Genetics and Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Mishima, Japan
| | - Gengqiang Xie
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Hui Wang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Nan Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Wu-Min Deng
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
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8
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Specchia V, D'Attis S, Puricella A, Bozzetti MP. dFmr1 Plays Roles in Small RNA Pathways of Drosophila melanogaster. Int J Mol Sci 2017; 18:ijms18051066. [PMID: 28509881 PMCID: PMC5454977 DOI: 10.3390/ijms18051066] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/09/2017] [Accepted: 05/10/2017] [Indexed: 11/16/2022] Open
Abstract
Fragile-X syndrome is the most common form of inherited mental retardation accompanied by other phenotypes, including macroorchidism. The disorder originates with mutations in the Fmr1 gene coding for the FMRP protein, which, with its paralogs FXR1 and FXR2, constitute a well-conserved family of RNA-binding proteins. Drosophila melanogaster is a good model for the syndrome because it has a unique fragile X-related gene: dFmr1. Recently, in addition to its confirmed role in the miRNA pathway, a function for dFmr1 in the piRNA pathway, operating in Drosophila gonads, has been established. In this review we report a summary of the piRNA pathways occurring in gonads with a special emphasis on the relationship between the piRNA genes and the crystal-Stellate system; we also analyze the roles of dFmr1 in the Drosophila gonads, exploring their genetic and biochemical interactions to reveal some unexpected connections.
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Affiliation(s)
- Valeria Specchia
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali (DiSTeBA)-University of Salento, 73100 Lecce, Italy.
| | - Simona D'Attis
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali (DiSTeBA)-University of Salento, 73100 Lecce, Italy.
| | - Antonietta Puricella
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali (DiSTeBA)-University of Salento, 73100 Lecce, Italy.
| | - Maria Pia Bozzetti
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali (DiSTeBA)-University of Salento, 73100 Lecce, Italy.
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