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1
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Pegler JL, Oultram JMJ, Grof CPL, Eamens AL. The Use of Arabidopsis thaliana to Characterize the Production and Action Stages of the Plant MicroRNA Pathway. Methods Mol Biol 2025; 2900:1-42. [PMID: 40380051 DOI: 10.1007/978-1-0716-4398-3_1] [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] [Indexed: 05/19/2025]
Abstract
Plant microRNAs are an endogenous class of small regulatory RNA central to the posttranscriptional control of gene expression as part of normal development to adapt to environmental stress and respond to pathogen challenges. The plant microRNA pathway is separated into two distinct stages: (1) production stage, which is localized to the nucleus of the cell and, in this cell compartment, the microRNA silencing signal is processed from its double-stranded RNA precursor transcript, and (2) action stage, which is localized to the cytoplasm of the cell. It is in this cellular compartment where the now mature microRNA functions as a regulatory RNA molecule to control target gene expression via its loading into the protein effector complex termed microRNA-induced silencing complex. Historical research indicated that the plant microRNA pathway was a highly structured, almost linear pathway that only required the functional activity of a small set of core, highly conserved pieces of protein machinery. However, contemporary research continues to illustrate that the plant microRNA pathway is highly dynamic, with such flexibility provided by an extremely large and functionally diverse set of auxiliary protein machinery that perform highly specific roles as part of either the production or action stage of the pathway. For example, recent research has elegantly demonstrated that plant microRNAs can regulate target gene expression via a translational repression mechanism of RNA silencing in addition to the standard messenger RNA cleavage-based mechanism: a mode of RNA silencing originally assigned to all plant microRNAs. Using Arabidopsis thaliana as our model system, we report on both the core and auxiliary sets of protein machinery now demonstrated functionally essential for the plant microRNA pathway.
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Affiliation(s)
- Joseph L Pegler
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW, Australia
| | - Jackson M J Oultram
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW, Australia
| | - Christopher P L Grof
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW, Australia
- School of Agriculture and Food Sustainability, The University of Queensland, St Lucia, QLD, Australia
| | - Andrew L Eamens
- Seaweed Research Group, School of Health, University of the Sunshine Coast, Maroochydore, QLD, Australia.
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2
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Li Y, Zhao L, Wang J, Ma L, Bai Y, Feng F. Argonaute-Based Nucleic Acid Detection Technology: Advantages, Current Status, Challenges, and Perspectives. ACS Sens 2024; 9:5665-5682. [PMID: 39526595 DOI: 10.1021/acssensors.4c01631] [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] [Indexed: 11/16/2024]
Abstract
Rapid and accurate detection is a prerequisite for precise clinical diagnostics, ensuring food safety, and facilitating biotechnological applications. The Argonaute system, as a cutting-edge technique, has been successfully repurposed in biosensing beyond the CRISPR/Cas system (clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins), which has been extensively researched, but recognition of PAM sequences remains restricted. Argonaute, as a programmable and target-activated nuclease, is repurposed for fabricating novel detection methods due to its unparalleled biological features. In this comprehensive review, we initially elaborate on the current methods for nucleic acid testing and programmable nucleases, followed by delving into the structure and nuclease activity of the Argonaute system. The advantages of Argonaute compared with the CRISPR/Cas system in nucleic acid detection are highlighted and discussed. Furthermore, we summarize the applications of Argonaute-based nucleic acid detection and provide an in-depth analysis of future perspectives and challenges. Recent research has demonstrated that Argonaute-based biosensing is an innovative and rapidly advancing technology that can overcome the limitations of existing methods and potentially replace them. In summary, the implementation of Argonaute and its integration with other technologies hold promise in developing customized and intelligent detection methods for nucleic acid testing across various aspects.
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Affiliation(s)
- Yaru Li
- School of Agriculture and Life Science, Shanxi Datong University, Datong 037009, China
| | - Lu Zhao
- School of Chemistry and Chemical Engineering, Shanxi Provincial Key Laboratory of Chemical Biosensing, Shanxi Datong University, Datong 037009, China
| | - Jiali Wang
- College of Food Science, Shanxi Normal University, Taiyuan 030031, China
| | - Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yunfeng Bai
- School of Agriculture and Life Science, Shanxi Datong University, Datong 037009, China
- School of Chemistry and Chemical Engineering, Shanxi Provincial Key Laboratory of Chemical Biosensing, Shanxi Datong University, Datong 037009, China
| | - Feng Feng
- School of Chemistry and Chemical Engineering, Shanxi Provincial Key Laboratory of Chemical Biosensing, Shanxi Datong University, Datong 037009, China
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3
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Limanówka P, Ochman B, Świętochowska E. Mechanisms Behind the Impact of PIWI Proteins on Cancer Cells: Literature Review. Int J Mol Sci 2024; 25:12217. [PMID: 39596284 PMCID: PMC11594409 DOI: 10.3390/ijms252212217] [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: 09/30/2024] [Revised: 11/09/2024] [Accepted: 11/12/2024] [Indexed: 11/28/2024] Open
Abstract
The P-Element-induced wimpy testis (PIWI) group of proteins plays a key role in RNA interference, particularly in the regulation of small non-coding RNAs. However, in recent years, PIWIs have gained attention in several diseases, mainly cancer. Therefore, the aim of this review was to evaluate current knowledge about the impact of PIWI proteins on cancer cells. PIWIs alter a number of pathways within cells, resulting in significant changes in cell behavior. Basic processes of cancer cells have been shown to be altered by either overexpression or inhibition of PIWIs. Regulation of apoptosis, metastasis, invasion, or proliferation of cancerous cells by these proteins proves their involvement in the progression of the malignancy. It has been revealed that PIWIs are also connected with cancer stem cells (CSCs), which proves their ability to become a therapeutic target. However, research on this topic is still fairly limited, and with significant differences between cancer types, it is necessary to refrain from making any decisive conclusions.
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Affiliation(s)
| | | | - Elżbieta Świętochowska
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 19 Jordana, 41-800 Zabrze, Poland; (P.L.); (B.O.)
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4
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Abajorga M, Yurkovetskiy L, Luban J. piRNA Defense Against Endogenous Retroviruses. Viruses 2024; 16:1756. [PMID: 39599869 PMCID: PMC11599104 DOI: 10.3390/v16111756] [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: 08/30/2024] [Revised: 10/30/2024] [Accepted: 11/08/2024] [Indexed: 11/29/2024] Open
Abstract
Infection by retroviruses and the mobilization of transposable elements cause DNA damage that can be catastrophic for a cell. If the cell survives, the mutations generated by retrotransposition may confer a selective advantage, although, more commonly, the effect of new integrants is neutral or detrimental. If retrotransposition occurs in gametes or in the early embryo, it introduces genetic modifications that can be transmitted to the progeny and may become fixed in the germline of that species. PIWI-interacting RNAs (piRNAs) are single-stranded, 21-35 nucleotide RNAs generated by the PIWI clade of Argonaute proteins that maintain the integrity of the animal germline by silencing transposons. The sequence specific manner by which piRNAs and germline-encoded PIWI proteins repress transposons is reminiscent of CRISPR, which retains memory for invading pathogen sequences. piRNAs are processed preferentially from the unspliced transcripts of piRNA clusters. Via complementary base pairing, mature antisense piRNAs guide the PIWI clade of Argonaute proteins to transposon RNAs for degradation. Moreover, these piRNA-loaded PIWI proteins are imported into the nucleus to modulate the co-transcriptional repression of transposons by initiating histone and DNA methylation. How retroviruses that invade germ cells are first recognized as foreign by the piRNA machinery, as well as how endogenous piRNA clusters targeting the sequences of invasive genetic elements are acquired, is not known. Currently, koalas (Phascolarctos cinereus) are going through an epidemic due to the horizontal and vertical transmission of the KoRV-A gammaretrovirus. This provides an unprecedented opportunity to study how an exogenous retrovirus becomes fixed in the genome of its host, and how piRNAs targeting this retrovirus are generated in germ cells of the infected animal. Initial experiments have shown that the unspliced transcript from KoRV-A proviruses in koala testes, but not the spliced KoRV-A transcript, is directly processed into sense-strand piRNAs. The cleavage of unspliced sense-strand transcripts is thought to serve as an initial innate defense until antisense piRNAs are generated and an adaptive KoRV-A-specific genome immune response is established. Further research is expected to determine how the piRNA machinery recognizes a new foreign genetic invader, how it distinguishes between spliced and unspliced transcripts, and how a mature genome immune response is established, with both sense and antisense piRNAs and the methylation of histones and DNA at the provirus promoter.
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Affiliation(s)
- Milky Abajorga
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Morningside Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Leonid Yurkovetskiy
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
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5
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Leão P, Little ME, Appler KE, Sahaya D, Aguilar-Pine E, Currie K, Finkelstein IJ, De Anda V, Baker BJ. Asgard archaea defense systems and their roles in the origin of eukaryotic immunity. Nat Commun 2024; 15:6386. [PMID: 39085212 PMCID: PMC11291487 DOI: 10.1038/s41467-024-50195-2] [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: 04/16/2024] [Accepted: 06/28/2024] [Indexed: 08/02/2024] Open
Abstract
Dozens of new antiviral systems have been recently characterized in bacteria. Some of these systems are present in eukaryotes and appear to have originated in prokaryotes, but little is known about these defense mechanisms in archaea. Here, we explore the diversity and distribution of defense systems in archaea and identify 2610 complete systems in Asgardarchaeota, a group of archaea related to eukaryotes. The Asgard defense systems comprise 89 unique systems, including argonaute, NLR, Mokosh, viperin, Lassamu, and CBASS. Asgard viperin and argonaute proteins have structural homology to eukaryotic proteins, and phylogenetic analyses suggest that eukaryotic viperin proteins were derived from Asgard viperins. We show that Asgard viperins display anti-phage activity when heterologously expressed in bacteria. Eukaryotic and bacterial argonaute proteins appear to have originated in Asgardarchaeota, and Asgard argonaute proteins have argonaute-PIWI domains, key components of eukaryotic RNA interference systems. Our results support that Asgardarchaeota played important roles in the origin of antiviral defense systems in eukaryotes.
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Affiliation(s)
- Pedro Leão
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, TX, USA.
- Department of Microbiology - RIBES, Radboud University, Nijmegen, The Netherlands.
| | - Mary E Little
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Kathryn E Appler
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, TX, USA
| | - Daphne Sahaya
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Emily Aguilar-Pine
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Kathryn Currie
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA
| | - Valerie De Anda
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, TX, USA
| | - Brett J Baker
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, TX, USA.
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6
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Pan X, Dai W, Wang Z, Li S, Sun T, Miao N. PIWI-Interacting RNAs: A Pivotal Regulator in Neurological Development and Disease. Genes (Basel) 2024; 15:653. [PMID: 38927589 PMCID: PMC11202748 DOI: 10.3390/genes15060653] [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: 04/13/2024] [Revised: 05/17/2024] [Accepted: 05/17/2024] [Indexed: 06/28/2024] Open
Abstract
PIWI-interacting RNAs (piRNAs), a class of small non-coding RNAs (sncRNAs) with 24-32 nucleotides (nt), were initially identified in the reproductive system. Unlike microRNAs (miRNAs) or small interfering RNAs (siRNAs), piRNAs normally guide P-element-induced wimpy testis protein (PIWI) families to slice extensively complementary transposon transcripts without the seed pairing. Numerous studies have shown that piRNAs are abundantly expressed in the brain, and many of them are aberrantly regulated in central neural system (CNS) disorders. However, the role of piRNAs in the related developmental and pathological processes is unclear. The elucidation of piRNAs/PIWI would greatly improve the understanding of CNS development and ultimately lead to novel strategies to treat neural diseases. In this review, we summarized the relevant structure, properties, and databases of piRNAs and their functional roles in neural development and degenerative disorders. We hope that future studies of these piRNAs will facilitate the development of RNA-based therapeutics for CNS disorders.
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Affiliation(s)
| | | | | | | | | | - Nan Miao
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen 361021, China; (X.P.); (W.D.); (Z.W.); (S.L.); (T.S.)
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7
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Graver BA, Chakravarty N, Solomon KV. Prokaryotic Argonautes for in vivo biotechnology and molecular diagnostics. Trends Biotechnol 2024; 42:61-73. [PMID: 37451948 DOI: 10.1016/j.tibtech.2023.06.010] [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: 04/20/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/18/2023]
Abstract
Prokaryotic Argonautes (pAgos) are an emerging class of programmable endonucleases that are believed to be more flexible than existing CRISPR-Cas systems and have significant potential for biotechnology. Current applications of pAgos include a myriad of molecular diagnostics and in vitro DNA assembly tools. However, efforts have historically been centered on thermophilic pAgo variants. To enable in vivo biotechnological applications such as gene editing, focus has shifted to pAgos from mesophilic organisms. We discuss what is known of pAgos, how they are being developed for various applications, and strategies to overcome current challenges to in vivo applications in prokaryotes and eukaryotes.
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Affiliation(s)
- Brett A Graver
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Namrata Chakravarty
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - Kevin V Solomon
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA.
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8
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Kola NS, Patel D, Thakur A. RNA-Based Vaccines and Therapeutics Against Intracellular Pathogens. Methods Mol Biol 2024; 2813:321-370. [PMID: 38888787 DOI: 10.1007/978-1-0716-3890-3_21] [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] [Indexed: 06/20/2024]
Abstract
RNA-based vaccines have sparked a paradigm shift in the treatment and prevention of diseases by nucleic acid medicines. There has been a notable surge in the development of nucleic acid therapeutics and vaccines following the global approval of the two messenger RNA-based COVID-19 vaccines. This growth is fueled by the exploration of numerous RNA products in preclinical stages, offering several advantages over conventional methods, i.e., safety, efficacy, scalability, and cost-effectiveness. In this chapter, we provide an overview of various types of RNA and their mechanisms of action for stimulating immune responses and inducing therapeutic effects. Furthermore, this chapter delves into the varying delivery systems, particularly emphasizing the use of nanoparticles to deliver RNA. The choice of delivery system is an intricate process involved in developing nucleic acid medicines that significantly enhances their stability, biocompatibility, and site-specificity. Additionally, this chapter sheds light on the current landscape of clinical trials of RNA therapeutics and vaccines against intracellular pathogens.
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Affiliation(s)
- Naga Suresh Kola
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Dhruv Patel
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Aneesh Thakur
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada.
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9
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Podder A, Ahmed FF, Suman MZH, Mim AY, Hasan K. Genome-wide identification of DCL, AGO and RDR gene families and their associated functional regulatory element analyses in sunflower (Helianthus annuus). PLoS One 2023; 18:e0286994. [PMID: 37294803 PMCID: PMC10256174 DOI: 10.1371/journal.pone.0286994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/27/2023] [Indexed: 06/11/2023] Open
Abstract
RNA interference (RNAi) regulates a variety of eukaryotic gene expressions that are engaged in response to stress, growth, and the conservation of genomic stability during developmental phases. It is also intimately connected to the post-transcriptional gene silencing (PTGS) process and chromatin modification levels. The entire process of RNA interference (RNAi) pathway gene families mediates RNA silencing. The main factors of RNA silencing are the Dicer-Like (DCL), Argonaute (AGO), and RNA-dependent RNA polymerase (RDR) gene families. To the best of our knowledge, genome-wide identification of RNAi gene families like DCL, AGO, and RDR in sunflower (Helianthus annuus) has not yet been studied despite being discovered in some species. So, the goal of this study is to find the RNAi gene families like DCL, AGO, and RDR in sunflower based on bioinformatics approaches. Therefore, we accomplished an inclusive in silico investigation for genome-wide identification of RNAi pathway gene families DCL, AGO, and RDR through bioinformatics approaches such as (sequence homogeneity, phylogenetic relationship, gene structure, chromosomal localization, PPIs, GO, sub-cellular localization). In this study, we have identified five DCL (HaDCLs), fifteen AGO (HaAGOs), and ten RDR (HaRDRs) in the sunflower genome database corresponding to the RNAi genes of model plant Arabidopsis thaliana based on genome-wide analysis and a phylogenetic method. The analysis of the gene structure that contains exon-intron numbers, conserved domain, and motif composition analyses for all HaDCL, HaAGO, and HaRDR gene families indicated almost homogeneity among the same gene family. The protein-protein interaction (PPI) network analysis illustrated that there exists interconnection among identified three gene families. The analysis of the Gene Ontology (GO) enrichment showed that the detected genes directly contribute to the RNA gene-silencing and were involved in crucial pathways. It was observed that the cis-acting regulatory components connected to the identified genes were shown to be responsive to hormone, light, stress, and other functions. That was found in HaDCL, HaAGO, and HaRDR genes associated with the development and growth of plants. Finally, we are able to provide some essential information about the components of sunflower RNA silencing through our genome-wide comparison and integrated bioinformatics analysis, which open the door for further research into the functional mechanisms of the identified genes and their regulatory elements.
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Affiliation(s)
- Anamika Podder
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Fee Faysal Ahmed
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md. Zahid Hasan Suman
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Afsana Yeasmin Mim
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Khadiza Hasan
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, Bangladesh
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10
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Stalker L, Backx AG, Tscherner AK, Russell SJ, Foster RA, LaMarre J. cDNA Cloning of Feline PIWIL1 and Evaluation of Expression in the Testis of the Domestic Cat. Int J Mol Sci 2023; 24:ijms24119346. [PMID: 37298298 DOI: 10.3390/ijms24119346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 05/12/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
The PIWI clade of Argonaute proteins is essential for spermatogenesis in all species examined to date. This protein family binds specific classes of small non-coding RNAs known as PIWI-interacting RNAs (piRNAs) which together form piRNA-induced silencing complexes (piRISCs) that are recruited to specific RNA targets through sequence complementarity. These complexes facilitate gene silencing through endonuclease activity and guided recruitment of epigenetic silencing factors. PIWI proteins and piRNAs have been found to play multiple roles in the testis including the maintenance of genomic integrity through transposon silencing and facilitating the turnover of coding RNAs during spermatogenesis. In the present study, we report the first characterization of PIWIL1 in the male domestic cat, a mammalian system predicted to express four PIWI family members. Multiple transcript variants of PIWIL1 were cloned from feline testes cDNA. One isoform shows high homology to PIWIL1 from other mammals, however, the other has characteristics of a "slicer null" isoform, lacking the domain required for endonuclease activity. Expression of PIWIL1 in the male cat appears limited to the testis and correlates with sexual maturity. RNA-immunoprecipitation revealed that feline PIWIL1 binds small RNAs with an average size of 29 nt. Together, these data suggest that the domestic cat has two PIWIL1 isoforms expressed in the mature testis, at least one of which interacts with piRNAs.
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Affiliation(s)
- Leanne Stalker
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Alanna G Backx
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Allison K Tscherner
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Stewart J Russell
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Robert A Foster
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W12, Canada
| | - Jonathan LaMarre
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
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11
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The epigenetic regulatory mechanism of PIWI/piRNAs in human cancers. Mol Cancer 2023; 22:45. [PMID: 36882835 PMCID: PMC9990219 DOI: 10.1186/s12943-023-01749-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 02/16/2023] [Indexed: 03/09/2023] Open
Abstract
PIWI proteins have a strong correlation with PIWI-interacting RNAs (piRNAs), which are significant in development and reproduction of organisms. Recently, emerging evidences have indicated that apart from the reproductive function, PIWI/piRNAs with abnormal expression, also involve greatly in varieties of human cancers. Moreover, human PIWI proteins are usually expressed only in germ cells and hardly in somatic cells, so the abnormal expression of PIWI proteins in different types of cancer offer a promising opportunity for precision medicine. In this review, we discussed current researches about the biogenesis of piRNA, its epigenetic regulatory mechanisms in human cancers, such as N6-methyladenosine (m6A) methylation, histone modifications, DNA methylation and RNA interference, providing novel insights into the markers for clinical diagnosis, treatment and prognosis in human cancers.
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12
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Argonaute 2 Restores Erectile Function by Enhancing Angiogenesis and Reducing Reactive Oxygen Species Production in Streptozotocin (STZ)-Induced Type-1 Diabetic Mice. Int J Mol Sci 2023; 24:ijms24032935. [PMID: 36769259 PMCID: PMC9918048 DOI: 10.3390/ijms24032935] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/22/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
Severe vascular and nerve damage from diabetes is a leading cause of erectile dysfunction (ED) and poor response to oral phosphodiesterase 5 inhibitors. Argonaute 2 (Ago2), a catalytic engine in mammalian RNA interference, is involved in neurovascular regeneration under inflammatory conditions. In the present study, we report that Ago2 administration can effectively improve penile erection by enhancing cavernous endothelial cell angiogenesis and survival under diabetic conditions. We found that although Ago2 is highly expressed around blood vessels and nerves, it is significantly reduced in the penis tissue of diabetic mice. Exogenous administration of the Ago2 protein restored erectile function in diabetic mice by reducing reactive oxygen species production-signaling pathways (inducing eNOS Ser1177/NF-κB Ser536 signaling) and improving cavernous endothelial angiogenesis, migration, and cell survival. Our study provides new evidence that Ago2 mediation may be a promising therapeutic strategy and a new approach for diabetic ED treatment.
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13
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Sohn EJ, Oh SO. P-Element-Induced Wimpy Testis Proteins and P-Element-Induced Wimpy Testis-Interacting RNAs Expression in Ovarian Cancer Stem Cells. Genet Test Mol Biomarkers 2023; 27:56-64. [PMID: 36853842 DOI: 10.1089/gtmb.2022.0113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Background: P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs) are a type of noncoding RNA and are predominantly expressed in germline cells. piRNAs function as gene regulators and potential biomarkers for the development of a number of malignancies. The biological importance of piRNAs in ovarian cancer is still unknown. In this study, we investigated the expression of piRNAs in ovarian cancer stem cells and compared it with that in adherent cells. Methods: To assess changes in the expression levels of PIWIL1/HIWI, PIWIL2/HILI, PIWIL3, and PIWIL4/HIWI2, we used quantitative reverse-transcription polymerase chain reaction (RT-qPCR) analysis. Changes in piRNA expression levels in ovarian cancer stem cells were analyzed using Arraystar piRNA microarray screening. Gene Ontology (GO) enrichment analysis was conducted to determine the potential functions of piRNAs. Results: Using microarray analysis, we identified a cohort of differentially expressed piRNAs. Fifteen piRNAs, including DQ570763 and DQ597396, were downregulated, and 58 piRNAs were upregulated when compared with those in adherent A2780 and SKOV3 cells (p > 0.05, >2.0, respectively). GO functions of the downregulated piRNAs (DQ570763 and DQ570797) suggest that their roles are commonly associated with the Golgi apparatus. In addition, A2780-SP and SKOV3-SP cells had higher PIWIL3 and PIWIL4 mRNA levels than adherent cells (A2780 and SKOV3). Moreover, we determined, using receiver operating characteristic plot, that the expression level of PIWIL4 was lower in responders than in nonresponders after treatment with platins in patients with ovarian cancer. Finally, in ovarian cancer, PIWIL4 expression was associated with somatic mutations of dynein axonemal heavy chain 2, signal induced proliferation associated 1 like 2, YTH N6-methyladenosine RNA-binding protein 1, TBC1 domain family member 8, and LPS responsive Beige-like anchor protein. Conclusion: Our study showed that PIWI proteins and piRNAs are potential diagnostic and prognostic biomarkers for ovarian cancer.
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Affiliation(s)
- Eun Jung Sohn
- College of Medicine, Pusan National University, Yangsan, Korea
| | - Sae-Ock Oh
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan, Korea
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14
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Li Q, Shen H, Yuan S, Dai X, Yang C. miRNAs and lncRNAs in tomato: Roles in biotic and abiotic stress responses. FRONTIERS IN PLANT SCIENCE 2023; 13:1094459. [PMID: 36714724 PMCID: PMC9875070 DOI: 10.3389/fpls.2022.1094459] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
Plants are continuously exposed to various biotic and abiotic stresses in the natural environment. To cope with these stresses, they have evolved a multitude of defenses mechanisms. With the rapid development of genome sequencing technologies, a large number of non-coding RNA (ncRNAs) have been identified in tomato, like microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). Recently, more and more evidence indicates that many ncRNAs are involved in plant response to biotic and abiotic stresses in tomato. In this review, we summarize recent updates on the regulatory roles of ncRNAs in tomato abiotic/biotic responses, including abiotic (high temperature, drought, cold, salinization, etc.) and biotic (bacteria, fungi, viruses, insects, etc.) stresses. Understanding the molecular mechanisms mediated by ncRNAs in response to these stresses will help us to clarify the future directions for ncRNA research and resistance breeding in tomato.
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Affiliation(s)
- Qian Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Heng Shen
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Shoujuan Yuan
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Xigang Dai
- School of Life Sciences, Jianghan University/Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, Wuhan, China
| | - Changxian Yang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
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15
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Identification of Circular RNAs of Testis and Caput Epididymis and Prediction of Their Potential Functional Roles in Donkeys. Genes (Basel) 2022; 14:genes14010066. [PMID: 36672807 PMCID: PMC9858477 DOI: 10.3390/genes14010066] [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: 11/16/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
Circular RNAs (circRNAs) are a class of noncoding RNAs with a covalently closed loop. Studies have demonstrated that circRNA can function as microRNA (miRNA) sponges or competing endogenous RNAs. Although circRNA has been explored in some species and tissues, the genetic basis of testis development and spermatogenesis in donkeys remain unknown. We performed RNA-seq to detect circRNA expression profiles of adult donkey testes. Length distribution and other characteristics were shown a total of 1971 circRNAs were differentially expressed and 12,648 and 6261 circRNAs were detected from the testis and caput epididymis, respectively. Among these circRNAs, 1472 circRNAs were downregulated and 499 circRNAs were upregulated in the testis. Moreover, KEGG pathway analyses and Gene Ontology were performed for host genes of circRNAs. A total of 39 upregulated circRNA host genes were annotated in spermatogenesis terms, including PIWIL2, CATSPERD, CATSPERB, SPATA6, and SYCP1. Other host genes were annotated in the focal adhesion, Rap1 signaling pathway. Downregulated expressed circRNA host genes participated in the TGF-β signaling pathway, GnRH signaling pathway, estrogen signaling pathway, and calcium signaling pathway. Our discoveries provide a solid foundation for identifying and characterizing critical circRNAs involved in testis development or spermatogenesis.
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16
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Chattopadhyay T, Biswal P, Lalruatfela A, Mallick B. Emerging roles of PIWI-interacting RNAs (piRNAs) and PIWI proteins in head and neck cancer and their potential clinical implications. Biochim Biophys Acta Rev Cancer 2022; 1877:188772. [PMID: 35931391 DOI: 10.1016/j.bbcan.2022.188772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 02/08/2023]
Abstract
Head and neck squamous cell carcinoma (HNSCC) are among the well-known neoplasms originating in the oral cavity, pharynx, and larynx. Despite advancements in chemotherapy, radiotherapy, and surgery, the survival rates of the patients are low, which has posed a major therapeutic challenge. A growing number of non-coding RNAs (ncRNAs), for instance, microRNAs, have been identified whose abnormal expression patterns have been implicated in HNSCC. However, more recently, several seminal research has shown that piwi-interacting RNAs (piRNAs), a promising and young class of small ncRNA, are linked to the emergence and progression of cancer. They can regulate transposable elements (TE) and gene expression through multiple mechanisms, making them potentially more powerful regulators than miRNAs. Hence, they can be more promising ncRNAs candidates for cancer therapeutic intervention. Here, we surveyed the roles and clinical implications of piRNAs and their PIWI proteins partners in tumorigenesis and associated molecular processes of cancer, with a particular focus on HNSCC, to offer a new avenue for diagnosis, prognosis, and therapeutic interventions for the malignancy, improving patient's outcomes.
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Affiliation(s)
- Trisha Chattopadhyay
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Priyajit Biswal
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Anthony Lalruatfela
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Bibekanand Mallick
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India.
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17
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Ahmed FF, Hossen MI, Sarkar MAR, Konak JN, Zohra FT, Shoyeb M, Mondal S. Genome-wide identification of DCL, AGO and RDR gene families and their associated functional regulatory elements analyses in banana (Musa acuminata). PLoS One 2021; 16:e0256873. [PMID: 34473743 PMCID: PMC8412350 DOI: 10.1371/journal.pone.0256873] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 08/17/2021] [Indexed: 12/15/2022] Open
Abstract
RNA silencing is mediated through RNA interference (RNAi) pathway gene families, i.e., Dicer-Like (DCL), Argonaute (AGO), and RNA-dependent RNA polymerase (RDR) and their cis-acting regulatory elements. The RNAi pathway is also directly connected with the post-transcriptional gene silencing (PTGS) mechanism, and the pathway controls eukaryotic gene regulation during growth, development, and stress response. Nevertheless, genome-wide identification of RNAi pathway gene families such as DCL, AGO, and RDR and their regulatory network analyses related to transcription factors have not been studied in many fruit crop species, including banana (Musa acuminata). In this study, we studied in silico genome-wide identification and characterization of DCL, AGO, and RDR genes in bananas thoroughly via integrated bioinformatics approaches. A genome-wide analysis identified 3 MaDCL, 13 MaAGO, and 5 MaRDR candidate genes based on multiple sequence alignment and phylogenetic tree related to the RNAi pathway in banana genomes. These genes correspond to the Arabidopsis thaliana RNAi silencing genes. The analysis of the conserved domain, motif, and gene structure (exon-intron numbers) for MaDCL, MaAGO, and MaRDR genes showed higher homogeneity within the same gene family. The Gene Ontology (GO) enrichment analysis exhibited that the identified RNAi genes could be involved in RNA silencing and associated metabolic pathways. A number of important transcription factors (TFs), e.g., ERF, Dof, C2H2, TCP, GATA and MIKC_MADS families, were identified by network and sub-network analyses between TFs and candidate RNAi gene families. Furthermore, the cis-acting regulatory elements related to light-responsive (LR), stress-responsive (SR), hormone-responsive (HR), and other activities (OT) functions were identified in candidate MaDCL, MaAGO, and MaRDR genes. These genome-wide analyses of these RNAi gene families provide valuable information related to RNA silencing, which would shed light on further characterization of RNAi genes, their regulatory elements, and functional roles, which might be helpful for banana improvement in the breeding program.
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Affiliation(s)
- Fee Faysal Ahmed
- Faculty of Science, Department of Mathematics, Jashore University of Science and Technology, Jashore, Bangladesh
- * E-mail:
| | - Md. Imran Hossen
- Faculty of Science, Department of Mathematics, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md. Abdur Rauf Sarkar
- Faculty of Biological Science and Technology, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Jesmin Naher Konak
- Faculty of Life Science, Department of Biochemistry and Molecular Biology, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Fatema Tuz Zohra
- Faculty of Agriculture, Laboratory of Fruit Science, Saga University, Honjo-machi, Saga, Japan
| | - Md. Shoyeb
- Faculty of Biological Science and Technology, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Samiran Mondal
- Faculty of Science, Department of Mathematics, Jashore University of Science and Technology, Jashore, Bangladesh
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18
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Jin S, Zhan J, Zhou Y. Argonaute proteins: structures and their endonuclease activity. Mol Biol Rep 2021; 48:4837-4849. [PMID: 34117606 DOI: 10.1007/s11033-021-06476-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 06/05/2021] [Indexed: 01/12/2023]
Abstract
Argonaute proteins are highly conserved and widely expressed in almost all organisms. They not only play a critical role in the biogenesis of small RNAs but also defend against invading nucleic acids via small RNA or DNA-mediated gene silencing pathways. One functional mechanism of Argonaute proteins is acting as a nucleic-acid-guided endonuclease, which can cleave targets complementary to DNA or RNA guides. The cleavage then leads to translational silencing directly or indirectly by recruiting additional silencing proteins. Here, we summarized the latest research progress in structural and biological studies of Argonaute proteins and pointed out their potential applications in the field of gene editing.
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Affiliation(s)
- Shujuan Jin
- Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Jian Zhan
- Institute for Glycomics, Griffith University, Brisbane, QLD, Australia
| | - Yaoqi Zhou
- Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
- Institute for Glycomics, Griffith University, Brisbane, QLD, Australia.
- Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518055, China.
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19
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Arraes FBM, Martins-de-Sa D, Noriega Vasquez DD, Melo BP, Faheem M, de Macedo LLP, Morgante CV, Barbosa JARG, Togawa RC, Moreira VJV, Danchin EGJ, Grossi-de-Sa MF. Dissecting protein domain variability in the core RNA interference machinery of five insect orders. RNA Biol 2020; 18:1653-1681. [PMID: 33302789 DOI: 10.1080/15476286.2020.1861816] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
RNA interference (RNAi)-mediated gene silencing can be used to control specific insect pest populations. Unfortunately, the variable efficiency in the knockdown levels of target genes has narrowed the applicability of this technology to a few species. Here, we examine the current state of knowledge regarding the miRNA (micro RNA) and siRNA (small interfering RNA) pathways in insects and investigate the structural variability at key protein domains of the RNAi machinery. Our goal was to correlate domain variability with mechanisms affecting the gene silencing efficiency. To this end, the protein domains of 168 insect species, encompassing the orders Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera, were analysed using our pipeline, which takes advantage of meticulous structure-based sequence alignments. We used phylogenetic inference and the evolutionary rate coefficient (K) to outline the variability across domain regions and surfaces. Our results show that four domains, namely dsrm, Helicase, PAZ and Ribonuclease III, are the main contributors of protein variability in the RNAi machinery across different insect orders. We discuss the potential roles of these domains in regulating RNAi-mediated gene silencing and the role of loop regions in fine-tuning RNAi efficiency. Additionally, we identified several order-specific singularities which indicate that lepidopterans have evolved differently from other insect orders, possibly due to constant coevolution with plants and viruses. In conclusion, our results highlight several variability hotspots that deserve further investigation in order to improve the application of RNAi technology in the control of insect pests.
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Affiliation(s)
| | - Diogo Martins-de-Sa
- Departamento De Biologia Celular, Universidade De Brasília, Brasília-DF, Brazil
| | - Daniel D Noriega Vasquez
- Plant-Pest Molecular Interaction Laboratory (LIMPP), Brasilia, Brasília-DF, Brazil.,Catholic University of Brasília, Brasília-DF, Brazil
| | - Bruno Paes Melo
- Plant-Pest Molecular Interaction Laboratory (LIMPP), Brasilia, Brasília-DF, Brazil.,Viçosa University, UFV, Viçosa-MG, Brazil
| | - Muhammad Faheem
- Plant-Pest Molecular Interaction Laboratory (LIMPP), Brasilia, Brasília-DF, Brazil.,Department of Biological Sciences, National University of Medical Sciences, Punjab, Pakistan
| | | | - Carolina Vianna Morgante
- Plant-Pest Molecular Interaction Laboratory (LIMPP), Brasilia, Brasília-DF, Brazil.,Embrapa Semiarid, Petrolina-PE, Brazil.,National Institute of Science and Technology, Jakarta Embrapa-Brazil
| | | | - Roberto Coiti Togawa
- Plant-Pest Molecular Interaction Laboratory (LIMPP), Brasilia, Brasília-DF, Brazil
| | - Valdeir Junio Vaz Moreira
- Biotechnology Center, Brazil.,Plant-Pest Molecular Interaction Laboratory (LIMPP), Brasilia, Brasília-DF, Brazil.,Departamento De Biologia Celular, Universidade De Brasília, Brasília-DF, Brazil
| | - Etienne G J Danchin
- National Institute of Science and Technology, Jakarta Embrapa-Brazil.,INRAE, Université Côte d'Azur, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France
| | - Maria Fatima Grossi-de-Sa
- Plant-Pest Molecular Interaction Laboratory (LIMPP), Brasilia, Brasília-DF, Brazil.,Catholic University of Brasília, Brasília-DF, Brazil.,National Institute of Science and Technology, Jakarta Embrapa-Brazil
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20
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Xu CM, Sun SC. Expression of Piwi Genes during the Regeneration of Lineus sanguineus (Nemertea, Pilidiophora, Heteronemertea). Genes (Basel) 2020; 11:E1484. [PMID: 33321919 PMCID: PMC7764242 DOI: 10.3390/genes11121484] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/18/2020] [Accepted: 12/08/2020] [Indexed: 12/19/2022] Open
Abstract
The transposon silencer piwi genes play important roles in germline determination and maintenance, gametogenesis, and stem-cell self-renewal, and the expression of certain piwi genes is indispensable for regeneration. Knowledge about piwi genes is needed for phylum Nemertea, which contains members (e.g., Lineus sanguineus) with formidable regeneration capacity. By searching the L. sanguineus genome, we identified six Argonaute genes including three ago (Ls-Ago2, Ls-Ago2a, and Ls-Ago2b) and three piwi (Ls-piwi1, Ls-piwi2, and Ls-piwi3) genes. In situ hybridization revealed that, in intact females, Ls-piwi2 and Ls-piwi3 were not expressed, while Ls-piwi1 was expressed in ovaries. During regeneration, Ls-piwi1 and Ls-pcna (proliferating cell nuclear antigen) had strong and similar expressions. The expression of Ls-piwi1 became indetectable while Ls-pcna continued to be expressed when the differentiation of new organs was finished. During anterior regeneration, expression signals of Ls-piwi2 and Ls-piwi3 were weak and only detected in the blastema stage. During posterior regeneration, no expression was observed for Ls-piwi2. To date, no direct evidence has been found for the existence of congenital stem cells in adult L. sanguineus. The "pluripotent cells" in regenerating tissues are likely to be dedifferentiated from other type(s) of cells.
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Affiliation(s)
| | - Shi-Chun Sun
- College of Fisheries, Institute of Evolution and Marine Biodiversity, Ocean University of China, 5 Yushan Road, Qingdao 266003, China;
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21
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Sun ZH, Wei JL, Cui ZP, Han YL, Zhang J, Song J, Chang YQ. Identification and functional characterization of piwi1 gene in sea cucumber, Apostichopus japonicas. Comp Biochem Physiol B Biochem Mol Biol 2020; 252:110536. [PMID: 33212209 DOI: 10.1016/j.cbpb.2020.110536] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 11/03/2020] [Accepted: 11/12/2020] [Indexed: 02/04/2023]
Abstract
The sea cucumber (Apostichopus japonicus) is an economically important mariculture species in Asia. However, the genetic breeding of sea cucumbers is difficult because the sexes cannot be identified by appearance. Therefore, studies on sex-related genes are helpful in revealing the mechanisms of sex determination and differentiation in sea cucumbers. P-element induced wimpy testis (piwi) is a germ cell marker involved in gametogenesis in vertebrates; however, the expression pattern and function during gametogenesis remain unclear in sea cucumbers. In this study, we identified a piwi homolog gene in A. japonicus (Ajpiwi1) and investigated its expression pattern, and function. Ajpiwi1 is a maternal factor and is ubiquitously expressed in adult tissues, including the ovary and testis. Ajpiwi1 expression is strong in early oocytes, spermatocytes, and spermatogonia; weak in mature oocytes; and undetected in spermatids and intra-gonadal somatic cells. The knockdown of Ajpiwi1 by RNA interference (RNAi) led to the downregulation of other conserved sex-related genes such as dmrt1, foxl2, and germ cell-less. Therefore, Ajpiwi1 might play a critical role during gametogenesis in A. japonicus. This study creates new possibilities for studying sex-related gene functions in the sea cucumber and builds a gene function research platform based on RNAi for the first time.
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Affiliation(s)
- Zhi-Hui Sun
- Key Laboratory of Mariculture& Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian 116023, China
| | - Jin-Liang Wei
- Key Laboratory of Mariculture& Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian 116023, China
| | - Zhou-Ping Cui
- Key Laboratory of Mariculture& Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian 116023, China
| | - Ya-Lun Han
- Key Laboratory of Mariculture& Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian 116023, China
| | - Jian Zhang
- Key Laboratory of Mariculture& Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian 116023, China
| | - Jian Song
- Key Laboratory of Mariculture& Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian 116023, China
| | - Ya-Qing Chang
- Key Laboratory of Mariculture& Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian 116023, China.
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22
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Zumajo-Cardona C, Ambrose BA. Phylogenetic analyses of key developmental genes provide insight into the complex evolution of seeds. Mol Phylogenet Evol 2020; 147:106778. [PMID: 32165160 DOI: 10.1016/j.ympev.2020.106778] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 02/06/2020] [Accepted: 02/26/2020] [Indexed: 11/30/2022]
Abstract
Gene duplication plays a decisive role in organismal diversification and in the appearance of novel structures. In plants the megagametophyte covered by the integuments, which after fertilization becomes the seed constitutes a novel structure: the ovule. In Arabidopsis thaliana, genetic mechanisms regulating ovule development, including the genetics underlying ovule initiation, ovule patterning and integument development, have been identified. Among seed plants, integuments are not only a novelty in evolution, but integuments also present an enormous morphological variation. This study is focused on the evolution of gene families that play a role in the proper morphological development of the integuments, BELL1 (BEL1), KANADIs (KAN1, KAN2, and KAN4/ATS), UNICORN (UCN) and SHORT INTEGUMENTS1 (SIN1). In Arabidopsis, BEL1 establishes the initiation of integument development. KAN1 and 2 act in the proper development of the outer integument. While ABERRANT TESTA SHAPE (ATS), is involved in the correct separation of both integuments. UCN acts in planar growth of the outer integument repressing ATS. SIN1 is involved in cell elongation in the integuments. The results of our analyses show that each of these genes has a different evolutionary history and that while gymnosperms appear to have a simpler ovule morphology, they have more homologues of these candidate genes than angiosperms. In addition, we present the conserved and novel motifs for each of these genes among seed plants and their selection constraints, which may be related to functional changes and to the diversity of ovule morphologies.
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Affiliation(s)
- Cecilia Zumajo-Cardona
- New York Botanical Garden, Bronx, NY 10458, USA; The Graduate Center, City University of New York, New York, NY 10016, USA
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23
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Kim KW. PIWI Proteins and piRNAs in the Nervous System. Mol Cells 2019; 42:828-835. [PMID: 31838836 PMCID: PMC6939654 DOI: 10.14348/molcells.2019.0241] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/29/2019] [Accepted: 12/06/2019] [Indexed: 12/13/2022] Open
Abstract
PIWI Argonaute proteins and Piwi-interacting RNAs (piRNAs) are expressed in all animal species and play a critical role in cellular defense by inhibiting the activation of transposable elements in the germline. Recently, new evidence suggests that PIWI proteins and piRNAs also play important roles in various somatic tissues, including neurons. This review summarizes the neuronal functions of the PIWI-piRNA pathway in multiple animal species, including their involvement in axon regeneration, behavior, memory formation, and transgenerational epigenetic inheritance of adaptive memory. This review also discusses the consequences of dysregulation of neuronal PIWI-piRNA pathways in certain neurological disorders, including neurodevelopmental and neurodegenerative diseases. A full understanding of neuronal PIWI-piRNA pathways will ultimately provide novel insights into small RNA biology and could potentially provide precise targets for therapeutic applications.
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Affiliation(s)
- Kyung Won Kim
- Convergence Program of Material Science for Medicine and Pharmaceutics, Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252,
Korea
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24
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Mohibi S, Chen X, Zhang J. Cancer the'RBP'eutics-RNA-binding proteins as therapeutic targets for cancer. Pharmacol Ther 2019; 203:107390. [PMID: 31302171 DOI: 10.1016/j.pharmthera.2019.07.001] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/02/2019] [Indexed: 12/11/2022]
Abstract
RNA-binding proteins (RBPs) play a critical role in the regulation of various RNA processes, including splicing, cleavage and polyadenylation, transport, translation and degradation of coding RNAs, non-coding RNAs and microRNAs. Recent studies indicate that RBPs not only play an instrumental role in normal cellular processes but have also emerged as major players in the development and spread of cancer. Herein, we review the current knowledge about RNA binding proteins and their role in tumorigenesis as well as the potential to target RBPs for cancer therapeutics.
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Affiliation(s)
- Shakur Mohibi
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, United States
| | - Xinbin Chen
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, United States
| | - Jin Zhang
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, United States.
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25
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Tan H, Zhu Y, Zheng X, Lu Y, Tao D, Liu Y, Ma Y. PIWIL1 suppresses circadian rhythms through GSK3β-induced phosphorylation and degradation of CLOCK and BMAL1 in cancer cells. J Cell Mol Med 2019; 23:4689-4698. [PMID: 31099187 PMCID: PMC6584488 DOI: 10.1111/jcmm.14377] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 03/16/2019] [Accepted: 04/21/2019] [Indexed: 02/05/2023] Open
Abstract
Circadian rhythms are maintained by series of circadian clock proteins, and post-translation modifications of clock proteins significantly contribute to regulating circadian clock. However, the underlying upstream mechanism of circadian genes that are responsible for circadian rhythms in cancer cells remains unknown. PIWIL1 participates in many physiological processes and current discoveries have shown that PIWIL1 is involved in tumorigenesis in various cancers. Here we report that PIWIL1 can suppress circadian rhythms in cancer cells. Mechanistically, by promoting SRC interacting with PI3K, PIWIL1 can activate PI3K-AKT signalling pathway to phosphorylate and inactivate GSK3β, repressing GSK3β-induced phosphorylation and ubiquitination of CLOCK and BMAL1. Simultaneously, together with CLOCK/BMAL1 complex, PIWIL1 can bind with E-BOX region to suppress transcriptional activities of clock-controlled genes promoters. Collectively, our findings first demonstrate that PIWIL1 negatively regulates circadian rhythms via two pathways, providing molecular connection between dysfunction of circadian rhythms and tumorigenesis.
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Affiliation(s)
- Hao Tan
- Department of Medical Genetics, State Key Laboratory of BiotherapyWest China Hospital, Sichuan University and Collaborative Innovation CenterChengduChina
| | - Yingchuan Zhu
- Department of Medical Genetics, State Key Laboratory of BiotherapyWest China Hospital, Sichuan University and Collaborative Innovation CenterChengduChina
| | - Xulei Zheng
- Department of Medical Genetics, State Key Laboratory of BiotherapyWest China Hospital, Sichuan University and Collaborative Innovation CenterChengduChina
| | - Yilu Lu
- Department of Medical Genetics, State Key Laboratory of BiotherapyWest China Hospital, Sichuan University and Collaborative Innovation CenterChengduChina
| | - Dachang Tao
- Department of Medical Genetics, State Key Laboratory of BiotherapyWest China Hospital, Sichuan University and Collaborative Innovation CenterChengduChina
| | - Yunqiang Liu
- Department of Medical Genetics, State Key Laboratory of BiotherapyWest China Hospital, Sichuan University and Collaborative Innovation CenterChengduChina
| | - Yongxin Ma
- Department of Medical Genetics, State Key Laboratory of BiotherapyWest China Hospital, Sichuan University and Collaborative Innovation CenterChengduChina
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Dias N, Cagliari D, Kremer FS, Rickes LN, Nava DE, Smagghe G, Zotti M. The South American Fruit Fly: An Important Pest Insect With RNAi-Sensitive Larval Stages. Front Physiol 2019; 10:794. [PMID: 31316391 PMCID: PMC6610499 DOI: 10.3389/fphys.2019.00794] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/06/2019] [Indexed: 01/04/2023] Open
Abstract
RNA interference (RNAi) technology has been used in the development of approaches for pest control. The presence of some essential genes, the so-called “core genes,” in the RNAi machinery is crucial for its efficiency and robust response in gene silencing. Thus, our study was designed to examine whether the RNAi machinery is functional in the South American (SA) fruit fly Anastrepha fraterculus (Diptera: Tephritidae) and whether the sensitivity to the uptake of double-stranded RNA (dsRNA) could generate an RNAi response in this fruit fly species. To prepare a transcriptome database of the SA fruit fly, total RNA was extracted from all the life stages for later cDNA synthesis and Illumina sequencing. After the de novo transcriptome assembly and gene annotation, the transcriptome was screened for RNAi pathway genes, as well as the duplication or loss of genes and novel target genes to dsRNA delivery bioassays. The dsRNA delivery assay by soaking was performed in larvae to evaluate the gene-silencing of V-ATPase, and the upregulation of Dicer-2 and Argonaute-2 after dsRNA delivery was analyzed to verify the activation of siRNAi machinery. We tested the stability of dsRNA using dsGFP with an in vitro incubation of larvae body fluid (hemolymph). We identified 55 genes related to the RNAi machinery with duplication and loss for some genes and selected 143 different target genes related to biological processes involved in post-embryonic growth/development and reproduction of A. fraterculus. Larvae soaked in dsRNA (dsV-ATPase) solution showed a strong knockdown of V-ATPase after 48 h, and the expression of Dicer-2 and Argonaute-2 responded with an increase upon the exposure to dsRNA. Our data demonstrated the existence of a functional RNAi machinery in the SA fruit fly, and we present an easy and robust physiological bioassay with the larval stages that can further be used for screening of target genes at in vivo organisms’ level for RNAi-based control of fruit fly pests. This is the first study that provides evidence of a functional siRNA machinery in the SA fruit fly.
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Affiliation(s)
- Naymã Dias
- Molecular Entomology and Applied Bioinformatics Laboratory, Faculty of Agronomy, Department of Crop Protection, Federal University of Pelotas, Pelotas, Brazil
| | - Deise Cagliari
- Molecular Entomology and Applied Bioinformatics Laboratory, Faculty of Agronomy, Department of Crop Protection, Federal University of Pelotas, Pelotas, Brazil
| | - Frederico Schmitt Kremer
- Bioinformatics and Proteomics Laboratory, Technological Development Center, Federal University of Pelotas, Pelotas, Brazil
| | - Leticia Neutzling Rickes
- Molecular Entomology and Applied Bioinformatics Laboratory, Faculty of Agronomy, Department of Crop Protection, Federal University of Pelotas, Pelotas, Brazil
| | - Dori Edson Nava
- Entomology Laboratory, Embrapa Clima Temperado, Pelotas, Brazil
| | - Guy Smagghe
- Faculty of Bioscience Engineering, Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - Moisés Zotti
- Molecular Entomology and Applied Bioinformatics Laboratory, Faculty of Agronomy, Department of Crop Protection, Federal University of Pelotas, Pelotas, Brazil
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Giebler M, Greither T, Müller L, Mösinger C, Behre HM. Altered PIWI-LIKE 1 and PIWI-LIKE 2 mRNA expression in ejaculated spermatozoa of men with impaired sperm characteristics. Asian J Androl 2019; 20:260-264. [PMID: 29286006 PMCID: PMC5952480 DOI: 10.4103/aja.aja_58_17] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
In about half the cases of involuntary childlessness, a male infertility factor is involved. The PIWI-LIKE genes, a subclade of the Argonaute protein family, are involved in RNA silencing and transposon control in the germline. Knockout of murine Piwi-like 1 and 2 homologs results in complete infertility in males. The aim of this study was to analyze whether the mRNA expression of human PIWI-LIKE 1-4 genes is altered in ejaculated spermatozoa of men with impaired sperm characteristics. Ninety male participants were included in the study, among which 47 were with normozoospermia, 36 with impaired semen characteristics according to the World Health Organization (WHO) manual, 5th edition, and 7 with azoospermia serving as negative control for the PIWI-LIKE 1-4 mRNA expression in somatic cells in the ejaculate. PIWI-LIKE 1-4 mRNA expression in the ejaculated spermatozoa of the participants was measured by quantitative real-time PCR. In nonazoospermic men, PIWI-LIKE 1-4 mRNA was measurable in ejaculated spermatozoa in different proportions. PIWI-LIKE 1 (100.0%) and PIWI-LIKE 2 (49.4%) were more frequently expressed than PIWI-LIKE 3 (9.6%) and PIWI-LIKE 4 (15.7%). Furthermore, a decreased PIWI-LIKE 2 mRNA expression showed a significant correlation with a decreased sperm count (P = 0.022) and an increased PIWI-LIKE 1 mRNA expression with a decreased progressive motility (P = 0.048). PIWI-LIKE 1 and PIWI-LIKE 2 mRNA expression exhibited a significant association with impaired sperm characteristics and may be a useful candidate for the evaluation of the impact of PIWI-LIKE 1-4 mRNA expression on male infertility.
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Affiliation(s)
- Maria Giebler
- Center for Reproductive Medicine and Andrology, Martin Luther University Halle-Wittenberg, Halle (Saale) 06120, Germany
| | - Thomas Greither
- Center for Reproductive Medicine and Andrology, Martin Luther University Halle-Wittenberg, Halle (Saale) 06120, Germany
| | - Lisa Müller
- Center for Reproductive Medicine and Andrology, Martin Luther University Halle-Wittenberg, Halle (Saale) 06120, Germany
| | - Carina Mösinger
- Center for Reproductive Medicine and Andrology, Martin Luther University Halle-Wittenberg, Halle (Saale) 06120, Germany
| | - Hermann M Behre
- Center for Reproductive Medicine and Andrology, Martin Luther University Halle-Wittenberg, Halle (Saale) 06120, Germany
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Mungamuri SK. Targeting the epigenome as a therapeutic strategy for pancreatic tumors. THERANOSTIC APPROACH FOR PANCREATIC CANCER 2019:211-244. [DOI: 10.1016/b978-0-12-819457-7.00011-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
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29
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Pegler JL, Grof CPL, Eamens AL. The Plant microRNA Pathway: The Production and Action Stages. Methods Mol Biol 2019; 1932:15-39. [PMID: 30701489 DOI: 10.1007/978-1-4939-9042-9_2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Plant microRNAs are an endogenous class of small regulatory RNA central to the posttranscriptional regulation of gene expression in plant development and environmental stress adaptation or in response to pathogen challenge. The plant microRNA pathway is readily separated into two distinct stages: (1) the production stage, which is localized to the plant cell nucleus and where the microRNA small RNA is processed from a double-stranded RNA precursor transcript, and (2) the action stage, which is localized to the plant cell cytoplasm and where the mature microRNA small RNA is loaded into an effector complex and is used by the complex as a sequence specificity guide to direct expression repression of target genes harboring highly complementary microRNA target sequences. Historical research indicated that the plant microRNA pathway was a highly structured, almost linear pathway requiring a small set of core machinery proteins. However, contemporary research has demonstrated that the plant microRNA pathway is highly dynamic, and to allow for this flexibility, a large and highly functionally diverse set of machinery proteins is now known to be required. For example, recent research has shown that plant microRNAs can regulate target gene expression via a translational repression mechanism of RNA silencing in addition to the standard messenger RNA cleavage-based mechanism of RNA silencing: a mode of RNA silencing originally assigned to all plant microRNAs. Using Arabidopsis thaliana as our model system, here we report on both the core and auxiliary sets of machinery proteins now known to be required for both microRNA production and microRNA action in plants.
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Affiliation(s)
- Joseph L Pegler
- Faculty of Science, Centre for Plant Science, School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - Christopher P L Grof
- Faculty of Science, Centre for Plant Science, School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - Andrew L Eamens
- Faculty of Science, Centre for Plant Science, School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia.
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Giebler M, Greither T, Behre HM. Differential Regulation of PIWI-LIKE 2 Expression in Primordial Germ Cell Tumor Cell Lines by Promoter Methylation. Front Genet 2018; 9:375. [PMID: 30294341 PMCID: PMC6158399 DOI: 10.3389/fgene.2018.00375] [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: 04/23/2018] [Accepted: 08/24/2018] [Indexed: 11/13/2022] Open
Abstract
PIWI-LIKE 2, a member of the ARGONAUTE protein family, is exclusively expressed in pre-pachytene and pachytene stages of spermatogenesis. PIWI-LIKE 2 acts in the germ cell development and the silencing of retrotransponsons to maintain the genomic integrity and stem cell character. In the present study we investigated DNA methylation as potential mechanism for the regulation of human PIWI-LIKE 2 expression in cell lines related to spermatozoa precursor cells. We detected a high methylation of the PIWI-LIKE 2 promoter in TCam-2 cells, while in NT2/D1 cells the promoter was hypomethylated. Concordantly, PIWI-LIKE 2 expression is higher in NT2/D1 cells than in TCam-2 cells. By demethylation of the promoter with 5'-Aza-2'-deoxycytidine, PIWI-LIKE 2 expression in TCam-2 was increased, while in NT2/D1 no alterations in PIWI-LIKE 2 expression could be detected. In conclusion, we analyzed the DNA methylation driving PIWI-LIKE 2 expression in undifferentiated germ cell tumors and demonstrated an epigenetic basis for PIWI-LIKE 2 expression in this cell type.
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Affiliation(s)
- Maria Giebler
- Center for Reproductive Medicine and Andrology, Martin Luther University of Halle-Wittenberg, Halle, Germany
| | - Thomas Greither
- Center for Reproductive Medicine and Andrology, Martin Luther University of Halle-Wittenberg, Halle, Germany
| | - Hermann M Behre
- Center for Reproductive Medicine and Andrology, Martin Luther University of Halle-Wittenberg, Halle, Germany
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Wang H, Wang B, Liu J, Li A, Zhu H, Wang X, Zhang Q. Piwil1 gene is regulated by hypothalamic-pituitary-gonadal axis in turbot (Scophthalmus maximus): A different effect in ovaries and testes. Gene 2018. [PMID: 29524575 DOI: 10.1016/j.gene.2018.03.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
As constituent factors of Piwi-interacting RNA (piRNA) pathways, Piwi proteins are essential for germline maintenance and gonadal development. Previous studies show that Piwi-piRNA pathways could be regulated by hypothalamic-pituitary-gonadal (HPG) axis, however, related studies have not been reported in marine species. Here we reported the identification of turbot (Scophthalmus maximus) piwil1 gene, which was abundantly expressed in testis and ovary in a tissue-specific manner. Phylogenetic and genomic structure analyses revealed that piwil1 was conserved in its sequence and function during vertebrate evolution. We also investigated the effects of HPG axis hormones, including human chorionic gonadotropin (hCG), estradiol-17β (E2) and 17α-methyltestosterone (MT), on gonadal piwil1 expression via in vivo and in vitro approaches. In ovary, hCG and E2 suppressed piwil1 expression both in vivo and in vitro, and MT increased piwil1 expression in vivo. In testis, hCG had upregulating effects on piwil1 expression in vivo and in vitro, and MT also increased piwil1 expression in vitro. In addition, E2 suppressed expression of piwil1 in vivo. These results indicated that the decreased or increased expression of piwil1 regulated by hormones might play a crucial role during gonadal differentiation and development in S. maximus.
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Affiliation(s)
- Huizhen Wang
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, 266003, Qingdao, Shandong, China
| | - Bo Wang
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, 266003, Qingdao, Shandong, China
| | - Jinxiang Liu
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, 266003, Qingdao, Shandong, China
| | - Aoyun Li
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, 266003, Qingdao, Shandong, China
| | - He Zhu
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, 266003, Qingdao, Shandong, China
| | - XuBo Wang
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, 266003, Qingdao, Shandong, China.
| | - Quanqi Zhang
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, 266003, Qingdao, Shandong, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, 266237, Qingdao, Shandong, China.
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32
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Zhao C, Zhu W, Yin S, Cao Q, Zhang H, Wen X, Zhang G, Xie W, Chen S. Molecular characterization and expression of Piwil1 and Piwil2 during gonadal development and treatment with HCG and LHRH-A 2 in Odontobutis potamophila. Gene 2018; 647:181-191. [DOI: 10.1016/j.gene.2018.01.038] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 12/04/2017] [Accepted: 01/09/2018] [Indexed: 12/12/2022]
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Zeng G, Zhang D, Liu X, Kang Q, Fu Y, Tang B, Guo W, Zhang Y, Wei G, He D. Co-expression of Piwil2/Piwil4 in nucleus indicates poor prognosis of hepatocellular carcinoma. Oncotarget 2018; 8:4607-4617. [PMID: 27894076 PMCID: PMC5354858 DOI: 10.18632/oncotarget.13491] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 10/28/2016] [Indexed: 01/08/2023] Open
Abstract
Purpose This study aimed to explore the localization and expression of P-element-induced wimpy testis-like 2 (piwil2)/Piwil4 in hepatocellular carcinoma (HCC) tissues, and analyze the correlation between co-expression pattern and prognosis of HCC. Results Piwil2 showed 100% positive expression in the cell nucleus, with the intensity higher than in the cytoplasm. Piwil4 showed a lower intensity of expression in the cell nucleus than in the cytoplasm. The molecular chaperone Piwil2/Piwil4 had four co-expression patterns: nuclear co-expression, nuclear and cytoplasmic co-expression, cytoplasmic co-expression, and non-coexpression. The survival rate and the overall survival sequentially increased. The prognostic phenotype of the nuclear co-expression of Piwil2/Piwil4 was worse than that of non-coexpression, and the intracellular localization and expression of Piwil2 and Piwil4 were not significantly different. Methods HCC pathological tissue samples with follow-up information (90 cases) and 2 normal control liver tissues were collected and made into a 92-site microarray. The expression of Piwil2 and Piwil4 was detected using the immunofluorescence double staining method. The differences in the expression and location of Piwil2 and Piwil4 in tumor cells were explored, and the influence of such differences on the long-term survival rate of HCC was studied using Kaplan-Meier survival curve and log-rank test. The clinical staging was analyzed according to the HCC international TNM staging criteria. Conclusions The nuclear co-expression of Piwil2/Piwil4 indicated that patients with HCC had a worse prognostic phenotype. The molecular chaperone Piwil2/Piwil4 seems promising as a molecular marker for prognosis judgment; a single marker (Piwil2/Piwil4) cannot be used for prognosis judgment.
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Affiliation(s)
- Guangping Zeng
- Department of Urology, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Key Laboratory of Pediatrics in Chongqing, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing 400014, China
| | - Deying Zhang
- Department of Urology, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Key Laboratory of Pediatrics in Chongqing, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing 400014, China
| | - Xing Liu
- Department of Urology, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Key Laboratory of Pediatrics in Chongqing, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing 400014, China
| | - Qing Kang
- Department of Urology, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Key Laboratory of Pediatrics in Chongqing, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing 400014, China
| | - Yiyao Fu
- Department of Urology, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Key Laboratory of Pediatrics in Chongqing, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing 400014, China
| | - Bo Tang
- Department of Urology, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Key Laboratory of Pediatrics in Chongqing, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing 400014, China
| | - Wenhao Guo
- Department of Urology, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Key Laboratory of Pediatrics in Chongqing, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing 400014, China
| | - Yuanyuan Zhang
- Wake Forest Institute for Regenerative Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27103, USA
| | - Guanghui Wei
- Department of Urology, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Key Laboratory of Pediatrics in Chongqing, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing 400014, China
| | - Dawei He
- Department of Urology, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Key Laboratory of Pediatrics in Chongqing, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing 400014, China
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Ernst C, Odom DT, Kutter C. The emergence of piRNAs against transposon invasion to preserve mammalian genome integrity. Nat Commun 2017; 8:1411. [PMID: 29127279 PMCID: PMC5681665 DOI: 10.1038/s41467-017-01049-7] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/14/2017] [Indexed: 01/09/2023] Open
Abstract
Transposable elements (TEs) contribute to the large amount of repetitive sequences in mammalian genomes and have been linked to species-specific genome innovations by rewiring regulatory circuitries. However, organisms need to restrict TE activity to ensure genome integrity, especially in germline cells to protect the transmission of genetic information to the next generation. This review features our current understandings of mammalian PIWI-interacting RNAs (piRNAs) and their role in TE regulation in spermatogenesis. Here we discuss functional implication and explore additional molecular mechanisms that inhibit transposon activity and altogether illustrate the paradoxical arms race between genome evolution and stability.
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Affiliation(s)
- Christina Ernst
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Duncan T Odom
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Claudia Kutter
- Department of Microbiology, Tumor and Cell Biology, Science for Life Laboratory, Karolinska Institute, Nobels väg 16, 171 77, Stockholm, Sweden.
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Abstract
Evolution of bacteria and archaea involves an incessant arms race against an enormous diversity of genetic parasites. Accordingly, a substantial fraction of the genes in most bacteria and archaea are dedicated to antiparasite defense. The functions of these defense systems follow several distinct strategies, including innate immunity; adaptive immunity; and dormancy induction, or programmed cell death. Recent comparative genomic studies taking advantage of the expanding database of microbial genomes and metagenomes, combined with direct experiments, resulted in the discovery of several previously unknown defense systems, including innate immunity centered on Argonaute proteins, bacteriophage exclusion, and new types of CRISPR-Cas systems of adaptive immunity. Some general principles of function and evolution of defense systems are starting to crystallize, in particular, extensive gain and loss of defense genes during the evolution of prokaryotes; formation of genomic defense islands; evolutionary connections between mobile genetic elements and defense, whereby genes of mobile elements are repeatedly recruited for defense functions; the partially selfish and addictive behavior of the defense systems; and coupling between immunity and dormancy induction/programmed cell death.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894;
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894;
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894;
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Ma X, Ji A, Zhang Z, Yang D, Liang S, Wang Y, Qin Z. Piwi1 is essential for gametogenesis in mollusk Chlamys farreri. PeerJ 2017; 5:e3412. [PMID: 28652931 PMCID: PMC5483327 DOI: 10.7717/peerj.3412] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/14/2017] [Indexed: 11/23/2022] Open
Abstract
Piwi (P-element induced wimpy testis) is an important gene involved in stem cell maintenance and gametogenesis in vertebrates. However, in most invertebrates, especially mollusks, the function of Piwi during gametogenesis remains largely unclear. To further understand the function of Piwi during gametogenesis, full-length cDNA of Piwi1 from scallop Chlamys farreri (Cf-Piwi1) was characterized, which consisted of a 2,637 bp open reading frame encoding an 878-amino acid protein. Cf-Piwi1 mRNA was mainly localized in the spermatogonia, spermatocytes, oogonia, oocytes of early development and intra-gonadal somatic cells. Additionally, the knockdown of Cf-Piwi1 by injection of Cf-Piwi1-dsRNA (double-stranded RNA) into scallop adductor led to a loss of germ cells in C. farreri gonads. Apoptosis was observed mainly in spermatocytes and oocytes of early development, as well as in a small number of spermatogonia and oogonia. Our findings indicate that Cf-Piwi1 is essential for gametogenesis in the scallop C. farreri.
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Affiliation(s)
- Xiaoshi Ma
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Ocean University of China, Qingdao, China
| | - Aichang Ji
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Ocean University of China, Qingdao, China
| | - Zhifeng Zhang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Ocean University of China, Qingdao, China
| | - Dandan Yang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Ocean University of China, Qingdao, China
| | - Shaoshuai Liang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Ocean University of China, Qingdao, China
| | - Yuhan Wang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Ocean University of China, Qingdao, China
| | - Zhenkui Qin
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Ocean University of China, Qingdao, China
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HILI destabilizes microtubules by suppressing phosphorylation and Gigaxonin-mediated degradation of TBCB. Sci Rep 2017; 7:46376. [PMID: 28393858 PMCID: PMC5385498 DOI: 10.1038/srep46376] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/15/2017] [Indexed: 02/05/2023] Open
Abstract
Human PIWIL2, aka HILI, is a member of PIWI protein family and overexpresses in various tumors. However, the underlying mechanisms of HILI in tumorigenesis remain largely unknown. TBCB has a critical role in regulating microtubule dynamics and is overexpressed in many cancers. Here we report that HILI inhibits Gigaxonin-mediated TBCB ubiquitination and degradation by interacting with TBCB, promoting the binding between HSP90 and TBCB, and suppressing the interaction between Gigaxonin and TBCB. Meanwhile, HILI can also reduce phosphorylation level of TBCB induced by PAK1. Our results showed that HILI suppresses microtubule polymerization and promotes cell proliferation, migration and invasion via TBCB for the first time, revealing a novel mechanism for HILI in tumorigenesis.
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Koonin EV. Evolution of RNA- and DNA-guided antivirus defense systems in prokaryotes and eukaryotes: common ancestry vs convergence. Biol Direct 2017; 12:5. [PMID: 28187792 PMCID: PMC5303251 DOI: 10.1186/s13062-017-0177-2] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 02/06/2017] [Indexed: 12/18/2022] Open
Abstract
Abstract Complementarity between nucleic acid molecules is central to biological information transfer processes. Apart from the basal processes of replication, transcription and translation, complementarity is also employed by multiple defense and regulatory systems. All cellular life forms possess defense systems against viruses and mobile genetic elements, and in most of them some of the defense mechanisms involve small guide RNAs or DNAs that recognize parasite genomes and trigger their inactivation. The nucleic acid-guided defense systems include prokaryotic Argonaute (pAgo)-centered innate immunity and CRISPR-Cas adaptive immunity as well as diverse branches of RNA interference (RNAi) in eukaryotes. The archaeal pAgo machinery is the direct ancestor of eukaryotic RNAi that, however, acquired additional components, such as Dicer, and enormously diversified through multiple duplications. In contrast, eukaryotes lack any heritage of the CRISPR-Cas systems, conceivably, due to the cellular toxicity of some Cas proteins that would get activated as a result of operon disruption in eukaryotes. The adaptive immunity function in eukaryotes is taken over partly by the PIWI RNA branch of RNAi and partly by protein-based immunity. In this review, I briefly discuss the interplay between homology and analogy in the evolution of RNA- and DNA-guided immunity, and attempt to formulate some general evolutionary principles for this ancient class of defense systems. Reviewers This article was reviewed by Mikhail Gelfand and Bojan Zagrovic.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA.
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Phosphate-binding pocket in Dicer-2 PAZ domain for high-fidelity siRNA production. Proc Natl Acad Sci U S A 2016; 113:14031-14036. [PMID: 27872309 DOI: 10.1073/pnas.1612393113] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The enzyme Dicer produces small silencing RNAs such as micro-RNAs (miRNAs) and small interfering RNAs (siRNAs). In Drosophila, Dicer-1 produces ∼22-24-nt miRNAs from pre-miRNAs, whereas Dicer-2 makes 21-nt siRNAs from long double-stranded RNAs (dsRNAs). How Dicer-2 precisely makes 21-nt siRNAs with a remarkably high fidelity is unknown. Here we report that recognition of the 5'-monophosphate of a long dsRNA substrate by a phosphate-binding pocket in the Dicer-2 PAZ (Piwi, Argonaute, and Zwille/Pinhead) domain is crucial for the length fidelity, but not the efficiency, in 21-nt siRNA production. Loss of the length fidelity, meaning increased length heterogeneity of siRNAs, caused by point mutations in the phosphate-binding pocket of the Dicer-2 PAZ domain decreased RNA silencing activity in vivo, showing the importance of the high fidelity to make 21-nt siRNAs. We propose that the 5'-monophosphate of a long dsRNA substrate is anchored by the phosphate-binding pocket in the Dicer-2 PAZ domain and the distance between the pocket and the RNA cleavage active site in the RNaseIII domain corresponds to the 21-nt pitch in the A-form duplex of a long dsRNA substrate, resulting in high-fidelity 21-nt siRNA production. This study sheds light on the molecular mechanism by which Dicer-2 produces 21-nt siRNAs with a remarkably high fidelity for efficient RNA silencing.
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van Houte S, Buckling A, Westra ER. Evolutionary Ecology of Prokaryotic Immune Mechanisms. Microbiol Mol Biol Rev 2016; 80:745-63. [PMID: 27412881 PMCID: PMC4981670 DOI: 10.1128/mmbr.00011-16] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Bacteria have a range of distinct immune strategies that provide protection against bacteriophage (phage) infections. While much has been learned about the mechanism of action of these defense strategies, it is less clear why such diversity in defense strategies has evolved. In this review, we discuss the short- and long-term costs and benefits of the different resistance strategies and, hence, the ecological conditions that are likely to favor the different strategies alone and in combination. Finally, we discuss some of the broader consequences, beyond resistance to phage and other genetic elements, resulting from the operation of different immune strategies.
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Affiliation(s)
- Stineke van Houte
- ESI and CEC, Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Angus Buckling
- ESI and CEC, Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Edze R Westra
- ESI and CEC, Department of Biosciences, University of Exeter, Exeter, United Kingdom
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PIWIL1 destabilizes microtubule by suppressing phosphorylation at Ser16 and RLIM-mediated degradation of Stathmin1. Oncotarget 2016; 6:27794-804. [PMID: 26317901 PMCID: PMC4695026 DOI: 10.18632/oncotarget.4533] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 07/03/2015] [Indexed: 02/05/2023] Open
Abstract
Human PIWIL1, alias HIWI, is a member of Piwi protein family and expressed in various tumors. However, the underlying mechanism of PIWIL1 in tumorigenesis remains largely unknown. Stathmin1 is a cytosolic phosphoprotein which has a critical role in regulating microtubule dynamics and is overexpressed in many cancers. Here we report that PIWIL1 can directly bind to Stathmin1. Meanwhile, PIWIL1 can up-regulate the expression of Stathmin1 through inhibiting ubiquitin-mediated degradation induced by an E3 ubiquitin ligase RLIM. Furthermore, PIWIL1 can also reduce phosphorylation level of Stathmin1 at Ser-16 through inhibiting the interaction between CaMKII and Stathmin1. Our results showed that PIWIL1 suppresses microtubule polymerization, and promotes cell proliferation and migration via Stathmin1 for the first time. Our study reveals a novel mechanism for PIWIL1 in tumorigenesis.
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Abstract
Short interfering RNAs (siRNAs) are as effective at targeting and silencing genes by RNA interference (RNAi) as long double-stranded RNAs (dsRNAs). siRNAs are widely used for assessing gene function in cultured mammalian cells or early developing vertebrate embryos. siRNAs are also promising reagents for developing gene-specific therapeutics. Specifically, the inhibition of HIV-1 replication is particularly well-suited to RNAi, as several stages of the viral life cycle and many viral and cellular genes can be targeted. The future success of this approach will depend on recent advances in siRNA-based silencing technologies.
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Affiliation(s)
- Hiroshi Takaku
- Department of Life & Environmental Sciences and High Technology Research Center, Chiba Institute of Technology, Chiba, Japan.
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Zhou Y, Zhong H, Xiao J, Yan J, Luo Y, Gan X, Yu F. Identification and comparative analysis of piRNAs in ovary and testis of Nile tilapia (Oreochromis niloticus). Genes Genomics 2016. [DOI: 10.1007/s13258-016-0400-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Zhou YR, Li LY, Li JM, Sun ZT, Xie L, Chen JP. ARGONAUTE SUBFAMILY GENES IN THE SMALL BROWN PLANTHOPPER, Laodelphax striatellus (HEMIPTERA: DELPHACIDAE). ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2016; 91:37-51. [PMID: 26446351 DOI: 10.1002/arch.21307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Argonaute (AGO) proteins are essential catalytic components of the RNA-induced silencing complex and play central roles in RNA interference. Using a combination of bioinformatics and rapid amplification of cDNA ends (RACE) methods, putative AGO subfamily members, ls-AGO1 and ls-AGO2, were cloned and characterized from the small brown planthopper, Laodelphax striatellus. The open reading frame (ORF) of ls-AGO1 is 2,820 bp long, encoding a putative protein of 939 amino acid residues, and ls-AGO2 contains an ORF of 2,490 bp, encoding 829 amino acid residues. The expected conserved PAZ and PIWI domains, and the conserved Asp-Asp-His (DDH) catalytic triad motif in the PIWI domain were observed in both ls-AGO1 and ls-AGO2. Reverse transcription-qPCR (RT-qPCR) results showed that both ls-AGO1 and ls-AGO2 were expressed in all developmental stages of L. striatellus with highest mRNA abundance in eggs. Expression of ls-AGO1 and ls-AGO2 was significantly decreased in adult insects in response to acquisition of rice black-streaked dwarf virus by second instar nymphs. mRNA expression of ls-AGO1 was significantly downregulated in response to low and high temperatures, but expression of ls-AGO2 was only affected by low temperature. ls-AGO1 and ls-AGO2 were initially downregulated when insects were transferred from rice to maize and to the wild grass Brachypodium distachyon, but expression showed partial or complete recovery 7 days after transfer. These results document that AGO subfamily members of L. striatellus are ubiquitously expressed at different developmental stages and respond to various stresses. Thus, AGO subfamily may act in regulating the stress-response of L. striatellus by controlling related gene expression.
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Affiliation(s)
- Yan-Ru Zhou
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, China
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Biotechnology in Plant Protection of MOA and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Lin-Ying Li
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Jun-Min Li
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Biotechnology in Plant Protection of MOA and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zong-Tao Sun
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Biotechnology in Plant Protection of MOA and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Li Xie
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Biotechnology in Plant Protection of MOA and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jian-Ping Chen
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Biotechnology in Plant Protection of MOA and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Stalker L, Russell SJ, Co C, Foster RA, LaMarre J. PIWIL1 Is Expressed in the Canine Testis, Increases with Sexual Maturity, and Binds Small RNAs. Biol Reprod 2015; 94:17. [PMID: 26658707 DOI: 10.1095/biolreprod.115.131854] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 12/02/2015] [Indexed: 01/23/2023] Open
Abstract
Spermatogenesis is a highly regulated process leading to the development of functional spermatozoa through meiotic division and subsequent maturation. Recent studies have suggested that a novel class of Argonaute proteins, known as the PIWI clade, plays important roles in multiple stages of spermatogenesis. PIWI proteins bind specific small noncoding RNAs, called PIWI-interacting RNAs (piRNAs). These piRNAs guide the PIWI-piRNA complex to retrotransposon targets that become expressed during meiosis. Retrotransposons are subsequently silenced, either through PIWI "slicer" activity or through PIWI-directed methylation of the retrotransposon locus. Most mammalian studies have employed mouse models where sterility follows PIWI inactivation. The goal of this study was to characterize canine PIWIL1 to determine whether expression pattern and functional characteristics support a similar function in that species. Canine PIWIL1 cDNA is a 2.6-kb transcript that encodes an 861-amino acid protein showing high homology to other mammalian PIWIL1 proteins and containing features consistent with PIWI family members (PAZ, PIWI domains). Analysis of PIWIL1 protein and transcript levels revealed that PIWIL1 expression is limited to the testes and is associated with sexual maturity, with mature dogs showing higher levels of PIWIL1 expression. Immunohistochemistry demonstrated expression primarily in seminiferous tubules and confirmed higher levels of PIWIL1 in mature dogs. Functional characterization by RNA immunoprecipitation demonstrated that canine PIWIL1 binds short RNAs consistent in size with piRNAs (27-32 nucleotides). Together, these studies represent the first characterization of a PIWI protein in the dog and suggest that it is a functional piRNA-binding protein most highly expressed in the mature testes.
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Affiliation(s)
- Leanne Stalker
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Stewart J Russell
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Carmon Co
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Robert A Foster
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Jonathan LaMarre
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
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Luangpraseuth-Prosper A, Lesueur E, Jouneau L, Pailhoux E, Cotinot C, Mandon-Pépin B. TOPAZ1, a germ cell specific factor, is essential for male meiotic progression. Dev Biol 2015; 406:158-71. [PMID: 26358182 DOI: 10.1016/j.ydbio.2015.09.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 09/01/2015] [Accepted: 09/04/2015] [Indexed: 11/19/2022]
Abstract
Topaz1 (Testis and Ovary-specific PAZ domain gene 1) is a germ cell specific gene highly conserved in vertebrates. The putative protein TOPAZ1 contains a PAZ domain, specifically found in PIWI, Argonaute and Zwille proteins. Consequently, Topaz1 is supposed to have a role during gametogenesis and may be involved in the piRNA pathway and contribute to silencing of transposable elements and maintenance of genome integrity. Here we report Topaz1 inactivation in mouse. Female fertility was not affected, but male sterility appeared exclusively in homozygous mutants in accordance with the high expression of Topaz1 in male germ cells. Pachytene Topaz1--deficient spermatocytes progress through meiosis without either derepression of retrotransposons or MSCI dysfunction, but become arrested before the post-meiotic round spermatid stage with extensive apoptosis. Consequently, an absence of spermatids and spermatozoa was observed in Topaz1(-/-) testis. Histological analysis also revealed that disturbances of spermatogenesis take place between post natal days 15 and 20, during the first wave of male meiosis and before the generation of haploid germ cells. Transcriptomic analysis at these two stages showed that TOPAZ1 influences the expression of one hundred transcripts, most of which are up-regulated in mutant testis at post natal day 20. Our results also showed that 10% of these transcripts are long non-coding RNA. This suggests that a highly regulated balance of lncRNAs seems to be essential during spermatogenesis for induction of appropriate male gamete production.
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Affiliation(s)
| | - Elodie Lesueur
- INRA, UMR 1198 Biologie du Développement et Reproduction, F-78350 Jouy-en-Josas, France.
| | - Luc Jouneau
- INRA, UMR 1198 Biologie du Développement et Reproduction, F-78350 Jouy-en-Josas, France.
| | - Eric Pailhoux
- INRA, UMR 1198 Biologie du Développement et Reproduction, F-78350 Jouy-en-Josas, France.
| | - Corinne Cotinot
- INRA, UMR 1198 Biologie du Développement et Reproduction, F-78350 Jouy-en-Josas, France.
| | - Béatrice Mandon-Pépin
- INRA, UMR 1198 Biologie du Développement et Reproduction, F-78350 Jouy-en-Josas, France.
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Wickstrom E. DNA and RNA derivatives to optimize distribution and delivery. Adv Drug Deliv Rev 2015; 87:25-34. [PMID: 25912659 DOI: 10.1016/j.addr.2015.04.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 04/13/2015] [Accepted: 04/15/2015] [Indexed: 12/27/2022]
Abstract
Synthetic, complementary DNA single strands and short interfering RNA double strands have been found to inhibit the expression of animal, plant, and viral genes in cells, animals, and patients, in a dose dependent and sequence specific manner. DNAs and RNAs, however, are readily digested in biological systems. Hence, chemists are obliged to design and synthesize nuclease-resistant analogs of normal DNA (Fig. 1).
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Wang HL, Chen BB, Cao XG, Wang J, Hu XF, Mu XQ, Chen XB. The clinical significances of the abnormal expressions of Piwil1 and Piwil2 in colonic adenoma and adenocarcinoma. Onco Targets Ther 2015; 8:1259-64. [PMID: 26064060 PMCID: PMC4455855 DOI: 10.2147/ott.s77003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Objective The objective of the present investigation was to study the clinical significances of the abnormal expressions of Piwil1 and Piwil2 protein in colonic adenoma and adenocarcinoma. Methods This study had applied immunohistochemical method to detect 45 cases of tissues adjacent to carcinoma (distance to cancerous tissue was above 5 cm), 41 cases of colonic adenoma and 92 cases of colon cancer tissues, and their Piwil1 and Piwil2 protein expression levels. Analysis The correlation of both expression and its relationship with clinicopathological features of colon cancer was analyzed. Results Positive expression rates of Piwil1 in tissues adjacent to carcinoma, colonic adenoma, and colon cancer were 11.1% (5/45), 53.7% (22/41), and 80.4% (74/92), respectively; the expression rates increased, and the comparisons between each two groups were statistically significant (P<0.05). In each group, the positive expression rates of Piwil2 were 24.4% (11/45 cases), 75.6% (31/41 cases), and 92.4% (85/92 cases); expression rates increased, and the comparisons between each two groups were statistically significant (P<0.05). Piwil1 expression and the correlation of the degree of differentiation, TNM stage, and lymph node metastasis were statistically significant (P<0.05). Piwil2 expression and the correlation of the degree of differentiation, tumor node metastasis (TNM) stage, and lymph node metastasis had no statistical significance (P>0.05). In colon cancer tissue, Piwil1 and Piwil2 expressions were positively correlated (r=0.262, P<0.05). Conclusion The results showed that the abnormal expression of Piwil1 and Piwil2 might play an important role in the process of colon cancer development.
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Affiliation(s)
- Hai-Ling Wang
- The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, People's Republic of China
| | - Bei-Bei Chen
- The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, People's Republic of China
| | - Xin-Guang Cao
- The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, People's Republic of China
| | - Jin Wang
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
| | - Xiu-Feng Hu
- The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, People's Republic of China
| | - Xiao-Qian Mu
- The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, People's Republic of China
| | - Xiao-Bing Chen
- The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, People's Republic of China
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Taubert H, Wach S, Jung R, Pugia M, Keck B, Bertz S, Nolte E, Stoehr R, Lehmann J, Ohlmann CH, Stöckle M, Wullich B, Hartmann A. Piwil 2 expression is correlated with disease-specific and progression-free survival of chemotherapy-treated bladder cancer patients. Mol Med 2015; 21:371-80. [PMID: 25998509 DOI: 10.2119/molmed.2014.00250] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 05/13/2015] [Indexed: 12/21/2022] Open
Abstract
Piwi-like 2 (Piwil 2) belongs to the family of Argonaute genes/proteins. The expression of Piwil 2 is associated with stem cells. A role in tumorigenesis and/or tumor progression is proposed for different cancers but not yet for bladder cancer (BCa). We investigated the Piwil 2 expression by immunohistochemistry in a cohort of 202 BCa patients treated by cystectomy and adjuvant chemotherapy. The association between Piwil 2 expression and disease-specific (DSS) or progression-free survival (PFS) was calculated using Kaplan Meier analyses and univariate/multivariate Cox's regression hazard models.In a multivariate Cox's regression, Piwil 2 expression, either in the cytoplasm or the nucleus, was significantly associated with DSS and PFS. A weak cytoplasmic staining pattern was associated with poor DSS and tumor progression (RR=2.7; P=0.004 and RR=2.4; P=0.027). Likewise,, absent nuclear Piwil 2 immunoreactivity was associated with poor DSS and tumor progression (RR=2.3; P=0.023 and RR=2.2; P=0.022). BCa patients whose tumors exhibited a combination of weak cytoplasmic and absent nuclear immunoreactivity had a 6-fold increased risk of tumor-related death (P=0.005) compared to patients with strong expression. Considering only patients with high grade G3 tumors, a 7.8-fold risk of tumor-associated death and a 3.6-fold risk of tumor progression were detected independently of the histologic tumor subtype or the chemotherapy regimen. In summary, a combination of weak cytoplasmic and absent nuclear expression of Piwil 2 is significantly associated with an increased risk of DSS and tumor progression. This implicates that Piwil 2 could be a valuable prognostic marker for high-risk BCa patients.
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Affiliation(s)
- Helge Taubert
- Department of Urology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Sven Wach
- Department of Urology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Rudolf Jung
- Department of Pathology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Michael Pugia
- Siemens Healthcare Diagnostics, Elkhart, Indiana, USA
| | - Bastian Keck
- Department of Urology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Simone Bertz
- Department of Pathology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Elke Nolte
- Department of Urology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Robert Stoehr
- Department of Pathology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Jan Lehmann
- Urologische Gemeinschaftspraxis, Prüner Gang and Department of Urology, Städtisches Krankenhaus, Kiel, Germany
| | | | - Michael Stöckle
- Department of Urology, Saarland University, Homburg, Germany
| | - Bernd Wullich
- Department of Urology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Arndt Hartmann
- Department of Pathology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
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