1
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Ashley CN, Broni E, Miller WA. ADAR Family Proteins: A Structural Review. Curr Issues Mol Biol 2024; 46:3919-3945. [PMID: 38785511 PMCID: PMC11120146 DOI: 10.3390/cimb46050243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
This review aims to highlight the structures of ADAR proteins that have been crucial in the discernment of their functions and are relevant to future therapeutic development. ADAR proteins can correct or diversify genetic information, underscoring their pivotal contribution to protein diversity and the sophistication of neuronal networks. ADAR proteins have numerous functions in RNA editing independent roles and through the mechanisms of A-I RNA editing that continue to be revealed. Provided is a detailed examination of the ADAR family members-ADAR1, ADAR2, and ADAR3-each characterized by distinct isoforms that offer both structural diversity and functional variability, significantly affecting RNA editing mechanisms and exhibiting tissue-specific regulatory patterns, highlighting their shared features, such as double-stranded RNA binding domains (dsRBD) and a catalytic deaminase domain (CDD). Moreover, it explores ADARs' extensive roles in immunity, RNA interference, and disease modulation, demonstrating their ambivalent nature in both the advancement and inhibition of diseases. Through this comprehensive analysis, the review seeks to underline the potential of targeting ADAR proteins in therapeutic strategies, urging continued investigation into their biological mechanisms and health implications.
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Affiliation(s)
- Carolyn N. Ashley
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA; (C.N.A.); (E.B.)
| | - Emmanuel Broni
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA; (C.N.A.); (E.B.)
| | - Whelton A. Miller
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA; (C.N.A.); (E.B.)
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
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2
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Juhlin CC. On the Chopping Block: Overview of DICER1 Mutations in Endocrine and Neuroendocrine Neoplasms. Surg Pathol Clin 2023; 16:107-118. [PMID: 36739158 DOI: 10.1016/j.path.2022.09.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Mutational inactivation of the DICER1 gene causes aberrant micro-RNA maturation, which in turn may have consequences for the posttranscriptional regulation of gene expression, thereby contributing to tumor formation in various organs. Germline DICER1 mutations cause DICER1 syndrome, a pleiotropic condition with an increased risk of various neoplastic conditions in the pleura, ovaries, thyroid, pituitary, pineal gland, and mesenchymal tissues. Somatic DICER1 mutations are also frequently observed in a wide variety of solid tumors, thereby highlighting the importance of this gene in tumor development. In this review, the importance of DICER1 inactivation in endocrine tumors is discussed.
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3
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Torrez RM, Ohi MD, Garner AL. Structural Insights into the Advances and Mechanistic Understanding of Human Dicer. Biochemistry 2023; 62:1-16. [PMID: 36534787 PMCID: PMC11467861 DOI: 10.1021/acs.biochem.2c00570] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The RNase III endoribonuclease Dicer was discovered to be associated with cleavage of double-stranded RNA in 2001. Since then, many advances in our understanding of Dicer function have revealed that the enzyme plays a major role not only in microRNA biology but also in multiple RNA interference-related pathways. Yet, there is still much to be learned regarding Dicer structure-function in relation to how Dicer and Dicer-like enzymes initiate their cleavage reaction and release the desired RNA product. This Perspective describes the latest advances in Dicer structural studies, expands on what we have learned from this data, and outlines key gaps in knowledge that remain to be addressed. More specifically, we focus on human Dicer and highlight the intermediate processing steps where there is a lack of structural data to understand how the enzyme traverses from pre-cleavage to cleavage-competent states. Understanding these details is necessary to model Dicer's function as well as develop more specific microRNA-targeted therapeutics for the treatment of human diseases.
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Affiliation(s)
- Rachel M. Torrez
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States; Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Melanie D. Ohi
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Amanda L. Garner
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
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4
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Ghossein CA, Dogan S, Farhat N, Landa I, Xu B. Expanding the spectrum of thyroid carcinoma with somatic DICER1 mutation: a survey of 829 thyroid carcinomas using MSK-IMPACT next-generation sequencing platform. Virchows Arch 2022; 480:293-302. [PMID: 34580763 PMCID: PMC10126990 DOI: 10.1007/s00428-021-03212-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 02/06/2023]
Abstract
DICER1 gene encodes an RNaseIII endoribonuclease essential for the cleavage of pre-microRNA to mature microRNA. Germline DICER1 mutation results in DICER syndrome, a cancer predisposition syndrome which manifests in the thyroid gland as early-onset multinodular goiter and increased risk for differentiated thyroid carcinoma. Recently, somatic DICER1 mutations were described in various thyroid neoplasms, including follicular adenoma, papillary thyroid carcinoma, follicular carcinoma, and poorly differentiated thyroid carcinoma. In this study, we identified and described 14 cases (1.7%) with somatic DICER1 mutations from a cohort of 829 patients with thyroid follicular cell-derived thyroid carcinomas which were sequenced using MSK-IMPACT targeted next-generation sequencing platform. We expanded the histologic spectrum of thyroid carcinomas with somatic DICER1 mutations to include Hurthle cell carcinoma, high-grade differentiated thyroid carcinoma, and anaplastic thyroid carcinoma. All patients were adults with a median age of diagnosis of 59 years (range: 22-82). Although rare, a subset of thyroid cancers, including the aggressive subtypes, display somatic DICER1 mutations, some of which have oncogenic potential.
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Affiliation(s)
- Charles A Ghossein
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Snjezana Dogan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Nada Farhat
- Department of Pathology, New York Eye and Ear Infirmary, Mount Sinai Hospital, New York, NY, USA
| | - Iñigo Landa
- Department of Medicine, Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital, and Harvard Medical School, Boston, MD, USA
| | - Bin Xu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
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5
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Loffer A, Singh J, Fukudome A, Mishra V, Wang F, Pikaard CS. A DCL3 dicing code within Pol IV-RDR2 transcripts diversifies the siRNA pool guiding RNA-directed DNA methylation. eLife 2022; 11:e73260. [PMID: 35098919 PMCID: PMC8846587 DOI: 10.7554/elife.73260] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/28/2022] [Indexed: 11/26/2022] Open
Abstract
In plants, selfish genetic elements, including retrotransposons and DNA viruses, are transcriptionally silenced by RNA-directed DNA methylation. Guiding the process are short interfering RNAs (siRNAs) cut by DICER-LIKE 3 (DCL3) from double-stranded precursors of ~30 bp that are synthesized by NUCLEAR RNA POLYMERASE IV (Pol IV) and RNA-DEPENDENT RNA POLYMERASE 2 (RDR2). We show that Pol IV's choice of initiating nucleotide, RDR2's initiation 1-2 nt internal to Pol IV transcript ends and RDR2's terminal transferase activity collectively yield a code that influences which precursor end is diced and whether 24 or 23 nt siRNAs are produced. By diversifying the size, sequence, and strand specificity of siRNAs derived from a given precursor, alternative patterns of DCL3 dicing allow for maximal siRNA coverage at methylated target loci.
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Affiliation(s)
- Andrew Loffer
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University BloomingtonBloomingtonUnited States
| | - Jasleen Singh
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University BloomingtonBloomingtonUnited States
| | - Akihito Fukudome
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University BloomingtonBloomingtonUnited States
- Howard Hughes Medical Institute, Indiana UniversityBloomingtonUnited States
| | - Vibhor Mishra
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University BloomingtonBloomingtonUnited States
- Howard Hughes Medical Institute, Indiana UniversityBloomingtonUnited States
| | - Feng Wang
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University BloomingtonBloomingtonUnited States
- Howard Hughes Medical Institute, Indiana UniversityBloomingtonUnited States
| | - Craig S Pikaard
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University BloomingtonBloomingtonUnited States
- Howard Hughes Medical Institute, Indiana UniversityBloomingtonUnited States
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6
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Leitão AL, Enguita FJ. A Structural View of miRNA Biogenesis and Function. Noncoding RNA 2022; 8:ncrna8010010. [PMID: 35202084 PMCID: PMC8874510 DOI: 10.3390/ncrna8010010] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 12/16/2022] Open
Abstract
Micro-RNAs (miRNAs) are a class of non-coding RNAs (ncRNAs) that act as post-transcriptional regulators of gene expression. Since their discovery in 1993, they have been the subject of deep study due to their involvement in many important biological processes. Compared with other ncRNAs, miRNAs are generated from devoted transcriptional units which are processed by a specific set of endonucleases. The contribution of structural biology methods for understanding miRNA biogenesis and function has been essential for the dissection of their roles in cell biology and human disease. In this review, we summarize the application of structural biology for the characterization of the molecular players involved in miRNA biogenesis (processors and effectors), starting from the X-ray crystallography methods to the more recent cryo-electron microscopy protocols.
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Affiliation(s)
- Ana Lúcia Leitão
- MEtRICs, Department of Sciences and Technology of Biomass, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal;
| | - Francisco J. Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
- Correspondence:
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7
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Paturi S, Deshmukh MV. A Glimpse of "Dicer Biology" Through the Structural and Functional Perspective. Front Mol Biosci 2021; 8:643657. [PMID: 34026825 PMCID: PMC8138440 DOI: 10.3389/fmolb.2021.643657] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/07/2021] [Indexed: 01/05/2023] Open
Abstract
The RNA interference pathway (RNAi) is executed by two core enzymes, Dicer and Argonaute, for accomplishing a tailored transcriptional and post-transcriptional gene regulation. Dicer, an RNase III enzyme, initiates the RNAi pathway, plays a pivotal role in fighting infection against pathogens, and acts as a housekeeping enzyme for cellular homeostasis. Here, we review structure-based functional insights of Dicer and its domains present in a diverse group of organisms. Although Dicer and its domains are evolutionarily conserved from microsporidian parasites to humans, recent cryo-electron microscopy structures of Homo sapiens Dicer and Drosophila melanogaster Dicer-2 suggest characteristic variations in the mechanism of the dsRNA substrate recognition. Interestingly, the necessity for more than one functionally distinct Dicer paralogs in insects and plants compared with a single Dicer in other eukaryotic life forms implies Dicer’s role in the interplay of RNAi and other defense mechanisms. Based on the structural and mechanistic information obtained during the last decade, we aim to highlight the significance of key Dicer domains that are crucial to Dicer specific recognition and precise cleavage of dsRNA substrates. Further, the role of Dicer in the formation of Argonaute-based RNA-induced silencing complex (RISC) assembly formation, Dicer’s ability to regulate a complex protein interaction network, and its role in other cellular processes, as well as its therapeutic potentials, are emphasized.
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Affiliation(s)
- Sneha Paturi
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Hyderabad, India
| | - Mandar V Deshmukh
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Hyderabad, India
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8
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Uebbing S, Kreiß M, Scholl F, Häfner AK, Sürün D, Garscha U, Werz O, Basavarajappa D, Samuelsson B, Rådmark O, Suess B, Steinhilber D. Modulation of microRNA processing by 5-lipoxygenase. FASEB J 2020; 35:e21193. [PMID: 33205517 DOI: 10.1096/fj.202002108r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/30/2020] [Accepted: 10/30/2020] [Indexed: 12/20/2022]
Abstract
The miRNA biogenesis is tightly regulated to avoid dysfunction and consequent disease development. Here, we describe modulation of miRNA processing as a novel noncanonical function of the 5-lipoxygenase (5-LO) enzyme in monocytic cells. In differentiated Mono Mac 6 (MM6) cells, we found an in situ interaction of 5-LO with Dicer, a key enzyme in miRNA biogenesis. RNA sequencing of small noncoding RNAs revealed a functional impact, knockout of 5-LO altered the expression profile of several miRNAs. Effects of 5-LO could be observed at two levels. qPCR analyses thus indicated that (a) 5-LO promotes the transcription of the evolutionarily conserved miR-99b/let-7e/miR-125a cluster and (b) the 5-LO-Dicer interaction downregulates the processing of pre-let-7e, resulting in an increase in miR-125a and miR-99b levels by 5-LO without concomitant changes in let-7e levels in differentiated MM6 cells. Our observations suggest that 5-LO regulates the miRNA profile by modulating the Dicer-mediated processing of distinct pre-miRNAs. 5-LO inhibits the formation of let-7e which is a well-known inducer of cell differentiation, but promotes the generation of miR-99b and miR-125a known to induce cell proliferation and the maintenance of leukemic stem cell functions.
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Affiliation(s)
- Stella Uebbing
- Department of Biology, Technical University, Darmstadt, Germany.,Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt/Main, Germany.,Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Marius Kreiß
- Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt/Main, Germany
| | - Friederike Scholl
- Department of Biology, Technical University, Darmstadt, Germany.,Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt/Main, Germany.,Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Ann-Kathrin Häfner
- Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt/Main, Germany
| | - Duran Sürün
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Ulrike Garscha
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University, Jena, Germany
| | - Oliver Werz
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University, Jena, Germany
| | - Devaraj Basavarajappa
- Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Bengt Samuelsson
- Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Olof Rådmark
- Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Beatrix Suess
- Department of Biology, Technical University, Darmstadt, Germany
| | - Dieter Steinhilber
- Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt/Main, Germany
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9
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Pokornowska M, Milewski MC, Ciechanowska K, Szczepańska A, Wojnicka M, Radogostowicz Z, Figlerowicz M, Kurzynska-Kokorniak A. The RNA-RNA base pairing potential of human Dicer and Ago2 proteins. Cell Mol Life Sci 2020; 77:3231-3244. [PMID: 31655860 PMCID: PMC7391396 DOI: 10.1007/s00018-019-03344-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 09/24/2019] [Accepted: 10/14/2019] [Indexed: 12/22/2022]
Abstract
The ribonuclease Dicer produces microRNAs (miRNAs) and small interfering RNAs that are handed over to Ago proteins to control gene expression by targeting complementary sequences within transcripts. Interestingly, a growing number of reports have demonstrated that the activity of Dicer may extend beyond the biogenesis of small regulatory RNAs. Among them, a report from our latest studies revealed that human Dicer facilitates base pairing of complementary sequences present in two nucleic acids, thus acting as a nucleic acid annealer. Accordingly, in this manuscript, we address how RNA structure influences the annealing activity of human Dicer. We show that Dicer supports hybridization between a small RNA and a complementary sequence of a longer RNA in vitro, even when both complementary sequences are trapped within secondary structures. Moreover, we show that under applied conditions, human Ago2, a core component of RNA-induced silencing complex, displays very limited annealing activity. Based on the available data from new-generation sequencing experiments regarding the RNA pool bound to Dicer in vivo, we show that multiple Dicer-binding sites within mRNAs also contain miRNA targets. Subsequently, we demonstrate in vitro that Dicer but not Ago2 can anneal miRNA to its target present within mRNA. We hypothesize that not all miRNA duplexes are handed over to Ago proteins. Instead, miRNA-Dicer complexes could target specific sequences within transcripts and either compete or cooperate for binding sites with miRNA-Ago complexes. Thus, not only Ago but also Dicer might be directly involved in the posttranscriptional control of gene expression.
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Affiliation(s)
- Maria Pokornowska
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Marek C Milewski
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Kinga Ciechanowska
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Agnieszka Szczepańska
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Marta Wojnicka
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Ziemowit Radogostowicz
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Marek Figlerowicz
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, 60-965, Poznan, Poland
| | - Anna Kurzynska-Kokorniak
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland.
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10
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Dicer up-regulation by inhibition of specific proteolysis in differentiating monocytic cells. Proc Natl Acad Sci U S A 2020; 117:8573-8583. [PMID: 32220961 PMCID: PMC7165444 DOI: 10.1073/pnas.1916249117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Dicer is a ribonuclease III enzyme in biosynthesis of miRNAs, regulators of gene expression involved in macrophage differentiation. We found a specific truncation of Dicer in monocytic cells resulting from apparently constitutive cleavage by a serine protease. Inhibition of this proteolytic truncation, which occurred during macrophage differentiation in presence of TLR ligands or prostaglandin E2, up-regulates full-length Dicer and promotes miR biosynthesis. Regulation of transcription of pri-miRNA is one mode to regulate biosynthesis of mature miRNA. Inhibition of constitutive proteolysis of Dicer, as described here, provides a second layer of regulation, at the level of miRNA processing. Our data provide insights to Dicer and miRNAs in macrophage polarization/differentiation, a key process in the innate immune response. Dicer is a ribonuclease III enzyme in biosynthesis of micro-RNAs (miRNAs). Here we describe a regulation of Dicer expression in monocytic cells, based on proteolysis. In undifferentiated Mono Mac 6 (MM6) cells, full-length Dicer was undetectable; only an ∼50-kDa fragment appeared in Western blots. However, when MM6 cells were treated with zymosan or LPS during differentiation with TGF-β and 1,25diOHvitD3, full-length Dicer became abundant together with varying amounts of ∼170- and ∼50-kDa Dicer fragments. Mass spectrometry identified the Dicer fragments and showed cleavage about 450 residues upstream from the C terminus. Also, PGE2 (prostaglandin E2) added to differentiating MM6 cells up-regulated full-length Dicer, through EP2/EP4 and cAMP. The TLR stimuli strongly induced miR-146a-5p, while PGE2 increased miR-99a-5p and miR-125a-5p, both implicated in down-regulation of TNFα. The Ser protease inhibitor AEBSF (4-[2-aminoethyl] benzene sulfonyl fluoride) up-regulated full-length Dicer, both in MM6 cells and in primary human blood monocytes, indicating a specific proteolytic degradation. However, AEBSF alone did not lead to a general increase in miR expression, indicating that additional mechanisms are required to increase miRNA biosynthesis. Finally, differentiation of monocytes to macrophages with M-CSF or GM-CSF strongly up-regulated full-length Dicer. Our results suggest that differentiation regimens, both in the MM6 cell line and of peripheral blood monocytes, inhibit an apparently constitutive Dicer proteolysis, allowing for increased formation of miRNAs.
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11
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Moura MO, Fausto AKS, Fanelli A, Guedes FADF, Silva TDF, Romanel E, Vaslin MFS. Genome-wide identification of the Dicer-like family in cotton and analysis of the DCL expression modulation in response to biotic stress in two contrasting commercial cultivars. BMC PLANT BIOLOGY 2019; 19:503. [PMID: 31729948 PMCID: PMC6858778 DOI: 10.1186/s12870-019-2112-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 10/31/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Dicer-like proteins (DCLs) are essential players in RNA-silencing mechanisms, acting in gene regulation via miRNAs and in antiviral protection in plants and have also been associated to other biotic and abiotic stresses. To the best of our knowledge, despite being identified in some crops, cotton DCLs haven't been characterized until now. In this work, we characterized the DCLs of three cotton species and analyzed their expression profiles during biotic stress. RESULTS As main results, 11 DCLs in the allotetraploid cotton Gossypium hirsutum, 7 and 6 in the diploid G. arboreum and G. raimondii, were identified, respectively. Among some DCLs duplications observed in these genomes, the presence of an extra DCL3 in the three cotton species were detected, which haven't been found in others eudicots. All the DCL types identified by in silico analysis in the allotetraploid cotton genome were able to generate transcripts, as observed by gene expression analysis in distinct tissues. Based on the importance of DCLs for plant defense against virus, responses of cotton DCLs to virus infection and/or herbivore attack using two commercial cotton cultivars (cv.), one susceptible (FM966) and another resistant (DO) to polerovirus CLRDV infection, were analyzed. Both cvs. Responded differently to virus infection. At the inoculation site, the resistant cv. showed strong induction of DCL2a and b, while the susceptible cv. showed a down-regulation of these genes, wherever DCL4 expression was highly induced. A time course of DCL expression in aerial parts far from inoculation site along infection showed that DCL2b and DCL4 were repressed 24 h after infection in the susceptible cotton. As CLRDV is aphid-transmitted, herbivore attack was also checked. Opposite expression pattern of DCL2a and b and DCL4 was observed for R and S cottons, showing that aphid feeding alone may induce DCL modulation. CONCLUSIONS Almost all the DCLs of the allotetraploide G. hirsutum cotton were found in their relative diploids. Duplications of DCL2 and DCL3 were found in the three species. All four classes of DCL responded to aphid attack and virus infection in G. hirsutum. DCLs initial responses against the virus itself and/or herbivore attack may be contributing towards virus resistance.
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Affiliation(s)
- Marianna O. Moura
- Departamento de Virologia, Instituto de Microbiologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-590 Brazil
| | - Anna Karoline S. Fausto
- Departamento de Virologia, Instituto de Microbiologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-590 Brazil
| | - Amanda Fanelli
- Departamento de Biotecnologia, Escola de Engenharia de Lorena/Universidade de São Paulo (EEL/USP), Lorena, SP 12602-810 Brazil
| | - Fernanda A. de F. Guedes
- Programa de Pós-graduação em Biotecnologia Vegetal, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-590 Brazil
| | - Tatiane da F. Silva
- Departamento de Biotecnologia, Escola de Engenharia de Lorena/Universidade de São Paulo (EEL/USP), Lorena, SP 12602-810 Brazil
| | - Elisson Romanel
- Departamento de Biotecnologia, Escola de Engenharia de Lorena/Universidade de São Paulo (EEL/USP), Lorena, SP 12602-810 Brazil
| | - Maite F. S. Vaslin
- Departamento de Virologia, Instituto de Microbiologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-590 Brazil
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12
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Kock L, Wu MK, Foulkes WD. Ten years of
DICER1
mutations: Provenance, distribution, and associated phenotypes. Hum Mutat 2019; 40:1939-1953. [DOI: 10.1002/humu.23877] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 07/08/2019] [Accepted: 07/19/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Leanne Kock
- Department of Human Genetics McGill University Montréal Québec Canada
- Cancer Axis Lady Davis Institute, Jewish General Hospital Montréal Québec Canada
| | - Mona K. Wu
- Department of Human Genetics McGill University Montréal Québec Canada
- Cancer Axis Lady Davis Institute, Jewish General Hospital Montréal Québec Canada
| | - William D. Foulkes
- Department of Human Genetics McGill University Montréal Québec Canada
- Cancer Axis Lady Davis Institute, Jewish General Hospital Montréal Québec Canada
- Cancer Research Program Research Institute of the McGill University Health Centre Montreal Quebec Canada
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13
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Vedanayagam J, Chatila WK, Aksoy BA, Majumdar S, Skanderup AJ, Demir E, Schultz N, Sander C, Lai EC. Cancer-associated mutations in DICER1 RNase IIIa and IIIb domains exert similar effects on miRNA biogenesis. Nat Commun 2019; 10:3682. [PMID: 31417090 PMCID: PMC6695490 DOI: 10.1038/s41467-019-11610-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 07/25/2019] [Indexed: 11/09/2022] Open
Abstract
Somatic mutations in the RNase IIIb domain of DICER1 arise in cancer and disrupt the cleavage of 5' pre-miRNA arms. Here, we characterize an unstudied, recurrent, mutation (S1344L) in the DICER1 RNase IIIa domain in tumors from The Cancer Genome Atlas (TCGA) project and MSK-IMPACT profiling. RNase IIIa/b hotspots are absent from most cancers, but are notably enriched in uterine cancers. Systematic analysis of TCGA small RNA datasets show that DICER1 RNase IIIa-S1344L tumors deplete 5p-miRNAs, analogous to RNase IIIb hotspot samples. Structural and evolutionary coupling analyses reveal constrained proximity of RNase IIIa-S1344 to the RNase IIIb catalytic site, rationalizing why mutation of this site phenocopies known hotspot alterations. Finally, examination of DICER1 hotspot endometrial tumors reveals derepression of specific miRNA target signatures. In summary, comprehensive analyses of DICER1 somatic mutations and small RNA data reveal a mechanistic aspect of pre-miRNA processing that manifests in specific cancer settings.
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Affiliation(s)
- Jeffrey Vedanayagam
- Department of Developmental Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Walid K Chatila
- Department of Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA.,Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, NY, 10065, USA.,Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Bülent Arman Aksoy
- Department of Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA.,Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, NY, 10065, USA.,Immunology and Microbiology Department, Medical University of South Carolina, Charleston, SC, 29412, USA
| | - Sonali Majumdar
- Department of Developmental Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Anders Jacobsen Skanderup
- Department of Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA.,Computational and Systems Biology, Agency for Science Technology and Research, Genome Institute of Singapore, 60 Biopolis Street, Singapore, 138672, Singapore
| | - Emek Demir
- Department of Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA.,Oregon Health and Science University, Computational Biology Program, Portland, OR, 97239, USA
| | - Nikolaus Schultz
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.,Departments of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Chris Sander
- Department of Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA. .,cBio Center, Dana-Farber Cancer Institute, Boston, MA, 02115, USA. .,Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.
| | - Eric C Lai
- Department of Developmental Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA. .,Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, NY, 10065, USA.
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14
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Garner AL, Lorenz DA, Sandoval J, Gallagher EE, Kerk SA, Kaur T, Menon A. Tetracyclines as Inhibitors of Pre-microRNA Maturation: A Disconnection between RNA Binding and Inhibition. ACS Med Chem Lett 2019; 10:816-821. [PMID: 31098005 DOI: 10.1021/acsmedchemlett.9b00091] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 04/22/2019] [Indexed: 12/21/2022] Open
Abstract
In a high-throughput screening campaign, we recently discovered the rRNA-binding tetracyclines, methacycline and meclocycline, as inhibitors of Dicer-mediated processing of microRNAs. Herein, we describe our biophysical and biochemical characterization of these compounds. Interestingly, although direct, albeit weak, binding to the pre-microRNA hairpins was observed, the inhibitory activity of these compounds was not due to RNA binding. Through additional biochemical and chemical studies, we revealed that metal chelation likely plays a principle role in their mechanism of inhibition. By exploring the activity of other known RNA-binding scaffolds, we identified additional disconnections between direct RNA interaction and inhibition of Dicer processing. Thus, the results presented within provide a valuable case study in the complexities of targeting RNA with small molecules, particularly with weak binding and potentially promiscuous scaffolds.
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15
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Lussi C, Sauter KS, Schweizer M. Homodimerisation-independent cleavage of dsRNA by a pestiviral nicking endoribonuclease. Sci Rep 2018; 8:8226. [PMID: 29844335 PMCID: PMC5974291 DOI: 10.1038/s41598-018-26557-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 05/09/2018] [Indexed: 12/12/2022] Open
Abstract
The glycoprotein Erns plays a central role in the biology of the pestivirus bovine viral diarrhea virus (BVDV). This soluble endonuclease mediates the escape from an interferon (IFN) response in the infected fetus, thereby permitting the establishment of persistent infection. Viral single-stranded (ss) and double-stranded (ds) RNA act as potent IFN inducing signals and we previously showed that Erns efficiently cleaves these substrates, thereby inhibiting an IFN response that is crucial for successful fetal infection. Considering that a large variety of RNases and DNases require dimerisation to cleave double-stranded substrates, the activity of Erns against dsRNA was postulated to depend on homodimer formation mediated by disulfide bonds involving residue Cys171. Here, we show that monomeric Erns is equally able to cleave dsRNA and to inhibit dsRNA-induced IFN synthesis as the wild-type form. Furthermore, both forms were able to degrade RNA within a DNA/RNA- as well as within a methylated RNA/RNA-hybrid, with the DNA and the methylated RNA strand being resistant to degradation. These results support our model that Erns acts as 'nicking endoribonuclease' degrading ssRNA within double-stranded substrates. This efficiently prevents the activation of IFN and helps to maintain a state of innate immunotolerance in persistently infected animals.
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Affiliation(s)
- Carmela Lussi
- Institute of Virology and Immunology, Laenggass-Str. 122, CH-3001, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Kay-Sara Sauter
- Institute of Virology and Immunology, Laenggass-Str. 122, CH-3001, Bern, Switzerland.,Department of Clinical Research, Faculty of Medicine, University of Bern, CH-3010, Bern, Switzerland
| | - Matthias Schweizer
- Institute of Virology and Immunology, Laenggass-Str. 122, CH-3001, Bern, Switzerland. .,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
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16
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Liu Z, Wang J, Cheng H, Ke X, Sun L, Zhang QC, Wang HW. Cryo-EM Structure of Human Dicer and Its Complexes with a Pre-miRNA Substrate. Cell 2018; 173:1191-1203.e12. [PMID: 29706542 DOI: 10.1016/j.cell.2018.03.080] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 01/02/2018] [Accepted: 03/28/2018] [Indexed: 12/26/2022]
Abstract
Human Dicer (hDicer) is a multi-domain protein belonging to the RNase III family. It plays pivotal roles in small RNA biogenesis during the RNA interference (RNAi) pathway by processing a diverse range of double-stranded RNA (dsRNA) precursors to generate ∼22 nt microRNA (miRNA) or small interfering RNA (siRNA) products for sequence-directed gene silencing. In this work, we solved the cryoelectron microscopy (cryo-EM) structure of hDicer in complex with its cofactor protein TRBP and revealed the precise spatial arrangement of hDicer's multiple domains. We further solved structures of the hDicer-TRBP complex bound with pre-let-7 RNA in two distinct conformations. In combination with biochemical analysis, these structures reveal a property of the hDicer-TRBP complex to promote the stability of pre-miRNA's stem duplex in a pre-dicing state. These results provide insights into the mechanism of RNA processing by hDicer and illustrate the regulatory role of hDicer's N-terminal helicase domain.
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Affiliation(s)
- Zhongmin Liu
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China 100084
| | - Jia Wang
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China 100084
| | - Hang Cheng
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China 100084; Joint Graduate Program of Peking-Tsinghua-NIBS, School of Life Sciences, Tsinghua University, Beijing, China 100084
| | - Xin Ke
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China 100084
| | - Lei Sun
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China 100084
| | - Qiangfeng Cliff Zhang
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China 100084
| | - Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China 100084.
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17
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De Wilde B, Beckers A, Lindner S, Kristina A, De Preter K, Depuydt P, Mestdagh P, Sante T, Lefever S, Hertwig F, Peng Z, Shi LM, Lee S, Vandermarliere E, Martens L, Menten B, Schramm A, Fischer M, Schulte J, Vandesompele J, Speleman F. The mutational landscape of MYCN, Lin28b and ALKF1174L driven murine neuroblastoma mimics human disease. Oncotarget 2017; 9:8334-8349. [PMID: 29492199 PMCID: PMC5823580 DOI: 10.18632/oncotarget.23614] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 10/28/2017] [Indexed: 12/27/2022] Open
Abstract
Genetically engineered mouse models have proven to be essential tools for unraveling fundamental aspects of cancer biology and for testing novel therapeutic strategies. To optimally serve these goals, it is essential that the mouse model faithfully recapitulates the human disease. Recently, novel mouse models for neuroblastoma have been developed. Here, we report on the further genomic characterization through exome sequencing and DNA copy number analysis of four of the currently available murine neuroblastoma model systems (ALK, Th-MYCN, Dbh-MYCN and Lin28b). The murine tumors revealed a low number of genomic alterations – in keeping with human neuroblastoma - and a positive correlation of the number of genetic lesions with the time to onset of tumor formation was observed. Gene copy number alterations are the hallmark of both murine and human disease and frequently affect syntenic genomic regions. Despite low mutational load, the genes mutated in murine disease were found to be enriched for genes mutated in human disease. Taken together, our study further supports the validity of the tested mouse models for mechanistic and preclinical studies of human neuroblastoma.
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Affiliation(s)
- Bram De Wilde
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | | | - Sven Lindner
- Department of Pediatric Oncology and Hematology, University Children's Hospital, Essen, Germany
| | - Althoff Kristina
- Department of Pediatric Oncology and Hematology, University Children's Hospital, Essen, Germany
| | - Katleen De Preter
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Pauline Depuydt
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Pieter Mestdagh
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Tom Sante
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Steve Lefever
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Falk Hertwig
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Zhiyu Peng
- BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, China
| | - Le-Ming Shi
- Center for Pharmacogenomics and Fudan-Zhangjiang Center for Clinical Genomics, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Sangkyun Lee
- Department of Computer Science, Artificial Intelligence Group, TU Dortmund, Dortmund, Germany
| | - Elien Vandermarliere
- Medical Biotechnology Center, VIB, Ghent, Belgium.,Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Lennart Martens
- Medical Biotechnology Center, VIB, Ghent, Belgium.,Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Alexander Schramm
- Department of Pediatric Oncology and Hematology, University Children's Hospital, Essen, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Johannes Schulte
- Pediatric Oncology and Hematology, Charité University Medicine, Berlin, Germany
| | - Jo Vandesompele
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Frank Speleman
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
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18
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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19
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Fukudome A, Fukuhara T. Plant dicer-like proteins: double-stranded RNA-cleaving enzymes for small RNA biogenesis. JOURNAL OF PLANT RESEARCH 2017; 130:33-44. [PMID: 27885504 DOI: 10.1007/s10265-016-0877-1] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 10/08/2016] [Indexed: 05/20/2023]
Abstract
Dicer, a double-stranded RNA (dsRNA)-specific endoribonuclease, plays an essential role in triggering both transcriptional and post-transcriptional gene silencing in eukaryotes by cleaving dsRNAs or single-stranded RNAs bearing stem-loop structures such as microRNA precursor transcripts into 21- to 24-nt small RNAs. Unlike animals, plants have evolved to utilize at least four Dicer-like (DCL) proteins. Extensive genetic studies have revealed that each DCL protein participates in a specific gene silencing pathway, with some redundancy. However, a mechanistic understanding of how the specific action of each DCL protein is regulated in its respective pathway is still in its infancy due to the limited number of biochemical studies on plant DCL proteins. In this review, we summarize and discuss the biochemical properties of plant DCL proteins revealed by studies using highly purified recombinant proteins, crude extracts, and immunoprecipitates. With help from co-factor proteins and an ATPase/DExH-box RNA-helicase domain, the microRNA-producing enzyme DCL1 recognizes bulges and terminal loop structures in its substrate transcripts to ensure accurate and efficient processing. DCL4 prefers long dsRNA substrates and requires the dsRNA-binding protein DRB4 for its activity. The short-dsRNA preference of DCL3 is well suited for short-RNA transcription and subsequent dsRNA formation by coupling between a plant-specific DNA-dependent RNA-polymerase IV and RNA-dependent RNA-polymerase 2 in the transcriptional gene silencing pathway. Inorganic phosphate also seems to play a role in differential regulation of DCL3 and DCL4 activities. Further development of biochemical approaches will be necessary for better understanding of how plant DCL proteins are fine-tuned in each small RNA biogenesis pathway under various physiological conditions.
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Affiliation(s)
- Akihito Fukudome
- Molecular and Environmental Plant Sciences, Department of Horticultural Sciences, Vegetable and Fruit Improvement Center, Texas A&M University, College Station, TX, 77843, USA
| | - Toshiyuki Fukuhara
- Department of Applied Biological Sciences and Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan.
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20
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Mickiewicz A, Sarzyńska J, Miłostan M, Kurzyńska-Kokorniak A, Rybarczyk A, Łukasiak P, Kuliński T, Figlerowicz M, Błażewicz J. Modeling of the catalytic core of Arabidopsis thaliana Dicer-like 4 protein and its complex with double-stranded RNA. Comput Biol Chem 2016; 66:44-56. [PMID: 27907832 DOI: 10.1016/j.compbiolchem.2016.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 10/11/2016] [Accepted: 11/16/2016] [Indexed: 12/20/2022]
Abstract
Plant Dicer-like proteins (DCLs) belong to the Ribonuclease III (RNase III) enzyme family. They are involved in the regulation of gene expression and antiviral defense through RNA interference pathways. A model plant, Arabidopsis thaliana encodes four DCL proteins (AtDCL1-4) that produce different classes of small regulatory RNAs. Our studies focus on AtDCL4 that processes double-stranded RNAs (dsRNAs) into 21 nucleotide trans-acting small interfering RNAs. So far, little is known about the structures of plant DCLs and the complexes they form with dsRNA. In this work, we present models of the catalytic core of AtDCL4 and AtDCL4-dsRNA complex constructed by computational methods. We built a homology model of the catalytic core of AtDCL4 comprising Platform, PAZ, Connector helix and two RNase III domains. To assemble the AtDCL4-dsRNA complex two modeling approaches were used. In the first method, to establish conformations that allow building a consistent model of the complex, we used Normal Mode Analysis for both dsRNA and AtDCL4. The second strategy involved template-based approach for positioning of the PAZ domain and manual arrangement of the Connector helix. Our results suggest that the spatial orientation of the Connector helix, Platform and PAZ relative to the RNase III domains is crucial for measuring dsRNA of defined length. The modeled complexes provide information about interactions that may contribute to the relative orientations of these domains and to dsRNA binding. All these information can be helpful for understanding the mechanism of AtDCL4-mediated dsRNA recognition and binding, to produce small RNA of specific size.
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Affiliation(s)
- Agnieszka Mickiewicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland; European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland
| | - Joanna Sarzyńska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland; European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland.
| | - Maciej Miłostan
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland; European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland
| | - Anna Kurzyńska-Kokorniak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Agnieszka Rybarczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland; Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland; European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland
| | - Piotr Łukasiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland; Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland; European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland
| | - Tadeusz Kuliński
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland; Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland; European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland
| | - Jacek Błażewicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland; Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland; European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland
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21
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Svobodova E, Kubikova J, Svoboda P. Production of small RNAs by mammalian Dicer. Pflugers Arch 2016; 468:1089-102. [PMID: 27048428 PMCID: PMC4893058 DOI: 10.1007/s00424-016-1817-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 03/20/2016] [Accepted: 03/24/2016] [Indexed: 01/16/2023]
Abstract
MicroRNA (miRNA) and RNA interference (RNAi) pathways employ RNase III Dicer for the biogenesis of small RNAs guiding post-transcriptional repression. Requirements for Dicer activity differ in the two pathways. The biogenesis of miRNAs requires a single Dicer cleavage of a short hairpin precursor to produce a small RNA with a precisely defined sequence, while small RNAs in RNAi come from a processive cleavage of a long double-stranded RNA (dsRNA) into a pool of small RNAs with different sequences. While Dicer is generally conserved among eukaryotes, its substrate recognition, cleavage, and biological roles differ. In Metazoa, a single Dicer can function as a universal factor for RNAi and miRNA pathways or as a factor adapted specifically for one of the pathways. In this review, we focus on the structure, function, and evolution of mammalian Dicer. We discuss key structural features of Dicer and other factors defining Dicer substrate repertoire and biological functions in mammals in comparison with invertebrate models. The key for adaptation of Dicer for miRNA or RNAi pathways is the N-terminal helicase, a dynamically evolving Dicer domain. Its functionality differs between mammals and invertebrates: the mammalian Dicer is well adapted to produce miRNAs while its ability to support RNAi is limited.
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Affiliation(s)
- Eliska Svobodova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4, 142 20, Czech Republic
| | - Jana Kubikova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4, 142 20, Czech Republic
| | - Petr Svoboda
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4, 142 20, Czech Republic.
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22
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Wu MK, Cotter MB, Pears J, McDermott MB, Fabian MR, Foulkes WD, O'Sullivan MJ. Tumor progression in DICER1-mutated cystic nephroma-witnessing the genesis of anaplastic sarcoma of the kidney. Hum Pathol 2016; 53:114-20. [PMID: 27036314 DOI: 10.1016/j.humpath.2016.03.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 01/29/2016] [Accepted: 03/02/2016] [Indexed: 12/15/2022]
Abstract
We report a 7-month-old female infant with a multicystic left renal tumor having histologic features predominantly of a cystic nephroma, but with microscopic cellular foci which contained atypical mitotic figures and anaplastic nuclei. Immunohistochemistry showed strong p53 reactivity in the anaplastic region. DICER1 sequencing confirmed 2 mutations: germ line mutation c.2450delC and c.5438A>G somatic within the tumor. Despite an initial consideration of cystic partially differentiated nephroblastoma, the presence of anaplasia ruled that possibility out, as this is not an acceptable feature for that diagnosis. Moreover, the germ line DICER1 mutation prompted consideration that this case represents a unique "nascent" anaplastic sarcoma of kidney, and further immunohistochemical workup demonstrated cytoplasmic, but no nuclear WT-1 reactivity in the cellular foci. The importance of meticulous sampling of cystic lesions is highlighted by this unprecedented case, which lends support to the recent recognition of anaplastic sarcoma of kidney as a DICER1-associated cancer.
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Affiliation(s)
- Mona K Wu
- Department of Medical Genetics, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC H3T 1E2, Canada
| | - Maura B Cotter
- Histology Laboratory, Our Lady's Children's Hospital, Crumlin, Dublin 12, Ireland
| | - Jane Pears
- Oncology Department, Our Lady's Children's Hospital, Crumlin, Dublin 12, Ireland
| | - Michael B McDermott
- Histology Laboratory, Our Lady's Children's Hospital, Crumlin, Dublin 12, Ireland
| | - Marc R Fabian
- Departments of Oncology and Experimental Medicine, McGill University, Montréal, QC H3T 1E2, Canada
| | - William D Foulkes
- Department of Medical Genetics, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC H3T 1E2, Canada; Program in Cancer Genetics, Departments of Oncology and Human Genetics, McGill University, Montréal, QC H3T 1E2, Canada
| | - Maureen J O'Sullivan
- Histology Laboratory, Our Lady's Children's Hospital, Crumlin, Dublin 12, Ireland; Trinity College, University of Dublin, Dublin 2, Ireland; The National Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin 12, Ireland.
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23
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Wu MK, de Kock L, Conwell LS, Stewart CJR, King BR, Choong CS, Hussain K, Sabbaghian N, MacRae IJ, Fabian MR, Foulkes WD. Functional characterization of multiple DICER1 mutations in an adolescent. Endocr Relat Cancer 2016; 23:L1-5. [PMID: 26545620 DOI: 10.1530/erc-15-0460] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 11/06/2015] [Indexed: 12/15/2022]
Affiliation(s)
- M K Wu
- Department of Medical Genetics, Lady Davis Institute Jewish General Hospital, McGill UniversityMontréal, QuebecCanadaDepartment Endocrinology and Diabetes, Lady Cilento Children's HospitalBrisbane, QueenslandAustraliaSchool of Medicine, University of QueenslandBrisbane, QueenslandAustraliaQueensland Children's Medical Research InstituteBrisbane, QueenslandAustraliaDepartment of Histopathology, King Edward Memorial HospitalPerthAustraliaJohn Hunter Children's HospitalLookout Road, Newcastle, New South WalesAustraliaSchool of Medicine and Public Health, Hunter Medical Research Institute, University of NewcastleRankin Park, New South WalesAustraliaSchool of Paediatrics and Child Health, University of Western AustraliaCrawley, Western AustraliaAustraliaDepartment of Paediatric Endocrinology and Diabetes, Princess Margaret Hospital for Children, Child and Adolescent Health ServiceSubiaco, Western AustraliaAustraliaGenetics and Epigenetics in Health and Disease Genetics and Genomic Medicine Programme UCL Institute of Child Health Great Ormond Street Hospital for ChildrenLondonUKThe Scripps Research Institute3215 Merryfield Row, San Diego, CaliforniaUSADepartments of Oncology and Experimental Medicine, McGill UniversityMontréal, QuebecCanadaProgram in Cancer Genetics, Departments of Oncology and Human Genetics, McGill UniversityMontréal, Quebec, H3T 1E2Canada
| | - L de Kock
- Department of Medical Genetics, Lady Davis Institute Jewish General Hospital, McGill UniversityMontréal, QuebecCanadaDepartment Endocrinology and Diabetes, Lady Cilento Children's HospitalBrisbane, QueenslandAustraliaSchool of Medicine, University of QueenslandBrisbane, QueenslandAustraliaQueensland Children's Medical Research InstituteBrisbane, QueenslandAustraliaDepartment of Histopathology, King Edward Memorial HospitalPerthAustraliaJohn Hunter Children's HospitalLookout Road, Newcastle, New South WalesAustraliaSchool of Medicine and Public Health, Hunter Medical Research Institute, University of NewcastleRankin Park, New South WalesAustraliaSchool of Paediatrics and Child Health, University of Western AustraliaCrawley, Western AustraliaAustraliaDepartment of Paediatric Endocrinology and Diabetes, Princess Margaret Hospital for Children, Child and Adolescent Health ServiceSubiaco, Western AustraliaAustraliaGenetics and Epigenetics in Health and Disease Genetics and Genomic Medicine Programme UCL Institute of Child Health Great Ormond Street Hospital for ChildrenLondonUKThe Scripps Research Institute3215 Merryfield Row, San Diego, CaliforniaUSADepartments of Oncology and Experimental Medicine, McGill UniversityMontréal, QuebecCanadaProgram in Cancer Genetics, Departments of Oncology and Human Genetics, McGill UniversityMontréal, Quebec, H3T 1E2Canada
| | - L S Conwell
- Department of Medical Genetics, Lady Davis Institute Jewish General Hospital, McGill UniversityMontréal, QuebecCanadaDepartment Endocrinology and Diabetes, Lady Cilento Children's HospitalBrisbane, QueenslandAustraliaSchool of Medicine, University of QueenslandBrisbane, QueenslandAustraliaQueensland Children's Medical Research InstituteBrisbane, QueenslandAustraliaDepartment of Histopathology, King Edward Memorial HospitalPerthAustraliaJohn Hunter Children's HospitalLookout Road, Newcastle, New South WalesAustraliaSchool of Medicine and Public Health, Hunter Medical Research Institute, University of NewcastleRankin Park, New South WalesAustraliaSchool of Paediatrics and Child Health, University of Western AustraliaCrawley, Western AustraliaAustraliaDepartment of Paediatric Endocrinology and Diabetes, Princess Margaret Hospital for Children, Child and Adolescent Health ServiceSubiaco, Western AustraliaAustraliaGenetics and Epigenetics in Health and Disease Genetics and Genomic Medicine Programme UCL Institute of Child Health Great Ormond Street Hospital for ChildrenLondonUKThe Scripps Research Institute3215 Merryfield Row, San Diego, CaliforniaUSADepartments of Oncology and Experimental Medicine, McGill UniversityMontréal, QuebecCanadaProgram in Cancer Genetics, Departments of Oncology and Human Genetics, McGill UniversityMontréal, Quebec, H3T 1E2Canada Department of Medical Genetics, Lady Davis Institute Jewish General Hospital, McGill UniversityMontréal, QuebecCanadaDepartment Endocrinology and Diabetes, Lady Cilento Children's HospitalBrisbane, QueenslandAustraliaSchool of Medicine, University of QueenslandBrisbane, QueenslandAustraliaQueensland Children's Medical Research InstituteBrisbane, QueenslandAustraliaDepartment of Histopathology, King Edward Memorial HospitalPerthAustraliaJohn Hunter Children's HospitalLookout Road, Newcastle, New South WalesAustraliaSchool of Medicine and Public Health, Hunter Medical Research Institute, University of NewcastleRanki
| | - C J R Stewart
- Department of Medical Genetics, Lady Davis Institute Jewish General Hospital, McGill UniversityMontréal, QuebecCanadaDepartment Endocrinology and Diabetes, Lady Cilento Children's HospitalBrisbane, QueenslandAustraliaSchool of Medicine, University of QueenslandBrisbane, QueenslandAustraliaQueensland Children's Medical Research InstituteBrisbane, QueenslandAustraliaDepartment of Histopathology, King Edward Memorial HospitalPerthAustraliaJohn Hunter Children's HospitalLookout Road, Newcastle, New South WalesAustraliaSchool of Medicine and Public Health, Hunter Medical Research Institute, University of NewcastleRankin Park, New South WalesAustraliaSchool of Paediatrics and Child Health, University of Western AustraliaCrawley, Western AustraliaAustraliaDepartment of Paediatric Endocrinology and Diabetes, Princess Margaret Hospital for Children, Child and Adolescent Health ServiceSubiaco, Western AustraliaAustraliaGenetics and Epigenetics in Health and Disease Genetics and Genomic Medicine Programme UCL Institute of Child Health Great Ormond Street Hospital for ChildrenLondonUKThe Scripps Research Institute3215 Merryfield Row, San Diego, CaliforniaUSADepartments of Oncology and Experimental Medicine, McGill UniversityMontréal, QuebecCanadaProgram in Cancer Genetics, Departments of Oncology and Human Genetics, McGill UniversityMontréal, Quebec, H3T 1E2Canada
| | - B R King
- Department of Medical Genetics, Lady Davis Institute Jewish General Hospital, McGill UniversityMontréal, QuebecCanadaDepartment Endocrinology and Diabetes, Lady Cilento Children's HospitalBrisbane, QueenslandAustraliaSchool of Medicine, University of QueenslandBrisbane, QueenslandAustraliaQueensland Children's Medical Research InstituteBrisbane, QueenslandAustraliaDepartment of Histopathology, King Edward Memorial HospitalPerthAustraliaJohn Hunter Children's HospitalLookout Road, Newcastle, New South WalesAustraliaSchool of Medicine and Public Health, Hunter Medical Research Institute, University of NewcastleRankin Park, New South WalesAustraliaSchool of Paediatrics and Child Health, University of Western AustraliaCrawley, Western AustraliaAustraliaDepartment of Paediatric Endocrinology and Diabetes, Princess Margaret Hospital for Children, Child and Adolescent Health ServiceSubiaco, Western AustraliaAustraliaGenetics and Epigenetics in Health and Disease Genetics and Genomic Medicine Programme UCL Institute of Child Health Great Ormond Street Hospital for ChildrenLondonUKThe Scripps Research Institute3215 Merryfield Row, San Diego, CaliforniaUSADepartments of Oncology and Experimental Medicine, McGill UniversityMontréal, QuebecCanadaProgram in Cancer Genetics, Departments of Oncology and Human Genetics, McGill UniversityMontréal, Quebec, H3T 1E2Canada Department of Medical Genetics, Lady Davis Institute Jewish General Hospital, McGill UniversityMontréal, QuebecCanadaDepartment Endocrinology and Diabetes, Lady Cilento Children's HospitalBrisbane, QueenslandAustraliaSchool of Medicine, University of QueenslandBrisbane, QueenslandAustraliaQueensland Children's Medical Research InstituteBrisbane, QueenslandAustraliaDepartment of Histopathology, King Edward Memorial HospitalPerthAustraliaJohn Hunter Children's HospitalLookout Road, Newcastle, New South WalesAustraliaSchool of Medicine and Public Health, Hunter Medical Research Institute, University of NewcastleRanki
| | - C S Choong
- Department of Medical Genetics, Lady Davis Institute Jewish General Hospital, McGill UniversityMontréal, QuebecCanadaDepartment Endocrinology and Diabetes, Lady Cilento Children's HospitalBrisbane, QueenslandAustraliaSchool of Medicine, University of QueenslandBrisbane, QueenslandAustraliaQueensland Children's Medical Research InstituteBrisbane, QueenslandAustraliaDepartment of Histopathology, King Edward Memorial HospitalPerthAustraliaJohn Hunter Children's HospitalLookout Road, Newcastle, New South WalesAustraliaSchool of Medicine and Public Health, Hunter Medical Research Institute, University of NewcastleRankin Park, New South WalesAustraliaSchool of Paediatrics and Child Health, University of Western AustraliaCrawley, Western AustraliaAustraliaDepartment of Paediatric Endocrinology and Diabetes, Princess Margaret Hospital for Children, Child and Adolescent Health ServiceSubiaco, Western AustraliaAustraliaGenetics and Epigenetics in Health and Disease Genetics and Genomic Medicine Programme UCL Institute of Child Health Great Ormond Street Hospital for ChildrenLondonUKThe Scripps Research Institute3215 Merryfield Row, San Diego, CaliforniaUSADepartments of Oncology and Experimental Medicine, McGill UniversityMontréal, QuebecCanadaProgram in Cancer Genetics, Departments of Oncology and Human Genetics, McGill UniversityMontréal, Quebec, H3T 1E2Canada Department of Medical Genetics, Lady Davis Institute Jewish General Hospital, McGill UniversityMontréal, QuebecCanadaDepartment Endocrinology and Diabetes, Lady Cilento Children's HospitalBrisbane, QueenslandAustraliaSchool of Medicine, University of QueenslandBrisbane, QueenslandAustraliaQueensland Children's Medical Research InstituteBrisbane, QueenslandAustraliaDepartment of Histopathology, King Edward Memorial HospitalPerthAustraliaJohn Hunter Children's HospitalLookout Road, Newcastle, New South WalesAustraliaSchool of Medicine and Public Health, Hunter Medical Research Institute, University of NewcastleRanki
| | - K Hussain
- Department of Medical Genetics, Lady Davis Institute Jewish General Hospital, McGill UniversityMontréal, QuebecCanadaDepartment Endocrinology and Diabetes, Lady Cilento Children's HospitalBrisbane, QueenslandAustraliaSchool of Medicine, University of QueenslandBrisbane, QueenslandAustraliaQueensland Children's Medical Research InstituteBrisbane, QueenslandAustraliaDepartment of Histopathology, King Edward Memorial HospitalPerthAustraliaJohn Hunter Children's HospitalLookout Road, Newcastle, New South WalesAustraliaSchool of Medicine and Public Health, Hunter Medical Research Institute, University of NewcastleRankin Park, New South WalesAustraliaSchool of Paediatrics and Child Health, University of Western AustraliaCrawley, Western AustraliaAustraliaDepartment of Paediatric Endocrinology and Diabetes, Princess Margaret Hospital for Children, Child and Adolescent Health ServiceSubiaco, Western AustraliaAustraliaGenetics and Epigenetics in Health and Disease Genetics and Genomic Medicine Programme UCL Institute of Child Health Great Ormond Street Hospital for ChildrenLondonUKThe Scripps Research Institute3215 Merryfield Row, San Diego, CaliforniaUSADepartments of Oncology and Experimental Medicine, McGill UniversityMontréal, QuebecCanadaProgram in Cancer Genetics, Departments of Oncology and Human Genetics, McGill UniversityMontréal, Quebec, H3T 1E2Canada
| | - N Sabbaghian
- Department of Medical Genetics, Lady Davis Institute Jewish General Hospital, McGill UniversityMontréal, QuebecCanadaDepartment Endocrinology and Diabetes, Lady Cilento Children's HospitalBrisbane, QueenslandAustraliaSchool of Medicine, University of QueenslandBrisbane, QueenslandAustraliaQueensland Children's Medical Research InstituteBrisbane, QueenslandAustraliaDepartment of Histopathology, King Edward Memorial HospitalPerthAustraliaJohn Hunter Children's HospitalLookout Road, Newcastle, New South WalesAustraliaSchool of Medicine and Public Health, Hunter Medical Research Institute, University of NewcastleRankin Park, New South WalesAustraliaSchool of Paediatrics and Child Health, University of Western AustraliaCrawley, Western AustraliaAustraliaDepartment of Paediatric Endocrinology and Diabetes, Princess Margaret Hospital for Children, Child and Adolescent Health ServiceSubiaco, Western AustraliaAustraliaGenetics and Epigenetics in Health and Disease Genetics and Genomic Medicine Programme UCL Institute of Child Health Great Ormond Street Hospital for ChildrenLondonUKThe Scripps Research Institute3215 Merryfield Row, San Diego, CaliforniaUSADepartments of Oncology and Experimental Medicine, McGill UniversityMontréal, QuebecCanadaProgram in Cancer Genetics, Departments of Oncology and Human Genetics, McGill UniversityMontréal, Quebec, H3T 1E2Canada
| | - I J MacRae
- Department of Medical Genetics, Lady Davis Institute Jewish General Hospital, McGill UniversityMontréal, QuebecCanadaDepartment Endocrinology and Diabetes, Lady Cilento Children's HospitalBrisbane, QueenslandAustraliaSchool of Medicine, University of QueenslandBrisbane, QueenslandAustraliaQueensland Children's Medical Research InstituteBrisbane, QueenslandAustraliaDepartment of Histopathology, King Edward Memorial HospitalPerthAustraliaJohn Hunter Children's HospitalLookout Road, Newcastle, New South WalesAustraliaSchool of Medicine and Public Health, Hunter Medical Research Institute, University of NewcastleRankin Park, New South WalesAustraliaSchool of Paediatrics and Child Health, University of Western AustraliaCrawley, Western AustraliaAustraliaDepartment of Paediatric Endocrinology and Diabetes, Princess Margaret Hospital for Children, Child and Adolescent Health ServiceSubiaco, Western AustraliaAustraliaGenetics and Epigenetics in Health and Disease Genetics and Genomic Medicine Programme UCL Institute of Child Health Great Ormond Street Hospital for ChildrenLondonUKThe Scripps Research Institute3215 Merryfield Row, San Diego, CaliforniaUSADepartments of Oncology and Experimental Medicine, McGill UniversityMontréal, QuebecCanadaProgram in Cancer Genetics, Departments of Oncology and Human Genetics, McGill UniversityMontréal, Quebec, H3T 1E2Canada
| | - M R Fabian
- Department of Medical Genetics, Lady Davis Institute Jewish General Hospital, McGill UniversityMontréal, QuebecCanadaDepartment Endocrinology and Diabetes, Lady Cilento Children's HospitalBrisbane, QueenslandAustraliaSchool of Medicine, University of QueenslandBrisbane, QueenslandAustraliaQueensland Children's Medical Research InstituteBrisbane, QueenslandAustraliaDepartment of Histopathology, King Edward Memorial HospitalPerthAustraliaJohn Hunter Children's HospitalLookout Road, Newcastle, New South WalesAustraliaSchool of Medicine and Public Health, Hunter Medical Research Institute, University of NewcastleRankin Park, New South WalesAustraliaSchool of Paediatrics and Child Health, University of Western AustraliaCrawley, Western AustraliaAustraliaDepartment of Paediatric Endocrinology and Diabetes, Princess Margaret Hospital for Children, Child and Adolescent Health ServiceSubiaco, Western AustraliaAustraliaGenetics and Epigenetics in Health and Disease Genetics and Genomic Medicine Programme UCL Institute of Child Health Great Ormond Street Hospital for ChildrenLondonUKThe Scripps Research Institute3215 Merryfield Row, San Diego, CaliforniaUSADepartments of Oncology and Experimental Medicine, McGill UniversityMontréal, QuebecCanadaProgram in Cancer Genetics, Departments of Oncology and Human Genetics, McGill UniversityMontréal, Quebec, H3T 1E2Canada
| | - W D Foulkes
- Department of Medical Genetics, Lady Davis Institute Jewish General Hospital, McGill UniversityMontréal, QuebecCanadaDepartment Endocrinology and Diabetes, Lady Cilento Children's HospitalBrisbane, QueenslandAustraliaSchool of Medicine, University of QueenslandBrisbane, QueenslandAustraliaQueensland Children's Medical Research InstituteBrisbane, QueenslandAustraliaDepartment of Histopathology, King Edward Memorial HospitalPerthAustraliaJohn Hunter Children's HospitalLookout Road, Newcastle, New South WalesAustraliaSchool of Medicine and Public Health, Hunter Medical Research Institute, University of NewcastleRankin Park, New South WalesAustraliaSchool of Paediatrics and Child Health, University of Western AustraliaCrawley, Western AustraliaAustraliaDepartment of Paediatric Endocrinology and Diabetes, Princess Margaret Hospital for Children, Child and Adolescent Health ServiceSubiaco, Western AustraliaAustraliaGenetics and Epigenetics in Health and Disease Genetics and Genomic Medicine Programme UCL Institute of Child Health Great Ormond Street Hospital for ChildrenLondonUKThe Scripps Research Institute3215 Merryfield Row, San Diego, CaliforniaUSADepartments of Oncology and Experimental Medicine, McGill UniversityMontréal, QuebecCanadaProgram in Cancer Genetics, Departments of Oncology and Human Genetics, McGill UniversityMontréal, Quebec, H3T 1E2Canada Department of Medical Genetics, Lady Davis Institute Jewish General Hospital, McGill UniversityMontréal, QuebecCanadaDepartment Endocrinology and Diabetes, Lady Cilento Children's HospitalBrisbane, QueenslandAustraliaSchool of Medicine, University of QueenslandBrisbane, QueenslandAustraliaQueensland Children's Medical Research InstituteBrisbane, QueenslandAustraliaDepartment of Histopathology, King Edward Memorial HospitalPerthAustraliaJohn Hunter Children's HospitalLookout Road, Newcastle, New South WalesAustraliaSchool of Medicine and Public Health, Hunter Medical Research Institute, University of NewcastleRanki
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de Kock L, Wang YC, Revil T, Badescu D, Rivera B, Sabbaghian N, Wu M, Weber E, Sandoval C, Hopman SMJ, Merks JHM, van Hagen JM, Bouts AHM, Plager DA, Ramasubramanian A, Forsmark L, Doyle KL, Toler T, Callahan J, Engelenberg C, Bouron-Dal Soglio D, Priest JR, Ragoussis J, Foulkes WD. High-sensitivity sequencing reveals multi-organ somatic mosaicism causing DICER1 syndrome. J Med Genet 2015; 53:43-52. [DOI: 10.1136/jmedgenet-2015-103428] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 09/18/2015] [Indexed: 12/30/2022]
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Comprehensive assessment of cancer missense mutation clustering in protein structures. Proc Natl Acad Sci U S A 2015; 112:E5486-95. [PMID: 26392535 DOI: 10.1073/pnas.1516373112] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Large-scale tumor sequencing projects enabled the identification of many new cancer gene candidates through computational approaches. Here, we describe a general method to detect cancer genes based on significant 3D clustering of mutations relative to the structure of the encoded protein products. The approach can also be used to search for proteins with an enrichment of mutations at binding interfaces with a protein, nucleic acid, or small molecule partner. We applied this approach to systematically analyze the PanCancer compendium of somatic mutations from 4,742 tumors relative to all known 3D structures of human proteins in the Protein Data Bank. We detected significant 3D clustering of missense mutations in several previously known oncoproteins including HRAS, EGFR, and PIK3CA. Although clustering of missense mutations is often regarded as a hallmark of oncoproteins, we observed that a number of tumor suppressors, including FBXW7, VHL, and STK11, also showed such clustering. Beside these known cases, we also identified significant 3D clustering of missense mutations in NUF2, which encodes a component of the kinetochore, that could affect chromosome segregation and lead to aneuploidy. Analysis of interaction interfaces revealed enrichment of mutations in the interfaces between FBXW7-CCNE1, HRAS-RASA1, CUL4B-CAND1, OGT-HCFC1, PPP2R1A-PPP2R5C/PPP2R2A, DICER1-Mg2+, MAX-DNA, SRSF2-RNA, and others. Together, our results indicate that systematic consideration of 3D structure can assist in the identification of cancer genes and in the understanding of the functional role of their mutations.
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Kurzynska-Kokorniak A, Koralewska N, Pokornowska M, Urbanowicz A, Tworak A, Mickiewicz A, Figlerowicz M. The many faces of Dicer: the complexity of the mechanisms regulating Dicer gene expression and enzyme activities. Nucleic Acids Res 2015; 43:4365-80. [PMID: 25883138 PMCID: PMC4482082 DOI: 10.1093/nar/gkv328] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 03/31/2015] [Indexed: 12/14/2022] Open
Abstract
There is increasing evidence indicating that the production of small regulatory RNAs is not the only process in which ribonuclease Dicer can participate. For example, it has been demonstrated that this enzyme is also involved in chromatin structure remodelling, inflammation and apoptotic DNA degradation. Moreover, it has become increasingly clear that cellular transcript and protein levels of Dicer must be strictly controlled because even small changes in their accumulation can initiate various pathological processes, including carcinogenesis. Accordingly, in recent years, a number of studies have been performed to identify the factors regulating Dicer gene expression and protein activity. As a result, a large amount of complex and often contradictory data has been generated. None of these data have been subjected to an exhaustive review or critical discussion. This review attempts to fill this gap by summarizing the current knowledge of factors that regulate Dicer gene transcription, primary transcript processing, mRNA translation and enzyme activity. Because of the high complexity of this topic, this review mainly concentrates on human Dicer. This review also focuses on an additional regulatory layer of Dicer activity involving the interactions of protein and RNA factors with Dicer substrates.
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Affiliation(s)
| | - Natalia Koralewska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Maria Pokornowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Anna Urbanowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Aleksander Tworak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Agnieszka Mickiewicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland Institute of Computing Science, Poznan University of Technology, Poznan 60-965, Poland
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Ipsaro JJ, Joshua-Tor L. From guide to target: molecular insights into eukaryotic RNA-interference machinery. Nat Struct Mol Biol 2015; 22:20-8. [PMID: 25565029 PMCID: PMC4450863 DOI: 10.1038/nsmb.2931] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 11/12/2014] [Indexed: 12/12/2022]
Abstract
Since its relatively recent discovery, RNA interference (RNAi) has emerged as a potent, specific and ubiquitous means of gene regulation. Through a number of pathways that are conserved in eukaryotes from yeast to humans, small noncoding RNAs direct molecular machinery to silence gene expression. In this Review, we focus on mechanisms and structures that govern RNA silencing in higher organisms. In addition to highlighting recent advances, we discuss parallels and differences among RNAi pathways. Together, the studies reviewed herein reveal the versatility and programmability of RNA-induced silencing complexes and emphasize the importance of both upstream biogenesis and downstream silencing factors.
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Affiliation(s)
- Jonathan J. Ipsaro
- W. M. Keck Structural Biology Laboratory Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor, NY 11724
| | - Leemor Joshua-Tor
- W. M. Keck Structural Biology Laboratory Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor, NY 11724
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Role of microRNAs in cancers of the female reproductive tract: insights from recent clinical and experimental discovery studies. Clin Sci (Lond) 2014; 128:153-80. [PMID: 25294164 DOI: 10.1042/cs20140087] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
microRNAs (miRNAs) are small RNA molecules that represent the top of the pyramid of many tumorigenesis cascade pathways as they have the ability to affect multiple, intricate, and still undiscovered downstream targets. Understanding how miRNA molecules serve as master regulators in these important networks involved in cancer initiation and progression open up significant innovative areas for therapy and diagnosis that have been sadly lacking for deadly female reproductive tract cancers. This review will highlight the recent advances in the field of miRNAs in epithelial ovarian cancer, endometrioid endometrial cancer and squamous-cell cervical carcinoma focusing on studies associated with actual clinical information in humans. Importantly, recent miRNA profiling studies have included well-characterized clinical specimens of female reproductive tract cancers, allowing for studies correlating miRNA expression with clinical outcomes. This review will summarize the current thoughts on the role of miRNA processing in unique miRNA species present in these cancers. In addition, this review will focus on current data regarding miRNA molecules as unique biomarkers associated with clinically significant outcomes such as overall survival and chemotherapy resistance. We will also discuss why specific miRNA molecules are not recapitulated across multiple studies of the same cancer type. Although the mechanistic contributions of miRNA molecules to these clinical phenomena have been confirmed using in vitro and pre-clinical mouse model systems, these studies are truly only the beginning of our understanding of the roles miRNAs play in cancers of the female reproductive tract. This review will also highlight useful areas for future research regarding miRNAs as therapeutic targets in cancers of the female reproductive tract.
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Stabilisation and characterisation of the isolated regulatory domain of human 5-lipoxygenase. Biochim Biophys Acta Mol Cell Biol Lipids 2014; 1842:1538-47. [DOI: 10.1016/j.bbalip.2014.07.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 07/22/2014] [Accepted: 07/28/2014] [Indexed: 11/18/2022]
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Nasal chondromesenchymal hamartomas arise secondary to germline and somatic mutations of DICER1 in the pleuropulmonary blastoma tumor predisposition disorder. Hum Genet 2014; 133:1443-50. [PMID: 25118636 DOI: 10.1007/s00439-014-1474-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 07/23/2014] [Indexed: 12/22/2022]
Abstract
Nasal chondromesenchymal hamartoma (NCMH) is a rare nasal tumor that typically presents in young children. We previously reported on NCMH occurrence in children with pleuropulmonary blastoma (PPB), a rare pulmonary dysembryonic sarcoma that is the hallmark neoplasm in the PPB-associated DICER1 tumor predisposition disorder. Original pathologic materials from individuals with a PPB, PPB-associated tumor and/or a DICER1 mutation were centrally reviewed by the International PPB Registry. Paraffin-embedded NCMH tumor tissue was available in three cases. Laser-capture microdissection was used to isolate mesenchymal spindle cells and cartilage in one case for Sanger sequencing of DICER1. Nine patients (5F/4M) had PPB and NCMH. NCMH was diagnosed at a median age of 10 years (range 6-21 years). NCMH developed 4.5-13 years after PPB. Presenting NCMH symptoms included chronic sinusitis and nasal congestion. Five patients had bilateral tumors. Local NCMH recurrences required several surgical resections in two patients, but all nine patients were alive at 0-16 years of follow-up. Pathogenic germline DICER1 mutations were found in 6/8 NCMH patients tested. In 2 of the patients with germline DICER1 mutations, somatic DICER1 missense mutations were also identified in their NCMH (E1813D; n = 2). Three additional PPB patients developed other nasal lesions seen in the general population (a Schneiderian papilloma, chronic sinusitis with cysts, and allergic nasal polyps with eosinophils). Two of these patients had germline DICER1 mutations. Pathogenic germline and somatic mutations of DICER1 in NCMH establishes that the genetic etiology of NCMH is similar to PPB, despite the disparate biological potential of these neoplasms.
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Cantini LP, Andino LM, Attaway CC, Butler B, Dumitriu A, Blackshaw A, Jakymiw A. Identification and characterization of Dicer1e, a Dicer1 protein variant, in oral cancer cells. Mol Cancer 2014; 13:190. [PMID: 25115815 PMCID: PMC4141963 DOI: 10.1186/1476-4598-13-190] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 08/05/2014] [Indexed: 01/15/2023] Open
Abstract
Background The human dicer1 gene has been predicted to produce several mRNA variants that encode truncated Dicer1 proteins of varying lengths. One of these Dicer1 variants, Dicer1e, was recently found to be differentially expressed in breast cancer cells. Because the expression and function of the Dicer1e protein variant has not been well characterized and the underlying molecular mechanisms for the development of oral squamous cell carcinomas (OSCCs) are poorly understood, the present study sought to characterize the biological role of Dicer1e and determine its relationship, if any, to OSCC pathogenesis. Methods Western blot analyses were used to examine Dicer1e expression levels in a panel of oral cancer cells/tissues and during epithelial-mesenchymal transition (EMT), followed by 5′/3′-RACE analyses to obtain the full-length Dicer1e transcript. Biochemical fractionation and indirect immunofluorescent studies were performed to determine the cellular localization of Dicer1e and the effects of Dicer1e silencing on cancer cell proliferation, clonogenicity, and drug sensitivity were also assessed. Results Dicer1e protein levels were found to be overexpressed in OSCC cell lines of epithelial phenotype and in OSCC tissues with its levels downregulated during EMT. Moreover, the Dicer1e protein was observed to predominantly localize in the nucleus. 5′/3′-RACE analyses confirmed the presence of the Dicer1e transcript and silencing of Dicer1e impaired both cancer cell proliferation and clonogenicity by inducing either apoptosis and/or G2/M cell cycle arrest. Lastly, Dicer1e knockdown enhanced the chemosensitivity of oral cancer cells to cisplatin. Conclusion The expression levels of Dicer1e influence the pathogenesis of oral cancer cells and alter their response to chemosensitivity, thus supporting the importance of Dicer1e as a therapeutic target for OSCCs. Electronic supplementary material The online version of this article (doi:10.1186/1476-4598-13-190) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | - Andrew Jakymiw
- Department of Oral Health Sciences and Center for Oral Health Research, Hollings Cancer Center, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC 29425, USA.
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Torrezan GT, Ferreira EN, Nakahata AM, Barros BDF, Castro MTM, Correa BR, Krepischi ACV, Olivieri EHR, Cunha IW, Tabori U, Grundy PE, Costa CML, de Camargo B, Galante PAF, Carraro DM. Recurrent somatic mutation in DROSHA induces microRNA profile changes in Wilms tumour. Nat Commun 2014; 5:4039. [PMID: 24909261 PMCID: PMC4062040 DOI: 10.1038/ncomms5039] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 05/06/2014] [Indexed: 12/16/2022] Open
Abstract
Wilms tumour (WT) is an embryonal kidney neoplasia for which very few driver genes have
been identified. Here we identify DROSHA mutations in 12% of WT samples (26/222) using whole-exome
sequencing and targeted sequencing of 10 microRNA (miRNA)-processing genes. A recurrent
mutation (E1147K) affecting a metal-binding residue of the RNase IIIb domain is detected in
81% of the DROSHA-mutated tumours.
In addition, we identify non-recurrent mutations in other genes of this pathway
(DGCR8, DICER1, XPO5 and TARBP2). By assessing the miRNA expression pattern of the
DROSHA-E1147K-mutated tumours
and cell lines expressing this mutation, we determine that this variant leads to a
predominant downregulation of a subset of miRNAs. We confirm that the downregulation occurs
exclusively in mature miRNAs and not in primary miRNA transcripts, suggesting that the
DROSHA E1147K mutation affects
processing of primary miRNAs. Our data underscore the pivotal role of the miRNA biogenesis
pathway in WT tumorigenesis, particularly the major miRNA-processing gene DROSHA. Wilms tumour (WT) is the most common paediatric kidney cancer and few driver
genes related to its development have been identified. Here, the authors identify
DROSHA mutations that may contribute to WT tumorigenesis through their effect on
primary microRNA processing.
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Affiliation(s)
- Giovana T Torrezan
- 1] Genomics and Molecular Biology Laboratory, International Research Center, A. C. Camargo Cancer Center, São Paulo, S.P., 01508-010, Brazil [2]
| | - Elisa N Ferreira
- 1] Genomics and Molecular Biology Laboratory, International Research Center, A. C. Camargo Cancer Center, São Paulo, S.P., 01508-010, Brazil [2]
| | - Adriana M Nakahata
- Genomics and Molecular Biology Laboratory, International Research Center, A. C. Camargo Cancer Center, São Paulo, S.P., 01508-010, Brazil
| | - Bruna D F Barros
- Genomics and Molecular Biology Laboratory, International Research Center, A. C. Camargo Cancer Center, São Paulo, S.P., 01508-010, Brazil
| | - Mayra T M Castro
- Genomics and Molecular Biology Laboratory, International Research Center, A. C. Camargo Cancer Center, São Paulo, S.P., 01508-010, Brazil
| | - Bruna R Correa
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, S.P., 01308-060, Brazil
| | - Ana C V Krepischi
- Genomics and Molecular Biology Laboratory, International Research Center, A. C. Camargo Cancer Center, São Paulo, S.P., 01508-010, Brazil
| | - Eloisa H R Olivieri
- Genomics and Molecular Biology Laboratory, International Research Center, A. C. Camargo Cancer Center, São Paulo, S.P., 01508-010, Brazil
| | - Isabela W Cunha
- Department of Pathology, A. C. Camargo Cancer Center, São Paulo, S.P., 01509-900, Brazil
| | - Uri Tabori
- Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8
| | - Paul E Grundy
- Cancer Control Alberta, Alberta Health Services, Edmonton, Alberta, Canada AB T5J 3H1
| | - Cecilia M L Costa
- Department of Pediatrics, A. C. Camargo Cancer Center, São Paulo, S.P., 01509-010, Brazil
| | - Beatriz de Camargo
- Pediatric Hematology-Oncology Research Program, Instituto Nacional de Cancer, INCA, Rio de Janeiro, R.J., 20231-050, Brazil
| | - Pedro A F Galante
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, S.P., 01308-060, Brazil
| | - Dirce M Carraro
- Genomics and Molecular Biology Laboratory, International Research Center, A. C. Camargo Cancer Center, São Paulo, S.P., 01508-010, Brazil
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33
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Liang YH, Lavoie M, Comeau MA, Abou Elela S, Ji X. Structure of a eukaryotic RNase III postcleavage complex reveals a double-ruler mechanism for substrate selection. Mol Cell 2014; 54:431-44. [PMID: 24703949 DOI: 10.1016/j.molcel.2014.03.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 12/23/2013] [Accepted: 02/27/2014] [Indexed: 11/19/2022]
Abstract
Ribonuclease III (RNase III) enzymes are a family of double-stranded RNA (dsRNA)-specific endoribonucleases required for RNA maturation and gene regulation. Prokaryotic RNase III enzymes have been well characterized, but how eukaryotic RNase IIIs work is less clear. Here, we describe the structure of the Saccharomyces cerevisiae RNase III (Rnt1p) postcleavage complex and explain why Rnt1p binds to RNA stems capped with an NGNN tetraloop. The structure shows specific interactions between a structural motif located at the end of the Rnt1p dsRNA-binding domain (dsRBD) and the guanine nucleotide in the second position of the loop. Strikingly, structural and biochemical analyses indicate that the dsRBD and N-terminal domains (NTDs) of Rnt1p function as two rulers that measure the distance between the tetraloop and the cleavage site. These findings provide a framework for understanding eukaryotic RNase IIIs.
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Affiliation(s)
- Yu-He Liang
- Biomolecular Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Mathieu Lavoie
- RNA Group/Groupe ARN, Département de microbiologie et d'infectiologie, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Marc-Andre Comeau
- RNA Group/Groupe ARN, Département de microbiologie et d'infectiologie, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Sherif Abou Elela
- RNA Group/Groupe ARN, Département de microbiologie et d'infectiologie, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada.
| | - Xinhua Ji
- Biomolecular Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
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34
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Hackl M, Jadhav V, Klanert G, Karbiener M, Scheideler M, Grillari J, Borth N. Analysis of microRNA transcription and post-transcriptional processing by Dicer in the context of CHO cell proliferation. J Biotechnol 2014; 190:76-84. [PMID: 24486028 PMCID: PMC4247382 DOI: 10.1016/j.jbiotec.2013.12.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 12/05/2013] [Accepted: 12/11/2013] [Indexed: 11/25/2022]
Abstract
The expression of Dicer is correlated to growth rate in different CHO cell lines. Global perturbation of microRNA levels via DICER knockdown or overexpression directly influences CHO growth behavior. This provides strong evidence that microRNAs are key growth regulators in CHO cell lines.
CHO cells are the mammalian cell line of choice for recombinant production of therapeutic proteins. However, their low rate of proliferation limits obtainable space-time yields due to inefficient biomass accumulation. We set out to correlate microRNA transcription to cell-specific growth-rate by microarray analysis of 5 CHO suspension cell lines with low to high specific growth rates. Global microRNA expression analysis and Pearson correlation studies showed that mature microRNA transcript levels are predominately up-regulated in a state of fast proliferation (46 positively correlated, 17 negatively correlated). To further validate this observation, the expression of three genes that are central to microRNA biogenesis (Dicer, Drosha and Dgcr8) was analyzed. The expression of Dicer, which mediates the final step in microRNA maturation, was found to be strongly correlated to growth rate. Accordingly, knockdown of Dicer impaired cell growth by reducing growth-correlating microRNA transcripts. Moderate ectopic overexpression of Dicer positively affected cell growth, while strong overexpression impaired growth, presumably due to the concomitant increase of microRNAs that inhibit cell growth. Our data therefore suggest that Dicer dependent microRNAs regulate CHO cell proliferation and that Dicer could serve as a potential surrogate marker for cellular proliferation.
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Affiliation(s)
- Matthias Hackl
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Vaibhav Jadhav
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Gerald Klanert
- ACIB GmbH, Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - Michael Karbiener
- RNA Biology Group, Institute for Genomics and Bioinformatics, Graz University of Technology, 8010 Graz, Austria
| | - Marcel Scheideler
- RNA Biology Group, Institute for Genomics and Bioinformatics, Graz University of Technology, 8010 Graz, Austria
| | - Johannes Grillari
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Nicole Borth
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria; ACIB GmbH, Austrian Centre of Industrial Biotechnology, Graz, Austria.
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35
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Neubacher S, Arenz C. Detection of microRNA maturation using unmodified pre-microRNA and branched rolling circle amplification. Methods Mol Biol 2014; 1095:109-119. [PMID: 24166307 DOI: 10.1007/978-1-62703-703-7_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The ever-increasing number of different miRNAs and their association with a vast number of cellular dysfunctions and diseases have initiated several groups to investigate miRNA maturation, which ultimately leads to down regulation of a target messenger RNA (mRNA) and its downstream product. A rapid, convenient, and reliable assay to detect the Dicer-mediated miRNA-maturation step may facilitate research in this field. Here we describe the in vitro detection of the Dicer-mediated miRNA maturation step using unmodified pre-miRNA and branched rolling circle amplification.
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Affiliation(s)
- Saskia Neubacher
- Institute for Chemistry, Humboldt Universität zu Berlin, Berlin, Germany
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36
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Ghersi D, Singh M. Interaction-based discovery of functionally important genes in cancers. Nucleic Acids Res 2013; 42:e18. [PMID: 24362839 PMCID: PMC3919581 DOI: 10.1093/nar/gkt1305] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A major challenge in cancer genomics is uncovering genes with an active role in tumorigenesis from a potentially large pool of mutated genes across patient samples. Here we focus on the interactions that proteins make with nucleic acids, small molecules, ions and peptides, and show that residues within proteins that are involved in these interactions are more frequently affected by mutations observed in large-scale cancer genomic data than are other residues. We leverage this observation to predict genes that play a functionally important role in cancers by introducing a computational pipeline (http://canbind.princeton.edu) for mapping large-scale cancer exome data across patients onto protein structures, and automatically extracting proteins with an enriched number of mutations affecting their nucleic acid, small molecule, ion or peptide binding sites. Using this computational approach, we show that many previously known genes implicated in cancers are enriched in mutations within the binding sites of their encoded proteins. By focusing on functionally relevant portions of proteins--specifically those known to be involved in molecular interactions--our approach is particularly well suited to detect infrequent mutations that may nonetheless be important in cancer, and should aid in expanding our functional understanding of the genomic landscape of cancer.
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Affiliation(s)
- Dario Ghersi
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA and Department of Computer Science, Princeton University, Princeton, NJ 08544, USA
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37
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Ge X, Zhao X, Nakagawa A, Gong X, Skeen-Gaar RR, Shi Y, Gong H, Wang X, Xue D. A novel mechanism underlies caspase-dependent conversion of the dicer ribonuclease into a deoxyribonuclease during apoptosis. Cell Res 2013; 24:218-32. [PMID: 24323044 DOI: 10.1038/cr.2013.160] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 10/15/2013] [Accepted: 10/16/2013] [Indexed: 01/04/2023] Open
Abstract
During C. elegans apoptosis, the dicer ribonuclease (DCR-1) is cleaved by the cell death protease CED-3 to generate a truncated DCR-1 (tDCR-1) with one and a half ribonuclease III (RNase III) domains, converting it into a deoxyribonuclease (DNase) that initiates apoptotic chromosome fragmentation. We performed biochemical and functional analyses to understand this unexpected RNase to DNase conversion. In full-length DCR-1, tDCR-1 DNase activity is suppressed by its N-terminal DCR-1 sequence. However, not all the sequence elements in the N-terminal DCR-1 are required for this suppression. Our deletion analysis reveals that a 20-residue α-helix sequence in DCR-1 appears to define a critical break point for the sequence required for suppressing tDCR-1 DNase activity through a structure-dependent mechanism. Removal of the N-terminal DCR-1 sequence from tDCR-1 activates a DNA-binding activity that also requires the one half RNase IIIa domain, and enables tDCR-1 to process DNA. Consistently, structural modeling of DCR-1 and tDCR-1 suggests that cleavage of DCR-1 by CED-3 may cause a conformational change that allows tDCR-1 to bind and process DNA, and may remove steric hindrance that blocks DNA access to tDCR-1. Moreover, a new DNase can be engineered using different RNase III domains, including the one from bacterial RNase III. Our results indicate that very distantly related RNase III enzymes have the potential to cleave DNA when processed proteolytically or paired with an appropriate partner that facilitates binding to DNA. We suggest the possibility that this phenomenon may be extrapolated to other ribonucleases.
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Affiliation(s)
- Xiao Ge
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiang Zhao
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Akihisa Nakagawa
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Xinqi Gong
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Riley Robert Skeen-Gaar
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Yong Shi
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Haipeng Gong
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xinquan Wang
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ding Xue
- 1] School of Life Sciences, Tsinghua University, Beijing 100084, China [2] Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
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38
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de Faria IJDS, Olmo RP, Silva EG, Marques JT. dsRNA sensing during viral infection: lessons from plants, worms, insects, and mammals. J Interferon Cytokine Res 2013; 33:239-53. [PMID: 23656598 DOI: 10.1089/jir.2013.0026] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Host defense systems often rely on direct and indirect pattern recognition to sense the presence of invading pathogens. Patterns can be molecules directly produced by the pathogen or indirectly generated by changes in host parameters as a consequence of infection. Viruses are intracellular pathogens that hijack the cellular machinery to synthesize their own molecules making direct recognition of viral molecules a great challenge. Antiviral systems in prokaryotes and eukaryotes commonly exploit aberrant nucleic acid sensing to recognize virus infection as host and viral nucleic acid metabolism can greatly differ. Indeed, the generation of dsRNA is often associated with viral infection. In this review, we discuss current knowledge on the mechanisms of viral dsRNA sensing utilized by 2 important antiviral defense systems, RNA interference (RNAi) and the vertebrate immune system. The major viral sensors of the vertebrate immune systems are RIG-like receptors, while RNAi pathways depend on Dicer proteins. These 2 families of sensors share a similar helicase domain with high specificity for dsRNA, which is necessary, but not sufficient for efficient recognition by these receptors. Additional intrinsic features to the dsRNA molecule are also necessary for activation of antiviral systems. Studies utilizing synthetic ligands, in vitro biochemistry and reporter systems have greatly helped increase our knowledge on intrinsic features of dsRNA recognition. However, characteristics such as subcellular localization are extrinsic to the dsRNA itself, but certainly influence the recognition in vivo. Thus, mechanisms of viral dsRNA recognition must address how cellular sensors are recruited to nucleic acids or vice versa. Accessory proteins are likely important for in vivo recognition of extrinsic features of viral RNA, but have mostly remained undiscovered due to the limitations of previous strategies. Hence, the identification of novel components of antiviral systems must take into account the complexities involved in viral recognition in vivo.
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39
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Sawh AN, Duchaine TF. A truncated form of dicer tilts the balance of RNA interference pathways. Cell Rep 2013; 4:454-63. [PMID: 23933256 DOI: 10.1016/j.celrep.2013.07.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 06/25/2013] [Accepted: 07/12/2013] [Indexed: 12/15/2022] Open
Abstract
The RNase III enzyme Dicer is responsible for key steps in the biogenesis of small RNA species in multiple RNA interference pathways. Here, we show that, in the adult C. elegans soma, half of the total DCR-1 protein is expressed as a truncated, stable C-terminal fragment named small DCR-1 (sDCR-1). sDCR-1 operates independently of full-length DCR-1 in two distinct RNAi pathways; it enhances exogenous RNAi (exoRNAi) and concurrently acts as a negative regulator of microRNA (miRNA) biogenesis. Enhancement of exoRNAi relies on sDCR-1 catalytic activity, whereas impinging on miRNA processing does not. Instead, sDCR-1 competes with pre-miRNA processing by interacting with the miRNA-dedicated Argonautes ALG-1 and ALG-2. Finally, triggering a strong exoRNAi response in the presence of elevated levels of sDCR-1 exacerbates the miRNA processing defect. Our results unveil a surprising role for a truncated form of DCR-1 in the modulation of multiple RNAi activities and in the regulation of mechanistic boundaries between pathways.
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Affiliation(s)
- Ahilya N Sawh
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, QC H3G 1Y6, Canada
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40
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Wu MK, Sabbaghian N, Xu B, Addidou-Kalucki S, Bernard C, Zou D, Reeve AE, Eccles MR, Cole C, Choong CS, Charles A, Tan TY, Iglesias DM, Goodyer PR, Foulkes WD. Biallelic DICER1 mutations occur in Wilms tumours. J Pathol 2013; 230:154-64. [PMID: 23620094 DOI: 10.1002/path.4196] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 03/20/2013] [Accepted: 03/29/2013] [Indexed: 12/21/2022]
Abstract
DICER1 is an endoribonuclease central to the generation of microRNAs (miRNAs) and short interfering RNAs (siRNAs). Germline mutations in DICER1 have been associated with a pleiotropic tumour predisposition syndrome and Wilms tumour (WT) is a rare manifestation of this syndrome. Three WTs, each in a child with a deleterious germline DICER1 mutation, were screened for somatic DICER1 mutations and were found to bear specific mutations in either the RNase IIIa (n = 1) or the RNase IIIb domain (n = 2). In the two latter cases, we demonstrate that the germline and somatic DICER1 mutations were in trans, suggesting that the two-hit hypothesis of tumour formation applies for these examples of WT. Among 191 apparently sporadic WTs, we identified five different missense or deletion somatic DICER1 mutations (2.6%) in four individual WTs; one tumour had two very likely deleterious somatic mutations in trans in the RNase IIIb domain (c.5438A>G and c.5452G>A). In vitro studies of two somatic single-base substitutions (c.5429A>G and c.5438A>G) demonstrated exon 25 skipping from the transcript, a phenomenon not previously reported in DICER1. Further we show that DICER1 transcripts lacking exon 25 can be translated in vitro. This study has demonstrated that a subset of WTs exhibits two 'hits' in DICER1, suggesting that these mutations could be key events in the pathogenesis of these tumours.
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Affiliation(s)
- M K Wu
- Department of Medical Genetics, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
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41
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DOLORS: versatile strategy for internal labeling and domain localization in electron microscopy. Structure 2013; 20:1995-2002. [PMID: 23217681 DOI: 10.1016/j.str.2012.10.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 10/11/2012] [Accepted: 10/31/2012] [Indexed: 11/22/2022]
Abstract
Single-particle electron microscopy (EM) is a powerful tool for studying the structures of large biological molecules. However, the achievable resolution does not always allow for direct recognition of individual protein domains. Labels that can be visualized by EM have been developed for protein termini, but tagging internal domains remains a challenge. We describe a robust strategy for determining the position of internal sites within EM maps, termed domain localization by RCT sampling (DOLORS). DOLORS uses monovalent streptavidin added posttranslationally to tagged sites in the target protein. Internal labels generally display less conformational flexibility than terminal labels, providing more precise positional information. Automated methods are used to rapidly generate assemblies of unique 3D models allowing the attachment sites of labeled domains to be accurately identified and thus provide an overall architectural map of the molecule.
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42
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Anglesio MS, Wang Y, Yang W, Senz J, Wan A, Heravi-Moussavi A, Salamanca C, Maines-Bandiera S, Huntsman DG, Morin GB. Cancer-associated somatic DICER1 hotspot mutations cause defective miRNA processing and reverse-strand expression bias to predominantly mature 3p strands through loss of 5p strand cleavage. J Pathol 2013; 229:400-9. [PMID: 23132766 DOI: 10.1002/path.4135] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Revised: 09/26/2012] [Accepted: 10/10/2012] [Indexed: 12/19/2022]
Abstract
Our group recently described recurrent somatic mutations of the miRNA processing gene DICER1 in non-epithelial ovarian cancer. Mutations appeared to be clustered around each of four critical metal-binding residues in the RNase IIIB domain of DICER1. This domain is responsible for cleavage of the 3' end of the 5p miRNA strand of a pre-mRNA hairpin. To investigate the effects of these cancer-associated 'hotspot' mutations, we engineered mouse DICER1-deficient ES cells to express wild-type and an allelic series of the mutant DICER1 variants. Global miRNA and mRNA profiles from cells carrying the metal-binding site mutations were compared to each other and to wild-type DICER1. The miRNA and mRNA profiles generated through the expression of the hotspot mutations were virtually identical, and the DICER1 hotspot mutation-carrying cells were distinct from both wild-type and DICER1-deficient cells. Further, miRNA profiles showed that mutant DICER1 results in a dramatic loss in processing of mature 5p miRNA strands but were still able to create 3p strand miRNAs. Messenger RNA (mRNA) profile changes were consistent with the loss of 5p strand miRNAs and showed enriched expression for predicted targets of the lost 5p-derived miRNAs. We therefore conclude that cancer-associated somatic hotspot mutations of DICER1, affecting any one of four metal-binding residues in the RNase IIIB domain, are functionally equivalent with respect to miRNA processing and are hypomorphic alleles, yielding a global loss in processing of mature 5p strand miRNA. We further propose that this resulting 3p strand bias in mature miRNA expression likely underpins the oncogenic potential of these hotspot mutations.
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Affiliation(s)
- M S Anglesio
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
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43
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Kashida S, Inoue T, Saito H. Three-dimensionally designed protein-responsive RNA devices for cell signaling regulation. Nucleic Acids Res 2012; 40:9369-78. [PMID: 22810207 PMCID: PMC3467064 DOI: 10.1093/nar/gks668] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The three-dimensional (3D) structures of many biomacromolecules have been solved to reveal the functions of these molecules. However, these 3D structures have rarely been applied to constructing efficient molecular devices that function in living cells. Here, we demonstrate a 3D structure-based molecular design principle for constructing short hairpin RNA (shRNA)-mediated genetic information converters; these converters respond to specific proteins and trigger the desired gene expression by modulating the function of the RNA-processing enzyme Dicer. The inhibitory effect on Dicer cleavage against the shRNA designed to specifically bind to U1A spliceosomal protein was correlated with the degree of steric hindrance between Dicer and the shRNA-protein complex in vitro: The level of the hindrance was predicted based on the models. Moreover, the regulation of gene expression was achieved by using the shRNA converters designed to bind to the target U1A or nuclear factor-κB (NF-κB) p50 proteins expressed in human cells. The 3D molecular design approach is widely applicable for developing new devices in synthetic biology.
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Affiliation(s)
- Shunnichi Kashida
- Laboratory of Gene Biodynamics, Graduate School of Biostudies, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
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44
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Affiliation(s)
- Allen W Nicholson
- Department of Biology, Temple University, Philadelphia, PA 19122, USA.
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45
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Hackl M, Jadhav V, Jakobi T, Rupp O, Brinkrolf K, Goesmann A, Pühler A, Noll T, Borth N, Grillari J. Computational identification of microRNA gene loci and precursor microRNA sequences in CHO cell lines. J Biotechnol 2012; 158:151-5. [PMID: 22306111 PMCID: PMC3314935 DOI: 10.1016/j.jbiotec.2012.01.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 01/11/2012] [Accepted: 01/13/2012] [Indexed: 11/05/2022]
Abstract
MicroRNAs (miRNAs) have recently entered Chinese hamster ovary (CHO) cell culture technology, due to their severe impact on the regulation of cellular phenotypes. Applications of miRNAs that are envisioned range from biomarkers of favorable phenotypes to cell engineering targets. These applications, however, require a profound knowledge of miRNA sequences and their genomic organization, which exceeds the currently available information of ~400 conserved mature CHO miRNA sequences. Based on these recently published sequences and two independent CHO-K1 genome assemblies, this publication describes the computational identification of CHO miRNA genomic loci. Using BLAST alignment, 415 previously reported CHO miRNAs were mapped to the reference genomes, and subsequently assigned to a distinct genomic miRNA locus. Sequences of the respective precursor-miRNAs were extracted from both reference genomes, folded in silico to verify correct structures and cross-compared. In the end, 212 genomic loci and pre-miRNA sequences representing 319 expressed mature miRNAs (approximately 50% of miRNAs represented matching pairs of 5' and 3' miRNAs) were submitted to the miRBase miRNA repository. As a proof-of-principle for the usability of the published genomic loci, four likely polycistronic miRNA cluster were chosen for PCR amplification using CHO-K1 and DHFR (-) genomic DNA. Overall, these data on the genomic context of miRNA expression in CHO will simplify the development of tools employing stable overexpression or deletion of miRNAs, allow the identification of miRNA promoters and improve detection methods such as microarrays.
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Affiliation(s)
- Matthias Hackl
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Vaibhav Jadhav
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Tobias Jakobi
- Centrum für Biotechnologie, Universität Bielefeld, 33594 Bielefeld, Germany
| | - Oliver Rupp
- Centrum für Biotechnologie, Universität Bielefeld, 33594 Bielefeld, Germany
| | - Karina Brinkrolf
- Centrum für Biotechnologie, Universität Bielefeld, 33594 Bielefeld, Germany
| | - Alexander Goesmann
- Centrum für Biotechnologie, Universität Bielefeld, 33594 Bielefeld, Germany
| | - Alfred Pühler
- Centrum für Biotechnologie, Universität Bielefeld, 33594 Bielefeld, Germany
| | - Thomas Noll
- AG Zellkulturtechnik, Technische Fakultät, Universität Bielefeld, 33549 Bielefeld, Germany
| | - Nicole Borth
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- ACIB GmbH, Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - Johannes Grillari
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
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46
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The molecular architecture of human Dicer. Nat Struct Mol Biol 2012; 19:436-40. [PMID: 22426548 PMCID: PMC3319852 DOI: 10.1038/nsmb.2268] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Accepted: 02/22/2012] [Indexed: 12/20/2022]
Abstract
Dicer is a multi-domain enzyme that generates small RNAs for gene silencing in eukaryotes. Current understanding of Dicer structure is restricted to simple forms of the enzyme, while that of the large and complex Dicer, widespread in eukarya, is unknown. Here, we describe a novel domain localization strategy developed to determine the structure of human Dicer by electron microscopy. A rearrangement of the nuclease core, compared to the archetypal Giardia Dicer, explains how metazoan Dicers generate 21–23 nucleotide products. The helicase domains form a clamp-like structure adjacent to the RNase III active site, facilitating recognition of pre-miRNA loops or translocation on long dsRNAs. Drosophila Dicer-2 displays similar features, revealing that the three-dimensional architecture is conserved. These results illuminate the structural basis for small RNA production in eukaryotes and provide a versatile new tool for determining structures of large molecular machines.
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47
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Ohishi K, Nakano T. A forward genetic screen to study mammalian RNA interference: essential role of RNase IIIa domain of Dicer1 in 3' strand cleavage of dsRNA in vivo. FEBS J 2012; 279:832-43. [PMID: 22221880 DOI: 10.1111/j.1742-4658.2012.08474.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
RNA interference is a major post-transcriptional regulatory pathway in many eukaryotes. The RNase III enzyme Dicer1 processes precursor RNAs into small RNA duplexes to be loaded onto Argonaute proteins, the effector components of RNA-induced silencing complex. Biochemical studies have shown that the RNase IIIa and RNase IIIb domains of Dicer1 cleave the 3' and 5' strands of dsRNAs, respectively, although the in vivo functional significance of this activity remains unclear. Genetic screening of mammalian cells is useful for studying molecular mechanisms at the cellular level. In the present study, we conducted a novel forward genetic screen for mammalian RNA interference components using Chinese hamster ovary cells and successfully obtained several Dicer1 mutant lines. One mutant bore an intriguing Dicer1 allele in which a conserved glutamic acid in the RNase IIIa domain was substituted with a lysine. Our detailed cell biological study demonstrated that the RNase IIIa domain of Dicer1 was essential for generating small RNAs embedded in the 3' stem of exogenous hairpin-like RNAs. In the mutant cells, the expression of endogenous mature microRNAs derived from the 3' stem of pre-microRNA was repressed more severely than that from the 5' stem. Moreover, appropriate processing and loading of small RNAs were required for the dissociation of Argonaute 2 from Dicer1. The data obtained in the present study demonstrate that this screening method represents a promising strategy for the identification of unknown components of mammalian RNA interference pathways and the study of the biological significance of these components at the cellular level.
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Affiliation(s)
- Kazuhito Ohishi
- Department of Pathology, Medical School, Osaka University, Japan
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Heravi-Moussavi A, Anglesio MS, Cheng SWG, Senz J, Yang W, Prentice L, Fejes AP, Chow C, Tone A, Kalloger SE, Hamel N, Roth A, Ha G, Wan ANC, Maines-Bandiera S, Salamanca C, Pasini B, Clarke BA, Lee AF, Lee CH, Zhao C, Young RH, Aparicio SA, Sorensen PHB, Woo MMM, Boyd N, Jones SJM, Hirst M, Marra MA, Gilks B, Shah SP, Foulkes WD, Morin GB, Huntsman DG. Recurrent somatic DICER1 mutations in nonepithelial ovarian cancers. N Engl J Med 2012; 366:234-42. [PMID: 22187960 DOI: 10.1056/nejmoa1102903] [Citation(s) in RCA: 326] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Germline truncating mutations in DICER1, an endoribonuclease in the RNase III family that is essential for processing microRNAs, have been observed in families with the pleuropulmonary blastoma-family tumor and dysplasia syndrome. Mutation carriers are at risk for nonepithelial ovarian tumors, notably sex cord-stromal tumors. METHODS We sequenced the whole transcriptomes or exomes of 14 nonepithelial ovarian tumors and noted closely clustered mutations in the region of DICER1 encoding the RNase IIIb domain of DICER1 in four samples. We then sequenced this region of DICER1 in additional ovarian tumors and in certain other tumors and queried the effect of the mutations on the enzymatic activity of DICER1 using in vitro RNA cleavage assays. RESULTS DICER1 mutations in the RNase IIIb domain were found in 30 of 102 nonepithelial ovarian tumors (29%), predominantly in Sertoli-Leydig cell tumors (26 of 43, or 60%), including 4 tumors with additional germline DICER1 mutations. These mutations were restricted to codons encoding metal-binding sites within the RNase IIIb catalytic centers, which are critical for microRNA interaction and cleavage, and were somatic in all 16 samples in which germline DNA was available for testing. We also detected mutations in 1 of 14 nonseminomatous testicular germ-cell tumors, in 2 of 5 embryonal rhabdomyosarcomas, and in 1 of 266 epithelial ovarian and endometrial carcinomas. The mutant DICER1 proteins had reduced RNase IIIb activity but retained RNase IIIa activity. CONCLUSIONS Somatic missense mutations affecting the RNase IIIb domain of DICER1 are common in nonepithelial ovarian tumors. These mutations do not obliterate DICER1 function but alter it in specific cell types, a novel mechanism through which perturbation of microRNA processing may be oncogenic. (Funded by the Terry Fox Research Institute and others.).
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Dicer Proteins and Their Role in Gene Silencing Pathways. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/b978-0-12-404741-9.00001-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
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Niederer F, Trenkmann M, Ospelt C, Karouzakis E, Neidhart M, Stanczyk J, Kolling C, Gay RE, Detmar M, Gay S, Jüngel A, Kyburz D. Down-regulation of microRNA-34a* in rheumatoid arthritis synovial fibroblasts promotes apoptosis resistance. ACTA ACUST UNITED AC 2011; 64:1771-9. [PMID: 22161761 DOI: 10.1002/art.34334] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVE To investigate the expression and effect of the microRNA-34 (miR-34) family on apoptosis in rheumatoid arthritis synovial fibroblasts (RASFs). METHODS Expression of the miR-34 family in synovial fibroblasts with or without stimulation with Toll-like receptor (TLR) ligands, tumor necrosis factor α (TNFα), interleukin-1β (IL-1β), hypoxia, or 5-azacytidine was analyzed by real-time polymerase chain reaction (PCR). Promoter methylation was studied by combined bisulfite restriction analysis. The effects of overexpression and silencing of miR-34a and miR-34a* on apoptosis were analyzed by annexin V/propidium iodide staining. Production of X-linked inhibitor of apoptosis protein (XIAP) was assessed by real-time PCR and immunohistochemistry analysis. Reporter gene assay was used to study the signaling pathways of miR-34a*. RESULTS Basal expression levels of miR-34a* were found to be reduced in synovial fibroblasts from RA patients compared to osteoarthritis patients, whereas levels of miR-34a, miR-34b/b*, and miR-34c/c* did not differ. Neither TNFα, IL-1β, TLR ligands, nor hypoxia altered miR-34a* expression. However, we demonstrated that the promoter of miR-34a/34a* was methylated and showed that transcription of the miR-34a duplex was induced upon treatment with demethylating agents. Enforced expression of miR-34a* led to an increased rate of FasL- and TRAIL-mediated apoptosis in RASFs. Moreover, levels of miR-34a* were highly correlated with expression of XIAP, which was found to be up-regulated in RA synovial cells. Finally, we identified XIAP as a direct target of miR-34a*. CONCLUSION Our data provide evidence of a methylation-specific down-regulation of proapoptotic miR-34a* in RASFs. Decreased expression of miR- 34a* results in up-regulation of its direct target XIAP, thereby contributing to resistance of RASFs to apoptosis.
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