1
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Oikawa K, Ohno SI, Ono K, Hirao K, Murakami A, Harada Y, Kumagai K, Sudo K, Takanashi M, Ishikawa A, Mineo S, Fujita K, Umezu T, Watanabe N, Murakami Y, Ogawa S, Schultz KA, Kuroda M. Liver-specific DICER1 syndrome model mice develop cystic liver tumors with defective primary cilia. J Pathol 2024; 264:17-29. [PMID: 38922876 DOI: 10.1002/path.6320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 05/01/2024] [Accepted: 05/20/2024] [Indexed: 06/28/2024]
Abstract
DICER1 syndrome is a tumor predisposition syndrome caused by familial genetic mutations in DICER1. Pathogenic variants of DICER1 have been discovered in many rare cancers, including cystic liver tumors. However, the molecular mechanisms underlying liver lesions induced by these variants remain unclear. In the present study, we sought to gain a better understanding of the pathogenesis of these variants by generating a mouse model of liver-specific DICER1 syndrome. The mouse model developed bile duct hyperplasia with fibrosis, similar to congenital hepatic fibrosis, as well as cystic liver tumors resembling those in Caroli's syndrome, intrahepatic cholangiocarcinoma, and hepatocellular carcinoma. Interestingly, the mouse model of DICER1 syndrome showed abnormal formation of primary cilia in the bile duct epithelium, which is a known cause of bile duct hyperplasia and cyst formation. These results indicated that DICER1 mutations contribute to cystic liver tumors by inducing defective primary cilia. The mouse model generated in this study will be useful for elucidating the potential mechanisms of tumorigenesis induced by DICER1 variants and for obtaining a comprehensive understanding of DICER1 syndrome. © 2024 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Keiki Oikawa
- Department of Molecular Pathology, Tokyo Medical University, Tokyo, Japan
| | - Shin-Ichiro Ohno
- Department of Molecular Pathology, Tokyo Medical University, Tokyo, Japan
| | - Kana Ono
- Department of Molecular Pathology, Tokyo Medical University, Tokyo, Japan
| | - Kaito Hirao
- Department of Molecular Pathology, Tokyo Medical University, Tokyo, Japan
| | - Ayano Murakami
- Department of Molecular Pathology, Tokyo Medical University, Tokyo, Japan
| | - Yuichirou Harada
- Department of Molecular Pathology, Tokyo Medical University, Tokyo, Japan
| | - Katsuyoshi Kumagai
- Department of Pre-clinical Research Center, Tokyo Medical University, Tokyo, Japan
| | - Katsuko Sudo
- Department of Pre-clinical Research Center, Tokyo Medical University, Tokyo, Japan
| | | | - Akio Ishikawa
- Department of Molecular Pathology, Tokyo Medical University, Tokyo, Japan
| | - Shouichirou Mineo
- Department of Molecular Pathology, Tokyo Medical University, Tokyo, Japan
| | - Koji Fujita
- Department of Molecular Pathology, Tokyo Medical University, Tokyo, Japan
| | - Tomohiro Umezu
- Department of Molecular Pathology, Tokyo Medical University, Tokyo, Japan
| | - Noriko Watanabe
- Department of Molecular Pathology, Tokyo Medical University, Tokyo, Japan
| | - Yoshiki Murakami
- Department of Molecular Pathology, Tokyo Medical University, Tokyo, Japan
| | - Shinichiro Ogawa
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Kris Ann Schultz
- Cancer and Blood Disorders, Children's Minnesota, Minneapolis, MN, USA
| | - Masahiko Kuroda
- Department of Molecular Pathology, Tokyo Medical University, Tokyo, Japan
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2
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Fan S, Liu J, Chofflet N, Bailey AO, Russell WK, Zhang Z, Takahashi H, Ren G, Rudenko G. Molecular mechanism of contactin 2 homophilic interaction. Structure 2024:S0969-2126(24)00222-3. [PMID: 38968938 DOI: 10.1016/j.str.2024.06.004] [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: 04/12/2024] [Revised: 05/23/2024] [Accepted: 06/10/2024] [Indexed: 07/07/2024]
Abstract
Contactin 2 (CNTN2) is a cell adhesion molecule involved in axon guidance, neuronal migration, and fasciculation. The ectodomains of CNTN1-CNTN6 are composed of six Ig domains (Ig1-Ig6) and four FN domains. Here, we show that CNTN2 forms transient homophilic interactions (KD ∼200 nM). Cryo-EM structures of full-length CNTN2 and CNTN2_Ig1-Ig6 reveal a T-shaped homodimer formed by intertwined, parallel monomers. Unexpectedly, the horseshoe-shaped Ig1-Ig4 headpieces extend their Ig2-Ig3 tips outwards on either side of the homodimer, while Ig4, Ig5, Ig6, and the FN domains form a central stalk. Cross-linking mass spectrometry and cell-based binding assays confirm the 3D assembly of the CNTN2 homodimer. The interface mediating homodimer formation differs between CNTNs, as do the homophilic versus heterophilic interaction mechanisms. The CNTN family thus encodes a versatile molecular platform that supports a very diverse portfolio of protein interactions and that can be leveraged to strategically guide neural circuit development.
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Affiliation(s)
- Shanghua Fan
- Department of Pharmacology and Toxicology; University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Nicolas Chofflet
- Synapse Development and Plasticity Research Unit, Institut de Recherches Cliniques de Montréal, Montreal, QC H2W 1R7, Canada; Integrated Program in Neuroscience, McGill University, Montreal, QC H3A 2B2, Canada
| | - Aaron O Bailey
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - William K Russell
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Ziqi Zhang
- Synapse Development and Plasticity Research Unit, Institut de Recherches Cliniques de Montréal, Montreal, QC H2W 1R7, Canada
| | - Hideto Takahashi
- Synapse Development and Plasticity Research Unit, Institut de Recherches Cliniques de Montréal, Montreal, QC H2W 1R7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3T 1J4, Canada; Division of Experimental Medicine, McGill University, Montreal, QC H3A 0G4, Canada.
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Gabby Rudenko
- Department of Pharmacology and Toxicology; University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA.
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3
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Wang F, Zhou C, Zhu Y, Keshavarzi M. The microRNA Let-7 and its exosomal form: Epigenetic regulators of gynecological cancers. Cell Biol Toxicol 2024; 40:42. [PMID: 38836981 PMCID: PMC11153289 DOI: 10.1007/s10565-024-09884-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/15/2024] [Indexed: 06/06/2024]
Abstract
Many types of gynecological cancer (GC) are often silent until they reach an advanced stage, and are therefore often diagnosed too late for effective treatment. Hence, there is a real need for more efficient diagnosis and treatment for patients with GC. During recent years, researchers have increasingly studied the impact of microRNAs cancer development, leading to a number of applications in detection and treatment. MicroRNAs are a particular group of tiny RNA molecules that regulate regular gene expression by affecting the translation process. The downregulation of numerous miRNAs has been observed in human malignancies. Let-7 is an example of a miRNA that controls cellular processes as well as signaling cascades to affect post-transcriptional gene expression. Recent research supports the hypothesis that enhancing let-7 expression in those cancers where it is downregulated may be a potential treatment option. Exosomes are tiny vesicles that move through body fluids and can include components like miRNAs (including let-7) that are important for communication between cells. Studies proved that exosomes are able to enhance tumor growth, angiogenesis, chemoresistance, metastasis, and immune evasion, thus suggesting their importance in GC management.
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Affiliation(s)
- Fei Wang
- Haiyan People's Hospital, Zhejiang Province, Jiaxing, 314300, Zhejiang, China
| | - Chundi Zhou
- Haiyan People's Hospital, Zhejiang Province, Jiaxing, 314300, Zhejiang, China
| | - Yanping Zhu
- Haiyan People's Hospital, Zhejiang Province, Jiaxing, 314300, Zhejiang, China.
| | - Maryam Keshavarzi
- School of Medicine, Tehran University of Medical Sciences, Tehran, Tehran, Iran.
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4
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Immanneni C, Calame D, Jiao S, Emrick LT, Holmgren M, Yano ST. ATP1A3 Disease Spectrum Includes Paroxysmal Weakness and Encephalopathy Not Triggered by Fever. Neurol Genet 2024; 10:e200150. [PMID: 38685976 PMCID: PMC11057438 DOI: 10.1212/nxg.0000000000200150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 02/23/2024] [Indexed: 05/02/2024]
Abstract
Background and Objectives Heterozygous pathogenic variants in ATP1A3, which encodes the catalytic alpha subunit of neuronal Na+/K+-ATPase, cause primarily neurologic disorders with widely variable features that can include episodic movement deficits. One distinctive presentation of ATP1A3-related disease is recurrent fever-triggered encephalopathy. This can occur with generalized weakness and/or ataxia and is described in the literature as relapsing encephalopathy with cerebellar ataxia. This syndrome displays genotype-phenotype correlation with variants at p.R756 causing temperature sensitivity of ATP1A3. We report clinical and in vitro functional evidence for a similar phenotype not triggered by fever but associated with protein loss-of-function. Methods We describe the phenotype of an individual with de novo occurrence of a novel heterozygous ATP1A3 variant, NM_152296.5:c.388_390delGTG; p.(V130del). We confirmed the pathogenicity of p.V130del by cell survival complementation assay in HEK293 cells and then characterized its functional impact on enzymatic ion transport and extracellular sodium binding by two-electrode voltage clamp electrophysiology in Xenopus oocytes. To determine whether variant enzymes reach the cell surface, we surface-biotinylated oocytes expressing N-tagged ATP1A3. Results The proband is a 7-year-old boy who has had 2 lifetime episodes of paroxysmal weakness, encephalopathy, and ataxia not triggered by fever. He had speech regression and intermittent hand tremors after the second episode but otherwise spontaneously recovered after episodes and is at present developmentally appropriate. The p.V130del variant was identified on clinical trio exome sequencing, which did not reveal any other variants possibly associated with the phenotype. p.V130del eliminated ATP1A3 function in cell survival complementation assay. In Xenopus oocytes, p.V130del variant Na+/K+-ATPases showed complete loss of ion transport activity and marked abnormalities of extracellular Na+ binding at room temperature. Despite this clear loss-of-function effect, surface biotinylation under the same conditions revealed that p.V130del variant enzymes were still present at the oocyte's cell membrane. Discussion This individual's phenotype expands the clinical spectrum of ATP1A3-related recurrent encephalopathy to include presentations without fever-triggered events. The total loss of ion transport function with p.V130del, despite enzyme presence at the cell membrane, indicates that haploinsufficiency can cause relatively mild phenotypes in ATP1A3-related disease.
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Affiliation(s)
- Chetan Immanneni
- From the Sam Houston State University College of Osteopathic Medicine (C.I.), Conroe, TX; Molecular Neurophysiology Unit (C.I., S.J., M.H.), National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, MD; Section of Pediatric Neurology and Developmental Neuroscience (D.C.), Department of Pediatrics; Department of Molecular and Human Genetics (D.C., L.T.E.), Baylor College of Medicine; Texas Children's Hospital (D.C.), Houston, TX; National Human Genome Research Institute (S.T.Y.), National Institutes of Health, Bethesda, MD; and Section of Pediatric Neurology (S.T.Y.), Department of Pediatrics, University of Chicago, IL
| | - Daniel Calame
- From the Sam Houston State University College of Osteopathic Medicine (C.I.), Conroe, TX; Molecular Neurophysiology Unit (C.I., S.J., M.H.), National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, MD; Section of Pediatric Neurology and Developmental Neuroscience (D.C.), Department of Pediatrics; Department of Molecular and Human Genetics (D.C., L.T.E.), Baylor College of Medicine; Texas Children's Hospital (D.C.), Houston, TX; National Human Genome Research Institute (S.T.Y.), National Institutes of Health, Bethesda, MD; and Section of Pediatric Neurology (S.T.Y.), Department of Pediatrics, University of Chicago, IL
| | - Song Jiao
- From the Sam Houston State University College of Osteopathic Medicine (C.I.), Conroe, TX; Molecular Neurophysiology Unit (C.I., S.J., M.H.), National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, MD; Section of Pediatric Neurology and Developmental Neuroscience (D.C.), Department of Pediatrics; Department of Molecular and Human Genetics (D.C., L.T.E.), Baylor College of Medicine; Texas Children's Hospital (D.C.), Houston, TX; National Human Genome Research Institute (S.T.Y.), National Institutes of Health, Bethesda, MD; and Section of Pediatric Neurology (S.T.Y.), Department of Pediatrics, University of Chicago, IL
| | - Lisa T Emrick
- From the Sam Houston State University College of Osteopathic Medicine (C.I.), Conroe, TX; Molecular Neurophysiology Unit (C.I., S.J., M.H.), National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, MD; Section of Pediatric Neurology and Developmental Neuroscience (D.C.), Department of Pediatrics; Department of Molecular and Human Genetics (D.C., L.T.E.), Baylor College of Medicine; Texas Children's Hospital (D.C.), Houston, TX; National Human Genome Research Institute (S.T.Y.), National Institutes of Health, Bethesda, MD; and Section of Pediatric Neurology (S.T.Y.), Department of Pediatrics, University of Chicago, IL
| | - Miguel Holmgren
- From the Sam Houston State University College of Osteopathic Medicine (C.I.), Conroe, TX; Molecular Neurophysiology Unit (C.I., S.J., M.H.), National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, MD; Section of Pediatric Neurology and Developmental Neuroscience (D.C.), Department of Pediatrics; Department of Molecular and Human Genetics (D.C., L.T.E.), Baylor College of Medicine; Texas Children's Hospital (D.C.), Houston, TX; National Human Genome Research Institute (S.T.Y.), National Institutes of Health, Bethesda, MD; and Section of Pediatric Neurology (S.T.Y.), Department of Pediatrics, University of Chicago, IL
| | - Sho T Yano
- From the Sam Houston State University College of Osteopathic Medicine (C.I.), Conroe, TX; Molecular Neurophysiology Unit (C.I., S.J., M.H.), National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, MD; Section of Pediatric Neurology and Developmental Neuroscience (D.C.), Department of Pediatrics; Department of Molecular and Human Genetics (D.C., L.T.E.), Baylor College of Medicine; Texas Children's Hospital (D.C.), Houston, TX; National Human Genome Research Institute (S.T.Y.), National Institutes of Health, Bethesda, MD; and Section of Pediatric Neurology (S.T.Y.), Department of Pediatrics, University of Chicago, IL
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5
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Stone HM, Unal E, Romano TA, Turner PE. Beluga whale and bottlenose dolphin ACE2 proteins allow cell entry mediated by spike protein from three variants of SARS-CoV-2. Biol Lett 2023; 19:20230321. [PMID: 38053365 PMCID: PMC10698476 DOI: 10.1098/rsbl.2023.0321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 11/14/2023] [Indexed: 12/07/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viruses infect numerous non-human species. Spillover of SARS-CoV-2 into novel animal reservoirs may present a danger to host individuals of these species, particularly worrisome in populations already endangered or threatened by extinction. In addition, emergence in new reservoirs could pose spillback threats to humans, especially in the form of virus variants that further mutate when infecting other animal hosts. Previous work suggests beluga whales (Delphinapterus leucas) and bottlenose dolphins (Tursiops truncatus) may be at risk owing to their formation of social groups, contact with humans, exposure to contaminated wastewater, and structure of their angiotensin-converting enzyme 2 (ACE2) proteins, which SARS-CoV-2 uses as a cellular receptor. We examined marine-mammal susceptibility to virus infection by challenging 293T cells expressing beluga or dolphin ACE2 with pseudovirions bearing the SARS-CoV-2 spike protein. Beluga and dolphin ACE2 were sufficient to allow cell entry by an early pandemic isolate (Wuhan-Hu-1) and two evolved variants (Delta B.1.617.2 and Omicron BA.1 strains). We conclude that SARS-CoV-2 poses a potential threat to marine mammal reservoirs that should be considered in surveillance efforts.
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Affiliation(s)
- H. M. Stone
- Graduate Program in Microbiology, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - E. Unal
- Sea Research Foundation, Inc. d/b/a Mystic Aquarium, Mystic, CT 06355, USA
- Department of Marine Sciences, University of Connecticut Avery Point Campus, Groton, CT 06340, USA
| | - T. A. Romano
- Sea Research Foundation, Inc. d/b/a Mystic Aquarium, Mystic, CT 06355, USA
- Department of Marine Sciences, University of Connecticut Avery Point Campus, Groton, CT 06340, USA
| | - P. E. Turner
- Graduate Program in Microbiology, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
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6
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Pelletier D, Chong AL, Wu M, Witkowski L, Albert S, Sabbaghian N, Fabian M, Foulkes W. DICER1 platform domain missense variants inhibit miRNA biogenesis and lead to tumor susceptibility. NAR Cancer 2023; 5:zcad030. [PMID: 37333613 PMCID: PMC10273190 DOI: 10.1093/narcan/zcad030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/10/2023] [Accepted: 05/31/2023] [Indexed: 06/20/2023] Open
Abstract
The endoribonuclease DICER1 plays an essential role in the microRNA (miRNA) biogenesis pathway, cleaving precursor miRNA (pre-miRNA) stem-loops to generate mature single-stranded miRNAs. Germline pathogenic variants (GPVs) in DICER1 result in DICER1 tumor predisposition syndrome (DTPS), a mainly childhood-onset tumor susceptibility disorder. Most DTPS-causing GPVs are nonsense or frameshifting, with tumor development requiring a second somatic missense hit that impairs the DICER1 RNase IIIb domain. Interestingly, germline DICER1 missense variants that cluster in the DICER1 Platform domain have been identified in some persons affected by tumors that also associate with DTPS. Here, we demonstrate that four of these Platform domain variants prevent DICER1 from producing mature miRNAs and as a result impair miRNA-mediated gene silencing. Importantly, we show that in contrast to canonical somatic missense variants that alter DICER1 cleavage activity, DICER1 proteins harboring these Platform variants fail to bind to pre-miRNA stem-loops. Taken together, this work sheds light upon a unique subset of GPVs causing DTPS and provides new insights into how alterations in the DICER1 Platform domain can impact miRNA biogenesis.
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Affiliation(s)
- Dylan Pelletier
- Department of Human Genetics, Medicine, McGill University, Montreal, QC, Canada
- Cancer Axis, Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
- Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Anne-Laure Chong
- Department of Human Genetics, Medicine, McGill University, Montreal, QC, Canada
- Cancer Axis, Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
| | - Mona Wu
- Department of Human Genetics, Medicine, McGill University, Montreal, QC, Canada
- Cancer Axis, Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
| | - Leora Witkowski
- Department of Human Genetics, Medicine, McGill University, Montreal, QC, Canada
| | - Sophie Albert
- Cancer Axis, Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
| | - Nelly Sabbaghian
- Department of Human Genetics, Medicine, McGill University, Montreal, QC, Canada
- Cancer Axis, Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
| | - Marc R Fabian
- Cancer Axis, Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - William D Foulkes
- Department of Human Genetics, Medicine, McGill University, Montreal, QC, Canada
- Cancer Axis, Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
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7
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Mann MM, Hsieh MK, Tang JD, Hart WS, Lazzara MJ, Klauda JB, Berger BW. Understanding how transmembrane domains regulate interactions between human BST-2 and the SARS-CoV-2 accessory protein ORF7a. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184174. [PMID: 37211321 PMCID: PMC10197439 DOI: 10.1016/j.bbamem.2023.184174] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/12/2023] [Accepted: 05/10/2023] [Indexed: 05/23/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID, replicates at intracellular membranes. Bone marrow stromal antigen 2 (BST-2; tetherin) is an antiviral response protein that inhibits transport of viral particles after budding within infected cells. RNA viruses such as SARS-CoV-2 use various strategies to disable BST-2, including use of transmembrane 'accessory' proteins that interfere with BST-2 oligomerization. ORF7a is a small, transmembrane protein present in SARS-CoV-2 shown previously to alter BST-2 glycosylation and function. In this study, we investigated the structural basis for BST-2 ORF7a interactions, with a particular focus on transmembrane and juxtamembrane interactions. Our results indicate that transmembrane domains play an important role in BST-2 ORF7a interactions and mutations to the transmembrane domain of BST-2 can alter these interactions, particularly single-nucleotide polymorphisms in BST-2 that result in mutations such as I28S. Using molecular dynamics simulations, we identified specific interfaces and interactions between BST-2 and ORF7a to develop a structural basis for the transmembrane interactions. Differences in glycosylation are observed for BST-2 transmembrane mutants interacting with ORF7a, consistent with the idea that transmembrane domains play a key role in their heterooligomerization. Overall, our results indicate that ORF7a transmembrane domain interactions play a key role along with extracellular and juxtamembrane domains in modulating BST-2 function.
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Affiliation(s)
- Madison M Mann
- Department of Chemical Engineering, University of Virginia, United States of America
| | - Min-Kang Hsieh
- Department of Chemical and Biomolecular Engineering, University of Maryland College Park, United States of America
| | - James D Tang
- Department of Chemical Engineering, University of Virginia, United States of America
| | - William S Hart
- Department of Chemical Engineering, University of Virginia, United States of America
| | - Matthew J Lazzara
- Department of Chemical Engineering, University of Virginia, United States of America
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland College Park, United States of America; Institute for Physical Science and Technology, Biophysics Program, University of Maryland College Park, United States of America.
| | - Bryan W Berger
- Department of Chemical Engineering, University of Virginia, United States of America; Department of Biomedical Engineering, University of Virginia, United States of America.
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8
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Torrez RM, Nagaraja S, Menon A, Chang L, Ohi MD, Garner AL. Comparative Biochemical Studies of Disease-Associated Human Dicer Mutations on Processing of a Pre-microRNA and snoRNA. Biochemistry 2023. [PMID: 37130292 DOI: 10.1021/acs.biochem.2c00687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Dicer is an RNase III enzyme that is responsible for the maturation of small RNAs such as microRNAs. As Dicer's cleavage products play key roles in promoting cellular homeostasis through the fine-tuning of gene expression, dysregulation of Dicer activity can lead to several human diseases, including cancers. Mutations in Dicer have been found to induce tumorigenesis and lead to the development of a rare pleiotropic tumor predisposition syndrome found in children and young adults called DICER1 syndrome. These patients harbor germline and somatic mutations in Dicer that lead to defective microRNA processing and activity. While most mutations occur within Dicer's catalytic RNase III domains, alterations within the Platform-PAZ (Piwi-Argonaute-Zwille) domain also cause loss of microRNA production. Using a combination of in vitro biochemical and cellular studies, we characterized the effect of disease-relevant Platform-PAZ-associated mutations on the processing of a well-studied oncogenic microRNA, pre-microRNA-21. We then compared these results to those of a representative from another Dicer substrate class, the small nucleolar RNA, snord37. From this analysis, we provide evidence that mutations within the Platform-PAZ domain result in differential impacts on RNA binding and processing, adding new insights into the complexities of Dicer processing of small RNA substrates.
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Affiliation(s)
- Rachel M Torrez
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, United States
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
| | - Shruti Nagaraja
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, United States
| | - Arya Menon
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, United States
| | - Louise Chang
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
| | - Melanie D Ohi
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, Michigan 48109, United States
| | - Amanda L Garner
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, United States
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9
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Wong MRE, Lim KH, Hee EXY, Chen H, Kuick CH, Jet AS, Chang KTE, Sulaiman NS, Low SY, Hartono S, Tran ANT, Ahamed SH, Lam CMJ, Soh SY, Hannan KM, Hannan RD, Coupland LA, Loh AHP. Targeting Mutant Dicer Tumorigenesis in Pleuropulmonary Blastoma via Inhibition of RNA Polymerase I. Transl Res 2023:S1931-5244(23)00041-5. [PMID: 36921796 DOI: 10.1016/j.trsl.2023.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 02/23/2023] [Accepted: 03/07/2023] [Indexed: 03/14/2023]
Abstract
DICER1 mutations predispose to increased risk for various cancers, particularly pleuropulmonary blastoma (PPB), the commonest lung malignancy of childhood. There is a paucity of directly actionable molecular targets as these tumors are driven by loss-of-function mutations of DICER1. Therapeutic development for PPB is further limited by a lack of biologically and physiologically-representative disease models. Given recent evidence of Dicer's role as a haploinsufficient tumor suppressor regulating RNA polymerase I (Pol I), Pol I inhibition could abrogate mutant Dicer-mediated accumulation of stalled polymerases to trigger apoptosis. Hence, we developed a novel sub-pleural orthotopic PPB patient-derived xenograft (PDX) model that retained both RNase IIIa and IIIb hotspot mutations and recapitulated the cardiorespiratory physiology of intra-thoracic disease, and with it evaluated the tolerability and efficacy of first-in-class Pol I inhibitor CX-5461. In PDX tumors, CX-5461 significantly reduced H3K9 di-methylation and increased nuclear p53 expression, within 24 hours' exposure. Following treatment at the maximum tolerated dosing regimen (12 doses, 30mg/kg), tumors were smaller and less hemorrhagic than controls, with significantly decreased cellular proliferation, and increased apoptosis. As demonstrated in a novel intra-thoracic tumor model of PPB, Pol I inhibition with CX-5461 could be a tolerable and clinically-feasible therapeutic strategy for mutant Dicer tumors, inducing anti-tumor effects by decreasing H3K9 methylation and enhancing p53-mediated apoptosis.
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Affiliation(s)
- Megan Rui En Wong
- VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore 229899
| | - Kia Hui Lim
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597
| | - Esther Xuan Yi Hee
- VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore 229899
| | - Huiyi Chen
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore 229899
| | - Chik Hong Kuick
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore 229899
| | - Aw Sze Jet
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore 229899
| | - Kenneth Tou En Chang
- VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore 229899; Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore 229899; Duke-NUS School of Medicine, Singapore 169857
| | - Nurfarhanah Syed Sulaiman
- VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore 229899; Department of Neurology, National Neuroscience Institute, Singapore 308433
| | - Sharon Yy Low
- VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore 229899; Department of Neurology, National Neuroscience Institute, Singapore 308433; Duke-NUS School of Medicine, Singapore 169857
| | - Septian Hartono
- Department of Oncologic Imaging, National Cancer Centre Singapore, Singapore 169610
| | - Anh Nguyen Tuan Tran
- Department of Oncologic Imaging, National Cancer Centre Singapore, Singapore 169610
| | - Summaiyya Hanum Ahamed
- Duke-NUS School of Medicine, Singapore 169857; Department of Diagnostic and Interventional Imaging, KK Women's and Children's Hospital, Singapore 229899
| | - Ching Mei Joyce Lam
- Duke-NUS School of Medicine, Singapore 169857; Department of Paediatric Subspecialties Haematology/Oncology Service, KK Women's and Children's Hospital, Singapore 229899
| | - Shui Yen Soh
- VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore 229899; Duke-NUS School of Medicine, Singapore 169857; Department of Paediatric Subspecialties Haematology/Oncology Service, KK Women's and Children's Hospital, Singapore 229899
| | - Katherine M Hannan
- Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, the Australian National University, Canberra, Australia; Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Ross D Hannan
- Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, the Australian National University, Canberra, Australia; Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, Australia; Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Lucy A Coupland
- Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, the Australian National University, Canberra, Australia
| | - Amos Hong Pheng Loh
- VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore 229899; Duke-NUS School of Medicine, Singapore 169857; Department of Paediatric Surgery, KK Women's and Children's Hospital, Singapore 229899.
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10
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Ricarte-Filho JC, Casado-Medrano V, Reichenberger E, Spangler Z, Scheerer M, Isaza A, Baran J, Patel T, MacFarland SP, Brodeur GM, Stewart DR, Baloch Z, Bauer AJ, Wasserman JD, Franco AT. DICER1 RNase IIIb domain mutations trigger widespread miRNA dysregulation and MAPK activation in pediatric thyroid cancer. Front Endocrinol (Lausanne) 2023; 14:1083382. [PMID: 36896180 PMCID: PMC9990750 DOI: 10.3389/fendo.2023.1083382] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 02/01/2023] [Indexed: 02/25/2023] Open
Abstract
DICER1 is a highly conserved RNase III endoribonuclease essential for the biogenesis of single-stranded mature microRNAs (miRNAs) from stem-loop precursor miRNAs. Somatic mutations in the RNase IIIb domain of DICER1 impair its ability to generate mature 5p miRNAs and are believed to drive tumorigenesis in DICER1 syndrome-associated and sporadic thyroid tumors. However, the DICER1-driven specific changes in miRNAs and resulting changes in gene expression are poorly understood in thyroid tissue. In this study, we profiled the miRNA (n=2,083) and mRNA (n=2,559) transcriptomes of 20 non-neoplastic, 8 adenomatous and 60 pediatric thyroid cancers (13 follicular thyroid cancers [FTC] and 47 papillary thyroid cancers [PTC]) of which 8 had DICER1 RNase IIIb mutations. All DICER1-mutant differentiated thyroid cancers (DTC) were follicular patterned (six follicular variant PTC and two FTC), none had lymph node metastasis. We demonstrate that DICER1 pathogenic somatic mutations were associated with a global reduction of 5p-derived miRNAs, including those particularly abundant in the non-neoplastic thyroid tissue such as let-7 and mir-30 families, known for their tumor suppressor function. There was also an unexpected increase of 3p miRNAs, possibly associated with DICER1 mRNA expression increase in tumors harboring RNase IIIb mutations. These abnormally expressed 3p miRNAs, which are otherwise low or absent in DICER1-wt DTC and non-neoplastic thyroid tissues, make up exceptional markers for malignant thyroid tumors harboring DICER1 RNase IIIb mutations. The extensive disarray in the miRNA transcriptome results in gene expression changes, which were indicative of positive regulation of cell-cycle. Moreover, differentially expressed genes point to increased MAPK signaling output and loss of thyroid differentiation comparable to the RAS-like subgroup of PTC (as coined by The Cancer Genome Atlas), which is reflective of the more indolent clinical behavior of these tumors.
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Affiliation(s)
- Julio C. Ricarte-Filho
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Victoria Casado-Medrano
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Erin Reichenberger
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Zachary Spangler
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Michele Scheerer
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Amber Isaza
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Julia Baran
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Tasleema Patel
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Suzanne P. MacFarland
- Division of Oncology, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
- Cancer Predisposition Program, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Garrett M. Brodeur
- Division of Oncology, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
- Cancer Predisposition Program, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, United States
| | - Douglas R. Stewart
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, United States
| | - Zubair Baloch
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Andrew J. Bauer
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
- Cancer Predisposition Program, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | | | - Aime T. Franco
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
- Cancer Predisposition Program, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, United States
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11
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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 DOI: 10.1021/acs.biochem.2c00570] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [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, 428 Church Street, Ann Arbor, Michigan 48109, United States.,Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
| | - Melanie D Ohi
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States.,Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, Michigan 48109, United States
| | - Amanda L Garner
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, United States
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12
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Jouravleva K, Golovenko D, Demo G, Dutcher RC, Hall TMT, Zamore PD, Korostelev AA. Structural basis of microRNA biogenesis by Dicer-1 and its partner protein Loqs-PB. Mol Cell 2022; 82:4049-4063.e6. [PMID: 36182693 PMCID: PMC9637774 DOI: 10.1016/j.molcel.2022.09.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/24/2022] [Accepted: 08/31/2022] [Indexed: 12/22/2022]
Abstract
In animals and plants, Dicer enzymes collaborate with double-stranded RNA-binding domain (dsRBD) proteins to convert precursor-microRNAs (pre-miRNAs) into miRNA duplexes. We report six cryo-EM structures of Drosophila Dicer-1 that show how Dicer-1 and its partner Loqs‑PB cooperate (1) before binding pre-miRNA, (2) after binding and in a catalytically competent state, (3) after nicking one arm of the pre-miRNA, and (4) following complete dicing and initial product release. Our reconstructions suggest that pre-miRNA binds a rare, open conformation of the Dicer‑1⋅Loqs‑PB heterodimer. The Dicer-1 dsRBD and three Loqs‑PB dsRBDs form a tight belt around the pre-miRNA, distorting the RNA helix to place the scissile phosphodiester bonds in the RNase III active sites. Pre-miRNA cleavage shifts the dsRBDs and partially closes Dicer-1, which may promote product release. Our data suggest a model for how the Dicer‑1⋅Loqs‑PB complex affects a complete cycle of pre-miRNA recognition, stepwise endonuclease cleavage, and product release.
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Affiliation(s)
- Karina Jouravleva
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Dmitrij Golovenko
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Gabriel Demo
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 62500, Czech Republic
| | - Robert C Dutcher
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, USA.
| | - Phillip D Zamore
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Howard Hughes Medical Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
| | - Andrei A Korostelev
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
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13
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Akkermans O, Delloye-Bourgeois C, Peregrina C, Carrasquero-Ordaz M, Kokolaki M, Berbeira-Santana M, Chavent M, Reynaud F, Raj R, Agirre J, Aksu M, White ES, Lowe E, Ben Amar D, Zaballa S, Huo J, Pakos I, McCubbin PTN, Comoletti D, Owens RJ, Robinson CV, Castellani V, Del Toro D, Seiradake E. GPC3-Unc5 receptor complex structure and role in cell migration. Cell 2022; 185:3931-3949.e26. [PMID: 36240740 PMCID: PMC9596381 DOI: 10.1016/j.cell.2022.09.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/22/2022] [Accepted: 09/15/2022] [Indexed: 11/09/2022]
Abstract
Neural migration is a critical step during brain development that requires the interactions of cell-surface guidance receptors. Cancer cells often hijack these mechanisms to disseminate. Here, we reveal crystal structures of Uncoordinated-5 receptor D (Unc5D) in complex with morphogen receptor glypican-3 (GPC3), forming an octameric glycoprotein complex. In the complex, four Unc5D molecules pack into an antiparallel bundle, flanked by four GPC3 molecules. Central glycan-glycan interactions are formed by N-linked glycans emanating from GPC3 (N241 in human) and C-mannosylated tryptophans of the Unc5D thrombospondin-like domains. MD simulations, mass spectrometry and structure-based mutants validate the crystallographic data. Anti-GPC3 nanobodies enhance or weaken Unc5-GPC3 binding and, together with mutant proteins, show that Unc5/GPC3 guide migrating pyramidal neurons in the mouse cortex, and cancer cells in an embryonic xenograft neuroblastoma model. The results demonstrate a conserved structural mechanism of cell guidance, where finely balanced Unc5-GPC3 interactions regulate cell migration.
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Affiliation(s)
- Onno Akkermans
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Céline Delloye-Bourgeois
- MeLis, University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5284, INSERM U1314, Institut NeuroMyoGène, 8 avenue Rockefeller 69008 Lyon, Lyon, France
| | - Claudia Peregrina
- Department of Biological Sciences, Institute of Neurosciences, IDIBAPS, CIBERNED, University of Barcelona, Barcelona, Spain
| | - Maria Carrasquero-Ordaz
- Department of Biochemistry, University of Oxford, Oxford, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Maria Kokolaki
- Department of Biochemistry, University of Oxford, Oxford, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Miguel Berbeira-Santana
- Department of Biochemistry, University of Oxford, Oxford, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Matthieu Chavent
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, Toulouse, France
| | - Florie Reynaud
- MeLis, University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5284, INSERM U1314, Institut NeuroMyoGène, 8 avenue Rockefeller 69008 Lyon, Lyon, France
| | - Ritu Raj
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Metin Aksu
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Eleanor S White
- Department of Biochemistry, University of Oxford, Oxford, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Edward Lowe
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Dounia Ben Amar
- MeLis, University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5284, INSERM U1314, Institut NeuroMyoGène, 8 avenue Rockefeller 69008 Lyon, Lyon, France
| | - Sofia Zaballa
- Department of Biological Sciences, Institute of Neurosciences, IDIBAPS, CIBERNED, University of Barcelona, Barcelona, Spain
| | - Jiandong Huo
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK; Division of Structural Biology, University of Oxford, Oxford, UK
| | - Irene Pakos
- Child Health Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Patrick T N McCubbin
- Department of Biochemistry, University of Oxford, Oxford, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Davide Comoletti
- Child Health Institute of New Jersey, New Brunswick, NJ 08901, USA; School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Raymond J Owens
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK; Division of Structural Biology, University of Oxford, Oxford, UK
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Valérie Castellani
- MeLis, University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5284, INSERM U1314, Institut NeuroMyoGène, 8 avenue Rockefeller 69008 Lyon, Lyon, France.
| | - Daniel Del Toro
- Department of Biological Sciences, Institute of Neurosciences, IDIBAPS, CIBERNED, University of Barcelona, Barcelona, Spain.
| | - Elena Seiradake
- Department of Biochemistry, University of Oxford, Oxford, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
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14
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Schell G, Roy B, Prall K, Dwivedi Y. miR-218: A Stress-Responsive Epigenetic Modifier. Noncoding RNA 2022; 8:ncrna8040055. [PMID: 35893238 PMCID: PMC9326663 DOI: 10.3390/ncrna8040055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 11/16/2022] Open
Abstract
Understanding the epigenetic role of microRNAs (miRNAs) has been a critical development in the field of neuropsychiatry and in understanding their underlying pathophysiology. Abnormalities in miRNA expression are often seen as key to the pathogenesis of many stress-associated mental disorders, including major depressive disorder (MDD). Recent advances in omics biology have further contributed to this understanding and expanded the role of miRNAs in networking a diverse array of molecular pathways, which are essentially related to the stress adaptivity of a healthy brain. Studies have highlighted the role of many such miRNAs in causing maladaptive changes in the brain's stress axis. One such miRNA is miR-218, which is debated as a critical candidate for increased stress susceptibility. miR-218 is expressed throughout the brain, notably in the hippocampus and prefrontal cortex (PFC). It is expressed at various levels through life stages, as seen by adolescent and adult animal models. Until now, a minimal number of studies have been conducted on human subjects to understand its role in stress-related abnormalities in brain circuits. However, several studies, including animal and cell-culture models, have been used to understand the impact of miR-218 on stress response and hypothalamic-pituitary-adrenal (HPA) axis function. So far, expression changes in this miRNA have been found to regulate signaling pathways such as glucocorticoid signaling, serotonergic signaling, and glutamatergic signaling. Recently, the developmental role of miR-218 has generated interest, given its increasing expression from adolescence to adulthood and targeting the Netrin-1/DCC signaling pathway. Since miR-218 expression affects neuronal development and plasticity, it is expected that a change in miR-218 expression levels over the course of development may negatively impact the process and make individuals stress-susceptible in adulthood. In this review, we describe the role of miR-218 in stress-induced neuropsychiatric conditions with an emphasis on stress-related disorders.
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15
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Yang X, Wang X, Li Z, Duan S, Li H, Jin J, Zhang Z, Gu W. An unexpected role for Dicer as a reader of the unacetylated DNA binding domain of p53 in transcriptional regulation. SCIENCE ADVANCES 2021; 7:eabi6684. [PMID: 34705508 PMCID: PMC8550248 DOI: 10.1126/sciadv.abi6684] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 09/04/2021] [Indexed: 06/02/2023]
Abstract
Here, we identified Dicer as a major cellular factor that recognizes the DNA binding domain (DBD) of p53 in a manner dependent on its acetylation status. Upon binding the unacetylated DBD, Dicer is recruited to the promoters of p53 target genes, where it represses p53-mediated transcriptional activation. Conversely, knockdown or knockout of endogenous Dicer leads to up-regulation of p53-mediated transcriptional activation without increasing its protein levels. Moreover, Dicer-mediated repression is independent of its intrinsic endoribonuclease activity; instead, Dicer directly represses transcription by recruiting the SUV39H1 histone methyltransferase. However, upon DNA damage, Dicer-mediated repression is abrogated by stress-induced acetylation at the DBD of p53. Notably, the inability of acetylation-defective p53-3KR in transcription is partially but significantly restored upon loss of Dicer expression. Our study reveals that Dicer acts as an unexpected acetylation “reader” for p53 and thus has important implications regarding the mechanism of acetylation-mediated regulation of p53 transcriptional program.
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Affiliation(s)
- Xin Yang
- Institute for Cancer Genetics, and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University, 1130 Nicholas Ave., New York, NY 10032, USA
| | - Xingwu Wang
- Institute for Cancer Genetics, and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University, 1130 Nicholas Ave., New York, NY 10032, USA
| | - Zhiming Li
- Institute for Cancer Genetics, and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University, 1130 Nicholas Ave., New York, NY 10032, USA
| | - Shoufu Duan
- Institute for Cancer Genetics, and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University, 1130 Nicholas Ave., New York, NY 10032, USA
| | - Huan Li
- Institute for Cancer Genetics, and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University, 1130 Nicholas Ave., New York, NY 10032, USA
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zhiguo Zhang
- Institute for Cancer Genetics, and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University, 1130 Nicholas Ave., New York, NY 10032, USA
- Department of Pediatrics and Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, 1130 Nicholas Ave., New York, NY 10032, USA
| | - Wei Gu
- Institute for Cancer Genetics, and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University, 1130 Nicholas Ave., New York, NY 10032, USA
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, 1130 Nicholas Ave., New York, NY 10032, USA
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16
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Shortridge MD, Varani G. Efficient NMR Screening Approach to Discover Small Molecule Fragments Binding Structured RNA. ACS Med Chem Lett 2021; 12:1253-1260. [PMID: 34413954 DOI: 10.1021/acsmedchemlett.1c00109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/07/2021] [Indexed: 01/27/2023] Open
Abstract
We describe a scalable nuclear magnetic resonance (NMR) screening approach to identify and prioritize small molecule fragments that bind to structured RNAs. This approach is target agnostic and, therefore, amenable to many RNA structures and libraries, and it provides initial hits for further synthetic elaboration and structure-based drug discovery efforts. We demonstrate the approach on the pre-miR-21 stem-loop, which is of significant interest in oncology and metabolic diseases. We screened the pre-miR-21 hairpin using a small (420 compounds) commercially available fragment library and identified 18 hits in the first round of triage screening. This was further refined to four fragments which passed all screening cascade filters. Among these four hits, a thiadiazole fragment was demonstrated to bind the Dicer cleavage site of pre-miR-21 by target-detected NMR experiments and through the observation of clear intermolecular NOEs.
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Affiliation(s)
- Matthew D. Shortridge
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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17
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Ford KM, Panwala R, Chen DH, Portell A, Palmer N, Mali P. Peptide-tiling screens of cancer drivers reveal oncogenic protein domains and associated peptide inhibitors. Cell Syst 2021; 12:716-732.e7. [PMID: 34051140 PMCID: PMC8298269 DOI: 10.1016/j.cels.2021.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 02/09/2021] [Accepted: 03/30/2021] [Indexed: 02/07/2023]
Abstract
Gene fragments derived from structural domains mediating physical interactions can modulate biological functions. Utilizing this, we developed lentiviral overexpression libraries of peptides comprehensively tiling high-confidence cancer driver genes. Toward inhibiting cancer growth, we assayed ~66,000 peptides, tiling 65 cancer drivers and 579 mutant alleles. Pooled fitness screens in two breast cancer cell lines revealed peptides, which selectively reduced cellular proliferation, implicating oncogenic protein domains important for cell fitness. Coupling of cell-penetrating motifs to these peptides enabled drug-like function, with peptides derived from EGFR and RAF1 inhibiting cell growth at IC50s of 27-63 μM. We anticipate that this peptide-tiling (PepTile) approach will enable rapid de novo mapping of bioactive protein domains and associated interfering peptides.
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Affiliation(s)
- Kyle M Ford
- Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA
| | - Rebecca Panwala
- Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA
| | - Dai-Hua Chen
- Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA
| | - Andrew Portell
- Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA
| | - Nathan Palmer
- Division of Biological Sciences, University of California, San Diego, San Diego, CA 92093, USA
| | - Prashant Mali
- Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA.
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18
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Awais MM, Shakeel M, Sun J. MicroRNA-Mediated Host-Pathogen Interactions Between Bombyx mori and Viruses. Front Physiol 2021; 12:672205. [PMID: 34025458 PMCID: PMC8137832 DOI: 10.3389/fphys.2021.672205] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/14/2021] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs), small non-coding RNAs of about 22 nucleotides, have been reported to regulate gene expression at the posttranscriptional level and are involved in several biological processes such as immunity, development, metabolism, and host-pathogen interactions. Apart from miRNAs encoded by the host, miRNAs produced by pathogens also regulate host genes to facilitate virus replication and evasion of the host defense responses. In recent years, accumulated studies suggest that viral infections alter the host miRNAs expression profile, and both cellular and viral miRNAs may play vital roles in host-pathogen interactions. Bombyx mori, one of the critical lepidopteran model species, is an economically important insect for silk production. The mechanism of interaction between B. mori and its pathogens and their regulation by miRNAs has been extensively studied. Therefore, in this review, we aim to highlight the recent information and understanding of the virus-encoding miRNAs and their functions in modulating viral and host (B. mori) genes. Additionally, the response of B. mori derived miRNAs to viral infection is also discussed. A detailed critical view about miRNAs’ regulatory roles in B. mori-virus interactions will help us understand molecular networks and develop a sustainable antiviral strategy.
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Affiliation(s)
- Mian Muhammad Awais
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding and Sub-Tropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Muhammad Shakeel
- Laboratory of Bio-Pesticide Innovation and Application of Guandong Province, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Jingchen Sun
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding and Sub-Tropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou, China
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19
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Wang S, Xu J, Guo Y, Cai Y, Ren X, Zhu W, Geng M, Meng L, Jiang C, Lu S. MicroRNA-497 Reduction and Increase of Its Family Member MicroRNA-424 Lead to Dysregulation of Multiple Inflammation Related Genes in Synovial Fibroblasts With Rheumatoid Arthritis. Front Immunol 2021; 12:619392. [PMID: 33841401 PMCID: PMC8034293 DOI: 10.3389/fimmu.2021.619392] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/10/2021] [Indexed: 01/26/2023] Open
Abstract
Objectives Mounting evidence has demonstrated that microRNAs (miRNAs) participate in rheumatoid arthritis (RA). The role of highly conserved miR-15/107 family in RA has not been clarified yet, and hence investigated in this study. Methods Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was used to evaluate the expression of miRNAs and genes. Cell counting kit 8 (CCK-8) and FACS were used to detect proliferation and apoptosis. Protein expression was detected by using Western blotting. mRNA deep sequencing and cytokine antibody array were used to analyze differentially expressed genes, signaling pathways and cytokines. Results The expression of miR-15a, miR-103, miR-497, and miR-646 was found decreased, while miR-424 increased in RA patients. MiR-424 and miR-497 were further investigated and the results showed that they could regulate the expression of multiple genes in rheumatoid arthritis synovial fibroblast (RASF) and affect signaling pathways. At the protein level, miR-497 mimic altered all the selected inflammation-related genes while miR-424 inhibitor only affected part of genes. MiR-497 mimic, rather than miR-424 inhibitor, had significant effects on proliferation and apoptosis of RASF. DICER1 was found to positively regulate the expression of miR-424 and miR-497, while DICER1 was also negatively regulated by miR-424. The increase of miR-424 could reduce miR-497 expression, thus forming a loop, which facilitated explaining the dysregulated miR-424 and miR-497 in RA. Conclusion The miR-424 and miR-497 of miR-15/107 family affect cell proliferation and apoptosis in RA, and the proposed miR-424-DICER1-miR-497 feedback loop provides a novel insight into regulating miRNA expression and a candidate target for controlling RA.
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Affiliation(s)
- Si Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Institute of Molecular and Translational Medicine (IMTM), Xi'an Jiaotong University Health Science Center, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, China
| | - Jing Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Institute of Molecular and Translational Medicine (IMTM), Xi'an Jiaotong University Health Science Center, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, China
| | - Yuanxu Guo
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Institute of Molecular and Translational Medicine (IMTM), Xi'an Jiaotong University Health Science Center, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, China
| | - Yongsong Cai
- Department of Joint Surgery, Xi'an Hong Hui Hospital, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Xiaoyu Ren
- Department of Joint Surgery, Xi'an Hong Hui Hospital, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Wenhua Zhu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Institute of Molecular and Translational Medicine (IMTM), Xi'an Jiaotong University Health Science Center, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, China
| | - Manman Geng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Institute of Molecular and Translational Medicine (IMTM), Xi'an Jiaotong University Health Science Center, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, China
| | - Liesu Meng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Institute of Molecular and Translational Medicine (IMTM), Xi'an Jiaotong University Health Science Center, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, China
| | - Congshan Jiang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Institute of Molecular and Translational Medicine (IMTM), Xi'an Jiaotong University Health Science Center, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, China
| | - Shemin Lu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Institute of Molecular and Translational Medicine (IMTM), Xi'an Jiaotong University Health Science Center, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, China
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20
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Lee M, Kim TI, Jang SJ, Cho KJ, Lee SM, Kim HR, Song JS. Pleuropulmonary Blastoma with Hotspot Mutations in RNase IIIb Domain of DICER 1: Clinicopathologic Study of 10 Cases in a Single-Institute Experience. Pathobiology 2021; 88:251-260. [PMID: 33567437 DOI: 10.1159/000512957] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 11/06/2020] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Pleuropulmonary blastoma (PPB) is a rare sarcomatous malignancy involving the lung and pleura which occurs in early childhood. Cystic PPB in the early stage can be misdiagnosed as other cystic diseases. Early detection of this entity is important for appropriate treatment and prevention of disease progression. Hotspot mutations in the ribonuclease IIIb (RNase IIIb) domain of DICER1 have been reported to have a crucial role as genetic factors of PPB and DICER1 familial syndrome. We reviewed the clinicopathologic findings of PPB and the status of DICER1 hotspot mutation and patients' clinical course. METHODS We retrospectively reviewed all patients with histologically confirmed PPB at Asan Medical Center between 2000 and 2017. Ten cases were identified in the database, and their clinicopathologic parameters were evaluated. PPB was classified into the following 3 pathologic subtypes: type I (purely cystic), type II (mixed cystic and solid), and type III (entirely solid). The status of DICER1 mutation in 2 hotspot regions of the RNase IIIb domain was evaluated by Sanger sequencing. RESULTS The most frequent PPB type was II (6 cases), followed by I and III (2 cases each). The age at diagnosis ranged from 16 months to 15 years. All patients underwent surgery, and all patients received adjuvant or neoadjuvant chemotherapy. Four of 7 patients had missense mutations in the RNase IIIb hotspot; the base and predicted corresponding amino acid changes were c.5113 G>A (p.E1705K), c.5407 G>A (p.E1803K), c.5425 G>A (p.G1809R), and c.5428 G>T (p.D1810Y). There was no particular association between the presence of the hotspot mutation and histologic type. Nine patients survived with no evidence of disease for a median interval of 93 (range, 13-199) months. Only 1 patient diagnosed with type III PPB at the age of 18 years had recurrence after 20.8 months and eventually died 66 months after the initial diagnosis. CONCLUSIONS Late detection of solid PPB is associated with poor prognosis. Considering the rarity of PPB disease and the importance of DICER1 hotspot mutation in pathogenesis, DICER1 hotspot mutation testing and identification in the early cystic stage can improve patient outcomes.
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Affiliation(s)
- Miseon Lee
- Department of Pathology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
| | - Tae-Im Kim
- Department of Pathology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
| | - Se Jin Jang
- Department of Pathology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
| | - Kyung-Ja Cho
- Department of Pathology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
| | - Sang Min Lee
- Department of Radiology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
| | - Hyeong Ryul Kim
- Department of Cardiovascular and Thoracic Surgery, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
| | - Joon Seon Song
- Department of Pathology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea,
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21
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Galka-Marciniak P, Urbanek-Trzeciak M, Nawrocka P, Kozlowski P. A pan-cancer atlas of somatic mutations in miRNA biogenesis genes. Nucleic Acids Res 2021; 49:601-620. [PMID: 33406242 PMCID: PMC7826265 DOI: 10.1093/nar/gkaa1223] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/28/2020] [Accepted: 12/04/2020] [Indexed: 02/07/2023] Open
Abstract
It is a well-known and intensively studied phenomenon that the levels of many miRNAs are differentiated in cancer. miRNA biogenesis and functional expression are complex processes orchestrated by many proteins cumulatively called miRNA biogenesis proteins. To characterize cancer somatic mutations in the miRNA biogenesis genes and investigate their potential impact on the levels of miRNAs, we analyzed whole-exome sequencing datasets of over 10 000 cancer/normal sample pairs deposited within the TCGA repository. We identified and characterized over 3600 somatic mutations in 29 miRNA biogenesis genes and showed that some of the genes are overmutated in specific cancers and/or have recurrent hotspot mutations (e.g. SMAD4 in PAAD, COAD and READ; DICER1 in UCEC; PRKRA in OV and LIN28B in SKCM). We identified a list of miRNAs whose level is affected by particular types of mutations in either SMAD4, SMAD2 or DICER1 and showed that hotspot mutations in the RNase domains in DICER1 not only decrease the level of 5p-miRNAs but also increase the level of 3p-miRNAs, including many well-known cancer-related miRNAs. We also showed an association of the mutations with patient survival. Eventually, we created an atlas/compendium of miRNA biogenesis alterations providing a useful resource for different aspects of biomedical research.
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Affiliation(s)
| | | | | | - Piotr Kozlowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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22
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Post-transcriptional tuning of FGF signaling mediates neural crest induction. Proc Natl Acad Sci U S A 2020; 117:33305-33316. [PMID: 33376218 DOI: 10.1073/pnas.2009997117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Ectodermal patterning is required for the establishment of multiple components of the vertebrate body plan. Previous studies have demonstrated that precise combinations of extracellular signals induce distinct ectodermal cell populations, such as the neural crest and the neural plate. Yet, we still lack understanding of how the response to inductive signals is modulated to generate the proper transcriptional output in target cells. Here we show that posttranscriptional attenuation of fibroblast growth factor (FGF) signaling is essential for the establishment of the neural crest territory. We found that neural crest progenitors display elevated expression of DICER, which promotes enhanced maturation of a set of cell-type-specific miRNAs. These miRNAs collectively target components of the FGF signaling pathway, a central player in the process of neural induction in amniotes. Inactivation of this posttranscriptional circuit results in a fate switch, in which neural crest cells are converted into progenitors of the central nervous system. Thus, the posttranscriptional attenuation of signaling systems is a prerequisite for proper segregation of ectodermal cell types. These findings demonstrate how posttranscriptional repression may alter the activity of signaling systems to generate distinct spatial domains of progenitor cells.
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23
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Kamihara J, Paulson V, Breen MA, Laetsch TW, Rakheja D, Shulman DS, Schoettler ML, Clinton CM, Ward A, Reidy D, Pinches RS, Weiser DA, Mullen EA, Schienda J, Meyers PA, DuBois SG, Nowak JA, Foulkes WD, Schultz KAP, Janeway KA, Vargas SO, Church AJ. DICER1-associated central nervous system sarcoma in children: comprehensive clinicopathologic and genetic analysis of a newly described rare tumor. Mod Pathol 2020; 33:1910-1921. [PMID: 32291395 DOI: 10.1038/s41379-020-0516-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 02/24/2020] [Accepted: 02/25/2020] [Indexed: 12/16/2022]
Abstract
The spectrum of neoplasms associated with DICER1 variants continues to expand, with the recent addition of primary "DICER1-associated central nervous system sarcoma" (DCS). DCS is a high-grade malignancy predominantly affecting pediatric patients. Six pediatric DCS were identified through a combination of clinical diagnostic studies, archival inquiry, and interinstitutional collaboration. Clinical, histologic, immunohistologic, and molecular features were examined. Genomic findings in the 6 DCS were compared with those in 14 additional DICER1-associated tumors sequenced with the same assay. The six patients presented at ages 3-15 years with CNS tumors located in the temporal (n = 2), parietal (n = 1), fronto-parietal (n = 1), and frontal (n = 2) lobes. All underwent surgical resection. Histologic examination demonstrated high-grade malignant spindle cell tumors with pleuropulmonary blastoma-like embryonic "organoid" features and focal rhabdomyoblastic differentiation; immature cartilage was seen in one case. Immunohistochemically, there was patchy desmin and myogenin staining, and patchy loss of H3K27me3, and within eosinophilic cytoplasmic globules, alfa-fetoprotein staining. Biallelic DICER1 variants were identified in all cases, with germline variants in two of five patients tested. DCS demonstrated genomic alterations enriched for Ras pathway activation and TP53 inactivation. Tumor mutational burden was significantly higher in the 6 DCS tumors than in 14 other DICER1-associated tumors examined (mean 12.9 vs. 6.8 mutations/Mb, p = 0.035). Postoperative care included radiation (n = 5) and chemotherapy (n = 3); at the last follow-up, three patients were alive without DCS, and three had died of disease. Our analysis expands the clinical, histologic, immunohistological, and molecular spectrum of DCS, identifying distinctive features that can aid in the diagnosis, multidisciplinary evaluation, and treatment of DCS.
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Affiliation(s)
- Junne Kamihara
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, USA
| | - Vera Paulson
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Laboratory Medicine, University of Washington Medical Center, Seattle, WA, USA
| | - Micheál A Breen
- Department of Radiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Theodore W Laetsch
- Department of Pediatrics, University of Texas Southwestern Medical Center and Children's Health, Dallas, TX, USA
| | - Dinesh Rakheja
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - David S Shulman
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, USA
| | - Michelle L Schoettler
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, USA
| | - Catherine M Clinton
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Abigail Ward
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Deirdre Reidy
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - R Seth Pinches
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - Daniel A Weiser
- Department of Pediatrics, Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY, USA
| | - Elizabeth A Mullen
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, USA
| | - Jaclyn Schienda
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Paul A Meyers
- Department of Pediatrics, Memorial Sloan-Kettering Cancer Center, Weill Cornell Medical College, New York, NY, USA
| | - Steven G DuBois
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, USA
| | - Jonathan A Nowak
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - William D Foulkes
- Department of Human Genetics, McGill University Health Centre/Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Kris Ann P Schultz
- Cancer and Blood Disorders and International Pleuropulmonary Blastoma/DICER1 Registry, Children's Minnesota, Minneapolis, MN, USA
| | - Katherine A Janeway
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, USA
| | - Sara O Vargas
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Alanna J Church
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
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24
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Wang X, Wendel JRH, Emerson RE, Broaddus RR, Creighton CJ, Rusch DB, Buechlein A, DeMayo FJ, Lydon JP, Hawkins SM. Pten and Dicer1 loss in the mouse uterus causes poorly differentiated endometrial adenocarcinoma. Oncogene 2020; 39:6286-6299. [PMID: 32843721 PMCID: PMC7541676 DOI: 10.1038/s41388-020-01434-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 08/02/2020] [Accepted: 08/13/2020] [Indexed: 12/14/2022]
Abstract
Endometrial cancer remains the most common gynecological malignancy in the United States. While the loss of the tumor suppressor, PTEN (phosphatase and tensin homolog), is well studied in endometrial cancer, recent studies suggest that DICER1, the endoribonuclease responsible for miRNA genesis, also plays a significant role in endometrial adenocarcinoma. Conditional uterine deletion of Dicer1 and Pten in mice resulted in poorly differentiated endometrial adenocarcinomas, which expressed Napsin A and HNF1B (hepatocyte nuclear factor 1 homeobox B), markers of clear-cell adenocarcinoma. Adenocarcinomas were hormone-independent. Treatment with progesterone did not mitigate poorly differentiated adenocarcinoma, nor did it affect adnexal metastasis. Transcriptomic analyses of DICER1 deleted uteri or Ishikawa cells revealed unique transcriptomic profiles and global miRNA downregulation. Computational integration of miRNA with mRNA targets revealed deregulated let-7 and miR-16 target genes, similar to published human DICER1-mutant endometrial cancers from TCGA (The Cancer Genome Atlas). Similar to human endometrial cancers, tumors exhibited dysregulation of ephrin-receptor signaling and transforming growth factor-beta signaling pathways. LIM kinase 2 (LIMK2), an essential molecule in p21 signal transduction, was significantly upregulated and represents a novel mechanism for hormone-independent pathogenesis of endometrial adenocarcinoma. This preclinical mouse model represents the first genetically engineered mouse model of poorly differentiated endometrial adenocarcinoma.
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Affiliation(s)
- Xiyin Wang
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jillian R H Wendel
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Robert E Emerson
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Russell R Broaddus
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Chad J Creighton
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Douglas B Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, USA
| | - Aaron Buechlein
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, USA
| | - Francesco J DeMayo
- National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, USA
| | - John P Lydon
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Shannon M Hawkins
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN, USA.
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25
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Zhang G, Chen F, Wu P, Li T, He M, Yin X, Shi H, Duan Y, Zhang T, Wang J, Xie K, Dai G. MicroRNA-7 Targets the KLF4 Gene to Regulate the Proliferation and Differentiation of Chicken Primary Myoblasts. Front Genet 2020; 11:842. [PMID: 33193566 PMCID: PMC7530283 DOI: 10.3389/fgene.2020.00842] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/13/2020] [Indexed: 12/17/2022] Open
Abstract
The proliferation and differentiation of chicken primary myoblasts (CPMs) play an important role in the development of skeletal muscle. In our previous research, RNA-seq analysis showed that microRNA-7 (miR-7) was relatively highly expressed in the proliferation phase of CPMs, but its expression level decreased significantly after CPMS-induced differentiation. Meanwhile, the mechanism by which the miR-7 regulates the proliferation and differentiation of CPMs is still unknown. In this study, we found that the expression levels of miR-7 and the Krüppel-like factor 4 (KLF4) gene were negatively correlated during the embryonic phase, and in vitro induced differentiation. A dual-luciferase assay and a rescue experiment show that there is a target relationship between miR-7 and the KLF4 gene. Meanwhile, the results show that overexpression of miR-7 inhibited the proliferation and differentiation of CPMs, while inhibition of miR-7 had the opposite effects. Furthermore, overexpression of the KLF4 gene was found to significantly promote the proliferation and differentiation of CPMs. Conversely, inhibition of the KLF4 gene was able to significantly decrease the proliferation and differentiation of CPMs. Our results demonstrate, for the first time, that miR-7 inhibits the proliferation and differentiation of myoblasts by targeting the KLF4 gene in chicken primary myoblasts.
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Affiliation(s)
- Genxi Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, China
| | - Fuxiang Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, China
| | - Pengfei Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, China
| | - TingTing Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, China
| | - Mingliang He
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, China
| | - Xuemei Yin
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, China
| | - Huiqiang Shi
- Jiangsu Jinghai Poultry Group Co., Ltd., Nantong, China
| | - Yanjun Duan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, China
| | - Tao Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, China
| | - Jinyu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, China
| | - Kaizhou Xie
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, China
| | - Guojun Dai
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, China
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26
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Zhang R, Boareto M, Engler A, Louvi A, Giachino C, Iber D, Taylor V. Id4 Downstream of Notch2 Maintains Neural Stem Cell Quiescence in the Adult Hippocampus. Cell Rep 2020; 28:1485-1498.e6. [PMID: 31390563 DOI: 10.1016/j.celrep.2019.07.014] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 04/14/2019] [Accepted: 07/02/2019] [Indexed: 12/31/2022] Open
Abstract
Neural stem cells (NSCs) in the adult mouse hippocampal dentate gyrus (DG) are mostly quiescent, and only a few are in cell cycle at any point in time. DG NSCs become increasingly dormant with age and enter mitosis less frequently, which impinges on neurogenesis. How NSC inactivity is maintained is largely unknown. Here, we found that Id4 is a downstream target of Notch2 signaling and maintains DG NSC quiescence by blocking cell-cycle entry. Id4 expression is sufficient to promote DG NSC quiescence and Id4 knockdown rescues Notch2-induced inhibition of NSC proliferation. Id4 deletion activates NSC proliferation in the DG without evoking neuron generation, and overexpression increases NSC maintenance while promoting astrogliogenesis at the expense of neurogenesis. Together, our findings indicate that Id4 is a major effector of Notch2 signaling in NSCs and a Notch2-Id4 axis promotes NSC quiescence in the adult DG, uncoupling NSC activation from neuronal differentiation.
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Affiliation(s)
- Runrui Zhang
- Embryology and Stem Cell Biology Lab, Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
| | - Marcelo Boareto
- Computational Biology Group, D-BSSE, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland; Swiss Institute of Bioinformatics (SIB), Mattenstrasse 26, 4058 Basel, Switzerland
| | - Anna Engler
- Embryology and Stem Cell Biology Lab, Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
| | - Angeliki Louvi
- Departments of Neurosurgery and Neuroscience, Yale Program on Neurogenetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Claudio Giachino
- Embryology and Stem Cell Biology Lab, Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
| | - Dagmar Iber
- Computational Biology Group, D-BSSE, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland; Swiss Institute of Bioinformatics (SIB), Mattenstrasse 26, 4058 Basel, Switzerland
| | - Verdon Taylor
- Embryology and Stem Cell Biology Lab, Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland.
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Lee YA, Im SW, Jung KC, Chung EJ, Shin CH, Kim JI, Park YJ. Predominant DICER1 Pathogenic Variants in Pediatric Follicular Thyroid Carcinomas. Thyroid 2020; 30:1120-1131. [PMID: 32228164 DOI: 10.1089/thy.2019.0233] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Background: Pediatric thyroid cancer has characteristics that are distinct from adulthood thyroid cancer. Due to its very low prevalence, little is known about the genetic characteristics of pediatric follicular thyroid cancer (FTC). Methods: We investigated genetic alterations in tumor tissues from 15 patients aged <20 years (median: 14.3 years; range: 2.4 - 19.0 years) using multifaceted approaches. Whole-exome sequencing, targeted next-generation sequencing using a cancer gene panel, and Sanger sequencing of the major exons of the H/K/N-RAS and DICER1 genes and the promoter region of the TERT gene were performed. Normal tissues or blood of patients with DICER1- or PTEN-positive tumors was also evaluated to determine whether the variant is germ line. Results: The median tumor size was 3.1 cm (range: 0.6 - 6.4 cm). Four patients exhibited angioinvasion and one extensive capsular invasion; none showed evidence of disease over a median of 8.1 years. Eight patients (53.3%) had DICER1 variants, including four with DICER1 syndrome (three patients were <10 years of age). One patient had a germ line PTEN frameshift variant with the diagnosis of PTEN hamartoma tumor syndrome. One patient had a PAX8/PPARγ rearrangement, and two patients had no genetic driver alteration other than multiple loss of heterozygosity with or without copy number alterations in their tumors. No RAS or TERT variants were found. Nodular hyperplasia and follicular adenoma (FA) coexisted in DICER1 variant-positive FTCs more frequently than variant-negative FTCs (p = 0.026). All DICER1 variant-positive FTCs had a somatic missense variant at metal binding sites (six at codon p.E1813 and two at codon p.D1709) within the RNase IIIb domain; seven had other missense, nonsense, or frameshift variants in the DICER1 gene. Six coexisting FAs of two patients with DICER1 syndrome (three of each) had additional somatic variants at metal binding sites within the RNase IIIb domain (codon p.E1705, p.D1709, p.D1810, or p.E1813), different from each other and from the indexed FTC tumor. Conclusions: Pediatric FTCs have distinct genomic alterations and pathogenesis compared with adults, particularly those characterized by DICER1 variants. The DICER1 variant should be considered in pediatric FTCs, especially in cases <10 years of age. In all DICER1 variant-positive FTCs and FAs, recurrent hotspot variants were found at metal binding sites within the RNase IIIb domain, suggesting they impact tumorigenesis.
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Affiliation(s)
- Young Ah Lee
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sun-Wha Im
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
| | - Kyeong Cheon Jung
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Eun-Jae Chung
- Department of Otorhinolaryngology-Head and Neck Surgery, and Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Choong Ho Shin
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jong-Il Kim
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea
- Seoul National University Cancer Research Institute, Seoul, Republic of Korea
| | - Young Joo Park
- Seoul National University Cancer Research Institute, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
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Tsai MH, Cheng HY, Nian FS, Liu C, Chao NH, Chiang KL, Chen SF, Tsai JW. Impairment in dynein-mediated nuclear translocation by BICD2 C-terminal truncation leads to neuronal migration defect and human brain malformation. Acta Neuropathol Commun 2020; 8:106. [PMID: 32665036 PMCID: PMC7362644 DOI: 10.1186/s40478-020-00971-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/19/2020] [Indexed: 02/06/2023] Open
Abstract
During brain development, the nucleus of migrating neurons follows the centrosome and translocates into the leading process. Defects in these migratory events, which affect neuronal migration, cause lissencephaly and other neurodevelopmental disorders. However, the mechanism of nuclear translocation remains elusive. Using whole exome sequencing (WES), we identified a novel nonsense BICD2 variant p.(Lys775Ter) (K775X) from a lissencephaly patient. Interestingly, most BICD2 missense variants have been associated with human spinal muscular atrophy (SMA) without obvious brain malformations. By in utero electroporation, we showed that BicD2 knockdown in mouse embryos inhibited neuronal migration. Surprisingly, we observed severe blockage of neuronal migration in cells overexpressing K775X but not in those expressing wild-type BicD2 or SMA-associated missense variants. The centrosome of the mutant was, on average, positioned farther away from the nucleus, indicating a failure in nuclear translocation without affecting the centrosome movement. Furthermore, BicD2 localized at the nuclear envelope (NE) through its interaction with NE protein Nesprin-2. K775X variant disrupted this interaction and further interrupted the NE recruitment of BicD2 and dynein. Remarkably, fusion of BicD2-K775X with NE-localizing domain KASH resumed neuronal migration. Our results underscore impaired nuclear translocation during neuronal migration as an important pathomechanism of lissencephaly.
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29
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Wijaya JC, Khanabdali R, Georgiou HM, Kalionis B. Ageing in human parturition: impetus of the gestation clock in the decidua†. Biol Reprod 2020; 103:695-710. [PMID: 32591788 DOI: 10.1093/biolre/ioaa113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 05/22/2020] [Accepted: 06/23/2020] [Indexed: 12/18/2022] Open
Abstract
Despite sharing many common features, the relationship between ageing and parturition remains poorly understood. The decidua is a specialized lining of endometrial tissue, which develops in preparation for pregnancy. The structure and location of the decidua support its role as the physical scaffold for the growing embryo and placenta, and thus, it is vital to sustain pregnancy. Approaching term, the physical support properties of the decidua are naturally weakened to permit parturition. In this review, we hypothesize that the natural weakening of decidual tissue at parturition is promoted by the ageing process. Studies of the ageing-related functional and molecular changes in the decidua at parturition are reviewed and classified using hallmarks of ageing as the framework. The potential roles of decidual mesenchymal stem/stromal cell (DMSC) ageing in labor are also discussed because, although stem cell exhaustion is also a hallmark of ageing, its role in labor is not completely understood. In addition, the potential roles of extracellular vesicles secreted by DMSCs in labor, and their parturition-related miRNAs, are reviewed to gain further insight into this research area. In summary, the literature supports the notion that the decidua ages as the pregnancy progresses, and this may facilitate parturition, suggesting that ageing is the probable impetus of the gestational clocks in the decidua. This conceptual framework was developed to provide a better understanding of the natural ageing process of the decidua during parturition as well as to encourage future studies of the importance of healthy ageing for optimal pregnancy outcomes.
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Affiliation(s)
- Joan C Wijaya
- Pregnancy Research Centre, Department of Maternal-Fetal Medicine, Royal Women's Hospital, Parkville, Victoria, Australia.,University of Melbourne Department of Obstetrics and Gynaecology, Royal Women's Hospital, Parkville, Victoria, Australia
| | - Ramin Khanabdali
- Pregnancy Research Centre, Department of Maternal-Fetal Medicine, Royal Women's Hospital, Parkville, Victoria, Australia.,University of Melbourne Department of Obstetrics and Gynaecology, Royal Women's Hospital, Parkville, Victoria, Australia.,Department of Process Development, Exopharm Limited, Melbourne, Victoria, Australia
| | - Harry M Georgiou
- Pregnancy Research Centre, Department of Maternal-Fetal Medicine, Royal Women's Hospital, Parkville, Victoria, Australia.,University of Melbourne Department of Obstetrics and Gynaecology, Royal Women's Hospital, Parkville, Victoria, Australia
| | - Bill Kalionis
- Pregnancy Research Centre, Department of Maternal-Fetal Medicine, Royal Women's Hospital, Parkville, Victoria, Australia.,University of Melbourne Department of Obstetrics and Gynaecology, Royal Women's Hospital, Parkville, Victoria, Australia
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30
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Kretov DA, Walawalkar IA, Mora-Martin A, Shafik AM, Moxon S, Cifuentes D. Ago2-Dependent Processing Allows miR-451 to Evade the Global MicroRNA Turnover Elicited during Erythropoiesis. Mol Cell 2020; 78:317-328.e6. [PMID: 32191872 PMCID: PMC7201373 DOI: 10.1016/j.molcel.2020.02.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 12/02/2019] [Accepted: 02/24/2020] [Indexed: 01/08/2023]
Abstract
MicroRNAs (miRNAs) are sequentially processed by two RNase III enzymes, Drosha and Dicer. miR-451 is the only known miRNA whose processing bypasses Dicer and instead relies on the slicer activity of Argonaute-2 (Ago2). miR-451 is highly conserved in vertebrates and regulates erythrocyte maturation, where it becomes the most abundant miRNA. However, the basis for the non-canonical biogenesis of miR-451 is unclear. Here, we show that Ago2 is less efficient than Dicer in processing pre-miRNAs, but this deficit is overcome when miR-144 represses Dicer in a negative-feedback loop during erythropoiesis. Loss of miR-144-mediated Dicer repression in zebrafish embryos and human cells leads to increased canonical miRNA production and impaired miR-451 maturation. Overexpression of Ago2 rescues some of the defects of miR-451 processing. Thus, the evolution of Ago2-dependent processing allows miR-451 to circumvent the global repression of canonical miRNAs elicited, in part, by the miR-144 targeting of Dicer during erythropoiesis.
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Affiliation(s)
- Dmitry A Kretov
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Isha A Walawalkar
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | | | - Andrew M Shafik
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Simon Moxon
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Daniel Cifuentes
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA.
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31
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Wright CB, Uehara H, Kim Y, Yasuma T, Yasuma R, Hirahara S, Makin RD, Apicella I, Pereira F, Nagasaka Y, Narendran S, Fukuda S, Albuquerque R, Fowler BJ, Bastos-Carvalho A, Georgel P, Hatada I, Chang B, Kerur N, Ambati BK, Ambati J, Gelfand BD. Chronic Dicer1 deficiency promotes atrophic and neovascular outer retinal pathologies in mice. Proc Natl Acad Sci U S A 2020; 117:2579-2587. [PMID: 31964819 PMCID: PMC7007521 DOI: 10.1073/pnas.1909761117] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Degeneration of the retinal pigmented epithelium (RPE) and aberrant blood vessel growth in the eye are advanced-stage processes in blinding diseases such as age-related macular degeneration (AMD), which affect hundreds of millions of people worldwide. Loss of the RNase DICER1, an essential factor in micro-RNA biogenesis, is implicated in RPE atrophy. However, the functional implications of DICER1 loss in choroidal and retinal neovascularization are unknown. Here, we report that two independent hypomorphic mouse strains, as well as a separate model of postnatal RPE-specific DICER1 ablation, all presented with spontaneous RPE degeneration and choroidal and retinal neovascularization. DICER1 hypomorphic mice lacking critical inflammasome components or the innate immune adaptor MyD88 developed less severe RPE atrophy and pathological neovascularization. DICER1 abundance was also reduced in retinas of the JR5558 mouse model of spontaneous choroidal neovascularization. Finally, adenoassociated vector-mediated gene delivery of a truncated DICER1 variant (OptiDicer) reduced spontaneous choroidal neovascularization in JR5558 mice. Collectively, these findings significantly expand the repertoire of DICER1 in preserving retinal homeostasis by preventing both RPE degeneration and pathological neovascularization.
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Affiliation(s)
- Charles B Wright
- Department of Ophthalmology and Visual Sciences, University of Kentucky, Lexington, KY 40506
| | - Hironori Uehara
- Department of Ophthalmology, Loma Linda University, Loma Linda, CA 92350
| | - Younghee Kim
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA 22903
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA 22903
| | - Tetsuhiro Yasuma
- Department of Ophthalmology and Visual Sciences, University of Kentucky, Lexington, KY 40506
| | - Reo Yasuma
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA 22903
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA 22903
| | - Shuichiro Hirahara
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA 22903
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA 22903
| | - Ryan D Makin
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA 22903
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA 22903
- Molecular and Cellular Basis of Disease Graduate Program, University of Virginia School of Medicine, Charlottesville, VA 22903
| | - Ivana Apicella
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA 22903
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA 22903
| | - Felipe Pereira
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA 22903
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA 22903
- Departamento de Oftalmologia e Ciências Visuais, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo 04039-032, Brazil
| | - Yosuke Nagasaka
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA 22903
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA 22903
| | - Siddharth Narendran
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA 22903
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA 22903
- Aravind Medical Research Foundation, Aravind Eye Care System, Madurai, Tamil Nadu 625020, India
| | - Shinichi Fukuda
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA 22903
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA 22903
- Department of Ophthalmology, University of Tsukuba, Ibaraki 305-8575, Japan
| | - Romulo Albuquerque
- Department of Ophthalmology and Visual Sciences, University of Kentucky, Lexington, KY 40506
| | - Benjamin J Fowler
- Department of Ophthalmology and Visual Sciences, University of Kentucky, Lexington, KY 40506
| | - Ana Bastos-Carvalho
- Department of Ophthalmology and Visual Sciences, University of Kentucky, Lexington, KY 40506
| | - Philippe Georgel
- Laboratoire d'ImmunoRhumatologie Moléculaire, INSERM UMR-S1109, LabEx Transplantex, Fédération de Médecine Translationnelle de Strasbourg, Université de Strasbourg, 67085 Strasbourg, France
- Fédération Hospitalo-Universitaire OMICARE, Université de Strasbourg, 67085 Strasbourg, France
| | - Izuho Hatada
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi 371-8512, Japan
| | - Bo Chang
- The Jackson Laboratory, Bar Harbor, ME 04609
| | - Nagaraj Kerur
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA 22903
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA 22903
| | | | - Jayakrishna Ambati
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA 22903
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA 22903
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, VA 22903
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22903
| | - Bradley D Gelfand
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA 22903;
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA 22903
- Department of Biomedical Engineering, University of Virginia School of Engineering, Charlottesville, VA 22904
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32
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Li BK, Vasiljevic A, Dufour C, Yao F, Ho BLB, Lu M, Hwang EI, Gururangan S, Hansford JR, Fouladi M, Nobusawa S, Laquerriere A, Delisle MB, Fangusaro J, Forest F, Toledano H, Solano-Paez P, Leary S, Birks D, Hoffman LM, Szathmari A, Faure-Conter C, Fan X, Catchpoole D, Zhou L, Schultz KAP, Ichimura K, Gauchotte G, Jabado N, Jones C, Loussouarn D, Mokhtari K, Rousseau A, Ziegler DS, Tanaka S, Pomeroy SL, Gajjar A, Ramaswamy V, Hawkins C, Grundy RG, Hill DA, Bouffet E, Huang A, Jouvet A. Pineoblastoma segregates into molecular sub-groups with distinct clinico-pathologic features: a Rare Brain Tumor Consortium registry study. Acta Neuropathol 2020; 139:223-241. [PMID: 31820118 DOI: 10.1007/s00401-019-02111-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/13/2019] [Accepted: 11/14/2019] [Indexed: 12/22/2022]
Abstract
Pineoblastomas (PBs) are rare, aggressive pediatric brain tumors of the pineal gland with modest overall survival despite intensive therapy. We sought to define the clinical and molecular spectra of PB to inform new treatment approaches for this orphan cancer. Tumor, blood, and clinical data from 91 patients with PB or supratentorial primitive neuroectodermal tumor (sPNETs/CNS-PNETs), and 2 pineal parenchymal tumors of intermediate differentiation (PPTIDs) were collected from 29 centres in the Rare Brain Tumor Consortium. We used global DNA methylation profiling to define a core group of PB from 72/93 cases, which were delineated into five molecular sub-groups. Copy number, whole exome and targeted sequencing, and miRNA expression analyses were used to evaluate the clinico-pathologic significance of each sub-group. Tumors designated as group 1 and 2 almost exclusively exhibited deleterious homozygous loss-of-function alterations in miRNA biogenesis genes (DICER1, DROSHA, and DGCR8) in 62 and 100% of group 1 and 2 tumors, respectively. Recurrent alterations of the oncogenic MYC-miR-17/92-RB1 pathway were observed in the RB and MYC sub-group, respectively, characterized by RB1 loss with gain of miR-17/92, and recurrent gain or amplification of MYC. PB sub-groups exhibited distinct clinical features: group 1-3 arose in older children (median ages 5.2-14.0 years) and had intermediate to excellent survival (5-year OS of 68.0-100%), while Group RB and MYC PB patients were much younger (median age 1.3-1.4 years) with dismal survival (5-year OS 37.5% and 28.6%, respectively). We identified age < 3 years at diagnosis, metastatic disease, omission of upfront radiation, and chr 16q loss as significant negative prognostic factors across all PBs. Our findings demonstrate that PB exhibits substantial molecular heterogeneity with sub-group-associated clinical phenotypes and survival. In addition to revealing novel biology and therapeutics, molecular sub-grouping of PB can be exploited to reduce treatment intensity for patients with favorable biology tumors.
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Affiliation(s)
- Bryan K Li
- Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, 555 University Ave., 10421B, Black, Toronto, ON, M5G 1X8, Canada
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON, Canada
- Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Alexandre Vasiljevic
- Faculté de Médecine, Université de Lyon, Lyon, France
- Service d'Anatomie et Cytologie Pathologiques, CHU de Lyon, Lyon, France
| | - Christelle Dufour
- Département de Cancérologie de l'Enfant et de l'Adolescent, Institut Gustave Roussy, Villejuif, Paris, France
| | - Fupan Yao
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON, Canada
- Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Ben L B Ho
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON, Canada
| | - Mei Lu
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON, Canada
| | - Eugene I Hwang
- Department of Oncology, Children's National Medical Center, Washington, DC, USA
| | - Sridharan Gururangan
- Department of Pediatrics, Preston A. Wells Jr. Center for Brain Tumor Therapy, UF Health Shands Hospital, University of Florida, Gainesville, FL, USA
| | - Jordan R Hansford
- Children's Cancer Centre, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia
| | - Maryam Fouladi
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Sumihito Nobusawa
- Department of Human Pathology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Annie Laquerriere
- Department of Pathology, Normandy Center for Genomic and Personalized Medicine, Rouen University Hospital, Normandie University, UNIROUEN, Inserm U1245, F 76000, Rouen, France
| | | | - Jason Fangusaro
- Department of Pediatric Hematology and Oncology, Children's Healthcare of Atlanta and the Emory University School of Medicine, Atlanta, GA, USA
| | - Fabien Forest
- Department of Pathology, CHU St. Etienne, Saint-Étienne, France
| | - Helen Toledano
- Department of Pediatric Hematology Oncology, Schneider Children's Medical Center of Israel, Petah Tikva, Israel
| | - Palma Solano-Paez
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON, Canada
- Hospital Infantil Virgen del Rocio, Seville, Spain
| | - Sarah Leary
- Cancer and Blood Disorders Center, Seattle Children's, Seattle, WA, USA
| | - Diane Birks
- Department of Pediatrics, University of Colorado Denver, Denver, CO, USA
| | - Lindsey M Hoffman
- Center for Cancer and Blood Disorders, Phoenix Children's Hospital, Phoenix, AZ, USA
| | - Alexandru Szathmari
- Département de Neurochirurgie Adulte et Pédiatrique, Hôpital Femme Mère Enfant, Hospices Civils de Lyon, Bron, France
| | | | - Xing Fan
- Department of Neurosurgery, University of Michigan, Ann Arbor, MI, USA
| | - Daniel Catchpoole
- Children's Cancer Research Unit, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Li Zhou
- Children's Cancer Research Unit, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Kris Ann P Schultz
- Cancer and Blood Disorder, Children's Hospitals and Clinics of Minnesota, Minneapolis, MN, USA
| | | | | | - Nada Jabado
- Departments of Pediatrics and Human Genetics, McGill University, Montreal, QC, Canada
| | - Chris Jones
- The Institute of Cancer Research, London, UK
| | - Delphine Loussouarn
- Service d'Anatomie et de Cytologie pathologiques, CHU Nantes, Nantes, France
| | - Karima Mokhtari
- Département de Neuropathologie, Hôpital Universitaire Pitie-Salpetriere, Paris, France
| | - Audrey Rousseau
- Département de Pathologie Cellulaire et Tissulaire, CHU d'Angers, Angers, France
| | - David S Ziegler
- Kids Cancer Centre, Sydney Children's Hospital, Sydney, NSW, Australia
- Children's Cancer Institute, Lowy Cancer Centre, University of New South Wales, Sydney, NSW, Australia
| | - Shinya Tanaka
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Hokkaido, Japan
| | - Scott L Pomeroy
- Department of Neurology, Harvard Medical School, Boston Children's Hospital, Boston, MA, USA
| | - Amar Gajjar
- Department of Oncology, Division of Neuro-Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Vijay Ramaswamy
- Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, 555 University Ave., 10421B, Black, Toronto, ON, M5G 1X8, Canada
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON, Canada
- Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Cynthia Hawkins
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON, Canada
- Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Division of Pathology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Richard G Grundy
- Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK
| | - D Ashley Hill
- Division of Pathology, Center for Cancer and Immunology Research, Children's National Medical Center, Washington, DC, USA
| | - Eric Bouffet
- Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, 555 University Ave., 10421B, Black, Toronto, ON, M5G 1X8, Canada
| | - Annie Huang
- Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, 555 University Ave., 10421B, Black, Toronto, ON, M5G 1X8, Canada.
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON, Canada.
- Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
- Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
| | - Anne Jouvet
- Service d'Anatomie et Cytologie Pathologiques, CHU de Lyon, Lyon, France
- Pathology and Molecular Biology, SFCE, Bordeaux, France
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Martínez de LaPiscina I, Hernández-Ramírez LC, Portillo N, Gómez-Gila AL, Urrutia I, Martínez-Salazar R, García-Castaño A, Aguayo A, Rica I, Gaztambide S, Faucz FR, Keil MF, Lodish MB, Quezado M, Pankratz N, Chittiboina P, Lane J, Kay DM, Mills JL, Castaño L, Stratakis CA. Rare Germline DICER1 Variants in Pediatric Patients With Cushing's Disease: What Is Their Role? Front Endocrinol (Lausanne) 2020; 11:433. [PMID: 32714280 PMCID: PMC7351020 DOI: 10.3389/fendo.2020.00433] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/02/2020] [Indexed: 12/14/2022] Open
Abstract
Context: The DICER1 syndrome is a multiple neoplasia disorder caused by germline mutations in the DICER1 gene. In DICER1 patients, aggressive congenital pituitary tumors lead to neonatal Cushing's disease (CD). The role of DICER1 in other corticotropinomas, however, remains unknown. Objective: To perform a comprehensive screening for DICER1 variants in a large cohort of CD patients, and to analyze their possible contribution to the phenotype. Design, setting, patients, and interventions: We included 192 CD cases: ten young-onset (age <30 years at diagnosis) patients were studied using a next generation sequencing panel, and 182 patients (170 pediatric and 12 adults) were screened via whole-exome sequencing. In seven cases, tumor samples were analyzed by Sanger sequencing. Results: Rare germline DICER1 variants were found in seven pediatric patients with no other known disease-associated germline defects or somatic DICER1 second hits. By immunohistochemistry, DICER1 showed nuclear localization in 5/6 patients. Variant transmission from one of the parents was confirmed in 5/7 cases. One patient had a multinodular goiter; another had a family history of melanoma; no other patients had a history of neoplasms. Conclusions: Our findings suggest that DICER1 gene variants may contribute to the pathogenesis of non-syndromic corticotropinomas. Clarifying whether DICER1 loss-of-function is disease-causative or a mere disease-modifier in this setting, requires further studies. Clinical trial registration: ClinicalTrials.gov: NCT00001595.
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Affiliation(s)
- Idoia Martínez de LaPiscina
- Section on Endocrinology, Metabolism, Nutrition and Renal Diseases, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, UPV/EHU, CIBERER, CIBERDEM, Barakaldo, Spain
| | - Laura C. Hernández-Ramírez
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Nancy Portillo
- Section on Endocrinology, Metabolism, Nutrition and Renal Diseases, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, UPV/EHU, CIBERER, CIBERDEM, Barakaldo, Spain
- Pediatric Endocrinology Service, Alto Deba Hospital, Arrasate, Spain
| | - Ana L. Gómez-Gila
- Pediatric Endocrinology Service, Virgen del Rocío University Hospital, Sevilla, Spain
| | - Inés Urrutia
- Section on Endocrinology, Metabolism, Nutrition and Renal Diseases, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, UPV/EHU, CIBERER, CIBERDEM, Barakaldo, Spain
| | - Rosa Martínez-Salazar
- Section on Endocrinology, Metabolism, Nutrition and Renal Diseases, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, UPV/EHU, CIBERER, CIBERDEM, Barakaldo, Spain
| | - Alejandro García-Castaño
- Section on Endocrinology, Metabolism, Nutrition and Renal Diseases, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, UPV/EHU, CIBERER, CIBERDEM, Barakaldo, Spain
| | - Aníbal Aguayo
- Section on Endocrinology, Metabolism, Nutrition and Renal Diseases, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, UPV/EHU, CIBERER, CIBERDEM, Barakaldo, Spain
| | - Itxaso Rica
- Section on Endocrinology, Metabolism, Nutrition and Renal Diseases, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, UPV/EHU, CIBERER, CIBERDEM, Barakaldo, Spain
- Pediatric Endocrinology Service, Cruces University Hospital, Barakaldo, Spain
| | - Sonia Gaztambide
- Section on Endocrinology, Metabolism, Nutrition and Renal Diseases, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, UPV/EHU, CIBERER, CIBERDEM, Barakaldo, Spain
- Endocrinology Service, Cruces University Hospital, Barakaldo, Spain
| | - Fabio R. Faucz
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Margaret F. Keil
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Maya B. Lodish
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, United States
- Division of Pediatric Endocrinology, Department of Pediatrics, Mission Hall, University of California, San Francisco, San Francisco, CA, United States
| | - Martha Quezado
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, United States
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN, United States
| | - Prashant Chittiboina
- Neurosurgery Unit for Pituitary and Inheritable Diseases, National Institute of Neurological Disorders and Stroke, Bethesda, MD, United States
| | - John Lane
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN, United States
| | - Denise M. Kay
- Newborn Screening Program, Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - James L. Mills
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Luis Castaño
- Section on Endocrinology, Metabolism, Nutrition and Renal Diseases, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, UPV/EHU, CIBERER, CIBERDEM, Barakaldo, Spain
- *Correspondence: Luis Castaño
| | - Constantine A. Stratakis
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, United States
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Oliver-Petit I, Bertozzi AI, Grunenwald S, Gambart M, Pigeon-Kerchiche P, Sadoul JL, Caron PJ, Savagner F. Multinodular goitre is a gateway for molecular testing of DICER1 syndrome. Clin Endocrinol (Oxf) 2019; 91:669-675. [PMID: 31408196 DOI: 10.1111/cen.14074] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 08/11/2019] [Accepted: 08/12/2019] [Indexed: 11/28/2022]
Abstract
BACKGROUND DICER1 syndrome is an autosomal dominant disorder that predisposes individuals to develop benign or malignant tumours from infancy to adulthood. There is low-to-moderate penetrance of tumour development, which is sex- and age-dependent. Multinodular goitre (MNG) is among the most highly penetrant phenotype of the disorder, especially in females. PATIENTS AND METHODS We report a series of eight families referred for childhood-onset of MNG or DICER1-related tumours with familial history of MNG in relatives. No additional families with these criteria stated were identified during the same date. We screened DNA samples from the probands and members of their family (40) for constitutional DICER1 variants using Next Generation Sequencing tools. RESULTS Germline pathogenic DICER1 gene variants were identified in all probands and several of their relatives: 64% presented with MNG/thyroidectomy as the phenotypic expression of the syndrome. DICER1 gene variants were identified in the RNAseIII and the PAZ domains. All tumour tissues studied presented clonal pathogenic variants in hotspot regions. Early identification of DICER1 variant carriers has permitted diagnosis and therapeutic scheme correction for two patients and cascade testing in relatives. CONCLUSIONS Multinodular goitre is uncommon in children. Childhood-onset MNG, multiple occurrences of the disease within the same family, or its association with rare benign or malignant tumours should raise suspicions of anomalies in the DICER1 gene, as proposed by recent international recommendations. Early detection of DICER1 pathogenic variants has important consequences in terms of therapeutic strategy, early tumour screening, and genetic counselling.
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Affiliation(s)
- Isabelle Oliver-Petit
- Endocrine, Genetics, Bone Diseases, and Pediatric Gynecology unit, Children's Hospital, CHU Toulouse, Toulouse, France
| | | | - Solange Grunenwald
- Department of Endocrinology and Metabolic Diseases, Cardio-Vascular and Metabolic Unit, CHU Larrey, Toulouse, France
| | - Marion Gambart
- Hematology and Oncology unit, Children's Hospital, CHU Toulouse, Toulouse, France
| | | | | | - Philippe J Caron
- Department of Endocrinology and Metabolic Diseases, Cardio-Vascular and Metabolic Unit, CHU Larrey, Toulouse, France
| | - Frédérique Savagner
- Biochemistry and Genetic laboratory, Federative Institute of Biology, CHU Toulouse, Toulouse, France
- Inserm UMR1048, I2MC, Toulouse, France
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35
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Cooperative adaptation to therapy (CAT) confers resistance in heterogeneous non-small cell lung cancer. PLoS Comput Biol 2019; 15:e1007278. [PMID: 31449515 PMCID: PMC6709889 DOI: 10.1371/journal.pcbi.1007278] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 07/22/2019] [Indexed: 12/12/2022] Open
Abstract
Understanding intrinsic and acquired resistance is crucial to overcoming cancer chemotherapy failure. While it is well-established that intratumor, subclonal genetic and phenotypic heterogeneity significantly contribute to resistance, it is not fully understood how tumor sub-clones interact with each other to withstand therapy pressure. Here, we report a previously unrecognized behavior in heterogeneous tumors: cooperative adaptation to therapy (CAT), in which cancer cells induce co-resistant phenotypes in neighboring cancer cells when exposed to cancer therapy. Using a CRISPR/Cas9 toolkit we engineered phenotypically diverse non-small cell lung cancer (NSCLC) cells by conferring mutations in Dicer1, a type III cytoplasmic endoribonuclease involved in small non-coding RNA genesis. We monitored three-dimensional growth dynamics of fluorescently-labeled mutant and/or wild-type cells individually or in co-culture using a substrate-free NanoCulture system under unstimulated or drug pressure conditions. By integrating mathematical modeling with flow cytometry, we characterized the growth patterns of mono- and co-cultures using a mathematical model of intra- and interspecies competition. Leveraging the flow cytometry data, we estimated the model’s parameters to reveal that the combination of WT and mutants in co-cultures allowed for beneficial growth in previously drug sensitive cells despite drug pressure via induction of cell state transitions described by a cooperative game theoretic change in the fitness values. Finally, we used an ex vivo human tumor model that predicts clinical response through drug sensitivity analyses and determined that cellular and morphologic heterogeneity correlates to prognostic failure of multiple clinically-approved and off-label drugs in individual NSCLC patient samples. Together, these findings present a new paradox in drug resistance implicating non-genetic cooperation among tumor cells to thwart drug pressure, suggesting that profiling for druggable targets (i.e. mutations) alone may be insufficient to assign effective therapy. Here, we provide mathematical and empirical evidence to support a potentially new paradigm in drug resistance, which we have termed “cooperative adaptation to therapy” (CAT). CAT is defined by a phenomenon wherein drug-sensitive cancer cells with different genetic and phenotypic features within a 3-dimensional heterogeneous tumor induce non-mutational resistance in their neighboring cells under pressure of cancer therapy. To develop this novel conclusion we deployed an interdisciplinary effort including an ex vivo human tumor model, a CRISPR/Cas9 platform with 3-dimensional in vitro experiments, and high throughput flow cytometry. Importantly, we wove these data together using a mathematical model of intra- and interspecies competition to understand how tumor heterogeneity influenced our observations. By estimating the model’s parameters, we determined that the combination of genetic clonal variants in co-cultures allowed for previously drug-sensitive cells to continue to grow despite drug pressure. We were thus able to characterize distinct growth regimens in mono- and co-cultures without and with drug pressure.
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36
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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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37
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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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38
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Abnormal Expression of DICER1 Leads to Dysregulation of Inflammatory Effectors in Human Synoviocytes. Mediators Inflamm 2019; 2019:6768504. [PMID: 31275058 PMCID: PMC6558604 DOI: 10.1155/2019/6768504] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 03/26/2019] [Accepted: 05/02/2019] [Indexed: 01/31/2023] Open
Abstract
Dysregulation of multiple microRNAs widely takes place during rheumatoid arthritis (RA) and experimental arthritides. This study is performed to explore the possible mechanism underlying DICER1 deficiency-mediated inflammation in human synoviocytes SW982. Firstly, RNAi of DICER1 led to increased COX2, MMP3, and MMP13 protein production, while DICER1 overexpression could reduce MMP13 expression. Secondly, the increase of IL-8 and decrease of TGF-β1 and TIMP1 were determined in the supernatant derived from DICER1 siRNA-treated cells, while DICER1 overexpression was found capable to reverse this effect. Ingenuity pathway analysis (IPA) software predicted that the Dicer1 deficiency-induced dysregulated cytokines in synoviocytes could possibly lead to the inflammatory disorders in the synovial tissue. Moreover, DICER1 deficiency could also reduce apoptosis, while DICER1 overexpression was found to decrease the proliferation and enhance apoptosis. In addition, DICER1 deficiency could lower the expression of multiple RA-related miRNAs such as miR-155. Meanwhile, DICER1 overexpression could rescue their low expression levels. And then, gain or loss of miR-155 function could regulate the protein levels of MMP3 and MMP13. These results indicated that DICER1 might play its role through regulating its downstream RA-related miRNAs. Our data demonstrated that DICER1 deficiency could cause multiple proinflammatory events in human synoviocytes SW982. This mechanism study might provide the possible target molecule to modify the inflammatory destruction and overproliferation in synoviocytes.
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39
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Yan H, Liang FS. miRNA inhibition by proximity-enabled Dicer inactivation. Methods 2019; 167:117-123. [PMID: 31077820 DOI: 10.1016/j.ymeth.2019.05.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 04/22/2019] [Accepted: 05/05/2019] [Indexed: 11/17/2022] Open
Abstract
microRNAs (miRNAs) are considered as master regulators of biological processes. Dysregulation of miRNA expression has been implicated in many human diseases. Driven by the key biological roles and the therapeutic potential, developing methods for miRNA regulation has become an intense research area. Due to favorable pharmacological properties, small molecule-based miRNA inhibition emerges as a promising strategy and significant progresses have been made. However, it remains challenging to regulate miRNA using small molecules because of the inherent difficulty in RNA targeting and inhibition. Herein we outline the workflow of generating bifunctional small molecule inhibitors blocking miRNA biogenesis through proximity-enabled inactivation of Dicer, an enzyme required for the processing of precursor miRNA (pre-miRNA) into mature miRNA. By conjugating a weak Dicer inhibitor with a pre-miRNA binder, the inhibitor can be delivered to the Dicer processing site associated with the targeted pre-miRNA, and as a result inhibiting Dicer-mediated pre-miRNA processing. This protocol can be applicable in producing bifunctional inhibitors for different miRNAs.
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Affiliation(s)
- Hao Yan
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, United States
| | - Fu-Sen Liang
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, United States.
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40
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Stewart DR, Best AF, Williams GM, Harney LA, Carr AG, Harris AK, Kratz CP, Dehner LP, Messinger YH, Rosenberg PS, Hill DA, Schultz KAP. Neoplasm Risk Among Individuals With a Pathogenic Germline Variant in DICER1. J Clin Oncol 2019; 37:668-676. [PMID: 30715996 PMCID: PMC6553836 DOI: 10.1200/jco.2018.78.4678] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2018] [Indexed: 01/08/2023] Open
Abstract
PURPOSE DICER1 syndrome is an autosomal-dominant, pleiotropic tumor-predisposition disorder caused by pathogenic germline variants in DICER1. We sought to quantify risk, hazard rates, and the probability of neoplasm incidence accounting for competing risks ("cumulative incidence") of neoplasms (benign and malignant) and standardized incidence ratios for malignant tumors in individuals with DICER1 pathogenic variation. PATIENTS AND METHODS We combined data from three large cohorts of patients who carry germline pathogenic variation in DICER1. To reduce ascertainment bias, we distinguished probands from nonprobands. Neoplasm diagnoses were confirmed by review of pathology reports and/or central review of surgical pathology materials. Standardized cancer incidence ratios were determined relative to the SEER program, which does not capture all DICER1-associated neoplasms. For all malignancies and benign tumors ("neoplasms," excluding type Ir pleuropulmonary blastoma and thyroid nodules), we used the Kaplan-Meier method and nonparametric cumulative incidence curves to estimate neoplasm-free survival. RESULTS We calculated the age at first neoplasm diagnosis (systematically ascertained cancers plus DICER1-associated neoplasms pleuropulmonary blastoma, cystic nephroma, and nasal chondromesenchymal hamartoma) in 102 female and male nonproband DICER1 carriers. By age 10 years, 5.3% (95% CI, 0.6% to 9.7%) of nonproband DICER1 carriers had developed a neoplasm (females, 4.0%; males, 6.6%). By age 50 years, 19.3% (95% CI, 8.4% to 29.0%) of nonprobands had developed a neoplasm (females, 26.5%; males, 10.2%). After age 10 years, female risk was elevated compared with male risk. Standardized cancer incidence ratio analysis of 102 nonproband DICER1 carriers, which represented 3,344 person-years of observation, showed significant cancer excesses overall, particularly of gynecologic and thyroid cancers. CONCLUSION This work provides the first quantitative analysis of site-specific neoplasm risk and excess malignancy risk in 102 systematically characterized nonproband DICER1 carriers. Our findings inform DICER1 syndrome phenotype, natural history, and genetic counseling.
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Affiliation(s)
| | | | - Gretchen M. Williams
- Children's Hospitals and Clinics of Minnesota, Minneapolis, MN
- International Pleuropulmonary Blastoma/DICER1 Registry, Minneapolis, MN
| | | | | | - Anne K. Harris
- Children's Hospitals and Clinics of Minnesota, Minneapolis, MN
- International Pleuropulmonary Blastoma/DICER1 Registry, Minneapolis, MN
- International Ovarian and Testicular Stromal Tumor Registry, Minneapolis, MN
| | | | - Louis P. Dehner
- International Pleuropulmonary Blastoma/DICER1 Registry, Minneapolis, MN
- International Ovarian and Testicular Stromal Tumor Registry, Minneapolis, MN
- Washington University, St. Louis, MO
| | - Yoav H. Messinger
- Children's Hospitals and Clinics of Minnesota, Minneapolis, MN
- International Pleuropulmonary Blastoma/DICER1 Registry, Minneapolis, MN
| | | | - D. Ashley Hill
- Children's National Health System, Washington, DC
- George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Kris Ann P. Schultz
- Children's Hospitals and Clinics of Minnesota, Minneapolis, MN
- International Pleuropulmonary Blastoma/DICER1 Registry, Minneapolis, MN
- International Ovarian and Testicular Stromal Tumor Registry, Minneapolis, MN
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41
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Pepe S, Korbonits M, Iacovazzo D. Germline and mosaic mutations causing pituitary tumours: genetic and molecular aspects. J Endocrinol 2019; 240:R21-R45. [PMID: 30530903 DOI: 10.1530/joe-18-0446] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 11/07/2018] [Indexed: 12/24/2022]
Abstract
While 95% of pituitary adenomas arise sporadically without a known inheritable predisposing mutation, in about 5% of the cases they can arise in a familial setting, either isolated (familial isolated pituitary adenoma or FIPA) or as part of a syndrome. FIPA is caused, in 15-30% of all kindreds, by inactivating mutations in the AIP gene, encoding a co-chaperone with a vast array of interacting partners and causing most commonly growth hormone excess. While the mechanisms linking AIP with pituitary tumorigenesis have not been fully understood, they are likely to involve several pathways, including the cAMP-dependent protein kinase A pathway via defective G inhibitory protein signalling or altered interaction with phosphodiesterases. The cAMP pathway is also affected by other conditions predisposing to pituitary tumours, including X-linked acrogigantism caused by duplications of the GPR101 gene, encoding an orphan G stimulatory protein-coupled receptor. Activating mosaic mutations in the GNAS gene, coding for the Gα stimulatory protein, cause McCune-Albright syndrome, while inactivating mutations in the regulatory type 1α subunit of protein kinase A represent the most frequent genetic cause of Carney complex, a syndromic condition with multi-organ manifestations also involving the pituitary gland. In this review, we discuss the genetic and molecular aspects of isolated and syndromic familial pituitary adenomas due to germline or mosaic mutations, including those secondary to AIP and GPR101 mutations, multiple endocrine neoplasia type 1 and 4, Carney complex, McCune-Albright syndrome, DICER1 syndrome and mutations in the SDHx genes underlying the association of familial paragangliomas and phaeochromocytomas with pituitary adenomas.
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Affiliation(s)
- Sara Pepe
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine, Queen Mary University of London, London, UK
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Márta Korbonits
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine, Queen Mary University of London, London, UK
| | - Donato Iacovazzo
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine, Queen Mary University of London, London, UK
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Dubbury SJ, Boutz PL, Sharp PA. CDK12 regulates DNA repair genes by suppressing intronic polyadenylation. Nature 2018; 564:141-145. [PMID: 30487607 PMCID: PMC6328294 DOI: 10.1038/s41586-018-0758-y] [Citation(s) in RCA: 174] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 10/11/2018] [Indexed: 12/28/2022]
Abstract
Mutations that attenuate homologous recombination (HR)-mediated repair promote tumorigenesis and sensitize cells to chemotherapeutics that cause replication fork collapse, a phenotype known as 'BRCAness'1. BRCAness tumours arise from loss-of-function mutations in 22 genes1. Of these genes, all but one (CDK12) function directly in the HR repair pathway1. CDK12 phosphorylates serine 2 of the RNA polymerase II C-terminal domain heptapeptide repeat2-7, a modification that regulates transcription elongation, splicing, and cleavage and polyadenylation8,9. Genome-wide expression studies suggest that depletion of CDK12 abrogates the expression of several HR genes relatively specifically, thereby blunting HR repair3-7,10,11. This observation suggests that the mutational status of CDK12 may predict sensitivity to targeted treatments against BRCAness, such as PARP1 inhibitors, and that CDK12 inhibitors may induce sensitization of HR-competent tumours to these treatments6,7,10,11. Despite growing clinical interest, the mechanism by which CDK12 regulates HR genes remains unknown. Here we show that CDK12 globally suppresses intronic polyadenylation events in mouse embryonic stem cells, enabling the production of full-length gene products. Many HR genes harbour more intronic polyadenylation sites than other expressed genes, and these sites are particularly sensitive to loss of CDK12. The cumulative effect of these sites accounts for the enhanced sensitivity of HR gene expression to CDK12 loss, and we find that this mechanism is conserved in human tumours that contain loss-of-function CDK12 mutations. This work clarifies the function of CDK12 and underscores its potential both as a chemotherapeutic target and as a tumour biomarker.
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Affiliation(s)
- Sara J Dubbury
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Paul L Boutz
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Phillip A Sharp
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Nourse J, Braun J, Lackner K, Hüttelmaier S, Danckwardt S. Large-scale identification of functional microRNA targeting reveals cooperative regulation of the hemostatic system. J Thromb Haemost 2018; 16:2233-2245. [PMID: 30207063 DOI: 10.1111/jth.14290] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Indexed: 12/22/2022]
Abstract
Essentials MicroRNAs (miRNAs) regulate the molecular networks controlling biological functions such as hemostasis. We utilized novel methods to analyze miRNA-mediated regulation of the hemostatic system. 52 specific miRNA interactions with 11 key hemostatic associated genes were identified. Functionality and drugability of miRNA-19b-3p against antithrombin were demonstrated in vivo. SUMMARY: Background microRNAs (miRNAs) confer robustness to complex molecular networks regulating biological functions. However, despite the involvement of miRNAs in almost all biological processes, and the importance of the hemostatic system for a multitude of actions in and beyond blood coagulation, the role of miRNAs in hemostasis is poorly defined. Objectives Here we comprehensively illuminate miRNA-mediated regulation of the hemostatic system in an unbiased manner. Methods In contrast to widely applied association studies, we used an integrative screening approach that combines functional aspects of miRNA silencing with biophysical miRNA interaction based on RNA pull-downs (miTRAP) coupled to next-generation sequencing. Results Examination of a panel of 27 hemostasis-associated gene 3'UTRs revealed the majority to possess substantial Dicer-dependent silencing capability, suggesting functional miRNA targeting. miTRAP revealed 150 specific miRNA interactions with 14 3'UTRs, of which 52, involving 40 miRNAs, were functionally confirmed. This includes cooperative miRNA regulation of key hemostatic genes comprising procoagulant (F7, F8, F11, FGA, FGG and KLKB1) and anticoagulant (SERPINA10, PROZ, SERPIND1 and SERPINC1) as well as fibrinolytic (PLG) components. Bioinformatic analysis of miRNA functionality reveals established and potential novel links between the hemostatic system and other pathologies, such as cancer, bone metabolism and renal function. Conclusions Our findings provide, along with an in-vivo proof of concept, deep insights into the network of miRNAs regulating the hemostatic system and present a foundation for biomarker discovery and novel targeted therapeutics for correction of de-regulated hemostasis and associated processes in the future. A repository of the miRNA targetome covering 14 hemostatic components is provided.
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Affiliation(s)
- J Nourse
- Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University, Mainz, Germany
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - J Braun
- Institute of Molecular Medicine, Martin Luther University Halle (Saale), Halle, Germany
| | - K Lackner
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - S Hüttelmaier
- Institute of Molecular Medicine, Martin Luther University Halle (Saale), Halle, Germany
| | - S Danckwardt
- Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University, Mainz, Germany
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
- German Center for Cardiovascular Research (DZHK), Rhine-Main, University Medical Center, Mainz, Germany
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44
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The Hippo Pathway Prevents YAP/TAZ-Driven Hypertranscription and Controls Neural Progenitor Number. Dev Cell 2018; 47:576-591.e8. [PMID: 30523785 DOI: 10.1016/j.devcel.2018.09.021] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 07/24/2018] [Accepted: 09/25/2018] [Indexed: 01/12/2023]
Abstract
The Hippo pathway controls the activity of YAP/TAZ transcriptional coactivators through a kinase cascade. Despite the critical role of this pathway in tissue growth and tumorigenesis, it remains unclear how YAP/TAZ-mediated transcription drives proliferation. By analyzing the effects of inactivating LATS1/2 kinases, the direct upstream inhibitors of YAP/TAZ, on mouse brain development and applying cell-number-normalized transcriptome analyses, we discovered that YAP/TAZ activation causes a global increase in transcription activity, known as hypertranscription, and upregulates many genes associated with cell growth and proliferation. In contrast, conventional read-depth-normalized RNA-sequencing analysis failed to detect the scope of the transcriptome shift and missed most relevant gene ontologies. Following a transient increase in proliferation, however, hypertranscription in neural progenitors triggers replication stress, DNA damage, and p53 activation, resulting in massive apoptosis. Our findings reveal a significant impact of YAP/TAZ activation on global transcription activity and have important implications for understanding YAP/TAZ function.
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45
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Alternative processing of its precursor is related to miR319 decreasing in melon plants exposed to cold. Sci Rep 2018; 8:15538. [PMID: 30341377 PMCID: PMC6195573 DOI: 10.1038/s41598-018-34012-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 10/09/2018] [Indexed: 01/02/2023] Open
Abstract
miRNAs are fundamental endogenous regulators of gene expression in higher organisms. miRNAs modulate multiple biological processes in plants. Consequently, miRNA accumulation is strictly controlled through miRNA precursor accumulation and processing. Members of the miRNA319 family are ancient ribo-regulators that are essential for plant development and stress responses and exhibit an unusual biogenesis that is characterized by multiple processing of their precursors. The significance of the high conservation of these non-canonical biogenesis pathways remains unknown. Here, we analyze data obtained by massive sRNA sequencing and 5′ - RACE to explore the accumulation and infer the processing of members of the miR319 family in melon plants exposed to adverse environmental conditions. Sequence data showed that miR319c was down regulated in response to low temperature. However, the level of its precursor was increased by cold, indicating that miR319c accumulation is not related to the stem loop levels. Furthermore, we found that a decrease in miR319c was inversely correlated with the stable accumulation of an alternative miRNA (#miR319c) derived from multiple processing of the miR319c precursor. Interestingly, the alternative accumulation of miR319c and #miR319c was associated with an additional and non-canonical partial cleavage of the miR319c precursor during its loop-to-base-processing. Analysis of the transcriptional activity showed that miR319c negatively regulated the accumulation of HY5 via TCP2 in melon plants exposed to cold, supporting its involvement in the low temperature signaling pathway associated with anthocyanin biosynthesis. Our results provide new insights regarding the versatility of plant miRNA processing and the mechanisms regulating them as well as the hypothetical mechanism for the response to cold-induced stress in melon, which is based on the alternative regulation of miRNA biogenesis.
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46
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Yan H, Bhattarai U, Song Y, Liang FS. Design, synthesis and activity of light deactivatable microRNA inhibitor. Bioorg Chem 2018; 80:492-497. [PMID: 29990897 DOI: 10.1016/j.bioorg.2018.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/25/2018] [Accepted: 07/01/2018] [Indexed: 12/28/2022]
Abstract
miRNAs are key cellular regulators and their dysregulation is associated with many human diseases. They are usually produced locally in a spatiotemporally controlled manner to target mRNAs and regulate gene expression. Thus, developing chemical tools for manipulating miRNA with spatiotemporal precise is critical for studying miRNA. Herein, we designed a strategy to control miRNA biogenesis with light controllable inhibitor targeting the pre-miRNA processing by Dicer. By conjugating two non-inhibiting units, a low affinity Dicer inhibitor and a pre-miRNA binder, through a photocleavable linker, the bifunctional molecule obtained could inhibit miRNA production. Taking advantage of the photocleavable property of the linker, the bifunctional inhibitor can be fragmented into separate non-inhibiting units and therefore be deactivated by light. We expect that this strategy could be applied to generate chemical biological tools that allow light-mediated spatiotemporal control of miRNA maturation and contribute to the study of miRNA function.
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Affiliation(s)
- Hao Yan
- Department of Chemistry and Chemical Biology, University of New Mexico, 300 Terrace Street NE, Albuquerque, NM 87131, United States
| | - Umesh Bhattarai
- Department of Chemistry and Chemical Biology, University of New Mexico, 300 Terrace Street NE, Albuquerque, NM 87131, United States
| | - Yabin Song
- Department of Chemistry and Chemical Biology, University of New Mexico, 300 Terrace Street NE, Albuquerque, NM 87131, United States
| | - Fu-Sen Liang
- Department of Chemistry and Chemical Biology, University of New Mexico, 300 Terrace Street NE, Albuquerque, NM 87131, United States.
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47
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López-Beas J, Capilla-González V, Aguilera Y, Mellado N, Lachaud CC, Martín F, Smani T, Soria B, Hmadcha A. miR-7 Modulates hESC Differentiation into Insulin-Producing Beta-like Cells and Contributes to Cell Maturation. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 12:463-477. [PMID: 30195784 PMCID: PMC6070677 DOI: 10.1016/j.omtn.2018.06.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 06/08/2018] [Accepted: 06/09/2018] [Indexed: 12/19/2022]
Abstract
Human pluripotent stem cells retain the extraordinary capacity to differentiate into pancreatic beta cells. For this particular lineage, more effort is still required to stress the importance of developing an efficient, reproducible, easy, and cost-effective differentiation protocol to obtain more mature, homogeneous, and functional insulin-secreting cells. In addition, microRNAs (miRNAs) have emerged as a class of small non-coding RNAs that regulate many cellular processes, including pancreatic differentiation. Some miRNAs are known to be preferentially expressed in islets. Of note, miR-375 and miR-7 are two of the most abundant pancreatic miRNAs, and they are necessary for proper pancreatic islet development. Here we provide new insight into specific miRNAs involved in pancreatic differentiation. We found that miR-7 is differentially expressed during the differentiation of human embryonic stem cells (hESCs) into a beta cell-like phenotype and that its modulation plays an important role in generating mature pancreatic beta cells. This strategy may be exploited to optimize the potential for in vitro differentiation of hESCs into insulin-producing beta-like cells for use in preclinical studies and future clinical applications as well as the prospective uses of miRNAs to improve this process.
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Affiliation(s)
- Javier López-Beas
- Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER), University of Pablo de Olavide-University of Seville-CSIC, Sevilla, Spain
| | - Vivian Capilla-González
- Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER), University of Pablo de Olavide-University of Seville-CSIC, Sevilla, Spain
| | - Yolanda Aguilera
- Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER), University of Pablo de Olavide-University of Seville-CSIC, Sevilla, Spain
| | - Nuria Mellado
- Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER), University of Pablo de Olavide-University of Seville-CSIC, Sevilla, Spain
| | - Christian C Lachaud
- Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER), University of Pablo de Olavide-University of Seville-CSIC, Sevilla, Spain
| | - Franz Martín
- Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER), University of Pablo de Olavide-University of Seville-CSIC, Sevilla, Spain; Centro de Investigación Biomédica en Red sobre Diabetes y Enfermedades Metabólicas-CIBERDEM, Madrid, Spain
| | - Tarik Smani
- Instituto de Biomedicina de Sevilla-IBiS, Universidad de Sevilla/HUVR/Junta de Andalucía/CSIC, Sevilla, Spain; Centro de Investigación Biomédica en Red sobre Enfermedades Cardiovaculares-CIBERCV, Madrid, Spain
| | - Bernat Soria
- Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER), University of Pablo de Olavide-University of Seville-CSIC, Sevilla, Spain; Centro de Investigación Biomédica en Red sobre Diabetes y Enfermedades Metabólicas-CIBERDEM, Madrid, Spain
| | - Abdelkrim Hmadcha
- Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER), University of Pablo de Olavide-University of Seville-CSIC, Sevilla, Spain; Centro de Investigación Biomédica en Red sobre Diabetes y Enfermedades Metabólicas-CIBERDEM, Madrid, Spain.
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48
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van der Veen AG, Maillard PV, Schmidt JM, Lee SA, Deddouche-Grass S, Borg A, Kjær S, Snijders AP, Reis e Sousa C. The RIG-I-like receptor LGP2 inhibits Dicer-dependent processing of long double-stranded RNA and blocks RNA interference in mammalian cells. EMBO J 2018; 37:e97479. [PMID: 29351913 PMCID: PMC5813259 DOI: 10.15252/embj.201797479] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 12/08/2017] [Accepted: 12/15/2017] [Indexed: 12/25/2022] Open
Abstract
In vertebrates, the presence of viral RNA in the cytosol is sensed by members of the RIG-I-like receptor (RLR) family, which signal to induce production of type I interferons (IFN). These key antiviral cytokines act in a paracrine and autocrine manner to induce hundreds of interferon-stimulated genes (ISGs), whose protein products restrict viral entry, replication and budding. ISGs include the RLRs themselves: RIG-I, MDA5 and, the least-studied family member, LGP2. In contrast, the IFN system is absent in plants and invertebrates, which defend themselves from viral intruders using RNA interference (RNAi). In RNAi, the endoribonuclease Dicer cleaves virus-derived double-stranded RNA (dsRNA) into small interfering RNAs (siRNAs) that target complementary viral RNA for cleavage. Interestingly, the RNAi machinery is conserved in mammals, and we have recently demonstrated that it is able to participate in mammalian antiviral defence in conditions in which the IFN system is suppressed. In contrast, when the IFN system is active, one or more ISGs act to mask or suppress antiviral RNAi. Here, we demonstrate that LGP2 constitutes one of the ISGs that can inhibit antiviral RNAi in mammals. We show that LGP2 associates with Dicer and inhibits cleavage of dsRNA into siRNAs both in vitro and in cells. Further, we show that in differentiated cells lacking components of the IFN response, ectopic expression of LGP2 interferes with RNAi-dependent suppression of gene expression. Conversely, genetic loss of LGP2 uncovers dsRNA-mediated RNAi albeit less strongly than complete loss of the IFN system. Thus, the inefficiency of RNAi as a mechanism of antiviral defence in mammalian somatic cells can be in part attributed to Dicer inhibition by LGP2 induced by type I IFNs. LGP2-mediated antagonism of dsRNA-mediated RNAi may help ensure that viral dsRNA substrates are preserved in order to serve as targets of antiviral ISG proteins.
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Affiliation(s)
| | | | | | - Sonia A Lee
- Immunobiology Laboratory, The Francis Crick Institute, London, UK
| | | | - Annabel Borg
- Structural Biology Platform, The Francis Crick Institute, London, UK
| | - Svend Kjær
- Structural Biology Platform, The Francis Crick Institute, London, UK
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49
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Kim Y, Kang YG, Choe JY, Lee D, Shin C, Hong SW, Lee DK. RNA Interference-Mediated Gene Silencing by Branched Tripodal RNAs Does Not Require Dicer Processing. Nucleic Acid Ther 2018; 28:44-49. [PMID: 29195056 DOI: 10.1089/nat.2017.0681] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Specific gene silencing through RNA interference (RNAi) holds great promise as the next-generation therapeutic development platform. Previously, we have shown that branched, tripodal interfering RNA (tiRNA) structures could simultaneously trigger RNAi-mediated gene silencing of three target genes with 38 nt-long guide strands associated with Argonaute 2. Herein, we show that the branched RNA structure can trigger effective gene silencing in Dicer knockout cell line, demonstrating that the Dicer-mediated processing is not required for tiRNA activity. The finding of this study confirms the flexibility of the structure of RNAi triggers as well as the length of the guide strand in RNAi-mediated gene silencing.
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Affiliation(s)
- Yanghee Kim
- 1 Global Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University , Suwon, Republic of Korea
| | - Young Gyu Kang
- 1 Global Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University , Suwon, Republic of Korea
| | - Jeong Yong Choe
- 1 Global Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University , Suwon, Republic of Korea
| | - Dooyoung Lee
- 2 Department of Agricultural Biotechnology, Seoul National University , Seoul, Republic of Korea
| | - Chanseok Shin
- 2 Department of Agricultural Biotechnology, Seoul National University , Seoul, Republic of Korea
| | - Sun Woo Hong
- 3 OliX Pharmaceuticals, Inc. , Suwon, Republic of Korea
| | - Dong-Ki Lee
- 1 Global Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University , Suwon, Republic of Korea
- 3 OliX Pharmaceuticals, Inc. , Suwon, Republic of Korea
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50
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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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