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Arima J, Yoshino H, Fukumoto W, Kawahara I, Saito S, Li G, Fukuda I, Iizasa S, Mitsuke A, Sakaguchi T, Inoguchi S, Matsushita R, Nakagawa M, Tatarano S, Yamada Y, Enokida H. LncRNA BCYRN1 as a Potential Therapeutic Target and Diagnostic Marker in Serum Exosomes in Bladder Cancer. Int J Mol Sci 2024; 25:5955. [PMID: 38892143 PMCID: PMC11172611 DOI: 10.3390/ijms25115955] [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: 03/29/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
Bladder cancer (BC) is a common genitourinary malignancy that exhibits silent morbidity and high mortality rates because of a lack of diagnostic markers and limited effective treatments. Here, we evaluated the role of the lncRNA brain cytoplasmic RNA 1 (BCYRN1) in BC. We performed loss-of-function assays to examine the effects of BCYRN1 downregulation in T24 and BOY BC cells. We found that BCYRN1 downregulation significantly inhibited the proliferation, migration, invasion, and three-dimensional spheroid formation ability and induced apoptosis in BC cells. Additionally, gene set enrichment analysis (GSEA) using RNA sequences from tumor fractions showed that BCYRN1 downregulation decreased the expression of mRNAs associated with the cell cycle. These findings were supported by observations of G2/M arrest in flow cytometry assays. Finally, we examined the expression of serum exosomal BCYRN1 as a biomarker. Clinically, BCYRN1 expression in serum exosomes from patients with BC (n = 31) was significantly higher than that in healthy donors (n = 19; mean difference: 4.1-fold higher, p < 0.01). Moreover, in patients who had undergone complete resection of BC, serum exosomal BCYRN1 levels were significantly decreased (n = 8). Thus, serum exosomal BCYRN1 may be a promising diagnostic marker and therapeutic target in patients with BC.
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Affiliation(s)
| | - Hirofumi Yoshino
- Department of Urology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8544, Japan
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2
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Zheng SM, Feng YC, Zhu Q, Li RQ, Yan QQ, Teng L, Yue YM, Han MM, Ye K, Zhang SN, Qi TF, Tang CX, Zhao XH, Zhang YY, Xu L, Xu R, Xing J, Baker M, Liu T, Thorne RF, Jin L, Preiss T, Zhang XD, Cang S, Gao JN. MILIP Binding to tRNAs Promotes Protein Synthesis to Drive Triple-Negative Breast Cancer. Cancer Res 2024; 84:1460-1474. [PMID: 38593213 PMCID: PMC11063688 DOI: 10.1158/0008-5472.can-23-3046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/04/2024] [Accepted: 02/07/2024] [Indexed: 04/11/2024]
Abstract
Patients with triple-negative breast cancer (TNBC) have a poor prognosis due to the lack of effective molecular targets for therapeutic intervention. Here we found that the long noncoding RNA (lncRNA) MILIP supports TNBC cell survival, proliferation, and tumorigenicity by complexing with transfer RNAs (tRNA) to promote protein production, thus representing a potential therapeutic target in TNBC. MILIP was expressed at high levels in TNBC cells that commonly harbor loss-of-function mutations of the tumor suppressor p53, and MILIP silencing suppressed TNBC cell viability and xenograft growth, indicating that MILIP functions distinctively in TNBC beyond its established role in repressing p53 in other types of cancers. Mechanistic investigations revealed that MILIP interacted with eukaryotic translation elongation factor 1 alpha 1 (eEF1α1) and formed an RNA-RNA duplex with the type II tRNAs tRNALeu and tRNASer through their variable loops, which facilitated the binding of eEF1α1 to these tRNAs. Disrupting the interaction between MILIP and eEF1α1 or tRNAs diminished protein synthesis and cell viability. Targeting MILIP inhibited TNBC growth and cooperated with the clinically available protein synthesis inhibitor omacetaxine mepesuccinate in vivo. Collectively, these results identify MILIP as an RNA translation elongation factor that promotes protein production in TNBC cells and reveal the therapeutic potential of targeting MILIP, alone and in combination with other types of protein synthesis inhibitors, for TNBC treatment. SIGNIFICANCE LncRNA MILIP plays a key role in supporting protein production in TNBC by forming complexes with tRNAs and eEF1α1, which confers sensitivity to combined MILIP targeting and protein synthesis inhibitors.
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Affiliation(s)
- Si Min Zheng
- General Surgery Department, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, P.R. China
- Translational Research Institute, Henan Provincial and Zhengzhou City Key Laboratory of Non-coding RNA and Cancer Metabolism, Henan International Join Laboratory of Non-coding RNA and Metabolism in Cancer, Henan Provincial People's Hospital, Academy of Medical Sciences, Zhengzhou University, Henan, P.R. China
| | - Yu Chen Feng
- School of Medicine and Public Health, The University of Newcastle, New South Wales, Australia
| | - Qin Zhu
- General Surgery Department, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, P.R. China
| | - Ruo Qi Li
- General Surgery Department, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, P.R. China
| | - Qian Qian Yan
- Translational Research Institute, Henan Provincial and Zhengzhou City Key Laboratory of Non-coding RNA and Cancer Metabolism, Henan International Join Laboratory of Non-coding RNA and Metabolism in Cancer, Henan Provincial People's Hospital, Academy of Medical Sciences, Zhengzhou University, Henan, P.R. China
| | - Liu Teng
- Translational Research Institute, Henan Provincial and Zhengzhou City Key Laboratory of Non-coding RNA and Cancer Metabolism, Henan International Join Laboratory of Non-coding RNA and Metabolism in Cancer, Henan Provincial People's Hospital, Academy of Medical Sciences, Zhengzhou University, Henan, P.R. China
| | - Yi Meng Yue
- Translational Research Institute, Henan Provincial and Zhengzhou City Key Laboratory of Non-coding RNA and Cancer Metabolism, Henan International Join Laboratory of Non-coding RNA and Metabolism in Cancer, Henan Provincial People's Hospital, Academy of Medical Sciences, Zhengzhou University, Henan, P.R. China
| | - Man Man Han
- Translational Research Institute, Henan Provincial and Zhengzhou City Key Laboratory of Non-coding RNA and Cancer Metabolism, Henan International Join Laboratory of Non-coding RNA and Metabolism in Cancer, Henan Provincial People's Hospital, Academy of Medical Sciences, Zhengzhou University, Henan, P.R. China
| | - Kaihong Ye
- Translational Research Institute, Henan Provincial and Zhengzhou City Key Laboratory of Non-coding RNA and Cancer Metabolism, Henan International Join Laboratory of Non-coding RNA and Metabolism in Cancer, Henan Provincial People's Hospital, Academy of Medical Sciences, Zhengzhou University, Henan, P.R. China
| | - Sheng Nan Zhang
- Translational Research Institute, Henan Provincial and Zhengzhou City Key Laboratory of Non-coding RNA and Cancer Metabolism, Henan International Join Laboratory of Non-coding RNA and Metabolism in Cancer, Henan Provincial People's Hospital, Academy of Medical Sciences, Zhengzhou University, Henan, P.R. China
| | - Teng Fei Qi
- Translational Research Institute, Henan Provincial and Zhengzhou City Key Laboratory of Non-coding RNA and Cancer Metabolism, Henan International Join Laboratory of Non-coding RNA and Metabolism in Cancer, Henan Provincial People's Hospital, Academy of Medical Sciences, Zhengzhou University, Henan, P.R. China
| | - Cai Xia Tang
- Translational Research Institute, Henan Provincial and Zhengzhou City Key Laboratory of Non-coding RNA and Cancer Metabolism, Henan International Join Laboratory of Non-coding RNA and Metabolism in Cancer, Henan Provincial People's Hospital, Academy of Medical Sciences, Zhengzhou University, Henan, P.R. China
| | - Xiao Hong Zhao
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, New South Wales, Australia
| | - Yuan Yuan Zhang
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, New South Wales, Australia
| | - Liang Xu
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, New South Wales, Australia
| | - Ran Xu
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, New South Wales, Australia
| | - Jun Xing
- General Surgery Department, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, P.R. China
| | - Mark Baker
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, New South Wales, Australia
| | - Tao Liu
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, New South Wales, Australia
| | - Rick F. Thorne
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, New South Wales, Australia
| | - Lei Jin
- School of Medicine and Public Health, The University of Newcastle, New South Wales, Australia
| | - Thomas Preiss
- Shine-Dalgarno Centre for RNA Innovation, John Curtin School of Medical Research, Australian National University, Canberra, Australia
- Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
| | - Xu Dong Zhang
- Translational Research Institute, Henan Provincial and Zhengzhou City Key Laboratory of Non-coding RNA and Cancer Metabolism, Henan International Join Laboratory of Non-coding RNA and Metabolism in Cancer, Henan Provincial People's Hospital, Academy of Medical Sciences, Zhengzhou University, Henan, P.R. China
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, New South Wales, Australia
| | - Shundong Cang
- Department of Oncology, Henan Provincial International Coalition Laboratory of Oncology Precision Treatment, Henan Provincial Academician Workstation of Non-coding RNA Translational Research, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan, P.R. China
| | - Jin Nan Gao
- General Surgery Department, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, P.R. China
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3
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Muslimov IA, Berardi V, Stephenson S, Ginzler EM, Hanly JG, Tiedge H. Autoimmune RNA dysregulation and seizures: therapeutic prospects in neuropsychiatric lupus. Life Sci Alliance 2022; 5:5/12/e202201496. [PMID: 36229064 PMCID: PMC9559755 DOI: 10.26508/lsa.202201496] [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: 04/22/2022] [Revised: 09/20/2022] [Accepted: 09/22/2022] [Indexed: 11/24/2022] Open
Abstract
Lupus autoimmunity frequently presents with neuropsychiatric manifestations, but underlying etiology remains poorly understood. Human brain cytoplasmic 200 RNA (BC200 RNA) is a translational regulator in neuronal synapto-dendritic domains. Here, we show that a BC200 guanosine-adenosine dendritic transport motif is recognized by autoantibodies from a subset of neuropsychiatric lupus patients. These autoantibodies impact BC200 functionality by quasi irreversibly displacing two RNA transport factors from the guanosine-adenosine transport motif. Such anti-BC autoantibodies, which can gain access to brains of neuropsychiatric lupus patients, give rise to clinical manifestations including seizures. To establish causality, naive mice with a permeabilized blood-brain barrier were injected with anti-BC autoantibodies from lupus patients with seizures. Animals so injected developed seizure susceptibility with high mortality. Seizure activity was entirely precluded when animals were injected with lupus anti-BC autoantibodies together with BC200 decoy autoantigen. Seizures are a common clinical manifestation in neuropsychiatric lupus, and our work identifies anti-BC autoantibody activity as a mechanistic cause. The results demonstrate potential utility of BC200 decoys for autoantibody-specific therapeutic interventions in neuropsychiatric lupus.
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Affiliation(s)
- Ilham A Muslimov
- Department of Physiology and Pharmacology, The Robert F Furchgott Center for Neural and Behavioral Science, State University of New York Downstate Health Sciences University, Brooklyn, NY, USA,Correspondence: ;
| | - Valerio Berardi
- Department of Physiology and Pharmacology, The Robert F Furchgott Center for Neural and Behavioral Science, State University of New York Downstate Health Sciences University, Brooklyn, NY, USA
| | - Stacy Stephenson
- Division of Comparative Medicine, State University of New York Downstate Health Sciences University, Brooklyn, NY, USA
| | - Ellen M Ginzler
- Department of Medicine, State University of New York Downstate Health Sciences University, Brooklyn, NY, USA
| | - John G Hanly
- Division of Rheumatology, Department of Medicine, Department of Pathology, Queen Elizabeth II Health Sciences Center and Dalhousie University, Halifax, Canada
| | - Henri Tiedge
- Department of Physiology and Pharmacology, The Robert F Furchgott Center for Neural and Behavioral Science, State University of New York Downstate Health Sciences University, Brooklyn, NY, USA,Department of Medicine, State University of New York Downstate Health Sciences University, Brooklyn, NY, USA,Department of Neurology, State University of New York Downstate Health Sciences University, Brooklyn, NY, USA,Correspondence: ;
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4
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Aleshkina D, Iyyappan R, Lin CJ, Masek T, Pospisek M, Susor A. ncRNA BC1 influences translation in the oocyte. RNA Biol 2021; 18:1893-1904. [PMID: 33491548 PMCID: PMC8583082 DOI: 10.1080/15476286.2021.1880181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/17/2020] [Accepted: 01/15/2021] [Indexed: 01/06/2023] Open
Abstract
Regulation of translation is essential for the diverse biological processes involved in development. Particularly, mammalian oocyte development requires the precisely controlled translation of maternal transcripts to coordinate meiotic and early embryo progression while transcription is silent. It has been recently reported that key components of mRNA translation control are short and long noncoding RNAs (ncRNAs). We found that the ncRNABrain cytoplasmic 1 (BC1) has a role in the fully grown germinal vesicle (GV) mouse oocyte, where is highly expressed in the cytoplasm associated with polysomes. Overexpression of BC1 in GV oocyte leads to a minute decrease in global translation with a significant reduction of specific mRNA translation via interaction with the Fragile X Mental Retardation Protein (FMRP). BC1 performs a repressive role in translation only in the GV stage oocyte without forming FMRP or Poly(A) granules. In conclusion, BC1 acts as the translational repressor of specific mRNAs in the GV stage via its binding to a subset of mRNAs and physical interaction with FMRP. The results reported herein contribute to the understanding of the molecular mechanisms of developmental events connected with maternal mRNA translation.
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Affiliation(s)
- D. Aleshkina
- Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Libechov, Czech Republic
| | - R. Iyyappan
- Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Libechov, Czech Republic
| | - Ch. J. Lin
- MRC Centre for Reproductive Health, The University of Edinburgh, Edinburgh, UK
| | - T. Masek
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - M. Pospisek
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - A. Susor
- Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Libechov, Czech Republic
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5
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Cui X, Pertile RAN, Du Z, Wei W, Sun Z, Eyles DW, Kesby JP. Developmental Inhibition of Long Intergenic Non-Coding RNA, HOTAIRM1, Impairs Dopamine Neuron Differentiation and Maturation. Int J Mol Sci 2021; 22:ijms22147268. [PMID: 34298885 PMCID: PMC8306845 DOI: 10.3390/ijms22147268] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 11/16/2022] Open
Abstract
The dopaminergic (DA) system is important for a range of brain functions and subcortical DA development precedes many cortical maturational processes. The dysfunction of DA systems has been associated with neuropsychiatric disorders such as schizophrenia, depression, and addiction. DA neuron cell fate is controlled by a complex web of transcriptional factors that dictate DA neuron specification, differentiation, and maturation. A growing body of evidence suggests that these transcriptional factors are under the regulation of newly discovered non-coding RNAs. However, with regard to DA neuron development, little is known of the roles of non-coding RNAs. The long non-coding RNA (lncRNA) HOX-antisense intergenic RNA myeloid 1 (HOTAIRM1) is present in adult DA neurons, suggesting it may have a modulatory role in DA systems. Moreover, HOTAIRM1 is involved in the neuronal differentiation in human stem cells suggesting it may also play a role in early DA neuron development. To determine its role in early DA neuron development, we knocked down HOTAIRM1 using RNAi in vitro in a human neuroblastoma cell line, and in vivo in mouse DA progenitors using a novel in utero electroporation technique. HOTAIRM1 inhibition decreased the expression of a range of key DA neuron specification factors and impaired DA neuron differentiation and maturation. These results provide evidence of a functional role for HOTAIRM1 in DA neuron development and differentiation. Understanding of the role of lncRNAs in the development of DA systems may have broader implications for brain development and neurodevelopmental disorders such as schizophrenia.
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Affiliation(s)
- Xiaoying Cui
- Queensland Centre for Mental Health Research, Wacol, QLD 4076, Australia; (X.C.); (D.W.E.)
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia; (R.A.N.P.); (Z.D.); (W.W.); (Z.S.)
| | - Renata Ap. Nedel Pertile
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia; (R.A.N.P.); (Z.D.); (W.W.); (Z.S.)
| | - Zilong Du
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia; (R.A.N.P.); (Z.D.); (W.W.); (Z.S.)
| | - Wei Wei
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia; (R.A.N.P.); (Z.D.); (W.W.); (Z.S.)
| | - Zichun Sun
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia; (R.A.N.P.); (Z.D.); (W.W.); (Z.S.)
| | - Darryl W. Eyles
- Queensland Centre for Mental Health Research, Wacol, QLD 4076, Australia; (X.C.); (D.W.E.)
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia; (R.A.N.P.); (Z.D.); (W.W.); (Z.S.)
| | - James P. Kesby
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia; (R.A.N.P.); (Z.D.); (W.W.); (Z.S.)
- QIMR Berghofer Medical Research Institute, Herston, QLD 4029, Australia
- Correspondence: ; Tel.: +61-7-3346-6363; Fax: +61-7-3346-6301
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6
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Keihani S, Kluever V, Fornasiero EF. Brain Long Noncoding RNAs: Multitask Regulators of Neuronal Differentiation and Function. Molecules 2021; 26:molecules26133951. [PMID: 34203457 PMCID: PMC8272081 DOI: 10.3390/molecules26133951] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/21/2021] [Accepted: 06/24/2021] [Indexed: 02/07/2023] Open
Abstract
The extraordinary cellular diversity and the complex connections established within different cells types render the nervous system of vertebrates one of the most sophisticated tissues found in living organisms. Such complexity is ensured by numerous regulatory mechanisms that provide tight spatiotemporal control, robustness and reliability. While the unusual abundance of long noncoding RNAs (lncRNAs) in nervous tissues was traditionally puzzling, it is becoming clear that these molecules have genuine regulatory functions in the brain and they are essential for neuronal physiology. The canonical view of RNA as predominantly a 'coding molecule' has been largely surpassed, together with the conception that lncRNAs only represent 'waste material' produced by cells as a side effect of pervasive transcription. Here we review a growing body of evidence showing that lncRNAs play key roles in several regulatory mechanisms of neurons and other brain cells. In particular, neuronal lncRNAs are crucial for orchestrating neurogenesis, for tuning neuronal differentiation and for the exact calibration of neuronal excitability. Moreover, their diversity and the association to neurodegenerative diseases render them particularly interesting as putative biomarkers for brain disease. Overall, we foresee that in the future a more systematic scrutiny of lncRNA functions will be instrumental for an exhaustive understanding of neuronal pathophysiology.
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7
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Booy EP, Gussakovsky D, Choi T, McKenna SA. The noncoding RNA BC200 associates with polysomes to positively regulate mRNA translation in tumor cells. J Biol Chem 2020; 296:100036. [PMID: 33410401 PMCID: PMC7949042 DOI: 10.1074/jbc.ra120.015775] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/30/2020] [Accepted: 11/04/2020] [Indexed: 12/19/2022] Open
Abstract
BC200 is a noncoding RNA elevated in a broad spectrum of tumor cells that is critical for cell viability, invasion, and migration. Overexpression studies have implicated BC200 and the rodent analog BC1 as negative regulators of translation in both cell-based and in vitro translation assays. Although these studies are consistent, they have not been confirmed in knockdown studies and direct evidence for this function is lacking. Herein, we have demonstrated that BC200 knockdown is correlated with a decrease in global translation rates. As this conflicts with the hypothesis that BC200 is a translational suppressor, we overexpressed BC200 by transfection of in vitro transcribed RNA and transient expression from transfected plasmids. In this context BC200 suppressed translation; however, an innate immune response confounded the data. To overcome this, breast cancer cells stably overexpressing BC200 and various control RNAs were developed by selection for genomic incorporation of a plasmid coexpressing BC200 and the neomycin resistance gene. Stable overexpression of BC200 was associated with elevated translation levels in pooled stable cell lines and isolated single-cell clones. Cross-linking sucrose density gradient centrifugation demonstrated an association of BC200 and its reported binding partners SRP9/14, CSDE1, DHX36, and PABPC1 with both ribosomal subunits and polysomal RNA, an association not previously observed owing to the labile nature of the interactions. In summary, these data present a novel understanding of BC200 function as well as optimized methodology that has far reaching implications in the study of noncoding RNAs, particularly within the context of translational regulatory mechanisms.
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Affiliation(s)
- Evan P Booy
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Daniel Gussakovsky
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Taegi Choi
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sean A McKenna
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada.
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Kahaei MS, Ghafouri-Fard S, Namvar A, Omrani MD, Sayad A, Taheri M. Association study of a single nucleotide polymorphism in brain cytoplasmic 200 long-noncoding RNA and psychiatric disorders. Metab Brain Dis 2020; 35:1095-1100. [PMID: 32488423 DOI: 10.1007/s11011-020-00582-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/19/2020] [Indexed: 12/25/2022]
Abstract
The Brain cytoplasmic 200 RNA (BC200 RNA) is neuron-specific lncRNA with putative roles in normal aging and in the pathogenesis of Alzheimer's disease. Its role in the neuron plasticity has also been documented. In the current study, we genotyped a single nucleotide polymorphism (SNP) within this lncRNA (rs4404327) in a population of Iranian patients with diverse neuropsychiatric conditions including substance addiction (n = 315), attention deficit hyperactive disorder (ADHD) (n = 53), bipolar 1 (BP1) (n = 131), bipolar 2 (BP2) (n = 68), major depressive disorder (MDD) (n = 56) and schizophrenia (SCZ) (n = 177) as well as age-/ sex-matched healthy controls. This SNP was associated with ADHD in co-dominant model (C/T vs. C/C) (OR (95% CI) = 3.7 (1.96-10), P value = 0.000193), dominant model (C/T + T/T vs. C/C) (OR (95% CI) = 4.43(2.02-9.72), P value = 1.37E-04) and multiplicative model (C vs. T) (OR (95% CI) = 3.20(1.64-6.25), P value = 4.316269E-04). Moreover, this SNP was associated with risk of BP1 in dominant model (OR (95% CI) = 1.67(1.08-2.62), P value = 0.02) and multiplicative model (OR (95% CI) = 1.51 (1.04-2.21), P value = 0.028). After correction for multiple comparisons (6 cohorts × 4 models), associations remained significant in ADHD but not in BP1. No other significant association was detected. The current project showed association between a certain SNP within BC200 RNA and ADHD. Further studies are required to assess these associations in larger cohorts of patients and find the underlying mechanism for this observation.
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Affiliation(s)
- Mir Salar Kahaei
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir Namvar
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mir Davood Omrani
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Arezou Sayad
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad Taheri
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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9
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Jang S, Shin H, Lee Y. Functional Analysis of RNA Motifs Essential for BC200 RNA-mediated Translational Regulation. BMB Rep 2020. [PMID: 31234958 PMCID: PMC7061212 DOI: 10.5483/bmbrep.2020.53.2.153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Brain cytoplasmic 200 RNA (BC200 RNA) is proposed to act as a local translational modulator by inhibiting translation after being targeted to neuronal dendrites. However, the mechanism by which BC200 RNA inhibits translation is not fully understood. Although a detailed functional analysis of RNA motifs is essential for understanding the BC200 RNA-mediated translation-inhibition mechanism, there is little relevant research on the subject. Here, we performed a systematic domain-dissection analysis of BC200 RNA to identify functional RNA motifs responsible for its translational-inhibition activity. Various RNA variants were assayed for their ability to inhibit translation of luciferase mRNA in vitro. We found that the 111–200-nucleotide region consisting of part of the Alu domain as well as the A/C-rich domain (consisting of both the A-rich and C-rich domains) is most effective for translation inhibition. Surprisingly, we also found that individual A-rich, A/C-rich, and Alu domains can enhance translation but at different levels for each domain, and that these enhancing effects manifest as cap-dependent translation.
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Affiliation(s)
- Seonghui Jang
- Department of Chemistry, KAIST, Daejeon 34141, Korea
- Korea Food Research Institute, Wanju 55365, Korea
| | - Heegwon Shin
- Department of Chemistry, KAIST, Daejeon 34141, Korea
| | - Younghoon Lee
- Department of Chemistry, KAIST, Daejeon 34141, Korea
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10
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Brain Cytoplasmic RNAs in Neurons: From Biosynthesis to Function. Biomolecules 2020; 10:biom10020313. [PMID: 32079202 PMCID: PMC7072442 DOI: 10.3390/biom10020313] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/13/2020] [Accepted: 02/13/2020] [Indexed: 01/10/2023] Open
Abstract
Flexibility in signal transmission is essential for high-level brain function. This flexibility is achieved through strict spatial and temporal control of gene expression in neurons. Given the key regulatory roles of a variety of noncoding RNAs (ncRNAs) in neurons, studying neuron-specific ncRNAs provides an important basis for understanding molecular principles of brain function. This approach will have wide use in understanding the pathogenesis of brain diseases and in the development of therapeutic agents in the future. Brain cytoplasmic RNAs (BC RNAs) are a leading paradigm for research on neuronal ncRNAs. Since the first confirmation of brain-specific expression of BC RNAs in 1982, their investigation has been an area of active research. In this review, we summarize key studies on the characteristics and functions of BC RNAs in neurons.
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11
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Kats IR, Klann E. Translating from cancer to the brain: regulation of protein synthesis by eIF4F. ACTA ACUST UNITED AC 2019; 26:332-342. [PMID: 31416906 PMCID: PMC6699409 DOI: 10.1101/lm.050047.119] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 07/03/2019] [Indexed: 12/27/2022]
Abstract
Formation of eukaryotic initiation factor 4F (eIF4F) is widely considered to be the rate-limiting step in cap-dependent translation initiation. Components of eIF4F are often up-regulated in various cancers, and much work has been done to elucidate the role of each of the translation initiation factors in cancer cell growth and survival. In fact, many of the basic mechanisms describing how eIF4F is assembled and how it functions to regulate translation initiation were first investigated in cancer cell lines. These same eIF4F translational control pathways also are relevant for neuronal signaling that underlies long-lasting synaptic plasticity and memory, and in neurological diseases where eIF4F and its upstream regulators are dysregulated. Although eIF4F is important in cancer and for brain function, there is not always a clear path to use the results of studies performed in cancer models to inform one of the roles that the same translation factors have in neuronal signaling. Issues arise when extrapolating from cell lines to tissue, and differences are likely to exist in how eIF4F and its upstream regulatory pathways are expressed in the diverse neuronal subtypes found in the brain. This review focuses on summarizing the role of eIF4F and its accessory proteins in cancer, and how this information has been utilized to investigate neuronal signaling, synaptic function, and animal behavior. Certain aspects of eIF4F regulation are consistent across cancer and neuroscience, whereas some results are more complicated to interpret, likely due to differences in the complexity of the brain, its billions of neurons and synapses, and its diverse cell types.
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Affiliation(s)
- Ilona R Kats
- Sackler Graduate Program, New York University School of Medicine, New York, New York 10016, USA.,Center for Neural Science, New York University, New York, New York 10003, USA
| | - Eric Klann
- Center for Neural Science, New York University, New York, New York 10003, USA.,NYU Neuroscience Institute, New York University School of Medicine, New York, New York 10016, USA
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12
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Neuronal BC RNA Transport Impairments Caused by Systemic Lupus Erythematosus Autoantibodies. J Neurosci 2019; 39:7759-7777. [PMID: 31405929 DOI: 10.1523/jneurosci.1657-18.2019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 05/02/2019] [Accepted: 06/24/2019] [Indexed: 12/27/2022] Open
Abstract
The etiology of the autoimmune disorder systemic lupus erythematosus (SLE) remains poorly understood. In neuropsychiatric SLE (NPSLE), autoimmune responses against neural self-antigens find expression in neurological and cognitive alterations. SLE autoantibodies often target nucleic acids, including RNAs and specifically RNA domains with higher-order structural content. We report that autoantibodies directed against neuronal regulatory brain cytoplasmic (BC) RNAs were generated in a subset of SLE patients. By contrast, anti-BC RNA autoantibodies (anti-BC abs) were not detected in sera from patients with autoimmune diseases other than SLE (e.g., rheumatoid arthritis or multiple sclerosis) or in sera from healthy subjects with no evidence of disease. SLE anti-BC abs belong to the IgG class of immunoglobulins and target both primate BC200 RNA and rodent BC1 RNA. They are specifically directed at architectural motifs in BC RNA 5' stem-loop domains that serve as dendritic targeting elements (DTEs). SLE anti-BC abs effectively compete with RNA transport factor heterogeneous nuclear ribonucleoprotein A2 (hnRNP A2) for DTE access and significantly diminish BC RNA delivery to synapto-dendritic sites of function. In vivo experiments with male BALB/c mice indicate that, upon lipopolysaccharide-induced opening of the blood-brain barrier, SLE anti-BC abs are taken up by CNS neurons where they significantly impede localization of endogenous BC1 RNA to synapto-dendritic domains. Lack of BC1 RNA causes phenotypic abnormalities including epileptogenic responses and cognitive dysfunction. The combined data indicate a role for anti-BC RNA autoimmunity in SLE and its neuropsychiatric manifestations.SIGNIFICANCE STATEMENT Although clinical manifestations of neuropsychiatric lupus are well recognized, the underlying molecular-cellular alterations have been difficult to determine. We report that sera of a subset of lupus patients contain autoantibodies directed at regulatory brain cytoplasmic (BC) RNAs. These antibodies, which we call anti-BC abs, target the BC RNA 5' domain noncanonical motif structures that specify dendritic delivery. Lupus anti-BC abs effectively compete with RNA transport factor heterogeneous nuclear ribonucleoprotein A2 (hnRNP A2) for access to BC RNAs. As a result, hnRNP A2 is displaced, and BC RNAs are impaired in their ability to reach synapto-dendritic sites of function. The results reveal an unexpected link between BC RNA autoantibody recognition and dendritic RNA targeting. Cellular RNA dysregulation may thus be a contributing factor in the pathogenesis of neuropsychiatric lupus.
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13
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Shin H, Lee J, Kim Y, Jang S, Kim M, Lee Y. Heterogeneous Sequences of Brain Cytoplasmic 200 RNA Formed by Multiple Adenine Nucleotide Insertions. Mol Cells 2019; 42:495-500. [PMID: 31250622 PMCID: PMC6602144 DOI: 10.14348/molcells.2019.0108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 06/06/2019] [Indexed: 11/27/2022] Open
Abstract
Brain cytoplasmic 200 RNA (BC200 RNA), originally identified as a neuron-specific non-coding RNA, is also observed in various cancer cells that originate from non-neural cells. Studies have revealed diverse functions of BC200 RNA in cancer cells. Accordingly, we hypothesized that BC200 RNA might be modified in cancer cells to generate cancerous BC200 RNA responsible for its cancer-specific functions. Here, we report that BC200 RNA sequences are highly heterogeneous in cancer cells by virtue of multiple adenine nucleotide insertions in the internal A-rich region. The insertion of adenine nucleotides enhances BC200 RNAmediated translation inhibition, possibly by increasing the binding affinity of BC200 RNA for eIF4A (eukaryotic translation initiation factor 4A).
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Affiliation(s)
- Heegwon Shin
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Jungmin Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Youngmi Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Seonghui Jang
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Meehyein Kim
- Virus Research and Testing Group, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114,
Korea
| | - Younghoon Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
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14
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Choquet K, Forget D, Meloche E, Dicaire MJ, Bernard G, Vanderver A, Schiffmann R, Fabian MR, Teichmann M, Coulombe B, Brais B, Kleinman CL. Leukodystrophy-associated POLR3A mutations down-regulate the RNA polymerase III transcript and important regulatory RNA BC200. J Biol Chem 2019; 294:7445-7459. [PMID: 30898877 PMCID: PMC6509492 DOI: 10.1074/jbc.ra118.006271] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 03/07/2019] [Indexed: 12/12/2022] Open
Abstract
RNA polymerase III (Pol III) is an essential enzyme responsible for the synthesis of several small noncoding RNAs, a number of which are involved in mRNA translation. Recessive mutations in POLR3A, encoding the largest subunit of Pol III, cause POLR3-related hypomyelinating leukodystrophy (POLR3–HLD), characterized by deficient central nervous system myelination. Identification of the downstream effectors of pathogenic POLR3A mutations has so far been elusive. Here, we used CRISPR-Cas9 to introduce the POLR3A mutation c.2554A→G (p.M852V) into human cell lines and assessed its impact on Pol III biogenesis, nuclear import, DNA occupancy, transcription, and protein levels. Transcriptomic profiling uncovered a subset of transcripts vulnerable to Pol III hypofunction, including a global reduction in tRNA levels. The brain cytoplasmic BC200 RNA (BCYRN1), involved in translation regulation, was consistently affected in all our cellular models, including patient-derived fibroblasts. Genomic BC200 deletion in an oligodendroglial cell line led to major transcriptomic and proteomic changes, having a larger impact than those of POLR3A mutations. Upon differentiation, mRNA levels of the MBP gene, encoding myelin basic protein, were significantly decreased in POLR3A-mutant cells. Our findings provide the first evidence for impaired Pol III transcription in cellular models of POLR3–HLD and identify several candidate effectors, including BC200 RNA, having a potential role in oligodendrocyte biology and involvement in the disease.
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Affiliation(s)
- Karine Choquet
- From the Department of Human Genetics, McGill University, Montréal, Québec H3A 0C7, Canada.,the Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec H3T 1E2, Canada.,the Montréal Neurological Institute, McGill University, Montréal, Québec H3A 2B4, Canada
| | - Diane Forget
- the Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec H2W 1R7, Canada
| | - Elisabeth Meloche
- the Montréal Neurological Institute, McGill University, Montréal, Québec H3A 2B4, Canada
| | - Marie-Josée Dicaire
- the Montréal Neurological Institute, McGill University, Montréal, Québec H3A 2B4, Canada
| | - Geneviève Bernard
- From the Department of Human Genetics, McGill University, Montréal, Québec H3A 0C7, Canada.,Pediatrics, McGill University, Montréal, Québec H3A 0G4, Canada.,the Department of Internal Medicine, Division of Medical Genetics, Montréal Children's Hospital, McGill University Health Center, Montréal, Québec H4A 3J1, Canada.,the Child Health and Human Development Program, and.,MyeliNeuroGene Laboratory, Research Institute, McGill University Health Center, Montréal, Québec H4A 3J1, Canada.,the Departments of Neurology and Neurosurgery and
| | - Adeline Vanderver
- the Division of Neurology, Children's Hospital of Philadelphia (CHOP), Philadelphia, Pennsylvania 19104
| | - Raphael Schiffmann
- the Institute of Metabolic Disease, Baylor Research Institute, Dallas, Texas 75204
| | - Marc R Fabian
- the Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec H3T 1E2, Canada
| | - Martin Teichmann
- INSERM U1212-CNRS UMR5320, Université de Bordeaux, Bordeaux, France, and
| | - Benoit Coulombe
- the Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec H2W 1R7, Canada.,the Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Bernard Brais
- From the Department of Human Genetics, McGill University, Montréal, Québec H3A 0C7, Canada.,the Montréal Neurological Institute, McGill University, Montréal, Québec H3A 2B4, Canada.,the Departments of Neurology and Neurosurgery and
| | - Claudia L Kleinman
- From the Department of Human Genetics, McGill University, Montréal, Québec H3A 0C7, Canada, .,the Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec H3T 1E2, Canada
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15
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Shin H, Kim Y, Kim M, Lee Y. BC200 RNA: An Emerging Therapeutic Target and Diagnostic Marker for Human Cancer. Mol Cells 2018; 41:993-999. [PMID: 30590906 PMCID: PMC6315322 DOI: 10.14348/molcells.2018.0425] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 11/14/2018] [Indexed: 12/17/2022] Open
Abstract
One of the most interesting findings from genome-wide expression analysis is that a considerable amount of noncoding RNA (ncRNA) is present in the cell. Recent studies have identified diverse biological functions of ncRNAs, which are expressed in a much wider array of forms than proteins. Certain ncRNAs associated with diseases, in particular, have attracted research attention as novel therapeutic targets and diagnostic markers. BC200 RNA, a 200-nucleotide ncRNA originally identified as a neuron-specific transcript, is abnormally over-expressed in several types of cancer tissue. A number of recent studies have suggested mechanisms by which abnormal expression of BC200 RNA contributes to the development of cancer. In this article, we first provide a brief review of a recent progress in identifying functions of BC200 RNA in cancer cells, and then offer examples of other ncRNAs as new therapeutic targets and diagnostic markers for human cancer. Finally, we discuss future directions of studies on BC200 RNA for new cancer treatments.
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Affiliation(s)
- Heegwon Shin
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Youngmi Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Meehyein Kim
- Virus Research and Testing Group, Korea Research Institute of Chemical Technology, Daejeon 34114,
Korea
| | - Younghoon Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
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16
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Prediction of secondary and tertiary structures of human BC200 RNA (BCYRN1) based on experimental and bioinformatic cross-validation. Biochem J 2018; 475:2727-2748. [PMID: 30072491 DOI: 10.1042/bcj20180239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 07/25/2018] [Accepted: 08/01/2018] [Indexed: 11/17/2022]
Abstract
Based on experimental and bioinformatic approaches, we present the first empirically established complete secondary structure of human BC200 RNA. BC200 RNA is a brain-specific non-messenger RNA with a confirmed regulatory role in dendritic translation in neurons. Although the involvement of human BC200 RNA in various types of tumour and Alzheimer's disease has been repeatedly confirmed, the exact secondary structure remains not fully elucidated. To determine the secondary structure of BC200 RNA in vitro, we performed partial hydrolysis with sequence-specific nucleases and lead-induced cleavage. We also examined the availabilities of putative single-stranded regions and base-pairing interactions via specific DNAzymes and RNase H assay. To determine the complete spatial folding of BC200 RNA, we used experimental data as constraints in structure prediction programs and performed a comparison of results obtained by several algorithms using different criteria. Based on the experimental-derived secondary structure of BC200 RNA, we also predicted the tertiary structure of BC200 RNA. The presented combination of experimental and bioinformatic approaches not only enabled the determination of the most reliable secondary and tertiary structures of human BC200 RNA (largely in agreement with the previous phylogenetic model), but also verified the compatibility and potential disadvantages of utilizing in silico structure prediction programs.
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17
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Samson J, Cronin S, Dean K. BC200 (BCYRN1) - The shortest, long, non-coding RNA associated with cancer. Noncoding RNA Res 2018; 3:131-143. [PMID: 30175286 PMCID: PMC6114260 DOI: 10.1016/j.ncrna.2018.05.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 05/14/2018] [Accepted: 05/17/2018] [Indexed: 12/22/2022] Open
Abstract
With the discovery that the level of RNA synthesis in human cells far exceeds what is required to express protein-coding genes, there has been a concerted scientific effort to identify, catalogue and uncover the biological functions of the non-coding transcriptome. Long, non-coding RNAs (lncRNAs) are a diverse group of RNAs with equally wide-ranging biological roles in the cell. An increasing number of studies have reported alterations in the expression of lncRNAs in various cancers, although unravelling how they contribute specifically to the disease is a bigger challenge. Originally described as a brain-specific, non-coding RNA, BC200 (BCYRN1) is a 200-nucleotide, predominantly cytoplasmic lncRNA that has been linked to neurodegenerative disease and several types of cancer. Here we summarise what is known about BC200, primarily from studies in neuronal systems, before turning to a review of recent work that aims to understand how this lncRNA contributes to cancer initiation, progression and metastasis, along with its possible clinical utility as a biomarker or therapeutic target.
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Affiliation(s)
| | | | - K. Dean
- School of Biochemistry and Cell Biology, Western Gateway Building, University College Cork, Cork, Ireland
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18
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Iacoangeli A, Adzovic L, Chen EQ, Latif Cattie R, Soff GA, Tiedge H. Regulatory BC200 RNA in peripheral blood of patients with invasive breast cancer. J Investig Med 2018; 66:1055-1063. [PMID: 29967012 DOI: 10.1136/jim-2018-000717] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2018] [Indexed: 01/10/2023]
Abstract
Regulatory brain cytoplasmic 200 RNA (BC200 RNA) is highly expressed in human mammary carcinoma cells. Here, we ask whether BC200 RNA becomes detectable in peripheral blood of patients with invasive breast cancer. Using quantitative reverse-transcription PCR (qRT-PCR) methodology, we observed that BC200 RNA blood levels were significantly elevated, in comparison with healthy subjects, in patients with invasive breast cancer prior to tumorectomy (p=0.001) and in patients with metastatic breast cancer (p=0.003). In patients with invasive breast cancer who had recently undergone tumorectomy, BC200 RNA blood levels were not distinguishable from levels in healthy subjects. However, normality analysis revealed a heterogeneous distribution of patients in this group, including a subgroup of individuals with high residual BC200 RNA blood levels. In blood from patients with invasive breast cancer, BC200 RNA was specifically detected in the mononuclear leukocyte fraction. The qRT-PCR approach is sensitive enough to detect as few as three BC200 RNA-expressing tumor cells. Our work establishes the potential of BC200 RNA detection in blood to serve as a molecular indicator of invasive breast malignancy.
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Affiliation(s)
- Anna Iacoangeli
- Department of Physiology and Pharmacology, SUNY Downstate Medical Center, Brooklyn, New York, USA
| | - Linda Adzovic
- Department of Physiology and Pharmacology, SUNY Downstate Medical Center, Brooklyn, New York, USA
| | - Emily Q Chen
- Department of Medicine, Division of Hematology/Oncology, SUNY Downstate Medical Center, Brooklyn, New York, USA
| | - Rabia Latif Cattie
- Department of Medicine, Division of Hematology/Oncology, SUNY Downstate Medical Center, Brooklyn, New York, USA
| | - Gerald A Soff
- Department of Medicine, Division of Hematology/Oncology, SUNY Downstate Medical Center, Brooklyn, New York, USA
| | - Henri Tiedge
- Department of Physiology and Pharmacology, SUNY Downstate Medical Center, Brooklyn, New York, USA
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19
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The Expression Alteration of BC1 RNA and its Interaction with Eukaryotic Translation Initiation Factor eIF4A Post-Status Epilepticus. Neurochem Res 2018; 43:1328-1338. [PMID: 29774448 DOI: 10.1007/s11064-018-2548-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 05/07/2018] [Accepted: 05/12/2018] [Indexed: 01/08/2023]
Abstract
Abnormal dendritic sprouting and synaptic remodelling are important pathological features of temporal lobe epilepsy. BC1 RNA is a translation repressor involved in the regulation of the dendritic protein synthesis and mRNA transport, which is essential for dendritic development and plasticity. The expression alteration of BC1 RNA in the pilocarpine induced epilepsy model remains unknown. It is unclear if the interactions between BC1 RNA and eukaryotic initiation factor 4A (eIF4A) exists in this model. The purpose of this study was to investigate the expression changes of BC1 RNA and its interactions with eIF4A post-status epilepticus (SE). Chloride lithium and pilocarpine were used to induce the SE rat model. Either a whole brain or hippocampus tissues were collected at different time points after SE. The expression patterns of BC1 was detected by qPCR and in situ hybridization. The levels of eIF4AI/II protein expression were analyzed via western blotting and immunohistochemistry. The BC1 RNA-eIF4AI/II interaction was determined by electrophoretic mobility shift assay (EMSA). We found that the BC1 RNA levels decreased in hippocampus 3d, 1w and 2w post-SE before the levels recovered. The eIF4AI/II began to rise 3d post-SE and reached the maximum level 1w post-SE. After 1w post-SE the levels decreased in the hippocampal CA1, CA3 and DG subregions. EMSA analysis showed that BC1 RNA specifically interacted with the eIF4AI/II. The BC1 RNA-eIF4AI/II complex reduced to the lowest level 1w post-SE. Our results suggested that BC1 has a negative regulatory correlation with eIF4AI/II, where BC1 RNA could be involved in epileptogenesis by regulating dendritic protein synthesis.
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20
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Epigenetics of Circadian Rhythms in Imprinted Neurodevelopmental Disorders. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 157:67-92. [PMID: 29933957 DOI: 10.1016/bs.pmbts.2017.11.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
DNA sequence information alone cannot account for the immense variability between chromosomal alleles within diverse cell types in the brain, whether these differences are observed across time, cell type, or parental origin. The complex control and maintenance of gene expression and modulation are regulated by a multitude of molecular and cellular mechanisms that layer on top of the genetic code. The integration of genetic and environmental signals required for regulating brain development and function is achieved in part by a dynamic epigenetic landscape that includes DNA methylation, histone modifications, and noncoding RNAs. These epigenetic mechanisms establish and maintain core biological processes, including genomic imprinting and entrainment of circadian rhythms. This chapter will focus on how the epigenetic layers of DNA methylation and long, noncoding RNAs interact with circadian rhythms at specific imprinted chromosomal loci associated with the human neurodevelopmental disorders Prader-Willi, Angelman, Kagami-Ogata, and Temple syndromes.
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21
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Shin H, Lee J, Kim Y, Jang S, Ohn T, Lee Y. Identifying the cellular location of brain cytoplasmic 200 RNA using an RNA-recognizing antibody. BMB Rep 2018; 50:318-322. [PMID: 28042783 PMCID: PMC5498142 DOI: 10.5483/bmbrep.2017.50.6.217] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Indexed: 11/20/2022] Open
Abstract
Brain cytoplasmic 200 RNA (BC200 RNA) is a neuron-specific non-coding RNA, implicated in the inhibition of local synaptodendritic protein synthesis, and is highly expressed in some cancer cells. Although BC200 RNA has been shown to inhibit translation in vitro, the cellular location of this inhibition is unknown. In this study, we used a BC200 RNA-recognizing antibody to identify the cellular locations of BC200 RNA in HeLa cervical carcinoma cells. We observed punctate signals in both the cytoplasm and nucleus, and further discovered that BC200 RNA co-localized with the p-body decapping enzyme, DCP1A, and the heterogeneous nuclear ribonucleoprotein E2 (hnRNP E2). The latter is a known BC200 RNA-binding partner protein and a constituent of p-bodies. This suggests that BC200 RNA is localized to p-bodies via hnRNP E2. [BMB Reports 2017; 50(6): 318-322].
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Affiliation(s)
- Heegwon Shin
- Department of Chemistry, KAIST, Daejeon 34141, Korea
| | - Jungmin Lee
- Department of Chemistry, KAIST, Daejeon 34141, Korea
| | - Youngmi Kim
- Department of Chemistry, KAIST, Daejeon 34141, Korea
| | - Seonghui Jang
- Department of Chemistry, KAIST, Daejeon 34141, Korea
| | - Takbum Ohn
- Department of Cellular and Molecular Medicine, Chosun University School of Medicine, Gwangju 61452, Korea
| | - Younghoon Lee
- Department of Chemistry, KAIST, Daejeon 34141, Korea
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22
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Muslimov IA, Eom T, Iacoangeli A, Chuang SC, Hukema RK, Willemsen R, Stefanov DG, Wong RKS, Tiedge H. BC RNA Mislocalization in the Fragile X Premutation. eNeuro 2018; 5:ENEURO.0091-18.2018. [PMID: 29766042 PMCID: PMC5952321 DOI: 10.1523/eneuro.0091-18.2018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 03/20/2018] [Accepted: 03/27/2018] [Indexed: 12/27/2022] Open
Abstract
Fragile X premutation disorder is caused by CGG triplet repeat expansions in the 5' untranslated region of FMR1 mRNA. The question of how expanded CGG repeats cause disease is a subject of continuing debate. Our work indicates that CGG-repeat structures compete with regulatory BC1 RNA for access to RNA transport factor hnRNP A2. As a result, BC1 RNA is mislocalized in vivo, as its synapto-dendritic presence is severely diminished in brains of CGG-repeat knock-in animals (a premutation mouse model). Lack of BC1 RNA is known to cause seizure activity and cognitive dysfunction. Our working hypothesis thus predicted that absence, or significantly reduced presence, of BC1 RNA in synapto-dendritic domains of premutation animal neurons would engender cognate phenotypic alterations. Testing this prediction, we established epileptogenic susceptibility and cognitive impairments as major phenotypic abnormalities of CGG premutation mice. In CA3 hippocampal neurons of such animals, synaptic release of glutamate elicits neuronal hyperexcitability in the form of group I metabotropic glutamate receptor-dependent prolonged epileptiform discharges. CGG-repeat knock-in animals are susceptible to sound-induced seizures and are cognitively impaired as revealed in the Attentional Set Shift Task. These phenotypic disturbances occur in young-adult premutation animals, indicating that a neurodevelopmental deficit is an early-initial manifestation of the disorder. The data are consistent with the notion that RNA mislocalization can contribute to pathogenesis.
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Affiliation(s)
- Ilham A. Muslimov
- The Robert F. Furchgott Center for Neural and Behavioral Science, State University of New York Downstate Medical Center, Brooklyn, New York 11203
- Department of Physiology and Pharmacology, State University of New York Downstate Medical Center, Brooklyn, New York 11203
| | - Taesun Eom
- The Robert F. Furchgott Center for Neural and Behavioral Science, State University of New York Downstate Medical Center, Brooklyn, New York 11203
- Department of Physiology and Pharmacology, State University of New York Downstate Medical Center, Brooklyn, New York 11203
| | - Anna Iacoangeli
- The Robert F. Furchgott Center for Neural and Behavioral Science, State University of New York Downstate Medical Center, Brooklyn, New York 11203
- Department of Physiology and Pharmacology, State University of New York Downstate Medical Center, Brooklyn, New York 11203
| | - Shih-Chieh Chuang
- The Robert F. Furchgott Center for Neural and Behavioral Science, State University of New York Downstate Medical Center, Brooklyn, New York 11203
- Department of Physiology and Pharmacology, State University of New York Downstate Medical Center, Brooklyn, New York 11203
| | - Renate K. Hukema
- Department of Clinical Genetics, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Rob Willemsen
- Department of Clinical Genetics, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Dimitre G. Stefanov
- Statistical Design and Analysis, Research Division, State University of New York Downstate Medical Center, Brooklyn, New York 11203
| | - Robert K. S. Wong
- The Robert F. Furchgott Center for Neural and Behavioral Science, State University of New York Downstate Medical Center, Brooklyn, New York 11203
- Department of Physiology and Pharmacology, State University of New York Downstate Medical Center, Brooklyn, New York 11203
- Department of Neurology, State University of New York Downstate Medical Center, Brooklyn, New York 11203
| | - Henri Tiedge
- The Robert F. Furchgott Center for Neural and Behavioral Science, State University of New York Downstate Medical Center, Brooklyn, New York 11203
- Department of Physiology and Pharmacology, State University of New York Downstate Medical Center, Brooklyn, New York 11203
- Department of Neurology, State University of New York Downstate Medical Center, Brooklyn, New York 11203
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23
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Chung A, Dahan N, Alarcon JM, Fenton AA. Effects of regulatory BC1 RNA deletion on synaptic plasticity, learning, and memory. ACTA ACUST UNITED AC 2017; 24:646-649. [PMID: 29142061 PMCID: PMC5688958 DOI: 10.1101/lm.045617.117] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 08/17/2017] [Indexed: 12/24/2022]
Abstract
Nonprotein coding dendritic BC1 RNA regulates translation of mRNAs in neurons. We examined two lines of BC1 knockout mice and report that loss of BC1 RNA exaggerates group I mGluR-stimulated LTD of the Schaffer collateral synapse, with one of the lines showing a much more enhanced DHPG-induced LTD than the other. When the animals were given the hippocampus-synaptic plasticity-dependent active place avoidance task, learning and memory were impaired in the BC1-KO line with the more severely altered DHPG-induced LTD. These findings indicate a role for BC1 RNA control of mGluR-dependent synaptic function in hippocampus and associated cognitive ability.
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Affiliation(s)
- Ain Chung
- Center for Neural Science, New York University, New York, New York 10003, USA
| | - Nessy Dahan
- Department of Pathology and Pharmacology, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA
| | - Juan Marcos Alarcon
- The Robert F. Furchgott Center for Neural and Behavioral Science, Brooklyn, New York 11203, USA.,Department of Pathology and Pharmacology, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA
| | - André A Fenton
- Center for Neural Science, New York University, New York, New York 10003, USA.,The Robert F. Furchgott Center for Neural and Behavioral Science, Brooklyn, New York 11203, USA.,Department of Physiology and Pharmacology, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA
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24
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Egbe NE, Dornelles TO, Paget CM, Castelli LM, Ashe MP. Farnesol inhibits translation to limit growth and filamentation in C. albicans and S. cerevisiae. MICROBIAL CELL 2017; 4:294-304. [PMID: 28913344 PMCID: PMC5597792 DOI: 10.15698/mic2017.09.589] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Candida albicans is a polymorphic yeast where the capacity to switch between yeast and filamentous growth is critical for pathogenicity. Farnesol is a quorum-sensing sesquiterpene alcohol that, via regulation of specific signalling and transcription components, inhibits filamentous growth in Candida albicans. Here we show that farnesol also inhibits translation at the initiation step in both Candida albicans and S. cerevisiae. In contrast to fusel alcohols, that target the eukaryotic initiation factor 2B (eIF2B), farnesol affects the interaction of the mRNA with the small ribosomal subunit leading to reduced levels of the 48S preinitiation ribosomal complex in S. cerevisiae. Therefore, farnesol targets a different step in the translation pathway than fusel alcohols to elicit a completely opposite physiological outcome by negating filamentous growth.
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Affiliation(s)
- Nkechi E Egbe
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Michael Smith Building, Oxford Rd., Manchester, M13 9PT, United Kingdom.,Current address: Department of Biological Sciences, Nigerian Defence Academy, PMB 2109, Kaduna, Nigeria
| | - Tawni O Dornelles
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Michael Smith Building, Oxford Rd., Manchester, M13 9PT, United Kingdom
| | - Caroline M Paget
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Michael Smith Building, Oxford Rd., Manchester, M13 9PT, United Kingdom
| | - Lydia M Castelli
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Michael Smith Building, Oxford Rd., Manchester, M13 9PT, United Kingdom.,Current address: Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, S10 2HQ, United Kingdom
| | - Mark P Ashe
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Michael Smith Building, Oxford Rd., Manchester, M13 9PT, United Kingdom
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25
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Kim Y, Lee J, Shin H, Jang S, Kim SC, Lee Y. Biosynthesis of brain cytoplasmic 200 RNA. Sci Rep 2017; 7:6884. [PMID: 28761139 PMCID: PMC5537265 DOI: 10.1038/s41598-017-05097-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/10/2017] [Indexed: 12/13/2022] Open
Abstract
Brain cytoplasmic 200 RNA (BC200 RNA), a neuron-specific non-coding RNA, is also highly expressed in a number of tumors of non-neuronal origin. However, the biosynthesis of BC200 RNA remains poorly understood. In this study, we show that the efficient transcription of BC200 RNA requires both internal and upstream promoter elements in cancer cells. The transcription complex seems to interact with a broad range of sequences within the upstream 100-bp region. The cellular levels and half-lives of BC200 RNA were found to differ across various cancer cell types, but there was no significant correlation between these parameters. Exogenously expressed BC200 RNA had a shorter half-life than that observed for the endogenous version in cancer cells, suggesting that BC200 RNA might be protected by some limiting factor(s) in cancer cells. Transient transfection experiments showed that the transcriptional activity of the exogenous BC200 RNA promoter element varied depending on the cancer cell type. However, the promoter activities together with the half-life data could not explain the differences in the levels of BC200 RNA among different cell types, suggesting that there is another level of transcriptional regulation beyond that detected by our transient transfection experiments.
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Affiliation(s)
- Youngmi Kim
- Department of Chemistry, KAIST, Daejeon, 34141, Korea
| | - Jungmin Lee
- Department of Chemistry, KAIST, Daejeon, 34141, Korea
| | - Heegwon Shin
- Department of Chemistry, KAIST, Daejeon, 34141, Korea
| | - Seonghui Jang
- Department of Chemistry, KAIST, Daejeon, 34141, Korea
| | - Sun Chang Kim
- Department of Biological Sciences, KAIST, Daejeon, 34141, Korea
| | - Younghoon Lee
- Department of Chemistry, KAIST, Daejeon, 34141, Korea.
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26
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Iacoangeli A, Dosunmu A, Eom T, Stefanov DG, Tiedge H. Regulatory BC1 RNA in cognitive control. ACTA ACUST UNITED AC 2017; 24:267-277. [PMID: 28620074 PMCID: PMC5473108 DOI: 10.1101/lm.045427.117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/12/2017] [Indexed: 12/27/2022]
Abstract
Dendritic regulatory BC1 RNA is a non-protein-coding (npc) RNA that operates in the translational control of gene expression. The absence of BC1 RNA in BC1 knockout (KO) animals causes translational dysregulation that entails neuronal phenotypic alterations including prolonged epileptiform discharges, audiogenic seizure activity in vivo, and excessive cortical oscillations in the γ frequency band. Here we asked whether BC1 RNA control is also required for higher brain functions such as learning, memory, or cognition. To address this question, we used odor/object attentional set shifting tasks in which prefrontal cortical performance was assessed in a series of discrimination and conflict learning sessions. Results obtained in these behavioral trials indicate that BC1 KO animals were significantly impaired in their cognitive flexibility. When faced with conflicting information sources, BC1 KO animals committed regressive errors as they were compromised in their ability to disengage from recently acquired memories even though recall of such memories was in conflict with new situational context. The observed cognitive deficits are reminiscent of those previously described in subtypes of human autism spectrum disorders.
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Affiliation(s)
- Anna Iacoangeli
- The Robert F. Furchgott Center for Neural and Behavioral Science, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA.,Department of Physiology and Pharmacology, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA
| | - Aderemi Dosunmu
- The Robert F. Furchgott Center for Neural and Behavioral Science, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA.,Department of Physiology and Pharmacology, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA
| | - Taesun Eom
- The Robert F. Furchgott Center for Neural and Behavioral Science, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA.,Department of Physiology and Pharmacology, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA
| | - Dimitre G Stefanov
- Statistical Design and Analysis, Research Division, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA
| | - Henri Tiedge
- The Robert F. Furchgott Center for Neural and Behavioral Science, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA .,Department of Physiology and Pharmacology, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA.,Department of Neurology, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA
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27
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Shin H, Lee J, Kim Y, Jang S, Lee Y, Kim S, Lee Y. Knockdown of BC200 RNA expression reduces cell migration and invasion by destabilizing mRNA for calcium-binding protein S100A11. RNA Biol 2017; 14:1418-1430. [PMID: 28277927 DOI: 10.1080/15476286.2017.1297913] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Although BC200 RNA is best known as a neuron-specific non-coding RNA, it is overexpressed in various cancer cells. BC200 RNA was recently shown to contribute to metastasis in several cancer cell lines, but the underlying mechanism was not understood in detail. To examine this mechanism, we knocked down BC200 RNA in cancer cells, which overexpress the RNA, and examined cell motility, profiling of ribosome footprints, and the correlation between cell motility changes and genes exhibiting altered ribosome profiles. We found that BC200 RNA knockdown reduced cell migration and invasion, suggesting that BC200 RNA promotes cell motility. Our ribosome profiling analysis identified 29 genes whose ribosomal occupations were altered more than 2-fold by BC200 RNA knockdown. Many (> 30%) of them were directly or indirectly related to cancer progression. Among them, we focused on S100A11 (which showed a reduced ribosome footprint) because its expression was previously shown to increase cellular motility. S100A11 was decreased at both the mRNA and protein levels following knockdown of BC200 RNA. An actinomycin-chase experiment showed that BC200 RNA knockdown significantly decreased the stability of the S100A11 mRNA without changing its transcription rate, suggesting that the downregulation of S100A11 was mainly caused by destabilization of its mRNA. Finally, we showed that the BC200 RNA-knockdown-induced decrease in cell motility was mainly mediated by S100A11. Together, our results show that BC200 RNA promotes cell motility by stabilizing S100A11 transcripts.
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Affiliation(s)
- Heegwon Shin
- a Department of Chemistry , KAIST , Daejeon , Korea
| | - Jungmin Lee
- a Department of Chemistry , KAIST , Daejeon , Korea
| | - Youngmi Kim
- a Department of Chemistry , KAIST , Daejeon , Korea
| | | | - Yunhee Lee
- a Department of Chemistry , KAIST , Daejeon , Korea.,b Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Daejeon , Korea
| | - Semi Kim
- a Department of Chemistry , KAIST , Daejeon , Korea.,b Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Daejeon , Korea
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28
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Jang S, Shin H, Lee J, Kim Y, Bak G, Lee Y. Regulation of BC200 RNA-mediated translation inhibition by hnRNP E1 and E2. FEBS Lett 2017; 591:393-405. [PMID: 28027391 DOI: 10.1002/1873-3468.12544] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 12/21/2016] [Accepted: 12/21/2016] [Indexed: 12/28/2022]
Abstract
The long noncoding RNA BC200 (brain cytoplasmic RNA, 200 nucleotides) acts as a translational modulator of local protein synthesis at dendrites. BC200 RNA has been shown to inhibit translation in vitro, but it remains unknown how this translation inhibition might be controlled in a cell. Here, we performed yeast three-hybrid screening and identified hnRNP E1 and hnRNP E2 as BC200 RNA-interacting proteins. We found that: these hnRNA proteins could restore BC200 RNA-inhibited translation; BC200 RNA interacts with hnRNP E1 and E2 mainly through its unique 3' C-rich domain; and the RNA binding specificities and modes of the two proteins differed somewhat. Our results offer new insights into the regulation of BC200 RNA-mediated translation inhibition.
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Affiliation(s)
| | | | - Jungmin Lee
- Department of Chemistry, KAIST, Daejeon, Korea
| | - Youngmi Kim
- Department of Chemistry, KAIST, Daejeon, Korea
| | - Geunu Bak
- Department of Chemistry, KAIST, Daejeon, Korea
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29
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Sosińska P, Mikuła-Pietrasik J, Książek K. The double-edged sword of long non-coding RNA: The role of human brain-specific BC200 RNA in translational control, neurodegenerative diseases, and cancer. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2015; 766:58-67. [DOI: 10.1016/j.mrrev.2015.08.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 07/29/2015] [Accepted: 08/28/2015] [Indexed: 12/14/2022]
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30
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Smalheiser NR. The RNA-centred view of the synapse: non-coding RNAs and synaptic plasticity. Philos Trans R Soc Lond B Biol Sci 2015; 369:rstb.2013.0504. [PMID: 25135965 PMCID: PMC4142025 DOI: 10.1098/rstb.2013.0504] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
If mRNAs were the only RNAs made by a neuron, there would be a simple mapping of mRNAs to proteins. However, microRNAs and other non-coding RNAs (ncRNAs; endo-siRNAs, piRNAs, BC1, BC200, antisense and long ncRNAs, repeat-related transcripts, etc.) regulate mRNAs via effects on protein translation as well as transcriptional and epigenetic mechanisms. Not only are genes ON or OFF, but their ability to be translated can be turned ON or OFF at the level of synapses, supporting an enormous increase in information capacity. Here, I review evidence that ncRNAs are expressed pervasively within dendrites in mammalian brain; that some are activity-dependent and highly enriched near synapses; and that synaptic ncRNAs participate in plasticity responses including learning and memory. Ultimately, ncRNAs can be viewed as the post-it notes of the neuron. They have no literal meaning of their own, but derive their functions from where (and to what) they are stuck. This may explain, in part, why ncRNAs differ so dramatically from protein-coding genes, both in terms of the usual indicators of functionality and in terms of evolutionary constraints. ncRNAs do not appear to be direct mediators of synaptic transmission in the manner of neurotransmitters or receptors, yet they orchestrate synaptic plasticity—and may drive species-specific changes in cognition.
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Affiliation(s)
- Neil R Smalheiser
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60612, USA
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31
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Niedner A, Edelmann FT, Niessing D. Of social molecules: The interactive assembly of ASH1 mRNA-transport complexes in yeast. RNA Biol 2014; 11:998-1009. [PMID: 25482892 PMCID: PMC4615550 DOI: 10.4161/rna.29946] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Asymmetric, motor-protein dependent transport of mRNAs and subsequent localized translation is an important mechanism of gene regulation. Due to the high complexity of such motile particles, our mechanistic understanding of mRNA localization is limited. Over the last two decades, ASH1 mRNA localization in budding yeast has served as comparably simple and accessible model system. Recent advances have helped to draw an increasingly clear picture on the molecular mechanisms governing ASH1 mRNA localization from its co-transcriptional birth to its delivery at the site of destination. These new insights help to better understand the requirement of initial nuclear mRNPs, the molecular basis of specific mRNA-cargo recognition via cis-acting RNA elements, the different stages of RNP biogenesis and reorganization, as well as activation of the motile activity upon cargo binding. We discuss these aspects in context of published findings from other model organisms.
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Affiliation(s)
- Annika Niedner
- a Institute of Structural Biology; Helmholtz Zentrum München - German Center for Environmental Health ; Neuherberg , Germany
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32
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Eom T, Muslimov IA, Tsokas P, Berardi V, Zhong J, Sacktor TC, Tiedge H. Neuronal BC RNAs cooperate with eIF4B to mediate activity-dependent translational control. ACTA ACUST UNITED AC 2014; 207:237-52. [PMID: 25332164 PMCID: PMC4210447 DOI: 10.1083/jcb.201401005] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Regulatory brain cytoplasmic RNAs cooperate with eukaryotic initiation factor 4B to couple translation to receptor activation in support of long-term plastic changes in neurons. In neurons, translational regulation of gene expression has been implicated in the activity-dependent management of synapto-dendritic protein repertoires. However, the fundamentals of stimulus-modulated translational control in neurons remain poorly understood. Here we describe a mechanism in which regulatory brain cytoplasmic (BC) RNAs cooperate with eukaryotic initiation factor 4B (eIF4B) to control translation in a manner that is responsive to neuronal activity. eIF4B is required for the translation of mRNAs with structured 5′ untranslated regions (UTRs), exemplified here by neuronal protein kinase Mζ (PKMζ) mRNA. Upon neuronal stimulation, synapto-dendritic eIF4B is dephosphorylated at serine 406 in a rapid process that is mediated by protein phosphatase 2A. Such dephosphorylation causes a significant decrease in the binding affinity between eIF4B and BC RNA translational repressors, enabling the factor to engage the 40S small ribosomal subunit for translation initiation. BC RNA translational control, mediated via eIF4B phosphorylation status, couples neuronal activity to translational output, and thus provides a mechanistic basis for long-term plastic changes in nerve cells.
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Affiliation(s)
- Taesun Eom
- Department of Physiology and Pharmacology, Department of Anesthesiology, and Department of Neurology, The Robert F. Furchgott Center for Neural and Behavioral Science, SUNY Downstate Medical Center, Brooklyn, NY 11203
| | - Ilham A Muslimov
- Department of Physiology and Pharmacology, Department of Anesthesiology, and Department of Neurology, The Robert F. Furchgott Center for Neural and Behavioral Science, SUNY Downstate Medical Center, Brooklyn, NY 11203
| | - Panayiotis Tsokas
- Department of Physiology and Pharmacology, Department of Anesthesiology, and Department of Neurology, The Robert F. Furchgott Center for Neural and Behavioral Science, SUNY Downstate Medical Center, Brooklyn, NY 11203 Department of Physiology and Pharmacology, Department of Anesthesiology, and Department of Neurology, The Robert F. Furchgott Center for Neural and Behavioral Science, SUNY Downstate Medical Center, Brooklyn, NY 11203
| | - Valerio Berardi
- Department of Physiology and Pharmacology, Department of Anesthesiology, and Department of Neurology, The Robert F. Furchgott Center for Neural and Behavioral Science, SUNY Downstate Medical Center, Brooklyn, NY 11203
| | - Jun Zhong
- Department of Physiology and Pharmacology, Department of Anesthesiology, and Department of Neurology, The Robert F. Furchgott Center for Neural and Behavioral Science, SUNY Downstate Medical Center, Brooklyn, NY 11203
| | - Todd C Sacktor
- Department of Physiology and Pharmacology, Department of Anesthesiology, and Department of Neurology, The Robert F. Furchgott Center for Neural and Behavioral Science, SUNY Downstate Medical Center, Brooklyn, NY 11203 Department of Physiology and Pharmacology, Department of Anesthesiology, and Department of Neurology, The Robert F. Furchgott Center for Neural and Behavioral Science, SUNY Downstate Medical Center, Brooklyn, NY 11203 Department of Physiology and Pharmacology, Department of Anesthesiology, and Department of Neurology, The Robert F. Furchgott Center for Neural and Behavioral Science, SUNY Downstate Medical Center, Brooklyn, NY 11203
| | - Henri Tiedge
- Department of Physiology and Pharmacology, Department of Anesthesiology, and Department of Neurology, The Robert F. Furchgott Center for Neural and Behavioral Science, SUNY Downstate Medical Center, Brooklyn, NY 11203 Department of Physiology and Pharmacology, Department of Anesthesiology, and Department of Neurology, The Robert F. Furchgott Center for Neural and Behavioral Science, SUNY Downstate Medical Center, Brooklyn, NY 11203
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33
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Emerging epigenetic mechanisms of long non-coding RNAs. Neuroscience 2013; 264:25-38. [PMID: 24342564 DOI: 10.1016/j.neuroscience.2013.12.009] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 12/04/2013] [Accepted: 12/05/2013] [Indexed: 01/15/2023]
Abstract
Long non-coding RNAs (lncRNAs) have been increasingly appreciated as an integral component of gene regulatory networks. Genome-wide features of their origin and expression patterns ascribed a prominent role for lncRNAs to the regulation of protein-coding genes, and also suggest a potential link to many human diseases. Recent studies have begun to unravel the intricate regulatory mechanism of lncRNAs occurring at multiple levels. The brain is one of the richest sources of lncRNAs, many of which have already shown a close relationship with genes or genetic loci implicated in a wide range of neurological disorders. This review describes recently emerging mechanistic principles of lncRNA functions to provide neuroscientists with molecular insights that will help future research on lncRNAs in the brain.
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34
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Iacoangeli A, Tiedge H. Translational control at the synapse: role of RNA regulators. Trends Biochem Sci 2012; 38:47-55. [PMID: 23218750 DOI: 10.1016/j.tibs.2012.11.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 11/01/2012] [Accepted: 11/05/2012] [Indexed: 12/31/2022]
Abstract
Translational control of gene expression is instrumental in the regulation of eukaryotic cellular form and function. Neurons in particular rely on this form of control because their numerous synaptic connections need to be independently modulated in an input-specific manner. Brain cytoplasmic (BC) RNAs implement translational control at neuronal synapses. BC RNAs regulate protein synthesis by interacting with eIF4 translation initiation factors. Recent evidence suggests that such regulation is required to control synaptic strength, and that dysregulation of local protein synthesis precipitates neuronal hyperexcitability and a propensity for epileptogenic responses. A similar phenotype results from lack of fragile X mental retardation protein (FMRP), indicating that BC RNAs and FMRP use overlapping and convergent modes of action in neuronal translational regulation.
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Affiliation(s)
- Anna Iacoangeli
- Department of Physiology and Pharmacology, The Robert F. Furchgott Center for Neural and Behavioral Science, State University of New York Health Science Center at Brooklyn, 450 Clarkson Avenue, Brooklyn, NY 11203, USA
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35
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Emerging roles of non-coding RNAs in brain evolution, development, plasticity and disease. Nat Rev Neurosci 2012; 13:528-41. [PMID: 22814587 DOI: 10.1038/nrn3234] [Citation(s) in RCA: 420] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Novel classes of small and long non-coding RNAs (ncRNAs) are being characterized at a rapid pace, driven by recent paradigm shifts in our understanding of genomic architecture, regulation and transcriptional output, as well as by innovations in sequencing technologies and computational and systems biology. These ncRNAs can interact with DNA, RNA and protein molecules; engage in diverse structural, functional and regulatory activities; and have roles in nuclear organization and transcriptional, post-transcriptional and epigenetic processes. This expanding inventory of ncRNAs is implicated in mediating a broad spectrum of processes including brain evolution, development, synaptic plasticity and disease pathogenesis.
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36
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Cencic R, Galicia-Vázquez G, Pelletier J. Inhibitors of translation targeting eukaryotic translation initiation factor 4A. Methods Enzymol 2012; 511:437-61. [PMID: 22713332 DOI: 10.1016/b978-0-12-396546-2.00020-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The RNA helicases eIF4AI and eIF4AII play key roles in recruiting ribosomes to mRNA templates during eukaryotic translation initiation. Small molecule inhibitors of eIF4AI and eIF4AII have been useful for chemically dissecting their role in translation in vitro and in vivo. Here, we describe a screen performed on a small focused library of kinase inhibitors to identify a novel helicase inhibitor. We describe assays that have been critical for characterizing novel RNA helicase inhibitors.
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Affiliation(s)
- Regina Cencic
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
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