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Book: Nuclear bodies and noncoding RNAS

Nakagawa, Shinichi / Hirose, Tetsuro

(Methods in molecular biology ; 1262 ; Springer protocols)

2015

Author's details	ed. by Shinichi Nakagawa ; Tetsuro Hirose
Series title	Methods in molecular biology ; 1262 Springer protocols
Collection
Language	English
Size	XII, 351 S., Ill., graph. Darst.
Publisher	Humana Press
Publishing place	New York u.a.
Publishing country	United States
Document type	Book
HBZ-ID	HT018526439
ISBN	978-1-4939-2252-9 ; 9781493922536 ; 1-4939-2252-1 ; 149392253X
Database	Catalogue ZB MED Medicine, Health

In stock of ZB MED Cologne/Königswinter

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Zs A 7042 -1262-	verfügbar in Königswinter	Königswinter

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Article ; Online: A guide to membraneless organelles and their various roles in gene regulation.

Hirose, Tetsuro / Ninomiya, Kensuke / Nakagawa, Shinichi / Yamazaki, Tomohiro

Nature reviews. Molecular cell biology

2022 Volume 24, Issue 4, Page(s) 288–304

Abstract: Membraneless organelles (MLOs) are detected in cells as dots of mesoscopic size. By undergoing phase separation into a liquid-like or gel-like phase, MLOs contribute to intracellular compartmentalization of specific biological functions. In eukaryotes, ... ...

Abstract	Membraneless organelles (MLOs) are detected in cells as dots of mesoscopic size. By undergoing phase separation into a liquid-like or gel-like phase, MLOs contribute to intracellular compartmentalization of specific biological functions. In eukaryotes, dozens of MLOs have been identified, including the nucleolus, Cajal bodies, nuclear speckles, paraspeckles, promyelocytic leukaemia protein (PML) nuclear bodies, nuclear stress bodies, processing bodies (P bodies) and stress granules. MLOs contain specific proteins, of which many possess intrinsically disordered regions (IDRs), and nucleic acids, mainly RNA. Many MLOs contribute to gene regulation by different mechanisms. Through sequestration of specific factors, MLOs promote biochemical reactions by simultaneously concentrating substrates and enzymes, and/or suppressing the activity of the sequestered factors elsewhere in the cell. Other MLOs construct inter-chromosomal hubs by associating with multiple loci, thereby contributing to the biogenesis of macromolecular machineries essential for gene expression, such as ribosomes and spliceosomes. The organization of many MLOs includes layers, which might have different biophysical properties and functions. MLOs are functionally interconnected and are involved in various diseases, prompting the emergence of therapeutics targeting them. In this Review, we introduce MLOs that are relevant to gene regulation and discuss their assembly, internal structure, gene-regulatory roles in transcription, RNA processing and translation, particularly in stress conditions, and their disease relevance.
MeSH term(s)	Organelles/metabolism ; Biomolecular Condensates ; RNA/metabolism ; Gene Expression Regulation ; Transcription Factors/metabolism
Chemical Substances	RNA (63231-63-0) ; Transcription Factors
Language	English
Publishing date	2022-11-23
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2031313-5
ISSN	1471-0080 ; 1471-0072
ISSN (online)	1471-0080
ISSN	1471-0072
DOI	10.1038/s41580-022-00558-8
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Zs.MG 26: Show issues

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Article ; Online: Interleukin-4 induced 1-mediated resistance to an immune checkpoint inhibitor through suppression of CD8

Hirose, Shiho / Mashima, Tetsuo / Yuan, Xunmei / Yamashita, Makiko / Kitano, Shigehisa / Torii, Shinichi / Migita, Toshiro / Seimiya, Hiroyuki

Cancer science

2024 Volume 115, Issue 3, Page(s) 791–803

Abstract: Cancer cells adopt multiple strategies to escape tumor surveillance by the host immune system and aberrant amino acid metabolism in the tumor microenvironment suppresses the immune system. Among the amino acid-metabolizing enzymes is an L-amino-acid ... ...

Abstract	Cancer cells adopt multiple strategies to escape tumor surveillance by the host immune system and aberrant amino acid metabolism in the tumor microenvironment suppresses the immune system. Among the amino acid-metabolizing enzymes is an L-amino-acid oxidase called interleukin-4 induced 1 (IL4I1), which depletes essential amino acids in immune cells and is associated with a poor prognosis in various cancer types. Although IL4I1 is involved in immune metabolism abnormalities, its effect on the therapeutic efficacy of immune checkpoint inhibitors is unknown. In this study, we established murine melanoma cells overexpressing IL4I1 and investigated their effects on the intratumor immune microenvironment and the antitumor efficacy of anti-programmed death-ligand 1 (PD-L1) antibodies (Abs) in a syngeneic mouse model. As a result, we found that IL4I1-overexpressing B16-F10-derived tumors showed resistance to anti-PD-L1 Ab therapy. Transcriptome analysis revealed that immunosuppressive genes were globally upregulated in the IL4I1-overexpressing tumors. Consistently, we showed that IL4I1-overexpressing tumors exhibited an altered subset of lymphoid cells and particularly significant suppression of cytotoxic T cell infiltration compared to mock-infected B16-F10-derived tumors. After treatment with anti-PD-L1 Abs, we also found a more prominent elevation of tumor-associated macrophage (TAM) marker, CD68, in the IL4I1-overexpressing tumors than in the mock tumors. Consistently, we confirmed an enhanced TAM infiltration in the IL4I1-overexpressing tumors and a functional involvement of TAMs in the tumor growth. These observations indicate that IL4I1 reprograms the tumor microenvironment into an immunosuppressive state and thereby confers resistance to anti-PD-L1 Abs.
MeSH term(s)	Mice ; Animals ; Melanoma/drug therapy ; Melanoma/genetics ; Melanoma/metabolism ; Immune Checkpoint Inhibitors/pharmacology ; Immune Checkpoint Inhibitors/therapeutic use ; Interleukin-4/metabolism ; CD8-Positive T-Lymphocytes ; Amino Acids/metabolism ; Tumor Microenvironment ; B7-H1 Antigen
Chemical Substances	Immune Checkpoint Inhibitors ; Interleukin-4 (207137-56-2) ; Amino Acids ; B7-H1 Antigen
Language	English
Publishing date	2024-01-22
Publishing country	England
Document type	Journal Article
ZDB-ID	2115647-5
ISSN	1349-7006 ; 1349-7006
ISSN (online)	1349-7006
ISSN	1349-7006
DOI	10.1111/cas.16073
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Development and evaluation of a novel water-based pigment marker for radiation therapy skin marking.

Nakayama, Shinichi / Hirose, Miduki / Kaneshige, Soichiro / Nakamura, Kenji / Matsuo, Yukinori / Monzen, Hajime

Radiological physics and technology

2023 Volume 16, Issue 4, Page(s) 543–551

Abstract: Skin marks are widely used in external radiation therapy to ensure the accuracy of the irradiation position. However, conventional skin markers contain harmful substance, so we developed an alternative skin marker. The purpose of this study was to ... ...

Abstract	Skin marks are widely used in external radiation therapy to ensure the accuracy of the irradiation position. However, conventional skin markers contain harmful substance, so we developed an alternative skin marker. The purpose of this study was to investigate the feasibility of using a novel water-based pigment marker comprising safe materials commonly used in cosmetics for clinical radiation therapy. We investigated various properties of the marker, namely marker longevity, color variety, line visibility, ink bleeding, and line durability, and improved the marker in response to the feel when drawing or being drawn on. The durability of the ink was evaluated by simultaneously applying the new marker and oil-based pen and comparing the period until the marks faded and became invisible. In clinical trial, we applied marks on the skin of 56 patients over three months to observe symptoms and visible changes in the skin. There were no complications of discomfort or pain, owing to the improvements in the marker tip. The marks drawn on the arms of volunteers with the new marker and the oil-based pen remained visible for a mean of 7.2 days and 3.6 days, respectively (P value < 0.001). The percentages of participants with no symptoms and no visible changes were 100%, respectively. We developed an alternative skin marker that complies with current regulatory standards by excluding crystal violet. The newly developed marker has features suitable for clinical use, such as resistance to smudging and water, marker tip shape and texture, and color variations.
MeSH term(s)	Humans ; Gentian Violet ; Reference Standards ; Skin
Chemical Substances	Gentian Violet (J4Z741D6O5)
Language	English
Publishing date	2023-10-15
Publishing country	Japan
Document type	Clinical Trial ; Journal Article
ZDB-ID	2433581-2
ISSN	1865-0341 ; 1865-0333
ISSN (online)	1865-0341
ISSN	1865-0333
DOI	10.1007/s12194-023-00743-0
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: ArcRNAs and the formation of nuclear bodies.

Nakagawa, Shinichi / Yamazaki, Tomohiro / Mannen, Taro / Hirose, Tetsuro

Mammalian genome : official journal of the International Mammalian Genome Society

2021 Volume 33, Issue 2, Page(s) 382–401

Abstract: Long noncoding RNAs (lncRNAs) have long been collectively and passively defined as transcripts that do not encode proteins. However, extensive functional studies performed over the last decade have enabled the classification of lncRNAs into multiple ... ...

Abstract	Long noncoding RNAs (lncRNAs) have long been collectively and passively defined as transcripts that do not encode proteins. However, extensive functional studies performed over the last decade have enabled the classification of lncRNAs into multiple categories according to their functions and/or molecular properties. Architectual RNAs (arcRNAs) are a group of lncRNAs that serve as architectural components of submicron-scale cellular bodies or nonmembranous organelles, which are composed of specific sets of proteins and nucleic acids involved in particular molecular processes. In this review, we focus on arcRNAs that function in the nucleus, which provide a structural basis for the formation of nuclear bodies, nonmembranous organelles in the cell nucleus. We will summarize the current list of arcRNAs and proteins associated with classic and more recently discovered nuclear bodies and discuss general rules that govern the formation of nuclear bodies, emphasizing weak multivalent interactions mediated by innately flexible biomolecules.
MeSH term(s)	Cell Nucleus/genetics ; Cell Nucleus/metabolism ; Nuclear Bodies ; RNA, Long Noncoding/genetics ; RNA, Long Noncoding/metabolism
Chemical Substances	RNA, Long Noncoding
Language	English
Publishing date	2021-06-03
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	1058547-3
ISSN	1432-1777 ; 0938-8990
ISSN (online)	1432-1777
ISSN	0938-8990
DOI	10.1007/s00335-021-09881-5
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Zs.A 3489: Show issues

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Article ; Online: Genetics and gene therapy in Dravet syndrome.

Higurashi, Norimichi / Broccoli, Vania / Hirose, Shinichi

Epilepsy & behavior : E&B

2021 Volume 131, Issue Pt B, Page(s) 108043

Abstract: Dravet syndrome is a well-established electro-clinical condition first described in 1978. A main genetic cause was identified with the discovery of a loss-of-function SCN1A variant in 2001. Mechanisms underlying the phenotypic variations have ... ...

Abstract	Dravet syndrome is a well-established electro-clinical condition first described in 1978. A main genetic cause was identified with the discovery of a loss-of-function SCN1A variant in 2001. Mechanisms underlying the phenotypic variations have subsequently been a main topic of research. Various genetic modifiers of clinical severities have been elucidated through many rigorous studies on genotype-phenotype correlations and the recent advances in next generation sequencing technology. Furthermore, a deeper understanding of the regulation of gene expression and remarkable progress on genome-editing technology using the CRISPR-Cas9 system provide significant opportunities to overcome hurdles of gene therapy, such as enhancing Na
MeSH term(s)	Epilepsies, Myoclonic/genetics ; Epilepsies, Myoclonic/therapy ; Epilepsy/genetics ; Epileptic Syndromes ; Genetic Therapy ; Humans ; NAV1.1 Voltage-Gated Sodium Channel/genetics ; Spasms, Infantile
Chemical Substances	NAV1.1 Voltage-Gated Sodium Channel
Language	English
Publishing date	2021-05-28
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2010587-3
ISSN	1525-5069 ; 1525-5050
ISSN (online)	1525-5069
ISSN	1525-5050
DOI	10.1016/j.yebeh.2021.108043
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Article ; Online: Mutant GABA(A) receptor subunits in genetic (idiopathic) epilepsy.

Hirose, Shinichi

Progress in brain research

2014 Volume 213, Page(s) 55–85

Abstract: The γ-aminobutyric acid receptor type A (GABAA receptor) is a ligand-gated chloride channel that mediates major inhibitory functions in the central nervous system. GABAA receptors function mainly as pentamers containing α, β, and either γ or δ subunits. ... ...

Abstract	The γ-aminobutyric acid receptor type A (GABAA receptor) is a ligand-gated chloride channel that mediates major inhibitory functions in the central nervous system. GABAA receptors function mainly as pentamers containing α, β, and either γ or δ subunits. A number of antiepileptic drugs have agonistic effects on GABAA receptors. Hence, dysfunctions of GABAA receptors have been postulated to play important roles in the etiology of epilepsy. In fact, mutations or genetic variations of the genes encoding the α1, α6, β2, β3, γ2, or δ subunits (GABRA1, GABRA6, GABRB2, GABRB3, GABRG2, and GABRD, respectively) have been associated with human epilepsy, both with and without febrile seizures. Epilepsy resulting from mutations is commonly one of following, genetic (idiopathic) generalized epilepsy (e.g., juvenile myoclonic epilepsy), childhood absence epilepsy, genetic epilepsy with febrile seizures, or Dravet syndrome. Recently, mutations of GABRA1, GABRB2, and GABRB3 were associated with infantile spasms and Lennox-Gastaut syndrome. These mutations compromise hyperpolarization through GABAA receptors, which is believed to cause seizures. Interestingly, most of the insufficiencies are not caused by receptor gating abnormalities, but by complex mechanisms, including endoplasmic reticulum (ER)-associated degradation, nonsense-mediated mRNA decay, intracellular trafficking defects, and ER stress. Thus, GABAA receptor subunit mutations are now thought to participate in the pathomechanisms of epilepsy, and an improved understanding of these mutations should facilitate our understanding of epilepsy and the development of new therapies.
MeSH term(s)	Animals ; Epilepsy, Generalized/genetics ; Humans ; Mutation ; Receptors, GABA-A/genetics
Chemical Substances	Receptors, GABA-A
Language	English
Publishing date	2014
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ISSN	1875-7855 ; 0079-6123
ISSN (online)	1875-7855
ISSN	0079-6123
DOI	10.1016/B978-0-444-63326-2.00003-X
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: [Central Institute for the Molecular Pathomechanisms of Epilepsies].

Hirose, Shinichi

Rinsho shinkeigaku = Clinical neurology

2013 Volume 53, Issue 11, Page(s) 946

MeSH term(s)	Action Potentials ; Animals ; Cell Differentiation ; Disease Models, Animal ; Epilepsies, Myoclonic/genetics ; Epilepsy/genetics ; Humans ; Induced Pluripotent Stem Cells ; NAV1.1 Voltage-Gated Sodium Channel/genetics ; Neurons/physiology
Chemical Substances	NAV1.1 Voltage-Gated Sodium Channel ; SCN1A protein, human
Language	Japanese
Publishing date	2013-09-05
Publishing country	Japan
Document type	Journal Article
ZDB-ID	604200-4
ISSN	1882-0654 ; 0009-918X
ISSN (online)	1882-0654
ISSN	0009-918X
DOI	10.5692/clinicalneurol.53.946
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Zs.MO 223: Show issues

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Article: [IVIG-steroids combination therapy for initial treatment of Kawasaki disease].

Yoshikane, Yukako / Hirose, Shinichi

Nihon rinsho. Japanese journal of clinical medicine

2018 Volume 74 Suppl 6, Page(s) 522–526

MeSH term(s)	Drug Combinations ; Humans ; Immunoglobulins, Intravenous/therapeutic use ; Mucocutaneous Lymph Node Syndrome/drug therapy ; Steroids/therapeutic use
Chemical Substances	Drug Combinations ; Immunoglobulins, Intravenous ; Steroids
Language	Japanese
Publishing date	2018-12-13
Publishing country	Japan
Document type	Journal Article
ZDB-ID	390903-7
ISSN	0047-1852
ISSN	0047-1852
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Article ; Online: The early macrophage response to pathogens requires dynamic regulation of the nuclear paraspeckle.

Azam, Sikandar / Armijo, Kaitlyn S / Weindel, Chi G / Chapman, Morgan J / Devigne, Alice / Nakagawa, Shinichi / Hirose, Tetsuro / Carpenter, Susan / Watson, Robert O / Patrick, Kristin L

Proceedings of the National Academy of Sciences of the United States of America

2024 Volume 121, Issue 9, Page(s) e2312587121

Abstract: To ensure a robust immune response to pathogens without risking immunopathology, the kinetics and amplitude of inflammatory gene expression in macrophages need to be exquisitely well controlled. There is a growing appreciation for stress-responsive ... ...

Abstract	To ensure a robust immune response to pathogens without risking immunopathology, the kinetics and amplitude of inflammatory gene expression in macrophages need to be exquisitely well controlled. There is a growing appreciation for stress-responsive membraneless organelles (MLOs) regulating various steps of eukaryotic gene expression in response to extrinsic cues. Here, we implicate the nuclear paraspeckle, a highly ordered biomolecular condensate that nucleates on the
MeSH term(s)	Humans ; Animals ; Mice ; Paraspeckles ; RNA, Long Noncoding/genetics ; RNA, Long Noncoding/metabolism ; Macrophages/metabolism
Chemical Substances	RNA, Long Noncoding
Language	English
Publishing date	2024-02-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2312587121
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