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Rodrigues MGF, Firmino AC, Valentim JJ, Pavan BE, Ferreira AFA, Monteiro LNH, Ramos ES, Soutello RVG. Correlation of genome methylation of fig tree accessions with natural nematode and rust incidence. BRAZ J BIOL 2024; 84. [DOI: 10.1590/1519-6984.263041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Abstract Commercial fig tree cultivation in Brazil involves a single cultivar, ‘Roxo-de-Valinhos’. The use of a single cultivar results in serious diseases and related problems. The aim of this study was to characterize fig accessions by analyzing the natural root-knot nematode and leaf rust incidence in relation to the epigenomic profile of the plant, since epigenetic variations affect plant–pathogen interactions. All plants were attacked by nematodes, indicating susceptibility; Meloidogyne incognita was the root-knot nematode species involved. Joint analysis of data showed that methylation and leaf rust incidence were correlated when observed in the same phenological phase, presenting initial evidence of the same factorial pressure loads in genotypes, suggesting similar behavior within these genotypes.
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Affiliation(s)
| | - A. C. Firmino
- Universidade Estadual Paulista “Júlio de Mesquita Filho”, Brasil
| | - J. J. Valentim
- Universidade Estadual Paulista “Júlio de Mesquita Filho”, Brasil
| | - B. E. Pavan
- Universidade Estadual Paulista “Júlio de Mesquita Filho”, Brasil
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Abid F, Saleem M, Leghari T, Rafi I, Maqbool T, Fatima F, Arshad AM, Khurshid S, Naz S, Hadi F, Tahir M, Akhtar S, Yasir S, Mobashar A, Ashraf M. Evaluation of in vitro anticancer potential of pharmacological ethanolic plant extracts Acacia modesta and Opuntia monocantha against liver cancer cells. BRAZ J BIOL 2024; 84:e252526. [DOI: 10.1590/1519-6984.252526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Abstract Acacia modesta (AM) and Opuntia monocantha (OM) are distributed in Pakistan, Afghanistan and India. Both of these plants have different pharmacological properties. This study was designed to evaluate anticancer potential of Acacia modesta (AM) and Opuntia monocantha (OM). Liver cancer cell line HepG2 was used for assessment of anticancer activity. For the evaluation of anti-proliferative effects, cell viability and cell death in all groups of cells were evaluated via MTT, crystal violet and trypan blue assays. For the evaluation of apoptosis ELISA of p53 performed. Furthermore, LDH assay to find out the ability of malignant cells to metabolize pyruvate to lactate and antioxidant enzymes activity (GSH, CAT and SOD) at the end HPLC was performed to find active compound of AM and OM. Cytotoxicity (MTT), Viability assays (trypan blue, crystal viability, MUSE analysis) showed more dead, less live cells in plant treated groups with increase of concentration. Scratch assay for the anti-migratory effect of these plants showed treated groups have not ability to heal scratch/wound. ELISA of p53 for cellular apoptosis showed more release of p53 in treated groups. Antioxidant assay via glutathione (GSH), superoxide dismutase (SOD), catalase (CAT) showed less anti-oxidative potential in treated cancer groups. LDH assay showed more lactate dehydrogenase release in treated groups compared with untreated. HPLC analysis showed the presence of phytochemicals such as steroids, alkaloids, phenols, flavonoids, saponins, tannins, anthraquinone and amino acids in AM and OM plant extracts. Based on all these findings, it can be concluded that ethanolic extracts of Acacia modesta and Opuntia monocantha have promising anti-cancer potential.
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Affiliation(s)
- F. Abid
- Government College University Faisalabad, Pakistan; The University of Lahore, Pakistan
| | - M. Saleem
- Government College University Faisalabad, Pakistan; University of the Punjab, Pakistan
| | | | - I. Rafi
- University of Lahore, Pakistan
| | | | | | | | | | - S. Naz
- University of Lahore, Pakistan
| | - F. Hadi
- University of Lahore, Pakistan
| | | | - S. Akhtar
- University of Lahore, Pakistan; University of Bradford, United Kingdom
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Li Y, Xie D, Li L, Jiang P. Comprehensive analysis of metabolic changes in spontaneously hypertensive rats. Clin Exp Hypertens 2023; 45:2190529. [PMID: 36922753 DOI: 10.1080/10641963.2023.2190529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
OBJECTIVES Hypertension is a chronic disease with multiple causative factors that involve metabolic disturbances and can cause various complications. However, the metabolic characteristics of hypertension at different stages are still unclear. This study aimed to explore the metabolic changes induced by hypertension at different ages. METHODS Spontaneously hypertensive rats (SHR) and Wistar Kyoto (WKY) rats were divided into four groups according to age: 5-week-old SHR (n = 6), 5-week-old WKY rats (n = 6), 32-week-old SHR (n = 6), and 32-week-old WKY rats (n = 6). Metabolites were analyzed in primary tissues (serum, heart, lung, kidney, brain, and brown adipose) using a non-targeted metabolomics approach. RESULTS Thirty-five metabolites and nine related metabolic pathways were identified in 5-week-old SHR, mainly related to the metabolism of amino acids. Fifty-one metabolites and seven related metabolic pathways were identified in the 32-week-old SHR, involving glycolysis, lipid, and amino acid metabolisms. CONCLUSION This experiment elucidates the metabolic profile of SHR at different ages and provides a basis for predicting and diagnosing hypertension. It also provides a reference for the pathogenesis of hypertension.
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Affiliation(s)
- Yanan Li
- Translational Pharmaceutical Laboratory, Jining First People's Hospital, Shandong First Medical University, Jining, China
| | - Dadi Xie
- Department of Endocrinology, Tengzhou Central People's Hospital, Tengzhou, China
| | - Luxi Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Pei Jiang
- Translational Pharmaceutical Laboratory, Jining First People's Hospital, Shandong First Medical University, Jining, China.,Institute of Translational Pharmacy, Jining Medical Research Academy, Jining, China
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Long L, Huang X, Yu S, Fan J, Li X, Xu R, Zhang X, Huang H. The research status and prospects of MUC1 in immunology. Hum Vaccin Immunother 2023; 19:2172278. [PMID: 36744407 DOI: 10.1080/21645515.2023.2172278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In immune processes, molecular - molecular interactions are complex. As MUC1 often appears to be an important molecule in inflammation and tumor immunity, it is necessary to summarize the leading countries, authors, journals, and the cooperation among these entities and, most importantly, to determine the main research directions related to MUC1 in this field and the associated research frontiers. A total of 3,397 related studies published from 2012-2021 were retrieved from the Web of Science core database. The search strategy is TS= (MUC1 OR Mucin-1) refined by WEB OF SCIENCE CATEGORY (IMMUNOLOGY) AND [excluding] PUBLICATION YEARS: (2022) AND DOCUMENT TYPES: (ARTICLE OR REVIEW) AND LANGUAGES: (ENGLISH) AND WEB OF SCIENCE INDEX: (Web of Science Core Collection. SCI), with a timespan of 2012 to 2021. Documented bibliometric visual analysis was performed by CiteSpace and VOSviewer. The number of studies has increased every year. There are 1,982 articles and 1,415 reviews from 89 countries and regions, 3,722 organizations, 1,042 journals, and 17,948 authors. The United States, China, and Germany are the major countries producing publications on this issue. The most published author is Finn OJ and the most influential author is June CH. The key words "chimeric antigen receptor" and "T-cell" highlight the current hot spots and future trends in this field. Research on MUC1 in the field of immunology is still evolving. Through the bibliometric analysis of the existing publications, the current research hotspots and future development trends in this field can be obtained.
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Affiliation(s)
- Linna Long
- Department of Histology & Embryology, Xiangya School of Medicine, Central South University, ChangSha, China
| | - Xueying Huang
- Department of Histology & Embryology, Xiangya School of Medicine, Central South University, ChangSha, China
| | - Siying Yu
- Department of Histology & Embryology, Xiangya School of Medicine, Central South University, ChangSha, China
| | - Jiahui Fan
- Department of Histology & Embryology, Xiangya School of Medicine, Central South University, ChangSha, China
| | - Xia Li
- Department of Histology & Embryology, Xiangya School of Medicine, Central South University, ChangSha, China.,Department of gynaecology, Xinjiang Cancer Hospital, Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Rong Xu
- Department of Histology & Embryology, Xiangya School of Medicine, Central South University, ChangSha, China
| | - Xiaorui Zhang
- Department of Histology & Embryology, Xiangya School of Medicine, Central South University, ChangSha, China
| | - He Huang
- Department of Histology & Embryology, Xiangya School of Medicine, Central South University, ChangSha, China
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5
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Thanapipatpong P, Vuttipongchaikij S, Chomtong T, Puangtame W, Napaumpaipond P, Gomez LD, Suttangkakul A. Alternative splicing regulates autophagy in response to environmental stresses in cucumber ( Cucumis sativus). All Life 2023; 16. [DOI: 10.1080/26895293.2023.2195987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023] Open
Affiliation(s)
| | - Supachai Vuttipongchaikij
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Center of Advanced Studies for Tropical Natural Resources, Kasetsart University, Bangkok, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok, Thailand
| | - Thitikorn Chomtong
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Wilasinee Puangtame
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | | | | | - Anongpat Suttangkakul
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Center of Advanced Studies for Tropical Natural Resources, Kasetsart University, Bangkok, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok, Thailand
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Kocaman A. Combined interactions of amino acids and organic acids in heavy metal binding in plants. Plant Signal Behav 2022; 18:2064072. [PMID: 35491815 DOI: 10.1080/15592324.2022.2064072] [Citation(s) in RCA: 1] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/04/2022] [Accepted: 04/04/2022] [Indexed: 05/30/2023]
Abstract
This research focused on the different approaches to the transport and internal chelation of metals with amino acids and organic acids in plants. Therefore, in the first phase, the plants studied were identified the characteristics of the bioaccumulation factors. Steria pumila, Echium angustifolium, Typha angustifolia, Sisymbrium austriacum were identified as hyperaccumulators (Cd, Ni), accumulators (Pb, Sn, and Se), excluders (Cr, Hg). On the other hand, the Sisymbrium austriacum only showed the characteristic of the accumulator for Cr. In the second phase, the combined effects of amino acids and organic acids on the chelation of heavy metals in plants were tested by a multi-linear regression model. Related to our hypothesis, Amino acids; Gly and Leu (Cd), Trp and Ile (Pb), Asp, Ser, and Leu (Cr), Ser (Hg), Trp and Glu (Ni), Asp, Thr, and Gly (Sn), Asn and Leu (Se), Organic acids; Malonic and Malic acid (Cd), Malonic acid (Pb), Oxalic and Malic acid (Cr), Oxalic, Succinic, Citric and Butyric acid (Hg), Malonic and Malic acid (Ni), Malonic, Maleic, and Malic acid (Sn), Malonic and Citric acid (Se) were concluded that had combined effect for heavy metal's phytochelation ability into plants.
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Affiliation(s)
- Ayhan Kocaman
- Engineering Faculty, Environmental Engineering Department, Karabük University, Karabük, Turkey
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Yue J, Lu Y, Sun Z, Guo Y, San León D, Pasin F, Zhao M. Methyltransferase-like (METTL) homologues participate in Nicotiana benthamiana antiviral responses. Plant Signal Behav 2023; 18:2214760. [PMID: 37210738 DOI: 10.1080/15592324.2023.2214760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/18/2023] [Accepted: 04/24/2023] [Indexed: 05/23/2023]
Abstract
Methyltransferase (MTase) enzymes catalyze the addition of a methyl group to a variety of biological substrates. MTase-like (METTL) proteins are Class I MTases whose enzymatic activities contribute to the epigenetic and epitranscriptomic regulation of multiple cellular processes. N6-adenosine methylation (m6A) is a common chemical modification of eukaryotic and viral RNA whose abundance is jointly regulated by MTases and METTLs, demethylases, and m6A binding proteins. m6A affects various cellular processes including RNA degradation, post-transcriptional processing, and antiviral immunity. Here, we used Nicotiana benthamiana and plum pox virus (PPV), an RNA virus of the Potyviridae family, to investigated the roles of MTases in plant-virus interaction. RNA sequencing analysis identified MTase transcripts that are differentially expressed during PPV infection; among these, accumulation of a METTL gene was significantly downregulated. Two N. benthamiana METTL transcripts (NbMETTL1 and NbMETTL2) were cloned and further characterized. Sequence and structural analyses of the two encoded proteins identified a conserved S-adenosyl methionine (SAM) binding domain, showing they are SAM-dependent MTases phylogenetically related to human METTL16 and Arabidopsis thaliana FIONA1. Overexpression of NbMETTL1 and NbMETTL2 caused a decrease of PPV accumulation. In sum, our results indicate that METTL homologues participate in plant antiviral responses.
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Affiliation(s)
- Jianying Yue
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Yan Lu
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhenqi Sun
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Yuqing Guo
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - David San León
- Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Fabio Pasin
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas - Universitat Politècnica de València (CSIC-UPV), Valencia, Spain
| | - Mingmin Zhao
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
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Abd El-hameed RH, Mohamed MS, Awad SM, Hassan BB, Khodair MAE, Mansour YE. Novel benzo chromene derivatives: design, synthesis, molecular docking, cell cycle arrest, and apoptosis induction in human acute myeloid leukemia HL-60 cells. J Enzyme Inhib Med Chem 2023; 38:405-422. [DOI: 10.1080/14756366.2022.2151592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Affiliation(s)
- Rania H. Abd El-Hameed
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Helwan University, Cairo, Egypt
| | - Mosaad S. Mohamed
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Helwan University, Cairo, Egypt
| | - Samir M. Awad
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Helwan University, Cairo, Egypt
| | - Bardes B. Hassan
- Department of Pathology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | | | - Yara E. Mansour
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Helwan University, Cairo, Egypt
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9
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Romano PS, Akematsu T, Besteiro S, Bindschedler A, Carruthers VB, Chahine Z, Coppens I, Descoteaux A, Lopes Alberto Duque T, He CY, Heussler V, Le Roch KG, Li F, Perrone Bezerra de Menezes J, Menna-barreto RFS, Mottram JC, Schmuckli-maurer J, Turk B, Tavares Veras PS, Salassa BN, Vanrell MC. Autophagy in protists and their hosts: When, how and why? Autophagy Reports 2023; 2. [PMID: 37064813 DOI: 10.1080/27694127.2022.2149211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Pathogenic protists are a group of organisms responsible for causing a variety of human diseases including malaria, sleeping sickness, Chagas disease, leishmaniasis, and toxoplasmosis, among others. These diseases, which affect more than one billion people globally, mainly the poorest populations, are characterized by severe chronic stages and the lack of effective antiparasitic treatment. Parasitic protists display complex life-cycles and go through different cellular transformations in order to adapt to the different hosts they live in. Autophagy, a highly conserved cellular degradation process, has emerged as a key mechanism required for these differentiation processes, as well as other functions that are crucial to parasite fitness. In contrast to yeasts and mammals, protist autophagy is characterized by a modest number of conserved autophagy-related proteins (ATGs) that, even though, can drive the autophagosome formation and degradation. In addition, during their intracellular cycle, the interaction of these pathogens with the host autophagy system plays a crucial role resulting in a beneficial or harmful effect that is important for the outcome of the infection. In this review, we summarize the current state of knowledge on autophagy and other related mechanisms in pathogenic protists and their hosts. We sought to emphasize when, how, and why this process takes place, and the effects it may have on the parasitic cycle. A better understanding of the significance of autophagy for the protist life-cycle will potentially be helpful to design novel anti-parasitic strategies.
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Affiliation(s)
- Patricia Silvia Romano
- Laboratorio de Biología de Trypanosoma cruzi y de la célula hospedadora. Instituto de Histología y Embriología de Mendoza. Universidad Nacional de Cuyo. (IHEM-CONICET-UNCUYO). Facultad de Ciencias Médicas. Universidad Nacional de Cuyo. Av. Libertador 80 , Mendoza, Argentina
| | - Takahiko Akematsu
- Department of Biosciences, College of Humanities and Sciences, Nihon University, Tokyo, Japan
| | | | | | - Vern B. Carruthers
- Department of Microbiology and Immunology, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Zeinab Chahine
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - Isabelle Coppens
- Department of Molecular Microbiology and Immunology. Department of Molecular Microbiology and Immunology. Johns Hopkins Malaria Research Institute. Johns Hopkins University Bloomberg School of Public Health. Baltimore, MD, USA
| | - Albert Descoteaux
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Laval, QC, Canada
| | - Thabata Lopes Alberto Duque
- Autophagy Inflammation and Metabolism Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA; Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Cynthia Y. He
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Volker Heussler
- Institute of Cell Biology.University of Bern. Baltzerstr, Bern, Switzerland
| | - Karine G. Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - Feng-Jun Li
- Department of Biological Sciences, National University of Singapore, Singapore
| | | | | | - Jeremy C. Mottram
- York Biomedical Research Institute, Department of Biology, University of York, York, UK
| | | | - Boris Turk
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Patricia Sampaio Tavares Veras
- Laboratory of Host-Parasite Interaction and Epidemiology, Gonçalo Moniz Institute, Fiocruz-Bahia, Brazil
- National Institute of Science and Technology of Tropical Diseases - National Council for Scientific Research and Development (CNPq), Brazil
| | - Betiana Nebai Salassa
- Laboratorio de Biología de Trypanosoma cruzi y de la célula hospedadora. Instituto de Histología y Embriología de Mendoza. Universidad Nacional de Cuyo. (IHEM-CONICET-UNCUYO). Facultad de Ciencias Médicas. Universidad Nacional de Cuyo. Av. Libertador 80 , Mendoza, Argentina
| | - María Cristina Vanrell
- Laboratorio de Biología de Trypanosoma cruzi y de la célula hospedadora. Instituto de Histología y Embriología de Mendoza. Universidad Nacional de Cuyo. (IHEM-CONICET-UNCUYO). Facultad de Ciencias Médicas. Universidad Nacional de Cuyo. Av. Libertador 80 , Mendoza, Argentina
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Liton PB, Boesze-battaglia K, Boulton ME, Boya P, Ferguson TA, Ganley IG, Kauppinnen A, Laurie GW, Mizushima N, Morishita H, Russo R, Sadda J, Shyam R, Sinha D, Thompson DA, Zacks DN. Autophagy in the eye: from physiology to pathophysology. Autophagy Reports 2023; 2. [PMID: 37034386 DOI: 10.1080/27694127.2023.2178996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
Autophagy is a catabolic self-degradative pathway that promotes the degradation and recycling of intracellular material through the lysosomal compartment. Although first believed to function in conditions of nutritional stress, autophagy is emerging as a critical cellular pathway, involved in a variety of physiological and pathophysiological processes. Autophagy dysregulation is associated with an increasing number of diseases, including ocular diseases. On one hand, mutations in autophagy-related genes have been linked to cataracts, glaucoma, and corneal dystrophy; on the other hand, alterations in autophagy and lysosomal pathways are a common finding in essentially all diseases of the eye. Moreover, LC3-associated phagocytosis, a form of non-canonical autophagy, is critical in promoting visual cycle function. This review collects the latest understanding of autophagy in the context of the eye. We will review and discuss the respective roles of autophagy in the physiology and/or pathophysiology of each of the ocular tissues, its diurnal/circadian variation, as well as its involvement in diseases of the eye.
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Affiliation(s)
- Paloma B. Liton
- Departments of Ophthalmology & Pathology, Duke School of Medicine, Duke University, Durham, NC 27705, USA
| | - Kathleen Boesze-Battaglia
- Department of Basic and Translational Sciences, University of Pennsylvania, School of Dental Medicine, Philadelphia, PA 19104, USA
| | - Michael E. Boulton
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | - Patricia Boya
- Department of Neuroscience and Movement Science. Faculty of Science and Medicine, University of Fribourg, 1700 Fribourg, Switzerland
| | - Thomas A. Ferguson
- Department of Ophthalmology and Visual Sciences, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Ian G. Ganley
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Anu Kauppinnen
- Faculty of Health and Sciences, School of Pharmacy, University of Eastern Finland, 70210 Kuopio, Finland
| | - Gordon W. Laurie
- Departments of Cell Biology, Ophthalmology and Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, 113-0033, Japan
| | - Hideaki Morishita
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, 113-0033, Japan
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Rossella Russo
- Preclinical and Translational Pharmacology, Glaucoma Unit, Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy
| | - Jaya Sadda
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Debasish Sinha
- Department of Ophthalmology, Cell Biology, and Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Wilmer Eye Institute, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Debra A. Thompson
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - David N. Zacks
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medical School, Ann Arbor, MI, USA
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Huang Y, Ge MX, Li YH, Li JL, Yu Q, Xiao FH, Ao HS, Yang LQ, Li J, He Y, Kong QP. Longevity-Associated Transcription Factor ATF7 Promotes Healthspan by Suppressing Cellular Senescence and Systematic Inflammation. Aging Dis 2023. [PMID: 37163432 DOI: 10.14336/AD.2022.1217] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
Aging is characterized by persistent low-grade systematic inflammation, which is largely responsible for the occurrence of various age-associated diseases. We and others have previously reported that long-lived people (such as centenarians) can delay the onset of or even escape certain major age-related diseases. Here, by screening blood transcriptome and inflammatory profiles, we found that long-lived individuals had a relatively lower inflammation level (IL6, TNFα), accompanied by up-regulation of activating transcription factor 7 (ATF7). Interestingly, ATF7 expression was gradually reduced during cellular senescence. Loss of ATF7 induced cellular senescence, while overexpression delayed senescence progress and senescence-associated secretory phenotype (SASP) secretion. We showed that the anti-senescence effects of ATF7 were achieved by inhibiting nuclear factor kappa B (NF-κB) signaling and increasing histone H3K9 dimethylation (H3K9me2). In Caenorhabditis elegans, ATF7 overexpression significantly suppressed aging biomarkers and extended lifespan. Our findings suggest that ATF7 is a longevity-promoting factor that lowers cellular senescence and inflammation in long-lived individuals.
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Affiliation(s)
- Yaqun Huang
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Department of Dermatology/National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410000, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
| | - Ming-Xia Ge
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Hong Li
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Jing-Lin Li
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Department of Dermatology/National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410000, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
| | - Qin Yu
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Fu-Hui Xiao
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Hong-Shun Ao
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Li-Qin Yang
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ji Li
- Department of Dermatology/National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410000, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
| | - Yonghan He
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Qing-Peng Kong
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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12
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Zhang H, Qin W, Romero H, Leonhardt H, Cardoso MC. Heterochromatin organization and phase separation. Nucleus 2023; 14:2159142. [PMID: 36710442 DOI: 10.1080/19491034.2022.2159142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The eukaryotic nucleus displays a variety of membraneless compartments with distinct biomolecular composition and specific cellular activities. Emerging evidence indicates that protein-based liquid-liquid phase separation (LLPS) plays an essential role in the formation and dynamic regulation of heterochromatin compartmentalization. This feature is especially conspicuous at the pericentric heterochromatin domains. In this review, we will describe our understanding of heterochromatin organization and LLPS. In addition, we will highlight the increasing importance of multivalent weak homo- and heteromolecular interactions in LLPS-mediated heterochromatin compartmentalization in the complex environment inside living cells.
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Affiliation(s)
- Hui Zhang
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Weihua Qin
- Human Biology and Bioimaging, Faculty of Biology, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Hector Romero
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Heinrich Leonhardt
- Human Biology and Bioimaging, Faculty of Biology, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - M. Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany,CONTACT M. Cristina Cardoso Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287Darmstadt, Germany
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13
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A J, S S S, K S, T S M. Extracellular vesicles in bacterial and fungal diseases - Pathogenesis to diagnostic biomarkers. Virulence 2023; 14:2180934. [PMID: 36794396 DOI: 10.1080/21505594.2023.2180934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
Intercellular communication among microbes plays an important role in disease exacerbation. Recent advances have described small vesicles, termed as "extracellular vesicles" (EVs), previously disregarded as "cellular dust" to be vital in the intracellular and intercellular communication in host-microbe interactions. These signals have been known to initiate host damage and transfer of a variety of cargo including proteins, lipid particles, DNA, mRNA, and miRNAs. Microbial EVs, referred to generally as "membrane vesicles" (MVs), play a key role in disease exacerbation suggesting their importance in pathogenicity. Host EVs help coordinate antimicrobial responses and prime the immune cells for pathogen attack. Hence EVs with their central role in microbe-host communication, may serve as important diagnostic biomarkers of microbial pathogenesis. In this review, we summarize current research regarding the roles of EVs as markers of microbial pathogenesis with specific focus on their interaction with host immune defence and their potential as diagnostic biomarkers in disease conditions.
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Affiliation(s)
- Jnana A
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Sadiya S S
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Satyamoorthy K
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Murali T S
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
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14
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Keuenhof KS, Kohler V, Broeskamp F, Panagaki D, Speese SD, Büttner S, Höög JL. Nuclear envelope budding and its cellular functions. Nucleus 2023; 14:2178184. [PMID: 36814098 DOI: 10.1080/19491034.2023.2178184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
The nuclear pore complex (NPC) has long been assumed to be the sole route across the nuclear envelope, and under normal homeostatic conditions it is indeed the main mechanism of nucleo-cytoplasmic transport. However, it has also been known that e.g. herpesviruses cross the nuclear envelope utilizing a pathway entitled nuclear egress or envelopment/de-envelopment. Despite this, a thread of observations suggests that mechanisms similar to viral egress may be transiently used also in healthy cells. It has since been proposed that mechanisms like nuclear envelope budding (NEB) can facilitate the transport of RNA granules, aggregated proteins, inner nuclear membrane proteins, and mis-assembled NPCs. Herein, we will summarize the known roles of NEB as a physiological and intrinsic cellular feature and highlight the many unanswered questions surrounding these intriguing nuclear events.
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Affiliation(s)
| | - Verena Kohler
- Institute of Molecular Biosciences, University of Graz, Austria,Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Filomena Broeskamp
- Department for Chemistry and Molecular biology, University of Gothenburg, Sweden
| | - Dimitra Panagaki
- Department for Chemistry and Molecular biology, University of Gothenburg, Sweden
| | - Sean D. Speese
- Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, 2720 S Moody Ave, Portland, OR, 97201, USA
| | - Sabrina Büttner
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Johanna L. Höög
- Department for Chemistry and Molecular biology, University of Gothenburg, Sweden,CONTACT Johanna L. Höög Department for Chemistry and Molecular biology, University of Gothenburg, Medicinaregatan 9C, Göteborg413 90, Sweden
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15
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Tang Y. Plant nuclear envelope as a hub connecting genome organization with regulation of gene expression. Nucleus 2023; 14:2178201. [PMID: 36794966 DOI: 10.1080/19491034.2023.2178201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
Eukaryotic cells organize their genome within the nucleus with a double-layered membrane structure termed the nuclear envelope (NE) as the physical barrier. The NE not only shields the nuclear genome but also spatially separates transcription from translation. Proteins of the NE including nucleoskeleton proteins, inner nuclear membrane proteins, and nuclear pore complexes have been implicated in interacting with underlying genome and chromatin regulators to establish a higher-order chromatin architecture. Here, I summarize recent advances in the knowledge of NE proteins that are involved in chromatin organization, gene regulation, and coordination of transcription and mRNA export. These studies support an emerging view of plant NE as a central hub that contributes to chromatin organization and gene expression in response to various cellular and environmental cues.
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Affiliation(s)
- Yu Tang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China,CONTACT Yu Tang Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
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16
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Barral A, Déjardin J. The chromatin signatures of enhancers and their dynamic regulation. Nucleus 2023; 14:2160551. [PMID: 36602897 DOI: 10.1080/19491034.2022.2160551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Enhancers are cis-regulatory elements that can stimulate gene expression from distance, and drive precise spatiotemporal gene expression profiles during development. Functional enhancers display specific features including an open chromatin conformation, Histone H3 lysine 27 acetylation, Histone H3 lysine 4 mono-methylation enrichment, and enhancer RNAs production. These features are modified upon developmental cues which impacts their activity. In this review, we describe the current state of knowledge about enhancer functions and the diverse chromatin signatures found on enhancers. We also discuss the dynamic changes of enhancer chromatin signatures, and their impact on lineage specific gene expression profiles, during development or cellular differentiation.
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Affiliation(s)
- Amandine Barral
- Institute for Regenerative Medicine, Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA,CONTACT Amandine Barral Institute for Regenerative Medicine, Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania. 3400 Civic Blvd, Philadelphia, Pennsylvania19104, USA
| | - Jérôme Déjardin
- Biology of repetitive sequences, Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, Montpellier, France,Jérôme Déjardin Biology of repetitive sequences, Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, 141 rue de la Cardonille, Montpellier34000, France
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17
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Chen T, Sun Z, Cui Y, Ji J, Li Y, Qu X. Identification of long noncoding RNA NEAT1 as a key gene involved in the extramedullary disease of multiple myeloma by bioinformatics analysis. Hematology 2023; 28:2164449. [PMID: 36657019 DOI: 10.1080/16078454.2022.2164449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
OBJECTIVE Long non-coding RNAs (lncRNAs) are involved in tumorigenesis and play a key role in cancer progression. To determine whether lncRNAs are involved in extramedullary disease of multiple myeloma (EMD), we analyzed the expression profile of lncRNAs in EMD. METHODS Three pairs of EMD patients and their intramedullary MM cells were screened by microarray first. We extracted data from gene chips and made an identification of lncRNAs and mRNAs with significant differences between EMD group and non EMD group. WGCNA confirmed the EMD related gene module and drew a heat map to further determine the key gene lncRNA-NEAT1. In the meantime, bone marrow and extramedullary samples (hydrothorax and ascites) were collected from 2 MM patients and subjected to single-cell RNA-seq. Single cell Transcriptome analysis was conducted to verify the gene expression difference of malignant plasma cells derived from intramedullary and extramedullary. Then we verified high expression level of lncRNA-NEAT1 in EMD patients by using quantitative real-time PCR (qRT-PCR) and analyzed the correlation between expression patterns and survival and molecular genetics analysis of the LncRNA (NEAT1) involved in MM patients. At last, cell experiments were conducted to observe the effects of down-regulation of NEAT1on the proliferation, cell cycle and PTEN pathway related proteins of multiple myeloma cell lines U266 and RPMI8226. RESULTS We identified one of the EMD related key gene is lncRNA-NEAT1. Compared with patients without extramedullary lesions, intramedullary MM cells in EMD patients expressed NEAT1 highly. The outcome of parallel single-cell RNA sequencing (RNA-seq) revealed NEAT1 level of plasma cells came from pleural effusion /ascites increased significantly compared with myeloma-stricken bone marrow. By survival and molecular genetic analysis, NEAT1 gene expression was not associated with OS and PFS in MM patients. However, the expression of NEAT1 is related to adverse therapeutic reactions and the progression of MM. We found that the expressions of NEAT1 were negatively associated with albumin levels and were positively associated with gain of chromosome 1q, IGH-CCND1, IGH@-FGFR3/WHSC1,and IGH-MAF gene fusion, respectively. At the level of cell experiment, CCK-8, soft agar clone formation experiment and CFSE staining showed that down regulating NEAT1 could inhibit the proliferation of U266 and RPMI8226 cells; Cell cycle detection showed that down-regulation of NEAT1 would interfere with the cell cycle process, and RPMI 8226 cells were blocked in G1 phase. Western blot analysis showed that when the expression of NEAT1 was down regulated in U266 and RPMI 8226 cells, the expression of PTEN and p-PTEN (phosphorylated phosphatase and tensin homologue) was up-regulated, and the expression of PI3K, p-PI3K (human phosphorylated inositol 3 kinase), Akt, p-Akt (phosphorylated protein kinase B). DISCUCCION AND CONCLUSION This study provides novel insights into the lncRNA-NEAT1 and reveals that NEAT1 maybe a potential lncRNA biomarkers in EMD.
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Affiliation(s)
- Ting Chen
- Department of Hematology, Key Laboratory of Hematology of Nanjing Medical University, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing, People's Republic of China.,Department of Hematology, Rugao Hospital, Nantong, People's Republic of China
| | - Zhengxu Sun
- Department of Hematology, Key Laboratory of Hematology of Nanjing Medical University, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing, People's Republic of China
| | - Yunqi Cui
- Department of Hematology, Key Laboratory of Hematology of Nanjing Medical University, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing, People's Republic of China
| | - Jiamei Ji
- Department of Hematology, Key Laboratory of Hematology of Nanjing Medical University, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing, People's Republic of China
| | - Yating Li
- Department of Hematology, Key Laboratory of Hematology of Nanjing Medical University, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing, People's Republic of China
| | - Xiaoyan Qu
- Department of Hematology, Key Laboratory of Hematology of Nanjing Medical University, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing, People's Republic of China
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Mann R, Notani D. Transcription factor condensates and signaling driven transcription. Nucleus 2023; 14:2205758. [PMID: 37129580 DOI: 10.1080/19491034.2023.2205758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Abstract
Transcription Factor (TF) condensates are a heterogenous mix of RNA, DNA, and multiple co-factor proteins capable of modulating the transcriptional response of the cell. The dynamic nature and the spatial location of TF-condensates in the 3D nuclear space is believed to provide a fast response, which is on the same pace as the signaling cascade and yet ever-so-specific in the crowded environment of the nucleus. However, the current understanding of how TF-condensates can achieve these feet so quickly and efficiently is still unclear. In this review, we draw parallels with other protein condensates and share our speculations on how the nucleus uses these TF-condensates to achieve high transcriptional specificity and fidelity. We discuss the various constituents of TF-condensates, their properties, and the known and unknown functions of TF-condensates with a particular focus on steroid signaling-induced transcriptional programs.
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Affiliation(s)
- Rajat Mann
- National Centre for Biological Sciences, TIFR, Bangalore, India
| | - Dimple Notani
- National Centre for Biological Sciences, TIFR, Bangalore, India
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19
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Wackers P, Dollé MET, van Oostrom CTM, van Kerkhof LWM. Exploration of genome-wide DNA methylation profiles in night shift workers. Epigenetics 2023; 18:2152637. [PMID: 36457290 DOI: 10.1080/15592294.2022.2152637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The past decades, studies indicated that night shift work is associated with adverse health effects, however, molecular mechanisms underlying these effects are poorly understood. A few previous studies have hypothesized a role for DNA-methylation (DNAm) in this relationship. We performed a cross-sectional epigenome-wide association study, to investigate if night shift work is associated with genome-wide DNAm changes and DNAm-based biological age acceleration, based on previously developed so-called 'epigenetic clocks.' Short term (2-6 years) and intermediate term (10-16 years) night shift workers, along with age and sex matched dayworkers (non-shift workers) were selected from the Lifelines Cohort Study. For genome-wide methylation analysis the Infinium Methylation EPIC array (Ilumina) was used. Linear regression analyses were used to detect differences in methylation at individual CpG-sites associated with night shift work. Pathway analysis was performed based on KEGG pathways and predictions of age acceleration in night shift workers were performed based on four previously developed epigenetic age calculators. Only in women, differences in methylation at individual CpG-sites were observed between night shift workers and non-shift workers. Most of these differentially methylated positions (DMPs) were observed in intermediate term night shift workers. Pathway analysis shows involvement of pathways related to circadian rhythm and cellular senescence. Increased age acceleration was observed only in short-term night shift workers (men and women). This might be indicative of adaptation to night shift work or a so-called healthy worker effect. In conclusion, these results show that DNA methylation changes are associated with night shift work, specifically in women.
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Affiliation(s)
- Paul Wackers
- Center for Health Protection, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Martijn E. T. Dollé
- Center for Health Protection, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Conny T.M. van Oostrom
- Center for Health Protection, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Linda W.M. van Kerkhof
- Center for Health Protection, National Institute for Public Health and the Environment, Bilthoven, The Netherlands,CONTACT Linda W.M. van Kerkhof Centre for Health Protection; National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA; Bilthoven, The Netherlands
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Niu Y, Xiao H, Wang B, Wang Z, Du K, Wang Y, Wang L. Angelica sinensis polysaccharides alleviate the oxidative burden on hematopoietic cells by restoring 5-fluorouracil-induced oxidative damage in perivascular mesenchymal progenitor cells. Pharm Biol 2023; 61:768-78. [PMID: 37148130 DOI: 10.1080/13880209.2023.2207592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
CONTEXT 5-Fluorouracil (5-FU)-injured stromal cells may cause chronic bone marrow suppression; however, the underlying mechanism remains unclear. Angelica sinensis polysaccharide (ASP), the main biologically active ingredient of the Chinese herb, Angelica sinensis (Oliv.) Diels (Apiaceae), may enrich the blood and promote antioxidation. OBJECTIVE This study investigated the protective antioxidative effects of ASP on perivascular mesenchymal progenitors (PMPs) and their interactions with hematopoietic cells. MATERIALS AND METHODS PMPs were dissociated from C57BL/6 mouse femur and tibia and were subsequently divided into the control, ASP (0.1 g/L), 5-FU (0.025 g/L), and 5-FU + ASP (pre-treatment with 0.1 g/L ASP for 6 h, together with 0.025 g/L 5-FU) then cultured for 48 h. Hematopoietic cells were co-cultured on these feeder layers for 24 h. Cell proliferation, senescence, apoptosis, and oxidative indices were detected, along with stromal osteogenic and adipogenic differentiation potentials. Intercellular and intracellular signaling was analyzed by real-time quantitative reverse transcription polymerase chain reaction and Western blotting. RESULTS ASP ameliorated the reactive oxygen species production/scavenge balance in PMPs; improved osteogenic differentiation; increased SCF, CXCL12, VLA-4/VCAM-1, ICAM-1/LFA1, and TPO/MPL, Ang-1/Tie-2 gene expression. Further, the ASP-treated feeder layer alleviated hematopoietic cells senescence (from 21.9 ± 1.47 to 12.1 ± 1.13); decreased P53, P21, p-GSK-3β, β-catenin and cyclin-D1 protein expression, and increased glycogen synthase kinase (GSK)-3β protein expression in co-cultured hematopoietic cells. DISCUSSION AND CONCLUSIONS ASP delayed oxidative stress-induced premature senescence of 5-FU-treated feeder co-cultured hematopoietic cells via down-regulation of overactivated Wnt/β-catenin signaling. These findings provide a new strategy for alleviating myelosuppressive stress.
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Affiliation(s)
- Yilin Niu
- Laboratory of Stem Cells and Tissue Engineering, Chongqing Medical University, Chongqing, China
| | - Hanxianzhi Xiao
- Laboratory of Stem Cells and Tissue Engineering, Chongqing Medical University, Chongqing, China
| | - Biyao Wang
- Laboratory of Stem Cells and Tissue Engineering, Chongqing Medical University, Chongqing, China
| | - Ziling Wang
- Laboratory of Stem Cells and Tissue Engineering, Chongqing Medical University, Chongqing, China
| | - Kunhang Du
- Laboratory of Stem Cells and Tissue Engineering, Chongqing Medical University, Chongqing, China
| | - Yaping Wang
- Laboratory of Stem Cells and Tissue Engineering, Chongqing Medical University, Chongqing, China
- Department of Histology and Embryology, Chongqing Medical University, Chongqing, China
| | - Lu Wang
- Laboratory of Stem Cells and Tissue Engineering, Chongqing Medical University, Chongqing, China
- Department of Histology and Embryology, Chongqing Medical University, Chongqing, China
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Wen J, Liu J, Wan L, Wang F. Long noncoding RNA/circular RNA regulates competitive endogenous RNA networks in rheumatoid arthritis: molecular mechanisms and traditional Chinese medicine therapeutic significances. Ann Med 2023; 55:973-89. [PMID: 36905646 DOI: 10.1080/07853890.2023.2172605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/13/2023] Open
Abstract
Rheumatoid arthritis (RA) is a systemic and autoimmune disease that is mainly featured abnormal fibroblast-like synoviocyte (FLS) proliferation and inflammatory cell infiltration. Abnormal expression or function of long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) are closely related to human diseases, including RA. There has been increasing evidence showing that in the competitive endogenous RNA (ceRNA) networks, both lncRNA and circRNA are vital in the biological functions of cells. Nevertheless, the exact mechanism of ceRNA in RA remains to be investigated. Herein, we summarized the molecular potencies of lncRNA/circRNA-mediated ceRNA networks in RA, with emphasis on the phenotypic regulation of ceRNA in the progression of RA, including regulation of proliferation, invasion, inflammation and apoptosis, as well as the role of ceRNA in traditional Chinese medicine (TCM) in the treatment of RA. In addition, we also discussed the future direction and potential clinical value of ceRNA in the treatment of RA, which may provide potential reference value for clinical trials of TCM therapy for the treatment of RA.Key messagesLong noncoding RNA/circular RNA can work as the competitive endogenous RNA sponge and participate in the pathogenesis of rheumatoid arthritis.Traditional Chinese medicine and its agents have shown potential roles in the prevention and treatment of rheumatoid arthritis via competitive endogenous RNA.
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Affiliation(s)
- Jianting Wen
- Department of Rheumatology and Immunology, First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China
- Institute of Rheumatology, Anhui Academy of Chinese Medicine, Hefei, Anhui, China
- Key Laboratory of Xin'an Medicine of the Ministry of Education, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Jian Liu
- Department of Rheumatology and Immunology, First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China
- Institute of Rheumatology, Anhui Academy of Chinese Medicine, Hefei, Anhui, China
- Department of Internal Medicine Application Foundation Research and Development, Anhui Province-Key Laboratory of Modern Chinese Medicine, Hefei, Anhui, China
| | - Lei Wan
- Department of Rheumatology and Immunology, First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China
- Institute of Rheumatology, Anhui Academy of Chinese Medicine, Hefei, Anhui, China
- Department of Internal Medicine Application Foundation Research and Development, Anhui Province-Key Laboratory of Modern Chinese Medicine, Hefei, Anhui, China
| | - Fanfan Wang
- Department of Rheumatology and Immunology, First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China
- Institute of Rheumatology, Anhui Academy of Chinese Medicine, Hefei, Anhui, China
- Department of Internal Medicine Application Foundation Research and Development, Anhui Province-Key Laboratory of Modern Chinese Medicine, Hefei, Anhui, China
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Yu Y, Wang S, Wang Z, Gao R, Lee J. Arabidopsis thaliana: a powerful model organism to explore histone modifications and their upstream regulations. Epigenetics 2023; 18:2211362. [PMID: 37196184 DOI: 10.1080/15592294.2023.2211362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 04/07/2023] [Accepted: 04/28/2023] [Indexed: 05/19/2023] Open
Abstract
Histones are subjected to extensive covalent modifications that affect inter-nucleosomal interactions as well as alter chromatin structure and DNA accessibility. Through switching the corresponding histone modifications, the level of transcription and diverse downstream biological processes can be regulated. Although animal systems are widely used in studying histone modifications, the signalling processes that occur outside the nucleus prior to histone modifications have not been well understood due to the limitations including non viable mutants, partial lethality, and infertility of survivors. Here, we review the benefits of using Arabidopsis thaliana as the model organism to study histone modifications and their upstream regulations. Similarities among histones and key histone modifiers such as the Polycomb group (PcG) and Trithorax group (TrxG) in Drosophila, Human, and Arabidopsis are examined. Furthermore, prolonged cold-induced vernalization system has been well-studied and revealed the relationship between the controllable environment input (duration of vernalization), its chromatin modifications of FLOWERING LOCUS C (FLC), following gene expression, and the corresponding phenotypes. Such evidence suggests that research on Arabidopsis can bring insights into incomplete signalling pathways outside of the histone box, which can be achieved through viable reverse genetic screenings based on the phenotypes instead of direct monitoring of histone modifications among individual mutants. The potential upstream regulators in Arabidopsis can provide cues or directions for animal research based on the similarities between them.
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Affiliation(s)
- Yang Yu
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Sihan Wang
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Ziqin Wang
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Renwei Gao
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Joohyun Lee
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
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Krusnauskas R, Stakaitis R, Steponaitis G, Almstrup K, Vaitkiene P. Identification and comparison of m6A modifications in glioblastoma non-coding RNAs with MeRIP-seq and Nanopore dRNA-seq. Epigenetics 2023; 18:2163365. [PMID: 36597408 DOI: 10.1080/15592294.2022.2163365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The most prominent RNA modification - N6-methyladenosine (m6A) - affects gene regulation and cancer progression. The extent and effect of m6A on long non-coding RNAs (lncRNAs) is, however, still not clear. The most established method for m6A detection is methylated RNA immunoprecipitation and sequencing (MeRIP-seq). However, Oxford Nanopore Technologies recently developed direct RNA-seq (dRNA-seq) method, allowing m6A identification at higher resolution and in its native form. We performed whole transcriptome sequencing of the glioblastoma cell line U87-MG with both MeRIP-seq and dRNA-seq. For MeRIP-seq, m6A peaks were identified using nf-core/chipseq, and for dRNA-seq - EpiNano pipeline. MeRIP-seq analysis revealed 5086 lncRNAs transcripts, while dRNA-seq identified 336 lncRNAs transcripts from which 556 and 198 were found to be m6A modified, respectively. While 24 lncRNAs with m6A overlapped between two methods. Gliovis database analysis revealed that the expression of the major part of identified overlapping lncRNAs was associated with glioma grade or patient survival prognosis. We found that the frequency of m6A occurrence in lncRNAs varied more than 9-fold throughout the provided list of 24 modified lncRNAs. The highest m6A frequency was detected in MIR1915HG, THAP9-AS1, MALAT1, NORAD1, and NEAT1 (49-88nt), while MIR99AHG, SNHG3, LOXL1-AS1, ILF3-DT showed the lowest m6A frequency (445-261nt). Taken together, (1) we provide a high accuracy list of 24 m6A modified lncRNAs of U87-MG cells; (2) we conclude that MeRIP-seq is more suitable for an initial m6A screening study, due to its higher lncRNA coverage, whereas dRNA-seq is most useful when more in-depth analysis of m6A quantity and precise location is of interest.Abbreviations: (dRNA-seq) direct RNA-seq, (GBM) glioblastoma, (LGG) low-grade glioma, (lncRNAs) long non-coding RNAs, (m6A) N6-methyladenosine, (MeRIP-seq) methylated RNA immunoprecipitation and sequencing, (ncRNA) non-coding RNA, (ONT) Oxford Nanopore Technologi; Lietuvos Mokslo Taryba.
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Affiliation(s)
- Raulas Krusnauskas
- Laboratory of Molecular Neurobiology, Neuroscience Institute, Lithuanian University of Health Sciences, Eiveniu str. 4, LT50161, Kaunas, Lithuania
| | - Rytis Stakaitis
- Laboratory of Molecular Neurooncology, Neuroscience Institute, Lithuanian University of Health Sciences, Eiveniu str. 4, LT50161, Kaunas, Lithuania
| | - Giedrius Steponaitis
- Laboratory of Molecular Neurooncology, Neuroscience Institute, Lithuanian University of Health Sciences, Eiveniu str. 4, LT50161, Kaunas, Lithuania
| | - Kristian Almstrup
- Department of Growth and Reproduction, Rigshospitalet, University of Copenhagen, GR-5064, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark.,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (Edmarc), Rigshospitalet, University of Copenhagen, GR-5064, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
| | - Paulina Vaitkiene
- Laboratory of Molecular Neurobiology, Neuroscience Institute, Lithuanian University of Health Sciences, Eiveniu str. 4, LT50161, Kaunas, Lithuania
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Legname G. Copper coordination modulates prion conversion and infectivity in mammalian prion proteins. Prion 2023; 17:1-6. [PMID: 36597284 DOI: 10.1080/19336896.2022.2163835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In mammals the cellular form of the prion protein (PrPC) is a ubiquitous protein involved in many relevant functions in the central nervous system. In addition to its physiological functions PrPC plays a central role in a group of invariably fatal neurodegenerative disorders collectively called prion diseases. In fact, the protein is a substrate in a process in which it converts into an infectious and pathological form denoted as prion. The protein has a unique primary structure where the unstructured N-terminal moiety possesses characteristic sequences wherein histidines are able to coordinate metal ions, in particular copper ions. These sequences are called octarepeats for their characteristic length. Moreover, a non-octarepeat fifth-copper binding site is present where copper coordination seems to control infectivity. In this review, I will argue that these sequences may play a significant role in modulating prion conversion and replication.
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