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Burkhalter MD, Stiff T, Maerz LD, Casar Tena T, Wiese H, Gerhards J, Sailer SA, Vu LAT, Duong Phu M, Donow C, Alupei M, Iben S, Groth M, Wiese S, Church JA, Jeggo PA, Philipp M. Cilia defects upon loss of WDR4 are linked to proteasomal hyperactivity and ubiquitin shortage. Cell Death Dis 2024; 15:660. [PMID: 39251572 PMCID: PMC11384789 DOI: 10.1038/s41419-024-07042-5] [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: 02/03/2024] [Revised: 08/07/2024] [Accepted: 08/29/2024] [Indexed: 09/11/2024]
Abstract
The WD repeat-containing protein 4 (WDR4) has repeatedly been associated with primary microcephaly, a condition of impaired brain and skull growth. Often, faulty centrosomes cause microcephaly, yet aberrant cilia may also be involved. Here, we show using a combination of approaches in human fibroblasts, zebrafish embryos and patient-derived cells that WDR4 facilitates cilium formation. Molecularly, we associated WDR4 loss-of-function with increased protein synthesis and concomitant upregulation of proteasomal activity, while ubiquitin precursor pools are reduced. Inhibition of proteasomal activity as well as supplementation with free ubiquitin restored normal ciliogenesis. Proteasome inhibition ameliorated microcephaly phenotypes. Thus, we propose that WDR4 loss-of-function impairs head growth and neurogenesis via aberrant cilia formation, initially caused by disturbed protein and ubiquitin homeostasis.
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Affiliation(s)
- Martin D Burkhalter
- Department of Experimental and Clinical Pharmacology and Pharmacogenomics, Section of Pharmacogenomics, Eberhard-Karls-University Tübingen, 72074, Tübingen, Germany
| | - Tom Stiff
- Genome Damage and Stability Centre, University of Sussex, Brighton, BN1 9RQ, UK
| | - Lars D Maerz
- Institute for Biochemistry and Molecular Biology, Ulm University, 89081, Ulm, Germany
| | - Teresa Casar Tena
- Institute for Biochemistry and Molecular Biology, Ulm University, 89081, Ulm, Germany
| | - Heike Wiese
- Core Unit Mass Spectrometry and Proteomics, Medical Faculty, Ulm University, 89081, Ulm, Germany
| | - Julian Gerhards
- Department of Experimental and Clinical Pharmacology and Pharmacogenomics, Section of Pharmacogenomics, Eberhard-Karls-University Tübingen, 72074, Tübingen, Germany
| | - Steffen A Sailer
- Department of Experimental and Clinical Pharmacology and Pharmacogenomics, Section of Pharmacogenomics, Eberhard-Karls-University Tübingen, 72074, Tübingen, Germany
| | - Linh Anna Trúc Vu
- Department of Experimental and Clinical Pharmacology and Pharmacogenomics, Section of Pharmacogenomics, Eberhard-Karls-University Tübingen, 72074, Tübingen, Germany
| | - Max Duong Phu
- Department of Experimental and Clinical Pharmacology and Pharmacogenomics, Section of Pharmacogenomics, Eberhard-Karls-University Tübingen, 72074, Tübingen, Germany
| | - Cornelia Donow
- Institute for Biochemistry and Molecular Biology, Ulm University, 89081, Ulm, Germany
| | - Marius Alupei
- Department of Dermatology, Ulm University, 89081, Ulm, Germany
| | - Sebastian Iben
- Department of Dermatology, Ulm University, 89081, Ulm, Germany
| | - Marco Groth
- Core Facility Next Generation Sequencing, Leibniz Institute on Aging-Fritz Lipmann Institute, 07745, Jena, Germany
| | - Sebastian Wiese
- Core Unit Mass Spectrometry and Proteomics, Medical Faculty, Ulm University, 89081, Ulm, Germany
| | - Joseph A Church
- Department of Pediatrics, Keck School of Medicine of University of Southern California, Children's Hospital Los Angeles, Los Angeles, CA, 90033, USA
| | - Penelope A Jeggo
- Genome Damage and Stability Centre, University of Sussex, Brighton, BN1 9RQ, UK
| | - Melanie Philipp
- Department of Experimental and Clinical Pharmacology and Pharmacogenomics, Section of Pharmacogenomics, Eberhard-Karls-University Tübingen, 72074, Tübingen, Germany.
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Zhiyan C, Min Z, Yida D, Chunying H, Xiaohua H, Yutong L, Huan W, Linjuan S. Bioinformatic analysis of hippocampal histopathology in Alzheimer's disease and the therapeutic effects of active components of traditional Chinese medicine. Front Pharmacol 2024; 15:1424803. [PMID: 39221152 PMCID: PMC11362046 DOI: 10.3389/fphar.2024.1424803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 07/17/2024] [Indexed: 09/04/2024] Open
Abstract
Background and aim Pathological changes in the central nervous system (CNS) begin before the clinical symptoms of Alzheimer's Disease (AD) manifest, with the hippocampus being one of the first affected structures. Current treatments fail to alter AD progression. Traditional Chinese medicine (TCM) has shown potential in improving AD pathology through multi-target mechanisms. This study investigates pathological changes in AD hippocampal tissue and explores TCM active components that may alleviate these changes. Methods GSE5281 and GSE173955 datasets were downloaded from GEO and normalized to identify differentially expressed genes (DEGs). Key functional modules and hub genes were analyzed using Cytoscape and R. Active TCM components were identified from literature and the Pharmacopoeia of the People's Republic of China. Enrichment analyses were performed on target genes overlapping with DEGs. Result From the datasets, 76 upregulated and 363 downregulated genes were identified. Hub genes included SLAMF, CD34, ELN (upregulated) and ATP5F1B, VDAC1, VDAC2, HSPA8, ATP5F1C, PDHA1, UBB, SNCA, YWHAZ, PGK1 (downregulated). Literature review identified 33 active components from 23 herbal medicines. Target gene enrichment and analysis were performed for six components: dihydroartemisinin, berberine, naringenin, calycosin, echinacoside, and icariside II. Conclusion Mitochondrial to synaptic vesicle dysfunction pathways were enriched in downregulated genes. Despite downregulation, UBB and SNCA proteins accumulate in AD brains. TCM studies suggest curcumin and echinacoside may improve hippocampal pathology and cognitive impairment in AD. Further investigation into their mechanisms is needed.
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Affiliation(s)
- Chen Zhiyan
- Graduate School of Beijing University of Chinese Medicine, Beijing, China
| | - Zhan Min
- Department of Neurology, China Academy of Chinese Medical Sciences Xiyuan Hospital, Beijing, China
| | - Du Yida
- Graduate School of Beijing University of Chinese Medicine, Beijing, China
| | - He Chunying
- China Academy of Chinese Medical Sciences, Beijing, China
| | - Hu Xiaohua
- China Academy of Chinese Medical Sciences, Beijing, China
| | - Li Yutong
- Graduate School of Beijing University of Chinese Medicine, Beijing, China
| | - Wang Huan
- China Academy of Chinese Medical Sciences, Beijing, China
| | - Sun Linjuan
- Department of Neurology, China Academy of Chinese Medical Sciences Xiyuan Hospital, Beijing, China
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Tomita T, Nakajima Y, Ohmiya Y, Miyazaki K. Novel three-dimensional live skin-like in vitro composite for bioluminescence reporter gene assay. FEBS J 2024. [PMID: 39148322 DOI: 10.1111/febs.17246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 05/20/2024] [Accepted: 08/02/2024] [Indexed: 08/17/2024]
Abstract
We genetically manipulated HaCaT cells, a spontaneously immortalised normal keratinocyte cell line, to stably express two different coloured luciferase reporter genes, driven by interleukin 8 (IL-8) and ubiquitin-C (UBC) promoters, respectively. Subsequently, we generated a three-dimensional (3D) skin-like in vitro composite (SLIC) utilising these cells, with the objective of monitoring bioluminescence emitted from the SLIC. This SLIC was generated on non-woven silica fibre membranes in differentiation medium. Immunohistochemical analyses of skin differentiation markers in the SLIC revealed the expression of keratins 2 and 10, filaggrin, and involucrin, indicating mature skin characteristics. This engineered SLIC was employed for real-time bioluminescence monitoring, allowing the assessment of time- and dose-dependent responses to UV stress, as well as to hydrophilic and hydrophobic chemical loads. Notably, evaluation of responses to hydrophobic substances has been challenging with conventional 2D cell culture methods, suggesting the need for a new approach, which this technology could address. Our observations suggest that engineered SLIC with constitutively expressing reporters driven by selected promoters which are tailored to specific objectives, significantly facilitates assays exploring the physiological functions of skin cells based on genetic response mechanisms. It also highlights new avenues for evaluating the physiological impacts of various compounds designed for topical application to human skin.
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Affiliation(s)
- Tatsunosuke Tomita
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Yoshihiro Nakajima
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Takamatsu, Japan
| | - Yoshihiro Ohmiya
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ikeda, Japan
- Osaka Institute of Technology (OIT), Omiya, Japan
| | - Koyomi Miyazaki
- Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
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Li X, Meng Z, Hua Y, Li Z, Yin B, Qian B, Yu H, Li Z, Zhou Y, Feng Z, Lu S, Ke S, Bai M, Fu Y, Ma Y. Identification and validation of ferroptosis-related hub genes and immune infiltration in liver ischemia-reperfusion injury. Genomics 2024; 116:110918. [PMID: 39147333 DOI: 10.1016/j.ygeno.2024.110918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 07/15/2024] [Accepted: 07/26/2024] [Indexed: 08/17/2024]
Abstract
Ischemia-reperfusion injury (IRI) is a cumulation of pathophysiological processes that involves cell and organelle damage upon blood flow constraint and subsequent restoration. However, studies on overall immune infiltration and ferroptosis in liver ischemia-reperfusion injury (LIRI) are limited. This study explored immune cell infiltration and ferroptosis in LIRI using bioinformatics and experimental validation. The GSE151648 dataset, including 40 matched pairs of pre- and post- transplant liver samples was downloaded for bioinformatic analysis. Eleven hub genes were identified by overlapping differentially expressed genes (DEGs), iron genes, and genes identified through weighted gene co-expression network analysis (WGCNA). Subsequently, the pathway enrichment, transcription factor-target, microRNA-mRNA and protein-protein interaction networks were investigated. The diagnostic model was established by logistic regression, which was validated in the GSE23649 and GSE100155 datasets and verified using cytological experiments. Moreover, several drugs targeting these genes were found in DrugBank, providing a more effective treatment for LIRI. In addition, the expression of 11 hub genes was validated using quantitative real-time polymerase chain reaction (qRT-PCR) in liver transplantation samples and animal models. The expression of the 11 hub genes increased in LIRI compared with the control. Five genes were significantly enriched in six biological process terms, six genes showed high enrichment for LIRI-related signaling pathways. There were 56 relevant transcriptional factors and two central modules in the protein-protein interaction network. Further immune infiltration analysis indicated that immune cells including neutrophils and natural killer cells were differentially accumulated in the pre- and post-transplant groups, and this was accompanied by changes in immune-related factors. Finally, 10 targeted drugs were screened. Through bioinformatics and further experimental verification, we identified hub genes related to ferroptosis that could be used as potential targets to alleviate LIRI.
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Affiliation(s)
- Xinglong Li
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhanzhi Meng
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yongliang Hua
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Department of Pediatric Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zihao Li
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Bing Yin
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Baolin Qian
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Hongjun Yu
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhongyu Li
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yongzhi Zhou
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhigang Feng
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; The First Department of General Surgery, Affiliated Hospital of Inner Mongolia Minzu University, Tongliao, China
| | - Shounan Lu
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shanjia Ke
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Miaoyu Bai
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yao Fu
- Department of Ultrasound, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yong Ma
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China.
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Kaminskaya AN, Evpak AS, Belogurov AA, Kudriaeva AA. Tracking of Ubiquitin Signaling through 3.5 Billion Years of Combinatorial Conjugation. Int J Mol Sci 2024; 25:8671. [PMID: 39201358 PMCID: PMC11354881 DOI: 10.3390/ijms25168671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 08/01/2024] [Accepted: 08/02/2024] [Indexed: 09/02/2024] Open
Abstract
Ubiquitination is an evolutionary, ancient system of post-translational modification of proteins that occurs through a cascade involving ubiquitin activation, transfer, and conjugation. The maturation of this system has followed two main pathways. The first is the conservation of a universal structural fold of ubiquitin and ubiquitin-like proteins, which are present in both Archaea and Bacteria, as well as in multicellular Eukaryotes. The second is the rise of the complexity of the superfamily of ligases, which conjugate ubiquitin-like proteins to substrates, in terms of an increase in the number of enzyme variants, greater variation in structural organization, and the diversification of their catalytic domains. Here, we examine the diversity of the ubiquitination system among different organisms, assessing the variety and conservation of the key domains of the ubiquitination enzymes and ubiquitin itself. Our data show that E2 ubiquitin-conjugating enzymes of metazoan phyla are highly conservative, whereas the homology of E3 ubiquitin ligases with human orthologues gradually decreases depending on "molecular clock" timing and evolutionary distance. Surprisingly, Chordata and Echinodermata, which diverged over 0.5 billion years ago during the Cambrian explosion, share almost the same homology with humans in the amino acid sequences of E3 ligases but not in their adaptor proteins. These observations may suggest that, firstly, the E2 superfamily already existed in its current form in the last common metazoan ancestor and was generally not affected by purifying selection in metazoans. Secondly, it may indicate convergent evolution of the ubiquitination system and highlight E3 adaptor proteins as the "upper deck" of the ubiquitination system, which plays a crucial role in chordate evolution.
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Affiliation(s)
- Alena N. Kaminskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (A.N.K.); (A.S.E.)
| | - Alena S. Evpak
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (A.N.K.); (A.S.E.)
| | - Alexey A. Belogurov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (A.N.K.); (A.S.E.)
- Department of Biological Chemistry, Russian University of Medicine, Ministry of Health of Russian Federation, 127473 Moscow, Russia
| | - Anna A. Kudriaeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (A.N.K.); (A.S.E.)
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Dutta G, Alex R, Singh A, Gowane GR, Vohra V, De S, Verma A, Ludri A. Functional transcriptome analysis revealed upregulation of MAPK-SMAD signalling pathways in chronic heat stress in crossbred cattle. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2024; 68:1371-1385. [PMID: 38720050 DOI: 10.1007/s00484-024-02672-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 02/14/2024] [Accepted: 03/01/2024] [Indexed: 07/26/2024]
Abstract
Animal geneticists and breeders have the impending challenge of enhancing the resilience of Indian livestock to heat stress through better selection strategies. Climate change's impact on livestock is more intense in tropical countries like India where dairy cattle crossbreeds are more sensitive to heat stress. The main reason for this study was to find the missing relative changes in transcript levels in thermo-neutral and heat stress conditions in crossbred cattle through whole-transcriptome analysis of RNA-Seq data. Differentially expressed genes (DEGs) identified based on the minimum log twofold change value and false discovery rate 0.05 revealed 468 up-regulated genes and 2273 down-regulated significant genes. Functional annotation and pathway analysis of these significant DEGs were compared based on Gene Ontology (Biological process), Kyoto Encyclopedia of Genes and Genome (KEGG), and Reactome pathways using g: Profiler, ShinyGO v0.76, and iDEP.951 web tools. On finding network visualization, the most over-represented and correlated pathways were neuronal and sensory organ development, calcium signalling pathway, Mitogen-activated protein kinase (MAPK) and Smad signalling pathway, Ras-proximate-1, or Ras-related protein 1 (Rap 1) signalling pathway, apoptosis, and oxidative stress. Similarly, down-regulated genes were most expressed in mRNA processing, immune system, B-cell receptor signalling pathway, Nucleotide oligomerization domain (NOD)-like receptors (NLRs) signalling pathway and nonsense-mediated decay (NMD) pathway. The heat stress-responsive genes identified in this study will facilitate our understanding of the molecular basis for climate resilience and heat tolerance in Indian dairy crossbreeds.
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Affiliation(s)
- Gaurav Dutta
- Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Rani Alex
- Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India.
| | - Ayushi Singh
- Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Gopal R Gowane
- Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Vikas Vohra
- Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Sachidanandan De
- Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Archana Verma
- Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Ashutosh Ludri
- Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India
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7
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Blake MJ, Steer CJ. Chimeric Livers: Interspecies Blastocyst Complementation and Xenotransplantation for End-Stage Liver Disease. Hepat Med 2024; 16:11-29. [PMID: 38379783 PMCID: PMC10878318 DOI: 10.2147/hmer.s440697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 02/10/2024] [Indexed: 02/22/2024] Open
Abstract
Orthotopic liver transplantation (OLT) currently serves as the sole definitive treatment for thousands of patients suffering from end-stage liver disease; and the existing supply of donor livers for OLT is drastically outpaced by the increasing demand. To alleviate this significant gap in treatment, several experimental approaches have been devised with the aim of either offering interim support to patients waiting on the transplant list or bioengineering complete livers for OLT by infusing them with fresh hepatic cells. Recently, interspecies blastocyst complementation has emerged as a promising method for generating complete organs in utero over a short timeframe. When coupled with gene editing technology, it has brought about a potentially revolutionary transformation in regenerative medicine. Blastocyst complementation harbors notable potential for generating complete human livers in large animals, which could be used for xenotransplantation in humans, addressing the scarcity of livers for OLT. Nevertheless, substantial experimental and ethical challenges still need to be overcome to produce human livers in larger domestic animals like pigs. This review compiles the current understanding of interspecies blastocyst complementation and outlines future possibilities for liver xenotransplantation in humans.
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Affiliation(s)
- Madelyn J Blake
- Department of Medicine, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Clifford J Steer
- Departments of Medicine, and Genetics, Cell Biology and Development, University of Minnesota Medical School, Minneapolis, MN, USA
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8
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Legrand JMD, Hobbs RM. Defining Gene Function in Spermatogonial Stem Cells Through Conditional Knockout Approaches. Methods Mol Biol 2023; 2656:261-307. [PMID: 37249877 DOI: 10.1007/978-1-0716-3139-3_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Mammalian male fertility is maintained throughout life by a population of self-renewing mitotic germ cells known as spermatogonial stem cells (SSCs). Much of our current understanding regarding the molecular mechanisms underlying SSC activity is derived from studies using conditional knockout mouse models. Here, we provide a guide for the selection and use of mouse strains to develop conditional knockout models for the study of SSCs, as well as their precursors and differentiation-committed progeny. We describe Cre recombinase-expressing strains, breeding strategies to generate experimental groups, and treatment regimens for inducible knockout models and provide advice for verifying and improving conditional knockout efficiency. This resource can be beneficial to those aiming to develop conditional knockout models for the study of SSC development and postnatal function.
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Affiliation(s)
- Julien M D Legrand
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Robin M Hobbs
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC, Australia.
- Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia.
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9
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Han SW, Ryu KY. Increased clearance of non-biodegradable polystyrene nanoplastics by exocytosis through inhibition of retrograde intracellular transport. JOURNAL OF HAZARDOUS MATERIALS 2022; 439:129576. [PMID: 35850071 DOI: 10.1016/j.jhazmat.2022.129576] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/28/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
Nanoplastics (NPs) are derived from microplastics and may cause health problems. We previously showed that 100 nm polystyrene (PS)-NPs enter cells, including mouse embryonic fibroblasts (MEFs), and their intracellular accumulation induces inflammatory and oxidative stress. Moreover, PS-NP uptake was found to occur via endocytosis, and they accumulated mostly at the juxtanuclear position, but never within the nucleus. We speculated that PS-NPs were cleared from cells when they were no longer exposed to PS-NPs. However, the effects of PS-NPs on the cellular machinery remain unknown. The accumulation of PS-NPs at the juxtanuclear position may be due to retrograde transport along microtubules. To confirm this, we treated PS-NP-exposed MEFs with inhibitors of histone deacetylase 6 (HDAC6), dynein, or microtubule polymerization and found greatly diminished intracellular and juxtanuclear accumulation. Moreover, rapid clearance of PS-NPs was observed when MEFs were treated with an HDAC6 inhibitor. PS-NPs were removed by exocytosis, as confirmed by treatment with an exocytosis inhibitor. Furthermore, inhibiting the retrograde transport of PS-NPs alleviated the activation of the antioxidant response pathway, inflammatory and oxidative stress, and reactive oxygen species generation. In summary, inhibition of the retrograde transport of non-biodegradable PS-NPs leads to their rapid export by exocytosis, which may reduce their cytotoxicity.
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Affiliation(s)
- Seung-Woo Han
- Department of Life Science, University of Seoul, Seoul 02504, Republic of Korea
| | - Kwon-Yul Ryu
- Department of Life Science, University of Seoul, Seoul 02504, Republic of Korea.
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Spears ME, Lee N, Hwang S, Park SJ, Carlisle AE, Li R, Doshi MB, Armando AM, Gao J, Simin K, Zhu LJ, Greer PL, Quehenberger O, Torres EM, Kim D. De novo sphingolipid biosynthesis necessitates detoxification in cancer cells. Cell Rep 2022; 40:111415. [PMID: 36170811 PMCID: PMC9552870 DOI: 10.1016/j.celrep.2022.111415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 07/21/2022] [Accepted: 09/02/2022] [Indexed: 11/29/2022] Open
Abstract
Sphingolipids play important signaling and structural roles in cells. Here, we find that during de novo sphingolipid biosynthesis, a toxic metabolite is formed with critical implications for cancer cell survival. The enzyme catalyzing the first step in this pathway, serine palmitoyltransferase complex (SPT), is upregulated in breast and other cancers. SPT is dispensable for cancer cell proliferation, as sphingolipids can be salvaged from the environment. However, SPT activity introduces a liability as its product, 3-ketodihydrosphingosine (3KDS), is toxic and requires clearance via the downstream enzyme 3-ketodihydrosphingosine reductase (KDSR). In cancer cells, but not normal cells, targeting KDSR induces toxic 3KDS accumulation leading to endoplasmic reticulum (ER) dysfunction and loss of proteostasis. Furthermore, the antitumor effect of KDSR disruption can be enhanced by increasing metabolic input (via high-fat diet) to allow greater 3KDS production. Thus, de novo sphingolipid biosynthesis entails a detoxification requirement in cancer cells that can be therapeutically exploited.
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Affiliation(s)
- Meghan E Spears
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Namgyu Lee
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Sunyoung Hwang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Sung Jin Park
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Anne E Carlisle
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Rui Li
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Mihir B Doshi
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Aaron M Armando
- School of Medicine, Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, San Diego, CA 92093, USA
| | - Jenny Gao
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Karl Simin
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Paul L Greer
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Oswald Quehenberger
- School of Medicine, Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, San Diego, CA 92093, USA
| | - Eduardo M Torres
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Dohoon Kim
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA.
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11
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El-Saafin F, Devys D, Johnsen SA, Vincent SD, Tora L. SAGA-Dependent Histone H2Bub1 Deubiquitination Is Essential for Cellular Ubiquitin Balance during Embryonic Development. Int J Mol Sci 2022; 23:ijms23137459. [PMID: 35806465 PMCID: PMC9267394 DOI: 10.3390/ijms23137459] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 06/30/2022] [Accepted: 06/30/2022] [Indexed: 12/24/2022] Open
Abstract
Ubiquitin (ub) is a small, highly conserved protein widely expressed in eukaryotic cells. Ubiquitination is a post-translational modification catalyzed by enzymes that activate, conjugate, and ligate ub to proteins. Substrates can be modified either by addition of a single ubiquitin molecule (monoubiquitination), or by conjugation of several ubs (polyubiquitination). Monoubiquitination acts as a signaling mark to control diverse biological processes. The cellular and spatial distribution of ub is determined by the opposing activities of ub ligase enzymes, and deubiquitinases (DUBs), which remove ub from proteins to generate free ub. In mammalian cells, 1–2% of total histone H2B is monoubiquitinated. The SAGA (Spt Ada Gcn5 Acetyl-transferase) is a transcriptional coactivator and its DUB module removes ub from H2Bub1. The mammalian SAGA DUB module has four subunits, ATXN7, ATXN7L3, USP22, and ENY2. Atxn7l3−/− mouse embryos, lacking DUB activity, have a five-fold increase in H2Bub1 retention, and die at mid-gestation. Interestingly, embryos lacking the ub encoding gene, Ubc, have a similar phenotype. Here we provide a current overview of data suggesting that H2Bub1 retention on the chromatin in Atxn7l3−/− embryos may lead to an imbalance in free ub distribution. Thus, we speculate that ATXN7L3-containing DUBs impact the free cellular ub pool during development.
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Affiliation(s)
- Farrah El-Saafin
- Olivia Newton-John Cancer Research Institute, Melbourne 3095, Australia;
| | - Didier Devys
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France;
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | | | - Stéphane D. Vincent
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France;
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
- Correspondence: (S.D.V.); (L.T.); Tel.: +33-3-88653425 (S.D.V.); +33-3-88653444 (L.T.)
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France;
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
- Correspondence: (S.D.V.); (L.T.); Tel.: +33-3-88653425 (S.D.V.); +33-3-88653444 (L.T.)
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12
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Lambert-Smith IA, Saunders DN, Yerbury JJ. Progress in biophysics and molecular biology proteostasis impairment and ALS. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 174:3-27. [PMID: 35716729 DOI: 10.1016/j.pbiomolbio.2022.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 05/19/2022] [Accepted: 06/09/2022] [Indexed: 12/11/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a rapidly progressive and fatal neurodegenerative disease that results from the loss of both upper and lower motor neurons. It is the most common motor neuron disease and currently has no effective treatment. There is mounting evidence to suggest that disturbances in proteostasis play a significant role in ALS pathogenesis. Proteostasis is the maintenance of the proteome at the right level, conformation and location to allow a cell to perform its intended function. In this review, we present a thorough synthesis of the literature that provides evidence that genetic mutations associated with ALS cause imbalance to a proteome that is vulnerable to such pressure due to its metastable nature. We propose that the mechanism underlying motor neuron death caused by defects in mRNA metabolism and protein degradation pathways converges on proteostasis dysfunction. We propose that the proteostasis network may provide an effective target for therapeutic development in ALS.
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Affiliation(s)
- Isabella A Lambert-Smith
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia; Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Darren N Saunders
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Justin J Yerbury
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia; Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia.
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13
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Sorrentino A, Menevse AN, Michels T, Volpin V, Durst FC, Sax J, Xydia M, Hussein A, Stamova S, Spoerl S, Heuschneider N, Muehlbauer J, Jeltsch KM, Rathinasamy A, Werner-Klein M, Breinig M, Mikietyn D, Kohler C, Poschke I, Purr S, Reidell O, Martins Freire C, Offringa R, Gebhard C, Spang R, Rehli M, Boutros M, Schmidl C, Khandelwal N, Beckhove P. Salt-inducible kinase 3 protects tumor cells from cytotoxic T-cell attack by promoting TNF-induced NF-κB activation. J Immunother Cancer 2022; 10:jitc-2021-004258. [PMID: 35606086 PMCID: PMC9174898 DOI: 10.1136/jitc-2021-004258] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2022] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Cancer immunotherapeutic strategies showed unprecedented results in the clinic. However, many patients do not respond to immuno-oncological treatments due to the occurrence of a plethora of immunological obstacles, including tumor intrinsic mechanisms of resistance to cytotoxic T-cell (TC) attack. Thus, a deeper understanding of these mechanisms is needed to develop successful immunotherapies. METHODS To identify novel genes that protect tumor cells from effective TC-mediated cytotoxicity, we performed a genetic screening in pancreatic cancer cells challenged with tumor-infiltrating lymphocytes and antigen-specific TCs. RESULTS The screening revealed 108 potential genes that protected tumor cells from TC attack. Among them, salt-inducible kinase 3 (SIK3) was one of the strongest hits identified in the screening. Both genetic and pharmacological inhibitions of SIK3 in tumor cells dramatically increased TC-mediated cytotoxicity in several in vitro coculture models, using different sources of tumor and TCs. Consistently, adoptive TC transfer of TILs led to tumor growth inhibition of SIK3-depleted cancer cells in vivo. Mechanistic analysis revealed that SIK3 rendered tumor cells susceptible to tumor necrosis factor (TNF) secreted by tumor-activated TCs. SIK3 promoted nuclear factor kappa B (NF-κB) nuclear translocation and inhibited caspase-8 and caspase-9 after TNF stimulation. Chromatin accessibility and transcriptome analyses showed that SIK3 knockdown profoundly impaired the expression of prosurvival genes under the TNF-NF-κB axis. TNF stimulation led to SIK3-dependent phosphorylation of the NF-κB upstream regulators inhibitory-κB kinase and NF-kappa-B inhibitor alpha on the one side, and to inhibition of histone deacetylase 4 on the other side, thus sustaining NF-κB activation and nuclear stabilization. A SIK3-dependent gene signature of TNF-mediated NF-κB activation was found in a majority of pancreatic cancers where it correlated with increased cytotoxic TC activity and poor prognosis. CONCLUSION Our data reveal an abundant molecular mechanism that protects tumor cells from cytotoxic TC attack and demonstrate that pharmacological inhibition of this pathway is feasible.
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Affiliation(s)
- Antonio Sorrentino
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
- Translational Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ayse Nur Menevse
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Tillmann Michels
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
- Translational Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Valentina Volpin
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
- Translational Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Julian Sax
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Maria Xydia
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Abir Hussein
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Slava Stamova
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Steffen Spoerl
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
- Department of Oral and Maxillofacial Surgery, University Hospital Regensburg, Regensburg, Germany
| | - Nicole Heuschneider
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Jasmin Muehlbauer
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
| | | | - Anchana Rathinasamy
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Melanie Werner-Klein
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
- Experimental Medicine and Therapy Research, University of Regensburg, Regensburg, Germany
| | - Marco Breinig
- Signalling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Helmholtz-University Group 'Cell Plasticity and Epigenetic Remodeling', German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Damian Mikietyn
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Christian Kohler
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Isabel Poschke
- Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
- DKTK CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Immune Monitoring Unit, National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Sabrina Purr
- Joint Immunotherapeutics Laboratory, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Olivia Reidell
- Research Department, iOmx Therapeutics, Munich/Martinsried, Germany
| | | | - Rienk Offringa
- Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Claudia Gebhard
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Rainer Spang
- Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Michael Rehli
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Michael Boutros
- Signalling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christian Schmidl
- Junior Group 'Epigenetic Immunooncology', Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Nisit Khandelwal
- Translational Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Research Department, iOmx Therapeutics, Munich/Martinsried, Germany
| | - Philipp Beckhove
- Division of Interventional Immunology, Leibniz Institute for Immunotherapy, Regensburg, Germany
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
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14
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Aisenberg WH, McCray BA, Sullivan JM, Diehl E, DeVine LR, Alevy J, Bagnell AM, Carr P, Donohue JK, Goretzki B, Cole RN, Hellmich UA, Sumner CJ. Multiubiquitination of TRPV4 reduces channel activity independent of surface localization. J Biol Chem 2022; 298:101826. [PMID: 35300980 PMCID: PMC9010760 DOI: 10.1016/j.jbc.2022.101826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 02/19/2022] [Accepted: 02/21/2022] [Indexed: 02/06/2023] Open
Abstract
Ubiquitin (Ub)-mediated regulation of plasmalemmal ion channel activity canonically occurs via stimulation of endocytosis. Whether ubiquitination can modulate channel activity by alternative mechanisms remains unknown. Here, we show that the transient receptor potential vanilloid 4 (TRPV4) cation channel is multiubiquitinated within its cytosolic N-terminal and C-terminal intrinsically disordered regions (IDRs). Mutagenizing select lysine residues to block ubiquitination of the N-terminal but not C-terminal IDR resulted in a marked elevation of TRPV4-mediated intracellular calcium influx, without increasing cell surface expression levels. Conversely, enhancing TRPV4 ubiquitination via expression of an E3 Ub ligase reduced TRPV4 channel activity but did not decrease plasma membrane abundance. These results demonstrate Ub-dependent regulation of TRPV4 channel function independent of effects on plasma membrane localization. Consistent with ubiquitination playing a key negative modulatory role of the channel, gain-of-function neuropathy-causing mutations in the TRPV4 gene led to reduced channel ubiquitination in both cellular and Drosophila models of TRPV4 neuropathy, whereas increasing mutant TRPV4 ubiquitination partially suppressed channel overactivity. Together, these data reveal a novel mechanism via which ubiquitination of an intracellular flexible IDR domain modulates ion channel function independently of endocytic trafficking and identify a contributory role for this pathway in the dysregulation of TRPV4 channel activity by neuropathy-causing mutations.
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Affiliation(s)
- William H Aisenberg
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Brett A McCray
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jeremy M Sullivan
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Erika Diehl
- Department of Chemistry, Biochemistry Section, Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Lauren R DeVine
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jonathan Alevy
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Anna M Bagnell
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Patrice Carr
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jack K Donohue
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Benedikt Goretzki
- Institute of Organic Chemistry and Macromolecular Chemistry, Cluster of Excellence 'Balance of the Microverse', Friedrich-Schiller-Universität, Jena, Germany; Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität, Frankfurt am Main, Germany
| | - Robert N Cole
- Institute of Organic Chemistry and Macromolecular Chemistry, Cluster of Excellence 'Balance of the Microverse', Friedrich-Schiller-Universität, Jena, Germany
| | - Ute A Hellmich
- Institute of Organic Chemistry and Macromolecular Chemistry, Cluster of Excellence 'Balance of the Microverse', Friedrich-Schiller-Universität, Jena, Germany; Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität, Frankfurt am Main, Germany
| | - Charlotte J Sumner
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
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15
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Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain. Nat Neurosci 2022; 25:306-316. [PMID: 35260865 DOI: 10.1038/s41593-022-01022-8] [Citation(s) in RCA: 166] [Impact Index Per Article: 83.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 01/25/2022] [Indexed: 12/31/2022]
Abstract
A key aspect of nearly all single-cell sequencing experiments is dissociation of intact tissues into single-cell suspensions. While many protocols have been optimized for optimal cell yield, they have often overlooked the effects that dissociation can have on ex vivo gene expression. Here, we demonstrate that use of enzymatic dissociation on brain tissue induces an aberrant ex vivo gene expression signature, most prominently in microglia, which is prevalent in published literature and can substantially confound downstream analyses. To address this issue, we present a rigorously validated protocol that preserves both in vivo transcriptional profiles and cell-type diversity and yield across tissue types and species. We also identify a similar signature in postmortem human brain single-nucleus RNA-sequencing datasets, and show that this signature is induced in freshly isolated human tissue by exposure to elevated temperatures ex vivo. Together, our results provide a methodological solution for preventing artifactual gene expression changes during fresh tissue digestion and a reference for future deeper analysis of the potential confounding states present in postmortem human samples.
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16
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Ubiquitination-Proteasome System (UPS) and Autophagy Two Main Protein Degradation Machineries in Response to Cell Stress. Cells 2022; 11:cells11050851. [PMID: 35269473 PMCID: PMC8909305 DOI: 10.3390/cells11050851] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/17/2022] [Accepted: 02/22/2022] [Indexed: 02/07/2023] Open
Abstract
In response to environmental stimuli, cells make a series of adaptive changes to combat the injury, repair the damage, and increase the tolerance to the stress. However, once the damage is too serious to repair, the cells will undergo apoptosis to protect the overall cells through suicidal behavior. Upon external stimulation, some intracellular proteins turn into unfolded or misfolded protein, exposing their hydrophobic regions to form protein aggregation, which may ultimately produce serious damage to the cells. Ubiquitin plays an important role in the degradation of these unnatural proteins by tagging with ubiquitin chains in the ubiquitin-proteasome or autophagy system. If the two processes fail to eliminate the abnormal protein aggregates, the cells will move to apoptosis and death. Dysregulation of ubiquitin-proteasome system (UPS) and autophagy may result in the development of numerous diseases. This review focuses on the molecular mechanisms of UPS and autophagy in clearance of intracellular protein aggregates, and the relationship between dysregulation of ubiquitin network and diseases.
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17
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Regulatory Networks of Prognostic mRNAs in Pediatric Acute Myeloid Leukemia. JOURNAL OF HEALTHCARE ENGINEERING 2022; 2022:2691997. [PMID: 35035819 PMCID: PMC8754609 DOI: 10.1155/2022/2691997] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 11/27/2021] [Accepted: 12/09/2021] [Indexed: 12/24/2022]
Abstract
Acute myeloid leukemia (AML) in children refers to a malignant tumor caused by the abnormal proliferation of immature myeloid cells in the bone marrow and peripheral blood. The prognosis of patients with pediatric acute myeloid leukemia (AML) remains poor, highlighting the need for improved targeted therapy. The expression data of lncRNAs, mRNAs, and miRNAs and survival information of pediatric AML patients were collected from The Cancer Genome Atlas (TCGA) database. Cox regression analysis was used to screen the lncRNAs, mRNAs, and miRNAs that significantly affect the overall survival (OS) of patients as OS-related genes (included lncRNAs, mRNAs, and miRNAs). Enrichment analysis and protein-protein interaction (PPI) network construction were performed for the OS-related mRNAs. We further established a ceRNAs regulatory network. In addition, the potential prognostic role of genes was further evaluated by risk score. We have identified 5275 lncRNAs, 176 miRNAs, and 6221 mRNAs that significantly affect the prognosis of pediatric AML patients. It is worth noting that OS-related mRNAs are mainly involved in ribosome, RNA transport, and spliceosome. We identified the top 10 most connected mRNAs in the PPI network as important mRNAs and constructed a ceRNAs regulatory network (including NCBP2, RPLP0, UBC, RPS2, and RPS9). The risk score and nomogram results suggest that NCBP2 may be a risk factor for pediatric AML, while RPLP0, UBC, RPS2, and RPS9 may be protective factors. Our results construct 5 gene signals as new prognostic indicators for predicting the survival of pediatric AML patients. Our research has demonstrated the ceRNAs regulatory network may become a new target for pediatric AML treatment.
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18
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UBC Mediated by SEPT6 Inhibited the Progression of Prostate Cancer. Mediators Inflamm 2021; 2021:7393029. [PMID: 34966246 PMCID: PMC8712179 DOI: 10.1155/2021/7393029] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/25/2021] [Accepted: 11/29/2021] [Indexed: 11/18/2022] Open
Abstract
Background Prostate cancer is one of the most common malignancies in men. Protein ubiquitination is an important mechanism for regulating protein activity and level in vivo. We aimed to study the mechanism of SEPT6 and UBC action in prostate cancer to identify new targets. Methods The ubiquitin-protein and the ubiquitin coding gene UBA52, UBA80, UBB, and UBC expressions were detected in clinical tissues and cells. Overexpression and knockdown of UBC were performed in prostate cancer DU145 cells. Cell Counting Kit 8 (CCK-8) assay was performed to detect cell proliferation. Cell cycle at 24 h was detected by flow cytometry. Clonal formation assay was used to measure cell clone number. Immunofluorescence (IF) was performed to detect the colocalization of SEPT6 and UBC in prostate cancer cells. Next, we overexpressed or knocked down SEPT6 expression in DU145 cells. Pearson correlation coefficient was applied to analyze the relationship between SEPT6 and UBC in prostate cancer tissue. oe-SEPT6+oe-UBC coexpressing cells were constructed to detect the upstream and downstream relationship between SEPT6 and UBC on prostate cancer cells. The tumor formation experiment was performed to explore SEPT6/UBC effect on prostate cancer. Results UBC was upregulated in prostate cancer tissues and cells. Overexpression of UBC promoted cell survival and proliferation. IF revealed the colocalization of SEPT6 and UBC in prostate cancer cells. UBC expression decreased after oe-SEPT6, while increased after sh-SEPT6, indicating that UBC was downstream of SEPT6. Pearson correlation coefficient analysis showed that SEPT6 was negatively correlated with UBC in prostate cancer tissues. SEPT6 as an upstream gene of UBC regulated prostate cancer cell behavior through UBC. The tumor formation experiment showed that SEPT6 could inhibit tumor growth. Conclusion In general, SEPT6 inhibited UBC expression, thereby reducing the overall ubiquitination level, affecting the expression level of downstream cell proliferation-related genes, and then affecting the progression of prostate cancer.
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19
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Khan RIN, Sahu AR, Malla WA, Praharaj MR, Hosamani N, Kumar S, Gupta S, Sharma S, Saxena A, Varshney A, Singh P, Verma V, Kumar P, Singh G, Pandey A, Saxena S, Gandham RK, Tiwari AK. Systems biology under heat stress in Indian cattle. Gene 2021; 805:145908. [PMID: 34411649 DOI: 10.1016/j.gene.2021.145908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 11/26/2022]
Abstract
Transcriptome profiling of Vrindavani and Tharparkar cattle (n = 5 each) revealed that more numbers of genes were dysregulated in Vrindavani than in Tharparkar. A contrast in gene expression was observed with 18.9 % of upregulated genes in Vrindavani downregulated in Tharparkar and 17.8% upregulated genes in Tharparkar downregulated in Vrindavani. Functional annotation of genes differentially expressed in Tharparkar and Vrindavani revealed that the systems biology in Tharparkar is moving towards counteracting the effects due to heat stress. Unlike Vrindavani, Tharparkar is not only endowed with higher expression of the scavengers (UBE2G1, UBE2S, and UBE2H) of misfolded proteins but also with protectors (VCP, Serp1, and CALR) of naïve unfolded proteins. Further, higher expression of the antioxidants in Tharparkar enables it to cope up with higher levels of free radicals generated as a result of heat stress. In this study, we found relevant genes dysregulated in Tharparkar in the direction that can counter heat stress.
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Affiliation(s)
- Raja Ishaq Nabi Khan
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Bareilly, India
| | - Amit Ranjan Sahu
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Bareilly, India
| | - Waseem Akram Malla
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Bareilly, India
| | - Manas Ranjan Praharaj
- Computational Biology and Genomics, National Institute of Animal Biotechnology, Hyderabad, India
| | - Neelima Hosamani
- Computational Biology and Genomics, National Institute of Animal Biotechnology, Hyderabad, India
| | - Shakti Kumar
- Computational Biology and Genomics, National Institute of Animal Biotechnology, Hyderabad, India
| | - Smita Gupta
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Bareilly, India
| | - Shweta Sharma
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Bareilly, India
| | - Archana Saxena
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Bareilly, India
| | - Anshul Varshney
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Bareilly, India
| | - Pragya Singh
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Bareilly, India
| | - Vinay Verma
- Division of Physiology and Climatology, Indian Veterinary Research Institute, Bareilly, India
| | - Puneet Kumar
- Division of Physiology and Climatology, Indian Veterinary Research Institute, Bareilly, India
| | - Gyanendra Singh
- Division of Physiology and Climatology, Indian Veterinary Research Institute, Bareilly, India
| | - Aruna Pandey
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Bareilly, India
| | - Shikha Saxena
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Bareilly, India
| | - Ravi Kumar Gandham
- Computational Biology and Genomics, National Institute of Animal Biotechnology, Hyderabad, India.
| | - Ashok Kumar Tiwari
- Division of Biological Standardization, Indian Veterinary Research Institute, Bareilly, India.
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20
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Larson EL, Joo DJ, Nelson ED, Amiot BP, Aravalli RN, Nyberg SL. Fumarylacetoacetate hydrolase gene as a knockout target for hepatic chimerism and donor liver production. Stem Cell Reports 2021; 16:2577-2588. [PMID: 34678209 PMCID: PMC8581169 DOI: 10.1016/j.stemcr.2021.09.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 11/15/2022] Open
Abstract
A reliable source of human hepatocytes and transplantable livers is needed. Interspecies embryo complementation, which involves implanting donor human stem cells into early morula/blastocyst stage animal embryos, is an emerging solution to the shortage of transplantable livers. We review proposed mutations in the recipient embryo to disable hepatogenesis, and discuss the advantages of using fumarylacetoacetate hydrolase knockouts and other genetic modifications to disable hepatogenesis. Interspecies blastocyst complementation using porcine recipients for primate donors has been achieved, although percentages of chimerism remain persistently low. Recent investigation into the dynamic transcriptomes of pigs and primates have created new opportunities to intimately match the stage of developing animal embryos with one of the many varieties of human induced pluripotent stem cell. We discuss techniques for decreasing donor cell apoptosis, targeting donor tissue to endodermal structures to avoid neural or germline chimerism, and decreasing the immunogenicity of chimeric organs by generating donor endothelium.
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Affiliation(s)
- Ellen L Larson
- Department of Surgery, Division of Transplant Surgery, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| | - Dong Jin Joo
- Department of Surgery, Division of Transplantation, Yonsei University College of Medicine, Seoul, South Korea
| | - Erek D Nelson
- Department of Surgery, Mayo Clinic, Rochester, MN, USA
| | - Bruce P Amiot
- Department of Surgery, Division of Transplant Surgery, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| | - Rajagopal N Aravalli
- Department of Electrical and Computer Engineering, College of Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Scott L Nyberg
- Department of Surgery, Division of Transplant Surgery, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA.
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21
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Polyubiquitin gene Ubb is required for upregulation of Piwi protein level during mouse testis development. Cell Death Dis 2021; 7:194. [PMID: 34312369 PMCID: PMC8313548 DOI: 10.1038/s41420-021-00581-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/18/2021] [Accepted: 07/10/2021] [Indexed: 02/07/2023]
Abstract
Testis development, including early embryonic gonad formation and late postnatal spermatogenesis, is essential for the reproduction of higher metazoans to generate fertile gametes, called sperm. We have previously reported that the polyubiquitin gene Ubb is required for fertility in both male and female mice. In particular, the Ubb-null male mice showed an azoospermia phenotype due to arrest of spermatogenesis at the pachytene stage. Here, we analyzed the whole testis proteome at postnatal day 20 to define the molecular mediators of the male-infertility phenotype caused by Ubb knockout. From the identified proteome, 564 proteins were significantly and differentially expressed in Ubb-knockout testes and, among these, 36 downregulated proteins were involved at different stages of spermatogenesis. We also found that levels of piRNA metabolic process-related proteins, including Piwil2 and Tdrd1, were downregulated in Ubb-null testes through functional gene ontology analysis. Further, protein-protein interaction mapping revealed that 24 testis development-related proteins, including Hsp90aa1, Eef1a1, and Pabpc1, were directly influenced by the depletion of ubiquitin. In addition, the reduced mRNA levels of these proteins were observed in Ubb-knockout testes, which closely resembled the global downregulation of piRNA-metabolic gene expression at the transcriptional and post-transcriptional levels. Together with proteomic and transcriptional analyses, our data suggest that Ubb expression is essential for the maintenance of testicular RNA-binding regulators and piRNA-metabolic proteins to complete spermatogenesis in mice.
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22
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Abstract
Ubiquitin (Ub) is one of the proteins that are highly conserved from yeast to humans. It is an essential core unit of the well-defined post-translational modification, called ubiquitination, which is involved in a variety of biological processes. In meta-zoans, Ub is encoded by two monoubiquitin genes and two polyubiquitin genes, in which a single Ub is fused to a ribosomal protein or Ub coding units are arranged in tandem repeats. In mice, polyubiquitin genes (Ubb and Ubc) play a pivotal role to meet the requirement of cellular Ub pools during embryonic development. In addition, expression levels of polyubiquitin genes are increased to adapt to environmental stimuli such as oxidative, heat-shock, and proteotoxic stress. Several researchers have reported about the perturbation of Ub pools through genetic alteration or exogenous Ub delivery using diverse model systems. To study Ub pool changes in a physiologically relevant manner, changing Ub pools via the regulation of endogenous polyubiquitin gene expression has recently been introduced. Furthermore, to understand the regulation of polyubiquitin gene expression more precisely, cis-acting elements and trans-acting factors, which are regulatory components of polyubiquitin genes, have been analyzed. In this review, we discuss how the role of polyu-biquitin genes has been studied during the past decade, es-pecially focusing on their regulation.
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Affiliation(s)
- Seung-Woo Han
- Department of Life Science, University of Seoul, Seoul 02504, Korea
| | - Byung-Kwon Jung
- Department of Life Science, University of Seoul, Seoul 02504, Korea
| | - Kwon-Yul Ryu
- Department of Life Science, University of Seoul, Seoul 02504, Korea
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23
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Martín-Villanueva S, Gutiérrez G, Kressler D, de la Cruz J. Ubiquitin and Ubiquitin-Like Proteins and Domains in Ribosome Production and Function: Chance or Necessity? Int J Mol Sci 2021; 22:ijms22094359. [PMID: 33921964 PMCID: PMC8122580 DOI: 10.3390/ijms22094359] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 12/11/2022] Open
Abstract
Ubiquitin is a small protein that is highly conserved throughout eukaryotes. It operates as a reversible post-translational modifier through a process known as ubiquitination, which involves the addition of one or several ubiquitin moieties to a substrate protein. These modifications mark proteins for proteasome-dependent degradation or alter their localization or activity in a variety of cellular processes. In most eukaryotes, ubiquitin is generated by the proteolytic cleavage of precursor proteins in which it is fused either to itself, constituting a polyubiquitin precursor, or as a single N-terminal moiety to ribosomal proteins, which are practically invariably eL40 and eS31. Herein, we summarize the contribution of the ubiquitin moiety within precursors of ribosomal proteins to ribosome biogenesis and function and discuss the biological relevance of having maintained the explicit fusion to eL40 and eS31 during evolution. There are other ubiquitin-like proteins, which also work as post-translational modifiers, among them the small ubiquitin-like modifier (SUMO). Both ubiquitin and SUMO are able to modify ribosome assembly factors and ribosomal proteins to regulate ribosome biogenesis and function. Strikingly, ubiquitin-like domains are also found within two ribosome assembly factors; hence, the functional role of these proteins will also be highlighted.
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Affiliation(s)
- Sara Martín-Villanueva
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41009 Seville, Spain;
- Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain;
| | - Gabriel Gutiérrez
- Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain;
| | - Dieter Kressler
- Unit of Biochemistry, Department of Biology, University of Fribourg, CH-1700 Fribourg, Switzerland
- Correspondence: (D.K.); (J.d.l.C.); Tel.: +41-26-300-86-45 (D.K.); +34-955-923-126 (J.d.l.C.)
| | - Jesús de la Cruz
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41009 Seville, Spain;
- Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain;
- Correspondence: (D.K.); (J.d.l.C.); Tel.: +41-26-300-86-45 (D.K.); +34-955-923-126 (J.d.l.C.)
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24
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Yu HC, Huang KY, Lu MC, Huang Tseng HY, Liu SQ, Lai NS, Huang HB. Down-Regulation of LOC645166 in T Cells of Ankylosing Spondylitis Patients Promotes the NF-κB Signaling via Decreasingly Blocking Recruitment of the IKK Complex to K63-Linked Polyubiquitin Chains. Front Immunol 2021; 12:591706. [PMID: 33717069 PMCID: PMC7946993 DOI: 10.3389/fimmu.2021.591706] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/11/2021] [Indexed: 01/01/2023] Open
Abstract
Ankylosing spondylitis (AS) is a chronic inflammatory disease that mainly affects the spine. AS is highly associated with the expression of HLA-B27. Up to 95% AS patients are HLA-B27-positive. However, only 1%-2% of the HLA-B27-positive carriers suffer from AS, implying that other factors may also govern the development of AS. Long non-coding RNAs (lncRNAs) can regulate the immune response via their binding proteins. In the present study, we have identified that the levels of lncRNA, LOC645166, in T cells of AS patients were reduced. Overexpression of LOC645166 in Jurkat cells down-regulated the IL-23p19 expression and suppressed the JAK2/STAT3 signaling in response to stimulation by phorbol 12-myristate 13-acetate. Suppression of STAT3 activation by LOC645166 was also observed when Jurkat cells or T cells of AS patient were treated with anti-CD3/CD28 antibodies. In order to explore the role of LOC645166 in the pathogenesis of AS, RNA pull-down assay plus proteomic approach and western blotting were performed and identified that LOC645166 prefers binding the K63-linked polyubiquitin chains. LOC645166 can suppress recruitment of the IKK complex to K63-linked polyubiquitin chains and diminish IKK2 activation, leading to down-regulation of NF-κB activation. Down-regulation of LOC645166 expression in T cells of AS patients up-regulates NF-kB activation via decreasingly impeding recruitment of the IKK complex to K63-linked polyubiquitin chains, allowing AS patients to exhibit more sensitivity to stimulation by the proinflammatory cytokines or by TLR ligands.
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Affiliation(s)
- Hui-Chun Yu
- Department of Medical Research, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chiayi, Taiwan
| | - Kuang-Yung Huang
- Division of Allergy, Immunology and Rheumatology, Department of Medicine, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chiayi, Taiwan
- School of Medicine, Tzu Chi University, Hualien, Taiwan
| | - Ming-Chi Lu
- Department of Medical Research, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chiayi, Taiwan
- Division of Allergy, Immunology and Rheumatology, Department of Medicine, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chiayi, Taiwan
- School of Medicine, Tzu Chi University, Hualien, Taiwan
| | - Hsien-Yu Huang Tseng
- Department of Medical Research, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chiayi, Taiwan
| | - Su-Qin Liu
- Division of Allergy, Immunology and Rheumatology, Department of Medicine, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chiayi, Taiwan
| | - Ning-Sheng Lai
- Division of Allergy, Immunology and Rheumatology, Department of Medicine, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chiayi, Taiwan
- School of Medicine, Tzu Chi University, Hualien, Taiwan
| | - Hsien-Bin Huang
- Department of Biomedical Sciences, National Chung Cheng University, Chiayi, Taiwan
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25
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Stress Response of Mouse Embryonic Fibroblasts Exposed to Polystyrene Nanoplastics. Int J Mol Sci 2021; 22:ijms22042094. [PMID: 33672484 PMCID: PMC7923411 DOI: 10.3390/ijms22042094] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/17/2021] [Accepted: 02/19/2021] [Indexed: 12/21/2022] Open
Abstract
Polystyrene (PS) nanoplastic exposure has been shown to affect the viability of neuronal cells isolated from mouse embryonic brains. However, the viability of mouse embryonic fibroblasts (MEFs) was not affected although PS nanoplastics accumulated in the cytoplasm. It is currently unknown whether MEFs do not respond to PS nanoplastics or their cellular functions are altered without compromising viability. Here, we found that PS nanoplastics entered the cells via endocytosis and were then released into the cytoplasm, probably by endosomal escape, or otherwise remained in the endosome. Oxidative and inflammatory stress caused by intracellular PS nanoplastics induced the antioxidant response pathway and activated the autophagic pathway. However, colocalization of the autophagic marker LC3B and PS nanoplastics suggested that PS nanoplastics in the cytoplasm might interfere with normal autophagic function. Furthermore, autophagic flux could be impaired, probably due to accumulation of PS nanoplastic-containing lysosomes or autolysosomes. Intriguingly, the level of accumulated PS nanoplastics decreased during prolonged culture when MEFs were no longer exposed to PS nanoplastics. These results indicate that accumulated PS nanoplastics are removed or exported out of the cells. Therefore, PS nanoplastics in the cytoplasm affect cellular functions, but it is temporal and MEFs can overcome the stress caused by PS nanoplastic exposure.
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26
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Bae HR, Choi MS, Kim S, Young HA, Gershwin ME, Jeon SM, Kwon EY. IFNγ is a Key Link between Obesity and Th1-Mediated AutoImmune Diseases. Int J Mol Sci 2020; 22:ijms22010208. [PMID: 33379198 PMCID: PMC7794719 DOI: 10.3390/ijms22010208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/23/2020] [Accepted: 12/24/2020] [Indexed: 12/22/2022] Open
Abstract
Obesity, a characteristic of metabolic syndrome, is also associated with chronic inflammation and the development of autoimmune diseases. However, the relationship between obesity and autoimmune diseases remains to be investigated in depth. Here, we compared hepatic gene expression profiles among high-fat diet (HFD) mice using the primary biliary cholangitis (PBC) mouse model based on the chronic expression of interferon gamma (IFNγ) (ARE-Del-/- mice). The top differentially expressed genes affected by upstream transcriptional regulators IFNγ, LPS, and TNFα displayed an overlap in HFD and ARE-Del-/- mice, indicating that obesity-induced liver inflammation may be dependent on signaling via IFNγ. The top pathways altered in HFD mice were mostly involved in the innate immune responses, which overlapped with ARE-Del-/- mice. In contrast, T cell-mediated signaling pathways were exclusively altered in ARE-Del-/- mice. We further evaluated the therapeutic effect of luteolin, known as anti-inflammatory flavonoid, in HFD and ARE-Del-/- mice. Luteolin strongly suppressed the MHC I and II antigen presentation pathways, which were highly activated in both HFD and ARE-Del-/- mice. Conversely, luteolin increased metabolic processes of fatty acid oxidation and oxidative phosphorylation in the liver, which were suppressed in ARE-Del-/- mice. Luteolin also strongly induced PPAR signaling, which was downregulated in HFD and ARE-Del-/- mice. Using human GWAS data, we characterized the genetic interaction between significant obesity-related genes and IFNγ signaling and demonstrated that IFNγ is crucial for obesity-mediated inflammatory responses. Collectively, this study improves our mechanistic understanding of the relationship between obesity and autoimmune diseases. Furthermore, it provides new methodological insights into how immune network-based analyses effectively integrate RNA-seq and microarray data.
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Affiliation(s)
- Heekyong R. Bae
- Omixplus, LLC., Gaithersburg, MD 20885, USA; (H.R.B.); (S.K.)
- Laboratory of Cancer Immunometabolism, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21701, USA;
- Department of Food Science and Nutrition, Center for Food and Nutritional Genomics Research, Kyungpook National University, Daegu 41566, Korea;
| | - Myung-Sook Choi
- Department of Food Science and Nutrition, Center for Food and Nutritional Genomics Research, Kyungpook National University, Daegu 41566, Korea;
| | - Suntae Kim
- Omixplus, LLC., Gaithersburg, MD 20885, USA; (H.R.B.); (S.K.)
| | - Howard A. Young
- Laboratory of Cancer Immunometabolism, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21701, USA;
| | - M. Eric Gershwin
- Division of Rheumatology, Allergy and Clinical Immunology, University of California at Davis, Davis, CA 95616, USA;
| | - Seon-Min Jeon
- R&D Center, APtechnologies Corp., Gyeonggi-do, Hwaseong-si 18469, Korea
- Correspondence: (S.-M.J.); (E.-Y.K.); Tel.: +82-53-950-7936 (S.-M.J.); +82-53-950-6231 (E.-Y.K.)
| | - Eun-Young Kwon
- Department of Food Science and Nutrition, Center for Food and Nutritional Genomics Research, Kyungpook National University, Daegu 41566, Korea;
- Correspondence: (S.-M.J.); (E.-Y.K.); Tel.: +82-53-950-7936 (S.-M.J.); +82-53-950-6231 (E.-Y.K.)
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27
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Aravalli RN. Generating liver using blastocyst complementation: Opportunities and challenges. Xenotransplantation 2020; 28:e12668. [PMID: 33372360 DOI: 10.1111/xen.12668] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/05/2020] [Accepted: 11/26/2020] [Indexed: 12/28/2022]
Abstract
Orthotopic liver transplantation (OLT) is the only definitive treatment option for many patients with end-stage liver disease. Current supply of donor livers for OLT is not keeping up with the growing demand. To overcome this problem, a number of experimental strategies have been developed either to provide a bridge to transplant for patients on the waiting list or to bioengineer whole livers for OLT by replenishing them with fresh supplies of hepatic cells. In recent years, blastocyst complementation has emerged as the most promising approach for generating whole organs and, in combination with gene editing technology, it has revolutionized regenerative medicine. This methodology was successful in producing xenogeneic organs in animal hosts. Blastocyst complementation has the potential to produce whole livers in large animals that could be xenotransplanted in humans, thereby reducing the shortage of livers for OLT. However, significant experimental and ethical barriers remain for the production of human livers in domestic animals, such as the pig. This review summarizes the current knowledge and provides future perspectives for liver xenotransplantation in humans.
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Affiliation(s)
- Rajagopal N Aravalli
- Department of Electrical and Computer Engineering, College of Science and Engineering, University of Minnesota, Minneapolis, MN, USA
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28
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Jung BK, Han SW, Park SH, Bae JS, Choi J, Ryu KY. Neurotoxic potential of polystyrene nanoplastics in primary cells originating from mouse brain. Neurotoxicology 2020; 81:189-196. [PMID: 33132133 DOI: 10.1016/j.neuro.2020.10.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 09/04/2020] [Accepted: 10/12/2020] [Indexed: 12/22/2022]
Abstract
Polystyrene (PS) and chemically modified compounds in the PS family have long been used in commercial and industrial fields. However, it is poorly understood whether nanoscale-PS microplastic or PS nanoplastic exposure leads to perturbations in fundamental cellular functions, such as proliferation, differentiation, and apoptosis. Herein, we cultured three types of primary cells, including mouse embryonic fibroblasts (MEFs), mixed neuronal cells isolated from embryonic cortex, and cortical astrocytes, and investigated the effects of their exposure to PS nanoplastics with a 100 nm diameter. Although PS nanoplastic exposure did not affect the viability of MEFs or astrocytes, it significantly reduced the viability of mixed neuronal cells. Consistent with the observed effect on cellular viability, levels of the apoptosis marker, cleaved caspase-3, were elevated exclusively in mixed neuronal cells. To investigate whether cells uptake PS nanoplastics into the cytoplasm, we exposed MEFs and neurons to fluorescent PS latex beads and monitored fluorescence over time. We found that PS nanoplastics were deposited and accumulated in the cytoplasm in a concentration-dependent manner. Although astrocytes were not apoptotic upon exposure to PS nanoplastics, they underwent reactive astrocytosis, with increased levels of lipocalin-2 and proinflammatory cytokines. Therefore, our findings suggested that the vulnerability of cells to the deposition and accumulation of PS nanoplastics in the cytoplasm was dependent on cell type. Furthermore, based on our data from primary cells originating from mouse brains, we suggest that reactive astrocytosis may contribute to the neuronal apoptosis seen in defective neurons with PS nanoplastics accumulated in the cell body.
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Affiliation(s)
- Byung-Kwon Jung
- Department of Life Science, University of Seoul, Seoul 02504, South Korea
| | - Seung-Woo Han
- Department of Life Science, University of Seoul, Seoul 02504, South Korea
| | - So-Hyun Park
- Department of Life Science, University of Seoul, Seoul 02504, South Korea
| | - Jin-Sil Bae
- Department of Life Science, University of Seoul, Seoul 02504, South Korea
| | - Jinhee Choi
- School of Environmental Engineering, University of Seoul, Seoul 02504, South Korea
| | - Kwon-Yul Ryu
- Department of Life Science, University of Seoul, Seoul 02504, South Korea.
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29
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Park CW, Bae JS, Ryu KY. Simultaneous Disruption of Both Polyubiquitin Genes Affects Proteasome Function and Decreases Cellular Proliferation. Cell Biochem Biophys 2020; 78:321-329. [PMID: 32705536 DOI: 10.1007/s12013-020-00933-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 07/13/2020] [Indexed: 12/26/2022]
Abstract
The ubiquitin (Ub) proteasome system is important for maintaining protein homeostasis and has various roles in cell signaling, proliferation, and cell cycle regulation. In mammals, Ub is encoded by two monoubiquitin and two polyubiquitin genes. Although reduced levels of Ub due to the disruption of one polyubiquitin gene are known to decrease cell proliferation, the effect of disrupting both polyubiquitin genes remains elusive. Polyubiquitin gene Ubc knockout mice are embryonically lethal and polyubiquitin gene Ubb knockout mice are infertile. Thus, it is difficult to study the effects of double knockouts (DKOs). In the present study, the CRISPR/Cas9 system was used to simultaneously knockout both polyubiquitin genes, UBB and UBC, in HEK293T and HeLa cells. In DKO cells, growth decreased significantly compared to the control cells. We observed reduced proteasome function and reduced levels of free Ub in DKO cells. However, the levels of purified proteasome were not different between control and DKO cells, although the mRNA levels of proteasomal subunits were significantly increased in latter. We propose that the reduction of Ub levels, by disruption of both polyubiquitin genes, resulted in an altered proteasomal status, leading to the reduced proteasome activity, and decreased cellular proliferation.
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Affiliation(s)
- Chul-Woo Park
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea
| | - Jin-Sil Bae
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea
| | - Kwon-Yul Ryu
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea.
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30
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Park CW, Jung BK, Ryu KY. Disruption of the polyubiquitin gene Ubb reduces the self-renewal capacity of neural stem cells. Biochem Biophys Res Commun 2020; 527:372-378. [PMID: 32321641 DOI: 10.1016/j.bbrc.2020.04.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 04/10/2020] [Indexed: 02/08/2023]
Abstract
Ubiquitin (Ub) is a highly conserved eukaryotic protein that plays pivotal roles in cellular signal transduction, differentiation, and proteolysis. Although we have previously reported that disruption of the polyubiquitin gene Ubb is associated with the dysregulated differentiation of neural stem cells (NSCs) into neurons, it is unclear how gene expression patterns are altered in Ubb knockout (KO) NSCs, and whether this altered gene expression contributes to Ubb KO neural phenotypes. To answer these questions, we used RNA-Seq to compare the transcriptomes of Ubb KO NSCs and Ubb heterozygous (HT) controls. We found that the expression levels of most proliferation markers were decreased in Ubb KO NSCs. To determine whether the reduced levels of proliferation markers were due to reduced self-renewal of NSCs, such as radial glia, we measured the levels of the radial glia marker, Pax6, in mouse embryonic brains at 14.5 dpc. We found that Pax6 levels were decreased and the ventricular zone was thinner in the embryonic brains of Ubb KO mice compared to those of wild-type (WT) control mice. To determine whether the decreased self-renewal of Ubb KO NSCs was caused by cell-autonomous defects and not due to their microenvironment, we transplanted NSCs into WT mouse brains using a cannula system. In mouse brain sections, immunoreactivity of the NSC marker, nestin, was much lower in Ubb KO NSCs than in Ubb HT controls. Therefore, our data suggest that cell-autonomous defects, due to the disruption of Ubb, lead to a decrease in the self-renewal capacity of NSCs and may contribute to their dysregulated differentiation into neurons.
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Affiliation(s)
- Chul-Woo Park
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea
| | - Byung-Kwon Jung
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea
| | - Kwon-Yul Ryu
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea.
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31
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A negative feedback mechanism links UBC gene expression to ubiquitin levels by affecting RNA splicing rather than transcription. Sci Rep 2019; 9:18556. [PMID: 31811203 PMCID: PMC6898720 DOI: 10.1038/s41598-019-54973-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 11/20/2019] [Indexed: 12/16/2022] Open
Abstract
UBC gene plays a critical role in maintaining ubiquitin (Ub) homeostasis. It is upregulated under stress conditions, and herein we report that it is downregulated upon Ub overexpression. Downregulation occurs in a dose-dependent manner, suggesting the existence of a fine-tuned Ub sensing mechanism. This “sensor” requires a conjugation competent ubiquitin to detect Ub levels. Searching the sensor among the transcription factors involved in basal and stress-induced UBC gene expression was unsuccessful. Neither HSF1 and HSF2, nor Sp1 and YY1 are affected by the increased Ub levels. Moreover, mutagenesis of their binding sites in the UBC promoter-driven reporter constructs does not impair the downmodulation effect. Epigenetic studies show that H2A and H2B ubiquitination within the UBC promoter region is unchanged upon ubiquitin overexpression. Noteworthy, quantification of nascent RNA molecules excludes that the downmodulation arises in the transcription initiation step, rather pointing towards a post-transcriptional mechanism. Indeed, a significantly higher fraction of unspliced UBC mRNA is detected in ubiquitin overexpressing cells, compared to empty vector transfected cells. Our findings suggest how increasing cellular ubiquitin levels may control the expression of UBC gene by negatively affecting the splicing of its pre-mRNA, providing a straightforward feedback strategy for the homeostatic control of ubiquitin pools.
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32
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Yang Y, Zeng C, Lu X, Song Y, Nie J, Ran R, Zhang Z, He C, Zhang W, Liu SM. 5-Hydroxymethylcytosines in Circulating Cell-Free DNA Reveal Vascular Complications of Type 2 Diabetes. Clin Chem 2019; 65:1414-1425. [PMID: 31575611 DOI: 10.1373/clinchem.2019.305508] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 08/06/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Long-term complications of type 2 diabetes (T2D), such as macrovascular and microvascular events, are the major causes for T2D-related disability and mortality. A clinically convenient, noninvasive approach for monitoring the development of these complications would improve the overall life quality of patients with T2D and help reduce healthcare burden through preventive interventions. METHODS A selective chemical labeling strategy for 5-hydroxymethylcytosines (5hmC-Seal) was used to profile genome-wide 5hmCs, an emerging class of epigenetic markers implicated in complex diseases including diabetes, in circulating cell-free DNA (cfDNA) from a collection of Chinese patients (n = 62). Differentially modified 5hmC markers between patients with T2D with and without macrovascular/microvascular complications were analyzed under a case-control design. RESULTS Statistically significant changes in 5hmC markers were associated with T2D-related macrovascular/microvascular complications, involving genes and pathways relevant to vascular biology and diabetes, including insulin resistance and inflammation. A 16-gene 5hmC marker panel accurately distinguished patients with vascular complications from those without [testing set: area under the curve (AUC) = 0.85; 95% CI, 0.73-0.96], outperforming conventional clinical variables such as urinary albumin. In addition, a separate 13-gene 5hmC marker panel could distinguish patients with single complications from those with multiple complications (testing set: AUC = 0.84; 95% CI, 0.68-0.99), showing superiority over conventional clinical variables. CONCLUSIONS The 5hmC markers in cfDNA reflected the epigenetic changes in patients with T2D who developed macrovascular/microvascular complications. The 5hmC-Seal assay has the potential to be a clinically convenient, noninvasive approach that can be applied in the clinic to monitor the presence and severity of diabetic vascular complications.
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Affiliation(s)
- Ying Yang
- Department of Clinical Laboratory, Center for Gene Diagnosis, and Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Chang Zeng
- Driskill Graduate Program in Life Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL.,Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Xingyu Lu
- Shanghai Epican Genetech Co. Ltd., Shanghai, China
| | - Yanqun Song
- Shanghai Epican Genetech Co. Ltd., Shanghai, China
| | - Ji Nie
- Department of Chemistry, The University of Chicago, Chicago, IL
| | - Ruoxi Ran
- Department of Clinical Laboratory, Center for Gene Diagnosis, and Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhou Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL; .,Department of Biochemistry and Molecular Biology; Institute for Biophysical Dynamics; and The Howard Hughes Medical Institute, The University of Chicago, Chicago, IL
| | - Wei Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL;
| | - Song-Mei Liu
- Department of Clinical Laboratory, Center for Gene Diagnosis, and Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China;
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High-affinity free ubiquitin sensors for quantifying ubiquitin homeostasis and deubiquitination. Nat Methods 2019; 16:771-777. [PMID: 31308549 PMCID: PMC6669086 DOI: 10.1038/s41592-019-0469-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 05/21/2019] [Indexed: 02/07/2023]
Abstract
Ubiquitin (Ub) conjugation is an essential post-translational modification that affects nearly all proteins in eukaryotes. The functions and mechanisms of ubiquitination are areas of extensive study, and yet the dynamics and regulation of even free (i.e., unconjugated) Ub are poorly understood. A major impediment has been the lack of simple and robust techniques to quantify Ub levels in cells and to monitor Ub release from conjugates. Here we describe avidity-based fluorescent sensors that address this need. The sensors bind specifically to free Ub, have Kd values down to 60 pM, and, in concert with a newly developed workflow, allow us to distinguish and quantify the pools of free, protein-conjugated, and thioesterified forms of Ub from cell lysates. Alternatively, free Ub in fixed cells can be visualized microscopically by staining with a sensor. Real-time assays using the sensors afford unprecedented flexibility and precision to measure deubiquitination of virtually any (poly)Ub conjugate.
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Mi Z, Guo B, Yin Z, Li J, Zheng Z. Disease classification via gene network integrating modules and pathways. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190214. [PMID: 31417727 PMCID: PMC6689581 DOI: 10.1098/rsos.190214] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 06/04/2019] [Indexed: 06/10/2023]
Abstract
Disease classification based on gene information has been of significance as the foundation for achieving precision medicine. Previous works focus on classifying diseases according to the gene expression data of patient samples, and constructing disease network based on the overlap of disease genes, as many genes have been confirmed to be associated with diseases. In this work, the effects of diseases on human biological functions are assessed from the perspective of gene network modules and pathways, and the distances between diseases are defined to carry out the classification models. In total, 1728 diseases are divided into 12 and 14 categories by the intensity and scope of effects on pathways, respectively. Each category is a mix of several types of diseases identified based on congenital and acquired factors as well as diseased tissues and organs. The disease classification models on the basis of gene network are parallel with traditional pathology classification based on anatomic and clinical manifestations, and enable us to look at diseases in the viewpoint of commonalities in etiology and pathology. Our models provide a foundation for exploring combination therapy of diseases, which in turn may inform strategies for future gene-targeted therapy.
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Affiliation(s)
- Zhilong Mi
- Beijing Advanced Innovation Center for Big Data and Brain Computing, Beihang University, Beijing 100191, People’s Republic of China
- LMIB and School of Mathematics and Systems Science, Beihang University, Beijing 100191, People’s Republic of China
- Peng Cheng Laboratory, Shenzhen, Guangdong Province 518055, People’s Republic of China
| | - Binghui Guo
- Beijing Advanced Innovation Center for Big Data and Brain Computing, Beihang University, Beijing 100191, People’s Republic of China
- LMIB and School of Mathematics and Systems Science, Beihang University, Beijing 100191, People’s Republic of China
- Peng Cheng Laboratory, Shenzhen, Guangdong Province 518055, People’s Republic of China
| | - Ziqiao Yin
- Beijing Advanced Innovation Center for Big Data and Brain Computing, Beihang University, Beijing 100191, People’s Republic of China
- LMIB and School of Mathematics and Systems Science, Beihang University, Beijing 100191, People’s Republic of China
- Shenyuan Honors College, Beihang University, Beijing 100191, People’s Republic of China
- Peng Cheng Laboratory, Shenzhen, Guangdong Province 518055, People’s Republic of China
| | - Jiahui Li
- Beijing Advanced Innovation Center for Big Data and Brain Computing, Beihang University, Beijing 100191, People’s Republic of China
- LMIB and School of Mathematics and Systems Science, Beihang University, Beijing 100191, People’s Republic of China
- Peng Cheng Laboratory, Shenzhen, Guangdong Province 518055, People’s Republic of China
| | - Zhiming Zheng
- Beijing Advanced Innovation Center for Big Data and Brain Computing, Beihang University, Beijing 100191, People’s Republic of China
- LMIB and School of Mathematics and Systems Science, Beihang University, Beijing 100191, People’s Republic of China
- Peng Cheng Laboratory, Shenzhen, Guangdong Province 518055, People’s Republic of China
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Han SW, Jung BK, Park SH, Ryu KY. Reversible Regulation of Polyubiquitin Gene UBC via Modified Inducible CRISPR/Cas9 System. Int J Mol Sci 2019; 20:ijms20133168. [PMID: 31261719 PMCID: PMC6651705 DOI: 10.3390/ijms20133168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/20/2019] [Accepted: 06/27/2019] [Indexed: 12/13/2022] Open
Abstract
Ubiquitin is required under both normal and stress conditions. Under stress conditions, upregulation of the polyubiquitin gene UBC is essential to meet the requirement of increased ubiquitin levels to confer stress resistance. However, UBC upregulation is usually observed only under stress conditions and not under normal conditions. Therefore, it has not been possible to upregulate UBC under normal conditions to study the effect of excess ubiquitin on cellular machinery. Recently, the CRISPR/Cas9 system has been widely used in biological research as a useful tool to study gene disruption effects. In this study, using an inducible CRISPR/Cas9 variant, a dCas9-VP64 fusion protein, combined with a single guide RNA (sgRNA) containing MS2 aptamer loops and MS2-p65-HSF1, we developed a system to increase the ubiquitin pool via upregulation of UBC. Although it is challenging to upregulate the expression of a gene that is already expressed at high levels, the significance of our system is that UBC upregulation can be induced in an efficient, reversible manner that is compatible with cellular processes, even under normal conditions. This system can be used to study ubiquitin pool dynamics and it will be a useful tool in identifying the role of ubiquitin under normal and stress conditions.
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Affiliation(s)
- Seung-Woo Han
- Department of Life Science, University of Seoul, Seoul 02504, Korea
| | - Byung-Kwon Jung
- Department of Life Science, University of Seoul, Seoul 02504, Korea
| | - So-Hyun Park
- Department of Life Science, University of Seoul, Seoul 02504, Korea
| | - Kwon-Yul Ryu
- Department of Life Science, University of Seoul, Seoul 02504, Korea.
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Proteomics of exhaled breath condensate in stable COPD and non-COPD controls using tandem mass tags (TMTs) quantitative mass spectrometry: A pilot study. J Proteomics 2019; 206:103392. [PMID: 31129269 DOI: 10.1016/j.jprot.2019.103392] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 05/04/2019] [Accepted: 05/14/2019] [Indexed: 01/08/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) is a type of obstructive lung disease characterized by long-term breathing problems and poor airflow. Exhaled breath condensate (EBC) is now a safe and clinically significant measurement which has a huge potential to measure biomarkers in COPD. Previous studies profiled the pooled EBC samples from COPD or control participants due to technological limitations. In our study, 32 COPD patients and 28 control individuals were enrolled, and their EBC were collected. After matching with sex, age and smoking history, EBC samples of 19 COPD patients and 19 control individuals were analyzed using tandem mass tags (TMTs) quantitative mass spectrometry individually. A total of 257 proteins were identified. Compared with control group, 24 proteins (15 upregulated and 9 downregulated) were differentially expressed in COPD patients. The GO analysis of these differential proteins expressed mostly in the cytoplasm, and the KEGG analysis showed they had a predominant role in inflammatory response. And ACTB, UBC, TUBB and CCT2 involving in cell motility and cytoskeleton played important role in the interaction-net of these proteins. To sum up, we found some proteins might be novel biomarkers of EBC in COPD and TMTs was available to analyze proteomics in individual EBC samples. SIGNIFICANCE: It is still difficult to understand the mechanism of airway inflammation in COPD. Exhaled breath condensate(EBC) might be a great study object, but due to technological limitations, researchers preferred to use pooled EBC samples. This study analyzed individual EBC samples, which would deepen our understanding of the pathogenesis of COPD. And this method can be applied to individual EBC samples for further airway investigations of different purpose and different complexity.
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Lim D, Park CW, Ryu KY, Chung H. Disruption of the polyubiquitin gene Ubb causes retinal degeneration in mice. Biochem Biophys Res Commun 2019; 513:35-40. [DOI: 10.1016/j.bbrc.2019.03.164] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 03/25/2019] [Indexed: 12/31/2022]
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Vaden JH, Tian T, Golf S, McLean JW, Wilson JA, Wilson SM. Chronic over‐expression of ubiquitin impairs learning, reduces synaptic plasticity, and enhancesGRIAreceptor turnover in mice. J Neurochem 2018; 148:386-399. [DOI: 10.1111/jnc.14630] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 11/01/2018] [Accepted: 11/06/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Jada H. Vaden
- Department of Neurobiology Evelyn F. McKnight Brain Institute Civitan International Research Center University of Alabama at Birmingham Birmingham Alabama USA
| | - Tina Tian
- Department of Neurobiology Evelyn F. McKnight Brain Institute Civitan International Research Center University of Alabama at Birmingham Birmingham Alabama USA
| | - Samantha Golf
- Department of Neurobiology Evelyn F. McKnight Brain Institute Civitan International Research Center University of Alabama at Birmingham Birmingham Alabama USA
| | - John W. McLean
- Department of Neurobiology Evelyn F. McKnight Brain Institute Civitan International Research Center University of Alabama at Birmingham Birmingham Alabama USA
| | - Julie A. Wilson
- Department of Neurobiology Evelyn F. McKnight Brain Institute Civitan International Research Center University of Alabama at Birmingham Birmingham Alabama USA
| | - Scott M. Wilson
- Department of Neurobiology Evelyn F. McKnight Brain Institute Civitan International Research Center University of Alabama at Birmingham Birmingham Alabama USA
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Gomes SIL, Gonçalves MFM, Bicho RC, Roca CP, Soares AMVM, Scott-Fordsmand JJ, Amorim MJB. High-throughput gene expression in soil invertebrate embryos - Mechanisms of Cd toxicity in Enchytraeus crypticus. CHEMOSPHERE 2018; 212:87-94. [PMID: 30142569 DOI: 10.1016/j.chemosphere.2018.08.068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/13/2018] [Accepted: 08/14/2018] [Indexed: 05/21/2023]
Abstract
Gene expression can vary with the organisms' life stage. It is known that embryos can be more sensitive to toxicant exposure, as previously demonstrated for Enchytraeus crypticus (Oligochaeta) exposed to cadmium (Cd), known to cause embryotoxicity and hatching delay. It was shown that Ca enters embryos via the L-type Ca channels in the cocoon membrane, this being affected in Cd exposed embryos (Cd-Ca competition is well-known). In the present study, the embryotoxic mechanisms of Cd were studied via high-throughput gene expression for E. crypticus. Cocoons (1-2 days old), instead of the adult organism, were exposed in Cd spiked LUFA 2.2 soil during 1 day. Results showed that Cd affected Ca homeostasis which is implicated in several other molecular processes. Several of the major modulators of Cd toxicity (e.g., impaired gene expression, cell cycle arrest, DNA and mitochondrial damage) were identified in the embryos showing its relevancy as a model in ecotoxicogenomics. The draft Adverse Outcome Pathway was improved. Previously was hypothesized that gene regulation mechanisms were activated to synthesize more Ca channel proteins - this was confirmed here. Further, novel evidences were that, besides the extracellular competition, Cd competes intracellularly which causes a reduction in Ca efflux, and potentiates Cd embryotoxicity.
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Affiliation(s)
- Susana I L Gomes
- Department of Biology & CESAM, University of Aveiro, 3810-193, Aveiro, Portugal.
| | | | - Rita C Bicho
- Department of Biology & CESAM, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Carlos P Roca
- Department of Bioscience, Aarhus University, Vejlsovej 25, PO BOX 314, DK-8600, Silkeborg, Denmark
| | - Amadeu M V M Soares
- Department of Biology & CESAM, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Janeck J Scott-Fordsmand
- Department of Bioscience, Aarhus University, Vejlsovej 25, PO BOX 314, DK-8600, Silkeborg, Denmark
| | - Mónica J B Amorim
- Department of Biology & CESAM, University of Aveiro, 3810-193, Aveiro, Portugal.
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Narita Y, Tsutiya A, Nakano Y, Ashitomi M, Sato K, Hosono K, Kaneko T, Chen RD, Lee JR, Tseng YC, Hwang PP, Ohtani-Kaneko R. Androgen induced cellular proliferation, neurogenesis, and generation of GnRH3 neurons in the brain of mature female Mozambique tilapia. Sci Rep 2018; 8:16855. [PMID: 30442908 PMCID: PMC6237963 DOI: 10.1038/s41598-018-35303-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 11/05/2018] [Indexed: 01/24/2023] Open
Abstract
The neuroplastic mechanisms in the fish brain that underlie sex reversal remain unknown. Gonadotropin-releasing hormone 3 (GnRH3) neurons control male reproductive behaviours in Mozambique tilapia and show sexual dimorphism, with males having a greater number of GnRH3 neurons. Treatment with androgens such as 11-ketotestosterone (KT), but not 17β-estradiol, increases the number of GnRH3 neurons in mature females to a level similar to that observed in mature males. Compared with oestrogen, the effect of androgen on neurogenesis remains less clear. The present study examined the effects of 11-KT, a non-aromatizable androgen, on cellular proliferation, neurogenesis, generation of GnRH3 neurons and expression of cell cycle-related genes in mature females. The number of proliferating cell nuclear antigen-positive cells was increased by 11-KT. Simultaneous injection of bromodeoxyuridine and 11-KT significantly increased the number of newly-generated (newly-proliferated) neurons, but did not affect radial glial cells, and also resulted in newly-generated GnRH3 neurons. Transcriptome analysis showed that 11-KT modulates the expression of genes related to the cell cycle process. These findings suggest that tilapia could serve as a good animal model to elucidate the effects of androgen on adult neurogenesis and the mechanisms for sex reversal in the fish brain.
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Affiliation(s)
- Yasuto Narita
- Department of Life Sciences, Toyo University, 1-1-1 Itakura, Oura, Gunma, 374-0193, Japan
| | - Atsuhiro Tsutiya
- Department of Life Sciences, Toyo University, 1-1-1 Itakura, Oura, Gunma, 374-0193, Japan
| | - Yui Nakano
- Department of Life Sciences, Toyo University, 1-1-1 Itakura, Oura, Gunma, 374-0193, Japan
| | - Moe Ashitomi
- Department of Life Sciences, Toyo University, 1-1-1 Itakura, Oura, Gunma, 374-0193, Japan
| | - Kenjiro Sato
- Department of Life Sciences, Toyo University, 1-1-1 Itakura, Oura, Gunma, 374-0193, Japan
| | - Kohei Hosono
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Toyoji Kaneko
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Ruo-Dong Chen
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei City, Taiwan, Republic of China
| | - Jay-Ron Lee
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei City, Taiwan, Republic of China
| | - Yung-Che Tseng
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei City, Taiwan, Republic of China
| | - Pung-Pung Hwang
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei City, Taiwan, Republic of China
| | - Ritsuko Ohtani-Kaneko
- Department of Life Sciences, Toyo University, 1-1-1 Itakura, Oura, Gunma, 374-0193, Japan.
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Szebeni GJ, Balog JA, Demjén A, Alföldi R, Végi VL, Fehér LZ, Mán I, Kotogány E, Gubán B, Batár P, Hackler L, Kanizsai I, Puskás LG. Imidazo[1,2- b]pyrazole-7-carboxamides Induce Apoptosis in Human Leukemia Cells at Nanomolar Concentrations. Molecules 2018; 23:E2845. [PMID: 30388846 PMCID: PMC6278434 DOI: 10.3390/molecules23112845] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 10/25/2018] [Accepted: 10/29/2018] [Indexed: 01/14/2023] Open
Abstract
Leukemia, the malignancy of the hematopoietic system accounts for 10% of cancer cases with poor overall survival rate in adults; therefore, there is a high unmet medical need for the development of novel therapeutics. Eight imidazo[1,2-b]pyrazole-7-carboxamides have been tested for cytotoxic activity against five leukemia cell lines: Acute promyelocytic leukemia (HL-60), acute monocytic leukemia (THP-1), acute T-lymphoblastic leukemia (MOLT-4), biphenotypic B myelomonocytic leukemia (MV-4-11), and erythroleukemia (K-562) cells in vitro. Imidazo[1,2-b]pyrazole-7-carboxamides hampered the viability of all five leukemia cell lines with different potential. Optimization through structure activity relationship resulted in the following IC50 values for the most effective lead compound DU385: 16.54 nM, 27.24 nM, and 32.25 nM on HL-60, MOLT-4, MV-4-11 cells, respectively. Human primary fibroblasts were much less sensitive in the applied concentration range. Both monolayer or spheroid cultures of murine 4T1 and human MCF7 breast cancer cells were less sensitive to treatment with 1.5⁻10.8 μM IC50 values. Flow cytometry confirmed the absence of necrosis and revealed 60% late apoptotic population for MV-4-11, and 50% early apoptotic population for HL-60. MOLT-4 cells showed only about 30% of total apoptotic population. Toxicogenomic study of DU385 on the most sensitive MV-4-11 cells revealed altered expression of sixteen genes as early (6 h), midterm (12 h), and late response (24 h) genes upon treatment. Changes in ALOX5AP, TXN, and SOD1 expression suggested that DU385 causes oxidative stress, which was confirmed by depletion of cellular glutathione and mitochondrial membrane depolarization induction. Imidazo[1,2-b]pyrazole-7-carboxamides reported herein induced apoptosis in human leukemia cells at nanomolar concentrations.
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Affiliation(s)
- Gábor J Szebeni
- Laboratory of Functional Genomics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary.
- Department of Physiology, Anatomy and Neuroscience, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.
| | - József A Balog
- Laboratory of Functional Genomics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary.
| | - András Demjén
- Avidin Ltd., Alsó kikötő sor 11/D, H-6726 Szeged, Hungary.
| | - Róbert Alföldi
- Avidin Ltd., Alsó kikötő sor 11/D, H-6726 Szeged, Hungary.
| | - Vanessza L Végi
- Laboratory of Functional Genomics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary.
- Avidin Ltd., Alsó kikötő sor 11/D, H-6726 Szeged, Hungary.
| | | | - Imola Mán
- Avidin Ltd., Alsó kikötő sor 11/D, H-6726 Szeged, Hungary.
| | - Edit Kotogány
- Laboratory of Functional Genomics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary.
| | - Barbara Gubán
- Department of Dermatology and Allergology, University of Szeged, Korányi fasor 6, H-6720 Szeged, Hungary.
| | - Péter Batár
- Department of Hematology, Institute of Internal Medicine, University of Debrecen, Nagyerdei Körút 98, 4032 Debrecen, Hungary.
| | - László Hackler
- Avidin Ltd., Alsó kikötő sor 11/D, H-6726 Szeged, Hungary.
| | - Iván Kanizsai
- Avidin Ltd., Alsó kikötő sor 11/D, H-6726 Szeged, Hungary.
| | - László G Puskás
- Laboratory of Functional Genomics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary.
- Avidin Ltd., Alsó kikötő sor 11/D, H-6726 Szeged, Hungary.
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Kang SD, Chatterjee S, Alam S, Salzberg AC, Milici J, van der Burg SH, Meyers C. Effect of Productive Human Papillomavirus 16 Infection on Global Gene Expression in Cervical Epithelium. J Virol 2018; 92:e01261-18. [PMID: 30045992 PMCID: PMC6158420 DOI: 10.1128/jvi.01261-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 07/20/2018] [Indexed: 12/29/2022] Open
Abstract
Human papillomavirus (HPV) infection is the world's most common sexually transmitted infection and is responsible for most cases of cervical cancer. Previous studies of global gene expression changes induced by HPV infection have focused on the cancerous stages of infection, and therefore, not much is known about global gene expression changes at early preneoplastic stages of infection. We show for the first time the global gene expression changes during early-stage HPV16 infection in cervical tissue using 3-dimensional organotypic raft cultures, which produce high levels of progeny virions. cDNA microarray analysis showed that a total of 594 genes were upregulated and 651 genes were downregulated at least 1.5-fold with HPV16 infection. Gene ontology analysis showed that biological processes including cell cycle progression and DNA metabolism were upregulated, while skin development, immune response, and cell death were downregulated with HPV16 infection in cervical keratinocytes. Individual genes were selected for validation at the transcriptional and translational levels, including UBC, which was central to the protein association network of immune response genes, and top downregulated genes RPTN, SERPINB4, KRT23, and KLK8 In particular, KLK8 and SERPINB4 were shown to be upregulated in cancer, which contrasts with the gene regulation during the productive replication stage. Organotypic raft cultures, which allow full progression of the HPV life cycle, allowed us to identify novel gene modulations and potential therapeutic targets of early-stage HPV infection in cervical tissue. Additionally, our results suggest that early-stage productive infection and cancerous stages of infection are distinct disease states expressing different host transcriptomes.IMPORTANCE Persistent HPV infection is responsible for most cases of cervical cancer. The transition from precancerous to cancerous stages of HPV infection is marked by a significant reduction in virus production. Most global gene expression studies of HPV infection have focused on the cancerous stages. Therefore, little is known about global gene expression changes at precancerous stages. For the first time, we measured global gene expression changes at the precancerous stages of HPV16 infection in human cervical tissue producing high levels of virus. We identified a group of genes that are typically overexpressed in cancerous stages to be significantly downregulated at the precancerous stage. Moreover, we identified significantly modulated genes that have not yet been studied in the context of HPV infection. Studying the role of these genes in HPV infection will help us understand what drives the transition from precancerous to cancerous stages and may lead to the development of new therapeutic targets.
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Affiliation(s)
- Sa Do Kang
- Department of Microbiology and Immunology, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Sreejata Chatterjee
- Department of Microbiology and Immunology, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Samina Alam
- Department of Microbiology and Immunology, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Anna C Salzberg
- Bioinformatics Core, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Janice Milici
- Department of Microbiology and Immunology, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Sjoerd H van der Burg
- Department of Medical Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Craig Meyers
- Department of Microbiology and Immunology, Penn State College of Medicine, Hershey, Pennsylvania, USA
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Solcia E, Necchi V, Sommi P, Ricci V. Proteasome-Rich PaCS as an Oncofetal UPS Structure Handling Cytosolic Polyubiquitinated Proteins. In Vivo Occurrence, in Vitro Induction, and Biological Role. Int J Mol Sci 2018; 19:ijms19092767. [PMID: 30223470 PMCID: PMC6164709 DOI: 10.3390/ijms19092767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 09/11/2018] [Indexed: 11/16/2022] Open
Abstract
In this article, we outline and discuss available information on the cellular site and mechanism of proteasome interaction with cytosolic polyubiquitinated proteins and heat-shock molecules. The particulate cytoplasmic structure (PaCS) formed by barrel-like particles, closely reproducing in vivo the high-resolution structure of 26S proteasome as isolated in vitro, has been detected in a variety of fetal and neoplastic cells, from living tissue or cultured cell lines. Specific trophic factors and interleukins were found to induce PaCS during in vitro differentiation of dendritic, natural killer (NK), or megakaryoblastic cells, apparently through activation of the MAPK-ERK pathway. Direct interaction of CagA bacterial oncoprotein with proteasome was shown inside the PaCSs of a Helicobacter pylori-infected gastric epithelium, a finding suggesting a role for PaCS in CagA-mediated gastric carcinogenesis. PaCS dissolution and autophagy were seen after withdrawal of inducing factors. PaCS-filled cell blebs and ectosomes were found in some cells and may represent a potential intercellular discharge and transport system of polyubiquitinated antigenic proteins. PaCS differs substantially from the inclusion bodies, sequestosomes, and aggresomes reported in proteinopathies like Huntington or Parkinson diseases, which usually lack PaCS. The latter seems more linked to conditions of increased cell proliferation/differentiation, implying an increased functional demand to the ubiquitin–proteasome system.
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Affiliation(s)
- Enrico Solcia
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy.
- Pathologic Anatomy Unit, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy.
| | - Vittorio Necchi
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy.
- Centro Grandi Strumenti, University of Pavia, 27100 Pavia, Italy.
| | - Patrizia Sommi
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy.
| | - Vittorio Ricci
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy.
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Bianchi M, Crinelli R, Arbore V, Magnani M. Induction of ubiquitin C ( UBC) gene transcription is mediated by HSF1: role of proteotoxic and oxidative stress. FEBS Open Bio 2018; 8:1471-1485. [PMID: 30186748 PMCID: PMC6120222 DOI: 10.1002/2211-5463.12484] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 05/16/2018] [Accepted: 06/26/2018] [Indexed: 12/14/2022] Open
Abstract
The polyubiquitin gene ubiquitin C (UBC) is considered a stress protective gene and is upregulated under various stressful conditions, which is probably a consequence of an increased demand for ubiquitin in order to remove toxic misfolded proteins. We previously identified heat shock elements (HSEs) within the UBC promoter, which are responsible for heat shock factor (HSF)1‐driven induction of the UBC gene and are activated by proteotoxic stress. Here, we determined the molecular players driving the UBC gene transcriptional response to arsenite treatment, mainly addressing the role of the nuclear factor‐erythroid 2‐related factor 2 (Nrf2)‐mediated antioxidant pathway. Exposure of HeLa cells to arsenite caused a time‐dependent increase of UBCmRNA, while cell viability and proteasome activity were not affected. Nuclear accumulation of HSF1 and Nrf2 transcription factors was detected upon both arsenite and MG132 treatment, while HSF2 nuclear levels increased in MG132‐treated cells. Notably, siRNA‐mediated knockdown of Nrf2 did not reduce UBC transcription under either basal or stressful conditions, but significantly impaired the constitutive and inducible expression of well‐known antioxidant response element‐dependent genes. A chromatin immunoprecipitation assay consistently failed to detect Nrf2 binding to the UBC promoter sequence. By contrast, depletion of HSF1, but not HSF2, significantly compromised stress‐induced UBC expression. Critically, HSF1‐mediated UBC trans‐activation upon arsenite exposure relies on transcription factor binding to previously mapped distal HSEs, as demonstrated to occur under proteasome inhibition. These data highlight HSF1 as the pivotal transcription factor that translates different stress signals into UBC gene transcriptional induction.
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Affiliation(s)
- Marzia Bianchi
- Department of Biomolecular Sciences, Biochemistry and Molecular Biology Section University of Urbino 'Carlo Bo' Italy
| | - Rita Crinelli
- Department of Biomolecular Sciences, Biochemistry and Molecular Biology Section University of Urbino 'Carlo Bo' Italy
| | - Vanessa Arbore
- Department of Biomolecular Sciences, Biochemistry and Molecular Biology Section University of Urbino 'Carlo Bo' Italy
| | - Mauro Magnani
- Department of Biomolecular Sciences, Biochemistry and Molecular Biology Section University of Urbino 'Carlo Bo' Italy
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Chen Q, Li Y, Wang J, Li R, Chen B. cpubi4 Is Essential for Development and Virulence in Chestnut Blight Fungus. Front Microbiol 2018; 9:1286. [PMID: 29963030 PMCID: PMC6013588 DOI: 10.3389/fmicb.2018.01286] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/25/2018] [Indexed: 12/03/2022] Open
Abstract
Ubiquitination plays key roles in eukaryotic growth, stress adaptation, and metabolic regulation. In our previous work, ubiquitin was found to be secreted in the hypovirus-infected strain of Cryphonectria parasitica, a phytopathogenic filamentous fungus responsible for the chestnut blight. Here we report the functional and molecular characterization of a polyubiquitin gene, cpubi4, in C. parasitica. The expression of cpubi4 was upregulated by the infection of a hypovirus. Deletion of cpubi4 resulted in abnormal morphology, reduced sporulation, attenuation of virulence, and significant reduction in ubiquitination. A total of 378 sites in 236 proteins were identified to be significantly decreased in ubiquitination in the absence of cpubi4. Quantitative proteome analysis revealed that 285 in 4,776 identified proteins changed in abundance (1.5-fold, P < 0.05) in the cpubi4 null mutant, as compared with the wild-type strain.
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Affiliation(s)
- Qi Chen
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Nanning, China.,College of Life Science and Technology, Guangxi University, Nanning, China
| | - Yongbing Li
- College of Life Science and Technology, Guangxi University, Nanning, China
| | - Jinzi Wang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Nanning, China.,College of Life Science and Technology, Guangxi University, Nanning, China
| | - Ru Li
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Nanning, China.,College of Life Science and Technology, Guangxi University, Nanning, China
| | - Baoshan Chen
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Nanning, China.,College of Life Science and Technology, Guangxi University, Nanning, China
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Chatterjee S, Chaubal R, Maitra A, Gardi N, Dutt A, Gupta S, Badwe RA, Majumder PP, Pandey P. Pre-operative progesterone benefits operable breast cancer patients by modulating surgical stress. Breast Cancer Res Treat 2018; 170:431-438. [PMID: 29564740 DOI: 10.1007/s10549-018-4749-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/08/2018] [Indexed: 02/08/2023]
Abstract
PURPOSE We have reported a survival benefit of single injection of hydroxyprogesterone prior to surgery for primary tumour in patients with node-positive operable breast cancer. Hydroxyprogesterone was meant to recapitulate the luteal phase of menstrual cycle in these women. We wanted to understand the molecular basis of action of hydroxyprogesterone on primary breast tumours in a peri-operative setting. METHODS We performed whole transcriptome sequencing (RNA-Seq) of primary breast tumour samples collected from patients before and after hydroxyprogesterone exposure and controls. Paired breast cancer samples were obtained from patients who were given hydroxyprogesterone before surgery and a group of patients who were subjected to only surgery. RESULTS A test of significance between the two groups revealed 207 significantly altered genes, after correction for multiple hypothesis testing. We found significantly contrasting gene expression patterns in exposed versus unexposed groups; 142 genes were up-regulated post-surgery among exposed patients, and down-regulated post-surgery among unexposed patients. Significantly enriched pathways included genes that respond to progesterone, cellular stress, nonsense-mediated decay of proteins and negative regulation of inflammatory response. These results suggest that cellular stress is modulated by hydroxyprogesterone. Network analysis revealed that UBC, a mediator of stress response, to be a major node to which many of the significantly altered genes connect. CONCLUSIONS Our study suggests that pre-operative exposure to progesterone favourably modulates the effect of surgical stress, and this might underlie its beneficial effect when administered prior to surgery.
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Affiliation(s)
- Shatakshee Chatterjee
- National Institute of Biomedical Genomics, P.O.: N.S.S., Kalyani, 741251, West Bengal, India
| | - Rohan Chaubal
- Tata Memorial Centre/Hospital, Parel, Mumbai, 400012, India
| | - Arindam Maitra
- National Institute of Biomedical Genomics, P.O.: N.S.S., Kalyani, 741251, West Bengal, India
| | - Nilesh Gardi
- Tata Memorial Centre/Hospital, Parel, Mumbai, 400012, India
| | - Amit Dutt
- Tata Memorial Centre/Hospital, Parel, Mumbai, 400012, India
| | - Sudeep Gupta
- Tata Memorial Centre/Hospital, Parel, Mumbai, 400012, India.
- Department of Medical Oncology, Tata Memorial Centre, Mumbai, 400012, India.
| | - Rajendra A Badwe
- Tata Memorial Centre/Hospital, Parel, Mumbai, 400012, India.
- Department of Surgical Oncology, Tata Memorial Centre, Mumbai, 400012, India.
| | - Partha P Majumder
- National Institute of Biomedical Genomics, P.O.: N.S.S., Kalyani, 741251, West Bengal, India.
| | - Priyanka Pandey
- National Institute of Biomedical Genomics, P.O.: N.S.S., Kalyani, 741251, West Bengal, India.
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Wu S, Liu Y, Guo W, Cheng X, Ren X, Chen S, Li X, Duan Y, Sun Q, Yang X. Identification and characterization of long noncoding RNAs and mRNAs expression profiles related to postnatal liver maturation of breeder roosters using Ribo-zero RNA sequencing. BMC Genomics 2018; 19:498. [PMID: 29945552 PMCID: PMC6020324 DOI: 10.1186/s12864-018-4891-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 06/19/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The liver is mainly hematopoietic in the embryo, and converts into a major metabolic organ in the adult. Therefore, it is intensively remodeled after birth to adapt and perform adult functions. Long non-coding RNAs (lncRNAs) are involved in organ development and cell differentiation, likely they have potential roles in regulating postnatal liver development. Herein, in order to understand the roles of lncRNAs in postnatal liver maturation, we analyzed the lncRNAs and mRNAs expression profiles in immature and mature livers from one-day-old and adult (40 weeks of age) breeder roosters by Ribo-Zero RNA-Sequencing. RESULTS Around 21,939 protein-coding genes and 2220 predicted lncRNAs were expressed in livers of breeder roosters. Compared to protein-coding genes, the identified chicken lncRNAs shared fewer exons, shorter transcript length, and significantly lower expression levels. Notably, in comparison between the livers of newborn and adult breeder roosters, a total of 1570 mRNAs and 214 lncRNAs were differentially expressed with the criteria of log2fold change > 1 or < - 1 and P values < 0.05, which were validated by qPCR using randomly selected five mRNAs and five lncRNAs. Further GO and KEGG analyses have revealed that the differentially expressed mRNAs were involved in the hepatic metabolic and immune functional changes, as well as some biological processes and pathways including cell proliferation, apoptotic and cell cycle that are implicated in the development of liver. We also investigated the cis- and trans- regulatory effects of differentially expressed lncRNAs on its target genes. GO and KEGG analyses indicated that these lncRNAs had their neighbor protein coding genes and trans-regulated genes associated with adapting of adult hepatic functions, as well as some pathways involved in liver development, such as cell cycle pathway, Notch signaling pathway, Hedgehog signaling pathway, and Wnt signaling pathway. CONCLUSIONS This study provides a catalog of mRNAs and lncRNAs related to postnatal liver maturation of chicken, and will contribute to a fuller understanding of biological processes or signaling pathways involved in significant functional transition during postnatal liver development that differentially expressed genes and lncRNAs could take part in.
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Affiliation(s)
- Shengru Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Yanli Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Wei Guo
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Xi Cheng
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Xiaochun Ren
- Dazhou Institute of Agricultural Sciences, Dazhou, 635000 Sichuan China
| | - Si Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Xueyuan Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Yongle Duan
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Qingzhu Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Xiaojun Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
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48
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Construction of the network of critical paths on Blood-stasis syndrome of hypertension based on mRNA sequencing. Eur J Integr Med 2018. [DOI: 10.1016/j.eujim.2018.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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49
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McHugh A, Fernandes K, South AP, Mellerio JE, Salas-Alanís JC, Proby CM, Leigh IM, Saville MK. Preclinical comparison of proteasome and ubiquitin E1 enzyme inhibitors in cutaneous squamous cell carcinoma: the identification of mechanisms of differential sensitivity. Oncotarget 2018; 9:20265-20281. [PMID: 29755650 PMCID: PMC5945540 DOI: 10.18632/oncotarget.24750] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 03/02/2018] [Indexed: 11/25/2022] Open
Abstract
Proteasome inhibitors have distinct properties and the biochemical consequences of suppressing ubiquitin E1 enzymes and the proteasome differ. We compared the effects of the proteasome inhibitors bortezomib, ixazomib and carfilzomib and the ubiquitin E1 enzyme inhibitor MLN7243/TAK-243 on cell viability and cell death in normal keratinocytes and cutaneous squamous cell carcinoma (cSCC) cell lines. The effects of both a pulse of treatment and more extended incubation were investigated. This is relevant to directly-delivered therapy (topical treatment/intratumoral injection) where the time of exposure can be controlled and a short exposure may better reflect systemically-delivered inhibitor pharmacokinetics. These agents can selectively kill cSCC cells but there are variations in the pattern of cSCC cell line sensitivity/resistance. Variations in the responses to proteasome inhibitors are associated with differences in the specificity of the inhibitors for the three proteolytic activities of the proteasome. There is greater selectivity for killing cSCC cells compared to normal keratinocytes with a pulse of proteasome inhibitor treatment than with a more extended exposure. We provide evidence that c-MYC-dependent NOXA upregulation confers susceptibility to a short incubation with proteasome inhibitors by priming cSCC cells for rapid BAK-dependent death. We observed that bortezomib-resistant cSCC cells can be sensitive to MLN7243-induced death. Low expression of the ubiquitin E1 UBA1/UBE1 participates in conferring susceptibility to MLN7243 by increasing sensitivity to MLN7243-mediated attenuation of ubiquitination. This study supports further investigation of the potential of proteasome and ubiquitin E1 inhibition for cSCC therapy. Direct delivery of inhibitors could facilitate adequate exposure of skin cancers.
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Affiliation(s)
- Angela McHugh
- Division of Cancer Research, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - Kenneth Fernandes
- Division of Cancer Research, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - Andrew P South
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Jemima E Mellerio
- St. John's Institute of Dermatology, King's College London, Guy's Campus, London, SE1 7EH, UK
| | - Julio C Salas-Alanís
- DEBRA Mexico, Azteca Guadalupe, Nuevo Leon, 67150 Mexico.,Hospital Regional "Lic. Adolfo Lopez Mateos", Colonia Florida, Del Alvaro Obregon, 01030 Ciudad de Mexico
| | - Charlotte M Proby
- Division of Cancer Research, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - Irene M Leigh
- Division of Cancer Research, School of Medicine, University of Dundee, Dundee DD1 9SY, UK.,Centre for Cutaneous Research, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Mark K Saville
- Division of Cancer Research, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
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50
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Cytoprotective role of ubiquitin against toxicity induced by polyglutamine-expanded aggregates. Biochem Biophys Res Commun 2018; 500:344-350. [PMID: 29654755 DOI: 10.1016/j.bbrc.2018.04.072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 04/10/2018] [Indexed: 11/21/2022]
Abstract
Ubiquitin (Ub) homeostasis is important for cellular function and survival, especially under stress conditions. Recently, we have demonstrated that Ubc-/- (Ub-deficient) mouse embryonic fibroblasts (MEFs) exhibited reduced viability under oxidative stress induced by arsenite, which was not due to dysregulation of the antioxidant response pathway, but rather due to the potential toxicity caused by the misfolded protein aggregates. However, it is still not clear whether Ub deficiency is directly related to the accumulation of toxic protein aggregates, as arsenite itself triggers protein aggregation and renders cells into aberrant conditions such as reduced proteasome function and inhibition of autophagic flux. Therefore, under arsenite treatment, the outcome could be derived from the combination of multiple defective pathways. Furthermore, it has also been suggested that ubiquitination status of misfolded proteins may not be important for the formation of inclusion bodies composed of misfolded protein aggregates. We therefore wondered whether Ub deficiency is sufficient to trigger the accumulation of toxic protein aggregates inside the cells. In this study, we ectopically expressed polyQ-expanded aggregates (Q103) in MEFs and observed inclusion body formation at the juxtanuclear region, which was independent of cellular Ub levels. In contrast to arsenite treatment, polyQ expression did not affect proteasome function. However, we observed an increased accumulation of Q103 aggregates in Ubc-/- MEFs, which was due to impaired autophagic clearance. Finally, we demonstrated that the increased accumulation of Q103 aggregates under Ub deficiency dramatically reduced the viability of cells. Therefore, our results suggest that the maintenance of proper levels of cellular Ub is important to protect cells against the toxicity induced by the accumulation of protein aggregates.
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