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Cui G, Li Y, Zheng L, Smith C, Bevan MW, Li Y. The peptidase DA1 cleaves and destabilizes WUSCHEL to control shoot apical meristem size. Nat Commun 2024; 15:4627. [PMID: 38821962 PMCID: PMC11143343 DOI: 10.1038/s41467-024-48361-7] [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: 02/20/2023] [Accepted: 04/29/2024] [Indexed: 06/02/2024] Open
Abstract
Stem cells in plants and animals are the source of new tissues and organs. In plants, stem cells are maintained in the central zone (CZ) of multicellular meristems, and large shoot meristems with an increased stem cell population hold promise for enhancing yield. The mobile homeodomain transcription factor WUSCHEL (WUS) is a central regulator of stem cell function in plant shoot meristems. Despite its central importance, the factors that directly modulate WUS protein stability have been a long-standing question. Here, we show that the peptidase DA1 physically interacts with and cleaves the WUS protein, leading to its destabilization. Furthermore, our results reveal that cytokinin signaling represses the level of DA1 protein in the shoot apical meristem, thereby increasing the accumulation of WUS protein. Consistent with these observations, loss of DA1 function results in larger shoot apical meristems with an increased stem cell population and also influences cytokinin-induced enlargement of shoot apical meristem. Collectively, our findings uncover a previously unrecognized mechanism by which the repression of DA1 by cytokinin signaling stabilizes WUS, resulting in the enlarged shoot apical meristems with the increased stem cell number during plant growth and development.
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Affiliation(s)
- Guicai Cui
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agriculture, University of Chinese Academy of Sciences, Beijing, China
| | - Yu Li
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Leiying Zheng
- College of Advanced Agriculture, University of Chinese Academy of Sciences, Beijing, China.
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
| | | | | | - Yunhai Li
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agriculture, University of Chinese Academy of Sciences, Beijing, China.
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2
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Jin S, Xu M, Gao X, Jiang S, Xiong Y, Zhang W, Qiao H, Wu Y, Fu H. Effects of Alkalinity Exposure on Antioxidant Status, Metabolic Function, and Immune Response in the Hepatopancreas of Macrobrachium nipponense. Antioxidants (Basel) 2024; 13:129. [PMID: 38275654 PMCID: PMC10812643 DOI: 10.3390/antiox13010129] [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: 12/13/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
The oriental river prawn Macrobrachium nipponense is an important freshwater economic species in China, producing huge economic benefits. However, M. nipponense shows lower alkali tolerance than fish species, thus genetic selection is urgently needed in order to improve alkali tolerance in this species. In the present study, the effects of alkalinity exposure on the hepatopancreas of M. nipponense were measured under the alkali concentrations of 0 (control), 4, 8, and 12 mmol/L with the exposure time of 96 h through histological observations, measurement of antioxidant enzymes, metabolic profiling analysis, and transcriptome profiling analysis. The present study identified that the low concentration of alkali treatment (<4 mmol/L) did not result in morphological changes in the hepatopancreas and activity changes in antioxidant enzymes, while high-alkali treatment (>8 mmol/L) damaged the normal structures of the lumen and vacuoles and significantly stimulated the levels of superoxide dismutase, catalase, and total antioxidant capacity, indicating these antioxidant enzymes play essential roles in the protection of the body from the damage caused by the alkali treatment. Metabolic profiling analysis revealed that the main enriched metabolic pathways of differentially expressed metabolites in the present study were consistent with the metabolic pathways caused by environmental stress in plants and other aquatic animals. Transcriptome profiling analysis revealed that the alkali concentration of <8 mmol/L did not lead to significant changes in gene expression. The main enriched metabolic pathways were selected from the comparison between 0 mmol/L vs. 12 mmol/L, and some significantly up-regulated genes were selected from these metabolic pathways, predicting these selected metabolic pathways and genes are involved in the adaptation to alkali treatment in M. nipponense. The expressions of Ras-like GTP-binding protein, Doublesex and mab-3 related transcription factor 1a, and Hypothetical protein JAY84 are sensitive to changes in alkali concentrations, suggesting these three genes participated in the process of alkali adaptation in M. nipponense. The present study identified the effects of alkalinity exposure on the hepatopancreas of M. nipponense, including the changes in antioxidant status and the expressions of metabolites and genes, contributing to further studies of alkali tolerance in this species.
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Affiliation(s)
- Shubo Jin
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (S.J.); (S.J.); (Y.X.); (W.Z.); (H.Q.); (Y.W.)
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; (M.X.); (X.G.)
| | - Mingjia Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; (M.X.); (X.G.)
| | - Xuanbin Gao
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; (M.X.); (X.G.)
| | - Sufei Jiang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (S.J.); (S.J.); (Y.X.); (W.Z.); (H.Q.); (Y.W.)
| | - Yiwei Xiong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (S.J.); (S.J.); (Y.X.); (W.Z.); (H.Q.); (Y.W.)
| | - Wenyi Zhang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (S.J.); (S.J.); (Y.X.); (W.Z.); (H.Q.); (Y.W.)
| | - Hui Qiao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (S.J.); (S.J.); (Y.X.); (W.Z.); (H.Q.); (Y.W.)
| | - Yan Wu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (S.J.); (S.J.); (Y.X.); (W.Z.); (H.Q.); (Y.W.)
| | - Hongtuo Fu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (S.J.); (S.J.); (Y.X.); (W.Z.); (H.Q.); (Y.W.)
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; (M.X.); (X.G.)
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3
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Burov AV, Rodin AA, Karpov VL, Morozov AV. The Role of Ubiquitin-Proteasome System in the Biology of Stem Cells. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:2043-2053. [PMID: 38462448 DOI: 10.1134/s0006297923120076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/17/2023] [Accepted: 11/18/2023] [Indexed: 03/12/2024]
Abstract
Selective degradation of cellular proteins by the ubiquitin-proteasome system (UPS) is one of the key regulatory mechanisms in eukaryotic cells. A growing body of evidence indicates that UPS is involved in the regulation of fundamental processes in mammalian stem cells, including proliferation, differentiation, cell migration, aging, and programmed cell death, via proteolytic degradation of key transcription factors and cell signaling proteins and post-translational modification of target proteins with ubiquitin. Studying molecular mechanisms of proteostasis in stem cells is of great importance for the development of new therapeutic approaches aimed at the treatment of autoimmune and neurodegenerative diseases, cancer, and other socially significant pathologies. This review discusses current data on the UPS functions in stem cells.
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Affiliation(s)
- Alexander V Burov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Andrey A Rodin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Vadim L Karpov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Alexey V Morozov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.
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4
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Zou Q, Liu M, Liu K, Zhang Y, North BJ, Wang B. E3 ubiquitin ligases in cancer stem cells: key regulators of cancer hallmarks and novel therapeutic opportunities. Cell Oncol (Dordr) 2023; 46:545-570. [PMID: 36745329 PMCID: PMC10910623 DOI: 10.1007/s13402-023-00777-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2023] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Human malignancies are composed of heterogeneous subpopulations of cancer cells with phenotypic and functional diversity. Among them, a unique subset of cancer stem cells (CSCs) has both the capacity for self-renewal and the potential to differentiate and contribute to multiple tumor properties. As such, CSCs are promising cellular targets for effective cancer therapy. At the molecular level, hyper-activation of multiple stemness regulatory signaling pathways and downstream transcription factors play critical roles in controlling CSCs establishment and maintenance. To regulate CSC properties, these stemness pathways are controlled by post-translational modifications including, but not limited to phosphorylation, acetylation, methylation, and ubiquitination. CONCLUSION In this review, we focus on E3 ubiquitin ligases and their roles and mechanisms in regulating essential hallmarks of CSCs, such as self-renewal, invasion and metastasis, metabolic reprogramming, immune evasion, and therapeutic resistance. Moreover, we discuss emerging therapeutic approaches to eliminate CSCs through targeting E3 ubiquitin ligases by chemical inhibitors and proteolysis-targeting chimera (PROTACs) which are currently under development at the discovery, preclinical, and clinical stages. Several outstanding issues such as roles for E3 ubiquitin ligases in heterogeneity and phenotypical/functional evolution of CSCs remain to be studied under pathologically and clinically relevant conditions. With the rapid application of functional genomic and proteomic approaches at single cell, spatiotemporal, and even single molecule levels, we anticipate that more specific and precise functions of E3 ubiquitin ligases will be delineated in dictating CSC properties. Rational design and proper translation of these mechanistic understandings may lead to novel therapeutic modalities for cancer procession medicine.
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Affiliation(s)
- Qiang Zou
- Department of Hepatobiliary Pancreatic Tumor Center, Chongqing University Cancer Hospital, Chongqing University Medical School, Chongqing, 400030, People's Republic of China
- Department of Gastroenterology & Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), 10 Changjiang Branch Road, Yuzhong District, Chongqing, 400042, People's Republic of China
| | - Meng Liu
- Department of Gastroenterology & Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), 10 Changjiang Branch Road, Yuzhong District, Chongqing, 400042, People's Republic of China
- Department of Gastroenterology, Chongqing University Cancer Hospital, Chongqing University Medical School, Chongqing, 400030, People's Republic of China
| | - Kewei Liu
- Department of Gastroenterology & Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), 10 Changjiang Branch Road, Yuzhong District, Chongqing, 400042, People's Republic of China
| | - Yi Zhang
- Department of Hepatobiliary Pancreatic Tumor Center, Chongqing University Cancer Hospital, Chongqing University Medical School, Chongqing, 400030, People's Republic of China.
| | - Brian J North
- Biomedical Sciences Department, Creighton University School of Medicine, Omaha, NE, 68178, USA.
| | - Bin Wang
- Department of Gastroenterology & Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), 10 Changjiang Branch Road, Yuzhong District, Chongqing, 400042, People's Republic of China.
- Institute of Pathology and Southwest Cancer Center, and Key Laboratory of Tumor Immunopathology of Ministry of Education of China, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, 400038, People's Republic of China.
- Jinfeng Laboratory, Chongqing, 401329, People's Republic of China.
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5
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Zhang M, Li K, Qu S, Guo Z, Wang Y, Yang X, Zhou J, Ouyang G, Weng R, Li F, Wu Y, Yang X. Integrative analyses of maternal plasma cell-free DNA nucleosome footprint differences reveal chromosomal aneuploidy fetuses gene expression profile. J Transl Med 2022; 20:536. [PMID: 36401256 PMCID: PMC9673457 DOI: 10.1186/s12967-022-03735-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 10/30/2022] [Indexed: 11/19/2022] Open
Abstract
Background Chromosomal aneuploidy is the most common birth defect. However, the developmental mechanism and gene expression profile of fetuses with chromosomal aneuploidy are relatively unknown, and the maternal immune changes induced by fetal aneuploidy remain unclear. The inability to obtain the placenta multiple times in real-time is a bottleneck in research on aneuploid pregnancies. Plasma cell-free DNA (cfDNA) carries the gene expression profile information of its source cells and may be used to evaluate the development of fetuses with aneuploidy and the immune changes induced in the mother owing to fetal aneuploidy. Methods Here, we carried out whole-genome sequencing of the plasma cfDNA of 101 pregnant women carrying a fetus with trisomy (trisomy 21, n = 42; trisomy 18, n = 28; trisomy 13, n = 31) based on non-invasive prenatal testing (NIPT) screening and 140 normal pregnant women to identify differential genes according to the cfDNA nucleosome profile in the region around the transcription start sites (TSSs). Results The plasma cfDNA promoter profiles were found to differ between aneuploid and euploid pregnancies. A total of 158 genes with significant differences were identified, of which 43 genes were upregulated and 98 genes were downregulated. Functional enrichment and signaling pathway analysis were performed based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases found that these signal pathways were mainly related to the coordination of developmental signals during embryonic development, the control of cell growth and development, regulation of neuronal survival, and immune regulation, such as the MAPK, Hippo, TGF-β, and Rap1 signaling pathways, which play important roles in the development of embryonic tissues and organs. Furthermore, based on the results of differential gene analysis, a total of 14 immune-related genes with significant differences from the ImmPort database were collected and analyzed. These significantly different immune genes were mainly associated with the maintenance of embryonic homeostasis and normal development. Conclusions These results suggest that the distribution characteristics of cfDNA nucleosomes in maternal plasma can be used to reflect the status of fetal development and changes of the immune responses in trisomic pregnancies. Overall, our findings may provide research ideas for non-invasive detection of the physiological and pathological states of other diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03735-7.
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6
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Wittorf KJ, Weber KK, Swenson SA, Buckley SM. Ubiquitin E3 ligase FBXO21 regulates cytokine-mediated signaling pathways, but is dispensable for steady-state hematopoiesis. Exp Hematol 2022; 114:33-42.e3. [PMID: 35987460 DOI: 10.1016/j.exphem.2022.08.002] [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: 06/16/2022] [Revised: 08/03/2022] [Accepted: 08/04/2022] [Indexed: 11/24/2022]
Abstract
Hematopoietic cell fate decisions such as self-renewal and differentiation are highly regulated through multiple molecular pathways. One pathway, the ubiquitin proteasome system (UPS), controls protein levels by tagging them with polyubiquitin chains and promoting their degradation through the proteasome. Ubiquitin E3 ligases serve as the substrate-recognition component of the UPS. By investigating the FBOX family of E3 ligases, we discovered that Fbxo21 was highly expressed in the hematopoietic stem and progenitor cell (HSPC) population, and exhibited low to no expression in mature myeloid populations. To determine the role of FBXO21 on HSPC maintenance, self-renewal, and differentiation, we generated shRNAs against FBXO21 and a hematopoiesis-specific Fbxo21 conditional knockout (cKO) mouse model. We found that silencing FBXO21 in HSPCs led to a loss in colony formation and an increase in cell differentiation in vitro. Additionally, stressing the HSPC populations in our Fbxo21 cKO mouse with 5-fluorouracil injections resulted in a decrease in survival, despite these populations exhibiting minimal alterations during steady-state hematopoiesis. Although FBXO21 has previously been proposed to regulate cytokine signaling via ASK and p38, our results indicate that depletion of FBXO21 led to altered ERK signaling in vitro. Together, these findings suggest ubiquitin E3 ligase FBXO21 regulates HSPCs through cytokine-mediated pathways.
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Affiliation(s)
- Karli J Wittorf
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE
| | - Kasidy K Weber
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE
| | - Samantha A Swenson
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE
| | - Shannon M Buckley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE.
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7
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Wang R, Amoyel M. mRNA Translation Is Dynamically Regulated to Instruct Stem Cell Fate. Front Mol Biosci 2022; 9:863885. [PMID: 35433828 PMCID: PMC9008482 DOI: 10.3389/fmolb.2022.863885] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 02/25/2022] [Indexed: 12/12/2022] Open
Abstract
Stem cells preserve tissue homeostasis by replacing the cells lost through damage or natural turnover. Thus, stem cells and their daughters can adopt two identities, characterized by different programs of gene expression and metabolic activity. The composition and regulation of these programs have been extensively studied, particularly by identifying transcription factor networks that define cellular identity and the epigenetic changes that underlie the progressive restriction in gene expression potential. However, there is increasing evidence that post-transcriptional mechanisms influence gene expression in stem cells and their progeny, in particular through the control of mRNA translation. Here, we review the described roles of translational regulation in controlling all aspects of stem cell biology, from the decision to enter or exit quiescence to maintaining self-renewal and promoting differentiation. We focus on mechanisms controlling global translation rates in cells, mTOR signaling, eIF2ɑ phosphorylation, and ribosome biogenesis and how they allow stem cells to rapidly change their gene expression in response to tissue needs or environmental changes. These studies emphasize that translation acts as an additional layer of control in regulating gene expression in stem cells and that understanding this regulation is critical to gaining a full understanding of the mechanisms that underlie fate decisions in stem cells.
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Affiliation(s)
| | - Marc Amoyel
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
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8
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Quiroga M, Rodríguez-Alonso A, Alfonsín G, Rodríguez JJE, Breijo SM, Chantada V, Figueroa A. Protein Degradation by E3 Ubiquitin Ligases in Cancer Stem Cells. Cancers (Basel) 2022; 14:cancers14040990. [PMID: 35205738 PMCID: PMC8870109 DOI: 10.3390/cancers14040990] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/09/2022] [Accepted: 02/11/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary The aim of this review was to discuss the fundamental role of E3 ubiquitin ligases in controlling cancer stem cells. It will be surmised that protein degradation controlled by the E3 ubiquitin ligases plays a fundamental role in the self-renewal, maintenance and differentiation of cancer stem cells, highlighting its potential as an effective therapeutic target for anticancer drug development. Abstract Cancer stem cells are a small subpopulation within the tumor with high capacity for self-renewal, differentiation and reconstitution of tumor heterogeneity. Cancer stem cells are major contributors of tumor initiation, metastasis and therapy resistance in cancer. Emerging evidence indicates that ubiquitination-mediated post-translational modification plays a fundamental role in the maintenance of cancer stem cell characteristics. In this review, we will discuss how protein degradation controlled by the E3 ubiquitin ligases plays a fundamental role in the self-renewal, maintenance and differentiation of cancer stem cells, highlighting the possibility to develop novel therapeutic strategies against E3 ubiquitin ligases targeting CSCs to fight cancer.
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9
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Basar MA, Beck DB, Werner A. Deubiquitylases in developmental ubiquitin signaling and congenital diseases. Cell Death Differ 2021; 28:538-556. [PMID: 33335288 PMCID: PMC7862630 DOI: 10.1038/s41418-020-00697-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/20/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023] Open
Abstract
Metazoan development from a one-cell zygote to a fully formed organism requires complex cellular differentiation and communication pathways. To coordinate these processes, embryos frequently encode signaling information with the small protein modifier ubiquitin, which is typically attached to lysine residues within substrates. During ubiquitin signaling, a three-step enzymatic cascade modifies specific substrates with topologically unique ubiquitin modifications, which mediate changes in the substrate's stability, activity, localization, or interacting proteins. Ubiquitin signaling is critically regulated by deubiquitylases (DUBs), a class of ~100 human enzymes that oppose the conjugation of ubiquitin. DUBs control many essential cellular functions and various aspects of human physiology and development. Recent genetic studies have identified mutations in several DUBs that cause developmental disorders. Here we review principles controlling DUB activity and substrate recruitment that allow these enzymes to regulate ubiquitin signaling during development. We summarize key mechanisms of how DUBs control embryonic and postnatal differentiation processes, highlight developmental disorders that are caused by mutations in particular DUB members, and describe our current understanding of how these mutations disrupt development. Finally, we discuss how emerging tools from human disease genetics will enable the identification and study of novel congenital disease-causing DUBs.
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Affiliation(s)
- Mohammed A Basar
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA
| | - David B Beck
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA
- Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Achim Werner
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA.
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Beck DB, Basar MA, Asmar AJ, Thompson JJ, Oda H, Uehara DT, Saida K, Pajusalu S, Talvik I, D'Souza P, Bodurtha J, Mu W, Barañano KW, Miyake N, Wang R, Kempers M, Tamada T, Nishimura Y, Okada S, Kosho T, Dale R, Mitra A, Macnamara E, Matsumoto N, Inazawa J, Walkiewicz M, Õunap K, Tifft CJ, Aksentijevich I, Kastner DL, Rocha PP, Werner A. Linkage-specific deubiquitylation by OTUD5 defines an embryonic pathway intolerant to genomic variation. SCIENCE ADVANCES 2021; 7:7/4/eabe2116. [PMID: 33523931 PMCID: PMC7817106 DOI: 10.1126/sciadv.abe2116] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 12/07/2020] [Indexed: 05/09/2023]
Abstract
Reversible modification of proteins with linkage-specific ubiquitin chains is critical for intracellular signaling. Information on physiological roles and underlying mechanisms of particular ubiquitin linkages during human development are limited. Here, relying on genomic constraint scores, we identify 10 patients with multiple congenital anomalies caused by hemizygous variants in OTUD5, encoding a K48/K63 linkage-specific deubiquitylase. By studying these mutations, we find that OTUD5 controls neuroectodermal differentiation through cleaving K48-linked ubiquitin chains to counteract degradation of select chromatin regulators (e.g., ARID1A/B, histone deacetylase 2, and HCF1), mutations of which underlie diseases that exhibit phenotypic overlap with OTUD5 patients. Loss of OTUD5 during differentiation leads to less accessible chromatin at neuroectodermal enhancers and aberrant gene expression. Our study describes a previously unidentified disorder we name LINKED (LINKage-specific deubiquitylation deficiency-induced Embryonic Defects) syndrome and reveals linkage-specific ubiquitin cleavage from chromatin remodelers as an essential signaling mode that coordinates chromatin remodeling during embryogenesis.
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Affiliation(s)
- David B Beck
- Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mohammed A Basar
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anthony J Asmar
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joyce J Thompson
- Unit on Genome Structure and Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hirotsugu Oda
- Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniela T Uehara
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ken Saida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Sander Pajusalu
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Inga Talvik
- Department of Neurology and Rehabilitation, Tallinn Children's Hospital, Tallinn, Estonia
| | - Precilla D'Souza
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joann Bodurtha
- Department of Genetic Medicine, Johns Hopkins Hospital, Baltimore, MD 21287, USA
| | - Weiyi Mu
- Department of Genetic Medicine, Johns Hopkins Hospital, Baltimore, MD 21287, USA
| | - Kristin W Barañano
- Department of Neurology, Johns Hopkins Hospital, Baltimore, MD 21287, USA
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Raymond Wang
- Division of Metabolic Disorders, CHOC Children's Specialists, Orange, CA 92868, USA
- Department of Pediatrics, University of California Irvine School of Medicine, Orange, CA 92967, USA
| | - Marlies Kempers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Tomoko Tamada
- Department of Pediatrics, Hiroshima Prefectural Rehabilitation Center, Hiroshima, Japan
| | - Yutaka Nishimura
- Department of General Perinatology, Hiroshima City Hiroshima Citizens Hospital, Hiroshima, Japan
| | - Satoshi Okada
- Department of Pediatrics, Hiroshima University, Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Tomoki Kosho
- Department of Medical Genetics, Shinshu University School of Medicine, Nagano, Japan
| | - Ryan Dale
- Bioinformatics and Scientific Programming Core, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Apratim Mitra
- Bioinformatics and Scientific Programming Core, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ellen Macnamara
- Undiagnosed Diseases Program, The Common Fund, Office of the Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Johji Inazawa
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Magdalena Walkiewicz
- National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD 20892, USA
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Cynthia J Tifft
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Undiagnosed Diseases Program, The Common Fund, Office of the Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ivona Aksentijevich
- Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel L Kastner
- Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pedro P Rocha
- Unit on Genome Structure and Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
- National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Achim Werner
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA.
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11
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Kaushal K, Ramakrishna S. Deubiquitinating Enzyme-Mediated Signaling Networks in Cancer Stem Cells. Cancers (Basel) 2020; 12:E3253. [PMID: 33158118 PMCID: PMC7694198 DOI: 10.3390/cancers12113253] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/23/2020] [Accepted: 11/02/2020] [Indexed: 12/11/2022] Open
Abstract
Cancer stem cells (CSCs) have both the capacity for self-renewal and the potential to differentiate and contribute to multiple tumor properties, such as recurrence, metastasis, heterogeneity, multidrug resistance, and radiation resistance. Thus, CSCs are considered to be promising therapeutic targets for cancer therapy. The function of CSCs can be regulated by ubiquitination and deubiquitination of proteins related to the specific stemness of the cells executing various stem cell fate choices. To regulate the balance between ubiquitination and deubiquitination processes, the disassembly of ubiquitin chains from specific substrates by deubiquitinating enzymes (DUBs) is crucial. Several key developmental and signaling pathways have been shown to play essential roles in this regulation. Growing evidence suggests that overactive or abnormal signaling within and among these pathways may contribute to the survival of CSCs. These signaling pathways have been experimentally shown to mediate various stem cell properties, such as self-renewal, cell fate decisions, survival, proliferation, and differentiation. In this review, we focus on the DUBs involved in CSCs signaling pathways, which are vital in regulating their stem-cell fate determination.
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Affiliation(s)
- Kamini Kaushal
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea;
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea;
- College of Medicine, Hanyang University, Seoul 04763, Korea
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12
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Kap1 regulates the self-renewal of embryonic stem cells and cellular reprogramming by modulating Oct4 protein stability. Cell Death Differ 2020; 28:685-699. [PMID: 32895487 DOI: 10.1038/s41418-020-00613-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 08/15/2020] [Accepted: 08/25/2020] [Indexed: 12/27/2022] Open
Abstract
Oct4 plays a crucial role in the regulation of self-renewal of embryonic stem cells (ESCs) and reprogramming of somatic cells to induced pluripotent stem cells. However, the molecular mechanisms underlying posttranslational regulation and protein stability of Oct4 remain unclear. Using affinity purification and mass spectrometry analysis, we identified Kap1 as an Oct4-binding protein. Silencing of Kap1 reduced the protein levels of Oct4 in ESCs, whereas the overexpression of Kap1 stimulated the levels of Oct4. In addition, Kap1 overexpression stimulated the self-renewal of ESCs and attenuated the spontaneous differentiation of ESCs in response to LIF withdrawal. Kap1 overexpression increased the stability of Oct4 by inhibiting the Itch-mediated ubiquitination of Oct4. Silencing of Kap1 augmented Itch-mediated ubiquitination and inhibited the stability of Oct4. We identified the lysine 133 (K133) residue in Oct4 as a ubiquitination site responsible for the Kap1-Itch-dependent regulation of Oct4 stability. Preventing ubiquitination at the lysine residue by mutation to arginine augmented the reprogramming of mouse embryonic fibroblasts to induced pluripotent stem cells. These results suggest that Kap1 plays a crucial role in the regulation of the pluripotency of ESCs and somatic cell reprogramming by preventing Itch-mediated ubiquitination and the subsequent degradation of Oct4.
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13
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Xing M, Liu Q, Mao C, Zeng H, Zhang X, Zhao S, Chen L, Liu M, Shen B, Guo X, Ma H, Chen H, Zhang J. The 18S rRNA m 6 A methyltransferase METTL5 promotes mouse embryonic stem cell differentiation. EMBO Rep 2020; 21:e49863. [PMID: 32783360 DOI: 10.15252/embr.201949863] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 07/21/2020] [Accepted: 07/23/2020] [Indexed: 12/12/2022] Open
Abstract
RNA modifications represent a novel layer of regulation of gene expression. Functional experiments revealed that N6 -methyladenosine (m6 A) on messenger RNA (mRNA) plays critical roles in cell fate determination and development. m6 A mark also resides in the decoding center of 18S ribosomal RNA (rRNA); however, the biological function of m6 A on 18S rRNA is still poorly understood. Here, we report that methyltransferase-like 5 (METTL5) methylates 18S rRNA both in vivo and in vitro, which is consistent with previous reports. Deletion of Mettl5 causes a dramatic differentiation defect in mouse embryonic stem cells (mESCs). Mechanistically, the m6 A deposited by METTL5 is involved in regulating the efficient translation of F-box and WD repeat domain-containing 7 (FBXW7), a key regulator of cell differentiation. Deficiency of METTL5 reduces FBXW7 levels and leads to the accumulation of its substrate c-MYC, thereby delaying the onset of mESC differentiation. Our study uncovers an important role of METTL5-mediated 18S m6 A in mESC differentiation through translation regulation and provides new insight into the functional significance of rRNA m6 A.
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Affiliation(s)
- Ming Xing
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Qi Liu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Cong Mao
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Hanyi Zeng
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Xin Zhang
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Shuqin Zhao
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Li Chen
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Mingxi Liu
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Bin Shen
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Honghui Ma
- Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Hao Chen
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Jun Zhang
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
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14
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Shende P, Gandhewar N. Current Trend and Pro-survival Approaches for Augmenting Stem Cell Viability. Curr Pharm Biotechnol 2020; 21:1154-1164. [PMID: 32297579 DOI: 10.2174/1389201021666200416130253] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 02/28/2020] [Accepted: 03/02/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Stem cells are of two types: embryonic and adult stem cells and they act as a repair system by replenishing body tissue. Stem cells differentiate into different types of cells, such as neural, hematopoietic, adipose, etc. and are used for the treatment of various conditions like myocardial infarction, spinal cord injury, Parkinson's disease and diabetes. METHODS This article focuses on recent research development that addresses the viability issues of stem cells. The efficiency of transplanted stem cells reduces due to conditions like hypoxia, inflammation, nutrient deprivation, immunogenicity, extracellular matrix loss on delivery and mechanical stress. RESULTS To increase the viability of stem cells, techniques like scaffolds of stem cells with hydrogel or alginate, pre-conditioning, different routes of administration and encapsulation, are implemented. CONCLUSION For the protection of stem cells against apoptosis, different pathways, namely Phosphoinositide 3-Kinase (PI3K/AKT), Hypoxia-Inducible Factor (HIF1), Mitogen-Activated Protein Kinases (MAPK) and Hippo, are discussed. DISCUSSION Activation of the PI3K/AKT pathway decreases the concentration of apoptotic factors, while the HIF pathway protects stem cells against the micro-environment of tissue (hypoxia).
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Affiliation(s)
- Pravin Shende
- Shobhaben Pratapbhai Patel School Pharmacy and Technology Management SVKM'S NMIMS, V.L Mehta Road, Vile Parle(W), Mumbai, India
| | - Nivedita Gandhewar
- Shobhaben Pratapbhai Patel School Pharmacy and Technology Management SVKM'S NMIMS, V.L Mehta Road, Vile Parle(W), Mumbai, India
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15
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Cell cycle-dependent localization of the proteasome to chromatin. Sci Rep 2020; 10:5801. [PMID: 32242037 PMCID: PMC7118148 DOI: 10.1038/s41598-020-62697-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 03/12/2020] [Indexed: 11/08/2022] Open
Abstract
An integrative understanding of nuclear events including transcription in normal and cancer cells requires comprehensive and quantitative measurement of protein dynamics that underlie such events. However, the low abundance of most nuclear proteins hampers their detailed functional characterization. We have now comprehensively quantified the abundance of nuclear proteins with the use of proteomics approaches in both normal and transformed human diploid fibroblasts. We found that subunits of the 26S proteasome complex were markedly down-regulated in the nuclear fraction of the transformed cells compared with that of the wild-type cells. The intranuclear proteasome abundance appeared to be inversely related to the rate of cell cycle progression, with restraint of the cell cycle being associated with an increase in the amount of proteasome subunits in the nucleus, suggesting that the nuclear proteasome content is dependent on the cell cycle. Furthermore, chromatin enrichment for proteomics (ChEP) analysis revealed enrichment of the proteasome in the chromatin fraction of quiescent cells and its apparent dissociation from chromatin in transformed cells. Our results thus suggest that translocation of the nuclear proteasome to chromatin may play an important role in control of the cell cycle and oncogenesis through regulation of chromatin-associated transcription factors.
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16
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Chang SY, Carpena NT, Mun S, Jung JY, Chung PS, Shim H, Han K, Ahn JC, Lee MY. Enhanced Inner-Ear Organoid Formation from Mouse Embryonic Stem Cells by Photobiomodulation. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 17:556-567. [PMID: 32258218 PMCID: PMC7118273 DOI: 10.1016/j.omtm.2020.03.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/09/2020] [Accepted: 03/10/2020] [Indexed: 12/18/2022]
Abstract
Photobiomodulation (PBM) stimulates different types of stem cells to migrate, proliferate, and differentiate in vitro and in vivo. However, little is known about the effects of PBM on the differentiation of embryonic stem cells (ESCs) toward the otic lineage. Only a few reports have documented the in vitro differentiation of ESCs into inner-ear hair cells (HCs) due to the complexity of HCs compared with other target cell types. In this study, we determined the optimal condition to differentiate the ESCs into the otic organoid using different culture techniques and PBM parameters. The efficiency of organoid formation within the embryoid body (EB) was dependent on the cell density of the hanging drop. PBM, using 630 nm wavelength light-emitting diodes (LEDs), further improved the differentiation of inner-ear hair cell-like cells coupled with reactive oxygen species (ROS) overexpression. Transcriptome analysis showed the factors that are responsible for the effect of PBM in the formation of otic organoids, notably, the downregulation of neural development-associated genes and the hairy and enhancer of split 5 (Hes5) gene, which inhibits the differentiation of prosensory cells to hair cells. These data enrich the current differentiation protocols for generating inner-ear hair cells.
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Affiliation(s)
- So-Young Chang
- Beckman Laser Institute Korea, Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea
| | - Nathaniel T Carpena
- Department of Otolaryngology-Head & Neck Surgery, College of Medicine, Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea
| | - Seyoung Mun
- Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea.,DKU-Theragen Institute for NGS Analysis (DTiNa), 119 Dandae-ro, Cheonan 31116, Republic of Korea
| | - Jae Yun Jung
- Beckman Laser Institute Korea, Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea.,Department of Otolaryngology-Head & Neck Surgery, College of Medicine, Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea
| | - Phil-Sang Chung
- Beckman Laser Institute Korea, Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea.,Department of Otolaryngology-Head & Neck Surgery, College of Medicine, Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea
| | - Hosup Shim
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea
| | - Kyudong Han
- Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea.,DKU-Theragen Institute for NGS Analysis (DTiNa), 119 Dandae-ro, Cheonan 31116, Republic of Korea
| | - Jin-Chul Ahn
- Beckman Laser Institute Korea, Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea.,Department of Biomedical Science, Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea
| | - Min Young Lee
- Beckman Laser Institute Korea, Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea.,Department of Otolaryngology-Head & Neck Surgery, College of Medicine, Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea
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17
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Loss of FBXO9 Enhances Proteasome Activity and Promotes Aggressiveness in Acute Myeloid Leukemia. Cancers (Basel) 2019; 11:cancers11111717. [PMID: 31684170 PMCID: PMC6895989 DOI: 10.3390/cancers11111717] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 10/30/2019] [Accepted: 11/01/2019] [Indexed: 12/11/2022] Open
Abstract
The hematopoietic system is maintained throughout life by stem cells that are capable of differentiating into all hematopoietic lineages. An intimate balance between self-renewal, differentiation, and quiescence is required to maintain hematopoiesis and disruption of this balance can result in malignant transformation. FBXO9, the substrate recognition component from the SCF E3 ubiquitin ligase family, is downregulated in patients with acute myeloid leukemia (AML) compared to healthy bone marrow, and this downregulation is particularly evident in patients with inv(16) AML. To study FBXO9 in malignant hematopoiesis, we generated a conditional knockout mouse model using a novel CRISPR/Cas9 strategy. Deletion of Fbxo9 in the murine hematopoietic system showed no adverse effects on stem and progenitor cell function but in AML lead to markedly accelerated and aggressive leukemia development in mice with inv(16). Not only did Fbxo9 play a role in leukemia initiation but it also functioned to maintain AML activity and promote disease progression. Quantitative mass spectrometry from primary tumors reveals tumors lacking Fbxo9 highly express proteins associated with metastasis and invasion as well as components of the ubiquitin proteasome system. We confirmed that the loss of FBXO9 leads to increased proteasome activity and tumors cells were more sensitive to in vitro proteasome inhibition with bortezomib, suggesting that FBXO9 expression may predict patients’ response to bortezomib.
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18
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Guillamot M, Ouazia D, Dolgalev I, Yeung ST, Kourtis N, Dai Y, Corrigan K, Zea-Redondo L, Saraf A, Florens L, Washburn MP, Tikhonova AN, Malumbres M, Gong Y, Tsirigos A, Park C, Barbieri C, Khanna KM, Busino L, Aifantis I. The E3 ubiquitin ligase SPOP controls resolution of systemic inflammation by triggering MYD88 degradation. Nat Immunol 2019; 20:1196-1207. [PMID: 31406379 PMCID: PMC7376385 DOI: 10.1038/s41590-019-0454-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 06/26/2019] [Indexed: 01/25/2023]
Abstract
The response to systemic infection and injury requires the rapid adaptation of hematopoietic stem cells (HSCs), which proliferate and divert their differentiation toward the myeloid lineage. Significant interest has emerged in understanding the signals that trigger the emergency hematopoietic program. However, the mechanisms that halt this response of HSCs, which is critical to restore homeostasis, remain unknown. Here we reveal that the E3 ubiquitin ligase Speckle-type BTB-POZ protein (SPOP) restrains the inflammatory activation of HSCs. In the absence of Spop, systemic inflammation proceeded in an unresolved manner, and the sustained response in the HSCs resulted in a lethal phenotype reminiscent of hyper-inflammatory syndrome or sepsis. Our proteomic studies decipher that SPOP restricted inflammation by ubiquitinating the innate signal transducer myeloid differentiation primary response protein 88 (MYD88). These findings unearth an HSC-intrinsic post-translational mechanism that is essential for reestablishing homeostasis after emergency hematopoiesis.
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Affiliation(s)
- Maria Guillamot
- Department of Pathology, NYU School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA.,These authors contributed equally: Maria Guillamot, Dahmane Ouazia.,Correspondence and requests for materials should be addressed to M.G., L.B. or I.A., ; ;
| | - Dahmane Ouazia
- Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,These authors contributed equally: Maria Guillamot, Dahmane Ouazia
| | - Igor Dolgalev
- Department of Pathology, NYU School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA.,Applied Bioinformatics Laboratories, Office of Science & Research, NYU School of Medicine, New York, NY, USA
| | - Stephen T. Yeung
- Department of Microbiology, NYU School of Medicine, New York, NY, USA
| | - Nikos Kourtis
- Department of Pathology, NYU School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Yuling Dai
- Department of Pathology, NYU School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Kate Corrigan
- Department of Pathology, NYU School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Luna Zea-Redondo
- Department of Pathology, NYU School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Anita Saraf
- The Stowers Institute of Medical Research, Kansas City, MO, USA
| | | | - Michael P. Washburn
- The Stowers Institute of Medical Research, Kansas City, MO, USA.,Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, Kansas City, KS, USA
| | - Anastasia N. Tikhonova
- Department of Pathology, NYU School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Marina Malumbres
- Department of Pathology, NYU School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Yixiao Gong
- Department of Pathology, NYU School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Aristotelis Tsirigos
- Department of Pathology, NYU School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA.,Applied Bioinformatics Laboratories, Office of Science & Research, NYU School of Medicine, New York, NY, USA
| | - Christopher Park
- Department of Pathology, NYU School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Christopher Barbieri
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.,Department of Urology, Weill Cornell Medicine, New York, NY, USA
| | - Kamal M. Khanna
- Department of Microbiology, NYU School of Medicine, New York, NY, USA
| | - Luca Busino
- Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,These authors contributed equally: Maria Guillamot, Dahmane Ouazia.,These authors jointly supervised this work: Luca Busino and Iannis Aifantis.,Correspondence and requests for materials should be addressed to M.G., L.B. or I.A., ; ;
| | - Iannis Aifantis
- Department of Pathology, NYU School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA.,These authors contributed equally: Maria Guillamot, Dahmane Ouazia.,These authors jointly supervised this work: Luca Busino and Iannis Aifantis.,Correspondence and requests for materials should be addressed to M.G., L.B. or I.A., ; ;
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19
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Strikoudis A, Lazaris C, Ntziachristos P, Tsirigos A, Aifantis I. Opposing functions of H2BK120 ubiquitylation and H3K79 methylation in the regulation of pluripotency by the Paf1 complex. Cell Cycle 2019; 16:2315-2322. [PMID: 28272987 DOI: 10.1080/15384101.2017.1295194] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Maintenance of stem cell plasticity is determined by the ability to balance opposing forces that control gene expression. Regulation of transcriptional networks, signaling cues and chromatin-modifying mechanisms constitute crucial determinants of tissue equilibrium. Histone modifications can affect chromatin compaction, therefore co-transcriptional events that influence their deposition determine the propensities toward quiescence, self-renewal, or cell specification. The Paf1 complex (Paf1C) is a critical regulator of RNA PolII elongation that controls gene expression and deposition of histone modifications, however few studies have focused on its role affecting stem cell fate decisions. Here we delineate the functions of Paf1C in pluripotency and characterize its impact in deposition of H2B ubiquitylation (H2BK120-ub) and H3K79 methylation (H3K79me), 2 fundamental histone marks that shape transcriptional regulation. We identify that H2BK120-ub is increased in the absence of Paf1C on its embryonic stem cell targets, in sharp contrast to H3K79me, suggesting opposite functions in the maintenance of self-renewal. Furthermore, we found that core pluripotency genes are characterized by a dual gain of H2BK120-ub and loss of H3K79me on their gene bodies. Our findings elucidate molecular mechanisms of cellular adaptation and reveal novel functions of Paf1C in the regulation of the self-renewal network.
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Affiliation(s)
- Alexandros Strikoudis
- a Department of Pathology , NYU School of Medicine , New York , NY , USA.,b Laura & Isaac Perlmutter Cancer Center , NYU School of Medicine , New York , NY , USA.,c Helen L. & Martin S. Kimmel Center for Stem Cell Biology , NYU School of Medicine , New York , NY , USA
| | - Charalampos Lazaris
- a Department of Pathology , NYU School of Medicine , New York , NY , USA.,b Laura & Isaac Perlmutter Cancer Center , NYU School of Medicine , New York , NY , USA.,c Helen L. & Martin S. Kimmel Center for Stem Cell Biology , NYU School of Medicine , New York , NY , USA
| | - Panagiotis Ntziachristos
- d Department of Biochemistry and Molecular Genetics , Feinberg School of Medicine and Robert H. Lurie Comprehensive Cancer Center, Northwestern University , Chicago , IL , USA
| | - Aristotelis Tsirigos
- a Department of Pathology , NYU School of Medicine , New York , NY , USA.,b Laura & Isaac Perlmutter Cancer Center , NYU School of Medicine , New York , NY , USA.,e Applied Bioinformatics Laboratories, Office of Science & Research , NYU School of Medicine , NY , USA
| | - Iannis Aifantis
- a Department of Pathology , NYU School of Medicine , New York , NY , USA.,b Laura & Isaac Perlmutter Cancer Center , NYU School of Medicine , New York , NY , USA.,c Helen L. & Martin S. Kimmel Center for Stem Cell Biology , NYU School of Medicine , New York , NY , USA
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20
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The Best for the Most Important: Maintaining a Pristine Proteome in Stem and Progenitor Cells. Stem Cells Int 2019; 2019:1608787. [PMID: 31191665 PMCID: PMC6525796 DOI: 10.1155/2019/1608787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 03/05/2019] [Indexed: 12/19/2022] Open
Abstract
Pluripotent stem cells give rise to reproductively enabled offsprings by generating progressively lineage-restricted multipotent stem cells that would differentiate into lineage-committed stem and progenitor cells. These lineage-committed stem and progenitor cells give rise to all adult tissues and organs. Adult stem and progenitor cells are generated as part of the developmental program and play critical roles in tissue and organ maintenance and/or regeneration. The ability of pluripotent stem cells to self-renew, maintain pluripotency, and differentiate into a multicellular organism is highly dependent on sensing and integrating extracellular and extraorganismal cues. Proteins perform and integrate almost all cellular functions including signal transduction, regulation of gene expression, metabolism, and cell division and death. Therefore, maintenance of an appropriate mix of correctly folded proteins, a pristine proteome, is essential for proper stem cell function. The stem cells' proteome must be pristine because unfolded, misfolded, or otherwise damaged proteins would interfere with unlimited self-renewal, maintenance of pluripotency, differentiation into downstream lineages, and consequently with the development of properly functioning tissue and organs. Understanding how various stem cells generate and maintain a pristine proteome is therefore essential for exploiting their potential in regenerative medicine and possibly for the discovery of novel approaches for maintaining, propagating, and differentiating pluripotent, multipotent, and adult stem cells as well as induced pluripotent stem cells. In this review, we will summarize cellular networks used by various stem cells for generation and maintenance of a pristine proteome. We will also explore the coordination of these networks with one another and their integration with the gene regulatory and signaling networks.
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21
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Mohammad K, Dakik P, Medkour Y, Mitrofanova D, Titorenko VI. Quiescence Entry, Maintenance, and Exit in Adult Stem Cells. Int J Mol Sci 2019; 20:ijms20092158. [PMID: 31052375 PMCID: PMC6539837 DOI: 10.3390/ijms20092158] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 04/24/2019] [Accepted: 04/28/2019] [Indexed: 12/13/2022] Open
Abstract
Cells of unicellular and multicellular eukaryotes can respond to certain environmental cues by arresting the cell cycle and entering a reversible state of quiescence. Quiescent cells do not divide, but can re-enter the cell cycle and resume proliferation if exposed to some signals from the environment. Quiescent cells in mammals and humans include adult stem cells. These cells exhibit improved stress resistance and enhanced survival ability. In response to certain extrinsic signals, adult stem cells can self-renew by dividing asymmetrically. Such asymmetric divisions not only allow the maintenance of a population of quiescent cells, but also yield daughter progenitor cells. A multistep process of the controlled proliferation of these progenitor cells leads to the formation of one or more types of fully differentiated cells. An age-related decline in the ability of adult stem cells to balance quiescence maintenance and regulated proliferation has been implicated in many aging-associated diseases. In this review, we describe many traits shared by different types of quiescent adult stem cells. We discuss how these traits contribute to the quiescence, self-renewal, and proliferation of adult stem cells. We examine the cell-intrinsic mechanisms that allow establishing and sustaining the characteristic traits of adult stem cells, thereby regulating quiescence entry, maintenance, and exit.
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Affiliation(s)
- Karamat Mohammad
- Department of Biology, Concordia University, 7141 Sherbrooke Street, West, SP Building, Room 501-13, Montreal, QC H4B 1R6, Canada.
| | - Paméla Dakik
- Department of Biology, Concordia University, 7141 Sherbrooke Street, West, SP Building, Room 501-13, Montreal, QC H4B 1R6, Canada.
| | - Younes Medkour
- Department of Biology, Concordia University, 7141 Sherbrooke Street, West, SP Building, Room 501-13, Montreal, QC H4B 1R6, Canada.
| | - Darya Mitrofanova
- Department of Biology, Concordia University, 7141 Sherbrooke Street, West, SP Building, Room 501-13, Montreal, QC H4B 1R6, Canada.
| | - Vladimir I Titorenko
- Department of Biology, Concordia University, 7141 Sherbrooke Street, West, SP Building, Room 501-13, Montreal, QC H4B 1R6, Canada.
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22
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Yang CK, Feng CC, Lo JF, Chen JW, Padma VV, Lai CH, Chen TS, Chen RJ, Liao PH, Huang CY. C-terminus of Hsc70-interacting protein (CHIP) enhances stemness properties of human Wharton’s jelly mesenchymal stem cell. Biotech Histochem 2018; 93:632-639. [PMID: 30260250 DOI: 10.1080/10520295.2018.1521990] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Affiliation(s)
- C-K Yang
- Division of Colorectal Surgery, Department of Surgery, Mackay Memorial Hospital, Taipei, Taiwan
| | - C-C Feng
- Graduate Institute of Clinical Medical Science, China Medical University, Taichung, Taiwan
| | - J-F Lo
- Institute of Oral Biology, National Yang-Ming University, Taipei, Taiwan
| | - J-W Chen
- Graduate Institute of Basic Medical Science, China Medical University, Taichung, Taiwan
| | - V. V Padma
- Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - C-H Lai
- Cardiology Department, Taichung Armed Forced General Hospital, Taichung, Taiwan
| | - T-S Chen
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - R-J Chen
- Department of Surgery, School of Medicine, Taipei Medical University, Taipei, Taiwan
| | - P-H Liao
- Graduate Institute of Basic Medical Science, China Medical University, Taichung, Taiwan
- Medical Research Center of Exosomes and Mitochondria’s Related-Diseases, China Medical University Hospital, Taichung, Taiwan
| | - C-Y Huang
- Division of Colorectal Surgery, Department of Surgery, Mackay Memorial Hospital, Taipei, Taiwan
- Graduate Institute of Basic Medical Science, China Medical University, Taichung, Taiwan
- Medical Research Center of Exosomes and Mitochondria’s Related-Diseases, China Medical University Hospital, Taichung, Taiwan
- Department of Clinical Laboratory, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People’s Hospital, Guangdong, China, and 11Department of Biological Science, Asia University, Taichung, Taiwan
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23
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Farhadian M, Rafat SA, Hasanpur K, Ebrahimi M, Ebrahimie E. Cross-Species Meta-Analysis of Transcriptomic Data in Combination With Supervised Machine Learning Models Identifies the Common Gene Signature of Lactation Process. Front Genet 2018; 9:235. [PMID: 30050559 PMCID: PMC6052129 DOI: 10.3389/fgene.2018.00235] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 06/13/2018] [Indexed: 01/13/2023] Open
Abstract
Lactation, a physiologically complex process, takes place in mammary gland after parturition. The expression profile of the effective genes in lactation has not comprehensively been elucidated. Herein, meta-analysis, using publicly available microarray data, was conducted identify the differentially expressed genes (DEGs) between pre- and post-peak milk production. Three microarray datasets of Rat, Bos Taurus, and Tammar wallaby were used. Samples related to pre-peak (n = 85) and post-peak (n = 24) milk production were selected. Meta-analysis revealed 31 DEGs across the studied species. Interestingly, 10 genes, including MRPS18B, SF1, UQCRC1, NUCB1, RNF126, ADSL, TNNC1, FIS1, HES5 and THTPA, were not detected in original studies that highlights meta-analysis power in biosignature discovery. Common target and regulator analysis highlighted the high connectivity of CTNNB1, CDD4 and LPL as gene network hubs. As data originally came from three different species, to check the effects of heterogeneous data sources on DEGs, 10 attribute weighting (machine learning) algorithms were applied. Attribute weighting results showed that the type of organism had no or little effect on the selected gene list. Systems biology analysis suggested that these DEGs affect the milk production by improving the immune system performance and mammary cell growth. This is the first study employing both meta-analysis and machine learning approaches for comparative analysis of gene expression pattern of mammary glands in two important time points of lactation process. The finding may pave the way to use of publically available to elucidate the underlying molecular mechanisms of physiologically complex traits such as lactation in mammals.
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Affiliation(s)
- Mohammad Farhadian
- Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Seyed A Rafat
- Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Karim Hasanpur
- Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | | | - Esmaeil Ebrahimie
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia.,Institute of Biotechnology, Shiraz University, Shiraz, Iran.,Division of Information Technology, Engineering and the Environment, School of Information Technology & Mathematical Sciences, University of South Australia, Adelaide, SA, Australia.,School of Biological Sciences, Faculty of Science and Engineering, Flinders University, Adelaide, SA, Australia
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24
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Kaushal K, Antao AM, Kim KS, Ramakrishna S. Deubiquitinating enzymes in cancer stem cells: functions and targeted inhibition for cancer therapy. Drug Discov Today 2018; 23:1974-1982. [PMID: 29864528 DOI: 10.1016/j.drudis.2018.05.035] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 05/15/2018] [Accepted: 05/29/2018] [Indexed: 12/28/2022]
Abstract
The ability of cancers to evade conventional treatments, such as chemotherapy and radiation therapy, has been attributed to a subpopulation of cancer stem cells (CSCs). CSCs are regulated by mechanisms similar to those that regulate normal stem cells (NSCs), including processes involving ubiquitination and deubiquitination enzymes (DUBs) that regulate the expression of various factors, such as Notch, Wnt, Sonic Hedgehog (Shh), and Hippo. In this review, we discuss the roles of various DUBs involved in the regulation of core stem cell transcription factors and CSC-related proteins that are implicated in the modulation of cellular processes and carcinogenesis. In addition, we discuss the various DUB inhibitors that have been designed to target processes relevant to cancer and CSC maintenance.
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Affiliation(s)
- Kamini Kaushal
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea
| | - Ainsley Mike Antao
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea
| | - Kye-Seong Kim
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea; College of Medicine, Hanyang University, Seoul, South Korea.
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea; College of Medicine, Hanyang University, Seoul, South Korea.
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25
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Park YC, Chapagain S, Jang CS. The microtubule-associated RING finger protein 1 (OsMAR1) acts as a negative regulator for salt-stress response through the regulation of OCPI2 (O. sativa chymotrypsin protease inhibitor 2). PLANTA 2018; 247:875-886. [PMID: 29260397 DOI: 10.1007/s00425-017-2834-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 12/15/2017] [Indexed: 05/02/2023]
Abstract
Our results suggest that a rice E3 ligase, OsMAR1, physically interacts with a cytosolic protein OCPI2 and may play an important role under salinity stress. Salt is an important abiotic stressor that negatively affects plant growth phases and alters development. Herein, we found that a rice gene, OsMAR1 (Oryza sativa microtubule-associated RING finger protein 1), encoding the RING E3 ligase was highly expressed in response to high salinity, water deficit, and ABA treatment. Fluorescence signals of its recombinant proteins were clearly associated with the microtubules in rice protoplasts. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) showed that OsMAR1 interacted with a cytosolic protein OCPI2 (O. sativa chymotrypsin protease inhibitor 2) and led to its degradation via the 26S proteasome. Heterogeneous overexpression of OsMAR1 in Arabidopsis showed retarded root growth compared with that of control plants, and then led to hypersensitivity phenotypes under high salinity stress. Taken together, OsMAR1 negatively regulates the salt-stress response via the regulation of the OCPI2 protein in rice.
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Affiliation(s)
- Yong Chan Park
- Plant Genomics Lab, Department of Applied Plant Sciences, Kangwon National University, Chuncheon, 200-713, Republic of Korea
| | - Sandeep Chapagain
- Plant Genomics Lab, Department of Applied Plant Sciences, Kangwon National University, Chuncheon, 200-713, Republic of Korea
| | - Cheol Seong Jang
- Plant Genomics Lab, Department of Applied Plant Sciences, Kangwon National University, Chuncheon, 200-713, Republic of Korea.
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26
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Wang X, Zhang Q, Wang Y, Zhuang H, Chen B. Clinical Significance of Ubiquitin Specific Protease 7 (USP7) in Predicting Prognosis of Hepatocellular Carcinoma and its Functional Mechanisms. Med Sci Monit 2018; 24:1742-1750. [PMID: 29574466 PMCID: PMC5882160 DOI: 10.12659/msm.909368] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) accounts for one of the most prevalent cancer types in the world. The ubiquitin specific protease 7 (USP7), a kind of deubiquitylating enzyme, has been reported to play multifaceted roles in different tumor types. The aim of this study was to investigate the expression and function of USP7 in HCC. MATERIAL AND METHODS Immunohistochemical staining and quantitative PCR were performed to explore the expression of USP7 in both HCC tissues and adjacent normal liver tissues. Chi-square test, univariate analysis, and multivariate analysis were conducted to statistically evaluate the clinical significance of USP7 in HCC. Proliferation, migration, and invasion capacities of HCC cells were assessed after overexpressing or silencing USP7. RESULTS Both the RNA and protein levels of USP7 were upregulated in HCC tissues compared to normal liver tissues. High expression of USP7 was correlated with advanced tumor stage and poor overall survival. Moreover, USP7 was identified as a novel independent prognostic factor for HCC patients. Cellular studies showed that USP7 could enhance the proliferation, migration, and invasion capacities of HCC cells, thereby promoting tumor progression. CONCLUSIONS High expression of USP7 is frequent in HCC tissues, which promotes tumor proliferation and invasion, and is correlated with a poor overall survival. Targeting USP7 may be a novel direction for the drug development of HCC therapy.
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Affiliation(s)
- Xujing Wang
- Department of Hepatopancreatobiliary Surgery, East Hospital Affiliated to Tongji University in Shanghai, Shanghai, China (mainland)
| | - Qiqi Zhang
- Department of Hepatopancreatobiliary Surgery, East Hospital Affiliated to Tongji University in Shanghai, Shanghai, China (mainland)
| | - Yongkun Wang
- Department of Hepatopancreatobiliary Surgery, East Hospital Affiliated to Tongji University in Shanghai, Shanghai, China (mainland)
| | - Huiren Zhuang
- Department of Hepatopancreatobiliary Surgery, East Hospital Affiliated to Tongji University in Shanghai, Shanghai, China (mainland)
| | - Bo Chen
- Department of Hepatopancreatobiliary Surgery, East Hospital Affiliated to Tongji University in Shanghai, Shanghai, China (mainland)
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27
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Saez I, Koyuncu S, Gutierrez-Garcia R, Dieterich C, Vilchez D. Insights into the ubiquitin-proteasome system of human embryonic stem cells. Sci Rep 2018; 8:4092. [PMID: 29511261 PMCID: PMC5840266 DOI: 10.1038/s41598-018-22384-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 02/22/2018] [Indexed: 12/27/2022] Open
Abstract
Human embryonic stem cells (hESCs) exhibit high levels of proteasome activity, an intrinsic characteristic required for their self-renewal, pluripotency and differentiation. However, the mechanisms by which enhanced proteasome activity maintains hESC identity are only partially understood. Besides its essential role for the ability of hESCs to suppress misfolded protein aggregation, we hypothesize that enhanced proteasome activity could also be important to degrade endogenous regulatory factors. Since E3 ubiquitin ligases are responsible for substrate selection, we first define which E3 enzymes are increased in hESCs compared with their differentiated counterparts. Among them, we find HECT-domain E3 ligases such as HERC2 and UBE3A as well as several RING-domain E3s, including UBR7 and RNF181. Systematic characterization of their interactome suggests a link with hESC identity. Moreover, loss of distinct up-regulated E3s triggers significant changes at the transcriptome and proteome level of hESCs. However, these alterations do not dysregulate pluripotency markers and differentiation ability. On the contrary, global proteasome inhibition impairs diverse processes required for hESC identity, including protein synthesis, rRNA maturation, telomere maintenance and glycolytic metabolism. Thus, our data indicate that high proteasome activity is coupled with other determinant biological processes of hESC identity.
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Affiliation(s)
- Isabel Saez
- Institute for Genetics and Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931, Cologne, Germany
| | - Seda Koyuncu
- Institute for Genetics and Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931, Cologne, Germany
| | - Ricardo Gutierrez-Garcia
- Institute for Genetics and Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931, Cologne, Germany
| | - Christoph Dieterich
- Department of Internal Medicine III and Klaus Tschira Institute for Computational Cardiology, Section of Bioinformatics and Systems Cardiology, Neuenheimer Feld 669, University Hospital, 69120, Heidelberg, Germany
| | - David Vilchez
- Institute for Genetics and Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931, Cologne, Germany.
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28
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García-Prat L, Sousa-Victor P, Muñoz-Cánoves P. Proteostatic and Metabolic Control of Stemness. Cell Stem Cell 2018; 20:593-608. [PMID: 28475885 DOI: 10.1016/j.stem.2017.04.011] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Adult stem cells, particularly those resident in tissues with little turnover, are largely quiescent and only activate in response to regenerative demands, while embryonic stem cells continuously replicate, suggesting profoundly different regulatory mechanisms within distinct stem cell types. In recent years, evidence linking metabolism, mitochondrial dynamics, and protein homeostasis (proteostasis) as fundamental regulators of stem cell function has emerged. Here, we discuss new insights into how these networks control potency, self-renewal, differentiation, and aging of highly proliferative embryonic stem cells and quiescent adult stem cells, with a focus on hematopoietic and muscle stem cells and implications for anti-aging research.
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Affiliation(s)
- Laura García-Prat
- Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), CIBER on Neurodegenerative Diseases (CIBERNED), E-08003 Barcelona, Spain; Spanish National Center on Cardiovascular Research (CNIC), E-28029 Madrid, Spain; Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Pedro Sousa-Victor
- Paul F. Glenn Center for Biology of Aging Research, Buck Institute for Research on Aging, Novato, CA 94945-1400, USA
| | - Pura Muñoz-Cánoves
- Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), CIBER on Neurodegenerative Diseases (CIBERNED), E-08003 Barcelona, Spain; Spanish National Center on Cardiovascular Research (CNIC), E-28029 Madrid, Spain; ICREA, E-08010 Barcelona, Spain.
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29
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Csizmok V, Forman-Kay JD. Complex regulatory mechanisms mediated by the interplay of multiple post-translational modifications. Curr Opin Struct Biol 2018; 48:58-67. [DOI: 10.1016/j.sbi.2017.10.013] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 10/07/2017] [Accepted: 10/13/2017] [Indexed: 12/18/2022]
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30
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Strand NS, Allen JM, Ghulam M, Taylor MR, Munday RK, Carrillo M, Movsesyan A, Zayas RM. Dissecting the function of Cullin-RING ubiquitin ligase complex genes in planarian regeneration. Dev Biol 2018; 433:210-217. [PMID: 29291974 DOI: 10.1016/j.ydbio.2017.10.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/25/2017] [Accepted: 10/11/2017] [Indexed: 12/26/2022]
Abstract
The ubiquitin system plays a role in nearly every aspect of eukaryotic cell biology. The enzymes responsible for transferring ubiquitin onto specific substrates are the E3 ubiquitin ligases, a large and diverse family of proteins, for which biological roles and target substrates remain largely undefined. Studies using model organisms indicate that ubiquitin signaling mediates key steps in developmental processes and tissue regeneration. Here, we used the freshwater planarian, Schmidtea mediterranea, to investigate the role of Cullin-RING ubiquitin ligase (CRL) complexes in stem cell regulation during regeneration. We identified six S. mediterranea cullin genes, and used RNAi to uncover roles for homologs of Cullin-1, -3 and -4 in planarian regeneration. The cullin-1 RNAi phenotype included defects in blastema formation, organ regeneration, lesions, and lysis. To further investigate the function of cullin-1-mediated cellular processes in planarians, we examined genes encoding the adaptor protein Skp1 and F-box substrate-recognition proteins that are predicted to partner with Cullin-1. RNAi against skp1 resulted in phenotypes similar to cullin-1 RNAi, and an RNAi screen of the F-box genes identified 19 genes that recapitulated aspects of cullin-1 RNAi, including ones that in mammals are involved in stem cell regulation and cancer biology. Our data provides evidence that CRLs play discrete roles in regenerative processes and provide a platform to investigate how CRLs regulate stem cells in vivo.
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Affiliation(s)
- Nicholas S Strand
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - John M Allen
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Mahjoobah Ghulam
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Matthew R Taylor
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Roma K Munday
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Melissa Carrillo
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Artem Movsesyan
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Ricardo M Zayas
- Department of Biology, San Diego State University, San Diego, CA 92182, USA.
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31
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Noormohammadi A, Calculli G, Gutierrez-Garcia R, Khodakarami A, Koyuncu S, Vilchez D. Mechanisms of protein homeostasis (proteostasis) maintain stem cell identity in mammalian pluripotent stem cells. Cell Mol Life Sci 2018; 75:275-290. [PMID: 28748323 PMCID: PMC11105389 DOI: 10.1007/s00018-017-2602-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 07/13/2017] [Accepted: 07/24/2017] [Indexed: 01/10/2023]
Abstract
Protein homeostasis, or proteostasis, is essential for cell function, development, and organismal viability. The composition of the proteome is adjusted to the specific requirements of a particular cell type and status. Moreover, multiple metabolic and environmental conditions challenge the integrity of the proteome. To maintain the quality of the proteome, the proteostasis network monitors proteins from their synthesis through their degradation. Whereas somatic stem cells lose their ability to maintain proteostasis with age, immortal pluripotent stem cells exhibit a stringent proteostasis network associated with their biological function and intrinsic characteristics. Moreover, growing evidence indicates that enhanced proteostasis mechanisms play a central role in immortality and cell fate decisions of pluripotent stem cells. Here, we will review new insights into the melding fields of proteostasis and pluripotency and their implications for the understanding of organismal development and survival.
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Affiliation(s)
- Alireza Noormohammadi
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph Stelzmann Strasse 26, 50931, Cologne, Germany
| | - Giuseppe Calculli
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph Stelzmann Strasse 26, 50931, Cologne, Germany
| | - Ricardo Gutierrez-Garcia
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph Stelzmann Strasse 26, 50931, Cologne, Germany
| | - Amirabbas Khodakarami
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph Stelzmann Strasse 26, 50931, Cologne, Germany
| | - Seda Koyuncu
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph Stelzmann Strasse 26, 50931, Cologne, Germany
| | - David Vilchez
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph Stelzmann Strasse 26, 50931, Cologne, Germany.
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32
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The ubiquitin ligase ITCH coordinates small intestinal epithelial homeostasis by modulating cell proliferation, differentiation, and migration. Differentiation 2017; 99:51-61. [PMID: 29309986 DOI: 10.1016/j.diff.2017.12.003] [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: 08/07/2017] [Revised: 11/09/2017] [Accepted: 12/13/2017] [Indexed: 12/20/2022]
Abstract
Maintenance of the intestinal mucosa is driven by local signals that coordinate epithelial proliferation, differentiation, and turnover in order to separate antigenic luminal contents from the host's immune system. Breaches in this barrier promote gastrointestinal pathologies ranging from inflammatory bowel disease to cancer. The ubiquitin ligase ITCH is known to regulate immune responses, and loss of function of ITCH has been associated with gastrointestinal inflammatory disorders, particularly in the colon. However, the small intestine appears to be spared from this pathology. Here we explored the physiological mechanism that underlies the preservation of mucosal homeostasis in the small intestine in mice lacking ITCH (Itcha18H/a18H). Histological analysis of the small intestines from young adult mice revealed architectural changes in animals deficient for ITCH, including villus blunting with cell crowding, crypt expansion, and thickening of the muscularis propria relative to age-matched mice sufficient for ITCH. These differences were more prominent in the distal part of the small intestine and were not dependent upon lymphoid cells. Underlying the observed changes in the epithelium were expansion of the Ki67+ proliferating transit amplifying progenitor population and increased numbers of terminally differentiated mucus-secreting goblet and anti-microbial producing Paneth cells, which are both important in controlling local inflammation in the small intestine and are known to be dysregulated in inflammatory bowel disease. Homeostasis in the small intestine of Itcha18H/a18H animals was maintained by increased cell turnover, including accelerated migration of epithelial cells along the crypt-villus axis and increased apoptosis of epithelial cells at the crypt-villus junction. Consistent with this enhanced turnover, Itcha18H/a18H mice carrying the Min mutation (Itcha18H/a18H; ApcMin/+) displayed a 76% reduction in tumor burden as compared to ApcMin/+ littermates with normal levels of ITCH. These findings highlight the role of ITCH as an important modulator of intestinal epithelial homeostasis.
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33
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Tang Y, Lv L, Li W, Zhang X, Jiang Y, Ge W, Zhou Y. Protein deubiquitinase USP7 is required for osteogenic differentiation of human adipose-derived stem cells. Stem Cell Res Ther 2017; 8:186. [PMID: 28807012 PMCID: PMC5557518 DOI: 10.1186/s13287-017-0637-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 07/09/2017] [Accepted: 07/21/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Human adipose-derived stem cells (hASCs) are multipotent progenitor cells with self-renewal capabilities and multilineage differentiation potential, including osteogenesis. Although protein deubiquitinases have been linked to stem cell fate determination, whether protein deubiquitination contributes to lineage commitment during osteogenic differentiation of hASCs remains to be investigated. The objective of this study was to evaluate the effects of the ubiquitin specific protease 7 (USP7) on osteogenic differentiation of hASCs. METHODS An osteocalcin promoter driven luciferase reporter system was established to initially discover the potential association between USP7 and hASC osteogenesis. To further characterize the function of USP7 in osteogenic differentiation of hASCs, a combination of in vitro and in vivo experiments were carried out through genetic depletion or overexpression of USP7 using a lentiviral strategy. Moreover, HBX 41,108, a cyanoindenopyrazine-derived deubiquitinase inhibitor of USP7, was utilized at different doses to further examine whether USP7 regulated osteogenic differentiation of hASCs through its enzymatic activity. RESULTS We demonstrated that USP7 depletion was associated with remarkable downregulation of the reporter gene activity. Genetic depletion of USP7 by lentiviral RNAi markedly suppressed hASC osteogenesis both in vitro and in vivo, while overexpression of USP7 enhanced the osteogenic differentiation of hASCs. Notably, chemical blockade via the small molecular inhibitor HBX 41,108 could efficiently mimic the effects of USP7 genetic depletion in a dose-dependent manner. CONCLUSIONS Taken together, our study revealed that protein deubiquitinase USP7 is an essential player in osteogenic differentiation of hASCs through its catalytic activity, and supported the pursuit of USP7 as a potential target for modulation of hASC-based stem cell therapy and bone tissue engineering.
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Affiliation(s)
- Yiman Tang
- Department of Prosthodontics, Peking University School and Hospital of Stomatology, 22 Zhongguancun Avenue South, Haidian District, Beijing, 100081, People's Republic of China
| | - Longwei Lv
- Department of Prosthodontics, Peking University School and Hospital of Stomatology, 22 Zhongguancun Avenue South, Haidian District, Beijing, 100081, People's Republic of China
| | - Wenyue Li
- Department of Prosthodontics, Peking University School and Hospital of Stomatology, 22 Zhongguancun Avenue South, Haidian District, Beijing, 100081, People's Republic of China
| | - Xiao Zhang
- Department of Prosthodontics, Peking University School and Hospital of Stomatology, 22 Zhongguancun Avenue South, Haidian District, Beijing, 100081, People's Republic of China
| | - Yong Jiang
- Department of General Dentistry II, Peking University School and Hospital of Stomatology, 22 Zhongguancun Avenue South, Haidian District, Beijing, 100081, People's Republic of China
| | - Wenshu Ge
- Department of General Dentistry II, Peking University School and Hospital of Stomatology, 22 Zhongguancun Avenue South, Haidian District, Beijing, 100081, People's Republic of China.
| | - Yongsheng Zhou
- Department of Prosthodontics, Peking University School and Hospital of Stomatology, 22 Zhongguancun Avenue South, Haidian District, Beijing, 100081, People's Republic of China. .,National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, Beijing, 100081, China.
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Park MH, Lee HJ, Lee HL, Son DJ, Ju JH, Hyun BK, Jung SH, Song JK, Lee DH, Hwang CJ, Han SB, Kim S, Hong JT. Parkin Knockout Inhibits Neuronal Development via Regulation of Proteasomal Degradation of p21. Am J Cancer Res 2017; 7:2033-2045. [PMID: 28656059 PMCID: PMC5485421 DOI: 10.7150/thno.19824] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 03/31/2017] [Indexed: 11/05/2022] Open
Abstract
PARK2 encodes for the E3 ubiquitin ligase parkin and is implicated in the development of Parkinson's disease (PD). Although the neuroprotective role of parkin is well known, the mechanism of PARK2's function in neural stem differentiation has not yet been thoroughly studied. Co-expressions network analysis showed that synaptosomal-associated protein 25 (SNAP-25) and brain-derived neurotrophic factor (BDNF) were positively correlated with parkin, but negatively correlated with p21 in human patient brain. We investigated a link between the ubiquitin E3 ligase parkin and proteasomal degradation of p21 for the control of neural stem cell differentiation. We found that the neurogenesis was lowered in PARK2 knockout (KO) mice compared with non-tg mice. Expression of the marker protein for neural cell differentiation such as class III beta tubulin (TUBBIII), glial fibrillary acidic protein (GFAP) and neurofilament, as well as SNAP25 and BDNF, was down regulated in PARK2 KO mice. Associated with the loss of differentiation function, p21 protein was highly accumulated in the neural stem cells of PARK2 KO mice. We discovered that p21 directly binds with parkin and is ubiquitinated by parkin which resulted in the loss of cell differentiation ability. Introduction of p21 shRNA in PARK2 KO mice significantly rescued the differentiation efficacy as well as SNAP25 and BDNF expression. c-Jun N-terminal kinase (JNK) pathway is implicated in neurogenesis and p21 degradation. We also defined the decreased p21 ubiquitination and differentiation ability were reversed after treatment with JNK inhibitor, SP600125 in PARK2 KO mice derived neural stem cells. Thus, the present study indicated that parkin knockout inhibits neural stem cell differentiation by JNK-dependent proteasomal degradation of p21.
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Nguyen DTT, Richter D, Michel G, Mitschka S, Kolanus W, Cuevas E, Wulczyn FG. The ubiquitin ligase LIN41/TRIM71 targets p53 to antagonize cell death and differentiation pathways during stem cell differentiation. Cell Death Differ 2017; 24:1063-1078. [PMID: 28430184 PMCID: PMC5442473 DOI: 10.1038/cdd.2017.54] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 03/04/2017] [Accepted: 03/17/2017] [Indexed: 12/13/2022] Open
Abstract
Rapidity and specificity are characteristic features of proteolysis mediated by the ubiquitin-proteasome system. Therefore, the UPS is ideally suited for the remodeling of the embryonic stem cell proteome during the transition from pluripotent to differentiated states and its inverse, the generation of inducible pluripotent stem cells. The Trim-NHL family member LIN41 is among the first E3 ubiquitin ligases to be linked to stem cell pluripotency and reprogramming. Initially discovered in C. elegans as a downstream target of the let-7 miRNA, LIN41 is now recognized as a critical regulator of stem cell fates as well as the timing of neurogenesis. Despite being indispensable for embryonic development and neural tube closure in mice, the underlying mechanisms for LIN41 function in these processes are poorly understood. To better understand the specific contributions of the E3 ligase activity for the stem cell functions of LIN41, we characterized global changes in ubiquitin or ubiquitin-like modifications using Lin41-inducible mouse embryonic stem cells. The tumor suppressor protein p53 was among the five most strongly affected proteins in cells undergoing neural differentiation in response to LIN41 induction. We show that LIN41 interacts with p53, controls its abundance by ubiquitination and antagonizes p53-dependent pro-apoptotic and pro-differentiation responses. In vivo, the lack of LIN41 is associated with upregulation of Grhl3 and widespread caspase-3 activation, two downstream effectors of p53 with essential roles in neural tube closure. As Lin41-deficient mice display neural tube closure defects, we conclude that LIN41 is critical for the regulation of p53 functions in cell fate specification and survival during early brain development.
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Affiliation(s)
- Duong Thi Thuy Nguyen
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Institute of Cell Biology and Neurobiology, Charitéplatz 1, Berlin 10117, Germany
| | - Daniel Richter
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Institute of Cell Biology and Neurobiology, Charitéplatz 1, Berlin 10117, Germany
| | - Geert Michel
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Forschungseinrichtung für Experimentelle Medizin, Krahmerstraße 6-10, Berlin 12207, Germany
| | - Sibylle Mitschka
- University of Bonn, Life &Medical Sciences Institute (LIMES), Molecular Immunology and Cell Biology, Carl-Troll-Straße 31, Bonn 53115, Germany
| | - Waldemar Kolanus
- University of Bonn, Life &Medical Sciences Institute (LIMES), Molecular Immunology and Cell Biology, Carl-Troll-Straße 31, Bonn 53115, Germany
| | - Elisa Cuevas
- UCL Institute of Child Health, Stem Cells &Regenerative Medicine Section, 30 Guilford Street, London WC1N 1EH, Great Britain, UK
| | - F Gregory Wulczyn
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Institute of Cell Biology and Neurobiology, Charitéplatz 1, Berlin 10117, Germany
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Qiu GZ, Sun W, Jin MZ, Lin J, Lu PG, Jin WL. The bad seed gardener: Deubiquitinases in the cancer stem-cell signaling network and therapeutic resistance. Pharmacol Ther 2017; 172:127-138. [DOI: 10.1016/j.pharmthera.2016.12.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Kotoku T, Kosaka K, Nishio M, Ishida Y, Kawaichi M, Matsuda E. CIBZ Regulates Mesodermal and Cardiac Differentiation of by Suppressing T and Mesp1 Expression in Mouse Embryonic Stem Cells. Sci Rep 2016; 6:34188. [PMID: 27659197 PMCID: PMC5034229 DOI: 10.1038/srep34188] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 09/08/2016] [Indexed: 11/24/2022] Open
Abstract
The molecular mechanisms underlying mesodermal and cardiac specification from embryonic stem cells (ESCs) are not fully understood. Here, we showed that the BTB domain-containing zinc finger protein CIBZ is expressed in mouse ESCs but is dramatically downregulated during ESC differentiation. CIBZ deletion in ESCs induced specification toward mesoderm phenotypes and their differentiation into cardiomyocytes, whereas overexpression of CIBZ delayed these processes. During ESC differentiation, CIBZ loss-and-gain-of-function data indicate that CIBZ negatively regulates the expressions of Brachyury (T) and Mesp1, the key transcriptional factors responsible for the specification of mammalian mesoderm and cardiac progenitors, respectively. Chromatin immunoprecipitation assays showed that CIBZ binds to T and Mesp1 promoters in undifferentiated ESCs, and luciferase assays indicate that CIBZ suppresses T and Mesp1 promoters. These findings demonstrate that CIBZ is a novel regulator of mesodermal and cardiac differentiation of ESCs, and suggest that CIBZ-mediated cardiac differentiation depends on the regulation of these two genes.
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Affiliation(s)
| | - Koji Kosaka
- Division of Gene Function in Animals, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
| | - Miki Nishio
- Functional Genomics and Medicine, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
| | - Yasumasa Ishida
- Functional Genomics and Medicine, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
| | - Masashi Kawaichi
- Division of Gene Function in Animals, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
| | - Eishou Matsuda
- Division of Gene Function in Animals, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
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Lee HJ, Gutierrez‐Garcia R, Vilchez D. Embryonic stem cells: a novel paradigm to study proteostasis? FEBS J 2016; 284:391-398. [DOI: 10.1111/febs.13810] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 06/22/2016] [Accepted: 07/08/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Hyun Ju Lee
- Cologne Excellence Cluster for Cellular Stress Responses in Aging‐Associated Diseases (CECAD) University of Cologne Germany
| | - Ricardo Gutierrez‐Garcia
- Cologne Excellence Cluster for Cellular Stress Responses in Aging‐Associated Diseases (CECAD) University of Cologne Germany
| | - David Vilchez
- Cologne Excellence Cluster for Cellular Stress Responses in Aging‐Associated Diseases (CECAD) University of Cologne Germany
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McDonnell KJ, Gallanis GT, Heller KA, Melas M, Idos GE, Culver JO, Martin SE, Peng DH, Gruber SB. A novel BAP1 mutation is associated with melanocytic neoplasms and thyroid cancer. Cancer Genet 2015; 209:75-81. [PMID: 26774355 DOI: 10.1016/j.cancergen.2015.12.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 11/11/2015] [Accepted: 12/12/2015] [Indexed: 12/28/2022]
Abstract
Germline mutations in the tumor suppressor gene, BRCA-1 associated protein (BAP1), underlie a tumor predisposition syndrome characterized by increased risk for numerous cancers including uveal melanoma, melanocytic tumors and mesothelioma, among others. In the present study we report the identification of a novel germline BAP1 mutation, c.1777C>T, which produces a truncated BAP1 protein product and segregates with cancer. Family members with this mutation demonstrated a primary clinical phenotype of autosomal dominant, early-onset melanocytic neoplasms with immunohistochemistry (IHC) of these tumors demonstrating lack of BAP1 protein expression. In addition, family members harboring the BAP1 c.1777C>T germline mutation developed other neoplastic disease including thyroid cancer. IHC analysis of the thyroid cancer, as well, demonstrated loss of BAP1 protein expression. Our investigation identifies a new BAP1 mutation, further highlights the relevance of BAP1 as a clinically important tumor suppressor gene, and broadens the range of cancers associated with BAP1 inactivation. Further study will be required to understand the full scope of BAP1-associated neoplastic disease.
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Affiliation(s)
- Kevin J McDonnell
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Gregory T Gallanis
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Kathleen A Heller
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Marilena Melas
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Gregory E Idos
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Julie O Culver
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Sue-Ellen Martin
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA; Keck School of Medicine, Department of Pathology, University of Southern California, Los Angeles, CA, USA
| | - David H Peng
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA; Department of Dermatology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Stephen B Gruber
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA.
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Demasi M, Simões V, Bonatto D. Cross-talk between redox regulation and the ubiquitin-proteasome system in mammalian cell differentiation. Biochim Biophys Acta Gen Subj 2014; 1850:1594-606. [PMID: 25450485 DOI: 10.1016/j.bbagen.2014.10.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 10/24/2014] [Accepted: 10/28/2014] [Indexed: 12/15/2022]
Abstract
BACKGROUND Embryogenesis and stem cell differentiation are complex and orchestrated signaling processes. Reactive oxygen species (ROS) act as essential signal transducers in cellular differentiation, as has been shown through recent discoveries. On the other hand, the ubiquitin-proteasome system (UPS) has long been known to play an important role in all cellular regulated processes, including differentiation. SCOPE OF REVIEW In the present review, we focus on findings that highlight the interplay between redox signaling and the UPS regarding cell differentiation. Through systems biology analyses, we highlight major routes during cardiomyocyte differentiation based on redox signaling and UPS modulation. MAJOR CONCLUSION Oxygen availability and redox signaling are fundamental regulators of cell fate upon differentiation. The UPS plays an important role in the maintenance of pluripotency and the triggering of differentiation. GENERAL SIGNIFICANCE Cellular differentiation has been a matter of intense investigation mainly because of its potential therapeutic applications. Understanding regulatory mechanisms underlying cell differentiation is an important issue. Correspondingly, the role of UPS and regulation of redox processes have been emerged as essential factors to control the fate of cells upon differentiation. This article is part of a Special Issue entitled Redox regulation of differentiation and de-differentiation.
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Affiliation(s)
- Marilene Demasi
- Laboratory of Biochemistry and Biophysics, Instituto Butantan, São Paulo, SP, Brazil.
| | - Vanessa Simões
- Department of Genetics and Evolutive Biology, IB, Universidade de São Paulo, São Paulo, Brazil
| | - Diego Bonatto
- Center of Biotechnology, Universidade Federal do Rio Grande do Sul., Porto Alegre, RS, Brazil.
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The role of ubiquitin and ubiquitin-like modification systems in papillomavirus biology. Viruses 2014; 6:3584-611. [PMID: 25254385 PMCID: PMC4189040 DOI: 10.3390/v6093584] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 09/17/2014] [Accepted: 09/18/2014] [Indexed: 12/12/2022] Open
Abstract
Human papillomaviruses (HPVs) are small DNA viruses that are important etiological agents of a spectrum of human skin lesions from benign to malignant. Because of their limited genome coding capacity they express only a small number of proteins, only one of which has enzymatic activity. Additionally, the HPV productive life cycle is intimately tied to the epithelial differentiation program and they must replicate in what are normally non-replicative cells, thus, these viruses must reprogram the cellular environment to achieve viral reproduction. Because of these limitations and needs, the viral proteins have evolved to co-opt cellular processes primarily through protein-protein interactions with critical host proteins. The ubiquitin post-translational modification system and the related ubiquitin-like modifiers constitute a widespread cellular regulatory network that controls the levels and functions of thousands of proteins, making these systems an attractive target for viral manipulation. This review describes the interactions between HPVs and the ubiquitin family of modifiers, both to regulate the viral proteins themselves and to remodel the host cell to facilitate viral survival and reproduction.
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