1
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Liu C, Xie Y, Chen X, Liu L, Liu C, Yin Z. BAF45D-binding to HOX genes was differentially targeted in H9-derived spinal cord neural stem cells. Sci Rep 2024; 14:29. [PMID: 38168763 PMCID: PMC10761701 DOI: 10.1038/s41598-023-50939-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 12/28/2023] [Indexed: 01/05/2024] Open
Abstract
Chromatin accessibility has been used to define how cells adopt region-specific neural fates. BAF45D is one of the subunits of a specialised chromatin remodelling BAF complex. It has been reported that BAF45D is expressed in spinal cord neural stem cells (NSCs) and regulates their fate specification. Within the developing vertebrate spinal cord, HOX genes exhibit spatially restricted expression patterns. However, the chromatin accessibility of BAF45D binding HOX genes in spinal cord NSCs is unclear. In the present study, we found that in H9-derived spinal cord NSCs, BAF45D targets TBX6, a gene that regulates spinal cord neural mesodermal progenitors. Furthermore, BAF45D binding to the NES gene is much more enriched in H9-derived spinal cord NSCs chromatin compared to ESCs chromatin. In addition, BAF45D binding to anterior and trunk/central HOX genes, but not to lumbosacral HOX genes, was much more enriched in NSCs chromatin compared to ESCs chromatin. These results may shed new light on the role of BAF45D in regulating region-specific spinal cord NSCs by targeting HOX genes.
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Affiliation(s)
- Chang Liu
- Department of Orthopedics, The First Affiliated Hospital, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Yuxin Xie
- Department of Histology and Embryology, Institute of Stem Cell and Tissue Engineering, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Xueying Chen
- Department of Histology and Embryology, Institute of Stem Cell and Tissue Engineering, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Lihua Liu
- Institute of Clinical Pharmacology, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Chao Liu
- Department of Histology and Embryology, Institute of Stem Cell and Tissue Engineering, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, Anhui, China.
| | - Zongsheng Yin
- Department of Orthopedics, The First Affiliated Hospital, Anhui Medical University, Hefei, 230032, Anhui, China.
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2
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Jeong DW, Park JW, Kim KS, Kim J, Huh J, Seo J, Kim YL, Cho JY, Lee KW, Fukuda J, Chun YS. Palmitoylation-driven PHF2 ubiquitination remodels lipid metabolism through the SREBP1c axis in hepatocellular carcinoma. Nat Commun 2023; 14:6370. [PMID: 37828054 PMCID: PMC10570296 DOI: 10.1038/s41467-023-42170-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 10/02/2023] [Indexed: 10/14/2023] Open
Abstract
Palmitic acid (PA) is the most common fatty acid in humans and mediates palmitoylation through its conversion into palmitoyl coenzyme A. Although palmitoylation affects many proteins, its pathophysiological functions are only partially understood. Here we demonstrate that PA acts as a molecular checkpoint of lipid reprogramming in HepG2 and Hep3B cells. The zinc finger DHHC-type palmitoyltransferase 23 (ZDHHC23) mediates the palmitoylation of plant homeodomain finger protein 2 (PHF2), subsequently enhancing ubiquitin-dependent degradation of PHF2. This study also reveals that PHF2 functions as a tumor suppressor by acting as an E3 ubiquitin ligase of sterol regulatory element-binding protein 1c (SREBP1c), a master transcription factor of lipogenesis. PHF2 directly destabilizes SREBP1c and reduces SREBP1c-dependent lipogenesis. Notably, SREBP1c increases free fatty acids in hepatocellular carcinoma (HCC) cells, and the consequent PA induction triggers the PHF2/SREBP1c axis. Since PA seems central to activating this axis, we suggest that levels of dietary PA should be carefully monitored in patients with HCC.
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Affiliation(s)
- Do-Won Jeong
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Korea
- Department of Physiology, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Jong-Wan Park
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Korea
- Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Kyeong Seog Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Korea
- Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, Seoul, 03080, Korea
| | - Jiyoung Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - June Huh
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Korea
| | - Jieun Seo
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Korea
- Department of Physiology, Seoul National University College of Medicine, Seoul, 03080, Korea
- Faculty of Engineering, Yokohama National University, Yokohama, 240-8501, Japan
| | - Ye Lee Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Korea
- Department of Physiology, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Joo-Youn Cho
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Korea
- Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, Seoul, 03080, Korea
| | - Kwang-Woong Lee
- Department of Surgery, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Junji Fukuda
- Faculty of Engineering, Yokohama National University, Yokohama, 240-8501, Japan
| | - Yang-Sook Chun
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Korea.
- Department of Physiology, Seoul National University College of Medicine, Seoul, 03080, Korea.
- Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, 03080, Korea.
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3
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Zhao T, Liu C, Liu L, Wang X, Liu C. Aging-accelerated differential production and aggregation of STAT3 protein in neuronal cells and neural stem cells in the male mouse spinal cord. Biogerontology 2023; 24:137-148. [PMID: 36550376 DOI: 10.1007/s10522-022-10004-z] [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: 10/10/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022]
Abstract
Aging-affected cellular compositions of the spinal cord are diverse and region specific. Age leads to the accumulation of abnormal protein aggregates and dysregulation of proteostasis. Dysregulated proteostasis and protein aggregates result from dysfunction of the ubiquitin-proteasome system (UPS) and autophagy. Understanding the molecular mechanisms of spinal cord aging is essential and important for scientists to discover new therapies for rejuvenation. We found age-related increases in STAT3 and decreases in Tuj1 in aging mouse spinal cords, which was characterized by increased expression of P16. Coaggregation of lysine-48 and lysine-63 ubiquitin with STAT3 was revealed in aging mouse spinal cords. STAT3-ubiquitin aggregates formed via lysine-48 and lysine-63 linkages were increased significantly in the aging spinal cords but not in central canal ependymal cells or neural stem cells in the spinal cord. These results highlight the increase in STAT3 and its region-specific aggregation and ubiquitin-conjugation during spinal cord aging.
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Affiliation(s)
- Tianyi Zhao
- Department of Histology and Embryology, School of Basic Medical Sciences, Institute of Stem Cell and Tissue Engineering, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Chang Liu
- Department of Orthopedics and Spine Surgery, The First Affiliated Hospital, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Lihua Liu
- Institute of Clinical Pharmacology, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Xinmeng Wang
- Department of Histology and Embryology, School of Basic Medical Sciences, Institute of Stem Cell and Tissue Engineering, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Chao Liu
- Department of Histology and Embryology, School of Basic Medical Sciences, Institute of Stem Cell and Tissue Engineering, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China.
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4
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Targeting CSC-related transcription factors by E3 ubiquitin ligases for cancer therapy. Semin Cancer Biol 2022; 87:84-97. [PMID: 36371028 DOI: 10.1016/j.semcancer.2022.11.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/07/2022] [Accepted: 11/07/2022] [Indexed: 11/10/2022]
Abstract
Evidence has revealed that transcription factors play essential roles in regulation of multiple cellular processes, including cell proliferation, metastasis, EMT, cancer stem cells and chemoresistance. Dysregulated expression levels of transcription factors contribute to tumorigenesis and malignant progression. The expression of transcription factors is tightly governed by several signaling pathways, noncoding RNAs and E3 ubiquitin ligases. Cancer stem cells (CSCs) have been validated in regulation of tumor metastasis, reoccurrence and chemoresistance in human cancer. Transcription factors have been verified to participate in regulation of CSC formation, including Oct4, SOX2, KLF4, c-Myc, Nanog, GATA, SALL4, Bmi-1, OLIG2, POU3F2 and FOX proteins. In this review article, we will describe the critical role of CSC-related transcription factors. We will further discuss which E3 ligases regulate the degradation of these CSC-related transcription factors and their underlying mechanisms. We also mentioned the functions and mechanisms of EMT-associated transcription factors such as ZEB1, ZEB2, Snail, Slug, Twist1 and Twist2. Furthermore, we highlight the therapeutic potential via targeting E3 ubiquitin ligases for modulation of these transcription factors.
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5
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Characterization of Novel Exopolysaccharides from Enterococcus hirae WEHI01 and Its Immunomodulatory Activity. Foods 2022; 11:foods11213538. [DOI: 10.3390/foods11213538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/23/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
Exopolysaccharide (EPS) from probiotic Enterococcus hirae WEHI01 was isolated and purified by anion exchange chromatography and gel chromatography, the results of which show that the EPS consists of four fractions, namely I01-1, I01-2, I01-3, and I01-4. As the main purification components, I01-2 and I01-4 were preliminarily characterized for their structure and their immunomodulatory activity was explored. The molecular weight of I01-2 was 2.28 × 104 Da, which consists mainly of galactose, and a few other sugars including glucose, arabinose, mannose, xylose, fucose, and rhamnose, while the I01-4 was composed of galactose only and has a molecular weight of 2.59 × 104 Da. Furthermore, the results of an evaluation of immunomodulatory activity revealed that I01-2 and I01-4 could improve the viability of macrophage cells, improve phagocytosis, boost NO generation, and encourage the release of cytokines including TNF-α and IL-6 in RAW 264.7 macrophages. These results imply that I01-2 and I01-4 could improve macrophage-mediated immune responses and might be useful in the production of functional food and medications.
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6
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Ubiquitin-Specific Protease 3 Deubiquitinates and Stabilizes Oct4 Protein in Human Embryonic Stem Cells. Int J Mol Sci 2021; 22:ijms22115584. [PMID: 34070420 PMCID: PMC8197518 DOI: 10.3390/ijms22115584] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/21/2021] [Accepted: 05/22/2021] [Indexed: 11/16/2022] Open
Abstract
Oct4 is an important mammalian POU family transcription factor expressed by early human embryonic stem cells (hESCs). The precise level of Oct4 governs the pluripotency and fate determination of hESCs. Several post-translational modifications (PTMs) of Oct4 including phosphorylation, ubiquitination, and SUMOylation have been reported to regulate its critical functions in hESCs. Ubiquitination and deubiquitination of Oct4 should be well balanced to maintain the pluripotency of hESCs. The protein turnover of Oct4 is regulated by several E3 ligases through ubiquitin-mediated degradation. However, reversal of ubiquitination by deubiquitinating enzymes (DUBs) has not been reported for Oct4. In this study, we generated a ubiquitin-specific protease 3 (USP3) gene knockout using the CRISPR/Cas9 system and demonstrated that USP3 acts as a protein stabilizer of Oct4 by deubiquitinating Oct4. USP3 interacts with endogenous Oct4 and co-localizes in the nucleus of hESCs. The depletion of USP3 leads to a decrease in Oct4 protein level and loss of pluripotent morphology in hESCs. Thus, our results show that USP3 plays an important role in controlling optimum protein level of Oct4 to retain pluripotency of hESCs.
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7
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Age-related changes in expression of lysine48 and lysine63 ubiquitin linkages in dopamine neurons of midbrain in mice. Neuroreport 2021; 32:569-576. [PMID: 33657079 DOI: 10.1097/wnr.0000000000001626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Ubiquitination of target proteins is mediated via different ubiquitin lysine (K) linkages and determines the protein fates. In particular, K48 ubiquitin linkage targets proteins for degradation, whereas K63 ubiquitin linkage plays a nondegradative role. Parkinson's disease is an age-onset neurodegenerative disorder, which shows selective loss of dopamine neurons in substantia nigra pars compacta (SNC) and ubiquitinated protein aggregates. However, age-related expression of K48 and K63 ubiquitin linkages in SNC dopamine neurons remains elusive. We thus sought to explore the expression of K48 and K63 ubiquitin linkages in dopamine neurons in SNCs of mice at different ages with morphological and biochemical assays. Here our results indicated that in 5-week-old mice, dopamine neurons presented higher levels of K48 and K63 ubiquitin linkages than nondopamine neural cells. Aging promoted the formation of protein aggregates that are positive for both K48 and K63 ubiquitin linkages, together with tyrosine hydroxylase, a dopamine neuron marker. Moreover, 21-month-old mice showed fewer neural cells and tyrosine hydroxylase positive neurons in the SNCs than younger mice. Through biochemical analysis, the 21-month-old mice were shown to express more K48 ubiquitin linkages and less tyrosine hydroxylase and NeuN than the 5-week-old mice. These results suggest the first time that expression of K48 and K63 ubiquitin lysine linkages in midbrain dopamine neurons is age-related and may be involved in the loss of dopamine neurons.
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8
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Wu Y, Zhang W. The Role of E3s in Regulating Pluripotency of Embryonic Stem Cells and Induced Pluripotent Stem Cells. Int J Mol Sci 2021; 22:1168. [PMID: 33503896 PMCID: PMC7865285 DOI: 10.3390/ijms22031168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 01/15/2021] [Accepted: 01/20/2021] [Indexed: 12/14/2022] Open
Abstract
Pluripotent embryonic stem cells (ESCs) are derived from early embryos and can differentiate into any type of cells in living organisms. Induced pluripotent stem cells (iPSCs) resemble ESCs, both of which serve as excellent sources to study early embryonic development and realize cell replacement therapies for age-related degenerative diseases and other cell dysfunction-related illnesses. To achieve these valuable applications, comprehensively understanding of the mechanisms underlying pluripotency maintenance and acquisition is critical. Ubiquitination modifies proteins with Ubiquitin (Ub) at the post-translational level to monitor protein stability and activity. It is extensively involved in pluripotency-specific regulatory networks in ESCs and iPSCs. Ubiquitination is achieved by sequential actions of the Ub-activating enzyme E1, Ub-conjugating enzyme E2, and Ub ligase E3. Compared with E1s and E2s, E3s are most abundant, responsible for substrate selectivity and functional diversity. In this review, we focus on E3 ligases to discuss recent progresses in understanding how they regulate pluripotency and somatic cell reprogramming through ubiquitinating core ESC regulators.
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Affiliation(s)
| | - Weiwei Zhang
- College of Life Sciences, Capital Normal University, Beijing 100048, China;
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9
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Cellular Functions of OCT-3/4 Regulated by Ubiquitination in Proliferating Cells. Cancers (Basel) 2020; 12:cancers12030663. [PMID: 32178477 PMCID: PMC7139964 DOI: 10.3390/cancers12030663] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 03/07/2020] [Accepted: 03/09/2020] [Indexed: 12/18/2022] Open
Abstract
Octamer-binding transcription factor 3/4 (OCT-3/4), which is involved in the tumorigenesis of somatic cancers, has diverse functions during cancer development. Overexpression of OCT-3/4 has been detected in various human somatic tumors, indicating that OCT-3/4 activation may contribute to the development and progression of cancers. Stem cells can undergo self-renewal, pluripotency, and reprogramming with the help of at least four transcription factors, OCT-3/4, SRY box-containing gene 2 (SOX2), Krüppel-like factor 4 (KLF4), and c-MYC. Of these, OCT-3/4 plays a critical role in maintenance of undifferentiated state of embryonic stem cells (ESCs) and in production of induced pluripotent stem cells (iPSCs). Stem cells can undergo partitioning through mitosis and separate into specific cell types, three embryonic germ layers: the endoderm, the mesoderm, and the trophectoderm. It has been demonstrated that the stability of OCT-3/4 is mediated by the ubiquitin-proteasome system (UPS), which is one of the key cellular mechanisms for cellular homeostasis. The framework of the mechanism is simple, but the proteolytic machinery is complicated. Ubiquitination promotes protein degradation, and ubiquitination of OCT-3/4 leads to regulation of cellular proliferation and differentiation. Therefore, it is expected that OCT-3/4 may play a key role in proliferation and differentiation of proliferating cells.
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10
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Gotoh M, Kaminuma O, Nakaya A, Saeki M, Nishimura T, Kitamura N, Hiroi T, Okubo K. Association of Basophil-Expressing Genes with Effectiveness of Sublingual Immunotherapy. J NIPPON MED SCH 2020; 87:49-52. [PMID: 31564689 DOI: 10.1272/jnms.jnms.2020_87-104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Basophils were reported to be associated with allergy pathogenesis and the efficacy of allergen immunotherapy. Using a purified cedar allergen, we recently studied the effectiveness of sublingual immunotherapy for patients with Japanese cedar pollinosis. Patients were classified as high responders (HR) and nonresponders (NR), and comprehensive microarray analysis was used to examine peripheral basophils in both groups. A total of 153 genes were differentially expressed in HR and NR patients. Most of these differentially expressed genes encoded intracellular molecules, and expression levels were higher in HR patients than in NR patients. mRNA expression of the gene encoding D4, zinc, and double plant homeodomain (PHD) fingers family 2 (DPF2) was significantly correlated with copy number variation (CNV). Genetic variation in the DPF2 gene and its expression in basophils might be associated with the efficacy of sublingual immunotherapy.
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Affiliation(s)
- Minoru Gotoh
- Department of Otorhinolaryngology, Nippon Medical School.,Allergy and Immunology Project, The Tokyo Metropolitan Institute of Medical Science
| | - Osamu Kaminuma
- Allergy and Immunology Project, The Tokyo Metropolitan Institute of Medical Science.,Department of Disease Model, Research Institute of Radiation Biology and Medicine, Hiroshima University
| | - Akihiro Nakaya
- Allergy and Immunology Project, The Tokyo Metropolitan Institute of Medical Science.,Department of Genome Informatics, Graduate School of Medicine, Osaka University
| | - Mayumi Saeki
- Allergy and Immunology Project, The Tokyo Metropolitan Institute of Medical Science
| | - Tomoe Nishimura
- Allergy and Immunology Project, The Tokyo Metropolitan Institute of Medical Science
| | - Noriko Kitamura
- Allergy and Immunology Project, The Tokyo Metropolitan Institute of Medical Science
| | - Takachika Hiroi
- Allergy and Immunology Project, The Tokyo Metropolitan Institute of Medical Science
| | - Kimihiro Okubo
- Department of Otorhinolaryngology, Nippon Medical School.,Allergy and Immunology Project, The Tokyo Metropolitan Institute of Medical Science
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11
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Liu Z, Liu L, Sun R, Liu C. BAF45D knockdown decreases cell viability, inhibits colony formation, induces cell apoptosis and S-phase arrest in human pancreatic cancer cells. Biosci Biotechnol Biochem 2020; 84:1146-1152. [PMID: 32024442 DOI: 10.1080/09168451.2020.1717923] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Pancreatic cancer, an extremely aggressive malignancy, is resistant to chemo- or radiotherapy. The rapid progression of pancreatic cancer without distinctive clinical sign makes early diagnosing and/or treating very difficult. BAF45D, a member of the d4 domain family, is involved in oncogenic processes. However, the role of BAF45D in pancreatic tumorigenesis is largely unclear. Our goal is to examine BAF45D protein expression after lentivirus-mediated Baf45d RNAi and explore the effects of BAF45D knockdown on cell proliferation, cell apoptosis, and cell cycle of human pancreatic cancer cells. Here our results showed that Baf45d RNAi downregulated BAF45D protein levels and decreased cell viability, increased cell apoptosis, and decreased colony formation in BxPC-3 cells. Moreover, BAF45D knockdown induced S-phase arrest in BxPC-3 cells. Our results here suggest that BAF45D may play a crucial role in tumorigenic properties of human pancreatic cancer cells.
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Affiliation(s)
- Zengyi Liu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Lihua Liu
- Institute of Clinical Pharmacology, Anhui Medical University, Hefei, China
| | - Ruyu Sun
- Department of Histology and Embryology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Chao Liu
- Department of Histology and Embryology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
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12
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de Dieuleveult M, Miotto B. Ubiquitin Dynamics in Stem Cell Biology: Current Challenges and Perspectives. Bioessays 2020; 42:e1900129. [PMID: 31967345 DOI: 10.1002/bies.201900129] [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: 07/29/2019] [Revised: 12/18/2019] [Indexed: 11/09/2022]
Abstract
Ubiquitination plays a central role in the regulation of stem cell self-renewal, propagation, and differentiation. In this review, the functions of ubiquitin dynamics in a myriad of cellular processes, acting along side the pluripotency network, to regulate embryonic stem cell identity are highlighted. The implication of deubiquitinases (DUBs) and E3 Ubiquitin (Ub) ligases in cellular functions beyond protein degradation is reported, including key functions in the regulation of mRNA stability, protein translation, and intra-cellular trafficking; and how it affects cell metabolism, the micro-environment, and chromatin organization is discussed. Finally, unsolved issues in the field are emphasized and will need to be tackled in order to fully understand the contribution of ubiquitin dynamics to stem cell self-renewal and differentiation.
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Affiliation(s)
- Maud de Dieuleveult
- Université de Paris, Institut Cochin, INSERM, U1016, CNRS, UMR8104, F-75014, Paris, France
| | - Benoit Miotto
- Université de Paris, Institut Cochin, INSERM, U1016, CNRS, UMR8104, F-75014, Paris, France
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13
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Wang Z, Huang J, Liu C, Liu L, Shen Y, Shen C, Liu C. BAF45D Downregulation in Spinal Cord Ependymal Cells Following Spinal Cord Injury in Adult Rats and Its Potential Role in the Development of Neuronal Lesions. Front Neurosci 2019; 13:1151. [PMID: 31736692 PMCID: PMC6828649 DOI: 10.3389/fnins.2019.01151] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 10/11/2019] [Indexed: 02/06/2023] Open
Abstract
The endogenous spinal cord ependymal cells (SCECs), which form the central canal (CC), are critically involved in proliferation, differentiation and migration after spinal cord injury (SCI) and represents a repair cell source in treating SCI. Previously, we reported that BAF45D is expressed in the SCECs and the spinal cord neurons in adult mice and knockdown of BAF45D fail to induce expression of PAX6, a neurogenic fate determinant, during early neural differentiation of human embryonic stem cells. However, the effects of SCI on expression of BAF45D have not been reported. The aim of this study is to explore the expression and potential role of BAF45D in rat SCI model. In this study, adult rats were randomly divided into intact, sham, and SCI groups. We first explored expression of BAF45D in the SCECs in intact adult rats. We then explored SCI-induced loss of motor neurons and lesion of neurites in the anterior horns induced by the SCI. We also investigated whether the SCI-induced lesions in SCECs are accompanied by the motor neuron lesions. Finally, we examined the effect of BAF45D knockdown on cell growth in neuro2a cells. Our data showed that BAF45D is expressed in SCECs, neurons, and oligodendrocytes but not astrocytes in the spinal cords of intact adult rats. After SCI, the structure of CC was disrupted and the BAF45D-positive SCEC-derivatives were decreased. During the early stages of SCI, when shape of CC was affected but there was no disruption in circular structure of the SCECs, it was evident that there was a significant reduction in the number of neurites and motor neurons in the anterior horns compared with those of intact rats. In comparison, a complete loss of SCECs accompanied by further loss of motor neurons but not neurites was observed at the later stage. BAF45D knockdown was also found to inhibit cell growth in neuro2a cells. These results highlight the decreased expression of BAF45D in SCI-injured SCECs and the potential role of BAF45D downregulation in development of neuronal lesion after SCI in adult rats.
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Affiliation(s)
- Zhenzhen Wang
- Department of Spine Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,School of Basic Medical Sciences, Anhui Medical University, Hefei, China.,Department of Histology and Embryology, Anhui Medical University, Hefei, China.,Institute of Stem Cell and Tissue Engineering, Anhui Medical University, Hefei, China
| | - Jian Huang
- Department of Spine Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,School of Basic Medical Sciences, Anhui Medical University, Hefei, China.,Department of Histology and Embryology, Anhui Medical University, Hefei, China.,Institute of Stem Cell and Tissue Engineering, Anhui Medical University, Hefei, China
| | - Chang Liu
- Department of Spine Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Lihua Liu
- Institute of Clinical Pharmacology, Anhui Medical University, Hefei, China
| | - Yuxian Shen
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Cailiang Shen
- Department of Spine Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Chao Liu
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China.,Department of Histology and Embryology, Anhui Medical University, Hefei, China.,Institute of Stem Cell and Tissue Engineering, Anhui Medical University, Hefei, China
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14
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Choi J, Baek KH. Cellular functions of stem cell factors mediated by the ubiquitin-proteasome system. Cell Mol Life Sci 2018; 75:1947-1957. [PMID: 29423528 PMCID: PMC11105287 DOI: 10.1007/s00018-018-2770-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 01/12/2018] [Accepted: 02/01/2018] [Indexed: 12/16/2022]
Abstract
Stem cells undergo partitioning through mitosis and separate into specific cells of each of the three embryonic germ layers: endoderm, mesoderm, and ectoderm. Pluripotency, reprogramming, and self-renewal are essential elements of embryonic stem cells (ESCs), and it is becoming evident that regulation of protein degradation mediated by the ubiquitin-proteasome system (UPS) is one of the key cellular mechanisms in ESCs. Although the framework of that mechanism may seem simple, it involves complicated proteolytic machinery. The UPS controls cell development, survival, differentiation, lineage commitment, migration, and homing processes. This review is centered on the connection between stem cell factors NANOG, OCT-3/4, SOX2, KLF4, C-MYC, LIN28, FAK, and telomerase and the UPS. Herein, we summarize recent findings and discuss potential UPS mechanisms involved in pluripotency, reprogramming, differentiation, and self-renewal. Interactions between the UPS and stem cell transcription factors can apply to various human diseases which can be treated by generating more efficient iPSCs. Such complexes may permit the design of novel therapeutics and the establishment of biomarkers that may be used in diagnosis and prognosis development. Therefore, the UPS is an important target for stem cell therapeutic product research.
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Affiliation(s)
- Jihye Choi
- Department of Biomedical Science, CHA Stem Cell Institute, CHA University, 335 Pangyo-Ro, Bundang-Gu, Seongnam-Si, Gyeonggi-Do, 13488, Republic of Korea
| | - Kwang-Hyun Baek
- Department of Biomedical Science, CHA Stem Cell Institute, CHA University, 335 Pangyo-Ro, Bundang-Gu, Seongnam-Si, Gyeonggi-Do, 13488, Republic of Korea.
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15
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Post-translational modification of OCT4 in breast cancer tumorigenesis. Cell Death Differ 2018; 25:1781-1795. [PMID: 29511337 PMCID: PMC6180041 DOI: 10.1038/s41418-018-0079-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 01/08/2018] [Accepted: 01/24/2018] [Indexed: 01/06/2023] Open
Abstract
Recurrence and drug resistance of breast cancer are still the main reasons for breast cancer-associated deaths. Cancer stem cell (CSC) model has been proposed as a hypothesis for the lethality of breast cancer. Molecular mechanisms underlying CSC maintenance are still unclear. In this study, we generated mammospheres derived from breast cancer MDA-MB231 cells and MCF7 cells to enrich CSCs and performed DNA microarray analysis. We found that the expression of carboxy terminus of HSP70-interacting protein (CHIP) E3 ubiquitin ligase was significantly downregulated in breast CSCs. CHIP depletion increased mammosphere formation, whereas CHIP overexpression reversed this effect. We identified interactomes by mass spectrometry and detected CHIP directly interacted with OCT4, a stemness factor. CHIP overexpression decreased OCT4 stability through proteasomal degradation. CHIP induced OCT4 ubiquitination, whereas H260Q, a catalytic CHIP mutant, did not. Interestingly, we determined that OCT4 was ubiquitinated at lysine 284, and CHIP overexpression did not degrade K284R mutant OCT4. CHIP overexpression decreased the proliferation and side population of breast cancer cells, but these were not occurred in K284R mutant OCT4 overexpressed cells. Only 1000 cells showing CHIP depletion or OCT4 overexpression sufficiently generated breast tumors and lung metastases in xenografted mice. Ubiquitination-defective mutant of OCT4(K284R) overexpressed cells drastically generated tumor burdens in mice. Patients with breast cancer who showed low CHIP expression had poor survival probability. Taken together, we suggest that CHIP-induced OCT4 ubiquitination is important in breast CSCs. Regulation of CHIP expression and OCT4 protein stability is a considerable approach for breast cancer therapy.
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16
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Vasileiou G, Vergarajauregui S, Endele S, Popp B, Büttner C, Ekici AB, Gerard M, Bramswig NC, Albrecht B, Clayton-Smith J, Morton J, Tomkins S, Low K, Weber A, Wenzel M, Altmüller J, Li Y, Wollnik B, Hoganson G, Plona MR, Cho MT, Thiel CT, Lüdecke HJ, Strom TM, Calpena E, Wilkie AOM, Wieczorek D, Engel FB, Reis A. Mutations in the BAF-Complex Subunit DPF2 Are Associated with Coffin-Siris Syndrome. Am J Hum Genet 2018; 102:468-479. [PMID: 29429572 DOI: 10.1016/j.ajhg.2018.01.014] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/17/2018] [Indexed: 12/31/2022] Open
Abstract
Variants affecting the function of different subunits of the BAF chromatin-remodelling complex lead to various neurodevelopmental syndromes, including Coffin-Siris syndrome. Furthermore, variants in proteins containing PHD fingers, motifs recognizing specific histone tail modifications, have been associated with several neurological and developmental-delay disorders. Here, we report eight heterozygous de novo variants (one frameshift, two splice site, and five missense) in the gene encoding the BAF complex subunit double plant homeodomain finger 2 (DPF2). Affected individuals share common clinical features described in individuals with Coffin-Siris syndrome, including coarse facial features, global developmental delay, intellectual disability, speech impairment, and hypoplasia of fingernails and toenails. All variants occur within the highly conserved PHD1 and PHD2 motifs. Moreover, missense variants are situated close to zinc binding sites and are predicted to disrupt these sites. Pull-down assays of recombinant proteins and histone peptides revealed that a subset of the identified missense variants abolish or impaire DPF2 binding to unmodified and modified H3 histone tails. These results suggest an impairment of PHD finger structural integrity and cohesion and most likely an aberrant recognition of histone modifications. Furthermore, the overexpression of these variants in HEK293 and COS7 cell lines was associated with the formation of nuclear aggregates and the recruitment of both wild-type DPF2 and BRG1 to these aggregates. Expression analysis of truncating variants found in the affected individuals indicated that the aberrant transcripts escape nonsense-mediated decay. Altogether, we provide compelling evidence that de novo variants in DPF2 cause Coffin-Siris syndrome and propose a dominant-negative mechanism of pathogenicity.
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Affiliation(s)
- Georgia Vasileiou
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Silvia Vergarajauregui
- Experimental Renal and Cardiovascular Research, Institute of Pathology, Department of Nephropathology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Sabine Endele
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Bernt Popp
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Christian Büttner
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Arif B Ekici
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Marion Gerard
- Génétique Clinique, Centre Hospitalier Universitaire de Caen, Caen 14000, France
| | - Nuria C Bramswig
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, 45122 Essen, Germany
| | - Beate Albrecht
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, 45122 Essen, Germany
| | - Jill Clayton-Smith
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9WL, UK
| | - Jenny Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's Hospital NHS Foundation Trust, Birmingham B15 2TG, UK
| | - Susan Tomkins
- Clinical Genetics Service, University Hospitals of Bristol NHS Foundation Trust, Bristol BS2 8HW, UK
| | - Karen Low
- Clinical Genetics Service, University Hospitals of Bristol NHS Foundation Trust, Bristol BS2 8HW, UK
| | - Astrid Weber
- Merseyside and Cheshire Clinical Genetics Service, Liverpool Women's NHS Foundation Hospital Trust, Liverpool L8 7SS, UK
| | | | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany
| | - Yun Li
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - George Hoganson
- Pediatric Genetics, University of Illinois Hospital, Chicago, IL 60612, USA
| | - Maria-Renée Plona
- Pediatric Genetics, University of Illinois Hospital, Chicago, IL 60612, USA
| | | | - Christian T Thiel
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Hermann-Josef Lüdecke
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, 45122 Essen, Germany; Institut für Humangenetik, Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Tim M Strom
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Eduardo Calpena
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Andrew O M Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Dagmar Wieczorek
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, 45122 Essen, Germany; Institut für Humangenetik, Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Felix B Engel
- Experimental Renal and Cardiovascular Research, Institute of Pathology, Department of Nephropathology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany.
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17
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Liu C, Sun R, Huang J, Zhang D, Huang D, Qi W, Wang S, Xie F, Shen Y, Shen C. The BAF45D Protein Is Preferentially Expressed in Adult Neurogenic Zones and in Neurons and May Be Required for Retinoid Acid Induced PAX6 Expression. Front Neuroanat 2017; 11:94. [PMID: 29163067 PMCID: PMC5681484 DOI: 10.3389/fnana.2017.00094] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/13/2017] [Indexed: 02/05/2023] Open
Abstract
Adult neurogenesis is important for the development of regenerative therapies for human diseases of the central nervous system (CNS) through the recruitment of adult neural stem cells (NSCs). NSCs are characterized by the capacity to generate neurons, astrocytes, and oligodendrocytes. To identify key factors involved in manipulating the adult NSC neurogenic fate thus has crucial implications for the clinical application. Here, we report that BAF45D is expressed in the subgranular zone (SGZ) of the dentate gyrus, the subventricular zone (SVZ) of the lateral ventricle, and the central canal (CC) of the adult spinal cord. Coexpression of BAF45D with glial fibrillary acidic protein (GFAP), a radial glial like cell marker protein, was identified in the SGZ, the SVZ and the adult spinal cord CC. Quantitative analysis data indicate that BAF45D is preferentially expressed in the neurogenic zone of the LV and the neurons of the adult CNS. Furthermore, during the neuroectoderm differentiation of H9 cells, BAF45D is required for the expression of PAX6, a neuroectoderm determinant that is also known to regulate the self-renewal and neuronal fate specification of adult neural stem/progenitor cells. Together, our results may shed new light on the expression of BAF45D in the adult neurogenic zones and the contribution of BAF45D to early neural development.
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Affiliation(s)
- Chao Liu
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China.,Department of Histology and Embryology, Anhui Medical University, Hefei, China.,Institute of Stem Cell and Tissue Engineering, Anhui Medical University, Hefei, China
| | - Ruyu Sun
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China.,Department of Histology and Embryology, Anhui Medical University, Hefei, China.,Institute of Stem Cell and Tissue Engineering, Anhui Medical University, Hefei, China
| | - Jian Huang
- Department of Spine Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Dijuan Zhang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China.,Department of Histology and Embryology, Anhui Medical University, Hefei, China.,Institute of Stem Cell and Tissue Engineering, Anhui Medical University, Hefei, China
| | - Dake Huang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Weiqin Qi
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Shenghua Wang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China.,Department of Histology and Embryology, Anhui Medical University, Hefei, China.,Institute of Stem Cell and Tissue Engineering, Anhui Medical University, Hefei, China
| | - Fenfen Xie
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China.,Department of Histology and Embryology, Anhui Medical University, Hefei, China.,Institute of Stem Cell and Tissue Engineering, Anhui Medical University, Hefei, China
| | - Yuxian Shen
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Cailiang Shen
- Department of Spine Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
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18
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Data in support of DPF2 regulates OCT4 protein level and nuclear distribution. Data Brief 2015; 5:599-604. [PMID: 26958616 PMCID: PMC4773415 DOI: 10.1016/j.dib.2015.10.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 10/12/2015] [Indexed: 02/08/2023] Open
Abstract
DPF2, also named ubi-d4/requiem (REQU), interacts with a protein complex containing OCT4. This paper provides data in support of the research article entitled “DPF2 regulates OCT4 protein level and nuclear distribution”. The highlights include: (1) Denature-immunoprecipitation assay revealed ubiquitination of OCT4 in pluripotent H9 cells, which was enhancedby MG132, a proteasome inhibitor. (2) Well colocalization of ectopic OCT4 and FLAG-Ub was found in HeLa cells, which was also increased by MG132. (3) MG132 treatment decreased DPF2 cytoplasmic expression in vivo. These data give insights into how proteasome inhibition contributes to studying ubiquitnation of OCT4.
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