1
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Ngule C, Shi R, Ren X, Jia H, Oyelami F, Li D, Park Y, Kim J, Hemati H, Zhang Y, Xiong X, Shinkle A, Vanderford NL, Bachert S, Zhou BP, Wang J, Song J, Liu X, Yang JM. NAC1 promotes stemness and regulates myeloid-derived cell status in triple-negative breast cancer. Mol Cancer 2024; 23:188. [PMID: 39243032 PMCID: PMC11378519 DOI: 10.1186/s12943-024-02102-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: 02/02/2024] [Accepted: 08/27/2024] [Indexed: 09/09/2024] Open
Abstract
Triple negative breast cancer (TNBC) is a particularly lethal breast cancer (BC) subtype driven by cancer stem cells (CSCs) and an immunosuppressive microenvironment. Our study reveals that nucleus accumbens associated protein 1 (NAC1), a member of the BTB/POZ gene family, plays a crucial role in TNBC by maintaining tumor stemness and influencing myeloid-derived suppressor cells (MDSCs). High NAC1 expression correlates with worse TNBC prognosis. NAC1 knockdown reduced CSC markers and tumor cell proliferation, migration, and invasion. Additionally, NAC1 affects oncogenic pathways such as the CD44-JAK1-STAT3 axis and immunosuppressive signals (TGFβ, IL-6). Intriguingly, the impact of NAC1 on tumor growth varies with the host immune status, showing diminished tumorigenicity in natural killer (NK) cell-competent mice but increased tumorigenicity in NK cell-deficient ones. This highlights the important role of the host immune system in TNBC progression. In addition, high NAC1 level in MDSCs also supports TNBC stemness. Together, this study implies NAC1 as a promising therapeutic target able to simultaneously eradicate CSCs and mitigate immune evasion.
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Affiliation(s)
- Chrispus Ngule
- Department of Toxicology and Cancer Biology, Department of Pharmacology and Nutritional Science, and Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
| | - Ruyi Shi
- Department of Toxicology and Cancer Biology, Department of Pharmacology and Nutritional Science, and Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
- Present Address: Department of Cell Biology and Genetics, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xingcong Ren
- Department of Toxicology and Cancer Biology, Department of Pharmacology and Nutritional Science, and Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
| | - Hongyan Jia
- Department of Toxicology and Cancer Biology, Department of Pharmacology and Nutritional Science, and Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
- Present Address: Department of Breast Surgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Felix Oyelami
- Department of Toxicology and Cancer Biology, Department of Pharmacology and Nutritional Science, and Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
| | - Dong Li
- Department of Toxicology and Cancer Biology, Department of Pharmacology and Nutritional Science, and Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
| | - Younhee Park
- Department of Toxicology and Cancer Biology, Department of Pharmacology and Nutritional Science, and Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
| | - Jinhwan Kim
- Department of Biochemistry, and Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
| | - Hami Hemati
- Department of Toxicology and Cancer Biology, Department of Pharmacology and Nutritional Science, and Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
| | - Yi Zhang
- Department of Toxicology and Cancer Biology, Department of Pharmacology and Nutritional Science, and Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
- Present Address: Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Xiaofang Xiong
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX, 77807, USA
| | - Andrew Shinkle
- Department of Toxicology and Cancer Biology, Department of Pharmacology and Nutritional Science, and Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
| | - Nathan L Vanderford
- Department of Toxicology and Cancer Biology, Department of Pharmacology and Nutritional Science, and Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
| | - Sara Bachert
- Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY, 40536, USA
| | - Binhua P Zhou
- Department of Biochemistry, and Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
| | - Jianlong Wang
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Jianxun Song
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX, 77807, USA.
| | - Xia Liu
- Department of Toxicology and Cancer Biology, Department of Pharmacology and Nutritional Science, and Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY, 40536, USA.
| | - Jin-Ming Yang
- Department of Toxicology and Cancer Biology, Department of Pharmacology and Nutritional Science, and Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY, 40536, USA.
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Vendrell X, de Castro P, Escrich L, Grau N, Gonzalez-Martin R, Quiñonero A, Escribá MJ, Domínguez F. Longitudinal profiling of human androgenotes through single-cell analysis unveils paternal gene expression dynamics in early embryo development. Hum Reprod 2024; 39:1186-1196. [PMID: 38622061 PMCID: PMC11145015 DOI: 10.1093/humrep/deae072] [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: 11/06/2023] [Revised: 03/12/2024] [Indexed: 04/17/2024] Open
Abstract
STUDY QUESTION How do transcriptomics vary in haploid human androgenote embryos at single cell level in the first four cell cycles of embryo development? SUMMARY ANSWER Gene expression peaks at the fourth cell cycle, however some androcytes exhibit unique transcriptional behaviors. WHAT IS KNOWN ALREADY The developmental potential of an embryo is determined by the competence of the oocyte and the sperm. However, studies of the contribution of the paternal genome using pure haploid androgenotes are very scarce. STUDY DESIGN, SIZE, DURATION This study was performed analyzing the single-cell transcriptomic sequencing of 38 androcytes obtained from 10 androgenote bioconstructs previously produced in vitro (de Castro et al., 2023). These results were analyzed through different bioinformatics software such as g: Profiler, GSEA, Cytoscape, and Reactome. PARTICIPANTS/MATERIALS, SETTING, METHODS Single cell sequencing was used to obtain the transcriptomic profiles of the different androcytes. The results obtained were compared between the different cycles studied using the DESeq2 program and functional enrichment pathways using g: Profiler, Cytoscape, and Reactome. MAIN RESULTS AND THE ROLE OF CHANCE A wave of paternally driven transcriptomic activation was found during the third-cell cycle, with 1128 upregulated and 225 downregulated genes and the fourth-cell cycle, with 1373 upregulated and 286 downregulated genes, compared to first-cell cycle androcytes. Differentially expressed routes related to cell differentiation, DNA-binding transcription, RNA biosynthesis and RNA polymerase II transcription regulatory complex, and cell death were found in the third and fourth with respect to the first-cell cycle. Conversely, in the fourth cell cycle, 153 downregulated and 332 upregulated genes were found compared with third cell cycle, associated with differentially expressed processes related to E-box binding and zinc finger protein 652 (ZNF652) transcription factor. Further, significant overexpression of LEUTX, PRAMEF1, DUXA, RFPL4A, TRIM43, and ZNF675 found in androgenotes, compared to biparental embryos, highlights the paternal contributions to zygote genome activation. LARGE SCALE DATA All raw sequencing data are available through the Gene Expression Omnibus (GEO) under accessions number: GSE216501. LIMITATIONS, REASONS FOR CAUTION Extrapolation of biological events from uniparental constructs to biparental embryos should be done with caution. Maternal and paternal genomes do not act independently of each other in a natural condition. The absence of one genome may affect gene transcription of the other. In this sense, the haploid condition of the bioconstructs could mask the transcriptomic patterns of the single cells. WIDER IMPLICATIONS OF THE FINDINGS The results obtained demonstrated the level of involvement of the human paternal haploid genome in the early stages of embryo development as well as its evolution at the transcriptomic level, laying the groundwork for the use of these bioconstructs as reliable models to dispel doubts about the genetic role played by the paternal genome in the early cycles of embryo development. STUDY FUNDING/COMPETING INTEREST(S) This study was funded by Instituto de Salud Carlos III (ISCIII) through the project 'PI22/00924', co-funded by European Regional Development Fund (ERDF); 'A way to make Europe'. F.D. was supported by the Spanish Ministry of Economy and Competitiveness through the Miguel Servet program (CPII018/00002). M.J.E. was supported by Instituto de Salud Carlos III (PI19/00577 [M.J.E.]) and FI20/00086. P.dC. was supported by a predoctoral grant for training in research into health (PFIS PI19/00577) from the Instituto de Salud Carlos III. All authors declare having no conflict of interest with regard to this trial.
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Affiliation(s)
- X Vendrell
- Reproductive Genetics Department, Sistemas Genómicos-Synlab, Valencia, Spain
| | - P de Castro
- Research Department, IVIRMA Global Research Alliance, IVI Foundation—Reproductive Biology and Bioengineering in Human Reproduction, IIS La Fe Health Research, Valencia, Spain
| | - L Escrich
- Embryology Department, IVIRMA Valencia, Valencia, Spain
| | - N Grau
- Embryology Department, IVIRMA Valencia, Valencia, Spain
| | - R Gonzalez-Martin
- Research Department, IVIRMA Global Research Alliance, IVI Foundation—Reproductive Biology and Bioengineering in Human Reproduction, IIS La Fe Health Research, Valencia, Spain
| | - A Quiñonero
- Research Department, IVIRMA Global Research Alliance, IVI Foundation—Reproductive Biology and Bioengineering in Human Reproduction, IIS La Fe Health Research, Valencia, Spain
| | - M J Escribá
- Research Department, IVIRMA Global Research Alliance, IVI Foundation—Reproductive Biology and Bioengineering in Human Reproduction, IIS La Fe Health Research, Valencia, Spain
- Embryology Department, IVIRMA Valencia, Valencia, Spain
| | - F Domínguez
- Research Department, IVIRMA Global Research Alliance, IVI Foundation—Reproductive Biology and Bioengineering in Human Reproduction, IIS La Fe Health Research, Valencia, Spain
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3
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Xie Q, Tong C, Xiong X. An overview of the co-transcription factor NACC1: Beyond its pro-tumor effects. Life Sci 2024; 336:122314. [PMID: 38030057 DOI: 10.1016/j.lfs.2023.122314] [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: 09/05/2023] [Revised: 11/20/2023] [Accepted: 11/26/2023] [Indexed: 12/01/2023]
Abstract
Nucleus accumbens-associated protein 1 (NACC1) is a member of the broad complex, tramtrack, bric-a-brac/poxvirus and zinc finger (BTB/POZ) protein families, mainly exerting its biological functions as a transcription co-regulator. NACC1 forms homo- or hetero-dimers through the BTB/POZ or BANP, E5R, and NACC1 (BEN) domain with other transcriptional regulators to regulate downstream signals. Recently, the overexpression of NACC1 has been observed in various tumors and is positively associated with tumor progression, high recurrence rate, indicating poor prognosis. NACC1 also regulates biological processes such as embryonic development, stem cell pluripotency, innate immunity, and related diseases. Our review combines recent research to summarize advancements in the structure, biological functions, and relative molecular mechanisms of NACC1. The future development of NACC1 clinical appliances is also discussed.
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Affiliation(s)
- Qing Xie
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Nanchang University, Nanchang, 330006, China; School of Basic Medical Sciences, Nanchang University, Nanchang, 330006, China
| | - Chang Tong
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Nanchang University, Nanchang, 330006, China
| | - Xiangyang Xiong
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Nanchang University, Nanchang, 330006, China; Province Key Laboratory of Tumor Pathogens and Molecular Pathology, Nanchang University, Nanchang 330006, China.
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4
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Wang L, Peng HY, Das JK, Kumar A, Ren Y, Ballard DJ, Xiong X, Yang W, Ren X, de Figueiredo P, Yang JM, Song J. NAC1 confines virus-specific memory formation of CD4 + T cells through the ROCK1-mediated pathway. J Med Virol 2023; 95:e28957. [PMID: 37465969 PMCID: PMC10391642 DOI: 10.1002/jmv.28957] [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: 05/15/2023] [Revised: 06/30/2023] [Accepted: 07/05/2023] [Indexed: 07/20/2023]
Abstract
Nucleus accumbens-associated protein 1 (NAC1), a transcriptional cofactor, has been found to play important roles in regulating regulatory T cells, CD8+ T cells, and antitumor immunity, but little is known about its effects on T-cell memory. In this study, we found that NAC1 expression restricts memory formation of CD4+ T cells during viral infection. Analysis of CD4+ T cells from wild-type (WT) and NAC1-deficient (-/- ) mice showed that NAC1 is essential for T-cell metabolism, including glycolysis and oxidative phosphorylation, and supports CD4+ T-cell survival in vitro. We further demonstrated that a deficiency of NAC1 downregulates glycolysis and correlates with the AMPK-mTOR pathway and causes autophagy defective in CD4+ T cells. Loss of NAC1 reduced the expression of ROCK1 and the phosphorylation and stabilization of BECLIN1. However, a forced expression of ROCK1 in NAC1-/- CD4+ T cells restored autophagy and the activity of the AMPK-mTOR pathway. In animal experiments, adoptively transferred NAC1-/- CD4+ T cells or NAC1-/- mice challenged with VACV showed enhanced formation of VACV-specific CD4+ memory T cells compared to adoptively transferred WT CD4+ T cells or WT mice. This memory T-cell formation enhancement was abrogated by forcing expression of ROCK1. Our study reveals a novel role for NAC1 as a suppressor of CD4+ T-cell memory formation and suggests that targeting NAC1 could be a new approach to promoting memory CD4+ T-cell development, which is critical for an effective immune response against pathogens.
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Affiliation(s)
- Liqing Wang
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Hao-Yun Peng
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Jugal Kishore Das
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Anil Kumar
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Yijie Ren
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Darby J Ballard
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Xiaofang Xiong
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Wen Yang
- Imgen BioSciences, Fall River, MA 02723, USA
| | - Xingcong Ren
- Department of Toxicology and Cancer Biology, Department of Pharmacology and Nutritional Science, and Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Paul de Figueiredo
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77845, USA
| | - Jin-Ming Yang
- Department of Toxicology and Cancer Biology, Department of Pharmacology and Nutritional Science, and Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Jianxun Song
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
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5
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Meharwade T, Joumier L, Parisotto M, Huynh V, Lummertz da Rocha E, Malleshaiah M. Cross-activation of FGF, NODAL, and WNT pathways constrains BMP-signaling-mediated induction of the totipotent state in mouse embryonic stem cells. Cell Rep 2023; 42:112438. [PMID: 37126449 DOI: 10.1016/j.celrep.2023.112438] [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: 05/03/2022] [Revised: 11/11/2022] [Accepted: 04/11/2023] [Indexed: 05/02/2023] Open
Abstract
Embryonic stem cells (ESCs) are an attractive model to study the relationship between signaling and cell fates. Cultured mouse ESCs can exist in multiple states resembling distinct stages of early embryogenesis, such as totipotent, pluripotent, primed, and primitive endoderm. The signaling mechanisms regulating the totipotent state and coexistence of these states are poorly understood. Here we identify bone morphogenetic protein (BMP) signaling as an inducer of the totipotent state. However, we discover that BMP's role is constrained by the cross-activation of FGF, NODAL, and WNT pathways. We exploit this finding to enhance the proportion of totipotent cells by rationally inhibiting the cross-activated pathways. Single-cell mRNA sequencing reveals that induction of the totipotent state is accompanied by suppression of primed and primitive endoderm states. Furthermore, reprogrammed totipotent cells we generate in culture resemble totipotent cells of preimplantation embryo. Our findings reveal a BMP signaling mechanism regulating both the totipotent state and heterogeneity of ESCs.
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Affiliation(s)
- Thulaj Meharwade
- Montreal Clinical Research Institute (IRCM), 110 Pine Avenue West, Montreal, QC H2W 1R7, Canada; Department of Biochemistry and Molecular Medicine, University of Montreal, C.P. 6128, Succursale Centre-ville, Montreal, QC H3C 3J7, Canada
| | - Loïck Joumier
- Montreal Clinical Research Institute (IRCM), 110 Pine Avenue West, Montreal, QC H2W 1R7, Canada; Department of Biochemistry and Molecular Medicine, University of Montreal, C.P. 6128, Succursale Centre-ville, Montreal, QC H3C 3J7, Canada
| | - Maxime Parisotto
- Montreal Clinical Research Institute (IRCM), 110 Pine Avenue West, Montreal, QC H2W 1R7, Canada
| | - Vivian Huynh
- Montreal Clinical Research Institute (IRCM), 110 Pine Avenue West, Montreal, QC H2W 1R7, Canada; Molecular Biology Program, University of Montreal, C.P. 6128, Succursale Centre-ville, Montreal, QC H3C 3J7, Canada
| | - Edroaldo Lummertz da Rocha
- Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Mohan Malleshaiah
- Montreal Clinical Research Institute (IRCM), 110 Pine Avenue West, Montreal, QC H2W 1R7, Canada; Department of Biochemistry and Molecular Medicine, University of Montreal, C.P. 6128, Succursale Centre-ville, Montreal, QC H3C 3J7, Canada; Molecular Biology Program, University of Montreal, C.P. 6128, Succursale Centre-ville, Montreal, QC H3C 3J7, Canada; The Division of Experimental Medicine, McGill University, 1001 Decarie Boulevard, Montreal, QC H4A 3J1, Canada; McGill Regenerative Medicine Network, 1160 Pine Avenue West, Montreal, QC H3A 1A3, Canada.
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6
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Liu K, Zhang J, Xiao Y, Yang A, Song X, Li Y, Chen Y, Hughes TR, Min J. Structural insights into DNA recognition by the BEN domain of the transcription factor BANP. J Biol Chem 2023; 299:104734. [PMID: 37086783 DOI: 10.1016/j.jbc.2023.104734] [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: 01/06/2023] [Revised: 04/12/2023] [Accepted: 04/15/2023] [Indexed: 04/24/2023] Open
Abstract
The BEN domain-containing transcription factors regulate transcription by recruiting chromatin-modifying factors to specific chromatin regions via their DNA-binding BEN domains. The BEN domain of BANP has been shown to bind to a CGCG DNA sequence or an AAA-containing MARs (matrix attachment regions) DNA sequence. Consistent with these in vivo observations, we identified an optimal DNA binding sequence of AAATCTCG by PBM (protein binding microarray), which was also confirmed by our ITC (Isothermal Titration Calorimetry) and mutagenesis results to uncover additional mechanistic details about DNA binding by the BEN domain of BANP. We then determined crystal structures of the BANP BEN domain in apo form and in complex with a CGCG-containing DNA, respectively, which revealed that the BANP BEN domain mainly used the electrostatic interactions to bind DNA with some base-specific interactions with the TC motifs. Our ITC results also showed that BANP bound to unmethylated and methylated DNAs with comparable binding affinities. Our complex structure of BANP-mCGCG revealed that the BANP BEN domain bound to the unmethylated and methylated DNAs in a similar mode and cytosine methylation did not get involved in binding, which is also consistent with our observations from the complex structures of the BEND6 BEN domain with the CGCG or CGmCG DNAs. Taken together, our results further elucidate the elements important for DNA recognition and transcriptional regulation by the BANP BEN domain-containing transcription factor.
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Affiliation(s)
- Ke Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China.
| | - Jin Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Yuqing Xiao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Ally Yang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
| | - Xiaosheng Song
- Structural Genomics Consortium and Department of Physiology, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Yanjun Li
- Structural Genomics Consortium and Department of Physiology, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Yunxia Chen
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Timothy R Hughes
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China; Structural Genomics Consortium and Department of Physiology, University of Toronto, Toronto, Ontario M5S 3E1, Canada.
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7
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Dong S, Wang X, Yang S, Guo F, Zhang J, Ji C, Shi L, Cheng Y, Hu Y, Li Z, Peng L, Guo L, Zhu W, Ren X, Yang JM, Zhang Y. Mechanistic Insights of NAC1 Nuclear Export and Its Role in Ovarian Cancer Resistance to Docetaxel. Biochem Pharmacol 2023; 211:115533. [PMID: 37019189 DOI: 10.1016/j.bcp.2023.115533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/14/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023]
Abstract
In this study, we uncovered the nuclear export of nucleus accumbens-associated protein-1 (NAC1) as a novel mechanism involved in ovarian cancer resistance to taxanes, the chemotherapeutic drugs commonly used in treatment of this malignancy. We showed that NAC1, a nuclear factor of the BTB/POZ gene family, has a nuclear export signal (NES) at the N terminus (aa 17-28), and this NES critically contributes to the NAC1 nuclear-cytoplasmic shuttling when tumor cells were treated with docetaxel. Mechanistically, the nuclear-exported NAC1 bound to cullin3 (Cul3) and Cyclin B1 via its BTB and BOZ domains respectively, and the cyto-NAC1-Cul3 E3 ubiquitin ligase complex promotes the ubiquitination and degradation of Cyclin B1, thereby facilitating mitotic exit and leading to cellular resistance to docetaxel. We also showed in in vitro and in vivo experiments that TP-CH-1178, a membrane-permeable polypeptide against the NAC1 NES motif, blocked the nuclear export of NAC1, interfered with the degradation of Cyclin B1 and sensitized ovarian cancer cells to docetaxel. This study not only reveals a novel mechanism by which the NAC1 nuclear export is regulated and Cyclin B1 degradation and mitotic exit are impacted by the NAC1-Cul3 complex, but also provides the nuclear-export pathway of NAC1 as a potential target for modulating taxanes resistance in ovarian cancer and other malignancies.
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8
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McCalla SG, Fotuhi Siahpirani A, Li J, Pyne S, Stone M, Periyasamy V, Shin J, Roy S. Identifying strengths and weaknesses of methods for computational network inference from single-cell RNA-seq data. G3 (BETHESDA, MD.) 2023; 13:jkad004. [PMID: 36626328 PMCID: PMC9997554 DOI: 10.1093/g3journal/jkad004] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 11/09/2022] [Accepted: 12/16/2022] [Indexed: 01/11/2023]
Abstract
Single-cell RNA-sequencing (scRNA-seq) offers unparalleled insight into the transcriptional programs of different cellular states by measuring the transcriptome of thousands of individual cells. An emerging problem in the analysis of scRNA-seq is the inference of transcriptional gene regulatory networks and a number of methods with different learning frameworks have been developed to address this problem. Here, we present an expanded benchmarking study of eleven recent network inference methods on seven published scRNA-seq datasets in human, mouse, and yeast considering different types of gold standard networks and evaluation metrics. We evaluate methods based on their computing requirements as well as on their ability to recover the network structure. We find that, while most methods have a modest recovery of experimentally derived interactions based on global metrics such as Area Under the Precision Recall curve, methods are able to capture targets of regulators that are relevant to the system under study. Among the top performing methods that use only expression were SCENIC, PIDC, MERLIN or Correlation. Addition of prior biological knowledge and the estimation of transcription factor activities resulted in the best overall performance with the Inferelator and MERLIN methods that use prior knowledge outperforming methods that use expression alone. We found that imputation for network inference did not improve network inference accuracy and could be detrimental. Comparisons of inferred networks for comparable bulk conditions showed that the networks inferred from scRNA-seq datasets are often better or at par with the networks inferred from bulk datasets. Our analysis should be beneficial in selecting methods for network inference. At the same time, this highlights the need for improved methods and better gold standards for regulatory network inference from scRNAseq datasets.
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Affiliation(s)
- Sunnie Grace McCalla
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Jiaxin Li
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Saptarshi Pyne
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Matthew Stone
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Viswesh Periyasamy
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Junha Shin
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Sushmita Roy
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53792, USA
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
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Meharwade T, Joumier L, Parisotto M, Malleshaiah M. Single-cell mass cytometry analysis reveals stem cell heterogeneity. Methods 2022; 208:9-18. [DOI: 10.1016/j.ymeth.2022.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/24/2022] [Accepted: 09/29/2022] [Indexed: 11/06/2022] Open
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10
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Wang L, Kumar A, Das JK, Ren Y, Peng HY, Ballard DJ, Xiong X, Davis JR, Ren X, Yang JM, Song J. Expression of NAC1 Restrains the Memory Formation of CD8 + T Cells during Viral Infection. Viruses 2022; 14:1713. [PMID: 36016335 PMCID: PMC9414488 DOI: 10.3390/v14081713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/02/2022] [Indexed: 01/02/2023] Open
Abstract
Nucleus accumbens-associated protein 1 (NAC1) is a transcription co-factor that has been shown to possess multiple roles in stem cell and cancer biology. However, little is known about its roles in regulation of the immune system. In the current study, we observed that expression of NAC1 impacted the survival of CD8+ T cells in vitro. NAC1-/- CD8+ T cells displayed lower metabolism, including reduced glycolysis and oxidative phosphorylation. In vivo, compared with wild-type (WT) mice, NAC1-/- mice produced a lower response to vaccinia virus (VACV) infection, and viral antigen (Ag)-specific CD8+ T cells decreased more slowly. Additionally, we observed that the NAC1-/- mice demonstrated a stronger memory formation of viral Ag-specific CD8+ T cells post-viral infection. Mechanically, we identified that compared with WT CD8+ T cells, the Interferon Regulatory Factor 4 (IRF4), a key transcription factor in T cell development, was highly expressed in NAC1-/- CD8+ T cells, insinuating that IRF4 could be a critical regulatory target of NAC1 in the memory formation of CD8+ T cells. Our results indicate that NAC1 restrains the memory formation of CD8+ T cells by modulating IRF4, and targeting NAC1 may be exploited as a new approach to boosting CD8+ T cell memory.
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Affiliation(s)
- Liqing Wang
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Anil Kumar
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Jugal Kishore Das
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Yijie Ren
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Hao-Yun Peng
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Darby Jane Ballard
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Xiaofang Xiong
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Jacob Rance Davis
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Xingcong Ren
- Department of Toxicology and Cancer Biology, Department of Pharmacology and Nutritional Science, and Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Jin-Ming Yang
- Department of Toxicology and Cancer Biology, Department of Pharmacology and Nutritional Science, and Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Jianxun Song
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
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11
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Abstract
POUV is a relatively newly emerged class of POU transcription factors present in jawed vertebrates (Gnathostomata). The function of POUV-class proteins is inextricably linked to zygotic genome activation (ZGA). A large body of evidence now extends the role of these proteins to subsequent developmental stages. While some functions resemble those of other POU-class proteins and are related to neuroectoderm development, others have emerged de novo. The most notable of the latter functions is pluripotency control by Oct4 in mammals. In this review, we focus on these de novo functions in the best-studied species harbouring POUV proteins-zebrafish, Xenopus (anamniotes) and mammals (amniotes). Despite the broad diversity of their biological functions in vertebrates, POUV proteins exert a common feature related to their role in safeguarding the undifferentiated state of cells. Here we summarize numerous pieces of evidence for these specific functions of the POUV-class proteins and recap available loss-of-function data.
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Affiliation(s)
- Evgeny I. Bakhmet
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russia
| | - Alexey N. Tomilin
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russia
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12
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Gordeev MN, Bakhmet EI, Tomilin AN. Pluripotency Dynamics during Embryogenesis and in Cell Culture. Russ J Dev Biol 2021. [DOI: 10.1134/s1062360421060059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Induction of Rosette-to-Lumen stage embryoids using reprogramming paradigms in ESCs. Nat Commun 2021; 12:7322. [PMID: 34916498 PMCID: PMC8677818 DOI: 10.1038/s41467-021-27586-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 11/19/2021] [Indexed: 01/01/2023] Open
Abstract
Blastocyst-derived stem cell lines were shown to self-organize into embryo-like structures in 3D cell culture environments. Here, we provide evidence that embryo-like structures can be generated solely based on transcription factor-mediated reprogramming of embryonic stem cells in a simple 3D co-culture system. Embryonic stem cells in these cultures self-organize into elongated, compartmentalized embryo-like structures reflecting aspects of the inner regions of the early post-implantation embryo. Single-cell RNA-sequencing reveals transcriptional profiles resembling epiblast, primitive-/visceral endoderm, and extraembryonic ectoderm of early murine embryos around E4.5-E5.5. In this stem cell-based embryo model, progression from rosette formation to lumenogenesis accompanied by progression from naïve- to primed pluripotency was observed within Epi-like cells. Additionally, lineage specification of primordial germ cells and distal/anterior visceral endoderm-like cells was observed in epiblast- or visceral endoderm-like compartments, respectively. The system presented in this study allows for fast and reproducible generation of embryo-like structures, providing an additional tool to study aspects of early embryogenesis.
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14
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Mehravar M, Ghaemimanesh F, Poursani EM. An Overview on the Complexity of OCT4: at the Level of DNA, RNA and Protein. Stem Cell Rev Rep 2021; 17:1121-1136. [PMID: 33389631 DOI: 10.1007/s12015-020-10098-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2020] [Indexed: 10/22/2022]
Abstract
OCT4 plays critical roles in self-renewal and pluripotency maintenance of embryonic stem cells, and is considered as one of the main stemness markers. It also has pivotal roles in early stages of embryonic development. Most studies on OCT4 have focused on the expression and function of OCT4A, which is the biggest isoform of OCT4 known so far. Recently, many studies have shown that OCT4 has various transcript variants, protein isoforms, as well as pseudogenes. Distinguishing the expression and function of these variants and isoforms is a big challenge in expression profiling studies of OCT4. Understanding how OCT4 is functioning in different contexts, depends on knowing of where and when each of OCT4 transcripts, isoforms and pseudogenes are expressed. Here, we review OCT4 known transcripts, isoforms and pseudogenes, as well as its interactions with other proteins, and emphasize the importance of discriminating each of them in order to understand the exact function of OCT4 in stem cells, normal development and development of diseases.
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Affiliation(s)
- Majid Mehravar
- Department of Anatomy and Developmental Biology, Development and Stem Cells Program, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Fatemeh Ghaemimanesh
- Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Ensieh M Poursani
- Hematology, Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran.
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15
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Nucleus Accumbens-Associated Protein 1 Binds DNA Directly through the BEN Domain in a Sequence-Specific Manner. Biomedicines 2020; 8:biomedicines8120608. [PMID: 33327466 PMCID: PMC7764960 DOI: 10.3390/biomedicines8120608] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/10/2020] [Accepted: 12/10/2020] [Indexed: 01/03/2023] Open
Abstract
Nucleus accumbens-associated protein 1 (NAC1) is a nuclear protein that harbors an amino-terminal BTB domain and a carboxyl-terminal BEN domain. NAC1 appears to play significant and diverse functions in cancer and stem cell biology. Here we demonstrated that the BEN domain of NAC1 is a sequence-specific DNA-binding domain. We selected the palindromic 6 bp motif ACATGT as a target sequence by using a PCR-assisted random oligonucleotide selection approach. The interaction between NAC1 and target DNA was characterized by gel shift assays, pull-down assays, isothermal titration calorimetry (ITC), chromatin-immunoprecipitation assays, and NMR chemical shifts perturbation (CSP). The solution NMR structure revealed that the BEN domain of human NAC-1 is composed of five conserved α helices and two short β sheets, with an additional hitherto unknown N-terminal α helix. In particular, ITC clarified that there are two sequential events in the titration of the BEN domain of NAC1 into the target DNA. The ITC results were further supported by CSP data and structure analyses. Furthermore, live cell photobleaching analyses revealed that the BEN domain of NAC1 alone was unable to interact with chromatin/other proteins in cells.
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16
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Wang H, Wang X, Zhang Y, Cheng R, Yuan J, Zhong Z. Systemic Delivery of NAC-1 siRNA by Neuropilin-Targeted Polymersomes Sensitizes Antiangiogenic Therapy of Metastatic Triple-Negative Breast Cancer. Biomacromolecules 2020; 21:5119-5127. [PMID: 33174734 DOI: 10.1021/acs.biomac.0c01253] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Antiangiogenic therapy with bevacizumab while being interesting for metastatic triple-negative breast cancer (mTNBC) is restrained by tumor hypoxia elevation and cancer stem cell enrichment. Here, we find that neuropilin-1 (NRP-1)-targeted delivery of nucleus accumbens-associated protein-1 (NAC-1) siRNA mediated by tLyP-1 peptide-functionalized chimaeric polymersomes (tLyP-1-Ps) effectively sensitizes antiangiogenic therapy of mTNBC in vivo. tLyP-1-Ps showed good encapsulation (up to 14.4 wt. %) of siNAC-1, giving robust tLyP-1-Ps-siNAC-1 nanoformulation with a defined size of 48.5 nm (PDI = 0.13) and a surface charge of -9.2 mV, and mediated efficient cytoplasmic transportation of siNAC-1 in MDA-MB-231 TNBC cells, resulting in significant silencing of NAC-1 mRNA and the corresponding oncoprotein. Transwell invasion and wound healing assays revealed that tLyP-1-Ps-siNAC-1 potently inhibited MDA-MB-231 cell invasion and migration. Intriguingly, tLyP-1-Ps-siNAC-1 was shown to markedly improve the bevacizumab therapy of mTNBC, significantly curbing lung metastasis and prolonging the survival time of the MDA-MB-231 metastatic model. The combination of targeted NAC-1 gene silencing and antiangiogenic therapy appears to be an innovative treatment for mTNBC.
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Affiliation(s)
- Hongyu Wang
- Biomedical Polymers Laboratory, College of Chemistry, Chemical Engineering and Materials Science, and State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou 215123, P. R. China
| | - Xiaohui Wang
- Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, P. R. China
| | - Yi Zhang
- Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, P. R. China
| | - Ru Cheng
- Biomedical Polymers Laboratory, College of Chemistry, Chemical Engineering and Materials Science, and State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou 215123, P. R. China
| | - Jiandong Yuan
- BrightGene Bio-Medical Technology Company, Ltd., Suzhou 215123, P. R. China
| | - Zhiyuan Zhong
- Biomedical Polymers Laboratory, College of Chemistry, Chemical Engineering and Materials Science, and State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou 215123, P. R. China
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17
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Choi H, Park HJ, Kim H, Kim J, Lee YK, Kim J. Nac1 facilitates pluripotency gene activation for establishing somatic cell reprogramming. Biochem Biophys Res Commun 2019; 518:253-258. [PMID: 31412978 DOI: 10.1016/j.bbrc.2019.08.043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 08/08/2019] [Indexed: 01/07/2023]
Abstract
Transcription factors play a central role in pluripotency transcription circuitry for establishing pluripotent reprogramming. Master transcription factors Oct4, Nanog, and Sox2 are known to form the core of the pluripotency transcription network. Other transcription factors also play critical roles for further refining the core circuitry for pluripotency in induced pluripotent stem (iPS) cells. Here, we reported that Nac1 interacted with the master pluripotent factors Oct4 and Nanog co-occupies gene promoters bound by these transcriptional factors for establishing pluripotency. Moreover, this interaction coordinates gene expression with H3K4me3 in the somatic cell reprogramming. Knockdown of Nac1 suppressed somatic cell reprogramming, whereas overexpression of Nac1 resulted in enhanced efficiency of induced pluripotent cell generation. Altogether, these results reveal the genome wide role for Nac1 in the contribution to the pluripotency circuitry and the regulation of the establishing pluripotent state.
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Affiliation(s)
- Hwan Choi
- Laboratory of Stem Cells & Cell reprogramming, Department of Biomedical Engineering, Dongguk University, Seoul, 100-715, Republic of Korea
| | - Hyeok Ju Park
- Database Laboratory, Department of Computer Science and Engineering, Dongguk University, Pildong-ro 1-gil 30, Jung-gu, Seoul, 04620, Republic of Korea
| | - Hongwon Kim
- Laboratory of Stem Cells & Cell reprogramming, Department of Biomedical Engineering, Dongguk University, Seoul, 100-715, Republic of Korea
| | - Junyeop Kim
- Laboratory of Stem Cells & Cell reprogramming, Department of Biomedical Engineering, Dongguk University, Seoul, 100-715, Republic of Korea
| | - Yong Kyu Lee
- Database Laboratory, Department of Computer Science and Engineering, Dongguk University, Pildong-ro 1-gil 30, Jung-gu, Seoul, 04620, Republic of Korea
| | - Jongpil Kim
- Laboratory of Stem Cells & Cell reprogramming, Department of Biomedical Engineering, Dongguk University, Seoul, 100-715, Republic of Korea; Department of Chemistry, Dongguk University, Seoul, 100-715, Republic of Korea.
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18
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Wang X, Ji C, Zhang H, Shan Y, Ren Y, Hu Y, Shi L, Guo L, Zhu W, Xia Y, Liu B, Rong Z, Wu B, Ming Z, Ren X, Song J, Yang J, Zhang Y. Identification of a small-molecule compound that inhibits homodimerization of oncogenic NAC1 protein and sensitizes cancer cells to anticancer agents. J Biol Chem 2019; 294:10006-10017. [PMID: 31101655 DOI: 10.1074/jbc.ra119.007664] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 05/09/2019] [Indexed: 12/13/2022] Open
Abstract
Nucleus accumbens-associated protein-1 (NAC1) is a transcriptional repressor encoded by the NACC1 gene, which is amplified and overexpressed in various human cancers and plays critical roles in tumor development, progression, and drug resistance. NAC1 has therefore been explored as a potential therapeutic target for managing malignant tumors. However, effective approaches for effective targeting of this nuclear protein remain elusive. In this study, we identified a core unit consisting of Met7 and Leu90 in NAC1's N-terminal domain (amino acids 1-130), which is critical for its homodimerization and stability. Furthermore, using a combination of computational analysis of the NAC1 dimerization interface and high-throughput screening (HTS) for small molecules that inhibit NAC1 homodimerization, we identified a compound (NIC3) that selectively binds to the conserved Leu-90 of NAC1 and prevents its homodimerization, leading to proteasomal NAC1 degradation. Moreover, we demonstrate that NIC3-mediated down-regulation of NAC1 protein sensitizes drug-resistant tumor cells to conventional chemotherapy and enhances the antimetastatic effect of the antiangiogenic agent bevacizumab both in vitro and in vivo These results suggest that small-molecule inhibitors of NAC1 homodimerization may effectively sensitize cancer cells to some anticancer agents and that NAC1 homodimerization could be further explored as a potential therapeutic target in the development of antineoplastic agents.
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Affiliation(s)
- XiaoHui Wang
- From the Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, 215123 Suzhou, Jiangsu, China
| | - Cheng Ji
- Department of Respiratory Medicine, First Affiliated Hospital, Soochow University, 215000 Suzhou, Jiangsu, China
| | - HongHan Zhang
- From the Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, 215123 Suzhou, Jiangsu, China
| | - Yu Shan
- Institute of Botany, Jiangsu Province and Chinese Academy of Science, 210014 Nanjing, Jiangsu, China
| | - YiJie Ren
- From the Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, 215123 Suzhou, Jiangsu, China
| | - YanWei Hu
- From the Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, 215123 Suzhou, Jiangsu, China
| | - LiangRong Shi
- Radiological Intervention Center, Department of Radiology, Xiangya Hospital, Central South University, 410013 Changsha, Hunan, China
| | - LingChuan Guo
- From the Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, 215123 Suzhou, Jiangsu, China
| | - WeiDong Zhu
- From the Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, 215123 Suzhou, Jiangsu, China
| | - YuJuan Xia
- From the Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, 215123 Suzhou, Jiangsu, China
| | - BeiJia Liu
- From the Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, 215123 Suzhou, Jiangsu, China
| | - ZiYun Rong
- From the Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, 215123 Suzhou, Jiangsu, China
| | - BiLian Wu
- From the Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, 215123 Suzhou, Jiangsu, China
| | - ZhiJun Ming
- From the Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, 215123 Suzhou, Jiangsu, China
| | - XingCong Ren
- Department of Cancer Biology and Toxicology, Markey Cancer Center, University of Kentucky College of Medicine, Lexington, Kentucky 40506
| | - JianXun Song
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, College Station, Texas 77843, and
| | - JinMing Yang
- Department of Cancer Biology and Toxicology, Markey Cancer Center, University of Kentucky College of Medicine, Lexington, Kentucky 40506
| | - Yi Zhang
- From the Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, 215123 Suzhou, Jiangsu, China,
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19
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Nakayama N, Sakashita G, Nariai Y, Kato H, Sinmyozu K, Nakayama JI, Kyo S, Urano T, Nakayama K. Cancer-related transcription regulator protein NAC1 forms a protein complex with CARM1 for ovarian cancer progression. Oncotarget 2018; 9:28408-28420. [PMID: 29983869 PMCID: PMC6033357 DOI: 10.18632/oncotarget.25400] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/16/2018] [Indexed: 01/07/2023] Open
Abstract
NAC1 is a cancer-related transcription regulator protein that is overexpressed in various carcinomas, including ovarian, cervical, breast, and pancreatic carcinomas. NAC1 knock-down was previously shown to result in the apoptosis of ovarian cancer cell lines and to rescue their sensitivity to chemotherapy, suggesting that NAC1 may be a potential therapeutic target, but protein complex formation of intranuclear NAC1 in ovarian cancer cells remain poorly understood. In this study, analysis of ovarian cancer cell lysates by fast protein liquid chromatography on a sizing column showed that the NAC1 peak corresponded to an apparent molecular mass of 300–500 kDa, which is larger than the estimated molecular mass (58 kDa) of the protein. Liquid chromatography-tandem mass spectrometry analysis identified CARM1 as interacting with NAC1 in the protein complex. Furthermore, tissue microarray analysis revealed a significant correlation between CARM1 and NAC1 expression levels. Ovarian cancer patients expressing high levels of NAC1 and CARM1 exhibited poor prognosis after adjuvant chemotherapy. Collectively, our results demonstrate that high expression levels of NAC1 and its novel binding partner CARM1 may serve as an informative prognostic biomarker for predicting resistance to chemotherapy for ovarian cancer.
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Affiliation(s)
- Naomi Nakayama
- Department of Biochemistry, Shimane University School of Medicine, Izumo, Japan
| | - Gyosuke Sakashita
- Department of Biochemistry, Shimane University School of Medicine, Izumo, Japan
| | - Yuko Nariai
- Department of Biochemistry, Shimane University School of Medicine, Izumo, Japan
| | - Hiroaki Kato
- Department of Biochemistry, Shimane University School of Medicine, Izumo, Japan
| | - Kaori Sinmyozu
- Proteomics Support Unit, RIKEN Center for Developmental Biology, Kobe, Japan.,Current address: National Cerebral and Cardiovascular Center, Osaka, Japan
| | - Jun-Ichi Nakayama
- Graduate School of Natural Sciences, Nagoya City University, Nagoya, Japan
| | - Satoru Kyo
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo, Japan
| | - Takeshi Urano
- Department of Biochemistry, Shimane University School of Medicine, Izumo, Japan
| | - Kentaro Nakayama
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo, Japan
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20
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Ruan Y, He J, Wu W, He P, Tian Y, Xiao L, Liu G, Wang J, Cheng Y, Zhang S, Yang Y, Xiong J, Zhao K, Wan Y, Huang H, Zhang J, Jian R. Nac1 promotes self-renewal of embryonic stem cells through direct transcriptional regulation of c-Myc. Oncotarget 2018; 8:47607-47618. [PMID: 28548937 PMCID: PMC5564591 DOI: 10.18632/oncotarget.17744] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 04/27/2017] [Indexed: 01/11/2023] Open
Abstract
The pluripotency transcriptional network in embryonic stem cells (ESCs) is composed of distinct functional units including the core and Myc units. It is hoped that dissection of the cellular functions and interconnections of network factors will aid our understanding of ESC and cancer biology. Proteomic and genomic approaches have identified Nac1 as a member of the core pluripotency network. However, previous studies have predominantly focused on the role of Nac1 in psychomotor stimulant response and cancer pathogenesis. In this study, we report that Nac1 is a self-renewal promoting factor, but is not required for maintaining pluripotency of ESCs. Loss of function of Nac1 in ESCs results in a reduced proliferation rate and an enhanced differentiation propensity. Nac1 overexpression promotes ESC proliferation and delays ESC differentiation in the absence of leukemia inhibitory factor (LIF). Furthermore, we demonstrated that Nac1 directly binds to the c-Myc promoter and regulates c-Myc transcription. The study also revealed that the function of Nac1 in promoting ESC self-renewal appears to be partially mediated by c-Myc. These findings establish a functional link between the core and c-Myc-centered networks and provide new insights into mechanisms of stemness regulation in ESCs and cancer.
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Affiliation(s)
- Yan Ruan
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, Third Military Medical University, Chongqing 400038, China.,Biomedical Analysis Center, Third Military Medical University, Chongqing 400038, China
| | - Jianrong He
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, Third Military Medical University, Chongqing 400038, China.,Department of Anesthesiology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Wei Wu
- Department of Cardiothoracic Surgery, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Ping He
- Department of Cardiothoracic Surgery, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Yanping Tian
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, Third Military Medical University, Chongqing 400038, China
| | - Lan Xiao
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, Third Military Medical University, Chongqing 400038, China
| | - Gaoke Liu
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, Third Military Medical University, Chongqing 400038, China
| | - Jiali Wang
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, Third Military Medical University, Chongqing 400038, China
| | - Yuda Cheng
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, Third Military Medical University, Chongqing 400038, China
| | - Shuo Zhang
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, Third Military Medical University, Chongqing 400038, China
| | - Yi Yang
- Experimental Center of Basic Medicine, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
| | - Jiaxiang Xiong
- Experimental Center of Basic Medicine, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
| | - Ke Zhao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Ying Wan
- Biomedical Analysis Center, Third Military Medical University, Chongqing 400038, China
| | - He Huang
- Department of Anesthesiology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Junlei Zhang
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, Third Military Medical University, Chongqing 400038, China
| | - Rui Jian
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, Third Military Medical University, Chongqing 400038, China
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21
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Dynamics of lineage commitment revealed by single-cell transcriptomics of differentiating embryonic stem cells. Nat Commun 2017; 8:1096. [PMID: 29061959 PMCID: PMC5653659 DOI: 10.1038/s41467-017-01076-4] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 08/15/2017] [Indexed: 01/01/2023] Open
Abstract
Gene expression heterogeneity in the pluripotent state of mouse
embryonic stem cells (mESCs) has been increasingly well-characterized. In contrast,
exit from pluripotency and lineage commitment have not been studied systematically
at the single-cell level. Here we measure the gene expression dynamics of retinoic
acid driven mESC differentiation from pluripotency to lineage commitment, using an
unbiased single-cell transcriptomics approach. We find that the exit from
pluripotency marks the start of a lineage transition as well as a transient phase of
increased susceptibility to lineage specifying signals. Our study reveals several
transcriptional signatures of this phase, including a sharp increase of gene
expression variability and sequential expression of two classes of transcriptional
regulators. In summary, we provide a comprehensive analysis of the exit from
pluripotency and lineage commitment at the single cell level, a potential stepping
stone to improved lineage manipulation through timing of differentiation
cues. Commitment to different fates by differentiating pluripotent cells
depends upon integration of external and internal signals. Here the authors analyse
the entry of mouse embryonic stem cells into retinoic acid-mediated differentiation
using single cell transcriptomics with high temporal resolution.
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22
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Zhang Y, Ren YJ, Guo LC, Ji C, Hu J, Zhang HH, Xu QH, Zhu WD, Ming ZJ, Yuan YS, Ren X, Song J, Yang JM. Nucleus accumbens-associated protein-1 promotes glycolysis and survival of hypoxic tumor cells via the HDAC4-HIF-1α axis. Oncogene 2017; 36:4171-4181. [PMID: 28319066 PMCID: PMC5537617 DOI: 10.1038/onc.2017.51] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 01/25/2017] [Accepted: 01/27/2017] [Indexed: 12/25/2022]
Abstract
Nucleus accumbens-associated protein-1 (NAC1), a nuclear factor of the BTB/POZ gene family, has emerging roles in cancer. In this study, we identified the NAC1-HDAC4-HIF-1α axis as an important pathway in regulating glycolysis and hypoxic adaptation in tumor cells. We show that nuclear NAC1 binds to histone deacetylase type 4 (HDAC4), hindering phosphorylation of HDAC4 at Ser246 and preventing its nuclear export that leads to cytoplasmic degradation of the deacetylase. Accumulation of HDAC4 in the nuclei results in an attenuation of HIF-1α acetylation, enhancing the stabilization and transcriptional activity of HIF-1α and strengthening adaptive response of cells to hypoxia. We also show the role of NAC1 in promoting glycolysis in a mouse xenograft model, and demonstrate that knockdown of NAC1 expression can reinforce the antitumor efficacy of bevacizumab, an inhibitor of angiogenesis. Clinical implication of the NAC1-HDAC4-HIF-1α pathway is suggested by the results showing that expression levels of these proteins are significantly correlative in human tumor specimens and associated with the disease progression. This study not only reveals an important function of NAC1 in regulating glycolysis, but also identifies the NAC1-HDAC4-HIF-1α axis as a novel molecular pathway that promotes survival of hypoxic tumor cells.
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Affiliation(s)
- Y Zhang
- Department of Pharmacology, College of Pharmaceutical Sciences, First Affiliated Hospital, Soochow University, Jiangsu, China
| | - Y-J Ren
- Department of Pharmacology, College of Pharmaceutical Sciences, First Affiliated Hospital, Soochow University, Jiangsu, China
| | - L-C Guo
- Department of Pharmacology, College of Pharmaceutical Sciences, First Affiliated Hospital, Soochow University, Jiangsu, China
| | - C Ji
- Department of Pharmacology, College of Pharmaceutical Sciences, First Affiliated Hospital, Soochow University, Jiangsu, China
| | - J Hu
- Department of Pharmacology, College of Pharmaceutical Sciences, First Affiliated Hospital, Soochow University, Jiangsu, China
| | - H-H Zhang
- Department of Pharmacology, College of Pharmaceutical Sciences, First Affiliated Hospital, Soochow University, Jiangsu, China
| | - Q-H Xu
- Department of Pharmacology, College of Pharmaceutical Sciences, First Affiliated Hospital, Soochow University, Jiangsu, China
| | - W-D Zhu
- Department of Pharmacology, College of Pharmaceutical Sciences, First Affiliated Hospital, Soochow University, Jiangsu, China
| | - Z-J Ming
- Department of Pharmacology, College of Pharmaceutical Sciences, First Affiliated Hospital, Soochow University, Jiangsu, China
| | - Y-S Yuan
- Engineering Research Center of Cell and Therapeutic Antibody, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - X Ren
- Department of Pharmacology and Microbiology and Immunology, The Penn State Hershey Cancer Institute, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - J Song
- Department of Pharmacology and Microbiology and Immunology, The Penn State Hershey Cancer Institute, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - J-M Yang
- Department of Pharmacology and Microbiology and Immunology, The Penn State Hershey Cancer Institute, The Pennsylvania State University College of Medicine, Hershey, PA, USA
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23
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Betschinger J. Charting Developmental Dissolution of Pluripotency. J Mol Biol 2016; 429:1441-1458. [PMID: 28013029 DOI: 10.1016/j.jmb.2016.12.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 12/14/2016] [Indexed: 02/06/2023]
Abstract
The formation of tissues and organs during metazoan development begs fundamental questions of cellular plasticity: How can the very same genome program have diverse cell types? How do cell identity programs unfold during development in space and time? How can defects in these mechanisms cause disease and also provide opportunities for therapeutic intervention? And ultimately, can developmental programs be exploited for bioengineering tissues and organs? Understanding principle designs of cellular identity and developmental progression is crucial for providing answers. Here, I will discuss how the capture of embryonic pluripotency in murine embryonic stem cells (ESCs) in vitro has allowed fundamental insights into the molecular underpinnings of a developmental cell state and how its ordered disassembly during differentiation prepares for lineage specification.
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Affiliation(s)
- Joerg Betschinger
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.
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24
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Liu L. Linking Telomere Regulation to Stem Cell Pluripotency. Trends Genet 2016; 33:16-33. [PMID: 27889084 DOI: 10.1016/j.tig.2016.10.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 10/18/2016] [Accepted: 10/31/2016] [Indexed: 12/31/2022]
Abstract
Embryonic stem cells (ESCs), somatic cell nuclear transfer ESCs, and induced pluripotent stem cells (iPSCs) represent the most studied group of PSCs. Unlimited self-renewal without incurring chromosomal instability and pluripotency are essential for the potential use of PSCs in regenerative therapy. Telomere length maintenance is critical for the unlimited self-renewal, pluripotency, and chromosomal stability of PSCs. While telomerase has a primary role in telomere maintenance, alternative lengthening of telomere pathways involving recombination and epigenetic modifications are also required for telomere length regulation, notably in mouse PSCs. Telomere rejuvenation is part of epigenetic reprogramming to pluripotency. Insights into telomere reprogramming and maintenance in PSCs may have implications for understanding of aging and tumorigenesis. Here, I discuss the link between telomere elongation and homeostasis to the acquisition and maintenance of stem cell pluripotency, and their regulatory mechanisms by epigenetic modifications.
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Affiliation(s)
- Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Department of Cell Biology and Genetics, College of Life Sciences, Collaborative Innovation Center for Biotherapy, Nankai University, Tianjin 300071, China.
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25
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Heemskerk I, Warmflash A. Pluripotent stem cells as a model for embryonic patterning: From signaling dynamics to spatial organization in a dish. Dev Dyn 2016; 245:976-90. [PMID: 27404482 DOI: 10.1002/dvdy.24432] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 06/29/2016] [Accepted: 07/06/2016] [Indexed: 12/13/2022] Open
Abstract
In vivo studies have identified the signaling pathways and transcription factors involved in patterning the vertebrate embryo, but much remains unknown about how these are organized in space and time to orchestrate embryogenesis. Recently, embryonic stem cells have been established as a platform for studying spatial pattern formation and differentiation dynamics in the early mammalian embryo. The ease of observing and manipulating stem cell systems promises to fill gaps in our understanding of developmental dynamics and identify aspects that are uniquely human. Developmental Dynamics 245:976-990, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Idse Heemskerk
- Department of Biosciences, Rice University, Houston, Texas
| | - Aryeh Warmflash
- Department of Biosciences, Rice University, Houston, Texas. .,Department of Bioengineering, Rice University, Houston, Texas.
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26
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Nakayama N, Kato H, Sakashita G, Nariai Y, Nakayama K, Kyo S, Urano T. Protein complex formation and intranuclear dynamics of NAC1 in cancer cells. Arch Biochem Biophys 2016; 606:10-5. [PMID: 27424155 DOI: 10.1016/j.abb.2016.07.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 07/01/2016] [Accepted: 07/11/2016] [Indexed: 10/21/2022]
Abstract
Nucleus accumbens-associated protein 1 (NAC1) is a cancer-related transcription regulator protein that is also involved in the pluripotency and differentiation of embryonic stem cells. NAC1 is overexpressed in various carcinomas including ovarian, cervical, breast, and pancreatic carcinomas. NAC1 knock-down was previously shown to result in the apoptosis of ovarian cancer cell lines and to rescue their sensitivity to chemotherapy, suggesting that NAC1 may be a potential therapeutic target, but protein complex formation and the dynamics of intranuclear NAC1 in cancer cells remain poorly understood. In this study, analysis of HeLa cell lysates by fast protein liquid chromatography (FPLC) on a sizing column showed that the NAC1 peak corresponded to an apparent molecular mass of 300-500 kDa, which is larger than the estimated molecular mass (58 kDa) of the protein. Furthermore, live cell photobleaching analyses with green fluorescent protein (GFP)-fused NAC1 proteins revealed the intranuclear dynamics of NAC1. Collectively our results demonstrate that NAC1 forms a protein complex to function as a transcriptional regulator in cancer cells.
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Affiliation(s)
- Naomi Nakayama
- Department of Biochemistry, Shimane University School of Medicine, Izumo 693-8501, Japan
| | - Hiroaki Kato
- Department of Biochemistry, Shimane University School of Medicine, Izumo 693-8501, Japan
| | - Gyosuke Sakashita
- Department of Biochemistry, Shimane University School of Medicine, Izumo 693-8501, Japan
| | - Yuko Nariai
- Department of Biochemistry, Shimane University School of Medicine, Izumo 693-8501, Japan
| | - Kentaro Nakayama
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo 693-8501, Japan
| | - Satoru Kyo
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo 693-8501, Japan
| | - Takeshi Urano
- Department of Biochemistry, Shimane University School of Medicine, Izumo 693-8501, Japan.
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