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Huang S, Yang J, Xie T, Jiang Y, Hong Y, Liu X, He X, Buratto D, Zhang D, Zhou R, Liang T, Bai X. Inhibition of DEF-p65 Interactions as a Potential Avenue to Suppress Tumor Growth in Pancreatic Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401845. [PMID: 38757623 PMCID: PMC11267266 DOI: 10.1002/advs.202401845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/28/2024] [Indexed: 05/18/2024]
Abstract
The limited success of current targeted therapies for pancreatic cancer underscores an urgent demand for novel treatment modalities. The challenge in mitigating this malignancy can be attributed to the digestive organ expansion factor (DEF), a pivotal yet underexplored factor in pancreatic tumorigenesis. The study uses a blend of in vitro and in vivo approaches, complemented by the theoretical analyses, to propose DEF as a promising anti-tumor target. Analysis of clinical samples reveals that high expression of DEF is correlated with diminished survival in pancreatic cancer patients. Crucially, the depletion of DEF significantly impedes tumor growth. The study further discovers that DEF binds to p65, shielding it from degradation mediated by the ubiquitin-proteasome pathway in cancer cells. Based on these findings and computational approaches, the study formulates a DEF-mimicking peptide, peptide-031, designed to disrupt the DEF-p65 interaction. The effectiveness of peptide-031 in inhibiting tumor proliferation has been demonstrated both in vitro and in vivo. This study unveils the oncogenic role of DEF while highlighting its prognostic value and therapeutic potential in pancreatic cancer. In addition, peptide-031 is a promising therapeutic agent with potent anti-tumor effects.
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Affiliation(s)
- Sicong Huang
- Department of Hepatobiliary and Pancreatic Surgerythe First Affiliated HospitalZhejiang University School of MedicineHangzhou310000China
- Key Laboratory of Pancreatic Disease of Zhejiang ProvinceHangzhou310000China
- Innovation Center for the Study of Pancreatic Diseases of Zhejiang ProvinceHangzhou310000China
| | - Jiaqi Yang
- Department of Hepatobiliary and Pancreatic Surgerythe First Affiliated HospitalZhejiang University School of MedicineHangzhou310000China
- Key Laboratory of Pancreatic Disease of Zhejiang ProvinceHangzhou310000China
- Innovation Center for the Study of Pancreatic Diseases of Zhejiang ProvinceHangzhou310000China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic DiseasesHangzhou310000China
| | - Teng Xie
- Institute of Quantitative Biology, College of Life SciencesZhejiang UniversityHangzhou310000China
- Shanghai Institute for Advanced StudyZhejiang UniversityShanghai200000China
| | - Yangwei Jiang
- Institute of Quantitative Biology, College of Life SciencesZhejiang UniversityHangzhou310000China
| | - Yifan Hong
- Department of Hepatobiliary and Pancreatic Surgerythe First Affiliated HospitalZhejiang University School of MedicineHangzhou310000China
- Key Laboratory of Pancreatic Disease of Zhejiang ProvinceHangzhou310000China
- Innovation Center for the Study of Pancreatic Diseases of Zhejiang ProvinceHangzhou310000China
| | - Xinyuan Liu
- Department of Hepatobiliary and Pancreatic Surgerythe First Affiliated HospitalZhejiang University School of MedicineHangzhou310000China
- Key Laboratory of Pancreatic Disease of Zhejiang ProvinceHangzhou310000China
- Innovation Center for the Study of Pancreatic Diseases of Zhejiang ProvinceHangzhou310000China
| | - Xuyan He
- Life Sciences InstituteZhejiang UniversityHangzhou310000China
| | - Damiano Buratto
- Institute of Quantitative Biology, College of Life SciencesZhejiang UniversityHangzhou310000China
- Shanghai Institute for Advanced StudyZhejiang UniversityShanghai200000China
| | - Dong Zhang
- Institute of Quantitative Biology, College of Life SciencesZhejiang UniversityHangzhou310000China
- Shanghai Institute for Advanced StudyZhejiang UniversityShanghai200000China
| | - Ruhong Zhou
- Department of Hepatobiliary and Pancreatic Surgerythe First Affiliated HospitalZhejiang University School of MedicineHangzhou310000China
- Institute of Quantitative Biology, College of Life SciencesZhejiang UniversityHangzhou310000China
- Shanghai Institute for Advanced StudyZhejiang UniversityShanghai200000China
- Department of ChemistryColumbia UniversityNew York10027USA
- Cancer CenterZhejiang UniversityHangzhou310000China
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgerythe First Affiliated HospitalZhejiang University School of MedicineHangzhou310000China
- Key Laboratory of Pancreatic Disease of Zhejiang ProvinceHangzhou310000China
- Innovation Center for the Study of Pancreatic Diseases of Zhejiang ProvinceHangzhou310000China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic DiseasesHangzhou310000China
- Cancer CenterZhejiang UniversityHangzhou310000China
| | - Xueli Bai
- Department of Hepatobiliary and Pancreatic Surgerythe First Affiliated HospitalZhejiang University School of MedicineHangzhou310000China
- Key Laboratory of Pancreatic Disease of Zhejiang ProvinceHangzhou310000China
- Innovation Center for the Study of Pancreatic Diseases of Zhejiang ProvinceHangzhou310000China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic DiseasesHangzhou310000China
- Cancer CenterZhejiang UniversityHangzhou310000China
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2
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Grant B, Sundaram Buitrago PA, Mercado BC, Yajima M. Characterization of p53/p63/p73 and Myc expressions during embryogenesis of the sea urchin. Dev Dyn 2024; 253:333-350. [PMID: 37698352 DOI: 10.1002/dvdy.656] [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: 04/11/2023] [Revised: 07/27/2023] [Accepted: 08/18/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND Some marine invertebrate organisms are considered not to develop tumors due to unknown mechanisms. To gain an initial insight into how tumor-related genes may be expressed and function during marine invertebrate development, we here leverage sea urchin embryos as a model system and characterize the expressions of Myc and p53/p63/p73 which are reported to function synergistically in mammalian models as an oncogene and tumor suppressor, respectively. RESULTS During sea urchin embryogenesis, a combo gene of p53/p63/p73 is found to be maternally loaded and decrease after fertilization both in transcript and protein, while Myc transcript and protein are zygotically expressed. p53/p63/p73 and Myc proteins are observed in the cytoplasm and nucleus of every blastomere, respectively, throughout embryogenesis. Both p53/p63/p73 and Myc overexpression results in compromised development with increased DNA damage after the blastula stage. p53/p63/p73 increases the expression of parp1, a DNA repair/cell death marker gene, and suppresses endomesoderm gene expressions. In contrast, Myc does not alter the expression of specification genes or oncogenes yet induces disorganized morphology. CONCLUSIONS p53/p63/p73 appears to be important for controlling cell differentiation, while Myc induces disorganized morphology yet not through conventional oncogene regulations or apoptotic pathways during embryogenesis of the sea urchin.
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Affiliation(s)
- Blaine Grant
- Department of Molecular Biology Cell Biology Biochemistry, Brown University, Providence, Rhode Island, USA
| | | | - Beatriz C Mercado
- Department of Molecular Biology Cell Biology Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Mamiko Yajima
- Department of Molecular Biology Cell Biology Biochemistry, Brown University, Providence, Rhode Island, USA
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Wang Y, Zhao Z, Yu H, Shi H, Tao B, He Y, Chen J, Peng J, Gan M, Lo LJ. Stability and function of RCL1 are dependent on the interaction with BMS1. J Mol Cell Biol 2024; 15:mjad046. [PMID: 37451810 PMCID: PMC11023236 DOI: 10.1093/jmcb/mjad046] [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: 02/25/2023] [Revised: 07/03/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023] Open
Abstract
During ribosome biogenesis, the small subunit (SSU) processome is responsible for 40S assembly. The BMS1/RCL1 complex is a core component of the SSU processome that plays an important role in 18S rRNA processing and maturation. Genetic studies using zebrafish mutants indicate that both Bms1-like (Bms1l) and Rcl1 are essential for digestive organ development. In spite of vital functions of this complex, the mutual dependence of these two nucleolar proteins for the stability and function remains elusive. In this study, we identified an RCL1-interacting domain in BMS1, which is conserved in zebrafish and humans. Moreover, both the protein stability and nucleolar entry of RCL1 depend on its interaction with BMS1, otherwise RCL1 degraded through the ubiquitination-proteasome pathway. Functional studies revealed that overexpression of RCL1 in BMS1-knockdown cells can partially rescue the defects in 18S rRNA processing and cell proliferation, and hepatocyte-specific overexpression of Rcl1 can resume zebrafish liver development in the bms1l substitution mutant bms1lsq163/sq163but not in the knockout mutant bms1lzju1/zju1, which is attributed to the nucleolar entry of Rcl1 in the former mutant. Our data demonstrate that BMS1 and RCL1 interaction is essential for not only pre-rRNA processing but also the communication between ribosome biogenesis and cell cycle regulation.
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Affiliation(s)
- Yong Wang
- Pathology Department of Taizhou Hospital, Zhejiang University, Taizhou 317000, China
| | - Zhenyu Zhao
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hongyan Yu
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hui Shi
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Boxiang Tao
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yinan He
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jun Chen
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jinrong Peng
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Meifu Gan
- Pathology Department of Taizhou Hospital, Zhejiang University, Taizhou 317000, China
| | - Li Jan Lo
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
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Wei J, Wang S, Zhu H, Cui W, Gao J, Gao C, Yu B, Liu B, Chen J, Peng J. Hepatic depletion of nucleolar protein mDEF causes excessive mitochondrial copper accumulation associated with p53 and NRF1 activation. iScience 2023; 26:107220. [PMID: 37456842 PMCID: PMC10339200 DOI: 10.1016/j.isci.2023.107220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/15/2023] [Accepted: 06/22/2023] [Indexed: 07/18/2023] Open
Abstract
Copper is an essential component in the mitochondrial respiratory chain complex IV (cytochrome c oxidases). However, whether any nucleolar factor(s) is(are) involved in regulating the mitochondrial copper homeostasis remains unclear. The nucleolar localized Def-Capn3 protein degradation pathway cleaves target proteins, including p53, in both zebrafish and human nucleoli. Here, we report that hepatic depletion of mDEF in mice causes an excessive copper accumulation in the mitochondria. We find that mDEF-depleted hepatocytes show an exclusion of CAPN3 from the nucleoli and accumulate p53 and NRF1 proteins in the nucleoli. Furthermore, we find that NRF1 is a CAPN3 substrate. Elevated p53 and NRF1 enhances the expression of Sco2 and Cox genes, respectively, to allow more copper acquirement in the mDefloxp/loxp, Alb:Cre mitochondria. Our findings reveal that the mDEF-CAPN3 pathway serves as a novel mechanism for regulating the mitochondrial copper homeostasis through targeting its substrates p53 and NRF1.
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Affiliation(s)
- Jinsong Wei
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shuai Wang
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Haozhe Zhu
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wei Cui
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jianan Gao
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ce Gao
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Bo Yu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Bojing Liu
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jun Chen
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jinrong Peng
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
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5
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Zhang Z, Yang C, Wang Z, Guo L, Xu Y, Gao C, Sun Y, Zhang Z, Peng J, Hu M, Jan Lo L, Ma Z, Chen J. Wdr5-mediated H3K4me3 coordinately regulates cell differentiation, proliferation termination, and survival in digestive organogenesis. Cell Death Discov 2023; 9:227. [PMID: 37407577 DOI: 10.1038/s41420-023-01529-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/05/2023] [Accepted: 06/22/2023] [Indexed: 07/07/2023] Open
Abstract
Food digestion requires the cooperation of different digestive organs. The differentiation of digestive organs is crucial for larvae to start feeding. Therefore, during digestive organogenesis, cell identity and the tissue morphogenesis must be tightly coordinated but how this is accomplished is poorly understood. Here, we demonstrate that WD repeat domain 5 (Wdr5)-mediated H3K4 tri-methylation (H3K4me3) coordinately regulates cell differentiation, proliferation and apoptosis in zebrafish organogenesis of three major digestive organs including intestine, liver, and exocrine pancreas. During zebrafish digestive organogenesis, some of cells in these organ primordia usually undergo differentiation without apoptotic activity and gradually reduce their proliferation capacity. In contrast, cells in the three digestive organs of wdr5-/- mutant embryos retain progenitor-like status with high proliferation rates, and undergo apoptosis. Wdr5 is a core member of COMPASS complex to implement H3K4me3 and its expression is enriched in digestive organs from 2 days post-fertilization (dpf). Further analysis reveals that lack of differentiation gene expression is due to significant decreases of H3K4me3 around the transcriptional start sites of these genes; this histone modification also reduces the proliferation capacity in differentiated cells by increasing the expression of apc to promote the degradation of β-Catenin; in addition, H3K4me3 promotes the expression of anti-apoptotic genes such as xiap-like, which modulates p53 activity to guarantee differentiated cell survival. Thus, our findings have discovered a common molecular mechanism for cell fate determination in different digestive organs during organogenesis, and also provided insights to understand mechanistic basis of human diseases in these digestive organs.
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Affiliation(s)
- Zhe Zhang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chun Yang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zixu Wang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Liwei Guo
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yongpan Xu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ce Gao
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yonghua Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zhenhai Zhang
- Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Jinrong Peng
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Minjie Hu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Li Jan Lo
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Zhipeng Ma
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Jun Chen
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
- Cancer Center, Zhejiang University, Hangzhou, 310058, China.
- Department of Plastic Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No. 3 Qingchun Road East, Hangzhou, 310016, China.
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6
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Xie A, Ma Z, Wang J, Zhang Y, Chen Y, Yang C, Chen J, Peng J. Upf3a but not Upf1 mediates the genetic compensation response induced by leg1 deleterious mutations in an H3K4me3-independent manner. Cell Discov 2023; 9:63. [PMID: 37369707 DOI: 10.1038/s41421-023-00550-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 03/29/2023] [Indexed: 06/29/2023] Open
Abstract
Genetic compensation responses (GCRs) can be induced by deleterious mutations in living organisms in order to maintain genetic robustness. One type of GCRs, homology-dependent GCR (HDGCR), involves transcriptional activation of one or more homologous genes related to the mutated gene. In zebrafish, ~80% of the genetic mutants produced by gene editing technology failed to show obvious phenotypes. The HDGCR has been proposed to be one of the main reasons for this phenomenon. It is triggered by mutant mRNA bearing a premature termination codon and has been suggested to depend on components of both the nonsense mRNA-mediated degradation (NMD) pathway and the complex of proteins associated with Set1 (COMPASS). However, exactly which specific NMD factor is required for HDGCR remains disputed. Here, zebrafish leg1 deleterious mutants are adopted as a model to distinguish the role of the NMD factors Upf1 and Upf3a in HDGCR. Four single mutant lines and three double mutant lines were produced. The RNA-seq data from 71 samples and the ULI-NChIP-seq data from 8 samples were then analyzed to study the HDGCR in leg1 mutants. Our results provide strong evidence that Upf3a, but not Upf1, is essential for the HDGCR induced by nonsense mutations in leg1 genes where H3K4me3 enrichment appears not to be a prerequisite. We also show that Upf3a is responsible for correcting the expression of hundreds of genes that would otherwise be dysregulated in the leg1 deleterious mutant.
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Affiliation(s)
- Aixuan Xie
- 1MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhipeng Ma
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Jinyang Wang
- 1MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuxi Zhang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yayue Chen
- 1MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chun Yang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jun Chen
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Jinrong Peng
- 1MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
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Tang Z, Wang K, Lo L, Chen J. Tg(Δ113p53:cmyc) Transgene Upregulates glut1 Expression to Promote Zebrafish Heart Regeneration. J Cardiovasc Dev Dis 2023; 10:246. [PMID: 37367411 DOI: 10.3390/jcdd10060246] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/28/2023] Open
Abstract
The heart switches its main metabolic substrate from glucose to fatty acids shortly after birth, which is one of reasons for the loss of heart regeneration capability in adult mammals. On the contrary, metabolic shifts from oxidative phosphorylation to glucose metabolism promote cardiomyocyte (CM) proliferation after heart injury. However, how glucose transportation in CMs is regulated during heart regeneration is still not fully understood. In this report, we found that the expression of Glut1 (slc2a1) was upregulated around the injury site of zebrafish heart, accompanied by an increase in glucose uptake at the injury area. Knockout of slc2a1a impaired zebrafish heart regeneration. Our previous study has demonstrated that the expression of Δ113p53 is activated after heart injury and Δ113p53+ CMs undergo proliferation to contribute to zebrafish heart regeneration. Next, we used the Δ113p53 promoter to generate the Tg(Δ113p53:cmyc) zebrafish transgenic line. Conditional overexpression of cmyc not only significantly promoted zebrafish CM proliferation and heart regeneration but also significantly enhanced glut1 expression at the injury site. Inhibiting Glut1 diminished the increase in CM proliferation in Tg(Δ113p53:cmyc) injured hearts of zebrafish. Therefore, our results suggest that the activation of cmyc promotes heart regeneration through upregulating the expression of glut1 to speed up glucose transportation.
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Affiliation(s)
- Zimu Tang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Kaiyuan Wang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Lijian Lo
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jun Chen
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Cancer Center, Zhejiang University, Hangzhou 310058, China
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8
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Yu S, Liu Z, Li M, Zhou D, Hua P, Cheng H, Fan W, Xu Y, Liu D, Liang S, Zhang Y, Xie M, Tang J, Jiang Y, Hou S, Zhou Z. Resequencing of a Pekin duck breeding population provides insights into the genomic response to short-term artificial selection. Gigascience 2023; 12:giad016. [PMID: 36971291 PMCID: PMC10041536 DOI: 10.1093/gigascience/giad016] [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: 09/29/2022] [Revised: 02/04/2023] [Accepted: 02/27/2023] [Indexed: 03/29/2023] Open
Abstract
BACKGROUND Short-term, intense artificial selection drives fast phenotypic changes in domestic animals and leaves imprints on their genomes. However, the genetic basis of this selection response is poorly understood. To better address this, we employed the Pekin duck Z2 pure line, in which the breast muscle weight was increased nearly 3-fold after 10 generations of breeding. We denovo assembled a high-quality reference genome of a female Pekin duck of this line (GCA_003850225.1) and identified 8.60 million genetic variants in 119 individuals among 10 generations of the breeding population. RESULTS We identified 53 selected regions between the first and tenth generations, and 93.8% of the identified variations were enriched in regulatory and noncoding regions. Integrating the selection signatures and genome-wide association approach, we found that 2 regions covering 0.36 Mb containing UTP25 and FBRSL1 were most likely to contribute to breast muscle weight improvement. The major allele frequencies of these 2 loci increased gradually with each generation following the same trend. Additionally, we found that a copy number variation region containing the entire EXOC4 gene could explain 1.9% of the variance in breast muscle weight, indicating that the nervous system may play a role in economic trait improvement. CONCLUSIONS Our study not only provides insights into genomic dynamics under intense artificial selection but also provides resources for genomics-enabled improvements in duck breeding.
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Affiliation(s)
- Simeng Yu
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zihua Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Ming Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Dongke Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Ping Hua
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Hong Cheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Wenlei Fan
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yaxi Xu
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Dapeng Liu
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Suyun Liang
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yunsheng Zhang
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ming Xie
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jing Tang
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Shuisheng Hou
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhengkui Zhou
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Prykhozhij SV, Caceres L, Ban K, Cordeiro-Santanach A, Nagaraju K, Hoffman EP, Berman JN. Loss of calpain3b in Zebrafish, a Model of Limb-Girdle Muscular Dystrophy, Increases Susceptibility to Muscle Defects Due to Elevated Muscle Activity. Genes (Basel) 2023; 14:492. [PMID: 36833417 PMCID: PMC9957097 DOI: 10.3390/genes14020492] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/06/2023] [Accepted: 02/14/2023] [Indexed: 02/17/2023] Open
Abstract
Limb-Girdle Muscular Dystrophy Type R1 (LGMDR1; formerly LGMD2A), characterized by progressive hip and shoulder muscle weakness, is caused by mutations in CAPN3. In zebrafish, capn3b mediates Def-dependent degradation of p53 in the liver and intestines. We show that capn3b is expressed in the muscle. To model LGMDR1 in zebrafish, we generated three deletion mutants in capn3b and a positive-control dmd mutant (Duchenne muscular dystrophy). Two partial deletion mutants showed transcript-level reduction, whereas the RNA-less mutant lacked capn3b mRNA. All capn3b homozygous mutants were developmentally-normal adult-viable animals. Mutants in dmd were homozygous-lethal. Bathing wild-type and capn3b mutants in 0.8% methylcellulose (MC) for 3 days beginning 2 days post-fertilization resulted in significantly pronounced (20-30%) birefringence-detectable muscle abnormalities in capn3b mutant embryos. Evans Blue staining for sarcolemma integrity loss was strongly positive in dmd homozygotes, negative in wild-type embryos, and negative in MC-treated capn3b mutants, suggesting membrane instability is not a primary muscle pathology determinant. Increased birefringence-detected muscle abnormalities in capn3b mutants compared to wild-type animals were observed following induced hypertonia by exposure to cholinesterase inhibitor, azinphos-methyl, reinforcing the MC results. These mutant fish represent a novel tractable model for studying the mechanisms underlying muscle repair and remodeling, and as a preclinical tool for whole-animal therapeutics and behavioral screening in LGMDR1.
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Affiliation(s)
- Sergey V. Prykhozhij
- Children’s Hospital of Eastern Ontario (CHEO) Research Institute & University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Lucia Caceres
- Department of Psychology & Neuroscience, Dalhousie University, Halifax, NS B3H 4J1, Canada
- AGADA BioSciences, Halifax, NS B3H 0A8, Canada
| | - Kevin Ban
- Children’s Hospital of Eastern Ontario (CHEO) Research Institute & University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | | | - Kanneboyina Nagaraju
- AGADA BioSciences, Halifax, NS B3H 0A8, Canada
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University—State University of New York, Binghamton, NY 13902, USA
| | - Eric P. Hoffman
- AGADA BioSciences, Halifax, NS B3H 0A8, Canada
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University—State University of New York, Binghamton, NY 13902, USA
| | - Jason N. Berman
- Children’s Hospital of Eastern Ontario (CHEO) Research Institute & University of Ottawa, Ottawa, ON K1H 8L1, Canada
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10
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The Role of Histo-Blood Group Antigens and Microbiota in Human Norovirus Replication in Zebrafish Larvae. Microbiol Spectr 2022; 10:e0315722. [PMID: 36314930 PMCID: PMC9769672 DOI: 10.1128/spectrum.03157-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Human norovirus (HuNoV) is the major agent for viral gastroenteritis, causing >700 million infections yearly. Fucose-containing carbohydrates named histo-blood group antigens (HBGAs) are known (co)receptors for HuNoV. Moreover, bacteria of the gut microbiota expressing HBGA-like structures have shown an enhancing effect on HuNoV replication in an in vitro model. Here, we studied the role of HBGAs and the host microbiota during HuNoV infection in zebrafish larvae. Using whole-mount immunohistochemistry, we visualized the fucose expression in the zebrafish gut for the HBGA Lewis X [LeX, α(1,3)-fucose] and core fucose [α(1,6)-fucose]. Costaining of HuNoV-infected larvae proved colocalization of LeX and to a lower extent core fucose with the viral capsid protein VP1, indicating the presence of fucose residues on infected cells. Upon blocking of fucose expression by a fluorinated fucose analogue, HuNoV replication was strongly reduced. Furthermore, by comparing HuNoV replication in conventional and germfree zebrafish larvae, we found that the natural zebrafish microbiome does not have an effect on HuNoV replication, contrary to earlier reports about the human gut microbiome. Interestingly, monoassociation with the HBGA-expressing Enterobacter cloacae resulted in a minor decrease in HuNoV replication, which was not triggered by a stronger innate immune response. Overall, we show here that fucose has an essential role for HuNoV infection in zebrafish larvae, as in the human host, but their natural gut microbiome does not affect viral replication. IMPORTANCE Despite causing over 700 million infections yearly, many gaps remain in the knowledge of human norovirus (HuNoV) biology due to an historical lack of efficient cultivation systems. Fucose-containing carbohydrate structures, named histo-blood group antigens, are known to be important (co)receptors for viral entry in humans, while the natural gut microbiota is suggested to enhance viral replication. This study shows a conserved mechanism of entry for HuNoV in the novel zebrafish infection model, highlighting the pivotal opportunity this model represents to study entry mechanisms and identify the cellular receptor of HuNoV. Our results shed light on the interaction of HuNoV with the zebrafish microbiota, contributing to the understanding of the interplay between gut microbiota and enteric viruses. The ease of generating germfree animals that can be colonized with human gut bacteria is an additional advantage of using zebrafish larvae in virology. This small animal model constitutes an innovative alternative to high-severity animal models.
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11
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Helwer R, Charette JM. The SSU Processome Component Utp25p is a Pseudohelicase. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000606. [PMID: 36212518 PMCID: PMC9539457 DOI: 10.17912/micropub.biology.000606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/19/2022] [Accepted: 09/19/2022] [Indexed: 11/09/2022]
Abstract
RNA helicases are involved in nearly all aspects of RNA metabolism and factor prominently in ribosome assembly. The SSU processome includes 10 helicases and many helicase-cofactors. Together, they mediate the structural rearrangements that occur as part of ribosomal SSU assembly. During the identification of the SSU processome component Utp25/Def, it was noticed that the protein displays some sequence similarity to DEAD-box RNA helicases and is essential for growth. Interestingly, mutational ablation showed that Utp25's DEAD-box motifs are dispensable. Here, we show that the Utp25 AlphaFold prediction displays considerable structural similarity to DEAD-box helicases and is the first fully validated pseudohelicase.
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Affiliation(s)
- Rafe Helwer
- Department of Chemistry, Brandon University, Brandon, Manitoba, Canada.
,
Children’s Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada.
,
CancerCare Manitoba Research Institute, Winnipeg, Manitoba, Canada
| | - J. Michael Charette
- Department of Chemistry, Brandon University, Brandon, Manitoba, Canada.
,
Children’s Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada.
,
CancerCare Manitoba Research Institute, Winnipeg, Manitoba, Canada.
,
Correspondence to: J. Michael Charette (
)
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12
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Babu S, Takeuchi Y, Masai I. Banp regulates DNA damage response and chromosome segregation during the cell cycle in zebrafish retina. eLife 2022; 11:74611. [PMID: 35942692 PMCID: PMC9363121 DOI: 10.7554/elife.74611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 07/05/2022] [Indexed: 11/25/2022] Open
Abstract
Btg3-associated nuclear protein (Banp) was originally identified as a nuclear matrix-associated region (MAR)-binding protein and it functions as a tumor suppressor. At the molecular level, Banp regulates transcription of metabolic genes via a CGCG-containing motif called the Banp motif. However, its physiological roles in embryonic development are unknown. Here, we report that Banp is indispensable for the DNA damage response and chromosome segregation during mitosis. Zebrafish banp mutants show mitotic cell accumulation and apoptosis in developing retina. We found that DNA replication stress and tp53-dependent DNA damage responses were activated to induce apoptosis in banp mutants, suggesting that Banp is required for regulation of DNA replication and DNA damage repair. Furthermore, consistent with mitotic cell accumulation, chromosome segregation was not smoothly processed from prometaphase to anaphase in banp morphants, leading to a prolonged M-phase. Our RNA- and ATAC-sequencing identified 31 candidates for direct Banp target genes that carry the Banp motif. Interestingly, a DNA replication fork regulator, wrnip1, and two chromosome segregation regulators, cenpt and ncapg, are included in this list. Thus, Banp directly regulates transcription of wrnip1 for recovery from DNA replication stress, and cenpt and ncapg for chromosome segregation during mitosis. Our findings provide the first in vivo evidence that Banp is required for cell-cycle progression and cell survival by regulating DNA damage responses and chromosome segregation during mitosis. In order for a cell to divide, it must progress through a series of carefully controlled steps known as the cell cycle. First, the cell replicates its DNA and both copies get segregated to opposite ends. The cell then splits into two and each new cell receives a copy of the duplicated genetic material. If any of the stages in the cell cycle become disrupted or mis-regulated this can lead to uncontrolled divisions that may result in cancer. Researchers have often used a structure within the eye known as the retina to study the cell cycle in zebrafish and other animals as cells in the retina rapidly divide in a highly controlled manner. A protein called Banp is known to help stop tumors from growing in humans and mice, but its normal role in the body, particularly the cell cycle, has remained unclear. To investigate, Babu et al. studied the retina of mutant zebrafish that were unable to make the Banp protein. The experiments revealed that two stress responses indicating DNA damage or defects in copying DNA were active in the retinal cells of the mutant zebrafish. This suggested that Banp allows cell to progress through the cell cycle by repairing any DNA damage that may arise during replication. Banp does this by activating the gene for another protein called Wrnip1. Babu et al. also found that Banp helps segregate the two copies of DNA during cell division by promoting the activation of two other proteins called Cenpt and Ncapg. Further experiments identified 31 genes that were directly regulated by Banp. These findings demonstrate that Banp is required for zebrafish cells to be able to accurately copy their DNA and divide in to two new cells. In the future, the work of Babu et al. will provide a useful resource to investigate how tumors grow and spread around the body, and may contribute to the development of new treatments for cancer.
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Affiliation(s)
- Swathy Babu
- Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - Yuki Takeuchi
- Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - Ichiro Masai
- Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
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13
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Ding F, Huang D, Wang M, Peng J. An 86 amino acids motif in CAPN3 is essential for formation of the nucleolus-localized Def-CAPN3 complex. Biochem Biophys Res Commun 2022; 623:66-73. [PMID: 35878425 DOI: 10.1016/j.bbrc.2022.06.032] [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: 05/16/2022] [Accepted: 06/09/2022] [Indexed: 11/17/2022]
Abstract
Digestive-organ expansion factor (Def) is a nucleolar protein that recruits cysteine proteinase Calpain3 (CAPN3) into the nucleolus to form the Def-CAPN3 complex in both human and zebrafish. This complex mediates the degradation of the tumor suppressor p53 and ribosome biogenesis factor mitotic phosphorylated protein 10 (Mpp10) in nucleolus, demonstrating the importance of this complex in regulating cell cycle and ribosome biogenesis. However, the Def and CAPN3 interacting motifs have yet been identified. In this report, by using a series of truncated or internally deleted human CAPN3 (hCAPN3) derivatives we identify that an essential motif of 86 amino acids (86-aa) (430-515aa) in hCAPN3 for its interaction with human Def (hDef), and this 86-aa motif is highly conserved in zebrafish Capn3b (zCapn3b) and is also required for the interaction between zebrafish Def (zDef) and zCapn3b. We further identify the 2/3 C-terminus of hDef is responsible for mediating the hDef-hCAPN3 interaction, and the corresponding region is conserved for the zDef and zCapn3b interaction. Our results lay the ground to resolve the structure of the Def-CAPN3 complex in the future.
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Affiliation(s)
- Feng Ding
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Delai Huang
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Mingyun Wang
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jinrong Peng
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
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14
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Mehta S, Campbell H, Drummond CJ, Li K, Murray K, Slatter T, Bourdon JC, Braithwaite AW. Adaptive homeostasis and the p53 isoform network. EMBO Rep 2021; 22:e53085. [PMID: 34779563 PMCID: PMC8647153 DOI: 10.15252/embr.202153085] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 10/12/2021] [Accepted: 10/28/2021] [Indexed: 12/25/2022] Open
Abstract
All living organisms have developed processes to sense and address environmental changes to maintain a stable internal state (homeostasis). When activated, the p53 tumour suppressor maintains cell and organ integrity and functions in response to homeostasis disruptors (stresses) such as infection, metabolic alterations and cellular damage. Thus, p53 plays a fundamental physiological role in maintaining organismal homeostasis. The TP53 gene encodes a network of proteins (p53 isoforms) with similar and distinct biochemical functions. The p53 network carries out multiple biological activities enabling cooperation between individual cells required for long‐term survival of multicellular organisms (animals) in response to an ever‐changing environment caused by mutation, infection, metabolic alteration or damage. In this review, we suggest that the p53 network has evolved as an adaptive response to pathogen infections and other environmental selection pressures.
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Affiliation(s)
- Sunali Mehta
- Department of Pathology, School of Medicine, University of Otago, Dunedin, New Zealand.,Maurice Wilkins Centre for Biodiscovery, University of Otago, Dunedin, New Zealand
| | - Hamish Campbell
- Department of Pathology, School of Medicine, University of Otago, Dunedin, New Zealand
| | - Catherine J Drummond
- Department of Pathology, School of Medicine, University of Otago, Dunedin, New Zealand.,Maurice Wilkins Centre for Biodiscovery, University of Otago, Dunedin, New Zealand
| | - Kunyu Li
- Department of Pathology, School of Medicine, University of Otago, Dunedin, New Zealand
| | - Kaisha Murray
- Dundee Cancer Centre, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Tania Slatter
- Department of Pathology, School of Medicine, University of Otago, Dunedin, New Zealand.,Maurice Wilkins Centre for Biodiscovery, University of Otago, Dunedin, New Zealand
| | - Jean-Christophe Bourdon
- Dundee Cancer Centre, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Antony W Braithwaite
- Department of Pathology, School of Medicine, University of Otago, Dunedin, New Zealand.,Maurice Wilkins Centre for Biodiscovery, University of Otago, Dunedin, New Zealand
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15
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Zhu Y, Wang Y, Tao B, Han J, Chen H, Zhu Q, Huang L, He Y, Hong J, Li Y, Chen J, Huang J, Lo LJ, Peng J. Nucleolar GTPase Bms1 displaces Ttf1 from RFB-sites to balance progression of rDNA transcription and replication. J Mol Cell Biol 2021; 13:902-917. [PMID: 34791311 PMCID: PMC8800533 DOI: 10.1093/jmcb/mjab074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/30/2021] [Accepted: 11/02/2021] [Indexed: 11/24/2022] Open
Abstract
18S, 5.8S, and 28S ribosomal RNAs (rRNAs) are cotranscribed as a pre-ribosomal RNA (pre-rRNA) from the rDNA by RNA polymerase I whose activity is vigorous during the S-phase, leading to a conflict with rDNA replication. This conflict is resolved partly by replication-fork-barrier (RFB)-sites sequences located downstream of the rDNA and RFB-binding proteins such as Ttf1. However, how Ttf1 is displaced from RFB-sites to allow replication fork progression remains elusive. Here, we reported that loss-of-function of Bms1l, a nucleolar GTPase, upregulates rDNA transcription, causes replication-fork stall, and arrests cell cycle at the S-to-G2 transition; however, the G1-to-S transition is constitutively active characterized by persisting DNA synthesis. Concomitantly, ubf, tif-IA, and taf1b marking rDNA transcription, Chk2, Rad51, and p53 marking DNA-damage response, and Rpa2, PCNA, Fen1, and Ttf1 marking replication fork stall are all highly elevated in bms1l mutants. We found that Bms1 interacts with Ttf1 in addition to Rc1l. Finally, we identified RFB-sites for zebrafish Ttf1 through chromatin immunoprecipitation sequencing and showed that Bms1 disassociates the Ttf1‒RFB complex with its GTPase activity. We propose that Bms1 functions to balance rDNA transcription and replication at the S-phase through interaction with Rcl1 and Ttf1, respectively. TTF1 and Bms1 together might impose an S-phase checkpoint at the rDNA loci.
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Affiliation(s)
- Yanqing Zhu
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Yong Wang
- Taizhou Hospital, Zhejiang University, Taizhou, 317000 China
| | - Boxiang Tao
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Jinhua Han
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058 China
| | - Hong Chen
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Qinfang Zhu
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Ling Huang
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Yinan He
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Jian Hong
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Yunqin Li
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Jun Chen
- College of Life Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Jun Huang
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058 China
| | - Li Jan Lo
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Jinrong Peng
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
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16
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Zhang C, Huang R, Ma X, Chen J, Han X, Li L, Luo L, Ruan H, Huang H. The Ribosome Biogenesis Factor Ltv1 Is Essential for Digestive Organ Development and Definitive Hematopoiesis in Zebrafish. Front Cell Dev Biol 2021; 9:704730. [PMID: 34692673 PMCID: PMC8528963 DOI: 10.3389/fcell.2021.704730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 09/13/2021] [Indexed: 11/13/2022] Open
Abstract
Ribosome biogenesis is a fundamental activity in cells. Ribosomal dysfunction underlies a category of diseases called ribosomopathies in humans. The symptomatic characteristics of ribosomopathies often include abnormalities in craniofacial skeletons, digestive organs, and hematopoiesis. Consistently, disruptions of ribosome biogenesis in animals are deleterious to embryonic development with hypoplasia of digestive organs and/or impaired hematopoiesis. In this study, ltv1, a gene involved in the small ribosomal subunit assembly, was knocked out in zebrafish by clustered regularly interspaced short palindromic repeats (CRISPRs)/CRISPR associated protein 9 (Cas9) technology. The recessive lethal mutation resulted in disrupted ribosome biogenesis, and ltv1 Δ14/Δ14 embryos displayed hypoplastic craniofacial cartilage, digestive organs, and hematopoiesis. In addition, we showed that the impaired cell proliferation, instead of apoptosis, led to the defects in exocrine pancreas and hematopoietic stem and progenitor cells (HSPCs) in ltv1 Δ14/Δ14 embryos. It was reported that loss of function of genes associated with ribosome biogenesis often caused phenotypes in a P53-dependent manner. In ltv1 Δ14/Δ14 embryos, both P53 protein level and the expression of p53 target genes, Δ113p53 and p21, were upregulated. However, knockdown of p53 failed to rescue the phenotypes in ltv1 Δ14/Δ14 larvae. Taken together, our data demonstrate that LTV1 ribosome biogenesis factor (Ltv1) plays an essential role in digestive organs and hematopoiesis development in zebrafish in a P53-independent manner.
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Affiliation(s)
- Chong Zhang
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Rui Huang
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Xirui Ma
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Jiehui Chen
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Xinlu Han
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Li Li
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Lingfei Luo
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Hua Ruan
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Honghui Huang
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
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17
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Zhao S, Huang D, Peng J. Nucleolus-localized Def-CAPN3 protein degradation pathway and its role in cell cycle control and ribosome biogenesis. J Genet Genomics 2021; 48:955-960. [PMID: 34452850 DOI: 10.1016/j.jgg.2021.06.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 12/25/2022]
Abstract
The nucleolus, as the 'nucleus of the nucleus', is a prominent subcellular organelle in a eukaryocyte. The nucleolus serves as the centre for ribosome biogenesis, as well as an important site for cell-cycle regulation, cellular senescence, and stress response. The protein composition of the nucleolus changes dynamically through protein turnover to meet the needs of cellular activities or stress responses. Recent studies have identified a nucleolus-localized protein degradation pathway in zebrafish and humans, namely the Def-CAPN3 pathway, which is essential to ribosome production and cell-cycle progression, by controlling the turnover of multiple substrates (e.g., ribosomal small-subunit [SSU] processome component Mpp10, transcription factor p53, check-point proteins Chk1 and Wee1). This pathway relies on the Ca2+-dependent cysteine proteinase CAPN3 and is independent of the ubiquitin-mediated proteasome pathway. CAPN3 is recruited by nucleolar protein Def from cytoplasm to nucleolus, where it proteolyzes its substrates which harbor a CAPN3 recognition-motif. Def depletion leads to the exclusion of CAPN3 and accumulation of p53, Wee1, Chk1, and Mpp10 in the nucleolus that result in cell-cycle arrest and rRNA processing abnormality. Here, we summarize the discovery of the Def-CAPN3 pathway and propose its biological role in cell-cycle control and ribosome biogenesis.
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Affiliation(s)
- Shuyi Zhao
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Delai Huang
- Department of Biology, University of Virginia, Charlottesville, VA 22904, United States
| | - Jinrong Peng
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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18
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Zhu Q, Tao B, Chen H, Shi H, Huang L, Chen J, Hu M, Lo LJ, Peng J. Rcl1 depletion impairs 18S pre-rRNA processing at the A1-site and up-regulates a cohort of ribosome biogenesis genes in zebrafish. Nucleic Acids Res 2021; 49:5743-5759. [PMID: 34019640 PMCID: PMC8191805 DOI: 10.1093/nar/gkab381] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/24/2021] [Accepted: 04/29/2021] [Indexed: 12/12/2022] Open
Abstract
Yeast Rcl1 is a potential endonuclease that mediates pre-RNA cleavage at the A2-site to separate 18S rRNA from 5.8S and 25S rRNAs. However, the biological function of Rcl1 in opisthokonta is poorly defined. Moreover, there is no information regarding the exact positions of 18S pre-rRNA processing in zebrafish. Here, we report that zebrafish pre-rRNA harbours three major cleavage sites in the 5′ETS, namely –477nt (A′-site), –97nt (A0-site) and the 5′ETS and 18S rRNA link (A1-site), as well as two major cleavage regions within the ITS1, namely 208–218nt (site 2) and 20–33nt (site E). We also demonstrate that depletion of zebrafish Rcl1 mainly impairs cleavage at the A1-site. Phenotypically, rcl1–/– mutants exhibit a small liver and exocrine pancreas and die before 15 days post-fertilization. RNA-seq analysis revealed that the most significant event in rcl1–/– mutants is the up-regulated expression of a cohort of genes related to ribosome biogenesis and tRNA production. Our data demonstrate that Rcl1 is essential for 18S rRNA maturation at the A1-site and for digestive organogenesis in zebrafish. Rcl1 deficiency, similar to deficiencies in other ribosome biogenesis factors, might trigger a common mechanism to upregulate the expression of genes responsible for ribosome biogenesis.
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Affiliation(s)
- Qinfang Zhu
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, China
| | - Boxiang Tao
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, China
| | - Hong Chen
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, China
| | - Hui Shi
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, China
| | - Ling Huang
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, China
| | - Jun Chen
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Minjie Hu
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA
| | - Li Jan Lo
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, China
| | - Jinrong Peng
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, China
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Loss-of-function of p53 isoform Δ113p53 accelerates brain aging in zebrafish. Cell Death Dis 2021; 12:151. [PMID: 33542214 PMCID: PMC7862496 DOI: 10.1038/s41419-021-03438-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 01/13/2021] [Accepted: 01/15/2021] [Indexed: 11/30/2022]
Abstract
Reactive oxygen species (ROS) stress has been demonstrated as potentially critical for induction and maintenance of cellular senescence, and been considered as a contributing factor in aging and in various neurological disorders including Alzheimer’s disease (AD) and amyotrophic lateral sclerosis (ALS). In response to low-level ROS stress, the expression of Δ133p53, a human p53 isoform, is upregulated to promote cell survival and protect cells from senescence by enhancing the expression of antioxidant genes. In normal conditions, the basal expression of Δ133p53 prevents human fibroblasts, T lymphocytes, and astrocytes from replicative senescence. It has been also found that brain tissues from AD and ALS patients showed decreased Δ133p53 expression. However, it is uncharacterized if Δ133p53 plays a role in brain aging. Here, we report that zebrafish Δ113p53, an ortholog of human Δ133p53, mainly expressed in some of the radial glial cells along the telencephalon ventricular zone in a full-length p53-dependent manner. EDU-labeling and cell lineage tracing showed that Δ113p53-positive cells underwent cell proliferation to contribute to the neuron renewal process. Importantly, Δ113p53M/M mutant telencephalon possessed less proliferation cells and more senescent cells compared to wild-type (WT) zebrafish telencephalon since 9-months old, which was associated with decreased antioxidant genes expression and increased level of ROS in the mutant telencephalon. More interestingly, unlike the mutant fish at 5-months old with cognition ability, Δ113p53M/M zebrafish, but not WT zebrafish, lost their learning and memory ability at 19-months old. The results demonstrate that Δ113p53 protects the brain from aging by its antioxidant function. Our finding provides evidence at the organism level to show that depletion of Δ113p53/Δ133p53 may result in long-term ROS stress, and finally lead to age-related diseases, such as AD and ALS in humans.
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Gao C, Peng J. All routes lead to Rome: multifaceted origin of hepatocytes during liver regeneration. CELL REGENERATION 2021; 10:2. [PMID: 33403526 PMCID: PMC7785766 DOI: 10.1186/s13619-020-00063-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 09/09/2020] [Indexed: 12/19/2022]
Abstract
Liver is the largest internal organ that serves as the key site for various metabolic activities and maintenance of homeostasis. Liver diseases are great threats to human health. The capability of liver to regain its mass after partial hepatectomy has widely been applied in treating liver diseases either by removing the damaged part of a diseased liver in a patient or transplanting a part of healthy liver into a patient. Vast efforts have been made to study the biology of liver regeneration in different liver-damage models. Regarding the sources of hepatocytes during liver regeneration, convincing evidences have demonstrated that different liver-damage models mobilized different subtype hepatocytes in contributing to liver regeneration. Under extreme hepatocyte ablation, biliary epithelial cells can undergo dedifferentiation to liver progenitor cells (LPCs) and then LPCs differentiate to produce hepatocytes. Here we will focus on summarizing the progresses made in identifying cell types contributing to producing new hepatocytes during liver regeneration in mice and zebrafish.
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Affiliation(s)
- Ce Gao
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jinrong Peng
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
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21
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The Δ133p53 Isoforms, Tuners of the p53 Pathway. Cancers (Basel) 2020; 12:cancers12113422. [PMID: 33218139 PMCID: PMC7698932 DOI: 10.3390/cancers12113422] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/12/2020] [Accepted: 11/16/2020] [Indexed: 02/07/2023] Open
Abstract
Simple Summary TP53, the most frequently mutated gene in human cancers, has a key role in the maintenance of the genetic stability and, thus, in preventing tumor development. The p53-dependent responses were long thought to be solely driven by canonical p53α. However, it is now known that TP53 physiologically expresses at least 12 p53 isoforms including Δ133p53α, Δ133p53β and Δ133p53γ. The Δ133p53 isoforms are potent modulators of the p53 pathway that regulate critical functions in cancer, physiological and premature aging, neurodegenerative diseases, immunity and inflammation, and tissue repair. This review aims to summarize the current knowledge on the Δ133p53 isoforms and how they contribute to multiple physiological and pathological mechanisms. Critically, further characterization of p53 isoforms may identify novel regulatory modes of p53 pathway functions that contribute to disease progression and facilitate the development of new therapeutic strategies. Abstract The TP53 gene is a critical tumor suppressor and key determinant of cell fate which regulates numerous cellular functions including DNA repair, cell cycle arrest, cellular senescence, apoptosis, autophagy and metabolism. In the last 15 years, the p53 pathway has grown in complexity through the discovery that TP53 differentially expresses twelve p53 protein isoforms in human cells with both overlapping and unique biologic activities. Here, we summarize the current knowledge on the Δ133p53 isoforms (Δ133p53α, Δ133p53β and Δ133p53γ), which are evolutionary derived and found only in human and higher order primates. All three isoforms lack both of the transactivation domains and the beginning of the DNA-binding domain. Despite the absence of these canonical domains, the Δ133p53 isoforms maintain critical functions in cancer, physiological and premature aging, neurodegenerative diseases, immunity and inflammation, and tissue repair. The ability of the Δ133p53 isoforms to modulate the p53 pathway functions underscores the need to include these p53 isoforms in our understanding of how the p53 pathway contributes to multiple physiological and pathological mechanisms. Critically, further characterization of p53 isoforms may identify novel regulatory modes of p53 pathway functions that contribute to disease progression and facilitate the development of new therapeutic strategies.
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p53 isoform Δ113p53 promotes zebrafish heart regeneration by maintaining redox homeostasis. Cell Death Dis 2020; 11:568. [PMID: 32703938 PMCID: PMC7378207 DOI: 10.1038/s41419-020-02781-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 07/08/2020] [Accepted: 07/13/2020] [Indexed: 12/14/2022]
Abstract
Neonatal mice and adult zebrafish can fully regenerate their hearts through proliferation of pre-existing cardiomyocytes. Previous studies have revealed that p53 signalling is activated during cardiac regeneration in neonatal mice and that hydrogen peroxide (H2O2) generated near the wound site acts as a novel signal to promote zebrafish heart regeneration. We recently demonstrated that the expression of the p53 isoform Δ133p53 is highly induced upon stimulation by low-level reactive oxygen species (ROS) and that Δ133p53 coordinates with full-length p53 to promote cell survival by enhancing the expression of antioxidant genes. However, the function of p53 signalling in heart regeneration remains uncharacterised. Here, we found that the expression of Δ113p53 is activated in cardiomyocytes at the resection site in the zebrafish heart in a full-length p53- and ROS signalling-dependent manner. Cell lineage tracing showed that Δ113p53-positive cardiomyocytes undergo cell proliferation and contribute to myocardial regeneration. More importantly, heart regeneration is impaired in Δ113p53M/M mutant zebrafish. Depletion of Δ113p53 significantly decreases the proliferation frequency of cardiomyocytes but has little effect on the activation of gata4-positive cells, their migration to the edge of the wound site, or apoptotic activity. Live imaging of intact hearts showed that induction of H2O2 at the resection site is significantly higher in Δ113p53M/M mutants than in wild-type zebrafish, which may be the result of reduced induction of antioxidant genes in Δ113p53M/M mutants. Our findings demonstrate that induction of Δ113p53 in cardiomyocytes at the resection site functions to promote heart regeneration by increasing the expression of antioxidant genes to maintain redox homeostasis.
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McElderry J, Carrington B, Bishop K, Kim E, Pei W, Chen Z, Ramanagoudr-Bhojappa R, Prakash A, Burgess SM, Liu PP, Sood R. Splicing factor DHX15 affects tp53 and mdm2 expression via alternate splicing and promoter usage. Hum Mol Genet 2020; 28:4173-4185. [PMID: 31691804 DOI: 10.1093/hmg/ddz261] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 10/18/2019] [Accepted: 10/24/2019] [Indexed: 12/21/2022] Open
Abstract
DHX15, a DEAH box containing RNA helicase, is a splicing factor required for the last step of splicing. Recent studies identified a recurrent mutational hotspot, R222G, in DHX15 in ∼ 6% of acute myeloid leukemia (AML) patients that carry the fusion protein RUNX1-RUNX1T1 produced by t (8;21) (q22;q22). Studies using yeast mutants showed that substitution of G for the residue equivalent to R222 leads to loss of its helicase function, suggesting that it is a loss-of-function mutation. To elucidate the role of DHX15 during development, we established the first vertebrate knockout model with CRISPR/Cas9 in zebrafish. Our data showed that dhx15 expression is enriched in the brain, eyes, pectoral fin primordia, liver and intestinal bulb during embryonic development. Dhx15 deficiency leads to pleiotropic morphological phenotypes in homozygous mutant embryos starting at 3 days post fertilization (dpf) that result in lethality by 7 dpf, revealing an essential role during embryonic development. RNA-seq analysis suggested important roles of Dhx15 in chromatin and nucleosome assembly and regulation of the Mdm2-p53 pathway. Interestingly, exons corresponding to the alternate transcriptional start sites for tp53 and mdm2 were preferentially expressed in the mutant embryos, leading to significant upregulation of their alternate isoforms, Δ113p53 (orthologous to Δ133p53 isoform in human) and mdm2-P2 (isoform using distal promoter P2), respectively. We speculate that these alterations in the Mdm2-p53 pathway contribute to the development of AML in patients with t(8;21) and somatically mutated DHX15.
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Affiliation(s)
- John McElderry
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Blake Carrington
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kevin Bishop
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Erika Kim
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wuhong Pei
- Developmental Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zelin Chen
- Developmental Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ramanagouda Ramanagoudr-Bhojappa
- Cancer Genomics Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anupam Prakash
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shawn M Burgess
- Developmental Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - P Paul Liu
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Raman Sood
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.,Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Chen F, Huang D, Shi H, Gao C, Wang Y, Peng J. Capn3 depletion causes Chk1 and Wee1 accumulation and disrupts synchronization of cell cycle reentry during liver regeneration after partial hepatectomy. ACTA ACUST UNITED AC 2020; 9:8. [PMID: 32588143 PMCID: PMC7306836 DOI: 10.1186/s13619-020-00049-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 04/16/2020] [Indexed: 01/20/2023]
Abstract
Recovery of liver mass to a healthy liver donor by compensatory regeneration after partial hepatectomy (PH) is a prerequisite for liver transplantation. Synchronized cell cycle reentry of the existing hepatocytes after PH is seemingly a hallmark of liver compensatory regeneration. Although the molecular control of the PH-triggered cell cycle reentry has been extensively studied, little is known about how the synchronization is achieved after PH. The nucleolus-localized protein cleavage complex formed by the nucleolar protein Digestive-organ expansion factor (Def) and cysteine proteinase Calpain 3 (Capn3) has been implicated to control wounding healing during liver regeneration through selectively cleaving the tumor suppressor p53 in the nucleolus. However, whether the Def-Capn3 complex participates in regulating the synchronization of cell cycle reentry after PH is unknown. In this report, we generated a zebrafish capn3b null mutant (capn3b∆19∆14). The homozygous mutant was viable and fertile, but suffered from a delayed liver regeneration after PH. Delayed liver regeneration in capn3b∆19∆14 was due to disruption of synchronized cell proliferation after PH. Mass spectrometry (MS) analysis of nuclear proteins revealed that a number of negative regulators of cell cycle are accumulated in the capn3b∆19∆14 liver after PH. Moreover, we demonstrated that Check-point kinase 1 (Chk1) and Wee1, two key negative regulators of G2 to M transition, are substrates of Capn3. We also demonstrated that Chk1 and Wee1 were abnormally accumulated in the nucleoli of amputated capn3b∆19∆14 liver. In conclusion, our findings suggest that the nucleolar-localized Def-Capn3 complex acts as a novel regulatory pathway for the synchronization of cell cycle reentry, at least partially, through inactivating Chk1 and Wee1 during liver regeneration after PH.
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Affiliation(s)
- Feng Chen
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Delai Huang
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.,Present address: Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Hui Shi
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.,Present address: Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ce Gao
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jinrong Peng
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
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Li Y, Li T, Tang Y, Zhan Z, Ding L, Song L, Yu T, Yang Y, Ma J, Zhang Y, Zhou Y, Gu S, Xu M, Gao Y, Li Y. The function of a heterozygous p53 mutation in a Li-Fraumeni syndrome patient. PLoS One 2020; 15:e0234262. [PMID: 32516327 PMCID: PMC7282642 DOI: 10.1371/journal.pone.0234262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/21/2020] [Indexed: 11/29/2022] Open
Abstract
p53 is one of the most extensively studied proteins in cancer research. Mutations in p53 generally abolish normal p53 function, and some mutants can gain new oncogenic functions. However, the mechanisms underlying p53 mutation-driven cancer remains to be elucidated. Our study investigated the function of a heterozygous p53 mutation (p.Asn268Glufs*4) in a Li-Fraumeni syndrome (LFS) patient. We used episomal technology to perform somatic reprogramming, and used molecular and cell biology methods to determine the p53 mutation levels in patient-originated induced pluripotent stem (iPS) cells at the RNA and protein levels. We found that p53 protein expression was not increased in this patient’s somatic cells compared with those of a healthy control. p53 mutation facilitates the proliferation of tumor cells by inhibiting apoptosis and promoting cell division. It can inhibit the efficiency of somatic reprogramming by inhibiting OCT4 expression during reprogramming stage. Moreover, not all p53 mutant iPS cell lines have mutant p53 RNA sequences. A small percentage of mutant p53 mRNA is present in the somatic cells from the patient and his mother. In summary, this p53 mutation can promote tumor cell proliferation, inhibit somatic reprogramming, and exhibit random p53 allelic expression of heterozygous mutations in the patient and iPS cells which may be one of the reasons why the people with p53 mutations develop cancer at random. This finding suggested that mutant p53 allelic expression should be added to the risk forecasting of cancer.
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Affiliation(s)
- Yang Li
- Department of Hematology & Oncology, Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ting Li
- Department of Hematology & Oncology, Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuejia Tang
- Department of Hematology & Oncology, Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhiyan Zhan
- Department of Hematology & Oncology, Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lixia Ding
- Department of Hematology & Oncology, Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lili Song
- Department of Hematology & Oncology, Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tingting Yu
- Molecular Biological Diagnostic Laboratory, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi Yang
- Department of Hematology & Oncology, Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Ma
- Department of Pathology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingwen Zhang
- Department of Hematology & Oncology, Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ying Zhou
- Department of Radiology, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Song Gu
- Department of General Surgery/Surgical Oncology Center, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Min Xu
- Department of General Surgery/Surgical Oncology Center, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- * E-mail: (YL); (YG); (MX)
| | - Yijin Gao
- Department of Hematology & Oncology, Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- * E-mail: (YL); (YG); (MX)
| | - Yanxin Li
- Department of Hematology & Oncology, Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- * E-mail: (YL); (YG); (MX)
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Huang W, Chen F, Ma Q, Xin J, Li J, Chen J, Zhou B, Chen M, Li J, Peng J. Ribosome biogenesis gene DEF/UTP25 is essential for liver homeostasis and regeneration. SCIENCE CHINA-LIFE SCIENCES 2020; 63:1651-1664. [PMID: 32303961 DOI: 10.1007/s11427-019-1635-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/17/2020] [Indexed: 12/19/2022]
Abstract
Hepatocytes are responsible for diverse metabolic activities in a liver. Proper ribosome biogenesis is essential to sustain the function of hepatocytes. There are approximately 200 factors involved in ribosome biogenesis; however, few studies have focused on the role of these factors in maintaining liver homeostasis. The digestive organ expansion factor (def) gene encodes a nucleolar protein Def that participates in ribosome biogenesis. In addition, Def forms a complex with cysteine protease Calpain3 (Capn3) and recruits Capn3 to the nucleolus to cleave protein targets. However, the function of Def has not been characterized in the mammalian digestive organs. In this report, we show that conditional knockout of the mouse def gene in hepatocytes causes cell morphology abnormality and constant infiltration of inflammatory cells in the liver. As age increases, the def conditional knockout liver displays multiple tissue damage foci and biliary hyperplasia. Moreover, partial hepatectomy leads to sudden acute death to the def conditional knockout mice and this phenotype is rescued by intragastric injection of the anti-inflammation drug dexamethasone one day before hepatectomy. Our results demonstrate that Def is essential for maintaining the liver homeostasis and liver regeneration capacity in mammals.
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Affiliation(s)
- Weidong Huang
- MOE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Feng Chen
- MOE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Quanxin Ma
- Academy of Chinese Medicine/Institute of Comparative Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Jiaojiao Xin
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Jiaqi Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Jun Chen
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Bin Zhou
- The State Key Laboratory of Cell Biology, CAS Center for Excellence on Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Minli Chen
- Academy of Chinese Medicine/Institute of Comparative Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053, China.
| | - Jun Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China.
| | - Jinrong Peng
- MOE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
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Huang Y, Huang CX, Wang WF, Liu H, Wang HL. Zebrafish miR-462-731 is required for digestive organ development. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 34:100679. [PMID: 32200130 DOI: 10.1016/j.cbd.2020.100679] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 02/24/2020] [Accepted: 02/26/2020] [Indexed: 02/06/2023]
Abstract
MicroRNAs (miRNAs), as important regulators of post-transcriptional gene expression, play important roles in the occurrence and function of organs. In this study, morpholino (MO) knockdown of miR-462/miR-731 was used to investigate the potential mechanisms of the miR-462-731 cluster during zebrafish liver development. The results showed significant reduction of digestive organs, especially liver and exocrine pancreas after the miR-462/miR-731 knockdown, and those phenotypes could be partially rescued by corresponding miRNA duplex. Acinar cells of the exocrine pancreas were also severely affected with pancreatic insufficiency. In particular, knockdown of miR-462 caused pancreas morphogenesis abnormity with specific bilateral exocrine pancreas. Additionally, it was found that miR-731 played a role in liver and exocrine pancreas development by directly targeting dkk3b, instead of the down-regulation of Wnt/β-catenin signaling. These findings contribute significantly to our understanding of molecular mechanisms of miR-462-731 cluster in development of digestive organs.
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Affiliation(s)
- Yan Huang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Chun-Xiao Huang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Wei-Feng Wang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Hong Liu
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Huan-Ling Wang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, Wuhan, Hubei, PR China.
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Martín B, Pappa S, Díez-Villanueva A, Mallona I, Custodio J, Barrero MJ, Peinado MA, Jordà M. Tissue and cancer-specific expression of DIEXF is epigenetically mediated by an Alu repeat. Epigenetics 2020; 15:765-779. [PMID: 32041475 DOI: 10.1080/15592294.2020.1722398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Alu repeats constitute a major fraction of human genome and for a small subset of them a role in gene regulation has been described. The number of studies focused on the functional characterization of particular Alu elements is very limited. Most Alu elements are DNA methylated and then assumed to lie in repressed chromatin domains. We hypothesize that Alu elements with low or variable DNA methylation are candidates for a functional role. In a genome-wide study in normal and cancer tissues, we pinpointed an Alu repeat (AluSq2) with differential methylation located upstream of the promoter region of the DIEXF gene. DIEXF encodes a highly conserved factor essential for the development of zebrafish digestive tract. To characterize the contribution of the Alu element to the regulation of DIEXF we analysed the epigenetic landscapes of the gene promoter and flanking regions in different cell types and cancers. Alternate epigenetic profiles (DNA methylation and histone modifications) of the AluSq2 element were associated with DIEXF transcript diversity as well as protein levels, while the epigenetic profile of the CpG island associated with the DIEXF promoter remained unchanged. These results suggest that AluSq2 might directly contribute to the regulation of DIEXF transcription and protein expression. Moreover, AluSq2 was DNA hypomethylated in different cancer types, pointing out its putative contribution to DIEXF alteration in cancer and its potential as tumoural biomarker.
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Affiliation(s)
- Berta Martín
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Stella Pappa
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Anna Díez-Villanueva
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Izaskun Mallona
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Joaquín Custodio
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - María José Barrero
- Center for Regenerative Medicine in Barcelona (CMRB), Avinguda de la Granvia de l'Hospitalet , Barcelona, Spain
| | - Miguel A Peinado
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Mireia Jordà
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
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Kansara K, Kumar A, Karakoti AS. Combination of humic acid and clay reduce the ecotoxic effect of TiO 2 NPs: A combined physico-chemical and genetic study using zebrafish embryo. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 698:134133. [PMID: 31505348 DOI: 10.1016/j.scitotenv.2019.134133] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/06/2019] [Accepted: 08/25/2019] [Indexed: 06/10/2023]
Abstract
The series of breakthroughs that have occurred within the realm of nanotechnology have been the source of several new products and technological interventions. One of the most salient examples in this regard is the widespread employment of titanium dioxide (TiO2) nanoparticles across a range of consumer goods. Given that waste is generated at every stage of the consumer-product cycle (from production to disposal), many items with TiO2 nanoparticles are likely to end up being discarded into water bodies. In order to understand the interaction of TiO2 NPs with aquatic ecosystem, the ecological fate and toxicity of TiO2 NPs was studied by exposing zebrafish embryos to a combination of abiotic factors (humic acid and clay) to assess its effect on the development of zebrafish embryos. The physiological changes were correlated with genetic marker analysis to holistically understand the effect on embryos development. Derjaguin-Landau-Verwey-Overbeek (DLVO) theory was used to analyze the interaction energy between TiO2 NPs and natural organic matter (NOM) for understanding the aggregation behavior of engineered nanoparticles (ENPs) in media. The study revealed that combination of HA and clay stabilized TiO2 NPs, compared to bare TiO2 and HA or clay alone. TiO2 NPs and TiO2 NPs + Clay significantly altered the expression of genes involved in development of dorsoventral axis and neural network of zebrafish embryos. However, the presence of HA and HA + clay showed protective effect on zebrafish embryo development. The complete system analysis demonstrated the possible ameliorating effects of abiotic factors on the ecotoxicity of ENPs.
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Affiliation(s)
- Krupa Kansara
- Biological & Life Sciences, School of Arts & Sciences, Ahmedabad University, Central Campus, Navrangpura, Ahmedabad 380009, Gujarat, India
| | - Ashutosh Kumar
- Biological & Life Sciences, School of Arts & Sciences, Ahmedabad University, Central Campus, Navrangpura, Ahmedabad 380009, Gujarat, India.
| | - Ajay S Karakoti
- Biological & Life Sciences, School of Arts & Sciences, Ahmedabad University, Central Campus, Navrangpura, Ahmedabad 380009, Gujarat, India.
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The Emerging Landscape of p53 Isoforms in Physiology, Cancer and Degenerative Diseases. Int J Mol Sci 2019; 20:ijms20246257. [PMID: 31835844 PMCID: PMC6941119 DOI: 10.3390/ijms20246257] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/26/2019] [Accepted: 12/09/2019] [Indexed: 12/13/2022] Open
Abstract
p53, first described four decades ago, is now established as a master regulator of cellular stress response, the “guardian of the genome”. p53 contributes to biological robustness by behaving in a cellular-context dependent manner, influenced by several factors (e.g., cell type, active signalling pathways, the type, extent and intensity of cellular damage, cell cycle stage, nutrient availability, immune function). The p53 isoforms regulate gene transcription and protein expression in response to the stimuli so that the cell response is precisely tuned to the cell signals and cell context. Twelve isoforms of p53 have been described in humans. In this review, we explore the interactions between p53 isoforms and other proteins contributing to their established cellular functions, which can be both tumour-suppressive and oncogenic in nature. Evidence of p53 isoform in human cancers is largely based on RT-qPCR expression studies, usually investigating a particular type of isoform. Beyond p53 isoform functions in cancer, it is implicated in neurodegeneration, embryological development, progeroid phenotype, inflammatory pathology, infections and tissue regeneration, which are described in this review.
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Zhang YX, Pan WY, Chen J. p53 and its isoforms in DNA double-stranded break repair. J Zhejiang Univ Sci B 2019; 20:457-466. [PMID: 31090271 DOI: 10.1631/jzus.b1900167] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
DNA double-stranded break (DSB) is one of the most catastrophic damages of genotoxic insult. Inappropriate repair of DNA DSBs results in the loss of genetic information, mutation, and the generation of harmful genomic rearrangements, which predisposes an organism to immunodeficiency, neurological damage, and cancer. The tumor repressor p53 plays a key role in DNA damage response, and has been found to be mutated in 50% of human cancer. p53, p63, and p73 are three members of the p53 gene family. Recent discoveries have shown that human p53 gene encodes at least 12 isoforms. Different p53 members and isoforms play various roles in orchestrating DNA damage response to maintain genomic integrity. This review briefly explores the functions of p53 and its isoforms in DNA DSB repair.
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Affiliation(s)
- Yu-Xi Zhang
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wen-Ya Pan
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jun Chen
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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Kansara K, Paruthi A, Misra SK, Karakoti AS, Kumar A. Montmorillonite clay and humic acid modulate the behavior of copper oxide nanoparticles in aqueous environment and induces developmental defects in zebrafish embryo. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 255:113313. [PMID: 31600709 DOI: 10.1016/j.envpol.2019.113313] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 09/24/2019] [Accepted: 09/26/2019] [Indexed: 06/10/2023]
Abstract
Copper oxide nanoparticles (CuO NPs) is one of the most commonly used metal oxide nanoparticles for commercial and industrial products. An increase in the manufacturing and use of the CuO NPs based products has increased the likelihood of their release into the aquatic environment. This has attracted major attention among researchers to explore their impact in human as well as environmental systems. CuO NPs, once released into the environment interact with the biotic and abiotic constituents of the ecosystem. Hence the objective of the study was to provide a holistic understanding of the effect of abiotic factors on the stability and aggregation of CuO NPs and its correlation with their effect on the development of zebrafish embryo. It has been observed that the bioavailability of CuO NPs decrease in presence of humic acid (HA) and heteroagglomeration of CuO NPs occurs with clay minerals. CuO NPs, CuO NPs + HA and CuO NPs + Clay significantly altered the expression of genes involved in development of dorsoventral axis and neural network of zebrafish embryos. However, the presence of HA with clay showed protective effect on zebrafish embryo development. These findings provide new insights into the interaction of NPs with abiotic factors and combined effects of such complexes on developing zebrafish embryos genetic markers.
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Affiliation(s)
- Krupa Kansara
- Biological and Life Sciences, School of Arts and Science, Ahmedabad University, Navrangpura, Ahmedabad, Gujarat, India
| | - Archini Paruthi
- Materials Science and Engineering, Indian Institute of Technology, Gandhinagar, Gujarat, India
| | - Superb K Misra
- Materials Science and Engineering, Indian Institute of Technology, Gandhinagar, Gujarat, India
| | - Ajay S Karakoti
- Biological and Life Sciences, School of Arts and Science, Ahmedabad University, Navrangpura, Ahmedabad, Gujarat, India; School of Engineering, The University of Newcastle, Australia.
| | - Ashutosh Kumar
- Biological and Life Sciences, School of Arts and Science, Ahmedabad University, Navrangpura, Ahmedabad, Gujarat, India.
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Functional interplay between p53 and Δ133p53 in adaptive stress response. Cell Death Differ 2019; 27:1618-1632. [PMID: 31659281 DOI: 10.1038/s41418-019-0445-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 10/10/2019] [Accepted: 10/15/2019] [Indexed: 01/20/2023] Open
Abstract
Apart from its well-known prodeath activity, p53 is also implicated in promoting cell survival. How p53 can mediate such seemingly opposing effects is largely unclear. We report here a novel mechanism in which p53-mediated proapoptosis is switched to antiapoptosis via its interaction with a p53 isoform, Δ133p53. We show that the expression of Δ133p53 is induced by mild or a moderate level of stress via an HIF1-dependent mechanism. Increased Δ133p53 levels contribute to the adaptive response by shifting the p53 binding at the Bcl2 promoter from suppressive responsive elements (RE) to activating REs, resulting in induction of Bcl2. In accordance with this mode of action, pretreatment of mice with mild stress induces Δ133p53 and Bcl2, which is associated with protection of animals from toxicity caused by high doses of DNA damage agents. Collectively, our work uncovers a novel functional interplay between p53 and Δ133p53 determining cell fate; survival or death in response to stress.
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Zhao S, Chen Y, Chen F, Huang D, Shi H, Lo LJ, Chen J, Peng J. Sas10 controls ribosome biogenesis by stabilizing Mpp10 and delivering the Mpp10-Imp3-Imp4 complex to nucleolus. Nucleic Acids Res 2019; 47:2996-3012. [PMID: 30773582 PMCID: PMC6451133 DOI: 10.1093/nar/gkz105] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 01/29/2019] [Accepted: 02/09/2019] [Indexed: 01/19/2023] Open
Abstract
Mpp10 forms a complex with Imp3 and Imp4 that serves as a core component of the ribosomal small subunit (SSU) processome. Mpp10 also interacts with the nucleolar protein Sas10/Utp3. However, it remains unknown how the Mpp10-Imp3-Imp4 complex is delivered to the nucleolus and what biological function the Mpp10-Sas10 complex plays. Here, we report that the zebrafish Mpp10 and Sas10 are conserved nucleolar proteins essential for the development of the digestive organs. Mpp10, but not Sas10/Utp3, is a target of the nucleolus-localized Def-Capn3 protein degradation pathway. Sas10 protects Mpp10 from Capn3-mediated cleavage by masking the Capn3-recognition site on Mpp10. Def interacts with Sas10 to form the Def-Sas10-Mpp10 complex to facilitate the Capn3-mediated cleavage of Mpp10. Importantly, we found that Sas10 determines the nucleolar localization of the Mpp10-Imp3-Imp4 complex. In conclusion, Sas10 is essential not only for delivering the Mpp10-Imp3-Imp4 complex to the nucleolus for assembling the SSU processome but also for fine-tuning Mpp10 turnover in the nucleolus during organogenesis.
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Affiliation(s)
- Shuyi Zhao
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yayue Chen
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Feng Chen
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Delai Huang
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hui Shi
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Li Jan Lo
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jun Chen
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jinrong Peng
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
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Huang Y, Lu Y, He Y, Feng Z, Zhan Y, Huang X, Liu Q, Zhang J, Li H, Huang H, Ma M, Luo L, Li L. Ikzf1 regulates embryonic T lymphopoiesis via Ccr9 and Irf4 in zebrafish. J Biol Chem 2019; 294:16152-16163. [PMID: 31511326 DOI: 10.1074/jbc.ra119.009883] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/26/2019] [Indexed: 12/16/2022] Open
Abstract
Ikzf1 is a Krüppel-like zinc-finger transcription factor that plays indispensable roles in T and B cell development. Although the function of Ikzf1 has been studied extensively, the molecular mechanism underlying T lymphopoiesis remains incompletely defined during the embryonic stage. Here we report that the genetic ablation of ikzf1 in mutant zebrafish resulted in abrogated embryonic T lymphopoiesis. This was ascribed to impaired thymic migration, proliferation, and differentiation of hematopoietic stem/progenitor cells (HSPCs). Ccr9a and Irf4a, two indispensable factors in T lymphopoiesis, were the direct targets of Ikzf1 and were absent in the ikzf1 mutants. Genetic deletion of either ccr9a or irf4a in the corresponding mutant embryos led to obvious T cell development deficiency, which was mainly caused by disrupted thymic migration of HSPCs. Restoration of ccr9a in ikzf1 mutants obviously promoted HSPC thymus homing. However, the HSPCs then failed to differentiate into T cells. Additional replenishment of irf4a efficiently induced HSPC proliferation and T cell differentiation. Our findings further demonstrate that Ikzf1 regulates embryonic T lymphopoiesis via Ccr9 and Irf4 and provide new insight into the genetic network of T lymphocyte development.
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Affiliation(s)
- Youkui Huang
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatic Science of Chongqing, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Yafang Lu
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatic Science of Chongqing, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Yuepeng He
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatic Science of Chongqing, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Zhi Feng
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatic Science of Chongqing, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Yandong Zhan
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatic Science of Chongqing, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xue Huang
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatic Science of Chongqing, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Qin Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jingjing Zhang
- Affiliated Hospital of Guangzhou Medical University, Zhanjiang, Guangdong 524001, China
| | - Hongtao Li
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatic Science of Chongqing, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Honghui Huang
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatic Science of Chongqing, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Ming Ma
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatic Science of Chongqing, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Lingfei Luo
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatic Science of Chongqing, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Li Li
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatic Science of Chongqing, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing 400715, China
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Loss of atrx cooperates with p53-deficiency to promote the development of sarcomas and other malignancies. PLoS Genet 2019; 15:e1008039. [PMID: 30970016 PMCID: PMC6476535 DOI: 10.1371/journal.pgen.1008039] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 04/22/2019] [Accepted: 02/20/2019] [Indexed: 12/24/2022] Open
Abstract
The SWI/SNF-family chromatin remodeling protein ATRX is a tumor suppressor in sarcomas, gliomas and other malignancies. Its loss of function facilitates the alternative lengthening of telomeres (ALT) pathway in tumor cells, while it also affects Polycomb repressive complex 2 (PRC2) silencing of its target genes. To further define the role of inactivating ATRX mutations in carcinogenesis, we knocked out atrx in our previously reported p53/nf1-deficient zebrafish line that develops malignant peripheral nerve sheath tumors and gliomas. Complete inactivation of atrx using CRISPR/Cas9 was lethal in developing fish and resulted in an alpha-thalassemia-like phenotype including reduced alpha-globin expression. In p53/nf1-deficient zebrafish neither peripheral nerve sheath tumors nor gliomas showed accelerated onset in atrx+/- fish, but these fish developed various tumors that were not observed in their atrx+/+ siblings, including epithelioid sarcoma, angiosarcoma, undifferentiated pleomorphic sarcoma and rare types of carcinoma. These cancer types are included in the AACR Genie database of human tumors associated with mutant ATRX, indicating that our zebrafish model reliably mimics a role for ATRX-loss in the early pathogenesis of these human cancer types. RNA-seq of p53/nf1- and p53/nf1/atrx-deficient tumors revealed that down-regulation of telomerase accompanied ALT-mediated lengthening of the telomeres in atrx-mutant samples. Moreover, inactivating mutations in atrx disturbed PRC2-target gene silencing, indicating a connection between ATRX loss and PRC2 dysfunction in cancer development. Somatic mutations in genes coding for epigenetic regulators such as ATRX are found across a diverse group of cancer types, suggesting their broad relevance in tumor induction and progression. However, tumors that have been linked to these chromatin remodelers can arise in many different molecular and cellular contexts, requiring studies with new experimental models to understand the extent and mechanisms of tumor development mediated by these regulatory proteins. Thus, we analyzed the tumor suppressive role of atrx in zebrafish that already harbored inactivating mutations of p53 and nf1. Homozygous deletion of atrx was lethal in developing fish, whereas the partial loss of this gene (atrx+/-) within the p53/nf1-deficient background led to a diverse spectrum of tumors not observed in animals that were wildtype for atrx, including epithelioid sarcoma, angiosarcoma, and rare carcinomas. Most of the cancer types we identified correspond to human tumors in the ATRX-mutant tumor sample cohort within the AACR Genie database, attesting to the relevance of our findings to human cancer. Further analysis revealed downregulation of telomerase during the lengthening of the telomeres through the ALT pathway, and disturbed function of the polycomb repressive complex 2 as key mechanistic components underlying atrx-linked tumorigenesis. These results demonstrate how a p53/nf1 compromised genetic background combined with ATRX haploinsufficiency leads to a broad spectrum of sarcomas and carcinomas associated with loss of this chromatin modulator.
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Ma Z, Zhu P, Shi H, Guo L, Zhang Q, Chen Y, Chen S, Zhang Z, Peng J, Chen J. PTC-bearing mRNA elicits a genetic compensation response via Upf3a and COMPASS components. Nature 2019; 568:259-263. [PMID: 30944473 DOI: 10.1038/s41586-019-1057-y] [Citation(s) in RCA: 289] [Impact Index Per Article: 57.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 03/01/2019] [Indexed: 12/26/2022]
Abstract
The genetic compensation response (GCR) has recently been proposed as a possible explanation for the phenotypic discrepancies between gene-knockout and gene-knockdown1,2; however, the underlying molecular mechanism of the GCR remains uncharacterized. Here, using zebrafish knockdown and knockout models of the capn3a and nid1a genes, we show that mRNA bearing a premature termination codon (PTC) promptly triggers a GCR that involves Upf3a and components of the COMPASS complex. Unlike capn3a-knockdown embryos, which have small livers, and nid1a-knockdown embryos, which have short body lengths2, capn3a-null and nid1a-null mutants appear normal. These phenotypic differences have been attributed to the upregulation of other genes in the same families. By analysing six uniquely designed transgenes, we demonstrate that the GCR is dependent on both the presence of a PTC and the nucleotide sequence of the transgene mRNA, which is homologous to the compensatory endogenous genes. We show that upf3a (a member of the nonsense-mediated mRNA decay pathway) and components of the COMPASS complex including wdr5 function in GCR. Furthermore, we demonstrate that the GCR is accompanied by an enhancement of histone H3 Lys4 trimethylation (H3K4me3) at the transcription start site regions of the compensatory genes. These findings provide a potential mechanistic basis for the GCR, and may help lead to the development of therapeutic strategies that treat missense mutations associated with genetic disorders by either creating a PTC in the mutated gene or introducing a transgene containing a PTC to trigger a GCR.
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Affiliation(s)
- Zhipeng Ma
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Peipei Zhu
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Hui Shi
- College of Animal Sciences, Zhejiang University, Hangzhou, China.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Liwei Guo
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Qinghe Zhang
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yanan Chen
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Shuming Chen
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zhe Zhang
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jinrong Peng
- College of Animal Sciences, Zhejiang University, Hangzhou, China.
| | - Jun Chen
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China.
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Chen YC, Liao BK, Lu YF, Liu YH, Hsieh FC, Hwang PP, Hwang SPL. Zebrafish Klf4 maintains the ionocyte progenitor population by regulating epidermal stem cell proliferation and lateral inhibition. PLoS Genet 2019; 15:e1008058. [PMID: 30933982 PMCID: PMC6459544 DOI: 10.1371/journal.pgen.1008058] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 04/11/2019] [Accepted: 02/28/2019] [Indexed: 01/06/2023] Open
Abstract
In the skin and gill epidermis of fish, ionocytes develop alongside keratinocytes and maintain body fluid ionic homeostasis that is essential for adaptation to environmental fluctuations. It is known that ionocyte progenitors in zebrafish embryos are specified from p63+ epidermal stem cells through a patterning process involving DeltaC (Dlc)-Notch-mediated lateral inhibition, which selects scattered dlc+ cells into the ionocyte progenitor fate. However, mechanisms by which the ionocyte progenitor population is modulated remain unclear. Krüppel-like factor 4 (Klf4) transcription factor was previously implicated in the terminal differentiation of mammalian skin epidermis and is known for its bifunctional regulation of cell proliferation in a tissue context-dependent manner. Here, we report novel roles for zebrafish Klf4 in the ventral ectoderm during embryonic skin development. We found that Klf4 was expressed in p63+ epidermal stem cells of the ventral ectoderm from 90% epiboly onward. Knockdown or knockout of klf4 expression reduced the proliferation rate of p63+ stem cells, resulting in decreased numbers of p63+ stem cells, dlc-p63+ keratinocyte progenitors and dlc+ p63+ ionocyte progenitor cells. These reductions subsequently led to diminished keratinocyte and ionocyte densities and resulted from upregulation of the well-known cell cycle regulators, p53 and cdkn1a/p21. Moreover, mutation analyses of the KLF motif in the dlc promoter, combined with VP16-klf4 or engrailed-klf4 mRNA overexpression analyses, showed that Klf4 can bind the dlc promoter and modulate lateral inhibition by directly repressing dlc expression. This idea was further supported by observing the lateral inhibition outcomes in klf4-overexpressing or knockdown embryos. Overall, our experiments delineate novel roles for zebrafish Klf4 in regulating the ionocyte progenitor population throughout early stem cell stage to initiation of terminal differentiation, which is dependent on Dlc-Notch-mediated lateral inhibition.
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Affiliation(s)
- Yi-Chung Chen
- Institute of Cellular and Organismic Biology (ICOB), Academia Sinica, Taipei, Taiwan, Republic of China
| | - Bo-Kai Liao
- Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan, Republic of China
| | - Yu-Fen Lu
- Institute of Cellular and Organismic Biology (ICOB), Academia Sinica, Taipei, Taiwan, Republic of China
| | - Yu-Hsiu Liu
- Institute of Cellular and Organismic Biology (ICOB), Academia Sinica, Taipei, Taiwan, Republic of China
- Department of Life Science, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Fang-Chi Hsieh
- Institute of Cellular and Organismic Biology (ICOB), Academia Sinica, Taipei, Taiwan, Republic of China
- Graduate Institute of Life Sciences, National Defense Medical Center, Taiwan, Republic of China
| | - Pung-Pung Hwang
- Institute of Cellular and Organismic Biology (ICOB), Academia Sinica, Taipei, Taiwan, Republic of China
| | - Sheng-Ping L. Hwang
- Institute of Cellular and Organismic Biology (ICOB), Academia Sinica, Taipei, Taiwan, Republic of China
- Department of Life Science, National Taiwan University, Taipei, Taiwan, Republic of China
- Graduate Institute of Life Sciences, National Defense Medical Center, Taiwan, Republic of China
- * E-mail:
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Lei J, Qi R, Tang Y, Wang W, Wei G, Nussinov R, Ma B. Conformational stability and dynamics of the cancer-associated isoform Δ133p53β are modulated by p53 peptides and p53-specific DNA. FASEB J 2019; 33:4225-4235. [PMID: 30540922 PMCID: PMC6404584 DOI: 10.1096/fj.201801973r] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/12/2018] [Indexed: 01/01/2023]
Abstract
p53 is a tumor suppressor protein that maintains genome stability, but its Δ133p53β and Δ160p53β isoforms promote breast cancer cell invasion. The sequence truncations in the p53 core domain raise key questions related to their physicochemical properties, including structural stabilities, interaction mechanisms, and DNA-binding abilities. Herein, we investigated the conformational dynamics of Δ133p53β and Δ160p53β with and without binding to p53-specific DNA by using molecular dynamics simulations. We observed that the core domains of the 2 truncated isoforms are much less stable than wild-type (wt) p53β, and the increased solvent exposure of their aggregation-triggering segment indicates their higher aggregation propensities than wt p53. We also found that Δ133p53β stability is modulable by peptide or DNA interactions. Adding a p53 peptide (derived from truncated p53 sequence 107-129) may help stabilize Δ133p53. Most importantly, our simulations of p53 isomer-DNA complexes indicate that Δ133p53β dimer, but not Δ160p53β dimer, could form a stable complex with p53-specific DNA, which is consistent with recent experiments. This study provides physicochemical insight into Δ133p53β, Δ133p53β-DNA complexes, Δ133p53β's pathologic mechanism, and peptide-based inhibitor design against p53-related cancers.-Lei, J., Qi, R., Tang, Y., Wang, W., Wei, G., Nussinov, R., Ma, B. Conformational stability and dynamics of the cancer-associated isoform Δ133p53β are modulated by p53 peptides and p53-specific DNA.
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Affiliation(s)
- Jiangtao Lei
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences–Ministry of Education, Department of Physics, Fudan University, Shanghai, China
| | - Ruxi Qi
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences–Ministry of Education, Department of Physics, Fudan University, Shanghai, China
| | - Yegen Tang
- Department of Chemistry, Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Wenning Wang
- Department of Chemistry, Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Guanghong Wei
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences–Ministry of Education, Department of Physics, Fudan University, Shanghai, China
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, USA; and
- Department of Human Genetics and Molecular Medicine, Sackler Institute of Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, USA; and
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Yi X, Yu J, Ma C, Dong G, Shi W, Li H, Li L, Luo L, Sampath K, Ruan H, Huang H. The effector of Hippo signaling, Taz, is required for formation of the micropyle and fertilization in zebrafish. PLoS Genet 2019; 15:e1007408. [PMID: 30608921 PMCID: PMC6334976 DOI: 10.1371/journal.pgen.1007408] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 01/16/2019] [Accepted: 12/10/2018] [Indexed: 11/18/2022] Open
Abstract
The mechanisms that ensure fertilization of egg by a sperm are not fully understood. In all teleosts, a channel called the 'micropyle' is the only route of entry for sperm to enter and fertilize the egg. The micropyle forms by penetration of the vitelline envelope by a single specialized follicle cell, the micropylar cell. The mechanisms underlying micropylar cell specification and micropyle formation are poorly understood. Here, we show that an effector of the Hippo signaling pathway, the Transcriptional co-activator with a PDZ-binding domain (Taz), plays crucial roles in micropyle formation and fertilization in zebrafish (Danio rerio). Genome editing mutants affecting taz can grow to adults. However, eggs from homozygous taz females are not fertilized even though oocytes in mutant females are histologically normal with intact animal-vegetal polarity, complete meiosis and proper ovulation. We find that taz mutant eggs have no micropyle. Taz protein is specifically enriched in mid-oogenesis in the micropylar cell located at the animal pole of wild type oocyte, where it might regulate the cytoskeleton. Taz protein and micropylar cells are not detected in taz mutant ovaries. Our work identifies a novel role for the Hippo/Taz pathway in micropylar cell specification in zebrafish, and uncovers the molecular basis of micropyle formation in teleosts.
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Affiliation(s)
- Xiaogui Yi
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Beibei, Chongqing, China
| | - Jia Yu
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Beibei, Chongqing, China
| | - Chao Ma
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Beibei, Chongqing, China
| | - Guoping Dong
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Beibei, Chongqing, China
| | - Wenpeng Shi
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Beibei, Chongqing, China
| | - Hongtao Li
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Beibei, Chongqing, China
| | - Li Li
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Beibei, Chongqing, China
| | - Lingfei Luo
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Beibei, Chongqing, China
| | - Karuna Sampath
- Cell & Developmental Biology Unit, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Hua Ruan
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Beibei, Chongqing, China
| | - Honghui Huang
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Beibei, Chongqing, China
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p53 Isoforms and Their Implications in Cancer. Cancers (Basel) 2018; 10:cancers10090288. [PMID: 30149602 PMCID: PMC6162399 DOI: 10.3390/cancers10090288] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 08/18/2018] [Accepted: 08/18/2018] [Indexed: 01/10/2023] Open
Abstract
In this review we focus on the major isoforms of the tumor-suppressor protein p53, dysfunction of which often leads to cancer. Mutations of the TP53 gene, particularly in the DNA binding domain, have been regarded as the main cause for p53 inactivation. However, recent reports demonstrating abundance of p53 isoforms, especially the N-terminally truncated ones, in the cancerous tissues suggest their involvement in carcinogenesis. These isoforms are ∆40p53, ∆133p53, and ∆160p53 (the names indicate their respective N-terminal truncation). Due to the lack of structural and functional characterizations the modes of action of the p53 isoforms are still unclear. Owing to the deletions in the functional domains, these isoforms can either be defective in DNA binding or more susceptive to altered ‘responsive elements’ than p53. Furthermore, they may exert a ‘dominant negative effect’ or induce more aggressive cancer by the ‘gain of function’. One possible mechanism of p53 inactivation can be through tetramerization with the ∆133p53 and ∆160p53 isoforms—both lacking part of the DNA binding domain. A recent report and unpublished data from our laboratory also suggest that these isoforms may inactivate p53 by fast aggregation—possibly due to ectopic overexpression. We further discuss the evolutionary significance of the p53 isoforms.
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Chen J, Tan X, Wang Z, Liu Y, Zhou J, Rong X, Lu L, Li Y. The ribosome biogenesis protein Esf1 is essential for pharyngeal cartilage formation in zebrafish. FEBS J 2018; 285:3464-3484. [DOI: 10.1111/febs.14622] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 06/10/2018] [Accepted: 08/01/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Jian‐Yang Chen
- Key Laboratory of Marine Drugs (Ocean University of China) Chinese Ministry of Education Qingdao China
- School of Medicine and Pharmacy Ocean University of China Qingdao China
- Laboratory for Marine Drugs and Biological Products Qingdao National Laboratory for Marine Science and Technology China
| | - Xungang Tan
- CAS Key Laboratory of Experimental Marine Biology Institute of Oceanology Chinese Academy of Sciences Qingdao China
| | - Zheng‐Hua Wang
- Key Laboratory of Marine Drugs (Ocean University of China) Chinese Ministry of Education Qingdao China
- School of Medicine and Pharmacy Ocean University of China Qingdao China
- Laboratory for Marine Drugs and Biological Products Qingdao National Laboratory for Marine Science and Technology China
- CAS Key Laboratory of Experimental Marine Biology Institute of Oceanology Chinese Academy of Sciences Qingdao China
| | - Yun‐Zhang Liu
- Key Laboratory of Marine Drugs (Ocean University of China) Chinese Ministry of Education Qingdao China
- School of Medicine and Pharmacy Ocean University of China Qingdao China
- Laboratory for Marine Drugs and Biological Products Qingdao National Laboratory for Marine Science and Technology China
| | - Jian‐Feng Zhou
- Key Laboratory of Marine Drugs (Ocean University of China) Chinese Ministry of Education Qingdao China
- School of Medicine and Pharmacy Ocean University of China Qingdao China
- Laboratory for Marine Drugs and Biological Products Qingdao National Laboratory for Marine Science and Technology China
| | - Xiao‐Zhi Rong
- Key Laboratory of Marine Drugs (Ocean University of China) Chinese Ministry of Education Qingdao China
- School of Medicine and Pharmacy Ocean University of China Qingdao China
- Laboratory for Marine Drugs and Biological Products Qingdao National Laboratory for Marine Science and Technology China
| | - Ling Lu
- Key Laboratory of Marine Drugs (Ocean University of China) Chinese Ministry of Education Qingdao China
- School of Medicine and Pharmacy Ocean University of China Qingdao China
- Laboratory for Marine Drugs and Biological Products Qingdao National Laboratory for Marine Science and Technology China
| | - Yun Li
- Key Laboratory of Marine Drugs (Ocean University of China) Chinese Ministry of Education Qingdao China
- School of Medicine and Pharmacy Ocean University of China Qingdao China
- Laboratory for Marine Drugs and Biological Products Qingdao National Laboratory for Marine Science and Technology China
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A mouse model of the Δ133p53 isoform: roles in cancer progression and inflammation. Mamm Genome 2018; 29:831-842. [PMID: 29992419 DOI: 10.1007/s00335-018-9758-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 07/05/2018] [Indexed: 01/19/2023]
Abstract
This review paper outlines studies on the Δ122p53 mouse, a model of the human Δ133p53 isoform, together with studies in other model organisms, cell culture, and where available, clinical investigations. In general, these studies imply that, in contrast to the canonical p53 tumor suppressor, Δ133p53 family members have oncogenic capability. Δ122p53 is multi-functional, conferring survival and proliferative advantages on cells, promoting invasion, metastasis and vascularization, as does Δ133p53. Cancers with high levels of Δ133p53 often have poor prognosis. Δ122p53 mediates its effects through the JAK-STAT and RhoA-ROCK signaling pathways. We propose that Δ133p53 isoforms have evolved as inflammatory signaling molecules to deal with the consequent tissue damage of p53 activation. However, if sustained expression of the isoforms occur, pathologies may result.
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Yi X, Yu J, Ma C, Li L, Luo L, Li H, Ruan H, Huang H. Yap1/Taz are essential for the liver development in zebrafish. Biochem Biophys Res Commun 2018; 503:131-137. [PMID: 29859190 DOI: 10.1016/j.bbrc.2018.05.196] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 05/29/2018] [Indexed: 10/14/2022]
Abstract
Hippo pathway regulates cell proliferation and differentiation. Yes-associated protein (Yap) and transcriptional coactivator with PDZ-binding motif (Taz) are effectors of Hippo pathway. The function of Yap/Taz in embryonic liver development has yet to be reported. Here yap1 and taz were found expressed in liver and other digestive organs in zebrafish embryos, and knockout of yap1 or taz did not lead to visible defects during embryogenesis. Interestingly, Taz was significantly increased in yap1 mutants, which may account for their normal development, albeit losing Yap1. However, yap1-/-; taz+/- embryos exhibited smaller digestive organs, and more than half of them showed bilateral livers and pancreas and non-looped intestines. Further analysis revealed that the disrupted gene function in yap1-/-; taz+/- embryos did not disturb liver bud formation, but instead impaired cell proliferation in liver and movement of the neighboring lateral plate mesoderm (LPM). Overexpression of wild type yap1 or taz could rescue the defective liver phenotypes in yap1-/-; taz+/- embryos, indicating that Yap1 cooperate with Taz to regulate the liver development. In addition, Yap1 was found to function in a Tead-dependent manner in the liver development. Our results suggest that Yap1/Taz regulate LPM movement and promote cell proliferation to ensure proper liver development in zebrafish.
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Affiliation(s)
- Xiaogui Yi
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, 2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Jia Yu
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, 2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Chao Ma
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, 2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Li Li
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, 2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Lingfei Luo
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, 2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Hongtao Li
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, 2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Hua Ruan
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, 2 Tiansheng Road, Beibei, Chongqing, 400715, China.
| | - Honghui Huang
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, 2 Tiansheng Road, Beibei, Chongqing, 400715, China.
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Zhan Y, Huang Y, Chen J, Cao Z, He J, Zhang J, Huang H, Ruan H, Luo L, Li L. The caudal dorsal artery generates hematopoietic stem and progenitor cells via the endothelial-to-hematopoietic transition in zebrafish. J Genet Genomics 2018; 45:S1673-8527(18)30099-7. [PMID: 29929848 DOI: 10.1016/j.jgg.2018.02.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 12/25/2017] [Accepted: 02/11/2018] [Indexed: 11/22/2022]
Abstract
Zebrafish hematopoietic stem and progenitor cells (HSPCs) originate from the hemogenic endothelium of the ventral wall of the dorsal aorta (DA) through the endothelial-to-hematopoietic transition (EHT) from approximately 30 to 60 hours post fertilization (hpf). However, whether other artery sites can generate HSPCs de novo remains unclear. In this study, using live imaging and lineage tracing, we found that the caudal dorsal artery (CDA) in the caudal hematopoietic tissue directly gave rise to HSPCs through EHT. This process initiated from approximately 60 hpf and terminated at approximately 156 hpf. Compared with that in the DA, fewer EHT events were observed in the CDA. The EHT events in the DA and CDA were similarly regulated by Runx1 but differentially influenced by blood flow (i.e., the EHT frequency in CDA was affected to a lesser extent when circulation was compromised in the tnnt2a-/- mutant). Therefore, the whole artery, including both DA and CDA, was endowed with the ability to produce HSPCs during a much longer time period. Coincidently, the lineage tracing results indicated that adult hematopoietic cells originated from the embryonic endothelium, and those produced later preferentially colonized the adult thymus. Collectively, our study revealed that the CDA serves as an additional source of hematopoiesis, and it shows similar but not identical properties with the DA.
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Affiliation(s)
- Yandong Zhan
- The State Key Laboratory Breeding Base of Bioresources and Eco-environments, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Youkui Huang
- The State Key Laboratory Breeding Base of Bioresources and Eco-environments, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Jingying Chen
- The State Key Laboratory Breeding Base of Bioresources and Eco-environments, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Zigang Cao
- The State Key Laboratory Breeding Base of Bioresources and Eco-environments, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Jianbo He
- The State Key Laboratory Breeding Base of Bioresources and Eco-environments, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Jingjing Zhang
- Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China
| | - Honghui Huang
- The State Key Laboratory Breeding Base of Bioresources and Eco-environments, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Hua Ruan
- The State Key Laboratory Breeding Base of Bioresources and Eco-environments, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Lingfei Luo
- The State Key Laboratory Breeding Base of Bioresources and Eco-environments, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing 400715, China.
| | - Li Li
- The State Key Laboratory Breeding Base of Bioresources and Eco-environments, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing 400715, China.
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p73 coordinates with Δ133p53 to promote DNA double-strand break repair. Cell Death Differ 2018; 25:1063-1079. [PMID: 29511339 PMCID: PMC5988805 DOI: 10.1038/s41418-018-0085-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 01/18/2018] [Accepted: 02/07/2018] [Indexed: 12/16/2022] Open
Abstract
Tumour repressor p53 isoform Δ133p53 is a target gene of p53 and an antagonist of p53-mediated apoptotic activity. We recently demonstrated that Δ133p53 promotes DNA double-strand break (DSB) repair by upregulating transcription of the repair genes RAD51, LIG4 and RAD52 in a p53-independent manner. However, Δ133p53 lacks the transactivation domain of full-length p53, and the mechanism by which it exerts transcriptional activity independently of full-length p53 remains unclear. In this report, we describe the accumulation of high levels of both Δ133p53 and p73 (a p53 family member) at 24 h post γ-irradiation (hpi). Δ133p53 can form a complex with p73 upon γ-irradiation. The co-expression of Δ133p53 and p73, but not either protein alone, can significantly promote DNA DSB repair mechanisms, including homologous recombination (HR), non-homologous end joining (NHEJ) and single-strand annealing (SSA). p73 and Δ133p53 act synergistically to promote the expression of RAD51, LIG4 and RAD52 by joining together to bind to region containing a Δ133p53-responsive element (RE) and a p73-RE in the promoters of all three repair genes. In addition to its accumulation at 24 hpi, p73 protein expression also peaks at 4 hpi. The depletion of p73 not only reduces early-stage apoptotic frequency (4–6 hpi), but also significantly increases later-stage DNA DSB accumulation (48 hpi), leading to cell cycle arrest in the G2 phase and, ultimately, cell senescence. In summary, the apoptotic regulator p73 also coordinates with Δ133p53 to promote DNA DSB repair, and the loss of function of p73 in DNA DSB repair may underlie spontaneous and carcinogen-induced tumorigenesis in p73 knockout mice.
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Development and growth of organs in living whole embryo and larval grafts in zebrafish. Sci Rep 2017; 7:16508. [PMID: 29184141 PMCID: PMC5705650 DOI: 10.1038/s41598-017-16642-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 11/15/2017] [Indexed: 11/25/2022] Open
Abstract
Age-related systemic environments influence neurogenesis and organ regeneration of heterochronic parabiotic partners; however, the difficulty of manipulating small embryos prevents the effects of aged systemic environments on primitive organs at the developmental stage from being analysed. Here, we describe a novel transplantation system to support whole living embryos/larvae as grafts in immunodeficient zebrafish by the intrusion of host blood vessels into the grafts, allowing bodies similar to those of heterochronic parabiosis to be generated by subcutaneous grafting. Although grafted embryos/larvae formed most organs, not all organogenesis was supported equally; although the brain, eyes and the intestine usually developed, the liver, testes and heart developed insufficiently or even occasionally disappeared. Removal of host germ cells stimulated testis development in grafted embryos. These results indicate that primitive testes are susceptible to the systemic environments that originated from the germ cells of aged hosts and imply that the primitive liver and heart are similar. Upon applying this method to embryonic lethal mutants, various types of organs, including testes that developed in germ-cell-removed recipients, and viable offspring were obtained from the mutants. This unique transplantation system will lead to new insights into the age-related systemic environments that are crucial for organogenesis in vertebrates.
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48
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Aryal NK, Wasylishen AR, Pant V, Riley-Croce M, Lozano G. Loss of digestive organ expansion factor ( Diexf) reveals an essential role during murine embryonic development that is independent of p53. Oncotarget 2017; 8:103996-104006. [PMID: 29262616 PMCID: PMC5732782 DOI: 10.18632/oncotarget.22087] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/10/2017] [Indexed: 01/01/2023] Open
Abstract
Increased levels of inhibitors of the p53 tumor suppressor such as Mdm2 and Mdm4 drive tumor development and thus serve as targets for therapeutic intervention. Recently, digestive organ expansion factor (Diexf) has been identified as a novel inhibitor of p53 in zebrafish. Here, we address the potential role of Diexf as a regulator of the p53 pathway in mammals by generating Diexf knockout mice. We demonstrate that, similar to Mdm2 and Mdm4, homozygous deletion of Diexf is embryonic lethal. However, unlike in Mdm2 and Mdm4 mice, loss of p53 does not rescue this phenotype. Moreover, Diexf heterozygous animals are not sensitive to sub-lethal ionizing radiation. Thus, we conclude that Diexf is an essential developmental gene in the mouse, but is not a significant regulator of the p53 pathway during development or in response to ionizing radiation.
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Affiliation(s)
- Neeraj K Aryal
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Genes and Development Program, The University of Texas MD Anderson Cancer Center, UT Health Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Amanda R Wasylishen
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Vinod Pant
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Maurisa Riley-Croce
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Guillermina Lozano
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Ma Z, Zhu P, Pang M, Guo L, Chang N, Zheng J, Zhu X, Gao C, Huang H, Cui Z, Xiong JW, Peng J, Chen J. A novel inducible mutagenesis screen enables to isolate and clone both embryonic and adult zebrafish mutants. Sci Rep 2017; 7:10381. [PMID: 28871129 PMCID: PMC5583359 DOI: 10.1038/s41598-017-10968-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 08/17/2017] [Indexed: 12/14/2022] Open
Abstract
Conventional genetic screens for recessive mutants are inadequate for studying biological processes in the adult vertebrate due to embryonic lethality. Here, we report that a novel inducible mutagenesis system enables to study gene function in both embryonic and adult zebrafish. This system yields genetic mutants with conditional ectopic over- or under-expression of genes in F1 heterozygotes by utilizing inducible Tet-On transcriptional activation of sense or anti-sense transcripts from entrapped genes by Tol2 transposase-meditated transgenesis. Pilot screens identified 37 phenotypic mutants displaying embryonic defects (34 lines), adult fin regeneration defects (7 lines), or defects at both stages (4 lines). Combination of various techniques (such as: generating a new mutant allele, injecting gene specific morpholino or mRNA etc) confirms that Dox-induced embryonic abnormalities in 10 mutants are due to dysfunction of entrapped genes; and that Dox-induced under-expression of 6 genes causes abnormal adult fin regeneration. Together, this work presents a powerful mutagenesis system for genetic analysis from zebrafish embryos to adults in particular and other model organisms in general.
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Affiliation(s)
- Zhipeng Ma
- Key laboratory for Molecular Animal Nutrition, Ministry of Education, Innovation Center for Signaling Network, College of Life Sciences, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, 310058, China
| | - Peipei Zhu
- Key laboratory for Molecular Animal Nutrition, Ministry of Education, Innovation Center for Signaling Network, College of Life Sciences, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, 310058, China
| | - Meijun Pang
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100871, China
| | - Liwei Guo
- Key laboratory for Molecular Animal Nutrition, Ministry of Education, Innovation Center for Signaling Network, College of Life Sciences, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, 310058, China
| | - Nannan Chang
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100871, China
| | - Jiyuan Zheng
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100871, China
| | - Xiaojun Zhu
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100871, China
| | - Ce Gao
- College of Animal Sciences, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, 310058, China
| | - Honghui Huang
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, 2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Zongbin Cui
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, 8 Dong Hu Nan Road, Wuhan, Hubei, 430072, P. R. China
| | - Jing-Wei Xiong
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100871, China.
| | - Jinrong Peng
- College of Animal Sciences, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, 310058, China.
| | - Jun Chen
- Key laboratory for Molecular Animal Nutrition, Ministry of Education, Innovation Center for Signaling Network, College of Life Sciences, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, 310058, China.
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50
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Bergen DJM, Stevenson NL, Skinner REH, Stephens DJ, Hammond CL. The Golgi matrix protein giantin is required for normal cilia function in zebrafish. Biol Open 2017; 6:1180-1189. [PMID: 28546340 PMCID: PMC5576078 DOI: 10.1242/bio.025502] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The Golgi is essential for glycosylation of newly synthesised proteins including almost all cell-surface and extracellular matrix proteoglycans. Giantin, encoded by the golgb1 gene, is a member of the golgin family of proteins that reside within the Golgi stack, but its function remains elusive. Loss of function of giantin in rats causes osteochondrodysplasia; knockout mice show milder defects, notably a cleft palate. In vitro, giantin has been implicated in Golgi organisation, biosynthetic trafficking, and ciliogenesis. Here we show that loss of function of giantin in zebrafish, using either morpholino or knockout techniques, causes defects in cilia function. Giantin morphants have fewer cilia in the neural tube and those remaining are longer. Mutants have the same number of cilia in the neural tube but these cilia are also elongated. Scanning electron microscopy shows that loss of giantin results in an accumulation of material at the ciliary tip, consistent with a loss of function of retrograde intraflagellar transport. Mutants show milder defects than morphants consistent with adaptation to loss of giantin. Summary: Morpholino knockdown of Golgb1/giantin leads to a severe cilopathy phenotype twinned with longer, misshapen cilia. Stable mutants have a very mild phenotype, indicative of compensation, but still have longer cilia.
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Affiliation(s)
- Dylan J M Bergen
- Cell Biology Laboratories, School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK.,School of Physiology, Pharmacology and Neuroscience, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
| | - Nicola L Stevenson
- Cell Biology Laboratories, School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
| | - Roderick E H Skinner
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
| | - David J Stephens
- Cell Biology Laboratories, School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
| | - Christina L Hammond
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
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