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Yang Z, Stemmer PM, Petriello MC. Proteomics-Based Identification of Interaction Partners of the Xenobiotic Detoxification Enzyme FMO3 Reveals Involvement in Urea Cycle. TOXICS 2022; 10:60. [PMID: 35202247 PMCID: PMC8877285 DOI: 10.3390/toxics10020060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/18/2022] [Accepted: 01/25/2022] [Indexed: 02/06/2023]
Abstract
The hepatic xenobiotic metabolizing enzyme flavin-containing monooxygenase 3 (FMO3) has been implicated in the development of cardiometabolic disease primarily due to its enzymatic product trimethylamine-N oxide (TMAO), which has recently been shown to be associated with multiple chronic diseases, including kidney and coronary artery diseases. Although TMAO may have causative roles as a pro-inflammatory mediator, the possibility for roles in metabolic disease for FMO3, irrespective of TMAO formation, does exist. We hypothesized that FMO3 may interact with other proteins known to be involved in cardiometabolic diseases and that modulating the expression of FMO3 may impact on these interaction partners. Here, we combine a co-immunoprecipitation strategy coupled to unbiased proteomic workflow to report a novel protein:protein interaction network for FMO3. We identified 51 FMO3 protein interaction partners, and through gene ontology analysis, have identified urea cycle as an enriched pathway. Using mice deficient in FMO3 on two separate backgrounds, we validated and further investigated expressional and functional associations between FMO3 and the identified urea cycle genes. FMO3-deficient mice showed hepatic overexpression of carbamoylphosphate synthetase (CPS1), the rate-limiting gene of urea cycle, and increased hepatic urea levels, especially in mice of FVB (Friend leukemia virus B strain) background. Finally, overexpression of FMO3 in murine AML12 hepatocytes led to downregulation of CPS1. Although there is past literature linking TMAO to urea cycle, this is the first published work showing that FMO3 and CPS1 may directly interact, implicating a role for FMO3 in chronic kidney disease irrespective of TMAO formation.
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Affiliation(s)
- Zhao Yang
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48202, USA; (Z.Y.); (P.M.S.)
| | - Paul M. Stemmer
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48202, USA; (Z.Y.); (P.M.S.)
- Department of Pharmaceutical Sciences, College of Pharmacy, Wayne State University, Detroit, MI 48202, USA
| | - Michael C. Petriello
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48202, USA; (Z.Y.); (P.M.S.)
- Department of Pharmacology, School of Medicine, Wayne State University, Detroit, MI 48202, USA
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Eliseeva IA, Sogorina EM, Smolin EA, Kulakovskiy IV, Lyabin DN. Diverse Regulation of YB-1 and YB-3 Abundance in Mammals. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:S48-S167. [PMID: 35501986 DOI: 10.1134/s000629792214005x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/13/2021] [Accepted: 09/17/2021] [Indexed: 06/14/2023]
Abstract
YB proteins are DNA/RNA binding proteins, members of the family of proteins with cold shock domain. Role of YB proteins in the life of cells, tissues, and whole organisms is extremely important. They are involved in transcription regulation, pre-mRNA splicing, mRNA translation and stability, mRNA packaging into mRNPs, including stress granules, DNA repair, and many other cellular events. Many processes, from embryonic development to aging, depend on when and how much of these proteins have been synthesized. Here we discuss regulation of the levels of YB-1 and, in part, of its homologs in the cell. Because the amount of YB-1 is immediately associated with its functioning, understanding the mechanisms of regulation of the protein amount invariably reveals the events where YB-1 is involved. Control over the YB-1 abundance may allow using this gene/protein as a therapeutic target in cancers, where an increased expression of the YBX1 gene often correlates with the disease severity and poor prognosis.
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Affiliation(s)
- Irina A Eliseeva
- Institute of Protein Research, Pushchino, Moscow Region, 142290, Russia.
| | | | - Egor A Smolin
- Institute of Protein Research, Pushchino, Moscow Region, 142290, Russia.
| | - Ivan V Kulakovskiy
- Institute of Protein Research, Pushchino, Moscow Region, 142290, Russia.
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Moscow, 119991, Russia
| | - Dmitry N Lyabin
- Institute of Protein Research, Pushchino, Moscow Region, 142290, Russia.
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Role of Extracellular Vesicles in Compromising Cellular Resilience to Environmental Stressors. BIOMED RESEARCH INTERNATIONAL 2021; 2021:9912281. [PMID: 34337063 PMCID: PMC8321721 DOI: 10.1155/2021/9912281] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/16/2021] [Accepted: 07/07/2021] [Indexed: 12/17/2022]
Abstract
Extracellular vesicles (EVs), like exosomes, are nanosized membrane-enveloped vesicles containing different bioactive cargo, such as proteins, lipids, mRNA, miRNA, and other small regulatory RNAs. Cell-derived EVs, including EVs originating from stem cells, may capture components from damaged cells or cells impacted by therapeutic treatments. Interestingly, EVs derived from stem cells can be preconditioned to produce and secrete EVs with different therapeutic properties, particularly with respect to heat-shock proteins and other molecular cargo contents. This behavior is consistent with stem cells that also respond differently to various microenvironments. Heat-shock proteins play roles in cellular protection and mediate cellular resistance to radiotherapy, chemotherapy, and heat shock. This review highlights the possible roles EVs play in mediating cellular plasticity and survival when exposed to different physical and chemical stressors, with a special focus on the respiratory distress due to the air pollution.
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Lyu H, Xu G, Peng X, Gong C, Peng Y, Song Q, Feng Q, Zheng S. Interacting C/EBPg and YBP regulate DNA methyltransferase 1 expression in Bombyx mori embryos and ovaries. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021; 134:103583. [PMID: 34010702 DOI: 10.1016/j.ibmb.2021.103583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 04/05/2021] [Accepted: 04/20/2021] [Indexed: 06/12/2023]
Abstract
DNA methylation is an important epigenetic modification. DNA methyltransferases (Dnmts), which catalyze the formation of 5-methylcytosine, play a role in ovarian and embryonic development in some insects. However, the underlying mechanism of Dnmt in mediating ovarian and embryonic development remains unclear. In this study, the regulation and function of Bombyx mori Dnmt1 were investigated. By progressively deleting the sequence upstream of Dnmt1, a region located between -580 and -560 region from the transcription initiation site was found to have the most transcriptional activity. Electrophoretic mobility shift assay and chromatin immunoprecipitation demonstrated that transcription factor Y box binding protein (YBP), a homolog of human Y box binding protein 1 (YBX1), bound to the -580 to -560 region. YBP knockdown and overexpression in a Bombyx cell line indicated that YBP activates Dnmt1 expression. Furthermore, GST-pulldown and co-immunoprecipitation demonstrated that YBP and ovarian CCAAT/enhancer binding protein (C/EBPg) could bind each other. Simultaneous knockdown of C/EBPg and YBP was more effective than single-gene RNAi in inhibiting Dnmt1 expression and reducing the hatching rate. These results demonstrated that the interaction of C/EBPg and YBP activated Dnmt1 expression. Correlated with the expression profiles of the studies genes, our results suggest that high-level expression and interaction of C/EBPg and YBP in ovaries and embryos enhance the expression of Dnmt1, thus ensuring high reproduction rate in B. mori.
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Affiliation(s)
- Hao Lyu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China; Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Guanfeng Xu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China; Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Xuezhen Peng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China; Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Chengcheng Gong
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China; Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Yuling Peng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China; Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Qisheng Song
- Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO, 65211, USA
| | - Qili Feng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China; Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Sichun Zheng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China; Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
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Wang W, Li Q, Huang G, Lin BY, Lin D, Ma Y, Zhang Z, Chen T, Zhou J. Tandem Mass Tag-Based Proteomic Analysis of Potential Biomarkers for Hepatocellular Carcinoma Differentiation. Onco Targets Ther 2021; 14:1007-1020. [PMID: 33603407 PMCID: PMC7886252 DOI: 10.2147/ott.s273823] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 01/28/2021] [Indexed: 01/27/2023] Open
Abstract
Purpose The poor prognosis of hepatocellular carcinoma (HCC) urgent us to discover early and effective biomarkers. In this study, we applied tandem mass tag (TMT)-based proteomic analysis to discover potential protein markers for HCC identification and differentiation. Patients and Methods Fifteen patients, well-differentiated (G1, N = 5), moderate-differentiated (G2, N = 5), and poorly differentiated (G3, N = 5), with 30 matched pair tissues (both tumor and adjacent non-tumor tissues derived from the same patient) were enrolled. All samples were subjected to TMT labeling and LC−MS/MS analysis. The identified proteins were subsequently assigned to GO and KEGG for predicting function. The identified protein candidates were validated using immunohistochemistry (IHC). Results A total of 1010 proteins were identified. Of these, 154 differentially expressed proteins (DEPs), 100 up-regulated and 54 down-regulated, were found between tumor and adjacent non-tumor tissues; 12 DEPs, 9 up-regulated and 3 down-regulated, were found between G1 and G3 tissues; 8 DEPs, 5 up-regulated and 3 down-regulated, were found between G1 and G2 tissues; 11 DEPs, 8 up-regulated and 3 down-regulated, were found between G2 and G3 tissues. Among them, ASS1 and CPS1 were significantly up-regulated while UROD and HBB were significantly down-regulated in G3 compared with G1 and G2 tumors. Three proteins, CYB5A, FKBP11 and YBX1, were significantly up-regulated in G1 compared with both G2 and G3 tumors. The 7 biomarker candidates were further verified by IHC. Conclusion A variety of DEPs related to the histological differentiation of HCC were identified, among which ASS1, CPS1, URPD and HBB proteins were potential biomarkers for distinguishing poorly differentiated HCC, while CYB5A, FKBP11 and YBX1 were potential biomarkers for distinguishing well-differentiated HCC. Our findings may further provide a new insight facilitating the diagnosis and prognosis of HCC.
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Affiliation(s)
- Wei Wang
- Department of Laboratory, Foshan Fourth People's Hospital, Foshan, 528000, People's Republic of China
| | - Qiang Li
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, 510000, People's Republic of China
| | - Ge Huang
- Intensive Care Unit, Foshan Fourth People's Hospital, Foshan, 528000, People's Republic of China
| | - Bing-Yao Lin
- Department of Laboratory, Foshan Fourth People's Hospital, Foshan, 528000, People's Republic of China
| | - Dongzi Lin
- Department of Laboratory, Foshan Fourth People's Hospital, Foshan, 528000, People's Republic of China
| | - Yan Ma
- Department of Laboratory, Foshan Fourth People's Hospital, Foshan, 528000, People's Republic of China
| | - Zhao Zhang
- Research and Development Centre, South China Institute of Biomedicine, Guangdonglongsee Biomedical Co., Ltd, Guangzhou, 510000, People's Republic of China
| | - Tao Chen
- Department of Laboratory, Foshan Fourth People's Hospital, Foshan, 528000, People's Republic of China
| | - Jie Zhou
- Department of Laboratory, Foshan Fourth People's Hospital, Foshan, 528000, People's Republic of China
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Key Enzymes in Pyrimidine Synthesis, CAD and CPS1, Predict Prognosis in Hepatocellular Carcinoma. Cancers (Basel) 2021; 13:cancers13040744. [PMID: 33670206 PMCID: PMC7916936 DOI: 10.3390/cancers13040744] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 02/05/2021] [Indexed: 02/06/2023] Open
Abstract
Patients with hepatocellular carcinoma (HCC) have a highly variable clinical course. Therefore, there is an urgent need to identify new prognostic markers to determine prognosis and select specific therapies. Recently, it has been demonstrated that dysregulation of the urea cycle (UC) is a common phenomenon in multiple types of cancer. Upon UC dysregulation, nitrogen is diverted toward the multifunctional enzyme carbamoyl-phosphate synthetase 2, aspartate transcarbamoylase, and dihydroorotase (CAD), and increases pyrimidine synthesis. In this study, we investigated the role of CAD and carbamoyl-phosphate synthetase 1 (CPS1), a rate-limiting enzyme of the UC highly expressed in hepatocytes, in HCC. We created a tissue microarray to analyze expression of both enzymes by immunohistochemistry in a large and well-characterized overall cohort of 871 HCCs of 561 patients that underwent surgery. CAD was induced in recurrent HCCs, and high expression predicted shorter overall survival. CPS1 was downregulated in HCC and further reduced in recurrent tumors and distant metastases. Additionally, low CPS1 was associated with short overall survival. A combined score of both enzymes was an independent prognostic marker in a multivariate Cox regression model (HR = 1.37, 95% confidence interval 1.06-1.75, p = 0.014). Inhibition of pyrimidine synthesis may represent a novel therapeutic strategy for HCC.
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Groot M, Lee H. Sorting Mechanisms for MicroRNAs into Extracellular Vesicles and Their Associated Diseases. Cells 2020; 9:cells9041044. [PMID: 32331346 PMCID: PMC7226101 DOI: 10.3390/cells9041044] [Citation(s) in RCA: 197] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/18/2020] [Accepted: 04/21/2020] [Indexed: 12/17/2022] Open
Abstract
Extracellular vesicles (EV) are secretory membranous elements used by cells to transport proteins, lipids, mRNAs, and microRNAs (miRNAs). While their existence has been known for many years, only recently has research begun to identify their function in intercellular communication and gene regulation. Importantly, cells have the ability to selectively sort miRNA into EVs for secretion to nearby or distant targets. These mechanisms broadly include RNA-binding proteins such as hnRNPA2B1 and Argonaute-2, but also membranous proteins involved in EV biogenesis such as Caveolin-1 and Neural Sphingomyelinase 2. Moreover, certain disease states have also identified dysregulated EV-miRNA content, shedding light on the potential role of selective sorting in pathogenesis. These pathologies include chronic lung disease, immune response, neuroinflammation, diabetes mellitus, cancer, and heart disease. In this review, we will overview the mechanisms whereby cells selectively sort miRNA into EVs and also outline disease states where EV-miRNAs become dysregulated.
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Affiliation(s)
- Michael Groot
- Department of Medicine, Boston University Medical Campus, Boston, MA 02118, USA;
| | - Heedoo Lee
- Department of Biology and Chemistry, Changwon National University, Changwon 51140, Korea
- Correspondence: ; Tel.: +82-55-213-3452
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Zhang W, Dong Z, Xu M, Zhang S, Liu C, Chen S. SWI/SNF complex subunit BAF60a represses hepatic ureagenesis through a crosstalk between YB-1 and PGC-1α. Mol Metab 2019; 32:85-96. [PMID: 32029232 PMCID: PMC6953711 DOI: 10.1016/j.molmet.2019.12.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/11/2019] [Accepted: 12/13/2019] [Indexed: 01/28/2023] Open
Abstract
Objective Ureagenesis predominantly occurs in the liver and functions to remove ammonia, and the dysregulation of ureagenesis leads to the development of hyperammonemia. Recent studies have shown that ureagenesis is under the control of nutrient signals, but the mechanism remains elusive. Therefore, intensive investigation of the molecular mechanism underlying ureagenesis will shed some light on the pathology of metabolic diseases related to ammonia imbalance. Methods Mice were fasted for 24 h or fed a high-fat diet (HFD) for 16 weeks. For human evaluation, we obtained a public data set including 41 obese patients with and without hepatic steatosis. We analyzed the expression levels of hepatic BAF60a under different nutrient status. The impact of BAF60a on ureagenesis and hyperammonemia was assessed by using gain- and loss-of-function strategies. The molecular chaperons mediating the effects of BAF60a on ureagenesis were validated by molecular biological strategies. Results BAF60a was induced in the liver of both fasted and HFD-fed mice and was positively correlated with body mass index in obese patients. Liver-specific overexpression of BAF60a inhibited hepatic ureagenesis, leading to the increase of serum ammonia levels. Mechanistically, BAF60a repressed the transcription of Cps1, a rate-limiting enzyme, through interaction with Y-box protein 1 (YB-1) and by switching the chromatin structure of Cps1 promoter into an inhibitory state. More importantly, in response to different nutrient status, PGC-1α (as a transcriptional coactivator) and YB-1 competitively bound to BAF60a, thus selectively regulating hepatic fatty acid β-oxidation and ureagenesis. Conclusion The BAF60a-YB-1 axis represses hepatic ureagenesis, thereby contributing to hyperammonemia under overnutrient status. Therefore, hepatic BAF60a may be a novel therapeutic target for the treatment of overnutrient-induced urea cycle disorders and their associated diseases. HFD-feeding increases hepatic BAF60a expression, while inhibits ureagenesis genes. BAF60a represses Cps1 transcription and ureagenesis, causing ammonia accumulation. YB-1 binds to BAF60a and mediates the inhibitory effects of BAF60a on ureagenesis. BAF60a mediates crosstalk between hepatic ureagenesis and fatty acid oxidation.
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Affiliation(s)
- Wenxiang Zhang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, 211198, China; School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu, 211198, China
| | - Zhewen Dong
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, 211198, China; School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu, 211198, China
| | - Mengyi Xu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, 211198, China; School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu, 211198, China
| | - Shiyao Zhang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, 211198, China; School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu, 211198, China
| | - Chang Liu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, 211198, China; School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu, 211198, China; State key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, Jiangsu, 211198, China.
| | - Siyu Chen
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, 211198, China; School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu, 211198, China; State key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, Jiangsu, 211198, China.
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Ang LT, Tan AKY, Autio MI, Goh SH, Choo SH, Lee KL, Tan J, Pan B, Lee JJH, Lum JJ, Lim CYY, Yeo IKX, Wong CJY, Liu M, Oh JLL, Chia CPL, Loh CH, Chen A, Chen Q, Weissman IL, Loh KM, Lim B. A Roadmap for Human Liver Differentiation from Pluripotent Stem Cells. Cell Rep 2019; 22:2190-2205. [PMID: 29466743 PMCID: PMC5854481 DOI: 10.1016/j.celrep.2018.01.087] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Revised: 12/08/2017] [Accepted: 01/29/2018] [Indexed: 01/02/2023] Open
Abstract
How are closely related lineages, including liver, pancreas, and intestines, diversified from a common endodermal origin? Here, we apply principles learned from developmental biology to rapidly reconstitute liver progenitors from human pluripotent stem cells (hPSCs). Mapping the formation of multiple endodermal lineages revealed how alternate endodermal fates (e.g., pancreas and intestines) are restricted during liver commitment. Human liver fate was encoded by combinations of inductive and repressive extracellular signals at different doses. However, these signaling combinations were temporally re-interpreted: cellular competence to respond to retinoid, WNT, TGF-β, and other signals sharply changed within 24 hr. Consequently, temporally dynamic manipulation of extracellular signals was imperative to suppress the production of unwanted cell fates across six consecutive developmental junctures. This efficiently generated 94.1% ± 7.35% TBX3+HNF4A+ human liver bud progenitors and 81.5% ± 3.2% FAH+ hepatocyte-like cells by days 6 and 18 of hPSC differentiation, respectively; the latter improved short-term survival in the Fah-/-Rag2-/-Il2rg-/- mouse model of liver failure.
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Affiliation(s)
- Lay Teng Ang
- Stem Cell & Regenerative Biology Group, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore.
| | - Antson Kiat Yee Tan
- Stem Cell & Regenerative Biology Group, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore
| | - Matias I Autio
- Human Genetics Group, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore; Cardiovascular Research Institute, National University of Singapore, Singapore 117599, Singapore
| | - Su Hua Goh
- Stem Cell & Regenerative Biology Group, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore
| | - Siew Hua Choo
- Stem Cell & Regenerative Biology Group, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore
| | - Kian Leong Lee
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Jianmin Tan
- Stem Cell & Regenerative Biology Group, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore
| | - Bangfen Pan
- Human Genetics Group, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore; Cardiovascular Research Institute, National University of Singapore, Singapore 117599, Singapore
| | - Jane Jia Hui Lee
- Stem Cell & Regenerative Biology Group, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Jen Jen Lum
- Stem Cell & Regenerative Biology Group, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore; School of Engineering, Temasek Polytechnic, Singapore 529757, Singapore
| | - Christina Ying Yan Lim
- Stem Cell & Regenerative Biology Group, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore
| | - Isabelle Kai Xin Yeo
- Stem Cell & Regenerative Biology Group, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore; School of Engineering, Temasek Polytechnic, Singapore 529757, Singapore
| | - Chloe Jin Yee Wong
- Stem Cell & Regenerative Biology Group, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore; School of Engineering, Temasek Polytechnic, Singapore 529757, Singapore
| | - Min Liu
- Humanized Mouse Unit, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore
| | - Jueween Ling Li Oh
- Stem Cell & Regenerative Biology Group, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore; School of Engineering, Temasek Polytechnic, Singapore 529757, Singapore
| | - Cheryl Pei Lynn Chia
- Stem Cell & Regenerative Biology Group, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore; School of Engineering, Temasek Polytechnic, Singapore 529757, Singapore
| | - Chet Hong Loh
- Stem Cell & Regenerative Biology Group, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore
| | - Angela Chen
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Department of Developmental Biology, Stanford-UC Berkeley Siebel Stem Cell Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Qingfeng Chen
- Humanized Mouse Unit, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore; Department of Microbiology, Yong Yoo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Irving L Weissman
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Department of Developmental Biology, Stanford-UC Berkeley Siebel Stem Cell Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kyle M Loh
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Department of Developmental Biology, Stanford-UC Berkeley Siebel Stem Cell Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Bing Lim
- Stem Cell & Regenerative Biology Group, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore.
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Chao HM, Chern E. Patient-derived induced pluripotent stem cells for models of cancer and cancer stem cell research. J Formos Med Assoc 2018; 117:1046-1057. [PMID: 30172452 DOI: 10.1016/j.jfma.2018.06.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 05/28/2018] [Accepted: 06/15/2018] [Indexed: 02/06/2023] Open
Abstract
Induced pluripotent stem cells (iPSCs) are embryonic stem cell-like cells reprogrammed from somatic cells by four transcription factors, OCT4, SOX2, KLF4 and c-MYC. iPSCs derived from cancer cells (cancer-iPSCs) could be a novel strategy for studying cancer. During cancer cell reprogramming, the epigenetic status of the cancer cell may be altered, such that it acquires stemness and pluripotency. The cellular behavior of the reprogrammed cells exhibits dynamic changes during the different stages of reprogramming. The cells may acquire the properties of cancer stem cells (CSCs) during the process of reprogramming, and lose their carcinogenic properties during reprogramming into a cancer-iPSCs. Differentiation of cancer-iPSCs by teratoma formation or organoid culturing could mimic the process of tumorigenesis. Some of the molecular mechanisms associated with cancer progression could be elucidated using the cancer-iPSC model. Furthermore, cancer-iPSCs could be expanded in culture system or bioreactors, and serve as cell sources for research, and as personal disease models for therapy and drug screening. This article introduces cancer studies that used the cell reprogramming strategy.
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Affiliation(s)
- Hsiao-Mei Chao
- niChe Lab for Stem Cell and Regenerative Medicine, Department of Biochemical Science and Technology, National Taiwan University, Taiwan; Department of Pathology, Wan Fang Hospital, Taipei Medical University, Taiwan
| | - Edward Chern
- niChe Lab for Stem Cell and Regenerative Medicine, Department of Biochemical Science and Technology, National Taiwan University, Taiwan.
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Murugesan SN, Yadav BS, Maurya PK, Chaudhary A, Singh S, Mani A. Expression and network analysis of YBX1 interactors for identification of new drug targets in lung adenocarcinoma. J Genomics 2018; 6:103-112. [PMID: 29973960 PMCID: PMC6030768 DOI: 10.7150/jgen.20581] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 08/31/2017] [Indexed: 12/27/2022] Open
Abstract
Y-Box Binding protein 1 (YBX-1) is known to be involved in various types of cancers. It's interactors also play major role in various cellular functions. Present work aimed to study the expression profile of the YBX-1 interactors during lung adenocarcinoma (LUAD). The differential expression analysis involved 57 genes from 95 lung adenocarcinoma samples, construction of gene network and topology analysis. A Total of 43 genes were found to be differentially expressed from which 17 genes were found to be down regulated and 26 genes were up-regulated. We observed that Polyadenylate-binding protein 1 (PABPC1), a protein involved in YBX1 translation, is highly correlated with YBX1. The interaction network analysis for a differentially expressed non-coding RNA Growth Arrest Specific 5 (GAS5) suggests that two proteins namely, Growth Arrest Specific 2 (GAS2) and Peripheral myelin protein 22 (PMP22) are potentially involved in LUAD progression. The network analysis and differential expression suggests that Collagen type 1 alpha 2 (COL1A2) can be potential biomarker and target for LUAD.
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Affiliation(s)
| | - Birendra Singh Yadav
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India-211004
| | - Pramod Kumar Maurya
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India-211004
| | - Amit Chaudhary
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India-211004
| | - Swati Singh
- Center of Bioinformatics, University of Allahabad, India-211002
| | - Ashutosh Mani
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India-211004
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12
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Chao HM, Huang HX, Chang PH, Tseng KC, Miyajima A, Chern E. Y-box binding protein-1 promotes hepatocellular carcinoma-initiating cell progression and tumorigenesis via Wnt/β-catenin pathway. Oncotarget 2018; 8:2604-2616. [PMID: 27911878 PMCID: PMC5356827 DOI: 10.18632/oncotarget.13733] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 11/22/2016] [Indexed: 12/14/2022] Open
Abstract
Y-box binding protein-1 (YB-1) is a pleiotropic molecule that binds DNA to regulate genes on a transcriptional level in the nucleus and binds RNA to modulate gene translation in the cytoplasm. In our previous studies, YB-1 was also characterized as a fetal hepatic protein that regulates the maturation of hepatocytes and is upregulated during liver regeneration. Moreover, YB-1 has been shown to be expressed in human hepatocellular carcinoma (HCC). However, the role of YB-1 in HCC remains unclear. Here, we aimed to characterize the role of YB-1 in HCC. Based on the results of loss-of-function in HCC and gain-of-function in mice liver using hydrodynamic gene delivery, YB-1 promoted hepatic cells proliferation in vitro and in vivo. YB-1 was also involved in HCC cell proliferation, migration, and drug-resistance. The results of extreme limiting dilution sphere forming analysis and cancer initiating cell marker analysis were also shown that YB-1 maintained HCC initiating cells population. YB-1 also induced the epithelial-mesenchymal transition and stemness-related gene expression. Knockdown of YB-1 suppressed the expression of Wnt ligands and β-catenin, impaired Wnt/β-catenin signaling pathway and reduced the numbers of HCC initiating cells. Moreover, YB-1 displayed nuclear localization particularly in the HCC initiating cells, the EpCAM+ cells or sphere cells. Our findings suggested that YB-1 was a key factor in HCC tumorigenesis and maintained the HCC initiating cell population.
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Affiliation(s)
- Hsiao-Mei Chao
- niChe Laboratory for Stem Cell and Regenerative Medicine, Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan.,Department of Pathology, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Hong-Xuan Huang
- niChe Laboratory for Stem Cell and Regenerative Medicine, Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Po-Hsiang Chang
- niChe Laboratory for Stem Cell and Regenerative Medicine, Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Kuo-Chang Tseng
- niChe Laboratory for Stem Cell and Regenerative Medicine, Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Atsushi Miyajima
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
| | - Edward Chern
- niChe Laboratory for Stem Cell and Regenerative Medicine, Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
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13
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Çeliktas M, Tanaka I, Tripathi SC, Fahrmann JF, Aguilar-Bonavides C, Villalobos P, Delgado O, Dhillon D, Dennison JB, Ostrin EJ, Wang H, Behrens C, Do KA, Gazdar AF, Hanash SM, Taguchi A. Role of CPS1 in Cell Growth, Metabolism and Prognosis in LKB1-Inactivated Lung Adenocarcinoma. J Natl Cancer Inst 2017; 109:1-9. [PMID: 28376202 DOI: 10.1093/jnci/djw231] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 09/09/2016] [Indexed: 02/06/2023] Open
Abstract
Background Liver kinase B1 ( LKB1 ) is a tumor suppressor in lung adenocarcinoma (LADC). We investigated the proteomic profiles of 45 LADC cell lines with and without LKB1 inactivation. Carbamoyl phosphate synthetase 1 (CPS1), the first rate-limiting mitochondrial enzyme in the urea cycle, was distinctively overexpressed in LKB1-inactivated LADC cell lines. We therefore assessed the role of CPS1 and its clinical relevance in LKB1-inactivated LADC. Methods Mass spectrometric profiling of proteome and metabolome and function of CPS1 were analyzed in LADC cell lines. CPS1 and LKB1 expression in tumors from 305 LADC and 160 lung squamous cell carcinoma patients was evaluated by immunohistochemistry. Kaplan-Meier and Cox regression analyses were applied to assess the association between overall survival and CPS1 and LKB1 expression. All statistical tests were two-sided. Results CPS1 knockdown reduced cell growth, decreased metabolite levels associated with nucleic acid biosynthesis pathway, and contributed an additive effect when combined with gemcitabine, pemetrexed, or CHK1 inhibitor AZD7762. Tissue microarray analysis revealed that CPS1 was expressed in 65.7% of LKB1-negative LADC, and only 5.0% of LKB1-positive LADC. CPS1 expression showed statistically significant association with poor overall survival in LADC (hazard ratio = 3.03, 95% confidence interval = 1.74 to 5.25, P < .001). Conclusions Our findings suggest functional relevance of CPS1 in LKB1-inactivated LADC and association with worse outcome of LADC. CPS1 is a promising therapeutic target in combination with other chemotherapy agents, as well as a prognostic biomarker, enabling a personalized approach to treatment of LADC.
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Affiliation(s)
- Müge Çeliktas
- Departments of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ichidai Tanaka
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Satyendra Chandra Tripathi
- Departments of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Johannes F Fahrmann
- Departments of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Pamela Villalobos
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Oliver Delgado
- Departments of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dilsher Dhillon
- Departments of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer B Dennison
- Departments of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Edwin J Ostrin
- Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hong Wang
- Departments of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carmen Behrens
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kim-Anh Do
- Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Adi F Gazdar
- Hamon Center for Therapeutic Oncology Research and Department of Pathology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
| | - Samir M Hanash
- Departments of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ayumu Taguchi
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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14
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Yang C, Fu R, Zhuang Z, Wang S. Studies on the biological functions of CPS1 in AFB1 induced hepatocarcinogenesis. Gene 2016; 591:255-261. [PMID: 27425868 DOI: 10.1016/j.gene.2016.07.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 06/23/2016] [Accepted: 07/12/2016] [Indexed: 01/10/2023]
Abstract
Carbamyl phosphate synthetase 1 (CPS1) was down-regulated in hepatocellular carcinoma (HCC), as treated by aflatoxin B1 (AFB1), a potent hepatocarcinogenesis mycotoxin. In this study, we firstly confirmed that AFB1 down-regulated the expression of CPS1 in a dose-dependent manner. At the meantime, both siRNA knock down of CPS1 and AFB1 treatment inhibited cell proliferation, and induced cell apoptosis. To further analysis the function of CPS1, the interacting proteins of CPS1 were searched by Co-IP, and three interacting proteins including type II cytoskeletal 1 (KRT1), albumin (ALB), and ubiquitin C (UBC) were found. Both KRT1 and ALB were new interacting proteins for CPS1. Our further study showed that CPS1 was regulating interacted and colocalized with KRT1 and ALB, and the intensity correlation was changed by AFB1. KRT1, ALB and CPS1 were all reported to play an important role in differentiation and tissue specialization. These results may offer an increasing understand that CPS1 might have a function in differentiation.
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Affiliation(s)
- Chi Yang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of the Education Ministry, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Institute of Edible Fungi, National and Local Joint Engineering Research Center for Breeding & Cultivation of Featured Edible Fungi, Fujian Academy of Agricultural Sciences, Fuzhou 350014, China
| | - Rao Fu
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of the Education Ministry, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhenhong Zhuang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of the Education Ministry, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shihua Wang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of the Education Ministry, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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15
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Dahl A, Iotchkova V, Baud A, Johansson Å, Gyllensten U, Soranzo N, Mott R, Kranis A, Marchini J. A multiple-phenotype imputation method for genetic studies. Nat Genet 2016; 48:466-72. [PMID: 26901065 PMCID: PMC4817234 DOI: 10.1038/ng.3513] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 01/25/2016] [Indexed: 12/15/2022]
Abstract
Genetic association studies have yielded a wealth of biological discoveries. However, these studies have mostly analyzed one trait and one SNP at a time, thus failing to capture the underlying complexity of the data sets. Joint genotype-phenotype analyses of complex, high-dimensional data sets represent an important way to move beyond simple genome-wide association studies (GWAS) with great potential. The move to high-dimensional phenotypes will raise many new statistical problems. Here we address the central issue of missing phenotypes in studies with any level of relatedness between samples. We propose a multiple-phenotype mixed model and use a computationally efficient variational Bayesian algorithm to fit the model. On a variety of simulated and real data sets from a range of organisms and trait types, we show that our method outperforms existing state-of-the-art methods from the statistics and machine learning literature and can boost signals of association.
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Affiliation(s)
- Andrew Dahl
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Valentina Iotchkova
- Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, UK
| | - Amelie Baud
- European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, UK
| | - Åsa Johansson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University, Uppsala, Sweden
| | - Ulf Gyllensten
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University, Uppsala, Sweden
| | - Nicole Soranzo
- Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Richard Mott
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Andreas Kranis
- Aviagen, Ltd., Newbridge, UK.,Roslin Institute, University of Edinburgh, Midlothian, UK
| | - Jonathan Marchini
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.,Department of Statistics, University of Oxford, Oxford, UK
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16
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Nohara K, Shin Y, Park N, Jeong K, He B, Koike N, Yoo SH, Chen Z. Ammonia-lowering activities and carbamoyl phosphate synthetase 1 (Cps1) induction mechanism of a natural flavonoid. Nutr Metab (Lond) 2015; 12:23. [PMID: 26075008 PMCID: PMC4465466 DOI: 10.1186/s12986-015-0020-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 06/04/2015] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVE Ammonia detoxification is essential for physiological well-being, and the urea cycle in liver plays a predominant role in ammonia disposal. Nobiletin (NOB), a natural dietary flavonoid, is known to exhibit various physiological efficacies. In the current study, we investigated a potential role of NOB in ammonia control and the underlying cellular mechanism. MATERIALS/METHODS C57BL/6 mice were fed with regular chow (RC), high-fat (HFD) or high-protein diet (HPD) and treated with either vehicle or NOB. Serum and/or urine levels of ammonia and urea were measured. Liver expression of genes encoding urea cycle enzymes and C/EBP transcription factors was determined over the circadian cycle. Luciferase reporter assays were carried out to investigate function of CCAAT consensus elements on the carbamoyl phosphate synthetase (Cps1) gene promoter. A circadian clock-deficient mouse mutant, Clock (Δ19/Δ19) , was utilized to examine a requisite role of the circadian clock in mediating NOB induction of Cps1. RESULTS NOB was able to lower serum ammonia levels in mice fed with RC, HFD or HPD. Compared with RC, HFD repressed the mRNA and protein expression of Cps1, encoding the rate-limiting enzyme of the urea cycle. Interestingly, NOB rescued CPS1 protein levels under the HFD condition via induction of the transcription factors C/EBPα and C/EBPβ. Expression of other urea cycle genes was also decreased by HFD relative to RC and again restored by NOB to varying degrees, which, in conjunction with Cps1 promoter reporter analysis, suggested a C/EBP-dependent mechanism for the co-induction of urea cycle genes by NOB. In comparison, HPD markedly increased CPS1 levels relative to RC, yet NOB did not further enrich CPS1 to a significant extent. Using the circadian mouse mutant Clock (Δ19/Δ19) , we also showed that a functional circadian clock, known to modulate C/EBP and CPS1 expression, was required for NOB induction of CPS1 under the HFD condition. CONCLUSION NOB, a dietary flavonoid, exhibits a broad activity in ammonia control across varying diets, and regulates urea cycle function via C/EBP-and clock-dependent regulatory mechanisms.
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Affiliation(s)
- Kazunari Nohara
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, 6431 Fannin Street, MSB 6.200, Houston, TX 77030 USA
| | - Youngmin Shin
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, 6431 Fannin Street, MSB 6.200, Houston, TX 77030 USA
| | - Noheon Park
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Kwon Jeong
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, 6431 Fannin Street, MSB 6.200, Houston, TX 77030 USA
| | - Baokun He
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, 6431 Fannin Street, MSB 6.200, Houston, TX 77030 USA
| | - Nobuya Koike
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto, 602-8566 Japan
| | - Seung-Hee Yoo
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, 6431 Fannin Street, MSB 6.200, Houston, TX 77030 USA
| | - Zheng Chen
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, 6431 Fannin Street, MSB 6.200, Houston, TX 77030 USA
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17
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LeMoine CMR, Walsh PJ. Ontogeny of ornithine-urea cycle gene expression in zebrafish (Danio rerio). Am J Physiol Regul Integr Comp Physiol 2013; 304:R991-1000. [PMID: 23576614 DOI: 10.1152/ajpregu.00411.2012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Although the majority of adult teleosts excrete most of their nitrogenous wastes as ammonia, several fish species are capable of producing urea early in development. In zebrafish, it is unclear whether this results from a functional ornithine-urea cycle (O-UC) and, if so, how it might be regulated. This study examined the spatiotemporal patterns of gene expression of four major O-UC enzymes: carbamoyl phosphate synthase III (CPSIII), ornithine transcarboxylase, arginosuccinate synthetase, and arginosuccinate lyase, using real-time PCR and whole mount in situ hybridization. In addition, we hypothesized that CPSIII gene expression was epigenetically regulated through methylation of its promoter, a widespread mode of differential gene regulation between tissues and life stages in vertebrates. Furthermore, to assess CPSIII functionality, we used morpholinos to silence CPSIII in zebrafish embryos and assessed their nitrogenous waste handling during development, and in response to ammonia injections. Our results suggest that mRNAs of O-UC enzymes are expressed early in zebrafish development and colocalize to the embryonic endoderm. In addition, the methylation status of CPSIII promoter is not consistent with the patterns of expression observed in developing larvae or adult tissues, suggesting other means of transcriptional regulation of this enzyme. Finally, CPSIII morphants exhibited a transient reduction in CPSIII enzyme activity 24 h postfertilization, which was paralleled by reduced urea production during development and in response to an ammonia challenge. Overall, we conclude that the O-UC is functional in zebrafish embryos, providing further evidence that the capacity to produce urea via the O-UC is widespread in developing teleosts.
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18
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Liver Stem Cells. Regen Med 2013. [DOI: 10.1007/978-94-007-5690-8_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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19
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Eliseeva IA, Kim ER, Guryanov SG, Ovchinnikov LP, Lyabin DN. Y-box-binding protein 1 (YB-1) and its functions. BIOCHEMISTRY (MOSCOW) 2012; 76:1402-33. [PMID: 22339596 DOI: 10.1134/s0006297911130049] [Citation(s) in RCA: 249] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review describes the structure and functions of Y-box binding protein 1 (YB-1) and its homologs. Interactions of YB-1 with DNA, mRNAs, and proteins are considered. Data on the participation of YB-1 in DNA reparation and transcription, mRNA splicing and translation are systematized. Results on interactions of YB-1 with cytoskeleton components and its possible role in mRNA localization are discussed. Data on intracellular distribution of YB-1, its redistribution between the nucleus and the cytoplasm, and its secretion and extracellular functions are summarized. The effect of YB-1 on cell differentiation, its involvement in extra- and intracellular signaling pathways, and its role in early embryogenesis are described. The mechanisms of regulation of YB-1 expression in the cell are presented. Special attention is paid to the involvement of YB-1 in oncogenic cell transformation, multiple drug resistance, and dissemination of tumors. Both the oncogenic and antioncogenic activities of YB-1 are reviewed. The potential use of YB-1 in diagnostics and therapy as an early cancer marker and a molecular target is discussed.
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Affiliation(s)
- I A Eliseeva
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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20
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Liu H, Dong H, Robertson K, Liu C. DNA methylation suppresses expression of the urea cycle enzyme carbamoyl phosphate synthetase 1 (CPS1) in human hepatocellular carcinoma. THE AMERICAN JOURNAL OF PATHOLOGY 2011; 178:652-61. [PMID: 21281797 DOI: 10.1016/j.ajpath.2010.10.023] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Revised: 09/10/2010] [Accepted: 10/14/2010] [Indexed: 12/31/2022]
Abstract
Carbamoyl phosphate synthetase 1 (CPS1) is a liver-specific, intramitochondrial, rate-limiting enzyme in the urea cycle. A previous study showed that CPS1 is the antigen for hepatocyte paraffin 1 antibody, a commonly used antibody in surgical pathology practice; and CPS1 expression appears to be down-regulated in liver cancer tissue and cell lines. The aim of this study is to understand how the CPS1 gene is regulated in liver carcinogenesis. In this report, we show that human hepatocellular carcinoma (HCC) cells do not express CPS1, whereas cultured human primary hepatocytes express abundant levels. In addition, CPS1 was silenced or down-regulated in liver tumor tissues compared with the matched noncancerous tissues. The expression of CPS1 in HCC cells was restored with a demethylation agent, 5-azacytidine. We show that two CpG dinucleotides, located near the transcription start site, and a CpG-rich region in the first intron were hypermethylated in HCC cells. The hypermethylation of the two CpG dinucleotides was also detected in HCC tumor tissues compared with noncancerous tissues. Further molecular analysis with mutagenesis indicated that the two CpG dinucleotides play a role in promoter activity of the CPS1 gene. In conclusion, our study demonstrates that DNA methylation is a key mechanism of silencing CPS1 expression in human HCC cells, and CPS1 gene hypermethylation of the two CpG dinucleotides is a potential biomarker for HCC.
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Affiliation(s)
- Hongyan Liu
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
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21
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Liver Stem Cells. Regen Med 2011. [DOI: 10.1007/978-90-481-9075-1_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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22
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Proteomic analysis of regenerating mouse liver following 50% partial hepatectomy. Proteome Sci 2009; 7:48. [PMID: 20040084 PMCID: PMC2813229 DOI: 10.1186/1477-5956-7-48] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 12/29/2009] [Indexed: 12/29/2022] Open
Abstract
Background Although 70% (or 2/3) partial hepatectomy (PH) is the most studied model for liver regeneration, the hepatic protein expression profile associated with lower volume liver resection (such as 50% PH) has not yet been reported. Therefore, the aim of this study was to determine the global protein expression profile of the regenerating mouse liver following 50% PH by differential proteomics, and thereby gaining some insights into the hepatic regeneration mechanism(s) under this milder but clinically more relevant condition. Results Proteins from sham-operated mouse livers and livers regenerating for 24 h after 50% PH were separated by SDS-PAGE and analyzed by nanoUPLC-Q-Tof mass spectrometry. Compared to sham-operated group, there were totally 87 differentially expressed proteins (with 50 up-regulated and 37 down-regulated ones) identified in the regenerating mouse livers, most of which have not been previously related to liver regeneration. Remarkably, over 25 differentially expressed proteins were located at mitochondria. Several of the mitochondria-resident proteins which play important roles in citric acid cycle, oxidative phosphorylation and ATP production were found to be down-regulated, consistent with the recently-proposed model in which the reduction of ATP content in the remnant liver gives rise to early stress signals that contribute to the onset of liver regeneration. Pathway analysis revealed a central role of c-Myc in the regulation of liver regeneration. Conclusions Our study provides novel evidence for mitochondria as a pivotal organelle that is connected to liver regeneration, and lays the foundation for further studies on key factors and pathways involved in liver regeneration following 50% PH, a condition frequently used for partial liver transplantation and conservative liver resection.
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