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White RR, Milholland B, MacRae SL, Lin M, Zheng D, Vijg J. Comprehensive transcriptional landscape of aging mouse liver. BMC Genomics 2015; 16:899. [PMID: 26541291 PMCID: PMC4636074 DOI: 10.1186/s12864-015-2061-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 10/10/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Mammalian aging is a highly complex process, a full mechanistic understanding of which is still lacking. One way to help understand the molecular changes underlying aging is through a comprehensive analysis of the transcriptome, the primary determinant of age-related phenotypic diversity. Previous studies have relied on microarray analysis to examine gene expression profiles in different tissues of aging organisms. However, studies have shown microarray-based transcriptional profiling is less accurate and not fully capable of capturing certain intricacies of the global transcriptome. METHODS Here, using directional whole transcriptome RNA-sequencing of aged mouse liver we have identified a comprehensive high-resolution profile of differentially expressed liver transcripts comprised of canonical protein-coding transcripts, transcript isoforms, and non-coding RNA transcripts, including pseudogenes, long non-coding RNAs and small RNA species. RESULTS Results show extensive age-related changes in every component of the mouse liver transcriptome and a pronounced increase in inter-individual variation. Functional annotation of the protein-coding mRNAs and isoforms indicated broad alterations in immune response, cell activation, metabolic processes, and RNA modification. Interestingly, multiple lncRNAs (Meg3, Rian, Mirg) from the Dlk-Dio3 microRNA locus were found up-regulated in aging liver, classifying this locus as a putative regulatory hotspot locus in aging liver. Moreover, integration of the altered non-coding RNAs and protein-coding transcripts into interaction networks of age-related change revealed inflammation, cellular proliferation, and metabolism as the dominant aging phenotypes in mouse liver. CONCLUSIONS Our analyses provide the first comprehensive dissection of the transcriptional landscape in aging mouse liver.
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Affiliation(s)
- Ryan R White
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA. .,Albert Einstein College of Medicine, Michael F. Price Center for Genetic and Translational Research, 1301 Morris Park Ave, Bronx, NY, 10461, USA.
| | - Brandon Milholland
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Sheila L MacRae
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Mingyan Lin
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA. .,Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA. .,Albert Einstein College of Medicine, Michael F. Price Center for Genetic and Translational Research, 1301 Morris Park Ave, Bronx, NY, 10461, USA.
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Hammad S, Ahmed H. Biomarker: the universe of chemically induced gene expression alterations in human hepatocyte. EXCLI JOURNAL 2014; 13:1275-7. [PMID: 26417340 PMCID: PMC4462829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 12/09/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Seddik Hammad
- Department of Forensic Medicine and Veterinary Toxicology, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt,*To whom correspondence should be addressed: Seddik Hammad, Department of Forensic Medicine and Veterinary Toxicology, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt, E-mail:
| | - Hassan Ahmed
- Division of Cerebral Circuitry, National Institute for Physiological Sciences, Okazaki, Japan
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Hu Y, Zhan Q, Liu HX, Chau T, Li Y, Wan YJ, Yvonne Wan YJ. Accelerated partial hepatectomy-induced liver cell proliferation is associated with liver injury in Nur77 knockout mice. THE AMERICAN JOURNAL OF PATHOLOGY 2014; 184:3272-83. [PMID: 25307349 DOI: 10.1016/j.ajpath.2014.08.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 07/29/2014] [Accepted: 08/18/2014] [Indexed: 12/17/2022]
Abstract
Nur77, encoded by Nr4a1 (alias Nur77), plays roles in cell death, survival, and inflammation. To study the role of Nur77 in liver regeneration, wild-type (WT) and Nur77 knockout (KO) mice were subjected to standard two-thirds partial hepatectomy (PH). Nur77 mRNA and protein levels were markedly induced at 1 hour after PH in WT livers, coinciding with ERK1/2 activation. Surprisingly, Nur77 KO mice exhibited a higher liver-to-body weight ratio than WT mice at 24, 48, and 72 hours after PH. Nur77 KO livers exhibited increase in Ki-67-positive hepatocytes at 24 hours, with early induction of cell-cycle genes. Despite accelerated regeneration, Nur77 KO livers paradoxically incurred necrosis, hepatocyte apoptosis, elevated serum alanine aminotransferase activity, and Kupffer cell accumulation. Microarray analysis revealed up-regulation of genes modulating inflammation, cell proliferation, and apoptosis but down-regulation (due to Nur77 deficiency) of glucose and lipid homeostasis genes. Levels of proinflammatory cytokines IL-6, IL-12, IL-23, and CCL2 were increased and levels of anti-inflammatory IL-10 were decreased, compared with WT. Activated NF-κB and STAT3 and mRNA levels of target genes Myc and Bcl2l1 were elevated in Nur77 KO livers. Overall, Nur77 appears essential for regulating early signaling of liver regeneration by modulating cytokine-mediated inflammatory, apoptotic, and energy mobilization processes. The accelerated liver regeneration observed in Nur77 KO mice is likely due to a compensatory effect caused by injury.
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Affiliation(s)
- Ying Hu
- Department of Medical Pathology and Laboratory Medicine, University of California, Davis Health Systems, Sacramento, California
| | - Qi Zhan
- Department of Gastroenterology and Hepatology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China; Guangzhou Digestive Disease Center, Guangzhou, China
| | - Hui-Xin Liu
- Department of Medical Pathology and Laboratory Medicine, University of California, Davis Health Systems, Sacramento, California
| | - Thinh Chau
- Department of Medical Pathology and Laboratory Medicine, University of California, Davis Health Systems, Sacramento, California
| | - Yuyuan Li
- Department of Gastroenterology and Hepatology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China; Guangzhou Digestive Disease Center, Guangzhou, China
| | - Yu-Jui Wan
- Department of Medical Pathology and Laboratory Medicine, University of California, Davis Health Systems, Sacramento, California; Department of Gastroenterology and Hepatology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China; Guangzhou Digestive Disease Center, Guangzhou, China.
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Hu Y, Liu HX, He Y, Fang Y, Fang J, Wan YJY. Transcriptome profiling and genome-wide DNA binding define the differential role of fenretinide and all-trans RA in regulating the death and survival of human hepatocellular carcinoma Huh7 cells. Biochem Pharmacol 2013; 85:1007-17. [PMID: 23396089 DOI: 10.1016/j.bcp.2013.01.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 01/27/2013] [Accepted: 01/28/2013] [Indexed: 12/17/2022]
Abstract
Fenretinide is significantly more effective in inducing apoptosis in cancer cells than all-trans retinoic acid (ATRA). The current study uses a genome-wide approach to understand the differential role fenretinide and ATRA have in inducing apoptosis in Huh7 cells. Fenretinide and ATRA-induced gene expressions and DNA bindings were profiled using microarray and chromatin immunoprecipitation with anti-RXRα antibody. The data showed that fenretinide was not a strong transcription regulator. Fenretinide only changed the expressions of 1 093 genes, approximately three times less than the number of genes regulated by ATRA (2 811). Biological function annotation demonstrated that both fenretinide and ATRA participated in pathways that determine cell fate and metabolic processes. However, fenretinide specifically induced Fas/TNFα-mediated apoptosis by increasing the expression of pro-apoptotic genes i.e., DEDD2, CASP8, CASP4, and HSPA1A/B; whereas, ATRA induced the expression of BIRC3 and TNFAIP3, which inhibit apoptosis by interacting with TRAF2. In addition, fenretinide inhibited the expression of the genes involved in RAS/RAF/ERK-mediated survival pathway. In contrast, ATRA increased the expression of SOSC2, BRAF, MEK, and ERK genes. Most genes regulated by fenretinide and ATRA were bound by RXRα, suggesting a direct effect. This study revealed that by regulating fewer genes, the effects of fenretinide become more specific and thus has fewer side effects than ATRA. The data also suggested that fenretinide induces apoptosis via death receptor effector and by inhibiting the RAS/RAF/ERK pathway. It provides insight on how retinoid efficacy can be improved and how side effects in cancer therapy can be reduced.
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Affiliation(s)
- Ying Hu
- Department of Medical Pathology and Laboratory Medicine, 4645 2nd Ave, Research Building III, University of California, Davis Health Systems, Sacramento, CA 95817, USA.
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Zhan Q, Fang Y, He Y, Liu HX, Fang J, Wan YJY. Function annotation of hepatic retinoid x receptor α based on genome-wide DNA binding and transcriptome profiling. PLoS One 2012; 7:e50013. [PMID: 23166811 PMCID: PMC3499475 DOI: 10.1371/journal.pone.0050013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 10/19/2012] [Indexed: 02/05/2023] Open
Abstract
Background Retinoid x receptor α (RXRα) is abundantly expressed in the liver and is essential for the function of other nuclear receptors. Using chromatin immunoprecipitation sequencing and mRNA profiling data generated from wild type and RXRα-null mouse livers, the current study identifies the bona-fide hepatic RXRα targets and biological pathways. In addition, based on binding and motif analysis, the molecular mechanism by which RXRα regulates hepatic genes is elucidated in a high-throughput manner. Principal Findings Close to 80% of hepatic expressed genes were bound by RXRα, while 16% were expressed in an RXRα-dependent manner. Motif analysis predicted direct repeat with a spacer of one nucleotide as the most prevalent RXRα binding site. Many of the 500 strongest binding motifs overlapped with the binding motif of specific protein 1. Biological functional analysis of RXRα-dependent genes revealed that hepatic RXRα deficiency mainly resulted in up-regulation of steroid and cholesterol biosynthesis-related genes and down-regulation of translation- as well as anti-apoptosis-related genes. Furthermore, RXRα bound to many genes that encode nuclear receptors and their cofactors suggesting the central role of RXRα in regulating nuclear receptor-mediated pathways. Conclusions This study establishes the relationship between RXRα DNA binding and hepatic gene expression. RXRα binds extensively to the mouse genome. However, DNA binding does not necessarily affect the basal mRNA level. In addition to metabolism, RXRα dictates the expression of genes that regulate RNA processing, translation, and protein folding illustrating the novel roles of hepatic RXRα in post-transcriptional regulation.
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Affiliation(s)
- Qi Zhan
- Department of Gastroenterology Hepatology, Guangzhou First Municipal People's Hospital, Guangzhou Medical College, Guangzhou, Guangdong Province, China
| | - Yaping Fang
- Applied Bioinformatics Laboratory, University of Kansas, Lawrence, Kansas, United States of America
| | - Yuqi He
- Department of Medical Pathology and Laboratory Medicine, University of California Davis, Davis Health Systems, Sacramento, California, United States of America
| | - Hui-Xin Liu
- Department of Medical Pathology and Laboratory Medicine, University of California Davis, Davis Health Systems, Sacramento, California, United States of America
| | - Jianwen Fang
- Applied Bioinformatics Laboratory, University of Kansas, Lawrence, Kansas, United States of America
| | - Yu-Jui Yvonne Wan
- Department of Gastroenterology Hepatology, Guangzhou First Municipal People's Hospital, Guangzhou Medical College, Guangzhou, Guangdong Province, China
- Department of Medical Pathology and Laboratory Medicine, University of California Davis, Davis Health Systems, Sacramento, California, United States of America
- * E-mail:
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Jackson P, Halappanavar S, Hougaard KS, Williams A, Madsen AM, Lamson JS, Andersen O, Yauk C, Wallin H, Vogel U. Maternal inhalation of surface-coated nanosized titanium dioxide (UV-Titan) in C57BL/6 mice: effects in prenatally exposed offspring on hepatic DNA damage and gene expression. Nanotoxicology 2011; 7:85-96. [PMID: 22117692 DOI: 10.3109/17435390.2011.633715] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We investigated effects of maternal pulmonary exposure to titanium dioxide (UV-Titan) on prenatally exposed offspring. Time-mated mice (C57BL/6BomTac) were inhalation exposed (1 h/day to 42 mg UV-Titan/m(3) aerosolised powder or filtered air) during gestation days (GDs) 8-18. We evaluated DNA strand breaks using the comet assay in bronchoalveolar lavage (BAL) cells and livers of the time-mated mice (5 and 26-27 days after inhalation exposure), and in livers of the offspring (post-natal days (PND) 2 and 22). We also analysed hepatic gene expression in newborns using DNA microarrays. UV-Titan exposure did not induce DNA strand breaks in time-mated mice or their offspring. Transcriptional profiling of newborn livers revealed changes in the gene expression related to the retinoic acid signalling pathway in the females, while gene expression in male offspring was unaffected. Changes may be a secondary response to maternal inflammation although no direct link was evident through gene expression analysis.
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Affiliation(s)
- Petra Jackson
- National Research Centre for the Working Environment, DK- 2100 Copenhagen Ø, Denmark
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