1
|
Liu P, Ewald J, Galvez JH, Head J, Crump D, Bourque G, Basu N, Xia J. Ultrafast functional profiling of RNA-seq data for nonmodel organisms. Genome Res 2021; 31:713-720. [PMID: 33731361 PMCID: PMC8015844 DOI: 10.1101/gr.269894.120] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 02/18/2021] [Indexed: 12/02/2022]
Abstract
Computational time and cost remain a major bottleneck for RNA-seq data analysis of nonmodel organisms without reference genomes. To address this challenge, we have developed Seq2Fun, a novel, all-in-one, ultrafast tool to directly perform functional quantification of RNA-seq reads without transcriptome de novo assembly. The pipeline starts with raw read quality control: sequencing error correction, removing poly(A) tails, and joining overlapped paired-end reads. It then conducts a DNA-to-protein search by translating each read into all possible amino acid fragments and subsequently identifies possible homologous sequences in a well-curated protein database. Finally, the pipeline generates several informative outputs including gene abundance tables, pathway and species hit tables, an HTML report to visualize the results, and an output of clean reads annotated with mapped genes ready for downstream analysis. Seq2Fun does not have any intermediate steps of file writing and loading, making I/O very efficient. Seq2Fun is written in C++ and can run on a personal computer with a limited number of CPUs and memory. It can process >2,000,000 reads/min and is >120 times faster than conventional workflows based on de novo assembly, while maintaining high accuracy in our various test data sets.
Collapse
Affiliation(s)
- Peng Liu
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec H9X 3V9, Canada
| | - Jessica Ewald
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec H9X 3V9, Canada
| | - Jose Hector Galvez
- Department of Human Genetics, McGill University, Montreal, Quebec H3A 0C7, Canada.,Canadian Center for Computational Genomics, McGill University, Montreal, Quebec H3A 0G1, Canada
| | - Jessica Head
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec H9X 3V9, Canada
| | - Doug Crump
- Environment and Climate Change Canada, National Wildlife Research Centre, Ottawa, Ontario K1A 0H3, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, Quebec H3A 0C7, Canada.,Canadian Center for Computational Genomics, McGill University, Montreal, Quebec H3A 0G1, Canada
| | - Niladri Basu
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec H9X 3V9, Canada
| | - Jianguo Xia
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec H9X 3V9, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec H3A 0C7, Canada
| |
Collapse
|
2
|
Zhu G, Fang C, Mo C, Wang Y, Huang Y, Li J. Transcriptomic analysis of granulosa cell populations proximal and distal to the germinal disc of chicken preovulatory follicles. Sci Rep 2021; 11:4683. [PMID: 33633274 PMCID: PMC7907084 DOI: 10.1038/s41598-021-84140-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 01/19/2021] [Indexed: 01/28/2023] Open
Abstract
Within the oocytes of chicken preovulatory follicles, the engulfed yolk constitutes 99% of the oocyte content, while the small germinal disc (GD) (which contains the nucleus and 99% ooplasm) occupies only less than 1%. Relative to the position of the GD, the single granulosa cell layer surrounding the oocyte can be sub-divided into two sub-populations: granulosa cells proximal (named Gp cells) and distal (Gd cells) to the GD. It was reported that Gp cells and Gd cells differ in their morphology, proliferative rate and steroidogenic capacity, however, the underlying mechanism controlling granulosa cell heterogeneity remains unclear. Here we analyzed the transcriptomes of Gd and Gp cells of preovulatory (F5 and F1) follicles in chicken ovaries. We found that: (1) genes associated with cell cycle and DNA replication (CDK1, CCNB3 etc.) have comparatively higher expression levels in Gp cells than in Gd cells, while genes associated with steroidogenesis (CYP51A1, DHCR24) are highly expressed in Gd cells, indicating that Gp cells are likely more mitotic and less steroidogenic than Gd cells; (2) genes associated with extracellular matrix remodeling, cell adhesion and sperm binding (ZP3, ZP2) are differentially expressed in Gp and Gd cells; (3) Furthermore, signaling molecules (WNT4/IHH) and receptors for NGF (NGFR), epidermal growth factor (EGFR), gonadotropins (FSHR/LHR) and prostaglandin (PTGER3) are abundantly but differentially expressed in Gp and Gd cells. Taken together, our data strongly supports the notion that Gp and Gd cells of preovulatory follicles differ in their proliferation rate, steroidogenic activity, ECM organization and sperm binding capacity, which are likely controlled by gonadotropins and local ovarian factors, such as GD-derived factors.
Collapse
Affiliation(s)
- Guoqiang Zhu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, People's Republic of China
| | - Chao Fang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, People's Republic of China
| | - Chunheng Mo
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, People's Republic of China
| | - Yajun Wang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, People's Republic of China
| | - Yan Huang
- The China Conservation and Research Center for the Giant Panda, Wolong, People's Republic of China.
| | - Juan Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, People's Republic of China.
| |
Collapse
|
3
|
Režen T, Zmrzljak UP, Bensa T, Tomaš TC, Cirnski K, Stojan J, Rozman D. Novel insights into biological roles of inducible cAMP early repressor ICER. Biochem Biophys Res Commun 2020; 530:396-401. [PMID: 32534736 DOI: 10.1016/j.bbrc.2020.05.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 05/03/2020] [Indexed: 11/16/2022]
Abstract
ICER corresponds to a group of alternatively spliced Inducible cAMP Early Repressors with high similarity, but multiple roles, including in circadian rhythm, and are involved in attenuation of cAMP-dependent gene expression. We present experimental and in silico data revealing biological differences between the isoforms with exon gamma (ICER) or without it (ICERγ). Both isoforms are expressed in the liver and the adrenal glands and can derive from differential splicing. In adrenals the expression is circadian, with maximum at ZT12 and higher amplitude of Icerγ. In the liver, the expression of Icerγ is lower than Icer in the 24 h time frame. Icer mRNA has a delayed early response to forskolin. The longer ICER protein binds to three DNA grooves of the Per1 promoter, while ICERγ only to two, as deduced by molecular modelling. This is in line with gel shift competition assays showing stronger binding of ICER to Per1 promotor. Only Icerγ siRNA provoked an increase of Per1 expression. In conclusion, we show that ICER and ICERγ have distinct biochemical properties in tissue expression, DNA binding, and response to forskolin. Data are in favour of ICERγ as the physiologically important form in hepatic cells where weaker binding of repressor might be preferred in guiding the cAMP-dependent response.
Collapse
Affiliation(s)
- Tadeja Režen
- Centre for Functional Genomics and Bio-Chip, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Slovenia; Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Slovenia
| | - Uršula Prosenc Zmrzljak
- Centre for Functional Genomics and Bio-Chip, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Slovenia; Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Slovenia
| | - Tjaša Bensa
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Slovenia
| | - Tanja Cvitanović Tomaš
- Centre for Functional Genomics and Bio-Chip, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Slovenia; Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Slovenia
| | - Katarina Cirnski
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Slovenia
| | - Jure Stojan
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Slovenia
| | - Damjana Rozman
- Centre for Functional Genomics and Bio-Chip, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Slovenia; Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Slovenia.
| |
Collapse
|
4
|
Qian L, Qi S, Cao F, Zhang J, Li C, Song M, Wang C. Effects of penthiopyrad on the development and behaviour of zebrafish in early-life stages. CHEMOSPHERE 2019; 214:184-194. [PMID: 30265925 DOI: 10.1016/j.chemosphere.2018.09.117] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 09/17/2018] [Accepted: 09/18/2018] [Indexed: 06/08/2023]
Abstract
The agricultural use of succinate dehydrogenase inhibitor (SDHI) fungicides has increased dramatically in the US and Europe. As the SDHI fungicides, boscalid, flutolanil and thifluzamide had been reported to induce a series of toxic effects on zebrafish. However, the toxic effects of penthiopyrad on zebrafish have not been reported yet. This study aimed to assess the acute toxicity of penthiopyrad to zebrafish in early-life stages and investigate behavioural response of larvae and the effects on lipid metabolism and pigmentation under sub-lethal exposure of penthiopyrad. Based on results of the acute toxicity tests of zebrafish embryo and larvae, penthiopyrad had an acute toxicity to early-life stages of zebrafish and induced a series of deformities during development. Based on the results of sub-lethal exposure for 8 days, penthiopyrad resulted in significant decreases in swimming velocity, acceleration speed, distance moved and inactive time of larvae at 0.3, 0.6 and 1.2 mg/L. Penthiopyrad induced the disorders of lipid metabolism via affecting fatty acid synthesis and β-oxidation, in accordance with remarkable changes in the content of triglycerides and cholesterol and the expression of key genes (hmgcrα, pparα1, srebf1, cyp51 and acca1) at 1.2 mg/L. In addition, the disorder of melanin synthesis and distribution was caused by penthiopyrad in larvae in accordance with changes in body colour and related gene expression at 8 dpe.
Collapse
Affiliation(s)
- Le Qian
- College of Sciences, China Agricultural University, Beijing, People's Republic of China
| | - Suzhen Qi
- Risk Assessment Laboratory for Bee Product Quality and Safety of Ministry of Agriculture, Institute of Agricultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100093, People's Republic of China
| | - Fangjie Cao
- College of Sciences, China Agricultural University, Beijing, People's Republic of China
| | - Jie Zhang
- College of Sciences, China Agricultural University, Beijing, People's Republic of China
| | - Changping Li
- Plant Protection Station, Beijing, People's Republic of China
| | - Min Song
- Institute of Agricultural Research, Taian, Shandong, People's Republic of China
| | - Chengju Wang
- College of Sciences, China Agricultural University, Beijing, People's Republic of China.
| |
Collapse
|
5
|
Cytochrome P450 metabolism of the post-lanosterol intermediates explains enigmas of cholesterol synthesis. Sci Rep 2016; 6:28462. [PMID: 27334049 PMCID: PMC4917857 DOI: 10.1038/srep28462] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 06/02/2016] [Indexed: 11/18/2022] Open
Abstract
Cholesterol synthesis is among the oldest metabolic pathways, consisting of the Bloch and Kandutch-Russell branches. Following lanosterol, sterols of both branches are proposed to be dedicated to cholesterol. We challenge this dogma by mathematical modeling and with experimental evidence. It was not possible to explain the sterol profile of testis in cAMP responsive element modulator tau (Crem τ) knockout mice with mathematical models based on textbook pathways of cholesterol synthesis. Our model differs in the inclusion of virtual sterol metabolizing enzymes branching from the pathway. We tested the hypothesis that enzymes from the cytochrome P450 (CYP) superfamily can participate in the catalysis of non-classical reactions. We show that CYP enzymes can metabolize multiple sterols in vitro, establishing novel branching points of cholesterol synthesis. In conclusion, sterols of cholesterol synthesis can be oxidized further to metabolites not dedicated to production of cholesterol. Additionally, CYP7A1, CYP11A1, CYP27A1, and CYP46A1 are parts of a broader cholesterol synthesis network.
Collapse
|
6
|
Identification of liver CYP51 as a gene responsive to circulating cholesterol in a hamster model. J Nutr Sci 2016; 5:e16. [PMID: 27110359 PMCID: PMC4831128 DOI: 10.1017/jns.2016.3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 01/05/2016] [Indexed: 12/17/2022] Open
Abstract
Hypercholesterolaemia is a risk factor for CVD, which is a leading cause of death in industrialised societies. The biosynthetic pathways for cholesterol metabolism are well understood; however, the regulation of circulating cholesterol by diet is still not fully elucidated. The present study aimed to gain more comprehensive understanding of the relationship between circulating cholesterol levels and molecular effects in target tissues using the hamster model. Male golden Syrian hamsters were fed with chow or diets containing 36 % energy from fat with or without 1 % cholesteyramine (CA) as a modulator of circulating cholesterol levels for 35 d. It was revealed that the expression of lanosterol 14α-demethylase (CYP51) instead of 3-hydroxy-3-methyl-glutaryl (HMG)-CoA reductase mRNA expression was responsive to circulating cholesterol in hamsters fed hypercholesterolaemic diets. The high-fat diet increased circulating cholesterol and down-regulated CYP51, but not HMG-CoA reductase. The CA diet decreased cholesterol and increased CYP51 expression, but HMG-CoA reductase expression was not affected. The high-fat diet and CA diet altered the expression level of cholesterol, bile acids and lipid metabolism-associated genes (LDL receptor, cholesterol 7α-hydroxylase (CYP7A1), liver X receptor (LXR) α, and ATP-binding cassette subfamily G member 5/8 (ABCG5/8)) in the liver, which were significantly correlated with circulating cholesterol levels. Correlation analysis also showed that circulating cholesterol levels were regulated by LXR/retinoid X receptor and PPAR pathways in the liver. Using the hamster model, the present study provided additional molecular insights into the influence of circulating cholesterol on hepatic cholesterol metabolism pathways during hypercholesterolaemia.
Collapse
Key Words
- ABCG5/, ATP-binding cassette subfamily G member 5/8
- CA, cholestyramine
- CYP51
- CYP51, lanosterol 14α-demethylase
- CYP7A1, cholesterol 7α-hydroxylase
- Circulating cholesterol
- HF + CA, high-fat + cholestyramine
- HF, high-fat
- HMG, 3-hydroxy-3-methyl-glutaryl
- Hamsters
- Hypercholesterolaemia
- IPA, Ingenuity Pathway Analysis
- LXRα, liver X receptor α
- RXR, retinoid X receptor
- SREBP, sterol regulatory element-binding protein
Collapse
|
7
|
Effect of itraconazole on mouse mesencephalic neurons. Int J Dev Neurosci 2015; 44:75-83. [DOI: 10.1016/j.ijdevneu.2015.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 05/13/2015] [Accepted: 06/06/2015] [Indexed: 01/14/2023] Open
|
8
|
Lorbek G, Perše M, Jeruc J, Juvan P, Gutierrez-Mariscal FM, Lewinska M, Gebhardt R, Keber R, Horvat S, Björkhem I, Rozman D. Lessons from hepatocyte-specific Cyp51 knockout mice: impaired cholesterol synthesis leads to oval cell-driven liver injury. Sci Rep 2015; 5:8777. [PMID: 25739789 PMCID: PMC4350092 DOI: 10.1038/srep08777] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 02/02/2015] [Indexed: 12/22/2022] Open
Abstract
We demonstrate unequivocally that defective cholesterol synthesis is an independent determinant of liver inflammation and fibrosis. We prepared a mouse hepatocyte-specific knockout (LKO) of lanosterol 14α-demethylase (CYP51) from the part of cholesterol synthesis that is already committed to cholesterol. LKO mice developed hepatomegaly with oval cell proliferation, fibrosis and inflammation, but without steatosis. The key trigger was reduced cholesterol esters that provoked cell cycle arrest, senescence-associated secretory phenotype and ultimately the oval cell response, while elevated CYP51 substrates promoted the integrated stress response. In spite of the oval cell-driven fibrosis being histologically similar in both sexes, data indicates a female-biased down-regulation of primary metabolism pathways and a stronger immune response in males. Liver injury was ameliorated by dietary fats predominantly in females, whereas dietary cholesterol rectified fibrosis in both sexes. Our data place defective cholesterol synthesis as a focus of sex-dependent liver pathologies.
Collapse
Affiliation(s)
- Gregor Lorbek
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Martina Perše
- Medical Experimental Centre, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Jera Jeruc
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Peter Juvan
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Francisco M Gutierrez-Mariscal
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Monika Lewinska
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Rolf Gebhardt
- Institute of Biochemistry, Faculty of Medicine, University of Leipzig, Leipzig, Germany
| | - Rok Keber
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Simon Horvat
- 1] Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia [2] National Institute of Chemistry, Ljubljana, Slovenia
| | - Ingemar Björkhem
- Department of Laboratory Medicine, Division of Clinical Chemistry, Karolinska Institute, Karolinska University Hospital, Huddinge, Sweden
| | - Damjana Rozman
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
9
|
Prediction of LDL cholesterol response to statin using transcriptomic and genetic variation. Genome Biol 2014; 15:460. [PMID: 25316374 PMCID: PMC4180544 DOI: 10.1186/s13059-014-0460-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 09/03/2014] [Indexed: 01/01/2023] Open
Abstract
Background Statins are widely prescribed for lowering LDL-cholesterol (LDLC) levels and risk of cardiovascular disease. There is, however, substantial inter-individual variation in the magnitude of statin-induced LDLC reduction. To date, analysis of individual DNA sequence variants has explained only a small proportion of this variability. The present study was aimed at assessing whether transcriptomic analyses could be used to identify additional genetic contributions to inter-individual differences in statin efficacy. Results Using expression array data from immortalized lymphoblastoid cell lines derived from 372 participants of the Cholesterol and Pharmacogenetics clinical trial, we identify 100 signature genes differentiating high versus low statin responders. A radial-basis support vector machine prediction model of these signature genes explains 12.3% of the variance in statin-mediated LDLC change. Addition of SNPs either associated with expression levels of the signature genes (eQTLs) or previously reported to be associated with statin response in genome-wide association studies results in a combined model that predicts 15.0% of the variance. Notably, a model of the signature gene associated eQTLs alone explains up to 17.2% of the variance in the tails of a separate subset of the Cholesterol and Pharmacogenetics population. Furthermore, using a support vector machine classification model, we classify the most extreme 15% of high and low responders with high accuracy. Conclusions These results demonstrate that transcriptomic information can explain a substantial proportion of the variance in LDLC response to statin treatment, and suggest that this may provide a framework for identifying novel pathways that influence cholesterol metabolism. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0460-9) contains supplementary material, which is available to authorized users.
Collapse
|
10
|
Wang W, Mutka AL, Zmrzljak UP, Rozman D, Tanila H, Gylling H, Remes AM, Huttunen HJ, Ikonen E. Amyloid precursor protein α- and β-cleaved ectodomains exert opposing control of cholesterol homeostasis via SREBP2. FASEB J 2013; 28:849-60. [PMID: 24249638 DOI: 10.1096/fj.13-239301] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Amyloid precursor protein (APP) is ubiquitously expressed. Studies in neuronal cells have implicated APP or its fragments as negative regulators of cholesterol metabolism. In the current study, APP acted, via its α-cleavage, as a positive regulator of sterol regulatory element-binding protein-2 (SREBP2) signaling in human astrocytic cells (U251MG), hepatic cells (HepG2), and primary fibroblasts, leading to an approximate 30% increase in SRE-dependent gene expression and, consequently, enhanced cholesterol biosynthesis and LDL receptor levels. This effect was mediated via the secretory ectodomain APPsα. The β-cleaved ectodomain, in turn, repressed SRE-dependent gene expression by up to ∼ 30%. This resulted in decreased cholesterol synthesis and LDL receptor content, establishing a physiological feedback loop in cholesterol-loaded cells, where APP undergoes preferential β-cleavage. Patients with familial Alzheimer's disease had decreased circulating lathosterol, reflecting hepatic cholesterol synthesis, and their fibroblasts had reduced LDL receptor content, which was alleviated by decreasing β-cleavage. These results show that APP regulates cholesterol metabolism in cells relevant for whole-body cholesterol balance and reveal that APP α- and β-cleavages produce opposing paracrine regulators of SREBP2 signaling.
Collapse
Affiliation(s)
- Wei Wang
- 2Institute of Biomedicine, Haartmaninkatu 8, FI-00014 University of Helsinki, Finland.
| | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Itraconazole inhibits HMEC-1 angiogenesis. Biomed Pharmacother 2012; 66:312-7. [DOI: 10.1016/j.biopha.2011.11.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 11/21/2011] [Indexed: 12/12/2022] Open
|
12
|
Lorbek G, Lewinska M, Rozman D. Cytochrome P450s in the synthesis of cholesterol and bile acids--from mouse models to human diseases. FEBS J 2011; 279:1516-33. [PMID: 22111624 DOI: 10.1111/j.1742-4658.2011.08432.x] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The present review describes the transgenic mouse models that have been designed to evaluate the functions of the cytochrome P450s involved in cholesterol and bile acid synthesis, as well as their link with disease. The knockout of cholesterogenic Cyp51 is embrionally lethal, with symptoms of Antley-Bixler syndrome occurring in mice, whereas the evidence for this association is conflicting in humans. Disruption of Cyp7a1 from classic bile acid synthesis in mice leads to either increased postnatal death or a milder phenotype with elevated serum cholesterol. The latter is similar to the case in humans, where CYP7A1 mutations associate with high plasma low-density lipoprotein and hepatic cholesterol content, as well as deficient bile acid excretion. Disruption of Cyp8b1 from an alternative bile acid pathway results in the absence of cholic acid and a reduced absorption of dietary lipids; however, the human CYP8B1 polymorphism fails to explain differences in bile acid composition. Unexpectedly, apparently normal Cyp27a1(-/-) mice still synthesize bile acids that originate from the compensatory pathway. In humans, CYP27A1 mutations cause cerebrotendinous xanthomatosis, suggesting that only mice can compensate for the loss of alternative bile acid synthesis. In line with this, Cyp7b1 knockouts are also apparently normal, whereas human CYP7B1 mutations lead to a congenital bile acid synthesis defect in children or spastic paraplegia in adults. Mouse knockouts of the brain-specific Cyp46a1 have reduced brain cholesterol excretion, whereas, in humans, CYP46A1 polymorphisms associate with cognitive impairment. At present, cytochrome P450 family 39 is poorly characterized. Despite important physiological differences between humans and mice, mouse models prove to be an invaluable tool for understanding the multifactorial facets of cholesterol and bile acid-related disorders.
Collapse
Affiliation(s)
- Gregor Lorbek
- Center for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | | | | |
Collapse
|
13
|
Košir R, Zmrzljak UP, Bele T, Acimovic J, Perse M, Majdic G, Prehn C, Adamski J, Rozman D. Circadian expression of steroidogenic cytochromes P450 in the mouse adrenal gland - involvement of cAMP-responsive element modulator in epigenetic regulation of Cyp17a1. FEBS J 2011; 279:1584-93. [DOI: 10.1111/j.1742-4658.2011.08317.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
14
|
Horvat S, Mcwhir J, Rozman D. Defects in cholesterol synthesis genes in mouse and in humans: lessons for drug development and safer treatments. Drug Metab Rev 2011; 43:69-90. [DOI: 10.3109/03602532.2010.540580] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
15
|
Acimovic J, Korosec T, Seliskar M, Bjorkhem I, Monostory K, Szabo P, Pascussi JM, Belic A, Urleb U, Kocjan D, Rozman D. Inhibition of human sterol Δ7-reductase and other postlanosterol enzymes by LK-980, a novel inhibitor of cholesterol synthesis. Drug Metab Dispos 2010; 39:39-46. [PMID: 20952551 DOI: 10.1124/dmd.110.035840] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Novel potential inhibitors of the postsqualene portion of cholesterol synthesis were screened in HepG2 cells. 2-(4-Phenethylpiperazin-1-yl)-1-(pyridine-3-yl)ethanol (LK-980) was identified as a prospective compound and was characterized further in cultures of human primary hepatocytes from seven donors. In vitro kinetic measurements show that the half-life of LK-980 is at least 4.3 h. LK-980 does not induce CYP3A4 mRNA nor enzyme activity. Target prediction was performed by gas chromatography-mass spectrometry, allowing simultaneous separation and quantification of nine late cholesterol intermediates. Experiments indicated that human sterol Δ(7)-reductase (DHCR7) is the major target of LK-980 (34-fold increase of 7-dehydrocholesterol), whereas human sterol Δ(14)-reductase (DHCR14), human sterol Δ(24)-reductase (DHCR24), and human sterol C5-desaturase (SC5DL) represent minor targets. In the absence of purified enzymes, we used the mathematical model of cholesterol synthesis to evaluate whether indeed more than a single enzyme is inhibited. In silico inhibition of only DHCR7 modifies the flux of cholesterol intermediates, resulting in a sterol profile that does not support experimental data. Partial inhibition of the DHCR14, DHCR24, and SC5DL steps, in addition to DHCR7, supports the experimental sterol profile. In conclusion, we provide experimental and computational evidence that LK-980, a novel inhibitor from the late portion of cholesterol synthesis, inhibits primarily DHCR7 and to a lesser extent three other enzymes from this pathway.
Collapse
Affiliation(s)
- Jure Acimovic
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Interplay between cholesterol and drug metabolism. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:146-60. [PMID: 20570756 DOI: 10.1016/j.bbapap.2010.05.014] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 05/17/2010] [Accepted: 05/24/2010] [Indexed: 12/14/2022]
Abstract
Cholesterol biosynthetic and metabolic pathways contain several branching points towards physiologically active molecules, such as coenzyme Q, vitamin D, glucocorticoid and steroid hormones, oxysterols, or bile acids. Sophisticated regulatory mechanisms are involved in maintenance of the homeostasis of not only cholesterol but also other cholesterogenic molecules. In addition to endogenous cues, cholesterol homeostasis needs to accommodate also to exogenous cues that are imported into the body, such as chemicals and medications. Steroid and nuclear receptors together with sterol regulatory element-binding protein (SREBP) mediate the fine tuning of biosynthetic and metabolic routes as well as transports of cholesterol and its derivatives. Similarly, drug/xenobiotic metabolism is the subject to the feedback regulation of cytochrome P450 enzymes and transporters. The regulatory mechanisms that maintain the homeostasis of cholesterogenic molecules and are involved in drug metabolism share similarities. Cholesterol and cholesterogenic compounds (bile acids, glucocorticoids, vitamin D, etc.) regulate the xenosensor signaling in drug-mediated induction of the major drug-metabolizing cytochrome P450 enzymes. The key cellular receptors, pregnane X receptor (PXR), constitutive androstane receptor (CAR), vitamin D receptor (VDR), and glucocorticoid receptor (GR) provide a functional cross-talk between the pathways maintaining cholesterol homeostasis and controlling the expression of drug-metabolizing enzymes. These receptors serve as metabolic sensors, resulting in a coordinate regulation of cholesterogenic compounds metabolism and of the defense against xenobiotic and endobiotic toxicity. Herein we present a comprehensive review of functional interactions between cholesterol homeostasis and drug metabolism involving the main nuclear and steroid receptors.
Collapse
|
17
|
Yang AJ, Li CC, Lu CY, Liu KL, Tsai CW, Lii CK, Chen HW. Activation of the cAMP/CREB/inducible cAMP early repressor pathway suppresses andrographolide-induced gene expression of the pi class of glutathione S-transferase in rat primary hepatocytes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2010; 58:1993-2000. [PMID: 20063885 DOI: 10.1021/jf902221j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Andrographolide (Ap) is a bioactive compound in Andrographis paniculata that is a Chinese herb. The pi class of glutathione S-transferase (GSTP) is one kind of phase II detoxification enzyme. Here we show that induction of GSTP protein and mRNA expression in rat primary hepatocytes by Ap was inhibited by forskolin and a variety of cAMP analogues. The inhibitory effect of the cAMP analogues was partially blocked by pretreatment with H89. In the presence of Ap, forskolin, or both, the expression of phospho-cAMP response element-binding protein (CREB) was increased. Ap alone had no effect on inducible cAMP early repressor (ICER) mRNA expression; however, Ap played a potentiating role in forskolin-induced ICER mRNA expression. An EMSA and immunoprecipitation assay showed that ICER binding to cAMP-response element (CRE) was increased in cells cotreated with Ap and forskolin for 3 and 8 h. Taken together, these results suggest that ICER is likely to be involved in the suppression of Ap-induced GSTP expression caused by the increase of cAMP in rat primary hepatocytes.
Collapse
Affiliation(s)
- Ai-Jen Yang
- Department of Nutrition, Chung Shan Medical University, Taichung, Taiwan
| | | | | | | | | | | | | |
Collapse
|
18
|
Kang JS, Yum YN, Kim JH, Park SN. Assessment of Biomarkers in Acetaminophen-Induced Hepatic Toxicity by siRNA. Biomol Ther (Seoul) 2009. [DOI: 10.4062/biomolther.2009.17.4.438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
|
19
|
Acimovic J, Fink M, Pompon D, Bjorkhem I, Hirayama J, Sassone-Corsi P, Golicnik M, Rozman D. CREM modulates the circadian expression of CYP51, HMGCR and cholesterogenesis in the liver. Biochem Biophys Res Commun 2008; 376:206-10. [DOI: 10.1016/j.bbrc.2008.08.126] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2008] [Accepted: 08/27/2008] [Indexed: 01/04/2023]
|
20
|
Ranheim T, Mattingsdal M, Lindvall JM, Holla OL, Berge KE, Kulseth MA, Leren TP. Genome-wide expression analysis of cells expressing gain of function mutant D374Y-PCSK9. J Cell Physiol 2008; 217:459-67. [PMID: 18570182 DOI: 10.1002/jcp.21519] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Proprotein convertase subtilisin/kexin type 9 (PCSK9) is a key regulator of serum cholesterol. The possibility that PCSK9 also functions in other pathways needs to be addressed. We have transfected HepG2 cells with mutant D374Y-PCSK9 or control vector. Gene expression signatures were determined using the Affymetrix GeneChip technology, and the expression pattern of selected genes was confirmed by quantitative real-time polymerase chain reaction (qRT-PCR). Data was normalized and analyzed using a model-based background adjustment for oligonucleotide expression arrays, then filtered based upon expression within treatments group, and subjected to moderated t-statistics. Five hundred twenty transcripts had altered expression levels between D374Y-PCSK9 and control vector. Among the 520 probes on our top list, 312 were found to have an assigned Gene Ontology (GO) term, and 96 were found in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Genome-wide expression profiling revealed that "steroid biosynthesis," "sterol metabolism," and "cholesterol biosynthsis" were affected by D374Y-PCSK9. Also, the GO biological process terms "response to stresss," "response to virus," "response to unfolded protein," and "immune response" were influenced by D374Y-PCSK9. Our results suggest that D374Y-PCSK9 results in up-regulation of genes involved in sterol biosynthesis and down-regulation of stress-response genes and specific inflammation pathways.
Collapse
Affiliation(s)
- Trine Ranheim
- Department of Medical Genetics, Rikshospitalet University Hospital, Oslo, Norway.
| | | | | | | | | | | | | |
Collapse
|
21
|
Korošec T, Ačimovič J, Seliškar M, Kocjan D, Tacer KF, Rozman D, Urleb U. Novel cholesterol biosynthesis inhibitors targeting human lanosterol 14α-demethylase (CYP51). Bioorg Med Chem 2008; 16:209-21. [DOI: 10.1016/j.bmc.2007.10.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2007] [Revised: 09/15/2007] [Accepted: 10/01/2007] [Indexed: 11/29/2022]
|
22
|
Abstract
By participating in pathways of cholesterol biosynthesis and elimination, different cytochrome P450 (P450 or CYP) enzymes play an important role in maintenance of cholesterol homeostasis. CYP51 is involved in cholesterol biosynthesis, whereas CYP 7A1, 27A1, 46A1, 7B1, 39A1, and 8B1 are the key enzymes in cholesterol catabolism to bile acids, the major route of cholesterol elimination in mammals. Cholesterol transformations to steroid hormones are also initiated by the P450 enzyme CYP11A1. Finally, one of the major drug-metabolizing P450s CYP3A4 seems to contribute to bile acid biosynthesis as well. The 9 P450s will be the focus of this review and assessed as drug targets for cholesterol lowering.
Collapse
Affiliation(s)
- Irina A Pikuleva
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-1031, USA.
| |
Collapse
|
23
|
Hoffmann JL, Torontali SP, Thomason RG, Lee DM, Brill JL, Price BB, Carr GJ, Versteeg DJ. Hepatic gene expression profiling using Genechips in zebrafish exposed to 17alpha-ethynylestradiol. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2006; 79:233-46. [PMID: 16872691 DOI: 10.1016/j.aquatox.2006.06.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2006] [Revised: 06/07/2006] [Accepted: 06/09/2006] [Indexed: 05/11/2023]
Abstract
Genomic, proteomic, and metabolomic technologies continue to receive increasing interest from environmental toxicologists. This interest is due to the great potential of these technologies to identify detailed modes of action and to provide assistance in the evaluation of a contaminant's risk to aquatic organisms. Our experimental model is the zebrafish (Danio rerio) exposed to reference endocrine disrupting compounds in order to investigate compound-induced changes in gene transcript profiles. Adult, female zebrafish were exposed to 0, 15, 40, and 100ng/L of 17alpha-ethynylestradiol (EE2) and concentration and time-dependent changes in hepatic gene expression were examined using Affymetrix GeneChip Zebrafish Genome Microarrays. At 24, 48, and 168h, fish were sacrificed and liver mRNA was extracted for gene expression analysis (24 and 168h only). In an effort to link gene expression changes to effects on higher levels of biological organization, body and ovary weights were measured and blood was collected for measurement of plasma steroid hormones (17beta-estradiol (E2), testosterone (T)) and vitellogenin (VTG) using ELISA. EE2 exposure significantly affected gene expression, GSI, E2, T, and VTG. We observed 1622 genes that were significantly affected (p< or =0.001) in a concentration-dependent manner by EE2 exposure at either 24 or 168h. Gene ontology (GO) analysis revealed that EE2 exposure affected genes involved in hormone metabolism, vitamin A metabolism, steroid binding, sterol metabolism, and cell growth. Plasma VTG was significantly increased at 24, 48, and 168h (p< or =0.05) at 40 and 100ng/L and at 15ng/L at 168h. E2 and T were significantly reduced following EE2 exposure at 48 and 168h. GSI was decreased in a concentration-dependent manner at 168h. In this study, we identified genes involved in a variety of biological processes that have the potential to be used as markers of exposure to estrogenic substances. Future work will evaluate the use of these genes in zebrafish exposed to weak estrogens to determine if these genes are indicative of exposure to estrogens with varying potencies.
Collapse
Affiliation(s)
- J L Hoffmann
- Miami Valley Innovation Center, The Procter and Gamble Company, P.O. Box 538707, Cincinnati, OH 45253-8707, USA
| | | | | | | | | | | | | | | |
Collapse
|