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Smetanina MA, Korolenya VA, Kel AE, Sevostyanova KS, Gavrilov KA, Shevela AI, Filipenko ML. Epigenome-Wide Changes in the Cell Layers of the Vein Wall When Exposing the Venous Endothelium to Oscillatory Shear Stress. EPIGENOMES 2023; 7:epigenomes7010008. [PMID: 36975604 PMCID: PMC10048778 DOI: 10.3390/epigenomes7010008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 03/29/2023] Open
Abstract
Epigenomic changes in the venous cells exerted by oscillatory shear stress towards the endothelium may result in consolidation of gene expression alterations upon vein wall remodeling during varicose transformation. We aimed to reveal such epigenome-wide methylation changes. Primary culture cells were obtained from non-varicose vein segments left after surgery of 3 patients by growing the cells in selective media after magnetic immunosorting. Endothelial cells were either exposed to oscillatory shear stress or left at the static condition. Then, other cell types were treated with preconditioned media from the adjacent layer's cells. DNA isolated from the harvested cells was subjected to epigenome-wide study using Illumina microarrays followed by data analysis with GenomeStudio (Illumina), Excel (Microsoft), and Genome Enhancer (geneXplain) software packages. Differential (hypo-/hyper-) methylation was revealed for each cell layer's DNA. The most targetable master regulators controlling the activity of certain transcription factors regulating the genes near the differentially methylated sites appeared to be the following: (1) HGS, PDGFB, and AR for endothelial cells; (2) HGS, CDH2, SPRY2, SMAD2, ZFYVE9, and P2RY1 for smooth muscle cells; and (3) WWOX, F8, IGF2R, NFKB1, RELA, SOCS1, and FXN for fibroblasts. Some of the identified master regulators may serve as promising druggable targets for treating varicose veins in the future.
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Affiliation(s)
- Mariya A Smetanina
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine (ICBFM) SB RAS, Novosibirsk 630090, Russia
- Department of Fundamental Medicine, V. Zelman Institute for Medicine and Psychology, Novosibirsk State University (NSU), Novosibirsk 630090, Russia
| | - Valeria A Korolenya
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine (ICBFM) SB RAS, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University (NSU), Novosibirsk 630090, Russia
| | - Alexander E Kel
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine (ICBFM) SB RAS, Novosibirsk 630090, Russia
- Department of Research & Development, GeneXplain GmbH, D-38302 Wolfenbüttel, Germany
| | - Ksenia S Sevostyanova
- Center of New Medical Technologies, Institute of Chemical Biology and Fundamental Medicine (ICBFM) SB RAS, Novosibirsk 630090, Russia
- Laboratory of Invasive Medical Technologies, Institute of Chemical Biology and Fundamental Medicine (ICBFM) SB RAS, Novosibirsk 630090, Russia
- Department of Surgical Diseases, V. Zelman Institute for Medicine and Psychology, Novosibirsk State University (NSU), Novosibirsk 630090, Russia
| | - Konstantin A Gavrilov
- Center of New Medical Technologies, Institute of Chemical Biology and Fundamental Medicine (ICBFM) SB RAS, Novosibirsk 630090, Russia
- Department of Surgical Diseases, V. Zelman Institute for Medicine and Psychology, Novosibirsk State University (NSU), Novosibirsk 630090, Russia
| | - Andrey I Shevela
- Center of New Medical Technologies, Institute of Chemical Biology and Fundamental Medicine (ICBFM) SB RAS, Novosibirsk 630090, Russia
- Laboratory of Invasive Medical Technologies, Institute of Chemical Biology and Fundamental Medicine (ICBFM) SB RAS, Novosibirsk 630090, Russia
- Department of Surgical Diseases, V. Zelman Institute for Medicine and Psychology, Novosibirsk State University (NSU), Novosibirsk 630090, Russia
| | - Maxim L Filipenko
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine (ICBFM) SB RAS, Novosibirsk 630090, Russia
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Diclofenac Disrupts the Circadian Clock and through Complex Cross-Talks Aggravates Immune-Mediated Liver Injury-A Repeated Dose Study in Minipigs for 28 Days. Int J Mol Sci 2023; 24:ijms24021445. [PMID: 36674967 PMCID: PMC9863319 DOI: 10.3390/ijms24021445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/28/2022] [Accepted: 12/30/2022] [Indexed: 01/14/2023] Open
Abstract
Diclofenac effectively reduces pain and inflammation; however, its use is associated with hepato- and nephrotoxicity. To delineate mechanisms of injury, we investigated a clinically relevant (3 mg/kg) and high-dose (15 mg/kg) in minipigs for 4 weeks. Initially, serum biochemistries and blood-smears indicated an inflammatory response but returned to normal after 4 weeks of treatment. Notwithstanding, histopathology revealed drug-induced hepatitis, marked glycogen depletion, necrosis and steatosis. Strikingly, the genomic study revealed diclofenac to desynchronize the liver clock with manifest inductions of its components CLOCK, NPAS2 and BMAL1. The > 4-fold induced CRY1 expression underscored an activated core-loop, and the dose dependent > 60% reduction in PER2mRNA repressed the negative feedback loop; however, it exacerbated hepatotoxicity. Bioinformatics enabled the construction of gene-regulatory networks, and we linked the disruption of the liver-clock to impaired glycogenesis, lipid metabolism and the control of immune responses, as shown by the 3-, 6- and 8-fold induced expression of pro-inflammatory CXCL2, lysozyme and ß-defensin. Additionally, diclofenac treatment caused adrenocortical hypertrophy and thymic atrophy, and we evidenced induced glucocorticoid receptor (GR) activity by immunohistochemistry. Given that REV-ERB connects the circadian clock with hepatic GR, its > 80% repression alleviated immune responses as manifested by repressed expressions of CXCL9(90%), CCL8(60%) and RSAD2(70%). Together, we propose a circuitry, whereby diclofenac desynchronizes the liver clock in the control of the hepatic metabolism and immune response.
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Wang B, Ran Z, Liu M, Ou Y. Prognostic Significance of Potential Immune Checkpoint Member HHLA2 in Human Tumors: A Comprehensive Analysis. Front Immunol 2019; 10:1573. [PMID: 31379814 PMCID: PMC6644528 DOI: 10.3389/fimmu.2019.01573] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/24/2019] [Indexed: 11/30/2022] Open
Abstract
Immunological checkpoint inhibitors have been immensely successfully applied in the treatment of cancer, however, a portion of tumor patients can't benefit from checkpoint therapy. The low PD-1/CTLA-4 positive rate and involvement of multiple immunosuppressive pathways are thought to be one of the reasons for treatment failure in non-responding patients. A new immune checkpoint molecule, HHLA2, which was widely expressed in PD-1 negative human tumors, may be a promising target for the improvement of recent immune therapy. Yet, the prognostic value and transcriptional regulatory mechanisms of HHLA2 remains unclear. In this study, we aimed to evaluate the prognostic value and transcriptional regulation mechanism of HHLA2 according to clinical and experimental data from multiple databases, including cBioPortal, TCGA, Cistrome, TIMER, Oncomine, Kaplan-Meier, GeneXplain. It was found that the expression of HHLA2 was significantly elevated in renal tumors, and significantly decreased in colorectal tumors. Pan-cancer survival analysis indicates that HHLA2 was an independent prognostic factor in 9/20 of human cancers. Especially in renal clear cell carcinoma (P = 3.0E-7). Through plotting survival curve in Kaplan-Meier Plotter, it was found that hypomethylation of HHLA2 DNA was a favorable prognostic factor for KIRC patients. Yet, the copy number variant of HHLA2 was not significantly correlated with the overall survival of KIRC patients. Finally, by analyzing the motif of HHLA2 co-expression genes, we identified 15 transcription factors that may be involved in the regulation of the HHLA2 co-expression network. Among these transcription factors, BATF in B lymphocyte and SMAD in monocyte were confirmed to be able to directly bind to HHLA2 DNA according to chip-seq experimental data from Cistrome database.
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Affiliation(s)
- Ben Wang
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhujie Ran
- School of Public Health and Community Medicine, Chongqing Medical University, Chongqing, China
| | - Mengmeng Liu
- Graduated School of Anhui University of Traditional Chinese Medicine, Hefei, China
| | - Yunsheng Ou
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Boyarskikh U, Pintus S, Mandrik N, Stelmashenko D, Kiselev I, Evshin I, Sharipov R, Stegmaier P, Kolpakov F, Filipenko M, Kel A. Computational master-regulator search reveals mTOR and PI3K pathways responsible for low sensitivity of NCI-H292 and A427 lung cancer cell lines to cytotoxic action of p53 activator Nutlin-3. BMC Med Genomics 2018; 11:12. [PMID: 29504919 PMCID: PMC5836833 DOI: 10.1186/s12920-018-0330-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Small molecule Nutlin-3 reactivates p53 in cancer cells by interacting with the complex between p53 and its repressor Mdm-2 and causing an increase in cancer cell apoptosis. Therefore, Nutlin-3 has potent anticancer properties. Clinical and experimental studies of Nutlin-3 showed that some cancer cells may lose sensitivity to this compound. Here we analyze possible mechanisms for insensitivity of cancer cells to Nutlin-3. METHODS We applied upstream analysis approach implemented in geneXplain platform ( genexplain.com ) using TRANSFAC® database of transcription factors and their binding sites in genome and using TRANSPATH® database of signal transduction network with associated software such as Match™ and Composite Module Analyst (CMA). RESULTS Using genome-wide gene expression profiling we compared several lung cancer cell lines and showed that expression programs executed in Nutlin-3 insensitive cell lines significantly differ from that of Nutlin-3 sensitive cell lines. Using artificial intelligence approach embed in CMA software, we identified a set of transcription factors cooperatively binding to the promoters of genes up-regulated in the Nutlin-3 insensitive cell lines. Graph analysis of signal transduction network upstream of these transcription factors allowed us to identify potential master-regulators responsible for maintaining such low sensitivity to Nutlin-3 with the most promising candidate mTOR, which acts in the context of activated PI3K pathway. These finding were validated experimentally using an array of chemical inhibitors. CONCLUSIONS We showed that the Nutlin-3 insensitive cell lines are actually highly sensitive to the dual PI3K/mTOR inhibitor NVP-BEZ235, while no responding to either PI3K -specific LY294002 nor Bcl-XL specific 2,3-DCPE compounds.
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Affiliation(s)
- Ulyana Boyarskikh
- Institute of Chemical Biology and Fundamental Medicine, SBRAN, Novosibirsk, Russia
| | | | | | | | | | | | | | | | | | - Maxim Filipenko
- Institute of Chemical Biology and Fundamental Medicine, SBRAN, Novosibirsk, Russia
| | - Alexander Kel
- Institute of Chemical Biology and Fundamental Medicine, SBRAN, Novosibirsk, Russia.
- Biosoft.ru, Ltd, Novosibirsk, Russia.
- geneXplain GmbH, D-38302, Wolfenbüttel, Germany.
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Orekhov AN, Oishi Y, Nikiforov NG, Zhelankin AV, Dubrovsky L, Sobenin IA, Kel A, Stelmashenko D, Makeev VJ, Foxx K, Jin X, Kruth HS, Bukrinsky M. Modified LDL Particles Activate Inflammatory Pathways in Monocyte-derived Macrophages: Transcriptome Analysis. Curr Pharm Des 2018; 24:3143-3151. [PMID: 30205792 PMCID: PMC6302360 DOI: 10.2174/1381612824666180911120039] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 08/28/2018] [Accepted: 09/04/2018] [Indexed: 12/27/2022]
Abstract
BACKGROUND A hallmark of atherosclerosis is its complex pathogenesis, which is dependent on altered cholesterol metabolism and inflammation. Both arms of pathogenesis involve myeloid cells. Monocytes migrating into the arterial walls interact with modified low-density lipoprotein (LDL) particles, accumulate cholesterol and convert into foam cells, which promote plaque formation and also contribute to inflammation by producing proinflammatory cytokines. A number of studies characterized transcriptomics of macrophages following interaction with modified LDL, and revealed alteration of the expression of genes responsible for inflammatory response and cholesterol metabolism. However, it is still unclear how these two processes are related to each other to contribute to atherosclerotic lesion formation. METHODS We attempted to identify the main mater regulator genes in macrophages treated with atherogenic modified LDL using a bioinformatics approach. RESULTS We found that most of the identified genes were involved in inflammation, and none of them was implicated in cholesterol metabolism. Among the key identified genes were interleukin (IL)-7, IL-7 receptor, IL- 15 and CXCL8. CONCLUSION Our results indicate that activation of the inflammatory pathway is the primary response of the immune cells to modified LDL, while the lipid metabolism genes may be a secondary response triggered by inflammatory signalling.
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Affiliation(s)
- Alexander N. Orekhov
- Address correspondence to this author at the Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Russian Academy of Medical Sciences, Moscow 125315, Russia; Tel: +7 903 169 08 66;, E-mail:
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6
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Lee EH, Oh JH, Selvaraj S, Park SM, Choi MS, Spanel R, Yoon S, Borlak J. Immunogenomics reveal molecular circuits of diclofenac induced liver injury in mice. Oncotarget 2017; 7:14983-5017. [PMID: 26934552 PMCID: PMC4924767 DOI: 10.18632/oncotarget.7698] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 11/25/2015] [Indexed: 12/12/2022] Open
Abstract
Diclofenac is a non-steroidal anti-inflammatory drug and its use can be associated with severe adverse reactions, notably myocardial infarction, stroke and drug-induced liver injury (DILI). In pursue of immune-mediated DILI mechanisms an immunogenomic study was carried out. Diclofenac treatment of mice at 30 mg/kg for 3 days caused significant serum ALT and AST elevations, hepatomegaly and degenerative changes including hepatic glycogen depletion, hydropic swelling, cholesterolosis and eosinophilic hepatocytes with one animal presenting subsegmental infarction due to portal vein thrombosis. Furthermore, portal/periportal induction of the rate limiting enzyme in ammonia detoxification, i.e. carbamoyl phosphate synthetase 1 was observed. The performed microarray studies informed on > 600 differential expressed genes of which 35, 37 and 50 coded for inflammation, 51, 44 and 61 for immune and 116, 129 and 169 for stress response, respectively after single and repeated dosing for 3 and 14 days. Bioinformatic analysis defined molecular circuits of hepatic inflammation with the growth hormone (Ghr)− and leptin receptor, the protein-tyrosine-phosphatase, selectin and the suppressor-of-cytokine-signaling (Socs) to function as key nodes in gene regulatory networks. Western blotting confirmed induction of fibronectin and M-CSF to hallmark tissue repair and differentiation of monocytes and macrophages. Transcript expression of the macrophage receptor with collagenous structure increased > 7-fold and immunohistochemistry of CD68 evidenced activation of tissue-resident macrophages. Importantly, diclofenac treatment prompted strong expression of phosphorylated Stat3 amongst individual animals and the associated 8- and 4-fold Soc3 and Il-6 induction reinforced Ghr degradation as evidenced by immunoblotting. Moreover, immunohistochemistry confirmed regulation of master regulatory proteins of diclofenac treated mice to suggest complex pro-and anti-inflammatory reactions in immune-mediated hepatic injury. The findings encourage translational research.
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Affiliation(s)
- Eun-Hee Lee
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon, 305-343, Republic of Korea
| | - Jung-Hwa Oh
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon, 305-343, Republic of Korea.,Department of Human and Environmental Toxicology, School of Engineering, Korea University of Science and Technology, Daejeon, 305-343, Republic of Korea
| | - Saravanakumar Selvaraj
- Centre for Pharmacology and Toxicology, Hannover Medical School, 30625 Hannover, Germany
| | - Se-Myo Park
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon, 305-343, Republic of Korea
| | - Mi-Sun Choi
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon, 305-343, Republic of Korea
| | - Reinhard Spanel
- Centre for Pharmacology and Toxicology, Hannover Medical School, 30625 Hannover, Germany.,Institute for Clinical Pathology, 41747 Viersen, Germany
| | - Seokjoo Yoon
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon, 305-343, Republic of Korea.,Department of Human and Environmental Toxicology, School of Engineering, Korea University of Science and Technology, Daejeon, 305-343, Republic of Korea
| | - Jürgen Borlak
- Centre for Pharmacology and Toxicology, Hannover Medical School, 30625 Hannover, Germany
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Abstract
In this chapter, we present an approach that allows a causal analysis of multiple "-omics" data with the help of an "upstream analysis" strategy. The goal of this approach is to identify master regulators in gene regulatory networks as potential drug targets for a pathological process. The data analysis strategy includes a state-of-the-art promoter analysis for potential transcription factor (TF)-binding sites using the TRANSFAC® database combined with an analysis of the upstream signal transduction pathways that control the activity of these TFs. When applied to genes that are associated with a switch to a pathological process, the approach identifies potential key molecules (master regulators) that may exert major control over and maintenance of transient stability of the pathological state. We demonstrate this approach on examples of analysis of multi-omics data sets that contain transcriptomics and epigenomics data in cancer. The results of this analysis helped us to better understand the molecular mechanisms of cancer development and cancer drug resistance. Such an approach promises to be very effective for rapid and accurate identification of cancer drug targets with true potential. The upstream analysis approach is implemented as an automatic workflow in the geneXplain platform ( www.genexplain.com ) using the open-source BioUML framework ( www.biouml.org ).
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Affiliation(s)
- Alexander E Kel
- Institute of Chemical Biology and Fundamental Medicine, SBRAN, Novosibirsk, Russia. .,Biosoft.ru, Ltd., Novosibirsk, Russia. .,geneXplain GmbH, Am Exer 10B, D-38302, Wolfenbüttel, Germany.
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Asano T, Narazaki H, Fujita A. Genome-wide DNA methylation profiling of CpG islands in a morpholino anthracycline derivative-resistant leukemia cell line: p38 α as a novel candidate for resistance. Pharmacol Res Perspect 2016; 5:e00285. [PMID: 28596837 PMCID: PMC5461645 DOI: 10.1002/prp2.285] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 11/12/2016] [Accepted: 11/27/2016] [Indexed: 11/18/2022] Open
Abstract
Effective leukemia treatment is seriously hampered by drug resistance. We previously showed that aberrant methylation of the topoisomerase IIα gene causes altered gene expression and acquired drug resistance in etoposide‐resistant leukemia cells. In this study, we analyzed the genome‐wide methylation status in resistant leukemia cells. We used MX2, which is a morpholino anthracycline derivative that functions as a topoisomerase IIα inhibitor. We established a human myelogenous leukemia cell line (K562/P) and a related cell line with resistance to MX2 (K562/MX2). Using these cell lines, we investigated the genome‐wide methylation status, compared expression profiles with a microarray, and analyzed the data using Gene Ontology and key node analysis. We demonstrate that the MX2‐resistant cell line was globally hypermethylated. Gene Ontology analysis identified genes involved in the immunological response and gene silencing that were responsible for methylation‐related altered gene expression in drug‐resistant cells. Key node analysis showed that p38α mitogen‐activated protein kinase was a novel enzyme involved in MX2‐related resistance. p38 kinase activity in resistant cells was increased compared to MX2‐sensitive parent cells. Blocking p38α activity using inhibitors and p38α knock down with small interfering RNA restored the sensitivity to MX2 in resistant cells with a decrease in p38 kinase activity as well as decreased expression of p38α mRNA and phosphorylated p38α protein. These findings may lead to a new strategy for treatment of drug‐resistant leukemia cells.
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Affiliation(s)
- Takeshi Asano
- Department of Pediatrics Nippon Medical School Tokyo Japan
| | | | - Atsushi Fujita
- Department of Pediatrics Nippon Medical School Tokyo Japan
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Genomics of human fatty liver disease reveal mechanistically linked lipid droplet-associated gene regulations in bland steatosis and nonalcoholic steatohepatitis. Transl Res 2016; 177:41-69. [PMID: 27376874 DOI: 10.1016/j.trsl.2016.06.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 05/13/2016] [Accepted: 06/08/2016] [Indexed: 12/11/2022]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a common disorder hallmarked by excessive lipid deposits. Based on our recent research on lipid droplet (LD) formation in hepatocytes, we investigated LD-associated gene regulations in NAFLD of different grades, that is, steatosis vs steatohepatitis by comparing liver biopsies from healthy controls (N = 13) and NAFLD patients (N = 102). On average, more than 700 differentially expressed genes (DEGs) were identified of which 146 are mechanistically linked to LD formation. We identified 51 LD-associated DEGs frequently regulated in patient samples (range ≥5 to ≤102) with the liver-receptor homolog-1(NR5A2), that is, a key regulator of cholesterol metabolism being commonly repressed among 100 patients examined. With bland steatosis, notable regulations involved hypoxia-inducible lipid droplet-associated-protein and diacylglycerol-O-acyltransferase-2 renowned for their role in LD-growth. Conversely, nonalcoholic steatohepatitis-associated DEGs coded for epidermal growth factor receptor and TLR4 signaling with decreased expression of the GTPase Rab5 and the lipid phosphohydrolase PPAP2B thus highlighting adaptive responses to inflammation, LDL-mediated endocytosis and lipogenesis, respectively. Studies with steatotic primary human hepatocyte cultures demonstrated induction of LD-associated PLIN2, CIDEC, DNAAF1, whereas repressed expression of CPT1A, ANGPTL4, and PKLR informed on burdened mitochondrial metabolism. Equally, repressed expression of the B-lymphocyte chemoattractant CXCL13 and STAT4 as well as induced FGF21 evidenced amelioration of steatosis-related inflammation. In-vitro/in-vivo patient sample comparisons confirmed C-reactive protein, SOCS3, NR5A2, and SOD2 as commonly regulated. Lastly, STRING network analysis highlighted potential "druggable" targets with PLIN2, CIDEC, and hypoxia-inducible lipid droplet-associated-protein being confirmed by immunofluorescence microscopy. In conclusion, steatosis and steatohepatitis specific gene regulations informed on the pathogenesis of NAFLD to broaden the perspective of targeted therapies.
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Kel AE, Stegmaier P, Valeev T, Koschmann J, Poroikov V, Kel-Margoulis OV, Wingender E. Multi-omics "upstream analysis" of regulatory genomic regions helps identifying targets against methotrexate resistance of colon cancer. EUPA OPEN PROTEOMICS 2016; 13:1-13. [PMID: 29900117 PMCID: PMC5988513 DOI: 10.1016/j.euprot.2016.09.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 09/05/2016] [Accepted: 09/08/2016] [Indexed: 11/25/2022]
Abstract
Upstream analysis strategy for multi-omics data is proposed. Drug targets are predicted by search for TFBS and analysis of signaling network. Methotrexate resistance data include transcriptomics, proteomics and epigenomics. Predicted targets are: TGFalpha, IGFBP7, alpha9-integrin. Predicted drugs are: zardaverine, divalproex and human metabolite nicotinamide N-oxide.
We present an “upstream analysis” strategy for causal analysis of multiple “-omics” data. It analyzes promoters using the TRANSFAC database, combines it with an analysis of the upstream signal transduction pathways and identifies master regulators as potential drug targets for a pathological process. We applied this approach to a complex multi-omics data set that contains transcriptomics, proteomics and epigenomics data. We identified the following potential drug targets against induced resistance of cancer cells towards chemotherapy by methotrexate (MTX): TGFalpha, IGFBP7, alpha9-integrin, and the following chemical compounds: zardaverine and divalproex as well as human metabolites such as nicotinamide N-oxide.
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Affiliation(s)
- Alexander E Kel
- Institute of Chemical Biology and Fundamental Medicine, SBRAS, Novosibirsk, Russia.,Biosoft.ru, Ltd, Novosibirsk, Russia.,geneXplain GmbH, D-38302 Wolfenbüttel, Germany
| | | | - Tagir Valeev
- Biosoft.ru, Ltd, Novosibirsk, Russia.,A.P. Ershov Institute of Informatics Systems, SB RAS, Novosibirsk, Russia
| | | | | | | | - Edgar Wingender
- geneXplain GmbH, D-38302 Wolfenbüttel, Germany.,Institute of Bioinformatics, University Medical Center Göttingen, D-37077 Göttingen, Germany
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11
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Ciribilli Y, Singh P, Spanel R, Inga A, Borlak J. Decoding c-Myc networks of cell cycle and apoptosis regulated genes in a transgenic mouse model of papillary lung adenocarcinomas. Oncotarget 2016; 6:31569-92. [PMID: 26427040 PMCID: PMC4741625 DOI: 10.18632/oncotarget.5035] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 09/21/2015] [Indexed: 11/25/2022] Open
Abstract
The c-Myc gene codes for a basic-helix-loop-helix-leucine zipper transcription factor protein and is reported to be frequently over-expressed in human cancers. Given that c-Myc plays an essential role in neoplastic transformation we wished to define its activity in lung cancer and therefore studied its targeted expression to respiratory epithelium in a transgenic mouse disease model. Using histological well-defined tumors, transcriptome analysis identified novel c-Myc responsive cell cycle and apoptosis genes that were validated as direct c-Myc targets using EMSA, Western blotting, gene reporter and ChIP assays.Through computational analyses c-Myc cooperating transcription factors emerged for repressed and up-regulated genes in cancer samples, namely Klf7, Gata3, Sox18, p53 and Elf5 and Cebpα, respectively. Conversely, at promoters of genes regulated in transgenic but non-carcinomatous lung tissue enriched binding sites for c-Myc, Hbp1, Hif1 were observed. Bioinformatic analysis of tumor transcriptomic data revealed regulatory gene networks and highlighted mortalin and moesin as master regulators while gene reporter and ChIP assays in the H1299 lung cancer cell line as well as cross-examination of published ChIP-sequence data of 7 human and 2 mouse cell lines provided strong evidence for the identified genes to be c-Myc targets. The clinical significance of findings was established by evaluating expression of orthologous proteins in human lung cancer. Taken collectively, a molecular circuit for c-Myc-dependent cellular transformation was identified and the network analysis broadened the perspective for molecularly targeted therapies.
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Affiliation(s)
- Yari Ciribilli
- Centre for Integrative Biology (CIBIO), University of Trento, 38123 Mattarello, Italy
| | - Prashant Singh
- Centre for Pharmacology and Toxicology, Hannover Medical School, 30625 Hannover, Germany
| | - Reinhard Spanel
- Centre for Pharmacology and Toxicology, Hannover Medical School, 30625 Hannover, Germany.,Institute of Pathology, 41747 Viersen, Germany
| | - Alberto Inga
- Centre for Integrative Biology (CIBIO), University of Trento, 38123 Mattarello, Italy
| | - Jürgen Borlak
- Centre for Pharmacology and Toxicology, Hannover Medical School, 30625 Hannover, Germany
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12
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Differences in the Early Development of Human and Mouse Embryonic Stem Cells. PLoS One 2015; 10:e0140803. [PMID: 26473594 PMCID: PMC4608779 DOI: 10.1371/journal.pone.0140803] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 09/30/2015] [Indexed: 01/22/2023] Open
Abstract
We performed a systematic analysis of gene expression features in early (10–21 days) development of human vs mouse embryonic cells (hESCs vs mESCs). Many development features were found to be conserved, and a majority of differentially regulated genes have similar expression change in both organisms. The similarity is especially evident, when gene expression profiles are clustered together and properties of clustered groups of genes are compared. First 10 days of mESC development match the features of hESC development within 21 days, in accordance with the differences in population doubling time in human and mouse ESCs. At the same time, several important differences are seen. There is a clear difference in initial expression change of transcription factors and stimulus responsive genes, which may be caused by the difference in experimental procedures. However, we also found that some biological processes develop differently; this can clearly be shown, for example, for neuron and sensory organ development. Some groups of genes show peaks of the expression levels during the development and these peaks cannot be claimed to happen at the same time points in the two organisms, as well as for the same groups of (orthologous) genes. We also detected a larger number of upregulated genes during development of mESCs as compared to hESCs. The differences were quantified by comparing promoters of related genes. Most of gene groups behave similarly and have similar transcription factor (TF) binding sites on their promoters. A few groups of genes have similar promoters, but are expressed differently in two species. Interestingly, there are groups of genes expressed similarly, although they have different promoters, which can be shown by comparing their TF binding sites. Namely, a large group of similarly expressed cell cycle-related genes is found to have discrepant TF binding properties in mouse vs human.
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Chen X, Yamamoto M, Fujii K, Nagahama Y, Ooshio T, Xin B, Okada Y, Furukawa H, Nishikawa Y. Differential reactivation of fetal/neonatal genes in mouse liver tumors induced in cirrhotic and non-cirrhotic conditions. Cancer Sci 2015; 106:972-81. [PMID: 26011625 PMCID: PMC4556385 DOI: 10.1111/cas.12700] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 05/06/2015] [Accepted: 05/17/2015] [Indexed: 12/13/2022] Open
Abstract
Hepatocellular carcinoma develops in either chronically injured or seemingly intact livers. To explore the tumorigenic mechanisms underlying these different conditions, we compared the mRNA expression profiles of mouse hepatocellular tumors induced by the repeated injection of CCl4 or a single diethylnitrosamine (DEN) injection using a cDNA microarray. We identified tumor-associated genes that were expressed differentially in the cirrhotic CCl4 model (H19, Igf2, Cbr3, and Krt20) and the non-cirrhotic DEN model (Tff3, Akr1c18, Gpc3, Afp, and Abcd2) as well as genes that were expressed comparably in both models (Ly6d, Slpi, Spink3, Scd2, and Cpe). The levels and patterns of mRNA expression of these genes were validated by quantitative RT-PCR analyses. Most of these genes were highly expressed in mouse livers during the fetal/neonatal periods. We also examined the mRNA expression of these genes in mouse tumors induced by thioacetamide, another cirrhotic inducer, and those that developed spontaneously in non-cirrhotic livers and found that they shared a similar expression profile as that observed in CCl4-induced and DEN-induced tumors, respectively. There was a close relationship between the expression levels of Igf2 and H19 mRNA, which were activated in the cirrhotic models. Our results show that mouse liver tumors reactivate fetal/neonatal genes, some of which are specific to cirrhotic or non-cirrhotic modes of pathogenesis.
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Affiliation(s)
- Xi Chen
- Division of Tumor Pathology, Department of Pathology, Asahikawa Medical University, Asahikawa, Japan
| | - Masahiro Yamamoto
- Division of Tumor Pathology, Department of Pathology, Asahikawa Medical University, Asahikawa, Japan
| | - Kiyonaga Fujii
- Division of Tumor Pathology, Department of Pathology, Asahikawa Medical University, Asahikawa, Japan
| | - Yasuharu Nagahama
- Division of Tumor Pathology, Department of Pathology, Asahikawa Medical University, Asahikawa, Japan
| | - Takako Ooshio
- Division of Tumor Pathology, Department of Pathology, Asahikawa Medical University, Asahikawa, Japan
| | - Bing Xin
- Division of Tumor Pathology, Department of Pathology, Asahikawa Medical University, Asahikawa, Japan
| | - Yoko Okada
- Division of Tumor Pathology, Department of Pathology, Asahikawa Medical University, Asahikawa, Japan
| | - Hiroyuki Furukawa
- Division of Gastroenterological and General Surgery, Department of Surgery, Asahikawa Medical University, Asahikawa, Japan
| | - Yuji Nishikawa
- Division of Tumor Pathology, Department of Pathology, Asahikawa Medical University, Asahikawa, Japan
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"Upstream Analysis": An Integrated Promoter-Pathway Analysis Approach to Causal Interpretation of Microarray Data. MICROARRAYS 2015; 4:270-86. [PMID: 27600225 PMCID: PMC4996392 DOI: 10.3390/microarrays4020270] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 05/11/2015] [Accepted: 05/14/2015] [Indexed: 11/16/2022]
Abstract
A strategy is presented that allows a causal analysis of co-expressed genes, which may be subject to common regulatory influences. A state-of-the-art promoter analysis for potential transcription factor (TF) binding sites in combination with a knowledge-based analysis of the upstream pathway that control the activity of these TFs is shown to lead to hypothetical master regulators. This strategy was implemented as a workflow in a comprehensive bioinformatic software platform. We applied this workflow to gene sets that were identified by a novel triclustering algorithm in naphthalene-induced gene expression signatures of murine liver and lung tissue. As a result, tissue-specific master regulators were identified that are known to be linked with tumorigenic and apoptotic processes. To our knowledge, this is the first time that genes of expression triclusters were used to identify upstream regulators.
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Leiherer A, Geiger K, Muendlein A, Drexel H. Hypoxia induces a HIF-1α dependent signaling cascade to make a complex metabolic switch in SGBS-adipocytes. Mol Cell Endocrinol 2014; 383:21-31. [PMID: 24275182 PMCID: PMC3969228 DOI: 10.1016/j.mce.2013.11.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 10/18/2013] [Accepted: 11/15/2013] [Indexed: 12/11/2022]
Abstract
To elucidate the complex impact of hypoxia on adipose tissue, resulting in biased metabolism, insulin resistance and finally diabetes we used mature adipocytes derived from a Simpson-Golabi-Behmel syndrome patient for microarray analysis. We found a significantly increased transcription rate of genes involved in glycolysis and a striking association between the pattern of upregulated genes and disease biomarkers for diabetes mellitus and insulin resistance. Although their upregulation turned out to be HIF-1α-dependent, we identified further transcription factors mainly AP-1 components to play also an important role in hypoxia response. Analyzing the regulatory network of mentioned transcription factors and glycolysis targets we revealed a clear hint for directing glycolysis to glutathione and glycogen synthesis. This metabolic switch in adipocytes enables the cell to prevent oxidative damage in the short term but might induce lipogenesis and establish systemic metabolic disorders in the long run.
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MESH Headings
- Adipocytes/metabolism
- Adipocytes/pathology
- Adipogenesis
- Arrhythmias, Cardiac/genetics
- Arrhythmias, Cardiac/metabolism
- Arrhythmias, Cardiac/pathology
- Biomarkers/metabolism
- Cell Hypoxia/genetics
- Gene Expression Profiling
- Gene Expression Regulation
- Genetic Diseases, X-Linked/genetics
- Genetic Diseases, X-Linked/metabolism
- Genetic Diseases, X-Linked/pathology
- Gigantism/genetics
- Gigantism/metabolism
- Gigantism/pathology
- Glutathione/biosynthesis
- Glycogen/biosynthesis
- Glycolysis
- Heart Defects, Congenital/genetics
- Heart Defects, Congenital/metabolism
- Heart Defects, Congenital/pathology
- Humans
- Hypoxia-Inducible Factor 1, alpha Subunit/genetics
- Hypoxia-Inducible Factor 1, alpha Subunit/metabolism
- Insulin Resistance
- Intellectual Disability/genetics
- Intellectual Disability/metabolism
- Intellectual Disability/pathology
- Oligonucleotide Array Sequence Analysis
- Protein Interaction Mapping
- Signal Transduction/genetics
- Transcription Factor AP-1/genetics
- Transcription Factor AP-1/metabolism
- Transcription, Genetic
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Affiliation(s)
- Andreas Leiherer
- Vorarlberg Institute for Vascular Investigation and Treatment (VIVIT), Feldkirch, Austria; Private University of the Principality of Liechtenstein, Triesen, Liechtenstein; Medical Central Laboratories, Feldkirch, Austria
| | - Kathrin Geiger
- Vorarlberg Institute for Vascular Investigation and Treatment (VIVIT), Feldkirch, Austria; Private University of the Principality of Liechtenstein, Triesen, Liechtenstein
| | - Axel Muendlein
- Vorarlberg Institute for Vascular Investigation and Treatment (VIVIT), Feldkirch, Austria; Private University of the Principality of Liechtenstein, Triesen, Liechtenstein
| | - Heinz Drexel
- Vorarlberg Institute for Vascular Investigation and Treatment (VIVIT), Feldkirch, Austria; Department of Medicine and Cardiology, Academic Teaching Hospital Feldkirch, Feldkirch, Austria; Private University of the Principality of Liechtenstein, Triesen, Liechtenstein; Drexel University College of Medicine, Philadelphia, USA.
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Zawacka-Pankau J, Grinkevich VV, Hünten S, Nikulenkov F, Gluch A, Li H, Enge M, Kel A, Selivanova G. Inhibition of glycolytic enzymes mediated by pharmacologically activated p53: targeting Warburg effect to fight cancer. J Biol Chem 2011; 286:41600-41615. [PMID: 21862591 DOI: 10.1074/jbc.m111.240812] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Unique sensitivity of tumor cells to the inhibition of glycolysis is a good target for anticancer therapy. Here, we demonstrate that the pharmacologically activated tumor suppressor p53 mediates the inhibition of glycolytic enzymes in cancer cells in vitro and in vivo. We showed that p53 binds to the promoters of metabolic genes and represses their expression, including glucose transporters SLC2A12 (GLUT12) and SLC2A1 (GLUT1). Furthermore, p53-mediated repression of transcription factors c-Myc and HIF1α, key drivers of ATP-generating pathways in tumors, contributed to ATP production block. Inhibition of c-Myc by p53 mediated the ablation of several glycolytic genes in normoxia, whereas in hypoxia down-regulation of HIF1α contributed to this effect. We identified Sp1 as a transcription cofactor cooperating with p53 in the ablation of metabolic genes. Using different approaches, we demonstrated that glycolysis block contributes to the robust induction of apoptosis by p53 in cancer cells. Taken together, our data suggest that tumor-specific reinstatement of p53 function targets the "Achilles heel" of cancer cells (i.e. their dependence on glycolysis), which could contribute to the tumor-selective killing of cancer cells by pharmacologically activated p53.
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Affiliation(s)
- Joanna Zawacka-Pankau
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Nobelsväg 16, Stockholm, SE 171 77, Sweden; Department of Biotechnology, Division of Molecular Diagnostics, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Kladki 24, 80-822 Gdansk, Poland.
| | - Vera V Grinkevich
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Nobelsväg 16, Stockholm, SE 171 77, Sweden
| | - Sabine Hünten
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Nobelsväg 16, Stockholm, SE 171 77, Sweden
| | - Fedor Nikulenkov
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Nobelsväg 16, Stockholm, SE 171 77, Sweden
| | | | - Hai Li
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Nobelsväg 16, Stockholm, SE 171 77, Sweden
| | - Martin Enge
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Nobelsväg 16, Stockholm, SE 171 77, Sweden
| | - Alexander Kel
- geneXplain GmbH, Am Exer 10b, D-38302 Wolfenbuettel, Germany
| | - Galina Selivanova
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Nobelsväg 16, Stockholm, SE 171 77, Sweden.
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