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Wu HQ, Cheng ML, Lai JM, Wu HH, Chen MC, Liu WH, Wu WH, Chang PMH, Huang CYF, Tsou AP, Shiao MS, Wang FS. Flux balance analysis predicts Warburg-like effects of mouse hepatocyte deficient in miR-122a. PLoS Comput Biol 2017; 13:e1005618. [PMID: 28686599 PMCID: PMC5536358 DOI: 10.1371/journal.pcbi.1005618] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 07/31/2017] [Accepted: 06/12/2017] [Indexed: 12/31/2022] Open
Abstract
The liver is a vital organ involving in various major metabolic functions in human body. MicroRNA-122 (miR-122) plays an important role in the regulation of liver metabolism, but its intrinsic physiological functions require further clarification. This study integrated the genome-scale metabolic model of hepatocytes and mouse experimental data with germline deletion of Mir122a (Mir122a–/–) to infer Warburg-like effects. Elevated expression of MiR-122a target genes in Mir122a–/–mice, especially those encoding for metabolic enzymes, was applied to analyze the flux distributions of the genome-scale metabolic model in normal and deficient states. By definition of the similarity ratio, we compared the flux fold change of the genome-scale metabolic model computational results and metabolomic profiling data measured through a liquid-chromatography with mass spectrometer, respectively, for hepatocytes of 2-month-old mice in normal and deficient states. The Ddc gene demonstrated the highest similarity ratio of 95% to the biological hypothesis of the Warburg effect, and similarity of 75% to the experimental observation. We also used 2, 6, and 11 months of mir-122 knockout mice liver cell to examined the expression pattern of DDC in the knockout mice livers to show upregulated profiles of DDC from the data. Furthermore, through a bioinformatics (LINCS program) prediction, BTK inhibitors and withaferin A could downregulate DDC expression, suggesting that such drugs could potentially alter the early events of metabolomics of liver cancer cells. For almost a century, researchers have known that cancer cells have an abnormal metabolism and utilize glucose differently than normal cells do. Aerobic glycolysis or the Warburg effect in cancer cells involves elevated glucose uptake with lactic acid production in the presence of oxygen. MicroRNAs have recently been discovered to be key metabolic regulators that mediate the fine tuning of genes that are involved directly or indirectly in cancer metabolism. MicroRNA-122 (miR-122) plays an important role in the regulation of liver metabolism, but its intrinsic physiological functions require further clarification. This study integrated the genome-scale metabolic modeling (GSMM) of hepatocytes and mouse experimental data with germline deletion of Mir122a (Mir122a–/–) to infer Warburg-like effects. In silico and in vivo observations indicated that DDC overexpression induced Warburg effect in hepatocyte. Furthermore, through a bioinformatics prediction, BTK inhibitors and withaferin A could downregulate DDC expression, suggesting that such drugs could potentially alter the early events of metabolomics of liver cancer cells.
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Won SJ, Yen CH, Hsieh HW, Chang SW, Lin CN, Huang CYF, Su CL. Using connectivity map to identify natural lignan justicidin A as a NF-κB suppressor. J Funct Foods 2017. [DOI: 10.1016/j.jff.2017.04.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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Lin SF, Chien JY, Kapupara K, Huang CYF, Huang SP. Oroxylin A promotes retinal ganglion cell survival in a rat optic nerve crush model. PLoS One 2017. [PMID: 28640893 PMCID: PMC5480866 DOI: 10.1371/journal.pone.0178584] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Purpose To investigate the effect of oroxylin A on the survival of retinal ganglion cells (RGC) and the activation of microglial cells in a rat optic nerve (ON) crush model. Methods Oroxylin A (15mg/Kg in 0.2ml phosphate-buffered saline) or phosphate-buffered saline (PBS control) was immediately administered after ON crush once by subcutaneous injection. Rats were euthanized at 2 weeks after the crush injury. The density of RGC was counted by retrograde labeling with FluoroGold and immunostaining of retina flat mounts for Brn3a. Electrophysiological visual function was assessed by flash visual evoked potentials (FVEP). TUNEL assay, immunoblotting analysis of glial fibrillary acidic protein (GFAP), inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) in the retinas, and immunohistochemistry of GFAP in the retinas and ED1 in the ON were evaluated. Results Two weeks after the insult, the oroxylin A-treated group had significantly higher FG labeled cells and Brn3a+ cells suggesting preserved RGC density in the central and mid-peripheral retinas compared with those of the PBS-treated group. FVEP measurements showed a significantly better preserved latency of the P1 wave in the ON-crushed, oroxylin A-treated rats than the ON-crushed, PBS treated rats. TUNEL assays showed fewer TUNEL positive cells in the ON-crushed, oroxylin A-treated rats. The number of ED1 positive cells was reduced at the lesion site of the optic nerve in the ON-crushed, oroxylin A-treated group. Increased GFAP expression in the retina was reduced greatly in ON-crushed, oroxylin A-treated group. Furthermore, administration of oroxylin A significantly attenuated ON crush insult-induced iNOS and COX-2 expression in the retinas. Conclusions These results demonstrated that oroxylin A hasss neuroprotective effects on RGC survival with preserved visual function and a decrease in microglial infiltration in the ONs after ON crush injury.
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Su CL, Tseng CL, Ramesh C, Liu HS, Huang CYF, Yao CF. Using gene expression database to uncover biology functions of 1,4-disubstituted 1,2,3-triazole analogues synthesized via a copper (I)-catalyzed reaction. Eur J Med Chem 2017; 132:90-107. [PMID: 28342400 DOI: 10.1016/j.ejmech.2017.03.034] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/14/2017] [Accepted: 03/15/2017] [Indexed: 12/18/2022]
Abstract
We have synthesized bioactive 1,4-disubstituted 1,2,3-triazole analogues containing 2H-1,4-benzoxazin-3-(4H)-one derivatives via 1,3-dipolar cycloaddition in the presence of CuI. All the reactions proceeded smoothly and afforded its desired products in excellent yields. Among these analogues, 3y exhibited a better cytotoxic effect on human hepatocellular carcinoma (HCC) Hep 3B cells and displayed less cytotoxicity on normal human umbilical vein endothelial cells, compared with Sorafenib, a targeted therapy for advanced HCC. 3y also induced stronger apoptosis and autophagy. Addition of curcumin enhanced 3y-induced cytotoxicity by further induction of autophagy. Using gene expression signatures of 3y to query Connectivity Map, a glycogen synthase kinase-3 inhibitor (AR-A014418) was predicted to display similar molecular action of 3y. Experiments further demonstrate that AR-A014418 acted like 3y, and vice versa. Overall, our data suggest the chemotherapeutic potential of 3y on HCC.
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Chen ST, Huang CH, Kok VC, Huang CYF, Ciou JS, Tsai JJP, Kurubanjerdjit N, Ng KL. Drug repurposing and therapeutic anti-microRNA predictions for inhibition of oxidized low-density lipoprotein-induced vascular smooth muscle cell-associated diseases. J Bioinform Comput Biol 2017; 15:1650043. [PMID: 28150521 DOI: 10.1142/s0219720016500438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Drug repurposing is a new method for disease treatments, which accelerates the identification of new uses for existing drugs with minimal side effects for patients. MicroRNA-based therapeutics are a class of drugs that have been used in gene therapy following the FDA's approval of the first anti-sense therapy. This study examines the effects of oxLDL on vascular smooth muscle cells (VSMCs) and identifies potential drugs and antimiRs for treating VSMC-associated diseases. The Connectivity Map (cMap) database is utilized to identify potential new uses of existing drugs. The success of the identifications was supported by MTT assay, clonogenic assay and clinical trial data. Specifically, 37 drugs, some of which are undergoing clinical trials, were identified. Three of the identified drugs exhibit IC50 activities. Among the 37 drugs' targets, three differentially expressed genes (DEGs) are identified as drug targets by using both the DrugBank and the NCBI PubChem Compound databases. Also, one DEG, DNMT1, which is regulated by 17 miRNAs, where these miRNAs are potential targets for developing antimiR-based miRNA therapy, is found.
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Sung PL, Jan YH, Lin SC, Huang CC, Lin H, Wen KC, Chao KC, Lai CR, Wang PH, Chuang CM, Wu HH, Twu NF, Yen MS, Hsiao M, Huang CYF. Periostin in tumor microenvironment is associated with poor prognosis and platinum resistance in epithelial ovarian carcinoma. Oncotarget 2016; 7:4036-47. [PMID: 26716408 PMCID: PMC4826188 DOI: 10.18632/oncotarget.6700] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 12/02/2015] [Indexed: 02/07/2023] Open
Abstract
The interplay between tumor microenvironment and cancer that causes chemoresistance remains unclear. By analyzing public available microarray datasets, we identified that periostin (POSTN) was overexpressed in cancer stroma in epithelial ovarian cancer (EOC) patients. Immunohistochemistry analysis showed overexpression of stromal POSTN is a powerful independent poor prognostic predictor for EOC patients. Furthermore, patients with high levels of stromal POSTN tend to have higher percentage of cisplatin resistance compared to those with low levels of stromal POSTN. Moreover, we found POSTN treatment can induce cisplatin resistant and activate AKT pathway in A2780 cells in vitro. Inhibition of AKT activity by AKT inhibitor MK-2206 abolished POSTN-induced AKT activation and cisplatin resistance in vitro. Taken together, we found high POSTN expression in cancer microenvironment is correlated with poor prognosis in EOC patients and associated with platinum resistance. The effect of POSTN in cancer stroma cells may activate AKT pathway in tumor and AKT inhibitor can be beneficial to augment the efficacy of existing cancer therapeutics.
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Chen MH, Yen CC, Cheng CT, Wu RC, Huang SC, Yu CS, Chung YH, Liu CY, Chang PMH, Chao Y, Chen MH, Chen YF, Chiang KC, Yeh TS, Chen TC, Huang CYF, Yeh CN. Identification of SPHK1 as a therapeutic target and marker of poor prognosis in cholangiocarcinoma. Oncotarget 2016; 6:23594-608. [PMID: 26090720 PMCID: PMC4695139 DOI: 10.18632/oncotarget.4335] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 05/30/2015] [Indexed: 01/01/2023] Open
Abstract
Cholangiocarcinoma (CCA) is characterized by a uniquely aggressive behavior and lack of effective targeted therapies. After analyzing the gene expression profiles of seven paired intrahepatic CCA microarrays, a novel sphingosine kinase 1 (SPHK1)/sphingosine-1-phosphate (S1P) pathway and a novel target gene, SPHK1, were identified. We hypothesized that therapeutic targeting of this pathway can be used to kill intrahepatic cholangiocarcinoma (CCA) cells. High levels of SPHK1 protein expression, which was evaluated by immunohistochemical staining of samples from 96 patients with intrahepatic CCA, correlated with poor overall survival. The SPHK1 inhibitor SK1-I demonstrated potent antiproliferative activity in vitro and in vivo. SK1-I modulated the balance of ceramide-sphinogosine-S1P and induced CCA apoptosis. Furthermore, SK1-I combined with JTE013, an antagonist of the predominant S1P receptor S1PR2, inhibited the AKT and ERK signaling pathways in CCA cells. Our preclinical data suggest SPHK1/S1P pathway targeting may be an effective treatment option for patients with CCA.
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Won SJ, Lin TY, Yen CH, Tzeng YH, Liu HS, Lin CN, Yu CH, Wu CS, Chen JT, Chen YT, Huang CYF, Su CL. A novel natural tautomeric pair of garcinielliptone FC suppressed nuclear factor κB and induced apoptosis in human colorectal cancer cells. J Funct Foods 2016. [DOI: 10.1016/j.jff.2016.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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Chen TC, Huang CYF. Use of In Situ Proximity Ligation Assays for Systems Analysis of Signaling Pathways. ACTA ACUST UNITED AC 2016; 71:17.18.1-17.18.11. [PMID: 27245426 DOI: 10.1002/cpcb.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Understanding signaling pathway networks via protein-protein interactions (PPIs) at the cellular level is a significant task that has not yet been completed. Here, a systems approach that computationally infers interlinked pathways from numerous PPIs is described. The endogenous PPIs can be empirically detected using an in situ proximity ligation assay (PLA), which detects and visualizes endogenous PPIs and post-translational modifications of proteins with a high sensitivity and specificity. This unit includes two parts: (1) conversion of gene lists into PPIs for investigation and (2) large-scale detection and analysis of endogenous PPIs for elucidating pathway networks. © 2016 by John Wiley & Sons, Inc.
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Lai CY, Yeh DW, Lu CH, Liu YL, Huang LR, Kao CY, Chen HY, Huang CYF, Chang CH, Luo Y, Xiang R, Chuang TH. Thiostrepton inhibits psoriasis-like inflammation induced by TLR7, TLR8, and TLR9. THE JOURNAL OF IMMUNOLOGY 2016. [DOI: 10.4049/jimmunol.196.supp.124.41] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Toll-like receptors 7, 8 and 9 (TLR7-9) comprise a subfamily of TLR. Activation of these TLRs has been linked to the pathogenesis of autoimmune diseases such as rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), and psoriasis. Thus antagonists of these TLRs are being investigated for their therapeutic applications on these diseases. Bortezomib is a proteasome inhibitor known to suppress activation of these TLRs. This drug is approved for the treatment of multiple myeloma, and its inhibitory effects on autoimmune disorders such as psoriasis, RA, and SLE have also been investigated in animal models. In an attempt to develop novel TLR7-9 inhibitors, we searched the Gene Expression Omnibus database for gene expression profiles in cells treated with bortezomib. These profiles were then used as an input to screen the Connectivity Map database for chemical compounds with similar functions as bortezomib. Here we report that the antibiotic thiostrepton is a novel TLR7–9 inhibitor. Like bortezomib, thiostrepton effectively inhibits TLR7–9 activation in cell-based assays and dendritic cells. In contrast to bortezomib, thiostrepton is less cytotoxic to dendritic cells, and its inhibitory activity is more specific to TLR7–9. Thiostrepton inhibits TLR9 localization in endosomes for activation via two mechanisms. One mechanism is similar to the proteasome inhibitory function of bortezomib, and the other is through inhibition of endosomal acidification. In different animal models, thiostrepton attenuated LL37- and imiquimod-induced psoriasis-like inflammation. These results indicated that thiostrepton is a novel and specific inhibitor to TLR7–9.
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Kan WC, Lu TL, Ling P, Lee TH, Cho CY, Huang CYF, Jeng WY, Weng YP, Chiang CY, Wu JB, Lu TJ. Pervanadate induces Mammalian Ste20 Kinase 3 (MST3) tyrosine phosphorylation but not activation. J Inorg Biochem 2016; 160:33-9. [PMID: 27118027 DOI: 10.1016/j.jinorgbio.2016.04.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 04/08/2016] [Accepted: 04/12/2016] [Indexed: 11/18/2022]
Abstract
The yeast Ste20 (sterile) protein kinase, which is a serine/threonine kinase, responds to the stimulation of the G proteincoupled receptor (GPCR) pheromone receptor. Ste20 protein kinase serves as the critical component that links signaling from the GPCR/G proteins to the mitogen-activated protein kinase (MAPK) cascade in yeast. The yeast Ste20p functions as a MAP kinase kinase kinase kinase (MAP4K) in the pheromone response. Ste20-like kinases are structurally conserved from yeast to mammals. The mechanism by which MAP4K links GPCR to the MAPK pathway is less clearly defined in vertebrates. In addition to MAP4K, the tyrosine kinase cascade bridges G proteins and the MAPK pathway in vertebrate cells. Mammalian Ste20 Kinase 3 (MST3) has been categorized into the Ste20 family and has been reported to function in the regulation of cell polarity and migration. However, whether MST3 tyrosine phosphorylation regulates diverse signaling pathways is unknown. In this study, the tyrosine phosphatase inhibitor pervanadate was found to induce MST3 tyrosine phosphorylation in intact cells, and the activity of tyrosine-phosphorylated MST3 was measured. This tyrosine-directed phosphorylation was independent of MST3 activity. Parameters including protein conformation, Triton concentration and ionic concentration influenced the sensitivity of MST3 activity. Taken together, our data suggests that the serine/threonine kinase MST3 undergoes tyrosinedirected phosphorylation. The tyrosine-phosphorylated MST3 may create a docking site for the structurally conserved SH2/SH3 (Src Homology 2 and 3) domains within the Src oncoprotein. The unusual tyrosinephosphorylated MST3 may recruit MST3 to various signaling components.
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Huang CH, Chang PMH, Hsu CW, Huang CYF, Ng KL. Drug repositioning for non-small cell lung cancer by using machine learning algorithms and topological graph theory. BMC Bioinformatics 2016; 17 Suppl 1:2. [PMID: 26817825 PMCID: PMC4895785 DOI: 10.1186/s12859-015-0845-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Non-small cell lung cancer (NSCLC) is one of the leading causes of death globally, and research into NSCLC has been accumulating steadily over several years. Drug repositioning is the current trend in the pharmaceutical industry for identifying potential new uses for existing drugs and accelerating the development process of drugs, as well as reducing side effects. Results This work integrates two approaches - machine learning algorithms and topological parameter-based classification - to develop a novel pipeline of drug repositioning to analyze four lung cancer microarray datasets, enriched biological processes, potential therapeutic drugs and targeted genes for NSCLC treatments. A total of 7 (8) and 11 (12) promising drugs (targeted genes) were discovered for treating early- and late-stage NSCLC, respectively. The effectiveness of these drugs is supported by the literature, experimentally determined in-vitro IC50 and clinical trials. This work provides better drug prediction accuracy than competitive research according to IC50 measurements. Conclusions With the novel pipeline of drug repositioning, the discovery of enriched pathways and potential drugs related to NSCLC can provide insight into the key regulators of tumorigenesis and the treatment of NSCLC. Based on the verified effectiveness of the targeted drugs predicted by this pipeline, we suggest that our drug-finding pipeline is effective for repositioning drugs.
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Huang CH, Ciou JS, Chen ST, Kok VC, Chung Y, Tsai JJP, Kurubanjerdjit N, Huang CYF, Ng KL. Identify potential drugs for cardiovascular diseases caused by stress-induced genes in vascular smooth muscle cells. PeerJ 2016; 4:e2478. [PMID: 27703845 PMCID: PMC5045879 DOI: 10.7717/peerj.2478] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 08/23/2016] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Abnormal proliferation of vascular smooth muscle cells (VSMC) is a major cause of cardiovascular diseases (CVDs). Many studies suggest that vascular injury triggers VSMC dedifferentiation, which results in VSMC changes from a contractile to a synthetic phenotype; however, the underlying molecular mechanisms are still unclear. METHODS In this study, we examined how VSMC responds under mechanical stress by using time-course microarray data. A three-phase study was proposed to investigate the stress-induced differentially expressed genes (DEGs) in VSMC. First, DEGs were identified by using the moderated t-statistics test. Second, more DEGs were inferred by using the Gaussian Graphical Model (GGM). Finally, the topological parameters-based method and cluster analysis approach were employed to predict the last batch of DEGs. To identify the potential drugs for vascular diseases involve VSMC proliferation, the drug-gene interaction database, Connectivity Map (cMap) was employed. Success of the predictions were determined using in-vitro data, i.e. MTT and clonogenic assay. RESULTS Based on the differential expression calculation, at least 23 DEGs were found, and the findings were qualified by previous studies on VSMC. The results of gene set enrichment analysis indicated that the most often found enriched biological processes are cell-cycle-related processes. Furthermore, more stress-induced genes, well supported by literature, were found by applying graph theory to the gene association network (GAN). Finally, we showed that by processing the cMap input queries with a cluster algorithm, we achieved a substantial increase in the number of potential drugs with experimental IC50 measurements. With this novel approach, we have not only successfully identified the DEGs, but also improved the DEGs prediction by performing the topological and cluster analysis. Moreover, the findings are remarkably validated and in line with the literature. Furthermore, the cMap and DrugBank resources were used to identify potential drugs and targeted genes for vascular diseases involve VSMC proliferation. Our findings are supported by in-vitro experimental IC50, binding activity data and clinical trials. CONCLUSION This study provides a systematic strategy to discover potential drugs and target genes, by which we hope to shed light on the treatments of VSMC proliferation associated diseases.
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Lai CY, Yeh DW, Lu CH, Liu YL, Huang LR, Kao CY, Chen HY, Huang CYF, Chang CH, Luo Y, Xiang R, Chuang TH. Identification of Thiostrepton as a Novel Inhibitor for Psoriasis-like Inflammation Induced by TLR7–9. THE JOURNAL OF IMMUNOLOGY 2015; 195:3912-21. [DOI: 10.4049/jimmunol.1500194] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 08/11/2015] [Indexed: 01/07/2023]
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Sung PL, Huang CYF, Hsiao M, Wen KC, Yen MS, Lee MH. Abstract 1922: Target mutation comparasion of WGA circulating tumor cell and primary tumor in epithelial ovarian cancer cell line using NGS. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-1922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction
Epithelial ovarian cancer is the third most common gynecologic cancer in the United States but a leading cause of gynecologic cancer deaths. Previous finding that numbers of circulating tumor cells (CTCs) in the blood of ovarian cancer patients are prognostically significant. Moreover, comprehensive analyses of ovarian cancer genomes may provide more information for precise cancer treatments. Genomic analysis of circulating tumor cells (CTC) can provide possible approach for EOC patients who lack primary tumor tissue or present with un-resectable metastatic diseases. The discordance between whole genome amplification of circulating tumors and primary tumor should be validated firstly and so we conducted a pilot analysis of CTC capture and targeted NGS in EOC cell lines.
Methods and materials
Under IRB approval, EOC cell lines, different numbers of SKOV-3 (serous adenocarcinoma) and ES-2 (clear cell carcinoma) were spiked in fresh blood samples (20 ml) of healthy donor and captured by CytoQuestTM CR system or negative enrichment method (Abnova, Taipei, Taiwan). CTCs were identified by pan-CK, CD45 and DAPI expression and stained with CEP8 FISH for aneuploidy. Spiked CTCs of two cell lines were captured and underwent whole genome amplification by PicoPLEX™ WGA kit (Rubicon Genomic, MI, USA). The WGA DNA product and DNA of two primary cell lines were prepared libraries for TruSight(TM) Tumor sequencing panel (Illumina Inc.MI,USA) according to manufacturer's instruction. Sequencing procedure were performed on MiSEQ system(Illumina Inc.) by a local service provider.
Results
SKOV-3 and ES-2 can be stained and captured with these antibodies. Mean recovery of these cells were more than 80% by both systems. However, ES-2 is less Pan-CK stained but still could be captured by this system. WGA products of each one, three and five ES-2 cells and one SKOV3 cell were prepared well for library. We choose one cell WGA product and DNA extracted from primary SKOV-3 and ES2 were subjected to targeted 26 genes mutational analysis composed in TruSight Tumor panel. Average coverage depth for each amplicon is minimum 1000x with 7000x means. We would like to show if any discordance appear due to the acquisition of DNA WGA in the single cells, of which the analysis is currently ongoing.
DISCUSSION
Our study would like to demonstrate the condition of variants calls of single tumor cells isolated from whole blood samples and primary tumor in a targeted mutation analysis using NGS after a highly automated isolation workflow. This approach provides a pilot workflow for studying the heterogeneity within the CTC population in blood samples of patients with tumor and their primary tumor and the results can also document the possibility of WGA-induced bias of a recently commercialized WGA kit.
Citation Format: Pi-Lin Sung, Chi-Ying F. Huang, Michael Hsiao, Kuo-Chang Wen, Ming-Shyen Yen, Mong-Hong Lee. Target mutation comparasion of WGA circulating tumor cell and primary tumor in epithelial ovarian cancer cell line using NGS. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1922. doi:10.1158/1538-7445.AM2015-1922
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Wu SM, Cheng WL, Liao CJ, Chi HC, Lin YH, Tseng YH, Tsai CY, Chen CY, Lin SL, Chen WJ, Yeh YH, Huang CYF, Chen MH, Yeh YC, Lin KH. Negative modulation of the epigenetic regulator, UHRF1, by thyroid hormone receptors suppresses liver cancer cell growth. Int J Cancer 2015; 137:37-49. [PMID: 25430639 DOI: 10.1002/ijc.29368] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 11/12/2014] [Indexed: 12/16/2022]
Abstract
The thyroid hormone, 3,3',5-triiodo-l-thyronine (T3 ), mediates several physiological processes, including embryonic development, cellular differentiation, metabolism and regulation of cell proliferation. Thyroid hormone (T3 ) and its receptor (TR) are involved in metabolism and growth. In addition to their developmental and metabolic functions, TRs play a tumor suppressor role, and therefore, their aberrant expression can lead to tumor transformation. Aberrant epigenetic silencing of tumor suppressor genes promotes cancer progression. The epigenetic regulator, Ubiquitin-like with PHD and ring finger domains 1 (UHRF1), is overexpressed in various cancers. In our study, we demonstrated that T3 negatively regulates UHRF1 expression, both in vitro and in vivo. Our results further indicate that UHRF1 regulation by T3 is indirect and mediated by Sp1. Sp1-binding elements of UHRF1 were identified at positions -664/-505 of the promoter region using the luciferase and chromatin immunoprecipitation assays. Notably, UHRF1 and Sp1 levels were elevated in subgroups of hepatocellular carcinoma patients and inversely correlated with TRα1 expression. Knockdown of UHRF1 expression should therefore provide a means to inhibit hepatoma cell proliferation. Expression of UHRF1 was downregulated by TRs, in turn, relieving silencing of the UHRF1 target gene, p21. Based on the collective findings, we propose that T3 /TR signaling induces hepatoma cell growth inhibition via UHRF1 repression.
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Chen TC, Lin KT, Chen CH, Lee SA, Lee PY, Liu YW, Kuo YL, Wang FS, Lai JM, Huang CYF. Using an in Situ Proximity Ligation Assay to Systematically Profile Endogenous Protein–Protein Interactions in a Pathway Network. J Proteome Res 2014; 13:5339-46. [DOI: 10.1021/pr5002737] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Ke CS, Liu HS, Yen CH, Huang GC, Cheng HC, Huang CYF, Su CL. Curcumin-induced Aurora-A suppression not only causes mitotic defect and cell cycle arrest but also alters chemosensitivity to anticancer drugs. J Nutr Biochem 2014; 25:526-39. [PMID: 24613085 DOI: 10.1016/j.jnutbio.2014.01.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Revised: 12/29/2013] [Accepted: 01/08/2014] [Indexed: 01/19/2023]
Abstract
Overexpression of oncoprotein Aurora-A increases drug resistance and promotes lung metastasis of breast cancer cells. Curcumin is an active anticancer compound in turmeric and curry. Here we observed that Aurora-A protein and kinase activity were reduced in curcumin-treated human breast chemoresistant nonmetastatic MCF-7 and highly metastatic cancer MDA-MB-231 cells. Curcumin acts in a similar manner to Aurora-A small interfering RNA (siRNA), resulting in monopolar spindle formation, S and G2/M arrest, and cell division reduction. Ectopic Aurora-A extinguished the curcumin effects. The anticancer effects of curcumin were enhanced by Aurora-A siRNA and produced additivity and synergism effects in cell division and monopolar phenotype, respectively. Combination treatment with curcumin overrode the chemoresistance to four Food and Drug Administration (FDA)-approved anticancer drugs (ixabepilone, cisplatin, vinorelbine, or everolimus) in MDA-MB-231 cells, which was characterized by a decrease in cell viability and the occurrence of an additivity or synergy effect. Ectopic expression of Aurora-A attenuated curcumin-enhanced chemosensitivity to these four tested drugs. A similar benefit of curcumin was observed in MCF-7 cells treated with ixabepilone, the primary systemic therapy to patients with invasive breast cancer (stages IIA-IIIB) before surgery. Antagonism effect was observed when MCF-7 cells were treated with curcumin plus cisplatin, vinorelbine or everolimus. Curcumin-induced enhancement in chemosensitivity was paralleled by significant increases (additivity or synergy effect) in apoptosis and cell cycle arrest at S and G2/M phases, the consequences of Aurora-A inhibition. These results suggest that a combination of curcumin with FDA-approved anticancer drugs warrants further assessment with a view to developing a novel clinical treatment for breast cancer.
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Sung PL, Cheng EE, Chen YJ, Chern SR, Shih CY, Chang CM, Wang PH, Yen MS, Huang CYF, Chen CP. Prenatal diagnosis of de novo monosomy 7q33-qter associated with hydrops fetalis, semilobar holoprosencephaly, and premaxillary dysgenesis. Taiwan J Obstet Gynecol 2014; 52:602-6. [PMID: 24411055 DOI: 10.1016/j.tjog.2013.10.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2013] [Accepted: 05/04/2013] [Indexed: 11/16/2022] Open
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Lan MY, Yang WLR, Lin KT, Lin JC, Shann YJ, Ho CY, Huang CYF. Using computational strategies to predict potential drugs for nasopharyngeal carcinoma. Head Neck 2013; 36:1398-407. [PMID: 24038431 DOI: 10.1002/hed.23464] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 05/06/2013] [Accepted: 08/13/2013] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Nasopharyngeal carcinoma (NPC) is a unique cancer. Refinement of current therapy by discovering potential drugs may be approached by several computational strategies. METHODS We collected NPC genes from published microarray data and the literature. The NPC disease network was constructed via a protein-protein interaction (PPI) network. The Connectivity Map (CMap) was used to predict potential chemicals, and support vector machines (SVMs) were further utilized to classify the effectiveness of tested drugs against NPC using their gene expression from CMap. RESULTS A highly interconnected network was obtained. Several chemically sensitive genes were identified and 87 drugs were predicted with the potential for treating NPC by SVM, in which nearly half of them have anticancer effects according to the literature. The 2 top-ranked drugs, thioridazine and vorinostat, were demonstrated to be effective in inhibiting NPC cells. CONCLUSION This in silico approach provides a promising strategy for screening potential therapeutic drugs for NPC treatment.
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Liu CH, Chen TC, Chen CH, Kao CY, Huang CYF. Differential network biology reveals a positive correlation between a novel protein-protein interaction and cancer cells migration. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2013; 2013:2700-3. [PMID: 24110284 DOI: 10.1109/embc.2013.6610097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This paper introduces a differential network biology for discovering tumor migration. We applied statistical methods to prioritize PPI candidates and an in situ proximity ligation assay to verify 67 endogenous PPIs among 21 interlinked pathways in two hepatocellular carcinoma (HCC) cells, Huh7 (minimally migratory cells) and Mahlavu (highly migratory cells). Differential network biology analysis was applied to determine the novel interaction, CRKL-FLT1, has a high centrality ranking, and the expression of this interaction is strongly correlated with the migratory ability of HCC and other cancer cell lines. Knockdown of CRKL and FLT1 in HCC cells leads to a decrease in cell migration. This study demonstrated that functional exploration of a disease network with differential network in interlinked pathways via PPIs can be used to discover tumor migration.
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Chen CC, Chu CB, Liu KJ, Huang CYF, Chang JY, Pan WY, Chen HH, Cheng YH, Lee KD, Chen MF, Kuo CC, Chen LT. Gene expression profiling for analysis acquired oxaliplatin resistant factors in human gastric carcinoma TSGH-S3 cells: The role of IL-6 signaling and Nrf2/AKR1C axis identification. Biochem Pharmacol 2013; 86:872-87. [DOI: 10.1016/j.bcp.2013.07.025] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 07/29/2013] [Accepted: 07/29/2013] [Indexed: 02/02/2023]
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Yeh CT, Huang WC, Rao YK, Ye M, Lee WH, Wang LS, Tzeng DT, Wu CH, Shieh YS, Huang CYF, Chen YJ, Hsiao M, Wu AT, Yang Z, Tzeng YM. A sesquiterpene lactone antrocin from Antrodia camphorata negatively modulates JAK2/STAT3 signaling via microRNA let-7c and induces apoptosis in lung cancer cells. Carcinogenesis 2013; 34:2918-28. [DOI: 10.1093/carcin/bgt255] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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Chen MH, Jan YH, Chang PMH, Chuang YJ, Yeh YC, Lei HJ, Hsiao M, Huang SF, Huang CYF, Chau GY. Expression of GOLM1 correlates with prognosis in human hepatocellular carcinoma. Ann Surg Oncol 2013; 20 Suppl 3:S616-24. [PMID: 23838921 DOI: 10.1245/s10434-013-3101-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Indexed: 01/18/2023]
Abstract
BACKGROUND Serum Golgi membrane protein 1 (GOLM1) is a novel biomarker for hepatocellular carcinoma (HCC). However, few studies have investigated the relationship between GOLM1 protein expression and clinicopathologic features in HCC patients. The aim of this study was to investigate the expression of GOLM1 in human HCC and its correlation with clinicopathologic parameters. METHODS Clinicopathologic data were obtained through a detailed retrospective review of the medical records of 193 patients with HCC who had undergone surgical resection between 1990 and 2006 at the Taipei Veterans General Hospital. Another 120 HCC tissue samples provided by the Taiwan Liver Cancer Network were used as validation cohort. Immunohistochemical staining was used to determine the expression of GOLM1 in archived formalin-fixed, paraffin-embedded tissue specimens. RESULTS GOLM1 expression was significantly higher in resected HCC tumor tissues than in corresponding normal liver tissues (p < 0.01). After a median follow-up of 51 months, multivariate analysis showed that portal vein invasion (hazard ratio [HR], 1.515; 95 % confidence interval [95 % CI], 1.008-2.277; p = 0.046) and high GOLM1 protein expression (HR, 1.696; 95 % CI, 1.160-2.479; p = 0.006) were independent prognostic factors for poor overall survival. High GOLM1 protein expression still significantly correlates with worse overall survival as well as disease-free survival in the validation cohort (p < 0.001 and p = 0.002). CONCLUSIONS Overexpression of GOLM1 is associated with poor prognosis in human HCC.
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Chang PMH, Yeh YC, Chen TC, Wu YC, Lu PJ, Cheng HC, Lu HJ, Chen MH, Chou TY, Huang CYF. High expression of CHRNA1 is associated with reduced survival in early stage lung adenocarcinoma after complete resection. Ann Surg Oncol 2013; 20:3648-54. [PMID: 23775407 DOI: 10.1245/s10434-013-3034-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Indexed: 12/23/2022]
Abstract
BACKGROUND Non-small cell lung cancer (NSCLC) is the leading cause of cancer deaths around the world, and a high recurrence rate after complete resection is an important issue reducing the cure rate and survival of patients with early stage NSCLC. Several pathologic biomarkers are associated with recurrence in early stage lung cancer after complete resection. METHODS We evaluated the expression and prognostic value of the α1 subunit of the nicotinic acetylcholine receptor (CHRNA1) as well as other pathologic features of tumor tissues resected from patients with stage I adenocarcinoma of the lung. RESULTS A high ratio (173/185) of CHRNA1 expression (93.5 %) was found in stage I lung adenocarcinoma. In the multivariate survival analysis, tumor necrosis, angiolymphatic invasion, perineural invasion, and CHRNA1 expression were independent poor prognostic factors for both recurrence-free and overall survival (OS). Patients expressing CHRNA1 had worse median recurrence-free survival (60.6 vs. 77.9 months, P = 0.03) and OS (65.1 vs. 77.9 months, P = 0.04) compared with CHRNA1-negative patients. CONCLUSIONS CHRNA1 expression could be directly tested from the tumor after complete resection. In early stage NSCLC, it could be a useful prognostic factor for recurrence and survival.
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