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ChIP assay

Isao Tamura, Kosuke Jozaki, Shun Sato, Yuichiro Shirafuta, Masahiro Shinagawa, Ryo Maekawa, Toshiaki Taketani, Hiromi Asada, Hiroshi Tamura, Norihiro Sugino
We have previously shown that decidualization of human endometrial stromal cells (ESCs) causes a genome-wide increase in the levels of acetylation of histone-H3 Lys-27 (H3K27ac). We also reported that the distal gene regions, more than 3 kb up or downstream of gene transcription start sites have increased H3K27ac levels. Insulin-like growth factor-binding protein-1 (IGFBP-1) is a specific decidualization marker and has increased H3K27ac levels in its distal upstream region (-4701 bp to -7501 bp). Here, using a luciferase reporter gene construct containing this IGFBP-1 upstream region, we tested the hypothesis that it is an IGFBP-1 enhancer...
February 16, 2018: Journal of Biological Chemistry
Sherona R Sirkisoon, Richard L Carpenter, Tadas Rimkus, Ashley Anderson, Alexandria Harrison, Allison M Lange, Guangxu Jin, Kounosuke Watabe, Hui-Wen Lo
Signal transducer and activator of transcription 3 (STAT3), glioma oncogene homolog 1 (GLI1), and truncated GLI1 (tGLI1) are oncogenic transcription factors playing important roles in breast cancer. tGLI1 is a gain-of-function GLI1 isoform. Whether STAT3 physically and/or functionally interacts with GLI1/tGLI1 has not been explored. To address this knowledge gap, we analyzed 47 node-positive breast cancer specimens using immunohistochemical staining and found that phosphorylated-STAT3 (Y705), GLI1, and tGLI1 are co-overexpressed in the majority of triple-negative breast carcinomas (64%) and HER2-enriched (68%) breast carcinomas, and in lymph node metastases (65%)...
February 16, 2018: Oncogene
Seong-Min Park, Eun-Young Choi, Dong-Hyuck Bae, Hyun Ahm Sohn, Seon-Young Kim, Youn-Jae Kim
BACKGROUND/AIMS: Recent studies have revealed that many long non-coding RNAs (lncRNAs) play oncogenic or tumor-suppressive roles in various cancers. Lung cancer is the leading cause of cancer-related death worldwide, and many lung cancer patients frequently relapse after surgery, even those in the early stages. However, the oncogenic or tumor-suppressive roles and clinical implications of lncRNAs in lung cancer have not been fully elucidated. METHODS: The association between an E2F-mediated cell proliferation enhancing lncRNA (EPEL) expression and lung cancer patient survival was accessed using public microarray data with clinical information...
February 9, 2018: Cellular Physiology and Biochemistry
Shenshen Wu, Qingtao Meng, Chengcheng Zhang, Hao Sun, Runze Lu, Na Gao, Hongbao Yang, Xiaobo Li, Michael Aschner, Rui Chen
The single nucleotide polymorphism (SNP), -397G>T (rs13278062) polymorphism, in the promoter of Death Receptor 4 (DR4) had been reported to be associated with a significantly increased risk for bladder cancer. However, the association of this SNP with the risk of colorectal cancer has not been reported. In this study, we performed a case-control study in 1,078 colorectal cancer patients and 1,175 matched healthy controls to evaluate the association of the potential functional genetic variants in DR4 with risk and survival of colorectal cancer...
February 15, 2018: International Journal of Cancer. Journal International du Cancer
P Dow, K Kotz, S Gruszka, J Holder, J Fiering
A more effective treatment of bacteremia requires a diagnostic platform that is both sensitive, accurate and rapid. Currently, clinical laboratory techniques require growth of bacteria prior to diagnosis, take days to complete, and leave empiric therapy and broad spectrum antibiotics as the only option at the onset of treatment. In order to bypass this growth requirement, we engineered a system that purifies bacteria from blood to improve performance in a bacteriophage-based luminescence assay. To perform the purification, we used acoustophoresis in plastic microfluidic chips, enabling future development into a low cost point-of-care system...
February 15, 2018: Lab on a Chip
Sharad Purohit, Ashok Sharma, Wenbo Zhi, Shan Bai, Diane Hopkins, Leigh Steed, Bruce Bode, Stephen W Anderson, John Chip Reed, R Dennis Steed, Jin-Xiong She
Soluble cytokine receptors may play an important role in development of microalbuminuria (MA) in type-1 diabetes (T1D). In this study, we measured 12 soluble receptors and ligands from TNF-α/IL6/IL2 pathways in T1D patients with MA ( n = 89) and T1D patients without MA ( n = 483) participating in the PAGODA study. Twelve proteins in the sera from T1D patients with and without MA were measured using multiplex Luminex assays. Ten serum proteins (sTNFR1, sTNFR2, sIL2Rα, MMP2, sgp130, sVCAM1, sIL6R, SAA, CRP, and sICAM1) were significantly elevated in T1D patients with MA...
2018: Frontiers in Immunology
Vinesh Vinayachandran, Rohit Reja, Matthew J Rossi, Bongsoo Park, Lila Rieber, Chitvan Mittal, Shaun Mahony, B Franklin Pugh
Gene expression is controlled by a variety of proteins that interact with the genome. Their precise organization and mechanism of action at every promoter remains to be worked out. To better understand the physical interplay among genome-interacting proteins, we examined the temporal binding of a functionally diverse subset of these proteins: nucleosomes (H3), H2AZ (Htz1), SWR (Swr1), RSC (Rsc1, Rsc3, Rsc58, Rsc6, Rsc9, Sth1), SAGA (Spt3, Spt7, Ubp8, Sgf11), Hsf1, TFIID (Spt15/TBP and Taf1), TFIIB (Sua7), TFIIH (Ssl2), FACT (Spt16), Pol II (Rpb3), and Pol II carboxyl-terminal domain (CTD) phosphorylation at serines 2, 5, and 7...
February 14, 2018: Genome Research
Wei Shi, Xiaoling Wang, Lihong Ruan, Jiamei Fu, Fang Liu, Jinfeng Qu
Endometrial cancer is the most common gynecological cancer. Epithelial-mesenchymal transition (EMT) plays a critical role in tumor invasion and metastasis, which limits the success of treatment. Here, we investigated the roles of forkhead box A2 (FOXA2) and microRNA-200a (miR-200a) in regulating the EMT of endometrial cancer cells RL95-2. Empty vector or FOXA2 was stably transfected into RL95-2 cells. MTT assay measured cell proliferation, apoptosis assay measured apoptosis, Transwell invasion assay measured cell invasion, and Western blot measured the protein expression of FOXA2, E-cadherin, and vimentin...
November 1, 2017: Die Pharmazie
Qiang Li, Hongjun Guo, Huihui Li, Qi Zhu, Yang Liu
In various tumors, aberrant expression of P54/nrb has been identified. However, the expression pattern and specific role of P54/nrb in rheumatoid arthritis (RA) has never been explored. Here, we first demonstrated that the expression of P54/nrb was markedly enhanced in the synovial tissues of RA patients. Functional study showed that P54/nrb could enhance the levels of inflammatory factors, including IL-1, IL-2, IL-6, IL-8 and TNFα. More importantly, we first found that overexpression of P54/nrb can induce the protein levels of P65, an important subunit of NF-κB...
May 1, 2017: Die Pharmazie
Weijiang Zhang, Jing Fei, Shuqian Yu, Jiayu Shen, Xiaoqing Zhu, Annapurna Sadhukhan, Weiguo Lu, Jianwei Zhou
The roles of long non-coding RNAs (lncRNAs), a class of long non-protein-coding RNAs, in the tumorigenesis of ovarian epithelial cells remain unknown. In this study, we discovered that the expression of long intergenic non-coding RNA 1088 (LINC01088) was clearly reduced in benign epithelial ovarian tumor tissues compared to matched normal ovarian tissues. This was shown by global cDNA gene chip scanning and real-time qPCR, and validated in 42 clinical specimens. Furthermore, we found that LINC01088 inhibited the growth of ovarian cancer xenografts in nude mice...
February 13, 2018: Scientific Reports
Xu Wang, Di Sun, Jiandong Tai, Si Chen, Miao Yu, Dong Ren, Lei Wang
BACKGROUND: Aberrant expression of transcription Factor AP-2 Gamma (TFAP2C) has been reported to be implicated in malignant process of many cancers. The purpose of this study is to investigate the clinical significance and biological roles of TFAP2C in colorectal cancer (CRC). METHODS: TFAP2C expression was evaluated by real-time PCR, Western blot and immunohistochemistry (IHC) respectively in clinical CRC tissues. Statistical analysis was performed to explore the correlation between TFAP2C expression and clinicopathological features, and overall and progression-free survival in CRC patients...
February 13, 2018: Journal of Experimental & Clinical Cancer Research: CR
Carlos Gaspar, Jonás I Silva-Marrero, María C Salgado, Isabel V Baanante, Isidoro Metón
Glutamate dehydrogenase (Gdh) plays a central role in ammonia detoxification by catalysing reversible oxidative deamination of L-glutamate into α-ketoglutarate using NAD+ or NADP+ as cofactor. To gain insight into transcriptional regulation of glud, the gene that codes for Gdh, we isolated and characterised the 5' flanking region of glud from gilthead sea bream (Sparus aurata). In addition, tissue distribution, the effect of starvation as well as short- and long-term refeeding on Gdh mRNA levels in the liver of S...
February 8, 2018: Journal of Molecular Endocrinology
Xiaolin Bu, Xinling Bi, Wuqing Wang, Yuling Shi, Qiang Hou, Jun Gu
Psoriasis is an autoimmune disease involving the excessive proliferation of keratinocytes mediated by T‑cells. Parathyroid hormone (PTH) has been identified as an essential factor in the treatment of psoriasis. In the present study, the mechanism underlying the effect of recombinant human parathyroid hormone (rhPTH) (1‑34) in keratinocytes was investigated. The effects of rhPTH (1‑34) on cell proliferation, cell cycle, and the secretion and expression of C‑X‑C motif chemokine 11 (CXCL11) and components of the Hedgehog signaling pathway were examined in HaCaT cells by MTT assay, flow cytometric analysis, ELISA and gene chip analysis...
February 7, 2018: Molecular Medicine Reports
S M Restaino, I M White
Surface enhanced Raman spectroscopy (SERS) has the potential to enable point-of-care sensing across the spectrum of chemical and biological analytes. In diagnostic assays, SERS has been demonstrated to increase the multiplexing density while reducing the burden of fluorescence hardware. One particular application of interest is the use of SERS to provide a multiplexed optical read-out following polymerase chain reaction (PCR). To date, however, the reported PCR-SERS assays require endpoint mixing with a plasmonic nanoparticle solution for detection, thus adding manual steps and preventing real-time, quantitative PCR...
February 13, 2018: Lab on a Chip
Fan Feng, Weiwei Qi, Yuanda Lv, Shumei Yan, Liming Xu, Wenyao Yang, Yue Yuan, Yihan Chen, Han Zhao, Rentao Song
Maize (Zea mays) endosperm is a primary tissue for nutrient storage and is highly differentiated during development. However, the regulatory networks of endosperm development and nutrient metabolism remain largely unknown. Maize opaque11 (o11) is a classic seed mutant with a small and opaque endosperm showing decreased starch and protein accumulation. We cloned O11 and found that it encodes an endosperm-specific bHLH transcription factor (TF). Loss-of-function of O11 significantly affected transcription of carbohydrate/amino acid metabolism and stress-response genes...
February 7, 2018: Plant Cell
Yi Xie, Jianmin Li, Chao Zhang
The aim of the present study was to investigate the correlation of STAT3 and AKT in HCC cells. HCC cells were transfected with si-STAT3 and si-AKT2 in vitro and the mRNA expression of STAT3 and AKT was detected by RT-PCR, and the protein expression was measured by western blot. MTT assays were used to evaluate cell proliferation, and Transwell assays were performed to detect the ability of migration and invasion. The relationship between STAT3 and AKT was analyzed by ChIP and Dual-luciferase reporter (DLR) assays...
March 2018: Oncology Letters
Dou Dou, Yan-Fen Shi, Qing Liu, Jie Luo, Ji-Xi Liu, Meng Liu, Ying-Ying Liu, Yuan-Liang Li, Xu-Dong Qiu, Huang-Ying Tan
AIM: To detect abnormal microRNA (miRNA) expression in type 1 gastric neuroendocrine neoplasms (g-NENs) and find potential target genes. METHODS: Tumour tissues from patients with type 1 g-NENs were used as experimental samples, and gastric mucosal tissues from the same patients obtained during gastroscopy review after several months were used as control samples. miRNA expression was examined with Agilent human miRNA chips and validated via RT-PCR. Three types of target gene prediction software (TargetScan, PITA, and microRNAorg) were used to predict potential target genes of the differentially expressed miRNAs, and a dual-luciferase reporter assay system was used for verification...
February 7, 2018: World Journal of Gastroenterology: WJG
Kavita Shalia, Dhananjaya Saranath, Jaipreet Rayar, Vinod K Shah, Manoj R Mashru, Surendra L Soneji
Background & objectives: Acute myocardial infarction (AMI) is a major health concern in India. The aim of the study was to identify single nucleotide polymorphisms (SNPs) associated with AMI in patients using dedicated chip and validating the identified SNPs on custom-designed chips using high-throughput microarray analysis. Methods: In pilot phase, 48 AMI patients and 48 healthy controls were screened for SNPs using human CVD55K BeadChip with 48,472 SNP probes on Illumina high-throughput microarray platform...
October 2017: Indian Journal of Medical Research
Kelly Maurer, Swathi Ramen, Lihuaa Shi, Li Song, Kathleen E Sullivan
The response to infection is managed in mammals by a coordinated immune response. Innate responses are rapid and hard wired and have been demonstrated to be regulated at the level of chromatin accessibility. This study examined primary human monocyte responses to LPS as a model of innate responses to bacteria. We utilized inhibitors of chromatin modifying enzymes to understand the inter-relationships of the chromatin complexes regulating transcription. Multiplex digital gene detection was utilized to quantitate changes in mRNA levels for genes induced by LPS...
February 9, 2018: Molecular Immunology
Carina Eklund, Ola Forslund, Keng-Ling Wallin, Joakim Dillner
BACKGROUND: Accurate and internationally comparable human papillomavirus (HPV) DNA detection and typing services are essential for HPV vaccine research and surveillance. OBJECTIVES: This study assessed the proficiency of different HPV typing services offered routinely in laboratories worldwide. STUDY DESIGN: The HPV Laboratory Network (LabNet) has designed international proficiency panels that can be regularly issued. The HPV genotyping proficiency panels of 2013 and 2014 contained 43 and 41 coded samples, respectively, composed of purified plasmids of sixteen HPV types (HPV 6, 11, 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, 68a and 68b) and 3 extraction controls...
February 9, 2018: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
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