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ChIP assay

Jing Qu, Lanyan Zhu, Zijing Zhou, Ping Chen, Shuyan Liu, Morgan L Locy, Victor J Thannickal, Yong Zhou
RATIONALE: Desmoplakin (DSP), the most abundant component of desmosomes which maintain the mechanical integrity of epithelium, is a GWAS-identified genetic risk locus in human idiopathic pulmonary fibrosis (IPF). IPF subjects express a significantly higher level of DSP than control subjects. OBJECTIVES: Determine potential mechanisms by which DSP is regulated in lung fibrosis Methods: Matrigel-coated soft and stiff polyacrylamide gels were made to simulate the stiffness of normal and fibrotic lungs...
June 20, 2018: American Journal of Respiratory and Critical Care Medicine
Xinzhao Xu, Pierrick Clement, Johnas Eklöf-Österberg, Nancy Kelley-Loughnane, Kasper Moth-Poulsen, Jorge Luis Chávez, Matteo Palma
Here we report on the fabrication of reconfigurable and solution processable nanoscale biosensors with multi-sensing capability, based on single walled carbon nanotubes (SWCNTs). Distinct DNA-wrapped (hence water-soluble) CNTs were immobilised from solution onto different pre-patterned electrodes on the same chip, via a low-cost dielectrophoresis (DEP) methodology. The CNTs were functionalised with specific, and different, aptamer sequences that were employed as selective recognition elements for biomarkers indicative of stress and neuro-trauma conditions...
June 20, 2018: Nano Letters
Jingjing Xu, Jun Zhou, Hanjue Dai, Fei Liu, Wenjing Li, Wenjuan Wang, Feng Guo
BACKGROUND: The carboxyl terminus of Hsc70-interacting protein (CHIP) is an E3 ubiquitin ligase that plays a controversial role in different cancers, either as a tumor suppressor or a tumor promoter. To date, the exact function and underlying mechanism of CHIP in colorectal cancer (CRC) is not yet clear. Here we aimed to determine whether CHIP could affect the biological behaviors of CRC cells and its underlying mechanisms. METHODS: Stably transfected CHIP overexpression and depletion DLD-1 and HT-29 cells were established using Lipofectamine 2000...
June 19, 2018: Journal of Translational Medicine
Xiaowei Diao, Xiubin Chen, Yurui Pi, Yu Zhang, Fangfang Wang, Ping Liu, Yanhong Gao, Xiaojun Wang, Sijun Yang, Shan Lu
Erythropoietin‑producing hepatocellular carcinoma cell surface type‑A receptor 3 (EPHA3) has been found to promote the proliferation and survival of prostate cancer (PCa) cell lines and prostate tumor development in nude mice. However, the regulation of EPHA3 in PCa remains largely unknown. This study is aimed to investigate the association between EPHA3 expression and androgen receptor (AR) signaling and the potential mechanism. We determined mRNA and protein levels of EPHA3 and AR signaling‑related genes in the PCa cell line 22Rv1 by reverse transcription‑polymerase chain reaction (RT‑PCR) and western blotting, respectively...
June 18, 2018: Oncology Reports
Nipin Sp, Dong Young Kang, Doh Hoon Kim, Jong Hwan Park, Hyo Gun Lee, Hye Jee Kim, Pramod Darvin, Yeong-Min Park, Young Mok Yang
Targeted cancer therapy with natural compounds is more effective than nontargeted therapy. Nobiletin is a flavonoid derived from citrus peel that has anticancer activity. Cluster of differentiation 36 (CD36) is a member of the class B scavenger receptor family that is involved in importing fatty acids into cells. CD36 plays a role in tumor angiogenesis by binding to its ligand, thrombospondin-1 (TSP-1), and then interacting with transforming growth factor beta 1 (TGFβ1). CD36 is implicated in tumor metastasis through its roles in fatty acid metabolism...
June 15, 2018: Nutrients
Qingguo Li, Yaqi Li, Jing Li, Yanlei Ma, Weixing Dai, Shaobo Mo, Ye Xu, Xinxiang Li, Sanjun Cai
F-box and WD repeat domain-containing 7 (FBW7) functions as a major tumor suppressor by targeting oncoproteins for degradations. FBW7 has been reported to be one of the most frequently mutated genes in colorectal cancer (CRC). However, its roles and possible mechanisms in the development of CRC are still unclear. In the present study, we adopted immunohistochemistry staining in tissue microarray (TMA), consisting of 276 samples from stage I-IV CRC patients, and analyzed the correlation between FBW7 expression and clinicopathological parameters, as well as overall survival (OS) and disease-free survival (DFS)...
2018: International Journal of Biological Sciences
Yong Qiu, Jing Zhang, Bing Li, Xianghua Wen, Peng Liang, Xia Huang
Antibiotic resistance genes (ARGs) in environment have become a growing public concern, due to their potential to be obtained by pathogens and their duplication along cell division. Horizontal gene transfer (HGT) was reported to be responsible for ARGs dissemination in microbes, but the HGT feature in environmental biofilm was still unclear due to insufficient assay tools. To address this challenge, we applied a novel microfluidic system to cultivate thin biofilm by continuous supply of nutrients and close contact between cells...
June 14, 2018: Science of the Total Environment
Anna Rita Bizzarri, Ilaria Moscetti, Salvatore Cannistraro
p53 is a powerful transcription factor playing a pivotal role in the prevention of cancer development and in maintaining genome integrity. This oncosuppressor is found to be functionally inactivated by mutations in many human tumors. Accordingly, wild type p53 and its oncogenic mutants represent valuable cancer biomarkers for diagnostic and prognostic purposes. We developed a highly sensitive biosensor, based on Surface Enhanced Raman Spectroscopy, for detection of wild type p53 and of p53R175H , which is one of the most frequent tumor-associated mutants of p53...
October 31, 2018: Analytica Chimica Acta
Jonathan Visentin, Lionel Couzi, Claire Dromer, Martine Neau-Cransac, Gwendaline Guidicelli, Vincent Veniard, Karine Nubret-le Coniat, Pierre Merville, Carmelo Di Primo, Jean-Luc Taupin
Human leukocyte antigen (HLA) donor-specific antibodies are key serum biomarkers for assessing the outcome of transplanted patients. Measuring their active concentration, i.e. the fraction that really interacts with donor HLA, and their affinity could help deciphering their pathogenicity. Surface plasmon resonance (SPR) is recognized as the gold-standard for measuring binding kinetics but also active concentrations, without calibration curves. SPR-based biosensors often suffer from non-specific binding (NSB) occurring with the sensor chip surface and the immobilized targets, especially for complex media such as human serum...
June 7, 2018: Biosensors & Bioelectronics
Mercedes Pérez-Ruiz, Irene Pedrosa-Corral, Sara Sanbonmatsu-Gámez, Cristina Gómez-Camarasa, José María Navarro-Marí
A new molecular assay (Viral CNS Flow Chip kit, Master Diagnóstica, Spain) has been developed for the detection of eight viruses causing acute meningitis and encephalitis, i.e. herpes simplex viruses 1-2, varicella zoster virus, human enterovirus, human parechovirus, Toscana virus, human cytomegalovirus and Epstein Barr virus. The new assay is a multiplex one-step RT-PCR followed by automatic flow-through hybridization, colorimetric detection and image analysis. The limit of detection was 50 copies/reaction, and 10 copies/reaction for human enterovirus and the other seven viruses, respectively...
June 11, 2018: Journal of Virological Methods
Hai-Yin Li, Xian-Wu Lin, Shao-Lei Geng, Wei-Hua Xu
The transforming growth factor-β (TGF-β) superfamily signaling pathway contains two general branches, known as TGF-β and bone morphogenetic protein (BMP), that regulate development in animals. It is well known that TGF-β superfamily signaling participates in the regulation of dauer (lifespan extension) in Caenorhabditis elegans, but little is known about the molecular mechanisms of lifespan extension in the pathway. Diapause, a programmed developmental arrest in insects, is similar to dauer in C. elegans...
June 11, 2018: Biochimica et Biophysica Acta
Wei Lv, Benhua Su, Yuyang Li, Chong Geng, Na Chen
KIAA0101 functions as a regulator of centrosome number in breast cancer. Here, we identify the role of KIAA0101 in breast cancer cell proliferation and cell cycle progression. KIAA0101 knockdown significantly inhibited cell growth, colony formation and G1/S phase transition. Further investigation indicated that KIAA0101 silencing suppressed the expression of CCNE2, CDK6 and CDKN1A. Luciferase reporter assay and ChIP assay demonstrated that Sp1 positively regulated the transcription of CCNE2, CDK6 and CDKN1A...
June 11, 2018: Biochemical and Biophysical Research Communications
Y Moritani, M Usui, K Sano, K Nakazawa, T Hanatani, M Nakatomi, T Iwata, T Sato, W Ariyoshi, T Nishihara, K Nakashima
OBJECTIVE AND BACKGROUND: Human periodontal ligament mesenchymal stem cells (hPDLMSCs) are reported to be responsible for homeostasis and regeneration of periodontal tissue. Although hPDLMSCs are commonly cultured in monolayers, monolayer cultures have been reported as inferior to 3-dimensional cultures such as spheroids, which are spherical clusters of cells formed by self-assembly. The aim of this study was to examine the osteogenic phenotype of spheroids of hPDLMSCs, compared with monolayer cultures of hPDLMSC, in vitro and in vivo...
June 14, 2018: Journal of Periodontal Research
Peiguo Yuan, Liqun Du, B W Poovaiah
During plant-pathogen interactions, plants have to relocate their resources including energy to defend invading organisms; as a result, plant growth and development are usually reduced. Arabidopsis signal responsive1 (AtSR1) has been documented as a negative regulator of plant immune responses and could serve as a positive regulator of plant growth and development. However, the mechanism by which AtSR1 balances plant growth and immunity is poorly understood. Here, we performed a global gene expression profiling using Affymetrix microarrays to study how AtSR1 regulates defense- and growth-related genes in plants with and without bacterial pathogen infection...
June 14, 2018: International Journal of Molecular Sciences
Wenjin Liang, Yong Liao, Zeming Li, Yan Wang, Siqi Zheng, Xiaochen Xu, Fulin Ran, Bo Tang, Zhenran Wang
In this study, we investigated the role of microRNA-644a (miR-644a) in the growth and survival of hepatocellular carcinoma (HCC) cells. MiR-644a levels were lower in HCC tissues than in adjacent peri-cancerous tissues (n = 135). MiR-644a expression was inversely correlated with heat shock factor 1 (HSF1) expression, tumour diameter and TNM stage. Moreover, HepG2 and SMMC-7721 cell lines showed lower miR-644a expression than normal L-O2 hepatocytes. MiR-644a overexpression in HepG2 and SMMC-7721 cells increased apoptosis by downregulating HSF1...
June 14, 2018: Cell Communication and Signaling: CCS
Yao Teng, Kui Zhu, Chunyang Xiong, Jianyong Huang
Mechanical phenotypes of cells are found to hold vital clues to reveal cellular functions and behaviors, which not only has great physiological significance but also is crucial for disease diagnosis. To this end, we developed a set of electrodeformation-based biomechanical microchip assays to quantify mechanical phenotypes on the single-cell level. By investigating the spatio-temporal dynamics of cancer cells driven by dielectrophoresis forces, we captured the key global viscoelastic indexes including cellular elasticity, viscosity, and transition time that was defined as the ratio of the transient viscosity and elasticity, simultaneously and thus explored their intrinsic correlation with cell cycle progression...
June 13, 2018: Analytical Chemistry
Xiaoru Xin, Mengying Wu, Qiuyu Meng, Chen Wang, Yanan Lu, Yuxin Yang, Xiaonan Li, Qidi Zheng, Hu Pu, Xin Gui, Tianming Li, Jiao Li, Song Jia, Dongdong Lu
BACKGROUND: Long noncoding RNA HULC is highly up-regulation in human hepatocellular carcinoma (HCC). However, the functions of HULC in hepatocarcinogenesis remains unclear. METHODS: RT-PCR, Western blotting, Chromatin immunoprecipitation (CHIP) assay, RNA Immunoprecipitation (RIP) and tumorignesis test in vitro and in vivo were performed. RESULTS: HULC is negatively associated with expression of PTEN or miR15a in patients of human liver cancer...
June 12, 2018: Molecular Cancer
Verena M Link, Casey E Romanoski, Dirk Metzler, Christopher K Glass
Cell-specific patterns of gene expression are determined by combinatorial actions of sequence-specific transcription factors at cis-regulatory elements. Studies indicate that relatively simple combinations of lineage-determining transcription factors (LDTFs) play dominant roles in the selection of enhancers that establish cell identities and functions. LDTFs require collaborative interactions with additional transcription factors to mediate enhancer function, but the identities of these factors are often unknown...
June 9, 2018: Nucleic Acids Research
Yanan You, Raquel Cuevas-Diaz Duran, Lihua Jiang, Xiaomin Dong, Shan Zong, Michael Snyder, Jia Qian Wu
Systematic study of the regulatory mechanisms of Hematopoietic Stem Cell and Progenitor Cell (HSPC) self-renewal is fundamentally important for understanding hematopoiesis and for manipulating HSPCs for therapeutic purposes. Previously, we have characterized gene expression and identified important transcription factors (TFs) regulating the switch between self-renewal and differentiation in a multipotent Hematopoietic Progenitor Cell (HPC) line, EML (Erythroid, Myeloid, and Lymphoid) cells. Herein, we report binding maps for additional TFs (SOX4 and STAT3) by using chromatin immunoprecipitation (ChIP)-Sequencing, to address the underlying mechanisms regulating self-renewal properties of lineage-CD34+ subpopulation (Lin-CD34+ EML cells)...
June 12, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Xue-Yin Pan, Yang Yang, Hong-Wu Meng, Hai-di Li, Xin Chen, Hui-Min Huang, Fang-Tian Bu, Hai-Xia Yu, Qin Wang, Cheng Huang, Xiao-Ming Meng, Jun Li
The activation of hepatic stellate cells (HSCs) is a central event in the progression of liver fibrosis. Multiple studies proved that DNA methylation might accelerate HSCs activation. However, the specific pathogenesis of liver fibrosis remains not fully addressed. Our laboratory performed Genome methylation screening to find out the methylated gene in mice with liver fibrosis. The pilot experiments showed that the promoter of prostacyclin synthase ( PTGIS ) gene was hypermethylated in CCl4 -induced liver fibrosis mouse model...
2018: Frontiers in Pharmacology
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