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1.
Genes Chromosomes Cancer ; 59(2): 73-83, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31408253

RESUMO

Hypoxia-induced epithelial-mesenchymal transition (EMT) involves the interplay between chromatin modifiers histone deacetylase 3 (HDAC3) and WDR5. The histone mark histone 3 lysine 4 acetylation (H3K4Ac) is observed in the promoter regions of various EMT marker genes (eg, CDH1 and VIM). To further define the genome-wide location of H3K4Ac, a chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) analysis was performed using a head and neck squamous cell carcinoma (HNSCC) FaDu cell line under normoxia and hypoxia. H3K4Ac was found to be located mainly around the transcription start site. Coupled with analysis of gene expression by RNA sequencing and using a HDAC3 knockdown cell line, 10 new genes (BMI1, GLI1, SMO, FOXF1, SIRT2, etc) that were labeled by H3K4Ac and regulated by HDAC3 were identified. Overexpression or knockdown of GLI1/SMO increased or repressed the in vitro migration and invasion activity in OECM-1/FaDu cells, respectively. In HNSCC patients, coexpression of GLI1 and SMO in primary tumors correlated with metastasis. Our results identify new EMT marker genes that may play a significant role in hypoxia-induced EMT and metastasis and further provide diagnostic and prognostic implications.

2.
Int J Hyg Environ Health ; 223(1): 171-178, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31548162

RESUMO

AIMS: Evidence concerning the impact of ambient particulate matter (PM) on mental health is just emerging and inconsistent. Air pollution with high PM levels has been frequently reported in China, however, no Chinese study has determined the association between PM exposures and anxiety hospitalizations. We examined the potential association between PM concentrations and anxiety admissions in 26 Chinese cities from January 2014 to December 2015. METHODS: A time-stratified case-crossover design was employed in the study. Anxiety hospitalizations were identified according to ICD-10 from the electronic hospitalization summary reports system in China. Conditional logistic regression was applied to estimate the relation between PM levels and anxiety admissions, stratified by age and sex. RESULTS: Positive associations between PM2.5/PM10 and admitted anxiety cases were observed. PM2.5 had the largest effect estimate at lag 5 days, with a per 10 µg/m3 increase corresponding to a 0.63% (95% CI, 0.26-1.00) increase in anxiety admissions. PM10's largest effect estimate was observed at lag 3 days, increasing 0.37% (95% CI, 0.12-0.62) anxiety admissions per 10 µg/m3. Females were more sensitive to PM2.5/PM10 concentrations than males, however, the effect modification by age was not significant. A marginally significant distinction in anxiety hospitalizations was found in patients with and without CVDs when they were exposed to PM2.5. CONCLUSIONS: Our findings indicate that short-term exposure to increased concentrations of PM2.5/PM10 exacerbates risks of anxiety hospitalizations in 26 Chinese cities. We observed effect modification by sex, with significantly stronger associations in female patients. This study offers the promise that reducing PM air pollution could probably reduce the huge disease burden from anxiety disorders.

3.
Sci Total Environ ; 698: 134149, 2020 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-31783450

RESUMO

Phosphate fertilizer applications are an important source of soil Cd in China. However, the input of Cd from phosphate fertilizer has always been neglected in China because of its low content. In this paper, we calculated the Cd input from phosphate fertilizer in China during 2006-2016. According to the data, the total phosphate fertilizer consumption and agriculture application rate tended to decrease after 2014. In 2016, the phosphate fertilizer application rate ranged from 12.14 to 99.38 kg/ha with a mean value of 42.70 kg/ha, and excessive fertilizer application occurred in Xinjiang, Henan, and Hubei Provinces. The Cd content in phosphate fertilizer was 0.75 mg/kg based on 1222 samples. The national Cd input from phosphate fertilizer was estimated to be 10.52 tons in 2016, with DAP/MAP being the largest contributor, accounting for 83.31% of the total input. These findings demonstrate the necessity of performing assessments to regulate the utilization of phosphate fertilizer in China, especially in Henan and Xinjiang Provinces.

4.
J Proteomics ; 211: 103560, 2020 Jan 16.
Artigo em Inglês | MEDLINE | ID: mdl-31669359

RESUMO

This paper reports a laser capture microdissection-tandem mass tag-quantitative proteomics analysis of Al-sensitive cells in root tips. Cherry tomato (Solanum lycopersicum var. cerasiforme 'LA2710') seedlings were treated under 15 µM Al3+ activity for 13 d. Root-tip longitudinal fresh frozen tissue sections of 10 µm thickness were prepared. The Al-sensitive root zone and cells were determined using histochemical analysis of root-tips and micro-sections. A procedure for collecting the Al-sensitive cells using laser capture microdissection-protein extraction-tandem mass tag-proteomics analysis was developed. Proteomics analysis of 18 µg protein/sample with three biological replicates per treatment condition identified 3879 quantifiable proteins each associated with two or more unique peptides. Quantified proteins constituted a broad range of Kyoto Encyclopedia of Genes and Genomes pathways when searched in the annotated tomato genome. Differentially expressed proteins between the Al-treated and non-Al treated control conditions were identified, including 128 Al-up-regulated and 32 Al-down-regulated proteins. Analysis of functional pathways and protein-protein interaction networks showed that the Al-down-regulated proteins are involved in transcription and translation, and the Al-up-regulated proteins are associated with antioxidant and detoxification and protein quality control processes. The proteomics data are available via ProteomeXchange with identifier PXD010459 under project title 'LCM-quantitative proteomics analysis of Al-sensitive tomato root cells'. SIGNIFICANCE: This paper presents an efficient laser capture microdissection-tandem mass tag-quantitative proteomics analysis platform for the analysis of Al sensitive root cells. The analytical procedure has a broad application for proteomics analysis of spatially separated cells from complex tissues. This study has provided a comprehensive proteomics dataset expressed in the epidermal and outer-cortical cells at root-tip transition zone of Al-treated tomato seedlings. The proteomes from the Al-sensitive root cells are valuable resources for understanding and improving Al tolerance in plants.

5.
Methods Mol Biol ; 2079: 3-12, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31728958

RESUMO

Many chimeric RNA prediction software packages are available to assist the scientific community in searching for cancer-specific chimeric RNAs. These packages predict a large number of false positive events, which significantly hampers experimental validation of predicted chimeric RNAs. Here, we describe the detailed steps for (1) prediction of chimeric RNAs using EricScript software, (2) characterization of chimeric RNAs to discard most probable false positive events, and (3) in silico validation of chimeric RNA to select the potential cancer-specific events.

6.
Methods Mol Biol ; 2079: 83-94, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31728963

RESUMO

Reverse-transcription polymerase chain reaction (RT-PCR) is a powerful combination of assays useful in detection and measurement of expressed RNA transcripts. RT-PCR consists of RNA isolation and reverse transcription into complementary DNA (cDNA), which can then be used as input to a variety of PCR-based procedures such as standard PCR, real-time or quantitative PCR (qPCR or qRT-PCR), or TaqMan PCR procedures. These assays are useful in detection of chimeric transcripts, especially when careful consideration is applied to experimental design. In this chapter, we provide guidelines and procedures for use of RT-PCR in detection and measurement of chimeric RNA expression.

7.
Methods Mol Biol ; 2079: 109-116, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31728965

RESUMO

Unbound, single-stranded RNA can be digested by RNase (A or T1) to ribonucleotides, whereas double-stranded RNA is not digested by RNase. Based on this principle, the RNase Protection Assay (RPA) is used to validate chimeric RNAs. Importantly, this assay does not employ reverse transcription (RT), thus avoiding potential false-positive results which could occur during RT such as template-switching. We first generate RNA probes with 32phosphate (P) or biotin that are complementary to the predicted nucleotide sequence of the chimeric RNA, then hybridize them to RNA samples. The labeled RNA probes can bind specifically with the target chimeric RNA in order to form double-stranded RNA. This newly formed RNA is resistant to digestion by RNase and therefore can be identified by high-resolution, denaturing polyacrylamide gel electrophoresis.

8.
Methods Mol Biol ; 2079: 117-124, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31728966

RESUMO

Chimeric RNAs as well as their fused protein products have therapeutic applications ranging from diagnostics to being used as therapeutic target. Many algorithms have been developed to identify chimeric RNAs, however, identification and validation of fused protein product of the chimeric RNA is still an emerging field. These chimeric proteins can be validated by searching and identifying them in publicly available proteomics datasets. Here we describe the detailed steps for (1) downloading and processing publicly available proteomics datasets, (2) developing fusion peptide database by performing in silico tryptic digestion of chimeric proteins, and (3) software used to identify chimeric peptides in the proteomics data.

9.
Methods Mol Biol ; 2079: 143-154, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31728968

RESUMO

Knockdown assays are widely used to study the functions of a gene of interest. RNA interference (RNAi) describes a set of well-known methods used to reduce the expression of a target gene by degrading its mRNA with short hairpin RNAs (shRNAs) or short interfering RNAs (siRNAs). Knockdown of chimeric RNAs present different challenges than standard RNAi targeting for regular genes. Most specifically, sequence homology restricts the targeting region to the chimeric junction and can result in off-target effects on the parental genes. In this chapter, we provide guidelines and procedures for RNAi design of chimeric RNAs, knockdown of chimeric RNAs, downstream experiments for chimeric RNA functional studies and necessary controls to accompany each set of experiments.

10.
Methods Mol Biol ; 2079: 155-166, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31728969

RESUMO

Cloning the open reading frame (ORF) of a protein-coding chimeric RNA into a mammalian expression vector is a simple, practiced way to study the function of the chimeric RNA. Here, we provide procedures for the insertion of the RRM2-C2orf48 fusion ORF into a mammalian expression vector, achieving the overexpression of the RRM2-C2orf48 fusion protein in a colon cancer cell line by retroviral transduction.

11.
Methods Mol Biol ; 2079: 167-175, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31728970

RESUMO

Cellular organelle fractionation, a basic technique in molecular biology, has been devised to separate various cell components, which can then be purified and analyzed biochemically. Isolation of proteins or RNAs from these fractions provides insight into fraction-specific or even organelle-specific expression, which may indicate potential modes of functionality or likelihood for a transcript to encode a protein. These findings can be further utilized to observe differences in expression between normal and diseased cell states, such as cancer. We utilize these techniques to observe expression of chimeric RNAs in these fractions. Within this chapter we describe the most frequently used cellular fractionation technique: the separation of the cytoplasmic fraction from the nuclear fraction in a cell.

12.
Methods Mol Biol ; 2079: 177-186, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31728971

RESUMO

Chimeric RNAs can be formed by trans-splicing from different transcripts or cis-splicing of adjacent genes (cis-SAGe). Cis-SAGe results from read-through transcription of two neighbor genes. To investigate the mechanisms underlying intergenic splicing of adjacent genes, it is important to develop an assay to detect transcriptional read-through. Here, we describe a general RT-PCR based method to confirm the process for cis-SAGe candidates. In this method, we use PCR to amplify cDNA that is reverse transcribed from the read-through precursor mRNA. The result provides a foundation for further downstream mechanistic studies.

13.
Methods Mol Biol ; 2079: 233-241, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31728975

RESUMO

Chimeric RNAs and their products have been shown to be closely associated with tumorigenicity and development in a variety of tumors, making them attractive diagnostic markers and therapeutic targets. In previous chapters, we introduced related research techniques and methods for studying chimeric RNAs. Here, we present an overview of the landscape of chimeric RNAs in bladder cancer and verification of two fusion transcripts which are associated with bladder cancer. We used bioinformatics to analyze the TCGA bladder urothelial carcinoma RNA-sequencing dataset, which contains 414 bladder cancer samples and 19 matched normal samples. We identified 19,547 chimeric RNAs and applied multiple criteria to avoid false positives, reducing this list to 271 high-confidence chimeric RNAs, 13 of which specifically expressed in cancer. We validated 6 of these chimeric in clinical bladder cancer samples, including CHFR-GOLGA3, which was found to be expressed significantly higher in bladder cancer samples in comparison to matched normal samples. We have determined that this chimeric RNA is produced by cis-splicing between adjacent genes (cis-SAGe). Further, we found that CHFR-GOLGA3 is mainly expressed in the nucleus, suggesting that it may not encode chimeric protein and instead act as noncoding RNA. Our findings establish the chimeric landscape of bladder cancer and provide a research strategy for how to conduct chimeric RNA research in other tumors.

14.
Methods Mol Biol ; 2079: 243-258, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31728976

RESUMO

Traditional gene fusions are involved in the development of various neoplasias. DUS4L-BCAP29, a chimeric fusion RNA, has been reported to be a cancer-related fusion in prostate and gastric cancers. This chimeric RNA is believed to play a tumorigenic role. Here, we showed that the DUS4L-BCAP29 fusion transcript exists in a variety of normal tissues. It is also present in noncancerous epithelial and fibroblast cell lines. Quantitatively, the fusion transcript has a similar expression level in noncancerous gastric and prostate cell lines and tissues to its expression in cancerous cell lines and tissues. Previously, a loss-of-function approach was used to report a probable functionality for this fusion. However, this approach is not sufficient to prove such functionality. Alternatively, a gain-of-function approach showed that overexpression of DUS4L-BCAP29 promotes cell growth and motility, even in noncancerous cell lines. Finally, we provide further evidence that the fusion transcript is a product of cis-splicing between adjacent genes. In summary, we believe that in contrast to traditional gene fusions, DUS4L-BCAP29 cannot be used as a cancer biomarker. Instead, it is a fusion transcript that exists in normal physiology and its progrowth effect is not unique to cancer situations.

15.
Nanotechnology ; 31(7): 072001, 2020 Feb 07.
Artigo em Inglês | MEDLINE | ID: mdl-31627201

RESUMO

Near infrared (NIR) excited lanthanide-doped upconversion nanoparticles (UCNPs) are emerging as a new type of fluorescent tag for biological applications, which can emit multi-photon ultraviolet, visible or NIR luminescence for imaging or activation of photosensitive molecules. Here, we present a comprehensive review on recent advances of UCNPs for a manifold of biological applications, including upconversion mechanisms, building bright multicolor upconversion nanocrystals, single nanoparticle and super resolution imaging, in vivo optical and multimodal imaging, photodynamic therapy, light-controlled drug release, biosensing, and toxicities. Our perspectives on the future development of UCNPs are also described.

16.
J Hazard Mater ; 383: 121153, 2020 Feb 05.
Artigo em Inglês | MEDLINE | ID: mdl-31518805

RESUMO

In this study, influences of cations (Na+, K+, Ca2+, and Mg2+), anions (NO3-, Cl-, and SO42-), and humic acid (HA) on the antimicrobial efficacy of silver nanoparticles (AgNPs)/Ag+ against Phanerochaete chrysosporium were investigated by observing cell viability and total Ag uptake. K+ enhanced the antimicrobial toxicity of AgNPs on P. chrysosporium, while divalent cations decreased the toxicity considerably, with preference of Ca2+ over Mg2+. Impact caused by a combination of monovalent and divalent electrolytes was mainly controlled by divalent cations. Compared to AgNPs, however, Ag+ with the same total Ag content exhibited stronger antimicrobial efficacy towards P. chrysosporium, regardless of the type of electrolytes. Furthermore, HA addition induced greater microbial activity under AgNP stress, possibly originating from stronger affinity of AgNPs over Ag+ to organic matters. The obtained results suggested that antimicrobial efficacy of AgNPs was closely related to water chemistry: addition of divalent electrolytes and HA reduced the opportunities directly for AgNP contact and interaction with cells through formation of aggregates, complexes, and surface coatings, leading to significant toxicity reduction; however, in monovalent electrolytes, the dominating mode of action of AgNPs could be toxic effects of the released Ag+ on microorganisms due to nanoparticle dissolution.

17.
J Hazard Mater ; 383: 121127, 2020 Feb 05.
Artigo em Inglês | MEDLINE | ID: mdl-31518810

RESUMO

The ecological toxicity of photocatalysts and toxicity reduction of Cr(VI) have attracted much attention. The development of environmentally-friendly photocatalysts with adsorption and internal hole-scavenging capacity for toxicity reduction of aqueous Cr(VI) via facile preparation method is desirable. In this study, visible-light-active BiOClxBr1-x, BiOClxI1-x and BiOBrxI1-x solid solutions were prepared by simple solvothermal strategy. The BiOCl0.3Br0.7, BiOCl0.7I0.3 and BiOBr0.7I0.3 solid solutions exhibited excellent adsorption capacity and photoreduction ability. The removal efficiency of Cr(VI) by BiOCl0.3Br0.7 was 97.7% within 60 min. BiOCl0.7I0.3 and BiOBr0.7I0.3 can remove Cr(VI) almost completely within less than 30 min, which were much higher than those by BiOCl (81.6%) and BiOBr (67.4%) due to joint effect of adsorption and photoreduction. More importantly, the toxicity evaluation confirmed nontoxicity of BiOClxBr1-x, BiOClxI1-x and BiOBrxI1-x, and rapid toxicity elimination process of Cr(VI).

18.
J Ethnopharmacol ; 246: 112227, 2020 Jan 10.
Artigo em Inglês | MEDLINE | ID: mdl-31509780

RESUMO

ETHNOPHARMACOLOGICAL RELEVANCE: Most cardiovascular diseases ultimately result in heart failure, an intractable problem in modern medicine. Yangxinshi tablet (YXS) is a Chinese medicine formula that is used clinically to treat coronary heart disease. However, the active compounds, potential targets, and pharmacological and molecular mechanism of its anti-heart failure activity remain unclear. Therefore, further investigation is required. AIM OF STUDY: Active ingredients and potential targets of YXS for treating heart failure have been reported previously. However, the molecular functions or biological processes of YXS in energy metabolism have not been discovered. To date, no experimental study to validate the potential anti-heart failure mechanism of YXS. The aim of this study was to study the therapeutic effect of YXS on rats with chronic ischemic heart failure by evaluating rat cardiac function and exercise tolerance, and to explore its potential mechanism by network pharmacology, western blotting, quantitative RT-PCR and histological analysis. MATERIALS AND METHODS: In this investigation, chronic ischemic heart failure rats were randomly assigned to five groups: control group (sham operation), model group (0.5% CMC-Na), trimetazidine group (positive control) and two YXS groups (low- and high-dose groups). Experimental rats were treated by gavage with 10 mg/kg/d (clinical equivalent dose) trimetazidine (TMZ), 500 mg/kg/d (clinical equivalent dose) YXS and 1000 mg/kg/d YXS, respectively, for 5 weeks. The cardiac functions of rats were detected by High-Resolution In Vivo Imaging System. We elucidated novel understanding of the active compounds of YXS in rat plasma and predicted the energy metabolism related targets and processes for heart failure. Then, we validated experimentally the targets and mechanism of YXS on these pathological processes in vivo. RESULTS: It was found that YXS was able to effectively improve cardiac LVIDs, LVEDV, LVESV and EF, decrease myocardial oxygen consumption and reduce myocardial infarct size in rats with chronic ischemic heart failure was similar to that of TMZ. We identified 63 major candidate targets for YXS that are closely to heart failure progression. Enrichment analysis revealed key targets for YXS associated to oxygen delivery, glucose utilization, and mitochondrial biogenesis. Meanwhile, we validated that YXS could promote the expression of downstream HIF-1α, PGC1α and GLUT4 by increasing phosphorylation of PI3K, Akt, mTOR, rpS6 and AMPK. The results show that YXS could activate related PI3K/Akt/mTOR/rpS6/HIF-1α and AMPK/PGC1α/GLUT4 signaling pathways in chronic ischemic heart failure rats. Further experiments demonstrated that YXS increased mitochondrial biogenesis in chronic ischemic heart failure rats and improved exercise tolerance CONCLUSION: YXS treated chronic ischemic heart failure through activating its targets which play pivotal roles in oxygen delivery, glucose utilization and mitochondrial biogenesis to improve energy metabolism through a multi-component, multi-level, multi-target, multi-pathway and multi-mechanism approaches.

19.
J Nanosci Nanotechnol ; 20(4): 2292-2300, 2020 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-31492239

RESUMO

Fluorine-free superhydrophobic cotton fabric was fabricated by coating polyacrylate (PA)/SiO2 nanocomposite. PA/SiO2 nanocomposite was prepared based on the modified SiO2 nanoparticles with double bonds and hexadecyl groups by solution polymerization of butyl acrylate (BA), methyl methacrylate (MMA) and octadecylmethacrylate (OMA). The obtained cotton fabric showed excellent superhydrophobicity with a water contact angle of 152.2±0.4° and a water shedding angle of 8.0±0.2°, due to the simultaneous introduction of surface topography constructed by modified SiO2 nanoparticles and low surface free energy PA adhesive layer and hexadecyl groups onto cotton fibers. The as-obtained products were characterized by Fourier-transform infrared spectrometry (FT-IR), thermal gravimetric analysis (TG), scanning electron microscopy (SEM) and size distribution analysis. The obtained superhydrophobic fabric coated by PA/SiO2 demonstrated good mechanical stability and self-cleaning. The PA/SiO2 coating treatment caused little loss in the tensile strength, breathability, and whiteness of the treated fabric. This approach with improved human/environmental friendliness can pave the potential way for the preparation of superhydrophobic surfaces.

20.
Int J Mol Sci ; 20(23)2019 Nov 28.
Artigo em Inglês | MEDLINE | ID: mdl-31795192

RESUMO

Colorectal cancer (CRC) is a kind of solid tumor and the third most common cancer type in the world. It is a heterogeneous disease characterized by genetic and epigenetic aberrations. The TP53 mutation is the key step driving the transition from adenoma to adenocarcinoma. The functional roles of TP53 mutation in tumor development have been comprehensively investigated. In CRC, TP53 mutation was associated with poor prognosis and chemoresistance. A gain of function (GOF) of p53 mutants promotes cell proliferation, migration and invasion through multiple mechanisms. Restoring wild type p53 function, depleting p53 mutants, or intervention by targeting the oncogenic downstreams provides potential therapeutic strategies. In this review, we comprehensively summarize the GOF of p53 mutants in CRC progression as well as in some other solid tumors, and discuss the current strategies targeting p53 mutants in malignancies.

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