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pcr array analysis reveals a novel expression profile of ferroptosis-related genes in idiopathic pulmonary fibrosis

BMC PULMONARY MEDICINE 2025年第1期25卷 1-17页

作者： Shen, Chenyou Wang, Wei Wei, Dong Yang, Xusheng Jiang, Cheng Sheng, Yating Chen, Yuan Sun, Jie Li, Xiaoshan Li, Guirong Ye, Shugao Chen, Jingyu Nanjing Med Univ Affiliated Wuxi Peoples Hosp Wuxi Peoples Hosp Lung Transplant CtrWuxi Med Ctr 299 Qingyang Rd Wuxi 214023 Jiangsu Peoples R China Nanjing Med Univ Wuxi Peoples Hosp Affiliated Wuxi Peoples Hosp Dept Sci ResWuxi Med Ctr 299 Qingyang Rd Wuxi 214023 Jiangsu Peoples R China Nanjing Med Univ Affiliated Wuxi Peoples Hosp Nanjing Med Univ Dept Neurol Wuxi Peoples HospWuxi Med Ctr Qingyang Rd 299 Wuxi 214023 Jiangsu Peoples R China

Background Idiopathic pulmonary fibrosis (IPF) is a chronic, irreversible, and fatal disease characterized by progressive interstitial lung fibrosis. Given its insidious onset and poor outcome, there is an urgent need to elucidate the molecular mechanisms underlying IPF and identify effective therapeutic targets and diagnosis and prognosis biomarkers. Ferroptosis is an iron-dependent form of programmed cell death that occurs as lipid peroxides accumulate. Growing evidence suggests that ferroptosis is important in IPF. Methods Human ferroptosis pcr array was performed on IPF and control lung tissue. The differentially expressed ferroptosis-related genes (DE-FRGs) were identified, underwent functional enrichment analyses, protein-protein interaction network construction, and potential drug target prediction. The DE-FRGs were validated and their value as diagnostic and prognostic blood biomarkers were evaluated using the Gene Expression Omnibus dataset GSE28042. Results The array identified 13 DE-FRGs. Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that the DE-FRGs were mainly related to iron ion transport, blood microparticles, and oxidoreductase activity, and were involved in porphyrin metabolism, necroptosis, and the p53 signaling pathway in addition to ferroptosis. The 13 DE-FRGs were analyzed using the Drug-Gene Interaction Database to explore novel IPF therapeutic agents, yielding 42 potential drugs. Four DE-FRGs (BBC3, STEAP3, EPRS, SLC39A8) in the peripheral blood of IPF patients from the GSE28042 dataset demonstrated the same expression pattern as that observed in the lung tissue array. The receiver operating characteristic analysis demonstrated that the area under the curve of STEAP3 and EPRS were > 0.75. The survival analysis demonstrated that STEAP3 and EPRS were significantly different between the IPF and control groups. Conclusions The FRG expression profiles in IPF and control lung tissue were characterized

关键词： Idiopathic pulmonary fibrosis Ferroptosis pcr array Bioinformatics analysis Drug targets Biomarkers

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pcr array analysis of gene expression profiles in chronic active Epstein- Barr virus infection

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MICROBES AND INFECTION 2014年第7期16卷 581-586页

作者： Murakami, Masanao Hashida, Yumiko Imajoh, Masayuki Maeda, Akihiko Kamioka, Mikio Senda, Yasutaka Sato, Tetsuya Fujieda, Mikiya Wakiguchi, Hiroshi Daibata, Masanori Kochi Univ Kochi Med Sch Dept Microbiol & Infect Kochi 7838505 Japan Kochi Univ Kochi Med Sch Dept Pediat Kochi 7838505 Japan Kochi Univ Kochi Med Sch Dept Lab Med Kochi 7838505 Japan Kochi Univ Kochi Med Sch Fac Med Kochi 7838505 Japan

To determine the host cellular gene expression profiles in chronic active Epstein Barr virus infection (CAEBV), peripheral blood samples were obtained from three patients with CAEBV and investigated using a pcr array analysis that focused on T-cell/B-cell activation. We identified six genes with expression levels that were tenfold higher in CAEBV patients compared with those in healthy controls. These results were verified by quantitative reverse transcription-pcr. We identified four highly upregulated genes, i.e., IL-10, IL-2, IFNGRI, and INHBA. These genes may be involved in inflammatory responses and cell proliferation, and they may contribute to the development and progression of CAEBV. (C) 2014 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

关键词： Epstein-Barr virus CAEBV Gene profile pcr array Cytokine

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Development and Utilization of a Custom pcr array Workflow: Analysis of Gene Expression in Mycoplasma genitalium and Guinea Pig (Cavia porcellus)

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MOLECULAR BIOTECHNOLOGY 2015年第2期57卷 172-183页

作者： Veselenak, Ronald L. Miller, Aaron L. Milligan, Gregg N. Bourne, Nigel Pyles, Richard B. Univ Texas Med Branch Dept Microbiol & Immunol Galveston TX 77555 USA Univ Texas Med Branch Dept Pediat Galveston TX 77555 USA

Transcriptome analysis is a powerful tool for evaluating molecular pathways central to maturation of specific biological processes and disease states. Recently, pcr-based arrays have supplemented microarray and RNA-seq methodologies for studying changes in gene expression levels. pcr arrays are a more cost efficient alternative, however commercially available assemblies are generally limited to only a few more widely researched species (e.g., rat, human, and mouse). Consequently, the investigation of emerging or under-studied species is hindered until such assays are created. To address this need, we present data documenting the success of a developed workflow with enhanced potential to create and validate novel RT-pcr arrays for underrepresented species with whole or partial genome annotation. Utilizing this enhanced workflow, we have achieved a success rate of 80 % for first-round designs for over 400 primer pairs. Of these, similar to 160 distinct targets were sequence confirmed. Proof of concept studies using two unique arrays, one targeting the pathogenic bacterium Mycoplasma genitalium and the other specific for the guinea pig (Cavia porcellus), allowed us to identify significant (P < 0.05) changes in mRNA expression validated by subsequent qpcr. This flexible and adaptable platform provides a valuable and cost-effective alternative for gene expression analysis.

关键词： pcr array Gene expression Transcription Mycoplasma genitalium Cavia porcellus Guinea pig Immune response

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Matrine induces programmed cell death and regulates expression of relevant genes based on pcr array analysis in C6 glioma cells

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MOLECULAR BIOLOGY REPORTS 2009年第4期36卷 791-799页

作者： Zhang, Shujun Qi, Jiping Sun, Libo Cheng, Binglin Pan, Shangha Zhou, Min Sun, Xueying Harbin Med Univ Hepatosplen Surg Ctr Dept Gen Surg Clin Med Sch 1 Harbin 150012 Peoples R China Harbin Med Univ Dept Pathol Clin Med Sch 1 Harbin 150012 Peoples R China Harbin Med Univ Dept Tradit Chinese Med Clin Med Sch 1 Harbin 150012 Peoples R China

Matrine, one of the main components extracted from Sophora flavescens Ait, has a wide range of pharmacological effects including anti-tumor activities on a number of cancer cell lines. This study has investigated whether matrine could also display anti-tumor action on rat C6 glioma cells. Exposure of C6 cells to matrine resulted in inhibition of proliferation and induction of apoptosis in a dose-dependent manner, as measured by the MTT assay and Flow cytometry. The Annexin V/PI staining further detected the apoptotic cells at both early and late phases of apoptosis. We used AO/EB staining to examine the programmed cell death of matrine-treated C6 cells, and showed that the death rate detected by AO/EB staining was higher than the apoptosis rate measured by Annexin V/PI staining, suggesting that autophagy, the Type II programmed cell death, may be involved in matrine-induced cell death, which was further confirmed by electronic microscopy. To explore the molecular mechanism, an apoptosis real-time pcr array was performed, which has demonstrated that 57 genes were at least 2-fold upregulated, and 11 genes were at least 2-fold downregulated in matrine-treated C6 cells, compared with untreated cells. However, the gene expression profiles could only partly and roughly explain molecular mechanisms of apoptosis and autophagy in matrine-treated C6 cells, thus further investigations are required to confirm the specific molecular pathways and related molecules responsible for the programmed cell death.

关键词： Matrine Glioma Apoptosis pcr array Programmed cell death

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The Stage-specific Testicular Germ Cell Apoptotic Response to Low-dose X-irradiation and 2,5-hexanedione Combined Exposure. I: Validation of the Laser Capture Microdissection Method for qRT-pcr array Application

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TOXICOLOGIC PATHOLOGY 2014年第8期42卷 1221-1228页

作者： Catlin, Natasha R. Huse, Susan M. Boekelheide, Kim Brown Univ Dept Pathol & Lab Med Providence RI 02912 USA

Over the past decade, laser capture microdissection (LCM) has grown as a tool for gene expression profiling of small numbers of cells from tumor samples and of specific cell populations in complex tissues. LCM can be used to study toxicant effects on selected cell populations within the testis at different stages of spermatogenesis. There are several LCM-related hurdles to overcome, including issues inherent to the method itself, as well as biases that result from amplifying the LCM-isolated RNA. Many technical issues associated with the LCM method are addressed here, including increasing RNA yield and obtaining more accurate quantification of RNA yields. We optimized the LCM method optimized to generate RNA quantities sufficient for quantitative reverse transcription polymerase chain reaction (qRT-pcr) array analysis without amplification and were able to validate the method through direct comparison of results from unamplified and amplified RNA from individual samples. The addition of an amplification step for gene expression studies using LCM RNA resulted in a bias, especially for low abundance transcripts. Although the amplification bias was consistent across samples, researchers should use caution when comparing results generated from amplified and unamplified LCM RNA. Here, we have validated the use of LCM-derived RNA with the qRT-pcr array, improving our ability to investigate cell-type and stage-specific responses to toxicant exposures.

关键词： laser capture microdissection testis amplification pcr array

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Responses of the zebrafish hypothalamic-pituitary-gonadal-liver axis pcr array to prochloraz are dependent on timing of sampling

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AQUATIC TOXICOLOGY 2016年 175卷 154-159页

作者： Dang, Yao Wang, Jianghua Giesy, John P. Liu, Chunsheng Huazhong Agr Univ Coll Fisheries Wuhan 430070 Peoples R China Collaborat Innovat Ctr Efficient & Hlth Prod Fish Changde 415000 Hunan Peoples R China Univ Hong Kong Sch Biol Sci Hong Kong Hong Kong Peoples R China Univ Saskatchewan Dept Vet Biomed Sci Saskatoon SK S7N 5B3 Canada Univ Saskatchewan Toxicol Ctr Saskatoon SK S7N 5B3 Canada Nanjing Univ Sch Environm State Key Lab Pollut Control & Resource Reuse Nanjing 210008 Jiangsu Peoples R China

A pcr array, based on expression of genes along the hypothalamic-pituitary-gonadal-liver(HPGL) axis of fish, has been suggested as a useful method for screening of endocrine-disrupting chemicals (EDCs). However, effects of circadian rhythm on responses of the HPGL axis to exposure to chemicals were unknown. In this study, profiles of expression of genes along the HPGL axis and concentrations of 17 beta-estradiol (E2) in blood plasma of female zebrafish were compared at two sampling times of day (8:00 AM and 7:00 PM). Prochloraz (PCZ) was selected as a model chemical to evaluate differences in responses of the HPGL axis at these two times of day. Profiles of responses of concentrations of E2 in plasma and expressions of genes along the HPGL axis genes were different between the two times of sampling. Concentrations of E2 were less, and abundances of mRNA for several genes along the HPGL axis were significantly greater or lesser when samples were collected at 7:00 PM than they were when samples were collected at 8:00 AM. Exposure to three concentrations of PCZ (3, 30 or 300 mu g/L) for 48 h resulted in significantly lesser concentrations of plasma E2 and caused compensatory up-regulation of genes included in hypothalamus, pituitary and ovary. Expressions of genes along the HPGL were more responsive to PCZ at 8:00 AM than they were when samples were collected at 7:00 PM. Correlations among parameters in samples collected at the two times indicated the effects might be due to different concentrations of E2 in plasma due to exposure to PCZ. (C) 2016 Elsevier B.V. All rights reserved.

关键词： HPGL axis pcr array Prochloraz Compensatory response Expressions of genes

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A 'bacteriocin pcr array' for identification of bacteriocin-related structural genes in lactic acid bacteria

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JOURNAL OF MICROBIOLOGICAL METHODS 2012年第2期88卷 197-204页

作者： Macwana, Sunita J. Muriana, Peter M. Oklahoma State Univ RM Kerr Food & Ag Prod Ctr Dept Anim Sci Stillwater OK 74078 USA Oklahoma State Univ Food & Agr Prod Res & Technol Ctr Stillwater OK 74078 USA

Bacteriocins have been identified in many strains of lactic acid bacteria (LAB) which are a source of natural food preservatives and microbial inhibitors. Our objectives were to use a pcr array of primers to identify bacteriocin structural genes in Back LAB. DNA sequence homology at the 5'- and 3'-ends of the various structural genes indicated that non-specific priming may allow pcr amplification of heterologous bacteriocin genes. Successful amplification was obtained by real-time pcr and confirmed by melting curve and agarose gel analysis. Sequence information specific to targeted bacteriocin structural genes from the intra-primer regions of amplimers was compared to sequences residing in GenBank. The bacteriocin pcr array allowed the successful amplification of bacteriocin structural genes from strains of Lactobacillus, Lactococcus, and Pediococcus including one whose amino acid sequence was unable to be determined by Edman degradation analysis. DNA sequence analysis identified as many as 3 bacteriocin structural genes within a given strain, identifying ten unique bacteriocin sequences that were previously uncharacterized (partial homology) and one that was 100% identical to sequences in GenBank. This study provides a rapid approach to sequence and identify bacteriocin structural genes among Bac(+) LAB using a microplate bacteriocin pcr array. (C) 2011 Elsevier B.V. All rights reserved.

关键词： Bacteriocin Real-time pcr Lactic acid bacteria pcr array DNA sequence

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Protective Effects Of Astragalus Polysaccharides On Oxidative Stress In High Glucose-Induced Or SOD2-Silenced H9C2 Cells Based On pcr array Analysis

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DIABETES METABOLIC SYNDROME AND OBESITY-TARGETS AND THERAPY 2019年 12卷 2209-2220页

作者： Sun, Qilin Wu, Xiaoyan Wang, Hao Chen, Wenjie Zhao, Xuelan Yang, Yehong Chen, Wei Fudan Univ Huashan Hosp Dept Geriatr 12 Wu Lu Mu Qi Rd Shanghai 200040 Peoples R China Fudan Univ Expt Teaching Ctr Basic Med Shanghai 200032 Peoples R China Fudan Univ Huashan Hosp Dept Endocrinol 12 Wu Lu Mu Qi Rd Shanghai 200040 Peoples R China

Background: Oxidative stress in cardiac myocytes is an important pathogenesis of diabetic cardiomyopathy (DCM). Previously, we reported that astragalus polysaccharide (APS) has protective effects against the oxidative stress of DCM. This study aimed to determine the effect of APS on the oxidative stress induced by hyperglycemia in H9C2 cells. Methods: Rat H9C2 cells were cultured in vitro and randomly divided into the control group, HG group, APS-HG group, siRNASOD2 group, and APS-siRNASOD2 group. The cellular ultrastructure was measured by transmission electron microscopy. Cell apoptosis was examined by TUNEL staining. Levels of reactive oxygen species (ROS) were detected by a quantitative fluorescence assay (DHE). 8-OH-dG and nitrotyrosine, the indicators of oxidative stress injury, were detected by immunohistochemistry. A pcr array was used to evaluate the expression levels of 84 oxidative stress genes in cultured cells, and the pcr array results were partially verified by Western blot. Results: APS treatment protected the H9C2 cell ultrastructure, reduced the level of cell apoptosis, inhibited cellular ROS production, and reduced the levels of oxidative stress injury indicators 8-OH-dG and nitrotyrosine in high glucose-induced or SOD2-silenced H9C2 cells. It also altered oxidative stress-related genes at the mRNA and protein levels. Conclusion: APS may improve antioxidant capacity and inhibit oxidative stress injury in high glucose induced H9C2 cells.

关键词： diabetic cardiomyopathy cardiomyocyte oxidative stress ROS pcr array astragalus polysaccharide

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pcr array of Specific RNA methylation associated genes Involved in Oxidative Stress of RPE Cells

PCR array of Specific RNA methylation associated genes Invol...

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2023第二十三届国际眼科学学术会议、2023第二十三届国际视光学学术会议、2023第十届国际角膜塑形学术论坛、中国研究型医院学会眼科学与视觉科学专业委员会2023学术年会(海口站)、海南省医学会眼科学分会2023年学术年会暨第51期海南眼科论坛、2023第二十三届上海国际眼科和视光技术及设备展览会(海口站)、2023中国民营眼科医院和视光诊治中心展示推广会

作者： Ke Mao Shanghai renji hospital

Purpose Methylation is the most prevalent RNA modification within protein-coding mRNAs in *** aim of this study was to identify RNA methylation associated genes variance from human retinal pigmented epithelial(RPE) cells under oxidative *** ARPE-19 cells were cultured with ox-LDL(100 mg/L),H2O2(100uM) or serum free medium for 48 ***-specific pcr array was conducted to analyze the differentially expressed RNA methylation associated genes(DEGs) between the different *** ResultsA total of 68 RNA methylation associated genes were identified,of which 11 were upregulated(METTL14,WTAP,FTO,NSUN1,NSUN2,NSUN5,DNMT2,TET2,Prrc2a,LRPPRC and e IF3I)and 8 were downregulated(TRMT61A,METTL1,VIRMA,HAKAI,YTHDF1,ALKBH1,Rtc and Ppc) in H2O2 group compared to control *** 7 genes were upregulated(METTL14,FTO,NSUN1,NSUN2,LRPPRC ei F3b and el F3l) and 6 were downregulated(VIRMA,TRMT61A,METTL1,CMTR1,YTHDF1 and ALYREF) in ox-LDL group compared to control *** western Blot experiments also confirmed pcr array *** ConclusionThis study identified several DEGs from oxidation-stimulated RPE cells,which may indicate the influence of oxidative damage on related miRNA methylation associated genes and explored potential regulatory gene targets for RPE degeneration study.

关键词： pcr array RNA methylasion Oxidative stress RPE cells

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pcr array analysis identified hyperproliferation but not autophagy or apoptosis in fibrous epulis

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JOURNAL OF CLINICAL LABORATORY ANALYSIS 2021年第6期35卷 e23784-e23784页

作者： Jiang, Yangyang Fang, Bing Xu, Bin Shanghai Jiao Tong Univ Shanghai Peoples Hosp 9 Dept Orthodont Sch Med Shanghai Peoples R China Univ Chinese Acad Sci Hwa Mei Hosp Dept Stomatol Ningbo Peoples R China

Background The pathogenesis of fibrous epulis is still quite unclear. Our recent genome-wide RNA sequencing analysis revealed that in fibrous epulis, RAS-PI3K-AKT-NF-kappa B pathway regulates the expression of Bcl-2 family and IAP family genes, leading to increased proliferation and the inhibition of apoptosis. The PI3K/AKT signaling pathway can promote autophagy in human gingival fibroblasts;therefore, the purpose of the present study was to identify whether autophagy is involved in the pathogenesis of fibrous epulis. Methods Differentially expressed genes (DEGs) between fibrous epulis lesions and normal gingival tissues were identified using the pcr array. The expression levels of eighteen autophagy-related (ATG) family genes, twelve B-cell lymphoma 2 (Bcl-2) family genes, and eleven cysteine-dependent aspartate-directed protease (caspase) family genes were validated using quantitative real-time pcr (qRT-pcr). Autophagy induction was determined by measuring microtubule-associated protein light chain 3 (LC3) conversion (LC3-I to LC3-II) by immunoblot analysis. Results The pcr array identified six upregulated genes, whereas no genes were expressed at significantly lower levels. The upregulated genes were BCL2, BCL2L1, CXCR4, HSP90AA1, HSPA8, and IGF1, which all belong to the "regulation of autophagy" group but not the "autophagy machinery components" group. qRT-pcr verified that the expression levels of BCL2, BCL2L1 (also known as BCL-XL), and BCL2L2 (also known as BCL-W) were significantly increased in fibrous epulis. No LC3-I to LC3-II conversion was observed. Conclusions The present study reveals that in fibrous epulis, Bcl-2 and Bcl-xL coordinately mediate gingival cell escape from apoptosis, leading to uncontrolled proliferation. Moreover, ATG family genes are not activated, and autophagy is not involved in this process.

关键词： apoptosis ATG family autophagy Bcl‐ 2 family caspase family fibrous epulis pcr array

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