Identification of tRNA-derived fragments and their potential roles in diabetic cataract rats

Epigenomics ◽  
2020 ◽  
Vol 12 (16) ◽  
pp. 1405-1418
Author(s):  
Xiaoyan Han ◽  
Lei Cai ◽  
Yi Lu ◽  
Dan Li ◽  
Jin Yang
Keyword(s):  
Real Time ◽  
Rna Sequencing ◽  
Small Rna ◽  
Real Time Pcr ◽  
Bioinformatics Analysis ◽  
Bioinformatic Analysis ◽  
Transfer Rna ◽  
Small Rna Sequencing ◽  
Quantitative Real Time Pcr ◽  
Diabetic Cataract

Aim: To illustrate the expression profile of transfer RNA-derived fragments and reveal their putative role in the pathogenesis of diabetic cataract (DC) rats. Materials & methods: Small RNA sequencing was conducted in the lens epithelium of rats lens. The data were validated by quantitative real-time PCR, and bioinformatic analysis was performed to explore the roles of the fragments in DC pathogenesis. Results: A total of 213 differentially expressed tRNA-related fragments were identified, in which 111 were upregulated and 102 were downregulated in DC rats. Bioinformatics analysis revealed that several associated pathways might participate in the development of DC rats. Conclusion: tRNA-derived fragments may be involved in the pathogenesis of DC rats.

scholarly journals The circRAB3IP Mediated by eIF4A3 and LEF1 Contributes to Enzalutamide Resistance in Prostate Cancer by Targeting miR-133a-3p/miR-133b/SGK1 Pathway

2021 ◽  
Vol 11 ◽  
Author(s):  
Dong Chen ◽  
Yaqin Wang ◽  
Feiya Yang ◽  
Adili Keranmu ◽  
Qingxin Zhao ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Real Time ◽  
Expression Pattern ◽  
Real Time Pcr ◽  
Bioinformatic Analysis ◽  
Biological Functions ◽  
Quantitative Real Time Pcr ◽  
Regulatory Effects

An increasing number of studies have shown that circRNAs are closely related to the carcinogenesis and development of prostate cancer (PCa). However, little is known about the effect of the biological functions of circRNAs on the enzalutamide resistance of PCa. Through bioinformatic analysis and experiments, we investigated the expression pattern of circRNAs in enzalutamide-resistant PCa cells. Quantitative real-time PCR was used to detect the expression of circRAB3IP, and plasmids that knock down or overexpress circRAB3IP were used to evaluate its effect on the enzalutamide sensitivity of PCa cells. Mechanistically, we explored the potential regulatory effects of eIF4A3 and LEF1 on the biogenesis of circRAB3IP. Our in vivo and in vitro data indicated that increased expression of circRAB3IP was found in enzalutamide-resistant PCa, and knockdown of circRAB3IP significantly enhanced enzalutamide sensitivity in PCa cells. However, upregulation of circRAB3IP resulted in the opposite effects. Further mechanistic research demonstrated that circRAB3IP could regulate the expression of serum and glucocorticoid-regulated kinase 1 (SGK1) by serving as a sponge that directly targets miR-133a-3p/miR-133b. Then, we showed that circRAB3IP partially exerted its biological functions via SGK1 signaling. Furthermore, we discovered that eIF4A3 and LEF1 might increase circRAB3IP expression in PCa.

scholarly journals Circular RNA sequencing indicates circ-IQGAP2 and circ-ZC3H6 as noninvasive biomarkers of primary Sjögren’s syndrome

Rheumatology ◽  
2020 ◽  
Vol 59 (9) ◽  
pp. 2603-2615 ◽  
Author(s):  
Fengxia Li ◽  
Zhenwei Liu ◽  
Bing Zhang ◽  
Shan Jiang ◽  
Qiongdan Wang ◽  
...  
Keyword(s):  
Receiver Operating Characteristic ◽  
Real Time ◽  
Rna Sequencing ◽  
Clinical Features ◽  
Real Time Pcr ◽  
Operating Characteristic ◽  
Receiver Operating Characteristic Analysis ◽  
Quantitative Real Time Pcr ◽  
Characteristic Analysis ◽  
Noninvasive Biomarkers

Abstract Objectives This study aims to characterize the expression profiles of circRNAs in primary Sjogren’s Syndrome (pSS) and examine the potential of noninvasive circular RNAs (circRNAs) as biomarkers of pSS. Methods We performed RNA sequencing of minor salivary gland (MSG) biopsies from four pSS and four non-pSS individuals (subjects undergoing MSG biopsies but not meeting 2012 or 2016 ACR classification criteria for SS). Differentially expressed circRNAs were identified by DESeq2, and confirmed by quantitative real-time PCR in the MSGs as well as in plasma exosomes in 37 pSS and 14 non-pSS subjects. Discriminatory capacity testing using receiver operating characteristic analysis was used to evaluate the performance of circRNAs as diagnostic biomarkers for pSS. Results Circ-IQGAP2 and circ-ZC3H6 had significantly upregulated expression in the MSGs of pSS patients, and this elevated expression was confirmed by quantitative real-time PCR of plasma exosome RNA. The expression of these circRNAs also showed significant correlation with both clinical features, serum IgG level and MSG focus scores. Receiver operating characteristic analysis showed that the indices comprised of both the two circRNAs and clinical features were better able to distinguish pSS from non-pSS subjects with high mean areas under the curve of 0.93 in the MSGs and 0.92 in the plasma exosomes. Conclusion This study indicated the potential roles of circ-IQGAP2 and circ-ZC3H6 as noninvasive biomarkers for the diagnosis of pSS.

scholarly journals Identification of Nutrient-Responsive Arabidopsis and Rapeseed MicroRNAs by Comprehensive Real-Time Polymerase Chain Reaction Profiling and Small RNA Sequencing

2009 ◽  
Vol 150 (3) ◽  
pp. 1541-1555 ◽  
Author(s):  
Bikram Datt Pant ◽  
Magdalena Musialak-Lange ◽  
Przemyslaw Nuc ◽  
Patrick May ◽  
Anja Buhtz ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Real Time ◽  
Rna Sequencing ◽  
Small Rna ◽  
Small Rna Sequencing ◽  
Chain Reaction ◽  
Polymerase Chain

scholarly journals Small RNA Sequencing Reveals Exosomal miRNAs Involved in the Treatment of Asthma by Scorpio and Centipede

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Binqing Tang ◽  
Yingen Wu ◽  
Hong Fang ◽  
Yuqin Wu ◽  
Kehua Shi
Keyword(s):  
Real Time ◽  
Small Rna ◽  
Real Time Pcr ◽  
Mapk Signaling ◽  
Lung Epithelial Cells ◽  
Mouse Lung ◽  
Control Group ◽  
Small Rna Sequencing ◽  
Inflammatory Signaling ◽  
Exosomal Mirnas

Asthma is a common respiratory disease with inflammation in the lungs. Exosomes and microRNAs (miRNAs) play crucial role in inflammation, whereas the role of exosomal miRNA in asthma remains unknown. Here, we aimed to identify the key exosomal miRNAs and their underlying mechanisms involved in scorpio and centipede (SC) treatment in asthma. Eighteen mice were randomly divided into three groups: control group, asthma group, and SC treatment group. Effect of SC was assessed by hematoxylin-eosin staining and real-time PCR. Exosomes from asthma and SC treatment groups were analyzed by small RNA-seq. Results revealed SC significantly alleviated the pathogenesis of asthma and suppressed the release of inflammatory cytokines. A total of 328 exosomal miRNAs were differentially expressed between the exosomes from asthma and SC-treated mice, including 118 up- and 210 downregulated in SC-treated mice. The altered exosomal miRNAs were primarily involved in the function of transcription, apoptotic process, and cell adhesion; and pathway of calcium, Wnt, and MAPK signaling. Real-time PCR verified exosomal miR-147 was downregulated, while miR-98-5p and miR-10a-5p were upregulated in SC-treated mice compared to asthma mice. Moreover, the target genes of miR-147-3p, miR-98-5p, and miR-10a-5p were mainly enriched in Wnt and MAPK inflammatory signaling. miR-10a-5p promoted the proliferation of mouse lung epithelial cells and downregulated the expression of Nfat5 and Map2k6. These data suggest SC-induced exosomal miRNAs might mediate the inflammatory signaling and might be involved in the SC treatment in asthma. The exosomal miRNAs might be promising candidates for the treatment of asthma.

Bioinformatic Analysis of Small RNA Sequencing Libraries

2019 ◽  
pp. 51-63
Author(s):  
Ricardo A. Chávez Montes ◽  
Fabiola Jaimes-Miranda ◽  
Stefan de Folter
Keyword(s):  
Rna Sequencing ◽  
Small Rna ◽  
Bioinformatic Analysis ◽  
Small Rna Sequencing

Screening of non-invasive miRNA biomarker candidates for metastasis of gastric cancer by small RNA sequencing of plasma exosomes

2019 ◽  
Vol 41 (5) ◽  
pp. 582-590 ◽  
Author(s):  
Yingyi Zhang ◽  
Ting Han ◽  
Dan Feng ◽  
Jie Li ◽  
Meihong Wu ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Rna Sequencing ◽  
Small Rna ◽  
Cancer Metastasis ◽  
Cell Types ◽  
Bioinformatic Analysis ◽  
Diagnostic Techniques ◽  
Small Rna Sequencing ◽  
High Relapse Rate ◽  
Gastric Cancer Patients

Abstract Gastric cancer remains one of the most lethal and prevalent malignancies, particularly in China. The majority of patients are diagnosed with gastric cancer at the late stages of the disease. Besides, the high relapse rate also contributes to the high mortality. Therefore, there exists an imperative need for the development of gastric cancer diagnostic techniques as well as novel indicators for gastric cancer metastasis. Exosomes, secreted by a variety of cell types, play critical roles in intercellular communication, which emerge as promising diagnostic biomarkers for gastric cancer. In this study, we present for the first time, at least to the best of our knowledge, the small RNA sequencing spectra of exosomes derived from the gastric cancer patient plasma using next-generation sequencing, focusing on the exploration of metastasis-related biomarkers. The exosomes enriched from patient plasma samples were well characterized by western blotting, transmission electron microscopy and nanoparticle-tracking analysis. In the following bioinformatic analysis of exosomal miRNAs, three candidates were proposed as the biomarkers for metastasis of gastric cancer, namely miR-10b-5p, miR-101-3p and miR-143-5p, for gastric cancer with lymph node metastasis, gastric cancer with ovarian metastasis and gastric cancer with liver metastasis, respectively. RT–qPCR was performed to test the accuracy of these candidates for validation. In conclusion, we successfully isolated and purified exosomes from plasma of patients with gastric cancer and identified several potential exosomal miRNA markers to distinguish gastric cancer patients with various kinds of metastasis.

scholarly journals Gene Expression Profile and Immunological Evaluation of Unique Hypothetical Unknown Proteins of Mycobacterium leprae by Using Quantitative Real-Time PCR

2012 ◽  
Vol 20 (2) ◽  
pp. 181-190 ◽  
Author(s):  
Hee Jin Kim ◽  
Kalyani Prithiviraj ◽  
Nathan Groathouse ◽  
Patrick J. Brennan ◽  
John S. Spencer
Keyword(s):  
Gene Expression ◽  
Real Time ◽  
Real Time Pcr ◽  
Specific Antigen ◽  
Mycobacterium Leprae ◽  
Bioinformatic Analysis ◽  
Cell Mediated Immunity ◽  
Quantitative Real Time Pcr ◽  
Content Type

ABSTRACTThe cell-mediated immunity (CMI)-basedin vitrogamma interferon release assay (IGRA) ofMycobacterium leprae-specific antigens has potential as a promising diagnostic means to detect those individuals in the early stages ofM. lepraeinfection. Diagnosis of leprosy is a major obstacle toward ultimate disease control and has been compromised in the past by the lack of specific markers. Comparative bioinformatic analysis among mycobacterial genomes identified potentialM. leprae-specific proteins called “hypothetical unknowns.” Due to massive gene decay and the prevalence of pseudogenes, it is unclear whether any of these proteins are expressed or are immunologically relevant. In this study, we performed cDNA-based quantitative real-time PCR to investigate the expression status of 131 putative open reading frames (ORFs) encoding hypothetical unknowns. Twenty-six of theM. leprae-specific antigen candidates showed significant levels of gene expression compared to that of ESAT-6 (ML0049), which is an important T cell antigen of low abundance inM. leprae. Fifteen of 26 selected antigen candidates were expressed and purified inEscherichia coli. The seroreactivity to these proteins of pooled sera from lepromatous leprosy patients and cavitary tuberculosis patients revealed that 9 of 15 recombinant hypothetical unknowns elicitedM. leprae-specific immune responses. These nine proteins may be good diagnostic reagents to improve both the sensitivity and specificity of detection of individuals with asymptomatic leprosy.

Bioinformatics analysis integrating metabolomics of m6A RNA microarray in intervertebral disc degeneration

Epigenomics ◽  
2020 ◽  
Vol 12 (16) ◽  
pp. 1419-1441
Author(s):  
Xiaoshuai Wang ◽  
Ningning Chen ◽  
Zefeng Du ◽  
Zemin Ling ◽  
Penghui Zhang ◽  
...  
Keyword(s):  
Intervertebral Disc ◽  
Real Time ◽  
Disc Degeneration ◽  
Real Time Pcr ◽  
Intervertebral Disc Degeneration ◽  
Wnt Pathway ◽  
Bioinformatics Analysis ◽  
Enzyme Activation ◽  
Quantitative Real Time Pcr ◽  
Gsk 3Β

Aim: To explore the potential functions and mechanism of N6.methyladenosine (m6A) abnormality of RNAs in nucleus pulposus from the intervertebral disc degeneration (IDD). Materials & methods: We performed rat model, m6A epitranscriptomic microarray, bioinformatics analysis and metabolomics. Results: In IDD, most of the differentially methylated RNAs showed a significant demethylation situation. The competing endogenous RNA network LOC102555094/ miR-431/ GSK-3β combining downstream Wnt pathway were identified in bioinformatics analysis. For metabolomics, activation of Wnt pathway led to reprogramming of glucose metabolism and enzyme activation of PKM2. Finally, quantitative real-time PCR and methylated RNA immunoprecipitation coupled with quantitative real-time PCR revealed the positive correlation between demethylation of LOC102555094 and expression of both FTO and ZFP217. Conclusion: LOC102555094 might be demethylated by ZFP217, activating FTO and LOC102555094/ miR-431/ GSK-3β/Wnt played a crucial role in IDD.

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