scholarly journals Circular RNA Expression Profiling Identifies Prostate Cancer- Specific circRNAs in Prostate Cancer

2018 ◽  
Vol 50 (5) ◽  
pp. 1903-1915 ◽  
Author(s):  
Qianlin Xia ◽  
Tao Ding ◽  
Guihong Zhang ◽  
Zehuan Li ◽  
Ling Zeng ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Polymerase Chain Reaction Analysis ◽  
Circular Rna ◽  
Differentially Expressed ◽  
Pcr Analysis ◽  
High Morbidity ◽  
Qrt Pcr ◽  
Diagnosis And Prognosis ◽  
Novel Biomarkers ◽  
Rna Expression Profiling

Background/Aims: Prostate cancer (PCa) is one of the main cancers that damage males’ health severely with high morbidity and mortality, but there is still no ideal molecular marker for the diagnosis and prognosis of prostate cancer. Methods: To determine whether the differentially expressed circRNAs in prostate cancer can serve as novel biomarkers for prostate cancer diagnosis, we screened differentially expressed circRNAs using SBC-ceRNA array in 4 pairs of prostate tumor and paracancerous tissues. A circRNA-miRNA-mRNA regulatory network for the differential circRNAs and their host genes was constructed by Cytoscape3.5.1 software. Quantitative real-time polymerase chain reaction analysis (qRT-PCR) was performed to confirm the microarray data. Results: We found 1021 differentially expressed circRNAs in PCa tumor using SBC-ceRNA array and confirmed the expression of circ_0057558, circ_0062019 and SLC19A1 in PCa cell lines and tumor tissues through qRT-PCR analysis. We demonstrated that combination of PSA level and two differentially expressed circRNAs showed significantly increased AUC, sensitivity and specificity (0.938, 84.5% and 90.9%, respectively) than PSA alone (AUC of serum PSA was 0.854). Moreover, circ_0057558 was correlated positively with total cholesterol. The functional network of circRNA-miRNA-mRNA analysis showed that circ_0057558 and circ_0034467 regulated miR-6884, and circ_0062019 and circ_0060325 regulated miR-5008. Conclusion: Our results demonstrated that differentially expressed circRNAs (circ_0062019 and circ_0057558) and host gene SLC19A1 of circ_0062019 could be used as potential novel biomarkers for prostate cancer.

scholarly journals ITRAQ-based quantitative proteomic analysis of Fusarium moniliforme (Fusarium verticillioides) in response to Phloridzin inducers

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Rong Zhang ◽  
Weitao Jiang ◽  
Xin Liu ◽  
Yanan Duan ◽  
Li Xiang ◽  
...  
Keyword(s):  
Fusarium Moniliforme ◽  
Abiotic Factors ◽  
Fusarium Verticillioides ◽  
Protein Profile ◽  
Sugar Metabolism ◽  
Differentially Expressed ◽  
Pcr Analysis ◽  
Differentially Expressed Proteins ◽  
Apple Replant Disease ◽  
Qrt Pcr

Abstract Background Apple replant disease (ARD) has been reported from all major fruit-growing regions of the world, and is often caused by biotic factors (pathogen fungi) and abiotic factors (phenolic compounds). In order to clarify the proteomic differences of Fusarium moniliforme under the action of phloridzin, and to explore the potential mechanism of F. moniliforme as the pathogen of ARD, the role of Fusarium spp. in ARD was further clarified. Methods In this paper, the quantitative proteomics method iTRAQ analysis technology was used to analyze the proteomic differences of F. moniliforme before and after phloridzin treatment. The differentially expressed protein was validated by qRT-PCR analysis. Results A total of 4535 proteins were detected, and 293 proteins were found with more than 1.2 times (P< 0.05) differences. In-depth data analysis revealed that 59 proteins were found with more than 1.5 times (P< 0.05) differences, and most proteins were consistent with the result of qRT-PCR. Differentially expressed proteins were influenced a variety of cellular processes, particularly metabolic processes. Among these metabolic pathways, a total of 8 significantly enriched KEGG pathways were identified with at least 2 affiliated proteins with different abundance in conidia and mycelium. Functional pathway analysis indicated that up-regulated proteins were mainly distributed in amino sugar, nucleotide sugar metabolism, glycolysis/ gluconeogenesis and phagosome pathways. Conclusions This study is the first to perform quantitative proteomic investigation by iTRAQ labeling and LC-MS/MS to identify differentially expressed proteins in F. moniliforme under phloridzin conditions. The results confirmed that F. moniliforme presented a unique protein profile that indicated the adaptive mechanisms of this species to phloridzin environments. The results deepened our understanding of the proteome in F. moniliforme in response to phloridzin inducers and provide a basis for further exploration for improving the efficiency of the fungi as biocontrol agents to control ARD.

scholarly journals Transcriptomic Analysis of Dark-Induced Senescence in Bermudagrass (Cynodon dactylon)

Plants ◽  
2019 ◽  
Vol 8 (12) ◽  
pp. 614
Author(s):  
Jibiao Fan ◽  
Yanhong Lou ◽  
Haiyan Shi ◽  
Liang Chen ◽  
Liwen Cao
Keyword(s):  
Leaf Senescence ◽  
Plant Hormone ◽  
Bioinformatics Analysis ◽  
Cynodon Dactylon ◽  
Differential Expression Analysis ◽  
Differentially Expressed ◽  
Pcr Analysis ◽  
Aesthetic Quality ◽  
Qrt Pcr

Leaf senescence induced by prolonged light deficiency is inevitable whenever turfgrass is cultivated in forests, and this negatively influences the survival and aesthetic quality of the turfgrass. However, the mechanism underlying dark-induced senescence in turfgrass remained obscure. In this study, RNA sequencing was performed to analyze how genes were regulated in response to dark-induced leaf senescence in bermudagrass. A total of 159,207 unigenes were obtained with a mean length of 948 bp. The differential expression analysis showed that a total of 59,062 genes, including 52,382 up-regulated genes and 6680 down-regulated genes were found to be differentially expressed between control leaves and senescent leaves induced by darkness. Subsequent bioinformatics analysis showed that these differentially expressed genes (DEGs) were mainly related to plant hormone (ethylene, abscisic acid, jasmonic acid, auxin, cytokinin, gibberellin, and brassinosteroid) signal transduction, N-glycan biosynthesis, and protein processing in the endoplasmic reticulum. In addition, transcription factors, such as WRKY, NAC, HSF, and bHLH families were also responsive to dark-induced leaf senescence in bermudagrass. Finally, qRT-PCR analysis of six randomly selected DEGs validated the accuracy of sequencing results. Taken together, our results provide basic information of how genes respond to darkness, and contribute to the understanding of comprehensive mechanisms of dark-induced leaf senescence in turfgrass.

scholarly journals Genomewide analysis of circular RNA in pituitaries of normal and heat-stressed sows

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Haojie Zhang ◽  
Baoyu Hu ◽  
Jiali Xiong ◽  
Ting Chen ◽  
Qianyun Xi ◽  
...  
Keyword(s):  
Heat Stress ◽  
Heat Shock ◽  
Heat Shock Protein ◽  
Noncoding Rna ◽  
Target Genes ◽  
Hormone Secretion ◽  
Circular Rna ◽  
Differentially Expressed ◽  
Pcr Analysis ◽  
Pituitary Hormone

Abstract Background As a newly characterized type of noncoding RNA, circular RNA (circRNA) has been shown to have functions in diverse biological processes of animals. It has been reported that several noncoding RNAs may regulate animals’ response to heat stress which can be easily induced by hyperthermia in summer. However, the expression and functions of circRNAs in the pituitary of sows and whether they participate in heat stress adaption are still unclear. Results In this study, we found that high temperature over the thermoneutral zone of sows during the summer increased the serum heat shock protein 70 (HSP70) level, decreased the superoxide dismutase (SOD) vitality and prolactin (PRL) concentration, and induced heat stress in sows. Then, we explored circRNA in the pituitary of heat-stressed and normal sows using RNA sequencing and bioinformatics analysis. In total, 12,035 circRNAs were detected, with 59 circRNAs differentially expressed, including 42 up-regulated and 17 down-regulated circRNAs in pituitaries of the heat-stressed sows. Six randomly selected circRNAs were identified through reverse transcription PCR followed by DNA sequencing and other 7 randomly selected differentially expressed circRNAs were verified by quantitative real-time PCR analysis. The predicted target genes regulated by circRNAs through sponging microRNAs (miRNAs) were enriched in metabolic pathway. Furthermore, the predicted circRNA–miRNA–mRNA interactions showed that some circRNAs might sponge miRNAs to regulate pituitary-specific genes and heat shock protein family members, indicating circRNA’s roles in pituitary hormone secretion and heat stress response. Conclusions Our results provided a meaningful reference to understand the functions of circRNA in the porcine pituitary and the mechanisms by which circRNA may participate in animals’ response to heat stress.

scholarly journals Serum Exosomal MicroRNAs as Potential Circulating Biomarkers for Endometriosis

2020 ◽  
Vol 2020 ◽  
pp. 1-10 ◽  
Author(s):  
Lu Zhang ◽  
Huihui Li ◽  
Ming Yuan ◽  
Dong Li ◽  
Chang Sun ◽  
...  
Keyword(s):  
Area Under The Curve ◽  
Roc Curves ◽  
Diagnostic Value ◽  
Pcr Analysis ◽  
Go Annotation ◽  
Qrt Pcr ◽  
Noninvasive Biomarker ◽  
Novel Biomarkers ◽  
Negative Controls ◽  
Exosomal Mirna

Background. A reliable noninvasive biomarker is not yet available for endometriosis diagnosis. Novel biomarkers for the diagnosis of endometriosis are urgently needed. The molecular constituents of exosomes, especially exosomal microRNAs (miRNAs), have considerable potential as novel biomarkers for clinical diagnosis. This study is aimed at exploring aberrant exosomal miRNA profiles by using miRNA microarray and at providing more accurate molecular biomarkers of endometriosis. Methods. Exosomes were isolated from the serum of patients with endometriosis and negative controls and identified by electron microscopy, nanoparticle tracking analysis, and Western blot. Exosomal miRNAs were profiled by miRNA microarrays. The expression of selective serum exosomal miRNA was validated by qRT-PCR. Receiver operating characteristic (ROC) curves were established to explore the diagnostic value of selective miRNAs. Finally, GO annotation and KEGG pathway enrichment analyses were used to display possible functions associated with the two miRNAs. Results. A total of 24 miRNAs showed differential levels of enrichment with P<0.05 and log2 fold change>1 by miRNA microarrays. Among the six selective miRNAs (i.e., miR-134-5p, miR-197-5p, miR-22-3p, miR-320a, miR-494-3p, and miR-939-5p), qRT-PCR analysis revealed that miR-22-3p and miR-320a were significantly upregulated in serum exosomes from patients with endometriosis compared with negative individuals. ROC curve revealed that the serum exosomal miR-22-3p and miR-320a yielded the area under the curve values of 0.855 and 0.827, respectively. Conclusion. Our results demonstrated that exosomal miR-22-3p and miR-320a were significantly increased in the sera of patients with endometriosis. The two miRNAs may be useful potential biomarkers for endometriosis diagnosis.

scholarly journals Detection of Tear Biomarkers for Future Prostate Cancer Diagnosis

2010 ◽  
Vol 3 (1) ◽  
pp. 26-29 ◽  
Author(s):  
Yong Li
Keyword(s):  
Prostate Cancer ◽  
Benign Prostate Hyperplasia ◽  
Specific Antigen ◽  
Clinical Proteomics ◽  
Prostate Hyperplasia ◽  
Psa Test ◽  
Diagnosis And Prognosis ◽  
Novel Biomarkers ◽  
Unique Source ◽  
Benign Prostate

Prostate cancer (CaP) continues to be the second leading cause of cancer-specific death in men in Western countries. The marker currently used for CaP detection is an increase in serum prostate specific antigen (PSA). However, the PSA test may give false positive or negative information and does not allow the differentiation of benign prostate hyperplasia (BPH), non-aggressive CaP and aggressive CaP. Tears are a unique source of body fluid and contain proteins, peptides, mucins and lipids, which is useful for studying clinical proteomics. Advances in the field of proteomics have greatly enhanced the study of tears, with a greater number of proteins now being identified in tears. Identification of novel biomarkers in tear is a new area of development. Modern advances in the field of proteomic techniques hold the promise of providing the clinical oncologists with new tools to find novel CaP biomarkers for early diagnosis and prognosis.

scholarly journals miR-10a-5p and miR-29b-3p as Extracellular Vesicle-Associated Prostate Cancer Detection Markers

Cancers ◽  
2019 ◽  
Vol 12 (1) ◽  
pp. 43 ◽  
Author(s):  
Thomas Stefan Worst ◽  
Christopher Previti ◽  
Katja Nitschke ◽  
Nicolle Diessl ◽  
Julia Christina Gross ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Cell Lines ◽  
Expression Profiling ◽  
Cell Types ◽  
Extracellular Vesicle ◽  
Tissue Samples ◽  
Prostate Cell ◽  
Qrt Pcr ◽  
Rna Expression Profiling ◽  
Biomarker Research

Extracellular vesicles (EVs) are shed by many different cell types. Their nucleic acids content offers new opportunities for biomarker research in different solid tumors. The role of EV RNA in prostate cancer (PCa) is still largely unknown. EVs were isolated from different benign and malignant prostate cell lines and blood plasma from patients with PCa (n = 18) and controls with benign prostatic hyperplasia (BPH) (n = 7). Nanoparticle tracking analysis (NTA), Western blot, electron microscopy, and flow cytometry analysis were used for the characterization of EVs. Non-coding RNA expression profiling of PC3 metastatic PCa cells and their EVs was performed by next generation sequencing (NGS). miRNAs differentially expressed in PC3 EVs were validated with qRT-PCR in EVs derived from additional cell lines and patient plasma and from matched tissue samples. 92 miRNAs were enriched and 48 miRNAs were depleted in PC3 EVs compared to PC3 cells, which could be confirmed by qRT-PCR. miR-99b-5p was significantly higher expressed in malignant compared to benign EVs. Furthermore, expression profiling showed miR-10a-5p (p = 0.018) and miR-29b-3p (p = 0.002), but not miR-99b-5p, to be overexpressed in plasma-derived EVs from patients with PCa compared with controls. In the corresponding tissue samples, no significant differences in the miRNA expression could be observed. We thus propose that EV-associated miR-10a-5p and miR-29b-3p could serve as potential new PCa detection markers.

scholarly journals Metabolic Reprogramming and Predominance of Solute Carrier Genes during Acquired Enzalutamide Resistance in Prostate Cancer

Cells ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 2535
Author(s):  
Shiv Verma ◽  
Eswar Shankar ◽  
E. Ricky Chan ◽  
Sanjay Gupta
Keyword(s):  
Prostate Cancer ◽  
Drug Resistance ◽  
Cancer Cells ◽  
Standard Of Care ◽  
Resistant Cell ◽  
Metabolic Reprogramming ◽  
Differentially Expressed ◽  
Pcr Analysis ◽  
Prostate Cancer Cells ◽  
Solute Carrier

Androgen deprivation therapy (ADT) is standard-of-care for advanced-stage prostate cancer, and enzalutamide (Xtandi®, Astellas, Northbrook, IL, USA), a second generation antiandrogen, is prescribed in this clinical setting. The response to this medication is usually temporary with the rapid emergence of drug resistance. A better understanding of gene expression changes associated with enzalutamide resistance will facilitate circumventing this problem. We compared the transcriptomic profile of paired enzalutamide-sensitive and resistant LNCaP and C4-2B prostate cancer cells for identification of genes involved in drug resistance by performing an unbiased bioinformatics analysis and further validation. Next-Gen sequencing detected 9409 and 7757 genes differentially expressed in LNCaP and C4-2B cells, compared to their parental counterparts. A subset of differentially expressed genes were validated by qRT-PCR. Analysis by the i-pathway revealed membrane transporters including solute carrier proteins, ATP-binding cassette transporters, and drug metabolizing enzymes as the most prominent genes dysregulated in resistant cell lines. RNA-Seq data demonstrated predominance of solute carrier genes SLC12A5, SLC25A17, and SLC27A6 during metabolic reprogramming and development of drug resistance. Upregulation of these genes were associated with higher uptake of lactic/citric acid and lower glucose intake in resistant cells. Our data suggest the predominance of solute carrier genes during metabolic reprogramming of prostate cancer cells in an androgen-deprived environment, thus signifying them as potentially attractive therapeutic targets.

scholarly journals Differential Transcription Profiling in Bone Marrow Mononuclear Cells Between Myasthenia Gravis Patients With or Without Thymoma

2021 ◽  
Author(s):  
Jingqun Tang ◽  
Ziming Ye ◽  
Yi Liu ◽  
Mengxiao Zhou ◽  
chao qin
Keyword(s):  
Stem Cells ◽  
Bone Marrow ◽  
Myasthenia Gravis ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Mononuclear Cells ◽  
Differentially Expressed ◽  
Pcr Analysis ◽  
Bone Marrow Mononuclear Cells ◽  
Qrt Pcr

Abstract PurposeDefective stem cells have been recognized as being associated with autoimmune diseases, such as systemic lupus erythematosus, rheumatoid arthritis, autoimmune cytopenias and myasthenia gravis (MG). However, the differential gene expression profile of bone marrow mononuclear cells (BMMCs) and the molecular mechanisms underlying MG pathogenesis have not been fully elucidated. Therefore, we investigated the abnormal expression and potential roles and mechanisms of mRNAs in BMMCs among patients with MG with or without thymoma.MethodsTranscription profiling of BMMCs in patients with MG without thymoma (M2) and patients with thymoma-associated MG (M1) was undertaken by using high-throughput RNA sequencing (RNA-Seq), and disease-related differentially expressed genes were validated by quantitative real-time polymerase chain reaction (qRT-PCR).ResultsRNA-Seq demonstrated 60 significantly upregulated and 65 significantly downregulated genes in M2 compared with M1. Five disease-related differentially expressed genes were identified and validated by qRT-PCR analysis. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed to predict the functions of aberrantly expressed genes. Recombination activating 1 (RAG1), RAG2, BCL2-like 11, phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform and repressor element-1-silencing transcription factor might play roles in MG pathogenesis involving the primary immunodeficiency signaling pathway, signaling pathways regulating pluripotency of stem cells and forkhead box O signaling pathway.ConclusionThe aberrantly expressed genes of BMMCs in M1 or M2 patients demonstrate the underlying mechanisms governing the pathogenesis of MG.

scholarly journals BZW1 Promotes Cell Proliferation in Prostate Cancer by Regulating TGF-β1/Smad Pathway

2020 ◽  
Author(s):  
Teng-Cheng Li ◽  
Zhuo-Lun Sun ◽  
Chu-Tian Xiao ◽  
Jie-Ying Wu ◽  
Ke Li
Keyword(s):  
Prostate Cancer ◽  
Cell Proliferation ◽  
Specific Antigen ◽  
High Expression ◽  
Pcr Analysis ◽  
Mrna Levels ◽  
Smad Pathway ◽  
Over Expression ◽  
Qrt Pcr ◽  
Tgf Β1

Abstract Background Recently, basic leucine zipper and the W2 domain-containing protein 1 (BZW1) is reported to be implicated in tumor progression. However, the role of BZW1 in prostate cancer remains unknown. This study is aimed to investigate the expression of BZW1 and its influence on cell proliferation in prostate cancer. Methods The expression levels of BZW1 were measured in 136 cases of prostate cancer and matched adjacent non-cancerous prostate tissues by quantificational real-time polymerase chain reaction (qRT-PCR) and immunohistochemistry (IHC). Then, the effect of BZW1 on cell proliferation was further explored. Results QRT-PCR analysis shown that the mRNA levels of BZW1 in prostate cancer were significantly greater compared with those in matched adjacent non-cancerous prostate tissues (P<0.001). IHC results shown the high-expression rate of BZW1 in prostate cancer and matched adjacent non-cancerous prostate tissues were 68.4% and 32.4%, and the difference was statistically significant (P<0.001). BZW1 high-expression significantly correlated with T stage, lymph node metastasis, prostate specific antigen (PSA) and Gleason score (P<0.05). Patients with BZW1 high-expression presented unfavorable prognosis compared with those with BZW1 low-expression (P=0.002). In addition, CCK-8 and Colony formation assays revealed that BZW1 over-expression significantly promoted cell proliferation in vitro. Tumor xenograft shown BZW1 knockdown significantly inhibited tumor growth in vivo. Moreover, BZW1 overexpression activated the TGF-β1/Smad1/Smad3 pathway. Conclusion BZW1 over-expression predicts poorer prognosis and promotes cell proliferation in prostate cancer by regulating TGF-β1/Smad pathway.

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