Detection of Potential Metastatic Prostate Cancer Circulating Biomarkers by Comparison of miRNA Profiles in DU145 Cells and Culture Medium

Fomicheva, K. A.; Osipyants, A. I.; Knyazev, E N; Samatov, Timur R.; Shkurnikov, M. Yu.

doi:10.1007/s10517-017-3715-0

Cited by 19 publications

(8 citation statements)

References 14 publications

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“…This is even more remarkable after excluding the numerous microRNAs already present in the fetal calf serum used for cell culturing ( Figure 1C). This evidences the need for considering appropriate controls for experiments [56], which is not always done and will result in false positive findings.…”

Section: Discussionmentioning

confidence: 99%

Identification and Validation Model for Informative Liquid Biopsy-Based microRNA Biomarkers: Insights from Germ Cell Tumor In Vitro, In Vivo and Patient-Derived Data

Lobo

Gillis

Berg

et al. 2019

Cells

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Liquid biopsy-based biomarkers, such as microRNAs, represent valuable tools for patient management, but often do not make it to integration in the clinic. We aim to explore issues impeding this transition, in the setting of germ cell tumors, for which novel biomarkers are needed. We describe a model for identifying and validating clinically relevant microRNAs for germ cell tumor patients, using both in vitro, in vivo (mouse model) and patient-derived data. Initial wide screening of candidate microRNAs is performed, followed by targeted profiling of potentially relevant biomarkers. We demonstrate the relevance of appropriate (negative) controls, experimental conditions (proliferation), and issues related to sample origin (serum, plasma, cerebral spinal fluid) and pre-analytical variables (hemolysis, contaminants, temperature), all of which could interfere with liquid biopsy-based studies and their conclusions. Finally, we show the value of our identification model in a specific scenario, contradicting the presumed role of miR-375 as marker of teratoma histology in liquid biopsy setting. Our findings indicate other putative microRNAs (miR-885-5p, miR-448 and miR-197-3p) fulfilling this clinical need. The identification model is informative to identify the best candidate microRNAs to pursue in a clinical setting.

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Section: Discussionmentioning

confidence: 99%

Identification and Validation Model for Informative Liquid Biopsy-Based microRNA Biomarkers: Insights from Germ Cell Tumor In Vitro, In Vivo and Patient-Derived Data

Lobo

Gillis

Berg

et al. 2019

Cells

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“…In human laryngeal carcinoma tissues, Sun et al (51) reported that miR-1225-5p promoted a G 1 /S cell cycle arrest and enhanced cell death. In addition, a previous study revealed that OTU deubiquitinase 5 suppression via hsa-miR-4417 and hsa-miR-6782 could maintain the viability of tumor cells and suppress programmed cell death (52). Song et al (53) demonstrated that, in hepatocellular carcinoma cells, miR-4417 can promote proliferation and suppress apoptosis by targeting tripartite motif-containing 35 and regulating the phosphorylation of pyruvate kinase muscle.…”

Section: Discussionmentioning

confidence: 99%

Bioinformatics identification of microRNAs involved in�polycystic ovary syndrome based on microarray data

Hou

Wang²,

Xu³

et al. 2019

Mol Med Report

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Polycystic ovary syndrome (PCOS) is the most common endocrine disease in women of reproductive age. MicroRNAs (miRNAs or miRs) serve important roles in the physiological and pathological process of PCOS. To identify PCOS-associated miRNAs, the dataset GSE84376 was extracted from the Gene Expression Omnibus database. Differentially expressed miRNAs (DE-miRNAs) were obtained from Gene-Cloud Biotechnology Information and potential target genes were predicted using TargetScan, DIANA-microT-CDS, miRDB and miRTarBase tools. Gene Ontology enrichment analysis was performed using Metascape and a protein-protein interaction network was constructed using Cytoscape. Transcription factors were obtained from FunRich. DE-miRNAs were verified by reverse transcription-quantitative PCR. At the screening phase, there were seven DE-miRNAs in the PCOS group not present in the control group. In total, 935 target genes were identified, which are involved in the development and maturation of oocytes. Mitogen-activated protein kinase 1, phosphatase and tensin homolog, cAMP responsive element binding protein 1, signal transducer and activator of transcription 3, interferon γ, Fms-related tyrosine kinase 1, transcription factor p65, insulin receptor substrate 1, DnaJ homolog superfamily C member 10 and casein kinase 2 α 1 were identified as the top 10 hub genes in the protein-protein interaction network. Specificity protein 1 was the most enriched transcription factor. At the validation phase, the levels of Homo sapiens (hsa)-miR-3188 and hsa-miR-3135b were significantly higher in the PCOS group than in the control group. In addition, the expression level of hsa-miR-3135b was significantly correlated with the number of oocytes retrieved, the fertilization rate and the cleavage rate (P<0.05). The present bioinformatics study on miRNAs may offer a novel understanding of the mechanism of PCOS, and may serve to identify novel miRNA therapeutic targets.

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“…RNA was isolated with miRNeasy Mini Kit (Qiagen) according to the manufacturer's protocol. The concentrations and the quality of the purified RNA were assessed using both Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific, USA) and Agilent Bioanalyzer 2100 (Agilent Genomics, USA) (Fomicheva et al, 2017). A260/A280 ratios were in range of 1.92.2.…”

Section: Methodsmentioning

confidence: 99%

LAMA4-Regulating miR-4274 and Its Host Gene SORCS2 Play a Role in IGFBP6-Dependent Effects on Phenotype of Basal-Like Breast Cancer

Shkurnikov

Никулин

Nersisyan

et al. 2019

Front. Mol. Biosci.

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Specificity of RNAi to selected target is challenged by off-target effects, both canonical and non-canonical. Notably, more than half of all human microRNAs are co-expressed with hosting them proteincoding genes. Here we dissect regulatory subnetwork centered on IGFBP6 gene, which is associated with low proliferative state and high migratory activity of basal-like breast cancer. We inhibited expression of IGFBP6 gene in a model cell line for basal-like breast carcinoma MDA-MB-231, then traced secondary and tertiary effects of this knockdown to LAMA4, a laminin encoding gene that contributes to the phenotype of triple-negative breast cancer. LAMA4-regulating miRNA miR-4274 and its host gene SORCS2 were highlighted as intermediate regulators of the expression levels of LAMA4, which correlated in a basal-like breast carcinoma sample subset of TCGA to the levels of SORCS2 negatively. Overall, our study points that the secondary and tertiary layers of regulatory interactions are certainly underappreciated. As these types of molecular event may significantly contribute to the formation of the cell phenotypes after RNA interference based knockdowns, further studies of multilayered molecular networks affected by RNAi are warranted.

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Detection of Potential Metastatic Prostate Cancer Circulating Biomarkers by Comparison of miRNA Profiles in DU145 Cells and Culture Medium

Cited by 19 publications

References 14 publications

Identification and Validation Model for Informative Liquid Biopsy-Based microRNA Biomarkers: Insights from Germ Cell Tumor In Vitro, In Vivo and Patient-Derived Data

Identification and Validation Model for Informative Liquid Biopsy-Based microRNA Biomarkers: Insights from Germ Cell Tumor In Vitro, In Vivo and Patient-Derived Data

Bioinformatics identification of microRNAs involved in�polycystic ovary syndrome based on microarray data

LAMA4-Regulating miR-4274 and Its Host Gene SORCS2 Play a Role in IGFBP6-Dependent Effects on Phenotype of Basal-Like Breast Cancer

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