miPrimer: an empirical-based qPCR primer design method for small noncoding microRNA

Kang, Shih-Ting; Hsieh, Yi-Shan; Feng, Chi-Ting; Chen, Yuting; Yang, Pok Eric; Chen, Wei-Ming

doi:10.1261/rna.061150.117

Cited by 14 publications

(5 citation statements)

References 33 publications

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“…Next, miR-26b-5p, miR-4530, and miR-28-5p were further validated by real-time miRNA quantification using stem-loop RT-PCR (21)(22)(23)(24)(25)(26)(27) in glioma cell lines A172 and SNB19 (Figures 2B,C). A set of endogenous RNAs SNOD48, SNOD44, SNOD47, and U6 served as endogenous controls in real-time miRNA quantification to normalize miRNA gene expression.…”

Section: Validation Of Mirna Array Results By Sitrpm7mentioning

confidence: 99%

TRPM7 Induces Mechanistic Target of Rap1b Through the Downregulation of miR-28-5p in Glioma Proliferation and Invasion

et al. 2019

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Objectives: Our previous findings demonstrate that channel-kinase transient receptor potential (TRP) ion channel subfamily M, member 7 (TRPM7) is critical in regulating human glioma cell migration and invasion. Since microRNAs (miRNAs) participate in complex regulatory networks that may affect almost every cellular and molecular process during glioma formation and progression, we explored the role of miRNAs in human glioma progression by comparing miRNA expression profiles due to differentially expressed TRPM7. Methods: First, we performed miRNA microarray analysis to determine TRPM7's miRNA targets upon TRPM7 silencing in A172 cells and validated the miRNA microarray data using A172, U87MG, U373MG, and SNB19 cell lines by stem-loop RT-qPCRs. We next determined whether TRPM7 regulates glioma cell proliferation and migration/invasion through different functional domains by overexpressing wild-type human TRPM7 (wtTRPM7), two mutants with TRPM7's α-kinase domain deleted (kinase-DK), or a point mutation in the ATP binding site of the α-kinase domain (K1648R-KR). In addition, we determined the roles of miR-28-5p in glioma cell proliferation and invasion by overexpressing or under expressing miR-28-5p in vitro. Lastly, we determined whether a Ras-related small GTP-binding protein (Rap1b) is a target of miR-28-5p in glioma tumorigenesis. Results: The miRNA microarray data revealed a list of 16 downregulated and 10 upregulated miRNAs whose transcripts are significantly changed by TRPM7 knock-down. Cell invasion was significantly reduced in two TRPM7 mutants with inactive kinase domain, kinase, and K1648R transfected glioma cells. miR-28-5p overexpression suppressed glioma cells' proliferation and invasion, and miR-28-5p under expression led to a significant increase in glioma cell proliferation and migration/invasion compared to that of the controls. miR-28-5p suppressed glioma cell proliferation and migration by targeting Rap1b. Co-transfection of siRap1b with miR28-5p inhibitor reduced the glioma cell proliferation and invasion, caused by the latter. Wan et al. TRPM7 Induces Rap1b in Glioma Conclusions: These results indicate that TRPM7's channel activity is required for glioma cell growth while the kinase domain is required for cell migration/invasion. TRPM7 regulates miR-28-5p expression, which suppresses cell proliferation and invasion in glioma cells by targeting Rap1b signaling.

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Section: Validation Of Mirna Array Results By Sitrpm7mentioning

confidence: 99%

TRPM7 Induces Mechanistic Target of Rap1b Through the Downregulation of miR-28-5p in Glioma Proliferation and Invasion

et al. 2019

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“…The diversity indices were constructed using Phyloseq 91 . To see structural segregation between groups, Partial Least Squares Discriminant Analysis (PLS-DA) model was generated using PRIMER7 92 . Functional metagenome of the oral microbiome based on BioCyc orthology abundance was inferred using PAPRICA and VOOM 93 , 94 .…”

Section: Methodsmentioning

confidence: 99%

Differences in the bacteriome of swab, saliva, and tissue biopsies in oral cancer

Gopinath

Menon

Chong

et al. 2021

Sci Rep

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Microbial dysbiosis has been implicated in the pathogenesis of oral cancer. We analyzed the compositional and metabolic profile of the bacteriome in three specific niches in oral cancer patients along with controls using 16SrRNA sequencing (Illumina Miseq) and DADA2 software. We found major differences between patients and control subjects. Bacterial communities associated with the tumor surface and deep paired tumor tissue differed significantly. Tumor surfaces carried elevated abundances of taxa belonging to genera Porphyromonas, Enterobacteriae, Neisseria, Streptococcus and Fusobacteria, whereas Prevotella, Treponema, Sphingomonas, Meiothermus and Mycoplasma genera were significantly more abundant in deep tissue. The most abundant microbial metabolic pathways were those related to fatty-acid biosynthesis, carbon metabolism and amino-acid metabolism on the tumor surface: carbohydrate metabolism and organic polymer degradation were elevated in tumor tissues. The bacteriome of saliva from patients with oral cancer differed significantly from paired tumor tissue in terms of community structure, however remained similar at taxonomic and metabolic levels except for elevated abundances of Streptococcus, Lactobacillus and Bacteroides, and acetoin-biosynthesis, respectively. These shifts to a pro-inflammatory profile are consistent with other studies suggesting oncogenic properties. Importantly, selection of the principal source of microbial DNA is key to ensure reliable, reproducible and comparable results in microbiome studies.

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“…In the present study, we utilized a novel multigene expression profiling platform, PanelChip (Quark Biosciences, Inc., Hsinchu, Taiwan) (26,27), to explore miRNAs that are differentially expressed in patients with RIF. We identified 6 miRNAs that could contribute to RIF.…”

mentioning

confidence: 99%

A novel platform for discovery of differentially expressed microRNAs in patients with repeated implantation failure

Chen

Lu²,

Yang³

et al. 2021

Fertility and Sterility

Self Cite

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Objective: To identify predictor microRNAs (miRNAs) from patients with repeated implantation failure (RIF). Design: Systemic analysis of miRNA profiles from the endometrium of patients undergoing in vitro fertilization (IVF). Setting: University research institute, private IVF center, and molecular testing laboratory. Patient(s): Twenty five infertile patients in the discovery cohort and 11 patients in the validation cohort. Interventions(s): None. Main Outcome Measure(s): A signature set of miRNA associated with the risk of RIF. Result(s): We designed a reproductive disease-related PanelChip to access endometrium miRNA profiles in patients undergoing IVF.Three major miRNA signatures, including hsa-miR-20b-5p, hsa-miR-155-5p, and hsa-miR-718, were identified using infinite combination signature search algorithm analysis from 25 patients in the discovery cohort undergoing IVF. These miRNAs were used as biomarkers in the validation cohort of 11 patients. Finally, the 3-miRNA signature was capable of predicting patients with RIF with an accuracy >90%. Conclusion(s):Our findings indicated that specific endometrial miRNAs can be applied as diagnostic biomarkers to predict RIF. Such information will definitely help to increase the success rate of implantation practice. (Fertil Steril Ò 2021;116:181-8. Ó2021 by American Society for Reproductive Medicine.) El resumen está disponible en Español al final del artículo.

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miPrimer: an empirical-based qPCR primer design method for small noncoding microRNA

Cited by 14 publications

References 33 publications

TRPM7 Induces Mechanistic Target of Rap1b Through the Downregulation of miR-28-5p in Glioma Proliferation and Invasion

TRPM7 Induces Mechanistic Target of Rap1b Through the Downregulation of miR-28-5p in Glioma Proliferation and Invasion

Differences in the bacteriome of swab, saliva, and tissue biopsies in oral cancer

A novel platform for discovery of differentially expressed microRNAs in patients with repeated implantation failure

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