Detection of microRNA: A Point-of-Care Testing Method Based on a pH-Responsive and Highly Efficient Isothermal Amplification

Feng, Chao; Mao, Xiaoxia; Shi, Hai; Bo, Bing; Chen, Xiaoxia; Chen, Tianshu; Zhu, Xiaoli; Li, Genxi

doi:10.1021/acs.analchem.7b00850

Cited by 90 publications

(60 citation statements)

References 20 publications

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“…Based on NRCA, Feng et al. (2017) further developed a new visible detection strategy for miR‐21 detection by introducing pH indicator for detection of NRCA byproduct H + (Figure ) . In their strategy, miR‐21 was designed as primer to initiate NRCA.…”

Section: Hcc‐associated Mirna Detection Based On Enzyme‐assisted Isotmentioning

confidence: 99%

Application of Isothermal Nucleic Acid Signal Amplification in the Detection of Hepatocellular Carcinoma‐Associated MicroRNA

et al. 2018

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Hepatocellular carcinoma (HCC) is a common type of malignant tumor with high incidence and mortality, and is the third leading cause of cancer‐related death in human. High‐precision detection of tumor markers, such as microRNA (miRNA), is expected to contribute to the early diagnosis of HCC as well as improve the survival rate of HCC patients. In recent years, great effort has been made to develop different methods to detect HCC‐associated miRNA, in which signal amplification strategies are incorporated to realize high sensitivity. Among them, isothermal nucleic acid signal amplification is an emerging signal amplification technology which has the advantages of high amplification efficiency, good reproducibility, and easy operation for real‐time analysis. Herein, we provide an overview of the advances in the application of isothermal nucleic acid signal amplification in HCC‐associated miRNA detection by highlighting several representative works in recent years.

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Section: Hcc‐associated Mirna Detection Based On Enzyme‐assisted Isotmentioning

confidence: 99%

Application of Isothermal Nucleic Acid Signal Amplification in the Detection of Hepatocellular Carcinoma‐Associated MicroRNA

et al. 2018

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“…Today, there are a few reports tackling these challenges, for example, by improving current detection methods, using electrochemical assays or developing pH‐based POC tests . However, these approaches still need error‐prone amplification steps prior to the miRNA detection, have rather tedious preparation steps, or are limited by the design of suitable primers .…”

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confidence: 99%

CRISPR/Cas13a‐Powered Electrochemical Microfluidic Biosensor for Nucleic Acid Amplification‐Free miRNA Diagnostics

et al. 2019

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Noncoding small RNAs, such as microRNAs, are becoming the biomarkers of choice for multiple diseases in clinical diagnostics. A dysregulation of these microRNAs can be associated with many different diseases, such as cancer, dementia, and cardiovascular conditions. The key for effective treatment is an accurate initial diagnosis at an early stage, improving the patient's survival chances. In this work, the first clustered regularly interspaced short palindromic repeats (CRISPR)/Cas13a‐powered microfluidic, integrated electrochemical biosensor for the on‐site detection of microRNAs is introduced. Through this unique combination, the quantification of the potential tumor markers microRNA miR‐19b and miR‐20a is realized without any nucleic acid amplification. With a readout time of 9 min and an overall process time of less than 4 h, a limit of detection of 10 pm is achieved, using a measuring volume of less than 0.6 µL. Furthermore, the feasibility of the biosensor platform to detect miR‐19b in serum samples of children, suffering from brain cancer, is demonstrated. The validation of the obtained results with a standard quantitative real‐time polymerase chain reaction method shows the ability of the electrochemical CRISPR‐powered system to be a low‐cost, easily scalable, and target amplification‐free tool for nucleic acid based diagnostics.

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“…From the fact that miRNAs regulate gene expression by binding the 3'-UTR of mRNAs 233 at the post-transcriptional level [6,[35][36][37], they are important in various biological 234 processes in the human body and identifying their regulation mechanisms plays a salient 235 role in diagnostics and therapeutics for a wide range of diseases. At the present, 236 although numerous studies have developed methods to identify the relationships of 237 miRNAs and mRNAs, most of them detect the correlations between the expression levels 238 of miRNAs and mRNAs while the methods discovering the cause-effect relationship 239 have a high computational complexity.…”

Section: Conclusion 232mentioning

confidence: 99%

“…A strong correlation between the expression 34 values of a miRNA and a mRNA in a dataset may be a spurious relationship, as it could 35 be confounded by a transcription factor. On the other hand, causal inference 36 June 2, 2018 2/15 approach [17][18][19] aims to estimate the intervention effects as in the gene knockdown 37 experiments. While these causal inference methods help remove spurious relationships, 38 they have high computational complexity and therefore they are not scalable in large 39 datasets.…”

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confidence: 99%

Identifying miRNA-mRNA regulatory relationships in breast cancer with invariant causal prediction

Pham

Zhang

Liu

et al. 2018

Preprint

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microRNAs (miRNAs) regulate gene expression at the post-transcriptional level and they play an important role in various biological processes in the human body. Therefore, identifying their regulation mechanisms is essential for the diagnostics and therapeutics for a wide range of diseases. There have been a large number of researches which use gene expression profiles to resolve this problem. However, the current methods have their own limitations. Some of them only identify the correlation of miRNA and mRNA expression levels instead of the causal or regulatory relationships while others infer the causality but with a high computational complexity. To overcome these issues, in this study, we propose a method to identify miRNA-mRNA regulatory relationships in breast cancer using the invariant causal prediction. The key idea of invariant causal prediction is that the cause miRNAs of their target mRNAs are the ones which have persistent causal relationships with the target mRNAs across different environments. In this research, we aim to find miRNA targets which are consistent across different breast cancer subtypes. Thus, first of all, we apply the Pam50 method to categorise BRCA samples into different "environment" groups based on different cancer subtypes. Then we use the invariant causal prediction method to find miRNA-mRNA regulatory relationships across subtypes. We validate the results with the miRNA-transfected experimental data and the results show that our method outperforms the state-of-the-art methods. In addition, we also integrate this new method with the Pearson correlation analysis method and Lasso in an ensemble method to take the advantages of these methods. We then validate the results of the ensemble method with the experimentally confirmed data and the ensemble method shows the best performance, even comparing to the proposed causal method. Functional enrichment analyses show that miRNAs in the regulatory relationship predicated by the proposed causal method tend to synergistically regulate target genes, indicating the usefulness of these methods, and the identified miRNA targets could be used in the design of wet-lab experiments to discover the causes of breast cancer.June 2, 2018 1/15 Author summaryCancer is a disease of cells in human body and it causes a high rate of deaths world wide. There has been evidence that non-coding RNAs are key players in the development and progression of cancer. Among the different types of non-coding RNAs, miRNAs, which are short non-coding RNAs, regulate gene expression and play an important role in different biological processes as well as various cancer types. To design better diagnostic and therapeutic plans for cancer patients, we need to know the roles of miRNAs in cancer initialisation and development, and their regulation mechanisms in the human body. In this study, we propose algorithms to identify miRNA-mRNA regulatory relationships in breast cancer. Comparing our methods with existing methods in predicting miRNA targets, our methods show a better perf...

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Detection of microRNA: A Point-of-Care Testing Method Based on a pH-Responsive and Highly Efficient Isothermal Amplification

Cited by 90 publications

References 20 publications

Application of Isothermal Nucleic Acid Signal Amplification in the Detection of Hepatocellular Carcinoma‐Associated MicroRNA

Application of Isothermal Nucleic Acid Signal Amplification in the Detection of Hepatocellular Carcinoma‐Associated MicroRNA

CRISPR/Cas13a‐Powered Electrochemical Microfluidic Biosensor for Nucleic Acid Amplification‐Free miRNA Diagnostics

Identifying miRNA-mRNA regulatory relationships in breast cancer with invariant causal prediction

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