Statistical Methods for Identifying Biomarkers from miRNA Profiles of Cancers

Potential role of circulating miR-21 in the diagnosis of hepatocellular carcinoma: a systematic review and meta-analysis

OBJECTIVE

Identify original articles that analyzed the diagnostic value of miR-21 in hepatocellular carcinoma without language restriction or publication date.

METHODOLOGY

We performed structured searches on PubMed, Web of Science, VHL, and EMBASE. The Standard Quality Assessment Criteria for Evaluating Primary Research Papers from a Variety of Fields was used to assess the quality of each study. Random effect models were used to study heterogeneity, evaluated based on the Higgins I2 statistic.

RESULTS

12 articles were evaluated and contained raw data from 1,329 individuals, of which 617 had HCC, 473 were healthy, and 239 had Chronic liver disease. The combined sensitivity and combined specificity of miR-21 for diagnosing HCC were, respectively, 0.83(95% CI:0.78-0.89) and 0.85(95% CI:0.80-0.90). The sensitivity and specificity, in that order, by type of control were 0.81 (95% CI: 0.71-0.91) and 0.88 (95% CI: 0.82-0.93) for CLDs and 0.86(95% CI: 0.81-0.91) and 0.83(95% CI:0.74-0.91) for Healthy controls.

CONCLUSION

miR-21 has a moderate overall performance in diagnosing HCC and may serve as a potential non-invasive marker for this early-stage disease. Thus, it may contribute to complementing the results of alpha-fetoprotein in the diagnosis and help to detect HCC at an earlier stage, increasing the survival chances of these patients.

Competing Endogenous RNA Network in Non-Keloid-Prone Individuals During Wound Healing

ABSTRACT

To study the interaction between differentially expressed long non-coding RNAs (lncRNAs), microRNAs, and messenger RNAs during wound healing in normal individuals. The GSE113621 dataset was downloaded from gene expression matrix, specimens regarding non-keloid-prone individuals were selected, including items before and 6 weeks after injury. A Pearson correlation coefficient of > 0.95 was selected as the index to screen targeting relationships among different RNAs. Cytoscape was used to construct a network diagram. The expression of 2547 lncRNAs was changed during the wound healing process-1479 were upregulated and 1068 were downregulated. After analyzing competitive endogenous RNA network, 4 upregulated (MEG8, MEG3, MIR181A1HG, MIR4435-2HG) lncRNAs were found expressed during wound healing. MEG8/MEG3 may regulate fibroblast proliferation, differentiation, and apoptosis through hsa-miR-296-3p/miR-6763-5p. In-depth mining of gene expression matrix data indicated that lncRNAs and a competitive endogenous RNA regulatory network participate in the wound healing process, possibly providing novel intervention targets and treatment options for delayed wound healing.

Secondary data mining of GEO database for long non-coding RNA and Competing endogenous RNA network in keloid-prone individuals

This study aimed to identify long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and messenger RNAs (mRNAs) differentially expressed (DE) during keloid formation, predict DElncRNA-DEmiRNA-DEmRNA interactions, and construct a competing endogenous RNA (ceRNA) network through secondary data mining of keloid-related sequencing and microarray data in the open-source Gene Expression Omnibus (GEO) database. The GSE113621 dataset was downloaded from the GEO database, |log₂FC|>1 and p<0.05 were set as screening criteria, genes expressed only in keloid-prone individuals were selected as research objects, and DEmRNAs, DElncRNAs, and DEmiRNAs before injury and 6 weeks after injury were screened. A Pearson correlation coefficient (PCC) of > 0.95 was selected as the index to predict the targeting relationships among lncRNAs, miRNAs, and mRNAs; and a network diagram was constructed using Cytoscape. The expression of 2356 lncRNAs was changed in the keloid-prone group—1306 were upregulated and 1050 were downregulated. Six lncRNAs, namely, 2 upregulated (DLEU2 and AP000317.2) and 4 downregulated (ADIRF-AS1, AC006333.2, AL137127.1 and LINC01725) lncRNAs, were expressed only in the keloid-prone group and were used to construct a ceRNA network. DLEU2 may regulate fibroblast proliferation, differentiation, and apoptosis through hsa-miR-30a-5p/hsa-miR-30b-5p. In-depth mining of GEO data indicated that lncRNAs and a ceRNA regulatory network participate in the wound healing process in keloid-prone individuals, possibly providing novel intervention targets and treatment options for keloid scars.

Detection of disease-associated microRNAs - application for autism spectrum disorders

Autism spectrum disorders (ASD) diagnostic procedure still lacks a uniform biological marker. This review gathers the information on microRNAs (miRNAs) specifically as a possible source of biomarkers of ASD. Extracellular vesicles, and their subset of exosomes, are believed to be a tool of cell-to-cell communication, and they are increasingly considered to be carriers of such a marker. The interest in studying miRNAs in extracellular vesicles grows in all fields of study and therefore should not be omitted in the field of neurodevelopmental disorders. The summary of miRNAs associated with brain cells and ASD either studied directly in the tissue or biofluids are gathered in this review. The heterogeneity in findings from different studies points out the fact that unified methods should be established, beginning with the determination of the accurate patient and control groups, through to sample collection, processing, and storage conditions. This review, based on the available literature, proposes the standardized approach to obtain the results that would not be affected by technical factors. Nowadays, the method of high-throughput sequencing seems to be the most optimal to analyze miRNAs. This should be followed by the uniformed bioinformatics procedure to avoid misvalidation. At the end, the proper validation of the obtained results is needed. With such an approach as is described in this review, it would be possible to obtain a reliable biomarker that would characterize the presence of ASD.