miRNA profiling in serum and tissue samples to assess noninvasive biomarkers for NSCLC clinical outcome

A spatially localized DNA linear classifier for cancer diagnosis

Molecular computing is an emerging paradigm that plays an essential role in data storage, bio-computation, and clinical diagnosis with the future trends of more efficient computing scheme, higher modularity with scaled-up circuity and stronger tolerance of corrupted inputs in a complex environment. Towards these goals, we construct a spatially localized, DNA integrated circuits-based classifier (DNA IC-CLA) that can perform neuromorphic architecture-based computation at a molecular level for medical diagnosis. The DNA-based classifier employs a two-dimensional DNA origami as the framework and localized processing modules as the in-frame computing core to execute arithmetic operations (e.g. multiplication, addition, subtraction) for efficient linear classification of complex patterns of miRNA inputs. We demonstrate that the DNA IC-CLA enables accurate cancer diagnosis in a faster (about 3 h) and more effective manner in synthetic and clinical samples compared to those of the traditional freely diffusible DNA circuits. We believe that this all-in-one DNA-based classifier can exhibit more applications in biocomputing in cells and medical diagnostics.

Diagnostic and prognostic value of microRNA-486 in patients with lung cancer: A systematic review and meta-analysis

PURPOSE

There are conflicting opinions on whether miR-486 could be used for cancer diagnosis and prognosis. Therefore, this present study investigated the potential effect of miR-486 on lung cancer diagnosis and prognosis.

METHODS

We researched PubMed, Embase, Wanfang and Chinese National Knowledge Infrastructure databases to select relevant publications. Specificity and sensitivity were obtained for the pooled and subgroup diagnostic meta-analysis while the hazard ratio was for prognostic meta-analysis. Publication analyses and sensitivity analyses were conducted to investigate possible sources of heterogeneity.

RESULTS

The overall sensitivity and specificity with 95% confidence intervals were 0.8 (0.8-0.9) and 0.9 (0.9-0.9). Results of subgroup analysis showed that high diagnostic efficacy might be obtained by miR-486 combined with other microRNAs (area under the curve (AUC): 0.9 (0.9-1.0)) to distinguish lung cancer patients from healthy controls (AUC: 1.0 (0.9-1.0)), especially for lung adenocarcinoma (AUC: 1.0 (1.0-1.0)) in the Asian population (AUC: 0.9 (0.9-1.0)). For prognosis prediction of miR-486 in overall non-small cell lung cancer, the overall hazard ratio with 95% confidence interval was 1.15 (0.85-1.54) for high versus low expression of miR-486, which indicated that a high miR-486 level was not related to the high risk of poor outcome. However, for the subgroup of progression-free survival and patients with chemotherapy, the hazard ratio was 0.41 (0.21-0.77), indicating that the higher miR-486 level would decrease the risk of poor progression-free survival for lung cancer patients with chemotherapy.

CONCLUSION

This study suggested circulating miR-486 combined with other microRNAs could be used as ideal biomarkers in early diagnosis and prognosis prediction for lung cancer, especially for lung adenocarcinoma in the Asian population.

microRNA-221 and tamoxifen resistance in luminal-subtype breast cancer patients: A case-control study

Background

Around 70% of breast cancers (BCs) are estrogen receptor-α (ERα)-positive. Adjuvant endocrine therapy is used to reduce estrogen levels and inhibit signal transduction through the ER. The anti-estrogen drugs that are most commonly used in endocrine therapy belong to the selective ER modulator (SERM) class and include tamoxifen. Although it has been used for three decades in cases of early-stage and ERα-positive BC, resistance to tamoxifen is a common problem. microRNAs (miRNAs) have a potential role in demonstrating BC resistance to tamoxifen therapy. Hence, there is a need to investigate the expression of miRNA-221 (miR-221) in luminal-subtype BC patients receiving tamoxifen therapy.

Methods

This case-control study investigated luminal-subtype BC patients who had undergone endocrine therapy for at least 1 year. The case group comprised patients with local or metastatic recurrence, and the control group comprised patients without local or metastatic recurrence.

Results

There was a significant difference in miR-221 expression (p = 0.005) between the case and control groups. There were no significant differences between the groups that were positive and negative for the progesterone receptor (PR) (p = 0.25), had high and low marker of proliferation Ki-67 levels (p = 0.60), were positive and negative for lymphovascular invasion (p = 0.14), and had stage 2 and stage 3 cancer (p = 0.25).

Conclusion

miR-221 expression was higher in tamoxifen-resistant BC cases. miR-221 is a potential biomarker of tamoxifen resistance.

•

Tamoxifen is used to treat early-stage and estrogen receptor-α-positive breast cancer.

•

Resistance to tamoxifen is a common problem.

•

Serum microRNA-221 levels were higher in patients with local recurrence and metastasis.

•

microRNA-221 is a potential serum biomarker of tamoxifen resistance.

miR-638 Serves as a Biomarker of 5-Fluorouracil Sensitivity to Neoadjuvant Chemotherapy in Breast Cancer

Purpose

Neoadjuvant chemotherapy (NAC) is widely used to treat breast cancer (BC). The prediction and evaluation of chemotherapy responses remains a significant challenge.

Methods

MicroRNAs (miRNAs) play a crucial role in cancer drug resistance. We used a miRNA microarray and identified that miR-638 is downregulated in chemoresistant cases. However, the exact role of miR-638 and the underlying mechanisms of chemoresistance remain unclear. Using real-time quantitative reverse transcription polymerase chain reaction, we found significant downregulation of miR-638 in chemoresistant patients compared with chemosensitive patients. To explore the function of miR-638, we overexpressed and inhibited miR-638 expression in MDA-MB-231 and MCF-7 cells by transfecting them with miR-638 mimics and miR-638 inhibitor, respectively. Cell proliferation and apoptosis were measured using MTS and flow cytometry, respectively. A minimal patient-derived xenograft (MiniPDX™) model was established to evaluate the chemosensitivity to different drugs.

Results

The results showed that cell proliferation decreased and cell apoptosis increased in cells transfected with the miR-638 mimic, and cell proliferation and apoptosis were reversed with transfection of miR-638 inhibitor compared with the control group. Among patients who received 5-fluorouracil (5-FU), miR-638 expression levels were lower in the chemoresistant group than in the chemosensitive group. The MiniPDX™ model showed that MDA-MB-231 cells overexpressing miR-638 were more susceptible to 5-FU treatment in vivo.

Conclusion

We provided evidence of acquired resistance to 5-FU caused by miR-638 deficiency. Alterations in miR-638 may be used with 5-FU chemotherapy during NAC for BC.

Identification of miRNA Signature in Breast Cancer to Predict Neoadjuvant Chemotherapy Response

Background: Chemotherapy failure causes high breast cancer recurrence and poor patient prognosis. Thus, we studied a cohort of novel biomarkers to predict chemotherapeutic response in breast cancer. In this study, miRNA expression profiling was performed on 10 breast cancer punctured specimens sensitive to chemotherapy (MP grade 4, 5) and 10 chemotherapy resistant (MP grade 1). Differentially expressed miRNAs were verified by qRT-PCR in 60 initial samples, 59 validated samples and 71 independent samples. A miRNA signature was generated using a Logistic regression model. A receiver operating characteristic (ROC) test was used to assess specificity and sensitivity of single miRNA and miRNA signature. Target genes regulated by miRNAs and their involved signaling pathways were analyzed using GO enrichment and KEGG software. MiRNAs expression were separately compared with ER, PR, HER2 immunohistochemical staining and different drugs. qRT-PCR showed that the high expression of miR-23a-3p, miR-200c-3p, miR-214-3p and the low expression of miR-451a and miR-638 were closely related to chemoresistance. According to the formula for calculating the drug resistance risk, patients in the high-risk group were more likely to develop chemotherapy resistance than the low-risk group. Bioinformatics analysis showed that 5 miRNAs and target genes are mainly involved in p53, ubiquitin-mediated proteolysis, mTOR, Wnt, cells skeletal protein regulation, cell adhesion and ErbB signaling pathways. miR-451a expression was associated with ER, HER-2 status and anthracyclines. A miRNA signature of chemotherapeutic response may be clinically valuable for improving current chemotherapy regimens of individual treatment for patients with breast cancer.

miRNAs in lung cancer. A systematic review identifies predictive and prognostic miRNA candidates for precision medicine in lung cancer

Lung cancer (LC) is the leading cause of cancer-related death worldwide and miRNAs play a key role in LC development. To better diagnose LC and to predict drug treatment responses we evaluated 228 articles encompassing 16,697 patients and 12,582 healthy controls. Based on the criteria of ≥3 independent studies and a sensitivity and specificity of >0.8 we found blood-borne miR-20a, miR-10b, miR-150, and miR-223 to be excellent diagnostic biomarkers for non-small cell LC whereas miR-205 is specific for squamous cell carcinoma. The systematic review also revealed 38 commonly regulated miRNAs in tumor tissue and the circulation, thus enabling the prediction of histological subtypes of LC. Moreover, theranostic biomarker candidates with proven responsiveness to checkpoint inhibitor treatments were identified, notably miR-34a, miR-93, miR-106b, miR-181a, miR-193a-3p, and miR-375. Conversely, miR-103a-3p, miR-152, miR-152-3p, miR-15b, miR-16, miR-194, miR-34b, and miR-506 influence programmed cell death-ligand 1 and programmed cell death-1 receptor expression, therefore providing a rationale for the development of molecularly targeted therapies. Furthermore, miR-21, miR-25, miR-27b, miR-19b, miR-125b, miR-146a, and miR-210 predicted response to platinum-based treatments. We also highlight controversial reports on specific miRNAs. In conclusion, we report diagnostic miRNA biomarkers for in-depth clinical evaluation. Furthermore, in an effort to avoid unnecessary toxicity we propose predictive biomarkers. The biomarker candidates support personalized treatment decisions of LC patients and await their confirmation in randomized clinical trials.

MirSNPs in clopidogrel metabolism genes predict cardiovascular disease risk: a case-control study and meta-analysis

Aim: The present study was conducted to decipher the inter-relationship of SNPs and miRNAs involved in pharmacogenomics of clopidogrel on predisposition to cardiovascular diseases (CVDs). Materials & methods: A case-control study was conducted on 410 cases and 386 controls to analyze the association of 13 mirSNPs on CVDs risk. Genotyping was performed by tetra-primer amplification refractory mutation system PCR and validated using Sanger DNA sequencing. miRNA expression analysis was performed using TaqMan assays. A meta-analysis was performed for PON1 rs662 with coronary artery disease. Results & conclusion: PON1 rs662, PON1 rs3917577, CYP3A5 rs15524, COL4A1 rs874204 and PTGIR rs1126510 polymorphisms showed association with CVDs. The miRNA hsa-miR-224-5p showed differential expression in the PON1 rs3917577 GG genotype. The meta-analysis showed the population-specific impact of PON1 rs662 on South Asian and Middle East populations.

Serum microRNA expression profiling revealing potential diagnostic biomarkers for lung adenocarcinoma

Background

Recent studies have demonstrated that microRNAs (miRNAs) in the blood circulation can serve as promising diagnostic markers for cancers. This four-stage study aimed at finding serum miRNAs as potential biomarkers for lung adenocarcinoma (LA) diagnosis.

Methods

The study was carried out between 2016 and 2017. The Exiqon miRNA qPCR panel (3 LA vs. 1 normal control [NC] pooled serum samples) was used for initial screening to acquire miRNA profiles. Thirty-five dysregulated miRNAs were further evaluated in the training (24 LA vs. 24 NCs) and testing stages (110 LA vs. 110 NCs) using quantitative real-time polymerase chain reaction assays.

Results

Four serum miRNAs (miR-133a-3p, miR-584-5p, miR-10b-5p, and miR-221-3p) were significantly overexpressed in LA patients compared with NCs. The diagnostic value of the four-miRNA panel was validated by an external cohort (36 LA vs. 36 NCs). The areas under the receiver operating characteristic curve of the four-miRNA panel in the training, testing, and external validation stages were 0.734, 0.803, and 0.894 respectively. Meanwhile, the expression level of miR-221-3p was much higher in LA tumor samples than that in the adjacent normal tissues (19 LA vs. 19 NCs). The expression level of miR-10b-5p was also elevated in the serum-derived exosomes samples (18 LA vs. 18 NCs). The expression of miR-133a-3p, miR-584-5p, and miR-10b-5p was significantly elevated in LA patients with epidermal growth factor receptor mutation compared with NCs.

Conclusion

The study established a four-miRNA signature in serum that could improve the diagnostic capability of LA.

Expression profile of miRNA in NSCLC tissues in middle-altitude area

Micro ribonucleic acid (miRNA) expression profile in non-small cell lung cancer (NSCLC) tissues in middle-altitude area was analyzed using the Affymetrix chip technique, to predict the target genes of abnormally-expressed miRNAs, and to analyze the target gene-related signaling pathways and cell biological functions regulated by them. The difference in miRNA expression profile in NSCLC tissues was analyzed using the Affymetrix chip technique. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was performed for the verification of some differentially-expressed miRNAs. The genes predicted by at least 6 out of 12 commonly used prediction methods of miRNA target genes, based on miRWalk2.0, were considered as target genes. The functions of differentially-expressed miRNA target genes were analyzed via Gene Ontology (GO) enrichment analysis, and the main signaling pathways involving target genes were analyzed via Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. There was abnormal expression of miRNAs in NSCLC tissues in the middle-altitude area. There were 140,405 target genes predicted for differentially-expressed miRNAs. The GO enrichment analysis of the functions of the target genes of differentially expressed miRNAs revealed that they mainly influence the binding process of intracellular components to protein, the positive regulation of biological process and the regulation of metabolic process. Moreover, these target genes were mainly enriched in the immunity, gene expression, metabolism and signal transduction, among which signal transduction was enriched with the most genes. The expression levels of miRNA-139-5p and miRNA-150-5p in lung cancer group were lower than those in the control group. The expression of miRNAs in NSCLC tissues in the middle-altitude area is abnormal, and most miRNAs are downregulated.

An estimate of the total number of true human miRNAs

While the number of human miRNA candidates continuously increases, only a few of them are completely characterized and experimentally validated. Toward determining the total number of true miRNAs, we employed a combined in silico high- and experimental low-throughput validation strategy. We collected 28 866 human small RNA sequencing data sets containing 363.7 billion sequencing reads and excluded falsely annotated and low quality data. Our high-throughput analysis identified 65% of 24 127 mature miRNA candidates as likely false-positives. Using northern blotting, we experimentally validated miRBase entries and novel miRNA candidates. By exogenous overexpression of 108 precursors that encode 205 mature miRNAs, we confirmed 68.5% of the miRBase entries with the confirmation rate going up to 94.4% for the high-confidence entries and 18.3% of the novel miRNA candidates. Analyzing endogenous miRNAs, we verified the expression of 8 miRNAs in 12 different human cell lines. In total, we extrapolated 2300 true human mature miRNAs, 1115 of which are currently annotated in miRBase V22. The experimentally validated miRNAs will contribute to revising targetomes hypothesized by utilizing falsely annotated miRNAs.

Circulating miRNAs as Diagnostic and Prognostic Biomarkers in Common Solid Tumors: Focus on Lung, Breast, Prostate Cancers, and Osteosarcoma

An early cancer diagnosis is essential to treat and manage patients, but it is difficult to achieve this goal due to the still too low specificity and sensitivity of classical methods (imaging, actual biomarkers), together with the high invasiveness of tissue biopsies. The discovery of novel, reliable, and easily collectable cancer markers is a topic of interest, with human biofluids, especially blood, as important sources of minimal invasive biomarkers such as circulating microRNAs (miRNAs), the most promising. MiRNAs are small non-coding RNAs and known epigenetic modulators of gene expression, with specific roles in cancer development/progression, which are next to be implemented in the clinical routine as biomarkers for early diagnosis and the efficient monitoring of tumor progression and treatment response. Unfortunately, several issues regarding their validation process are still to be resolved. In this review, updated findings specifically focused on the clinical relevance of circulating miRNAs as prognostic and diagnostic biomarkers for the most prevalent cancer types (breast, lung, and prostate cancers in adults, and osteosarcoma in children) are described. In addition, deep analysis of pre-analytical, analytical, and post-analytical issues still affecting the circulation of miRNAs' validation process and routine implementation is included.

Molecular predictors of brain metastasis-related microRNAs in lung adenocarcinoma

Brain metastasis (BM) is a major complication of lung adenocarcinoma (LAD). An investigation of the pathogenic mechanisms of BM, as well as the identification of appropriate molecular markers, is necessary. The aim of this study was to determine the expression patterns of microRNAs (miRNAs) in LAD with BM, and to investigate the biological role of these miRNAs during tumorigenesis. miRNA array profiles were used to identify BM-associated miRNAs. These miRNAs were independently validated in 155 LAD patients. Several in vivo and in vitro assays were performed to verify the effects of miRNAs on BM. We identified six miRNAs differentially expressed in patients with BM as compared to patients with BM. Of these, miR-4270 and miR-423-3p were further investigated. miR-4270 and miR-423-3p directly targeted MMP19 and P21, respectively, to influence cell viability, migration, and colony formation in vitro. miR-4270 downregulation and miR-423-3p upregulation was associated with an increased risk of BM in LAD patients. Thus, our results suggested that miR-4270 and miR-423-3p might play an important role in BM pathogenesis in LAD patients, and that these miRNAs might be useful prognostic and clinical treatment targets.

Brain metastasis (BM) is a major complication of lung carcinoma. Here, we aimed to identify the key miRNAs involved in BM lung cancer. We first profiled miRNA expression in 32 tissues from NSCLC patients with BM and 55 tissues from NSCLC patients without BM. We independently validated our results in 68 additional tissues from NSCLC patients. Based on our results, we identified a panel of miRNAs that distinguish BM lung adenocarcinomas from non-BM We report here for the first time that either miR-4270 downregulation or miR-423-3p upregulation significantly increased cell proliferation, colony formation, and migration in vitro. miR-4270 and miR-423-3p increased the risk of BM in mouse models by targeting MMP19 and P21, respectively. Our results suggested that miR-4270 and miR-423-3p might be useful markers of BM in lung adenocarcinoma.

MiR-486 as an effective biomarker in cancer diagnosis and prognosis: a systematic review and meta-analysis

Purpose

MiR-486 was found to be associated with cancer’s diagnosis and prognosis. This meta-analysis aimed to investigate the potential effect of miR-486 on cancer detection and prognosis.

Materials and Methods

We searched PubMed, Cochrane library, Embase, Chinese National Knowledge Infrastructure (CNKI) and Wanfang databases to find all correlated articles. The STATA 11.0 was applied to estimate the pooled effects, heterogeneity and publication bias.

Results

The pooled sensitivity (SEN), specificity (SPE) and Area under the curve (AUC) were 82% (95% CI: 78–85%), 88% (95% CI: 83–92%) and 0.91 (95% CI: 0.88–0.93). Subgroup analysis indicated miR-486 from circulating samples exhibited higher diagnostic accuracy with the AUC was 0.90 (95% CI: 0.87–0.92) than miR-486 from other specimen with the AUC of 0.78 (95% CI: 0.75–0.82) and miR-486 obtained a better diagnostic value in the Asian population with the AUC of 0.94 (95% CI: 0.91–0.95) than the Caucasian and Caucasian/African population with the AUC of 0.80 (95% CI: 0.76–0.83) and 0.89 (95% CI: 0.86–0.91) respectively. MiR-486 obtained high value for the diagnosis of non-small cell lung cancer with SEN, SPE and AUC were 0.82 (95% CI: 0.0.77–0.87), 0.90 (95% CI: 0.84–0.94) as well as 0.92 (95% CI: 0.89–0.94) respectively. For the 7 prognostic tests, the pooled hazard ratio (HR) was 0.48 (95% CI: –0.13–1.08) for low versus high miR-486 expression.

Conclusions

This meta-analysis indicated that miR-486 can be used as ideal biomarkers in the cancer’s diagnosis. However, Low miR-486 expression did not increase the risk of poor outcome.

A meta-analysis: microRNAs' prognostic function in patients with nonsmall cell lung cancer

Accumulating papers have demonstrated that microRNAs play an important role in the progression of lung cancer, mainly as oncogenic and tumor suppressive. Therefore, microRNAs may influence the survival of lung cancer patients. In this meta‐analysis, we evaluated the role of microRNAs in affecting the overall survival in nonsmall cell lung cancer (NSCLC) patients, which may provide valuable information for the treatment of nonsmall cell lung cancer. We used keywords to retrieve literatures from online databases PUBMED,EMBASE and Web of Science and included 12 studies into our investigation according to pre‐set criteria. Then, we analyzed the data with stata13.1 to evaluate the microRNAs role on the prognosis of NSCLC patients. NSCLC patients with higher microRNAs expression levels tend to show lower overall survival. HR (hazard ratio): 2.49, 95% CI (confidence interval): 1.84–3.37. Besides, both oncogenic and tumor suppressive microRNAs have an evident influence on prognosis with HR values of 2.60 (95% CI: 2.12–3.19) and 0.41 (95% CI: 0.05–0.34), respectively. microRNAs, especially from tissue, have an influence on overall survival of NSCLC patients, which indicates that microRNAs could serve as potential prognostic markers for NSCLC and may provide a treatment strategy for advanced NSCLC patients.

Clinical significance of circulating miRNA detection in lung cancer

Lung cancer is the most common cancer in the world and the leading cause of tumor death among males. MicroRNAs (miRNAs) are single-stranded RNAs of approximately 22 nucleotides and constituted a new class of gene regulators in humans. As a novel class of emerging biomarkers, the aberrant expression of miRNA has been detected in various tumors. miRNAs are secreted into circulation by microvesicles from the broken tumor cells and act as either oncogenes or tumor suppressors in tumor tissues. In this review, we summarized different circulating miRNAs and their expression level as well as predictable values in lung cancer patients which were investigated in recent 5 years. Circulating miRNAs are found to be dysregulated and have association with clinicopathological parameters and overall survival in lung cancer patients. In conclusion, circulating miRNAs have the potential for distinguishing lung cancer patients from healthy individuals, with the advantages of stabilities, noninvasiveness and cost-effectiveness.