Construction of a Potential Breast Cancer-Related miRNA-mRNA Regulatory Network

Circulating miRNAs signature on breast cancer: the MCC-Spain project

PURPOSE

To build models combining circulating microRNAs (miRNAs) able to identify women with breast cancer as well as different types of breast cancer, when comparing with controls without breast cancer.

METHOD

miRNAs analysis was performed in two phases: screening phase, with a total n = 40 (10 controls and 30 BC cases) analyzed by Next Generation Sequencing, and validation phase, which included 131 controls and 269 cases. For this second phase, the miRNAs were selected combining the screening phase results and a revision of the literature. They were quantified using RT-PCR. Models were built using logistic regression with LASSO penalization.

RESULTS

The model for all cases included seven miRNAs (miR-423-3p, miR-139-5p, miR-324-5p, miR-1299, miR-101-3p, miR-186-5p and miR-29a-3p); which had an area under the ROC curve of 0.73. The model for cases diagnosed via screening only took in one miRNA (miR-101-3p); the area under the ROC curve was 0.63. The model for disease-free cases in the follow-up had five miRNAs (miR-101-3p, miR-186-5p, miR-423-3p, miR-142-3p and miR-1299) and the area under the ROC curve was 0.73. Finally, the model for cases with active disease in the follow-up contained six miRNAs (miR-101-3p, miR-423-3p, miR-139-5p, miR-1307-3p, miR-331-3p and miR-21-3p) and its area under the ROC curve was 0.82.

CONCLUSION

We present four models involving eleven miRNAs to differentiate healthy controls from different types of BC cases. Our models scarcely overlap with those previously reported.

Analysis of mRNA-miRNA interaction network reveals the role of CAFs-derived exosomes in the immune regulation of oral squamous cell carcinoma

BACKGROUND

Cancer-associated fibroblasts (CAFs) have significant tumor regulatory functions, and CAFs-derived exosomes (CAFs-Exo) released from CAFs play an important role in the progression of oral squamous cell carcinoma (OSCC). However, a lack of comprehensive molecular biological analysis leaves the regulatory mechanisms of CAFs-Exo in OSCC unclear.

METHODS

We used platelet derived growth factor-BB (PDGF-BB) to induce the transformation of human oral mucosa fibroblast (hOMF) into CAFs, and extracted exosomes from the supernatant of CAFs and hOMF. We validated the effect of CAFs-Exo on tumor progression by exosomes co-culture with Cal-27 and tumor-forming in nude mice. The cellular and exosomal transcriptomes were sequenced, and immune regulatory genes were screened and validated using mRNA-miRNA interaction network analysis in combination with publicly available databases.

RESULTS

The results showed that CAFs-Exo had a stronger ability to promote OSCC proliferation and was associated with immunosuppression. We discovered that the presence of immune-related genes in CAFs-Exo may regulate the expression of PIGR, CD81, UACA, and PTTG1IP in Cal-27 by analyzing CAFs-Exo sequencing data and publicly available TCGA data. This may account for the ability of CAFs-Exo to exert immunomodulation and promote OSCC proliferation.

CONCLUSIONS

CAFs-Exo was found to be involved in tumor immune regulation through hsa-miR-139-5p, ACTR2 and EIF6, while PIGR, CD81, UACA and PTTG1IP may be potentially effective targets for the treatment of OSCC in the future.

Statistics and network-based approaches to identify molecular mechanisms that drive the progression of breast cancer

Breast cancer (BC) is one of the most malignant tumors and the leading cause of cancer-related death in women worldwide. So, an in-depth investigation on the molecular mechanisms of BC progression is required for diagnosis, prognosis and therapies. In this study, we identified 127 common differentially expressed genes (cDEGs) between BC and control samples by analyzing five gene expression profiles with NCBI accession numbers GSE139038, GSE62931, GSE45827, GSE42568 and GSE54002, based-on two statistical methods LIMMA and SAM. Then we constructed protein-protein interaction (PPI) network of cDEGs through the STRING database and selected top-ranked 7 cDEGs (BUB1, ASPM, TTK, CCNA2, CENPF, RFC4, and CCNB1) as a set of key genes (KGs) by cytoHubba plugin in Cytoscape. Several BC-causing crucial biological processes, molecular functions, cellular components, and pathways were significantly enriched by the estimated cDEGs including at-least one KGs. The multivariate survival analysis showed that the proposed KGs have a strong prognosis power of BC. Moreover, we detected some transcriptional and post-transcriptional regulators of KGs by their regulatory network analysis. Finally, we suggested KGs-guided three repurposable candidate-drugs (Trametinib, selumetinib, and RDEA119) for BC treatment by using the GSCALite online web tool and validated them through molecular docking analysis, and found their strong binding affinities. Therefore, the findings of this study might be useful resources for BC diagnosis, prognosis and therapies.

Integrative analysis of TCGA data identifies miRNAs as drug-specific survival biomarkers

Biomarkers predictive of drug-specific outcomes are important tools for personalized medicine. In this study, we present an integrative analysis to identify miRNAs that are predictive of drug-specific survival outcome in cancer. Using the clinical data from TCGA, we defined subsets of cancer patients who suffered from the same cancer and received the same drug treatment, which we call cancer-drug groups. We then used the miRNA expression data in TCGA to evaluate each miRNA’s ability to predict the survival outcome of patients in each cancer-drug group. As a result, the identified miRNAs are predictive of survival outcomes in a cancer-specific and drug-specific manner. Notably, most of the drug-specific miRNA survival markers and their target genes showed consistency in terms of correlations in their expression and their correlations with survival. Some of the identified miRNAs were supported by published literature in contexts of various cancers. We explored several additional breast cancer datasets that provided miRNA expression and survival data, and showed that our drug-specific miRNA survival markers for breast cancer were able to effectively stratify the prognosis of patients in those additional datasets. Together, this analysis revealed drug-specific miRNA markers for cancer survival, which can be promising tools toward personalized medicine.

Differentially expressed miRNAs in bone after methotrexate treatment

Previous studies have shown that administration of antimetabolite methotrexate (MTX) caused a reduced trabecular bone volume and increased marrow adiposity (bone/fat switch), for which the underlying molecular mechanisms and recovery potential are unclear. Altered expression of microRNAs (miRNAs) has been shown to be associated with dysregulation of osteogenic and/or adipogenic differentiation by disrupting target gene expression. First, the current study confirmed the bone/fat switch following MTX treatment in precursor cell culture models in vitro. Then, using a rat intensive 5-once daily MTX treatment model, this study aimed to identify miRNAs associated with bone damage and recovery (in a time course over Days 3, 6, 9, and 14 after the first MTX treatment). RNA isolated from bone samples of treated and control rats were subjected to miRNA array and reverse transcription-polymerase chain reaction validation, which identified five upregulated miRNA candidates, namely, miR-155-5p, miR-154-5p, miR-344g, miR-6215, and miR-6315. Target genes of these miRNAs were predicted using TargetScan and miRDB. Then, the protein-protein network was established via STRING database, after which the miRNA-key messenger RNA (mRNA) network was constructed by Cytoscape. Functional annotation and pathway enrichment analyses for miR-6315 were performed by DAVID database. We found that TGF-β signaling was the most significantly enriched pathway and subsequent dual-luciferase assays suggested that Smad2 was the direct target of miR-6315. Our current study showed that miR-6315 might be a vital regulator involved in bone and marrow fat formation. Also, this study constructed a comprehensive miRNA-mRNA regulatory network, which may contribute to the pathogenesis/prognosis of MTX-associated bone loss and bone marrow adiposity.

MicroRNAs in Prion Diseases-From Molecular Mechanisms to Insights in Translational Medicine

MicroRNAs (miRNAs) are small non-coding RNA molecules able to post-transcriptionally regulate gene expression via base-pairing with partially complementary sequences of target transcripts. Prion diseases comprise a singular group of neurodegenerative conditions caused by endogenous, misfolded pathogenic (prion) proteins, associated with molecular aggregates. In humans, classical prion diseases include Creutzfeldt-Jakob disease, fatal familial insomnia, Gerstmann-Sträussler-Scheinker syndrome, and kuru. The aim of this review is to present the connections between miRNAs and prions, exploring how the interaction of both molecular actors may help understand the susceptibility, onset, progression, and pathological findings typical of such disorders, as well as the interface with some prion-like disorders, such as Alzheimer's. Additionally, due to the inter-regulation of prions and miRNAs in health and disease, potential biomarkers for non-invasive miRNA-based diagnostics, as well as possible miRNA-based therapies to restore the levels of deregulated miRNAs on prion diseases, are also discussed. Since a cure or effective treatment for prion disorders still pose challenges, miRNA-based therapies emerge as an interesting alternative strategy to tackle such defying medical conditions.