Explaining Gene Expression Using Twenty-One MicroRNAs

Transcriptome Complexity Disentangled: A Regulatory Molecules Approach

Transcription factors (TFs) and microRNAs (miRNAs) are fundamental regulators of gene expression, cell state, and biological processes. This study investigated whether a small subset of TFs and miRNAs could accurately predict genome-wide gene expression. We analyzed 8895 samples across 31 cancer types from The Cancer Genome Atlas and identified 28 miRNA and 28 TF clusters using unsupervised learning. Medoids of these clusters could differentiate tissues of origin with 92.8% accuracy, demonstrating their biological relevance. We developed Tissue-Agnostic and Tissue-Aware models to predict 20,000 gene expressions using the 56 selected medoid miRNAs and TFs. The Tissue-Aware model attained an R 2 of 0.70 by incorporating tissue-specific information. Despite measuring only 1/400th of the transcriptome, the prediction accuracy was comparable to that achieved by the 1000 landmark genes. This suggests the transcriptome has an intrinsically low-dimensional structure that can be captured by a few regulatory molecules. Our approach could enable cheaper transcriptome assays and analysis of low-quality samples. It also provides insights into genes that are heavily regulated by miRNAs/TFs versus alternative mechanisms. However, model transportability was impacted by dataset discrepancies, especially in miRNA distribution. Overall, this study demonstrates the potential of a biology-guided approach for robust transcriptome representation.

MiR-1270 Suppresses the Malignant Progression of Breast Cancer via Targeting MMD2

We aimed to detect the clinical significance of microRNA-1270 (miR-1270) in breast cancer (BCa) development and its potential influence on malignant phenotypes of BCa cells. The miR-1270 level in paired BCa and paracancerous tissues was detected. The Kaplan-Meier method was used for the prognosis analysis of miR-1270 in BCa. The biofunctions of miR-1270 in apoptosis and proliferation of breast cancer cells were evaluated. Downstream target of miR-1270 was predicted and confirmed. The involvement of monocyte to macrophage differentiation associated 2 (MMD2) in BCa development was finally illustrated. miR-1270 was lowly expressed in BCa tissues. Lowly expressed miR-1270 was associated with tumor staging, larger tumor size, and also worse prognostic results in patients with BCa. miR-1270 overexpression suppressed proliferation and increased apoptotic rate of BCa cells. Further exploration showed that MMD2 might be the target of miR-1270. MMD2 was upregulated in BCa tissues and negatively correlated to miR-1270 level. Importantly, MMD2 significantly neutralized the above biofunctions of miR-1270 in malignant phenotypes of BCa. Lowly expressed miR-1270 is a hallmark of poor prognosis in patients with BCa. It inhibits proliferative ability and increases apoptosis in BCa by negatively regulating the MMD2 level.

miR-1207-5p Can Contribute to Dysregulation of Inflammatory Response in COVID-19 via Targeting SARS-CoV-2 RNA

The present study focuses on the role of human miRNAs in SARS-CoV-2 infection. An extensive analysis of human miRNA binding sites on the viral genome led to the identification of miR-1207-5p as potential regulator of the viral Spike protein. It is known that exogenous RNA can compete for miRNA targets of endogenous mRNAs leading to their overexpression. Our results suggest that SARS-CoV-2 virus can act as an exogenous competing RNA, facilitating the over-expression of its endogenous targets. Transcriptomic analysis of human alveolar and bronchial epithelial cells confirmed that the CSF1 gene, a known target of miR-1207-5p, is over-expressed following SARS-CoV-2 infection. CSF1 enhances macrophage recruitment and activation and its overexpression may contribute to the acute inflammatory response observed in severe COVID-19. In summary, our results indicate that dysregulation of miR-1207-5p-target genes during SARS-CoV-2 infection may contribute to uncontrolled inflammation in most severe COVID-19 cases.