What is the topic of your doctoral research? Why is it important to study the topic?
The topic of my thesis is the study of miRNA genes and their cell-type-specific expression and transcriptional regulation. MiRNAs are largely studied as biomarkers to monitor biological contexts such as disease progression, development, disease outcome, etc. Our study serves to characterize the synthesis of miRNA genes, and thus, can help to understand their modes of actions.
What are the key findings or observations of your doctoral research?
The main findings of the thesis were:
In the first study, we characterized miRNA gene loci, showing that miRNAs are transcribed from alternative TSS that are used in a cell and stimulus-specific manner. In addition, we demonstrated that TSS activities, as measured with GRO-seq technology, are differentially regulated in individual cells by SEs within the miRNA loci. Lastly, we showed that miRNA transcriptional regulation is physically constrained by the chromatin 3D conformation.
The second study proved that miRNA gene profiles could be quantified from the H3K36me3 ChIP-seq methodology. We characterize miRNA gene signatures in three contexts including the cardiac tissue, cancer cell lines, and cardiomyocytes carrying a mutation in the GATA4 TF. We found that hsa-mir-1-1, an established cardiac miRNA, was upregulated in GATA4 mutants. We defined SEs at miRNA loci and found that GATA4 mutant active SEs colocalized with endothelial SEs instead of cardiac SEs.
In the third study, our results highlight concordant regulation of well established immune-aging-miRNAs, including mmu-mir-146a in splenic single-cell datasets. We made available pre-analyzed miRNA gene expression profiles from 10x Genomics 3’ scRNA-seq TMS (93217 cells) and Tabula Sapiens (17129 cells) data sets, allowing further characterization of miRNA regulatory networks in aging and across species at the single-cell resolution. Lastly, we performed single-cell genomics characterization in the LDLR-/-ApoB100/100 mice to address the role of miRNA gene expression at early and late atherosclerotic stages. We found functionally distinct macrophage subtypes displaying specific miRNA gene expression changes, exemplified by mmu-mir-23b~24-2~27b up-regulation in Trem2+ lipid-associated macrophages.
How can the results of your doctoral research be utilised in practice?
We provided a map of miRNA gene activities in multitude of cellular contexts, in bulk and single-cell next-generation sequencing datasets.
What are the key research methods and materials used in your doctoral research?
My background is in molecular biology techniques and next-generation sequencing dataset analysis and integration. My research utilizes state-of-the-art methods in bulk and single-cell next-generation sequencing datasets.
The doctoral dissertation of Ana Hernández de Sande, MSc, entitled Genome-wide Study of primary miRNA expression will be examined at the Faculty of Health Sciences at Kuopio campus. The Opponent in the public examination will be Docent Anna Vähärautio of the University of Helsinki, and the Custos will be Professor Merja Heinäniemi of the University of Eastern Finland.