Biology subjects

Laitinen, P.

Publications and source records attributed to Laitinen, P..

3 recordsLinked to original sources

bioRxiv2025

Investigating the Intracellular Compartmental Dynamics of miRNAs in Response to Hypoxia

MicroRNAs (miRNAs) are a class of small non-coding RNAs (ncRNAs) with established functions in cytoplasmic gene regulation, where they interact with mRNA transcripts, impeding their translation--a process known as post-transcriptional gene silencing (PTGS). Recent studies have found that miRNAs and other components involved in PTGS are abundantly present in the nucleus of the cells, where they also play important roles in gene regulation. However, the understanding of their function in the nucleus is not well characterized, particularly in response to cellular stress. We conducted nuclear-cytoplasmic fractionation of primary human endothelial cells (ECs) to assess the distribution of miRNAs during hypoxia. The onset of hypoxia led to changes in miRNA expression in both nuclear and cytoplasmic compartments. Notably, a larger proportion of deregulated miRNAs were identified in the nucleus than in the cytoplasm upon hypoxia exposure. We focused on these nuclear-enriched, differentially expressed miRNAs to investigate their cellular functions and their effects on target mRNAs in different compartments. The data indicated a more pronounced alteration in nuclear mRNA expression compared to cytoplasmic expression, pointing towards a nuclear-specific role for these miRNAs. Several miRNAs influenced target mRNAs associated with pathways of cell proliferation and inflammation. Functional assays under hypoxia showed that miR-5091 and miR-7974 reduced EC cell proliferation, while miR-1246 increased it. Additionally, miR-3662 was found to regulate the secretion levels of specific cytokines, impacting the inflammatory response. Overall, our findings highlight the significant role of miRNAs in the nuclear compartment of ECs in modulating the hypoxic response and provide insights into their multifaceted functions.

molecular biology↗

bioRxiv2024

The critical role of isomiRs in accurate differential expression analysis of miRNA-seq data

MicroRNAs (miRNAs) are crucial for the regulation of gene expression and are promising biomarkers and therapeutic targets. miRNA isoforms (isomiRs) differ in their start/end offsets, which can impact the target gene selection and non-canonical function of the miRNA species. In addition, isomiRs frequently differ in their expression patterns from their parent miRNAs, yet their roles and tissue-specific responses are currently understudied, leading to their typical omission in miRNA research. Here, we evaluate the expression differences of isomiRs across conditions and their impact on standard miRNA-seq quantification results. We analyze 28 public miRNA-seq datasets, showing significant expression pattern differences between the isomiRs and their corresponding reference miRNAs, leading to misinterpretation of differential expression signals for both. As a case study, we generate a new dataset assessing isomiR abundance under hypoxia in human endothelial cells between the nuclear and cytosolic compartments. The results suggest that isomiRs are dramatically altered in their nuclear localization in response to hypoxia, indicating a potential non-canonical effect of the species, which would be missed without isomiR-aware analysis. Our results call for a comprehensive re-evaluation of the miRNA-seq analysis practices.

bioinformatics↗

bioRxiv2021

isomiRs-specific differential expression is the rule, not the exception: Are we missing hundreds of species in microRNA analysis?

MicroRNAs (miRNAs) are small RNA molecules that act as regulators of gene expression through targeted mRNA degradation. They are involved in many biological and pathophysiological processes and are widely studied as potential biomarkers and therapeutics agents for human diseases, including cardiovascular disorders. Recently discovered isoforms of miRNAs (isomiRs) exist in high quantities and are very diverse. Despite having few differences with their corresponding reference miRNAs, they display specific functions and expression profiles, across tissues and conditions. However, they are still overlooked and understudied, as we lack a comprehensive view on their condition-specific regulation and impact on differential expression analysis. Here, we show that isomiRs can have major effects on differential expression analysis results, as their expression is independent of their host miRNA genes or reference sequences. We present two miRNA-seq datasets from human umbilical vein endothelial cells, and assess isomiR expression in response to senescence and compartment-specificity (nuclear/cytosolic) under hypoxia. We compare three different methods for miRNA analysis, including isomiR-specific analysis, and show that ignoring isomiRs induces major biases in differential expression. Moreover, isomiR analysis permits higher resolution of complex signal dissection, such as the impact of hypoxia on compartment localization, and differential isomiR type enrichments between compartments. Finally, we show important distribution differences across conditions, independently of global miRNA expression signals. Our results raise concerns over the quasi exclusive use of miRNA reference sequences in miRNA-seq processing and experimental assays. We hope that our work will guide future isomiR expression studies, which will correct some biases introduced by golden standard analysis, improving the resolution of such assays and the biological significance of their downstream studies.

bioinformatics↗