Effects of overexpression on miRNA isoforms and the targetome
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE213724 | GEO | 2026/08/13
REPOSITORIES: GEO
Similar Datasets
Project description:Overexpression of miR-183-5p|+2, but not of the other two isomiRs |0 and |+1, was observed to reduce cell cycle and cell proliferation in different triple-negative breast cancer cell lines. Therefore, we hypothesized that the |+2 isoform has targets distinct from the other two isoforms. To test this hypothesis, we overexpressed separately the three different isoforms or negative controls (siAllstar or mimic-Cltr) and performed Mass Spectrometry to identify differentially regulated proteins. Interestingly, a gene set enrichment analysis of the changes in protein expression revealed significant downregulation of transcriptional targets of E2F specifically in cells transfected with the |+2 isoform prompting us to validate the predicted isomiR specific target E2F1. Subsequently, we could show that direct targeting of E2F1 by miR-183-5p|+2 is responsible for the impact of the isomiR on cell cycle and proliferation.
2022-05-26 | PXD026763 | Pride
Project description:miRNAs are small noncoding RNA molecules that play an important role in post-transcriptional regulation of gene expression. Length and/or sequence variants of the same miRNA are termed isomiRs. While most isomiRs are functionally redundant compared to their canonical counterparts, so-called 5âisomiRs exhibit a shifted 5â end and therefore a shifted seed sequence resulting in a different target spectrum. However, not much is known about the functional relevance of these isoforms. Analysis of miRNA-seq data from breast cancer cell lines identified six pairs of highly expressed miRNAs and associated 5âisomiRs. Among them, hsa-miR-140-3p was of particular interest because its 5âisomiR showed higher expression compared to the canonical miRNA annotated in miRbase. This miRNA has previously been shown to control stemness of breast cancer cells. MiRNAseq data of breast cancer patients (TCGA dataset) showed that both the canonical hsa-miR-140-3p and its 5âisomiR-140-3p were highly expressed in patients compared to normal breast tissue. In the current work, we present the functional characterization of 5âisomiR-140-3p and the cellular phenotypes associated with its overexpression in MCF10A and MDA-MB-231 cell lines in comparison to the canonical hsa-miR-140-3p. Contrary to the effect of the canonical hsa miR 140-3p, overexpression of the 5âisomiR-140-3p led to a decrease in cell viability. The latter observation was supported by cell cycle analysis, where the 5âisomiR-140-3p but not the hsa-miR-140-3p caused cell cycle arrest in G0/G1-phase. Additionally, 5âismoiR-140-3p overexpression was found to cause a decrease in cell migration in MCF10A cells. We identified three novel direct target genes of the 5â isomiR-140-3p; COL4A1, ITGA6 and MARCKSL1. Finally, we have shown that knocking down these genes partially phenocopied the effects of the 5âisomiR-140-4p overexpression, where COL4A1 and ITGA6 knockdown led to reduced cell viability and cell cycle arrest, while MARCKSL1 knockdown resulted in a decrease in the migratory potential of cells. In summary, this work presents evidence that there is a functional synergy between the canonical hsa-miR-140-3p and the newly identified 5âisomiR-140-3p in suppressing growth and progression of breast cancer by simultaneously targeting genes related to differentiation, proliferation, and migration. With this array, we aimed to address the question which genes are regulated by either of the two forms of the miRNA. Samples were measured in one biological replicate of cells transfected with mimic-ctrl1 and mimic-ctrl2 (Dharmacon) as control samples and two biological replicates of cells transfected with hsa-miR-140-3p and 5'isomiR-140-3p (Exiqon) in 30nM concentration using Lipofectamin 2000 as transfection reagent.
2015-10-31 | E-GEOD-74539 | biostudies-arrayexpress
Project description:Annotated canonical miRNAs (anomiRs) are critical regulators of COVID-19 pathogenesis. 5’ isomiRs, which exhibit a shifted 5’ end and distinct seed region compared to their cognate anomiRs, represent an essential component of the miRNAome. However, little is known about their repertoire and expression dynamics following SARS-CoV-2 infection. Herein, we performed an integrative analysis to investigate the expression and regulation of 5’ isomiRs in SARS-CoV-2-infected human lung cells. Using Argonaute (AGO) immunoprecipitated small-RNA sequencing data, we established a repertoire of AGO-loaded 5’ isomiRome encompassing 826 5’ isomiRs from SARS-CoV-2-infected lung cells. A total of 54 5’ isomiRs were differentially expressed, with the majority showing dysregulation 24 hours after SARS-CoV-2 infection. Compared to anomiRs, 5’ isomiRs were preferentially induced at 24 hours post SARS-CoV-2 infection, including six 5’ isomiRs derived from miR-4485 precursor. By focusing on a 5’ isomiR of miR-4485-3p exhibiting one nucleotide downstream shift of the 5’ end (miR-4485-3p|+1), we demonstrated that miR-4485-3p|+1 overexpression significantly repressed genes involved in cellular processes relating to cell cycle, cytoplasmic translation, and carbohydrate derivative metabolic process. Importantly, transcriptome integration further revealed that these cellular processes repressed by miR-4485-3p|+1 overexpression were strongly downregulated at 24 hours following SARS-CoV-2 infection. Moreover, 26 out of 43 (60.5%) hub genes co-repressed by miR-4485-3p|+1 and SARS-CoV-2 infection in these three cellular processes have reported association with COVID-19 in the literature. Taken together, our findings reveal the repertoire and expression alterations of AGO-loaded 5’ isomiRs in SARS-CoV-2-infected lung cells. The identified regulatory effects of miR-4485-3p|+1 highlight potential roles of 5’ isomiRs in COVID-19 pathogenesis.
2025-12-02 | GSE309153 | GEO
Project description:miRNAs are small noncoding RNA molecules that play an important role in post-transcriptional regulation of gene expression. Length and/or sequence variants of the same miRNA are termed isomiRs. While most isomiRs are functionally redundant compared to their canonical counterparts, so-called 5’isomiRs exhibit a shifted 5’ end and therefore a shifted seed sequence resulting in a different target spectrum. However, not much is known about the functional relevance of these isoforms. Analysis of miRNA-seq data from breast cancer cell lines identified six pairs of highly expressed miRNAs and associated 5’isomiRs. Among them, hsa-miR-140-3p was of particular interest because its 5’isomiR showed higher expression compared to the canonical miRNA annotated in miRbase. This miRNA has previously been shown to control stemness of breast cancer cells. MiRNAseq data of breast cancer patients (TCGA dataset) showed that both the canonical hsa-miR-140-3p and its 5’isomiR-140-3p were highly expressed in patients compared to normal breast tissue. In the current work, we present the functional characterization of 5’isomiR-140-3p and the cellular phenotypes associated with its overexpression in MCF10A and MDA-MB-231 cell lines in comparison to the canonical hsa-miR-140-3p. Contrary to the effect of the canonical hsa miR 140-3p, overexpression of the 5’isomiR-140-3p led to a decrease in cell viability. The latter observation was supported by cell cycle analysis, where the 5’isomiR-140-3p but not the hsa-miR-140-3p caused cell cycle arrest in G0/G1-phase. Additionally, 5’ismoiR-140-3p overexpression was found to cause a decrease in cell migration in MCF10A cells. We identified three novel direct target genes of the 5’ isomiR-140-3p; COL4A1, ITGA6 and MARCKSL1. Finally, we have shown that knocking down these genes partially phenocopied the effects of the 5’isomiR-140-4p overexpression, where COL4A1 and ITGA6 knockdown led to reduced cell viability and cell cycle arrest, while MARCKSL1 knockdown resulted in a decrease in the migratory potential of cells. In summary, this work presents evidence that there is a functional synergy between the canonical hsa-miR-140-3p and the newly identified 5’isomiR-140-3p in suppressing growth and progression of breast cancer by simultaneously targeting genes related to differentiation, proliferation, and migration. With this array, we aimed to address the question which genes are regulated by either of the two forms of the miRNA.
2015-10-31 | GSE74539 | GEO
Project description:The product of genomic loci coding for micro RNAs (miRNAs) produce many isoforms (isomiRs). IsomiRs differing at their 5’ end have different seed regions and therefore are expected to target different genes. We used microarrays to study the effect of different isomiRs in the context of breast cancer. The product of genomic loci coding for micro RNAs (miRNAs) produce many isoforms (isomiRs). IsomiRs differing at their 5’ end have different seed regions and therefore are expected to target different genes. We used microarrays to study the effect of different isomiRs in the context of breast cancer. Breast cancer MDA-MB-231 cells were cultured and were subject to a negative control treatment or transfected with one of the three selected isomiRs: the archetype miRNA, the miR-183-5p|2|-2| or the miR-183-5p|+2|+2| isomiR. Each treatment was done in triplicate. RNA was extracted and hybridized on Affymetrix microarrays.
2015-09-23 | E-GEOD-71950 | biostudies-arrayexpress
Project description:Due to alternative processing pathway and post-transcriptional modifications, precursor miRNAs maturate into various sequence isoforms (isomiRs). These sequence variations may result in the changes of the miRNA seed site, target genes, involvement in signaling pathways and thus function. It is important to mention that knowledge about the targets of isomiR is still poor. To date, isomiR research has only been performed in melanoma, breast, and gastric cancer, but there are no experimental studies conducted in colorectal cancer. Here, we aimed to evaluate the putative targets and functional role in vitro of miR-1246 and its two 5’ isoforms (ISO-miR-1246_a and ISO-miR-1246_G). To our best knowledge, this is the first study showing the important role of 5’isoforms of miR-1246 in colorectal carcinogenesis, while acting on different targetomes and being involved in distinct signaling pathways.
2024-02-26 | GSE220728 | GEO
Project description:Due to alternative processing pathway and post-transcriptional modifications, precursor miRNAs maturate into various sequence isoforms (isomiRs). These sequence variations may result in the changes of the miRNA seed site, target genes, involvement in signaling pathways and thus function. It is important to mention that knowledge about the targets of isomiR is still poor. To date, isomiR research has only been performed in melanoma, breast, and gastric cancer, but there are no experimental studies conducted in colorectal cancer. Here, we aimed to evaluate the putative targets and functional role in vitro of miR-1246 and its two 5’ isoforms (ISO-miR-1246_a and ISO-miR-1246_G). To our best knowledge, this is the first study showing the important role of 5’isoforms of miR-1246 in colorectal carcinogenesis, while acting on different targetomes and being involved in distinct signaling pathways.
2024-02-26 | GSE237144 | GEO
Project description:Trypanosoma cruzi (T. cruzi), the causative agent of Chagas disease, remains a major global health threat lacking effective therapies. Macrophages are key effector cells in the host response to T. cruzi infection, yet their incomplete clearance of T. cruzi contributes to Chagas disease pathogenesis. 5’ isomiRs, miRNA isoforms with shifted 5’ ends and altered seed sequences, have emerged as important regulators in diverse diseases. However, their expression alternations in T. cruzi-infected macrophages remain largely unknown. Here, we performed comparative analyses of 5’ isomiR expression in T. cruzi-infected macrophages. We found that T. cruzi infection induced a pronounced and selective increase in miRNA 5’-end heterogeneity in THP-1-derived macrophages, but not in cardiomyocytes or epithelial cells. Comparative 5’ isomiRome analyses further identified 68 differentially expressed 5’ isomiRs in THP-1 macrophages, most of which were specific to T. cruzi infection compared with other pathogens. Among these, 56 5’ isomiRs were associated with Argonaute proteins, including three originating from the miR-1246 precursor. Focusing on miR-1246|+1, a 5’ isomiR generated by a one-nucleotide downstream shift at the 5’ end, we showed that its overexpression significantly downregulated target genes involved in NF-κB signaling, cytokine responses, and cell migration. Notably, miR-1246|+1 broadly suppressed NF-κB family transcription factors and their downstream effector genes, thereby inhibiting pro-inflammatory M1 macrophage phenotype. Collectively, these findings reveal cell type- and pathogen-specific reprogramming of the 5’ isomiR landscape in T. cruzi-infected macrophages and identify miR-1246|+1 as a potential post-transcriptional regulator of macrophage inflammatory polarization.
2026-08-26 | GSE328447 | GEO
Project description:The microRNAome is comprised of annotated canonical miRNAs (anomiR) and a variety of recently identified microRNA isoforms (isomiR). While anomiR is well-studied in the last two decades, the functionality of most isomiRs is largely illusive. Here, we conducted both computional and experimental assays to estimate the functionality of isomiRs expressed in brains.
2022-12-01 | GSE119381 | GEO
Project description:Chronic obstructive pulmonary disease (COPD) and interstitial lung disease (ILD) are clinically and molecularly heterogeneous diseases. We utilized clustering and integrative network analyses to elucidate roles for microRNAs (miRNAs) and miRNA isoforms (isomiRs) in COPD and ILD pathogenesis. Short RNA sequencing was performed on 351 lung tissue samples of COPD (n=145), ILD (n=144) and controls (n=64). Five distinct subclusters of samples were identified including 1 COPD-predominant cluster and 2 ILD-predominant clusters which associated with different clinical measurements of disease severity. Utilizing 262 samples with gene expression and SNP microarrays, we built disease-specific genetic and expression networks to predict key miRNA regulators of gene expression. Members of miR-449/34 family, known to promote airway differentiation by repressing the Notch pathway, were among the top connected miRNAs in both COPD and ILD networks. Genes associated with miR-449/34 members in the disease networks were enriched among genes that increase in expression with airway differentiation at an air-liquid interface. A highly expressed isomiR containing a novel seed sequence was identified at the miR-34c-5p locus. 47% of the anticorrelated predicted targets for this isomiR were distinct from the canonical seed sequence for miR-34c-5p. Overexpression of the canonical miR-34c-5p and the miR-34c-5p isomiR with an alternative seed sequence down-regulated NOTCH1 and NOTCH4. However, only overexpression of the isomiR down-regulated genes involved in Ras signaling such as CRKL and GRB2. Overall, these findings elucidate molecular heterogeneity inherent across COPD and ILD patients and further suggest roles for miR-34c in regulating disease-associated gene-expression.
2023-04-30 | GSE201121 | GEO