Biology subjects

Karedath, T.

Publications and source records attributed to Karedath, T..

4 recordsLinked to original sources

bioRxiv2019

Regulation of circular RNA circNFATc3 in cancer cells alters proliferation, migration and oxidative phosphorylation

Circular RNAs were once considered artifacts of transcriptome sequencing but have recently been identified as functionally relevant in multiple cancers. Although there is still no clear main function of circRNAs, several studies have revealed that circRNAs are expressed in a variety of eukaryotic organisms, demonstrate conservation across species, and are expressed in a regulated manner often independent of their parental linear isoforms. circNFATC3, an abundant and uncharacterized circular isoform of NFATC3 gene (which is formed form backsplicing of exon 2 and 3) in solid tumors was identified from transcriptomic data. Here we show that circNFATC3 gain of and loss of function experiments using RNAi mediated circRNA silencing and circular mini vector-mediated overexpression of circularized constructs in breast and ovarian cancer cell lines affects molecular phenotypes. Knockdown of circNFATC3 induces a reduction in cell proliferation, invasion, migration, and oxidative phosphorylation. Gain of function of circNFATc3 in MDA-MB -231 cells and SKOV3 cells shows a significant increase in cell proliferation, migration, and respiration. The above results suggest that circNFATC3 is a functionally relevant circular RNA in cancer

molecular biology↗

bioRxiv2018

Identification of human genetic variants controlling circular RNA expression

Circular RNAs (circRNAs) are abundant in eukaryotic transcriptomes and have been linked to various human disorders. However, understanding genetic control of circular RNA expression is in early stages. Here we present the first integrated analysis of circRNAs and genome sequence variation from lymphoblastoid cell lines of the 1000 genomes project. We identified thousands of circRNAs in the RNA-seq data and show their association with local single nucleotide polymorphic sites, referred to as circQTLs, which influence the circRNA transcript abundance. Strikingly, we found that circQTLs exist independently of eQTLs with most circQTLs having no effect on mRNA expression. Only a fraction of the polymorphic sites are shared and linked to both circRNA and mRNA expression with mostly similar effects on circular and linear RNA. A shared intronic QTL, rs55928920, of HMSD gene drives the circular and linear expression in opposite directions, potentially modulating circRNA levels at the expense of mRNA. Finally, circQTLs and eQTLs are largely independent and exist in separate linkage disequilibrium (LD) blocks with circQTLs highly enriched for functional genomic elements and regulatory regions. This study reveals a previously uncharacterized role of DNA sequence variation in human circular RNA regulation.

genomics↗

bioRxiv2018

TGF-β Mediated Cell Adhesion Dynamics and Epithelial to Mesenchymal Transition in 3D and 2D Ovarian Cancer Models

BackgroundThree-dimensional (3D) tumor cultures in vitro have recently regained attention as they have been acclaimed to have higher similarity to in vivo tumors than cells grown in conventional monolayers (2D). Cancer cells in 2D monolayers fail to mimic the exact tumor microenvironment existing in the real clinical samples. The 3D anchorage-independent cancer models can better explain the cell adhesion properties in ovarian cancer cells.\n\nResultsTranscriptome profiling of 3D models compared to 2D models in various cancer cell lines shows differential expression of TGF-{beta}-mediated and cell adhesion pathways. Presence of TGF-{beta} in these cell lines shows an increased invasion potential which is specific to cell type. We decided to choose two ovarian cancer cell lines as model systems to study Epithelial to Mesenchymal Transition (EMT) and cancer invasion based on their invasion potential and ability to switch the cadherins expression. TGF-{beta} modulation in EMT and cancer invasion was successfully depicted in both 2D and 3D models of SKOV3 and CAOV3 cell lines. Functional evaluations in 3D and 2D models demonstrate that the addition of the exogenous TGF-{beta} can induce EMT and invasion in cancer cells by turning them into aggressive phenotypes. TGF-{beta} receptor kinase I inhibitor (LY364947) can revert TGF-{beta} effect in these cells.\n\nConclusionsIn a nutshell, TGF-{beta} can induce EMT and migration, increase aggressiveness, increase cell survival, alter cell characteristics, remodel the Extracellular Matrix (ECM) and increase cell metabolism favorable for tumor invasion and metastasis.

cancer biology↗

bioRxiv2018

Silencing of ANKRD12 circRNA induces molecular and functional changes associated with invasive phenotypes

Circular RNAs (circRNA) that form through non-canonical backsplicing events of pre-mRNA transcripts are evolutionarily conserved and abundantly expressed across species. However, the functional relevance of circRNAs remains a topic of debate. In this study, we identified and characterized a circular RNA derived from Exon 2 and Exon 8 of the ANKRD12 gene, termed here as circANKRD12. We show that this circRNA is abundantly expressed in breast and ovarian cancers. The circANKRD12 is RNase R resistant and predominantly localized in the cytoplasm in contrast to its source gene mRNA. We confirmed the expression of this circRNA across a variety of cancer cell lines and provide evidence for its functional relevance through downstream regulation of several tumor invasion genes. We show that silencing of circANKRD12 induces a phenotypic change by significantly regulating cell cycle, increasing invasion and migration, altering the metabolism in cancer cells. These results reveal the functional significance of circANKRD12 and provide evidence of a regulatory role for this circRNA in cancer progression.

cancer biology↗