Project description:Mitochondrial ribosomal proteins of the large subunit (MRPLs) are critical for mitochondrial protein synthesis and cellular energy metabolism. The role of MRPL37, a member of the MRPL family, in hepatocellular carcinoma (HCC) progression was investigated using SNU-398 HCC cells. In this study, we performed RNA sequencing (RNA-seq) to characterize transcriptomic changes following shRNA-mediated knockdown of MRPL37. The dataset includes RNA profiles from SNU-398 cells with MRPL37 knockdown and corresponding control cells. This analysis aims to elucidate the molecular mechanisms by which MRPL37 regulates mitochondrial function and energy metabolism in HCC. These data provide insights into the role of MRPL37 in HCC progression and may facilitate the identification of novel therapeutic targets for liver cancer.
Project description:Through deep sequencing and functional screening in zebrafish, we find that miR-221 is essential for angiogenesis. miR-221 knockdown phenocopied defects associated with loss of the tip cell-expressed Flt4 receptor. Furthermore, miR-221 was required for tip cell proliferation and migration, as well as tip cell potential in mosaic blood vessels. miR-221 knockdown also prevented “hyper-angiogenesis” defects associated with Notch deficiency and miR-221 expression was inhibited by Notch signaling. Finally, miR-221 promoted tip cell behavior through repression of two targets: cyclin-dependent kinase inhibitor 1b (cdkn1b) and phosphoinositide-3-kinase regulatory subunit 1 (pik3r1). These results identify miR-221 as an important regulatory node through which tip cell migration and proliferation are controlled during angiogenesis. Identification of endothelial-expressed microRNA from FACS-isolated zebrafish endothelial cells.
Project description:To evaluate involvement of miR-221 and miR-222 in lung cancer, we investigated the effects of miR-221 and miR-222 overexpression on six lung cancer cell lines as well as one immortalized normal human bronchial epithelial cell line. Two cell lines, H3255 and H1299 with no replicates were studied. Cells were transfected with miR-221, miR-222, or miR control. Microarray analysis was done to identify genes differentially expressed in lung cancer cells after the transfection of miR-221 or miR-222.
Project description:Hepatocellular carcinoma (HCC) is the third leading malignancy worldwide. MiR-221 have oncogenic functions and play a seminal role in carcinogenesis regulation including in high risk- human HCC. However, the molecular mechanism and biological functions of miR-221 has not been investigated thoroughly in HCC. In the present work, the role of miR-221 in HCC was evaluated using microarray and miR-221target genes expressions were analyzed in miR-221 inhibitor transfected HCC cell lines HepG2, Huh-7, WRL-68. Finally, we found that 89 upregulated and 52 downregulated genes by miR-221 in HCC cell lines.l
Project description:Patients with advanced hepatocellular carcinoma (HCC) are currently treated by Sorafenib and Regorafenib but efficacy of these multikinase inhibitors is disappointing. Thus, new drugs and therapies are needed to improve HCC management in clinic. We recently reported the remarkable capacity of miR-4510 to impede the growth of HCC and hepatoblastoma cells in vitro and in vivo through GPC3 targeting and Wnt pathway inactivation (Cartier F et al, Oncotarget 2017). Here, we used a label-free proteomic approach to identify new targets of miR-4510 in HCC-deriving Huh7 cells. We transfected HCC-derived Huh7 cells with either a synthetic miR-4510 mimic or a small RNA control, extracted total proteins 24hr later and comparatively analyzed proteomes of control and miR-4510-transfected cells using a quantitative label-free approach.
Project description:Hepatocellular carcinoma (HCC) remains a significant clinical challenge due to limited diagnostic and therapeutic options. Non-coding RNAs, such as microRNAs (miRNAs), play key roles in cancer biology. Our previous findings showed that miR-423-5p exerts anti-cancer effects on HCC patients treated with sorafenib by promoting autophagy. In this study, we investigated the molecular mechanisms underlying its activity by generating SNU-387 HCC cell line stably overexpressing miR-423-5p and conducting a comprehensive proteomic analysis. Mass spectrometry profiling identified 698 differentially expressed proteins (DEPs) in miR-423-5p-overexpressing cells compared to controls. Functional enrichment analysis revealed significant alterations in metabolic pathways, particularly purine/pyrimidine metabolism and gluconeogenesis. To relate these findings to clinical context, we integrated experimentally validated and predicted miR-423-5p targets with The Cancer Genome Atlas (TCGA) Liver Hepatocellular Carcinoma (LIHC) dataset. Seven candidate proteins were significantly associated with patient prognosis (log-rank p < 0.05 for both overall and disease-free survival). These targets were downregulated in our miR-423-5p model but found to be upregulated in stage III HCC tissues from TCGA data.
Project description:Wild type or Elf4-/- peritoneal macrophages were infected with VSV, followed by whole genome RNA-seq analysis. 293T cells were transfected with miR-221 or empty vector, followed by whole genome RNA-seq analysis. Conclusions:Overexpression of miR-221 in cells facilitated viral infection and inhibited the production of IFNβ.
Project description:MiR-221 overexpression leads to activation of apoptosis, growth arrest and reduced invasivness in PCa cells. Interaction of miR-221 with potential target genes was analyzed by a genome wide expression profiling.. Regulation of selected genes and proteins identified in the gene array analysis was confirmed by Real Time RT-PCR assay (IRF1, IRF2 SOCS3, STAT1), and Western Blotting. In total, 282 genes were upregulated and 64 downregulated based on a more than 2-fold difference to untransfected PC-3 cells. Regulated genes are involved in apoptosis, hemostasis, oxidative stress response, tumorigenesis and inflammation. We confirmed dysregulation of IRF-2 SOCS3, STAT1,IRF9. These results indicate that miR-221 overexpression might lead to activation of the JAK/STAT pathway and downregulation of miR-221 might contribute to tumorigenesis in PCa cells. pre-miR-221 transfected PC-3 cells vs unstimulated control cells - total samples analysed are 4.
Project description:MicroRNAs are noncoding RNA species comprising 18–23 nucleotides that regulate host-virus interaction networks. Here, we showed that enterovirus A71 infection in human rhabdomyosarcoma (RD) involved miR-197 expression. miR-197 can regulate virus replication in the context of viral RNA synthesis via the transfection of its mimic into RD cells. We employed a mass spectrometry-based quantitative proteomic stable isotope labeling with amino acids in cell culture (SILAC) approach for the identification of miR-197 target genes by transfecting mimetic miR-197 into RD cells, and the differential expression of prospective target proteins was identified. A total of 1,822 genes were repeatedly and considerably downregulated in miR-197-transfected RD cells, 106 of which were predicted to have seed sites by TargetScan. Seven of the selected 8 genes potentially related to viral replication and immune response were confidently validated as direct miR-197 targets using a luciferase (untranslated region (3'-UTR)) reporter assay. The expression of three selected endogenous molecules (ITGAV, ETF1, and MAP2K1 (MEK1)) was significantly reduced when RD cells were transfected with an miR-197 mimic. Our results provide a database of miR-197 targets, which is potentially of interest in the area of viral pathogenesis and other research fields.