Project description:Ultimately, autism is classified as an early neurodevelopmental disorder, highly heterogeneous and with a heritability of between 40% and 90%. Transcriptome studies have already been done in subjects with autism, but we decided to perform such a study on our own cohort of Sicilian subjects with autism. the results obtained show the involvement of differentially expressed genes involving inflammatory mechanisms and the mitochondrilae system.
Project description:The ATP binding cassette (ABC) transporter family is widely distributed in vertebrates and is essential for drug resistance, cell signaling and energy homeostasis. There is growing evidence that various ABC transporters contribute to the growth and development of tumors but relatively little is known about how the ABC transporter family behaves in hepatocellular carcinoma (HCC). ABCC6 transporter was downregulated in HCC tissues and that it was associated with successful treatment for HCC patients. Cellular model studies have shown that ABCC6 plays a role in the migration and cytoskeleton rearrangement of HepG2 hepatocarcinoma cells, highlighting its role in cancer biology. Abcc6-silenced HepG2 cells are used as cell model to obtain more deep information about the molecular mechanisms underlying the observed results. MTT and colony formation assays, showed the effects of Abcc6 on HepG2 cell proliferation. Western blotting analysis, real-time PCR, and immunofluorescence were used to find the E-cadherin, Vimentin, and N-cadherin markers associated with the epithelial-to-mesenchymal transition (EMT). Colony formation experiments in the current study showed that Abcc6 decreased HepG2 cell viability. The migratory and invasion activities were dramatically slowed down by Abcc6 silencing, according to the Transwell and wound-healing assays. In tumor cells, EMT has been shown to be crucial for enhancing migration and invasion and is frequently characterized by a loss of epithelial markers (E-cadherin) and an increase in mesenchymal markers (Vimentin and N-cadherin). In the western blotting examination, E-cadherin expression was considerably elevated compared to the control group, while N-cadherin and Vimentin expression were downregulated. This led to the hypothesis that the underlying mechanism of Abcc6 knockdown prevents migration and invasion in HepG2 cells and is linked to the suppression of EMT. In conclusion all evidence suggested that ABC transporters play a more active role in cancer biology.
Project description:Autism spectrum disorder (ASD) is considered a neurodevelopmental disorder and the pathogenic mechanisms responsible are still unknown, but it is believed to have a rather heterogeneous etiology involving both non-genetic and genetic factors. In this study, we performed a systematic analysis of miRNAs and functional analysis of pathways, to ex-plore their possible roles and/or mechanisms involved in pathology, as well as their pos-sible role as prenatal and/or postnatal, prognostic, and diagnostic biomarkers. We performed analyses on peripheral blood mononuclear cells from 12 Sicilian patients with ASD and 15 healthy controls and subjected them to small RNA sequencing. Differen-tial expression analysis was performed using DESeq2 (version 1.44.0), with significance defined as |fold change| ≥ 1.5 and adjusted p ≤ 0.05. Ingenuity Pathway Analysis (IPA) was applied to evaluate functional enrichment, focusing Diseases and Bio-Functions. A total of 998 miRNAs were identified as differentially expressed in patients with ASD (424 upregulated and 553 downregulated). IPA revealed enrichment in pathways re-lated to psychological and neurological diseases. IPA network analysis of differentially expressed miRNAs and their predicted targets identified multiple enriched interaction networks; we focused on three networks related to inflammation, cell survival and mech-anotransduction, synaptic plasticity, and neuronal excitability. We identified four miR-NAs: miR-296-3p, miR-27a, miR-146a-5p, and miR-29b-3p. The variance shown in the principal component analysis suggests that most miR-RNAs are expressed very differently in ASD compared to normal individuals. This preliminary study high-lighted and confirmed that inflammatory, autoimmune, and infectious mechanisms play a decisive role in ASD, emphasizing the specific function of miRNAs that regulate S100 family genes, neuronal migration, and the creation of communication systems.
Project description:Whole-genome transcriptome measurements are pivotal for characterizing carcinogenic mechanisms of chemicals and predicting toxic classes, such as genotoxicity, from in vitro and in vivo assays. DNA microarrays have evolved as the gold standard for this purpose. In recent years deep sequencing technologies have been developed that hold the promise of measuring the transcriptome with RNA-seq in a more accurate and unbiased manner than microarrays. So far, however, few applications have been published that assess the performance of RNA-seq within a toxicogenomics context. Here, we applied RNA-seq for the characterization of the in vitro transcriptomic responses in HepG2 cells upon exposure to benzo[a]pyrene (BaP), a well-known DNA damaging carcinogen. We demonstrate the performance of RNA-seq with respect to the identification of differentially expressed genes and associated pathways, in comparison with microarray technology. RNA-seq data generates more complete and thus accurate data on differentially expressed genes and affected pathways than microarrays. Additionally, we highlight the potential of RNA-seq for characterizing mechanisms related to alternative splicing and thereby gathering new information. Exposure to BaP alters the isoform distribution for many genes, including regulators of cell death and DNA repair such as TP53, BCL2 and XPA, which are relevant for genotoxic responses. Finally, we demonstrate that RNA-seq enables to investigate allele-specific gene expression, although no changes for that could be observed. Our results provide evidence that RNA-seq is a powerful tool for toxicology which, compared to microarrays, is capable of adding valuable information at the transcriptome level for characterizing toxic effects caused by chemicals. Examination of 2 biological replicates at 2 different timepoints
Project description:This SuperSeries is composed of the following subset Series: GSE36242: Transcriptomic response to benzo[a]pyrene treatment in HepG2 cells (RNA-Seq) GSE36243: Transcriptomic response to benzo[a]pyrene treatment in HepG2 cells (Affymetrix) Refer to individual Series
Project description:The experimental work unveils novel targets of hsa-miR-125a-5p relevant in hepatocellular carcinoma (HCC). In particular, a genome-wide perspective of the whole miR-125a targetome has been achieved. First, two different HCC cell lines were subjected to a miRNA boosting by mimic transfections, resulting in many de-regulated genes, as observed by a transcriptomic approach. Then, the merging of down-regulated genes with results from bioinformatic predictive tools yielded a number of miR-125a direct targets candidates. Finally, those potential targets were further experimentally validated. This study could pave the way to piece together the RNA regulatory networks governed by miR-125a impacting on hepatocarcinogenesis and be exploited in the future for identifying novel biomarkers and therapeutic targets in HCC.
Project description:Introduction: Parkinson's disease (PD) is characterized by bradykinesia, tremor, and rigidity; in addition, postural instability sets in as the disease progresses. Non-motor symptoms of the disease include cognitive, behavioral, and neuropsychiatric changes, sensory and sleep disturbances that may precede the motor symptoms of the disease itself. The peculiar pathological features of PD are decreased dopaminergic neurons and dopamine levels in the substantia nigra pars compacta and pontine locus ceruleus. The study of the transcriptome plays a major role in the identification of genes and gene regulatory mechanisms in multifactorial neurodegenerative diseases such as Parkinson's disease itself. Therefore, we proposed to study the transcriptome directly in the midbrain containing the "Substantia nigra.The study was performed in 8 subjects with PD and 6 normal control subjects, using next-generation sequencing (NGS) technologies. Results: With the use of an ad hoc bioinformatics pipeline, gene expression profiles in the different PD subjects were obtained and compared to those of controls. In detail, the results obtained from the data analysis indicated 92 differentially expressed genes (FDR-adjusted p value ≤0.05 and fold-change less than -1.5 or greater than +1.5) of which 33 genes were up-regulated while 59 were down-regulated. Conclusions: Functional analysis of the differentially expressed genes revealed several genes involved in different canonical pathways indicating their likely significant role in Parkinson's disease.
Project description:Huntington's disease (HD) is an autosomal dominant neurodegenerative disease caused by the expansion of the CAG nucleotide repeat in the first exon of the huntingtin (HTT) gene, with an onset between the second and third decades of life and slow progression. The pathogenesis of several of HD involves dysregulation of gene expression, which depends on several molecular processes ranging from transcription to protein stability. To elucidate potential variations in gene expression in HD, a transcriptome study was conducted on 15 HD subjects and 15 controls, all of Sicilian origin, starting from peripheral blood mononuclear cell samples. A total of 7179 different statistically significant genes were identified between the two cohorts. Gene Set Enrichment Analysis (GSEA) and Gene Ontology (GO) terms were employed to explore the pathways influenced by differentially expressed mRNAs. GSEA revealed GO pathways strongly associated with HD, i.e. all GO biological process terms encompassing ribosome functions and structure are all highly negatively expressed phenotypes, with a large number of genes being dysregulated. This leads to the hypothesis that the processing chain leading to protein translation (via ribosomes) from mRNA is somehow impaired. In addition, genes and non-coding RNAs (ncRNAs) that play a regulatory role in various transcriptional processes were dysregulated. We can hypothesize that the whole process, from transcription to translation, is somehow compromised in HD subjects who have been genetically diagnosed with the expansion of the CAG triplet of the first exon of the HTT gene.
Project description:Cardiac myocyte-specific ERalpha KO mice were generated to assess the role of ERα in the heart. Female ERαHKO mice displayed a modest cardiac phenotype, but unexpectedly, an the most striking obesity phenotype developed was obesity in female ERαHKO but not male ERαHKO mice. In female ERαHKO mice we identified cardiac dysfunction, mild glucose and insulin intolerance, and reduced ERα gene expression in skeletal muscle and white adipose tissue (WAT). RNA-seq analysis was conducted on the ventricles and WAT of male and female ERαHKO mice to further elucidate the transcriptomic alterations associated with the shift in metabolic profiles in the tissues of interest.
Project description:In order to characterize the differentially expressed miRNAs after the p53 activation , small RNA-seq were used after the overexpression of p53 in HepG2 cells. Four samples of HepG2 cells were subjected to small RNA-seq in two biological replicates.The HepG2 cells were treated with 1µg/ml doxorubicin for 24 hours to induce the expression of p53. The experimental group(dox-treated HepG2ï¼HepG2_24h_rep1 and HepG2_24h_rep2) and control group(untreated HepG2: HepG2_0h_rep1 and HepG2_0h_rep2) were subjected to small RNA-seq to identify the p53-regulated miRNAs.