biostudies-arrayexpressGenomix4Life VentolaHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15153Huntington's disease (HD) is a late-onset, progressive, neurodegenerative disorder, usually in the second decade of life, with a fatal outcome in about 6 to 20 years after onset. Many studies have focused on the dysregulation of noncoding RNAs (ncRNAs), such as microRNAs (miRNAs), which play a regulatory function on messenger RNAs (mRNAs) by degrading or inhibiting them. Since abnormal gene expression underlies many diseases, miRNAs are thought to exert influence on several aspects. Differential expression analysis was conducted on patient vs. control samples using the Bioconductor DESeq2 package. Instead, to perform miRNA-target analysis, clusterProfiler was used to study functional target analysis. Specifically, clusterProfiler analysis was based on Gene Ontology (GO - Cellular Component (CC), Biological Process (BP) and Molecular Function (MF)) and KEGG pathway database, selecting a set of miRNAs with padj≤0.05 and |fold-change|≥1.5. Differential expression analysis between the two groups revealed 270 miRNAs were significantly upregulated (fold change ≥ 1.5), while 519 were significantly downregulated (fold change ≤ -1.5). The enrichment analysis allowed us to identify a large number of functional terms associated with the target genes of dysregulated miRNAs. In particular, among the terms we focused on: positive regulation of cell development and nucleocytoplasmic transport, vacuolar membrane and chromosome, centromeric region and, finally DNA-binding transcription factor binding and nuclear receptor binding.biostudies-arrayexpressSequencing - The pooled samples were subject to cluster generation and sequencing using an Illumina NovaSeq 6000 System (Illumina, Santa Clara, CA, USA) in a 1 × 75 single-end format.Sample Collection - A miRNA analysis on peripheral blood mononuclear cells (PBMCs) was performed by RNA-seq in 30 subjects, including 15 HD patients and 15 healthy controls. The subjects were recruited at the Oasi Research Institute - IRCCS (Troina, Italy).Nucleic Acid Extraction - PBMCs separation was performed using Ficoll-Paque (Ficoll Plaque PLUS–GE Healthcare Life Sciences, Piscataway, NJ, USA.Total RNA extraction from PBMC was performed using TRIzol reagent (TRIzol Reagent, Invitrogen Life Technologies, Carlsbad, CA, USA), according to the manufacturer’s instructions. RNA was stored at −80 ◦C until further processing.RNA concentration and purity were evaluated using NanoDrop™ 2000/2000c (Thermo Fisher Scientific),whereas sample integrity was analyzed by TapeStation 4200 (Agilent Technologies) using RNA ScreenTape Assay. 2.7.Library Construction - Indexed libraries were prepared from 250 ng purified RNA using QIAseq miRNA Library Kit (Qiagen) according to the manufacturer’s instructions. Libraries were quantified using the TapeStation 4200 (Agilent Technologies) and Qubit fluorometer (Invitrogen Co.), then pooled such that each index-tagged sample was present in equimolar amounts.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - R was utilized to normalize the data, using negative binomial generalized linear models, considering all genes expressed in ≥ 30% of all samples.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsRIllumina NovaSeq 6000<b>Background/Objectives</b>: Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder caused by a CAG nucleotide repeat expansion in the Huntingtin (<i>HTT</i>) gene. Dysregulation of microRNAs (miRNAs), key post-transcriptional regulators of gene expression, has been implicated in HD pathogenesis, although their specific roles remain incompletely understood. <b>Methods</b>: Peripheral blood mononuclear cells from Sicilian HD patients and matched healthy controls were subjected to small RNA sequencing. Differential expression analysis was conducted using DESeq2 (version 1.44.0), with significance defined as |fold change| ≥ 1.5 and adjusted <i>p</i> ≤ 0.05. Ingenuity Pathway Analysis (IPA) was applied to assess functional enrichment, focusing on neurological diseases, inflammatory processes, and miRNA-RNA messenger (mRNA) interaction networks. <b>Results</b>: A total of 790 differentially expressed miRNAs were identified in HD patients (270 upregulated and 520 downregulated). IPA revealed enrichment in pathways related to organismal injury, neurological disease, and inflammatory responses. Four major regulatory networks linked differentially expressed miRNAs to neurodegenerative processes, with target genes involved in neuroinflammation, cellular stress responses, and metabolic dysfunction. Cross-referencing with previous RNA-seq data identified 5721 high-confidence miRNA-mRNA interactions, implicating 721 target genes across 54 key canonical pathways. <b>Conclusions</b>: HD patients exhibit a distinct and reproducible peripheral blood miRNA expression signature. These dysregulated miRNAs may represent accessible biomarkers and provide mechanistic insights into HD pathogenesis, with potential applications for diagnosis, prognosis, and therapeutic development.RNA-seq of coding RNAHomo sapiensDysregulation of miRNAs in Sicilian Patients with Huntington’s DiseaseMichele Salemi, Francesca Antonia Schillaci, Maria Grazia Salluzzo, Giovanna Marchese, Giovanna Maria Ventola, Concetta Simona Perrotta, Vincenzo Di Stefano, Giuseppe Lanza and Raffaele FerriGenomix4Life VentolafalseDysregulation of miRNAs in patients with Huntington's DiseaseHuntington's disease (HD) is a late-onset, progressive, neurodegenerative disorder, usually in the second decade of life, with a fatal outcome in about 6 to 20 years after onset. Many studies have focused on the dysregulation of noncoding RNAs (ncRNAs), such as microRNAs (miRNAs), which play a regulatory function on messenger RNAs (mRNAs) by degrading or inhibiting them. Since abnormal gene expression underlies many diseases, miRNAs are thought to exert influence on several aspects. Differential expression analysis was conducted on patient vs. control samples using the Bioconductor DESeq2 package. Instead, to perform miRNA-target analysis, clusterProfiler was used to study functional target analysis. Specifically, clusterProfiler analysis was based on Gene Ontology (GO - Cellular Component (CC), Biological Process (BP) and Molecular Function (MF)) and KEGG pathway database, selecting a set of miRNAs with padj≤0.05 and |fold-change|≥1.5. Differential expression analysis between the two groups revealed 270 miRNAs were significantly upregulated (fold change ≥ 1.5), while 519 were significantly downregulated (fold change ≤ -1.5). The enrichment analysis allowed us to identify a large number of functional terms associated with the target genes of dysregulated miRNAs. In particular, among the terms we focused on: positive regulation of cell development and nucleocytoplasmic transport, vacuolar membrane and chromosome, centromeric region and, finally DNA-binding transcription factor binding and nuclear receptor binding.2025-10-10T00:00:00Z2025-10-10T12:51:49.281Z2025-05-19T20:51:49.025ZE-MTAB-15153ERP172733EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_000418410.3390/diagnostics15192454