biostudies-arrayexpressGiovanna Maria VentolaHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16206Autism 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.biostudies-arrayexpressSample Collection - A miRNA analysis on peripheral blood mononuclear cells (PBMCs) was performed by RNA-seq in 27 subjects, including 12 ASD patients and 15 healthy controls. The subjects were recruited at the Oasi Research Institute - IRCCS (Troina, Italy) and originated from the same region (Sicily) to minimize environmental influences.Sequencing - Equimolar pooling of indexed libraries was performed, followed by cluster generation and sequencing on an Illumina NovaSeq 6000 platform (Illumina, San-ta Clara, CA, USA) in a single-end 1 × 75 format.Nucleic Acid Extraction - Total RNA was isolated from peripheral blood mononuclear cells (PBMCs) using the TRIzol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA), following the manu-facturer’s protocol. RNA concentration and purity were assessed with the NanoDrop™ 2000/2000c (Thermo Fisher Scientific, Waltham, MA, USA), whereas RNA integrity was evaluated with the Agilent TapeStation 4200 (Agilent Technologies, Santa Clara, CA, USA) using the RNA ScreenTape Assay 2.7. Extracted RNA was stored at −80 °C until further use.Library Construction - Indexed libraries were generated from 250 ng of total RNA using the QIAseq miRNA Li-brary Kit (Qiagen), according to the manufacturer’s guidelines. Library quality and con-centration were evaluated with the Agilent TapeStation 4200 and Qubit fluorometer (Invi-trogen), respectively.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Identification and quantification of microRNAs were performed with the sRNAbench library mode, using the Homo sapiens miRBase reference (release 22.1). Data normalization was performed in R, applying negative binomial generalized linear models and retaining genes expressed in at least 30% of samples. Differential expression analysis was con-ducted between ASD and control samples using the DESeq2 (version 1.50.1) package (Bi-oconductor version 3.22)UnknownTranscriptomicsGenomicsProteomicsRIllumina NovaSeq 6000RNA-seq of coding RNAHomo sapiensGiovanna Maria VentolafalseDysregulation of miRNAs in Sicilian Patients with Autism Spectrum DisorderAutism 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.2026-05-11T00:00:00Z2026-05-13T14:10:57.08Z2025-11-19T15:53:45.21ZE-MTAB-16206ERP185345EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184