Elevated mRNA expression of CASPR3 in patients with schizophrenia

Identification of genetic features that are associated with amplitude of low-frequency fluctuation changes in schizophrenia using omics analysis

Genetic risk for schizophrenia is thought to trigger variation in clinical features of schizophrenia, but biological processes associated with neuronal activity in brain regions remain elusive. In this study, gene expression features were mapped to various sub-regions of the brain by integrating low-frequency amplitude features and gene expression data from the schizophrenia brain and using gene co-expression network analysis of the Allen Transcriptome Atlas of the human brain from six donors to identify genetic features of brain regions and important associations with neuronal features. The results indicate that changes in the dynamic amplitude of low-frequency fluctuation (dALFF) are mainly associated with transcriptome signature factors such as cortical layer synthesis, immune response, and expanded membrane transport. Further modular disease enrichment analysis revealed that the same set of signature genes associated with dALFF levels was enriched for multiple neurological biological processes. Finally, genetic profiling of individual modules identified multiple core genes closely related to schizophrenia, also potentially associated with neuronal activity. Thus, this paper explores genetic features of brain regions in the schizophrenia closely related to low-frequency amplitude ratio levels based on imaging genetics, which suggests structural endophenotypes associated with schizophrenia.

miRNA analysis with Prost! reveals evolutionary conservation of organ-enriched expression and post-transcriptional modifications in three-spined stickleback and zebrafish

MicroRNAs (miRNAs) can have organ-specific expression and functions; they can originate from dedicated miRNA genes, from non-canonical miRNA genes, or from mirror-miRNA genes and can also experience post-transcriptional variation. It remains unclear, however, which mechanisms of miRNA production or modification are organ-specific and the extent of their evolutionary conservation. To address these issues, we developed the software Prost! (PRocessing Of Short Transcripts), which, among other features, helps quantify mature miRNAs, accounts for post-transcriptional processing, such as nucleotide editing, and identifies mirror-miRNAs. Here, we applied Prost! to annotate and analyze miRNAs in three-spined stickleback (Gasterosteus aculeatus), a model fish for evolutionary biology reported to have a miRNome larger than most teleost fish. Zebrafish (Danio rerio), a distantly related teleost with a well-known miRNome, served as comparator. Our results provided evidence for the existence of 286 miRNA genes and 382 unique mature miRNAs (excluding mir430 gene duplicates and the vaultRNA-derived mir733), which doesn't represent a miRNAome larger than other teleost miRNomes. In addition, small RNA sequencing data from brain, heart, testis, and ovary in both stickleback and zebrafish identified suites of mature miRNAs that display organ-specific enrichment, many of which are evolutionarily-conserved in the brain and heart in both species. These data also supported the hypothesis that evolutionarily-conserved, organ-specific mechanisms may regulate post-transcriptional variations in miRNA sequence. In both stickleback and zebrafish, miR2188-5p was edited frequently with similar nucleotide changes in the seed sequence with organ specific editing rates, highest in the brain. In summary, Prost! is a new tool to identify and understand small RNAs, to help clarify a species' miRNA biology as shown here for an important model for the evolution of developmental mechanisms, and to provide insight into organ-enriched expression and the evolutionary conservation of miRNA post-transcriptional modifications.