First Computational Characterization of HTR5A-AS1: a Schizophrenia-Linked Antisense RNA with Synaptic Functions

Background/Objectives: Schizophrenia is a highly heritable psychiatric disorder that affects approximately 1% of the global population. Genome-wide association studies (GWAS) have mapped most schizophrenia risk variants to noncoding regions, highlighting the role of regulatory processes and noncoding RNAs in schizophrenia pathology. Despite this, and schizophrenia’s association with 5-hydroxytryptamine (serotonin) system dysfunction, HTR5A-AS1, a long noncoding RNA (lncRNA) antisense to the serotonin receptor (HTR, 5-hydroxytryptamine receptor) gene HTR5A, remains virtually unstudied. This study provides the first systematic characterization of HTR5A-AS1, validating its transcript structure and investigating its genetic associations, expression dynamics, developmental regulation, and potential synaptic and GABAergic functions in schizophrenia. Methods: Transcriptome-wide association study (TWAS) summary statistics were integrated with postmortem RNA sequencing (RNA-seq), BrainSpan developmental transcriptomes, UCSC Genome Browser annotations, and functional prediction tools. These complementary approaches enabled validation of the transcript’s structure, quantification of regional and developmental expression, and assessment of potential molecular functions. Results: HTR5A-AS1 showed significant TWAS associations with schizophrenia in the hippocampus and dorsolateral prefrontal cortex (dlPFC). In postmortem schizophrenia donor tissue, expression was significantly reduced in the hippocampus, with a non-significant but directionally similar decrease in the dlPFC. Developmental transcriptomes revealed region-specific developmental trajectories, with steep increases during adolescence, aligning with the age range of typical schizophrenia onset. HTR5A-AS1 was strongly co-expressed with HTR5A, and functional predictions implicated involvement in synaptic and GABAergic signaling, consistent with cortico-hippocampal circuit disruption in schizophrenia. Conclusions: These findings provide the first evidence that HTR5A-AS1 is a bona fide antisense transcript with developmental and synaptic roles that may contribute to schizophrenia risk. Future single-cell and functional perturbation studies are needed to test causality and define mechanisms of regulation.