Disease Context–Dependent Directional Dysregulation Observed in Human Orphan Genes

Human orphan genes lack identifiable orthologs and remain poorly characterized. We investigated patient-level disease-associated expression changes of human orphan gene transcripts using paired RNA-sequencing data from 220 patients across four cohorts: psoriasis, laryngeal squamous cell carcinoma (LSCC), hepatocellular carcinoma (HCC), and lung adenocarcinoma (LAC). RNA-seq reads were quantified against a combined GRCh37-based reference containing 2,190 human orphan transcripts and 196,317 other transcripts. Significant upregulation versus downregulation of orphan transcripts was observed in 21 versus 3 patients with psoriasis, 26 versus 27 with LSCC, 19 versus 51 with HCC, and 69 versus 0 with LAC (Benjamini-Hochberg-adjusted P < 0.01). These patterns were largely preserved after excluding zero-abundance transcripts and aggregating transcripts into 1,226 orphan gene loci. Rank-based analysis changed the predominant direction in some cohorts, most notably LAC, but retained marked between-cohort differences and bidirectionality within several cohorts. Expression-matched non-orphan controls showed substantially fewer significant directional changes in three cohorts and failed to reproduce the orphan-gene pattern in LAC, indicating that low abundance alone cannot explain the observations. Clinical variables did not readily account for this heterogeneity. Patient-level directional heterogeneity is an underappreciated feature of human orphan gene expression that can be obscured by conventional group-level differential-expression analysis in studies of human disease.