T88. LARGE-SCALE LYMPHOBLASTOID CELL LINE TRANSCRIPTOMIC PROFILING OF AUTISM RECAPITULATES PROTEIN FOLDING AND MITOCHONDRIAL ALTERATIONS

Abstract

Background Autism spectrum disorder (ASD) is a common, heritable, polygenic neurodevelopmental disorder, with hundreds of robustly associated risk genes and loci. Transcriptomic profiling of post-mortem cortex has identified characteristic ASD molecular signatures, including upregulation of protein folding pathways and downregulation of mitochondrial and synaptic gene expression, enriched for ASD genetic risk. However, as brain tissue is clinically inaccessible, whether these (or other) characteristic transcriptomic biomarkers are reflected in peripheral tissues remains unknown — a critical gap, as tractable peripheral biomarkers could greatly advance diagnosis, stratification, and precision medicine. Methods We leveraged RNA-sequencing of lymphoblastoid cell lines (LCLs) from > 1600 sibling-proband pairs (N=3826 individuals) in the Simons Simplex Cohort (SSC). Gene expression was quantified using Salmon, and extensive sample-level quality control (QC) was conducted using metrics compiled across RNA-SeQC and PicardTools. Following data QC and filtering, we calculated a “direct” ASD transcriptomic effect (“delta ASD”) as the within-family difference in expression for probands versus unaffected siblings, correcting for sex, batch, and technical covariates, thereby accounting for shared familial genetic and environmental factors. Gene set enrichment analyses (GSEA) were then run using cameraPR on delta ASD t-statistics to assess enrichment for gene ontology (GO) pathways and previously identified ASD-associated brain gene co-expression modules. Results Delta ASD analysis identified 1139 nominally significant differentially expressed genes (p < 0.05), including 515 upregulated and 624 downregulated in probands relative to siblings. Of these, 9 were significant following correction for multiple comparisons, including genes implicated in innate immune signaling (TLR9; t = −3.75), translational regulation (EEF2; t = −3.71), and RNA processing (DHX35; t = 4.16) — themes independently recovered at the pathway level by GSEA. LCL transcriptomes recapitulated protein folding upregulation observed in post-mortem ASD cortex, with significant GSEA enrichment of a brain isoform co-expression module enriched for ubiquitin-proteasome mediated protein quality control (p = 0.03, normalized enrichment score [NES] = 1.49), further supported by GO GSEA enrichment of chaperone-mediated protein folding and proteasome pathways. Notably, upregulation of a curated mitochondrial gene set (p = 0.03; NES = 1.71), corroborated by GO enrichment of mitochondrial oxidative phosphorylation pathways, suggests altered mitochondrial function in ASD LCLs, contrasting with the downregulation of mitochondrial co-expression modules reported in post-mortem brain. Downregulated GO pathways included cytoplasmic translation, ribosome biogenesis, and glycolysis. Discussion Together, these results implicate dysregulation of protein folding and mitochondrial function as peripheral molecular signatures of ASD, partially recapitulating transcriptomic patterns observed in post-mortem brain tissue, highlighting the potential of LCL-based transcriptomics as a tractable, clinically accessible window into ASD neurobiology.