Whole-Blood RNA-seq in Adult-Onset Focal Dystonia: Differential Expression, Cell-Type Deconvolution, and Pathway Analyses

Author

yaoyuan caoFollow

Abstract

Background: Although adult-onset focal dystonia (AOFD) is the third most common movement disorder, its etiology remains poorly understood. Clinical diagnosis is performed solely based on clinical features, often leading to significant delays in diagnosis and treatment. While Genome-Wide Association Studies (GWAS) have identified specific genetic risk loci, these common variants explain only a fraction of the heritability and lack functional context. Consequently, identifying objective blood-based biomarkers that reflect the downstream biology of this disease is critical. Recent independent proteomic studies indicate immune and metabolic dysregulation in AOFD plasma; therefore, a comprehensive transcriptomic investigation is warranted to better characterize the systemic molecular footprint.

Methods: PAXgene whole-blood RNA-sequencing data from a large multicenter cohort recruited by the Dystonia Coalition were analyzed. To exclude potential Alzheimer’s disease (AD) co-pathology, controls were defined as “AT-negative” (confirmed negative for plasma amyloid-beta and phosphorylated-tau). Data processing followed a standardized STAR/Salmon bioinformatics workflow. Samples that failed to meet strict numeric quality control (QC) thresholds (such as mapping rate and RNA Integrity Number (RIN)) were excluded. Differential expression was modeled using DESeq2, incorporating Surrogate Variable Analysis (SVA) to correct for latent technical confounders, as SVA outperformed Principal Component Analysis (PCA) in capturing batch effects. Cell-type composition and functional contributions were inferred using CIBERSORTx-based deconvolution.

Results: Using a false discovery rate (FDR) < 0.05, the analysis found 2,196 differentially expressed genes. The AOFD transcriptomic signature is characterized by the widespread downregulation of cytoplasmic translation and mitochondrial respiratory pathways (e.g., NDUFA7), along with significantly upregulated RNA splicing (e.g., FUS) and stress response signaling. Sensitivity analyses confirmed that these effects were robust across different QC strategies and racial backgrounds. Deconvolution revealed a significantly remodeled immune compartment, with expanded monocytes, and reduced CD4+ T cells and NK cells. Crucially, cell-type-specific enrichment indicated that the global translational suppression signal was largely driven by lymphopenia, while expanded neutrophils exhibited a suppressed functional signature (S100A8/A9).

Interpretation: In this study, we identified a robust systemic molecular footprint for AOFD in peripheral blood. By correcting for latent confounders and utilizing rigorous control definitions, we uncovered a complex interplay among metabolic suppression, splicing dysregulation, and myeloid-biased immune remodeling. These findings validate previous proteomic signals and suggest potential molecular biomarkers for future clinical applications.

Committee Chair

Carlos Cruchaga

Committee Members

Laura Ibanez, Dan Moran

Degree

Master of Science (MS)

Author's Department

Biomedical Engineering

Author's School

McKelvey School of Engineering

Document Type

Thesis

Date of Award

Winter 12-17-2025

Language

English (en)

Author's ORCID

https://orcid.org/0009-0003-4727-1991

Recommended Citation

cao, yaoyuan, "Whole-Blood RNA-seq in Adult-Onset Focal Dystonia: Differential Expression, Cell-Type Deconvolution, and Pathway Analyses" (2025). McKelvey School of Engineering Theses & Dissertations. 1294.
https://openscholarship.wustl.edu/eng_etds/1294