Developing a disease-specific accessible transcriptional signature as a biomarker for ataxia with oculomotor apraxia type 2

• Published in: Molecular medicine (Cambridge, Mass.) Vol. 31; no. 1; pp. 205 - 14
• Main Authors: Ngo, Kathie J., Wong, Darice Y., Huang, Alden Y., Lee, Hane, Nelson, Stanley F., Fogel, Brent L.
• Format: Journal Article
• Language: English
• Published: London BioMed Central 24.05.2025; BMC
• Subjects: Adult; AOA2; Apraxias - congenital; Ataxia - diagnosis; Ataxia - genetics; Ataxia with oculomotor apraxia type 2; Biomarker; Biomarkers; Biomedical and Life Sciences; Biomedicine; Cogan Syndrome - diagnosis; Cogan Syndrome - genetics; DNA Helicases; Female; Gene Expression Profiling; Gene Regulatory Networks; Humans; Male; Middle Aged; Molecular Medicine; Multifunctional Enzymes - genetics; Mutation; RNA Helicases - genetics; RNA-sequencing; Senataxin; Transcriptome; WGCNA; RNA-sequencing; Senataxin; AOA2; Ataxia with oculomotor apraxia type 2; Biomarker; WGCNA
• ISSN: 1528-3658; 1076-1551; 1528-3658
• DOI: 10.1186/s10020-025-01257-8

Background Genetic ataxias are clinically heterogenous neurodegenerative conditions often involving rare or private mutations and it is often difficult to assign pathogenicity to rare gene variants solely based on DNA sequencing. An effective functional assay from an easy-to-obtain biospecimen would aid this assessment and be of high clinical value. SETX encodes a ubiquitous DNA/RNA helicase crucial for resolving R-loops and maintaining genome stability. Loss-of-function mutations cause a recessive disorder, Ataxia with Oculomotor Apraxia Type 2 (AOA2). Methods Here we utilize Weighted Gene Co-expression Network Analysis (WGCNA) from patient blood to construct an AOA2-specific transcriptomic signature as a biomarker to evaluate SETX variants in patients clinically suspected of having AOA2. Results WGCNA from peripheral blood RNA of 11 AOA2 patients from 7 families initially identified a single gene module that was modestly effective in distinguishing individuals with AOA2 from controls (sensitivity 73%, specificity 97%) and was able to robustly differentiate AOA2 patients from those with genetically distinct, yet phenotypically similar, neurological disorders (sensitivity 100%, specificity 100%). An independent derivation of the transcriptional biomarker identified a dual module model that was able to better distinguish individuals with AOA2 from controls (sensitivity 100%, specificity 97%). As validation, we examined a second cohort of 21 patients from 13 families and demonstrate that this dual module transcriptional biomarker could discriminate patients clinically suspected of AOA2 from controls (57%, 95%CI: 34%—78%). Overall, the transcriptional biomarker was able to separate AOA2 subjects ( n  = 32) from controls ( n  = 35) with 72% sensitivity and 97% specificity. Notably, this transcriptomic biomarker enabled verification of the first pathogenic SETX mutation found in a non-canonical transcript, expanding the spectrum of mutations that contribute to AOA2. Conclusions Our study identified a transcriptional biomarker that was able to differentiate AOA2 from controls and from other related neurological disorders, consequently expanding the spectrum of known pathogenic mutations. This proof-of-concept study illustrates that transcriptional biomarkers may be used to validate variants of uncertain significance in known genetic diseases.