Biomarkers of Immune Dysregulation and Post-Treatment Inflammation in Spinal Muscular Atrophy

Spinal Muscular Atrophy (SMA) is a neurodegenerative disorder primarily affecting motor neurons, but immune dysfunction may contribute to disease progression and treatment response. While AAV9-delivered SMN1 gene therapy (e.g., Zolgensma) improves survival, long-term motor outcomes remain variable. This study integrates bulk and single-cell RNA sequencing (scRNA-seq) to define immune dysregulation in SMA. We analyzed peripheral blood from infants with SMA (n = 7 for bulk RNA-seq; n = 4 for scRNA-seq, <25 mo of age) along with age-matched healthy controls (n = 4 for bulk RNA-seq; n = 6 for scRNA-seq). We profiled differentially expressed genes, immune pathways, cell–cell interactions, and gene regulatory networks. SMA samples showed distinct transcriptomic signatures and elevated immune activation compared to controls. NECTIN1 was identified as a transcriptomic biomarker of disease progression, while HSPA7 was validated from prior reports. A 6- to 7-mo inflection point marked a transition from metabolic regulation to immune activation in SMA infants. NF-κB–related inflammatory gene expression was significantly elevated post–gene therapy relative to both pretreatment and healthy controls, with IL1B and RNF19B emerging as key transcriptomic mediators. scRNA-seq revealed early dysfunction and G1-phase arrest in CD4+ T-cells, along with a switch to RELB-mediated noncanonical NF-κB signaling. In symptomatic infants, CD8+ T-cells showed higher proliferation and exhaustion, with co-upregulation of TBX21 and EOMES, genes consistent with chronic stimulation and a trajectory toward terminal differentiation. Immune dysregulation is a central feature of SMA and may influence treatment response. These findings support future development of adjunct immunomodulatory strategies to enhance gene therapy efficacy and suggest that immune signatures may correlate with motor function outcomes.