Single-nucleus transcriptomic characterization of muscle in Spinal Muscular Atrophy


Translational Research

Poster Number: S117


Sophie Rengarajan, MD, PhD, Stanford University Medical Center, Elena Monti, PhD, Stanford University, Colin Holbrook, Stanford University, Marwa Zafarullah, PhD, Stanford University, Lisa Ghiglieri, Stanford University Medical Center, Tina Dong, PhD, Stanford University Medical Center, Xu Yin Wang, PhD, Sanford Burnam Prebys Medical Discovery Institute, John W. Day, MD, PhD, Stanford University Medical Center, Helen M. Blau, PhD, Stanford University

Spinal muscular atrophy (SMA) is caused by loss of survival motor neuron protein (SMN), which leads to progressive reduction in motor neurons, muscle denervation, and muscle atrophy. There are three FDA-approved drugs that restore SMN and thereby stabilize disease and extend lifespan. However, most patients have residual muscle atrophy and weakness, highlighting the need for adjunctive treatments to improve strength.

We sought to identify markers of disease progression and potential therapeutic targets to boost muscle regeneration by performing single nuclei RNA sequencing on human muscle samples from a cohort of 7 adults with SMA. Within our cohort, 6 patients had received SMN-restoring treatment (nusinersen) prior to biopsy.

We isolated 86,833 nuclei with an average of 1,080 transcripts and 588 genes per nucleus. After pre-processing and doublet removal, we performed unsupervised Leiden clustering. Broad muscle-specific cell types were identified including fast and slow myonuclei, satellite cells, immune cells and stromal cells. Among clusters of myonuclei, we identified denervated and regenerating populations. Genes involved in “Actomyosin Structure Organization,” “Sarcomere Organization” and “Myofibril Assembly” were upregulated in SMA, consistent with a regenerating state.

Of particular interest, the gerozyme 15-PGDH, which we recently identified and showed is induced in skeletal muscles upon injury and with aging (PNAS, 2017; Science, 2021; Science Translational Medicine, 2023) was expressed in 6 of 7 samples. Inhibition of 15-PGDH has previously been shown to improve strength in aged mice and mice with sciatic nerve damage. Moreover, mice with severe SMA (delta 7) treated with SMN restoration also exhibit a significant increase in muscle strength. These results suggest that 15-PGDH inhibition may be a therapeutic target for SMA.