Combining multi-omics and drug perturbation profiles to identify novel treatments that improve disease phenotypes in spinal muscular atrophy

Abstract

Spinal muscular atrophy (SMA) is a neuromuscular disorder caused by loss of survival motor neuron (SMN) protein. While SMN restoration therapies are beneficial, they are not a cure. We aimed to identify novel treatments to alleviate muscle pathology combining transcriptomics, proteomics and perturbational datasets. This revealed potential drug candidates for repurposing in SMA. One of the lead candidates, harmine, was further investigated in cell and animal models, improving multiple disease phenotypes, including SMN expression and lifespan. Our work highlights the potential of multiple, parallel data driven approaches for development of novel treatments for use in combination with SMN restoration therapies. RESULTS Early restoration of Smn in SMA mice restores muscle protein and transcript expression.We first set out to determine the effect of early SMN restoration on the proteomic and transcriptomic profiles of SMA skeletal muscle, with the intent to design therapeutic strategies against the genes and proteins that remain unchanged. To do so, the severe Taiwanese Smn-/-;SMN2 SMA mouse model 24 received a facial intravenous (IV) injection at post-natal day (P) 0 and P2 of the previously described Pip6a-PMO or Pip6a-scrambled pharmacological compounds (10 g/g) 25,26. Pip6a is a cell-penetrating peptide (CPP) either conjugated to an SMN2 exon 7 inclusion-promoting ASO (PMO) or a scrambled ASO 25,26. We harvested the tibialis anterior (TA) from P2 (pre-symptomatic) untreated Smn-/-;SMN2 and wild type (WT) mice, P7 (symptomatic) untreated Smn-/-;SMN2 and WT mice and P7 Pip6a-scrambled-and Pip6a-PMO-treated Smn-/-;SMN2 mice. TAs were then cut in two, whereby one half was used for transcriptomics and the other for proteomics. qPCR analysis of the ratio of FL SMN2 over total SMN2 confirms a significant increase in FL SMN2 expression in P7 Pip6a-PMO-treated Smn-/-;SMN2 mice compared to age-matched untreated and Pip6a-scrambled-treated Smn-/-;SMN2 mice ( Fig. 1a).Despite differences between transcriptomic and proteomic methodologies highlighted by hierarchical clustering and combined Principal Component Analysis (PCA) ( Supplementary Fig. 1), we were able to find clear separation of experimental groups and agreement between transcriptomic and proteomic profiles once the variance attributed to the differences in methodologies was removed ( Fig. 1b). At P7, we observed clear separation of Smn-/-;SMN2-and WT samples, where only P7 Pip6a-PMO treated Smn-/-

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“…The gene expression profiles of GSE150563 (GSM4551578-GSM4551583) were downloaded from the Gene Expression Omnibus (GEO) database ( ), and gene expression data of harmine untreated WT mice (WTU) and three harmine treated WT mice (WTT) were obtained ( 18 ). The sequencing organism samples are Mus musculus .…”