Biology subjects

Spitali, P.

Publications and source records attributed to Spitali, P..

3 recordsLinked to original sources

bioRxiv2026

Spatial transcriptomics maps region and isoform specific brain alterations in mdx and mdx4cv models of Duchenne muscular dystrophy

Duchenne muscular dystrophy (DMD) is accompanied by cognitive and neurodevelopmental difficulties. To investigate how the loss of different dystrophin isoforms affects gene expression across brain regions, we performed spatial transcriptomics on brains from mdx and mdx4cv mouse models (lacking Dp427 or Dp427+Dp140 respectively) and healthy controls aged 2 weeks. Both dystrophic models showed transcriptional changes converging on myelin and oligodendrocyte biology and oxidative phosphorylation, but with distinct regional patterns. In mdx mice, myelin genes were upregulated in the amygdala and hippocampus and downregulated in fiber tract regions, while mitochondrial genes were upregulated in most regions but downregulated in the thalamus and isocortex. In mdx4cv mice, myelin genes were broadly upregulated and mitochondrial genes downregulated across almost all regions. Direct comparison between mdx and mdx4cv mice demonstrated that the additional loss of Dp140 expanded localized myelin upregulation across the brain and shifts the mitochondrial response toward widespread downregulation. These differences in regional changes between the mouse models is in line with their dystrophin isoform(s) loss. Our findings provide a molecular basis for the brain-related impairments of DMD and a foundation for future therapeutic studies.

neuroscience↗

bioRxiv2025

Evaluating exon-skipping therapies targeting the central nervous system in Duchenne muscular dystrophy using high-resolution spatial transcriptomics

Duchenne muscular dystrophy (DMD) is marked by progressive muscle degeneration due to dystrophin deficiency. Despite cognitive impairments in up to one-third of patients, central nervous system (CNS)-targeted dystrophin restoration remains relatively underexplored compared to muscle-focused therapies. Since dystrophin is expressed in the brain during development and postnatally, it is important to assess which aspects of CNS pathology could be rescued. However, studying Dmd is difficult due to its size, low-abundance transcripts, and with multiple isoforms, limiting the sensitivity and isoform resolution of standard sequencing methods. To overcome these limitations, we applied Xenium spatial transcriptomics to target splice junctions, enabling isoform-specific and exon 51 skipping events detection across brain regions and cell types. Using this approach, we analyzed mdx52 mice lacking the full-length and Dp140 isoforms, treated with two exon 51 skipping therapies (antisense oligonucleotides or AAV-U7ex51). We observed distinct spatial expression patterns in the wild type brain between the full-length isoforms (Dp427c/m/p1) and shorter isoforms (Dp71 and Dp40). The full-length isoforms were predominantly expressed in cortex layers 2/3-6b and the CA1 region, while the shorter isoforms were localized to cortex layer 1 and the dentate gyrus. Among the exon skipping therapies tested, U7ex51 delivered neonatally induced broad exon skipping in neurons and effectively restored full-length isoforms in the targeted cells. This study introduces the first subcellular-resolution spatial transcriptomic atlas of dystrophin presence and rescue in the CNS and demonstrates a framework for evaluating gene therapies in spatially and transcriptionally complex tissues such as the brain.

neuroscience↗

bioRxiv2022

Spatial transcriptomics reveal markers of histopathological changes in Duchenne muscular dystrophy mouse models

Duchenne muscular dystrophy (DMD) is caused by mutations in the DMD gene, leading to lack of dystrophin. Chronic muscle damage eventually leads to histological alterations in skeletal muscles. The identification of genes and cell types driving tissue remodeling is a key step to develop effective therapies. Here we use spatial transcriptomics in two DMD mouse models differing in disease severity to identify gene expression signatures underlying skeletal muscle pathologies and directly link this to the muscle histology. Deconvolution analysis allowed the identification of cell types contributing to histological alterations. We show how the expression of specific genes is enriched in areas of muscle regeneration (Myl4, Sparc, Hspg2), fibrosis (Vim, Fn1, Thbs4) and calcification (Bgn, Ctsk, Spp1). Finally, our analysis of differentiation dynamics in the severely affected D2-mdx muscle shows a subset of the muscle fibers are predicted to become affected in its future state. Genes associated with tissue remodeling could enable to design new diagnostic and therapeutic strategies for DMD.

genomics↗