Spatial Transcriptomics in DMD Mice

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Summary

In this study examining Duchenne muscular dystrophy, researchers identified how gene mutations lead to muscle damage and subsequent skeletal muscle alterations. Using spatial transcriptomics on two mouse models with varying disease severity, they linked gene expression directly to muscle changes. Their analysis highlighted specific genes associated with muscle regeneration, fibrosis, and calcification. The results, further validated by smFISH, also pointed out which muscle fibers are likely to deteriorate in future stages of the disease.

Research Criteria

The study aimed to bridge the gap between histological alterations, cell types, and gene expression in Duchenne muscular dystrophy. The researchers used spatial transcriptomics (ST) to directly link histology to gene expression, allowing them to identify molecular markers associated with the histopathological changes observed in mdx and D2-mdx mice.

Sample Type

Mouse quadriceps muscles.

Result—Histology-Related Clusters are Revealed Using Spatial Transcriptomics

In an intricate exploration of quadriceps muscle tissue from both healthy and dystrophic mice, researchers employed spatial transcriptomics to discern nuanced histological distinctions. The quadriceps, comprising the rectus femoris, vastus lateralis, vastus medialis, and occasionally the vastus intermedius, displayed uniform tissue composition in healthy specimens, contrasted starkly by the heterogeneity in dystrophic tissues marked by fiber size variations, inflammation, fibrosis, and other anomalies. Through meticulous analysis, 7028 spots were identified, each with a median of 1122 genes. Clustering based on gene expression profiles illuminated clusters emblematic of healthy muscle fibers in wildtype models, marked by genes like Myh4 and Mylpf. Concurrently, clusters indicative of connective tissue, slow twitch muscle fibers, erythrocytes, and immune responses were discerned. Dystrophic samples, particularly the mdx and D2-mdx variants, unveiled additional clusters mirroring the histopathological aberrations inherent to them, including inflammation, calcification, and necrosis. This comprehensive study underscores the potency of spatial transcriptomics in capturing the intricate tapestry of muscle tissue morphology and pathology.

Fig.1 Spatial transcriptomics was used to characterize muscle tissue in DMD and wildtype mouse models¹.

Result—Untangling the Knot: Cell Type Enrichment in Annotated Clusters

Delving into the cellular underpinnings of transcriptomic signatures, researchers utilized a deconvolution approach with a snRNAseq reference dataset from the tibialis anterior muscle of wildtype mice and a Dmd exon 51 deletion mouse model. This technique revealed the cellular composition driving observed gene expression patterns in muscle tissue. Predominantly, type IIx and IIb myonuclei emerged as the chief contributors to the gene expression signature. In the dystrophic mdx and D2-mdx mice, there was a marked surge in macrophages compared to their wildtype counterparts. The study also accentuated the muscle regenerative prowess inherent to the BL10 background, as evidenced by heightened levels of myoblasts, muscle satellite cells, and regenerative myonuclei. Conversely, the DBA/2J background displayed a reduced regenerative capacity. Through meticulous mapping, the research pinpointed the spatial congruence of specific markers with their respective clusters, such as the neuromuscular junction in the DBA/2J tissue and macrophage markers in mdx mice. This nuanced analysis underscores the pivotal role of distinct cell types in sculpting the transcriptomic milieu of muscle tissue.

Fig.2 Deconvolution of geographical data using a snRNAseq reference dataset indicates cell type enrichment in several mouse models as well as specific clusters¹.

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At Creative Biolabs, we are renowned for our mastery in delivering intricate single-cell RNA sequencing and spatial gene expression solutions. Our single-cell RNA sequencing services are impeccably crafted to unravel the intricacies of transcriptomic diversity within diverse cell populations, unveiling nuances at life's fundamental level. Complementing these capabilities, our advanced spatial gene expression services chart the transcriptome within tissue samples, providing unprecedented insights into physiological development and disease pathology within a structural context. By harmonizing these cutting-edge technologies, we empower researchers to delve into the complexities of cellular function and interactions across both spatial and temporal dimensions, catalyzing pioneering breakthroughs in life sciences research and discovery.

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Reference

1. Heezen, Laura GM, et al. "Spatial transcriptomics reveal markers of histopathological changes in Duchenne muscular dystrophy mouse models." Nature Communications 14.1 (2023): 4909.