By Josine de Winter

Publication

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

L G M Heezen, T Abdelaal, M van Putten, A Aartsma-Rus, A Mahfouz, P Spitali

Nat Commun 2023 Aug 15;14(1):4909.

doi: 10.1038/s41467-023-40555-9.

https://www.nature.com/articles/s41467-023-40555-9 

Summary

Duchenne muscular dystrophy (DMD) is an X-linked, recessive and fatal neuromuscular disorder caused by mutations in the DMD gene. These out-of-frame mutations lead to the lack of dystrophin, a protein that acts as a linker between the extracellular matrix and the cytoskeleton. The loss of dystrophin leaves the muscle fibres more vulnerable to contraction-induced damage. DMD muscle fibres undergo multiple cycles of degeneration and regeneration, but once the regenerative capacity of the muscle fibres is reached these are substituted by fibrotic and adipose tissue.

Previous studies have used cellular and molecular approaches such as cell specific staining, bulk proteomics and transcriptomics to study the tissue changes described above. However, there were no studies available where histological and gene expression data were simultaneously and spatially investigated.

The authors have performed spatial transcriptomics experiments using Visium from 10x Genomics in order to obtain whole transcriptome profiling that can be directly linked to the histology in individual tissue sections. Clustering of the 55µm Visium spots was based on both the histology and gene expression profiles. Hereafter, by applying a deconvolution algorithm, the authors show how different cell types contribute to aforementioned clusters such as connective tissue and inflamed/calcified fibers clusters.

The histological image that is directly linked to the transcriptomic profile allowed the authors to identify molecular markers that underlie the histopathological tissue changes observed in mdx and D2-mdx mice. The authors show increased expression of specific genes in areas of muscle regeneration (Myl4, Sparc, Hspg2), fibrosis (Vim, Fn1, Thbs4) and calcification (Bgn, Ctsk, Spp1). These findings were confirmed using a more sensitive approach that holds a higher resolution, smFISH (HiPlex RNAscope).  Finally, the authors applied RNA velocity analysis on the spatial data of the D2-mdx mouse to predict differentiation dynamics.  

About the author

Laura Heezen is in the final year of her PhD trajectory in the labs of Dr Pietro Spitali, Dr Ahmed Mahfouz and Prof Annemieke Aartsma-Rus. She pioneered the application of spatial transcriptomics on dystrophic skeletal muscle. Her research focuses on the identification of underlying mechanisms, pathways, genes and/or cell types involved in the histopathological tissue changes in various neuromuscular disorders, with a special focus on Duchenne muscular dystrophy. In the NMD Biomarker Group, we are, amongst other things, expanding the work on spatial analysis to better understand neuromuscular disorders (NMD Biomarker Group (nmd-biomarkers.org)).