Background:
Homozygous VcpR155H/R155H mice show profound weakness and severe pathology leading to premature death before three weeks of age. We previously showed that a lipid-enriched diet reversed lethality and improved muscle strength and pathology in homozygous VCP R155H offspring. However, the genetic changes underlying this process are not yet defined.
Methods:
We performed single-nuclei RNA sequencing (using Parse Biosciences) on 100,000 nuclei from skeletal muscles and hearts of three mouse groups: Vcp R155H/R155H mice on either 1) normal or 2) high-fat diet compared to 3) wild-type littermates on normal diet. Data was processed using Trailmaker and a custom pipeline including quality control, deep learning integration with scDREAMER, annotation with CellTypist, subsetting and principle component analysis (PCA), and gene-set enrichment analysis (GSEA).
Results:
Overall, we define the transcriptional changes present in R155H/R155H VCP disease vs wildtype. In addition, we observe a transcriptional trajectory between the three groups with the VcpR155H/R155H mice on a high-fat diet residing between those on a normal diet and wild-type mice, especially among the quadriceps muscle samples. We identify several genes that co-vary along this trajectory as a potential biomarkers. The mutation also caused significant changes in cell type populations, most notably the decreased proportion of Type IIb muscle cells. We also observed distinct levels of autophagy‑related gene expression across the different genotype–diet groups.
Conclusion:
In summary, this work provides an atlas of transcriptional changes in a murine model of VCP disease and identifies potential biomarkers. Our findings also demonstrate that a lipid-enriched diet partially restores the transcriptional changes, correlating with the observed reversal of early lethality and improvement in muscle health in affected mice. Collectively, these results underscore the beneficial role of dietary lipid enrichment and highlight new molecular insights that may inform future strategies for managing VCP-associated disorders.