Ketogenic diet containing medium-chain triglyceride ameliorates transcriptome disruption in skeletal muscles of rat models of duchenne muscular dystrophy

Yuri Fujikura; Keitaro Yamanouchi; Hidetoshi Sugihara; Masaki Hatakeyama; Tomoki Abe; Satoru Ato; Katsutaka Oishi

doi:10.1016/j.bbrep.2022.101378

Ketogenic diet containing medium-chain triglyceride ameliorates transcriptome disruption in skeletal muscles of rat models of duchenne muscular dystrophy

Biochem Biophys Rep. 2022 Nov 11:32:101378. doi: 10.1016/j.bbrep.2022.101378. eCollection 2022 Dec.

Authors

Yuri Fujikura¹, Keitaro Yamanouchi², Hidetoshi Sugihara², Masaki Hatakeyama³, Tomoki Abe¹, Satoru Ato^{1

4}, Katsutaka Oishi^{1

5

6

7}

Affiliations

¹ Healthy Food Science Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8566, Japan.
² Department of Veterinary Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan.
³ Miyagi Health Innovation, Sendai, Miyagi, 980-0021, Japan.
⁴ Japan Society for the Promotion of Science, Tokyo, Japan.
⁵ Department of Applied Biological Science, Graduate School of Science and Technology, Tokyo University of Science, Chiba, Noda, Japan.
⁶ Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Kashiwa, Japan.
⁷ School of Integrative and Global Majors (SIGMA), University of Tsukuba, Tsukuba, Ibaraki, Japan.

Abstract

Duchenne muscular dystrophy (DMD) is a myopathy characterized by progressive muscle weakness caused by a mutation in the dystrophin gene on the X chromosome. We recently showed that a medium-chain triglyceride-containing ketogenic diet (MCTKD) improves skeletal muscle myopathy in a CRISPR/Cas9 gene-edited rat model of DMD. We examined the effects of the MCTKD on transcription profiles in skeletal muscles of the model rats to assess the underlying mechanism of the MCTKD-induced improvement in DMD. DMD rats were fed MCTKD or normal diet (ND) from weaning to 9 months, and wild-type rats were fed with the ND, then tibialis anterior muscles were sampled for mRNA-seq analysis. Pearson correlation heatmaps revealed a one-node transition in the expression profile between DMD and wild-type rats. A total of 10,440, 11,555 and 11,348 genes were expressed in the skeletal muscles of wild-type and ND-fed DMD rats the MCTKD-fed DMD rats, respectively. The MCTKD reduced the number of DMD-specific mRNAs from 1624 to 1350 and increased the number of mRNAs in common with wild-type rats from 9931 to 9998. Among 2660 genes were differentially expressed in response to MCTKD intake, the mRNA expression of 1411 and 1249 of them was respectively increased and decreased. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses suggested that the MCTKD significantly suppressed the mRNA expression of genes associated with extracellular matrix organization and inflammation. This suggestion was consistent with our previous findings that the MCTKD significantly suppressed fibrosis and inflammation in DMD rats. In contrast, the MCTKD significantly increased the mRNA expression of genes associated with oxidative phosphorylation and ATP production pathways, suggesting altered energy metabolism. The decreased and increased mRNA expression of Sln and Atp2a1 respectively suggested that Sarco/endoplasmic reticulum Ca²⁺-ATPase activation is involved in the MCTKD-induced improvement of skeletal muscle myopathy in DMD rats. This is the first report to examine transcription profiles in the skeletal muscle of CRISPR/Cas9 gene-edited DMD model rats and the effect of MCTKD feeding on it.

Keywords: DAPC, dystrophin-associated glycoprotein complex; DEG, differentially expressed gene; DMD, Duchenne muscular dystrophy; Duchenne muscular dystrophy; FPKM, fragments per kilobase of exons per million mapped reads; GO, gene ontology; KD, ketogenic diet; KR, ketogenic ratio; Ketogenic diet; Ketone bodies; MCT, medium-chain triglycerides; MCTKD, medium-chain triglycerides containing ketogenic diet; ND, normal diet; PC, principal component; SERCA, sarco/endoplasmic reticulum (SR) Ca2+ ATPase; Skeletal muscle; TA, tibialis anterior; Transcriptome; WT, wild type.