snRNA‐Seq and Spatial Transcriptome Reveal Cell–Cell Crosstalk Mediated Metabolic Regulation in Porcine Skeletal Muscle

Abstract

ABSTRACT Background Cell–cell crosstalk between myogenic, adipogenic and immune cells in skeletal muscle to regulate energy metabolism and lipid deposition has received considerable attention. The specific mechanisms of interaction between the different cells in skeletal muscle are still unclear. Methods Using integrated analysis of snRNA‐seq and spatial transcriptome, the gene expression profile of longissimus dorsi (LD) muscle was compared between adult Taoyuan black (TB, obese, native Chinese breed) and Duroc (lean) pigs. Results TB pig had more intramuscular fat (IMF) deposition (3.91%, p = 0.0244) and higher slow myofiber proportion (17.13%, p 0.4, p < 0.05) between secretory and metabolism‐related DEGs with spatial aggregation was verified by regression analysis for random region extraction (area of 25 spots, n = 400) from spatial transcriptome, and we speculated that the alteration of secretory proteins forming the microenvironment might regulate myofiber metabolism via target genes such as IRS1, PLPP1 and SLC38A2. Conclusions Our study provides new insights into skeletal muscle microenvironment that contributes to metabolic regulation and new methods and resources to study cell–cell communication in skeletal muscle.

Keywords

• intercellular interaction
• metabolic regulation
• microenvironment
• skeletal muscle
• snRNA‐seq
• spatial transcriptome