# Delineating transcriptomic signatures of in vitro human skeletal muscle models in comparison to in vivo references

## TL;DR

This study compares in vitro human skeletal muscle models to real muscle tissue, finding that they retain some traits of their source cells and differ in metabolism and gene regulation.

## Contribution

The study provides a comprehensive transcriptomic comparison of in vitro skeletal muscle models to in vivo references, revealing novel insights into model limitations and potential improvements.

## Key findings

- In vitro models retain epigenetic memory from their source material.
- Transdifferentiation models fail to induce specific myogenic regulatory factors.
- Differences in lipid metabolism are observed between in vitro models and in vivo muscle.

## Abstract

A pivotal question at the heart of stem cell research is how faithful cellular models recapitulate human tissues. Skeletal muscle, the largest organ in the human body, has been modeled by various in vitro systems. Here, we sought to delineate the state-of-the-art of muscle models by performing a large-scale analysis of transcriptome datasets, covering over 400 samples across 39 studies, including bulk and single-cell RNA sequencing of 2D and 3D models and their in vivo counterparts. By comparing these models to in vivo muscle, we highlighted failed upregulation of myogenic factors and retention of epigenetic memory from the in vitro source material. We featured differences in lipid metabolism and depletion of multiple fibroblast growth factor (FGF) ligands in the in vitro models. Finally, we revealed model-dependent variation in myogenic progenitors. Our analyses highlight targetable processes to improve the models while paving the way for similar studies on other cell types.

•In vitro skeletal muscle models retain epigenetic memory from their source material•hPSC-derived and transdifferentiation models differ from in vivo in lipid metabolism•Transdifferentiation model fails to induce specific myogenic regulatory factors•2D and 3D models generate PAX7+ cells at different degrees of quiescence

In vitro skeletal muscle models retain epigenetic memory from their source material

hPSC-derived and transdifferentiation models differ from in vivo in lipid metabolism

Transdifferentiation model fails to induce specific myogenic regulatory factors

2D and 3D models generate PAX7+ cells at different degrees of quiescence

In this article, Yilmaz and colleagues perform a large-scale transcriptomics metaanalysis with over 400 samples comparing established in vitro skeletal muscle models to in vivo skeletal muscle samples from adult, embryonic, and fetal biopsies. They highlight differences across bulk and single-cell RNA sequencing datasets in expression of transcription factors, epigenetic complexes, metabolic processes, signaling pathways and in quiescence signatures.