# Proteomics of Duchenne Muscular Dystrophy Patient iPSC-Derived Skeletal Muscle Cells Reveal Differential Expression of Cytoskeletal and Extracellular Matrix Proteins

## TL;DR

This study uses patient-derived stem cells to analyze protein differences in Duchenne Muscular Dystrophy, identifying key proteins for further research.

## Contribution

The study introduces a 3D organoid system for more consistent proteomic analysis of DMD patient-derived muscle cells.

## Key findings

- 3007 and 2709 proteins were detected in 2D and 3D DMD patient probes, respectively.
- 83 and 338 proteins were differentially expressed in 2D and 3D DMD probes compared to controls.
- Proteins like Myosin-9 and Collagen 18A were identified as specifically altered in DMD.

## Abstract

Proteomics of dystrophic muscle samples is limited by the amount of protein that can be extracted from patient biopsies. Cells and tissues derived from patient-derived induced pluripotent stem cells (iPSCs) can be an expandable alternative source. We have patterned iPSCs from three Duchenne muscular dystrophy (DMD) patient lines into skeletal muscle cells using a two-dimensional as well as our three-dimensional organoid differentiation system. Probes with sufficient protein amounts could be extracted and prepared for mass spectrometry. In total, 3007 proteins in 2D and 2709 proteins in 3D were detected in DMD patient probes. A total of 83 proteins in 2D and 338 proteins in 3D can be described as differentially expressed between DMD and control patient probes in a post hoc test. We have identified and we propose Myosin-9, Collagen 18A, Tropomyosin 1, BASP1, RUVBL1, and NCAM1 as proteins specifically altered in their expression in DMD for further investigation. Proteomics of skeletal muscle organoids resulted in greater consistency of results between cell lines in comparison to the two-dimensional myogenic differentiation protocol.