20.500.12556/RUL-168472 In situ spatial transcriptomic analysis of human skeletal muscle using the Xenium platform Traditional transcriptomic studies often overlook the complex heterogeneity of skeletal muscle, as they typically isolate RNA from mixed muscle fibre and cell populations, resulting in an averaged transcriptomic profile that obscures fibre type-specific differences. This study assessed the potential of the recently developed Xenium platform for high-resolution spatial transcriptomic analysis of human skeletal muscle histological sections. Human vastus lateralis muscle samples from two individuals were analysed using the Xenium platform and Human Multi-Tissue and Cancer Panel targeting 377 genes complemented by staining of successive sections for Myosin Heavy Chain isoforms to differentiate between type 1 and type 2 muscle fibres. Manual segmentation of muscle fibres allowed accurate comparisons of transcript densities across fibre types and subcellular regions, overcoming limitations in the platform’s automated segmentation. The analysis revealed higher transcript density in type 1 fibres, particularly in nuclear and perinuclear areas, and identified 191 out of 377 genes with differential expression between muscle fibres and perimysium. Genes such as PROX1, S100A1, LGR5, ACTA2, and LPL exhibited higher expression in type 1 fibres, whereas PEBP4, CAVIN1, GATM, and PVALB in type 2 fibres. We demonstrated that the Xenium platform is capable of high-resolution spatial in situ transcriptomic analysis of skeletal muscle histological sections. This study demonstrates that, with manual segmentation, the Xenium platform effectively performs fibre type-specific transcriptomic analysis, providing new insights into skeletal muscle biology. spatial transcriptomic skeletal muscle xenium platform muscle fibre segmentation genetika skeletne mišice transkriptomika true false true Angleški jezik Slovenski jezik Članek v reviji 2025-04-15 08:56:29 2025-04-15 08:56:29 2025-04-16 04:22:14 0000-00-00 00:00:00 2025 0 0 Str. 291-302 iss. 3 Vol. 399 2025 0000-00-00 Zaloznikova Objavljeno NiDoloceno 0000-00-00 0000-00-00 0000-00-00 575 0302-766X 10.1007/s00441-024-03945-z 221773059 RAZ_Umek_Nejc_2025.pdf RAZ_Umek_Nejc_2025.pdf 1 6BEE0EAF6DF1762EB21CA5B81D9FE9A0 891d7aafa1b0b6f4c053bbe1e3bd9cfbcae872e127911d6721753930e425241f 3c86dbb8-19c7-11f0-b232-0050569b8976 https://repozitorij.uni-lj.si/Dokument.php?lang=slv&id=201974 https://link.springer.com/article/10.1007/s00441-024-03945-z 1 a49d0173-19c5-11f0-b232-0050569b8976 https://repozitorij.uni-lj.si/Dokument.php?lang=slv&id=201972 Medicinska fakulteta Biotehniška fakulteta 0 0 0