biostudies-arrayexpressSteven WoodsHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16598PBMCs from MED patients carrying the MATN3 T195K mutation and unaffected controls were reprogrammed into hiPSCs using Sendai virus. Data includes three differentiation stages: pluripotent hiPSCs, iMSCs, and Day 21 cartilage pellets. Sequencing was performed at the University Genomics Core Facility.biostudies-arrayexpressSample Collection - Cells harvested into QIAGEN RLT buffer. Pellets homogenized with molecular grinding resin and plastic pestle.Growth Protocol - hESC/hiPSC cultured in TeSR™-E8™ on vitronectin. Differentiation to iMSCs via MesenPRO RS™. 3D pellets (200k cells) cultured in medium with TGFβ3 and BMP2.Nucleic Acid Extraction - RNA extracted using QIAGEN RNeasy mini kit, as per manufacturers instructions.Library Construction - mRNA libraries were prepared using the Illumina stranded mRNA prep kit.Sequencing - Paired-end sequences generated using an Illumina HiSeq 4000 as per manufacturers instructions.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesUnknownTranscriptomicsGenomicsProteomicsIllumina HiSeq 4000Multiple epiphyseal dysplasia (MED), caused by mutations in MATN3, is a chondrodysplasia affecting the cartilage growth plate and is characterised by delayed epiphyseal ossification, short stature, and early onset osteoarthritis. Here we generated an in vitro human pluripotent stem cell (hPSC) model of cartilage growth-plate development to identify pathogenic mechanisms underlying MED. hPSCs were differentiated to chondrocytes via a mesenchymal intermediate, followed by TGFβ3+BMP2 induced chondrogenic pellet culture. MATN3-mutant hPSCs were generated by reprogramming MED patient PBMCs or by CRISPR-Cas9 gene editing to introduce a MATN3 mutation in a hESC line. RNAseq was used to assess chondrogenesis and identify MED pathogenic mechanisms. Transmission electron microscopy (TEM) was used to assess extracellular matrix assembly. The resultant hPSC-derived cartilage pellets displayed a typical cartilage morphology and strongly expressed cartilage matrix markers, e.g., collagen II and matrilin-3. Matrilin-3 protein was detected within both the matrix and cells of heterozygous mutant hPSC-cartilage pellets. RNAseq of mutant hPSC-cartilage pellets revealed significant enrichment for ‘ECM organisation’ and ‘cholesterol biosynthesis’ pathway genes as well as sightly increased expression of some unfolded protein response (UPR) marker genes. MATN3 mutant hPSC-derived cartilage pellets displayed abnormal matrix assembly, distended ER, accumulation of lipid droplets, and increased cholesterol content. Our model revealed mutant matrilin-3 induces cholesterol biosynthesis pathway upregulation and abnormal matrix assembly during MED pathogenesis. This study provides new insights into the molecular mechanisms underlying MED and highlights potential therapeutic targets.RNA-seq of coding RNAHomo sapiensHuman pluripotent stem cell model of multiple epiphyseal dysplasia with MATN3 mutation identifies altered Matrix organisation and upregulation of the cholesterol biosynthesis pathwayIan DonaldsonSteven WoodsSusan KimberSteven Woods, Nicola Bates, Stuart Cain, Paul EA Humphreys, Fabrizio E Mancini, Brenda Aguero Burgos, Peter Harley, Rayed Ali A. Alqahtani, Witchayapon Kamprom, Aleksandr Mironov, Antony Adamson, Ian J Donaldson, Geert Mortier, Kate Chandler, Anna Nicolaou, Clair Baldock, Jean-Marc Schwartz, Susan J Kimber.falseRNA-seq profiling of MED patient-derived (MATN3 T195K) and unaffected iPSC-chondrogenesisPBMCs from MED patients carrying the MATN3 T195K mutation and unaffected controls were reprogrammed into hiPSCs using Sendai virus. Data includes three differentiation stages: pluripotent hiPSCs, iMSCs, and Day 21 cartilage pellets. Sequencing was performed at the University Genomics Core Facility.2026-02-12T00:00:00Z2026-02-12T02:01:02.452Z2026-01-29T09:52:02.428ZE-MTAB-16598ERP188292EFO_0002944EFO_0004170EFO_0003789EFO_0005518EFO_0003738EFO_000418410.1101/2025.09.01.673425