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Series GSE194295 Query DataSets for GSE194295
Status Public on Nov 04, 2022
Title Batch effect during human bone marrow stromal cell propagation prevails donor variation and culture duration impact on phenotype, transcriptome and function [MethylCap-seq]
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary Donor variation is a prominent critical issue limiting applicability of cell-based therapies. We asked whether reference protocols for pre-clinical bone marrow stromal cell (BMSC) propagation using human platelet lysate (hPL) to replace xenogeneic fetal bovine serum (FBS) might also reduce donor variability for osteo-chondral regeneration. We therefore investigated the impact of donor variability, hPL- vs FBS driven propagation and exhaustive proliferation, on BMSC epigenome, transcriptome, phenotype, coagulation risk and osteochondral regenerative function. Polychromatic flow cytometry revealed maintained canonical fibroblastic phenotype in all cells tested. We confirmed significantly declining proliferative potential in FBS-expanded BMSC after proliferative challenge. Notably, BMSC propagation under the aegis of hPL, compared to FBS, significantly increased BMSC proliferation, created significantly different gene expression trajectories and diverging surface marker signatures, already after just one culture passage. We observed limited but measurable effects on DNA methylation irrespective of culture duration. Moreover, expansion under xenogenic serum conditions resulted in significant loss of function during 3D cartilage organoid-like disk formation and significantly increased clotting risk. Superior chondrogenic function under hPL conditions was maintained over culture duration. As an additional observation, platelet blood group and isoagglutinin levels showed phenotypic changes but only minor impact on BMSC chondrogenesis and clotting behaviour.
 
Overall design MethylCap-seq analysis of Bone marrow derived Mesenchymal stromal cells from four different donors cultivated in either FBS medium or hPL at two different passages (p1 and p4/5)
 
Contributor(s) Poupardin R, Strunk D
Citation(s) 35326396
Submission date Jan 24, 2022
Last update date Jul 14, 2023
Contact name Rodolphe Poupardin
E-mail(s) rodolphe.poupardin@pmu.ac.at
Organization name Paracelsus Medizinische Privatuniversität
Lab Institute for Cell Therapy
Street address Strubergasse 22
City Salzburg
ZIP/Postal code 5020
Country Austria
 
Platforms (1)
GPL18460 Illumina HiSeq 1500 (Homo sapiens)
Samples (20)
GSM5832735 FBS_P1_1_1089
GSM5832736 FBS_P1_2_1090
GSM5832737 FBS_P1_3_1091
This SubSeries is part of SuperSeries:
GSE194303 Batch effect during human bone marrow stromal cell propagation prevails donor variation and culture duration impact on phenotype, transcriptome and function
Relations
BioProject PRJNA800084

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Supplementary file Size Download File type/resource
GSE194295_Counts_QSEA_hPL_vs_FBS.csv.gz 169.4 Mb (ftp)(http) CSV
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Raw data are available in SRA
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