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Status |
Public on Aug 24, 2020 |
Title |
Comparison of Regulatory Type of Macrophages and PCMO Cells from perspective of RNAseq data. |
Organism |
Homo sapiens |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
Gene expression plasticity is central for macrophages? timely responses to cues from the microenvironment permitting phenotypic adaptation from pro-inflammatory (M1) to wound healing and tissue-regenerative (M2, with several subclasses). Regulatory macrophages (Mreg) are a distinct macrophage type, partially sharing some functionalities with both M1 and M2 cells. Mreg possess immunoregulatory, anti-inflammatory, and angiogenic properties, and are considered as a potential allogeneic cell therapy product to treat clinical conditions, e.g., non-healing diabetic foot ulcers. In this study we characterized clinically relevant regulatory macrophages, Mreg and Mreg_UKR, programmable cells of monocytic origin (PCMO) and comparator macrophages (M1, M2a and M0) using flow-cytometry, RT-qPCR, phagocytosis and secretome measurements, and finally RNA-Seq. We demonstrate that conventional phenotyping has a limited potential in deciphering all classes of produced cells. This limitation was ameliorated when global transcriptome characterization by RNA-Seq was employed. Using this approach we prove that macrophage manufacturing processes can result in a highly reproducible cell phenotype. At the same time, minor changes introduced in a protocol can consistently effect the phenotype of the end product as well. Additionally, we have identified a novel constellation of potential process specific biomarkers, which will not only support further clinical product development, but will lead to a better understanding of macrophage biology, differentiation and polarized activation.
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Overall design |
There are 7 immune cell types, comprised of 1 reference (CD14) and 6 differentiated types: M0, M1, M2a, Mreg, Mreg_UKR, and PCMO. There are 9 anonymized human donors, with a minimum of 3 donors per cell type. The donors act as biological replicates for the purpose of differential expression statistics.
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Contributor(s) |
Gurvich OL, Puttonen KA, Bailey A, Kailaanmäki A, Skirdenko V, Sivonen M, Pietikanen S, Kekarainen T |
Citation(s) |
32820219 |
BioProject |
PRJNA552427 |
Submission date |
Feb 27, 2020 |
Last update date |
Aug 24, 2020 |
Contact name |
Tuija Kekarainen |
Organization name |
Kuopio Center for Gene and Cell Therapy
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Department |
Cell Therapy Unit
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Lab |
Bioteknia 1
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Street address |
Microkatu 1
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City |
Kuopio |
State/province |
Northern Savonia |
ZIP/Postal code |
70210 |
Country |
Finland |
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Platforms (1) |
GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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Samples (37)
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Relations |
SRA |
SRP213590 |
Supplementary file |
Size |
Download |
File type/resource |
GSE146028_raw_counts.tsv.gz |
1.5 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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