The BioInvestigationIndex (BII)

Title:

Dermal and adipose stem cells treated with the NSAID indomethacin and/or other drugs. [original title: RNA-Seq Analysis Reveals Different Dynamics of Differentiation of Human Dermis- and Adipose-derived Stromal Stem Cells]

Organism(s):

Homo sapiens

Description:

Background: Tissue regeneration and recovery in the adult body depends on self-renewal and differentiation of stem and progenitor cells. Mesenchymal stem cells (MSCs) that have the ability to differentiate into various cell types, have been isolated from the stromal fraction of virtually all tissues. However, little is known about the true identity of MSCs. MSC populations exhibit great tissue-, location- and patient-specific variation in gene expression and are heterogeneous in cell composition. Methodology/Principal findings: Our aim was to analyze the dynamics of differentiation of two closely related stromal cell types, adipose tissue-derived MSCs and dermal fibroblasts (FBs) along adipogenic, osteogenic and chondrogenic lineages using multiplex RNA-seq technology. We found that undifferentiated donor-matched MSCs and FBs are distinct populations that stay different upon differentiation into adipocytes, osteoblasts and chondrocytes. The changes in lineage-specific gene expression occur early in differentiation and persist over time in both MSCs and FBs. Further, MSCs and FBs exhibit similar dynamics of adipogenic and osteogenic differentiation but different dynamics of chondrogenic differentiation. Conclusion: Our findings suggest that stromal stem cells including adipose-derived MSCs and dermal FBs exploit different molecular mechanisms of differentiation to reach a common cell fate. The early mechanisms of differentiation are lineage-specific and are similar for adipogenic and osteogenic differentiation but are distinct for chondrogenic differentiation between MSCs and FBs. A total of 91 samples were analyzed by multiplex RNA-seq. Samples represented replicates from two patients, two cell types and three differentiation protocols, as indicated by the sample annotation. 5 barcodes were unused, but the corresponding FASTQ files are included for completeness.

Design(s):

transcription profiling by high throughput sequencing

Experimental factor(s):

drug 3 conc 4 recorded
none 10 ug/ml 10 mM 6.25 ug/ml
drug 1 conc 4 recorded
none 1 uM 100 nM 10 ng/ml
drug 1 3 recorded
none dexamethasone TGF-beta 1
drug 2 3 recorded
none 3-isobutyl-1-methylxanthine L-ascorbic acid 2-phosphate
drug 3 3 recorded
none insulin (human) glycerol 2-phosphate
patient code name 3 recorded
Daphne Charlotte none
NSAID 2 recorded
none indometacin
treatment 5 recorded
Noninduced Adipogenesis Osteogenesis Blank Chondrogenesis
barcode 96 recorded
ACGAGC AGGGTC CCTAGA ACTTAT AAAGTT TTGGAC GGGCGA AACCTA ATGGCG TTTAGG TCAAAG ACAATA CCAGAC AAGTAC GTTGCC AACGCC GTAATG CAAAGT CGCTTG CGCACC CTCCAT CCTTTC GCCTAG CATCCC CTGTGT ACGTTG TAGAGA TAAGGG GAGATC ACACCC CGTATT TATTGT GCCCTC TGCAAT GCAGGA TTCATA TCGTAA TTCCGC GGCTGC ATCAAC GTCCCG CCGCTA TGTCAC CCGACG TCTACC TCACTT ATTTGC GACACT TGAAGC CTTCTG AGTCGT GCGTCC AAAACG AGGACT ACCTGA ATGCTT CTCGCA AGTTTA ATTCCA GAATTA TGTGCG GAGGAG TCGGGT GCGAAT CTGAAA GATCTT TTAACT TGGATG CCATCT ATCTCT GTGGTA TAGCAT CGGCAG AATAAA TACTTC AAGCGG GTCGGT GGGTTT TGATCA GCTGTG TGCGGA GCTCAA ATACAG AGCGAG CGAGTA CACAAG GGTACA TATGTA GAACGC TAGTCG CGTGGC CAACAA GGACAT CATGAT GTATAC AGATGG
day 9 recorded
d0 d3 d2 d1 d6 d4 none d7 d5
cell type 3 recorded
dermal fibroblast mesenchymal stem cell of adipose none
drug 2 conc 3 recorded
none 500 uM 50 uM

Publication(s):

Jger K, Islam S, Zajac P, Linnarsson S, Neuman T
RNA-Seq Analysis Reveals Different Dynamics of Differentiation of Human Dermis- and Adipose-Derived Stromal Stem Cells. PubMed:22723894

Sample attribute(s):

patient code name 3 recorded
Daphne Charlotte none
barcode 96 recorded
ACGAGC AGGGTC CCTAGA ACTTAT AAAGTT TTGGAC GGGCGA AACCTA ATGGCG TTTAGG TCAAAG ACAATA CCAGAC AAGTAC GTTGCC AACGCC GTAATG CAAAGT CGCTTG CGCACC CTCCAT CCTTTC GCCTAG CATCCC CTGTGT ACGTTG TAGAGA TAAGGG GAGATC ACACCC CGTATT TATTGT GCCCTC TGCAAT GCAGGA TTCATA TCGTAA TTCCGC GGCTGC ATCAAC GTCCCG CCGCTA TGTCAC CCGACG TCTACC TCACTT ATTTGC GACACT TGAAGC CTTCTG AGTCGT GCGTCC AAAACG AGGACT ACCTGA ATGCTT CTCGCA AGTTTA ATTCCA GAATTA TGTGCG GAGGAG TCGGGT GCGAAT CTGAAA GATCTT TTAACT TGGATG CCATCT ATCTCT GTGGTA TAGCAT CGGCAG AATAAA TACTTC AAGCGG GTCGGT GGGTTT TGATCA GCTGTG TGCGGA GCTCAA ATACAG AGCGAG CGAGTA CACAAG GGTACA TATGTA GAACGC TAGTCG CGTGGC CAACAA GGACAT CATGAT GTATAC AGATGG
day 9 recorded
d0 d3 d2 d1 d6 d4 none d7 d5
cell type 3 recorded
dermal fibroblast mesenchymal stem cell of adipose none (blank)
Organism 1 recorded
Homo sapiens