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Series GSE128490 Query DataSets for GSE128490
Status Public on Mar 17, 2020
Title RNA-Seq Analysis of Murine Chondrocytes Reveals Pathways Associated with Cartilage Regeneration and Degeneration
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Objectives: Understanding the molecular mechanisms underlying cartilage degeneration and regeneration is helpful for improving therapeutic strategies for treating osteoarthritis (OA). We report transcripts and pathways differentially expressed in chondrocytes obtained from genotypically and phenotypically distinct mouse strains.

Methods: We performed RNA-sequencing and computational analysis on chondrocytes derived from LG/J (large, healer, n=16) and SM/J (small, non-healer, n=16) mouse strains. We validated the expression of candidate genes using real-time PCR and immunostaining.

Results: Of those nearly 6,000 differentially expressed genes between LG/J and SM/J, 138 genes (99 protein-coding) were up-regulated and 145 (103 protein-coding) were down-regulated with log2 fold changes of 2 or more. Interestingly, we found the top up-regulated gene ontology biological pathways in the chondrocytes from the LG/J mice were related to chondrocyte development, cartilage condensation, and regulation of chondrocyte differentiation. In contrast, the top upregulated pathways in the SM/J mice were mostly inflammation related. Real-time PCR confirmed the expression pattern of a number of differentially expressed genes. Immunostaining of two candidate genes revealed that Tnfrsf23 and Car2 were respectively increased in LG/J and SM/J strains.

Conclusions: The enrichment of genes and pathways related chondrocyte differentiation, cartilage development and cartilage condensation in LG/J appear to be responsible for their superior healing potential. The enrichment of pathways related to cytokine production, immune cell activation and inflammation in SM/J suggests a compromised chondrocyte proliferation and/or survival ability and a higher sensitivity to inflammation and OA. Tnfrsf23 and Car2 warrant further investigation to discern their specific role(s) in chondrocyte function and OA.
Overall design chondrocyte mRNA profiles of 21-day old LG/j and SM/j mice were generated by RNA-sequencing and validated by real-time PCR and immunohistochemistry.

Please see PubMed ID 16688532 for information on strain origins.
Contributor(s) Duan X, Tycksen E, Rai MF
Citation(s) 31945456
Submission date Mar 18, 2019
Last update date Jun 17, 2020
Contact name Muhammad Farooq Rai
Organization name Washington University School of Medicine
Department Orthopaedic Surgery
Lab Linda Sandell
Street address 660 S. Euclid Ave.
City St. Louis
State/province MO
ZIP/Postal code 63110
Country USA
Platforms (1)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (32)
GSM3677486 lg-f1
GSM3677487 lg-f2
GSM3677488 lg-f3
BioProject PRJNA527836
SRA SRP188755

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE128490_RAW.tar 107.7 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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