Combining segmental bulk- and single-cell RNA-sequencing to define the chondrocyte gene expression signature in the murine knee joint.

Chondrocytes are a key player in the development of Knee Osteoarthritis (KOA), a disease which affects more than one-third of the people aged over 65, and is currently debilitating over 100 million individuals globally. Therefore, a key milestone towards understanding and combating KOA – and a long-standing problem in pre-clinical research – is the extraction of the very rare chondrocytes’ from the murine knee joint and analysis of their gene expression signature.

By a new cutting strategy of the murine femur into three different segments we isolated the cells (Charité – Universitätsmedizin Berlin) and analyzed them by joining modern mathematical biology (ZIB) and state-of-the-art high-throughput single cell technology (DRFZ). Thereby we could differentiate genes important for cartilage development, endochondral bone growth, extracellular matrix organization and other joint development processes.

The accessibility of this method to the pre-clinical research community opens up new possibilities to study key questions regarding disease: molecular factors, phenotypic switching, drug targeting and interactions, pathogenesis, and therapeutic targets. The researchers will continue to work together in the future to develop more novel techniques towards gaining deeper insights into KOA disease progression.