Constructing lineage hierarchies of the PPB tumor
To further understand the internal correlation of tumor cells in both
subtypes, we constructed differentiation trajectories of cells in
pseudotemporal order using Monocle after renaming the clusters of two
subtypes to obtain two tightly connected differentiation tumor lineages.
In the skeletal muscle lineage, FABP7hisatellite myogenic cells (clusters 6 and 9,FABP7hiPAX7hiMYF5hiMSChi )
were more primordial and at the start of their trajectory. Highly
expressed genes, such as PAX7 and MYF5 , were stable in the
early and middle stages of the pseudotime and then declined rapidly
(Fig.4B). ITM2Ahi satellite myogenic cells
(clusters 2 and 4,ITM2AhiPAX7hiMYF5hiMSChi )
emerged slightly later, but were still more primitive thanMYOGhi differentiated myocytes (cluster 5) that
dominated on the terminal branch of the trajectory (Fig.4A,4B). The
cartilage lineage was similar to the muscle cells. NaïveSOX9hiPAX9hiPAX1hiprechondrocytes (clusters 1, 3, 8, and 11) drove sequential
differentiation and generatedMGPhiOGNhi chondrocytes
(cluster 7) and DKK2hiTNMDhichondrocytes (cluster 10) (Fig.4C,4D). However, there was no evidence to
order the time sequence of these two chondrocyte subpopulations and we
could not define the detailed difference between them, although they
converged on the same branch in the trajectory. Interestingly, whether
in cartilage or muscle subtypes, when primitive cells occupying the
trunk of the trajectory developed into differentiated daughter cells,
they first produced a small branch filled with daughter cells and then a
large branch again from the trunk. The mechanism was not well understood
and might be related to cell activation.