They are called crown galls or burls. The cause is bacteria which have invaded the tree structure, and cause genetic modifications to the tree. The result is that the infected parts of the tree grow in a disorganized way.
They may be harmless, or they may kill the tree completely, depending what parts become infected.
There is no known cure. If you remove the tree and destroy it, the bacteria will remain in the soil for a few years, so don't plant another tree straight away.