In a large, heavy bottomed pot, melt the butter over medium heat until it bubbles. Add the onions and cook, undisturbed, for 3-5 minutes until you get color on them. Stir and cook 3 minutes further. Remove from pot and reserve.
Crumble the beef into the same pot. Allow to cook, undisturbed, for about 5 minutes or until the bottom of the beef develops some good brown color. Stir and let cook for 3 more minutes. Stir the onions back in and sprinkle with salt and pepper. Do not drain the grease.
Add tomato paste and bone broth. Turn heat down to low, cover, and let cook for about an hour.
When ready to serve, cook penne pasta according to package directions. Stir into beef sauce, fold in shredded cheese and serve hot.