We know they both been in the Root for sometime. One thing they like to do to destroy the emotion of a fellow ninja is to have then killed the best friend they grew up with in mortal combat. That's why Itachi is in control and not like those other emotional Uchiha. That's why Itachi thought highly of Shisui and about self sacrifice.
They killed there best friends in order to unlock the Mangekyō Sharingan. It's simple really.