$qb->select('DISTINCT m')
->from('MessageBundle:AssignmentUser', 'au')
->innerJoin('au.assignment', 'a', 'WITH', 'a.status = (:assigned)')
->innerJoin('au.user', 'u')
->innerJoin('a.message', 'm')
->where('u.id = (:user_id)')
->setParameter('assigned', 'assigned')
->setParameter('user_id', $yourSpecificUserId)
->orderBy("m.createdAt", "desc");
Lihat Symfony2 / Doctrine multiple joins return error untuk detailnya.