One of the themes in this work is that of the locked room. The theme is nothing new to detective fiction, poetry, or fairy tales, (ie, Sleeping Beauty, The Rape of the Lock). Here, Avi also includes a historical spin on the genre by weaving in real life events of Poe's life.
The locked room, according to James McGlathery, represents "the female sex organs. Turning the lock in the key to enter the room represents intercourse. Finally, the hidden chamber...represents exploring formerly inaccessible areas of existance."
In this case, the body of Sis is in the locked room. Though you probably don't want to introduce the more sexually-charged aspects of this theme to middle schoolers, it might still be broachable by examining the fears and uncertainity about the opposite sex by exploring the more palatable elements of this aspect of maturing.