As in every other iteration of the franchise, the concept of Ghost Hacking, that someone's memories or personality could be rewritten, and the damage that can do to their sense of self, not to mention being programmed to do things against their will, such as killing others. One character is Driven to Suicide, and it's unclear if it is due to his realization that everything he knows about himself is a lie, or if the suicide was simply another bit of reprogramming done to him in order for Kuze to cover his tracks.
On that note, the blase way that the Section 9 personnel react to Cummings killing himself, looking on the act with something that might be described as jaded curiosity more than actual concern.
Kuze's 'living network' and people that go into creating it are minor Body Horror combined with Dissonant Serenity (the connected people appear to be in a trance even during a gun battle) and Fridge Horror (how does Kuze get the people for this?)