Dungeons and Dragons

Make them live in terrible conditions, and look like monsters at first glance. This way your players will react to them as standard dungeons & dragons monsters, by which I mean kill them all. Afterwards, they find council chambers, crude medical facilities, nurseries, etc that imply that their society was surprisingly egalitarian and had a budding democratic government.

Give just enough of a hint beforehand so that they could have resolved things peacefully if they had been paying attention.

If harming your players emotionally is the goal.

If he's experimenting on humans, and depending on how much of their minds are retained from however he's transforming people; it could be that some of them recall bits of their previous religions and have bastardized them together with The Professor being the central antagonistic deity responsible for all their woes, and the gibbering horror as a living martyr for giving up of its sanity in order to banish the professor from the lab.

The lab could even be seen as a sort of corrupted garden of eden.

I'd say take some inspiration from Full Metal Alchemist as well, unless you haven't watched FMA/FMA:Brotherhood yet. Then I'd say, watch that and then take inspiration from a particular episode.

Where dies their water cine from, where does their poop go?

These as silly as they sound are important. Say a river flows into the lap, maybe an old drainage system. Niw they have 1 oltace to get water. Do they need some ti cast purify on it? If yes that person is very very important and would respected.

That's just 1 option for water, but yoy get the idea. They must havr food water and way to remove waste.

Quite a few people have commented about possible societal models for such a community. So I'll extend this by adding some thoughts about specific environmental challenges.

One would assume that the conditions in the lower levels are not very nice, so maybe rampant drug usage could be a thing. Some mongrels might be in pain due to the procedure and abuse pain killers. Others may just want to escape reality. Someone has to supply these. Maybe they're a misguided individual who wants to help their peers, maybe they're a stone cold profiteer who will make for an amazing miniboss. Who knows?

Another important factor is food. Mushrooms grow in dark places and could make up a lot of the diet of the mongrel folk. Or a former botanist could experiment with plants that grow under these conditions. Maybe there's even some animal husbandry going on. Or if you want there to be a darker twist, cannibalism is always an option. Maybe it's even part of their society. Being chosen to be the next meal is a great honor.

Lastly, what do the mongrels do for fun? Do they enjoy pit fights?If so, the players could take the wrong way into the arena room and face a crowd of cheering mongrels and some tough opposing fighters. Are there storytellers who remember some fragments of their human lives? Perhaps even some trash collectors who are willing to sell their strange goods even to outsiders?

Maybe model them after orc society in lord of the rings. Or perhaps the nomadic hobbits, depending on the atmosphere you're aiming for.

Alternatively, set it up like a prison state where the citizens (inmates) have become institutionalised over generations and anyone upsetting their serfdom way of life is unwelcomed.

Some good ideas here, but if I did this with my group, I'd have to deal with them volunteering for the process.

Have you seen the movie Us? Not too give any spoilers if you haven't, but you might get some good ideas from that.