One of the most promising treatments in this category is a drug called CM-AT made by a startup called Curemark. Dr. Joan Fallon, the company's founder and CEO, observed that many autistics show a strong preference for foods high in carbohydrates and low in protein. A diagnostic test revealed that some autistic children lack enzymes that digest protein. As a result, these children produce fewer of the essential amino acids that are the building blocks for brain development and neuroreception. Fallon believes this deficiency is linked to the most severe symptoms of autism, and she says an early observational study of CM-AT, an orally ingested powder that delivers protein-digesting protease, showed "significant improvements." Curemark is enrolling patients in phase III clinical trials at 10 to 12 sites—the largest autism trial to date.
Seemed related and interesting so thought I would mention it.
The other thing I found interesting was the mention of epigenetics, which I think I'm going to do some further research on. The basic premise is that the environment can influence gene expression. So many diseases may be a combination of both genetics and environmental influences (pollution, viruses, diet, etc.). Perhaps that's why it is so hard to pin down a single cause for Crohn's, autism, and many other diseases.