Not withstanding other contributing factors like epigenetics, vitamin D, stress etc., I agree that nutrition is likely at the core of most chronic disease conditions.
Through my readings I am finding that there are two key nutritional factors that seem to contribute to systemic inflamation:
1/Excessive carbohydrate, particularly High GI, consumption and unfounded fears of fat consumption, the end result being an overwhelming dependance on glucose metabolism and a progressive burnout of glucose control systems and a resultant elevated blood glucose levels, it has been shown that even "Normal range" high end glucose levels have a strong corrolation to heart disease and some autoimmune conditions.
Note high insulin levels and diabetes are the end result of decades of struggle endured by the body trying to mitigate the inflamation caused by mildly high blood glucose levels.
2/Excessive intake of Omega 6 polyunsaturated oils, there are a number of issues here, firstly these oils are highly unstable and prone to rapid oxidation as soon as they are removed from within their naturally packaged form, seeds, once extracted they are then bleached, deodorised and bottled, but for the most part are already rancid before you even open the bottle, so that is already a problem consuming oxidised oils is going to be an inflamation issue straight away. Secondly, they have been promoted as healthy and their increased consumption has been pushed by manufacturers on the foundation of selective science, along with the fact that Omega 3 levels have fallen to virtually zero due to changes in agriculture, i.e. factory farming, resulting in consumption ratios in excess of 20:1, where the ideal 06:O3 ratio is less than 4:1 and preferably as close to 1:1 as you can get, there have been some studies that indicate the actual ratio is more important than the absolute volume. This is then further aggravated by unfounded fears of saturated fat consumption, so when it comes to our body's doing building and repair work, if it can't get adequate supplies of the right material, then it uses what it has available, so in cell membranes which are primarily comprised of saturated fats and small amounts of O6's & O3's, the end result is an excessive proportion of O6's are represented and this is important because the O6's & O3's seem to play a significant role in cell signaling and transport of materials into and out of cells. So if we think of it like a building, then saturated fats form the walls and the Omega's form the doors & windows, too many doors and windows and it becomes difficult to maintain adequate security in the building, likewise with our cells, they effectively become leaky, so the body ramps up other measures like the immune system and cholesterol to help plug the gaps.
The Liver is definately a key part of the process as well and in the high carb consumption there is high fructose corn syrup (HFCS), fructose in moderate quantities in a balanced diet is fine, but the excessive consumption through HFCS and ordinary sucrose results in an overload in the liver which must process most of the fructose to triglycerides mostly because of excessive blood glucose already, transport out is impaired (can't remember mecanism at moment) and this results in a logjam in the liver impairing it's functions. The other thing about fructose is it has the ability to block leptin receptors in the brain causing the satiety response to fail, hence we just keep eating it and putting on weight, this is believed to be a hibernation type response allowing us to gorge on in season fruit as it is only available for a short period and then store this away, just doesn't work so well when there is a year round supply of fructose.
When you throw other nutritional antigens like Gluten type compounds, Casein, Soy into a damaged gut, then these become the key activation triggers for a variety of antibody type responses, often in conjunction with bacterial incursions as well.
Anyway that's some of the things I have looked at, not saying it is all right, but think it is part of the problem.
And yes, one can easily get lost in the endochrine system.
I am just an interested individual trying to crack the autoimmune nut.
Partner has Graves Disease, 5 years, showing good test results, looking forward to potential remission in the near future.
3 friends have MS, 1 just recently diagnosed, severity 7/10.