How does multiple sclerosis affect the hypothalamus?

It shouldn't: Since the hypothalamus is not really a white matter structure, it should not effect thje hypothalamus directly but it could effect neurons that go into and leave the hypothalamus. Since thie hypothalamus controls temperature, feeding behavior, sexual behavior and heart rate and blood pressure, if a brain region needs input from the hypothalamus it may not get it.

FATIGUE AND SLEEP: This is a complex question. We are finding that sleep disorders, such as narcolepsy and restless leg syndrome can be associated with ms, and some research suggests that hypocretin-i secreting cell loss may well be autoimmune. Although not usually recognized, interferon-beta meds do cause fatigue secondary to hypothalamic effects. Congrats, your question is highly sophisticated.