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I was reading about the necessity of niche formations to adequate development of blood progenitors and this idea reminded me of the patchy inactivation of the X chromosome which followed that maybe, if some of these pathways passed through X coded proteins, this might make women have different niches, that could account for the seemingly greater occurrence of auto-immune diseases in women.

Is there any sense to this idea? Was this ever researched?

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Yes, here is an article on it: "The role of X-chromosome inactivation in female predisposition to autoimmunity"

Below see the method and results summarised.

Using a DNA methylation assay, we have examined the X-chromosome inactivation patterns in peripheral blood from normal females (n = 30), female patients with a variety of autoimmune diseases (n = 167). No differences between patients and controls were observed. However, locally skewed X-chromsome inactivation may exist in the thymus, and therefore the underlying hypothesis remains to be disproved.

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Not very assuring finding, but the size of sample and the heterogeneity of diseases maybe influenced the results. I have to read it again with more attention, but thanks. –  user27221 Jul 25 '13 at 18:41
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