The molecules that silence a woman’s second X chromosome can confuse the immune system, a new study suggests.

Women are much more likely than men to have their immune system turn against them, resulting in an array of so-called autoimmune diseases, like lupus and multiple sclerosis. A study published on Thursday offers an explanation rooted in the X chromosome.

The research, published in the journal Cell, suggests that a special set of molecules that act on the extra X chromosome carried by women can sometimes confuse the immune system.

Independent experts said that the molecules are unlikely to be the sole reason autoimmune disease skews female. But if the results hold up in further experiments, it might be possible to base new treatments on these molecules, rather than on the current drugs that blunt the entire immune system.

“Maybe that’s a better strategy,” said Dr. Howard Chang, a geneticist and dermatologist at Stanford who led the new study.

Male and female embryos carry 22 identical pairs of chromosomes. The 23rd pair is different: Females carry two Xs, while males carry an X and a Y, which lead to the development of male sex organs.

Each chromosome holds genes that, when “switched on,” produce proteins to do work inside of cells. You might expect that women, with two copies of X, would make twice as many X proteins as men do. Instead, they produce about the same level. That’s because one of the two X chromosomes is silenced.

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