That is an interesting article in that it suggests that after HSCT the thymus is involute and the T cell reconstruction is due to memory cells that
are remnants after the HSCT treatment:
In adult humans, the thymus is involuted, which suggests that extrathymic differentiation of T-cell progenitors, peripheral expansion of mature T
cells, or both are the principal mechanisms of T-cell reconstitution after transplantation. Dreger et al17 showed a lack of naive CD45RA+ cells after AHSCT, suggesting that most circulating T cells after AHSCT in humans are activated memory CD45RO+ cells rather than naive T cells. The deficient numbers of naive T cells predict the inability to elicit immune responses against new antigens after AHSCT.
I think this article was written before the acceptance of the discovery of regulatory T cells. These cells act as moderators of the immune system and prevent autoimunity from occuring. Here is a pretty good paper that descibes these cells:http://www.smccd.edu/accounts/digennaroc/biology430/Articles/Regulatory_T-cells.pdf
So, this peaked my interest to see what happens to regulatory T-cells (tregs) after HSCT. According to the paper below, the regulatory T-cell subpopulation quickly becomes normal within 9 months.http://www.jci.org/articles/view/41072
Prospective monitoring of CD4+ T cell subsets revealed that Tregs rapidly expanded and achieved normal levels by 9 months after HSCT, but Treg levels subsequently declined in patients with prolonged CD4+ lymphopenia.
Granted this is for allogenic HSCT, but it may be that the Treg/Teffector cell population increases after HSCT which would explain why the non-myeoblative procedure works also (note that Tregs are a type of CD4+ cell, but are usually a small proportion, about 5% if memory serves me correctly).
At any rate, it seems people with MS have defective regulatory T cells. http://www.ncbi.nlm.nih.gov/pubmed/17099776
So it could be that the cause of MS is not simply autoreactive T-cells but could be because the role of the regulatory T-cells are deficient in people with MS and allows autoimunity to happen.
Incidentally, to tie this all together, it appears the Vitamin D has the ability to enhance regulatory T-cell function:http://www.plosone.org/article/info:doi/10.1371/journal.pone.0006635