Brain is immunopriveleged tissue which is populated by the immune cells during early embryogenesis and unless there is an ongoing inflammation/tissue damage there should be no influx of the immune cells from the periphery. In addition, other factors, such as type of the host (NSG and its modifications vs NOG vs SCID, etc), age post-engraftment, and the source of human cells (cord blood stem cells, fetal liver, PBMC) may affect your results.

Thanks. I gave them infection. And I see a lot of mouse specific CD68 and Iba1 in the brain. Its just that, none of the human specific antibodies are showing up. These are the NSG mice with CD45+ engraftment levels between 50-70%. I am trying different antigen retrieval methods now to confirm. Lets see if anything shows up. Thanks.

Which cells do you use to engraft your mice: cd34 or pbmc?

We bought the mice. They use CD34.

I doubt you'll see any human cells in the brain, especially macrophages (myeloid lineage development is not very robust in NSG mice). 

Alright. Well that's ok. I have to check it anyway. I am doing immunostaining for spleen and intestine in parallel. Plus mouse markers should be alright. Thanks for all your advice. Really appreciate it.

So here is what I have till date. I don't see human specific CD4,CD3 and CD8 in the brain. But it is most probably due to the antibodies I have been using. I used peripheral tissue and human spleen sections for positive controls and even those show up negative. I can't find any more human specific antibodies that I haven't tried. But peripheral tissue and human spleen were positive for CD68, CD45 and HLA-DR-LN3. All of these were absent in the brain. Brain was only positive for IBA-1 which showed up robustly in the infected brains and only slightly in control brains (but its was there).

After a few antigen retrieval methods and using different kinds of antibodies, I found that the human macrophages are only present in the meningial layers of these mice. Thank you Dr. Misharin for your comments here.