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Page 200 Walker. Neuroimmunol Neuroinflammation 2020;7:194-214 I http://dx.doi.org/10.20517/2347-8659.2020.09

rich repeat-containing protein (Lrrc3), Geranyltranstransferase (FPPS), microfibril-associated glycoprotein
3 (Mfap3), P2ry12, P2ry13, Plexin domain-containing protein 1 (Plxdc1), prostate transmembrane protein,
androgen induced 1 (Prmepa1), Ras-related protein Rab-39 (Rab39), Spalt-like transcription factor 1
(Sali1), Selectin-P ligand, CD162 (Selplg), Siglech (SIGLEC-H), Toll-like receptor-3 (Tlr3), and TMEM119.
A panel of 134 neurodegeneration-related genes were defined (for complete list refer to supplementary
[24]
data in reference ). It was noted that 75% of these genes were associated with plasma membrane or
extracellular space proteins. It was concluded that this was due to changes in the way microglia interact
with the degenerative environment. Other genes included transcription factors Bhihe40 (Clast-5), retinoid
X receptor gamma (Rxrγ), Hif1a and melanocyte inducing transcription factor (MITF), and 10 lysosome-
associated genes including cathepsins (Ctsb, Ctsl and Ctsz). In a number of the models analyzed, increased
expression of ApoE was consistently detected, and microglial responses to Aβ were highly dependent on
Trem2 signaling. The central role for TREM2 in microglial responses has been demonstrated in network
analysis showing TYROBP (DAP12), the essential adaptor protein that mediates TREM2 signaling, is a
central hub gene for many of the above-listed inflammatory genes [31,48] .

A recent publication employing single-nucleus transcriptomics combined with proteomic validation
[26]
studies comparing AD model mice and human AD materials showed that there were large differences
in the glial phenotypes between AD mice and human AD samples. These investigators confirmed that the
“Disease Associated Microglia” signature was dependent on expression of TREM2. There was increased
expression of a number of “homeostatic” genes, including P2RY12, TMEM119 and CX3CR1, which have
been downregulated in AD mouse models. This study also identified an amyloid-driven oligodendrocyte
signature showing disruption in myelination, possibly driven by enhanced white-matter inflammation.
In addition to the previously mentioned TREM2, APOE, HLA-DRA, and Alpha-2 macroglobulin (A2M),
this study identified a number of additional markers that could be characterized in AD brains. These
include Suppressor of Cytokine Signaling-6 (SOCS6), ZFP36 ring finger protein like 2 (ZFP36L2), SELPLG
(Selectin-P ligand, CD162), sortilin related receptor 1 (SORL1), and chitinase-3-like protein 1 (CHI3L1),
which were upregulated, and SLC11A1 (natural resistance-associated macrophage protein-1), S100A8 (S100
calcium binding protein A8), HAMP (Hepcidin), FTH1, SLC2A3 (Glucose transporter-3), Interleukin-1
beta (IL1B), Interferon Induced Transmembrane Protein 2 (IFITM2), S100 Calcium Binding Protein A9
(S100A9), regulator of G-protein signaling 1 (RGS1) and SLC25A37.

Differences between old and middle-aged human microglia
Noticeable differences in gene expression profiles were identified in microglia isolated from middle aged
(young-mean age 53) and old brains (aged-mean age 94) . This study produced RNA sequencing profiles
[49]
of aged brain microglia and compared the results with those in another published study to show that
1060 genes were significantly upregulated in aged microglia and 1174 were downregulated . Many of the
[50]
significantly upregulated genes included those with genetic associations to AD risk [Table 2].

Prominent in the upregulated group were Cathepsin D (CTSD), Progranulin (GRN), Lymphotoxin beta
receptor (LTBR), Translocator protein (TSPO), Cytochrome B245 alpha (CYBA), CD14 (LPS receptor),
C1QA, C1QC and interferon regulatory factor-7 (IRF7), while prominent in the downregulated group were
CD83, FLT1 (vascular endothelial growth factor receptor-1), nuclear factor kappa-light-chain-enhancer
of activated B cells (NFKB), interleukin-1 beta (IL1B), cycloxygenase-2 (PTGS2), CCL4 (macrophage
inflammatory protein-1 beta), CCL2 (monocyte chemoattractant protein-1), CCL3 (macrophage
inflammatory protein-1 alpha), Toll-like receptor-4 (TLR4), prostaglandin E receptor-1 (PTGER1),
transforming growth factor beta receptor 2 (TGFBR2) and mannose receptor C-type 1-CD206 (MRC1).

A similar approach was carried out comparing the RNA sequencing profiles of aged human microglia bulk
isolated from the human parietal cortex in 39 autopsy cases. Data were compared with available datasets