Microglia constantly monitor the brain environment, and many alterations of brain homeostasis can induce a microglial response. Several transcriptomic studies describe distinct signatures for microglia that define their states from healthy to disease-associated. These transcriptomic profiles are essential to an elucidation of which genes and proteins are required to trigger specific responses depending on the alterations faced by microglia and the surrounding cells with which they communicate. Using single-cell sequencing in
5xFAD mice, Keren-Shaul et al. (2017) showed a unique subtype of microglia, referred to as Disease-Associated Microglia (DAM), localized near the amyloid plaques [
26]. Using
Trem2−/− mice, they identified two sequential but distinct stages in the switch to a DAM phenotype. The first step is
Trem2-independent and requires the activation of genes that include
Tyrobp and
Apoe. The second step was found to be
Trem2-dependent and associated with phagocytosis. A report published by Krasemann et al. (2017) identified a similar signature in microglia acquiring a neurodegeneration-associated phenotype (MGnD) in models of amyotrophic lateral sclerosis (ALS), multiple sclerosis (MS), and AD, and pointed to microRNA-155 (
miR-155) as an effector of the MGnD phenotype [
25]. This study and a report from Butovsky et al. [
128] showed that ablation of
Trem2,
Apoe, or
miR-155 locks microglia into a homeostatic state blocking the formation of MGnD. Of note, our recent reports placed
miR-155 at the intersection of a multiplex of AD pathogenic components involving innate immunity, viral response, synaptic physiology, and pro-amyloidogenic pathways [
129]. Although similar, the study by Krasemann et al. (2017) contrasts with Keren-Shaul et al. (2017), in which
Apoe upregulation appeared to be independent of
Trem2. More recently, Chen et al. (2020) used a combination of spatial transcriptomics and in situ sequencing to avoid one of the main drawbacks of these types of analyses, i.e., averaging the transcriptomes between microglia which are and are not recruited around the amyloid plaques [
114]. They investigated the transcriptional changes occurring in a 100 μm diameter around the amyloid plaques of
APPNL-G-F mice and defined a plaque-induced gene (PIG) network of 57 genes in which
Trem2,
Tyrobp,
Apoe, and other complement-related genes were among the upregulated genes. When performed in human AD brain slices, both
Tyrobp and
Apoe transcripts were confirmed as enriched, but, unexpectedly,
Trem2 was not among the human PIGs. As stated above, our lab showed that the absence of
Tyrobp in
APP/PSEN1;Tyrobp−/− mice represses the induction of many genes involved in this DAM switch, including
Trem2, complement (
C1qa,
C1qb,
C1qc, and
Itgax),
Clec7a and
Cst7 (Fig.
3) [
32]. Furthermore, we recently provided evidence that concurrent upregulation in microglia of both
Tyrobp and
Apoe is interconnected during microglial sensing of amyloid deposits and that these events take place independent of
Trem2 but are dependent on
Tyrobp (Fig.
3) [
30]. The damage-associated signatures described in all DAM, MGnD, and PIG microglia suggest that microglial transition from a homeostatic to a disease-associated state is choreographed by multiple components and involves TREM2, TYROBP, and APOE. Our data confirmed the two stages described by Keren-Shaul et al. (2017), in which the first stage would eventually correspond to a sensing of the amyloid plaques by the microglia and where both
Tyrobp and
Apoe are upregulated. The first stage is independent of
Trem2 and would be followed by a second stage that is dependent on
Trem2 and mostly associated with phagocytosis.