RNA‐sequencing reveals oligodendrocyte and neuronal transcripts in microglia relevant to central nervous system disease

Abstract

Expression profiling of distinct central nervous system (CNS) cell populations has been employed to facilitate disease classification and to provide insights into the molecular basis of brain pathology. One important cell type implicated in a wide variety of CNS disease states is the resident brain macrophage (microglia). In these studies, microglia are often isolated from dissociated brain tissue by flow sorting procedures (FACS) or from postnatal glial cultures by mechanic isolation. Given the highly dynamic and state-dependent functions of these cells, the use of FACS or short-term culture methods may not accurately capture the biology of brain microglia. In the current study, we performed RNA-sequencing using Cx3cr1+/GFP labeled microglia isolated from the brainstem of 6-week old mice to compare the transcriptomes of FACS-sorted versus laser-captured (LCM) microglia. While both isolation techniques resulted in a large number of shared (common) transcripts, we identified transcripts unique to FACS-isolated and LCM-captured microglia. In particular, ~50% of these LCM-isolated microglial transcripts represented genes typically associated with neurons and glia. While these transcripts clearly localized to microglia using complementary methods, they were not translated into protein. Following the induction of murine experimental autoimmune encephalomyelitis (EAE), increased oligodendrocyte and neuronal transcripts were detected in microglia, while only the myelin basic protein oligodendrocyte transcript was increased in microglia after traumatic brain injury (TBI). Collectively, these findings have implications for the design and interpretation of microglia transcriptome-based investigations.

Microglia from offspring of dams with allergic asthma exhibit epigenomic alterations in genes dysregulated in autism

“…S1C) in our microglial isolations due to the inherent microglial-neuronal interactions including phagocytosis that occur in brain. While our microglia isolations were above the purity of another published microglial transcriptome study (Zhao et al, 2017), we cannot be certain that the higher expression of some of the typically neuronal genes were cell intrinsic to microglia rather than a result of increased neuronal phagocytosis in the MAA brain (Solga et al, 2015), although either explanation is of interest for understanding the pathogenesis. While the function of many of these neurotransmitter receptors on microglia is largely unknown (Schafer et al, 2013), their overall increase in expression following MAA suggests that microglia have altered sensitivity in the juvenile MAA brain.…”

“…One potential limitation of our study was a low level of neuronal contamination (0.2-2% in control versus 0.5-4% in MAA, Supporting Information Figure S1C) in our microglial isolations due to the inherent microglial-neuronal interactions including phagocytosis that occur in brain. While our microglia isolations were above the purity of another published microglial transcriptome study (Zhao et al, 2017), we cannot be certain that the higher expression of some of the typically neuronal genes were cell intrinsic to microglia rather than a result of increased phagocytosis of neurons in the MAA brain (Solga et al, 2015), although either explanation is of interest for understanding the pathogenesis.…”

The microglial reaction signature revealed by RNAseq from individual mice

“…In this study, Table S9), therefore these genes are pertinent specific biomarkers of microglial reaction for multiple disease conditions. Another study revealed that <0.5% of the detected genes differed between FACS isolated homeostatic microglia from WT and CX3CR1 1/GFP microglia (Solga et al, 2015). Another study revealed that <0.5% of the detected genes differed between FACS isolated homeostatic microglia from WT and CX3CR1 1/GFP microglia (Solga et al, 2015).…”

The role of microglia and macrophages in glioma maintenance and progression

“…SDF-1 operating through the CXCR4 receptor promotes optic glioma cell survival, such that CXCR4 inhibition reduces tumor growth in vivo . A more complete characterization of TAMs support of tumor maintenance has been performed using optimized RNA-sequencing methods 41,42 .…”