. Single-Cell RNA Sequencing of Microglia throughout the Mouse Lifespan and in the Injured Brain Reveals Complex Cell-State Changes. Immunity. 2019 Jan 15;50(1):253-271.e6. Epub 2018 Nov 21 PubMed.


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  1. This is a very exciting piece of research. I’ve eagerly awaited these data sets. A few points that make this work so novel, and will ensure that it is cited widely in the coming years:

    1. Single-cell microglia analysis—obviously interesting and follows nicely from the DAM paper from Keren-Shaul et al., 2017.
    2. Age-related changes in ssMicro transcripts—this highlights different populations of microglia that, one can now hypothesize, play specific and different roles at different stages of development. The addition of the senescent age (over 500 days) pairs nicely with the aging astrocyte transcriptomes published earlier in the year by Clarke et al., 2018, and Boisvert et al., 2018
    3. Sex-specific ssMicro transcripts. This is going to be extremely helpful for investigations into microglia functions going forward. We obviously know there are differences in female/male responses and disease progression, not just for AD, but for other chronic neurodegenerative diseases too, so having these baseline “control” data is key to making new hypotheses moving forward.
    4. Disease-response ssMicro transcriptomes. The capstone to this work was the response of the microglia to the mouse demyelinating EAE model. The most exciting piece for me! This really put to bed one of the most intriguing pieces of data in our original Nature paper (Liddelow et al., 2017) that Ben Barres and I were unable to make sense of. That is, when we used the colony-stimulating factor 1 receptor inhibitor drug PLX3397 to ablate microglia, we were able to remove 99 percent of microglia as per FACS, but the astrocyte response to inflammatory insult (modeled with LPS injection) was maintained. We thought that perhaps the PLX drug did not kill microglia but might instead simply have downregulated microglia-specific markers we were using for FACS/IF, or that the small subset of microglia that remained were the ones that would have mounted a response to the inflammation anyway. These new data show that the latter is likely the cause, i.e., if you look for TNFα, Il1α, and C1q, there is only a small population of microglia in the disease state that expresses all three.

    Note that the authors provide an easily searchable online portal. This means I can check genes easily on the fly while at meetings, or while out running and thinking of an idea. The portal also couples nicely with the earlier datasets published by the McCarrol and Macosko labs, e.g., DropViz.org.


    . A Unique Microglia Type Associated with Restricting Development of Alzheimer's Disease. Cell. 2017 Jun 15;169(7):1276-1290.e17. Epub 2017 Jun 8 PubMed.

    . Normal aging induces A1-like astrocyte reactivity. Proc Natl Acad Sci U S A. 2018 Feb 20;115(8):E1896-E1905. Epub 2018 Feb 7 PubMed.

    . The Aging Astrocyte Transcriptome from Multiple Regions of the Mouse Brain. Cell Rep. 2018 Jan 2;22(1):269-285. PubMed.

    . Neurotoxic reactive astrocytes are induced by activated microglia. Nature. 2017 Jan 26;541(7638):481-487. Epub 2017 Jan 18 PubMed.

  2. Microglial scRNA-Seq was performed across the mouse life span from E14.5 through P540. After cluster analysis, care was taken to specify at what age, and where, in the brain varied clusters were detected. It was observed that maximal microglial heterogeneity occurred during development, significantly resolved during healthy young adulthood, and then selectively and differentially re-emerged during either aging or focal injury. Particularly compelling observations included a select microglial phenotype associated with presumptive white-matter tracts before myelination, a finding of special interest given recent reports from Marco Prinz and Xinhoa Piao’s labs that microglia provide signals to promote myelination (Hagemeyer et al., 2017; Giera et al., 2018). 

    Another fascinating cluster was seen only at E14.5 and exhibited a phenotype consistent with that of highly proliferative cells, including elevated expression of fatty-acid-binding proteins and glycolytic machinery genes. The investigators' dedication in spatiotemporal localization of cells expressing transcriptomic phenotypes will provide both information and a strategic template for conducting such studies. In this analysis, the absence of sexual dimorphism was notable, consistent with previous reports that microglial sexual dimorphism is commonly elicited by stress conditions such as germ-free state. 

    Data from this paper will constitute a fascinating comparison with those coming from Olah, Phil DeJager et al., currently on bioRχiv. They isolated and sequenced more than 15,000 microglia from human samples, both autopsy and biopsy, from young and aged individuals. Many overall technical conclusions were shared between the two groups. In particular, scRNA-Seq represents an essential step for clarifying the population structures and transcriptomic phenotypes of microglia. DeJager compared their data with those they'd previously obtained by co-expression module analysis of cortical tissue from autopsy samples. They concluded that the scRNA-Seq data set was essential to developing robust insights into microglial phenotypes and heterogeneity in human brain. Of particular interest, Olah/DeJager evaluated four transcriptomic clusters found only in samples from brain donors more than 90 years of age. These transcriptomes bore resemblance to that described by Mathys et al., 2018, in a mouse model of neurodegeneration.

    Neither Hammond et al. nor Olah et al. yielded substantial support for the existence of a “DAM” transcriptome (Keren-Shaul et al., 2017). In particular, Hammond found genes diagnostic of the DAM transcriptome distributed among a number of distinct transcriptomic phenotypes (characterized by varying subsets of non-DAM genes). Olah did not observe clustering of transcriptomic states to be associated with a coherent co-expression pattern of DAM genes. Selection of scRNA-Seq platform and mouse disease model, as well as human versus mouse species variation and preferred analytic scheme, doubtless contributed to these differing observations among the reports.


    . Microglia contribute to normal myelinogenesis and to oligodendrocyte progenitor maintenance during adulthood. Acta Neuropathol. 2017 Sep;134(3):441-458. Epub 2017 Jul 6 PubMed.

    . Microglial transglutaminase-2 drives myelination and myelin repair via GPR56/ADGRG1 in oligodendrocyte precursor cells. Elife. 2018 May 29;7 PubMed.

    . Temporal Tracking of Microglia Activation in Neurodegeneration at Single-Cell Resolution. Cell Rep. 2017 Oct 10;21(2):366-380. PubMed.

    . A Unique Microglia Type Associated with Restricting Development of Alzheimer's Disease. Cell. 2017 Jun 15;169(7):1276-1290.e17. Epub 2017 Jun 8 PubMed.

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  1. Microglia Reveal Formidable Complexity, Deep Culpability in AD