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Cited by 1,268Neuroinflammation and Neurodegeneration MechanismsSingle-cell and spatial transcriptomicsMultiple Sclerosis Research Studies

An environment-dependent transcriptional network specifies human microglia identity

Open access
Gosselin, David, Skola, Dylan, Coufal, Nicole G., Holtman, Inge R., Schlachetzki, Johannes C. M., Sajti, Eniko, Jaeger, Baptiste N., O’Connor, Carolyn +9 more·2017·Science
DOI 10.1126/science.aal3222PMC PMC5858585
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Abstract

Of mice and men's microglia: Microglia are immune system cells that function in protecting and maintaining the brain. Gosselin et al. examined the epigenetics and RNA transcripts from single microglial cells and observed consistent profiles among samples despite differences in age, sex, and diagnosis. Mouse and human microglia demonstrated similar microglia-specific gene expression profiles, as well as a shared environmental response among microglia collected either immediately after surgery (ex vivo) or after culturing (in vitro). Interestingly, those genes exhibiting differences in expression between humans and mice or after culturing were often implicated in neurodegenerative diseases. Science , this issue p. eaal3222

AI snapshot

Written from the paper’s full text.

TL;DR

The study maps transcriptomes and regulatory landscapes of human microglia ex vivo and after culture, showing that brain environment maintains a large microglia-specific expression program. It also finds broad conservation with mouse microglia alongside species-biased genes and disease-risk gene expression.

Key findings

  • From 19 surgical samples, a human microglia signature of 881 transcripts was defined as >10-fold higher than cortex at FDR 0.05; intersecting with 46 public disease datasets showed significant enrichment/depletion in 28, including AD, FTLD, HAND, schizophrenia, and Parkinson’s.
  • Disease risk genes were often microglia-preferential: 28/48 AD genes, 48/81 MS genes, and about one-third of PD and schizophrenia genes.
  • Human and mouse microglia transcriptomes correlated at r=0.806; 13,253/15,768 ortholog pairs were within 4-fold, while 400 human- and 293 mouse-biased mRNAs differed >10-fold at FDR 0.05. Mouse microglia signature had 900 genes >10-fold over other macrophages; ~53% (477/900) had comparable human expression.
  • Culture caused rapid remodeling: >300 genes induced and >700 repressed >10-fold; at 2-fold, 2,263 up and 3,702 down. 33% of conserved signature and 31% of AD-risk genes fell >2-fold; 424/740 ex vivo super-enhancers were lost and 541 gained. TGF-β1 restored >2-fold expression of 429 of 2,398 culture-down genes.

Methods

  • Microglia isolated from resected brain tissue of 19 individuals (epilepsy, tumors, acute ischemia), purified by FACS as live CD11b+CD45LowCD64+CX3CR1High; mouse C57BL/6 microglia as CD11b+CD45Low. Samples analyzed ex vivo and after 6h, 24h, or 7d culture.
  • RNA-seq, ATAC-seq, and ChIP-seq for H3K4me2, H3K27ac, and PU.1; analyses included differential expression, motif enrichment, super-enhancer identification, ortholog mapping, and comparisons with cortex, public disease datasets, mouse macrophages, and developmental microglia.

Limitations

  • The authors note that more individuals are needed to link genetic variation to expression, that the full set of brain-derived maintenance signals is unknown, and that culture and current iPSC-derived microglia-like cells do not preserve the ex vivo phenotype; TGF-β1 effects were modest.
  • The text also makes evident limitations: samples came from heterogeneous surgical indications (epilepsy, tumor, ischemia), human macrophage RNA-seq datasets were insufficient to build a matched human microglia-specific signature, and analyses of sex differences were mostly limited to X/Y-linked genes.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1126/science.aal3222

Cites

78 of 78 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 58 cited sources checked · 0 supported · 0 flagged

  • Findingown data

    Using a stringent cutoff of 10-fold increased expression relative to cortex tissue at a false discovery rate of 0.05, a microglial gene signature in the human brain comprising 881 transcripts was defined.

    “Using a stringent cutoff of 10-fold increased expression relative to cortex tissue at a false discovery rate (FDR) of 0.05, we defined a microglial gene signature in the human brain comprising 881 transcripts (Fig. 1A, Table S2).”
    Quote in the paperSubstantial claim
    • Rests on an assumption: Human microglia isolated from surgically resected brain tissue of patients with epilepsy, brain tumors, or acute ischemic events are representative of normal human microglia.
    • Rests on an assumption: The ex vivo isolation procedure, including Percoll gradient centrifugation and FACS purification, does not substantially alter the microglial transcriptome.
  • Findingown data

    Gene ontology analysis of the extended microglia gene signature returned significant functional enrichment for CNS-related categories such as regulation of neurogenesis, synaptic signaling, CNS development, response to transforming growth factor beta, and regulation of neurotransmitter transport.

    “Gene ontology analysis of this extended microglia gene signature returned significant functional enrichment for CNS-related categories such as regulation of neurogenesis, synaptic signaling, CNS development, response to transforming growth factor beta (TGF-β), and regulation of neurotransmitter transport (Fig. 2C).”
    Quote in the paperNot a substantial claim
  • Findingown data

    Intersection of the microglia signature gene list with 46 publicly available data sets for differentially regulated genes in neurodegenerative and behavioral disorders revealed significant enrichment or depletion of microglia signature genes in 28 of the 46 data sets.

    “We then intersected this gene list with 46 publicly available data sets for differentially regulated genes in neurodegenerative and behavioral disorders derived from microarray or RNA-seq analysis of intact tissue (39–53). Two-sided Fisher’s exact tests revealed significant enrichment or depletion of microglia signature genes in 28 of the 46 data sets (Table S3).”
    Quote in the paperSubstantial claim0 of 10 sources checked
    • cites [39] Avramopoulos D Szymanski M Wang R Bassett S Gene expression reveals overlap between normal aging and Alzheimer's disease genes Neurobiol Aging 32 2319 e2327 2334 2011 PMC2945399 20570407 source
    • cites [40] Blalock EM Incipient Alzheimer's disease: microarray correlation analyses reveal major transcriptional and tumor suppressor responses Proc Natl Acad Sci U S A 101 2173 2178 2004 14769913 PMC357071 source
    • cites [41] Capurro A Bodea LG Schaefer P Luthi-Carter R Perreau VM Computational deconvolution of genome wide expression data from Parkinson's and Huntington's disease brain tissues using population-specific expression analysis Front Neurosci 8 441 2014 25620908 PMC4288238 source
    • cites [42] Colangelo V Gene expression profiling of 12633 genes in Alzheimer hippocampal CA1: transcription and neurotrophic factor down-regulation and up-regulation of apoptotic and pro-inflammatory signaling J Neurosci Res 70 462 473 2002 12391607 source

      Queued — the background check reaches it, usually within a day.

    • cites [43] Liang WS Altered neuronal gene expression in brain regions differentially affected by Alzheimer's disease: a reference data set Physiol Genomics 33 240 256 2008 18270320 PMC2826117 source

      Not checked in the free run.

    • cites [44] McClintick JN Ethanol treatment of lymphoblastoid cell lines from alcoholics and non-alcoholics causes many subtle changes in gene expression Alcohol 48 603 610 2014 25129674 PMC4730944 source
    • cites [45] Mishra M Gene expression analysis of frontotemporal lobar degeneration of the motor neuron disease type with ubiquitinated inclusions Acta Neuropathol 114 81 94 2007 17569064 source
    • cites [46] Satoh J Yamamoto Y Asahina N Kitano S Kino Y RNA-Seq data mining: downregulation of NeuroD6 serves as a possible biomarker for alzheimer's disease brains Dis Markers 2014 123165 2014 25548427 PMC4274867 source
    • cites [47] Webster JA Genetic control of human brain transcript expression in Alzheimer disease Am J Hum Genet 84 445 458 2009 19361613 PMC2667989 source
    • cites [48] Borjabad A Significant effects of antiretroviral therapy on global gene expression in brain tissues of patients with HIV-1-associated neurocognitive disorders PLoS Pathog 7 e1002213 2011 21909266 PMC3164642 source
  • Findingown data

    For multiple sclerosis, 48 of 81 genes associated with risk alleles were preferentially expressed in microglia.

    “For MS, 48 of 81 genes associated with risk alleles were preferentially expressed in microglia (Fig. S5).”
    Quote in the paperSubstantial claim
  • Findingown data

    Different subsets of the microglia signature gene set were upregulated or downregulated in cortex in Parkinson's disease.

    “Interestingly, different subsets of the microglia signature gene set were upregulated or downregulated in cortex in PD (Fig. 1C).”
    Quote in the paperNot a substantial claim
  • May combine two claims. 38
  • Classified as probably not a substantial claim. 15

  • May combine two claims.

    Findingown data

    A dominant signature was observed for PU.1 in both species, with highly significant enrichment also observed for motifs assigned to CTCF, IRF, RUNX, MEF2, C/EBP, AP-1, SMAD and MAF factors.

    “A dominant signature was observed for PU.1 in both species, with highly significant enrichment also observed for motifs assigned to CTCF, IRF, RUNX, MEF2, C/EBP, AP-1, SMAD and MAF factors (Fig. 3B, Fig. S10B).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Many genes associated with Alzheimer's disease, Parkinson's disease, multiple sclerosis and schizophrenia risk alleles were preferentially expressed in microglia, with the relative proportion varying by disorder.

    “Characterization of the microglia transcriptome, in conjunction with parallel whole brain cortical gene expression profiling, also enabled evaluation of the relative expression levels of genes associated with AD, PD, multiple sclerosis (MS) and Scz risk alleles (54). Many of these genes were preferentially expressed in microglia, with the relative proportion varying by disorder (Fig. 1D and Fig. S”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [54] Welter D The NHGRI GWAS Catalog, a curated resource of SNP-trait associations Nucleic acids research 42 D1001 1006 2014 24316577 PMC3965119 source

      Not checked in the free run.

  • May combine two claims.

    Findingown data

    Comparison of human and mouse microglia transcriptomes revealed overall similarities in patterns of gene expression (Pearson's r = 0.806), with the majority of orthologous gene pairs (13,253 of 15,768) expressed within a 4-fold range.

    “Overall, the microglia transcriptome comparison between the two species revealed overall similarities in patterns of gene expression (Pearson’s r = 0.806), with the majority of orthologous genes pairs (13,253 of 15,768) expressed within a 4-fold range.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Hundreds of genes in the microglia gene signature exhibited significant overlaps with sets of genes that were positively correlated with Braak stage in Alzheimer's disease, were upregulated in frontotemporal lobar degeneration in frontal cortex, were upregulated in HIV-associated neurocognitive disorder, or were upregulated in schizophrenia.

    “For example, hundreds of genes in the microglia gene signature exhibited significant overlaps with sets of genes that were positively correlated with Braak stage in AD, were upregulated in frontotemporal lobar degeneration (FTLD) in frontal cortex, were upregulated in HIV-associated neurocognitive disorder (HAND) or were upregulated in Scz (Fig. 1C).”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    Relative expression values for the 30 most highly expressed genes across each of the patients indicated substantial individual variation for some transcripts.

    “Relative expression values for the 30 most highly expressed genes across each of the patients are illustrated in Figure 1B, indicating substantial individual variation for some transcripts.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    When all transcripts were considered, Pearson correlation coefficients were in the range of 0.94 to 0.98, indicating no substantial outliers among samples.

    “When all transcripts were considered (i.e., including genes expressed at ≤ 2 log2 TPM), Pearson correlation coefficients were in the range of 0.94 to 0.98 (Fig. S3D), indicating no substantial outliers among samples.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    An additional 35 factors were associated with super-enhancers, some of which have been linked to functional roles in microglia, including SALL1, STAT3 and RELA.

    “An additional 35 factors were associated with SEs, some of which have been linked to functional roles in microglia, including SALL1, STAT3 and RELA (Fig. 3D).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    At a cutoff of 10-fold difference and an FDR of 0.05, 400 orthologous mRNAs were preferentially expressed in human microglia and 293 mRNAs were more highly expressed in mouse microglia.

    “At a cutoff of 10-fold difference and an FDR of 0.05, 400 orthologous mRNAs were preferentially expressed in human microglia and 293 mRNAs were more highly expressed in mouse microglia (Fig. 2A).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    This definition captures a mouse microglia gene signature set that is larger but mostly inclusive of previously described microglia signature sets.

    “This definition captures a mouse microglia gene signature set that is larger but mostly inclusive of previously described microglia signature sets (27, 57, 58).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites [27] Butovsky O Identification of a unique TGF-beta-dependent molecular and functional signature in microglia Nat Neurosci 17 131 143 2014 24316888 PMC4066672 source

      Not checked in the free run.

    • cites [57] Chiu IM A neurodegeneration-specific gene-expression signature of acutely isolated microglia from an amyotrophic lateral sclerosis mouse model Cell Rep 4 385 401 2013 23850290 PMC4272581 source

      Not checked in the free run.

    • cites [58] Hickman SE The microglial sensome revealed by direct RNA sequencing Nat Neurosci 16 1896 1905 2013 24162652 PMC3840123 source

      Not checked in the free run.

  • May combine two claims.

    Findingown data

    Notable examples of species-biased expression included higher expression in human microglia of regulators of the complement system (C2, C3, VSIG4, SERPING1) and genes involved in brain structure development (SYNDIG1, GLDN, CTTNBP2, ROBO3), whereas genes more highly expressed in mouse microglia included Hexb, Sparc, and Sall3.

    “Notable examples included higher expression in human microglia of regulators of the complement system (e.g., C2, C3, VSIG4, SERPING1) and genes involved in brain structure development, including SYNDIG1, GLDN, CTTNBP2, and ROBO3. In contrast, genes more highly expressed in mouse microglia included Hexb, Sparc, and Sall3.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Of 39 Alzheimer's disease-associated and expressed genes, 11 were higher in human microglia whereas three were increased in mouse microglia.

    “Comparing the expression of genes linked to human neurodegenerative and behavioral disorders, of the 39 AD-associated and expressed genes, 11 were higher in human microglia whereas three were increased in mouse microglia (Fig. 2E).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Of the top 25 most expressed genes, APOC1 and MPZL1 were essentially not expressed in C57BL/6 microglia, and SORL1 was nearly 20 times lower in mouse than human.

    “Interestingly, of the top 25 most expressed, two genes, APOC1 and MPZL1, were essentially not expressed in C57BL/6 microglia; the expression of a third one, SORL1, was nearly 20 times lower in mouse than human (Fig. 2F).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    SPI1 (encoding PU.1) was the most highly expressed ETS domain transcription factor, and the top motifs were nearly perfect matches for its consensus recognition sequence.

    “SPI1 (encoding PU.1) was the most highly expressed ETS domain transcription factor, and the top motifs were nearly perfect matches for its consensus recognition sequence.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingown data

    A small set of genes exhibited significant sex-specific differences in gene expression, and these were mostly related to X- and Y-linked genes.

    “A small set of genes exhibited significant sex-specific differences in gene expression, and these were mostly related to X- and Y-linked genes (Fig. S4).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Of the 2,398 genes downregulated > 2-fold in vitro, TGF-β1 induced expression > 2-fold of 429, including Sall1, Tmem119, and P2ry12.

    “Of the 2,398 genes downregulated > 2-fold in vitro, Tgf-β1 induced expression > 2-fold of 429, including Sall1, Tmem119, and P2ry12.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    Similar results were observed for Pu.1 binding sites in mouse microglia.

    “Similar results were observed for Pu.1 binding sites in mouse microglia.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    For individuals with both ex vivo and in vitro samples available, gene expression within culture conditions (mean Pearson correlation = 0.95) was more correlated (p = 0.008 by permutation test) than between the ex vivo and in vitro samples of the same individual (mean Pearson correlation = 0.89).

    “For the individuals with both ex vivo and in vitro samples available, gene expression within culture conditions (mean Pearson correlation = 0.95) was more correlated (p=0.008 by permutation test) than between the ex vivo and in vitro samples of the same individual (mean Pearson correlation = 0.89).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingcitation

    A subset of mRNAs encoding transcription factors was expressed in primitive macrophages and maintained high levels of expression in brain microglia.

    “A subset of mRNAs encoding these factors was expressed in primitive macrophages and maintained high levels of expression in brain microglia (Fig. 6A).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    More than 2,000 genes were downregulated more than 4-fold at 6 h following plating, with some genes exhibiting partial recovery at the 7-day time point.

    “Remarkably, more than 2,000 genes were downregulated more than 4-fold at 6 h following plating, with some genes exhibiting partial recovery at the 7-day time point (Figs. 4E, S13D).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Of the 31,164 ATAC-seq peaks associated with at least 16 normalized H3K27ac tags, approximately 14% exhibited a loss of H3K27ac and approximately 20% a gain of H3K27ac, indicating remodeling of the regulatory landscape in vitro.

    “Overall, of the 31,164 ATAC-seq peaks associated with at least 16 normalized H3K27ac tags (i.e., high confidence sites), ~14% exhibited a loss of H3K27ac and ~20% a gain of H3K27ac (Fig. 5D), indicating remodeling of the regulatory landscape in vitro.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    While SPI1 levels increased slightly, the majority of the mRNAs encoding transcription factors recognizing enriched motifs in microglia enhancers exhibited significant reductions in vitro.

    “While SPI1 levels increased slightly, the majority of the mRNAs encoding transcription factors recognizing enriched motifs in microglia enhancers exhibited significant reductions in vitro.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Examining differences in ex vivo and in vitro microglia, we observe rapid and profound alterations in gene expression by 6 h, characterized by activation of genes associated with acute inflammatory responses and decreased expression of genes associated with diverse immune functions.

    “Examining differences in ex vivo and in vitro microglia, we observe rapid and profound alterations in gene expression by 6 h, characterized by activation of genes associated with acute inflammatory responses and decreased expression of genes associated with diverse immune functions.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Of the non-redundant set of 291 microglia transcripts associated with differentially regulated genes in AD, PD, HAND, SCZ or FTD, 117 were downregulated in vitro whereas 29 were upregulated in vitro.

    “Of the non-redundant set of 291 microglia transcripts associated with differentially regulated genes in AD, PD, HAND, SCZ or FTD, 117 were downregulated in vitro whereas 29 were upregulated in vitro (Fig. 6D).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    PU.1 was localized at 51.2% of ATAC-seq-defined regions of open chromatin associated with H3K4me2 and at 60.9% of regions exhibiting these features plus H3K27ac.

    “with PU.1 being localized at 51.2% of ATAC-seq-defined regions of open chromatin associated with H3K4me2 and at 60.9% of regions exhibiting these features plus H3K27ac.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Substantial subsets of microglia-specific genes exhibit altered expression in neurodegenerative and behavioral diseases and are associated with non-coding risk variants.

    “Substantial subsets of these genes exhibit altered expression in neurodegenerative and behavioral diseases and are associated with non-coding risk variants.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Most treatment conditions produced some effect on gene expression, but none resulted in preservation of the ex vivo molecular phenotype.

    “Although most treatment conditions produced some effect on gene expression, none resulted in preservation of the ex vivo molecular phenotype (Fig. S16).”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    We observed substantial individual variation in genes linked to disease risk.

    “Although we also observed substantial individual variation in genes linked to disease risk”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Findingnone given

    It has not yet been possible to maintain primary human microglia in a serum-free environment.

    “It has not yet been possible to maintain primary human microglia in a serum-free environment.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    At a 2-fold cutoff, 2,263 genes were upregulated in vitro and 3,702 genes were downregulated at an FDR of 0.05.

    “At a 2-fold cutoff, 2,263 genes were upregulated in vitro and 3,702 genes were downregulated at a FDR of 0.05.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    A similar proportion (30%) of genes associated with Parkinson's disease displayed more than 2-fold reduction in expression in vitro, whereas more limited changes for genes associated with multiple sclerosis and schizophrenia were observed.

    “A similar proportion (30%) of genes associated with PD also displayed such reduction in vitro, whereas more limited changes for genes associated with MS and Scz were observed (Fig. S12).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    A paired analysis of samples for which both ex vivo and 7-day in vitro microglia populations were obtained revealed more than 300 genes induced greater than 10-fold and more than 700 genes repressed more than 10-fold in vitro at an FDR of 0.05.

    “A paired analysis of samples for which both ex vivo and 7-day in vitro microglia populations were obtained revealed more than 300 genes induced greater than 10-fold and more than 700 genes that were repressed more than 10-fold in vitro (FDR 0.05).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    424 of the 740 super-enhancers defined ex vivo were lost and 541 new super-enhancers were observed in vitro.

    “Extending this analysis, 424 of the 740 SEs defined ex vivo were lost and 541 new SEs were observed (Fig. 5E).”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Microglia are the resident macrophage population of the central nervous system that perform functions required for typical development, homeostasis, plasticity, immunity and repair.

    “Microglia are the resident macrophage population of the central nervous system (CNS) that perform functions required for typical development, as well as homeostasis, plasticity, immunity and repair (1–5).”
    Quote in the paperNot a substantial claim0 of 5 sources checked
    • cites [1] Rivest S Regulation of innate immune responses in the brain Nat Rev Immunol 9 429 439 2009 19461673 source
    • cites [2] Katsumoto A Lu H Miranda AS Ransohoff RM Ontogeny and functions of central nervous system macrophages J Immunol 193 2615 2621 2014 25193935 PMC4157312 source
    • cites [3] Shemer A Erny D Jung S Prinz M Microglia Plasticity During Health and Disease: An Immunological Perspective Trends Immunol 36 614 624 2015 26431939 source
    • cites [4] Schafer DP Stevens B Microglia Function in Central Nervous System Development and Plasticity Cold Spring Harb Perspect Biol 7 a020545 2015 26187728 PMC4588063 source

      Not checked in the free run.

    • cites [5] Casano AM Peri F Microglia: multitasking specialists of the brain Dev Cell 32 469 477 2015 25710533 source

  • May combine two claims.

    Interpretationown data

    The second most enriched motif was assigned to CTCF; the motif was nearly a perfect match for the CTCF consensus recognition site, and CTCF was the only transcription factor expressed in microglia known to recognize this motif.

    “The assignment of the second most enriched motif to CTCF was unexpected because CTCF is ubiquitously expressed and is thought to primarily play roles in the organization of broad domains of chromatin architecture. However, the identified motif was nearly a perfect match for the CTCF consensus recognition site, and CTCF was the only transcription factor expressed in microglia known to recognize”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    Within cell-specific enhancers, DNA sequences provide information about the identities of key lineage-determining transcription factors and the activity states of signaling pathways that control the functions of signal-dependent transcription factors.

    “Within cell-specific enhancers, DNA sequences provide information about the identities of key LDTFs and the activity states of signaling pathways that control the functions of SDTFs (31, 33–35).”
    Quote in the paperSubstantial claim0 of 4 sources checked
    • cites [31] Heinz S Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities Molecular cell 38 576 589 2010 20513432 PMC2898526 source

      Not checked in the free run.

    • cites [33] Kaikkonen MU Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription Molecular cell 51 310 325 2013 23932714 PMC3779836 source

      Not checked in the free run.

    • cites [34] C. Roadmap Epigenomics et al Integrative analysis of 111 reference human epigenomes Nature 518 317 330 2015 25693563 PMC4530010 source

      Not checked in the free run.

    • cites [35] Romanoski CE Glass CK Stunnenberg HG Wilson L Almouzni G Epigenomics: Roadmap for regulation Nature 518 314 316 2015 25693562 source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Studies in mice indicate that microglia are derived from yolk sac progenitor cells that populate the brain early in development.

    “Studies in mice indicate that microglia are derived from yolk sac progenitor cells that populate the brain early in development (18, 19).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [18] Ginhoux F Fate mapping analysis reveals that adult microglia derive from primitive macrophages Science 330 841 845 2010 20966214 PMC3719181 source

      Not checked in the free run.

    • cites [19] Schulz C A lineage of myeloid cells independent of Myb and hematopoietic stem cells Science 336 86 90 2012 22442384 source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The locations and sequence content of enhancers provide insights into how non-coding genetic variation may affect gene expression and cellular phenotypes.

    “Furthermore, the locations and sequence content of enhancers provide insights into how non-coding genetic variation may affect gene expression and cellular phenotypes (32, 36–38).”
    Quote in the paperNot a substantial claim0 of 4 sources checked
    • cites [32] Heinz S Effect of natural genetic variation on enhancer selection and function Nature 503 487 492 2013 24121437 PMC3994126 source

      Not checked in the free run.

    • cites [36] Kasowski M Extensive variation in chromatin states across humans Science 342 750 752 2013 24136358 PMC4075767 source

      Not checked in the free run.

    • cites [37] McVicker G Identification of genetic variants that affect histone modifications in human cells Science 342 747 749 2013 24136359 PMC3947669 source
    • cites [38] Kilpinen H Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription Science 342 744 747 2013 24136355 PMC5502466 source

  • Classified as probably not a substantial claim.

    Premisecitation

    Dysregulation of microglia functions contributes to the pathogenesis of neurodegenerative diseases including Alzheimer's disease, Parkinson's disease and Huntington's disease.

    “Dysregulation of microglia functions contribute to the pathogenesis of neurodegenerative diseases, including Alzheimer’s disease (AD) (6–8), Parkinson’s disease (PD) (9–12) and Huntington’s disease (HD) (13–15).”
    Quote in the paperSubstantial claim0 of 10 sources checked
    • cites [6] Malm TM Jay TR Landreth GE The evolving biology of microglia in Alzheimer's disease Neurotherapeutics 12 81 93 2015 25404051 PMC4322081 source
    • cites [7] Derecki NC Katzmarski N Kipnis J Meyer-Luehmann M Microglia as a critical player in both developmental and late-life CNS pathologies Acta Neuropathol 128 333 345 2014 25056803 PMC4131160 source
    • cites [8] Mosher KI Wyss-Coray T Microglial dysfunction in brain aging and Alzheimer's disease Biochem Pharmacol 88 594 604 2014 24445162 PMC3972294 source

      Not checked in the free run.

    • cites [9] Hirsch EC Vyas S Hunot S Neuroinflammation in Parkinson's disease Parkinsonism Relat Disord 18 Suppl 1 S210 212 2012 22166438 source
    • cites [10] Croisier E Moran LB Dexter DT Pearce RK Graeber MB Microglial inflammation in the parkinsonian substantia nigra: relationship to alpha-synuclein deposition J Neuroinflammation 2 14 2005 15935098 PMC1177985 source

      Not checked in the free run.

    • cites [11] Collins LM Toulouse A Connor TJ Nolan YM Contributions of central and systemic inflammation to the pathophysiology of Parkinson's disease Neuropharmacology 62 2154 2168 2012 22361232 source
    • cites [12] Saijo K A Nurr1/CoREST pathway in microglia and astrocytes protects dopaminergic neurons from inflammation-induced death Cell 137 47 59 2009 19345186 PMC2754279 source
    • cites [13] Crotti A Mutant Huntingtin promotes autonomous microglia activation via myeloid lineage-determining factors Nat Neurosci 2014 PMC4113004 24584051 source

      Not checked in the free run.

    • cites [14] Politis M Microglial activation in regions related to cognitive function predicts disease onset in Huntington's disease: a multimodal imaging study Hum Brain Mapp 32 258 270 2011 21229614 PMC6870088 source
    • cites [15] Tai YF Microglial activation in presymptomatic Huntington's disease gene carriers Brain 130 1759 1766 2007 17400599 source

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    The variance in gene expression noted in these samples likely overestimates the variance in the isolation of microglia and implies a high degree of precision in the RNA-Seq data set.

    “On the basis of these observations, the variance in gene expression noted in these samples likely overestimates the variance in the isolation of microglia and implies a high degree of precision in the RNA-Seq data set.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    Common super-enhancers are associated with genes that play essential roles in the development and function of virtually all macrophages, whereas mouse microglia-specific super-enhancers are associated with genes known to play restricted or selected roles in this cell type.

    “Common SEs were associated with genes that are known to play essential roles in the development and function of virtually all macrophages whereas mouse microglia-specific SEs were associated with genes known to play restricted or selected roles in this cell type (25).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [25] Gosselin D Environment drives selection and function of enhancers controlling tissue-specific macrophage identities Cell 159 1327 1340 2014 25480297 PMC4364385 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Microglia may play roles in neurodevelopmental and psychiatric diseases such as autism, schizophrenia and depression.

    “In addition, microglia may play roles in neurodevelopmental and psychiatric diseases such as autism, schizophrenia (Scz) and depression (16, 17).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [16] Bilimoria PM Stevens B Microglia function during brain development: New insights from animal models Brain Res 2014 25463024 source
    • cites [17] Frick LR Williams K Pittenger C Microglial dysregulation in psychiatric disease Clin Dev Immunol 2013 608654 2013 23690824 PMC3652125 source

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Interpretationcitation

    rs6733839 is a non-coding risk allele for Alzheimer's disease that lies within an enhancer-like region approximately 25 kb upstream of the BIN1 transcriptional start site, suggesting regulatory function.

    “rs6733839 is a non-coding risk allele for AD (59) that lies within an enhancer-like region approximately 25 kb upstream of the BIN1 transcriptional start site, suggesting regulatory function.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [59] Lambert JC Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease Nature genetics 45 1452 1458 2013 24162737 PMC3896259 source

      Not checked in the free run.

  • May combine two claims.

    Study design and conductnone given

    Isolated human microglia exhibited a high degree of viability and RNA integrity.

    “Isolated microglia exhibited a high degree of viability and RNA integrity.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing).

    Study design and conductreasoning

    More individuals will be required to power analyses linking genetic variation to gene expression.

    “more individuals will be required to power analyses linking genetic variation to gene expression.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    Transcriptomic analysis of mouse microglia transferred to a tissue culture environment for 7 days documented significant changes in expression of hundreds of genes, with a preferential reduction in expression of microglia-specific genes.

    “Transcriptomic analysis of mouse microglia transferred to a tissue culture environment for 7 days documented significant changes in expression of hundreds of genes, with a preferential reduction in expression of microglia-specific genes (25).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [25] Gosselin D Environment drives selection and function of enhancers controlling tissue-specific macrophage identities Cell 159 1327 1340 2014 25480297 PMC4364385 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing).

    Interpretationreasoning

    More complex culture conditions, such as co-culture with neurons and astrocytes in three-dimensional or organoid contexts, will be required to more precisely model the in vivo phenotype.

    “It is likely that more complex culture conditions, such as co-culture with neurons and astrocytes in three-dimensional or organoid contexts, will be required to more precisely model the in vivo phenotype.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationreasoning

    As a small number of transcription factors thought to play important roles in microglia are divergently expressed, such as CIITA and RUNX2 proteins, there is also the potential for significant trans effects at the subsets of genes regulated by these factors.

    “However, as a small number of transcription factors thought to play important roles in microglia are divergently expressed, such as CIITA and RUNX2 proteins, there is also the potential for significant trans effects at the subsets of genes regulated by these factors.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationown data

    Collectively, these findings provide evidence that the transcriptional mechanisms that control gene expression are largely conserved between human and mouse microglia and that differences in gene expression are primarily driven by species-specific organization of cis regulatory elements at target genes.

    “Collectively, these findings provide evidence that the transcriptional mechanisms that control gene expression are largely conserved between human and mouse microglia and that differences in gene expression are primarily driven by species-specific organization of cis regulatory elements at target genes.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Study design and conductown data

    Cultured microglia remained positive for Iba1 staining, whereas no expression of markers for astrocytes or neurons was observed, indicating that changes in RNA expression were not due to contaminating cells.

    “Cultured microglia remained positive for Iba1 staining, whereas no expression of markers for astrocytes or neurons was observed, indicating that changes in RNA expression were not due to contaminating cells (Fig. S13A).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    The frequency distribution of many of these motifs is consistent with the corresponding transcription factors forming ternary complexes with PU.1 or functioning as collaborative binding partners.

    “The frequency distribution of many of these motifs is consistent with the corresponding transcription factors forming ternary complexes with PU.1 (e.g., the IRF motif, Fig. S10C) or functioning as collaborative binding partners (e.g., CTCF, AP-1 and RUNX motifs, Fig. S10C).”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: Motif enrichment in open chromatin indicates binding and activity of the corresponding transcription factors.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Recent studies have derived microglia-like cells from human induced pluripotent stem cells (iPSCs) in a defined media that more closely resembles cerebrospinal fluid.

    “Recent studies have derived microglia like cells from human induced pluripotent stem cells (iPSCs) in a defined media that more closely resembles cerebrospinal fluid (65).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [65] Muffat J Efficient derivation of microglia-like cells from human pluripotent stem cells Nat Med 22 1358 1367 2016 27668937 PMC5101156 source

      Not checked in the free run.

51 of 51

  • The paper relies on this without support.

    Human microglia isolated from surgically resected brain tissue of patients with epilepsy, brain tumors, or acute ischemic events are representative of normal human microglia.

    “Microglia were isolated from brain tissue resected for treatment of epilepsy, brain tumors or acute ischemic events in 19 individuals.”
    “As judged by neuropathological diagnostic evaluation, none of the samples displayed evidence of pathological microgliosis (i.e. loss of tiled distribution, process retraction and enlarged cell bodies) despite the occasional presence of reactive cells (Fig. S1).”

  • The paper relies on this without support.

    The ex vivo isolation procedure, including Percoll gradient centrifugation and FACS purification, does not substantially alter the microglial transcriptome.

    “A microglia-rich cell fraction was isolated by Percoll gradient centrifugation and further purified by FACS, with final gating on live-CD11b+CD45LowCD64+CX3CR1High single cells (Fig. S2A).”
    “On the basis of these observations, the variance in gene expression noted in these samples likely overestimates the variance in the isolation of microglia and implies a high degree of precision in the RNA-Seq data set.”

  • The paper relies on this without support.

    Motif enrichment in open chromatin indicates binding and activity of the corresponding transcription factors.

    “De novo motif analysis of ATAC-seq peaks associated with H3K4me2 was performed to identify the most highly enriched transcription factor recognition motifs associated with poised or active chromatin.”
    “The frequency distribution of many of these motifs is consistent with the corresponding transcription factors forming ternary complexes with PU.1 (e.g., the IRF motif, Fig. S10C) or functioning as collaborative binding partners (e.g., CTCF, AP-1 and RUNX motifs, Fig. S10C).”

  • The paper relies on this without support.

    Current efforts to reprogram various starting cell populations to microglia-like cells largely achieve an in vitro phenotype.

    “Importantly, current efforts to reprogram various starting cell populations to microglia-like cells largely achieve an in vitro phenotype.”
4 of 4

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • ATAC-seq and H3K27ac profiles from PU.1 nuclei matched closely with profiles previously reported for ex vivo microglia.

    “ATAC-seq and H3K27ac ChIP-seq profiles generated from PU.1 nuclei were highly correlated with those previously defined in ex vivo microglia”

    From Brain cell type–specific enhancer–promoter interactome maps and disease <b>-</b> risk association (2019) · cites this paper as [14]

    The “Enhancer landscape of human microglia” section reports that ATAC-seq and ChIP-seq data, including H3K27ac, were highly correlated across human individuals and mouse biological replicates. It does not report a comparison between profiles generated from PU.1 nuclei and previously defined ex vivo microglia profiles; its PU.1 ChIP-seq experiments used microglia isolated from six individuals. (LLM, conf=0.85)

    Experimental — accuracy not yet measured

  • Recent transcriptome-wide studies of bulk ex vivo human microglia have consistently suggested that microglia change with age and have transcriptomes enriched for disease-related genes.

    “Recent transcriptome-wide studies of bulk ex vivo human microglia have consistently suggested that microglia change with age and have transcriptomes that are enriched for disease-related genes3–5.”

    From Single cell RNA sequencing of human microglia uncovers a subset associated with Alzheimer’s disease (2020) · cites this paper as [4]

    The Human microglia transcriptomes section reports that many disease-risk genes were preferentially expressed in microglia, supporting the disease-related enrichment claim. But it also says no strong gene-expression patterns related to age emerged; the Discussion describes age as having a relatively minor influence on the overall expression pattern. Thus this paper does not support the claim that its data suggested age-related transcriptomic change. (LLM, conf=0.88)

    Experimental — accuracy not yet measured

  • The microglial enhancer at BIN1 is PLAC-linked to the BIN1 promoter, binds PU.1, and carries rs6733839, an AD-risk variant with the second-highest score after APOE that fine mapping marked as causal.

    “The BIN1 microglia-specific enhancer is PLAC-linked to the BIN1 promoter (Fig. 4A), binds to PU.1 (14) and contains the AD-risk variant rs6733839, which has the second highest AD-risk score after APOE and was fine-mapped as a casual variant (Fig. 3A).”

    From Brain cell type–specific enhancer–promoter interactome maps and disease <b>-</b> risk association (2019) · cites this paper as [14]

  • Microglia are highly sensitive to perturbations in their environment.

    “As the tissue-resident macrophages of the brain, microglia are highly sensitive to perturbations in their environment13,14.”

    From Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain (2022) · cites this paper as [13]

  • Previous reports comparing cell isolation protocols or cells postisolation have often focused on aspects such as cell viability and/or yield over whether the isolated cells are truly reflective of their in vivo state.

    “Previous reports comparing cell isolation protocols or cells postisolation have often focused on aspects such as cell viability and/or yield4,62 over whether the isolated cells are truly reflective of their in vivo state13,14.”

    From Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain (2022) · cites this paper as [13]

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Authors
Gosselin, D., Skola, D., Coufal, N. G., Holtman, I. R., Schlachetzki, J. C. M., Sajti, E., Jaeger, B. N., O’Connor, C., Fitzpatrick, C., Pasillas, M. P., Pena, M., Adair, A., Gonda, D. D., Levy, M. L., Ransohoff, R. M., Gage, F. H., & Glass, C. K.
Affiliations
  • University of California San Diego (US)
  • Salk Institute for Biological Studies (US)
  • University Medical Center Groningen (NL)
  • Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA.
  • Biogen (United States) (US)
Corresponding author
  • Gosselin, David
  • Skola, Dylan
  • Coufal, Nicole G.
  • Holtman, Inge R.
  • Schlachetzki, Johannes C. M.
  • Glass, Christopher K.
ORCID
Venue
Science
Publisher
American Association for the Advancement of Science (AAAS)
Published
2017-06-23
Volume
356
Issue
6344
ISSN
  • 0036-8075 (ISSN-L)
  • 1095-9203
DOI
10.1126/science.aal3222
PMC
PMC5858585
OpenAlex
W2619332462
Semantic Scholar
7b09a8c02f1443df2339a07b52615cddd29b752a
Cited by
1,220
References
77
Citations by year
2026: 131 · 2025: 123 · 2024: 175 · 2023: 112 · 2022: 138 · 2021: 142 · 2020: 142 · 2019: 120 · 2018: 107 · 2017: 29
FWCI
53.50
Type
journal article
Language
en
Open access
Locations
  • Science (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • eScholarship (California Digital Library) (submittedVersion)
  • University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion)
Funders
NIH (NS096170, GM085764)
Topics
  • Life Sciences › Neuroscience › Neurology › Neuroinflammation and Neurodegeneration Mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
  • Health Sciences › Medicine › Pathology and Forensic Medicine › Multiple Sclerosis Research Studies
Keywords
human microglia, transcriptional regulatory networks, epigenetic landscape, neurodegenerative diseases, behavioral disorders, non-coding variants, transcriptome, macrophage migration, CNS homeostasis
MeSH terms
Animals, Brain Neoplasms, Cells, Cultured, Environment, Epilepsy, Female, Gene Expression Regulation, Humans, Male, Mice, Inbred C57BL, Microglia, Gene Expression Profiling, Mice, Gene Regulatory Networks

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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-11-06.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-11-06.

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