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Cited by 9Neuroinflammation and Neurodegeneration MechanismsMicroRNA in disease regulationNeurogenesis and neuroplasticity mechanisms

Mouse microglia express unique miRNA-mRNA networks to facilitate age-specific functions in the developing central nervous system

Open access
Walsh, Alexander D., Stone, Sarrabeth, Freytag, Saskia, Aprico, Andrea, Kilpatrick, Trevor J., Ansell, Brendan R. E., Binder, Michele D.·2023·Communications Biology
DOI 10.1038/s42003-023-04926-8PMC PMC10203306
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Abstract

Microglia regulate multiple processes in the central nervous system, exhibiting a considerable level of cellular plasticity which is facilitated by an equally dynamic transcriptional environment. While many gene networks that regulate microglial functions have been characterised, the influence of epigenetic regulators such as small non-coding microRNAs (miRNAs) is less well defined. We have sequenced the miRNAome and mRNAome of mouse microglia during brain development and adult homeostasis, identifying unique profiles of known and novel miRNAs. Microglia express both a consistently enriched miRNA signature as well as temporally distinctive subsets of miRNAs. We generated robust miRNA-mRNA networks related to fundamental developmental processes, in addition to networks associated with immune function and dysregulated disease states. There was no apparent influence of sex on miRNA expression. This study reveals a unique developmental trajectory of miRNA expression in microglia during critical stages of CNS development, establishing miRNAs as important modulators of microglial phenotype.

Verified 2026-11-06 · 1 reference not checked yet

AI snapshot

Written from the paper’s full text.

TL;DR

This study profiles miRNA and mRNA in mouse microglia at postnatal days 6 and 15 and 8 weeks, identifying a core microglial miRNA signature plus age-specific subsets and miRNA–mRNA networks linked to neurodevelopment and immune pathways. It reports no sex-specific miRNA differences and only six sex-linked mRNA differences, and highlights novel candidate chr3_29427.

Key findings

  • Across all mice, 1073 miRNAs were expressed; 213 miRNAs were upregulated in microglia versus CD45−ve bulk cells, and 299 miRNAs were enriched in at least one age group, with 84 enriched at all ages and 129 enriched in a single age group (68 of these adult-specific).
  • Microglial mRNA sequencing identified 15,660 robustly expressed transcripts; integrated networks contained 24 miRNAs and 234 target mRNAs, enriched for cell cycle, neurogenesis, axon guidance, myelination, p53, Hippo, PI3K-Akt and JAK-STAT pathways, including miR-3473b–Padi2 and miR-29a-3p–Hmgcr interactions.
  • Pairwise age comparisons found 185 differentially expressed miRNAs, with the largest difference between P6 and 8-week microglia; 14 miRNAs were sequentially upregulated and 37 sequentially downregulated from P6 to adult.
  • Of 54 novel miRNA sequences, 24 were enriched in microglia; the top novel candidate chr3_29427 had 14 predicted interactions, including Birc5 and Cdca5. No miRNAs and only six mRNAs were differentially expressed between male and female microglia, all six mRNAs X- or Y-linked.

Methods

  • Microglia were isolated by CD45+ve immunopanning from whole brains of male and female C57Bl/6 mice at P6, P15 and 8 weeks, alongside CD45−ve bulk CNS cells; CIBERSORTx estimated an average of 2.8% non-microglial contamination per sample.
  • miRNA and mRNA libraries were sequenced on MGISEQ2000-RS; reads were processed with miRDeep2, STAR and featureCounts, and differential expression used limma/edgeR with TMM normalisation and TREAT at a minimum ±2-fold change and FDR < 0.05.
  • miRNA–mRNA networks were built from strongly negative Pearson correlations (R² > 0.8, FDR < 0.05), filtered by multiMiR experimental evidence or, for novel miRNAs, RNAhybrid prediction (minimum free energy <25 kcal/mol, P < 0.05), followed by KEGG/GO enrichment and qPCR validation.

Limitations

  • The paper states that the miRNA–mRNA networks are based on in silico correlations and may not represent genuine cellular interactions; in vitro and in vivo experiments are needed to support them.
  • The paper notes that microglial isolation methods can alter activation status and gene expression, that whole-brain sampling may dilute region-specific sexually dimorphic signatures, and that sex effects may emerge after immune challenge or at older ages beyond the 8-week endpoint.
  • Evident from the text: the CD45−ve comparator is a mixed CNS population rather than purified cell types, novel miRNA targets are prediction-based without experimental validation, and some qPCR validation used small groups (n = 3).

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

Integrity signals

Registry

Crossref · 10.1038/s42003-023-04926-8

Cites

91 of 92 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

7 of 40 cited sources checked · 4 supported · 0 flagged · accuracy not yet measured

  • Premisecitation

    A comprehensive developmental study by Hanamsagar et al. (2017) observed that transcriptionally, male and female microglia are quite similar until early adulthood (P60).

    “A comprehensive developmental study by Hanamsagar et al. (2017) observed that transcriptionally, male and female microglia are quite similar until early adulthood (P60).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Hanamsagar et al. (2017) source
  • Premisecitation

    Other reported transcriptional differences studies come mainly from adult mice (12 weeks and older).

    “Other reported transcriptional differences studies come mainly from adult mice, (12 weeks and older) reinforcing the idea that the effects of sex are more prevalent with age34,68,70.”
    Quote in the paperNot a substantial claim2 of 3 sources checked
    • cites [34] Villa, A. et al. Sex-specific features of microglia from adult mice. Cell Rep. 23, 3501–3511 (2018). source
    • cites [68] Guneykaya, D. et al. Transcriptional and translational differences of microglia from male and female brains. Cell Rep. 24, 2773–2783.e6 (2018). source
    • cites [70] Thion, M. S. et al. Microbiome influences prenatal and adult microglia in a sex-specific manner. Cell 172, 500–516.e16 (2018). source

      The Results section, “Adult Microglia Acquire Sexually Dimorphic Transcriptomic Signatures” (page unavailable), reports greater sex-linked transcriptional differences in adult than embryonic mouse microglia. It does not establish that other studies mainly used mice aged 12 weeks or older; the Methods section instead describes an antibiotic-treatment group studied between 7 and 8 weeks of age. (LLM, conf=0.83)

      Experimental — accuracy not yet measured
  • Findingown data

    The six mRNAs differentially expressed between sexes across all age groups were all X- or Y-linked.

    “six mRNAs which were differentially expressed between sexes were observed across all age groups, all of which were X- or Y-linked”
    Quote in the paperNot a substantial claim
  • Findingown data

    The largest difference in miRNA expression was observed between P6 and 8-week microglia.

    “with the largest difference observed between P6 and 8-week microglia”
    Quote in the paperNot a substantial claim
  • Findingown data

    A total of 84 miRNAs were enriched in microglia at all ages compared to CD45−ve bulk cells.

    “Two hundred and ninety-nine miRNAs were defined as enriched in at least one age group, with 84 enriched at all ages, indicative of a common signature of microglial miRNA expression”
    • Also stated in: § Discussion · plain
      “84 miRNAs were observed to be significantly enriched in microglia at all ages compared to other CNS cell types.”
    Quote in the paperSubstantial claim
  • Classified as probably not a substantial claim. 26
  • May combine two claims. 22
  • The quote only partly states this claim. 1

  • Classified as probably not a substantial claim.

    Premisecitation

    Previous reports indicate sexual dimorphism in microglial genetics.

    “based on previous reports of sexual dimorphism in microglial genetics34–36”
    Quote in the paperSubstantial claim2 of 3 sources checked
    • cites [34] Villa, A. et al. Sex-specific features of microglia from adult mice. Cell Rep. 23, 3501–3511 (2018). source
    • cites [35] Kodama, L. et al. Microglial microRNAs mediate sex-specific responses to tau pathology. Nat. Neurosci. 23, 167–171 (2020). source
    • cites [36] Han, J., Fan, Y., Zhou, K., Blomgren, K. & Harris, R. A. Uncovering sex differences of rodent microglia. J. Neuroinflamm 18, 74 (2021). source

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

    Premisecitation

    Innate differences between male and female microglia are exacerbated during immune challenge and stress and are suggested to be a prominent influence in observed sex biases of neurological disease.

    “Importantly, these innate differences are exacerbated during immune challenge and stress and are suggested to be a prominent influence in observed sex biases of neurological disease34,36,68,69.”
    Quote in the paperNot a substantial claim2 of 3 sources checked
    • cites [34] Villa, A. et al. Sex-specific features of microglia from adult mice. Cell Rep. 23, 3501–3511 (2018). source

      The Abstract and Discussion describe intrinsic sex-specific microglial features and suggest a role in sex biases in brain disease. The Discussion also suggests that male microglia have an enhanced capacity to react to inflammatory stimuli, and the Results show different effects of female and male microglia after ischemia. The paper does not establish that sex differences are exacerbated during immune challenge and stress generally. (LLM, conf=0.84)

      Experimental — accuracy not yet measured
    • cites [36] Han, J., Fan, Y., Zhou, K., Blomgren, K. & Harris, R. A. Uncovering sex differences of rodent microglia. J. Neuroinflamm 18, 74 (2021). source

      In “Sex differences of microglia in response to exogenous stimuli” (page unavailable), the review reports a sex difference after inflammatory stimulation where unstimulated microglia had similar levels, and describes sex-specific responses to stress. It does not establish that stress exacerbates pre-existing differences. The Conclusions suggest microglial differences may contribute to sex biases in neurological disease, but describe them as a possible partial influence rather than a prominent one. (LLM, conf=0.82)

      Experimental — accuracy not yet measured
    • cites [68] Guneykaya, D. et al. Transcriptional and translational differences of microglia from male and female brains. Cell Rep. 24, 2773–2783.e6 (2018). source

  • May combine two claims.

    Findingown data

    chr3_29427 was strongly enriched across all ages and observed to increase in expression with age.

    “was strongly enriched across all ages and observed to increase with expression with age”
    Quote in the paperNot a substantial claim

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

    Findingown data

    miR-1895, miR-511-3p and miR-6983-5p were also highly enriched in microglia but have less well-defined functions.

    “Also identified as highly enriched were miR-1895, miR-511-3p and miR-6983-5p, which have less well-defined functions in microglia”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Extended qPCR validated temporal expression patterns: miR-21a-3p enriched across all ages; miR-29a-3p, miR-29b-3p and miR-3473b enriched specifically at P6 and P15; miR-10a-5p increased throughout development.

    “Extended qPCR analysis also validated specific patterns of observed temporal miRNA expression, including examples of candidates enriched across all ages (miR-21a-3p), enriched specifically at P6 and P15 (miR-29a-3p, miR-29b-3p, miR-3473b) and exhibiting increased expression (and enrichment) throughout development (miR-10a-5p)”
    Quote in the paperSubstantial claim

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

    Findingown data

    Overall, 1073 unique miRNAs were expressed across all mice (minimum CPM of 1 in at least 5 samples).

    “Overall, 1073 unique miRNAs were expressed across all mice, with a minimum count per million (CPM) of 1 in at least 5 samples.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Fourteen miRNAs were sequentially upregulated and 37 miRNAs were sequentially downregulated between P6 and adult microglia.

    “This analysis identified 14 miRNAs that were sequentially upregulated, and 37 miRNAs that were sequentially downregulated between P6 and adult microglia”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Fourteen miRNA-mRNA interactions passed the criteria for novel miRNA networks, all of which included chr3_29427.

    “Fourteen miRNA–mRNA interactions passed these criteria, all of which included the top novel miRNA candidate chr3_29427”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Specific miRNA targets of myelination genes included Padi2 (regulated by miR-3473b) and Hmgcr (regulated by miR-29a-3p).

    “Specific miRNA targets of myelination genes included Padi2 (regulated by miR-3473b) and Hmgcr (regulated miR-29a-3p).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    A total of 129 miRNAs were enriched in microglia in a single age group, with 68 specific to adult cells.

    “Conversely, 129 miRNAs were enriched in a single age group, with 68 of these specific to adult cells”
    • Also stated in: § Discussion · plain
      “our study identified 129 miRNAs that were specifically enriched in a single age group.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    qPCR validated strong enrichment of chr3_29427 but did not validate increasing expression with age.

    “We validated its strong enrichment (but not increasing expression with age) by qPCR”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Our study identified 6 differentially expressed mRNA transcripts across development, all of which are located on sex chromosomes and specifically differentiated in adult mice.

    “Conversely, our study identified 6 differentially expressed mRNA transcripts across development, all of which are located on sex chromosomes and specifically differentiated in adult mice.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The miRNAome is composed of both a relatively unchanging subset of highly enriched miRNAs and subsets of miRNAs that exhibit age-dependent expression profiles.

    “This miRNAome is composed of both a relatively unchanging subset of highly enriched miRNAs and subsets of miRNAs that exhibit age-dependent expression profiles.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    miR-10a-5p is uniquely enriched in adult mice and is predicted to target Mcm5.

    “miR-10a-5p, is uniquely enriched in adult mice and is predicted to target and therefore potentially inhibit Mcm5”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Study design and conductown data

    Microglial samples were highly pure, with qPCR showing high expression of Tmem119 and Cx3cr1 in purified CD45+ve cells.

    “qPCR expression analyses demonstrated that microglial-specific markers such as Tmem119 and Cx3cr1 were highly expressed by purified CD45+ve cells”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Study design and conductown data

    The study constructed miRNA-mRNA networks using stringent correlation thresholds and experimental validation of miRNA-mRNA interactions.

    “miRNA–mRNA networks in this study were constructed using both stringent correlation thresholds and experimental validation of miRNA–mRNA interactions.”
    Quote in the paperSubstantial claim

  • The quote only partly states this claim.

    Interpretationown data

    The miRNA-mRNA networks implicate both previously annotated and novel miRNAs in the regulation of key neurodevelopmental processes, including neurogenesis and myelination.

    “We have constructed a miRNA–mRNA network for microglia, which implicates both previously annotated and novel miRNAs in the regulation of key neurodevelopmental processes, including neurogenesis and myelination.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim. May combine two claims.

    Study design and conductown data

    miRNA-mRNA pairs were selected if strongly negatively correlated (R2 > 0.8, FDR < 0.05) and filtered for experimental evidence of interaction via multiMiR.

    “we selected putative miRNA–mRNA pairs that were strongly negatively correlated (R2 > 0.8, FDR < 0.05). miRNA–mRNA pairs were further filtered for experimental evidence of interaction as reported in the existing literature and relevant databases (collated by multiMiR)”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites multiMiR

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • May combine two claims.

    Premisecitation

    Mcm5 is an established regulator of microglial cell cycle that is strongly expressed during embryonic and early postnatal microglial development.

    “Mcm5, an established regulator of microglial cell cycle that is strongly expressed during embryonic and early postnatal microglial development”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [21] Matcovitch-Natan, O. et al. Microglia development follows a stepwise program to regulate brain homeostasis. Science 353, aad8670 (2016). source
    • cites [38] Bennett, M. L. et al. New tools for studying microglia in the mouse and human CNS. Proc. Natl Acad. Sci. USA 113, E1738–E1746 (2016). source

      Not checked in the free run.

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

    Study design and conductown data

    One sample did not pass RNA quality control and was excluded from library preparation.

    “One sample did not pass RNA quality control and so was excluded from library preparation.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Study design and conductown data

    The study used RNAhybrid to predict novel miRNA interactions, filtering for minimum free fold energy <25 kcal/mol (P < 0.05).

    “we calculated predicted interactions using the hybridisation tool RNAhybrid, filtering for those that were predicted to bind with minimum free fold energy <25 kcal/mol (P < 0.05)”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [33] Krüger, J. & Rehmsmeier, M. RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Res. 34, W451–W454 (2006). source

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

    Premisenone given

    PADI2 regulates citrullination of myelin basic protein (MBP), which alters myelin ultrastructure.

    “PADI2 regulates citrullination of myelin basic protein (MBP), which alters myelin ultrastructure.”
    Quote in the paperNot a substantial claim

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

    Study design and conductcitation

    Mouse cohorts in this study were balanced for sex.

    “Mouse cohorts in this study were balanced for sex based on previous reports of sexual dimorphism in microglial genetics34–36.”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites [34] Villa, A. et al. Sex-specific features of microglia from adult mice. Cell Rep. 23, 3501–3511 (2018). source

      Not checked in the free run.

    • cites [35] Kodama, L. et al. Microglial microRNAs mediate sex-specific responses to tau pathology. Nat. Neurosci. 23, 167–171 (2020). source
    • cites [36] Han, J., Fan, Y., Zhou, K., Blomgren, K. & Harris, R. A. Uncovering sex differences of rodent microglia. J. Neuroinflamm 18, 74 (2021). source

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Study design and conductown data

    miRNA-mRNA interactions were screened for experimental evidence of interaction in any cellular system using multimiR.

    “To further validate significant negative correlations, miRNA–mRNA interactions were screened for experimental evidence of interaction in any cellular system using multimiR (ver 1.140, 10.18129/B9.bioc.multiMiR) with default settings.”
    Quote in the paperSubstantial claim

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

    Interpretationreasoning

    Dimorphism may be more prevalent post-activation, whether induced by isolation, immune challenge or in ageing-related neurodegeneration.

    “Specifically, dimorphism may be more prevalent post-activation, whether induced by isolation, immune challenge or in ageing-related neurodegeneration.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim. May combine two claims.

    Study design and conductcitation

    RNA-seq sample size was determined to match or exceed those of similar studies, such that comparisons between age groups were 12 vs 12 (matched for sex), and between tissue types were 36 vs 36 (correcting for animal, age and sex).

    “RNA-seq sample size was determined to match or exceed those of similar studies34,35, such that comparisons between age groups were 12 vs 12 (matched for sex), and between tissue types were 36 vs 36 (correcting for animal, age and sex).”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [34] Villa, A. et al. Sex-specific features of microglia from adult mice. Cell Rep. 23, 3501–3511 (2018). source

      Not checked in the free run.

    • cites [35] Kodama, L. et al. Microglial microRNAs mediate sex-specific responses to tau pathology. Nat. Neurosci. 23, 167–171 (2020). source

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

    Interpretationreasoning

    These predicted novel candidates may be critical regulators of unique microglial biology.

    “These predicted novel candidates may be critical regulators of unique microglial biology and warrant future functional validation in vitro and in vivo.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Study design and conductcitation

    All regression analyses were set up as mixed effects models including age, sex, and cell type (microglia or CD45−ve bulk) as fixed effects and mouse ID as a random effect.

    “All regression analyses were set up as mixed effects models including age, sex, and cell type (microglia or CD45−ve bulk) as fixed effects and mouse ID as a random effect73.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [73] Law, C. W. et al. A guide to creating design matrices for gene expression experiments. F1000research 9, 1444 (2020). source

      Not checked in the free run.

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

    Premisecitation

    Different methods of isolation (e.g., immunopanning, FACS, magnetic bead sorting) can differentially alter the activation status of microglia and hence gene expression, potentially contributing to differing reports of baseline sexual dimorphism in studies of microglia.

    “While an unavoidable caveat, it has been shown that different methods of isolation (ie. immunopanning, FACS, magnetic bead sorting) can differentially alter the activation status of microglia and hence gene expression, potentially contributing to differing reports of baseline sexual dimorphism in studies of microglia40.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [40] Eggen, B. J. L., Boddeke, E. W. G. M. & Kooistra, S. M. Regulation of microglia identity from an epigenetic and transcriptomic point of view. Neuroscience 405, 3–13 (2019). source

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

    Premisecitation

    PI3k-Akt and JAK-STAT signalling are central regulators of microglial mediated neuroinflammation.

    “This included PI3k-Akt and JAK-STAT signalling, central regulators of microglial mediated neuroinflammation63,64.”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [63] Yan, Z., Gibson, S. A., Buckley, J. A., Qin, H. & Benveniste, E. N. Role of the JAK/STAT signaling pathway in regulation of innate immunity in neuroinflammatory diseases. Clin. Immunol. 189, 4–13 (2018). source

      Not checked in the free run.

    • cites [64] Cianciulli, A. et al. Microglia mediated neuroinflammation: focus on PI3K modulation. Biomol 10, 137 (2020). source

      Not checked in the free run.

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

    Premisecitation

    miR-6983 is downregulated in oligodendrocytes during experimental autoimmune encephalomyelitis (EAE), an animal model of demyelination, and is associated with disrupted ferroptosis pathways that are implicated in demyelination and neurodegeneration.

    “miR-6983 is downregulated in oligodendrocytes during experimental autoimmune encephalomyelitis (EAE), an animal model of demyelination, and is associated with disrupted ferroptosis pathways that are implicated in demyelination and neurodegeneration65.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [65] Ma, Q., Matsunaga, A., Ho, B., Oksenberg, J. R. & Didonna, A. Oligodendrocyte-specific Argonaute profiling identifies microRNAs associated with experimental autoimmune encephalomyelitis. J. Neuroinflamm. 17, 297 (2020). source

  • Classified as probably not a substantial claim.

    Study design and conductown data

    The networks identified are based on in silico correlations, which may not necessarily represent genuine interactions in cells and tissues.

    “Furthermore, we acknowledge that the networks we have identified are based on in silico correlations, which may not necessarily represent genuine interactions in cells and tissues.”
    Quote in the paperSubstantial claim

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

    Premisecitation

    Aspects of sexual dimorphism in microglial gene expression are region-dependent.

    “In addition, aspects of sexual dimorphism in microglial gene expression are region-dependent36,68.”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [36] Han, J., Fan, Y., Zhou, K., Blomgren, K. & Harris, R. A. Uncovering sex differences of rodent microglia. J. Neuroinflamm 18, 74 (2021). source

      Not checked in the free run.

    • cites [68] Guneykaya, D. et al. Transcriptional and translational differences of microglia from male and female brains. Cell Rep. 24, 2773–2783.e6 (2018). source

  • Classified as probably not a substantial claim.

    Study design and conductnone given

    All groups contained an equal number of male and female mice to allow for the identification of any sex-specific miRNAs.

    “In addition, all groups contained an equal number of male and female mice to allow for the identification of any sex-specific miRNAs.”
    Quote in the paperSubstantial claim

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

    Premisecitation

    Microglial cells are dynamic and respond quickly to changes in their local environment.

    “Microglial cells are dynamic and respond quickly to changes in their local environment15.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [15] Gosselin, D. et al. Environment drives selection and function of enhancers controlling tissue-specific macrophage identities. Cell 159, 1327–1340 (2014). source

      Not checked in the free run.

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

    Study design and conductown data

    Based on multidimensional scaling (MDS) analysis, one mouse was identified as an outlier, and its miRNA/mRNA data was removed from downstream analysis.

    “Based on multidimensional scaling (MDS) analysis one mouse was identified as an outlier, and its miRNA/mRNA data was removed from downstream analysis.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    Knockdown of Dypls3 inhibits microglial phagocytosis and migration.

    “Knockdown of Dypls3 inhibits microglial phagocytosis and migration”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [58] Manivannan, J., Tay, S. S. W., Ling, E.-A. & Dheen, S. T. Dihydropyrimidinase-like 3 regulates the inflammatory response of activated microglia. Neuroscience 253, 40–54 (2013). source

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

    Premisecitation

    Transcriptomics studies have defined subsets of mRNAs and miRNAs that are differentially expressed between male and female microglia, in steady state and particularly following immune challenge in adult mice.

    “Transcriptomics studies have defined subsets of mRNAs and miRNAs that are differentially expressed between male and female microglia, in steady state and particularly following immune challenge in adult mice34,35,68–70.”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites [34] Villa, A. et al. Sex-specific features of microglia from adult mice. Cell Rep. 23, 3501–3511 (2018). source

      Not checked in the free run.

    • cites [35] Kodama, L. et al. Microglial microRNAs mediate sex-specific responses to tau pathology. Nat. Neurosci. 23, 167–171 (2020). source
    • cites [68] Guneykaya, D. et al. Transcriptional and translational differences of microglia from male and female brains. Cell Rep. 24, 2773–2783.e6 (2018). source

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

    Study design and conductnone given

    Samples with an RNA integrity score (RIN) greater than 7 were used for library construction.

    “Samples with an RNA integrity score (RIN) greater than 7 were used for library construction.”
    Quote in the paperNot a substantial claim

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

    Premisecitation

    Sex hormones influence the developmental trajectories of male and female microglia, manifesting in differential regional densities, morphology, phagocytic capacity and metabolic influx.

    “There is growing evidence to suggest that sex hormones influence the developmental trajectories of male and female microglia manifesting in differential regional densities, morphology, phagocytic capacity and metabolic influx67.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [67] Bordt, E. A., Ceasrine, A. M. & Bilbo, S. D. Microglia and sexual differentiation of the developing brain: a focus on ontogeny and intrinsic factors. Glia 68, 1085–1099 (2020). source

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

    Premisecitation

    BIRC5 has been previously characterised as highly expressed by proliferating microglia during development and in response to injury.

    “BIRC5 has been previously characterised as highly expressed by proliferating microglia during development and in response to injury66.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [66] Capuccini, B. et al. Transcriptomic profiling of microglia reveals signatures of cell activation and immune response, during experimental cerebral malaria. Sci. Rep. 6, 39258 (2016). source

  • May combine two claims.

    Premisecitation

    Functional and structural differences between male and female microglia have been consistently observed, but transcriptomic results are less congruent.

    “Interestingly, while functional and structural differences between male and female microglia have been consistently observed, transcriptomic results are less congruent67.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [67] Bordt, E. A., Ceasrine, A. M. & Bilbo, S. D. Microglia and sexual differentiation of the developing brain: a focus on ontogeny and intrinsic factors. Glia 68, 1085–1099 (2020). source
42 of 42

  • The paper relies on this without support.

    The timepoints P6, P15 and 8 weeks represent critical stages in CNS development in the mouse.

    “These timepoints represent critical stages in CNS development in the mouse.”

  • The paper relies on this without support.

    miRNAs are canonically negatively correlated with their mRNA targets.

    “Given that miRNAs are canonically negatively correlated with their mRNA targets”

  • The paper relies on this without support.

    CD45−ve bulk CNS cells are primarily comprised of neurons, oligodendrocytes and astrocytes.

    “the CD45−ve bulk CNS cells (primarily comprised of neurons, oligodendrocytes and astrocytes)”

  • The paper relies on this without support.

    miR-511-3p is encoded by and co-regulated with the CD206 gene and is associated with anti-inflammatory (M2-like) activation in tumour and lung associated macrophage populations.

    “miR-511-3p has been characterised in tumour and lung associated macrophage populations, encoded by and co-regulated with the CD206 gene, where it is associated with anti-inflammatory (M2-like) activation.”
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?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • Fig. 9 caption names the wrong comparison

    Minor

    The Fig. 9 caption says its unpaired tests compared microglia with CD45−ve bulk cells, whereas the methods say those tests compared male and female microglia.

  • Novel miRNA identifier changes in Fig. 8

    Minor

    The network and its predicted targets are attributed to chr3_29427, but the caption identifies the miRNA plotted against those targets as chr3_295427.

2 of 2

Cites

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Related

Authors
Walsh, A. D., Stone, S., Freytag, S., Aprico, A., Kilpatrick, T. J., Ansell, B. R. E., & Binder, M. D.
Affiliations
  • The University of Queensland (AU)
  • Florey Institute of Neuroscience and Mental Health (AU)
  • The University of Melbourne (AU)
Corresponding author
Binder, Michele D.
ORCID
Venue
Communications Biology
Publisher
Springer Science and Business Media LLC
Published
2023-05-22
Volume
6
Issue
1
Pages
555-555
ISSN
2399-3642 (ISSN-L)
DOI
10.1038/s42003-023-04926-8
PMC
PMC10203306
OpenAlex
W4377288917
Semantic Scholar
3dc544a1c2b30a6e4010c8dead8a3cff9b225101
Cited by
9
References
91
Citations by year
2026: 5 · 2025: 2 · 2024: 2
FWCI
1.00
Type
journal article
Language
en
Open access
Licence
Locations
  • Communications Biology (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Minerva Access (University of Melbourne) (submittedVersion, cc-by)
Funders
  • Strong
  • Australian Government
  • Multiple Sclerosis Australia (21-3-038, APP1175775, 21‐6‐008)
  • State Government of Victoria
  • Medical Research Council
  • National Health and Medical Research Council (1175775)
Topics
  • Life Sciences › Neuroscience › Neurology › Neuroinflammation and Neurodegeneration Mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › MicroRNA in disease regulation
  • Life Sciences › Neuroscience › Developmental Neuroscience › Neurogenesis and neuroplasticity mechanisms
Keywords
microglia, microRNA, miRNA-mRNA regulatory network, brain development, central nervous system development, miRNAome, microglial plasticity, microglial phenotype, epigenetic regulation
MeSH terms
Age Factors, Animals, Central Nervous System, RNA, Messenger, Microglia, MicroRNAs, Mice

About these checks

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.

Cited sources are checked by gpt-6-sol.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

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