PreprintCited by 9Neuroinflammation and Neurodegeneration MechanismsInflammasome and immune disordersAlzheimer's disease research and treatments

INPP5D/SHIP1 regulates inflammasome activation in human microglia

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Chou, Vicky, Fancher, Seeley B., Pearse, Richard V., Lee, Hyo, Lam, Matti, Seyfried, Nicholas T., Bennett, David A., De Jager, Phillip L. +2 more·2023·bioRxiv (Cold Spring Harbor Laboratory)

Abstract

Microglia and neuroinflammation are implicated in the development and progression of Alzheimer’s disease (AD). To better understand microglia-mediated processes in AD, we studied the function of INPP5D/SHIP1, a gene linked to AD through GWAS. Immunostaining and single nucleus RNA sequencing confirmed that INPP5D expression in the adult human brain is largely restricted to microglia. Examination of prefrontal cortex across a large cohort revealed reduced full length INPP5D protein levels in AD patient brains compared to cognitively normal controls. The functional consequences of reduced INPP5D activity were evaluated in human induced pluripotent stem cell derived microglia (iMGLs), using both pharmacological inhibition of the phosphatase activity of INPP5D and genetic reduction in copy number. Unbiased transcriptional and proteomic profiling of iMGLs suggested an upregulation of innate immune signaling pathways, lower levels of scavenger receptors, and altered inflammasome signaling with INPP5D reduction. INPP5D inhibition induced the secretion of IL-1ß and IL-18, further implicating inflammasome activation. Inflammasome activation was confirmed through visualization of inflammasome formation through ASC immunostaining in INPP5D-inhibited iMGLs, increased cleaved caspase-1 and through rescue of elevated IL-1ß and IL-18 with caspase-1 and NLRP3 inhibitors. This work implicates INPP5D as a regulator of inflammasome signaling in human microglia.

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Crossref · 10.1101/2023.02.25.530025

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  • iMGs with biallelic INPP5D loss-of-function alleles and microglia from AD brain tissue both show a reduction in RNA levels of NF-kB pathway genes.

    “For example, iMGs with biallelic INPP5D LOF alleles and microglia from AD brain tissue both show a reduction in RNA levels of NF-kB pathway genes.”

    From Microglial function, INPP5D/SHIP1 signaling, and NLRP3 inflammasome activation: implications for Alzheimer’s disease (2023) · cites this paper as [161]

    The section on chronic genetic reduction reports loss-of-function mutations in a single INPP5D allele, not biallelic loss. The section on acute inhibition reports upregulated NF-κB signaling in treated iMGLs, while the AD brain analysis reports reduced INPP5D protein rather than reduced NF-κB-pathway RNA in microglia. (LLM, conf=0.89)

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  • Overexpression of INPP5D in iMGs showed an elevation in RNA levels of NF-kB pathway genes.

    “In accord, overexpression of INPP5D in iMGs showed an elevation in RNA levels of NF-kB pathway genes, suggesting that microglia from AD brains may display changes relevant to reduced SHIP1 activity [161].”

    From Microglial function, INPP5D/SHIP1 signaling, and NLRP3 inflammasome activation: implications for Alzheimer’s disease (2023) · cites this paper as [161]

    The section on acute INPP5D inhibition (page unavailable) reports increased NF-κB pathway activity after treating iMGLs with 3AC, an INPP5D inhibitor. It does not report this elevation after INPP5D overexpression; the claimed direction of manipulation is opposite to the one studied. (LLM, conf=0.88)

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  • SHIP1 may be aggregated and perhaps aqueous-insoluble in the AD brain.

    “suggesting that SHIP1 may be aggregated (and perhaps aqueous-insoluble) in the AD brain [161].”

    From Microglial function, INPP5D/SHIP1 signaling, and NLRP3 inflammasome activation: implications for Alzheimer’s disease (2023) · cites this paper as [161]

    In “INPP5D expression is restricted to human microglia and reduced in Alzheimer’s disease” (page unavailable), the authors suggest that TBS-soluble extracts may not capture all full-length INPP5D/SHIP1. They note that many proteins form insoluble aggregates in high-pathology brains, but do not show that SHIP1 itself aggregates; their urea-extract analysis instead finds lower SHIP1 levels in AD brain. (LLM, conf=0.84)

    Experimental — accuracy not yet measured
  • AD brains displayed increased immunostaining for SHIP1 compared to age and sex-matched brain tissue from non-cognitively impaired individuals when a C-terminally directed antibody to SHIP1 was used.

    “However, we found that AD brains displayed increased immunostaining for SHIP1 compared to age and sex-matched brain tissue from non-cognitively impaired individuals when a C-terminally directed antibody to SHIP1 was used.”

    From Microglial function, INPP5D/SHIP1 signaling, and NLRP3 inflammasome activation: implications for Alzheimer’s disease (2023) · cites this paper as [161]

    The section on INPP5D expression reports an age- and sex-matched comparison of AD and non-cognitively impaired brain tissue, and the Figure 1 legend documents INPP5D immunostaining of human brain sections. But the paper does not report increased staining in AD with a C-terminally directed antibody; its quantified Western blots instead show reduced full-length INPP5D protein in AD. Those blots are a different assay, so they do not directly contradict the claimed staining result. (LLM, conf=0.83)

    Experimental — accuracy not yet measured
  • Peptide-level mass spectrometry analyses of TBS- and urea-solubilized postmortem brain lysates revealed a reduction of peptides encoding the phosphatase domain of SHIP1 in the AD brain.

    “Peptide-level mass spectrometry analyses of TBS- and urea-solubilized postmortem brain lysates revealed a reduction of peptides encoding the phosphatase domain of SHIP1 in the AD brain [161].”

    From Microglial function, INPP5D/SHIP1 signaling, and NLRP3 inflammasome activation: implications for Alzheimer’s disease (2023) · cites this paper as [161]

    The section “INPP5D expression is restricted to human microglia and reduced in Alzheimer's disease” (page unavailable) reports reduced full-length SHIP1/INPP5D protein in AD brain using TBS- and urea-solubilized postmortem tissue. It identifies Western blotting, not peptide-level mass spectrometry, as the method; it does not report a reduction specifically in peptides encoding the phosphatase domain. (LLM, conf=0.89)

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Authors
Chou, V., Fancher, S. B., Pearse, R. V., Lee, H., Lam, M., Seyfried, N. T., Bennett, D. A., De Jager, P. L., Menon, V., & Young-Pearse, T. L.
Affiliations
  • Brigham and Women's Hospital (US)
  • Columbia University Irving Medical Center (US)
  • Emory University (US)
  • Rush University Medical Center (US)
Venue
bioRxiv (Cold Spring Harbor Laboratory)
Publisher
openRxiv
Published
2023-02-26
OpenAlex
W4322207826
Cited by
8
References
79
Citations by year
2026: 3 · 2025: 1 · 2024: 1 · 2023: 3
Type
posted content
Language
en
Open access
Locations
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (submittedVersion)
Funders
  • Brigham and Women's Hospital
  • Emory University
  • National Institutes of Health
  • Harvard Stem Cell Institute
  • National Institute on Aging (R01AG017917, F31AG063398, U01AG046152, R01AG015819, P30AG010161, U01AG061356, P30AG072975)
Topics
  • Life Sciences › Neuroscience › Neurology › Neuroinflammation and Neurodegeneration Mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Inflammasome and immune disorders
  • Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
Keywords
INPP5D, SHIP1, microglia, inflammasome activation, Alzheimer's disease, neuroinflammation, IL-1β, IL-18, caspase-1, NLRP3 inflammasome, ASC, induced pluripotent stem cell-derived microglia, phosphatase activity, prefrontal cortex, innate immune signaling, scavenger receptors

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