Dataset Information

Integrated Multi-Omic Analysis Reveals KDM5B as a Regulator of Microglial Reactivity to Immunomodulatory Stimuli

ABSTRACT: Microglia maintain brain homeostasis through coordinated pathways, including cell migration, phagocytosis, and secretion of immune-related signaling factors. Microglial reactivity is associated with a variety of functional outcomes that are highly context-dependent with epigenetic regulation through DNA methylation and histone modificationsimplicated in this complex control of microglial plasticity. Specifically, in relation to histone methylation, lysine-specific demethylase 5B (KDM5B) has been associated with several pathophysiological states, including neurodevelopmental and inflammatory disorders, cancer, and alcohol use disorder; however, the cell-type-specific role of KDM5B in microglial reactivity has not been investigated. In this study, transcriptomic and proteomic analyses were used to characterize the effects of KDM5B depletion on microglial pathways in clustered regularly interspaced short palindromic repeats (CRISPR)-edited adult-derived murine microglial cells. Additionally, various immunomodulatory stimuli, including lipopolysaccharide, interleukin-4, and alcohol, were used to study the effects of KDM5B depletion on immune reactivity in microglia using deep proteomics and bioinformatic analysis. Through this comprehensive characterization, KDM5B-depleted microglia exhibited broad remodeling of immune reactivity, including reduced intracellular and secreted inflammatory responses to lipopolysaccharide as well as distinct modulation of alcohol- and interleukin-4-induced pathways, that was functionally demonstrated by altered cytokine secretion profiles. Results from this study provide critical insight into KDM5B-mediated immunological effects on microglial function.

INSTRUMENT(S):

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Cell Culture

SUBMITTER: Stanley Stevens

LAB HEAD: Dr. Stanley

PROVIDER: PXD058485 | Pride | 2026-03-02

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	10-14-2021_Slot2-1_1_1532_DIA_90m_10th_2ul_KDM5B_01.d.zip	Other
	10-15-2021_Slot2-2_1_1534_DIA_90m_10th_2ul_KDM5B_02.d.zip	Other
	10-15-2021_Slot2-3_1_1536_DIA_90m_10th_2ul_KDM5B_03.d.zip	Other
	10-15-2021_Slot2-4_1_1538_DIA_90m_10th_2ul_WTB_01.d.zip	Other
	10-15-2021_Slot2-5_1_1540_DIA_90m_10th_2ul_WTB_02.d.zip	Other

Items per page:

1 - 5 of 34

Publications

Integrated Multi-Omic Analysis Reveals KDM5B as a Regulator of Microglial Reactivity to Immunomodulatory Stimuli.

Wohlfahrt Jessica J Wolf Tiara T Winters Alexis M AM Burkhardt Brant R BR Liu Bin B Guergues Jennifer J Stevens Stanley M SM

Journal of proteome research 20260204

Microglia maintain brain homeostasis through coordinated pathways, including cell migration, phagocytosis, and secretion of immune-related signaling factors. Microglial reactivity is associated with a variety of functional outcomes that are highly context-dependent withepigenetic regulation through DNA methylation and histone modifications implicated in this complex control of microglial plasticity. Specifically, in relation to histone methylation, lysine-specific demethylase 5B (KDM5B) has been ...[more]

PMID: 41640052

Similar Datasets

Project description:The biological significance of microglia are highlighted by their critical role as the resident immune cells of the central nervous system. In this capacity, microglia maintain homeostasis through various pathways that include cell migration, phagocytosis as well as secretion of immune-related and signaling factors into the extracellular environment. Microglial reactivity is associated with a variety of functional outcomes that are highly context-dependent and therefore microglia can exhibit a wide range of phenotypes. Epigenetic regulation through DNA methylation and histone modifications has recently been implicated in this complex control of microglial reactivity. Specifically, in relation to histone methylation status, the histone demethylase KDM5B has been implicated in many pathophysiological states including alcohol use disorder (AUD), cancer, and inflammatory disorders; however, the cell type-specific role of KDM5B in microglial reactivity has yet to be fully investigated. In this study, transcriptomic and proteomic analyses were used to characterize the effects of KDM5B knockdown on microglial pathways using CRISPR editing of adult-derived murine microglial cells to generate a Kdm5b knockout pool. From this multi-omic analysis, over 34,000 genes and 9,000 proteins were identified across all replicates of wild-type (WT) and KDM5B-depleted microglia. Additionally, various stimuli including LPS, IL4, and alcohol were used to study the effects of KDM5B knockdown on immune reactivity in microglia using deep proteomic analysis. Through this deep characterization, an overall decrease in inflammatory and immune reactivity pathways was observed in KDM5B-depleted microglia, which was then functionally validated through measurement of secreted factors including TNFα, IL6, IL4, IL10, IL16, and SPP1. The results from this study has provided critical insight into KDM5B-mediated effects on microglial function as well as a molecular framework for future studies aimed to understand epigenetic regulation of microglia and implications in neurodegenerative disease pathogenesis and progression.

Project description:Alzheimer’s disease (AD) is a progressive neurodegenerative disorder marked by the buildup of amyloid-β and tau protein tangles. Alcohol use has been identified as a risk factor for AD; however, the molecular mechanisms underlying this potential causal link remain elusive. An emerging area of research focuses on the role of microglia, the brain's innate immune cells, in AD pathogenesis, with evidence suggesting that alcohol exposure may prime microglia to exhibit an exaggerated immune response when they are subsequently exposed to proinflammatory stimuli. We used a single 10-day chronic-plus-binge alcohol exposure model in male and female C57BL/J mice aged 8- to 10-weeks old. One month later, tauopathy was induced via adenoviral vector (AAV)-mediated overexpression of h-p301L tau. After 2.5 months, the mice underwent behavioral and cognitive testing. Two weeks later, microglia were collected using fluorescence-activated cell sorting (FACS) and processed for unbiased mass spectrometry and deep proteomic analysis to determine the molecular pathways related to microglial reactivity. Microglia from mice exposed to alcohol in young adulthood exhibited a blunted immune response when challenged with AAV-mediated delivery and accumulation of human tau later in life. This was characterized by decreased expression of MHC II- and interferon-associated proteins and bioinformatic prediction of inhibited inflammation-related pathways in the absence of gross histological, behavioral, or cognitive deficits. These results demonstrate unique, temporally specific microglial reactivity to tau that is modulated by early life alcohol exposure, implicating a microglial response that could negatively affect the mechanisms necessary for tau clearance and potentially exacerbate tau pathogenesis. This study provides novel insights into the long-term effects of early alcohol exposure on microglial function and the complexity of context-dependent microglial involvement in tau pathology. Consideration of early life environmental factors is critical for understanding and potentially mitigating the risk of neurodegenerative diseases, such as AD.

Project description:Microglia colonize the brain parenchyma at early stages of development and accumulate in specific regions where they actively participate in cell death, angiogenesis, neurogenesis and synapse elimination. A recurring feature of embryonic microglial distribution is their association with developing axon tracts which, together with in vitro data, supports the idea of a physiological role for microglia in neurite development. Yet the demonstration of this role of microglia is still lacking. Here, we have studied the consequences of microglial dysfunction on the formation of the corpus callosum, the largest connective structure in the mammalian brain, which shows consistent microglial accumulation during development. We studied two models of microglial dysfunction: the loss-of-function of DAP12, a key microglial-specific signaling molecule, and a model of maternal inflammation by peritoneal injection of LPS at E15.5. We performed transcriptional profiling of maternally inflamed and Dap12-mutant microglia at E17.5. We found that both treatments principally down-regulated genes involved in nervous system development and function, particularly in neurite formation. We then analyzed the functional consequences of these microglial dysfunctions on the formation of the corpus callosum. We also took advantage of the Pu.1-/- mouse line, which is devoid of microglia. We now show that all three models of altered microglial activity resulted in the same defasciculation phenotype. Our study demonstrates that microglia are actively involved in the fasciculation of corpus callosum axons. To investigate possible roles for microglial during brain development, we challenged microglial function by two complementary approaches. First, we induced maternal inflammation by peritoneal injection of LPS into pregnant dams. Next, we analyzed the consequences of a loss of function of DAP12, a signaling molecule specifically expressed in microglia that is crucial for several aspects of microglia biology (references in Wakselman et al., 2008). We compared the gene expression profiles of microglia from control, maternally-inflamed by LPS (MI), and Dap12-mutated embryos. We isolated RNA from FACS sorted maternally inflamed (by LPS) and Dap12-mutant microglia at E17.5 pooled per pregnant dam; as a control we included PBS treated and untreated (UT) microglia. We compared gene expression between maternally inflamed microlgia (PBSvsLPS) and DAP12-mutant microglia (UTvsDAP12KO).