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RNA-seq for iPSC-derived macrophages with/without Lipopolysaccharide (LPS) stimulation.

ABSTRACT: RNA-seq for iPSC-derived macrophages with/without Lipopolysaccharide (LPS) stimulation.

PROVIDER: PRJNA995504 | ENA |

REPOSITORIES: ENA

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RNA-seq for iPSC-derived macrophages with/without Lipopolysaccharide (LPS) stimulation.

Project description:Wiskott-Aldrich syndrome (WAS) is an immunodeficiency disorder caused by the dysfunction of the Wiskott-Aldrich syndrome protein (WASP). Although the effect of WASP on actin -polymerization is well studied, less is known about its role in other intracellular systems. Here we show that WASP interacts with the nucleolus in macrophages. Using induced pluripotent stem cells and the CRISPR-Cas system, we show that knocking out WASP results in reduced nucleolar size, loss of roundness, decreased sub-nucleolar structure percentage, and impaired ribosomal RNA transcription. Furthermore, we identified interactions between WASP and two nucleolar proteins, including nucleophosmin 1 (NPM1) and fibrillarin (FBL). Previous research has demonstrated that a loss of NPM1 results in heightened cytokine expression following lipopolysaccharide (LPS) stimulation. We found that WASP-deficient cells presented less NPM1 and more cytokine expression in response to LPS stimulation, providing new insights on the role of the nucleolus in immune functions. Together, our study provides new information on WASP in nucleolar function and its control of inflammatory cytokine expression in response to inflammatory stimuli.

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LPS stimulation reveals male and female dimorphism in human iPSC-derived macrophages

Project description:Clinical disparities in the inflammatory responses between males and females have been reported for decades, revealing sex-biased disease severity and patient outcomes. However, the underlying mechanisms driving these differences are understudied and poorly understood, despite the growing potential for improved diagnoses and treatment strategies. In this study, we used male and female iPSC-derived macrophages to identify transcriptomic changes in response to the common bacterial antigen lipopolysaccharide (LPS). Bulk RNA sequencing identified 67 genes differentially expressed between male and female macrophages in the absence of inflammation, the majority of which mapped to the sex chromosomes. This sexual dimorphism was amplified by LPS stimulation, with genes predominantly located on autosomes, leading to divergent patterns in secreted protein production that were consistent with clinical findings following LPS exposure. Although future validation with a larger patient cohort is needed, these data collectively suggest that iPSC-derived macrophages can serve as a meaningful tool for understanding and improving treatment of sex-biased pathophysiological conditions.

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Lactic acid modifies gene expression and chromatin accessibility of bone marrow-derived macrophages during lipopolysaccharide stimulation (RNA-seq and ATAC-seq)

Project description:Lactic acid (LA) has emerged as an important modulator of immune cell function. We performed ATAC-seq to profile the chromatin landscape of bone marrow-derived macrophages (BMDMs) upon lipopolysaccharide (LPS) stimulation with or without LA. Additionally, we also report the genome-wide RNA sequencing analysis in bone marrow-derived macrophages (BMDMs) where LA effect in macrophage inflammatory response was examined in BMDMs upon lipopolysaccharide (LPS) stimulation in the presence or absence of LA. To further examine LA effect due to low pH, hydrochloric acid (HCl) was used to adjust similar pH conditions (i.e. pH 6.5) as in media with LA.

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Expression data from bone marrow neutrophils with or without LPS stimulation in wild type and miR-125a deficient mice

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LPS stimulation reveals male and female dimorphism in human iPSC-derived macrophages

Project description:LPS stimulation reveals male and female dimorphism in human iPSC-derived macrophages

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LPS stimulation of APOE knock-out iPSC-derived microglia with different ApoE isoforms

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Wild-type bone-marrow derived macrophages response to Escherichia coli lipopolysaccharide (LPS)

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