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Rifaximin Alleviates MASH by Suppressing Deoxycholic Acid-Triggered Macrophage-Hepatocyte Dialogue [snRNA-Seq]

ABSTRACT: Metabolic dysfunction-associated steatohepatitis (MASH) is characterized by a complex interplay between gut microbiota-derived metabolites and hepatic immune infiltration. This study investigates the therapeutic mechanism of rifaximin, an oral non systemic antibiotic, in the context of MASH progression and its modulation by bile acid signaling. Our preliminary data indicated that while rifaximin significantly ameliorates MASH features, deoxycholic acid (DCA), a secondary bile acid and potent S1PR2 agonist reverses these beneficial effects. To systematically dissect the specific cellular populations involved, we performed single-nucleus RNA sequencing (snRNA-seq) and bulk RNA-seq on liver tissues from mice under various conditions, including HFF-induced MASH, rifaximin treatment, and rifaximin treatment supplemented with DCA reconstitution. The snRNA-seq analysis primarily focused on the hepatic immune landscape, specifically the dynamics of monocyte-derived macrophages

ORGANISM(S): Mus musculus

PROVIDER: GSE317519 | GEO | 2026/09/01

REPOSITORIES: GEO

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Rifaximin Alleviates MASH by Suppressing Deoxycholic Acid-Triggered Macrophage-Hepatocyte Dialogue

Project description:Metabolic dysfunction-associated steatohepatitis (MASH) is characterized by a complex interplay between gut microbiota-derived metabolites and hepatic immune infiltration. This study investigates the therapeutic mechanism of rifaximin, an oral non systemic antibiotic, in the context of MASH progression and its modulation by bile acid signaling. Our preliminary data indicated that while rifaximin significantly ameliorates MASH features, deoxycholic acid (DCA), a secondary bile acid and potent S1PR2 agonist reverses these beneficial effects. To systematically dissect the specific cellular populations involved, we performed single-nucleus RNA sequencing (snRNA-seq) and bulk RNA-seq on liver tissues from mice under various conditions, including HFF-induced MASH, rifaximin treatment, and rifaximin treatment supplemented with DCA reconstitution. The snRNA-seq analysis primarily focused on the hepatic immune landscape, specifically the dynamics of monocyte-derived macrophages (MoMFs).

2026-09-01 | GSE317518 | GEO

The Microbial Metabolite Deoxycholic Acid Modulates Cholesterol Metabolism in the Germ-Free Mouse

Project description:Deoxycholic acid (DCA) is a secondary bile acid produced by a small number of commensal species of bacteria present in the mammalian gut. Elevated DCA concentration correlates with disease states including colon cancer and cholesterol gallstones, but the associated mechanisms are not fully understood. Both primary and secondary bile acids are also capable of affecting gene expression through nuclear receptors such as FXR. To better understand the impact of a commensal-derived secondary bile acid on host metabolism we fed DCA to germ-free (GF) mice, which normally lack DCA, and compared the hepatic transcriptomes of bile acid fed GF mice to GF mice receiving a control diet, as well as to those of conventionally housed control animals. Interestingly, the feeding of DCA to GF mice, but not the feeding of cholic acid (CA) from which DCA is derived, results in an up-regulation of genes of cholesterol biosynthetic pathways. GF mice normally have elevated hepatic cholesterol compared to conventionally housed mice. Despite increase in the expression of cholesterol biosynthetic genes, the DCA fed GF mice showed a markedly decreased level of hepatic cholesterol equivalent to the hepatic cholesterol concentration of conventionally colonized animals. Total cholesterol in the serum was unaffected by DCA, but there was a decrease in the HDL lipoprotein fraction as well as an increase in the non-HDL lipoprotein fraction of the serum cholesterol. DCA, but not CA, is sufficient to modulate host lipoprotein metabolism. Taken together, these results suggests that a minor component of the gut microbiome has a significant impact on cholesterol homeostasis through secondary metabolism of bile acids and suggests a possible therapeutic intervention route through the microbial metabolic pathways. two mouse strains, three diets, one time point

2015-01-08 | E-GEOD-34730 | biostudies-arrayexpress

The Microbial Metabolite Deoxycholic Acid Modulates Cholesterol Metabolism in the Germ-Free Mouse

2015-01-08 | GSE34730 | GEO

Exposure of Barrett's associated adenocarcinoma cell lines SKGT4 to deoxycholic acid (DCA)

2010-02-20 | GSE13376 | GEO

Exposure of squamous esophageal cell line HET-1A to deoxycholic acid (DCA)

Project description:The involvment of bile acids such as deoxycholic acid (DCA) in gastro-esophageal reflux disease and subsequent Barrettâ??s metaplsia has been postulated. This study examines gene expression induced by exposure to DCA in esophageal cells and may be utilised in cross-comparisions with data derived from gene expression studies of Barrettâ??s esophagus and associated adenocarcinoma. Additionally this study may be used to assess divergence in response to bile acids by comparisons with similar study performed in SKGT4 barrett''s assocaited adenocarcinoma cell line. HET-1A cells were exposed to 300um DCA over 24 hours in duplicate experiments including matched timepoint controls

2010-02-28 | E-GEOD-13378 | biostudies-arrayexpress

Exposure of Barrett's associated adenocarcinoma cell lines SKGT4 to deoxycholic acid (DCA)

Project description:The involvment of bile acids such as deoxycholic acid (DCA) in gastro-esophageal reflux disease and subsequent Barrettâs metaplsia has been postulated. This study examines gene expression induced by exposure to DCA in esophageal cells and may be utilised in cross-comparisons with data derived from gene expression studies of Barrettâs esophagus and associated adenocarcinoma. SKGT4 cells were exposed to 300um DCA over 24 hours in duplicate experiments including matched timepoint controls. RNA samples were taken at 4, 8, 12 and 24 hours from DCA (DCA) exposed and resting (REST) timepoint controls.

2010-02-28 | E-GEOD-13376 | biostudies-arrayexpress

Exposure of squamous esophageal cell line HET-1A to deoxycholic acid (DCA)

Project description:The involvment of bile acids such as deoxycholic acid (DCA) in gastro-esophageal reflux disease and subsequent Barrett’s metaplsia has been postulated. This study examines gene expression induced by exposure to DCA in esophageal cells and may be utilised in cross-comparisions with data derived from gene expression studies of Barrett’s esophagus and associated adenocarcinoma. Additionally this study may be used to assess divergence in response to bile acids by comparisons with similar study performed in SKGT4 barrett''s assocaited adenocarcinoma cell line.

2010-02-20 | GSE13378 | GEO

Transcription profiling of SKGT4 and HET-1A cell lines exposed to deoxycholic acid (DCA)

Project description:This SuperSeries is composed of the following subset Series: GSE13376: Exposure of Barrett's associated adenocarcinoma cell lines SKGT4 to deoxycholic acid (DCA) GSE13378: Exposure of squamous esophageal cell line HET-1A to deoxycholic acid (DCA) Refer to individual Series

2010-03-02 | E-GEOD-13400 | biostudies-arrayexpress

Effect of the bile acids chenodeoxycholic acid and deoxycholic acid on the transcriptome of Mycobacterium avium strain MAC101

Project description:The bile acids chenodeoxycholic acid (CDCA) and deoxycholic acid (DCA) were added to the growth medium of cultures of M.avium strain MAC101 and RNA was islated after 1.5 hours of incubation. RNAseq was performed with Illumina sequencing. With a FDR rate threshold of 0.05 showing a large number of genes whose expression was induced by the treatment. The signature sets of induced genes or both bile acids are shown to be very different. there are also common responses in various genes that function in cholesterol catabolism.

2026-09-01 | GSE304386 | GEO

Effect of the bile acids chenodeoxycholic acid (CDCA), deoxycholic acid (DCA) and cholic acid (CA) on the transcriptome of Mycobacterium avium strain MAC101

Project description:The bile acids chenodeoxycholic acid (CDCA), deoxycholic acid (DCA) andcholic acid (CA) were added to the growth medium of cultures of M.avium strain MAC101 and RNA was islated after 1.5 hours or 24 hours of incubation. RNAseq was performed with Illumina sequencing. With a FDR rate threshold of 0.05 showing a large number of genes whose expression was induced by the treatment. The signature sets of induced genes or both bile acids are shown to be very different. there are also common responses in various genes that function in cholesterol catabolism. As a control cholesterol in a similar concentration was used but this had only a very moderate effect on the transcriptome at 1.5 hours.

2026-09-01 | GSE306124 | GEO

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