Single-cell transcriptomes identifies characteristic features of mouse macrophages in liver Mallory-Denk bodies formation

C/EBPβ transcription factor promotes alcohol-induced liver fibrosis in males via HDL remodeling

BACKGROUND

Alcohol-associated liver disease (ALD) is the main cause of alcohol-associated mortality. However, the mechanism of ALD development is poorly understood. Epigenetic changes are thought to play an important role in ALD. We aimed to define the epigenetic changes induced by alcohol and predict drivers of these changes.

METHODS

Mice were fed high-fat diet with or without 20% of alcohol in the drinking water for 20 weeks (WDA model). scATAC-seq data set was analyzed using Signac R package. To test the role of C/EBPβ, Cebpb-floxed mice were treated with AAV8-TBG-Cre or AAV8-control.

RESULTS

We analyzed differentially accessible regions in livers from control and alcohol-fed mice and found that activity of C/EBPβ transcription factor was associated with alcohol-induced epigenetic changes in hepatocytes. C/EBPβ protein levels were significantly upregulated in multiple models of ALD and human ALD samples. Using hepatocyte-specific Cebpb knockout mice we found that Cebpb loss protected male mice from alcohol-induced fibrosis development. We found no protection in female mice, suggesting that this mechanism is specific to male ALD. In vitro studies suggested that the protective effect of Cebpb loss was mediated by altered hepatocyte-macrophage cross talk. Cebpb knockout in hepatocytes reduced a profibrotic and promoted a pro-resolving phenotype in macrophages, thus modulating ALD development. We further identified the mediators of the cross talk. Cebpb knockout altered the expression of several HDL protein components, increasing APOA1 and apolipoprotein M and reducing apolipoprotein E and SAA levels in male mice. HDL secreted by Cebpb knockout hepatocytes was sufficient to confer anti-inflammatory and antifibrotic changes to macrophages.

CONCLUSIONS

Taken together, alcohol-induced C/EBPβ activation is a key driver of ALD fibrosis in males via C/EBPβ-dependent HDL remodeling.

Single-cell transcriptomic analysis reveals characteristic feature of macrophage reprogramming in liver Mallory-Denk bodies pathogenesis

Chronic liver diseases are highly linked with mitochondrial dysfunction and macrophage infiltration. Mallory-Denk bodies (MDBs) are protein aggregates associated with hepatic inflammation, and MDBs pathogenesis could be induced in mice by feeding 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC). Here, we investigate the macrophage heterogeneity and the role of macrophage during MDBs pathogenesis on DDC-induced MDBs mouse model by single-nucleus RNA sequencing (snRNA-seq). We defined liver macrophages into four distinct subsets including monocyte-derived macrophages (MDMs) subset and three Kupffer cells (KCs) subsets (Gpnmbhigh KCs, Peam1high KCs, and Gpnmblow Pecam1low KCs). Particularly, we identified a novel Gpnmbhigh KCs subset as lipid-associated macrophage (LAM) with high expression of Trem2, CD63, and CD9. Interestingly, LAM showed a potential immunosuppressive characteristic by expressing anti-inflammatory genes IL-7R during the MDBs formation. Using contact and transwell co-culture systems, the released mtDNA from hepatocytes was found to induce the activation of inflammasome in macrophages. Furthermore, we revealed the damaged DNA could activate the NOD-like receptor family pyrin domain containing-3 (NLRP3) inflammasome and subsequently form apoptosis-associated speck-like protein containing a caspase recruit domain (ASC) specks of liver macrophages. Collectively, our results firstly revealed macrophage heterogeneity and inflammasome activation by mtDNA from injured liver during MDBs pathogenesis, providing crucial understanding of pathogenesis of chronic liver disease.

Alcohol-induced epigenetic changes prevent fibrosis resolution after alcohol cessation in miceresolution

BACKGROUND AND AIMS

Alcohol-associated liver disease is a major cause of alcohol-associated mortality. Recently, we identified hepatic demethylases lysine demethylase (KDM)5B and KDM5C as important epigenetic regulators of alcohol response in the liver. In this study, we aimed to investigate the role of KDM5 demethylases in alcohol-associated liver disease resolution.

APPROACH AND RESULTS

We showed that alcohol-induced liver steatosis rapidly resolved after alcohol cessation. In contrast, fibrosis persisted in the liver for up to 8 weeks after the end of alcohol exposure. Defects in fibrosis resolution were in part due to alcohol-induced KDM5B and KDM5C-dependent epigenetic changes in hepatocytes. Using cell-type-specific knockout mice, we found that adeno-associated virus-mediated knockout of KDM5B and KDM5C demethylases in hepatocytes at the time of alcohol withdrawal promoted fibrosis resolution. Single-cell ATAC sequencing analysis showed that during alcohol-associated liver disease resolution epigenetic cell states largely reverted to control conditions. In addition, we found unique epigenetic cell states distinct from both control and alcohol states and identified associated transcriptional regulators, including liver X receptor (LXR) alpha (α). In vitro and in vivo analysis confirmed that knockout of KDM5B and KDM5C demethylases promoted LXRα activity, likely through regulation of oxysterol biosynthesis, and this activity was critical for the fibrosis resolution process. Reduced LXR activity by small molecule inhibitors prevented fibrosis resolution in KDM5-deficient mice.

CONCLUSIONS

In summary, KDM5B and KDM5C demethylases prevent liver fibrosis resolution after alcohol cessation in part through suppression of LXR activity.

The crosstalking immune cells network creates a collective function beyond the function of each cellular constituent during the progression of hepatocellular carcinoma

Abundance of data on the role of inflammatory immune responses in the progression or inhibition of hepatocellular carcinoma (HCC) has failed to offer a curative immunotherapy for HCC. This is largely because of focusing on detailed specific cell types and missing the collective function of the hepatic immune system. To discover the collective immune function, we take systems immunology approach by performing high-throughput analysis of snRNAseq data collected from the liver of DIAMOND mice during the progression of nonalcoholic fatty liver disease (NAFLD) to HCC. We report that mutual signaling interactions of the hepatic immune cells in a dominant-subdominant manner, as well as their interaction with structural cells shape the immunological pattern manifesting a collective function beyond the function of the cellular constituents. Such pattern discovery approach recognized direct role of the innate immune cells in the progression of NASH and HCC. These data suggest that discovery of the immune pattern not only detects the immunological mechanism of HCC in spite of dynamic changes in immune cells during the course of disease but also offers immune modulatory interventions for the treatment of NAFLD and HCC.

New discoveries in the field of metabolism by applying single-cell and spatial omics

Single-cell multi-Omics (SCM-Omics) and spatial multi-Omics (SM-Omics) technologies provide state-of-the-art methods for exploring the composition and function of cell types in tissues/organs. Since its emergence in 2009, single-cell RNA sequencing (scRNA-seq) has yielded many groundbreaking new discoveries. The combination of this method with the emergence and development of SM-Omics techniques has been a pioneering strategy in neuroscience, developmental biology, and cancer research, especially for assessing tumor heterogeneity and T-cell infiltration. In recent years, the application of these methods in the study of metabolic diseases has also increased. The emerging SCM-Omics and SM-Omics approaches allow the molecular and spatial analysis of cells to explore regulatory states and determine cell fate, and thus provide promising tools for unraveling heterogeneous metabolic processes and making them amenable to intervention. Here, we review the evolution of SCM-Omics and SM-Omics technologies, and describe the progress in the application of SCM-Omics and SM-Omics in metabolism-related diseases, including obesity, diabetes, nonalcoholic fatty liver disease (NAFLD) and cardiovascular disease (CVD). We also conclude that the application of SCM-Omics and SM-Omics approaches can help resolve the molecular mechanisms underlying the pathogenesis of metabolic diseases in the body and facilitate therapeutic measures for metabolism-related diseases. This review concludes with an overview of the current status of this emerging field and the outlook for its future.

Disulfiram Ophthalmic Solution Inhibited Macrophage Infiltration by Suppressing Macrophage Pseudopodia Formation in a Rat Corneal Alkali Burn Model

FROUNT is an intracellular protein that promotes pseudopodia formation by binding to the chemokine receptors CCR2 and CCR5 on macrophages. Recently, disulfiram (DSF), a drug treatment for alcoholism, was found to have FROUNT inhibitory activity. In this study, we investigated the effect of DSF eye drops in a rat corneal alkali burn model. After alkali burn, 0.5% DSF eye drops (DSF group) and vehicle eye drops (Vehicle group) were administered twice daily. Immunohistochemical observations and real-time reverse transcription-polymerase chain reaction (RT-PCR) analyses were performed at 6 h and 1, 4, and 7 days after alkali burn. Results showed a significant decrease in macrophage accumulation in the cornea in the DSF group, but no difference in neutrophils. RT-PCR showed decreased expression of macrophage-associated cytokines in the DSF group. Corneal scarring and neovascularization were also suppressed in the DSF group. Low-vacuum scanning electron microscopy imaging showed that macrophage length was significantly shorter in the DSF group, reflecting the reduced extension of pseudopodia. These results suggest that DSF inhibited macrophage infiltration by suppressing macrophage pseudopodia formation.