Identification of CYP46A1 as a new regulator of lipid metabolism through CRISPR-based whole-genome screening

Insights into the effect of benzotriazoles in liver using integrated metabolomic and transcriptomic analysis

Benzotriazoles (BTRs) are a class of benzoheterocyclic chemicals that are frequently used as metal-corrosive inhibitors, both in industry and daily use. However, the exposure effect information on BTRs remains relatively limited. In this study, an integrated metabolomic and transcriptomic approach was utilized to evaluate the effect of three BTRs, benzotriazole, 6-chloro-1-hydroxi-benzotriazole, and 1-hydroxy-benzotriazole, in the mouse liver with results showing disrupted basal metabolic processes and vitamin and cofactor metabolism after 28 days. The expression of several genes that are related to the inflammatory response and aryl hydrocarbon receptor pathways, such as Gstt2 and Arntl, was altered by the exposure to BTRs. Exposure to BTRs also affected metabolites and genes that are involved in the immune system and xenobiotic responses. The altered expression of several cytochrome P450 family genes reveal a potential detoxification mechanism in the mouse liver. Taken together, our findings provide new insights into the multilayer response of the mouse liver to BTRs exposure as well as a resource for further exploration of the molecular mechanisms by which the response occurs.

Heterogeneity of foam cell biogenesis across diseases

Foam cells are dysfunctional, lipid-laden macrophages associated with chronic inflammation of diverse origin. The long-standing paradigm that foam cells are cholesterol-laden derives from atherosclerosis research. We previously showed that, in tuberculosis, foam cells surprisingly accumulate triglycerides. Here, we utilized bacterial (Mycobacterium tuberculosis), fungal (Cryptococcus neoformans), and human papillary renal cell carcinoma (pRCC) models. We applied mass spectrometry-based imaging to assess the spatial distribution of storage lipids relative to foam-cell-rich areas in lesional tissues, and characterized lipid-laden macrophages generated under corresponding in vitro conditions. The in vivo data were consistent with in vitro findings showing that cryptococcus-infected macrophages accumulated triglycerides, while macrophages exposed to pRCC-conditioned-medium accumulated both triglycerides and cholesterol. Moreover, cryptococcus- and mycobacterium-infected macrophages accumulated triglycerides by different mechanisms. Collectively, our data indicate that the mechanisms of foam cell formation are disease-microenvironment-specific. Since foam cells are potential therapeutic targets, recognizing that their formation is disease-specific opens new biomedical research directions.

Drug targets regulate systemic metabolism and provide new horizons to treat nonalcoholic steatohepatitis

Nonalcoholic steatohepatitis (NASH), is the advanced stage of nonalcoholic fatty liver disease (NAFLD) with rapidly rising global prevalence. It is featured with severe hepatocyte apoptosis, inflammation and hepatic lipogenesis. The drugs directly targeting the processes of steatosis, inflammation and fibrosis are currently under clinical investigation. Nevertheless, the long-term ineffectiveness and remarkable adverse effects are well documented, and new concepts are required to tackle with the root causes of NASH progression. We critically assess the recently validated drug targets that regulate the systemic metabolism to ameliorate NASH. Thermogenesis promoted by mitochondrial uncouplers restores systemic energy expenditure. Furthermore, regulation of mitochondrial proteases and proteins that are pivotal for intracellular metabolic homeostasis normalize mitochondrial function. Secreted proteins also improve systemic metabolism, and NASH is ameliorated by agonizing receptors of secreted proteins with small molecules. We analyze the drug design, the advantages and shortcomings of these novel drug candidates. Meanwhile, the structural modification of current NASH therapeutics significantly increased their selectivity, efficacy and safety. Furthermore, the arising CRISPR-Cas9 screen strategy on liver organoids has enabled the identification of new genes that mediate lipid metabolism, which may serve as promising drug targets. In summary, this article discusses the in-depth novel mechanisms and the multidisciplinary approaches, and they provide new horizons to treat NASH.

Microarray analysis identifies coding and non-coding RNA markers of liver injury in whole body irradiated mice

Radiation injury from medical, accidental, or intentional sources can induce acute and long-term hepatic dysregulation, fibrosis, and cancer. This long-term hepatic dysregulation decreases quality of life and may lead to death. Our goal in this study is to determine acute changes in biological pathways and discover potential RNA biomarkers predictive of radiation injury. We performed whole transcriptome microarray analysis of mouse liver tissue (C57BL/6 J) 48 h after whole-body irradiation with 1, 2, 4, 8, and 12 Gray to identify significant expression changes in mRNAs, lncRNAs, and miRNAs, We also validated changes in specific RNAs through qRT-PCR. We used Ingenuity Pathway Analysis (IPA) to identify pathways associated with gene expression changes. We observed significant dysregulation of multiple mRNAs across all doses. In contrast, miRNA dysregulation was observed upwards of 2 Gray. The most significantly upregulated mRNAs function as tumor suppressors: Cdkn1a, Phlda3, and Eda2r. The most significantly downregulated mRNAs were involved in hemoglobin synthesis, inflammation, and mitochondrial function including multiple members of Hbb and Hba. The most significantly upregulated miRNA included: miR-34a-5p, miR-3102-5p, and miR-3960, while miR-342-3p, miR-142a-3p, and miR-223-3p were most significantly downregulated. IPA predicted activation of cell cycle checkpoint control pathways and inhibition of pathways relevant to inflammation and erythropoietin. Clarifying expression of mRNA, miRNA and lncRNA at a short time point (48 h) offers insight into potential biomarkers, including radiation markers shared across organs and animal models. This information, once validated in human models, can aid in development of bio-dosimetry biomarkers, and furthers our understanding of acute pathway dysregulation.

Identification of MAP3K4 as a novel regulation factor of hepatic lipid metabolism in non-alcoholic fatty liver disease

Background

Non-alcoholic fatty liver disease (NAFLD) is a metabolic disorder with abnormal lipid metabolism. The present study was to identify regulatory genes related to lipid droplets (LDs) abnormal accumulation in NAFLD.

Methods

transcriptomic analysis and bioinformatics analysis (GEO database) were used to identify potential genes in abnormal lipid metabolism of NAFLD. A candidate gene MAP3K4 expression were detected by immunohistochemistry staining in NAFLD and controls. RNA interference and immunoblotting were used to verify the roles of MAP3K4 in the formation of hepatic LDs.

Results

A total of 134 candidate genes were screened, including 44 up-regulated genes and 90 down-regulated genes. 29 genes in the protein–protein interaction (PPI) were selected as hub genes, including MAP3K4. The expression levels of MAP3K4 were positively correlated with NAFLD activity score (r = 0.702, p = 0.002). Furthermore, we found a positive correlation of MAP3K4 expression with serum total cholesterol (r = 0.564, p = 0.023), uric acid levels (r = 0.520, p = 0.039), and body mass index (r = 0.574, p = 0.020). Downregulation of MAP3K4 decreased LDs accumulation in HepG2 cells and reduced the expression of CGI-58 and Plin-2 by imbibition of JNK and group IVA cytosolic phospholipase A2 (cPLA2) activation.

Conclusion

The study revealed a number of regulatory genes related to hepatic lipid metabolism of NAFLD, and demonstrated that MAP3K4 played a pivotal role in the hepatic lipogenesis of NAFLD.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12967-022-03734-8.

Insights into the architecture of human-induced polygenic selection in Duroc pigs

Background

As one of the most utilized commercial composite boar lines, Duroc pigs have been introduced to China and undergone strongly human-induced selection over the past decades. However, the efficiencies and limitations of previous breeding of Chinese Duroc pigs are largely understudied. The objective of this study was to uncover directional polygenic selection in the Duroc pig genome, and investigate points overlooked in the past breeding process.

Results

Here, we utilized the Generation Proxy Selection Mapping (GPSM) on a dataset of 1067 Duroc pigs with 8,766,074 imputed SNPs. GPSM detected a total of 5649 putative SNPs actively under selection in the Chinese Duroc pig population, and the potential functions of the selection regions were mainly related to production, meat and carcass traits. Meanwhile, we observed that the allele frequency of variants related to teat number (NT) relevant traits was also changed, which might be influenced by genes that had pleiotropic effects. First, we identified the direction of selection on NT traits by \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\hat{G}$$\end{document}G^, and further pinpointed large-effect genomic regions associated with NT relevant traits by selection signature and GWAS. Combining results of NT relevant traits-specific selection signatures and GWAS, we found three common genome regions, which were overlapped with QTLs related to production, meat and carcass traits besides “teat number” QTLs. This implied that there were some pleiotropic variants underlying NT and economic traits. We further found that rs346331089 has pleiotropic effects on NT and economic traits, e.g., litter size at weaning (LSW), litter weight at weaning (LWW), days to 100 kg (D100), backfat thickness at 100 kg (B100), and loin muscle area at 100 kg (L100) traits.

Conclusions

The selected loci that we identified across methods displayed the past breeding process of Chinese Duroc pigs, and our findings could be used to inform future breeding decision.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40104-022-00751-x.

Transcriptomic analysis reveals a novel regulatory factor of ECHDC1 involved in lipid metabolism of non-alcoholic fatty liver disease

Non-alcoholic fatty liver disease (NAFLD) is the highest incidence of chronic liver disease worldwide characterized by lipid accumulation in the liver. The full understanding of the lipogenesis of NAFLD is extreme importance. Here, whole-genome transcriptome analysis was performed on liver tissues of NAFLD patients and healthy controls to identify the differentially expressed genes and find new pathways and target genes related to the lipogenesis of NAFLD. Combined with the Gene Expression Omnibus (GEO) database, we found 86 overlapping genes, many of which are related to lipid metabolism of NAFLD. ECHDC1 is one of 86 overlapping genes, and its role in NAFLD has not been reported. The expression of ECHDC1 was significantly increased in liver tissue of patients with NAFLD than that of healthy controls, and oil Red O intensity was positively correlated with the expression levels of ECHDC1. Inhibition of ECHDC1 expression in HepG2 cells by RNAi significantly reduced intracellular lipid droplet number in vitro. In summary, this study analyzed pathogenic factors related to NAFLD at the whole-genome level and demonstrated that ECHDC1 may be involved in the occurrence and development of NAFLD by regulating hepatic lipid metabolism.

IRX3 plays an important role in the pathogenesis of metabolic-associated fatty liver disease by regulating hepatic lipid metabolism

Metabolic-associated fatty liver disease (MAFLD) affects approximately a quarter of the global population. Identification of the key genes and pathways involved in hepatic lipid metabolism is of the utmost importance for the diagnosis, treatment, and prevention of MAFLD. In this study, differentially expressed genes were identified through whole-genome transcriptional analysis of liver tissue from MAFLD patients and healthy controls, and a series of lipid metabolism-related molecules and pathways were obtained through pathway analysis. Subsequently, we focused on Iroquois homeobox protein 3 (IRX3), one of 13 transcription factors that were screened from the 331 differentially expressed genes. The transcription factor IRX3 was significantly decreased in the liver tissue of patients with MAFLD when compared with healthy controls. Pearson's correlation analysis showed that the expression levels of IRX3 in liver tissue were negatively correlated with serum total cholesterol, triglycerides, low-density lipoprotein cholesterol, and uric acid levels. The overexpression and interference of IRX3 induced the increased and decreased lipid droplet accumulation in vitro, respectively. Moreover, interference of IRX3 expression increased mitochondrial fragmentation and reduced the activity of the mitochondrial respiratory chain complex IV. In summary, the study demonstrated that IRX3 regulated hepatic lipid metabolism of MAFLD, and also revealed the effect of IRX3 on mitochondria might be an important mechanism by which IRX3 regulated hepatic lipid metabolism of MAFLD.