Biology subjects

Argemi, J.

Publications and source records attributed to Argemi, J..

4 recordsLinked to original sources

bioRxiv2025

Alpha diversity analysis of hepatic transcriptome reveals novel pathways inalcohol-related hepatitis

Next generation sequencing can identify novel gene expression patterns in disease. Beyond differentially expressed genes analysis, we investigated the ability of within-population diversity (-diversity) of the transcriptome to reveal new biological information in alcohol-related liver disease (ALD), comparing Differential Shannon diversity (DSD) to transcriptome heterogeneity changes. RNA sequencing data from normal livers and patients with early silent ALD and severe AH were analyzed. -diversity indices and Percent Shannon Diversity of a gene, which refers to this genes contribution to total Shannon entropy were calculated. Ingenuity pathway analysis identified canonical pathways determined by differentially expressed genes (DEG) and DSD approaches. ALD significantly decreased hepatic transcriptome -diversity correlating with increased relative contribution of select genes. These changes were driven by lower abundance gene expression loss. DEG and DSD analyses showed overlapping genes and canonical pathways, but DSD also identified novel genes and pathways not highlighted by DEG. Importantly, DSD more effectively identified differences between preclinical ALD and AH severity stages. ALD decreases hepatic transcriptome heterogeneity, favoring pathways associated with organ damage or damage response. Preclinical and clinical ALD led to differential heterogeneity patterns that may provide new disease insights. DSD analysis identified enriched pathways missed by standard DEG analyses, potentially yielding novel insight into disease mechanisms and biomarkers. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=53 SRC="FIGDIR/small/681263v1_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@d2d3a3org.highwire.dtl.DTLVardef@14496a8org.highwire.dtl.DTLVardef@1ff0dfeorg.highwire.dtl.DTLVardef@1efa8f3_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2025

Calpain-4 Knockdown Modulates Cholesterol Metabolism and LXRα Nuclear Localization in Alcohol-Related Liver Disease

Background & AimsEthanol affects lipid metabolism through multiple pathways, leading to fatty liver development in most ALD patients. Recent studies have highlighted the role of calpain, a calcium-dependent protease, in liver inflammation and fibrosis. Calpain activity is regulated by its essential subunit, Capns1, (calpain-4, Capn4), which stabilizes and modulates the activity of its catalytic isoforms, calpain-1 and calpain-2. This study investigated calpains impact on lipid metabolism in ALD. Approach & ResultsSix-week-old C57Bl6/J mice were injected with rAAV8 vectors encoding Capn4 shRNA or control vectors. After four weeks, mice underwent a 10-day period of ad libitum ethanol consumption, followed by a single gavaged ethanol administration on day 11. Following Capn4 knockdown, microvesicular steatosis was attenuated. While triglycerides and free fatty acids levels showed no significant changes, cholesterol levels were significantly reduced in the ethanol (EtOH) group with Capn4 knockdown. Cpt1a expression increased significantly in the EtOH group with Capn4 knockdown. Western blot analysis revealed increased Cleaved-HMGCR to Pro-HMGCR ratio in Capn4 knockdown mice, suggesting reduced HMGCR activity and suppressed cholesterol biosynthesis. LXR expression was mainly increased in the cytoplasm in the EtOH group, and following Capn4 knockdown, it was relocalized to the nucleus via its activation. In addition, RNA sequencing analysis suggests that Capn4 knockdown contributes to the reprogramming of ethanol-induced disruptions in metabolic and homeostatic pathways, primarily those involving cholesterol metabolism. ConclusionsFurther investigation into the relationship between Capn4 and cholesterol biosynthesis proteins may provide insights into using calpain inhibitors as a therapeutic approach for alcohol-related hepatitis.

molecular biology↗

bioRxiv2025

Histone methyl-transferase G9a inhibition boosts the efficacy of immune checkpoint inhibitors in experimental hepatocellular carcinoma

Background and AimsImmune checkpoint inhibitors (ICI) have revolutionized cancer therapy. Yet, their efficacy in hepatocellular carcinoma (HCC) remains limited, partly due to tumor-intrinsic mechanisms of immune evasion. This study focused on the identification of potential epigenetic drivers of immune resistance in HCC evaluating the therapeutic potential of targeting the histone methyltransferase G9a (EHMT2). Approach and ResultsWe analyzed G9a expression across multiple human HCC cohorts and found that elevated G9a levels were inversely correlated with the most relevant immune-related gene expression signatures predictive of ICI responsiveness. Using HCC cell lines and orthotopic models implemented in immunocompetent mice, we assessed the effects of pharmacologic inhibition of G9a with two innovative epigenetic inhibitors, CM272 and EZM8266. G9a blockade enhanced tumor cell immunogenicity by restoring IFN{gamma} responsiveness, increasing MHC-I surface expression, and promoting chemokine-mediated (CXCL10) recruitment of T cells. Mechanistically, G9a inhibition induced a viral mimicry response through derepressing endogenous retroviral elements and the accumulation of cytosolic double-stranded RNA. In vivo, G9a inhibition synergized with anti-PD-1 therapy to suppress tumor growth, significantly enhancing CD8 T cell infiltration. Notably, in a clinically-relevant post-hepatectomy HCC recurrence model, the combination therapy overcame immune resistance. ConclusionsG9a functions as a central epigenetic barrier to antitumor immunity in HCC. Pharmacologic G9a inhibition reprograms the tumor microenvironment, enhances immunogenicity, and sensitizes tumors to ICIs. These findings provide strong preclinical rationale for integrating G9a-targeted therapies with immunotherapy, particularly in perioperative settings.

pharmacology and toxicology↗

bioRxiv2022

Ceramide synthase 6 (CerS6) promotes alcohol-induced fatty liver by promoting metabolic dysfunction and upregulating lipid droplet-associated proteins

ObjectiveAlcohol-associated liver disease (ALD) is the leading cause of liver-related mortality worldwide. Current strategies to manage ALD largely focus on advanced stage disease, however, metabolic changes such as glucose intolerance are apparent at the earliest stage of alcoholic steatosis and increase the risk of disease progression. Ceramides impair insulin signaling and accumulate in ALD, and metabolic pathways involving ceramide synthase 6 (CerS6) are perturbed in ALD during hepatic steatosis. In this study, we aimed to investigate the role of CerS6 in ALD development. MethodsC57BL/6 WT and CerS6 KO mice of both sexes were fed either a Lieber-DeCarli control (CON) or 15% ethanol (EtOH) diet for 6 weeks. In vivo metabolic tests including glucose and insulin tolerance tests (GTT and ITT) were performed. The mice were euthanized, and liver histology and lipid levels in serum and liver were measured. For in vitro studies, CerS6 was deleted in human hepatocytes and were incubated with EtOH and/or C16:0-ceramides. RNAseq analysis was performed in mice and in liver from patients with different stages of ALD and diseased controls. ResultsAfter six weeks on an EtOH diet, CerS6 KO mice had reduced body weight, food intake, and %fat mass compared to WT mice. Male (but not female) EtOH-fed KO mice showed significantly higher O2 consumption, CO2 production, respiratory exchange ratio, and energy expenditure (P<0.05 for all) during the dark period compared to EtOH-fed WT mice. In response to EtOH, WT mice developed mild hepatic steatosis, while steatosis was alleviated in KO mice as determined by H&E and ORO staining. KO mice showed significantly decreased long-chain ceramide species, especially C16:0 ceramides, in the serum and liver tissues compared to WT mice. CerS6 deletion decreased serum TG and NEFA only in male not female mice. CerS6 deletion improved glucose tolerance and insulin resistance in EtOH-fed mice of both sexes. RNAseq analysis revealed that 74 genes are significantly upregulated and 66 genes are downregulated by CerS6 deletion in EtOH-fed male mice, with key network pathways including TG biosynthetic process, positive regulation of lipid localization, and fat cell differentiation. Similar to RNAseq results, absence of CerS6 significantly decreased mRNA expression of lipid droplet associated proteins in EtOH-fed mice. In vitro, EtOH stimulation significantly increased PLIN2 protein expression in VL-17A cells while CerS6 deletion inhibited EtOH-mediated PLIN2 upregulation. C16:0-ceramide treatment significantly increased PLIN2 protein expression compared to CON. Importantly, progression of ALD in humans was associated with increased CerS6 hepatic expression. ConclusionsOur findings demonstrate that CerS6 deletion attenuates EtOH-induced weight gain and hepatic steatosis and improves glucose homeostasis in mice fed an EtOH diet. Notably, we unveil that CerS6 plays a major role as a regulator of lipid droplet biogenesis in alcoholic intra-hepatic lipid droplet formation. Together, our data suggest that CerS6 may be targeted for treatment for early stage ALD.

pathology↗