The liver is a major store of glycogen and is essential in maintaining systemic glucose homeostasis. In healthy individuals, glycogen synthesis and breakdown in the liver are tightly regulated. Abnormal glycogen metabolism results in prominent pathological changes in the liver, often manifesting as hepatic glycogenosis or glycogen inclusions. This can occur in genetic glycogen storage disease or acquired conditions with insulin dysregulation such as diabetes mellitus and non-alcoholic fatty liver disease or medication effects. Some primary hepatic tumors such as clear cell hepatocellular carcinoma also demonstrate excessive glycogen accumulation. This review provides an overview of the pathological manifestations and molecular mechanisms of liver diseases associated with abnormal glycogen accumulation.

Increasing evidence implicates ceramides in the pathogenesis of metabolic dysfunction-associated steatohepatitis (MASH). However, the therapeutic potential of liver-targeted ceramide lowering remains unclear. In this study, we demonstrate that elevated ceramide levels in MASH patients and mouse models are closely associated with the activation of hepatic de novo ceramide synthesis. The analysis of human hepatic single-nucleus RNA sequencing (snRNA-seq) data revealed predominant up-regulation of SPTLC2 , which encodes a subunit of the rate-limiting enzyme in the de novo ceramide synthesis pathway, in hepatocytes. By targeted inhibition of SPTLC2 with lipid nanoparticle–mediated siRNA delivery to hepatocytes, we reduced both hepatic and circulating ceramide levels. This intervention suppressed hepatic lipid uptake and lipogenesis, thereby alleviating MASH progression. Therapeutic efficacy was demonstrated in an 8-week methionine-choline–deficient diet-induced MASH model and validated in a 1-year choline-deficient high-fat diet–induced MASH model. Our findings highlight hepatocyte Sptlc2 as a promising therapeutic target for MASH.

Intra and inter-pathologist variability poses a significant challenge in metabolic dysfunction-associated steatohepatitis (MASH) biopsy evaluation, leading to suboptimal selection of patients and confounded assessment of histological response in clinical trials. We evaluated the utility of an artificial intelligence (AI) digital pathology (DP) platform to help pathologists improve the reliability of fibrosis staging. A total of 120 digitized histology slides from two trials (NCT03517540, NCT03912532) were analyzed by four expert hepatopathologists, with and without AI assistance in a randomized, crossover design. We utilized an AI DP platform consisting of unstained second harmonic generation/two photon excitation fluorescence (SHG/TPEF) images and AI quantitative fibrosis (qFibrosis) values. AI assistance significantly improved inter-pathologist kappa for fibrosis staging, particularly for early fibrosis (F0-F2), with reduced variance around the median reads. Intra-pathologist kappa was unchanged. AI assistance increased pathologist concordance for identifying clinical trial inclusion cases (F2-F3) from 45% to 71%, exclusion cases (F0/F1/F4) from 38% to 55%, and evaluation of fibrosis response to treatment from 49% to 61%. SHG/TPEF images, qFibrosis continuous values, and qFibrosis stage were considered useful by at least three out of four pathologists in 83%, 55%, and 38% of cases, respectively. In the context of a clinical trial, the increase in inter-pathologist concordance was modeled to result in a ∼25% reduction in the potential need for adjudication as well as a ∼45% increase in the study power for a kappa improvement from ∼0.4 to ∼0.7. The use of AI DP enhances inter-rater reliability of fibrosis staging for MASH. This indicates that the SHG/TPEF-based AI DP tool is useful for assisting pathologists in assessing fibrosis, thereby enhancing clinical trial efficiency and reliability of fibrosis readouts in response to treatments. Implementing an AI DP platform as a tool for pathologists significantly improved inter-pathologist agreement on fibrosis staging, particularly for early-stage fibrosis (F0-F2), which is critical for clinical trial eligibility. The second harmonic generation imaging technology used in conjunction with AI quantitative scores provided enhanced visualization of fibrosis with an indication of severity along the disease continuum. This led to increased pathologist confidence in fibrosis staging and, therefore, increased pathologist concordance for the classification of clinical trial inclusion/exclusion and evaluation of treatment, compared to a standard scoring method based on traditional stains without AI assistance. Improved pathologist concordance with AI assistance could streamline clinical trial processes, reducing the need for adjudication and enhancing study power, potentially decreasing required sample sizes. Continued exploration of the utility of AI assistance across a broader range of pathologists and in prospective clinical trials will be essential for validating the effectiveness of AI assistance.

Lifestyle and environmental-related exposures are important risk factors for hepatocellular carcinoma (HCC), suggesting that epigenetic dysregulation significantly underpins HCC. We profiled 30 surgically resected tumours and the matched adjacent normal tissues to understand the aberrant epigenetic events associated with HCC. We identified tumour differential enhancers and the associated genes by analysing H3K27 acetylation (H3K27ac) chromatin immunoprecipitation sequencing (ChIP-seq) and Hi-C/HiChIP data from the resected tumour samples of 30 patients with early-stage HCC. This epigenome dataset was analysed with previously reported genome and transcriptome data of the overlapping group of patients from the same cohort. We performed patient-specific differential expression testing using multiregion sequencing data to identify genes that undergo both enhancer and gene expression changes. Based on the genes selected, we identified two patient groups and performed a recurrence-free survival analysis. We observed large-scale changes in the enhancer distribution between HCC tumours and the adjacent normal samples. Many of the gain-in-tumour enhancers showed corresponding upregulation of the associated genes and vice versa, but much of the enhancer and gene expression changes were patient-specific. A subset of the upregulated genes was activated in a subgroup of patients’ tumours. Recurrence-free survival analysis revealed that the patients with a more robust upregulation of those genes showed a worse prognosis. We report the genomic enhancer signature associated with differential prognosis in HCC. Findings that cohere with oncofoetal reprogramming in HCC were underpinned by genome-wide enhancer rewiring. Our results present the epigenetic changes in HCC that offer the rational selection of epigenetic-driven gene targets for therapeutic intervention or disease prognostication in HCC. Lifestyle and environmental-related exposures are the important risk factors of hepatocellular carcinoma (HCC), suggesting that tumour-associated epigenetic dysregulations may significantly underpin HCC. We profiled tumour tissues and their matched normal from 30 patients with early-stage HCC to study the dysregulated epigenetic changes associated with HCC. By also analysing the patients’ RNA-seq and clinical data, we found the signature genes – with epigenetic and transcriptomic dysregulation – associated with worse prognosis. Our findings suggest that systemic approaches are needed to consider the surrounding cellular environmental and epigenetic changes in HCC tumours.

The top cause of mortality in patients with nonalcoholic fatty liver disease (NAFLD) is cardiovascular complications. However, mechanisms of NAFLD‐associated vasculopathy remain understudied. Here, we show that blood outgrowth endothelial cells (BOECs) from NAFLD subjects exhibit global transcriptional upregulation of chemokines and human leukocyte antigens. In mouse models of diet‐induced NAFLD, we confirm heightened endothelial expressions of CXCL12 in the aortas and the liver vasculatures, and increased retention of infiltrated leukocytes within the vessel walls. To elucidate endothelial‐immune crosstalk, we performed immunoprofiling by single‐cell analysis, uncovering T cell intensification in NAFLD patients. Functionally, treatment with a CXCL12‐neutralizing antibody is effective at moderating the enhanced chemotactic effect of NAFLD BOECs in recruiting CD8⁺ T lymphocytes. Interference with the CXCL12‐CXCR4 axis using a CXCR4 antagonist also averts the impact of immune cell transendothelial migration and restores endothelial barrier integrity. Clinically, we detect threefold more circulating damaged endothelial cells in NAFLD patients than in healthy controls. Our work provides insight into the modulation of interactions with effector immune cells to mitigate endothelial injury in NAFLD.