Esophageal adenocarcinoma (EAC) and gastric cancer (GC) remain major causes of cancer-related mortality worldwide, largely because of late-stage diagnosis. Barrett’s esophagus (BE) is the established precursor setting for EAC, whereas gastric intestinal metaplasia is an important precursor lesion in the intestinal-type gastric carcinogenesis pathway. Aberrant DNA methylation arises early in both pathways and may offer greater sensitivity and specificity than histology or serology alone, while also illuminating the biology of neoplastic progression. This review evaluates the evidence and translational potential of DNA methylation biomarkers in upper gastrointestinal adenocarcinoma.

PubMed, Web of Science, and EMBASE were searched for studies published before May 2026 addressing DNA methylation biomarkers in BE, EAC, gastric intestinal metaplasia, and GC. Tissue-based, minimally invasive, and circulating biomarkers were reviewed, with emphasis on diagnostic performance, progression risk, biological significance, and clinical translation.

Methylation alterations accumulate during progression from precancerous lesions to invasive cancer and distinguish disease states in tissue and minimally invasive specimens. Methylation-based assays show promising diagnostic performance in BE and EAC, including nonendoscopic cytology-based approaches and risk-stratification assays, and circulating methylated DNA shows potential for noninvasive detection of EAC and GC. However, heterogeneity in populations, specimens, assay platforms, and study designs, together with limited prospective validation, remains a barrier to implementation.

The field is moving rapidly from discovery toward practice: Cytosponge-TFF3 with biomarker panels has been evaluated in real-world UK surveillance pathways, the EsoCheck/EsoGuard methylation assay is clinically available, and Esopredict is the first epigenetic prognostic assay clinically validated to risk-stratify BE, while multicancer early detection assays undergo prospective evaluation. Multicenter studies of clinical utility and cost-effectiveness remain the decisive step before routine adoption.

Anal canal melanoma (ACM) is a rare, aggressive malignancy with an ominous prognosis. However, its associated factors are largely unknown. Therefore, we investigated potential independent associations of sex and self-reported race with ACM and physiological anal canal pigmentation.

Two case-control cohorts from a single institution in Miami, Florida, were evaluated. The biopsy cohort comprised 117 sequential patients evaluated prospectively for melanocytic cells/pigment and anal intraepithelial neoplasia (AIN)/squamous intraepithelial lesion (SIL) in anal transitional zone biopsies between January 2021 and August 2022. The melanoma cohort consisted of 28 patients diagnosed with ACM between January 2003 and August 2021 and 116 of the patients in the pigmentation cohort. Multivariable logistic regression analysis was conducted to examine independent factor associations.

In the biopsy cohort, anal transitional melanocytic cells/pigment were identified in 48% (26/54) of Black patients compared to 17% (10/59) of White patients. Multivariable analysis demonstrated that White race was inversely associated with mucosal pigmentation (odds ratio (OR) = 0.19, 95% confidence interval (CI): 0.08–0.48, P < 0.001). Conversely, White race was associated with ACM (OR = 6.25, 95% CI: 2.07–18.81, P = 0.001). Male sex was also inversely associated with ACM (OR = 0.18, 95% CI: 0.07–0.47, P < 0.001). No significant correlations were observed between mucosal pigmentation and AIN/SIL or human immunodeficiency virus status.

Anal transitional zone pigmentation is more prevalent in self-reported Black individuals but is not associated with neoplastic squamous cell precursors. White (versus Black) individuals and female (versus male) individuals both have a significant association with ACM.

Celiac disease remains underdiagnosed despite an established diagnostic pathway, reflecting phenotypic heterogeneity, delayed recognition, and dependence on resource-intensive testing. This narrative review synthesizes evidence on artificial intelligence and phenomics in celiac disease (CD) across four operational layers: electronic health record phenotyping, Human Phenotype Ontology-based semantic encoding, machine-learning pre-screening from routine clinical data, and deep-learning-assisted histopathology. A targeted literature search of PubMed/MEDLINE, Embase, and Google Scholar covered publications from January 2010 through December 2025, using combinations of CD/coeliac disease with artificial intelligence, machine learning, deep learning, phenomics, Human Phenotype Ontology, computable phenotype, electronic health records, and natural language processing, supplemented by targeted searches and citation chaining. We present a curated minimum viable CD phenome and discuss clinical actionability, age-specific considerations, and current pediatric validation gaps. Selected models have demonstrated promising CD detection or pre-screening performance in specific datasets, but prospective, multicenter evidence with external validation remains insufficient to establish clinical utility. Artificial intelligence should augment expert clinical care rather than replace it.

Metabolic dysfunction-associated fatty liver disease (MAFLD) is a multifactorial disorder driven by complex interactions among genetic, epigenetic, transcriptional, proteomic, metabolic, and microbiome factors. Single-omics technologies have provided valuable insights into disease mechanisms, yet each layer captures only a partial view of MAFLD pathogenesis. Recent advances in multi-omics integration allow systematic dissection of molecular networks, cell differentiation trajectories, intercellular communication, and spatial organization, revealing causal links between molecular alterations and tissue phenotypes. Horizontal integration connects different omic layers within the same biological state, while longitudinal integration captures dynamic changes across disease stages. Emerging spatial transcriptomics, proteomics, and metabolomics techniques further enable in situ mapping of cellular and molecular heterogeneity, uncovering spatially defined pathogenic niches and regulatory hubs. Collectively, these integrated approaches offer a multidimensional framework for understanding MAFLD progression, identifying potential biomarkers, and guiding precision therapeutic strategies. Future efforts should focus on standardized multi-omics pipelines, interdisciplinary collaboration, and functional validation to translate these insights into clinical applications.

Metabolic dysfunction-associated steatotic liver disease affects roughly 38% of adults, yet approved agents do not correct the upstream redox-metabolic perturbations—a depressed nicotinamide adenine dinucleotide (NAD+/NADH) ratio, saturated lipid excess, and endoplasmic reticulum (ER) stress—that drive hepatocyte injury. Cytochrome b5 reductase 3 (CYB5R3) couples NADH oxidation to fatty acid desaturation, nuclear factor erythroid 2-related factor 2 (NRF2)-linked antioxidant and cholesterol-handling pathways, NAD+/sirtuin signaling, and ER-phagy, and is the sole electron input to mitochondrial amidoxime-reducing component 1 (mARC1). This review grades every link in the axis across the steatosis–cirrhosis–hepatocellular carcinoma spectrum, reporting effect estimates with sample sizes and test statistics alongside a study-level appraisal of clinical relevance. The common MTARC1 p.A165T variant protects against all-cause cirrhosis (odds ratio, 0.91; 95% CI, 0.89–0.94; P = 2.3 × 10−11; 12,361 cases, 790,095 controls), with lower hepatic fat, liver enzyme levels, and low-density lipoprotein cholesterol levels. Germline mARC1 deletion reduces picrosirius red fibrosis area by 24%–50% depending on diet, without altering histological disease activity, whereas partial protein reduction confers no protection. Critically, therapeutic hepatocyte-directed knockdown loses its anti-fibrotic effect when started at higher disease burden and in the choline-deficient model: efficacy depends on the depth, compartment, and timing of inhibition. Deep, hepatocyte-restricted mARC1 inhibition by GalNAc-conjugated oligonucleotides—which also avoids a male-predominant cardiac liability—is therefore the most credible near-term strategy, only in pre-cirrhotic F2–F3 disease. CYB5R3 activation, and its combination with mARC1 inhibition, remain unproven, and no clinical trial of this axis has been reported. Falsifiable in vivo and pharmacodynamic biomarker roadmaps are proposed, together with the efficacy, delivery, and safety uncertainties specific to advanced cirrhosis and a non-invasive pharmacodynamic framework.

Biliary atresia (BA) is the leading cause of pediatric obstructive cholestasis and a major indication for liver transplantation in infants. Organoid models are increasingly used to investigate BA pathogenesis and therapeutic responses, but incomplete methodological and clinical reporting may limit cross-study comparison and translational interpretation. This study aimed to map the landscape of BA-related organoid research, identify major reporting gaps, and propose the Biliary Atresia Minimum Reporting Standard (BA-MRS) as a preliminary framework for improving reporting completeness.

PubMed, Scopus, and Web of Science Core Collection were searched on March 8, 2026, in accordance with the PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews) and the 2024 Joanna Briggs Institute (JBI) Manual for Evidence Synthesis. Reporting completeness was assessed using a 36-item BA-MRS across six domains, scored as fully reported, partially reported, not reported, or not applicable.

Twenty-six studies published between 2020 and 2026 were included. Fibrosis and epithelial–mesenchymal transition were the most frequently studied themes, whereas only one study linked organoid findings to post-Kasai outcomes. BA case/model definition, ethics approval, and differentiation protocols were fully reported in all applicable studies (100%). In contrast, contamination monitoring (3.8%), core biliary function assays (34.6%), and clinical outcome linkage (26.3%) were poorly reported. Culture System and Sample Acquisition showed the lowest domain-level fully reported rates (58.1% and 63.2%, respectively).

BA organoid research has progressed beyond early model development, but reporting remains insufficient for robust comparison, reproducibility, and clinically meaningful interpretation. BA-MRS may serve as a preliminary framework for improving standardized reporting in future studies.

Biliary atresia (BA) is a severe pediatric cholangiopathy characterized by rapidly progressive liver fibrosis. This study aimed to characterize scar-associated macrophages and investigate the role of plasminogen (PLG)–plasminogen receptor with a C-terminal lysine (PLGRKT) signaling in BA-associated fibrogenesis.

Single-cell RNA sequencing and spatial transcriptomics were applied to liver tissues from patients with BA and non-BA controls. Key findings were validated in an independent cohort using quantitative polymerase chain reaction and multiplex immunohistochemistry. The functional role of the PLGRKT pathway was further examined using primary human peripheral blood mononuclear cell-derived macrophages with small interfering RNA (siRNA)-mediated PLGRKT knockdown, together with co-culture systems involving LX-2 hepatic stellate cells and human liver organoids. In vivo therapeutic potential was evaluated in a murine bile duct ligation model of cholestatic liver fibrosis using macrophage-targeted Plgrkt–Trem2 antibody–siRNA conjugates.

In BA, scar-associated macrophages (SAMs) increased with fibrosis progression and co-localized with hepatic stellate cells in fibrotic areas. PLGRKT was upregulated in BA liver tissue and increased during monocyte-to-macrophage differentiation. In primary human macrophages, PLG induced a PLGRKT-dependent pro-fibrotic phenotype, and conditioned medium from these cells increased COL1A1 deposition in hepatic stellate cells and human liver organoids. In vivo, macrophage-targeted Plgrkt–Trem2 antibody–siRNA conjugates reduced SAM accumulation and attenuated bile duct ligation-induced liver fibrosis.

These findings support a role for SAMs and the PLGRKT–SAM axis in BA-associated liver fibrosis and suggest that PLGRKT warrants further investigation as a potential macrophage-directed anti-fibrotic target.

Although hepatitis B surface antigen (HBsAg)-specific B cells have been partially characterized in chronic hepatitis B (CHB), the role of naïve B cells and their potential relevance to functional cure remain insufficiently explored. Here, we aimed to characterize the naïve B-cell subsets in functionally cured and uncured patients with CHB.

In this retrospective study, we applied single-cell RNA sequencing to compare peripheral B-cell profiles in functionally cured and uncured CHB patients. Key findings were validated by flow cytometry in an independent cohort and further supported in a nucleos(t)ide analog monotherapy cohort stratified by HBsAg levels.

Single-cell RNA sequencing characterized two naïve B-cell subsets, designated IL-4R+SELL+ and IL-4R−SELL− naïve B cells, which were differentially distributed between functionally cured and uncured patients. Functionally cured patients showed higher frequencies of total B cells and IL-4R+SELL+ naïve B cells than uncured patients. In contrast, functionally uncured patients exhibited persistent hyperactivation of type I interferon signaling in both naïve and memory B cells. The IL-4R+SELL+ subset showed a transcriptional signature associated with germinal center biology and exhibited stronger ligand–receptor interactions with CD40LG+CD4+ T cells. Notably, the frequency of the IL-4R+SELL+ subset was inversely correlated with HBsAg levels. Consistently, patients with lower HBsAg levels also exhibited significantly higher frequencies of IL-4R+SELL+ naïve B cells compared with those with high HBsAg levels.

Collectively, these findings indicate that the IL-4R+SELL+ naïve B-cell subset is characterized by germinal center-related responses and enhanced T-cell-mediated help and may serve as an immunological component associated with functional cure in CHB.