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Spatially resolved multiplex protein profiling reveals DNA methylation-dependent microenvironmental remodeling in liver fibrosis
PNAS Nexus. 2026 Feb 25;5(3):pgag047. doi: 10.1093/pnasnexus/pgag047. eCollection 2026 Mar.
ABSTRACT
Liver fibrosis is a significant health concern that affects βΌ300 million people globally, characterized by the excessive accumulation of extracellular matrix (ECM) components in the liver. A major contributor to liver fibrosis is fatty liver disease, which can progress to steatohepatitis when the accumulation of fat in the liver causes inflammation, cell death, and scarring. Long-standing steatohepatitis leads to liver fibrosis as scar tissue builds up and replaces healthy liver tissue, potentially progressing to life-threatening conditions, such as cirrhosis, liver failure, or hepatocellular carcinoma. DNA methylation plays a critical role in the progression of fatty liver disease and liver fibrosis by altering gene expression without modifying the DNA sequence. The integration of spatial analysis with protein profiling enhances our ability to explore the spatial organization of cellular interactions and protein expression in liver diseases, fostering a deeper understanding of the disease mechanisms. Multiplex immunofluorescence (mIF) imaging was performed to understand the spatial organization of 10 molecular targets and the cellular interaction between them across four distinct liver tissue types: wild-type (WT) regular, WT high-fat, fibrosis regular, and fibrosis high-fat. Notably, fibrotic high-fat samples displayed increased pan-cytokeratin and vascular cell adhesion molecule-1 (VCAM-1) expression, suggesting diet-aggravated injury and inflammation. Our findings highlight the interplay between epigenetic regulation, ECM remodeling, and cellular crosstalk in liver fibrosis. The spatial profiling approach provides insights into microenvironmental changes, revealing how DNA methylation influences protein localization and fibrotic progression. These results underscore the potential of spatial omics in elucidating disease mechanisms and guiding targeted therapies for metabolic liver disorders.
PMID:41834947 | PMC:PMC12988774 | DOI:10.1093/pnasnexus/pgag047
Tumor-informed liquid biopsy detection of structural variants in high grade serous ovarian cancer
Oncoscience. 2026 Mar 5;13:44-54. doi: 10.18632/oncoscience.645. eCollection 2026.
ABSTRACT
BACKGROUND: High grade serous ovarian cancer (HGSOC) recurs frequently and commercial tests have emerged for tumor-informed, cell-free DNA (cfDNA)-based detection of minimal residual disease. These tests are based on somatic single nucleotide variants prevalent in many cancers and thus are not well matched to HGSOC, which is dominated by structural genomic rearrangements. The purpose of this study was to evaluate the feasibility of a structural-variant (SV)-informed, cfDNA-based method for detecting clonal and subclonal HGSOC disease burden.
METHODS: A method was developed for detecting patient-specific SV breakpoints using digital droplet PCR (ddPCR) with custom tumor-informed primer/probe pairs. Test parameters were first estimated using synthetic cfDNA generated by ultrasonication of genomic DNA from ovarian cancer cell lines. The optimized workflow was implemented in which whole genome sequencing of multisite pre-treatment HGSOC biopsies performed and high confidence SVs were called by multiple published SV callers. Real-time PCR and ddPCR were used for assay development.
RESULTS: Following the optimized workflow, tumor-specific SV breakpoint-spanning primers/probe sets of four HGSOC patients' multisite biopsies were designed and validated by real-time PCR and ddPCR. Together with four HGSOCs, a total of 29 SVs breakpoints-spanning tumor-informed primers/probe sets were designed and validated in multisite biopsies. 15 validated tumor-specific SVs were selected for quantification in their corresponding liquid biopsies using the validated ddPCR, and 9 had measurements in liquid biopsies.
CONCLUSIONS: Our result shows the detection of SVs from pre-treatment cfDNA using tumor-informed breakpoints-spanning ddPCR is feasible and may enable a novel and sensitive method for monitoring on-treatment disease burden.
PMID:41835357 | PMC:PMC12981705 | DOI:10.18632/oncoscience.645