bims-dinmec 2026-04-26 papers

Issue of 2026–04–26
three papers selected by
Lorena Ancona, Humanitas Research

iScience. 2026 May 15. 29(5): 115425

Pan-cancer differentially methylated regions are promising biomarkers for non-invasive diagnosis in multiple cancers.

Zhixian Zhu, Yuanhui Sun, Xionghui Zhou, Guoliang Li.

DNA methylation is a well-established biomarker for cancer diagnosis, and most studies have focused on cancer-type-specific markers. However, methylation biomarkers applicable to multiple cancer types remain largely unexplored, posing a challenge for multi-cancer detection. Here, we identified pan-cancer differentially methylated regions (DMRs) by analyzing 197 whole-genome bisulfite sequencing datasets spanning 11 malignancies. Compared to cancer-type-specific DMRs, pan-cancer DMRs exhibited conserved methylation alterations across tumor types and significantly greater differential methylation in both tissue and cell-free DNA (cfDNA). A diagnostic model leveraging pan-cancer DMRs accurately detected seven cancer types in a plasma cfDNA dataset (n = 1,108), achieving 77% sensitivity and 96.9% specificity in the test set, with sensitivities of 69.6% and 70.4% for stage I and II patients, respectively. Overall, our findings establish pan-cancer DMRs as promising biomarkers for non-invasive diagnosis of multiple cancer types.

Keywords: cancer; diagnostics; genomics

DOI: https://doi.org/10.1016/j.isci.2026.115425

Adv Genet (Hoboken). 2026 Mar;7(1): e00069

PDMSA: A Web-Based Tool for Pan-Cancer Survival Analysis Using DNA Methylation Levels as Biomarkers.

Weiwei Guo, Ying Shi, Shanshan Wu, Hong Yang, Anqi Lin, Peng Luo.

DNA methylation levels are intimately associated with tumor development, progression, and therapeutic outcomes. Accurate analysis of the relationship between DNA methylation levels and tumor prognosis facilitates comprehensive investigation of tumor development mechanisms, enabling optimization of clinical decision-making and subsequent enhancement of cancer patient survival rates. However, current web-based tools for analyzing tumor methylation levels and survival prognosis exhibit significant limitations. We have developed a web-based tool called Pan-cancer DNA Methylation Survival Analysis (PDMSA) implemented in Shiny, which integrates DNA methylation data and clinical information from large public databases (TCGA and GEO). PDMSA currently encompasses tumor DNA methylation data from 30 TCGA datasets and 15 GEO datasets, consisting of 16 205 211 records that span 39 cancer types, 45 datasets, 19 909 genes, and 8369 samples. The tool executes prognostic Kaplan-Meier survival analysis and Cox regression analysis utilizing two distinct cutoff value grouping methods, offering customizable visualization options for the results. As a user-friendly analytical platform, PDMSA serves as a comprehensive tool for biomedical researchers to investigate the relationship between methylation levels at specific gene loci and tumor survival outcomes, thereby facilitating the advancement of precision medicine in oncology. Access PDMSA at robinl-lab.com/PDMSA.

Keywords: DNA methylation; R Shiny; biomarker; cancer; survival analysis

DOI: https://doi.org/10.1002/ggn2.202500069

J Liq Biopsy. 2026 Jun;12 100465

Liquid biopsies for the diagnosis of early-stage gastric cancer: A 5-year systematic review.

Efthymia Papaioannou, Despoina Ioannou, Theodora Papamitsou, Matthaios Bobos, Michalis Aivaliotis, Konstantina Psatha, Evangelos Karamitrousis.

Gastric cancer remains one of the leading causes of cancer-related mortality worldwide, largely due to its late-stage diagnosis. Liquid biopsy has emerged as a promising, minimally invasive method for early cancer detection, leveraging circulating biomarkers such as nucleic acids, extracellular vesicles, and tumor cells.
Objective: This systematic review aimed to evaluate the emerging role of liquid biopsy as a diagnostic tool for the early detection of primary gastric cancer, focusing on the past five years of published research.
Methods: Following PRISMA guidelines and based on the PICO framework, a comprehensive literature search was conducted across PubMed and Scopus databases, yielding 620 articles. After screening and eligibility assessment, 16 studies were included. Quality evaluation was performed using the QUADAS-2 tool and Analytical Validation Summaries.
Results: The included studies demonstrated consistently high diagnostic performance of various liquid biopsy-derived biomarkers. Notably, circulating non-coding RNAs-particularly miRNAs, circRNAs, lncRNAs, and tsRNAs-showed high sensitivity and specificity in early-stage gastric cancer detection. DNA methylation signatures, cfDNA fragmentomics, lipidomic profiles, and folate receptor-positive CTCs, also emerged as valuable diagnostic modalities. Most studies reported area under the curve (AUC) values exceeding 0.85, with several outperforming conventional serum markers, such as CEA and CA19-9.
Conclusions: Liquid biopsy holds significant promise as a non-invasive, accurate diagnostic approach for early gastric cancer. RNA-based and cfDNA-based biomarkers, in particular, exhibit strong potential for integration into routine screening protocols. Further large-scale, prospective validation studies are warranted to support clinical translation and standardization.

Keywords: Biomarkers; Gastric cancer; Liquid biopsy; Oncology

DOI: https://doi.org/10.1016/j.jlb.2026.100465