Current Applications of Liquid Biopsy in Gastrointestinal Cancer Disease-From Early Cancer Detection to Individualized Cancer Treatment

Clinical Applications of Circulating Tumor DNA Profiling in GI Cancers

Over the next few years, the analysis of circulating tumor DNA (ctDNA) through liquid biopsy is expected to enter clinical practice and revolutionize the approach to biomarker testing and treatment selection in GI cancers. In fact, growing evidence support the use of ctDNA testing as a noninvasive, effective, and highly specific tool for molecular profiling in GI cancers. Analysis of blood ctDNA has been investigated in multiple settings including early tumor detection, minimal residual disease evaluation, tumor diagnosis and evaluation of prognostic/predictive biomarkers for targeted treatment selection, longitudinal monitoring of treatment response, and identification of resistance mechanisms. Here, we review the clinical applications, advantages, and limitations of ctDNA profiling for precision oncology in GI cancers.

Correlation of Endoscopic and Histopathological Diagnoses in Upper Gastrointestinal Tract Lesions: A Cross-Sectional Study

Introduction Gastrointestinal tract (GIT) endoscopy with biopsy is essential for diagnosing and managing various GIT diseases, including malignancies and inflammatory conditions. This study aimed to analyze the spectrum of histopathological lesions in the GIT and their correlation with the endoscopic findings. Methodology This retrospective observational study was conducted at a tertiary medical college involving 114 patients who underwent GIT endoscopy between June 2023 and June 2024. This study focused on lesion types across different GIT sites (esophagus, stomach, and duodenum) and the agreement between endoscopic and histological diagnoses. Results Lesions were most prevalent in the stomach (52.6% of cases, n=60), followed by the duodenum (35.1%, n=40) and esophagus (12.3%, n=14). Significant correlations were found between endoscopic and histological diagnoses in the esophagus (concordance for esophagitis was 100%) and stomach (concordance for gastritis was 95%). In the duodenum, the concordance was high for duodenitis (100%) but lower for other lesions such as neuroendocrine tumors (71.43%). However, Cohen's kappa values indicated poor overall agreement across all sites (κ=0.49), reflecting variability in diagnostic accuracy. Conclusion This study highlights the reliability of endoscopic procedures for diagnosing upper GIT lesions, particularly in the esophagus and stomach, while emphasizing the challenges in diagnosing duodenal lesions. These findings support the need for targeted screening and further research to enhance diagnostic accuracy and patient outcomes in GIT diseases.

Combining non-invasive liquid biopsy and a methylation analysis to assess surgical risk for early esophageal cancer

Background

While the widespread use of endoscopic submucosal dissection (ESD) has significantly reduced the incidence of early esophageal cancer (ESCA), the limited ability of ESD to strip deep infiltrating esophageal lesions results in a considerable risk of intraoperative perforation. Circulating-free DNA (cfDNA) is widely used in modern tumor screening due to its non-invasive detection capabilities. A methylation analysis offers vital insights into the condition and advancement of malignancies due to its unique positioning, such as a marker of cancer. This study investigated the potential of combining a non-invasive liquid biopsy technique, along with a methylation analysis, to assess the surgical perforation risk of ESCA patients.

Methods

In this study, we conducted an analysis of gene expression differences between stage I esophageal squamous carcinoma samples and healthy tissue samples using data from The Cancer Genome Atlas (TCGA) database. We also identified the genes associated with progression-free survival (PFS) in esophageal squamous carcinoma. Integrating the framework of the methylation analysis, we explored the methylated sites of these distinct genes. To refine this process, we used the Shiny Methylation Analysis Resource Tool (SMART) to conduct a comprehensive analysis of these sites. We then confirmed the stability of the methylation sites in different lesion conditions using methylation-specific quantitative polymerase chain reaction (MS-qPCR) with paraffin tissue samples collected after ESD.

Results

We analyzed RNA-sequencing data from 42 early stage ESCA patients and 17 controls, identifying 1,263 up-regulated and 460 down-regulated genes. Functional analyses revealed involvement in key pathways such as cell cycle regulation and immune responses. Furthermore, we identified 38 differentially expressed genes associated with PFS. Using SMART analysis, we found 217 hyper-methylated regions in 38 genes, suggesting potential early markers for ESCA. Validation experiments confirmed the reliability of 29 hyper-methylated regions in FFPE tissue samples and 6 regions in cfDNA. A LunaCAM model showed high accuracy [area under the curve (AUC) =0.89] in discriminating early ESCA. Integrated assessment of six highly methylated regions significantly improved predictive performance, with 90.56% sensitivity, highlighting the importance of combinatorial biomarker evaluation for early cancer detection.

Conclusions

This study established a novel approach that integrates non-invasive testing with a methylation analysis to assess the surgical risk of early ESCA patients. The significance of changes in methylation sites in relation to lesion status should not be underestimated, as they have the potential to offer vital insights for proactive risk assessments before surgery.