Endoscopic liquid biopsies of gastric fluid in a large human patient cohort reveal DNA content as a candidate tumor biomarker in gastric cancer
- Laboratory of Medical Genomics, A. C. Camargo Cancer Center, Brazil
- Masters in Health and Life Sciences, Franciscana University, Brazil
- Endoscopy Section, A. C. Camargo Cancer Center, Brazil
- Department of Pathology, A. C. Camargo Cancer Center, Brazil
- Research Support Center, A. C. Camargo Cancer Center, Brazil
- Laboratory of Computational Biology, A. C. Camargo Cancer Center, Brazil
- Postgraduation Program in Applied of Sciences of Adult Health & Alpha Gatroenterology Institute, Hospital das Clínicas, Faculty of Medicine, Federal University of Minas Gerais, Brazil
- University of Latvia, Institute of Clinical and Preventive Medicine and Center for Gastric Diseases GASTRO, Latvia
- Rutgers Cancer Institute, New Brunswick, United States
- Division of Surgical Oncology, Department of Surgery, Rutgers Robert Wood Johnson Medical School, United States
- Rutgers Cancer Institute, United States
- Division of Hematology/Oncology, Department of Medicine, Rutgers New Jersey Medical School, United States
- Division of Medical Oncology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, United States
- Department of Abdominal Surgery, A. C. Camargo Cancer Center, Brazil
- Division of Surgical Oncology, Department of Surgery, Rutgers New Jersey Medical School, United States
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, United States
Figures
Figure 1
gfDNA concentrations observed in all subjects with available data, grouped according to sex, and presence of gastric cancer.
Non-cancer subjects have normal gastric mucosa or minor peptic diseases (excludes pre-neoplastic disease). Statistical comparisons were performed using the Kruskal–Wallis test, followed by pairwise Mann–Whitney U tests with Benjamini–Hochberg correction. P-values < 0.05 were considered significant. Error bars indicate median gfDNA concentration (ng/µL) with interquartile ranges.
Figure 2
gfDNA concentration according to disease diagnosis and tumor stage.
(A) gfDNA concentration (ng/µL) in patients with no endoscopic findings: Normal (N) or presenting minor peptic diseases (PD) – N+PD; preneoplastic conditions (PN), or gastric cancer (Cancer). (B) gfDNA concentrations (ng/µL) for early-stage disease patients – T0-T2 (T0 +Tis + T1+T2), as compared to more advanced disease stages T3 and T4. Statistical comparisons were performed using the Kruskal–Wallis test, followed by pairwise Mann–Whitney U tests with Benjamini–Hochberg correction. P-values < 0.05 were considered significant. Error bars indicate mean gfDNA concentration (ng/µL) and 95% confidence intervals.
Figure 3
Analysis of receiver operating characteristics (ROC) and area under the curve (AUC) for gfDNA levels between cancer patients and non-cancer individuals.
(A) ROC curve of gfDNA between the cancer patients and non-cancer individuals. (B) ROC curve of gfDNA between cancer versus non-cancer and cancer + preneoplastic conditions versus peptic diseases + normal.
Figure 4
gfDNA analysis according to patient survival and infiltration of inflammatory cells.
(A) For a total of 148 non-metastatic GC patients, cutoff gfDNA concentrations determined by a log-rank test (1.28 ng/µL) discriminate survival free of tumor progression (p=0.009). (B) For a subset of 32 cases, for which representative biopsy H&E slides were available, inflammatory cell infiltrates in the gastric tumors were inspected by experienced pathologists and (C) have shown that more intense inflammatory infiltrates in tumors are characteristic of subjects with higher gfDNA concentrations (p=0.001). gfDNA value distributions were compared using the non‑parametric Mann–Whitney U test.P‑values < 0.05 were considered statistically significant. Error bars indicate mean gfDNA concentration (ng/µL) and 95% confidence intervals.
Author response image 1
Tables
Table 1
Clinical and demographic attributes of participating subjects (n=941).
| Non-gastric cancer*(n=705, 74.9%) | Gastric cancer(n=236, 25.1%) | ||
|---|---|---|---|
| Age | ≤45 | 130 (18.4%) | 34 (14.4%) |
| 45–60 | 224 (31.8%) | 83 (35.2%) | |
| ≥60 | 343 (48.7%) | 119 (50.4%) | |
| Missing data | 8 (1.1%) | 0 | |
| Sex | Male | 330 (46.8%) | 150 (63.6%) |
| Female | 367 (52.1%) | 86 (36.4%) | |
| Missing data | 8 (1.1%) | 0 | |
| †BMI | Underweight | 10 (1.4%) | 9 (3.8%) |
| Normal weight | 206 (29.2%) | 91 (38.6%) | |
| Overweight | 310 (44%) | 84 (35.6%) | |
| Obese | 177 (25.1%) | 51 (21.6%) | |
| Missing data | 2 (0.3%) | 1 (0.4%) | |
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*
Includes all patients diagnosed as presenting normal mucosa, with peptic diseases or pre-neoplastic lesions.
-
†
Body-mass index (BMI): Underweight, BMI <18.5; Normal weight, BMI = 18.5–24.9; Overweight, BMI = 25–29.9; Obese, BMI ≥30.
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Chemical compound, drug | Phenol Chloroform | Sigma Sigma | P4682 472476 | Used to remove proteins and lipids during DNA extraction. |
| Software, algorithm | R statistical environment GraphPad | R Core Team Prism | RRID:SCR_025679 RRID:SCR_002798 | Version 4.2.0, 2022 Version 10.4.1 (532) Dec. 2024 |
| Other | Proteinase-K | Bioline | BIO37037 | Enzyme used for protein digestion during DNA extraction. |
Author response table 1
| Diagnosis group | Mean gfDNA and 95% Confidence Interval |
|---|---|
| Normal mucosa and peptic diseases (N=606) | 10.77ng//muL; 95% CI: 9.23 to 12.33; |
| Preneoplastic conditions (N=99) | 10.10ng//muL; 95% Cl: 7.59 to 12.60 |
| T2 and below (N=65) | 15.12ng//muL; 95% Cl: 9.73 to 20.50 |
| T3 and above (N=154) | 30.75ng//muL; 95% Cl: 14.24 to 36.62 |
Additional files
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MDAR checklist
- https://cdn.elifesciences.org/articles/107103/elife-107103-mdarchecklist1-v1.docx
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Supplementary file 1
Analysis of CT values for bacteria and human target genes.
- https://cdn.elifesciences.org/articles/107103/elife-107103-supp1-v1.xlsx
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Supplementary file 2
Performance metrics of the ROC/AUC curves shown in Figure 3.
- https://cdn.elifesciences.org/articles/107103/elife-107103-supp2-v1.xlsx
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Supplementary file 3
gfDNA concentration and intensity of inflammatory cell infiltrates.
- https://cdn.elifesciences.org/articles/107103/elife-107103-supp3-v1.xlsx
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Endoscopic liquid biopsies of gastric fluid in a large human patient cohort reveal DNA content as a candidate tumor biomarker in gastric cancer
eLife 14:RP107103.
https://doi.org/10.7554/eLife.107103.3
