Using Tumor Marker Gene Variants to Improve the Diagnostic Accuracy of DUPAN-2 and Carbohydrate Antigen 19-9 for Pancreatic Cancer

Abstract

Purpose: Circulating carbohydrate antigen 19-9 (CA19-9) levels reflect FUT3 and FUT2 fucosyltransferase activity. Measuring the related glycan, DUPAN-2, can be useful in individuals unable to synthesize CA19-9. We hypothesized that similar to CA19-9, FUT functional groups determined by variants in FUT3 and FUT2 influence DUPAN-2 levels, and having tumor marker reference ranges for each functional group would improve diagnostic performance.

Materials and methods: Using a training/validation study design, FUT2/FUT3 genotypes were determined in 938 individuals from Johns Hopkins Hospital: 607 Cancer of the Pancreas Screening (CAPS) study subjects with unremarkable pancreata and 331 with pancreatic ductal adenocarcinoma (PDAC). Serum DUPAN-2 and CA19-9 levels were measured by immunoassay.

Results: In controls, three functional FUT groups were identified with significant differences in DUPAN-2 levels: FUT3-intact, FUT3-null/FUT2-intact, and FUT3-null/FUT2-null. DUPAN-2 training set diagnostic cutoffs for each FUT group yielded higher diagnostic sensitivity in the validation set for patients with stage I/II PDAC than uniform cutoffs (60.4% [95% CI, 50.2 to 70.0] v 39.8% [30.0 to 49.8]), at approximately 99% (96.7 to 99.6) specificity. Combining FUT/CA19-9 and FUT/DUPAN-2 tests yielded 78.4% (72.3 to 83.7) sensitivity for stage I/II PDAC, at 97.7% (95.3 to 99.1) specificity in the combined sets, with higher AUC (stage I/II: 0.960 v 0.935 for CA19-9 + DUPAN-2 without the FUT test; P < .001); for stage I PDAC, sensitivity was 62.0% (49.1 to 73.2; AUC, 0.919 v 0.883; P = .03). CA19-9 levels in FUT3-null/FUT2-null PDAC subjects were higher than in FUT3-null/FUT2-intact subjects (median/IQR; 24.9/57.4 v <1/2.3 U/mL; P = .0044). In a simulated CAPS cohort, AUC precision recall (AUC_PR) scores were 0.51 for CA19-9 alone, 0.64 for FUT/CA19-9, 0.73 for CA19-9/DUPAN-2, and 0.84 for FUT/CA19-9/DUPAN-2.

Conclusion: Using a tumor marker gene test to individualize CA19-9 and DUPAN-2 reference ranges achieves high diagnostic performance for stage I/II pancreatic cancer.

FIG 1.

The effect of FUT functional groups on CA19-9 and DUPAN-2 synthesis. Synthetic pathway for Lewis antigens and related molecules in subjects with (A) normal FUT2 and FUT3 function (as predicted by the gene sequencing); (B) FUT3± and FUT2-intact; FUT3± indicates heterozygous for a null variant (lower CA19-9 levels), FUT2-intact meaning at least one functional FUT2 allele; (C) FUT2-null/FUT3 not null (higher CA19-9 levels); (D) FUT3-null/FUT2-intact (absent CA19-9/higher DUPAN-2 levels); (E) FUT3-null/FUT2-null (absent CA19-9 levels/highest DUPAN-2 levels). CA19-9, carbohydrate antigen 19-9.

FIG 2.

FUT functional group–stratified DUPAN-2 levels. (A) DUPAN-2 levels among controls classified into three functional FUT groups. In both the testing and validation set controls, DUPAN-2 levels differ significantly between each group. (B and C) Within each FUT group, DUPAN-2 levels are significantly higher among PDAC cases compared with controls (P < .05) in (B) the training set and (C) the validation set. The control box plots show the mean, and the 25th and the 75th percentile of values. Note that the y-axis scale is different for each group and the horizontal line at the 500 U/mL level indicates a change in the y-axis scale. PDAC, pancreatic ductal adenocarcinoma.

FIG 3.

Diagnostic performance of CA19-9 and DUPAN-2, alone and with FUT group classification. Receiver operating characteristic curve analysis for stage I PDAC of CA19-9 alone versus CA19-9 by FUT group determined by the (A) FUT TMGT, (B) DUPAN-2 alone versus DUPAN-2 by FUT group, and (C) CA19-9 and DUPAN-2 combined (either test-positive) without FUT group, versus by FUT group. (D-F) Stage I/II PDAC versus controls. FUT group defined by FUT2/3 gene variants. CA19-9, carbohydrate antigen 19-9; PDAC, pancreatic ductal adenocarcinoma; TMGT, tumor marker gene test.