Integrating next-generation sequencing to endoscopic retrograde cholangiopancreatography (ERCP)-obtained biliary specimens improves the detection and management of patients with malignant bile duct strictures

Abstract

Objective: Despite improvements in imaging, serum CA19-9 and pathological evaluation, differentiating between benign and malignant bile duct strictures remains a diagnostic conundrum. Recent developments in next-generation sequencing (NGS) have opened new opportunities for early detection and management of cancers but, to date, have not been rigorously applied to biliary specimens.

Design: We prospectively evaluated a 28-gene NGS panel (BiliSeq) using endoscopic retrograde cholangiopancreatography-obtained biliary specimens from patients with bile duct strictures. The diagnostic performance of serum CA19-9, pathological evaluation and BiliSeq was assessed on 252 patients (57 trainings and 195 validations) with 346 biliary specimens.

Results: The sensitivity and specificity of BiliSeq for malignant strictures was 73% and 100%, respectively. In comparison, an elevated serum CA19-9 and pathological evaluation had sensitivities of 76% and 48%, and specificities of 69% and 99%, respectively. The combination of BiliSeq and pathological evaluation increased the sensitivity to 83% and maintained a specificity of 99%. BiliSeq improved the sensitivity of pathological evaluation for malignancy from 35% to 77% for biliary brushings and from 52% to 83% for biliary biopsies. Among patients with primary sclerosing cholangitis (PSC), BiliSeq had an 83% sensitivity as compared with pathological evaluation with an 8% sensitivity. Therapeutically relevant genomic alterations were identified in 20 (8%) patients. Two patients with ERBB2-amplified cholangiocarcinoma received a trastuzumab-based regimen and had measurable clinicoradiographic response.

Conclusions: The combination of BiliSeq and pathological evaluation of biliary specimens increased the detection of malignant strictures, particularly in patients with PSC. Additionally, BiliSeq identified alterations that may stratify patients for specific anticancer therapies.

Keywords: ampulla; bile duct; cholangiocarcinoma; dysplasia; genomics; molecular; pancreas; pancreatic cancer; precision medicine.

Figure 1

Correlative findings of both training and validation cohorts for pathological examination of biliary brushings/biopsies and individual genomic alterations from BiliSeq testing with corresponding patient follow-up. Genomic alterations identified through BiliSeq testing were associated with a higher sensitivity (74% vs 50%) and higher specificity (100% vs 99%) for at least high-grade biliary dysplasia involving the bile duct system. In decreasing order, the most prevalent genomic alterations included KRAS, TP53, CDKN2A, SMAD4, PIK3CA, GNAS and others.

Figure 2

Radiographic response to trastuzumab for two patients with ERBB2 amplification by BiliSeq testing. Axial CT images of an elderly female (patient 157) with ERBB2-amplified metastatic intrahepatic cholangiocarcinoma (A) before and (B) after 1 year with gemcitabine, cisplatin and trastuzumab therapy with decrease in size of the rim-enhancing hypodense hepatic metastasis from 2.1 cm to 0.3 cm. A similar response was seen in a middle age male (patient 166) with 2.6 cm rim-enhancing hypodense hepatic metastasis from a perihilar cholangiocarcinoma (C) that harboured an ERBB2 amplification. (D) After the combination of first-line therapy and trastuzumab, the patient’s metastatic lesion decreased in size to 0.7 cm in 8 months.