Next-generation sequencing mutation analysis on biliary brush cytology for differentiation of benign and malignant strictures in primary sclerosing cholangitis

Self-Calibrated Stimulated Raman Scattering Spectroscopy for Rapid Cholangiocarcinoma Diagnosis

Cholangiocarcinoma (CCA) is an aggressive malignancy with poor clinical outcomes. The current "gold standard" diagnostic approach, endoscopic retrograde cholangiopancreatography (ERCP)-obtained biopsy, has a relatively low sensitivity (i.e., ∼50%). Here, we developed a bile-based diagnostic system using transient stimulated Raman scattering (T-SRS). Except for the tolerance to autofluorescence inherited from traditional SRS spectroscopy, T-SRS features quantum-limit spectral line shapes and is further improved with self-calibration ability in this research. These advantages make the acquired Raman spectra insensitive to the drifting of the excitation parameters, facilitating long-term reliability. Based on the T-SRS spectra in the C-H stretching region from 76 bile samples accumulated over more than 1 year, we demonstrated high accuracy (i.e., 85 ± 3%) and sensitivity (i.e., 87 ± 9%) for classification between CCA and benign diseases. The T-SRS acquisition only requires ∼9-μL bile samples and features a drastically improved time cost. This study suggests that the self-calibrated T-SRS analysis of the bile sample offers a promising approach for rapid CCA diagnosis.

Mutational Analysis of Bile Cell-Free DNA in Primary Sclerosing Cholangitis: A Pilot Study

BACKGROUND

Primary sclerosing cholangitis (PSC) is a chronic liver disease characterised by inflammation and fibrosis of the bile ducts, conferring an increased risk of cholangiocarcinoma (CCA). However, detecting CCA early in PSC patients remains challenging due to the limited sensitivity of conventional diagnostic methods, including imaging or bile duct brush cytology during endoscopic retrograde cholangiopancreatography (ERCP). This study aims to evaluate the potential of bile cell-free DNA (cfDNA) mutational analysis, termed the Bilemut assay, as a tool for CCA detection in PSC patients.

METHODS

Sixty-three PSC patients undergoing ERCP due to biliary strictures were prospectively recruited. Bile samples were collected, and cfDNA was extracted and analysed using the Oncomine Pan-Cancer Cell-Free assay. Twenty healthy liver donors were included for comparison. Samples with a mutant allele frequency (MAF) ≥ 0.1% were considered positive. Correlations between mutational status and clinical characteristics were assessed.

RESULTS

cfDNA mutational analysis was successful in all bile samples. Mutations predominantly in KRAS, GNAS, and TP53 were detected in 36.5% (23/63) of PSC patients, compared to 10% (2/20) of healthy donors (p = 0.0269). The clinical characteristics of Bilemut-positive and -negative patients were comparable, though there was a trend towards a lower prevalence of inflammatory bowel disease in the Bilemut-positive group. Among PSC patients diagnosed with CCA during follow-up, 75% were Bilemut-positive, suggesting an association between mutational status and malignancy risk.

CONCLUSIONS

Mutational analysis of cfDNA obtained from bile collected from PSC patients undergoing ERCP is feasible. Implementing the Bilemut assay may help identify patients needing closer surveillance and further imaging studies.

Next-generation sequencing improves the detection of malignant biliary strictures and changes management

BACKGROUND AND AIMS

Malignant biliary strictures (MBSs) pose diagnostic and therapeutic challenges due to the frequent indeterminate results after initial sampling. A next-generation sequencing (NGS) panel (BiliSeq) offers promise in MBS detection, but real-world performance remains uncertain. This study aimed to assess standard sampling techniques alone and with BiliSeq for malignancy detection in biliary strictures and to evaluate management changes based on NGS.

METHODS

This retrospective cohort study included 77 patients with biliary strictures undergoing BiliSeq during ERCP. Sensitivity, specificity, positive predictive values, and negative predictive values were calculated, and sensitivity was compared between tests by using the McNemar test. Clinical impact was defined by identifying MBS patients with negative cytology/pathology correctly identified by BiliSeq.

RESULTS

Among 77 patients (28 malignant, 49 benign) who underwent BiliSeq testing during ERCP, primary sclerosing cholangitis was present in 24 patients (31.2%). A mass was detected in 35.7% of MBS cases versus 6.1% of benign cases (P = .001). BiliSeq sensitivity for malignancy was 75% (95% CI, 55.1%-89.3%), surpassing the combination of cytology and biopsy (42.9%; 95% CI, 24.5%-62.8%; P = .03). Combining BiliSeq with cytology/biopsy improved sensitivity from 42.9% to 85.7% (P < .001). Among MBS patients with negative cytology/biopsy findings (n = 16), BiliSeq altered management in 75%.

CONCLUSIONS

NGS and pathologic evaluation enhanced MBS detection sensitivity, leading to management changes in 75% of cases when pathology test results were negative.

The Catheter Flushing Method Shows a Similar Diagnostic Yield to the Conventional Method in Brushing Cytology for Biliary Strictures

Background/Objectives: Endobiliary brushing is usually performed in the diagnosis of indeterminate biliary strictures; however, in this setting, brush cytology is limited by a low diagnostic yield and sensitivity. Here, we compared the catheter flushing method (CFM) with the conventional cytologic method (CCM) in terms of cellularity and diagnostic performance. Methods: Endobiliary brushings were obtained during endoscopic retrograde cholangiopancreatography (ERCP) from patients with biliary strictures enrolled at six tertiary hospitals. Additionally, the CFM was performed after brushing. Using liquid-based cytologic preparations of samples, we assessed the diagnostic performance of the CCM using Pap staining and the CFM using methionyl-transfer RNA synthetase 1 (MARS1) immunofluorescence staining. Results: From a total of 399 patients (malignant, 253; benign, 146), 374 CCM samples and 361 CFM samples contained adequate cells, with no significant difference in diagnostic yield (93.7% vs. 90.5%, respectively; p = 0.088). The sensitivity of the CFM (90.3%) was significantly higher than that of the CCM (75.1%; p < 0.001), with no significant difference in accuracy between methods (81.2% vs. 82.6%, respectively; p = 0.608). Conclusions: The diagnostic yield of the CFM was comparable to that of the CCM. Additionally, the diagnostic performance of the CFM was comparable to that of the CCM. These findings indicate that the CFM could be an additional brush cytology method for sample collection in patients with indeterminate biliary strictures. Incorporating both the CCM and CFM might be expected to improve the diagnostic yield of brush cytology in the biliary strictures. Further prospective comparative studies between the CCM and CFM using the same staining method are needed to validate these findings.

Implementing Massive Parallel Sequencing into Biliary Samples Obtained through Endoscopic Retrograde Cholangiopancreatography for Diagnosing Malignant Bile Duct Strictures

Despite advancements in radiologic, laboratory, and pathological evaluations, differentiating between benign and malignant bile duct strictures remains a diagnostic challenge. Recent developments in massive parallel sequencing (MPS) have introduced new opportunities for early cancer detection and management, but these techniques have not yet been rigorously applied to biliary samples. We prospectively evaluated the Oncomine Comprehensive Assay (OCA) and the Oncomine Pan-Cancer Cell-Free Assay (OPCCFA) using biliary brush cytology and bile fluid obtained via endoscopic retrograde cholangiopancreatography from patients with bile duct strictures. The diagnostic performance of MPS testing was assessed and compared to the pathological findings of biliary brush cytology and primary tissue. Mutations in TP53, BRAF, CTNNB1, SMAD4, and K-/N-RAS identified in biliary brush cytology samples were also detected in the corresponding bile fluid samples from patients with extrahepatic cholangiocarcinoma. These mutations were also identified in the bile fluid samples, but with variant allele frequencies lower than those in the corresponding biliary brush cytology samples. In control patients diagnosed with gallstones, neither the biliary brush cytology samples nor the bile fluid samples showed any pathogenic mutations classified as tier 1 or 2. Our study represents a prospective investigation into the role of MPS-based molecular testing in evaluating bile duct strictures. MPS-based molecular testing shows promise in identifying actionable genomic alterations, potentially enabling the stratification of patients for targeted chemotherapeutic treatments. Future research should focus on integrating OCA and OPCCFA testing, as well as similar MPS-based assays, into existing surveillance and management protocols for patients with bile duct strictures.

Role of endoscopy in hepatology

The growing and evolving field of EUS and advanced hepatobiliary endoscopy has amplified traditional upper gastrointestinal endoscopy and unveiled novel options for remaining unsolved hepatobiliary issues, both diagnostically and therapeutically. This conceptually appealing and fascinating integration of endoscopy within the practice of hepatology is referred to as 'endo-hepatology'. Endo-hepatology focuses on the one hand on disorders of the liver parenchyma and liver vasculature and of the hepatobiliary tract on the other hand. Applications hanging under the umbrella of endohepatology involve amongst others EUS-guided liver biopsy, EUS-guided portal pressure measurement, EUS-guided portal venous blood sampling, EUS-guided coil & glue embolization of gastric varices and spontaneous portosystemic shunts as well as ERCP in the challenging context of (decompensated cirrhosis) and intraductal cholangioscopy for primary sclerosing cholangitis. Although endoscopic proficiency however does not necessarily equal in an actual straightforward end-solution for currently persisting (complex) hepatobiliary situations. Therefore, endohepatology continues to generate high-quality data to validate and standardize procedures against currently considered (best available) "golden standards" while continuing to search and trying to provide novel minimally invasive solutions for persisting hepatological stalemate situations. In the current review, we aim to critically appraise the status and potential future directions of endo-hepatology.

NGS of brush cytology samples improves the detection of high-grade dysplasia and cholangiocarcinoma in patients with primary sclerosing cholangitis: A retrospective and prospective study

BACKGROUND

Biliary dysplasia, a precursor of cholangiocarcinoma (CCA), is a common complication of primary sclerosing cholangitis. Patients with high-grade dysplasia (HGD) or early CCA who have received oncological treatment are candidates for liver transplantation. The preoperative diagnosis of CCA or HGD is challenging, and the sensitivity of biliary brush cytology (BC) is limited.

METHODS

By using next-generation sequencing (NGS), we retrospectively analyzed archived tissue samples (n=62) obtained from explanted liver tissue and CCA samples to identify oncogenic mutations that occur during primary sclerosing cholangitis carcinogenesis. BC samples were prospectively collected from patients with primary sclerosing cholangitis (n=97) referred for endoscopic retrograde cholangiography to measure the diagnostic utility of NGS combined with BC compared with traditional cytology alone.

RESULTS

Mutations in KRAS, GNAS, FLT3, RNF43, TP53, ATRX, and SMAD4 were detected in archived CCA or HGD samples. KRAS, GNAS, TP53, CDKN2A, FBXW7, BRAF, and ATM mutations were detected in prospectively collected brush samples from patients with histologically verified CCA or HGD. One patient with low-grade dysplasia in the explanted liver had KRAS and GNAS mutations in brush sample. No mutations were observed in brush samples or archived tissues in liver transplantation cases without biliary neoplasia. While KRAS mutations are common in biliary neoplasms, they were also observed in patients without biliary neoplasia during surveillance.

CONCLUSIONS

In summary, NGS of BC samples increased the sensitivity of detecting biliary neoplasia compared with traditional cytology. Performing NGS on BC samples may help diagnose HGD or early CCA, benefiting the timing of liver transplantation.

The importance of protein domain mutations in cancer therapy

Cancer is a complex disease that is caused by multiple genetic factors. Researchers have been studying protein domain mutations to understand how they affect the progression and treatment of cancer. These mutations can significantly impact the development and spread of cancer by changing the protein structure, function, and signalling pathways. As a result, there is a growing interest in how these mutations can be used as prognostic indicators for cancer prognosis. Recent studies have shown that protein domain mutations can provide valuable information about the severity of the disease and the patient's response to treatment. They may also be used to predict the response and resistance to targeted therapy in cancer treatment. The clinical implications of protein domain mutations in cancer are significant, and they are regarded as essential biomarkers in oncology. However, additional techniques and approaches are required to characterize changes in protein domains and predict their functional effects. Machine learning and other computational tools offer promising solutions to this challenge, enabling the prediction of the impact of mutations on protein structure and function. Such predictions can aid in the clinical interpretation of genetic information. Furthermore, the development of genome editing tools like CRISPR/Cas9 has made it possible to validate the functional significance of mutants more efficiently and accurately. In conclusion, protein domain mutations hold great promise as prognostic and predictive biomarkers in cancer. Overall, considerable research is still needed to better define genetic and molecular heterogeneity and to resolve the challenges that remain, so that their full potential can be realized.

Molecular testing of cytology specimens: Issues in specimen adequacy and clinical utility

BACKGROUND

Next generation sequencing (NGS) is standard of care for workup of many neoplasms including adenocarcinomas of the lung. Molecular testing of cytology samples is used for many types of neoplasms but the value of such testing for the selection of "first"- and "second-line" treatment protocols is incompletely understood.

METHODS

Fifty-six sequentially performed cytology specimens (49 fine needle aspirates and 7 fluids) submitted for molecular analysis were reviewed by a medical oncologist to determine specimen adequacy and utility of results for therapy selection. Chart review was performed to determine availability of microsatellite instability status, tumor mutational burden, and presence of driver mutations treatable with targeted therapy in a "first"- or "second-line" application.

RESULTS

Forty of 56 cases were successfully sequenced and 34% (19/56) had targetable mutations detected by NGS. Ten of these 19 cases (53%) received targeted therapy for their tumor type with five of 10 patients receiving "first-line" therapy and five (50%) "second-line" therapy. Twenty-two mutations were detected where no targeted therapy for the patient's tumor type existed but targeted therapies were available for other tumor types. Of these specimens, only one patient received treatment using protocols associated with a second tumor type. Total mutation burden and microsatellite instability status results were obtained in 29 of 56 cases (52%).

CONCLUSIONS

71% (40/56) of cytologic specimens were adequate for sequencing with 34% (19/56) demonstrating a targetable mutation and 53% of these patients receiving therapy targeted to the driver mutation of their tumor type.

Endoscopic Diagnosis of Extra-Luminal Cancers

The last 2 decades have seen an emergence of endoscopic technologies and techniques allowing for minimally invasive modalities for assessing and sampling lesions outside of the gastrointestinal lumen, including the chest, abdomen, and pelvis. Incorporating these new endoscopic approaches has revolutionized the diagnosis and staging of extra-luminal malignancies and has enabled more accessible and safer tissue acquisition.

Endoscopic procedures in hepatology: Current trends and new developments

Gastrointestinal endoscopy has long been a reliable backbone in the diagnosis and management of hepatobilary disorders and their complications. However, with evolving non-invasive testing, personalised medicine has reframed the utility and necessity of endoscopic screening. Conversely, the growing interest and use of endoscopic ultrasound (EUS) and advanced endoscopy within gastrointestinal units has also opened novel diagnostic and therapeutic avenues for patients with various hepatobiliary diseases. The integration of "advanced endoscopy" within the practice of hepatology is nowadays referred to as "endo-hepatology". In essence, endo-hepatology consists of two pillars: one focusing primarily on disorders of the liver parenchyma, vascular disorders, and portal hypertension, which is mainly captured via EUS, while the other targets the hepatobiliary tract via endoscopic retrograde cholangiopancreatography and advanced imaging. Applications under the umbrella of endo-hepatology include, amongst others, EUS-guided liver biopsy, EUS-guided portal pressure gradient measurement, coil and glue embolisation of gastric varices as well as cholangioscopy. As such endo-hepatology could become an attractive concept wherein advanced endoscopy might reinforce the medical management of patients with hepatobiliary disorders and their complications after initial basic work-up. In this review, we discuss current trends and future developments within endo-hepatology and the remaining hurdles to overcome.

Recent Advances in the Management of Primary Sclerosing Cholangitis

Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease characterized by fibroinflammatory damage to the biliary tree, typically in the setting of inflammatory bowel disease, with an increased risk of liver failure and cholangiocarcinoma. A complex pathophysiology, heterogeneity in clinical features, and the rare nature of the disease have contributed to the lack of effective therapy to date. However, recent innovations in the characterization and prognostication of patients with PSC, in addition to new tools for medical management and emerging pharmacologic agents, give rise to the potential for meaningful progress in the next several years. This review summarizes current concepts in PSC and highlights particular areas in need of further study.

Efficient Establishment of Bile-Derived Organoids From Biliary Cancer Patients

Patient-derived tumor organoids have considerable potential as an in vitro diagnostic tool for drug susceptibility testing. In the present study, we investigated whether bile collected for diagnostic purposes could be a potential source for the establishment of biliary cancer organoids. Among 68 cases of biliary cancer, we successfully generated 60 bile-derived organoids (BDOs) from individual patients. Consistent with previous reports that described biliary cancer organoids from surgical tissues, the BDOs showed diverse morphologies such as simple cysts, multiloculated cysts, thick capsulated cysts, and solid masses. They also harbored mutations in KRAS and TP53 at frequencies of 15% and 55%, respectively. To enrich the cancer organoids by removing contaminated noncancerous components of BDOs, we attempted to verify the effectiveness of 3 different procedures, including repeat passage, xenografting, and selection with an MDM2 inhibitor for TP53 mutation-harboring BDOs. By monitoring the sequence and expression of mutated TP53, we found that all these procedures successfully enriched the cancer organoids. Our data suggest that BDOs can be established with minimal invasiveness from almost all patients with biliary cancers, including inoperable cases. Thus, despite some limitations with respect to the characterization of BDOs and methods for the enrichment of cancer cell-derived organoids, our data suggest that BDOs could have potential applications in personalized medicine.