Evaluating Pancreatic and Biliary Neoplasms with Small Biopsy-Based Next Generation Sequencing (NGS): Doing More with Less

Adequacy of EUS-guided fine-needle aspiration and fine-needle biopsy for next-generation sequencing in pancreatic malignancies: A systematic review and meta-analysis

Background and Objectives

A majority of pancreatic malignancies are unresectable at the time of presentation and require EUS-guided fine-needle aspiration or fine-needle biopsy (EUS-FNA/FNB) for diagnosis. With the advent of precision therapy, there is an increasing need to use EUS-FNA/FNB sample for genetic analysis. Next-generation sequencing (NGS) is a preferred technology to detect genetic mutations with high sensitivity in small specimens. We performed a meta-analysis to evaluate the adequacy of EUS-FNA/FNB for NGS in pancreatic malignancies.

Methods

PubMed, Embase, Cochrane Library, and Web of Science were searched from database inception to November 11, 2023. The primary outcome was the proportion of sufficient sample acquired by EUS-FNA/FNB in pancreatic malignancies for NGS. Secondary outcomes were the proportion of sufficient sample for NGS in pancreatic ductal adenocarcinoma (PDAC) and the detection rates of mutations in KRAS, TP53, CDKN2A, and SMAD4 and actionable mutations in PDAC. The pooled proportions were calculated using a random-effects model. Potential sources of heterogeneity were investigated with subgroup analyses and meta-regression.

Results

Twenty studies with 881 samples were included. The pooled adequacy of EUS-FNA/FNB sample for NGS was 89.9% (95% CI, 80.8%-96.7%) in pancreatic malignancies and 92.0% (95% CI, 81.3%-98.8%) in PDAC. Screening sample suitability before NGS testing was associated with lower adequacy in subgroup analysis (79.7% vs. 98.4%, P = 0.001). The pooled prevalences of mutations in KRAS, TP53, CDKN2A, and SMAD4 in PDAC were 87.4% (95% CI, 83.2%-91.2%), 62.6% (95% CI, 53.2%-71.7%), 20.6% (95% CI, 11.9%-30.8%), and 19.4% (95% CI, 11.2%-29.1%), respectively. The pooled prevalence of potentially actionable mutations in PDAC was 14.5% (95% CI, 8.2%-22.0%).

Conclusions

In the majority of cases, EUS-FNA/FNB can acquire adequate sample for NGS and identify tumor-specific mutations in patients with pancreatic malignancies. Strict pre-analysis screening criteria may negatively impact the sample adequacy and the success rate for NGS.

Duodenal Fluid Analysis as a Rewarding Approach to Detect Low-Abundance Mutations in Biliopancreatic Cancers

Diagnosis of biliopancreatic cancers by the available serum tumor markers, imaging, and histopathological tissue specimen examination remains a challenge. Circulating cell-free DNA derived from matched pairs of secretin-stimulated duodenal fluid (DF) and plasma from 10 patients with biliopancreatic diseases and 8 control subjects was analyzed using AmpliSeq™ HD technology for Ion Torrent Next-Generation Sequencing to evaluate the potential of liquid biopsy with DF in biliopancreatic cancers. The median cfDNA concentration was greater in DF-derived than in plasma-derived samples. A total of 13 variants were detected: 11 vs. 1 were exclusive for DF relative to the plasma source, and 1 was shared between the two body fluids. According to the four-tier systems, 10 clinical tier-I-II (76.9%), 1 tier-III (7.7%), and 2 tier-IV (15.4%) variants were identified. Notably, the 11 tier-I-III variants were exclusively found in DF-derived cfDNA from five patients with biliopancreatic cancers, and were detected in seven genes (KRAS, TP53, BRAF, CDKN2A, RNF43, GNAS, and PIK3CA); 82% of the tier-I-III variants had a low abundance, with a VAF < 6%. The mutational profiling of DF seems to be a reliable and promising tool for identifying cancer-associated alterations in malignant cancers of the biliopancreatic tract.

Rim enhancement of pancreatic ductal adenocarcinoma: investigating the relationship with DCE-MRI-based radiomics and next-generation sequencing

Purpose

To identify the clinical and genetic variables associated with rim enhancement of pancreatic ductal adenocarcinoma (PDAC) and to develop a dynamic contrast-enhanced (DCE) MRI-based radiomics model for predicting the genetic status from next-generation sequencing (NGS).

Materials and methods

Patients with PDAC, who underwent pretreatment pancreatic DCE-MRI between November 2019 and July 2021, were eligible in this prospective study. Two radiologists evaluated presence of rim enhancement in PDAC, a known radiological prognostic indicator, on DCE MRI. NGS was conducted for the tissue from the lesion. The Mann-Whitney U and Chi-square tests were employed to identify clinical and genetic variables associated with rim enhancement in PDAC. For continuous variables predicting rim enhancement, the cutoff value was set based on the Youden's index from the receiver operating characteristic (ROC) curve. Radiomics features were extracted from a volume-of-interest of PDAC on four DCE maps (Ktrans, Kep, Ve, and iAUC). A random forest (RF) model was constructed using 10 selected radiomics features from a pool of 392 original features. This model aimed to predict the status of significant NGS variables associated with rim enhancement. The performance of the model was validated using test set.

Results

A total of 55 patients (32 men; median age 71 years) were randomly assigned to the training (n = 41) and test (n = 14) sets. In the training set, KRAS, TP53, CDKN2A, and SMAD4 mutation rates were 92.3%, 61.8%, 14.5%, and 9.1%, respectively. Tumor size and KRAS variant allele frequency (VAF) differed between rim-enhancing (n = 12) and nonrim-enhancing (n = 29) PDACs with a cutoff of 17.22%. The RF model's average AUC from 10-fold cross-validation for predicting KRAS VAF status was 0.698. In the test set comprising 6 tumors with low KRAS VAF and 8 with high KRAS VAF, the RF model's AUC reached 1.000, achieving a sensitivity of 75.0%, specificity of 100% and accuracy of 87.5%.

Conclusion

Rim enhancement of PDAC is associated with KRAS VAF derived from NGS-based genetic information. For predicting the KRAS VAF status in PDAC, a radiomics model based on DCE maps showed promising results.

Genetic and therapeutic landscapes in cohort of pancreatic adenocarcinomas: next-generation sequencing and machine learning for full tumor exome analysis

About 7% of all cancer deaths are caused by pancreatic cancer (PCa). PCa is known for its lowest survival rates among all oncological diseases and heterogenic molecular profile. Enormous amount of genetic changes, including somatic mutations, exceeds the limits of routine clinical genetic laboratory tests and further stagnates the development of personalized treatments. We aimed to build a mutational landscape of PCa in the Russian population based on full exome next-generation sequencing (NGS) of the limited group of patients. Applying a machine learning model on full exome individual data we received personalized recommendations for targeted treatment options for each clinical case and summarized them in the unique therapeutic landscape.

Expression of EGFR, PD-L1, and the mismatch repair proteins before and following therapy in malignant serous effusions with metastatic high-grade serous tubo-ovarian carcinoma

AIM

To compare the immunochemical expression of EGFR, PD-L1, and the mismatch repair (MMR) proteins MLH1, PMS2, MSH2, and MSH6 between matched malignant effusions obtained before and following the administration of chemotherapy in patients with high-grade serous tubo-ovarian carcinoma (HGSC).

METHODS

In the enrolled HGSCs, matched formalin-fixed and paraffin-embedded cell blocks (CBs) from effusions sampled before (treatment-naïve patients) and during recurrence (following chemotherapy administration), in addition to their matched HGSC tissues obtained from the ovaries at initial diagnosis (treatment-naïve patients), were subjected to EGFR, PD-L1, and MMR immunochemical analysis.

RESULTS

EGFR was more often overexpressed in effusions obtained after chemotherapy administration compared to both effusions (100% vs. 57.1%) and their matched tubo-ovarian tumors (100% vs. 7.1%) from treatment-naïve patients, respectively. EGFR immunochemistry was concordant in just 9.1% of the effusions sampled during recurrence and their paired ovarian samples before recurrence. Whereas all HGSC treatment-naïve samples (ovarian lesions and effusions) were PD-L1 negative, 3/11 (27.3%) malignant effusions obtained during recurrence showed PD-L1 overexpression. Lastly, none of the tested HGSC samples exhibited MMR deficiency.

CONCLUSION

Measuring biomarkers using CBs from malignant effusions may provide clinicians with significant information related to HGSC prognosis and therapy selection, especially in patients with resistance to chemotherapy.

A real-time interpretable artificial intelligence model for the cholangioscopic diagnosis of malignant biliary stricture (with videos)

BACKGROUND AND AIMS

It is crucial to accurately determine malignant biliary strictures (MBSs) for early curative treatment. This study aimed to develop a real-time interpretable artificial intelligence (AI) system to predict MBSs under digital single-operator cholangioscopy (DSOC).

METHODS

A novel interpretable AI system called MBSDeiT was developed consisting of 2 models to identify qualified images and then predict MBSs in real time. The overall efficiency of MBSDeiT was validated at the image level on internal, external, and prospective testing data sets and subgroup analyses, and at the video level on the prospective data sets; these findings were compared with those of the endoscopists. The association between AI predictions and endoscopic features was evaluated to increase the interpretability.

RESULTS

MBSDeiT can first automatically select qualified DSOC images with an area under the curve (AUC) of .963 and .968 to .973 on the internal testing data set and the external testing data sets, and then identify MBSs with an AUC of .971 on the internal testing data set, an AUC of .978 to .999 on the external testing data sets, and an AUC of .976 on the prospective testing data set, respectively. MBSDeiT accurately identified 92.3% of MBSs in prospective testing videos. Subgroup analyses confirmed the stability and robustness of MBSDeiT. The AI system achieved superior performance to that of expert and novice endoscopists. The AI predictions were significantly associated with 4 endoscopic features (nodular mass, friability, raised intraductal lesion, and abnormal vessels; P < .05) under DSOC, which is consistent with the endoscopists' predictions.

CONCLUSIONS

The study findings suggest that MBSDeiT could be a promising approach for the accurate diagnosis of MBSs under DSOC.

Research trends in cholangiocarcinoma treatments during the last 3 decades

Background

Over the past 30 years, numerous studies have focused on the treatment of cholangiocarcinoma (CCA), and these treatments have greatly evolved.

Objectives

To better understand the research trends, we evaluated the most influential publications and attempted to identify their characteristics using bibliometric methods.

Methods

The most influential publications were identified from the Clarivate Analytics Web of Science Core Collection database. The general characteristics of included papers were identified, and the research trends were explored via the bibliometric method.

Results

The average total number of citations for of the listed publications were 312 (range from 165 to 1922). The highest number of papers were published during period II (2001-2010, n = 50), followed by period III (2011-2020, n = 28), and period I (1991-2000, n = 22). The United States and Germany have made remarkable achievements in this field. Institutionally, Mayo Clinic and Memorial Sloan-Kettering Cancer Center were the leading institutions, with Blumgart and Zhu from the United States being the most influential authors. Close collaboration was established between the leading countries, institutions, and authors. The Annals of Surgery contributed the most to the papers with the highest total number of citations. Surgery predominated during period I (n = 14, 63.6%), with a gradual decline occurring during periods II (n = 19, 41.3%, P = 0.085) and period III (n = 3, 9.4%, P = 0.002). Contrastingly, the number of publications related to systemic therapy has increased significantly since period II and peaked in period III.

Conclusions

Surgery remains the most important treatment for CCA. However systemic therapy has become a research and clinical application hotspot. These findings will contribute to the translation of treatments for CCA and provide researchers with relevant research directions.

Endoscopic Ultrasound-Guided Tissue Acquisition of Pancreaticobiliary Cancer Aiming for a Comprehensive Genome Profile

In recent years, cancer genomic medicine centered on comprehensive genome profile (CGP) analysis has become widely used in the field of pancreatic cancer. Endoscopic ultrasound-guided tissue acquisition (EUS-TA) has played an important role in pancreatic cancer, and recently, more EUS-TA tissue samples are considered for CGP analysis. Differences exist between the Oncoguide NCC Oncopanel System and Foundation One CDx Cancer Genome Profile, which are CGP tests approved by insurance programs in Japan, including the analysis criteria, optimal needle selection for meeting these criteria, and puncture target. It is important to understand not only the specimen collection factors, but also the specimen processing factors that can increase the success rate of CGP testing. Furthermore, cancer genome medicine is expected to enter an era of increasing turbulence in the future, and endoscopists need to respond flexibly to these changes. Herein, we review the current status of cancer genome medicine in pancreatic and biliary tract cancers and cancer gene panel testing using EUS-TA.

Targeted next-generation sequencing has incremental value in the diagnostic work-up of patients with suspect pancreatic masses; a multi-center prospective cross sectional study

BACKGROUND

The diagnostic process of patients with suspect pancreatic lesions is often lengthy and prone to repeated diagnostic procedures due to inconclusive results. Targeted Next-Generation Sequencing (NGS) performed on cytological material obtained with fine needle aspiration (FNA) or biliary duct brushing can speed up this process. Here, we study the incremental value of NGS for establishing the correct diagnosis, and subsequent treatment plan in patients with inconclusive diagnosis after regular diagnostic work-up for suspect pancreatic lesions.

METHODS

In this prospective cross-sectional cohort study, patients were screened for inclusion in four hospitals. NGS was performed with AmpliSeq Cancer Hotspot Panel v2 and v4b in patients with inconclusive cytology results or with an uncertain diagnosis. Diagnostic results were evaluated by the oncology pancreatic multidisciplinary team. The added value of NGS was determined by comparing diagnosis (malignancy, cystic lesion or benign condition) and proposed treatment plan (exploration/resection, neoadjuvant chemotherapy, follow-up, palliation or repeated FNA) before and after integration of NGS results. Final histopathological analysis or a 6-month follow-up period were used as the reference standard in case of surgical intervention or non-invasive treatment, respectively.

RESULTS

In 50 of the 53 included patients, cytology material was sufficient for NGS analysis. Diagnosis before and after integration of NGS results differed in 24% of the patients. The treatment plan was changed in 32% and the diagnosis was substantiated by the NGS data in 44%. Repetition of FNA/brushing was prevented in 14% of patients. All changes in treatment plan were correctly made after integration of NGS. Integration of NGS increased overall diagnostic accuracy from 68% to 94%.

INTERPRETATION

This study demonstrates the incremental diagnostic value of NGS in patients with an initial inconclusive diagnosis. Integration of NGS results can prevent repeated EUS/FNA, and can also rigorously change the final diagnosis and treatment plan.

Proposal of a novel pipeline involving precise bronchoscopy of distal peripheral pulmonary lesions for genetic testing

Next-generation sequencing (NGS) has become increasingly more important for lung cancer management. We now expect biopsies to be sensitive, safe, and yielding sufficient samples for NGS. In this study, we propose ultraselective biopsy (USB) with sample volume adjustment (SVA) as a novel method that integrates an ultrathin bronchoscope, radial probe endobronchial ultrasound, and the direct oblique method for ultraselective navigation, and adjustment of sample volume for NGS. Our purpose was to estimate the diagnostic potential and the applicability of USB-SVA for amplicon-based NGS analysis. The diagnostic yield of bronchoscopy in forty-nine patients with malignant peripheral pulmonary lesions (PPLs) was retrospectively analyzed, and amplicon-based NGS analysis was performed on samples from some patients using USB. The diagnostic yields of distal PPLs in the USB group were significantly higher than those in the non-USB group (90.5% vs. 50%, respectively, p = 0.015). The extracted amounts of nucleic acids were at least five times the minimum requirement and the sequence quality met the criteria for the Oncomine™ Target Test. Only the tumor cell content of some samples was insufficient. The feasibility of the pipeline for USB, SVA, and amplicon-based NGS in distal PPLs was demonstrated.