Next-generation sequencing of endoscopic ultrasound guided microbiopsies from pancreatic cystic neoplasms

Targeted next-generation sequencing of EUS-guided through-the-needle-biopsy sampling from pancreatic cystic lesions

BACKGROUND AND AIMS

Recent advances have introduced molecular subtyping of pancreatic cystic lesions (PCLs) as a possible amendment to the diagnostic algorithm. The study evaluated the feasibility and diagnostic accuracy of molecular analysis and subtyping of PCLs using the recently introduced EUS-guided through-the-needle-biopsy (TTNB) sampling.

METHODS

We prospectively included 101 patients in the study who presented with PCLs >15 mm in the largest cross-section. EUS-guided TTNB samples were obtained by a micro-biopsy forceps introduced through a 19-gauge needle. The TTNB samples were analyzed by next-generation sequencing (NGS) for point mutations in tumor suppressors and oncogenes using a 51-gene customized hotspot panel. Sensitivity and specificity were calculated with the histologic diagnosis as reference.

RESULTS

After initial microscopic evaluation of the samples, 91 patients had residual TTNB samples available for NGS. Of these, 49 harbored mutations, most frequently in KRAS and GNAS, reflecting an excess frequency of intraductal papillary mucinous neoplasms (IPMNs) in the study population. A sensitivity and specificity of 83.7% (95% confidence interval [CI], 70.3-92.7) and 81.8% (95% CI, 48.2-97.7), respectively, were demonstrated for the diagnosis of a mucinous cyst and 87.2% (95% CI, 74.2-95.2) and 84.6% (95% CI, 54.5-98.1) for the diagnosis of an IPMN.

CONCLUSIONS

Thus, molecular analysis of TTNB samples by NGS has high sensitivity and specificity for diagnosing mucinous cysts and IPMNs. Although the procedure comes with a risk of adverse events of 9.9%, TTNB samples are a robust alternative to cyst fluid for a combined histologic and molecular diagnosis of PCLs. (Clinical trial registration number: NCT03578445.).

Diminished Immune Surveillance during Histologic Progression of Intraductal Papillary Mucinous Neoplasms Offers a Therapeutic Opportunity for Cancer Interception

PURPOSE

Intraductal papillary mucinous neoplasms (IPMN) are bona fide precursors to pancreatic ductal adenocarcinoma (PDAC). While genomic alterations during multistep IPMN progression have been well cataloged, the accompanying changes within the tumor immune microenvironment (TIME) have not been comprehensively studied. Herein, we investigated TIME-related alterations during IPMN progression, using multiplex immunofluorescence (mIF) coupled with high-resolution image analyses.

EXPERIMENTAL DESIGN

Two sets of formalin-fixed, paraffin-embedded tissue samples from surgically resected IPMNs were analyzed. The training set of 30 samples consisted of 11 low-grade IPMN (LG-IPMN), 17 high-grade IPMN (HG-IPMN), and 2 IPMN with PDAC, while a validation set of 93 samples comprised of 55 LG-IPMN and 38 HG-IPMN. The training set was analyzed with two panels of immuno-oncology-related biomarkers, while the validation set was analyzed with a subset of markers found significantly altered in the training set.

RESULTS

Cell types indicative of enhanced immune surveillance, including cytotoxic and memory T cells, and antigen-experienced T cells and B cells, were all found at higher densities within isolated LG-IPMNs compared with HG-IPMNs. Notably, the TIME of LG-IPMNs that had progressed at the time of surgical resection (progressor LGD) resembled that of the synchronous HG-IPMNs, underscoring that attenuated immune surveillance occurs even in LG-IPMNs destined for progression.

CONCLUSIONS

Our findings provide a basis for interception of cystic neoplasia to PDAC, through maintenance of sustained immune surveillance using vaccines and other prevention approaches.

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

Simple Summary

Pancreatic cancer and cholangiocarcinoma are aggressive diseases mostly diagnosed at an advanced and inoperable stage. This review presents the value of next-generation sequencing (NGS) when performed on small biopsies—including fine-needle aspiration/biopsy samples, brushings, pancreatic juice and bile, and also blood—in the field of pancreatobiliary neoplasia. NGS could guide physicians while evaluating pancreatic solid and cystic lesions or suspicious biliary strictures, performing surveillance in high-risk individuals, or monitoring the disease and assessing prognosis in already diagnosed cancer patients. Evidence suggests that NGS performed on small biopsies is a robust tool for the diagnosis and pre-operative risk stratification of pancreatic and biliary lesions, whereas it also carries significant prognostic and therapeutic value. However, effective standardization of the pre-analytical and analytical assay parameters used for each clinical scenario is needed to fully implement NGS into routine practice and provide more personalized management in patients with suspected or established pancreatobiliary neoplasia.

Abstract

Pancreatic cancer and cholangiocarcinoma are lethal diseases mainly diagnosed at an inoperable stage. As pancreatobiliary surgical specimens are often unavailable for further molecular testing, this review aimed to highlight the diagnostic, prognostic, and therapeutic impact of next-generation sequencing (NGS) performed on distinct small biopsies, including endoscopic ultrasound fine-needle aspirations and biopsies of pancreatic solid and cystic lesions, biliary duct brushings, and also “liquid biopsies” such as the pancreatic juice, bile, and blood. NGS could clarify indeterminate pancreatic lesions or biliary strictures, for instance by identifying TP53 or SMAD4 mutations indicating high-grade dysplasia or cancer. It could also stratify pancreatic cystic lesions, by distinguishing mucinous from non-mucinous cysts and identifying high-risk cysts that should be excised in surgically fit patients, whereas the combination of cytology, elevated cystic CEA levels and NGS could improve the overall diagnostic accuracy. When NGS is performed on the pancreatic juice, it could stratify high-risk patients under surveillance. On the plasma, it could dynamically monitor the disease course and response to therapy. Notably, the circulating tumor DNA (ctDNA) levels have been associated with staging, grading, and survival. Lastly, NGS has shown potential in identifying potentially actionable molecular alterations. In conclusion, NGS applied on small biopsies could carry significant diagnostic, prognostic, and therapeutic value.

Through-the-needle biopsy of pancreatic cystic lesions: current evidence and implications for clinical practice

INTRODUCTION

There is increasing evidence to support the efficacy of endoscopic ultrasound (EUS)-guided through-the-needle biopsy (TTNB) technique as a means of sampling pancreatic cystic lesions (PCLs). Results provide evidence demonstrating the benefits of this procedure over standard EUS fine-needle aspiration (FNA), thus supporting a push for its widespread implementation in clinical practice. Though this technique has demonstrated advantages, achieving these advantages in clinical practice is contingent upon careful considerations to ensure safety and efficacy.

AREAS COVERED

The purpose of this review is to assess the level of evidence supporting the use of through-the-needle biopsy, revise its main technical and procedural characteristics, and to develop suggested guidelines outlining the safe assimilation of this device in clinical practice.

EXPERT OPINION

EUS-TTNB enables more definitive and accurate diagnosis of PCLs by providing higher-quality histological samples. However, EUS-TTNB is not appropriate for all PCLs. Selection of suitable patients as well as morphology and risk factors of the cystic lesion is a crucial component of achieving the described benefits of this procedure while minimizing risks of adverse effects. Subjects with weak or absent indications for this procedure are susceptible to a range of complications and may even result in fatality.

Cystic pancreatic lesions, the endless dilemma

Cystic pancreatic lesions involve a wide variety of pathological entities that include neoplastic and non-neoplastic lesions. The proper diagnosis, differentiation, and staging of these cystic lesions are considered a crucial issue in planning further management. There are great challenges for their diagnostic models. In our time, new emerging methods for this diagnosis have been discovered. Endoscopic ultrasonography-guided fine-needle aspiration cytology with chemical and molecular analysis of cyst fluid and EUS-guided fine needle-based confocal laser endomicroscopy, through the needle microforceps biopsy, and single-operator cholangioscopy/pancreatoscopy are promising methods that have been used in the diagnosis of cystic pancreatic lesions. Hereby we discuss the diagnosis of cystic pancreatic lesions and the benefits of various diagnostic models.

Molecular heterogeneity of pancreatic intraductal papillary mucinous neoplasms and implications for novel endoscopic tissue sampling strategies

AIMS

Intraductal papillary mucinous neoplasms (IPMNs) may be precursor lesions of pancreatic cancer. The path towards malignancy is associated with mutations in tumour suppressor-and oncogenes that may serve as biomarkers during diagnostic investigation. A novel micro forceps has made it possible to obtain biopsies from the cyst wall for analysis by next generation sequencing (NGS), providing an opportunity for early detection and intervention. However, the impact of spatial tumour heterogeneity on the representability of the biopsies has not been determined. The primary aim is to characterise the impact of molecular heterogeneity of the luminal cyst wall on tissue sampling strategies with small biopsies.

METHODS

We performed NGS and immunohistochemical phenotyping on 18 resected IPMNs with varying degrees of dysplasia and for a subset, concomitant carcinoma, using a commercially available NGS-panel of 51 oncogenes. We simulated endoscopic biopsies by performing punch biopsies (PBs) of the cyst wall from resected specimens.

RESULTS

In total, 127 NGS analyses were performed. Concomitant KRAS and GNAS was a common feature of the IPMNs. Mutations in KRAS and GNAS were associated with low-grade dysplasia whereas alterations in TP53, SMAD4, CDKN2A and PIK3CA were associated with high-grade dysplasia and/or carcinoma. The mutational analysis of the PBs from the cyst wall was compared with the whole lesion. No difference was detected between PBs and whole lesions when the cumulated mutational profile in increasing order of randomly performed PBs was compared.

CONCLUSIONS

Small IPMN biopsies from the cyst wall are adequate to yield a molecular diagnosis.

Defining the Comprehensive Genomic Landscapes of Pancreatic Ductal Adenocarcinoma Using Real-World Endoscopic Aspiration Samples

PURPOSE

Most patients with pancreatic ductal adenocarcinoma (PDAC) present with surgically unresectable cancer. As a result, endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) is the most common biospecimen source available for diagnosis in treatment-naïve patients. Unfortunately, these limited samples are often not considered adequate for genomic analysis, precluding the opportunity for enrollment on precision medicine trials.

EXPERIMENTAL DESIGN

Applying an epithelial cell adhesion molecule (EpCAM)-enrichment strategy, we show the feasibility of using real-world EUS-FNA for in-depth, molecular-barcoded, whole-exome sequencing (WES) and somatic copy-number alteration (SCNA) analysis in 23 patients with PDAC.

RESULTS

Potentially actionable mutations were identified in >20% of patients. Further, an increased mutational burden and higher aneuploidy in WES data were associated with an adverse prognosis. To identify predictive biomarkers for first-line chemotherapy, we developed an SCNA-based complexity score that was associated with response to platinum-based regimens in this cohort.

CONCLUSIONS

Collectively, these results emphasize the feasibility of real-world cytology samples for in-depth genomic characterization of PDAC and show the prognostic potential of SCNA for PDAC diagnosis.

Diagnostic accuracy of EUS-guided through-the-needle-biopsies and simultaneously obtained fine needle aspiration for cytology from pancreatic cysts: A systematic review and meta-analysis

OBJECTIVES

To address the diagnostic accuracy of endoscopic ultrasound guided through-the-needle-biopsies (TTNBs) and simultaneously obtained cytology samples from pancreatic cysts compared to the final histopathological diagnosis of the surgical specimen, and to give an overview of ancillary tests performed on TTNBs.

METHODS

A literature search was conducted in MEDLINE, Embase and Scopus. Studies were included in the meta-analysis, if they had data for TTNB, cytology and a surgical specimen of pancreatic cysts as reference standard. The assessment of the risk of bias and quality of the included studies was conducted using the modified QUADAS-2 tool.

RESULTS

Ten studies with 99 patients were included in the meta-analysis. Data regarding study design and clinicopathological features were extracted systematically. For TTNB, pooled sensitivity was 0.86 (95 % CI 0.62-0.96), specificity 0.95 (95 % CI 0.79-0.99) and area under the curve (AUC) 0.86 for the diagnosis of a mucinous cyst and pooled sensitivity was 0.78 (95 % CI 0.61-0.89), specificity 0.99 (95 % CI 0.90-0.99) and AUC 0.92 for the diagnosis of a high-risk cyst. For a specific diagnosis, pooled sensitivity was 0.69 (95 % CI 0.50-0.83), specificity 0.47 (95 % CI 0.28-0.68) and AUC 0.49. For cytology performed simultaneously, pooled sensitivity was 0.46 (95 % CI 0.35-0.57), specificity 0.90 (95 % CI 0.46-0.99) and AUC 0.64 for the diagnosis of mucinous cysts, and pooled sensitivity was 0.38 (95 % CI 0.23-0.55), specificity 0.99 (95 % CI 0.90-0.99) and AUC 0.84 for the diagnosis of a high-risk cyst. For a specific diagnosis, pooled sensitivity was 0.29 (95 % CI 0.21-0.39), specificity 0.45 (95 % CI 0.25-0.66) and AUC 0.30. Furthermore, immunohistochemical stains can be useful to establish the specific cyst subtype.

CONCLUSIONS

TTNBs have a higher sensitivity and specificity than cytology for the diagnosis of mucinous cyst and high- risk cysts of the pancreas.

Clinical impact of endoscopic ultrasound-guided through-the-needle microbiopsy in patients with pancreatic cysts

BACKGROUND

The limited data on the utility of endoscopic ultrasound (EUS)-guided through-the-needle biopsies (TTNBs) in patients with pancreatic cystic lesions (PCLs) originate mainly from retrospective studies. Our aim was to determine the clinical impact of TTNBs, their added diagnostic value, and the adverse event rate in a prospective setting.

METHODS

This was a prospective, single-center, open-label controlled study. Between February 2018 and August 2019, consecutive patients presenting with a PCL of 15 mm or more and referred for EUS were included. Primary outcome was a change in clinical management of PCLs following TTNB compared with cross-sectional imaging and cytology. Adverse events were defined according to the ASGE lexicon.

RESULTS

101 patients were included. TTNBs led to a change in clinical management in 11.9 % of cases (n = 12). Of these, 10 had serous cysts and surveillance was discontinued, while one of the remaining two cases underwent surgery following diagnosis of a mucinous cystic neoplasm. The diagnostic yield of TTNBs for a specific cyst diagnosis was higher compared with FNA cytology (69.3 % vs. 20.8 %, respectively; P < 0.001). The adverse event rate was 9.9 % (n = 10; 95 % confidence interval 5.4 % - 17.3 %), with the most common event being acute pancreatitis (n = 9). Four of the observed adverse events were severe, including one fatal outcome.

CONCLUSIONS

TTNBs resulted in a change of clinical management in about one in every 10 patients; however, the associated adverse event risk was substantial. Further studies are warranted to elucidate in which subgroups of patients the clinical benefit outweighs the risks.

Endoscopic ultrasound-guided through-the-needle microforceps biopsy improves diagnostic yield for pancreatic cystic lesions: a systematic review and meta-analysis

Background and study aims  Given variable diagnostic yield of endoscopic ultrasound (EUS)-guided fine-needle aspiration (FNA) for pancreatic cystic lesions (PCLs), a through-the-needle (TTN) microforceps biopsy device passed through a 19-gauge FNA needle has been devised to improve tissue sampling. This was a systematic review and meta-analysis to evaluate the feasibility, diagnostic yield, and safety of EUS-guided TTN microforceps biopsy for diagnosis of PCLs. Methods  Individualized searches were developed in accordance with PRISMA and MOOSE guidelines. This was a cumulative meta-analysis performed by calculating pooled proportions with rates estimated using random effects models. Measured outcomes included pooled technical success, diagnostic yield, accuracy, and procedure-associated adverse events (AEs) as well as comparison to conventional FNA. Results  Eleven studies (n = 518 patients; mean age 64.13 ± 5.83 years; 58.19 % female) were included. Mean PCL size was 33.39 ± 3.72 mm with the pancreatic head/uncinate (35.50 %) being the most common location. A mean of 2.47 ± 0.92 forceps passes were performed with a mean of 2.79 ± 0.81 microbiopsies obtained per lesion. Pooled technical success was 97.12 % (95 % CI, 93.73-98.71; I ²  = 34.49) with a diagnostic yield of 79.60 % (95 % CI, 72.62-85.16; I ²  = 56.00), and accuracy of 82.76 % [(95 % CI, 77.80-86.80; I ²  = 0.00). The pooled serious adverse event rate was 1.08 % (95 % CI, 0.43-2.69; I ²  = 0.00). Compared to conventional FNA, TTN microforceps biopsy resulted in significant improvement in diagnostic yield [OR 4.79 (95 % CI: 1.52-15.06; P  = 0.007)] and diagnostic accuracy [OR 8.69 (95 % CI, 1.12-67.12; P  = 0.038)], respectively. Conclusions  EUS-guided TTN microforceps biopsy appears to be safe and effective for diagnosis of PCLs with improvement in diagnostic yield and accuracy when compared to FNA alone.

Diagnostic yield of EUS-guided through-the-needle biopsy in pancreatic cysts: a meta-analysis

BACKGROUND AND AIMS

There is currently limited evidence supporting the use of EUS-guided through-the-needle biopsy for sampling pancreatic cystic lesions. The aim of this meta-analysis was to provide a pooled estimate of the diagnostic performance of through-the-needle biopsy for sampling of pancreatic cysts.

METHODS

A bibliographic search on the main databases was performed in September 2019. Pooled effects were calculated using a random-effects model by means of the DerSimonian and Laird test. The primary outcome was sample adequacy. Additional endpoints were diagnostic accuracy, optimal histologic core procurement, mean number of needle passes, pooled specificity, and sensitivity. Adverse event rates were also analyzed.

RESULTS

Eleven studies enrolling 490 patients were included. Eight articles compared through-the-needle biopsy with cytology/cystic fluid analysis. Most patients were female, and the body/tail was the most frequent location of cystic lesions. Sample adequacy with through-the-needle biopsy was 85.3% (78.2%-92.5%), and subanalysis performed according to cyst morphology, size, and location confirmed the result. Through-the-needle biopsy clearly outperformed FNA both in terms of sample adequacy (odds ratio, 4.83; 95% confidence interval, 1.63-14.31; P =.004) and diagnostic accuracy (odds ratio, 3.44; 95% confidence interval, 1.32-8.96; P =.01). The pooled diagnostic accuracy rate, sensitivity, and specificity of through-the-needle biopsy were 78.8%, 82.2%, and 96.8%, respectively. A mean of 3.121 (2.98-3.25) passes through the cyst was needed to obtain adequate histologic samples. The incidence rates of mild bleeding and pancreatitis were 4% and 2%, respectively.

CONCLUSION

Our meta-analysis speaks in favor of the use of through-the-needle biopsy as a safe and effective tool in EUS-guided tissue acquisition of pancreatic cysts.

EUS-guided through-the-needle microbiopsy of pancreatic cysts: Technical aspects (with video)

Pancreatic cystic lesions are frequently encountered and diagnostically challenging as some of the cysts may have malignant potential (mucinous) while others are completely benign (serous). EUS-guided through-the-needle biopsy (EUS-TTNB) of the cyst wall has recently been introduced as an alternative to cyst fluid cytology. Several studies have shown that microbiopsies outperform cytology in terms of distinction between mucinous and nonmucinous lesions, but also in determining the specific cyst diagnosis. However, little is known about the technical aspects of tissue sampling with TTNB. Herein, we summarize our experience with the procedure in a tertiary referral center and discuss indications, technical aspects, and safety of the procedure. Most adverse events (AEs) associated with the procedure are mild, but there is emerging evidence that the rate of postprocedural pancreatitis is higher compared to standard fine-needle aspiration. The added diagnostic yield should therefore be placed in perspective with an increased risk of AEs. Prospective studies are warranted to fully identify which patient groups could benefit from EUS-TTNB.