Mutation analysis by deep sequencing of pancreatic juice from patients with pancreatic ductal adenocarcinoma

Abstract

BackgroundReliable methods are needed to identify patients with early-stage cancer or high-grade precancerous lesions in the pancreas. Analysis of pancreatic juice to detect somatic mutations could represent one such approach. Here we investigated the concordance between mutations found in the primary tumor and pancreatic juice from the same patient.MethodsAmplicon-based targeted deep sequencing was performed on samples from 21 patients with pancreatic ductal adenocarcinoma (PDAC) who had undergone Whipple’s operation. Mutation profiles were determined in formalin-fixed sections of the primary tumor and in pancreatic juice sampled from the main pancreatic duct during surgery.ResultsUsing a cut-off of 3% for variant allele frequency, KRAS mutations were detected in 20/21 primary tumors (95%) and in 15/21 (71%) juice samples. When also considering low-frequency variants, KRAS mutations were found in 20/21 juice samples. Most juice samples exhibited multiple KRAS variants not seen in the primary tumor, and only in 11 cases (52%) did the most abundant variant of the juice correspond to the KRAS mutation detected in the tumor. TP53 mutations were found in 16 tumors (76%) and six juice samples (29%). Among the positive juice samples, only one exhibited more than a single TP53 mutation. Detection of both KRAS and TP53 mutations was fully concordant in the primary tumor and juice sample in 7/21 cases (33%).ConclusionsPancreatic juice from PDAC patients is rich in KRAS mutations often not seen in the primary tumor and possibly reflecting precancerous lesions in other regions of the pancreas. The inclusion of TP53 mutation detection and additional markers must therefore be considered for fully exploiting the clinical potential of pancreatic juice samples in early cancer detection.Electronic supplementary materialThe online version of this article (10.1186/s12885-018-5195-7) contains supplementary material, which is available to authorized users.

Pancreatic Macrophages: Critical Players in Obesity-Promoted Pancreatic Cancer

“…However, there is also evidence that at least a fraction of human PDACs can develop outside the PanIN-PDAC sequence paradigm [5][6][7]. Several studies have shown that Kras mutations can be detected at higher frequency in pancreatic juice and stool of patients with PDAC compared to normal patients and patients with benign pancreatic pathologies [8][9][10], making this disease potentially amenable to prevention or early interception.…”

Identification and Validation of T-cell Receptors Targeting RAS Hotspot Mutations in Human Cancers for Use in Cell-based Immunotherapy

“…RAS mutations can potentially serve as good targets for immunotherapies since the mutations are usually in hotspot mutations and are common among cancer patients with various types of cancer (19)(20)(21)(22)(23)(24)(25)(26)(27)(28). We have previously detected T cell reactivity against RAS hotspot driver mutations and identified the accompanying TCR from reactive TILs from 3 patients (17,52).…”

“…Author Manuscript Published OnlineFirst on June 24, 2021; DOI: 10.1158/1078-0432.CCR-21-0849 colon cancer express a RAS mutation (19)(20)(21)(23)(24)(25)(26)(27)(28). The human RAS super-family proteins (KRAS/NRAS/HRAS) have an identical amino acid sequence in positions 1 through 86 (20,25), and over 99% of all mutations in this gene family occur at positions 12, 13 or 61 (COSMIC database (29)) within the domains responsible for GTP dephosphorylation into GDP, resulting in constitutive activation of the RAS protein (20)(21)(22)(23)25,28,30).…”

The Diagnostic Accuracy of Mutant KRAS Detection from Pancreatic Secretions for the Diagnosis of Pancreatic Cancer: A Meta-Analysis

“…This method has a reported sensitivity of up to 82% for the detection of KRAS mutation in PDAC patients [ 53 , 54 ], however, it is likely to have a lower specificity given the propensity for mucus to be generated by benign or malignant colorectal polyps which also frequently harbour KRAS mutation [ 24 ]. The development of more advanced KRAS mutant detection methods will also improve test sensitivity [ 55 ]. This is the case for droplet digital PCR [ 56 ], a method ideally suited to the detection of mutations existing in samples such as pancreatic secretions which contain low levels of nucleic acid and suffer from abundant protein contamination.…”

“…This is the case for droplet digital PCR [ 56 ], a method ideally suited to the detection of mutations existing in samples such as pancreatic secretions which contain low levels of nucleic acid and suffer from abundant protein contamination. Alternatively, incorporation of multiple genetic indicators such as panels of mutations, DNA methylation status [ 46 , 54 ] or simultaneous tumour marker assessment [ 55 ] could be used to improve sensitivity.…”