Whole-exome sequencing of neoplastic cysts of the pancreas reveals recurrent mutations in components of ubiquitin-dependent pathways

Abstract

More than 2% of adults harbor a pancreatic cyst, a subset of which progresses to invasive lesions with lethal consequences. To assess the genomic landscapes of neoplastic cysts of the pancreas, we determined the exomic sequences of DNA from the neoplastic epithelium of eight surgically resected cysts of each of the major neoplastic cyst types: serous cystadenomas (SCAs), intraductal papillary mucinous neoplasms (IPMNs), mucinous cystic neoplasms (MCNs), and solid pseudopapillary neoplasms (SPNs). SPNs are low-grade malignancies, and IPMNs and MCNs, but not SCAs, have the capacity to progress to cancer. We found that SCAs, IPMNs, MCNs, and SPNs contained 10 ± 4.6, 27 ± 12, 16 ± 7.6, and 2.9 ± 2.1 somatic mutations per tumor, respectively. Among the mutations identified, E3 ubiquitin ligase components were of particular note. Four of the eight SCAs contained mutations of the von Hippel-Lindau gene (VHL), a key component of the VHL ubiquitin ligase complex that has previously been associated with renal cell carcinomas, SCAs, and other neoplasms. Six of the eight IPMNs and three of the eight MCNs harbored mutations of RNF43, a gene coding for a protein with intrinsic E3 ubiquitin ligase activity that has not previously been found to be genetically altered in any human cancer. The preponderance of inactivating mutations in RNF43 unequivocally establish it as a suppressor of both IPMNs and MCNs. SPNs contained remarkably few genetic alterations but always contained mutations of CTNNB1, previously demonstrated to inhibit degradation of the encoded protein (β-catenin) by E3 ubiquitin ligases. These results highlight the essential role of ubiquitin ligases in these neoplasms and have important implications for the diagnosis and treatment of patients with cystic tumors.

Integration of KRAS testing in the diagnosis of pancreatic cystic lesions: a clinical experience of 618 pancreatic cysts

“…Further, the presence of either a GNAS or KRAS mutation was identified in 496% of IPMNs. In another study by Wu et al 24 , sequencing of cyst epithelium of the four major neoplastic cysts defined a panel of genes that could be used to classify each cyst type. IPMNs were characterized by mutations in KRAS, GNAS and the E3 ubiquitin ligase, RNF43.…”

Light scattering spectroscopy identifies the malignant potential of pancreatic cysts during endoscopy

“…Recently genetic mutations in genes such as guanine nucleotide binding protein, alpha stimulating (GNAS), and mutational profiles of targeted next-generation sequencing of cancer genes, have been suggested as an adjunct to cytology and CEA to improve the diagnosis of mucinous cysts and to identify early malignancy within lesions by analyzing cyst fluid 45–47 . These studies are quite promising in substantiating the feasibility of detecting DNA mutations in IPMN using cyst fluid, even when these molecules are at low concentrations, though the performance of these genetic markers needs to be further evaluated in prospective in vivo clinical studies.…”

The value of mutational profiling of the cytocentrifugation supernatant fluid from fine-needle aspiration of pancreatic solid mass lesions

“…A panel of 16 microsatellite markers was used for this purpose. These markers targeted common sites for tumor-suppressor genes associated with pancreaticobiliary cancers and have previously undergone analytic and clinical validation for pancreaticobiliary disease as reported in prior studies, [16][17][18][19][20][21][22][23] and present at the following chromosomal locations: 1p (CMM1, Lmyc), 3p (VHL, OGG1), 5q (MCC, APC), 9p (CDKN2A, CDKN2B), 10q (PTEN, MXI1), 17p (TP53), 17q (NME1, RNF43), 21q, 22q (NF2) using quantitative fluorescent PCR/capillary electrophoresis.…”

“…For this purpose, panels of pancreatic cancer biomarkers have been developed. 14,15 Furthermore, the molecular analysis might prove to be of great help in addressing problems related to low sample volumes, few cells for evaluation and/or sampling inadequacy.…”

“…[16][17][18][19][20][21][22][23] The use of these techniques nonetheless requires the presence of not only an adequate amount of cellular material, but also cellular material that shows cytomorphological atypia, in order to be selected for microdissection. In fact, paucicellular or acellular specimens not only do not provide optimal material for cytological evaluation but also, at times, fail to provide material for cell-based DNA mutational analysis.…”