A Combined DNA/RNA-based Next-Generation Sequencing Platform to Improve the Classification of Pancreatic Cysts and Early Detection of Pancreatic Cancer Arising From Pancreatic Cysts.
Journal
Annals of surgery
ISSN: 1528-1140
Titre abrégé: Ann Surg
Pays: United States
ID NLM: 0372354
Informations de publication
Date de publication:
01 10 2023
01 10 2023
Historique:
medline:
11
9
2023
pubmed:
22
5
2023
entrez:
22
5
2023
Statut:
ppublish
Résumé
We report the development and validation of a combined DNA/RNA next-generation sequencing (NGS) platform to improve the evaluation of pancreatic cysts. Despite a multidisciplinary approach, pancreatic cyst classification, such as a cystic precursor neoplasm, and the detection of high-grade dysplasia and early adenocarcinoma (advanced neoplasia) can be challenging. NGS of preoperative pancreatic cyst fluid improves the clinical evaluation of pancreatic cysts, but the recent identification of novel genomic alterations necessitates the creation of a comprehensive panel and the development of a genomic classifier to integrate the complex molecular results. An updated and unique 74-gene DNA/RNA-targeted NGS panel (PancreaSeq Genomic Classifier) was created to evaluate 5 classes of genomic alterations to include gene mutations (e.g., KRAS, GNAS, etc.), gene fusions and gene expression. Further, CEA mRNA ( CEACAM5 ) was integrated into the assay using RT-qPCR. Separate multi-institutional cohorts for training (n=108) and validation (n=77) were tested, and diagnostic performance was compared to clinical, imaging, cytopathologic, and guideline data. Upon creation of a genomic classifier system, PancreaSeq GC yielded a 95% sensitivity and 100% specificity for a cystic precursor neoplasm, and the sensitivity and specificity for advanced neoplasia were 82% and 100%, respectively. Associated symptoms, cyst size, duct dilatation, a mural nodule, increasing cyst size, and malignant cytopathology had lower sensitivities (41-59%) and lower specificities (56-96%) for advanced neoplasia. This test also increased the sensitivity of current pancreatic cyst guidelines (IAP/Fukuoka and AGA) by >10% and maintained their inherent specificity. PancreaSeq GC was not only accurate in predicting pancreatic cyst type and advanced neoplasia but also improved the sensitivity of current pancreatic cyst guidelines.
Sections du résumé
OBJECTIVE
We report the development and validation of a combined DNA/RNA next-generation sequencing (NGS) platform to improve the evaluation of pancreatic cysts.
BACKGROUND AND AIMS
Despite a multidisciplinary approach, pancreatic cyst classification, such as a cystic precursor neoplasm, and the detection of high-grade dysplasia and early adenocarcinoma (advanced neoplasia) can be challenging. NGS of preoperative pancreatic cyst fluid improves the clinical evaluation of pancreatic cysts, but the recent identification of novel genomic alterations necessitates the creation of a comprehensive panel and the development of a genomic classifier to integrate the complex molecular results.
METHODS
An updated and unique 74-gene DNA/RNA-targeted NGS panel (PancreaSeq Genomic Classifier) was created to evaluate 5 classes of genomic alterations to include gene mutations (e.g., KRAS, GNAS, etc.), gene fusions and gene expression. Further, CEA mRNA ( CEACAM5 ) was integrated into the assay using RT-qPCR. Separate multi-institutional cohorts for training (n=108) and validation (n=77) were tested, and diagnostic performance was compared to clinical, imaging, cytopathologic, and guideline data.
RESULTS
Upon creation of a genomic classifier system, PancreaSeq GC yielded a 95% sensitivity and 100% specificity for a cystic precursor neoplasm, and the sensitivity and specificity for advanced neoplasia were 82% and 100%, respectively. Associated symptoms, cyst size, duct dilatation, a mural nodule, increasing cyst size, and malignant cytopathology had lower sensitivities (41-59%) and lower specificities (56-96%) for advanced neoplasia. This test also increased the sensitivity of current pancreatic cyst guidelines (IAP/Fukuoka and AGA) by >10% and maintained their inherent specificity.
CONCLUSIONS
PancreaSeq GC was not only accurate in predicting pancreatic cyst type and advanced neoplasia but also improved the sensitivity of current pancreatic cyst guidelines.
Identifiants
pubmed: 37212422
doi: 10.1097/SLA.0000000000005904
pii: 00000658-990000000-00471
pmc: PMC10481930
mid: NIHMS1901398
doi:
Substances chimiques
RNA
63231-63-0
DNA
9007-49-2
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
e789-e797Subventions
Organisme : NIDDK NIH HHS
ID : P30 DK120531
Pays : United States
Organisme : NCI NIH HHS
ID : P50 CA062924
Pays : United States
Organisme : NCI NIH HHS
ID : R37 CA263622
Pays : United States
Organisme : NCI NIH HHS
ID : U01 CA200466
Pays : United States
Informations de copyright
Copyright © 2023 The Author(s). Published by Wolters Kluwer Health, Inc.
Déclaration de conflit d'intérêts
A.D.S. has received an honorarium from Foundation Medicine Inc. M.N.N. and Y.E.N. own intellectual property related to the PancreaSeq technology and receive royalties from University of Pittsburgh. R.H.H. has the potential to receive royalty payments from Thrive Earlier Detection for the GNAS invention in an arrangement reviewed and approved by the Johns Hopkins University in accordance with its conflict-of-interest policies. The remaining authors report no conflicts of interest.
Références
Ayoub F, Davis AM, Chapman CG. Pancreatic cysts-an overview and summary of society guidelines, 2021. JAMA. 2021;325:391–392.
Singhi AD, Wood LD, Parks E, et al. Recurrent rearrangements in PRKACA and PRKACB in intraductal oncocytic papillary neoplasms of the pancreas and bile duct. Gastroenterology. 2020;158:573–582 e2.
Tanaka M, Fernandez-Del Castillo C, Kamisawa T, et al. Revisions of international consensus Fukuoka guidelines for the management of IPMN of the pancreas. Pancreatology. 2017;17:738–753.
European Study Group on Cystic Tumours of the Pancreas. European evidence-based guidelines on pancreatic cystic neoplasms. Gut. 2018;67:789–804.
Vege SS, Ziring B, Jain R, et al. American gastroenterological association institute guideline on the diagnosis and management of asymptomatic neoplastic pancreatic cysts. Gastroenterology. 2015;148:819–822; quize12–13.
Elta GH, Enestvedt BK, Sauer BG, et al. ACG Clinical Guideline: Diagnosis and Management of Pancreatic Cysts. Am J Gastroenterol. 2018;113:464–479.
Singhi AD, Zeh HJ, Brand RE, et al. American Gastroenterological Association guidelines are inaccurate in detecting pancreatic cysts with advanced neoplasia: a clinicopathologic study of 225 patients with supporting molecular data. Gastrointest Endosc. 2016;83:1107–1117 e2.
Dbouk M, Brewer Gutierrez OI, Lennon AM, et al. Guidelines on management of pancreatic cysts detected in high-risk individuals: an evaluation of the 2017 Fukuoka guidelines and the 2020 International Cancer of the Pancreas Screening (CAPS) consortium statements. Pancreatology. 2021;21:613–621.
Rosenbaum MW, Jones M, Dudley JC, et al. Next-generation sequencing adds value to the preoperative diagnosis of pancreatic cysts. Cancer Cytopathol. 2017;125:41–47.
Singhi AD, McGrath K, Brand RE, et al. Preoperative next-generation sequencing of pancreatic cyst fluid is highly accurate in cyst classification and detection of advanced neoplasia. Gut. 2018;67:2131–2141.
Springer S, Masica DL, Dal Molin M, et al. A multimodality test to guide the management of patients with a pancreatic cyst. Sci Transl Med. 2019;11:eaav4772.
Springer S, Wang Y, Dal Molin M, et al. A combination of molecular markers and clinical features improve the classification of pancreatic cysts. Gastroenterology. 2015;149:1501–1510.
Rift CV, Melchior LC, Kovacevic B, et al. Targeted next generation sequencing of endoscopic ultrasound-guided through-the-needle-biopsies from pancreatic cystic lesions. Gastrointest Endosc. 2023;97:50–58.
Singhi AD, Nikiforova MN, Fasanella KE, et al. Preoperative GNAS and KRAS testing in the diagnosis of pancreatic mucinous cysts. Clin Cancer Res. 2014;20:4381–4389.
Nikiforova MN, Khalid A, Fasanella KE, et al. Integration of KRAS testing in the diagnosis of pancreatic cystic lesions: a clinical experience of 618 pancreatic cysts. Mod Pathol. 2013;26:1478–1487.
Schmitz D, Kazdal D, Allgauer M, et al. KRAS/GNAS-testing by highly sensitive deep targeted next generation sequencing improves the endoscopic ultrasound-guided workup of suspected mucinous neoplasms of the pancreas. Genes Chromosomes Cancer. 2021;60:489–497.
Jones M, Zheng Z, Wang J, et al. Impact of next-generation sequencing on the clinical diagnosis of pancreatic cysts. Gastrointest Endosc. 2016;83:140–148.
Paniccia A, Polanco PM, Boone BA, et al. Prospective, multi-institutional, real-time next-generation sequencing of pancreatic cyst fluid reveals diverse genomic alterations that improve the clinical management of pancreatic cysts. Gastroenterology. 2023;164:117–133.
Lee JW, Hruban RH, Brosens LAA, et al. RNA sequencing identifies frequent mitogen-activated protein kinase-associated fusion genes in intraductal tubulopapillary neoplasms of the pancreas. Gastroenterology. 2023;164:1310–1313.
Krasinskas AM, Moser AJ, Saka B, et al. KRAS mutant allele-specific imbalance is associated with worse prognosis in pancreatic cancer and progression to undifferentiated carcinoma of the pancreas. Mod Pathol. 2013;26:1346–1354.
Lokuhetty D, White V, Watanabe R, et al. Digestive System Tumours: WHO Classification of Tumours. International Agency for Research on Cancer; 2019.
Nikiforova MN, Wald AI, Roy S, et al. Targeted next-generation sequencing panel (ThyroSeq) for detection of mutations in thyroid cancer. J Clin Endocrinol Metab. 2013;98:E1852–E1860.
Beadling C, Wald AI, Warrick A, et al. A multiplexed amplicon approach for detecting gene fusions by next-generation sequencing. J Mol Diagn. 2016;18:165–175.
Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods. 2001;25:402–408.
Cancer Genome Atlas Research Network. Electronic address aadhe, Cancer Genome Atlas Research N. Integrated genomic characterization of pancreatic ductal adenocarcinoma. Cancer Cell. 2017;32:185–203 e13.
Cerami E, Gao J, Dogrusoz U, et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2012;2:401–404.
Tate JG, Bamford S, Jubb HC, et al. COSMIC: the Catalogue Of Somatic Mutations In Cancer. Nucleic Acids Res. 2019;47:D941–D947.
Singhi AD, George B, Greenbowe JR, et al. Real-time targeted genome profile analysis of pancreatic ductal adenocarcinomas identifies genetic alterations that might be targeted with existing drugs or used as biomarkers. Gastroenterology. 2019;156:2242–2253 e4.
DeLong ER, DeLong DM, Clarke-Pearson DL. Comparing the areas under two or more correlated receiver operating characteristic curves: a nonparametric approach. Biometrics. 1988;44:837–845.
Brugge WR, Lewandrowski K, Lee-Lewandrowski E, et al. Diagnosis of pancreatic cystic neoplasms: a report of the cooperative pancreatic cyst study. Gastroenterology. 2004;126:1330–1336.
Faias S, Cravo M, Chaves P, et al. Comparative analysis of glucose and carcinoembryonic antigen in the diagnosis of pancreatic mucinous cysts: a systematic review and meta-analysis. Gastrointest Endosc. 2021;94:235–247.
Scheiman JM, Hwang JH, Moayyedi P. American Gastroenterological Association technical review on the diagnosis and management of asymptomatic neoplastic pancreatic cysts. Gastroenterology. 2015;148:824–48 e22.
Roldan J, Harrison JM, Qadan M, et al. Evolving trends in pancreatic cystic tumors: a 3-decade single-center experience with 1290 resections. Ann Surg. 2023;277:491–497.
Kim SA, Kim MS, Kim MS, et al. Pleomorphic solid pseudopapillary neoplasm of the pancreas: degenerative change rather than high-grade malignant potential. Hum Pathol. 2014;45:166–174.
Hackeng WM, Brosens LAA, Kim JY, et al. Non-functional pancreatic neuroendocrine tumours: ATRX/DAXX and alternative lengthening of telomeres (ALT) are prognostically independent from ARX/PDX1 expression and tumour size. Gut. 2022;71:961–973.
Singhi AD, Liu TC, Roncaioli JL, et al. Alternative lengthening of telomeres and loss of DAXX/ATRX expression predicts metastatic disease and poor survival in patients with pancreatic neuroendocrine tumors. Clin Cancer Res. 2017;23:600–609.
Pea A, Yu J, Marchionni L, et al. Genetic analysis of small well-differentiated pancreatic neuroendocrine tumors identifies subgroups with differing risks of liver metastases. Ann Surg. 2020;271:566–573.
Roy S, LaFramboise WA, Liu TC, et al. Loss of chromatin-remodeling proteins and/or cdkn2a associates with metastasis of pancreatic neuroendocrine tumors and reduced patient survival times. Gastroenterology. 2018;154:2060–2063 e8.