TY - JOUR
T1 - Molecular characterization of organoids derived from pancreatic intraductal papillary mucinous neoplasms
AU - Huang, Bo
AU - Trujillo, Maria A.
AU - Fujikura, Kohei
AU - Qiu, Miaozhen
AU - Chen, Fei
AU - Felsenstein, Matthäus
AU - Zhou, Cancan
AU - Skaro, Michael
AU - Gauthier, Christian
AU - Macgregor-Das, Anne
AU - Hutchings, Danielle
AU - Hong, Seung Mo
AU - Hruban, Ralph H.
AU - Eshleman, James R.
AU - Thompson, Elizabeth D.
AU - Klein, Alison P.
AU - Goggins, Michael
AU - Wood, Laura D.
AU - Roberts, Nicholas J.
N1 - Funding Information:
We wish to acknowledge funding support from the following sources: Rolfe Pancreatic Cancer Foundation; Susan Wojcicki and Denis Troper; NIH/NCI P50 CA62924; NIH/NIDDK K08 DK107781; NIH NCI R00 CA190889; Sol Goldman Pancreatic Cancer Research Center; Burroughs‐Wellcome Fund; the Maryland‐Genetic, Epidemiology and Medicine Training Program (MD‐GEM); DFG‐German Research Foundation; BIH‐Charité Junior Clinician Scientist Program; Buffone Family Gastrointestinal Cancer Research Fund; Kaya Tuncer Career Development Award in Gastrointestinal Cancer Prevention; AGA–Bernard Lee Schwartz Foundation Research Scholar Award in Pancreatic Cancer; Sidney Kimmel Foundation for Cancer Research Kimmel Scholar Award; AACR–Incyte Corporation Career Development Award for Pancreatic Cancer Research; American Cancer Society Research Scholar Grant; Emerson Collective Cancer Research Fund; Joseph C Monastra Foundation; The Gerald O Mann Charitable Foundation (Harriet and Allan Wulfstat, Trustees); and Art Creates Cures Foundation.
Funding Information:
We wish to acknowledge funding support from the following sources: Rolfe Pancreatic Cancer Foundation; Susan Wojcicki and Denis Troper; NIH/NCI P50 CA62924; NIH/NIDDK K08 DK107781; NIH NCI R00 CA190889; Sol Goldman Pancreatic Cancer Research Center; Burroughs-Wellcome Fund; the Maryland-Genetic, Epidemiology and Medicine Training Program (MD-GEM); DFG-German Research Foundation; BIH-Charit? Junior Clinician Scientist Program; Buffone Family Gastrointestinal Cancer Research Fund; Kaya Tuncer Career Development Award in Gastrointestinal Cancer Prevention; AGA?Bernard Lee Schwartz Foundation Research Scholar Award in Pancreatic Cancer; Sidney Kimmel Foundation for Cancer Research Kimmel Scholar Award; AACR?Incyte Corporation Career Development Award for Pancreatic Cancer Research; American Cancer Society Research Scholar Grant; Emerson Collective Cancer Research Fund; Joseph C Monastra Foundation; The Gerald O Mann Charitable Foundation (Harriet and Allan Wulfstat, Trustees); and Art Creates Cures Foundation.
Publisher Copyright:
© 2020 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
PY - 2020/11/1
Y1 - 2020/11/1
N2 - Intraductal papillary mucinous neoplasms (IPMNs) are commonly identified non-invasive cyst-forming pancreatic neoplasms with the potential to progress into invasive pancreatic adenocarcinoma. There are few in vitro models with which to study the biology of IPMNs and their progression to invasive carcinoma. Therefore, we generated a living biobank of organoids from seven normal pancreatic ducts and ten IPMNs. We characterized eight IPMN organoid samples using whole genome sequencing and characterized five IPMN organoids and seven normal pancreatic duct organoids using transcriptome sequencing. We identified an average of 11,344 somatic mutations in the genomes of organoids derived from IPMNs, with one sample harboring 61,537 somatic mutations enriched for T→C transitions and T→A transversions. Recurrent coding somatic mutations were identified in 15 genes, including KRAS, GNAS, RNF43, PHF3, and RBM10. The most frequently mutated genes were KRAS, GNAS, and RNF43, with somatic mutations identified in six (75%), four (50%), and three (37.5%) IPMN organoid samples, respectively. On average, we identified 36 structural variants in IPMN derived organoids, and none had an unstable phenotype (> 200 structural variants). Transcriptome sequencing identified 28 genes differentially expressed between normal pancreatic duct organoid and IPMN organoid samples. The most significantly upregulated and downregulated genes were CLDN18 and FOXA1. Immunohistochemical analysis of FOXA1 expression in 112 IPMNs, 113 mucinous cystic neoplasms, and 145 pancreatic ductal adenocarcinomas demonstrated statistically significant loss of expression in low-grade IPMNs (p < 0.0016), mucinous cystic neoplasms (p < 0.0001), and pancreatic ductal adenocarcinoma of any histologic grade (p < 0.0001) compared to normal pancreatic ducts. These data indicate that FOXA1 loss of expression occurs early in pancreatic tumorigenesis. Our study highlights the utility of organoid culture to study the genetics and biology of normal pancreatic duct and IPMNs.
AB - Intraductal papillary mucinous neoplasms (IPMNs) are commonly identified non-invasive cyst-forming pancreatic neoplasms with the potential to progress into invasive pancreatic adenocarcinoma. There are few in vitro models with which to study the biology of IPMNs and their progression to invasive carcinoma. Therefore, we generated a living biobank of organoids from seven normal pancreatic ducts and ten IPMNs. We characterized eight IPMN organoid samples using whole genome sequencing and characterized five IPMN organoids and seven normal pancreatic duct organoids using transcriptome sequencing. We identified an average of 11,344 somatic mutations in the genomes of organoids derived from IPMNs, with one sample harboring 61,537 somatic mutations enriched for T→C transitions and T→A transversions. Recurrent coding somatic mutations were identified in 15 genes, including KRAS, GNAS, RNF43, PHF3, and RBM10. The most frequently mutated genes were KRAS, GNAS, and RNF43, with somatic mutations identified in six (75%), four (50%), and three (37.5%) IPMN organoid samples, respectively. On average, we identified 36 structural variants in IPMN derived organoids, and none had an unstable phenotype (> 200 structural variants). Transcriptome sequencing identified 28 genes differentially expressed between normal pancreatic duct organoid and IPMN organoid samples. The most significantly upregulated and downregulated genes were CLDN18 and FOXA1. Immunohistochemical analysis of FOXA1 expression in 112 IPMNs, 113 mucinous cystic neoplasms, and 145 pancreatic ductal adenocarcinomas demonstrated statistically significant loss of expression in low-grade IPMNs (p < 0.0016), mucinous cystic neoplasms (p < 0.0001), and pancreatic ductal adenocarcinoma of any histologic grade (p < 0.0001) compared to normal pancreatic ducts. These data indicate that FOXA1 loss of expression occurs early in pancreatic tumorigenesis. Our study highlights the utility of organoid culture to study the genetics and biology of normal pancreatic duct and IPMNs.
KW - RNA
KW - cancer
KW - expression
KW - intraductal papillary mucinous neoplasm
KW - mutations
KW - organoids, DNA
KW - pancreas
KW - pancreatic
KW - precursor
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U2 - 10.1002/path.5515
DO - 10.1002/path.5515
M3 - Article
C2 - 32696980
AN - SCOPUS:85090528563
VL - 252
SP - 252
EP - 262
JO - Investigative and Cell Pathology
JF - Investigative and Cell Pathology
SN - 0022-3417
IS - 3
ER -