Global genomic analysis of intraductal papillary mucinous neoplasms of the pancreas reveals significant molecular differences compared to ductal adenocarcinoma

Abstract

Objective: To determine whether intraductal papillary mucinous neoplasms of the pancreas (IPMNs) have a different genetic background compared with ductal adenocarcinoma (PDAC).

Summary background data: The biologic and clinical behavior of IPMNs and IPMN-associated adenocarcinomas is different from PDAC in having a less aggressive tumor growth and significantly improved survival. Up to date, the molecular mechanisms underlying the clinical behavior of IPMNs are incompletely understood.

Methods: 128 cystic pancreatic lesions were prospectively identified during the course of 2 years. From the corresponding surgical specimens, 57 IPMNs were separated and subdivided by histologic criteria into those with low-grade dysplasia, moderate dysplasia, high-grade dysplasia, and invasive cancer. Twenty specimens were suitable for DNA isolation and subsequent performance of array CGH.

Results: While none of the IPMNs with low-grade dysplasia displayed detectable chromosomal aberrations, IPMNs with moderate and high-grade dysplasia showed frequent copy number alterations. Commonly lost regions were located on chromosome 5q, 6q, 10q, 11q, 13q, 18q, and 22q. The incidence of loss of chromosome 5q, 6q, and 11q was significantly higher in IPMNs with high-grade dysplasia or invasion compared with PDAC. Ten of 13 IPMNs with moderate dysplasia or malignancy had loss of part or all of chromosome 6q, with a minimal deleted region between linear positions 78.0 and 130.0.

Conclusions: This study is the first to use array CGH to characterize IPMNs. Recurrent cytogenetic alterations were identified and were different than those described in PDAC. Array CGH may help distinguish between these 2 entities and give insight into the differences in their biology and prognosis.

Figure 1

WHO Histologic Grading of IPMNs Used For Array CGH. Morphologic features of IPMNs often vary within different areas of the same pathologic specimen. Thus, each subject was classified based on a section from the tissue sample used for the array CGH analysis according to their histologic grade using current nomenclature. Hematoxylin & Eosin staining of (A) IPMN with low-grade dysplasia, (B) IPMN with moderate dysplasia, (C) IPMN with high-grade dysplasia, and (D) IPMN with moderate dysplasia (dashed arrow) with associated invasive adenocarcinoma of colloid type (solid arrow). Images shown using 4× objectives; insets show higher-power images using a 20× objective.

Figure 2

Array CGH Data for Chromosome 6q. Summary of all array CGH results concerning copy number changes on chromosome 6. (A); A representative array CGH chromosome 6 tracing from a tumor with partial loss of 6q, shown as the log2 ratio of tumor/normal fluorescence. (B); Black bars indicate extent of loss of chromosomal material on chromosome 6. 4/5 IPMNs with moderate dysplasia and 6/8 IPMNs with high-grade dysplasia or invasion showed loss of parts or loss of the whole long arm of chromosome 6. The numbers on the top of each bar^– refer to the patients described in detail in Supplemental Table 1 [see Table, Supplemental Digital Content 1, http://links.lww.com/A790]. Patients 1 through 7 had low-grade IPMNs with no genetic alterations detected by array CGH.

Figure 3

FISH Verification of Array CGH Findings. FISH analysis of paraffin sections of a representative tumor with relative 6q loss (A) and 18q loss (B). 6q loss is seen as fewer copies of the red 6q probe relative to the green 6p probe in tumor epithelium. 18q loss is seen as fewer copies of the red 18q probe relative to the green 6p probe in tumor epithelium. There is significant polysomy for both chromosomes.

Figure 4

Sequencing for KRAS Mutation at Codon 12. Sequence chromatograms of KRAS codon 12. (A); Codon 12 of a control sample consisting of DNA deriving from normal pancreas. (B); Example for a KRAS mutation at codon 12 in an IPMN specimen with low-grade dysplasia showing the sequence change GGT > GAT. (C); and (D); show KRAS mutations in IPMN with moderate dysplasia, high-grade dysplasia and invasion respectively.