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Molecular signatures of pancreatic cancer.

Pancreatic cancer is the fourth leading cause of cancer death in both men and women in the United States. In 2010, it is estimated that 43140 Americans will be diagnosed and 36800 patients will die of pancreatic cancer. (1) Most pancreatic cancers are pancreatic ductal adenocarcinomas and the 5-year survival rate for patients with localized disease after surgical resection is 20% and for those with metastatic disease, the survival rate is only 2%. (1) The poor survival rate is attributed to the late detection of pancreatic cancers; 85% of patients present with advanced disease that is unresectable. Although significant resources have been committed to improving the survival of patients with pancreatic cancer in the past decades, there has been no significant improvement in survival. (1) Research into the molecular mechanisms of pancreatic cancer has revealed that the disease is due to both genetic and epigenetic changes. The introduction of genome- and epigenome-wide screening techniques has expanded the numbers of genes linked to pancreatic cancer. (2-6) In this review, we briefly summarize recent research findings on genetics and epigenetics of pancreatic cancer in the context of histologic variants, precursor lesions, and familial pancreatic cancer.


A recent comprehensive study of the pancreatic cancer genome profiled the genetic abnormalities of pancreatic ductal adenocarcinomas. In this study, Jones and colleagues7 sequenced 20661 protein-coding genes in 24 ductal adenocarcinomas and demonstrated an average of 48 nonsilent mutations, 6 amplifications, and 8 homozygous deletions per pancreatic cancer. These mutations were associated with 12 core signaling pathways.7 Based on the frequency of genetically affected genes in pancreatic cancers, a genetic "topographic map" of the pancreatic cancers can be generated in which the most frequent mutations are represented as 4 "mountains" (high-frequency driver genes) involving KRAS2, CDKN2A/p16, SMAD4/DPC4, and TP53, with numerous "hills" (low-frequency driver genes) involving SMARC4A, CDH1, EPHA3, FBXW7, EGFR, IDH1, and NF1. (7)

1. Oncogenes and Pancreatic Cancer

The most frequently mutated oncogene in pancreatic cancers is KRAS2 (mutated in >95% of pancreatic cancers), which is activated by point mutations, most often in codon 12. (7,8) The KRAS2 gene is located on chromosome arm 12p and encodes a membrane-bound guanosine triphosphate (GTP)-binding protein. This GTP-binding protein mediates various cellular functions, such as proliferation, cellular survival, motility, and cytoskeletal remodeling. Activating KRAS2 gene mutations abolish the regulated GTPase activity of the Kras protein, which results in constitutive signaling. (9) Mutations in the KRAS2 gene are observed in the earliest pancreatic intraepithelial neoplasia (PanIN) lesions and are considered to be one of the earliest genetic events in pancreatic tumorigenesis. (7,10,11) Several additional signaling pathways downstream from KRAS2, including BRAF-MAPK and PI3K-AKT, may also be activated by mutations. The BRAF pathway is activated by a point mutation at V600E. BRAF gene mutations are observed in 5% of pancreatic cancers that do not possess a KRAS2 mutation. (12) These cancers are often microsatellite unstable. Similarly, amplifications in the AKT2 gene are seen in 10% to 20% of pancreatic cancers. (13,14) Amplifications of other oncogenes such as CMYC7, (15) and GATA6 (15,16) are less frequent.

2. Tumor Suppressor Genes in Pancreatic Cancer

Three tumor suppressor genes, CDKN2A/p16, TP53, and SMAD4/DPC4, are commonly inactivated in pancreatic cancers. (7,17-20) CDKN2A/p16 on chromosome arm 9p is inactivated in more than 95% of pancreatic cancers by several different mechanisms, such as homozygous deletion of both alleles of the gene; intragenic mutation in 1 allele, coupled with loss of the other allele; or promoter hypermethylation. (17,21,22) The p16 protein inhibits progression of the cell cycle at the G1-S checkpoint binding of cyclin-dependant kinases (CDKs), including CDK4 and CDK6. (23) The TP53 gene on chromosome arm 17p is inactivated in 50% to 75% of pancreatic cancers. (7,19,24,25)

p53 proteins play several key roles including maintaining G2-M arrest, regulating G1-S checkpoint, inducing apoptosis, regulating senescence, repairing DNA, and changing cellular metabolism. (26) Inactivation of the TP53 gene typically occurs through intragenic mutations of 1 allele, accompanied with loss of the other allele. (19) Functional loss of the p53 protein enables cellular survival and division in the presence of DNA damage; this facilitates the accumulation of further genetic abnormalities. (26)

SMAD4/DPC4 on chromosome arm 18q is inactivated in 55% of pancreatic cancers. (27,28) SMAD4/DPC4 is inactivated by homozygous deletion and by intragenic mutations accompanied by loss of the other allele. (28,29) SMAD4 (DPC4) protein has a critical function in the signal transduction cascade that involves transforming growth factor [beta] (TGF-[beta]) and multiple targets in the TGF-[beta] pathway. Binding of the TGF-[beta] ligand to its receptor triggers a series of reactions including binding of the transcription factor SMAD2/3 to SMAD4. Through multiple target genes, the TGF-[beta] pathway normally regulates cellular growth. Loss of SMAD4 function abolishes the SMAD4-dependant TGF-[beta] pathway and gives rise to unregulated cellular proliferation. (30) Loss of SMAD4 nuclear labeling by immunohistochemistry is generally observed late in pancreatic carcinogenesis, such as in PanIN-3 precursor lesions and infiltrating adenocarcinomas. (31) Both SMAD4/ DPC4 mutation and loss of SMAD4 expression are markers of poor prognosis in pancreatic cancers. (32,33) In contrast to SMAD4/DPC4 mutation, mutations in TP53 and CDKN2A/p16 have not been shown to predict survival. (33) Loss of SMAD4 protein expression can also be used in the differential diagnosis of carcinomas of unknown primary tumor; SMAD4/DPC4 mutations with loss of nuclear SMAD4 labeling frequently occur in pancreatic adenocarcinomas, but not in extrapancreatic malignancies. (34) SMAD4 mutations have recently been associated with poor prognosis and with the development of widespread metastases in pancreatic cancer. (33,35)

An additional tumor suppressor pathway that can be altered in pancreatic cancers involves STK11/LKB1 on chromosome arm 19p. Germline mutations of STK11/LKB1 are responsible for Peutz-Jeghers syndrome and are associated with intraductal papillary mucinous neoplasms (IPMNs) and invasive pancreatic cancer. In addition to germline mutations, somatic mutations of STK11/LKB1 are observed in 5% of patients with sporadic IPMNs and pancreatic cancers. (36,37) Other tumor suppressor genes, including TGFBR2, (38) MAP2K4/MKK4, (39,40) FBXW7, (12) and ACVR1B4, are inactivated in a small subset of pancreatic cancers. The genetically altered genes involved in pancreatic cancer are summarized in Table 1.

3. Genetics of Precursor Lesions

There are 3 histologically recognized precursor lesions of pancreatic cancer: PanINs, IPMNs, and mucinous cystic neoplasms (MCNs). (42-45) Pancreatic intraepithelial neoplasia lesions are microscopic papillary or flat noninvasive epithelial neoplasms (<0.5 cm) arising in pancreatic ducts characterized by mucin-containing cuboidal to columnar cells.

Pancreatic intraepithelial neoplasia lesions can be further classified according to the degree of cytologic and architectural atypia as PanIN-1, PanIN-2, and PanIN3. (43,44) Two distinct genetic events occur in early low-grade PanIN lesions (PanIN-1): telomere shortening and KRAS2 gene mutations. (8,10,11,46,47) Activating point mutations of KRAS2 occur in approximately 45% of PanIN-1 lesions. (8,10,11,47) Telomere shortening is found in approximately 90% of PanIN-1 lesions and may contribute to global chromosomal abnormalities in PanINs. (46) Inactivating mutations of CDKN2A/p16 begin to occur in PanIN-2 lesions, while inactivation of TP53, SMAD4/DPC4, and BRCA2 are generally associated with higher-grade PanIN lesions (PanIN-3). (31,48)

Intraductal papillary mucinous neoplasms are mucin-producing epithelial neoplasms, usually with papillary architecture; they arise from the main pancreatic duct or branch ducts. (44) These neoplasms are larger lesions than PanINs ([greater than or equal to] 1 cm) and therefore can be detected by imaging. (44) Activating point mutations of KRAS2 occur in approximately 50% of IPMNs with low-grade dysplasia, and the prevalence of KRAS2 mutations increases with the degree of dysplasia. (49-51) Inactivating mutations of CDKN2A/p16 and TP53 are found in IPMNs with high-grade dysplasia. (52) Loss of SMAD4 expression is observed in only a small subset of IPMNs (3%), whereas SMAD4 loss in PanIN3 occurs in approximately 30% of cases. (53) As described above, somatic mutations of STK11/LKB1, with loss of the wild-type allele and corresponding inactivation of STK11 protein, occur in a small proportion of IPMNs. (36,37,53)

Mucinous cystic neoplasms occur predominantly in women. (42) In contrast to IPMNs, MCNs do not have a connection with the pancreatic duct. In addition, MCNs are unique among pancreatic precursor lesions because of an associated ovarian-type stroma. (42) Compared with PanINs and IPMNs, the genetic alterations of MCNs have not been well defined. Studies of MCNs (54-56) have reported a range in the prevalence of KRAS2 mutations and p53 overexpression, with the prevalence of abnormalities increasing with increasing degrees of dysplasia. One observation is that SMAD4 mutation and loss of nuclear expression do not occur in most noninvasive MCNs. As with cancers arising from PanIN-3 lesions, SMAD4 expression is lost when infiltrating cancers arise from MCNs. (29) This suggests that inactivation of SMAD4/ DPC4 occurs in the late stages of neoplastic progression from MCNs. (29)

4. Genetics of Histologic Variants of Pancreatic Cancer

Several histologic variants of pancreatic cancer have been described, which include adenosquamous carcinoma, colloid carcinoma, medullary carcinoma, signet ring cell carcinoma, undifferentiated carcinoma, and undifferentiated carcinoma with osteoclast-like giant cells. (42)

Recognition of these variants is clinically important. Indeed, colloid and medullary carcinomas typically have better prognoses than the typical infiltrating ductal adenocarcinomas, and adenosquamous and undifferentiated carcinomas have worse prognoses than the typical ductal adenocarcinomas. (57-59) Furthermore, medullary carcinomas have distinct mechanisms of pathogenesis. We will briefly describe the genetic characteristics of these histologic variants, but we recommend a more comprehensive review for more in-depth discussion. (60)

Adenosquamous carcinomas contain both glandular and squamous components. (42) The squamous component, by definition, comprises at least 30% of the neoplasm. Adenosquamous carcinomas share similar genetic features with ductal adenocarcinomas, including KRAS2 mutations and inactivation of CDKN2A/p16, SMAD4/ DPC4, and/or TP53. (58) The squamous component expresses p63, which is a helpful finding for identifying squamous components. Recognition of adenosquamous carcinoma is clinically important because it is associated with worse survival than adenocarcinomas. (58)

Medullary carcinomas are characterized by well-defined pushing border, syncytial growth pattern, and poorly differentiated cancer cells. (59,61,62) Similar to medullary carcinomas of the colorectum, medullary carcinomas of the pancreas are often microsatellite unstable; this is caused either by germline or somatic mutation of the mismatch repair genes MHL1 and MSH2 or by epigenetic silencing of MLH1 by promoter methylation. (22,59,61,62) Medullary carcinomas are associated with a better prognosis than ductal adenocarcinomas. Medullary colorectal cancers (with microsatellite instability) respond poorly to 5-fluorouracil-based chemotherapy, but it is not known if this 5-fluorouracil resistance applies to medullary carcinoma of the pancreas. (63)

Colloid carcinomas are characterized by well-differentiated neoplastic cells floating in pools of extracellular mucin; by definition, the mucin pools should comprise at least 80% of the tumor. (57) The neoplastic cells have intestinal differentiation and label with antibodies to MUC2 and/or CDX2. (64,65) Colloid carcinomas are associated with a better prognosis than ductal adenocarcinomas. (57)

Undifferentiated carcinomas lack histologic features of differentiation. (42,59-61) The median survival time for patients with undifferentiated pancreatic adenocarcinoma is only 5 months after surgical resection. (66) Undifferentiated carcinomas are noncohesive cancers characterized by the loss of E-cadherin protein expression. (67) The expression of L1CAM, COX2, and EGFR proteins in undifferentiated carcinomas have been noted as possible future targets of inhibitor-based treatments. (68)

Undifferentiated carcinomas with osteoclast-like giant cells are composed of cytologically benign, multinucleated, osteoclast-like giant cells admixed with atypical pleomorphic mononuclear cells. (42) Frequently, undifferentiated carcinomas with osteoclast-like giant cells occur in association with noninvasive precursor lesions and share mutations with the associated noninvasive precursor lesions. (69-73)

5. Genetics of Familial Pancreatic Cancer

Up to 10% of pancreatic cancers have a familial basis. (74) Several cohort and case-control studies (75,76) report that individuals with first-degree relatives who have pancreatic cancer are at significantly greater risk for pancreatic cancer, a risk that increases with the number of affected relatives. Thus, the risk for pancreatic cancer in individuals with 1 first-degree relative with pancreatic cancer is 2-fold higher than that for an individual without an affected first-degree relative; persons with 2 affected first-degree relatives have a 6-fold increased risk; and persons with 3 or more affected first-degree relatives have a 14- to 32-fold increased risk for pancreatic cancer. (75,76)

Several genetic syndromes are linked to the development of familial pancreatic cancer. Hereditary breast and ovarian cancer syndrome is an autosomal, dominantly inherited disease characterized by early development of breast and ovarian cancer and germline mutation of BRCA2 and BRCA1. (74) Germline mutation of BRCA2 increases risk for pancreatic cancer 3.5- to 10-fold. (77-79) BRCA2 is a member of the Fanconi anemia gene family, and the function of the BRCA2 gene product is to repair DNA interstrand cross-links and double-strand breaks. (80) Pancreatic cancer cells with BRCA2 mutation are hypersensitive to DNA interstrand cross-linking agents, including mitomycin C, cisplatin, and poly ADP-ribose polymerase (PARP) inhibitors. (81-83)

Peutz-Jeghers syndrome is an autosomal, dominantly inherited disease characterized by hamartomatous polyps of the gastrointestinal tract and pigmented macules of the lips and buccal mucosa. (84) Germline mutations of STK11/ LKB1 are responsible for Peutz-Jeghers syndrome, and patients with this syndrome have a very high lifetime risk for pancreatic cancer (up to 132-fold). (84,85) As we described above, pancreatic cancers in patients with Peutz-Jeghers syndrome develop as IPMNs.

Familial atypical multiple mole melanoma (FAMMM) is an autosomal, dominantly inherited disorder characterized by multiple nevi and atypical nevi and an increased risk for malignant melanoma. (86,87) Germline mutations of CDKN2A/p16 cause FAMMM, and patients with FAMMM and mutated CDKN2A/p16 have a 47-fold increased risk for pancreatic cancer. (88)

Hereditary pancreatitis is characterized by recurrent attacks of pancreatitis at a young age. Germline mutations of PRSS1 are associated with a markedly increased risk for hereditary pancreatitis and a 53-fold increased risk for pancreatic cancer. (89-92) Variants in SPINK1 are associated with a moderate increased risk for pancreatitis.

Hereditary nonpolyposis colorectal cancer syndrome (HNPCC) is an autosomal, dominantly inherited disease characterized by early onset of right-sided colon cancer as well as an increased risk for endometrial cancer and carcinomas of the small intestine, stomach, endometrium, ovary, bile duct, and kidney. (93) Germline mutations of mismatch repair genes, including MLH1, MSH2, PMS1, PMS2, and MSH6, are associated with HNPCC. When pancreatic cancers arise in patients with HNPCC, they usually have a characteristic medullary phenotype.

Familial adenomatous polyposis (FAP) syndrome is an autosomal, dominantly inherited disease characterized by the presence of more than hundreds of polyps in the colon at an early age. (94,95) Germline mutation of APC is linked with FAP. Patients with FAP have a 4-fold increased risk for pancreatic cancer. (96)

Genetic syndromes associated with familial pancreatic cancer are summarized in Table 2.


Epigenetics is defined as heritable changes in gene expression without accompanying changes in DNA sequence. (97) The main epigenetic mechanisms that may affect gene expression include DNA methylation, histone modification, and microRNA expression.

1. DNA Methylation

DNA methylation is the covalent binding of a methyl group ([CH3.sub.-]) to the 5-carbon of cytosine residues. This methyl-group binding is catalyzed and maintained by a family of enzymes, DNA methyltransferases (DNMTs), including DNMT1, DNMT3A, and DNMT3B. DNMT1 is involved in preserving parental methylation patterns and transferring these patterns to offspring. DNMT3A and DNMT3B are involved in de novo methylation. (98-100) Approximately 80% of pancreatic cancers overexpress dnmt1 protein. (101)

A major pattern of DNA methylation occurs in CpG islands. CpG islands are stretches of DNA with a high CG nucleotide content (>50%). (102) The CpG islands are frequently located near the transcriptional start sites of genes. About 60% of human genes have associated CpG islands; for many years CpG islands were thought to be unmethylated except during genomic imprinting and X-chromosome inactivation, (103) but more recent evidence indicates that some CpG islands are methylated in a tissue-specific manner, (104) and CpG island methylation increases with age at many loci. (105,106) Aberrant hypermethylation of promoter CpG islands is tightly associated with gene silencing and may be associated with loss of tumor suppressor function in cancer. (107)

Aberrant Hypermethylation in Pancreatic Cancer.--Several classic tumor suppressor genes, as well as increasing numbers of functionally important genes, show aberrant promoter CpG island hypermethylation in a subset of pancreatic cancers. The first tumor suppressor gene that was shown to undergo promoter hypermethylation and silencing in pancreatic cancer was CDKN2A/ p16.21 Other genetically inactivated tumor suppressor genes in pancreatic cancers, including TP53, SMAD4/ DPC4, and STK11/LKB1, have not been shown to undergo epigenetic silencing by DNA methylation.

MLH1 on chromosome arm 3p undergoes DNA methylation in pancreatic cancers and is associated with microsatellite instability in medullary carcinomas. (22,108,109) The CDH1 gene on chromosome arm 16q, which encodes E-cadherin protein, shows aberrant methylation in a small fraction of pancreatic cancers. (22)

SPARC, located on chromosome arm 5q, encodes a calcium-binding protein that interacts with extracellular matrix. (110) SPARC has effects on cellular migration, proliferation, angiogenesis during wound healing, cell-matrix adhesion, and tissue remodeling. (110) In pancreatic and other cancers, SPARC expression is usually lost through abnormal DNA methylation. (110) Pancreatic cancer-associated peritumoral fibroblasts often express SPARC, and patients with pancreatic cancer and SPARC-expressing peritumoral fibroblasts were reported to have a poorer survival in 1 study. (111)

Other cancer-related genes that have been shown to undergo abnormal methylation and induced gene silencing include RELN, (112) CCND2, (105) TFPI2, (113) RUNX3, (114) SOCS 1, (115) and TSLC1/IGSF4. (116)

Genome-wide screening has made it possible to identify epigenetic alterations in novel genes within the setting of pancreatic cancer. Ueki and colleagues (4) used methylated CpG island amplification with representational difference analysis to identify differentially methylated CpG islands in pancreatic cancer. PENK (preproenkephalin) on chromosome arm 8q was one of the genes identified by this method, and more than 90% of pancreatic cancers in this study had aberrantly methylated PENK. (4,117) Using oligonucleotide microarrays, Sato and colleagues (5) identified a total of 475 candidate genes that were induced by a DNMT inhibitor (5-aza-2'-deoxycytidine) in 4 pancreatic cancer cell lines, but not in HPDE (a nonneoplastic pancreatic ductal epithelial cell line). Of these 475 genes, UCHL1 on chromosome arm 4p was methylated in all 42 pancreatic cancers studied. (5) RPRM on chromosome arm 2q was methylated in 80% of pancreatic cancers studied and was associated with a worse prognosis. (118) More recently, Omura and colleagues (3) applied the methylated CpG island amplification technique to an Agilent 44K promoter microarray (Agilent Technologies, Santa Clara, California) and identified 606 differentially methylated genes in pancreatic cancer cell lines compared with normal pancreas.

A selected list of genes that are aberrantly hypermethylated in pancreatic cancer is summarized in Table 3.

Aberrant Methylation in Precursor Lesions.--The discovery of abnormal methylation in pancreatic cancer has been followed by the investigation of methylation in precursor lesions. Many genes that are epigenetically silenced in pancreatic cancers also are silenced or have reduced expression in precursor lesions of pancreatic cancer. For example, global gene expression profiles of IPMN were compared with those of normal pancreatic ductal epithelial samples. (119) CDKN1C/p57KIP2 on chromosome arm 11p codes for an inhibitor of cyclin/CDK complexes and negative regulator of cellular proliferation. (120,121) Partial methylation of the CDKN1C/p57KIP2 promoter CpG islands in IPMNs and pancreatic cancer cell lines was correlated with a corresponding decrease in CDKN1C protein expression. (119)

Other genes identified in precursor lesions include PENK, CDKN2A/p16, STK11/LKB1, SPARC, SFRP1/SARP2 (chromosome arm 8p), TSLC1, RELN (chromosome arm 7q), TFPI2, CLDN5 (chromosome arm 22q), and UCHL1 in IPMNs (37,122,123); PENK, CDKN2A/p16, CLDN5, NPTX2, RPRM, SFRP1/SARP2, and LHX1 (chromosome arm 11p) in PanINs (117,118,124); and CDKN2A/p16 in MCNs. (56) A selected list of genes that are aberrantly hypermethylated in pancreatic precursor lesions is summarized in Table 4.

The degree of methylation for these genes positively correlates with the degree of cytologic and architectural atypia. These findings suggest that aberrant CpG island methylation begins in the earliest stages of precursor lesions, such as PanINs, IPMNs, and MCNs, and their prevalence progressively increases during pancreatic carcinogenesis.

Aberrant Hypomethylation in Pancreatic Cancer.--In addition to hypermethylation as a mechanism of carcinogenesis, aberrant loss of methylation (hypomethylation of DNA) is also common in pancreatic adenocarcinomas. Hypomethylation can be detected at the genomic scale (global hypomethylation) and at the sequence-specific level (regional hypomethylation). Although global DNA hypomethylation associated with cancer was first described in the early 1980s, (125,126) its significance is not known, but it may contribute to genomic instability. Folate and vitamin [B.sub.12] deficiency can cause global DNA hypomethylation, which is associated with decreased levels of the methyl-group donor S-adenosylmethionine. Decreased DNA methylation results in decreased thymidilate synthesis from uracil. (127) Misplacement of uracil into thymidine leads to an imbalance of nucleotide pools and an increased frequency of DNA strand breaks; this can lead to genomic instability that can promote the development of cancer. (128,129) Pancreatic cancers with defective methylenetetrahydrofolate reductase genotypes have more DNA hypomethylation, which is associated with increased chromosomal loss and genomic instability. (130)

DNA hypomethylation occurs at the 5' regions of certain genes in pancreatic cancer and is associated with overexpression of the encoded protein. Thus, whereas hypermethylation results in overregulation and silencing of gene and protein expression, hypomethylation can result in loss of regulation and the promotion of gene and protein expression. S100A4 is linked with hypomethylation at specific CpG sites within the first intron and is associated with protein overexpression. (131,132) Other frequently hypomethylated genes, including CLDN4 (chromosome arm 7q, encoding claudin-4), LCN2 (chromosome arm 9q, encoding lipocalin-2), SFN/14-3-3[sigma] (chromosome arm 18q), TFF2 (chromosome arm 21q, encoding trefoil factor 2), MSLN (chromosome arm 16p, encoding mesothelin), and PSCA (chromosome arm 8q, encoding prostate stem cell antigen), are overexpressed in pancreatic cancer cells in comparison with normal pancreatic duct.132 With oligonucleotide microarray technologies, 2 additional genes, S100P (chromosome arm 4p) and SERPINB5 (chromosome arm 18q, encoding maspin), have been identified as being hypomethylated and are overexpressed.6 A selected list of genes that are aberrantly hypomethylated in pancreatic cancer is summarized in Table 3.

2. MicroRNAs

MicroRNAs (miRNAs) are a recently described family of small, nonprotein-coding RNA molecules (18 to 24 nucleotides) that regulate transcription of target messenger RNAs. (133) More than 400 miRNAs in the human genome have been described and many are implicated in the regulation of cellular differentiation, proliferation, and apoptosis. (23) Aberrant miRNA expression has been described in many types of cancers. (134,135) Several mechanisms are involved in aberrant miRNA expression, including genetic (amplification and deletion) (136-138) and epigenetic (chromatin modification, DNA methylation) alterations (139-141) and transcription factor regulation. (142,143)

Pancreatic ductal adenocarcinomas have been shown to aberrantly express numerous miRNAs, including miR200, miR-34, miR-21, miR-155, miR-221, and miR-222. (144-151) For example, Li and colleagues (152) have demonstrated hypomethylation and overexpression of miR-200a and miR-200b. Aberrant expression of some of these miRNAs is evident in PanINs. For example, miR-155 overexpression is evident in PanIN-2 lesions and aberrant miR-21 expression is evident in PanIN-3 lesions. (153) Similarly, Habbe et al (154) have reported abnormal miR-21 and miR155 expression in IPMN lesions.


Pancreatic ductal adenocarinoma continues to be a fatal cancer that is difficult to treat. In the past decade, major advances have been made in the understanding of the earliest histologic and molecular changes that occur in precursor lesions and cancers of the pancreas. Subclassification of pancreatic adenocarcinomas according to their histologic features and molecular alterations could have important therapeutic and prognostic importance. In addition, the identification of molecular signatures that identify the earliest changes of carcinogenesis may lead to the earlier detection of pancreatic cancer. The survival data for pancreatic cancer clearly illustrate that patients do much better with earlier detection and surgical resection regardless of adjuvant chemotherapy or radiotherapy intervention. Understanding the signature of molecular alterations that occur before the development of invasive pancreatic cancer may lead to improved detection and survival in pancreatic cancer.

This work was supported by National Institutes of Health (NIH) grants (P50-CA62924, R01-CA120432, RO1-CA97075) and the Michael Rolfe Foundation.


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Seung-Mo Hong, MD, PhD; Jason Y. Park, MD, PhD; Ralph H. Hruban, MD; Michael Goggins, MD

Accepted for publication January 25, 2011.

From the Departments of Pathology (Drs Hong, Hruban, and Goggins), Medicine (Dr Goggins), and Oncology (Drs Hruban and Goggins), The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland; and the Department of Pathology, University of Texas Southwestern Medical Center, Dallas (Dr Park).

The authors have no relevant financial interest in the products or companies described in this article.

Presented at the 9th Spring Seminar of the Korean Pathologists Association of North America; March 18-20, 2010;Washington, DC; in conjunction with the 99th Annual Meeting of the United States and Canadian Academy of Pathology.

Reprints: Michael Goggins, MD, Department of Pathology, Johns Hopkins Medical Institutions, 1550 Orleans St, CRB2, Room 342, Baltimore, MD 21231 (e-mail:
Table 1. List of Selected Genes That Are Genetically Altered in
Pancreatic Cancer

 Mechanism of
 Genetic Genetic
Gene Symbol Gene Name Alteration Alteration

CDKN2A/p16 Cyclin-dependent Inactivation Homozygous
 kinase inhibitor deletion
 2A (41%),

KRAS2 v-Ki-ras-2 Kirsten Activation Point mutation
 rat sarcoma
 viral oncogene

TP53 Tumor protein p53 Inactivation Intragenic
 mutation in 1
 allele and
 loss in the
 other allele

SMAD4/DPC4 Mothers against Inactivation Homozygous
 decapentaplegic, deletion
 drosophila, (50%),
 homolog of, 4 intragenic
 mutation in 1
 allele and loss
 in the other
 allele (50%)

AKT2 v-akt murine Activation Amplification
 thymoma viral
 homolog 2

MLH1 mutL homolog 1, Inactivation Heterozygous
 colon cancer, mutations
 type 2 (E coli)
BRCA2 Breast cancer 2, Inactivation Homozygous
 early onset deletion

STK11/LKB1 Serine/threonine Inactivation Homozygous
 kinase 11 deletion,
 mutation in 1
 allele and
 loss in the
 other allele
BRAF v-raf murine Activation Point mutation
 sarcoma viral
 homolog B1
TGFBR2 Transforming Inactivation Homozygous
 growth factor, deletion,
 [beta] receptor II homozygous
 (70/80 kDa) frameshift
MAP2K4 Mitogen-activated Inactivation Homozygous
 protein kinase deletions,
 kinase 4 missense

 Known or in Primary
 Chromosome Predicted Pancreatic
Gene Symbol Site Function Cancer, % Source, y

CDKN2A/p16 9p21 Cyclin- 95 Caldas et
 dependent al, (17)
 kinase 1994

KRAS2 12p12.1 Signal Hruban et
 transduction, al, (8)
 proliferation, 1993
 cell survival,
 and motility
TP53 17p13.1 Cell cycle 50-70 Redston et
 arrest, al, (19) 1994
 apoptosis, Moore et
 senescence, al, (24) 2001
 DNA repair, Scarpa et
 metabolism al, (25) 1993

SMAD4/DPC4 18q21.1 Signal 55 Iacobuzio-
 Donahue transmission
 et al, (27)
 Hahn et al,
 (28) 1996

AKT2 19q13. AKT pathway, 10-20 Ruggeri et
 1-q13.2 hormone al, (13) 1998
 metabolism Cheng et
 al, (14) 1996

MLH1 3p21.3 DNA mismatch 3-15 Goggins et
 repair al, (59) 1998
 Wilentz et
 al, (61) 2000
BRCA2 13q12.3 DNA repair, 7 Goggins et
 proliferation, al,155 1996
STK11/LKB1 19p13.3 Apoptosis 5 Su et
 regulation al, (36)

BRAF 7q34 Signal 5 Calhoun et
 transduction, al, (12) 2003
 cell growth

TGFBR2 3p22 Signal 4 Goggins et
 transduction al, (38)

MAP2K4 17p11.2 MAPK pathway 2 Su et al,
 (39) 1998
 Teng et
 al, (40)

Abbreviation: MAPK, mitogen-activated protein kinase.

Table 2. Genetic Syndromes Associated With Familial Pancreatic Cancer

 Relative Risk
 of Developing
 Gene Pancreatic Histologic Feature of
Genetic Syndrome Symbol Cancer (Fold) Pancreatic Neoplasm

No familial history None 1 Ductal adenocarcinoma
Familial APC 4 Intraductal papillary
adenomatous mucinous neoplasm,
polyposis ductal adenocarcinoma,
Familial atypical CDKN2A/ 13-22 Ductal adenocarcinoma
multiple mole p16

Familial pancreatic Unknown 2-32 Ductal adenocarcinoma

Hereditary breast BRCA2, 3.5-10 Ductal adenocarcinoma
and ovarian BRCA1,
cancer FANCC,

Hereditary PRSS1, 53 Ductal adenocarcinoma
pancreatitis SPINK1

Hereditary MLH1, Increased Medullary carcinoma
nonpolyposis MSH2
colorectal cancer

Peutz-Jeghers SKT11/ 132 Intraductal papillary
syndrome LKB1 mucinous neoplasm,
 ductal adenocarcinoma

Genetic Syndrome Extrapancreatic Cancer

No familial history Unknown
Familial Colorectum, small
adenomatous intestine, stomach

Familial atypical Melanoma
multiple mole

Familial pancreatic

Hereditary breast Breast, ovary, prostate
and ovarian

Hereditary None

Hereditary Colorectum, small
nonpolyposis intestine,
colorectal cancer endometrium

Peutz-Jeghers Small intestine,
syndrome colorectum,
 esophagus, stomach,
 bile duct, lung, breast,
 ovary, uterus

Genetic Syndrome Source, y

No familial history
Familial Giardiello et
adenomatous al, (96) 1993

Familial atypical Gruis et al, (86)
multiple mole 1995 de Snoo et
melanoma al, (88) 2008

Familial pancreatic Amundadottir et
cancer al, (75) 2004 Klein
 et al, (76) 2004

Hereditary breast Hruban et al, (77)
and ovarian 1999 Hahn et al, (78)
cancer 2003 van Asperen
 et al, (79) 2005

Hereditary de las Heras-Castano
pancreatitis et al, (89) 2009
 Lowenfels et al, (90)
 1997 Schneider et
 al, (91) 2002 Whitcomb
 et al, (92) 1996

Hereditary Wilentz et
nonpolyposis al, (61) 2000
colorectal cancer

Peutz-Jeghers Zbuk and Eng, (84)
syndrome 2007 Giardiello et
 al, (85) 2000

Table 3. List of Selected Genes That Are Aberrantly Methylated
in Pancreatic Cancer

 Epigenetic Chromosome
Gene Gene Name Alteration Site

PENK Preproenkephalin Hypermethylation 8q23-q24

UCHL1 Ubiquitin Hypermethylation 4p14

 esterase L1

MDF-1 MAD (yeast Hypermethylation 11q13
 Mitosis Arrest

NPTX2 Neuronal Hypermethylation 7q21.3-q22.1
 pentraxin II

SPARC/ON Secreted Hypermethylation 5q31.3-q32

RPRM Reprimo, TP53- Hypermethylation 2q23.3
 dependent G2

BNIP3 BCL2/adenovirus Hypermethylation 10q26.3
 E1B 19 kDa
 protein 3

miR9-1 MicroRNA 9-1 Hypermethylation 1q22

SERPINB5 Serpin peptidase Hypomethylation 18q21.3
 inhibitor, clade
 B, member 5

CCND2 Cyclin D2 Hypermethylation 12p13

ZNF415 Zinc finger Hypermethylation 19q13.42
 protein 415

CLDN4 Claudin-4 Hypomethylation 7q11.23

SFN Stratifin Hypomethylation 1p35

LCN2 Lipocalin-2 Hypomethylation 9q34

TFPI2 Tissue factor Hypermethylation 7q22
 inhibitor 2

CNTNAP2 Contactin- Hypermethylation 7q35-q36
 protein-like 2

CDKN1C/p57 Cyclin-dependent Hypermethylation 11p15.5
 kinase inhibitor

SIP1 Survival of Hypermethylation 14q13-q21
 motor neuron

 protein 1

ELOVL4 Elongation of Hypermethylation 6q14
 fatty acids
 yeast)-like 4

TFF2 Trefoil factor 2 Hypomethylation 21q22.3

FOXE1 Forkhead box E1 Hypermethylation 9q22
 factor 2)

S100P S100 calcium- Hypomethylation 4p16
 binding protein

RARB Retinoic acid Hypermethylation 3p24
 receptor, b

S100A4 S100 calcium- Hypomethylation 1q21
 binding protein

CDKN2A/p16 Cyclin-dependent Hypermethylation 9p21
 kinase inhibitor

MSLN Mesothelin Hypomethylation 16p13.3

SOCS1 Suppressor of Hypermethylation 16p13.13
 signaling 1

PSCA Prostate stem Hypomethylation 8q24.2
 cell antigen

CADM1/TSLC1 Cell adhesion Hypermethylation 11q23.2
 molecule 1

 in Primary
 Methylation or
 in Pancreatic Xenografted
 Cancer Cell Pancreatic
 Known or Lines, Cancer,
 Predicted No./Total No./Total
Gene Function (%) (%)

PENK Neuropeptide 11/11 (100) 43/47 (91)

UCHL1 Ubiquitin 22/22 (100) 42/42 (100)

MDF-1 Glycogen 45/47 (96) Not
 metabolism determined

NPTX2 Neuronal 21/22 (95) 20/20 (100)

SPARC/ON Cell-cycle 16/17 (94) 21/24 (88)

RPRM P53-induced 20/22 (91) 16/20 (80)
 G2/M cellcycle

BNIP3 Hypoxia- 9/10 (90) 8/10 (80)
 induced cell

miR9-1 miRNA 42/47 (89) Not
 translation determined

SERPINB5 Regulation 20/23 (87) 32/34 (94)
 of cell
 and cell

CCND2 Cell-cycle 19/22 (86) 71/109 (65)

ZNF415 40/47 (86) Not

CLDN4 Cell 17/20 (85) 33/37 (89)

SFN P53-induced 17/20 (85) 36/37 (97)
 G2/M cellcycle

LCN2 Epithelial 17/20 (85) 34/37 (92)

TFPI2 Serine 14/17 (82) 102/140 (73)

CNTNAP2 Higher 39/47 (82) Not
 cortical determined

CDKN1C/p57 Cyclin- 7/9 (78) Not
 dependent determined

SIP1 Assembly of 11/15 (73) 34/35 (97)

ELOVL4 Fatty acid 32/47 (68) Not
 synthesis determined

TFF2 Secretory 13/20 (65) 31/37 (84)

FOXE1 Thyroid 14/22 (64) 15/20 (75)

S100P Cell-cycle 13/23 (57) 30/34 (88)

RARB Cell-growth 5/9 (56) 4/36 (11)

S100A4 Motility, 10/20 (50) 28/37 (76)

CDKN2A/p16 Cyclin- 3/9 (33) 5/36 (14)

MSLN Cell surface 8/20 (40) 34/37 (29)

SOCS1 Inhibitor 6/19 (32) 13/60 (22)
 of JAK/
 STAT pathway

PSCA Cell surface 6/20 (30) 20/37 (54)

CADM1/TSLC1 Cell-cell, 4/17 (24) 25/91 (27)

Gene Source, y

PENK Ueki et al,
 (4) 2001
 Fukushima et
 al,1 (17) 2002

UCHL1 Sato et al, (5)

MDF-1 Omura et
 al, (3) 2008

NPTX2 Sato et
 al, (5) 2003

SPARC/ON Sato et
 al, (110)

RPRM Sato et
 al, (118)

BNIP3 Okami et
 al, (156)

miR9-1 Omura et
 al, (3) 2008

SERPINB5 Sato et
 al, (132)
 Fitzgerald et
 al, (157)
 2003 Ohike
 et al,1 (58)

CCND2 Matsubayashi
 et al, (105)

ZNF415 Omura et
 al, (3) 2008

CLDN4 Sato et
 al, (132)

SFN Sato et
 al, (132) 2003
 al, (159) 2003

LCN2 Sato et
 al, (132)

TFPI2 Sato et
 al, (113)

CNTNAP2 Omura et
 al, (3) 2008

CDKN1C/p57 Sato et
 al, (119)

SIP1 Li et
 al, (152) 2010

ELOVL4 Omura et
 al, (3) 2008

TFF2 Sato et
 al, (132)

FOXE1 Sato et
 al, (5) 2003

S100P Sato et
 al, (132)

RARB Ueki et
 al, (22) 2000

S100A4 Rosty et
 al, (131) 2002
 Sato et
 al, (132) 2003

CDKN2A/p16 Schutte et
 al, (21) 1997
 Ueki et
 al, (22) 2000

MSLN Sato et
 al, (132) 2003

SOCS1 Fukushima et
 al, (115) 2003

PSCA Sato et
 al, (132) 2003

CADM1/TSLC1 Jansen et
 al, (116) 2002

Abbreviations: JAK/STAT, Janus kinase/signal transducer and
activator of transcription; miRNA, microRNA; snRNP, small
nuclear ribonucleoprotein.

Table 4. List of Selected Genes That Are Aberrantly Hypermethylated
in Pancreatic Precursor Lesions

 Methylation in
 (PanIN-1 or
 Dysplasia of
 Precursor IPMN or MCN),
Gene Symbol Gene Name Lesions No./Total (%)

PENK Preproenkephalin IPMN 1/6 (17)

 PanIN 5/67 (7)

 PanIN 1/38 (3)

CDKN2A/p16 Cyclin-dependent IPMN 0/6 (0)
 kinase inhibitor
 PanIN 4/63 (6)

 PanIN 3/38 (8)

 MCN 1/10 (10)

SPARC/ON Secreted protein, IPMN 7/12 (58)
 acidic, cysteinerich
 PanIN 10/36 (21)

SFRP1/SARP2 Secreted frizzled- IPMN 6/12 (50)
 related protein 1
 PanIN 2/37 (5)

NPTX2 Neuronal pentraxin PanIN 2/35 (8)

CADM1/ Cell adhesion IPMN 6/12 (50)

TSLC1 molecule 1

RELN Reelin IPMN 3/12 (25)

TFPI2 Tissue factor IPMN 3/12 (25)
 pathway inhibitor 2

CLDN5 Claudin-5 IPMN 4/12 (33)

 PanIN 3/35 (9)

UCHL1 Ubiquitin carboxyl- IPMN 7/12 (58)
 terminal esterase
 L1 (ubiquitin

RPRM Reprimo, TP53- PanIN 8/36 (22)
 dependent G2 arrest
 mediator candidate

LHX1 LIM homeobox 1 PanIN 3/37 (8)

 Methylation in in HighModerateGrade

 Grade Dysplasia
 Dysplasia (PanIN-3 or
 (PanIN-2 or High-Grade
 Moderate- Dysplasia of Methylation
 Grade IPMN or in Precursor
 Dysplasia of MCN), in Total,
 IPMN or MCN), No./Total No./Total
Gene Symbol No./Total (%) (%) (%)

PENK 4/12 (33) 27/32 (84) 32/50 (64)

 5/22 (23) 6/13 (46) 16/108 (15)

 1/14 (7) 7/12 (58) 9/64 (14)

CDKN2A/p16 0/12 (0) 7/32 (22) 7/50 (14)

 1/22 (5) 3/14 (21) 8/99 (8)

 1/15 (7) 3/11 (27) 7/64 (11)

 1/4 (25) NA 2/14 (14)

SPARC/ON 7/12 (58) 16/22 (73) 30/48 (63)

 3/14 (21) 3/10 (30) 16/60 (27)

SFRP1/SARP2 8/12 (67) 21/23 (91) 35/57 (61)

 3/15 (20) 10/12 (83) 15/64 (23)

NPTX2 6/13 (46) 4/12 (33) 12/60 (20)

CADM1/ 8/12 (67) 21/23 (91) 35/57 (61)


RELN 4/12 (33) 11/23 (48) 18/57 (32)

TFPI2 5/12 (42) 20/23 (87) 28/57 (49)

CLDN5 5/12 (42) 15/23 (65) 24/57 (42)

 1/15 (7) 4/11 (36) 8/61 (13)

UCHL1 10/12 (83) 21/23 (19) 38/57 (67)

RPRM 3/15 (20) 8/12 (67) 19/63 (30)

LHX1 1/15 (7) 5/12 (42) 9/64 (14)

Gene Symbol Source, y

PENK Sato et
 al, (122) 2002
 Fukushima et
 al, (117) 2002
 Sato et
 al, (124) 2008

CDKN2A/p16 Sato et
 al, (122) 2002

 Fukushima et
 al, (117) 2002
 Sato et
 al, (124) 2008
 Kim et
 al, (56) 2003

SPARC/ON Hong et
 al, (123) 2008

 Sato et
 al, (124) 2008

SFRP1/SARP2 Hong et
 al, (123) 2008
 Sato et
 al, (124) 2008

NPTX2 Sato et
 al, (124) 2008

CADM1/ Hong et
 al, (123)
TSLC1 2008

RELN Hong et
 al, (123) 2008

TFPI2 Hong et
 al, (123) 2008

CLDN5 Hong et
 al, (123) 2008
 Sato et
 al, (124) 2008

UCHL1 Hong et
 al, (123) 2008

RPRM Sato et
 al, (118)

LHX1 Sato et
 al, (124) 2008

Abbreviations: IPMN, intraductal papillary mucinous neoplasm; MCN,
mucinous cystic neoplasm; NA, not applicable; PanIN, pancreatic
intraepithelial neoplasia.
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Author:Hong, Seung-Mo; Park, Jason Y.; Hruban, Ralph H.; Goggins, Michael
Publication:Archives of Pathology & Laboratory Medicine
Date:Jun 1, 2011
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