US20190055610A1

US20190055610A1 - Genes frequently altered in pancreatic neuroendocrine tumors

Info

Publication number: US20190055610A1
Application number: US16/179,136
Authority: US
Inventors: Bert Vogelstein; Kenneth W. Kinzler; Victor Velculescu; Luis Diaz; Nickolas Papadopoulos; Yuchen Jiao; Ralph Hruban
Original assignee: Johns Hopkins University
Current assignee: Johns Hopkins University
Priority date: 2011-01-04
Filing date: 2018-11-02
Publication date: 2019-02-21
Also published as: WO2012094401A2; US10144971B2; US20140045881A1; WO2012094401A3

Abstract

Pancreatic Neuroendocrine Tumors (PanNETs) are a rare but clinically important form of pancreatic neoplasia. To explore the genetic basis of PanNETs, we determined the exomic sequences of ten non-familial PanNETs and then screened the most commonly mutated genes in 58 additional PanNETs. Remarkably, the most frequently mutated genes specify proteins implicated in chromatin remodeling: 44% of the tumors had somatic inactivating mutations in MEN-1, which encodes menin, a component of a histone methyltransferase complex; and 43% had mutations in genes encoding either of the two subunits of a transcription/chromatin remodeling complex consisting of DAXX (death-domain associated protein) and ATRX (alpha thalassemia/mental retardation syndrome X-linked). Clinically, mutations in the MEN1 and DAXX/ATRX genes were associated with better prognosis. We also found mutations in genes in the mTOR (mammalian target of rapamycin) pathway in 14% of the tumors, a finding that could potentially be used to stratify patients for treatment with mTOR inhibitors.

Description

This application is a divisional of U.S. application Ser. No. 13/977,810, filed Oct. 24, 2013, which is a national stage application, filed under 35 U.S.C. § 371 of International Application No. PCT/US2012/020199, filed Jan. 4, 2012, which claims priority to U.S. Provisional Application No. 61/429,666, filed Jan. 4, 2011, the contents of each of which are hereby incorporated by reference in their entireties.
This invention was made with government support under CA 57345, CA 62924, and CA 121113 awarded by National Institutes of Health. The government has certain rights in the invention.

TECHNICAL FIELD OF THE INVENTION

This invention is related to the area of identifying, treating, and predicting outcome for pancreatic tumors. In particular, it relates to pancreatic neuroendocrine tumors.

BACKGROUND OF THE INVENTION

Pancreatic Neuroendocrine Tumors (PanNETs) are the second most common malignancy of the pancreas. The ten-year survival rate is only 40% (1-3). They are usually sporadic, but they can arise in multiple endocrine neoplasia type 1 and more rarely in other syndromes, including von Hippel-Lindau (VHL) syndrome and tuberous sclerosis (4). “Functional” PanNETs secrete hormones that cause systemic effects, while “Nonfunctional” PanNETs do not and therefore cannot always be readily distinguished from other neoplasms of the pancreas. Non-functional PanNETs grow silently and patients may present with either an asymptomatic abdominal mass or symptoms of abdominal pain secondary to compression by a large tumor. Surgical resection is the treatment of choice, but many patients present with unresectable tumors or extensive metastatic disease, and medical therapies are relatively ineffective.
There is currently insufficient information about this tumor to either predict prognosis of patients diagnosed with PanNETs or to develop companion diagnostics and personalized treatments to improve disease management. Biallelic inactivation of the MEN1 gene, usually by a mutation in one allele coupled with loss of the remaining wild-type allele, occurs in 25-30% of PanNETs (5, 6). Chromosomal gains and losses, and expression analyses, have identified candidate loci for genes involved in the development of PanNETs, but these have not been substantiated by genetic or functional analyses (7-9).
There is a continuing need in the art to identify appropriate therapies and to predict outcome of patients with pancreatic tumors.

SUMMARY OF THE INVENTION

According to one aspect of the invention a method is provided for determining an appropriate therapy for an individual with a pancreatic neuroendocrine tumor. Tumor tissue or tumor cells or nucleic acid shed from the tumor are tested for a mutation in a gene selected from the group consisting of Rheb, AMPK, mTOR (FRAP1), TSC1, TSC2, IRS1, PI3KCA, AKT, PTEN, ERK1/2, p38MAPK, MK2, LKB1, GSK3β, RPS6KB1 (S6K1), and 4E-BP1. Identification of the presence of the mutation is a factor considered for treating the individual with an mTOR inhibitor.
Another aspect of the invention is a method for predicting outcome for a patient with a pancreatic neuroendocrine tumor. The pancreatic neuroendocrine tumor, or cells or nucleic acids shed from the tumor, are tested for the presence of an inactivating mutation in MEN1, DAXX, or ATRX. A mutation in at least one of these genes is a positive prognostic indicator.
An additional aspect of the invention is an isolated nucleic acid which comprises at least 20 nucleotides of a gene selected from MEN1, DAXX, ATRX, PTEN, TSC2, PIK3CA, and TP53. The nucleic acid comprises a mutation shown in Table 1.
Yet another aspect of the invention is a method of identifying a pancreatic neuroendocrine tumor. The pancreatic neuroendocrine tumor, or cells or nucleic acids shed from the tumor, is tested for any of the mutations shown in Table S2 or Table 1. Identification of any one of the mutations may be used to identify the tumor. Such markers can be used as a personal marker of the tumor, for example, for monitoring disease.
Yet another aspect of the invention is a method for distinguishing between a pancreatic neuroendocrine and a pancreatic ductal adenocarcinoma. The pancreatic neuroendocrine tumor, or cells or nucleic acids shed from the tumor, are tested for one or more mutations in one or more characteristic genes of each of a first group of genes and a second group of genes. The first group consists of MEN1, DAXX, and ATRX, and the second group consists of KRAS, CDKN2A, TGFBR1, SMAD3, and SMAD4. A mutation in the first group indicates a pancreatic neuroendocrine tumor. A mutation in the second group indicates a pancreatic ductal adenocarcinoma. Mutations can be detected using nucleic acid based or protein based assays.
These and other embodiments which will be apparent to those of skill in the art upon reading the specification provide the art with diagnostic and prognostic tools for better care of pancreatic tumor patients.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A-1D. FIGS. 1A-1B provide examples of traces showing mutations in DNA isolated from cancer cells (bottom panels of each), but not from normal cells of the same patient (top panels of each). FIG. 1C: Immunohistochemical staining with antibodies against DAXX shows lack of nuclear staining in cancer cells with the indicated mutation. Staining in the non-neoplastic cells (stroma) served as an internal control. FIG. 1D: Similar staining of another tumor with an antibody against ATRX protein. In both FIGS. 1C and 1D, although shown in black and white, nuclei that do not react with antibodies were blue because of the counterstain, while those that do react were brown.

FIG. 2A-2B: Kaplan-Meier plots of overall survival in patients with metastatic PanNETs. (FIG. 2A) Patients with a DAXX or ATRX gene mutation vs. patients in whom both genes were wild-type (WT) (Hazard Ratio 0.22, 95% CI 0.06 to 0.84, p=0.03). (FIG. 2B) Patients with mutations in MEN1 as well as either DAXXor ATRX vs. those in which all three genes were WT (Hazard Ratio 0.07, 95% CI 0.008 to 0.51, p=0.01).

FIGS. 3A-3C. (Table (1)) show mutations in MEN1, DAXX, ATRX, PTEN, TSC2, PIK3CA, and TP53 in human pancreatic neuroendocrine tumors.

FIGS. 4A-4C. (Table (S1)) show a summary of sequence analysis of PanNETs

FIGS. 5A-5H. (Table (S2)) show mutations identified in the discovery set

FIG. 6. Table (S3) showing a comparison of commonly mutated genes in Pan NETs and PDAC.

FIG. 7. Table (S4) showing a comparison of somatic point mutations spectra in PanNETs and PaCa.

FIG. 8. Table (S5) showing immunohistochemistry (IHC) of ATRX and DAXX.

FIG. 9. Table (S6) showing patient characteristics.

FIG. 10. Table (S7) showing survival estimates.

FIGS. 11A-11F. (Table (S8)) show primers used for PCR amplification and sequencing (SEQ ID NO: 1-291, in the order presented).

DETAILED DESCRIPTION OF THE INVENTION

The inventors have used whole exome sequencing of pancreatic neuroendocrine tumors to identify tumor suppressor genes and to illuminate the genetic differences between the two major cancers of the pancreas. The mutations may be used to aid prognosis and provide a way to prioritize patients for therapy with mTOR inhibitors.
Samples from patients can be tested to determine an appropriate therapy, to predict outcome or course of disease, and to identify a pancreatic tumor or tumor type. Suitable samples for genetic testing include tumor cells, tumor tissues, biopsy samples, circulating tumor cells, circulating plasma DNA from cancer cells, archived samples, nucleic acids shed into a body fluid, such as gastroduodenal fluid or lymph. Collection and preparation of such samples for genetic testing is known in the art and any such techniques may be used.
Mutations can be identified in any available genetic material, including, for example, genomic DNA, cDNA, and RNA. Techniques for testing for mutations are legion and any such techniques may be used. Mutations can be identified by sequencing, by hybridization to probes, by amplification using specific primers, by primer extension, by ligation assay, etc. Combinations of such techniques can be used as well. Any technique can be selected and applied using the ordinary skill level in the art. Identified mutation can be used as a personal marker of the tumor, for example, for monitoring disease. Other uses are discussed below.
Mutations in the mTOR signaling pathway occur in pancreatic neuroendocrine tumors. The mutations may be in any gene of the pathway, including but not limited to Rheb, AMPK, mTOR (FRAP1), TSC1, TSC2, IRS1, PI3KCA, AKT, PTEN, ERK1/2, p38MAPK, MK2, LKB1, GSK3β, RPS6KB1 (S6K1), and 4E-BP1. Identification of mutations in this pathway can be used to identify patients that are likely to benefit most from use of mTOR inhibitors such as evorolimus, rapamycin, deforolimus, and temsirolimus.
Mutations in other genes, particularly MEN1, DAXX, and ATRX, have been found to be positive prognostic indicators. These appear to be tumor suppressor genes because of their mutational spectra. They also appear to be strong prognostic indicators of longer survival, either alone or in combination.
Nucleic acids can be used as probes or primers for mutations identified. Typically these probes or primers are oligonucleotides of at least 18, 20, 25, or 30 bases in length. Typically they are less than 100, 50, or 40 bases in length. If they contain one of the mutated bases they can be used as specific primers or probes for the mutation. Specific mutations are identified in Table 1. The oligonucleotides can optionally be labeled with a detectable moiety, such as a radioactive or fluorescent moiety. Alternatively, primers can be used which do not contain a mutation but may bracket a mutation, so that an amplicon is formed that contains the mutation. Adjacent primers to a mutation may also be used in assays employing a single base extension reaction. Amplicons may be of any size, but typically will be less than 500 base pairs, less than 250 bp, or less than 100 bp. Typically an amplicon will be greater than 35 bp, greater than 50 bp, or greater than 75 bp. Identification of any of the specific mutations listed in FIG. 3 or 4 (Tables 1 or S1) can be used to identify a pancreatic neuroendocrine tumor. The nucleic acid probes or primers may be used to identify them or other methods such as sequencing may be used.
Interestingly, different mutation spectra have been found for pancreatic neuroendocrine tumors and pancreatic ductal adenocarcinomas. Mutations in certain genes are highly characteristic of each type of pancreatic cancer. In the case of pancreatic neuroendocrine tumors, mutations in MEN1, DAXX, and ATRX occur frequently, but almost never in pancreatic ductal adenocarcinomas. Conversely, mutations in KRAS, CDKN2A, TGFBR1, SMAD3, and SMAD4 occur frequently in pancreatic ductal adenocarcinomas, but almost never in pancreatic neuroendocrine tumors. MTOR mutations occur much more frequently, but not exclusively, in pancreatic neuroendocrine tumors than in pancreatic ductal adenocarcinomas. Mutations in TP53 occur far more frequently, but not exclusively, in pancreatic ductal adenocarcinomas than in pancreatic neuroendocrine tumors. Thus these distinct mutation patterns can be used to distinguish these two tumors of the pancreas. These mutation patterns can be determined using nucleic acid based tests, using protein and/or antibody based tests, or using a combination of such tests. For example, immunohistochemical assays can be used to detect inactivating mutations in MEN1, DAXX, and ATRX. Absence of labeling indicates an inactivating mutation.
The above disclosure generally describes the present invention. All references disclosed herein are expressly incorporated by reference. A more complete understanding can be obtained by reference to the following specific examples which are provided herein for purposes of illustration only, and are not intended to limit the scope of the invention.

Example 1—Sample Selection, Preparation, and Decoding

To gain insights into the genetic basis of this tumor type, we determined the exomic sequence of 18,000 protein-coding genes in a Discovery set of ten well-characterized sporadic PanNETs. A clinically homogeneous set of tumors of high neoplastic cellularity is essential for the successful identification of genes and pathways involved in any tumor type. Thus, we excluded small cell and large neuroendocrine carcinomas and studied only samples that were not part of a familial syndrome. We macrodisected them to achieve a neoplastic cellularity of >80%. DNA from the enriched neoplastic samples and from matched non-neoplastic tissue from ten patients was used to prepare fragment libraries suitable for massively parallel sequencing. The coding sequences were enriched by capture with the SureSelect Enrichment System and sequenced using an Illumina GAIIx platform (10). The average coverage of each base in the targeted regions was 101-fold and 94.8% of the bases were represented by at least 10 reads (table S1).

Example 2—Mutation Analysis in Discovery Set

We identified 157 somatic mutations in 158 genes among the ten tumors used in the Discovery set. The mutations per tumor ranged from 8 to 23, with a mean of 16 (table S2). There were some obvious differences between the genetic landscapes of PanNETs and those of pancreatic ductal adenocarcinomas (PDAC, ref 11). First, there were 60% fewer genes mutated per tumor in PanNETs than in PDACs. Second, the genes most commonly affected by mutation in PDACs (KRAS, TGF-β pathway, CDKN2A, TP53) were rarely altered in PanNETs and vice versa (table S3). Third, the spectrum of mutations in PDAC and PanNET were different, with C to T transitions more common in PDACs than in PanNETs, and C to G transversions more common in PanNETs than in PDACs (table S4). This suggests that PanNETs are exposed to different environmental carcinogens or that they harbor different repair pathways than PDACs.

Example 3—Mutation Analysis in Validation Set

Four genes were mutated in at least two tumors in the Discovery set: MEN1 in five, DAXX in three, PTEN in two, and TSC2 in two. Somatic mutations in each of these genes were confirmed by Sanger sequencing. The sequences of these genes were then determined by Sanger sequencing in a Validation set consisting of 58 additional PanNETs and their corresponding normal tissues (FIG. 1a,b ). Although ATRX was mutated in only one sample in the Discovery set, it was included in the list of genes for further evaluation in the Validation set because its product forms a heterodimer with DAXX and therefore is part of the same pathway. Similarly, PIK3CA was included because it is considered to be part of the mTOR pathway that includes PTEN and TSC2 (12-14). In total, somatic mutations in MEN1, DAXX, ATRX, PTEN, TSC2, and PIK3CA were identified in 44.1%, 25%, 17.6%, 7.3%, 8.8%, and 1.4% PanNETs, respectively (Table 1).

Example 4—MEN1 Mutations

Of the 30 mutations in MEN1, 25 were inactivating mutations (18 insertions or deletions (indels), 5 nonsense and 2 splice-site mutations), while five were missense. At least 11 were homozygous; in the others, the presence of “contaminating” DNA from normal cells made it difficult to reliably distinguish heterozygous from homozygous changes. MEN1 encodes menin which is a nuclear protein that acts as a scaffold to regulate gene transcription by coordinating chromatin remodeling. It is an essential component of the MLL SET1-like histone methyltransfarase (HMT) complex (15-19).

Example 5—DAXX and ATRX Mutations

DAXX was mutated in 17 and ATRX in 12 different PanNETs out of the 68 tested; thus, 42.6% of PanNETs had mutations in this pathway. There were 11 insertions or deletions (indels) and 4 nonsense mutations in DAXX, and six indels and 3 nonsense mutations in ATRX. The three ATRX missense mutations were within the conserved helicase domain and the DAXX missence mutations were non-conserved changes. Five DAXX and four ATRX mutations were homozygous, indicating loss of the other allele. The high ratio of inactivating to missense mutations in both genes unequivocally establishes them as PanNET tumor suppressor genes.
Loss of immunolabelling for DAXX and ATRX correlated with mutation of the respective gene (FIG. 1c, d and table S5). From these data, we assume that both copies of DAXX are generally inactivated, one by mutation and the other either by loss of the non-mutated allele or by epigenetic silencing. We also assume that both copies of ATRX are inactivated, one by mutation and the other by chromosome X inactivation. Recently, it has been shown that DAXX is an H3.3-specific histone chaperone (20). ATRX codes for a protein that at the amino-terminus has an ADD (ATRX-DNMTT3-DNMT3L) domain and a carboxy-terminal helicase domain. Almost all missense disease-causing mutations are within these two domains (21). DAXX and ATRX interact and both are required for H3.3 incorporation at the telomeres and ATRX is also required for suppression of telomeric repeat-containing RNA expression (22-24). ATRX was recently shown to target CpG islands and G-rich tandem repeats (25), which exist close to telomeric regions.

Example 6—PTEN, TSC2, PIK3CA Mutations and Therapeutic Selection

We identified five PTEN mutations, two indels and three missense; six TSC2 mutations, one indel, one nonsense and three missense; and one PIK3CA missense mutation. Previously published expression analyses have suggested that the PIK3CA/AKT/mTOR axis is altered in most PanNETs (26). Our data suggests that, at least at the genetic level, only a subset of PanNETs have alterations of this pathway. This finding may have direct clinical application through prioritization of patients for therapy with mTOR pathway inhibitors. Everolimus (Afinitor, RAD-001, 40-O-(hydroxyethyl)-rapamycin) has been shown to increase progression-free survival in a subset of PanNET patients with advanced disease (27). If the mutational status of genes coding for proteins in the mTOR pathway predicts clinical response to mTOR inhibitors, it should be possible to select patients who would benefit most from an mTOR inhibitor through analysis of these genes in patients' tumors (29, 30).

Example 7—Prognosis

All 68 tumors evaluated in this study were from patients undergoing aggressive intervention (table S6) and included patients undergoing curative resection as well as those with metastatic disease. Interestingly, mutations in MEN1, DAXX/ATRX or the combination of both MEN1 and DAXX/ATRX showed prolonged survival relative to those patients without these mutations (FIG. 2A and table S7). This was particularly evident in patients with metastatic disease and with mutations in both MEN1 and DAXX/ATRX: 100% of patients with these mutations survived at least ten years while over 60% of the patients without these mutations died within five years of diagnosis (FIG. 2B). One possible explanation for the difference in survival is that mutations in MEN1 and DAXX/ATRX identify a biologically specific subgroup of PanNETs.

Example 8—Materials and Methods

Preparation of Illumina Genomic DNA Libraries

Fresh-frozen surgically resected tumor and normal tissues were obtained from patients under an Institutional Review Board protocol. Genomic DNA libraries were prepared following Illumina's (Illumina, San Diego, Calif.) suggested protocol with the following modifications. (1) 3 micrograms (μg) of genomic DNA from tumor or normal cells in 100 microliters (μl) of TE was fragmented in a Covaris sonicator (Covaris, Woburn, Mass.) to a size of 100-500 bp. To remove fragments shorter than 150 bp, DNA was mixed with 25 μl of 5×Phusion HF buffer, 416 μl of ddH2O, and 84 μl of NT binding buffer and loaded into NucleoSpin column (cat#636972, Clontech, Mountain View, Calif.). The column was centrifuged at 14000 g in a desktop centrifuge for 1 min, washed once with 600 μl of wash buffer (NT3 from Clontech), and centrifuged again for 2 min to dry completely. DNA was eluted in 45 μl of elution buffer included in the kit. (2) Purified, fragmented DNA was mixed with 40 μl of H2O, 10 μl of End Repair Reaction Buffer, 5 μl of End Repair Enzyme Mix (cat# E6050, NEB, Ipswich, Mass.). The 100 μl end-repair mixture was incubated at 20° C. for 30 min, purified by a PCR purification kit (Cat #28104, Qiagen) and eluted with 42 μl of elution buffer (EB). (3) To A-tail, all 42 μl of end-repaired DNA was mixed with 5 μl of 10×dA Tailing Reaction Buffer and 3 μl of Klenow (exo−) (cat# E6053, NEB, Ipswich, Mass.). The 50 μl mixture was incubated at 37° C. for 30 min before DNA was purified with a MinElute PCR purification kit (Cat #28004, Qiagen). Purified DNA was eluted with 25 μl of 70° C. EB. (4) For adaptor ligation, 25 μl of A-tailed DNA was mixed with 10 μl of PE-adaptor (Illumina), 10 μl of 5× Ligation buffer and 5 μl of Quick T4 DNA ligase (cat# E6056, NEB, Ipswich, Mass.). The ligation mixture was incubated at 20° C. for 15 min. (5) To purify adaptor-ligated DNA, 50 μl of ligation mixture from step (4) was mixed with 200 μl of NT buffer and cleaned up by NucleoSpin column. DNA was eluted in 50 μl elution buffer. (6) To obtain an amplified library, ten PCRs of 50 μl each were set up, each including 29 μl of H2O, 10 μl of 5× Phusion HF buffer, 1 μl of a dNTP mix containing 10 mM of each dNTP, 2.5 μl of DMSO, 1 μl of Illumina PE primer # 1, 1 μl of Illumina PE primer #2, 0.5 μl of Hotstart Phusion polymerase, and 5 μl of the DNA from step (5). The PCR program used was: 98° C. 2 minute; 6 cycles of 98° C. for 15 seconds, 65° C. for 30 seconds, 72° C. for 30 seconds; and 72° C. for 5 min. To purify the PCR product, 500 μl PCR mixture (from the ten PCR reactions) was mixed with 1000 μl NT buffer from a NucleoSpin Extract II kit and purified as described in step (1). Library DNA was eluted with 70° C. elution buffer and the DNA concentration was estimated by absorption at 260 nm.

Exome and Targeted Subgenomic DNA Capture

Human exome capture was performed following a protocol from Agilent's SureSelect Paired-End Version 2.0 Human Exome Kit (Agilent, Santa Clara, Calif.) with the following modifications. (1) A hybridization mixture was prepared containing 25 μl of SureSelect Hyb # 1, 1 μl of SureSelect Hyb # 2, 10 μl of SureSelect Hyb # 3, and 13 μl of SureSelect Hyb #4. (2) 3.4 μl (0.5 μg) of the PE-library DNA described above, 2.5 μl of SureSelect Block #1, 2.5 μl of SureSelect Block #2 and 0.6 μl of Block #3; was loaded into one well in a 384-well Diamond PCR plate (cat# AB-1111, Thermo-Scientific, Lafayette, Colo.), sealed with microAmp clear adhesive film (cat#4306311; ABI, Carlsbad, Calif.) and placed in GeneAmp PCR system 9700 thermocycler (Life Sciences Inc., Carlsbad Calif.) for 5 minutes at 95° C., then held at 65° C. (with the heated lid on). (3) 25-30 μl of hybridization buffer from step (1) was heated for at least 5 minutes at 65° C. in another sealed plate with heated lid on. (4) 5 μl of SureSelect Oligo Capture Library, 1 μl of nuclease-free water, and 1 μl of diluted RNase Block (prepared by diluting RNase Block 1:1 with nuclease-free water) were mixed and heated at 65° C. for 2 minutes in another sealed 384-well plate. (5) While keeping all reactions at 65° C., 13 μl of Hybridization Buffer from Step (3) was added to the 7 μl of the SureSelect Capture Library Mix from Step (4) and then the entire contents (9 μl) of the library from Step (2). The mixture was slowly pipetted up and down 8 to 10 times. (6) The 384-well plate was sealed tightly and the hybridization mixture was incubated for 24 hours at 65° C. with a heated lid.
After hybridization, five steps were performed to recover and amplify captured DNA library: (1) Magnetic beads for recovering captured DNA: 50 μl of Dynal MyOne Streptavidin C1 magnetic beads (Cat #650.02, Invitrogen Dynal, AS Oslo, Norway) was placed in a 1.5 ml microfuge tube and vigorously resuspended on a vortex mixer. Beads were washed three times by adding 200 μl of SureSelect Binding buffer, mixed on a vortex for five seconds, then removing and discarding supernatant after placing the tubes in a Dynal magnetic separator. After the third wash, beads were resuspended in 200 μl of SureSelect Binding buffer. (2) To bind captured DNA, the entire hybridization mixture described above (29 μl) was transferred directly from the thermocycler to the bead solution and mixed gently; the hybridization mix/bead solution was incubated an Eppendorf thermomixer at 850 rpm for 30 minutes at room temperature. (3) To wash the beads, the supernatant was removed from beads after applying a Dynal magnetic separator and the beads was resuspended in 500 μl SureSelect Wash Buffer #1 by mixing on vortex mixer for 5 seconds and incubated for 15 minutes at room temperature. Wash Buffer#1 was then removed from beads after magnetic separation. The beads were further washed three times, each with 500 μl pre-warmed SureSelect Wash Buffer #2 after incubation at 65° C. for 10 minutes. After the final wash, SureSelect Wash Buffer #2 was completely removed. (4) To elute captured DNA, the beads were suspended in 50 μl SureSelect Elution Buffer, vortex-mixed and incubated for 10 minutes at room temperature. The supernatant was removed after magnetic separation, collected in a new 1.5 ml microcentrifuge tube, and mixed with 50 μl of SureSelect Neutralization Buffer. DNA was purified with a Qiagen MinElute column and eluted in 17 μl of 70° C. EB to obtain 15 μl of captured DNA library. (5) The captured DNA library was amplified in the following way: 15 PCR reactions each containing 9.5 μl of H2O, 3 μl of 5× Phusion HF buffer, 0.3 μl of 10 mM dNTP, 0.75 μl of DMSO, 0.15 μl of Illumina PE primer #1, 0.15 μl of Illumina PE primer #2, 0.15 μl of Hotstart Phusion polymerase, and 1 μl of captured exome library were set up. The PCR program used was: 98° C. for 30 seconds; 14 cycles of 98° C. for 10 seconds, 65° C. for 30 seconds, 72° C. for 30 seconds; and 72° C. for 5 min. To purify PCR products, 225 μl PCR mixture (from 15 PCR reactions) was mixed with 450 μl NT buffer from NucleoSpin Extract II kit and purified as described above. The final library DNA was eluted with 30 μl of 70° C. elution buffer and DNA concentration was estimated by OD260 measurement.

Somatic Mutation Identification by Massively Parallel Sequencing

Captured DNA libraries were sequenced with the Illumina GAIIx Genome Analyzer, yielding 150 (2×75) base pairs from the final library fragments. Sequencing reads were analyzed and aligned to human genome hg18 with the Eland algorithm in CASAVA 1.6 software (Illumina). A mismatched base was identified as a mutation only when (i) it was identified by more than three distinct tags; (ii) the number of distinct tags containing a particular mismatched base was at least 16% of the total distinct tags; and (iii) it was not present in >0.5% of the tags in the matched normal sample. SNP search databases included http://www.ncbi.nlm.nih.gov/projects/SNP/ and http://browser.1000genomes.org/index.html.

Evaluation of Genes in Additional Tumors and Matched Normal Controls.

For the ATRX, DAXX, MEN1, PIK3CA, PTEN, TP53 and TSC2 genes, the coding region was sequenced in a validation Set, comprising a series of additional pancreatic neuroendocrine tumors and matched controls. PCR amplification and Sanger sequencing were performed following protocols described previously (1) using the primers listed in table S8.

Immunohistochemistry

Immunohistochemical labeling for ATRX and DAXX proteins was performed on formalin-fixed, paraffin-embedded sections of PanNETs. Heat-induced antigen retrieval was performed in a steamer using citrate buffer (pH 6.0) (Vector Laboratories) for 30 min followed by 10 min of cooling. Endogenous peroxidase was blocked for 10 min with dual endogenous enzyme-blocking reagent (Dako). Serial sections were then incubated with primary antibody; anti-ATRX (1:400 dilution; catalog no. HPA001906, Sigma-Aldrich) and anti-DAXX (1:75 dilution; catalog no. HPA008736, Sigma-Aldrich) for 1 h at room temperature. The sections were then incubated for 30 min with secondary antibody (Leica Microsystems) followed by detection with 3,3′-Diaminobenzidine (Sigma-Adrich) for 8 min. Sections were washed with phosphate-buffered saline with 0.1% Tween-20. Finally, sections were counterstained with Harris hematoxylin, subsequently rehydrated and mounted. Only nuclear labeling of either protein was considered positive. At least 50% of the cells needed to have nuclear labeling for the marker to be considered positive. Internal controls included islets of Langerhans and endothelial cells (including within intra-tumoral vessels) which demonstrated strong nuclear labeling for both ATRX and DAXX.

Clinical Correlations

Clinical information on the patients evaluated in this study were obtained from the Johns Hopkins Hospital and the Memorial Sloan-Kettering Comprehensive Cancer Center in the context of approved IRB protocols. Clinical data were collected retrospectively and compared with mutational status. Overall survival was calculated from the time of diagnosis until death. Patients who were alive at the time of analysis were censored at the date of last observation. Survival curves were plotted by the Kaplan-Meier method and compared using the Mantel-Cox log-rank test (Prism, GraphPad Software, La Jolla, Calif.).

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The disclosure of each reference cited is expressly incorporated herein.

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Claims

We claim:

1. A method for predicting outcome of a pancreatic neuroendocrine tumor in a patient, comprising:

testing the pancreatic neuroendocrine tumor, or cells or nucleic acids shed from the tumor, for the presence of an inactivating mutation in MEN1, DAXX, or ATRX, wherein a mutation in at least one of these genes is a positive prognostic indicator.