Circulating Tumor DNA as a Clinical Test in Resected Pancreatic Cancer

PURPOSE

In research settings, circulating tumor DNA (ctDNA) shows promise as a tumor-specific biomarker for pancreatic ductal adenocarcinoma (PDAC). This study aims to perform analytical and clinical validation of a KRAS ctDNA assay in a Clinical Laboratory Improvement Amendments (CLIA) and College of American Pathology-certified clinical laboratory.

EXPERIMENTAL DESIGN

Digital-droplet PCR was used to detect the major PDAC-associated somatic KRAS mutations (G12D, G12V, G12R, and Q61H) in liquid biopsies. For clinical validation, 290 preoperative and longitudinal postoperative plasma samples were collected from 59 patients with PDAC. The utility of ctDNA status to predict PDAC recurrence during follow-up was assessed.

RESULTS

ctDNA was detected preoperatively in 29 (49%) patients and was an independent predictor of decreased recurrence-free survival (RFS) and overall survival (OS). Patients who had neoadjuvant chemotherapy were less likely to have preoperative ctDNA than were chemo-naïve patients (21% vs. 69%; P < 0.001). ctDNA levels dropped significantly after tumor resection. Persistence of ctDNA in the immediate postoperative period was associated with a high rate of recurrence and poor median RFS (5 months). ctDNA detected during follow-up predicted clinical recurrence [sensitivity 90% (95% confidence interval (CI), 74%-98%), specificity 88% (95% CI, 62%-98%)] with a median lead time of 84 days (interquartile range, 25-146). Detection of ctDNA during postpancreatectomy follow-up was associated with a median OS of 17 months, while median OS was not yet reached at 30 months for patients without ctDNA (P = 0.011).

CONCLUSIONS

Measurement of KRAS ctDNA in a CLIA laboratory setting can be used to predict recurrence and survival in patients with PDAC.

Cytosine deamination is a major cause of baseline noise in next-generation sequencing

BACKGROUND AND OBJECTIVES

As next-generation sequencing (NGS) becomes a major sequencing platform in clinical diagnostic laboratories, it is critical to identify artifacts that constitute baseline noise and may interfere with detection of low-level gene mutations. This is especially critical for applications requiring ultrasensitive detection, such as molecular relapse of solid tumors and early detection of cancer. We recently observed a ~10-fold higher frequency of C:G > T:A mutations than the background noise level in both wild-type peripheral blood and formalin-fixed paraffin-embedded samples. We hypothesized that these might represent cytosine deamination events, which have been seen using other platforms.

METHODS

To test this hypothesis, we pretreated samples with uracil N-glycosylase (UNG). Additionally, to test whether some of the cytosine deamination might be a laboratory artifact, we simulated the heat associated with polymerase chain reaction thermocycling by subjecting samples to thermocycling in the absence of polymerase. To test the safety of universal UNG pretreatment, we tested known positive samples treated with UNG.

RESULTS

UNG pretreatment significantly reduced the frequencies of these mutations, consistent with a biologic source of cytosine deamination. The simulated thermocycling-heated samples demonstrated significantly increased frequencies of C:G > T:A mutations without other baseline base substitutions being affected. Samples with known mutations demonstrated no decrease in our ability to detect these after treatment with UNG.

CONCLUSION

Baseline noise during NGS is mostly due to cytosine deamination, the source of which is likely to be both biologic and an artifact of thermocycling, and it can be reduced by UNG pretreatment.

False positives in multiplex PCR-based next-generation sequencing have unique signatures

Next-generation sequencing shows great promise by allowing rapid mutational analysis of multiple genes in human cancers. Recently, we implemented the multiplex PCR-based Ion AmpliSeq Cancer Hotspot Panel (>200 amplicons in 50 genes) to evaluate EGFR, KRAS, and BRAF in lung and colorectal adenocarcinomas. In 10% of samples, automated analysis identified a novel G873R substitution mutation in EGFR. By examining reads individually, we found this mutation in >5% of reads in 50 of 291 samples and also found similar events in 18 additional amplicons. These apparent mutations are present only in short reads and within 10 bases of either end of the read. We therefore hypothesized that these were from panel primers promiscuously binding to nearly complementary sequences of nontargeted amplicons. Sequences around the mutations matched primer binding sites in the panel in 18 of 19 cases, thus likely corresponding to panel primers. Furthermore, because most primers did not show this effect, we demonstrated that next-generation sequencing may be used to better design multiplex PCR primers through iterative elimination of offending primers to minimize mispriming. Our results indicate the need for careful sequence analysis to avoid false-positive mutations that can arise in multiplex PCR panels. The AmpliSeq Cancer panel is a valuable tool for clinical diagnostics, provided awareness of potential artifacts.

Genetic profiling by single-nucleotide polymorphism-based array analysis defines three distinct subtypes of orbital meningioma

Orbital meningiomas can be classified as primary optic nerve sheath (ON) meningiomas, primary intraorbital ectopic (Ob) meningiomas and spheno-orbital (Sph-Ob) meningiomas based on anatomic site. Single-nucleotide polymorphism (SNP)-based array analysis with the Illumina 300K platform was performed on formalin-fixed, paraffin-embedded tissue from 19 orbital meningiomas (5 ON, 4 Ob and 10 Sph-Ob meningiomas). Tumors were World Health Organization (WHO) grade I except for two grade II meningiomas, and one was NF2-associated. We found genomic alterations in 68% (13 of 19) of orbital meningiomas. Sph-Ob tumors frequently exhibited monosomy 22/22q loss (70%; 7/10) and deletion of chromosome 1p, 6q and 19p (50% each; 5/10). Among genetic alterations, loss of chromosome 1p and 6q were more frequent in clinically progressive tumors. Chromosome 22q loss also was detected in the majority of Ob meningiomas (75%; 3/4) but was infrequent in ON meningiomas (20%; 1/5). In general, Ob tumors had fewer chromosome alterations than Sph-Ob and ON tumors. Unlike Sph-Ob meningiomas, most of the Ob and ON meningiomas did not progress even after incomplete excision, although follow-up was limited in some cases. Our study suggests that ON, Ob and Sph-Ob meningiomas are three molecularly distinct entities. Our results also suggest that molecular subclassification may have prognostic implications.

Rb loss is characteristic of prostatic small cell neuroendocrine carcinoma

PURPOSE

Small cell neuroendocrine carcinoma of the prostate is likely to become increasingly common with recent advances in pharmacologic androgen suppression. Thus, developing molecular markers of small cell differentiation in prostate cancer will be important to guide the diagnosis and therapy of this aggressive tumor.

EXPERIMENTAL DESIGN

We examined the status of RB1, TP53, and PTEN in prostatic small cell and acinar carcinomas via immunohistochemistry (IHC), copy-number alteration analysis, and sequencing of formalin-fixed paraffin-embedded specimens.

RESULTS

We found retinoblastoma (Rb) protein loss in 90% of small cell carcinoma cases (26 of 29) with RB1 allelic loss in 85% of cases (11 of 13). Of acinar tumors occurring concurrently with prostatic small cell carcinoma, 43% (3 of 7) showed Rb protein loss. In contrast, only 7% of primary high-grade acinar carcinomas (10 of 150), 11% of primary acinar carcinomas with neuroendocrine differentiation (4 of 35), and 15% of metastatic castrate-resistant acinar carcinomas (2 of 13) showed Rb protein loss. Loss of PTEN protein was seen in 63% of small cell carcinomas (17 of 27), with 38% (5 of 13) showing allelic loss. By IHC, accumulation of p53 was observed in 56% of small cell carcinomas (14 of 25), with 60% of cases (6 of 10) showing TP53 mutation.

CONCLUSIONS

Loss of RB1 by deletion is a common event in prostatic small cell carcinoma and can be detected by a validated IHC assay. As Rb protein loss rarely occurs in high-grade acinar tumors, these data suggest that Rb loss is a critical event in the development of small cell carcinomas and may be a useful diagnostic and potential therapeutic target.

Abstract A05: Estrogen synthesis and metabolism within the lungs of non-small cell lung cancer patients

Although results from recent studies suggest that the female hormone estrogen promotes lung cancer development, the molecular mechanisms underlying this oncogenic activity remain to be elucidated. Previous data from this group demonstrate that estrogen is metabolized extensively within the murine lung. Exposure to tobacco smoke accelerates the production of 4-hydroxyestrogen, a putative carcinogenic estrogen metabolite that is generated primarily by CYP1B1. While these data suggest that mutagenic estrogen metabolites may contribute to lung tumorigenesis in mice, their relevance to humans remains unknown. The purpose of the present study was to determine the capacity of the human lung to synthesize and metabolize estrogen and to compare the profile of estrogen metabolites in tumor tissue from non-small cell lung cancer (NSCLC) patients with that of adjacent normal tissue.

Quantitative RT-PCR analyses revealed expression of estrogen synthesis (CYP17A1, CYP21, HSD17B3 and HSD17B7) and metabolism (CYP1B1, GSTA4, GSTT1, NQO1 and COMT) genes in 50-100% of both normal lung specimens and tumors. Transcripts for the estrogen synthesis genes CYP19 and HSD3B1 were present only in tumors, while expression of GSTM1 and CYP1A1 was detected in less than 30% of both normal and tumor tissues. Expression of ERα and ERβ was comparable in both tissue types. However, tumors exhibited decreased levels of HSD17B3 (converts androstenedione to testosterone) and progesterone receptor transcripts as compared to normal tissue.

In order to determine if the detected genes are functional, the estrogen metabolite profile of human lung tissue was established using liquid chromatography/tandem mass spectrometry (LC-MS2) technology. Examination of paired normal and tumor specimens from 9 female patients with NSCLC indicated the presence of 3 estrogens (E1, E2 and E3) and 6 estrogen metabolites (2-OHE1, 2-OHE2, 4-OHE1, 4-OHE2, 2-OMeE1 and 2-OMeE2). With the exception of 2-OMeEs, putative protective estrogen metabolites, the levels of all estrogen species examined were elevated 1.5-2 fold in tumor tissue as compared to adjacent normal tissue (P&lt;0.05 by Wilcoxon signed rank test). In summary, these findings demonstrate for the first time that estrogen is metabolized within the human lung. The differential gene expression profile and altered estrogen metabolite levels in tumor versus adjacent normal tissue suggest that estrogen metabolism may play an important role in the development of human lung tumors and serve as a promising target for lung cancer prevention. Future studies will confirm these results in a larger number of patients and evaluate the potential of using gene expression signatures and estrogen metabolite profiles as biomarkers for the early detection of lung cancer. (This work was supported by the Keystone Initiative in Personalized Risk and Prevention, the Estate of Jane Villon and the Kitty Jackson Fund.)

Citation Format: Jing Peng, Xia Xu, Sibele Meireles, Stacy Mosier, Michael Slifker, Karthik Devarajan, Margie Clapper. Estrogen synthesis and metabolism within the lungs of non-small cell lung cancer patients. [abstract]. In: Proceedings of the Twelfth Annual AACR International Conference on Frontiers in Cancer Prevention Research; 2013 Oct 27-30; National Harbor, MD. Philadelphia (PA): AACR; Can Prev Res 2013;6(11 Suppl): Abstract nr A05.

Abstract 195: Effect of sulindac and/or atorvastatin on colorectal adenomas in the Apc+/Min-FCCC mouse model varies depending on the presence or absence of adenomas at the time of drug initiation

While treatment with sulindac plus atorvastatin has been shown to be more efficacious than either agent alone in inhibiting chemically-induced colorectal tumors, the effectiveness of this same drug combination against sporadic colorectal cancer has not been evaluated. The goal of this study was to assess the chemopreventive activity of sulindac plus atorvastatin, in combination, in a unique strain of Apc+/Min-FCCC mice that spontaneously develops colorectal adenomas at a high multiplicity and incidence. Male Apc+/Min-FCCC mice (6-8 weeks of age) were subjected to colonoscopic examinations at baseline (prior to treatment) and randomized to receive either control chow or chow supplemented with sulindac (300 ppm), atorvastatin (100 ppm) or sulindac plus atorvastatin for 100 days. All drugs were well tolerated, with no significant change in body weight observed among the treatment groups. At the time of euthanasia, gross small intestinal (SI) and colonic tumors were identified and the height, width and length of the colonic tumors was measured using calipers. Only the colon was submitted for histopathological evaluation. The multiplicity of gross SI tumors was decreased in animals administered sulindac (54%) or sulindac plus atorvastatin (41%), as compared to those receiving either control diet or atorvastatin alone (P ≤ 0.00024). Based on the results of the colonoscopic evaluation, mice were categorized as being tumor-free or tumor-bearing at baseline. Treatment with atorvastatin, alone or in combination, lead to a 2.4-3.6-fold increase in the percentage of mice that were tumor-free both at baseline and at the time of euthanasia: control 12.5%; sulindac 9.1%; atorvastatin 44.4% and sulindac plus atorvastatin 30%. Interestingly, atorvastatin completely inhibited the formation of microadenomas in mice that were tumor-free at baseline (P = 0.002). In mice that were tumor-bearing at baseline, only the sulindac plus atorvastatin combination therapy reduced the multiplicity of colon adenomas significantly as compared to that of controls (Mean ± SEM, 3.7 ± 0.7 and 6.4 ± 1.2, respectively) (P = 0.049). The effect of drug exposure on tumor volume was evaluated at the time of euthanasia. Colon tumor volume was reduced 2-fold in mice treated with sulindac as compared to that of mice administered control diet or diet supplemented with atorvastatin or sulindac plus atorvastatin in combination (P &lt; 0.03). These data suggest that the chemopreventive activity of sulindac and/or atorvastatin against colorectal adenomas is dictated in part by the status of the animal (tumor-free or tumor-bearing) at the time treatment is initiated. Additional experimentation is required to establish the patient subgroup and drug schedule that will yield optimal therapeutic activity in a clinical setting. (Supported by NIH R21CA129467)

Citation Format: Wen-Chi Chang, Christina Ferrara, Stacy Mosier, Harry Cooper, Karthik Devarajan, Harvey Hensley, Tianyu Li, Margie Clapper. Effect of sulindac and/or atorvastatin on colorectal adenomas in the Apc+/Min-FCCC mouse model varies depending on the presence or absence of adenomas at the time of drug initiation. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 195. doi:10.1158/1538-7445.AM2013-195

Genetic and pathologic evolution of early secondary gliosarcoma

Gliosarcoma is a subset of glioblastoma with glial and mesenchymal components. True secondary gliosarcomas (i.e. progressing from lower-grade precursors) in the absence of radiation therapy are very rare. We report the unique case of a 61-year-old male who developed a fibrillary astrocytoma (WHO grade II). In the absence of adjuvant therapy the tumor recurred 3 years later as a gliosarcoma comprising an infiltrating glial component and a curious, early high-grade sarcomatous component surrounding intratumoral vessels. DNA was extracted from formalin fixed paraffin-embedded tissues from the precursor low-grade glioma and from the glioma and sarcomatous components at progression. Samples were hybridized separately to a 300 k Illumina SNP array. IDH1(R132H) mutant protein immunohistochemistry was positive in all tissue components. Alterations identified in all samples included dup(1)(q21q41), del(1)(q41qter), del(2)(q31.1), del(2)(q36.3qter), del(4)(q35.1qter), dup(7)(q22.2q36.3), del(7)(q36.3qter), del(9)(p21.3pter), dup(10)(p13pter), del(10)(q26.13q26.3), dup(17) (q12qter), and copy neutral LOH(20)(p11.23p11.21). The recurrent tumor had additional alterations, including del(3)(p21.31q13.31), del(18)(q21.2qter), and a homozygous del(9)(p21.3)(CDKN2A locus) and the sarcoma component had, in addition, del(4)(p14pter), del(6)(q12qter), del(11)(q24.3qter), and del(16)(p11.2pter). In conclusion, unique copy number alterations were identified during tumor progression from a low-grade glioma to gliosarcoma. A subset of alterations developed specifically in the sarcomatous component.

Disseminated oligodendroglial-like leptomeningeal tumor of childhood: a distinctive clinicopathologic entity

Rare, generally pediatric oligodendroglioma-like neoplasms with extensive leptomeningeal dissemination have been interpreted variably as glial, oligodendroglial or glioneuronal. The clinicopathologic features have not been fully characterized. We studied 36 patients, 12 females and 24 males with a median age of 5 years (range 5 months-46 years). MRI demonstrated leptomeningeal enhancement, frequently with cystic or nodular T2 hyperintense lesions within the spinal cord/brain along the subpial surface. A discrete intraparenchymal lesion, usually in the spinal cord, was found in 25 (of 31) (81 %). Tumors contained oligodendroglioma-like cells with low-mitotic activity (median 0 per 10 high power fields, range 0-4), and rare ganglion/ganglioid cells in 6 cases (17 %). Tumors were mostly low-grade, with anaplastic progression in 8 (22 %). Immunohistochemistry demonstrated strong reactivity for OLIG2 (7 of 9) (78 %), and moderate/strong S100 (11 of 12) (92 %), GFAP (12 of 31) (39 %) and synaptophysin (19 of 27) (70 %). NeuN, EMA, and mutant IDH1 (R132H) protein were negative. Median MIB1 labeling index was 1.5 % (range <1-30 %). FISH (n = 13) or SNP array (n = 2) demonstrated 1p loss/intact 19q in 8 (53 %), 1p19q co-deletion in 3 (20 %), and no 1p or 19q loss in 4 (27 %). Clinical follow-up (n = 24) generally showed periods of stability or slow progression, but a subset of tumors progressed to anaplasia and behaved more aggressively. Nine patients (38 %) died 3 months-21 years after diagnosis (median total follow-up 5 years). We report a series of a neoplasm with distinct clinicopathologic and molecular features. Although most progress slowly, a significant fraction develop aggressive features.

Progesterone binding in a clinical isolate of Pseudomonas aeruginosa

We have undertaken the characterization of progestin binding component(s) in the cytosol prepared from Pseudomonas aeruginosa isolated from an immunocompromised patient. Incubation of P. aeruginosa cytosol aliquots at 0 degrees C with 20 nM [3H]R5020 (a synthetic progestin) revealed the presence of saturable binding. The [3H]R5020 binding reached an equilibrium after 1 h at 0 degrees C and showed saturation at 30-50 nM with a Kd value of 7.7 nM. At 0 degrees C, beta-mercaptoethanol increased the [3H]R5020 binding by 20% but sodium molybdate had no effect. The [3H]R5020-macromolecular complex was stable for up to 4 h at 37 degrees C. Steroid binding specificity analysis revealed that [3H]R5020 binding could be eliminated in the presence of 2 microM progesterone, estradiol, or dihydrotestosterone but that the synthetic glucocorticoid, triamcinolone acetonide, did not compete. Postlabeling of the cytosol fractions obtained after 10-30% glycerol gradient analysis demonstrated association of the radioactivity with a molecule that sedimented as a 6-8 S protease-sensitive moiety which was unaltered in the presence of RNase or DNase. When cells were grown in the presence of 100 nM progesterone, a 50% inhibition in the number of resulting colonies was observed. In addition to its evolutionary significance, the presence of this steroid binding molecule suggests a potential in the endocrine manipulation in the treatment of infections caused by P. aeruginosa.