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Novel Methylated DNA Markers Discriminate Advanced Neoplasia in Pancreatic Cysts: Marker Discovery, Tissue Validation, and Cyst Fluid Testing
Majumder, Shounak; Taylor, William R; Yab, Tracy C; Berger, Calise K; Dukek, Brian A; Cao, Xiaoming; Foote, Patrick H; Wu, Chung Wah; Mahoney, Douglas W; Aslanian, Harry R; Fernández-Del Castillo, Carlos; Doyle, Leona A; Farrell, James J; Fisher, William E; Lee, Linda S; Lee, Yvonne N; Park, Walter; Rodrigues, Clifton; Gould Rothberg, Bonnie Elyssa; Salem, Ronald R; Simeone, Diane M; Urs, Sumithra; Van Buren, George; Smyrk, Thomas C; Allawi, Hatim T; Lidgard, Graham P; Raimondo, Massimo; Chari, Suresh T; Kendrick, Michael L; Kisiel, John B; Topazian, Mark D; Ahlquist, David A
OBJECTIVES:Pancreatic cystic lesions (PCLs) may be precancerous. Those likely to harbor high-grade dysplasia (HGD) or pancreatic cancer (PC) are targets for surgical resection. Current algorithms to predict advanced neoplasia (HGD/PC) in PCLs lack diagnostic accuracy. In pancreatic tissue and cyst fluid (CF) from PCLs, we sought to identify and validate novel methylated DNA markers (MDMs) that discriminate HGD/PC from low-grade dysplasia (LGD) or no dysplasia (ND). METHODS:From an unbiased whole-methylome discovery approach using predefined selection criteria followed by multistep validation on case (HGD or PC) and control (ND or LGD) tissues, we identified discriminant MDMs. Top candidate MDMs were then assayed by quantitative methylation-specific polymerase chain reaction on archival CF from surgically resected PCLs. RESULTS:Of 25 discriminant MDMs identified in tissue, 13 were selected for validation in 134 CF samples (21 cases [8 HGD, 13 PC], 113 controls [45 ND, 68 LGD]). A tree-based algorithm using 2 CF-MDMs (TBX15, BMP3) achieved sensitivity and specificity above 90%. Discrimination was significantly better by this CF-MDM panel than by mutant KRAS or carcinoembryonic antigen, with areas under the receiver operating characteristic curve of 0.93 (95% confidence interval: 0.86-0.99), 0.71 (0.57-0.85), and 0.72 (0.60-0.84), respectively. Cutoffs for the MDM panel applied to an independent CF validation set (31 cases, 56 controls) yielded similarly high discrimination, areas under the receiver operating characteristic curve = 0.86 (95% confidence interval: 0.77-0.94, P = 0.2). DISCUSSION:Novel MDMs discovered and validated in tissue accurately identify PCLs harboring HGD/PC. A panel of 2 MDMs assayed in CF yielded results with potential to enhance current risk prediction algorithms. Prospective studies are indicated to optimize and further evaluate CF-MDMs for clinical use.
PMCID:7294458
PMID: 31306149
ISSN: 1572-0241
CID: 5080702
Metabolic Regulation of Redox Balance in Cancer
Purohit, Vinee; Simeone, Diane M; Lyssiotis, Costas A
Reactive oxygen species (ROS) are chemically active free radicals produced by partial reduction of oxygen that can activate discrete signaling pathways or disrupt redox homeostasis depending on their concentration. ROS interacts with biomolecules, including DNA, and can cause mutations that can transform normal cells into cancer cells. Furthermore, certain cancer-causing mutations trigger alterations in cellular metabolism that can increase ROS production, resulting in genomic instability, additional DNA mutations, and tumor evolution. To prevent excess ROS-mediated toxicity, cancer-causing mutations concurrently activate pathways that manage this oxidative burden. Hence, an understanding of the metabolic pathways that regulate ROS levels is imperative for devising therapies that target tumor cells. In this review, we summarize the dual role of metabolism as a generator and inhibitor of ROS in cancer and discuss current strategies to target the ROS axis.
PMCID:6678865
PMID: 31288436
ISSN: 2072-6694
CID: 4136182
Multiplex Enrichment and Detection of Rare KRAS Mutations in Liquid Biopsy Samples using Digital Droplet Pre-Amplification
Pratt, Erica D; Cowan, Robert W; Manning, Sara L; Qiao, Edmund; Cameron, Heather; Schradle, Kara; Simeone, Diane M; Zhen, David B
Oncology research is increasingly incorporating molecular detection of circulating tumor DNA (ctDNA) as a tool for cancer surveillance and early detection. However, noninvasive monitoring of conditions with low tumor burden remains challenging, as the diagnostic sensitivity of most ctDNA assays is inversely correlated with total DNA concentration and ctDNA abundance. Here we present the Multiplex Enrichment using Droplet Pre-Amplification (MED-Amp) method, which combines single-molecule emulsification and short-round polymerase chain reaction (PCR) preamplification with digital droplet PCR detection of mutant DNA template. The MED-Amp assay increased mutant signal by over 50-fold with minimal distortion in allelic frequency. We demonstrate detection of as few as three mutant copies in wild-type DNA concentrations ranging from 5 to 50 ng. The MED-Amp assay successfully detected KRAS mutant ctDNA in 86% plasma samples obtained from patients with metastatic pancreatic ductal adenocarcinoma. This assay for high-sensitivity rare variant detection is appropriate for liquid biopsy samples or other limited clinical biospecimens.
PMID: 31072097
ISSN: 1520-6882
CID: 5080692
ATDC is required for the initiation of KRAS-induced pancreatic tumorigenesis
Wang, Lidong; Yang, Huibin; Zamperone, Andrea; Diolaiti, Daniel; Palmbos, Phillip L; Abel, Ethan V; Purohit, Vinee; Dolgalev, Igor; Rhim, Andrew D; Ljungman, Mats; Hadju, Christina H; Halbrook, Christopher J; Bar-Sagi, Dafna; di Magliano, Marina Pasca; Crawford, Howard C; Simeone, Diane M
Pancreatic adenocarcinoma (PDA) is an aggressive disease driven by oncogenic KRAS and characterized by late diagnosis and therapeutic resistance. Here we show that deletion of the ataxia-telangiectasia group D-complementing (Atdc) gene, whose human homolog is up-regulated in the majority of pancreatic adenocarcinoma, completely prevents PDA development in the context of oncogenic KRAS. ATDC is required for KRAS-driven acinar-ductal metaplasia (ADM) and its progression to pancreatic intraepithelial neoplasia (PanIN). As a result, mice lacking ATDC are protected from developing PDA. Mechanistically, we show ATDC promotes ADM progression to PanIN through activation of β-catenin signaling and subsequent SOX9 up-regulation. These results provide new insight into PDA initiation and reveal ATDC as a potential target for preventing early tumor-initiating events.
PMID: 31048544
ISSN: 1549-5477
CID: 3854942
ATDC mediates a TP63-regulated basal cancer invasive program
Palmbos, Phillip L; Wang, Yin; Bankhead Iii, Armand; Kelleher, Alan J; Wang, Lidong; Yang, Huibin; Ahmet, McKenzie L; Gumkowski, Erica R; Welling, Samuel D; Magnuson, Brian; Leflein, Jacob; Lorenzatti Hiles, Guadalupe; Abel, Ethan V; Dziubinski, Michele L; Urs, Sumithra; Day, Mark L; Ljungman, Mats E; Simeone, Diane M
Basal subtype cancers are deadly malignancies but the molecular events driving tumor lethality are not completely understood. Ataxia-telangiectasia group D complementing gene (ATDC, also known as TRIM29), is highly expressed and drives tumor formation and invasion in human bladder cancers but the factor(s) regulating its expression in bladder cancer are unknown. Molecular subtyping of bladder cancer has identified an aggressive basal subtype, which shares molecular features of basal/squamous tumors arising in other organs and is defined by activation of a TP63-driven gene program. Here, we demonstrate that ATDC is linked with expression of TP63 and highly expressed in basal bladder cancers. We find that TP63 binds to transcriptional regulatory regions of ATDC and KRT14 directly, increasing their expression, and that ATDC and KRT14 execute a TP63-driven invasive program. In vivo, ATDC is required for TP63-induced bladder tumor invasion and metastasis. These results link TP63 and the basal gene expression program to ATDC and to aggressive tumor behavior. Defining ATDC as a molecular determinant of aggressive, basal cancers may lead to improved biomarkers and therapeutic approaches.
PMID: 30643195
ISSN: 1476-5594
CID: 3595232
Low dose photodynamic therapy harmonizes with radiation therapy to induce beneficial effects on pancreatic heterocellular spheroids
Bulin, Anne-Laure; Broekgaarden, Mans; Simeone, Diane; Hasan, Tayyaba
Photodynamic therapy (PDT) has seen long standing interest as a therapy for resistant cancers, but the main Achilles' heel for its successful clinical exploitation is the use of poorly penetrating visible light. This limitation could be overcome by using radioluminescent nanoparticles, which can be excited during radiation therapy (RT) with penetrating X-rays. When infused in tumors, X-ray activated-nanoscintillators act as internal light sources and excite nearby photosensitizers. Recent studies demonstrated that it is realistic to achieve low dose PDT with current nanoscintillators. However, as the origin of enhanced RT efficacy with nanoscintillators may have varying origins, we aimed to answer the basic question: Is a combination of low-dose PDT beneficial to the RT efficacy in clinically relevant models of cancer? Pancreatic cancer (PanCa) remains a lethal disease for which RT is part of the palliative care and for which PDT demonstrated promising results in clinical trial. We thus evaluated the combination of low-dose PDT and RT delivered in absence of nanoscintillators on various heterocellular spheroid models that recapitulate the clinical heterogeneity of PanCa. Although therapeutic effects emerged at different timepoints in each model, the RT/PDT combination uniformly achieved favorable outcomes. With RT providing stunted tumor growth while PDT drove adjuvant apoptotic and necrotic cell death, the combination produced significantly smaller and less viable PanCa spheroids. In conclusion, the beneficial RT/PDT treatment outcomes encourage the further development of nanoscinitillators for X-ray-activated PDT. Assessment of such combination treatments should encompass multiparametric and temporally-spaced assessment of treatment effects in preclinical cancer models.
PMCID:6499000
PMID: 31080554
ISSN: 1949-2553
CID: 3864782
Evaluating Susceptibility to Pancreatic Cancer: ASCO Provisional Clinical Opinion
Stoffel, Elena M; McKernin, Shannon E; Brand, Randall; Canto, Marcia; Goggins, Michael; Moravek, Cassadie; Nagarajan, Arun; Petersen, Gloria M; Simeone, Diane M; Yurgelun, Matthew; Khorana, Alok A
PURPOSE/OBJECTIVE:An ASCO provisional clinical opinion (PCO) offers timely clinical direction to ASCO's membership and other health care providers. This PCO addresses identification and management of patients and family members with possible predisposition to pancreatic adenocarcinoma. METHODS:ASCO convened an Expert Panel and conducted a systematic review of the literature published from January 1998 to June 2018. Results of the databases searched were supplemented with hand searching of the bibliographies of systematic reviews and selected seminal articles and contributions from Expert Panel members' curated files. PROVISIONAL CLINICAL OPINION/UNASSIGNED:All patients diagnosed with pancreatic adenocarcinoma should undergo assessment of risk for hereditary syndromes known to be associated with an increased risk for pancreatic adenocarcinoma. Assessment of risk should include a comprehensive review of family history of cancer. Individuals with a family history of pancreatic cancer affecting two first-degree relatives meet criteria for familial pancreatic cancer (FPC). Individuals (cancer affected or unaffected) with a family history of pancreatic cancer meeting criteria for FPC, those with three or more diagnoses of pancreatic cancer in same side of the family, and individuals meeting criteria for other genetic syndromes associated with increased risk for pancreatic cancer have an increased risk for pancreatic cancer and are candidates for genetic testing. Germline genetic testing for cancer susceptibility may be discussed with individuals diagnosed with pancreatic cancer, even if family history is unremarkable. Benefits and limitations of pancreatic cancer screening should be discussed with individuals whose family history meets criteria for FPC and/or genetic susceptibility to pancreatic cancer. Additional information is available at www.asco.org/gastrointestinal-cancer-guidelines .
PMID: 30457921
ISSN: 1527-7755
CID: 3480712
A Phase I/II Open-Label Multicenter Single-Arm Study of FABLOx (Metronomic 5-Fluorouracil Plus nab-Paclitaxel, Bevacizumab, Leucovorin, and Oxaliplatin) in Patients with Metastatic Pancreatic Cancer
Sahai, Vaibhav; Saif, M Wasif; Kalyan, Aparna; Philip, Philip A; Rocha-Lima, Caio M; Ocean, Allyson; Ondovik, Michael S; Simeone, Diane M; Banerjee, Sibabrata; Bhore, Rafia; Louis, Chrystal U; Picozzi, Vincent
Purpose: To evaluate safety and preliminary efficacy of metronomic 5-fluorouracil plus nab-paclitaxel, bevacizumab, leucovorin, and oxaliplatin (FABLOx) in patients with newly diagnosed metastatic pancreatic cancer (MPC). Methods: A total of 12 treatment-naive patients (aged 18-65 years, Eastern Cooperative Oncology Group performance status [ECOG PS] ≤1) with MPC received 5-fluorouracil 180 mg/m2 per day (days 1-14 continuous infusion); nab-paclitaxel 75 mg/m2, leucovorin 20 mg/m2, and oxaliplatin 40 mg/m2 (days 1, 8, and 15); and bevacizumab 5 mg/kg (days 1 and 15) administered intravenously in each 28-day cycle. The primary end-point was incidence of dose-limiting toxicities (DLTs) in cycle 1. Safety was further evaluated as a secondary end-point; preliminary efficacy was also examined. Results: Two DLTs (grade 3 anemia requiring transfusion and grade 3 mucositis unresponsive to treatment within 4 days of onset) were observed in one of six patients enrolled in dose cohort 1. Cohort 1 was expanded from 6 to 12 patients to further evaluate safety, per the investigators' recommendation. All patients discontinued treatment. The most common grade ≥3 adverse events were abdominal pain, fatigue, mucositis, and decreased neutrophil count. Objective response rate was 33% (four partial responses). Median progression-free survival (PFS) and overall survival (OS) were 5.6 (95% confidence interval [CI], 1.7-11.3) and 9.9 (95% CI, 4.4-13.2) months, respectively; 1-year PFS and OS rates were 12.2% (95% CI, 0.7-40.8) and 38.9% (95% CI, 12.6-65.0). Conclusion: FABLOx is feasible and tolerable in patients newly diagnosed with MPC. However, preliminary efficacy data are inconclusive for continued investigation in a phase II trial.
PMCID:6761587
PMID: 31559379
ISSN: 2475-3246
CID: 4105642
Pancreatic Microtumors: A Novel 3D Ex Vivo Testing Platform
Goodwin, Mackenzie Lee; Urs, Sumi Kanthraj; Simeone, Diane M
The tumor microenvironment plays a vital role in therapeutic resistance in pancreatic adenocarcinoma. We have created a 3D model to study the tumor microenvironment ex vivo that integrates tumor cells with tumor associated macrophages (TAMs) and cancer associated fibroblasts (CAFs). The microtumor model recreates the complex histology of a primary tumor and can be analyzed histologically or with viability assays for therapeutic testing. Microtumors demonstrate increased resistance to gemcitabine when compared to tumor cells alone in a 3D spheroid, highlighting the contribution of TAMs and CAFs when designing models for therapeutic testing.
PMID: 30378045
ISSN: 1940-6029
CID: 3400832
Adaptive platform trials: definition, design, conduct and reporting considerations The Adaptive Platform Trials Coalition [Review]
Angus, Derek C.; Alexander, Brian M.; Berry, Scott; Buxton, Meredith; Lewis, Roger; Paoloni, Melissa; Webb, Steven A. R.; Arnold, Steven; Barker, Anna; Berry, Donald A.; Bonten, Marc J. M.; Brophy, Mary; Butler, Christopher; Cloughesy, Timothy F.; Derde, Lennie P. G.; Esserman, Laura J.; Ferguson, Ryan; Fiore, Louis; Gaffey, Sarah C.; Gaziano, J. Michael; Giusti, Kathy; Goossens, Herman; Heritier, Stephane; Hyman, Bradley; Krams, Michael; Larholt, Kay; LaVange, Lisa M.; Lavori, Philip; Lo, Andrew W.; London, Alex John; Manax, Victoria; McArthur, Colin; O\Neill, Genevieve; Parmigiani, Giovanni; Perlmutter, Jane; Petzold, Elizabeth A.; Ritchie, Craig; Rowan, Kathryn M.; Seymour, Christopher W.; Shapiro, Nathan, I; Simeone, Diane M.; Smith, Bradley; Spellberg, Bradley; Stern, Ariel Dora; Trippa, Lorenzo; Trusheim, Mark; Viele, Kert; Wen, Patrick Y.; Woodcock, Janet
ISI:000488208500015
ISSN: 1474-1776
CID: 4135822