Somatic Mutational Analysis in Endoscopic Ultrasound-Guided Biopsy of Pancreatic Adenocarcinoma: Assessing Yield and Impact

INTRODUCTION

We sought to determine the yield of somatic mutational analysis from endoscopic ultrasound (EUS)-guided biopsies of pancreatic adenocarcinoma compared with that of surgical resection and to assess the impact of these results on oncologic treatment.

METHODS

We determined the yield of EUS sampling and surgical resection. We evaluated the potential impact of mutational analysis by identifying actionable mutations and its direct impact by reviewing actual treatment decisions.

RESULTS

Yield of EUS sampling was 89.5%, comparable with the 95.8% yield of surgical resection. More than a quarter in the EUS cohort carried actionable mutations, and of these, more than 1 in 6 had treatment impacted by mutational analysis.

DISCUSSION

EUS sampling is nearly always adequate for somatic testing and may have substantial potential and real impact on treatment decisions.

Dynamics of Nucleation in Solids: A Self-Consistent Phase Field Approach

We derive a phase field method for computing rigorously the nucleation rate and the incubation time from the sole knowledge of the free energy of the system in the metastable regime. Our theoretical results are assessed against experimental data relative to demixing of an iron-chromium alloy. Our work clarifies the notions of nucleation rate and incubation time extensively used in classical nucleation theory (CNT) processes in solids. Our work thus emerges as an alternative to CNT but of more general applicability, and enables us to model the nucleation process across the whole range of condition encountered in first order phase transitions, an aspect in which CNT fails.

Abstract PR012: Perioperative liver biopsy captures features of the liver pre-metastatic niche and predicts metastatic outcome after pancreatic cancer resection

Pancreatic cancer (PC) has a high propensity for liver metastasis (LM), a rapidly lethal event, often seen early after resection of the primary tumor. Mounting pre-clinical evidence implicates the establishment of microenvironmental alterations in the liver or other target organs prior to emergence of clinically evident metastases, termed “pre-metastatic niches”, which is a crucial first step in metastatic progression. To determine the translational relevance of these findings, we evaluated liver biopsies from PC patients obtained during pancreatectomy to characterize the cellular, molecular and metabolic features that define the pre-metastatic niche and that may, in turn, be used as biomarkers to stratify the metastatic risk, and as therapeutic targets to interrupt the metastatic cascade. Thus, liver biopsies from 49 patients with localized PC were analyzed by transcriptomics, metabolomics, histopathology, flow cytometry, and in selected patients by single cell RNA sequencing. Patients underwent routine surveillance in a prospective manner to determine which patients developed early (<6 months) or late (>6 months) LM, extrahepatic metastasis, or remained disease-free. Eighteen patients with non-cancerous pancreatic lesions undergoing pancreatectomy were used as controls (non-PC). Single cell transcriptomics analyses and immuno-profiling revealed that, in contrast to non-PC livers, tumor-free, pre-metastatic livers from PC patients exhibited enhanced inflammation evidenced by enrichment of neutrophils, CD11B+ cells, and CD3+ T cells, as well as expansion and activation of a CD11B+ subset of NK cells. Furthermore, immune and metabolic profiling of PC pre-metastatic livers identified features that predicted future patterns of metastasis: high Ki67 proliferation index, neutrophil extracellular trap (NET) formation, and upregulated sortilin-1 gene expression, all of which correlated with earlier LM. Conversely, widespread lobular inflammation, with abundant lobular CD3+ T cells, as well as intact creatine metabolism and steatosis associated with no recurrence, isolated extrahepatic recurrence or later LM. We combined the above variables to develop a decision tree-based prediction model, which performed best for identification of early LM (AUC 0.85). Taken together, these data demonstrate that in patients with apparently localized PC, pre-treatment liver biopsies may confirm the presence of human hepatic pre-metastatic niche and reveal features that correlate with timing and patterns of recurrence (early or late LM, extrahepatic, or no recurrence), after resection of PC. These liver profiles represent novel biomarkers that may be used to provide prognostic information and guide subsequent treatment of PC.

Citation Format: Linda Bojmar, Constantinos P. Zambirinis, Jonathan Hernandez, Jayasree Chakraborty, Samer Hanna, Diane Simeone, David Kelsen, Haiying Zhang, Irina R Matei, Per Sandström, Robert Schwartz, William R. Jarnagin, David Lyden. Perioperative liver biopsy captures features of the liver pre-metastatic niche and predicts metastatic outcome after pancreatic cancer resection [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr PR012.

491 BASECAMP-1: an observational study to identify relapsed solid tumor patients with human leukocyte antigen (HLA) loss of heterozygosity (LOH) and leukapheresis for future CAR T-cell therapy

Background

Solid tumors comprise >90% of cancers. Metastatic colorectal cancer, non-small cell lung cancer, and pancreatic cancer are among the leading causes of cancer-related mortality (5-year overall survival: 14%, 6%, and 3%, respectively).1Chimeric antigen receptor (CAR) T-cell therapy demonstrated clinical outcomes in hematologic malignancies.2 3 However, translating engineered T-cell therapies to solid tumors proves difficult due to a lack of tumor-specific targets that discriminate cancer cells from normal cells. In previous studies, the use of a carcinoembryonic antigen T-cell receptors and mesothelin CARs both resulted in dose-limiting on-target, off-tumor toxicities.4 5 TmodTM CAR T-cell therapy addresses these challenges by leveraging dual receptors to create a robust AND NOT signal integrator capable of killing tumor cells, while leaving healthy cells intact (figure 1).6 Tmod platform technology is a versatile system that may be applied to T cells and natural killer cells in autologous and allogeneic settings.HLA LOH offers a definitive tumor versus normal discriminator target for CAR T-cell therapy.6 7 The 2 receptors comprise an activator that recognizes an antigen present on the surface of normal and tumor cells and a blocker that recognizes a second surface antigen from an allele lost only in tumor cells. HLA LOH has been observed in ~13% across all solid tumors and up to 33% of pancreatic cancers.8 New technologies have shown higher HLA LOH rates; however, it is unclear whether patients with HLA LOH in their primary tumor tissues are at higher risk for recurrence. BASECAMP-1 is an observational study with key objectives: 1) To determine and identify patients with somatic HLA LOH eligible for Tmod CAR T-cell therapy, and 2) Subsequent leukapheresis and manufacturing feasibility for future Tmod CAR T-cell trials.

Methods

BASECAMP-1 (NCT04981119) patient eligibility has 2 parts (figure 2): 1) Patients will be initially screened to identify germline HLA-A*02 heterozygosity by central next-generation sequencing (NGS). If HLA-A*02 heterozygosity is confirmed, primary archival tumor tissue will be analyzed by xT-Onco NGS testing9 to determine if somatic tumor HLA-A*02 LOH is present; 2) If the tumor demonstrates HLA-A*02 LOH and the patient screens eligible, the patient will undergo leukapheresis. Patients enrolled in the study who undergo leukapheresis will be evaluated for safety 7 days post-leukapheresis and followed for relapsed status. Banked T cells will be available for subsequent autologous Tmod CAR T-cell therapy at the time of relapse.

Abstract 491 Figure 1

Illustration of the Tmod T cell engaging with tumor cells with somatic loss of HLA-A*02 and with normal cells

Abstract 491 Figure 2

Study schema. HLA, human leukocyte antigen; LOH, loss of heterozygosity; NGS, next generation sequencing

Trial Registration

NCT04981119

References

American Cancer Society. Cancer Facts & Figures 2021. Atlanta: American Cancer Society; 2021.

Neelapu S, Locke F, Bartlett N, et al. Axicabtagene ciloleucel CAR T-cell therapy in refractory large B-cell lymphoma. N Engl J Med 2017;377(26):2531–2544.

Maude S, Laetsch T, Buechner J, et al. Tisagenlecleucel in children and young adults with B-cell lymphoblastic leukemia. N Engl J Med 2018;378(5):439–448.

Parkhurst M, Yang J, Langan R, et al. T cells targeting carcinoembryonic antigen can mediate regression of metastatic colorectal cancer but induce severe transient colitis. Mol Ther 2011;19(3):620–626.

Haas AR, Tanyi JL, O’Hara MH, et al. Phase I study of lentiviral-transduced chimeric antigen receptor-modified T cells recognizing mesothelin in advanced solid cancers. Mol Ther. 2019;27(11):1919–1929.

Hamburger A, DiAndreth B, Cui J, et al. Engineered T cells directed at tumors with defined allelic loss. Mol Immunol 2020;128:298–310.

Hwang M, Mog B, Douglass J, et al. Targeting loss of heterozygosity for cancer-specific immunotherapy. Proc Natl Acad Sci U S A 2021;118(12):e2022410118.

The Cancer Genome Atlas (TCGA) Research Network. https://www.cancer.gov/tcga. Accessed June 2021.

Perera J, Mapes B, Lau D, et al. Detection of human leukocyte antigen class I loss of heterozygosity in solid tumor types by next-generation DNA sequencing. J Immunother Cancer 2019;7(suppl 1):103.

Clinical and genomic characterisation of mismatch repair deficient pancreatic adenocarcinoma

OBJECTIVE

To describe the clinical, pathological and genomic characteristics of pancreatic cancer with DNA mismatch repair deficiency (MMRD) and proficiency (MMRP).

DESIGN

We identified patients with MMRD and MMRP pancreatic cancer in a clinical cohort (N=1213, 519 with genetic testing, 53 with immunohistochemistry (IHC)) and a genomic cohort (N=288 with whole-genome sequencing (WGS)).

RESULTS

12 out of 1213 (1.0%) in the clinical cohort were MMRD by IHC or WGS. Of the 14 patients with Lynch syndrome, 3 (21.4%) had an MMRP pancreatic cancer by IHC, and 4 (28.6%) were excluded because tissue was unavailable for testing. MMRD cancers had longer overall survival after surgery (weighted HR after coarsened exact matching 0.11, 95% CI 0.02 to 0.78, p=0.001). One patient with an unresectable MMRD cancer has an ongoing partial response 3 years after starting treatment with PD-L1/CTLA-4 inhibition. This tumour showed none of the classical histopathological features of MMRD. 9 out of 288 (3.1%) tumours with WGS were MMRD. Despite markedly higher tumour mutational burden and neoantigen loads, MMRD cancers were significantly less likely to have mutations in usual pancreatic cancer driver genes like KRAS and SMAD4, but more likely to have mutations in genes that drive cancers with microsatellite instability like ACV2RA and JAK1. MMRD tumours were significantly more likely to have a basal-like transcriptional programme and elevated transcriptional markers of immunogenicity.

CONCLUSIONS

MMRD pancreatic cancers have distinct clinical, pathological and genomic profiles. Patients with MMRD pancreatic cancer should be considered for basket trials targeting enhanced immunogenicity or the unique genomic drivers in these malignancies.

Symmetry Breaking Resulting from Long-Range Interactions in Out of Equilibrium Systems: Elastic Properties of Irradiated AgCu

This work presents a consistent formulation of the phase-field approach to model the behavior of nonmiscible alloys under irradiation which includes elastic strain fields, an example of a long-range interaction. Simulations show that the spatial isotropy that is characteristic of radiation-induced patterns breaks down as a result of the elastic strain energy. The consequence of this is the emergence of superlattice structures under irradiation liable to modify macroscopic material properties. This approach is assessed against the experimental study of a AgCu alloy under irradiation: we compare our simulation results to measured solubility limits and Young moduli.

Predicting Nonequilibrium Patterns beyond Thermodynamic Concepts: Application to Radiation-Induced Microstructures

In this work, we derive an analytical model to predict the appearance of all possible radiation-induced steady states and their associated microstructures in immiscible A_{c[over ¯]}B_{1-c[over ¯]} alloys, an example of a nonequilibrium dynamical system. This model is assessed against numerical simulations and experimental results which show that different microstructures characterized by the patterning of A-rich precipitates can emerge under irradiation. We demonstrate that the steady-state microstructure is governed by irradiation conditions and also by the average initial concentration of the alloy c[over ¯]. Such a dependence offers new leverage for tailoring materials with specific microstructures overcoming limitations imposed by the equilibrium thermodynamic phase diagram.

Abstract P6-08-24: Family history of pancreatic cancer and the prevalence of pathogenic germline variants in a contemporary cohort of newly diagnosed breast cancers

Introduction: Several studies have found a relationship between familial breast cancer (BC) and pancreatic cancer (PC). Known genes associated with both BC and PC include BRCA1, BRCA2, PALB2, ATM, STK11, and possibly others. For carriers of pathogenic germline variants (PGVs) in these genes with family history of PC (FHPC), pancreas surveillance is recommended and can lead to an earlier detection of disease. Current genetics practice typically involves use of multi-gene panel (MGP) testing covering all of these genes linked to both cancers, but not all patients have had complete testing leading to likely under appreciation of PC risk in BC cohorts. With improved treatment options and survival for BC and ovarian cancer in PGV carriers, we may begin to observe an increased prevalence of PC in this group. The purpose of our study was to evaluate the clinicopathologic characteristics including genetic testing uptake and outcomes in BC patients with and without a family history of pancreatic cancer (FHPC).

Methods: We queried the Institutional Breast Cancer Database, which includes patients diagnosed with BC between January 2010 and December 2018. Variables analyzed included FHPC in a first or second-degree relative, and other clinical and tumor characteristics. Statistical analyses included Pearson’s Chi Square and logistic regression.

Results: A total of 232 BC patients (7%) had a positive FHPC, including 115 (50%) with a first-degree relative and 117 (50%) with other relatives affected. When comparing BC patients with and without any FHPC, those with FHPC were 1.93 times more likely to be of White race (p<0.001), and 1.68 times more likely to have undergone genetic testing (p<0.001). Genetic testing in those with FHPC included BRCA1/2 only for 33%, multi-gene testing for 23%, and no genetic testing in 44% PGVs were identified in 9/129 (7%) tested patients including 2 BRCA1, 6 BRCA2, and 1 PALB2. Age, previous history of BC or other cancer, surgery type, tumor stage, histology, size, grade, and ER/PR/HER2neu status were not statistically different between the patients who had FHPC versus no FHPC. The 4% rate of BC recurrence was the same in both groups.

Conclusions: Within a contemporary cohort of newly diagnosed breast cancer patients, 7% had a positive FHPC. Although these patients were more likely than those without FHPC to have genetic testing, the majority, 77%, had incomplete or no genetic testing suggesting likely under-diagnosis of PC risk. Our study underscores the importance of querying and documenting FHPC in patients with BC and the consideration of germline testing and evaluation for pancreas surveillance in these patients and their family members.

Citation Format: Annie Wang, Jessica Everett, Jennifer Chun, Elianna Kaplowitz, Diane Simeone, Freya Schnabel. Family history of pancreatic cancer and the prevalence of pathogenic germline variants in a contemporary cohort of newly diagnosed breast cancers [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-08-24.

Management of patients with increased risk for familial pancreatic cancer: updated recommendations from the International Cancer of the Pancreas Screening (CAPS) Consortium

BACKGROUND AND AIM

The International Cancer of the Pancreas Screening Consortium met in 2018 to update its consensus recommendations for the management of individuals with increased risk of pancreatic cancer based on family history or germline mutation status (high-risk individuals).

METHODS

A modified Delphi approach was employed to reach consensus among a multidisciplinary group of experts who voted on consensus statements. Consensus was considered reached if ≥75% agreed or disagreed.

RESULTS

Consensus was reached on 55 statements. The main goals of surveillance (to identify high-grade dysplastic precursor lesions and T1N0M0 pancreatic cancer) remained unchanged. Experts agreed that for those with familial risk, surveillance should start no earlier than age 50 or 10 years earlier than the youngest relative with pancreatic cancer, but were split on whether to start at age 50 or 55. Germline ATM mutation carriers with one affected first-degree relative are now considered eligible for surveillance. Experts agreed that preferred surveillance tests are endoscopic ultrasound and MRI/magnetic retrograde cholangiopancreatography, but no consensus was reached on how to alternate these modalities. Annual surveillance is recommended in the absence of concerning lesions. Main areas of disagreement included if and how surveillance should be performed for hereditary pancreatitis, and the management of indeterminate lesions.

CONCLUSIONS

Pancreatic surveillance is recommended for selected high-risk individuals to detect early pancreatic cancer and its high-grade precursors, but should be performed in a research setting by multidisciplinary teams in centres with appropriate expertise. Until more evidence supporting these recommendations is available, the benefits, risks and costs of surveillance of pancreatic surveillance need additional evaluation.

Abstract B15: Therapeutic potential of targeting amino acid metabolism in pancreatic cancer

Background: A wide range of cancers, including pancreatic cancer, display altered expression of amino acid transporter LAT-1. LAT-1 overexpression has been shown to be an important prognostic factor and predicts chemo resistance in pancreatic cancer (Kaira K, 2012; Altan B, 2018). Radiolabeled amino acids for PET imaging, including 3-18F-l-α-methyl-tyrosine ([18F] FAMT), have successfully leveraged cancer’s aberrant LAT1 expression and amino acid uptake for decades. SM-88 is a denatured D/L racemic form of α-methyl-tyrosine designed for selective uptake and disruption of protein synthesis in cancer cells, as well as disruption of catecholamine production via inhibition of tyrosine hydroxylase. Catecholamines have been reported to potentially have a role in driving pancreatic cancer progression and changes in the tumor immune status (Renz B, Cancer Cell 2018; Calvani M, Oncotarget 2014). Initial clinical and preclinical results with SM-88 indicate that this agent could pose a novel approach in the treatment of pancreatic cancer.

Methods and Results: Initial xenograft models of human gastrointestinal cancers using monotherapy SM-88 showed a >50% decrease in tumor growth at three weeks of treatment (p<0.05). Ongoing preclinical experiments are testing the full pharmacodynamic effects of SM-88 on pancreatic cancer cells, as well as potential effects on the tumor microenvironment due to catecholamine interruption. In results from the ongoing phase 2 trial of SM-88 in heavily pretreated metastatic pancreatic cancer patients, SM-88 has shown monotherapy antitumor activity based on RECIST 1.1 criteria. Additionally, 16/24 patients demonstrated a reduction in circulating tumor cells, with the median nadir decline of 63%. LAT1 has been reported to be important in EMT transition and mesenchymal cell survival (Holldorsson S, Cancer letters 2017); examination of the impact of SM-88 on this important emerging biomarker is ongoing.

Conclusion: Altered amino acid (LAT1) metabolism has been shown to be a negative prognosticator in pancreatic cancer outcomes and progression. Targeting LAT1 and amino acid pathways has been identified as a therapeutic approach in multiple cancers (Fuchs BC, Semin Ca Biol 2005). Initial and ongoing studies of SM-88 may clarify the potential utility of this approach in the treatment of pancreatic cancer.

Citation Format: Martin Fernandez-Zapico, Dae Won Kim, Philip Philip, Alexander Vandell, Jonathan Eckard, Ron Korn, Giuseppe Del Priore, Diane Simeone. Therapeutic potential of targeting amino acid metabolism in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2019 Sept 6-9; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2019;79(24 Suppl):Abstract nr B15.

Impacting Pancreatic Cancer Therapy in Heterotypic in Vitro Organoids and in Vivo Tumors with Specificity-Tuned, NIR-Activable Photoimmunonanoconjugates: Towards Conquering Desmoplasia?

Despite untiring efforts to develop therapies for pancreatic ductal adenocarcinoma (PDAC), survival statistics remain dismal, necessitating distinct approaches. Photodynamic priming (PDP), which improves drug delivery and combination regimens, as well as tumor photodestruction are key attributes of photodynamic therapy (PDT), making it a distinctive clinical option for PDAC. Localized, high-payload nanomedicine-assisted delivery of photosensitizers (PSs), with molecular specificity and controlled photoactivation, thus becomes critical in order to reduce collateral toxicity during more expansive photodynamic activation procedures with curative intent. As such, targeted photoactivable lipid-based nanomedicines are an ideal candidate but have failed to provide greater than two-fold cancer cell selectivity, if at all, due to their extensive multivariant physical, optical, and chemical complexity. Here, we report (1) a systematic multivariant tuning approach to engineer (Cet, anti-EGFR mAb) photoimmunonanoconjugates (PINs), and (2) stroma-rich heterotypic PDAC in vitro and in vivo models incorporating patient-derived pancreatic cancer-associated fibroblasts (PCAFs) that recapitulate the desmoplasia observed in the clinic. These offer a comprehensive, disease-specific framework for the development of Cet-PINs. Specificity-tuning of the PINs, in terms of PS lipid anchoring, electrostatic modulation, Cet orientation, and Cet surface densities, achieved ∼16-fold binding specificities and rapid penetration of the heterotypic organoids within 1 h, thereby providing a ∼16-fold enhancement in molecular targeted NIR photodestruction. As a demonstration of their inherent amenability for multifunctionality, encapsulation of high payloads of gemcitabine hydrochloride, 5-fluorouracil, and oxaliplatin within the Cet-PINs further improved their antitumor efficacy in the heterotypic organoids. In heterotypic desmoplastic tumors, the Cet-PINs efficiently penetrated up to 470 μm away from blood vessels, and photodynamic activation resulted in substantial tumor necrosis, which was not elicited in T47D tumors (low EGFR) or when using untargeted constructs in both tumor types. Photodynamic activation of the Cet-PINs in the heterotypic desmoplastic tumors resulted in collagen photomodulation, with a 1.5-fold reduction in collagen density, suggesting that PDP may also hold potential for conquering desmoplasia. The in vivo safety profile of photodynamic activation of the Cet-PINs was also substantially improved, as compared to the untargeted constructs. While treatment using the Cet-PINs did not cause any detriment to the mice's health or to healthy proximal tissue, photodynamic activation of untargeted constructs induced severe acute cachexia and weight loss in all treated mice, with substantial peripheral skin necrosis, muscle necrosis, and bowel perforation. This study is the first report demonstrating the true value of molecular targeting for NIR-activable PINs. These constructs integrate high payload delivery, efficient photodestruction, molecular precision, and collagen photomodulation in desmoplastic PDAC tumors in a single treatment using a single construct. Such combined PIN platforms and heterocellular models open up an array of further multiplexed combination therapies to synergistically control desmoplastic tumor progression and extend PDAC patient survival.

A model of defect cluster creation in fragmented cascades in metals based on morphological analysis

The impacts of ions and neutrons in metals cause cascades of atomic collisions that expand and shrink, leaving microstructure defect debris, i.e. interstitial or vacancy clusters or loops of different sizes. In De Backer et al (2016 Europhys. Lett. 115 26001), we described a method to detect the first morphological transition, i.e. the cascade fragmentation in subcascades, and a model of primary damage combining the binary collision approximation and molecular dynamics (MD). In this paper including W, Fe, Be, Zr and 20 other metals, we demonstrate that the fragmentation energy increases with the atomic number and decreases with the atomic density following a unique power law. Above the fragmentation energy, the cascade morphology can be characterized by the cross pair correlation functions of the multitype point pattern formed by the subcascades. We derive the numbers of pairs of subcascades and observed that they follow broken power laws. The energy where the power law breaks indicates the second morphological transition when cascades are formed by branches decorated by chaplets of small subcascades. The subcascade interaction is introduced in our model of primary damage by adding pairwise terms. Using statistics obtained on hundreds of MD cascades in Fe, we demonstrate that the interaction of subcascades increases the proportion of large clusters in the damage created by high energy cascades. Finally, we predict the primary damage of 500 keV Fe ion in Fe and obtain cluster size distributions when large statistics of MD cascades are not feasible.

Optical properties of Ar ions irradiated nanocrystalline ZrC and ZrN thin films

Thin nanocrystalline ZrC and ZrN films (<400 nm), grown on (100) Si substrates at a substrate temperature of 500 °C by the pulsed laser deposition (PLD) technique, were irradiated by 800 keV Ar ion irradiation with fluences from 1 × 10¹⁴ at/cm² up to 2 × 10¹⁵ at/cm². Optical reflectance data, acquired from as-deposited and irradiated films, in the range of 500 - 50000 cm^-1 (0.06 - 6 eV), was used to assess the effect of irradiation on the optical and electronic properties. Both in ZrC and ZrN films we observed that irradiation affects the optical properties of the films mostly at low frequencies, which is dominated by the free carriers response. In both materials, we found a significant reduction in the free carriers scattering rate, i.e. possible increase in mobility, at higher irradiation flux. This is consistent with our previous findings that irradiation affects the crystallite size and the micro-strain, but it does not induce major structural changes.

Abstract A10: Biomarker independant microfluidic Labyrinth for the high throughput enrichment and characterization of circulating tumor cells in pancreatic cancer

Introduction and Objective: Pancreatic cancer is a devastating disease with a 5-year survival rate of less than 6%. By the time of diagnosis, less than 15% of patients have surgically resectable tumors, which is one reason why it has the highest mortality rate among all cancer types. Emerging evidence has pointed the importance of circulating tumor cells (CTCs) in the spread of cancers and metastasis. CTCs are believed to be the most promising cancer biomarkers available in blood. Recent reports also show that these cells could be a good surrogate biomarker for not only prognosis, but also for cancer detection and development of personalized treatment. We have developed an inertial microfluidic-based separation technique for high throughput and label-free isolation of CTCs.

Methods: To investigate the isolation efficiency of our technology before running cancer patients’ samples, PANC-1 cells labeled with cell tracker dye were spiked into 1 mL of whole blood. Using this optimized platform we isolate CTCs from pancreatic cancer patients, followed by downstream analysis . CTCs are characterized using immunocytochemistry for heterogeneity studies among CTC population.

Results: Our microfluidic device consists of a size based separation platform in which CTCs are separated from other blood components. This high throughput label free separation device was designed and developed by our lab. After more than 20 generations of device revision, an optimized flow rate of 2.5 ml/min for PANC-1 pancreatic cancer cell line has yielded a 95% recovery of these cells from whole blood, with cancer cells traveling to the second outlet and 80% of the White Blood Cells (WBC) to the first outlet. We have successfully isolated CTCs from over 100 pancreatic cancer patients. Among several patients we were able to characterize different subpopulations using the epithelial marker CK-19 and EpCAM, and the EMT-like marker ZEB1.

Conclusion: The implementation of our engineering technology to the study of pancreatic cancer can present novel ways to confront major hurdles in cancer research, such as early detection and the lack of effective therapeutics. The isolation and expansion of CTCs, the heterogeneous population of cells that promote metastasis, can provide meaningful information to elucidate the process of pancreatic tumorigenesis to preempt its fatal result.

Citation Format: Lianette Rivera-Baez, Eric Lin, Meghna Waghray, Shamileh Fouladdel, Ebrahim Azizi, Max Wicha, Vaibhav Sahai, Diane Simeone, Sunitha Nagrath.{Authors}. Biomarker independant microfluidic Labyrinth for the high throughput enrichment and characterization of circulating tumor cells in pancreatic cancer. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2016 May 12-15; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(24 Suppl):Abstract nr A10.

Patterning in systems driven by nonlocal external forces

This work focuses on systems displaying domain patterns resulting from competing external and internal dynamics. To this end, we introduce a Lyapunov functional capable of describing the steady states of systems subject to external forces, by adding nonlocal terms to the Landau Ginzburg free energy of the system. Thereby, we extend the existing methodology treating long-range order interactions, to the case of external nonlocal forces. By studying the quadratic term of this Lyapunov functional, we compute the phase diagram in the temperature versus external field and we determine all possible modulated phases (domain patterns) as a function of the external forces and the temperature. Finally, we investigate patterning in chemical reactive mixtures and binary mixtures under irradiation, and we show that the last case opens the path toward micro-structural engineering of materials.

Structural Changes in the Local Environment of Uranium Atoms in the Three Phases of U4O9

The crystal structure of U4O9 remains an enigma because of its differences with U(4+) and U(5+) coordination polyhedral mixtures, as shown in the XANES experimental results. To better understand this crystal structure, its diffraction pattern was measured at seven different temperatures using neutron diffraction before being independently refined by Rietveld's method and pair distribution function analysis. The O cuboctahedron-a structural element consisting of 13 oxygen atoms-is a specific feature of the U4O9 crystal structure. The volume of the cuboctahedron decreases when the temperature increases, whereas the overall volume of the crystal cell increases. This feature can be correlated with the two U4O9 phase transitions that induce sharp changes in the cuboctahedron geometry, suggesting that this structural element has internal dynamics. In particular, these structural modifications in the γ phase suggest that the high-temperature phase can be described as a mixture of U(4+) and U(5+) coordination polyhedra, the latter having U-O distances shorter than 2.2 Å, that are absent in the former. These changes in uranium polyhedra as a function of temperature are tentatively interpreted using steric arguments. They also raise the question of charge localization on the different U ion sites in the low-temperature phases of U4O9.

Abstract 3018: Cotargeting MEK and CDK4/6 to treat pancreatic adenocarcinoma

Hyperactivation of KRAS and inactivation of CDKN2A [p16] play a prominent role in tumor initiation and progression in a broad spectrum of human cancers. In pancreatic adenocarcinoma, KRAS mutation occurs in 90-95% of cases and is often coupled with inactivation of CDKN2A (&gt;90% incidence), typically by homozygous deletion. Based on the high incidence of these genetic events, the present study addresses the hypothesis that dual targeting of MEK and CDK4/6 represents a viable therapeutic strategy for the treatment of pancreatic adenocarcinoma. A panel of primary and high passage xenograft models was screened for in vitro synergy to the antiproliferative effects of the MEK inhibitor trametinib and the CDK4/6 inhibitor palbociclib. Two models that emerged as highly sensitive to this combination treatment strategy, L3.6pl and UM59, both exhibited G1 cell cycle arrest that was significantly more pronounced in response to the combination compared to either single agent. In vivo studies were subsequently carried out to evaluate the efficacy of this combination in tumor-bearing mice. Mice implanted subcutaneously with L3.6pl or UM59 cells were treated daily by oral gavage for ten days with trametinib (3 mg/kg), palbociclib (100 mg/kg), or the combination of these two agents at these doses. Consistent with in vitro synergy observations, both models proved to be exceptional responders in vivo to this combination treatment strategy, showing a robust response to the combination not seen with either single agent. These results suggest that the combined inhibition of MEK and CDK4/6 may offer a valuable therapeutic strategy for the treatment of pancreatic adenocarcinoma. Studies are ongoing to identify molecular determinants of response in pancreatic tumors that are highly sensitive to this combination approach to guide future patient enrichment strategies.

Citation Format: Joel D. Maust, Diane Simeone, Judith Sebolt-Leopold. Cotargeting MEK and CDK4/6 to treat pancreatic adenocarcinoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3018.

Abstract 1572: Sensitive and robust targeted sequencing of pancreatic precancer and tumors using microfluidic single-molecule enrichment

Pancreatic ductal adenocarcinoma (PDAC) arises from two precursor lesions, pancreatic intraepithelial neoplasias and pancreatic cysts, such as intraductal papillary mucinous neoplasias (IPMNs). Since cyst lesions are readily detected on cross sectional imaging, early diagnosis of IPMN-associated PDAC and intervention may be feasible. However, clinical guidelines dictating which IPMNs are high-risk and require surgical resection are suboptimal. Recently, the genomic signature of IPMN-associated carcinomas has been described opening the possibility for targeted genomic analysis. Previous groups have sought to achieve this using conventional methods. However, since IPMN tissue and cyst fluid are limited in quantity and contain inhibitors of PCR, we developed a novel microfluidics-based approach to achieve sensitive and specific targeted amplification and Illumina library construction.

We have optimized a novel method to enrich targeted genomic regions for next generation sequencing (NGS) platforms featuring microfluidic partitioning of the sample into uniform picoliter volume droplets containing single molecules of target DNA. All droplets contain all of the primers and PCR reagents, ensuring that every target molecule from the sample is amplified, and after endpoint PCR results in a highly uniform yield that facilitates efficient use of the NGS platform. In addition, the primers contain ‘Illumina tails’ that enable easy sample indexing and loading directly onto a MiSeq without additional library preparation.

Here we detail the successful customization and use of the ThunderBolts Cancer Panel, which targets 230 commonly mutated regions in 50 cancer associated genes, with additional primers for commonly mutated genes in PDAC. Addition of the 37 PDAC-relevant primer pairs to the commercially available core panel was very straightforward and resulted in sequencing metrics similar to those of the core panel alone (100% coverage at 100x depth, mean read depth of 2500). Cyst fluid from 30 patients with IPMN resected under Sendai criteria were analyzed. We describe the mutational signature of cyst fluid and relate the presence and quantity of mutations in KRAS, GNAS and PIK3CA to the presence of invasive carcinoma and high grade dysplasia on pathology. Finally, unbiased and high resolution sequencing was obtained using this protocol with as little as 8ng of input DNA.

Using picodroplet PCR technology we were able to achieve unprecedented sequencing performance on ultra-low sample inputs. Given the ease of use and customization of the panel, the same platform may be readily adapted to other applications in which samples are limited or are difficult to amplify. Future studies will utilize this platform for an expanded analysis of pancreatic cyst fluid with additional primers.

Citation Format: Angelina I. Londoño-Joshi, Erica Pratt, Robert W. Cowan, Michael L. Samuels, Steve Kotsopoulos, Jeff Olson, Francis Long, Michelle A. Anderson, Diane Simeone, Andrew D. Rhim. Sensitive and robust targeted sequencing of pancreatic precancer and tumors using microfluidic single-molecule enrichment. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1572. doi:10.1158/1538-7445.AM2015-1572

Abstract LB-061: Bmi1 is required for the initiation of pancreatic cancer through an Ink4a-independent mechanism

Pancreatic ductal adenocarcinoma (PDAC) is the fourth leading cause of cancer related death in the United States. Many characteristic mutations in PDAC are known, but this information has so far failed to produce the development of effective treatments, highlighting the need for deeper understanding of the processes that drive tumorigenesis.

B-cell specific Moloney murine leukemia virus insertion site 1 (Bmi1), a Polycomb repressive group protein, is upregulated in PDAC and associated with poor prognosis. Our lab has shown that despite an oncogenic K-ras mutation, mice with pancreas specific loss of Bmi1 do not develop precancerous lesions, termed PanINs (Pancreatic Intraepithelial Neoplasia). This lack of PanIN development was also seen in the presence of pancreatitis, which is usually known to synergize with oncogenic K-ras to speed PanIN development. In other cancer types, Bmi1's effect on tumorigenesis was mechanistically linked to its regulation of the Ink4a/ARF genetic locus. However, we found that in PDAC, PanIN initiation was independent of Bmi1 control this locus. Further, impairment in the regulation of ROS generation was seen in vitro in pancreatic cancer cell lines lacking Bmi1. Regulating ROS generation is a vital step in the neoplastic process and has been shown in other systems to be controlled by Bmi1.

Overall, in this work we have shown that expression of the Polycomb group protein Bmi1 is necessary for the initiation of pancreatic precancerous lesions, and that the mechanism of Bmi1 requirement is independent of its repression of the Ink4a/ARF genetic locus. Given the recent pre-clinical development of a Bmi1 inhibitor, this work could provide rationale for future treatment of pancreatic cancer, a truly devastating disease.

Citation Format: Heather Schofield, Filip Bednar, Meredith Collins, Wei Yan, Yaqing Zhang, Nikhil Shyam, Jaime Eberle, Kenneth Olive, Nabeel Bardeesy, Daisuke Nakada, Diane Simeone, Sean Morrison, Marina Pasca di Magliano. Bmi1 is required for the initiation of pancreatic cancer through an Ink4a-independent mechanism. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-061. doi:10.1158/1538-7445.AM2015-LB-061

Abstract 1748: Usp9x as a novel therapeutic target in human pancreatic cancer

Usp9x regulates tumor cell survival and responsiveness to targeted-, chemo- and radio-therapy in a broad number of tumors through effects on multiple proteins.

The role of Usp9x in human pancreatic cancer is largely unknown, although a recent study demonstrated that Usp9x co-operated in promoting KrasG12D tumorigenesis in mice. To examine Usp9x tumorigenicity and therapeutic potential of Usp9x inhibition in human pancreatic cancer vs. mouse pancreatic tumor models we developed 3D cultures of cell lines established from constitutive (8041) and doxycycline-inducible (4668) KrasG12D/Tp53R172H mouse pancreatic tumors, established human cell lines (BxPC3, PANC1 and MIAPACA2) and spontaneously immortalized human pancreatic patient tumor derived cell lines (UM2, UM6, UM16 and UM76). The effect of Usp9x knockdown (KD), overexpression (OE) or Usp9x activity inhibition by our small molecule deubiquitinase inhibitor EOAI3402143 (G9) were assessed by growth in 2D and 3D culture and anti-tumor efficacy studies in mouse (8041) and human (MIAPACA2) xenograft models. Usp9x KD in constitutive KrasG12D/Tp53R172H 8041 cells led to a 3-fold increase in the number of colonies formed in 3D and Usp9x KD sustained 3D colony growth even after withdrawal of mutant Kras support in KrasG12D/Tp53R172H inducible 4668 cells. Usp9x-OE in 8041 cells decreased 3D colony growth by 2.5-fold. These results contrast with outcomes in human pancreatic tumors where Usp9x KD induced either rapid apoptosis (in MIAPACA2) or reduced 3D colony formation by &gt;50% (in PANC1). Usp9x-OE in PANC1 cells enhanced 3D colony growth (2-fold) and increased invasion activity in Boyden chambers (3.5-fold). Mechanistically, we found differential effects of Usp9x on mutant Kras protein expression levels in mouse vs human cells. In vivo G9 treatment (15 mg/kg, every other day) of mouse 8041 xenografts showed a statistically insignificant trend towards tumor growth inhibition but effectively inhibited MIAPACA2 tumor growth in mice. Usp9x KD in human pancreatic patient tumor cell lines inhibited 3D colony growth by &gt;75% and this activity was phenocopied by G9 with nM efficacy. We conclude that Usp9x acts as a tumor promoter in established human pancreatic cancer and a tumor suppressor in murine cells from genetically engineered pancreatic tumors, possibly through differential regulation of mutant Kras. Overall, these results suggest that Usp9x may be a novel therapeutic target in pancreatic cancer.

Note: This abstract was not presented at the meeting.

Citation Format: Anupama Pal, Marina Pasca Di Magliano, Diane Simeone, Luke Peterson, Harish Potu, Moshe Talpaz, Nicholas Donato. Usp9x as a novel therapeutic target in human pancreatic cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1748. doi:10.1158/1538-7445.AM2015-1748

Abstract 1594: Application of label-free microfluidic technologies for the enrichment, expansion and characterization of circulating tumor cells in pancreatic cancer

Introduction and Objective: Pancreatic cancer is a devastating disease with a 5-year survival rate of less than 6%. By the time of diagnosis, less than 15% of patients have surgically resectable tumors, which is one reason why it has the highest mortality rate among all cancer types. Emerging evidence has pointed the importance of circulating tumor cells (CTCs) in the spread of cancers and metastasis. CTCs are believed to be the most promising cancer biomarkers available in blood. Recent reports also show that these cells could be a good surrogate biomarker for not only prognosis, but also for cancer detection and development of personalized treatment. We have developed an inertial microfluidic-based separation technique for high throughput and label-free isolation of CTCs.

Methods: To investigate the isolation efficiency of our technology before running cancer patients’ samples, PANC-1 cells labeled with cell tracker dye were spiked into 1 mL of whole blood. Using this optimized platform we isolate CTCs from pancreatic cancer patients, followed by downstream analysis. CTCs are characterized using immunocytochemistry for heterogeneity studies among CTC population.

Results: Our microfluidic device consists of a size based separation platform in which CTCs are separated from other blood components. This high throughput label free separation device was designed and developed by our lab. After more than 20 generations of device revision, an optimized flow rate of 2.5 ml/min for PANC-1 pancreatic cancer cell line has yielded a 95% recovery of these cells from whole blood, with cancer cells traveling to the second outlet and 80% of the White Blood Cells (WBC) to the first outlet. We have successfully isolated CTCs from over 100 pancreatic cancer patients. Among several patients we were able to characterize different subpopulations using the epithelial marker CK-19 and EpCAM, and the EMT-like marker ZEB1.

Conclusion: The implementation of our engineering technology to the study of pancreatic cancer can present novel ways to confront major hurdles in cancer research, such as early detection and the lack of effective therapeutics. The isolation and expansion of CTCs, the heterogeneous population of cells that promote metastasis, can provide meaningful information to elucidate the process of pancreatic tumorigenesis to preempt its fatal result.

Citation Format: Lianette Rivera-Baez, Eric Lin, Hyeun Joong Yoon, Meghna Waghray, Shamileh Fouladdel, Ebrahim Azizi, Max Wicha, Diane Simeone, Sunitha Nagrath. Application of label-free microfluidic technologies for the enrichment, expansion and characterization of circulating tumor cells in pancreatic cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1594. doi:10.1158/1538-7445.AM2015-1594

Abstract B24: ATDC (Trim29) drives invasive bladder cancer formation

Bladder cancer is a common and deadly malignancy, but incomplete understanding of the molecular events driving tumor development and metastasis has limited development of effective treatments. Ataxia-Telangiectasia Group D Complementing (ATDC; also named TRIM29) is highly expressed in many cancer types, including bladder and pancreas. To determine the role of ATDC in tumorigenesis, we developed a novel transgenic mouse model in which ATDC was overexpressed in multiple tissue types. The dominant phenotype in these mice was the development of both papillary and invasive bladder carcinoma beginning at approximately 8 months of age. In this model, invasive bladder tumors were histologically indistinguishable and shared a similar gene expression signature with human invasive bladder cancers. We also found that ATDC was highly expressed in ~70% human bladder cancers where it marked invasive tumors and correlated with worse survival after chemotherapy (p = 0.002). Furthermore, ATDC knockdown decreased proliferation, invasion and tumor growth in multiple human bladder cancer cell lines and in an in vivo orthotopic bladder tumor model. ATDC-induced bladder tumorigenesis was mediated by upregulation of DNA methyltransferase 3A (DNMT3A), which drove PTEN promoter methylation and silencing, events which promoted invasion and proliferation in both transgenic mice and human bladder cancers. These findings establish ATDC as a novel driver and therapeutic target in bladder cancer. In addition, the ATDC transgenic mouse model should serve as an important and unique new model to study bladder cancer development, progression and therapeutic responses.

Citation Format: Phillip Palmbos, Lidong Wang, Huibin Yang, Jake LeFlein, John E. Wilkinson, Chandan Kumar-Sinha, L. Priya Kunju, Stephanie Daignault, Xue-Ru Wu, Yair Lotan, Monica Liebert, Mats Ljungman, Diane Simeone. ATDC (Trim29) drives invasive bladder cancer formation. [abstract]. In: Proceedings of the AACR Special Conference: The Translational Impact of Model Organisms in Cancer; Nov 5-8, 2013; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2014;12(11 Suppl):Abstract nr B24.