Mapping three-dimensional intratumor proteomic heterogeneity in uterine serous carcinoma by multiregion microsampling.

BACKGROUND: Although uterine serous carcinoma (USC) represents a small proportion of all uterine cancer cases, patients with this aggressive subtype typically have high rates of chemotherapy resistance and disease recurrence that collectively result in a disproportionately high death rate. The goal of this study was to provide a deeper view of the tumor microenvironment of this poorly characterized uterine cancer variant through multi-region microsampling and quantitative proteomics. METHODS: Tumor epithelium, tumor-involved stroma, and whole "bulk" tissue were harvested by laser microdissection (LMD) from spatially resolved levels from nine USC patient tumor specimens and underwent proteomic analysis by mass spectrometry and reverse phase protein arrays, as well as transcriptomic analysis by RNA-sequencing for one patient's tumor. RESULTS: LMD enriched cell subpopulations demonstrated varying degrees of relatedness, indicating substantial intratumor heterogeneity emphasizing the necessity for enrichment of cellular subpopulations prior to molecular analysis. Known prognostic biomarkers were quantified with stable levels in both LMD enriched tumor and stroma, which were shown to be highly variable in bulk tissue. These USC data were further used in a comparative analysis with a data generated from another serous gynecologic malignancy, high grade serous ovarian carcinoma, and have been added to our publicly available data analysis tool, the Heterogeneity Analysis Portal ( https://lmdomics.org/ ). CONCLUSIONS: Here we identified extensive three-dimensional heterogeneity within the USC tumor microenvironment, with disease-relevant biomarkers present in both the tumor and the stroma. These data underscore the critical need for upfront enrichment of cellular subpopulations from tissue specimens for spatial proteogenomic analysis.

Improving Risk Assessment for Metastatic Disease in Endometrioid Endometrial Cancer Patients Using Molecular and Clinical Features: An NRG Oncology/Gynecologic Oncology Group Study.

Objectives: A risk assessment model for metastasis in endometrioid endometrial cancer (EEC) was developed using molecular and clinical features, and prognostic association was examined. Methods: Patients had stage I, IIIC, or IV EEC with tumor-derived RNA-sequencing or microarray-based data. Metastasis-associated transcripts and platform-centric diagnostic algorithms were selected and evaluated using regression modeling and receiver operating characteristic curves. Results: Seven metastasis-associated transcripts were selected from analysis in the training cohorts using 10-fold cross validation and incorporated into an MS7 classifier using platform-specific coefficients. The predictive accuracy of the MS7 classifier in Training-1 was superior to that of other clinical and molecular features, with an area under the curve (95% confidence interval) of 0.89 (0.80-0.98) for MS7 compared with 0.69 (0.59-0.80) and 0.71 (0.58-0.83) for the top evaluated clinical and molecular features, respectively. The performance of MS7 was independently validated in 245 patients using RNA sequencing and in 81 patients using microarray-based data. MS7 + MI (myometrial invasion) was preferrable to individual features and exhibited 100% sensitivity and negative predictive value. The MS7 classifier was associated with lower progression-free and overall survival (p ≤ 0.003). Conclusion: A risk assessment classifier for metastasis and prognosis in EEC patients with primary tumor derived MS7 + MI is available for further development and optimization as a companion clinical support tool.

Extensive three-dimensional intratumor proteomic heterogeneity revealed by multiregion sampling in high-grade serous ovarian tumor specimens.

Enriched tumor epithelium, tumor-associated stroma, and whole tissue were collected by laser microdissection from thin sections across spatially separated levels of ten high-grade serous ovarian carcinomas (HGSOCs) and analyzed by mass spectrometry, reverse phase protein arrays, and RNA sequencing. Unsupervised analyses of protein abundance data revealed independent clustering of an enriched stroma and enriched tumor epithelium, with whole tumor tissue clustering driven by overall tumor "purity." Comparing these data to previously defined prognostic HGSOC molecular subtypes revealed protein and transcript expression from tumor epithelium correlated with the differentiated subtype, whereas stromal proteins (and transcripts) correlated with the mesenchymal subtype. Protein and transcript abundance in the tumor epithelium and stroma exhibited decreased correlation in samples collected just hundreds of microns apart. These data reveal substantial tumor microenvironment protein heterogeneity that directly bears on prognostic signatures, biomarker discovery, and cancer pathophysiology and underscore the need to enrich cellular subpopulations for expression profiling.

An Integrated Scenario Ensemble-Based Framework for Hurricane Evacuation Modeling: Part 1-Decision Support System.

This article introduces a new integrated scenario-based evacuation (ISE) framework to support hurricane evacuation decision making. It explicitly captures the dynamics, uncertainty, and human-natural system interactions that are fundamental to the challenge of hurricane evacuation, but have not been fully captured in previous formal evacuation models. The hazard is represented with an ensemble of probabilistic scenarios, population behavior with a dynamic decision model, and traffic with a dynamic user equilibrium model. The components are integrated in a multistage stochastic programming model that minimizes risk and travel times to provide a tree of evacuation order recommendations and an evaluation of the risk and travel time performance for that solution. The ISE framework recommendations offer an advance in the state of the art because they: (1) are based on an integrated hazard assessment (designed to ultimately include inland flooding), (2) explicitly balance the sometimes competing objectives of minimizing risk and minimizing travel time, (3) offer a well-hedged solution that is robust under the range of ways the hurricane might evolve, and (4) leverage the substantial value of increasing information (or decreasing degree of uncertainty) over the course of a hurricane event. A case study for Hurricane Isabel (2003) in eastern North Carolina is presented to demonstrate how the framework is applied, the type of results it can provide, and how it compares to available methods of a single scenario deterministic analysis and a two-stage stochastic program.

An Integrated Scenario Ensemble-Based Framework for Hurricane Evacuation Modeling: Part 2-Hazard Modeling.

Hurricane track and intensity can change rapidly in unexpected ways, thus making predictions of hurricanes and related hazards uncertain. This inherent uncertainty often translates into suboptimal decision-making outcomes, such as unnecessary evacuation. Representing this uncertainty is thus critical in evacuation planning and related activities. We describe a physics-based hazard modeling approach that (1) dynamically accounts for the physical interactions among hazard components and (2) captures hurricane evolution uncertainty using an ensemble method. This loosely coupled model system provides a framework for probabilistic water inundation and wind speed levels for a new, risk-based approach to evacuation modeling, described in a companion article in this issue. It combines the Weather Research and Forecasting (WRF) meteorological model, the Coupled Routing and Excess STorage (CREST) hydrologic model, and the ADvanced CIRCulation (ADCIRC) storm surge, tide, and wind-wave model to compute inundation levels and wind speeds for an ensemble of hurricane predictions. Perturbations to WRF's initial and boundary conditions and different model physics/parameterizations generate an ensemble of storm solutions, which are then used to drive the coupled hydrologic + hydrodynamic models. Hurricane Isabel (2003) is used as a case study to illustrate the ensemble-based approach. The inundation, river runoff, and wind hazard results are strongly dependent on the accuracy of the mesoscale meteorological simulations, which improves with decreasing lead time to hurricane landfall. The ensemble envelope brackets the observed behavior while providing "best-case" and "worst-case" scenarios for the subsequent risk-based evacuation model.

Low frequency water level correction in storm surge models using data assimilation.

Research performed to-date on data assimilation (DA) in storm surge modeling has found it to have limited value for predicting rapid surge responses (e.g., those accompanying tropical cyclones). In this paper, we submit that a well-resolved, barotropic hydrodynamic model is typically able to capture the surge event itself, leaving slower processes that determine the large scale, background water level as primary sources of water level error. These "unresolved drivers" reflect physical processes not included in the model's governing equations or forcing terms, such as far field atmospheric forcing, baroclinic processes, major ocean currents, steric variations, or precipitation. We have developed a novel, efficient, optimal interpolation-based DA scheme, using observations from coastal water level gages, that dynamically corrects for the presence of unresolved drivers. The methodology is applied for Hurricane Matthew (2016) and results demonstrate it is highly effective at removing water level residuals, roughly halving overall surge errors for that storm. The method is computationally efficient, well-suited for either hindcast or forecast applications and extensible to more advanced techniques and datasets.

Race-specific molecular alterations correlate with differential outcomes for black and white endometrioid endometrial cancer patients.

BACKGROUND: The objective of this study was to identify molecular alterations associated with disease outcomes for white and black patients with endometrioid endometrial cancer (EEC). METHODS: EEC samples from black (n = 17) and white patients (n = 13) were analyzed by proteomics (liquid chromatography-tandem mass spectrometry) and transcriptomics (RNA-seq). Coordinate alterations were validated with RNA-seq data from black (n = 49) and white patients (n = 216). Concordantly altered candidates were further tested for associations with race-specific progression-free survival (PFS) in black (n = 64) or white patients (n = 267) via univariate and multivariate Cox regression modeling and log-rank testing. RESULTS: Discovery analyses revealed significantly altered candidate proteins and transcripts between black and white patients, suggesting modulation of tumor cell viability in black patients and cell death signaling in black and white patients. Eighty-nine candidates were validated as altered between these patient cohorts, and a subset significantly correlated with differential PFS. White-specific PFS candidates included serpin family A member 4 (SERPINA4; hazard ratio [HR], 0.89; Wald P value = .02), integrin subunit α3 (ITGA3; HR, 0.76; P = .03), and Bet1 Golgi vesicular membrane trafficking protein like (BET1L; HR, 0.48; P = .04). Black-specific PFS candidates included family with sequence similarity 228 member B (FAM228B; HR, 0.13; P = .001) and HEAT repeat containing 6 (HEATR6; HR, 4.94; P = .047). Several candidates were also associated with overall survival (SERPINA4 and ITGA3) as well as PFS independent of disease stage, grade and myometrial invasion (SERPINA4, BET1L and FAM228B). CONCLUSIONS: This study has identified and validated molecular alterations in tumors from black and white EEC patients, including candidates significantly associated with altered disease outcomes within these patient cohorts. Cancer 2017;123:4004-12. © 2017 American Cancer Society.

Establishment and characterization of a platinum- and paclitaxel-resistant high grade serous ovarian carcinoma cell line.

High grade serous ovarian cancer (HGSOC) patients have a high recurrence rate after surgery and adjuvant chemotherapy due to inherent or acquired drug resistance. Cell lines derived from HGSOC tumors that are resistant to chemotherapeutic agents represent useful pre-clinical models for drug discovery. Here, we describe establishment of a human ovarian carcinoma cell line, which we term WHIRC01, from a patient-derived mouse xenograft established from a chemorefractory HGSOC patient who did not respond to carboplatin and paclitaxel therapy. This newly derived cell line is platinum- and paclitaxel-resistant with cisplatin, carboplatin, and paclitaxel half-maximal lethal doses of 15, 130, and 20 µM, respectively. Molecular characterization of this cell line was performed using targeted DNA exome sequencing, transcriptomics (RNA-seq), and mass spectrometry-based proteomic analyses. Results from exomic sequencing revealed mutations in TP53 consistent with HGSOC. Transcriptomic and proteomic analyses of WHIRC01 showed high level of alpha-enolase and vimentin, which are associated with cell migration and epithelial-mesenchymal transition. WHIRC01 represents a chemorefractory human HGSOC cell line model with a comprehensive molecular profile to aid future investigations of drug resistance mechanisms and screening of chemotherapeutic agents.