Integrated Molecular Characterization of Uterine Carcinosarcoma

SummaryWe performed genomic, epigenomic, transcriptomic, and proteomic characterizations of uterine carcinosarcomas (UCSs). Cohort samples had extensive copy-number alterations and highly recurrent somatic mutations. Frequent mutations were found in TP53, PTEN, PIK3CA, PPP2R1A, FBXW7, and KRAS, similar to endometrioid and serous uterine carcinomas. Transcriptome sequencing identified a strong epithelial-to-mesenchymal transition (EMT) gene signature in a subset of cases that was attributable to epigenetic alterations at microRNA promoters. The range of EMT scores in UCS was the largest among all tumor types studied via The Cancer Genome Atlas. UCSs shared proteomic features with gynecologic carcinomas and sarcomas with intermediate EMT features. Multiple somatic mutations and copy-number alterations in genes that are therapeutic targets were identified

Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH -Mutant Molecular Profiles

Cholangiocarcinoma (CCA) is an aggressive malignancy of the bile ducts, with poor prognosis and limited treatment options. Here, we describe the integrated analysis of somatic mutations, RNA expression, copy number, and DNA methylation by The Cancer Genome Atlas of a set of predominantly intrahepatic CCA cases and propose a molecular classification scheme. We identified an IDH mutant-enriched subtype with distinct molecular features including low expression of chromatin modifiers, elevated expression of mitochondrial genes, and increased mitochondrial DNA copy number. Leveraging the multi-platform data, we observed that ARID1A exhibited DNA hypermethylation and decreased expression in the IDH mutant subtype. More broadly, we found that IDH mutations are associated with an expanded histological spectrum of liver tumors with molecular features that stratify with CCA. Our studies reveal insights into the molecular pathogenesis and heterogeneity of cholangiocarcinoma and provide classification information of potential therapeutic significance

Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma

SummaryWe describe a comprehensive genomic characterization of adrenocortical carcinoma (ACC). Using this dataset, we expand the catalogue of known ACC driver genes to include PRKAR1A, RPL22, TERF2, CCNE1, and NF1. Genome wide DNA copy-number analysis revealed frequent occurrence of massive DNA loss followed by whole-genome doubling (WGD), which was associated with aggressive clinical course, suggesting WGD is a hallmark of disease progression. Corroborating this hypothesis were increased TERT expression, decreased telomere length, and activation of cell-cycle programs. Integrated subtype analysis identified three ACC subtypes with distinct clinical outcome and molecular alterations which could be captured by a 68-CpG probe DNA-methylation signature, proposing a strategy for clinical stratification of patients based on molecular markers

Stereo-Based Endoscopic Tracking of Cardiac Surface Deformation

Abstract. We propose an image-based motion tracking algorithm that can be used with stereo endoscopic and microscope systems. The tracking problem is considered to be a time-varying optimization of a parametric function describing the disparity map. This algorithm could be used as part of a virtual stabilization system that can be employed to compensate residual motion of the heart during robot-assisted off-pump coronary artery bypass surgery (CABG). To test the appropriateness of our methods for this application, we processed an image sequence of a beating pig heart obtained by the stereo endoscope used in the da Vinci robotic surgery system. The tracking algorithm was able to detect the beating of the heart itself as well as the respiration of the lungs.

Predictive Value of the National Institutes of Health Stroke Scale and the Mini-Mental State Examination for Neurologic Outcome After Coronary Artery Bypass Graft Surgery

ObjectiveWe intended to define the role of the National Institutes of Health Stroke Scale and the Mini-Mental State Examination in identifying adverse neurologic outcomes in a large international sample of patients undergoing cardiac surgery.MethodsWe evaluated 4707 patients undergoing cardiac surgery with cardiopulmonary bypass at 72 centers in 17 countries between November 1996 and June 2000. Prespecified overt neurologic outcomes were categorized as type I (clinically diagnosed stroke, transient ischemic attack, encephalopathy, or coma) or type II (deterioration of intellectual function). The National Institutes of Health Stroke Scale and Mini-Mental State Examination were administered preoperatively and on postoperative day 3, 4, or 5. Receiver operating characteristic curves were plotted to determine the predictive value of worsening in National Institutes of Health Stroke Scale and Mini-Mental State Examination scores with respect to type I and II outcomes.ResultsThe receiver operating characteristic area under the curve for changes in National Institutes of Health Stroke Scale score (n = 4620) was 0.89 for type I outcomes and 0.66 for type II outcomes. A 1-point worsening in National Institutes of Health Stroke Scale score provided excellent discrimination (86% specificity; 84% sensitivity) of type I outcomes. The receiver operating characteristic area under the curve for changes in Mini-Mental State Examination score (n = 4707) was 0.75 for type I outcomes and 0.71 for type II outcomes. A 2-point worsening in Mini-Mental State Examination score provided only fair discrimination (73% specificity; 62% sensitivity) of type II outcomes.ConclusionWe used baseline controls and postoperative worsening in National Institutes of Health Stroke Scale and Mini-Mental State Examination scores to predict both serious adverse neurologic outcome and deterioration of intellectual function. Our findings provide the only reference for evaluating these tests that are used in cardiac surgical clinical trials

Predictive value of the National Institutes of Health Stroke Scale and the Mini-Mental State Examination for neurologic outcome after coronary artery bypass graft surgery

OBJECTIVE: We intended to define the role of the National Institutes of Health Stroke Scale and the Mini-Mental State Examination in identifying adverse neurologic outcomes in a large international sample of patients undergoing cardiac surgery. METHODS: We evaluated 4707 patients undergoing cardiac surgery with cardiopulmonary bypass at 72 centers in 17 countries between November 1996 and June 2000. Prespecified overt neurologic outcomes were categorized as type I (clinically diagnosed stroke, transient ischemic attack, encephalopathy, or coma) or type II (deterioration of intellectual function). The National Institutes of Health Stroke Scale and Mini-Mental State Examination were administered preoperatively and on postoperative day 3, 4, or 5. Receiver operating characteristic curves were plotted to determine the predictive value of worsening in National Institutes of Health Stroke Scale and Mini-Mental State Examination scores with respect to type I and II outcomes. RESULTS: The receiver operating characteristic area under the curve for changes in National Institutes of Health Stroke Scale score (n = 4620) was 0.89 for type I outcomes and 0.66 for type II outcomes. A 1-point worsening in National Institutes of Health Stroke Scale score provided excellent discrimination (86% specificity; 84% sensitivity) of type I outcomes. The receiver operating characteristic area under the curve for changes in Mini-Mental State Examination score (n = 4707) was 0.75 for type I outcomes and 0.71 for type II outcomes. A 2-point worsening in Mini-Mental State Examination score provided only fair discrimination (73% specificity; 62% sensitivity) of type II outcomes. CONCLUSION: We used baseline controls and postoperative worsening in National Institutes of Health Stroke Scale and Mini-Mental State Examination scores to predict both serious adverse neurologic outcome and deterioration of intellectual function. Our findings provide the only reference for evaluating these tests that are used in cardiac surgical clinical trials