An In Vivo Screen Identifies PYGO2 as a Driver for Metastatic Prostate Cancer

Advanced prostate cancer displays conspicuous chromosomal instability and rampant copy number aberrations, yet the identity of functional drivers resident in many amplicons remain elusive. Here, we implemented a functional genomics approach to identify new oncogenes involved in prostate cancer progression. Through integrated analyses of focal amplicons in large prostate cancer genomic and transcriptomic datasets as well as genes upregulated in metastasis, 276 putative oncogenes were enlisted into an in vivo gain-of-function tumorigenesis screen. Among the top positive hits, we conducted an in-depth functional analysis on Pygopus family PHD finger 2 (PYGO2), located in the amplicon at 1q21.3. PYGO2 overexpression enhances primary tumor growth and local invasion to draining lymph nodes. Conversely, PYGO2 depletion inhibits prostate cancer cell invasion in vitro and progression of primary tumor and metastasis in vivo In clinical samples, PYGO2 upregulation associated with higher Gleason score and metastasis to lymph nodes and bone. Silencing PYGO2 expression in patient-derived xenograft models impairs tumor progression. Finally, PYGO2 is necessary to enhance the transcriptional activation in response to ligand-induced Wnt/β-catenin signaling. Together, our results indicate that PYGO2 functions as a driver oncogene in the 1q21.3 amplicon and may serve as a potential prognostic biomarker and therapeutic target for metastatic prostate cancer.Significance: Amplification/overexpression of PYGO2 may serve as a biomarker for prostate cancer progression and metastasis. Cancer Res; 78(14); 3823-33. ©2018 AACR

ACE-ASIA - Regional climatic and atmospheric chemical effects of Asian dust and pollution

Although continental-scale plumes of Asian dust and pollution reduce the amount of solar radiation reaching the earth's surface and perturb the chemistry of the atmosphere, our ability to quantify these effects has been limited by a lack of critical observations, particularly of layers above the surface. Comprehensive surface, airborne, shipboard, and satellite measurements of Asian aerosol chemical composition, size, optical properties, and radiative impacts were performed during the Asian Pacific Regional Aerosol Characterization Experiment (ACE-Asia) study. Measurements within a massive Chinese dust storm at numerous widely spaced sampling locations revealed the highly complex structure of the atmosphere, in which layers of dust, urban pollution, and biomass-burning smoke may be transported long distances as distinct entities or mixed together. The data allow a first-time assessment of the regional climatic and atmospheric chemical effects of a continental-scale mixture of dust and pollution. Our results show that radiative flux reductions during such episodes are sufficient to cause regional climate change

Considering sex as a biological variable in preclinical research

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154390/1/fsb2fj201600781r.pd

Multiscale simulations of tropospheric chemistry in the eastern Pacific and on the U.S. West Coast during spring 2002

Regional modeling analysis for the Intercontinental Transport and Chemical Transformation 2002 (ITCT 2K2) experiment over the eastern Pacific and U.S. West Coast is performed using a multiscale modeling system, including the regional tracer model Chemical Weather Forecasting System (CFORS), the Sulfur Transport and Emissions Model 2003 (STEM-2K3) regional chemical transport model, and an off-line coupling with the Model of Ozone and Related Chemical Tracers (MOZART) global chemical transport model. CO regional tracers calculated online in the CFORS model are used to identify aircraft measurement periods with Asian influences. Asian-influenced air masses measured by the National Oceanic and Atmospheric Administration (NOAA) WP-3 aircraft in this experiment are found to have lower ΔAcetone/ΔCO, ΔMethanol /ΔCO, and ΔPropane/ ΔEthyne ratios than air masses influenced by U.S. emissions, reflecting differences in regional emission signals. The Asian air masses in the eastern Pacific are found to usually be well aged (\u3e5 days), to be highly diffused, and to have low NOy levels. Chemical budget analysis is performed for two flights, and the O3 net chemical budgets are found to be negative (net destructive) in the places dominated by Asian influences or clear sites and positive in polluted American air masses. During the trans-Pacific transport, part of gaseous HNO3 was converted to nitrate particle, and this conversion was attributed to NOy decline. Without the aerosol consideration, the model tends to overestimate HNO3 background concentration along the coast region. At the measurement site of Trinidad Head, northern California, high- concentration pollutants are usually associated with calm wind scenarios, implying that the accumulation of local pollutants leads to the high concentration. Seasonal variations are also discussed from April to May for this site. A high-resolution nesting simulation with 12-km horizontal resolution is used to study the WP-3 flight over Los Angeles and surrounding areas. This nested simulation significantly improved the predictions for emitted and secondary generated species. The difference of photochemical behavior between the coarse (60-km) and nesting simulations is discussed and compared with the observation. Copyright 2004 by the American Geophysical Union

Contrasting CO2 and water vapour fluxes in dry forest and pasture sites of central Argentina

The dry forests of South America are a key player of the global carbon cycle and the regional water cycle, but they are being intensively deforested. We used eddy covariance measurements to compare the temporal patterns of CO2 and water vapour fluxes and their relationships with environmental variables in dry forest and pastures sites of central Argentina. Ecosystem fluxes showed clear contrasts in magnitude, timing and response to environmental controls between ecosystems. The dry forest displayed higher daily gross primary productivity (GPP, 10.6 vs. 7.8 g CO2 m−2 d−1) and ecosystem respiration (Reco, 9.1 vs. 7.0 g CO2 m−2 d−1) and lower net ecosystem exchange (NEE, −1.5 vs. −0.7 g CO2 m−2 d−1) than the pasture. These differences were explained by a lower tolerance of the pasture to cool temperatures and drought. The lowest NEE rates were observed between 26°C and 34°C in the pasture, but below this range, NEE increased sharply, switching to a carbon source with temperatures <20°C. By contrast, the dry forest remained as a strong carbon sink down to 18°C. The pasture also showed a stronger drop of GPP with drought compared with the dry forest, becoming a carbon source with soil wetness <25% of soil available water. Rainfall was strongly coupled with GPP in both ecosystems, but the dry forest responded to longer rainfall integration periods. This study helps to understand how ecosystems can respond to climate change, improve global scale modelling and increase the productivity and resilience of rangelands.Fil: Nosetto, Marcelo Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi". Universidad Nacional de San Luis. Facultad de Ciencias Físico, Matemáticas y Naturales. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi"; ArgentinaFil: Luna Toledo, Emanuel Santiago. Instituto Nacional de Tecnología Agropecuaria; Argentina. Universidad Nacional de Chilecito; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Magliano, Patricio Nicolás. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi". Universidad Nacional de San Luis. Facultad de Ciencias Físico, Matemáticas y Naturales. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi"; ArgentinaFil: Figuerola, Patricia Irene. Universidad Nacional de Chilecito; ArgentinaFil: Blanco, Lisandro Javier. Instituto Nacional de Tecnología Agropecuaria; ArgentinaFil: Jobbagy Gampel, Esteban Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi". Universidad Nacional de San Luis. Facultad de Ciencias Físico, Matemáticas y Naturales. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi"; Argentin

Effects of the agility boot camp with cognitive challenge (ABC-C) exercise program for Parkinson’s disease

Few exercise interventions practice both gait and balance tasks with cognitive tasks to improve functional mobility in people with PD. We aimed to investigate whether the Agility Boot Camp with Cognitive Challenge (ABC-C), that simultaneously targets both mobility and cognitive function, improves dynamic balance and dual-task gait in individuals with Parkinson's disease (PD). We used a cross-over, single-blind, randomized controlled trial to determine efficacy of the exercise intervention. Eighty-six people with idiopathic PD were randomized into either an exercise (ABC-C)-first or an active, placebo, education-first intervention and then crossed over to the other intervention. Both interventions were carried out in small groups led by a certified exercise trainer (90-min sessions, 3 times a week, for 6 weeks). Outcome measures were assessed Off levodopa at baseline and after the first and second interventions. A linear mixed-effects model tested the treatment effects on the Mini-BESTest for balance, dual-task cost on gait speed, SCOPA-COG, the UPDRS Parts II and III and the PDQ-39. Although no significant treatment effects were observed for the Mini-BESTest, SCOPA-COG or MDS-UPDRS Part III, the ABC-C intervention significantly improved the following outcomes: anticipatory postural adjustment sub-score of the Mini-BESTest (p = 0.004), dual-task cost on gait speed (p = 0.001), MDS-UPDRS Part II score (p = 0.01), PIGD sub-score of MDS-UPDRS Part III (p = 0.02), and the activities of daily living domain of the PDQ-39 (p = 0.003). Participants with more severe motor impairment or more severe cognitive dysfunction improved their total Mini-BESTest scores after exercise. The ABC-C exercise intervention can improve specific balance deficits, cognitive-gait interference, and perceived functional independence and quality of life, especially in participants with more severe PD, but a longer period of intervention may be required to improve global cognitive and motor function

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment