Subtle Controllers: MicroRNAs Drive Pancreatic Tumorigenesis and Progression: A Dissertation

Pancreatic ductal adenocarcinoma (PDAC) is among the most lethal malignancies in the United States, with an average five-year survival rate of just 6.7%. One unifying aspect of PDAC is mutational activation of the KRAS oncogene, which occurs in over 90% of PDAC. Therefore, inhibiting KRAS function is likely an effective therapeutic strategy for this disease, and current research in our lab and others is focused on identifying downstream effectors of KRAS signaling that may be therapeutic targets. miRNAs are powerful regulators of gene expression that can behave as oncogenes or tumor suppressors. Dysregulation of miRNA expression is commonly observed in human tumors, including PDAC. The mir-17~92 cluster of miRNAs is an established oncogene in a variety of tumor contexts, and members of the mir-17~92 cluster are upregulated in PDAC, but their role has not been explored in vivo. This dissertation encompasses two studies exploring the role of miRNAs in pancreatic tumorigenesis. In Chapter II, I demonstrate that deletion of the mir-17~92 cluster impairs PDAC precursor lesion formation and maintenance, and correlates with reduced ERK signaling in these lesions. mir-17~92 deficient tumors and cell lines are also less invasive, which I attribute to the loss of the miR-19 family of miRNAs. In Chapter III, I find that Dicer heterozygosity inhibits PDAC metastasis, and that this phenotype is attributable to an increased sensitivity to anoikis. Ongoing experiments will determine whether shifts in particular miRNA signatures between cell lines can be attributed to this phenotype. Together these findings illustrate the importance of miRNA biogenesis, and the mir-17~92 cluster in particular, in supporting PDAC development and progression

MicroRNAs of the mir-17~92 cluster regulate multiple aspects of pancreatic tumor development and progression

Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy characterized by resistance to currently employed chemotherapeutic approaches. Members of the mir-17~92 cluster of microRNAs (miRNAs) are upregulated in PDAC, but the precise roles of these miRNAs in PDAC are unknown. Using genetically engineered mouse models, we show that loss of mir-17~92 reduces ERK pathway activation downstream of mutant KRAS and promotes the regression of KRASG12D-driven precursor pancreatic intraepithelial neoplasias (PanINs) and their replacement by normal exocrine tissue. In a PDAC model driven by concomitant KRASG12D expression and Trp53 heterozygosity, mir-17~92 deficiency extended the survival of mice that lacked distant metastasis. Moreover, mir-17~92-deficient PDAC cell lines display reduced invasion activity in transwell assays, form fewer invadopodia rosettes than mir-17~92-competent cell lines and are less able to degrade extracellular matrix. Specific inhibition of miR-19 family miRNAs with antagomirs recapitulates these phenotypes, suggesting that miR-19 family miRNAs are important mediators of PDAC cell invasion. Together these data demonstrate an oncogenic role for mir-17~92 at multiple stages of pancreatic tumorigenesis and progression; specifically, they link this miRNA cluster to ERK pathway activation and precursor lesion maintenance in vivo and identify a novel role for miR-19 family miRNAs in promoting cancer cell invasion

A Bioinformatics Method Identifies Prominent Off-targeted Transcripts in RNAi Screens

Because off-target effects hamper interpretation and validation of RNAi screens, we developed a bioinformatics method, Genome-wide Enrichment of Seed Sequence matches (GESS), to identify candidate off-targeted transcripts from direct analysis of primary screening data. GESS identified a prominent off-targeted transcript in several screens, including MAD2 in a screen for components of the spindle assembly checkpoint. We demonstrate how incorporation of the results of GESS analysis can enhance the validation rate in RNAi screens

Activation of WNT/beta-Catenin Signaling Enhances Pancreatic Cancer Development and the Malignant Potential Via Up-regulation of Cyr61

Pancreatic ductal adenocarcinoma (PDAC), a poor prognostic cancer, commonly develops following activating mutations in the KRAS oncogene. Activation of WNT signaling is also commonly observed in PDAC. To ascertain the impact of postnatal activation of WNT-stimulated signaling pathways in PDAC development, we combined the Elastase-tva-based RCAS-TVA pancreatic cancer model with the established LSL-KrasG12D, Ptf1a-cre model. Delivery of RCAS viruses encoding beta-cateninS37A and WNT1 stimulated the progression of premalignant pancreatic intraepithelial neoplasias (PanIN) and PDAC development. Moreover, mice injected with RCAS-beta-cateninS37A or RCAS-Wnt1 had reduced survival relative to RCAS-GFP-injected controls (P \u3c .05). Ectopic expression of active beta-catenin, or its DNA-binding partner TCF4, enhanced transformation associated phenotypes in PDAC cells. In contrast, these phenotypes were significantly impaired by the introduction of ICAT, an inhibitor of the beta-catenin/TCF4 interaction. By gene expression profiling, we identified Cyr61 as a target molecule of the WNT/beta-catenin signaling pathway in pancreatic cancer cells. Nuclear beta-catenin and CYR61 expression were predominantly detected in moderately to poorly differentiated murine and human PDAC. Indeed, nuclear beta-catenin- and CYR61-positive PDAC patients demonstrated poor prognosis (P \u3c .01). Knockdown of CYR61 in a beta-catenin-activated pancreatic cancer cell line reduced soft agar, migration and invasion activity. Together, these data suggest that the WNT/beta-catenin signaling pathway enhances pancreatic cancer development and malignancy in part via up-regulation of CYR61

Using Remotely Sensed Data and Watershed and Hydrodynamic Models to Evaluate the Effects of Land Cover Land Use Change on Aquatic Ecosystems in Mobile Bay, AL

Alabama coastal systems have been subjected to increasing pressure from a variety of activities including urban and rural development, shoreline modifications, industrial activities, and dredging of shipping and navigation channels. The impacts on coastal ecosystems are often observed through the use of indicator species. One such indicator species for aquatic ecosystem health is submerged aquatic vegetation (SAV). Watershed and hydrodynamic modeling has been performed to evaluate the impact of land cover land use (LCLU) change in the two counties surrounding Mobile Bay (Mobile and Baldwin) on SAV stressors and controlling factors (temperature, salinity, and sediment) in the Mobile Bay estuary. Watershed modeling using the Loading Simulation Package in C++ (LSPC) was performed for all watersheds contiguous to Mobile Bay for LCLU scenarios in 1948, 1992, 2001, and 2030. Remotely sensed Landsat-derived National Land Cover Data (NLCD) were used in the 1992 and 2001 simulations after having been reclassified to a common classification scheme. The Prescott Spatial Growth Model was used to project the 2030 LCLU scenario based on current trends. The LSPC model simulations provided output on changes in flow, temperature, and sediment for 22 discharge points into the estuary. These results were inputted in the Environmental Fluid Dynamics Computer Code (EFDC) hydrodynamic model to generate data on changes in temperature, salinity, and sediment on a grid throughout Mobile Bay and adjacent estuaries. The changes in the aquatic ecosystem were used to perform an ecological analysis to evaluate the impact on SAV habitat suitability. This is the key product benefiting the Mobile Bay coastal environmental managers that integrates the influences of temperature, salinity, and sediment due to LCLU driven flow changes with the restoration potential of SAVs. Data products and results are being integrated into NOAA s EcoWatch and Gulf of Mexico Data Atlas online systems for dissemination to coastal resource managers and stakeholders. Objective 1: Develop and utilize Land Use scenarios for Mobile and Baldwin Counties, AL as input to models to predict the affects on water properties (temperature,salinity,)for Mobile Bay through 2030. Objective 2: Evaluate the impact of land use change on seagrasses and SAV in Mobile Bay. Hypothesis: Urbanization will significantly increase surface flows and impact salinity and temperature variables that effect seagrasses and SAVs

mTORC2 signaling drives the development and progression of pancreatic cancer

mTOR signaling controls several critical cellular functions and is deregulated in many cancers, including pancreatic cancer. To date, most efforts have focused on inhibiting the mTORC1 complex. However, clinical trials of mTORC1 inhibitors in pancreatic cancer have failed, raising questions about this therapeutic approach. We employed a genetic approach to delete the obligate mTORC2 subunit Rictor and identified the critical times during which tumorigenesis requires mTORC2 signaling. Rictor deletion resulted in profoundly delayed tumorigenesis. Whereas previous studies showed most pancreatic tumors were insensitive to rapamycin, treatment with a dual mTORC1/2 inhibitor strongly suppressed tumorigenesis. In late-stage tumor-bearing mice, combined mTORC1/2 and PI3K inhibition significantly increased survival. Thus, targeting mTOR may be a potential therapeutic strategy in pancreatic cancer

A MODELING SYSTEM TO ASSESS LAND COVER LAND USE CHANGE EFFECTS ON SAV HABITAT IN THE MOBILE BAY ESTUARY

Estuarine ecosystems are largely influenced by watersheds directly connected to them. In the Mobile Bay, Alabama watersheds we examined the effect of land cover and land use (LCLU) changes on discharge rate, water properties, and submerged aquatic vegetation, including freshwater macrophytes and seagrasses, throughout the estuary. LCLU scenarios from 1948, 1992, 2001, and 2030 were used to influence watershed and hydrodynamic models and evaluate the impact of LCLU change on shallow aquatic ecosystems. Overall, our modeling results found that LCLU changes increased freshwater flows into Mobile Bay altering temperature, salinity, and total suspended sediments (TSS). Increased urban land uses coupled with decreased agricultural/pasture lands reduced TSS in the water column. However, increased urbanization or agricultural/ pasture land coupled with decreased forest land resulted in higher TSS concentrations. Higher sediment loads were usually strongly correlated with higher TSS levels, except in areas where a large extent of wetlands retained sediment discharged during rainfall events. The modeling results indicated improved water clarity in the shallow aquatic regions of Mississippi Sound and degraded water clarity in the Wolf Bay estuary. This integrated modeling approach will provide new knowledge and tools for coastal resource managers to manage shallow aquatic habitats that provide critical ecosystem services

MicroRNA-378 controls classical brown fat expansion to counteract obesity

Both classical brown adipocytes and brown-like beige adipocytes are considered as promising therapeutic targets for obesity; however, their development, relative importance and functional coordination are not well understood. Here we show that a modest expression of miR-378/378* in adipose tissue specifically increases classical brown fat (BAT) mass, but not white fat (WAT) mass. Remarkably, BAT expansion, rather than miR-378 per se, suppresses formation of beige adipocytes in subcutaneous WAT. Despite this negative feedback, the expanded BAT depot is sufficient to prevent both genetic and high-fat diet-induced obesity. At the molecular level, we find that miR-378 targets phosphodiesterase Pde1b in BAT but not in WAT. Indeed, miR-378 and Pde1b inversely regulate brown adipogenesis in vitro in the absence of phosphodiesterase inhibitor isobutylmethylxanthine. Our work identifies miR-378 as a key regulatory component underlying classical BAT-specific expansion and obesity resistance, and adds novel insights into the physiological crosstalk between BAT and WAT

Evaluating the Impact of Land Use Change on Submerged Aquatic Vegetation Stressors in Mobile Bay

Alabama coastal systems have been subjected to increasing pressure from a variety of activities including urban and rural development, shoreline modifications, industrial activities, and dredging of shipping and navigation channels. The impacts on coastal ecosystems are often observed through the use of indicator species. One such indicator species for aquatic ecosystem health is submerged aquatic vegetation (SAV). Watershed and hydrodynamic modeling has been performed to evaluate the impact of land use change in Mobile and Baldwin counties on SAV stressors and controlling factors (temperature, salinity, and sediment) in Mobile Bay. Watershed modeling using the Loading Simulation Package in C++ (LSPC) was performed for all watersheds contiguous to Mobile Bay for land use scenarios in 1948, 1992, 2001, and 2030. Landsat-derived National Land Cover Data (NLCD) were used in the 1992 and 2001 simulations after having been reclassified to a common classification scheme. The Prescott Spatial Growth Model was used to project the 2030 land use scenario based on current trends. The LSPC model simulations provided output on changes in flow, temperature, and sediment for 22 discharge points into the Bay. Theses results were inputted in the Environmental Fluid Dynamics Computer Code (EFDC) hydrodynamic model to generate data on changes in temperature, salinity, and sediment on a grid with four vertical profiles throughout Mobile Bay. The changes in the aquatic ecosystem were used to perform an ecological analysis to evaluate the impact on SAV habitat suitability. This is the key product benefiting the Mobile Bay coastal environmental managers that integrates the influences of temperature, salinity, and sediment due to land use driven flow changes with the restoration potential of SAVs

Watershed and Hydrodynamic Modeling for Evaluating the Impact of Land Use Change on Submerged Aquatic Vegetation and Seagrasses in Mobile Bay

There is a continued need to understand how human activities along the northern Gulf of Mexico coast are impacting the natural ecosystems. The gulf coast is experiencing rapid population growth and associated land cover/land use change. Mobile Bay, AL is a designated pilot region of the Gulf of Mexico Alliance (GOMA) and is the focus area of many current NASA and NOAA studies, for example. This is a critical region, both ecologically and economically to the entire United States because it has the fourth largest freshwater inflow in the continental USA, is a vital nursery habitat for commercially and recreational important fisheries, and houses a working waterfront and port that is expanding. Watershed and hydrodynamic modeling has been performed for Mobile Bay to evaluate the impact of land use change in Mobile and Baldwin counties on the aquatic ecosystem. Watershed modeling using the Loading Simulation Package in C (LSPC) was performed for all watersheds contiguous to Mobile Bay for land use Scenarios in 1948, 1992, 2001, and 2030. The Prescott Spatial Growth Model was used to project the 2030 land use scenario based on observed trends. All land use scenarios were developed to a common land classification system developed by merging the 1992 and 2001 National Land Cover Data (NLCD). The LSPC model output provides changes in flow, temperature, sediments and general water quality for 22 discharge points into the Bay. These results were inputted in the Environmental Fluid Dynamics Computer Code (EFDC) hydrodynamic model to generate data on changes in temperature, salinity, and sediment concentrations on a grid with four vertical profiles throughout the Bay s aquatic ecosystems. The models were calibrated using in-situ data collected at sampling stations in and around Mobile bay. This phase of the project has focused on sediment modeling because of its significant influence on light attenuation which is a critical factor in the health of submerged aquatic vegetation. The impact of land use change on sediment concentrations was evaluated by analyzing the LSPC and EFDC sediment simulations for the four land use scenarios. Such analysis was also performed for storm and non-storm periods. In- situ data of total suspended sediments (TSS) and light attenuation were used to develop a regression model to estimate light attenuation from TSS. This regression model was used to derive marine light attenuation estimates throughout Mobile bay using the EFDC TSS outputs. The changes in sediment concentrations and associated impact on light attenuation in the aquatic ecosystem were used to perform an ecological analysis to evaluate the impact on seagreasses and Submerged Aquatic Vegetation (SAV) habitat. This is the key product benefiting the Mobile Bay coastal environmental managers that integrates the influences of sediments due to land use driven flow changes with the restoration potential of SAVs