The identification of microRNAs to predict glioma prognosis

Until now, personalised medicine for patients in oncology has been focused on the use of DNA-based techniques such as mutation detection and fluorescence in situ hybridisation, fluorescence-activated cell sorting and immuno-staining for classifying tumours. MicroRNAs are short non-coding RNAs that are involved in post-translational regulation of gene expression. Their expression levels are often altered in cancer. Due to their functional importance and stability in biological samples, they represent another tool that could be used to aid patient management. Glioblastoma is a disease that has had little improvement in survival over the past decade in comparison to other cancers. A number of new drugs have been explored but even successful trials have shown limited success. This thesis is focused on identification of microRNAs as signatures for prognosis prediction in glioblastoma. It is separated into four parts; the identification of a microRNA signature that can be used to predict prognosis in glioblastoma; the alignment of glioblastoma microRNA expression with the microRNA expression of oligodendrocyte precursors and its involvement in patient outcome; the use of the expression pattern of the most abundant and robust prognostic microRNA in glioma (miR-9) to delineate glioblastoma subtype and finally the identification of a microRNA signature to predict prognosis in patients treated with the anti-angiogenic drug bevacizumab. The research aims to create signatures suitable for clinical practice, with a small number of predictors, and where possible the function of the microRNAs has been predicted and reviewed to provide confirmation of their role in glioma biology. The key findings of this research are the formation of robust signatures using microRNAs in a disease where few markers are available and proof of a technique that can be used in future drug studies to improve performance at clinical trials

Weighted risk assessment of critical source areas for soil phosphorus losses through surface runoff mechanisms

This work was supported by the NERC QUADRAT DTP [grant number 2280708].Peer reviewedPublisher PD

Do Space Tech Pack Program Evaluation: Improving Digital Access and Equity

The Do Space Library received funding from the Emergency Connectivity Fund from the Federal Communications Commission to conduct the Teck Pack Program in Omaha, Nebraska, between June 30, 2022 to June 29, 2023. As part of the Tech Pack Program, 945 Omaha residents received a computing device and free internet access for one year. Along with this infrastructure, they received computer basics training and technology tutoring. This innovative program directly addresses the challenges experienced by those without access. In the city of Omaha, Nebraska, according to data from the U.S. Census Bureau’s American Community Survey for 2021, over 9,000 households (4.6%) do not have a computer or smart device and over 18,000 households (9.0%) do not have an internet subscription of any kind. The Tech Pack Program alleviated this challenge for one year for some of these households. Do Space partnered with the Center for Public Affairs Research (CPAR) at the University of Nebraska at Omaha to evaluate the Tech Pack Program. An online application to the program and three surveys were administered to track participation and outcomes from the program. The survey demonstrates that participants used the Tech Pack Program for work related purposes (17% - 19%); household related activities like paying bills, banking, ordering groceries, or shopping for the households (20% - 22%); getting news and participating in local activities (21% - 23%); creating or fostering relationships with family and friends (14% - 15%); and practicing computing and internet skills (23% - 26%). Over the course of the program many participants became more comfortable using digital devices, navigating the internet, and becoming familiar with computer and internet related terms. A range of questions about the economic security of participants also show that over the course of the program positive gains were made. Respondents reported feeling more in control of their economic future, having stronger economic support networks, and financial situations getting better. One participant shared about the program, “…it has given me a path to my dream career.” Additionally, respondents reported increasingly using the Tech Pack Program to support their health and well-being, including accessing information about cultural events (46% - 55%), learning new skills (42% - 48%), accessing financial services (55% - 61%), and getting health information not related to COVID-19 (52% - 57%), as just some examples. By the last survey, over 65% reported that participating in the program improved their life “a great deal.” Tech Pack Program participants were quick to share their gratitude and satisfaction with the program. Their quotes and open-ended responses demonstrate the overwhelming and positive impact of the Tech Pack Program. Overall, the findings suggest that providing individuals with digital devices and teaching them useful technological skills enables greater opportunity for long-term success. To fully participate in our society, we recognize that digital access and equity is essential. Not only does digital equity ensure access to basic resources critical to social, economic, and physical well-being, but digital equity also enhances the creation of social capital and promotes economic security. This innovative and straightforward program resulting in improvements in the lives of its participants is a model for future programming to overcome the digital divide

Grassland Reseeding: Impact on Soil Surface Nutrient Accumulation and Using LiDAR-Based Image Differencing to Infer Implications for Water Quality

Publication history: Accepted - 2 November 2022; Published - 4 November 2022.Long-term phosphorus (P) accumulation in agricultural soils presents a challenge for water quality improvement. P is commonly elevated in soils managed for intensive livestock production due to repeated overapplication of slurry and fertilisers. High legacy nutrient accumulations result in poor water quality via transport pathways such as surface runoff, subsurface drainage, and soil erosion. To achieve environmental water quality targets, improved management strategies are required for targeting and reducing excess agricultural P sources. Reseeding of old swards is known to improve grassland productivity and enhance overall soil health. However, soil disturbance associated with reseeding could have positive and negative impacts on other soil functions that affect the nutrient balance (including improved microbial activity, but also increasing the potential for sediment and nutrient losses). This study investigates the impact of reseeding and inversion tillage in addressing soil surface nutrient surpluses and identifies potential trade-offs between production, environment (through soil erosion and associated sediment and nutrient losses), and soil health. At a study site in the Blackwater catchment in Northern Ireland, we collected highresolution (35 m) gridded soil samples pre- and post-reseeding for nutrient analyses and combined this with GIS-based interpolation. We found that decreases in sub-field scale surface nutrient content (0–7.5 cm depth) occurred following tillage and reseeding, but that this was spatially variable. In addition, the magnitude of changes in nutrient content was variable between P and other sampled nutrients. LiDAR-based image differencing indicated variability in the magnitude of soil erosion and sediment loss also at sub-field scale. Information on the identified deposition and erosion zones (from LiDAR analysis) was combined with mass wasting data to determine accumulation rates and losses of nutrients in-field and confirmed some of the identified patterns in soil surface nutrient content changes post-reseeding. We conclude that while inversion tillage and reseeding are essential agricultural practices, environmental trade-offs exist through potential nutrient and sediment losses. LiDAR-based image differencing was found to be a useful tool in helping to quantify these risks. Quantifying sediment and nutrient losses as a result of inversion tillage and reseeding induced soil erosion aids in understanding potential trends in water quality statuses.This research was funded by the NERC QUADRAT DTP, grant number 2280708

Grassland Reseeding - Improving Grassland Productivity and Reducing Excess Soil-Surface Nutrient Accumulations

Publication history: Published online 10 February 2022Long-term phosphorus (P) accumulation in agricultural soils presents a challenge for water quality improvement. P is commonly elevated in soils managed for intensive livestock production due to the repeated over-application of slurry and fertilizers. High legacy nutrient accumulations can result in poor water quality via transport pathways such as surface runoff, subsurface drainage, and soil erosion. To achieve the EU Water Framework Directive (WFD) aims, improved management strategies are required for diffuse and point P sources. Reseeding is known to improve grassland productivity and enhance overall soil health. However, soil disturbance associated with reseeding could have positive and negative effects on several other soil functions that affect the nutrient balance (including improved microbial activity, but also increasing the potential for sediment and nutrient losses). This study investigated the role of reseeding in addressing nutrient surpluses in surface soils and identified potential trade-offs between production, environment, and soil health. At a study site in the Blackwater catchment in Northern Ireland, we collected high-resolution gridded soil samples pre- and post-reseeding for nutrient analyses and combined this with GIS-based interpolation. We found that decreases in sub-field scale nutrient content occurred following reseeding, but that this was spatially variable. This indicates that this strategy is effective in reducing soil surface P accumulations. However, more research is needed to determine whether this P becomes available for grass uptake during re-growth or whether it increases the pool of mobile P, which can be lost in surface runoff, subsurface drainage, and soil erosionThis research was funded by the NERC QUADRAT DTP, grant number 2280708

Tumor-derived fibulin-3 activates pro-invasive NF-kappa B signaling in glioblastoma cells and their microenvironment

Molecular profiling of glioblastomas has revealed the presence of key signaling hubs that contribute to tumor progression and acquisition of resistance. One of these main signaling mechanisms is the NF-κB pathway, which integrates multiple extracellular signals into transcriptional programs for tumor growth, invasion, and maintenance of the tumor-initiating population. We show here that an extracellular protein released by glioblastoma cells, fibulin-3, drives oncogenic NF-κB in the tumor and increases NF-κB activation in peritumoral astrocytes. Fibulin-3 expression correlates with a NF-κB-regulated “invasive signature” linked to poorer survival, being a possible tissue marker for regions of active tumor progression. Accordingly, fibulin-3 promotes glioblastoma invasion in a manner that requires NF-κB activation both in the tumor cells and their microenvironment. Mechanistically, we found that fibulin-3 activates the metalloprotease ADAM17 by competing with its endogenous inhibitor, TIMP3. This results in sustained release of soluble TNFα by ADAM17, which in turn activates TNF receptors and canonical NF-κB signaling. Taken together, our results underscore fibulin-3 as a novel extracellular signal with strong activating effect on NF-κB in malignant gliomas. Because fibulin-3 is produced de novo in these tumors and is absent from normal brain we propose that targeting the fibulin-3/NF-κB axis may provide a novel avenue to disrupt oncogenic NF-κB signaling in combination therapies for malignant brain tumors

Prediction of clinical outcome in glioblastoma using a biologically relevant nine-microRNA signature

Background Glioblastoma is the most aggressive primary brain tumor, and is associated with a very poor prognosis. In this study we investigated the potential of microRNA expression profiles to predict survival in this challenging disease. Methods MicroRNA and mRNA expression data from glioblastoma (n = 475) and grade II and III glioma (n = 178) were accessed from The Cancer Genome Atlas. LASSO regression models were used to identify a prognostic microRNA signature. Functionally relevant targets of microRNAs were determined using microRNA target prediction, experimental validation and correlation of microRNA and mRNA expression data. Results A 9-microRNA prognostic signature was identified which stratified patients into risk groups strongly associated with survival (p = 2.26e−09), significant in all glioblastoma subtypes except the non-G-CIMP proneural group. The statistical significance of the microRNA signature was higher than MGMT methylation in temozolomide treated tumors. The 9-microRNA risk score was validated in an independent dataset (p = 4.50e−02) and also stratified patients into high- and low-risk groups in lower grade glioma (p = 5.20e−03). The majority of the 9 microRNAs have been previously linked to glioblastoma biology or treatment response. Integration of the expression patterns of predicted microRNA targets revealed a number of relevant microRNA/target pairs, which were validated in cell lines. Conclusions We have identified a novel, biologically relevant microRNA signature that stratifies high- and low-risk patients in glioblastoma. MicroRNA/mRNA interactions identified within the signature point to novel regulatory networks. This is the first study to formulate a survival risk score for glioblastoma which consists of microRNAs associated with glioblastoma biology and/or treatment response, indicating a functionally relevant signatur

A validated microRNA profile with predictive potential in glioblastoma patients treated with bevacizumab

Purpose: We investigated whether microRNA expression data from glioblastoma could be used to produce a profile that defines a bevacizumab responsive group of patients. Patients and Methods: TCGA microRNA expression data from tumors resected at first diagnosis of glioblastoma in patients treated with bevacizumab at any time during the course of their disease were randomly separated into training (n=50) and test (n=37) groups for model generation. MicroRNA-seq data for 51 patients whose treatment included bevacizumab in the BELOB trial were used as an independent validation cohort. Results: Using penalized regression we identified 8 microRNAs as potential predictors of overall survival in the training set. We dichotomized the response score based on the most prognostic minimum of a density plot of the response scores (log-rank HR=0.16, p=1.2e-5) and validated the profile in the test cohort (one-sided log-rank HR=0.34, p=0.026). Analysis of the profile using all samples in the TCGA glioblastoma dataset, regardless of treatment received, (n=473) showed that the prediction of patient benefit was not significant (HR=0.84, p=0.083) suggesting the profile is specific to bevacizumab. Further independent validation of our microRNA profile in RNA-seq data from patients treated with bevacizumab (alone or in combination with CCNU) at glioblastoma recurrence in the BELOB trial confirmed that our microRNA profile predicted patient benefit from bevacizumab (HR=0.59, p=0.043). Conclusion: We have identified and validated an 8-microRNA profile that predicts overall survival in patients with glioblastoma treated with bevacizumab. This may be useful for identifying patients who are likely to benefit from this agent

Quick fabrication VCSELs for characterisation of epitaxial material

A systematic analysis of the performance of VCSELs, fabricated with a decreasing number of structural elements, is used to assess the complexity of fabrication (and therefore time) required to obtain sufficient information on epitaxial wafer suitability. Initially, sub-mA threshold current VCSEL devices are produced on AlGaAs-based material, designed for 940 nm emission, using processing methods widely employed in industry. From there, stripped-back Quick Fabrication (QF) devices, based on a bridge-mesa design, are fabricated and this negates the need for benzocyclcobutane (BCB) planarisation. Devices are produced with three variations on the QF design, to characterise the impact on laser performance from removing time-consuming process steps, including wet thermal oxidation and mechanical lapping used to reduce substrate thickness. An increase in threshold current of 1.5 mA for oxidised QF devices, relative to the standard VCSELs, and a further increase of 1.9 mA for unoxidised QF devices are observed, which is a result of leakage current. The tuning of the emission wavelength with current increases by ~0.1 nm/mA for a VCSEL with a 16 μm diameter mesa when the substrate is unlapped, which is ascribed to the increased thermal resistance. Generally, relative to the standard VCSELs, the QF methods employed do not significantly impact the threshold lasing wavelength and the differences in mean wavelengths of the device types that are observed are attributed to variation in cavity resonance with spatial position across the wafer, as determined by photovoltage spectroscopy measurements

Gain measurements on vertical cavity surface emitting laser material using segmented contact technique

We report direct measurements of the optical gain profile for a vertical cavity surface emitting laser (VCSEL) epitaxial structure, by characterising the transverse electric (TE) in-plane net modal gain using the segmented contact method