Bayesian hierarchical analysis on crash prediction models

Ph.DDOCTOR OF PHILOSOPH

Double Strand Breaks Can Initiate Gene Silencing and SIRT1-Dependent Onset of DNA Methylation in an Exogenous Promoter CpG Island

Chronic exposure to inducers of DNA base oxidation and single and double strand breaks contribute to tumorigenesis. In addition to the genetic changes caused by this DNA damage, such tumors often contain epigenetically silenced genes with aberrant promoter region CpG island DNA hypermethylation. We herein explore the relationships between such DNA damage and epigenetic gene silencing using an experimental model in which we induce a defined double strand break in an exogenous promoter construct of the E-cadherin CpG island, which is frequently aberrantly DNA hypermethylated in epithelial cancers. Following the onset of repair of the break, we observe recruitment to the site of damage of key proteins involved in establishing and maintaining transcriptional repression, namely SIRT1, EZH2, DNMT1, and DNMT3B, and the appearance of the silencing histone modifications, hypoacetyl H4K16, H3K9me2 and me3, and H3K27me3. Although in most cells selected after the break, DNA repair occurs faithfully with preservation of activity of the promoter, a small percentage of the plated cells demonstrate induction of heritable silencing. The chromatin around the break site in such a silent clone is enriched for most of the above silent chromatin proteins and histone marks, and the region harbors the appearance of increasing DNA methylation in the CpG island of the promoter. During the acute break, SIRT1 appears to be required for the transient recruitment of DNMT3B and subsequent methylation of the promoter in the silent clones. Taken together, our data suggest that normal repair of a DNA break can occasionally cause heritable silencing of a CpG island–containing promoter by recruitment of proteins involved in silencing. Furthermore, with contribution of the stress-related protein SIRT1, the break can lead to the onset of aberrant CpG island DNA methylation, which is frequently associated with tight gene silencing in cancer

Examining Road Traffic Mortality Status in China: A Simulation Study

Background Data from the Chinese police service suggest substantial reductions in road traffic injuries since 2002, but critics have questioned the accuracy of those data, especially considering conflicting data reported by the health department. Methods To address the gap between police and health department data and to determine which may be more accurate, we conducted a simulation study based on the modified Smeed equation, which delineates a non-linear relation between road traffic mortality and the level of motorization in a country or region. Our goal was to simulate trends in road traffic mortality in China and compare performances in road traffic safety management between China and 13 other countries. Results Chinese police data indicate a peak in road traffic mortalities in 2002 and a significant and a gradual decrease in population-based road traffic mortality since 2002. Health department data show the road traffic mortality peaked in 2012. In addition, police data suggest China’s road traffic mortality peaked at a much lower motorization level (0.061 motor vehicles per person) in 2002, followed by a reduction in mortality to a level comparable to that of developed countries. Simulation results based on health department data suggest high road traffic mortality, with a mortality peak in 2012 at a moderate motorization level (0.174 motor vehicles per person). Comparisons to the other 13 countries suggest the health data from China may be more valid than the police data. Conclusion Our simulation data indicate China is still at a stage of high road traffic mortality, as suggested by health data, rather than a stage of low road traffic mortality, as suggested by police data. More efforts are needed to integrate safety into road design, improve road traffic management, improve data quality, and alter unsafe behaviors of pedestrians, drivers and passengers in China

Analyzing drivers’ preferences and choices for the content and format of variable message signs (VMS)

Background Recent advance in variable message signs (VMS) technology has made it viable to provide spatio-temporal information on traffic and network conditions to drivers. There is a debate whether VMS diverts drivers’ attention away from the road and may cause unnecessary distraction in their driving tasks due to inconsistent VMS contents and formats. There are also other external factors such as weather conditions, visibility and time of day that may affect the integrity and reliability of the VMS. In China, only about 23% drivers were persuaded by VMS to follow route diversion. Objective In order to capture the full benefits of VMS, the aim of this paper is therefore to identify the factors affecting VMS by examining what kinds of VMS contents, formats and their interactions are more preferable to drivers, specifically in China. Methods A revealed preference (RP) questionnaire and stated preference (SP) survey consisting of 1154 samples from private and taxi drivers was conducted and analyzed using discrete choice model. Results The results revealed that the information showed by amber-on-black on text format, white-on-blue on graph format or the suggested route diversion information showed by single line are preferred by drivers in fog weather. In addition, highly educated drivers or drivers with no occupation are more prone to the qualitative delay time on a text-graph format in fog weather. In normal weather, drivers with working trip purpose are mostly preferred to receive the information on a congested traffic condition with a reason on a text-only format. However, the congested traffic condition along with the information on the apparent causes shown by red-on-black or green-on-black on a text-only format was least preferred by drivers. Regarding current and adjacent road traffic information, drivers prefer to receive the suggested route diversion on a graph-only format in fog weather and the qualitative delay time on a text-graph format in normal weather. Irrespective to weather conditions, male drivers incline to the qualitative delay time on a text-graph format. Conclusions The findings of this study could assist traffic authorities to design the most acceptable VMS for displaying traffic information for the purpose of improving road traffic efficiency and provide the theory evidence for the design of in-vehicle personalized information service system

Alterations of immune response of non-small lung cancer with azacytidine

Innovative therapies are needed for advanced Non-Small Cell Lung Cancer (NSCLC). We have undertaken a genomics based, hypothesis driving, approach to query an emerging potential that epigenetic therapy may sensitize to immune checkpoint therapy targeting PD-L1/PD-1 interaction. NSCLC cell lines were treated with the DNA hypomethylating agent azacytidine (AZA - Vidaza) and genes and pathways altered were mapped by genome-wide expression and DNA methylation analyses. AZA-induced pathways were analyzed in The Cancer Genome Atlas (TCGA) project by mapping the derived gene signatures in hundreds of lung adeno (LUAD) and squamous cell carcinoma (LUSC) samples. AZA up-regulates genes and pathways related to both innate and adaptive immunity and genes related to immune evasion in a several NSCLC lines. DNA hypermethylation and low expression of IRF7, an interferon transcription factor, tracks with this signature particularly in LUSC. In concert with these events, AZA up-regulates PD-L1 transcripts and protein, a key ligand-mediator of immune tolerance. Analysis of TCGA samples demonstrates that a significant proportion of primary NSCLC have low expression of AZA-induced immune genes, including PD-L1. We hypothesize that epigenetic therapy combined with blockade of immune checkpoints - in particular the PD-1/PD-L1 pathway - may augment response of NSCLC by shifting the balance between immune activation and immune inhibition, particularly in a subset of NSCLC with low expression of these pathways. Our studies define a biomarker strategy for response in a recently initiated trial to examine the potential of epigenetic therapy to sensitize patients with NSCLC to PD-1 immune checkpoint blockade

Lysine-Specific Demethylase 1 Mediates AKT Activity and Promotes Epithelial-to-Mesenchymal Transition in PIK3CA-Mutant Colorectal Cancer

Activation of the epithelial-mesenchymal transition (EMT) program is a critical mechanism for initiating cancer progression and migration. Colorectal cancers (CRCs) contain many genetic and epigenetic alterations that can contribute to EMT. Mutations activating the PI3K/AKT signaling pathway are observed in >40% of patients with CRC contributing to increased invasion and metastasis. Little is known about how oncogenic signaling pathways such as PI3K/AKT synergize with chromatin modifiers to activate the EMT program. Lysine Specific Demethylase 1 (LSD1) is a chromatin-modifying enzyme that is overexpressed in colorectal cancer (CRC) and enhances cell migration. In this study we determine that LSD1 expression is significantly elevated in CRC patients with mutation of the catalytic subunit of PI3K, PIK3CA, compared to CRC patients with WT PIK3CA. LSD1 enhances activation of the AKT kinase in CRC cells through a non-catalytic mechanism, acting as a scaffolding protein for the transcription-repressing CoREST complex. Additionally, growth of PIK3CA mutant CRC cells is uniquely dependent on LSD1. Knockdown or CRISPR knockout of LSD1 blocks AKT-mediated stabilization of the EMT-promoting transcription factor Snail and effectively blocks AKT-mediated EMT and migration. Overall we uniquely demonstrate that LSD1 mediates AKT activation in response to growth factors and oxidative stress, and LSD1-regulated AKT activity promotes EMT-like characteristics in a subset of PIK3CA mutant cells. Implications Our data supports the hypothesis that inhibitors targeting the CoREST complex may be clinically effective in CRC patients harboring PIK3CA mutations

Targeting enhancer switching overcomes non-genetic drug resistance in acute myeloid leukaemia.

Non-genetic drug resistance is increasingly recognised in various cancers. Molecular insights into this process are lacking and it is unknown whether stable non-genetic resistance can be overcome. Using single cell RNA-sequencing of paired drug naïve and resistant AML patient samples and cellular barcoding in a unique mouse model of non-genetic resistance, here we demonstrate that transcriptional plasticity drives stable epigenetic resistance. With a CRISPR-Cas9 screen we identify regulators of enhancer function as important modulators of the resistant cell state. We show that inhibition of Lsd1 (Kdm1a) is able to overcome stable epigenetic resistance by facilitating the binding of the pioneer factor, Pu.1 and cofactor, Irf8, to nucleate new enhancers that regulate the expression of key survival genes. This enhancer switching results in the re-distribution of transcriptional co-activators, including Brd4, and provides the opportunity to disable their activity and overcome epigenetic resistance. Together these findings highlight key principles to help counteract non-genetic drug resistance