Lung cancer is a particularly devastating disease, accounting for the most deaths among all cancer types in the United States. Despite a reduction in the country’s smoking rates, cigarette smoking remains the number one risk factor for lung cancer. Additionally arsenic exposure, which occurs primarily through contaminated drinking water in the U.S., is associated with increased lung cancer incidence. The nucleotide excision repair (NER) pathway is critical for maintenance of genomic fidelity, removing DNA lesions that could otherwise promote DNA mutations and drive carcinogenesis. Tobacco smoking introduces significant amounts of DNA damage and produces characteristic DNA mutations found in lung cancers of smokers, and arsenic increases lung cancer risk in smokers beyond the risk of smoking along. The contributions of these chemicals to DNA damage and cancer have been well documented, but few studies have examined their effects on DNA repair pathways, particularly the nucleotide excision repair (NER) pathway. Arsenic, while not directly mutagenic, promotes the carcinogenicity of other compounds including agents that produce DNA damage that is repaired by the NER pathway. In this dissertation I investigated the effects of cigarette smoke condensate (CSC, a whole-smoke tobacco surrogate) and arsenic on NER. I observed that CSC or arsenic treatment inhibited NER as measured by a slot-blot assay using UV-induced photolesions as model substrates to measure NER. The abundance of Xeroderma Pigmentosum complementation group C (XPC), a critical NER protein, was significantly reduced in all lines treated with either chemical, while XPA protein was unaffected. CSC and arsenic also affected RNA levels of certain NER genes. Finally, proteasome-regulated XPC turnover was affected by CSC and arsenic treatment, suggesting a potential mechanism for XPC protein inhibition. The observed impairment of NER by CSC is critically important in tobacco cancer etiology – CSC introduces DNA damage, some of which is repaired exclusively by NER, and CSC inhibits the NER pathway as well, providing a two-sided assault on cellular genetic fidelity. I then adapted the NER assay to measure repair in lymphocytes isolated from human subjects of a study investigating the high incidence of lung cancer in Appalachian Kentucky. I observed an age-dependent decline in NER efficiency that was modulated by subject smoking status and a reduced NER efficiency among current smokers in the lung cancer patient population compared to control subjects in the youngest age group, suggesting individual DNA repair capacity measured with this repair assay may be a biomarker for lung cancer susceptibility.

ADVANCED IMAGING ANALYSIS FOR PREDICTING TUMOR RESPONSE AND IMPROVING CONTOUR DELINEATION UNCERTAINTY By Rebecca Nichole Mahon, MS A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at Virginia Commonwealth University. Virginia Commonwealth University, 2018 Major Director: Dr. Elisabeth Weiss, Professor, Department of Radiation Oncology Radiomics, an advanced form of imaging analysis, is a growing field of interest in medicine. Radiomics seeks to extract quantitative information from images through use of computer vision techniques to assist in improving treatment. Early prediction of treatment response is one way of improving overall patient care. This work seeks to explore the feasibility of building predictive models from radiomic texture features extracted from magnetic resonance (MR) and computed tomography (CT) images of lung cancer patients. First, repeatable primary tumor texture features from each imaging modality were identified to ensure a sufficient number of repeatable features existed for model development. Then a workflow was developed to build models to predict overall survival and local control using single modality and multi-modality radiomics features. The workflow was also applied to normal tissue contours as a control study. Multiple significant models were identified for the single modality MR- and CT-based models, while the multi-modality models were promising indicating exploration with a larger cohort is warranted. Another way advances in imaging analysis can be leveraged is in improving accuracy of contours. Unfortunately, the tumor can be close in appearance to normal tissue on medical images creating high uncertainty in the tumor boundary. As the entire defined target is treated, providing physicians with additional information when delineating the target volume can improve the accuracy of the contour and potentially reduce the amount of normal tissue incorporated into the contour. Convolution neural networks were developed and trained to identify the tumor interface with normal tissue and for one network to identify the tumor location. A mock tool was presented using the output of the network to provide the physician with the uncertainty in prediction of the interface type and the probability of the contour delineation uncertainty exceeding 5mm for the top three predictions.

Secreted proteins play important roles in many cellular functions and molecular processes. Because secreted proteins potentially enter the blood stream, they can serve as valuable measures of health and disease useful for disease diagnosis and prognosis, therapeutic target identification, and patient stratification in personalized medicine. Consequently, significant interest exists in secreted protein analysis within complex biospecimens, particularly blood but significant bioanalytical challenges including the wide protein dynamic range >10 orders of magnitude remain. The cellular secretome therefore represents a viable alternative to direct biomarker discovery in biofluids. Finally, cellular systems are amenable to labeling for the production of intact stable isotope labeled (SIL) proteins that can be used as global internal standards for quantitative proteomics. In this dissertation, two secretome-focused studies were undertaken. The first study involving candidate biomarker discovery in radiation-induced autophagy utilized the p53-null and inducible H1299 non-small cell lung cancer (NSCLC) secretome. The study identified 364 secreted proteins that were mainly associated with exosomes (N=224) and chaperone activity (N=21). CHGB and SCG2 were identified as potential population-based biomarkers (for patient stratification) due to their consistent overexpression in p53-null H1299 cell secretomes compared to p53-wt cells before and after radiation. FAM3C, CANX, EIF5A, GPI, and TXNRD1 were identified as candidate biomarkers for patient prognosis following radiotherapy due to their differential expression only in response to radiation treatment. In the second study, a comprehensive glycoproteomics characterization of the SILAC-labeled HepG2 secretome was undertaken. 1635 SIL proteins, 492 of which were major plasma proteins including 192 cancer biomarkers were identified with high sequence coverage spanning six orders of magnitude. EDTA plasma spiked with the SIL secretomes yielded 63 proteins that were quantified with H/L ratios in all samples out of 1405 total proteins identified. Additionally, LC-MS/MS analysis of the Con A and WGA enriched 72h secretome:plasma sample afforded an opportunity to clearly distinguish between glycoproteins in plasma and the HepG2 secretome that share/differ in N-glycan structures. Collectively, the two studies reveal the suitability of the H1299 cancer cell secretome as an experimental model for biomarker studies and support the HepG2 secretome as a viable platform for producing SIL glycoproteins.

Abstract Purpose: The purpose of this paper is to quantify if using an average intensity projection (AIP) scan or a 30% phase (mid-ventilation surrogate, MidV) scan as the reference image for patient position verification affects reproducibility of lung cancer patient alignment under free-breathing cone beam computed tomography (CBCT) image guidance and to analyze the effects of common clinical issues on registration variability. Methods: AIPs were retrospectively created for 16 lung patients (14 SBRT, 2 conventional treatments) originally planned/treated using the 30% phase MidV surrogate scan as reference. The study included 3-5 CBCTs from each patient. Registrations were performed between the AIP-CBCT and between the MidV-CBCT by 5 individuals (student, medical physics resident, medical resident, medical physicist, and attending physician) using MIM 6.2 image registration platform (Beachwood, OH). The images were rigidly registered, internal tumor volume (ITV) contours were displayed, and no rotational adjustments were allowed to reflect real treatment conditions. Additionally, the registrations for AIP-CBCT and MidV-CBCT were repeated 3 times by one individual for intra-observer variability assessment. Patient setup rotations, tumor volume, tumor motion, and breathing variability were estimated for correlation with registration variability. Results: The magnitude of the average intra-observer standard deviations from the lateral (LAT), anterior-posterior (AP), and superior-inferior (SI) directions for the AIP/CBCT and MidV/CBCT registrations were 0.9 mm and 1.2 mm, respectively. The magnitude of the average inter-observer standard deviations for the AIP/CBCT and MidV/CBCT were 1.7 mm and 1.8 mm, respectively. Average discrepancies over the whole population were found to be small; however, some individual patients presented high variability. Patient-specific cases with high variability were analyzed and observations on its potential causes are discussed. Conclusion: The differences in alignment using AIP versus MidV as the reference images are, when averaged over the population studied, very small and clinically irrelevant for PTV margins > 5mm; however, individual patients may be impacted in a clinically relevant manner if smaller margins, 3 mm and below, are used instead.

As a validation study, this study addressed an under-researched area of bronchopulmonary cancer mortality and incidence. The association between altitude and bronchopulmonary cancer mortality and incidence was investigated using data from the Centers for Disease Control and Prevention Wide-ranging Online Data for Epidemiologic Research. The theoretical framework for my study was Bronfenbrenner's ecological model. This model emphasizes the relevance of social and physical environments that influence patterns of disease and injury and shape responses to these patterns of disease and injury. The age-adjusted bronchopulmonary cancer mortality and incidence rates per 100,000 people in the highest elevation and lowest elevation states were investigated. The data used in this study spans from 2006 to 2014. In this study, bivariate statistics were used to analyze the data. The relevant technique of performing an unpaired t-test was used. After performing age, gender, and race-stratified analysis, no significant difference in cancer mortality and incidence was found within the following three groups: Black or African American, Asian or Pacific Islander, and American Indian or Alaska Native. This was a new finding, as previous studies did not stratify for race. Cancer mortality and incidence were found to be lower in both the male and female groups for the highest elevation states. Cancer mortality and incidence were also found to be lower in all age categories for the highest elevation states. A positive social change impact of this study is that this research provides the groundwork for future studies to probe what in the environment is lowering the bronchopulmonary cancer mortality and incidence for the White population.

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De nombreuses études ont impliqué des TLR dans le développement et la progression tumorale. Précédemment, il a été démontré que les cellules tumorales expriment TLR7, un récepteur à ARNsb, et qu’une forte expression de TLR7 par les cellules tumorales de patients atteints de cancer du poumon est associée à un mauvais pronostic. Dans un modèle murin de cancer du poumon, cet effet pro-tumoral a été reproduit lors de l’injection d’agoniste de TLR7. Mes travaux de thèse ont eu pour objectif de déterminer les mécanismes impliqués dans les effets pro-tumoraux de TLR7. La stimulation de ce récepteur au niveau des cellules tumorales induit une production plus importante de CCL2 et GM-CSF, ainsi qu’un fort recrutement de MDSC au site de la tumeur. Ces MDSC, de par leurs propriétés immunosuppressives sont responsables de l’effet pro-tumoral à la suite de la stimulation de TLR7. Nous avons également mis évidence que la stimulation de TLR7 était pro-métastatique dans un modèle murin de cancer du poumon et que les MDSC étaient également impliquées dans cet effet. Ces effets pro-métastatiques associés au TLR7 ont été confirmés chez l’homme, grâce à l’étude de transcrits de molécules associées à l’invasion, l’angiogénèse, la transition épithélio-mésenchymateuse et les métastases. Enfin nous avons démontré la présence de ligand de TLR7 chez les patients atteints de cancer du poumon et démontré que l’injection intratumorale de virus respiratoires, IAV et RSV, a un effet pro-tumoral dans notre modèle de cancer du poumon. Ces virus respiratoires pourraient donc être à l’origine de la surexpression de TLR7 et du mauvais pronostic associé à ce récepteur chez les patients atteints de cancer du poumon. Ces recherches ont donc permis de mettre en évidence de nouveaux facteurs aggravants dans le cancer du poumon, dont les virus respiratoires, et de découvrir les mécanismes impliqués. / Numerous studies have implicated some TLR in tumor development. Previously, we have demonstrated that lung tumor cells express TLR7, a receptor for ssRNA, and that high TLR7 expression confers to NSCLC patients bad clinical outcome. In mice models of lung cancer, we further demonstrated that the injection of TLR7 agonists led to a pro-tumoral effect.My thesis work has firstly demonstrated the mechanisms involved in the pro-tumoral effects of TLR7 in lung cancer: TLR7 stimulation on tumor cells induces a high production of CCL2 and GM -CSF, as well as a sharp MDSC recruitment within the tumor. These MDSC, by their immunosuppressive properties, are implicated in the pro-tumoral effect upon TLR7 stimulation. We also demonstrated that TLR7 stimulation was pro-metastatic in a mice model of lung cancer and that MDSC were also involved in this effect. These pro-metastatic effects associated with TLR7 have been confirmed in humans through the studies of transcripts and proteins involved in invasion, angiogenesis, Epithelial–mesenchymal transition and metastasis. Finally, we demonstrated that TLR7 ligands are present in tumor microenvironment of lung cancer patients and that intratumoral injection of respiratory viral infections such as IAV and RSV, have a pro-tumoral effect in lung cancer mice model. These respiratory viruses could therefore be at the origin of the overexpression of TLR7 and the poor clinical outcome associated with this receptor in lung cancer patients. This research has thus made possible to highlight new aggravating factors in lung cancer, including respiratory viruses, and to discover the mechanisms involved.

Lung cancer is the second most common cancer type and is associated with high mortality rates. The survival rate for lung cancer patients has increased slowly in the last decade mainly as the result of the development of novel targeted and immune therapies. However, non-small cell lung cancer patients lacking known or actionable driver mutations and small cell lung cancer patients with recurrent disease are still in urgent need of new therapies. Drug repurposing is an efficient way to identify new therapies since it uses clinically relevant small molecule drugs. Determination of off-targets of small molecules is a novel approach towards drug repurposing as unintended targets can play important roles for a new clinical application. Here we apply functional proteomics and systems pharmacology approaches to determine target profiles and differential mechanisms of action, independent of the intended targets, of small molecules with similar chemical structures. Using chemical proteomics, we elucidated the differential target profiles of two clinical CDK4/6 inhibitors: palbociclib and ribociclib. We observed that palbociclib, but not ribociclib, is a dual protein and lipid kinase inhibitor that in addition to the intended cell cycle pathway modulates the PI3K/AKT and autophagy pathways. Furthermore, we investigated the off-targets of two MET/VEGFR inhibitors, foretinib and cabozantinib. Foretinib, but not cabozantinib, was found to reduce cell viability and induce cell cycle arrest and apoptosis in lung cancer cell lines. Using a systems pharmacology approach, which included chemical proteomics, phosphoproteomics and RNA-Seq, integrated data analysis and subsequent functional validation revealed a complex polypharmacology mechanism of action of foretinib, which involves the simultaneous inhibition of MEK, AURKB and FER protein kinases. Because AURKB is an important protein kinase for the proliferation of MYC-amplified small cell lung cancer cells, we were able to design a drug combination of foretinib with barasertib, a much more potent AURKB inhibitor, that enhanced specifically the cell death of MYC-amplified small cell lung cancer cells. In summary, we show that small structural changes of closely related clinical drugs can result in pronounced differences in their target profiles and anticancer activities through differential polypharmacology mechanisms and that an integrated systems pharmacology approach can identify new repurposing opportunities for these drugs in cancers with high unmet medical need.

The goal of this study was to identify novel drug repurposing opportunities in cancer by utilizing the off-target profiles of clinically relevant kinase inhibitors. This was based on the observation that the global target profiles of compounds are largely ignored and that many compounds have activity that cannot be explained by their cognate target alone. Additionally, by utilizing clinically relevant compounds, any results would hold a high potential for eventual clinical implementation. We utilized a systems pharmacology approach utilizing cell viability-based drug screening to identify compounds with beneficial off-target activity and then using chemical and phosphoproteomics in order to elucidate the mechanisms of action of these compounds. We found that tivantinib has off-target activity in NSCLC cells through inhibition of GSK3. Based on tivantinib’s ability to inhibit GSK3, we hypothesized that tivantinib would therefore have activity in acute myeloid leukemia (AML). We found that tivantinib had potent activity in AML through inhibition of GSK3. We also identified a highly synergistic combination with ABT-199 by drug synergy screening which was effective in HL60 cells and patient derived AML cells. We also found that the anaplastic lymphoma kinase (ALK) inhibitor, ceritinib, had activity across several ALK-negative lung cancer cell lines. We utilized integrated functional proteomics to identify the new targets and network-wide signaling effects. Combining pharmacological inhibitors and RNA interference revealed a polypharmacology mechanism involving the noncanonical targets IGF1R, FAK1, RSK1 and RSK2. Mutating the downstream signaling hub YB1 protected cells from ceritinib. Consistent with YB1 signaling being known to cause taxol resistance, combination of ceritinib with paclitaxel displayed strong synergy, particularly in cells expressing high FAK autophosphorylation, which we show to be prevalent in lung cancer. Together, we present a systems chemical biology platform for elucidating multikinase inhibitor mechanisms, synergistic drug combinations, mechanistic biomarker candidates and identifying novel drug repurposing opportunities.

In order to study the incidence of Estrogen Receptors (ER) in breast carcinoma, lung carcinoma and melanoma, an in situ hybridisation technique for ER mRNA (ER mRNA-ISH) was developed. Various technical aspects of the procedure including tissue fixation, hybridisation conditions, and demonstration technique were investigated in order to obtain an optimum technique for routine use. ISH results were compared with ER immunohistochemistry using the monoclonal antibodies ER1D5 and D5. Commercially available biotin labelled antisense oligonucleotides to ER, Poly A (total mRNA), and sense chromogranin (negative control) were applied to frozen and formalin-fixed paraffin sections of breast carcinomas. For frozen sections, various fixatives including formalin, alcohol, Schoobridge, Zamboni's and acetic- alcohol were compared. A direct streptavidin- eroxidase and an indirect demonstration method using anti-biotin were also compared. The effect of differing formamide concentrations and post hybridisation stringency washings were analysed. An optimised ISH technique was then applied to frozen sections of 21 cases of breast carcinoma and 11 cases of lung carcinoma. Results were compared to H222 staining on adjacent sections. The ISH technique was also optimised for use on formalin-fixed, paraffin-embedded sections of 28 breast carcinomas and 17 melanomas. The results were compared with ER1D5 and D5 immunohistochemistry done on adjacent sections. The occurrence of endogenous biotin was also studied on a range of normal tissues. Consistent ISH results were obtained when formamide was omitted from the hybridisation cocktail, high stringency post hybridisation washes were discarded, room temperature hybridisations and an indirect demonstration method were used. Fixation of frozen sections in acetic/ethanol gave more consistent results with good morphology and resulted in positive nucleolar staining in 90% of breast and 45% of lung carcinomas. Positive nucleolar staining was also present in frozen sections of one metastatic melanoma. In formalin fixed paraffin sections, acid hydrolysis and pronase treatment were required prior to ISH. Cytoplasmic and/or nucleolar ER mRNA-ISH staining was seen in 87% of breast carcinoma and 97% of melanoma studied. ER1D5 was present in 54% of breast carcinomas but was absent in all melanomas. D5, on the other hand, was found in 88% of the melanomas. In conclusion, ER mRNA-ISH can be successfully done on acetic/alcohol fixed frozen sections and formalin fixed paraffin sections. Formamide, high stringency washes and elevated hybridisation temperatures are detrimental to a successful ISH reaction and an indirect demonstration method (using anti-biotin) is preferred. Unfortunately, endogenous biotin can cause false positive ISH reactions and needs to be considered during interpretation. Results show that the localisation of ER mRNA in the nucleolus is specific. Both ER mRNA-ISH and ER immunohistochemistry indicate that melanomas and some lung carcinomas contain a receptor possibly similar to that in breast carcinomas. / Thesis (M.Sc.)--Department of Anatomical Sciences, 2004.