CONTEXTE : Le cancer colorectal (CCR) reste l’un des cancers les plus diagnostiqués au Canada et dans le monde. Malgré les efforts en matière de dépistage, la moitié des cancers colorectaux sont encore diagnostiqués à des stades avancés de la maladie, réduisant ainsi les chances de survie à ce cancer. La prévention du CCR reste encore primordiale et les efforts doivent être maintenus pour l’identification de ses facteurs de risque modifiables. Durant cette dernière décennie, on a assisté à un cumul d’évidence sur l’association entre l’enrichissement colorectal en une bactérie spécifique, Fusobacterium nucleatum (F. nucleatum), et le CCR. Ce qui a ressuscité le débat sur l’association même entre la maladie parodontale (MP) et le CCR, puisque F. nucleatum est non seulement une bactérie commensale de la bouche, mais surtout l’une des principaux agents pathogènes de la MP. Des études épidémiologiques antérieures avaient en effet déjà suggéré que le la MP serait associée au risque de CCR, mais leurs résultats sont restés non concluants à cause de leurs défaillances méthodologiques. La diffusion des bactéries parodontopathogènes, comme F. nucleatum, et de leurs produits de virulence de la bouche vers le côlon et la libération des médiateurs d’inflammation chronique dans la circulation générale sont les mécanismes incriminés dans l’association entre la MP et le CCR. OBJECTIFS: 1) Vérifier l’association entre la MP et le CCR; 2) Synthétiser la littérature sur l’association entre la détection de la bactérie F. nucleatum dans le côlon et le CCR et; 3) Vérifier la faisabilité d’investiguer l’expression concomitante de F. nucleatum, dans les deux milieux buccal et colorectal, en présence de lésions néoplasiques colorectales. Ces deux derniers objectifs sont un préambule à l’investigation du rôle des bactéries causales de la MP, précisément F. nucleatum, comme mécanisme d’association entre la MP et le CCR. MÉTHODES: Nous avons entrepris trois projets de recherche distincts qui répondent aux trois objectifs respectifs de recherche cités ci-dessus: 1) Une étude cas-témoins à base populationnelle (Projet COLDENT) a inclut 348 cas incidents de CCR et 310 témoins qui lui sont appariés dans des catégories d’âge et de sexe. Des données ont été collectées sur l’exposition à la MP et aux principaux facteurs de risque du CCR; 2) Une revue systématique avec méta-analyse d’études observationnelles ayant investigué la bactérie, F. nucleatum, dans des échantillons colorectaux, chez des cas de CCR et des témoins exempts de lésions cancéreuses ou précancéreuses colorectales; 6 et 3) Une étude pilote cas-témoins à base hospitalière, auprès de 22 cas de néoplasies colorectales et 21 témoins, examinés par coloscopie. Des échantillons de salive et des biopsies de muqueuse colorectale, ainsi que des données sur l’exposition à la MP et aux principaux facteurs de risque du CCR ont été collectées. RÉSULTATS: Les résultats de notre étude cas-témoins populationnelle suggèrent que le taux d’incidence de CCR était augmenté chez les personnes avec un historique positif de MP comparé aux personnes sans historique de MP, en ajustant pour la majorité des facteurs de confusion potentiels (Rapport des taux ajusté = 1,45 ; Intervalle de confiance (IC) à 95 % : 1,04-2,01). Les résultats de notre revue systématique incluant 24 études observationnelles ont montré que dans la majorité des études où la charge de F. nucleatum dans les échantillons colorectaux était quantifiée, celle-ci était significativement plus élevée chez les cas de CCR que chez les témoins. Les résultats de la méta-analyse de 12 études observationnelles qui ont rapporté le pourcentage des échantillons colorectaux où F. nucleatum était détecté montrent une association significativement positive entre la détection de la bactérie F. nucleatum dans le côlon et le CCR (Rapport de cotes combiné = 8,3; IC à 95 % = 5,2-13; Indice d’hétérogénéité I2 = 26,3 %; p pour hétérogénéité = 0,18). Enfin, les résultats préliminaires de l’étude de faisabilité appuient la faisabilité et l’utilité de mener une étude subséquente pour investiguer F. nucleatum dans la salive et le côlon en présence de néoplasies colorectales afin de vérifier son rôle dans l’association entre la MP et le CCR, mais des ajustements doivent être apportés à la méthodologie initiale. CONCLUSION: Nos résultats suggèrent que l’exposition à la MP peut augmenter le risque de CCR, bien qu’on ne puisse encore confirmer de lien causal. On espère que ce travail sensibilise les cliniciens, décideurs en santé et public à l’importance de prévenir et de contrôler les maladies buccodentaires, notamment la MP, pour la prévention même de maladies systémiques encore plus fatales, tels que le CCR. / BACKGROUND: Colorectal cancer (CRC) remains one of the most diagnosed cancers in Canada and around the world. Despite screening efforts, half of colorectal cancers are still diagnosed at advanced stages of the disease, thus reducing the chances of survival from this cancer. Prevention of CRC still remains essential, and efforts must be maintained to identify its modifiable risk factors. Over the past decade, there has been an accumulation of evidence on the association between colorectal enrichment in a specific bacterium, Fusobacterium nucleatum (F. nucleatum), and CRC. This has sparked debate on the association between periodontal disease (PD) and CRC, since F. nucleatum is not only a commensal bacterium of the mouth, but above all one of the main pathogens of PD. Previous epidemiological studies had indeed already suggested that PD would be associated with the risk of CRC, but their results remained inconclusive because of their methodological flaws. Dissemination of periodontal pathogen bacteria such as F. nucleatum, and of their virulence products, from the mouth to the colon and the release of chronic inflammatory mediators into the bloodstream are suggested as the mechanisms involved in the association between PD and CRC. OBJECTIVES: 1) To verify the association between PD and CRC; 2) To synthesize the literature on the association between the detection of the bacterium F. nucleatum in the colon and CRC; and 3) To verify the feasibility of investigating the concomitant expression of F. nucleatum, in both oral and colorectal environments, in the presence of colorectal neoplasms. These last two objectives are a preamble to the investigation of the role of the causative bacteria of PD, specifically F. nucleatum, as a mechanism of association between PD and CRC. METHODS: We undertook three separate research projects that address the three respective research objectives listed above: 1) A population-based case-control study (COLDENT Project) included 348 incident cases of CRC and 310 age and sex frequency-matched controls. Data were collected on PD and on major risk factors for CRC; 2) A systematic review with meta-analysis of observational studies that have investigated the bacterium F. nucleatum in colorectal samples, in CRC cases and colorectal cancerous or precancerous-free controls; and 3) A pilot hospital-based case-control study, with 22 cases of colorectal neoplasms and 21 controls, examined by colonoscopy. Saliva samples and colorectal mucosal biopsies as well as data on exposure to PD and major risk factors for CRC were collected. 8 RESULTS: The results of our population-based case-control study suggest that the rate of CRC was increased in people with a positive history of PD compared to people without a history of PD, adjusting for the majority of potential confounders (adjusted rate ratio = 1.45; 95% Confidence interval (CI): 1.04-2.01). The results of our systematic review including 24 observational studies showed that in most studies where the load of F. nucleatum in colorectal samples was quantified, it was significantly higher in CRC cases than in controls. The results of the meta-analysis of 12 observational studies that reported the percentage of colorectal samples where F. nucleatum was detected show a significantly positive association between the detection of the bacterium F. nucleatum in the colon and CRC (pooled odds ratio = 8.3; 95% CI = 5.2-13; heterogeneity index I 2 = 26.3%; p for heterogeneity = 0.18). Finally, the preliminary results of the feasibility study support the feasibility and utility of conducting a subsequent study to investigate F. nucleatum in saliva and colon in the presence of colorectal neoplasms to verify its role in the association between PD and CCR, but adjustments need to be made to the original methodology. CONCLUSION: Our results suggest that exposure to PD may increase the risk of CRC, although a causal relationship cannot yet be confirmed. It is hoped that this work will sensitize clinicians, health policy makers and the public to the importance of preventing and controlling oral diseases, including PD, for the prevention of even more fatal systemic diseases, such as CRC.

The detection of plasma cell–free tumor DNA (ctDNA) is prognostic in colorectal cancer (CRC) and has potential for early prediction of disease recurrence. In clinical routine, ctDNA-based diagnostics are limited by the low concentration of ctDNA and error rates of standard next-generation sequencing (NGS) approaches. We evaluated the potential to increase the stability and yield of plasma cell–free DNA (cfDNA) for routine diagnostic purposes using different blood collection tubes and various manual or automated cfDNA extraction protocols. Sensitivity for low-level ctDNA was measured in KRAS-mutant cfDNA using an error-reduced NGS procedure. To test the applicability of rapid evaluation of ctDNA persistence in clinical routine, we prospectively analyzed postoperative samples of 67 CRC (stage II) patients. ctDNA detection was linear between 0.0045 and 45%, with high sensitivity (94%) and specificity (100%) for mutations at 0.1% VAF. The stability and yield of cfDNA were superior when using Streck BCT tubes and a protocol by Zymo Research. Sensitivity for ctDNA increased 1.5-fold by the integration of variant reads from triplicate PCRs and with PCR template concentration. In clinical samples, ctDNA persistence was found in ∼9% of samples, drawn 2 weeks after surgery. Moreover, in a retrospective analysis of 14 CRC patients with relapse during adjuvant therapy, we successfully detected ctDNA (median 0.38% VAF; range 0.18–5.04% VAF) in 92.85% of patients significantly prior (median 112 days) to imaging-based surveillance. Using optimized pre-analytical conditions, the detection of postoperative ctDNA is feasible with excellent sensitivity and allows the prediction of CRC recurrence in routine oncology testing.

Colorectal cancer is one of the most prevalent malignancies globally and recently introduced digital pathology enables the use of machine learning as an aid for fast diagnostics. This project aimed to develop a deep neural network model to specifically identify and differentiate dysplasia in the epithelium of colorectal polyps and was posed as a binary classification problem. The available dataset consisted of 80 whole slide images of different H&E-stained polyp sections, which were parted info smaller patches, annotated by a pathologist. The best performing model was a pre-trained ResNet-18 utilising a weighted sampler, weight decay and augmentation during fine tuning. Reaching an area under precision-recall curve of 0.9989 and 97.41% accuracy on previously unseen data, the model’s performance was determined to underperform compared to the task’s intra-observer variability and be in alignment with the inter-observer variability. Final model made publicly available at https://github.com/stinabr/classification-of-colorectal-polyps.

Despite a decade of publications investigating the effect of germline polymorphisms on both toxicity related to treatment with 5-fluorouracil-based (5-FU) chemotherapy and prognosis following diagnosis with colorectal cancer (CRC), few genetic biomarkers have been identified convincingly. For 5-FU toxicity and CRC prognosis, in four results chapters, this thesis aims to validate previously-reported genetic biomarkers, identify new markers, determine the mechanistic basis of associated polymorphisms, and expand upon methods in the field. The first three results chapters investigate genetic biomarkers for the prediction of toxicity caused by 5-FU-based treatment, particularly for the 5-FU prodrug capecitabine (Xeloda®, Roche). In the first, a systematic review and meta-analysis is performed for all variants that have been previously studied for an association with toxicity caused by any 5-FU-based drug regimen. 16 studies are analysed, including 36 previously-studied variants. Four variants show strong evidence of affecting a patient’s risk of global (any) 5-FU-related toxicity upon analysis of both the existing data and over 900 patients from the QUASAR2 trial of capecitabine +/- bevacizumab (Avastin®, Roche/Genentech): DPYD 2846, DPYD *2A, TYMS 5’VNTR and TYMS 3’UTR. Next, 1,456 polymorphisms in 25 genes involved in the activation, action or degradation of 5-FU are investigated in 1,046 patients from QUASAR2. At a Bonferroni-corrected p-value threshold of 3.43e-05, three novel associations with capecitabine-related toxicity are identified in DPYD (rs12132152, rs7548189, A551T) and the previously-identified TYMS 5’VNTR and 3’UTR toxicity polymorphisms are refined to a tagging SNP (rs2612091) downstream of TYMS and intronic to the adjacent ENOSF1, the latter of which appears to be functional. Finally, a genome-wide investigation of 4.77 million directly genotyped or imputed SNPs identifies one variant (rs2093152 on chr20) as significantly associated with capecitabine-related diarrhoea (p<5e-08), though no associations meet this threshold for global toxicity. In the study of CRC prognosis, a severe left truncation to the VICTOR trial is defined and shown to probably reduce statistical power but not bias effect estimates. Applying standard and novel genome-wide analysis approaches, a set of 43 SNPs are prioritised for future work. With over one million new CRC cases annually, this work helps define biomarkers that could become broadly applicable in the clinical setting.

Au cours de la dernière décennie, la pathologie numérique a été améliorée grâce aux avancées des algorithmes d'analyse d'images et de la puissance de calcul. Néanmoins, le diagnostic par un expert à partir d'images histopathologiques reste le gold standard pour un nombre considérable de maladies notamment le cancer. Ce type d'images préserve la structure des tissus aussi proches que possible de leur état vivant. Ainsi, cela permet de quantifier les objets biologiques et de décrire leur organisation spatiale afin de fournir une description plus précise des tissus malades. L'analyse automatique des images histopathologiques peut avoir trois objectifs: le diagnostic assisté par ordinateur, l'évaluation de la sévérité des maladies et enfin l'étude et l'interprétation des mécanismes sous-jacents des maladies et leurs impacts sur les objets biologiques. L'objectif principal de cette thèse est en premier lieu de comprendre et relever les défis associés à l'analyse automatisée des images histologiques. Ensuite, ces travaux visent à décrire les populations d'objets biologiques présents dans les images et leurs relations et interactions à l'aide des statistiques spatiales et également à évaluer la significativité de leurs différences en fonction de la maladie par des tests statistiques. Après une étape de séparation des populations d'objets biologiques basée sur la couleur des marqueurs, une extraction automatique de leurs emplacements est effectuée en fonction de leur type, qui peut être ponctuel ou surfacique. Les statistiques spatiales, basées sur la distance pour les données ponctuelles, sont étudiées et une fonction originale afin de mesurer les interactions entre deux types de données est proposée. Puisqu'il a été montré dans la littérature que la texture d'un tissu est altérée par la présence d'une maladie, les méthodes fondées sur les motifs binaires locaux sont discutées et une approche basée sur une modification de la résolution de l'image afin d'améliorer leur description est introduite. Enfin, les statistiques descriptives et déductives sont appliquées afin d'interpréter les caractéristiques extraites et d'étudier leur pouvoir discriminant dans le cadre de l'étude des modèles animaux de cancer colorectal. Ce travail préconise la mesure des associations entre différents types d'objets biologiques pour mieux comprendre et comparer les mécanismes sous-jacents des maladies et leurs impacts sur la structure des tissus. En outre, nos expériences confirment que l'information de texture joue un rôle important dans la différenciation des deux modèles d'implantation d'une même maladie. / During the last decade, digital pathology has been improved thanks to the advance of image analysis algorithms and calculus power. However, the diagnosis from histopathology images by an expert remains the gold standard in a considerable number of diseases especially cancer. This type of images preserves the tissue structures as close as possible to their living state. Thus, it allows to quantify the biological objects and to describe their spatial organization in order to provide a more specific characterization of diseased tissues. The automated analysis of histopathological images can have three objectives: computer-aided diagnosis, disease grading, and the study and interpretation of the underlying disease mechanisms and their impact on biological objects. The main goal of this dissertation is first to understand and address the challenges associated with the automated analysis of histology images. Then it aims at describing the populations of biological objects present in histology images and their relationships using spatial statistics and also at assessing the significance of their differences according to the disease through statistical tests. After a color-based separation of the biological object populations, an automated extraction of their locations is performed according to their types, which can be point or areal data. Distance-based spatial statistics for point data are reviewed and an original function to measure the interactions between point and areal data is proposed. Since it has been shown that the tissue texture is altered by the presence of a disease, local binary patterns methods are discussed and an approach based on a modification of the image resolution to enhance their description is introduced. Finally, descriptive and inferential statistics are applied in order to interpret the extracted features and to study their discriminative power in the application context of animal models of colorectal cancer. This work advocates the measure of associations between different types of biological objects to better understand and compare the underlying mechanisms of diseases and their impact on the tissue structure. Besides, our experiments confirm that the texture information plays an important part in the differentiation of two implemented models of the same disease.

Animal testing is still the common method to test the efficacy of new drugs, but tissue engineered in vitro models are becoming more acceptable for replacing and reducing animal testing in anti-cancer drug screening by developing in vitro three-dimensional (3D) tumour models for anti-cancer drug testing. In this study, three-dimensional (3D) culture methods were developed to mimic the tumour microenvironment. 3D culturing is to seed, maintain and expand cultured cells in three-dimensional space, in contrast to the traditional two-dimensional (2D) method in which the cells attach to the bottom of culture containers as monolayers. To mimic the intercellular interplay for tumour study, cell co-culture was applied. In this thesis, perfusion culture showed a better homeostasis for 3D tumour model growth over 17 days, with a more controllable working platform and a more reliable response-dose correlation for data interpretation. In the Matrigel sandwich system, the co-culture of breast cancer cells and endothelial cells demonstrated the morphology featuring a vascular network and tumour structures, with the thickness of the three-dimensional structure around 100µm and tubule length 200-400 µm, and maintained for 10 days. The comparisons studies between Matrigel sandwich and other methods suggest that though not fully characterised, Matrigel is still a valuable scaffold choice for developing co-culture 3D tumour model. Finally, the combination of perfusion and co-culture showed the potential of applying this model in angiogenesis assay, with a drug response profile combining cell viability and morphology to mimic in vivo tumour physiology.

Une dérégulation de la voie de signalisation Ras/Raf/MEK/ERK1/2 est observée dans plus de 30% des cancers et des mutations activatrices de RAS sont observées dans 30% à 50% des adénomes colorectaux. À la suite d’une analyse extensive de biopsies de tumeurs colorectales humaines par micromatrices tissulaires (TMA), nous avons observé que 44% des tissus cancéreux exprimaient MEK1/2 phosphorylés, contre 10% des tissus normaux. L'analyse des TMA a également révélé que 79% des tumeurs arboraient un marquage nucléaire de MEK1/2 phosphorylés, contre 4 % pour les tissus normaux. Bien que la voie MEK/ERK1/2 soit fréquemment activée dans les cancers, le rôle précis des isoformes de MEK1 et de MEK2 n'a jamais été clairement établie. De même, l'impact de cette localisation nucléaire aberrante de phospho-MEK1/2, dans l'initiation et la progression des cancers colorectaux, est inconnu. Lors d'un premier projet, nous avons démontré, que l’expression de MEK1 ou MEK2 activé est suffisante pour transformer in vitro des cellules intestinales épithéliales de rat (IEC-6). L'expression des mutants actifs de MEK1 ou MEK2 est suffisante pour induire une dérégulation de la prolifération cellulaire et engendrer la formation d'adénocarcinomes invasifs dans un modèle de greffe orthotopique du côlon chez la souris. Nous avons également démontré que l'inhibition de MEK2 par shRNA supprime complètement la prolifération des lignées humaines de cancer du côlon, alors que la suppression de MEK1 a peu d'effet sur la capacité de prolifération. Le deuxième projet, nous a permis d'observer que l'expression d'un mutant nucléaire de MEK1 dans les cellules IEC-6 transforme drastiquement les cellules. Une augmentation de prolifération, une résistance à l'anoikose, un dérèglement du cycle cellulaire, de l'instabilité chromosomique (CIN), de la tétra/aneuploïdie sont observés. La caractérisation des mécanismes responsables de cette localisation aberrante de MEK1/2 phosphorylés, a permis d'identifier la protéine Sef, un régulateur de la localisation cytoplasmique de MEK/ERK1/2. Nous avons démontré que l'expression d'une forme oncogénique de Ras (H-RasV12) inhibe l'expression de Sef, engendrant alors une accumulation nucléaire de MEK1/2 activés. Plus encore, la réexpression de Sef restaure la localisation cytoplasmique de MEK1/2 et renverse les propriétés tumorigéniques ainsi que l'aneuploïdie induite par Ras activé. Un troisième projet, visant la caractérisation des mécanismes associés à la CIN et à l'aneuploïde engendrés par l'activation aberrante de la voie de Ras-ERK1/2, a permis d'observer que l'hyperactivation de ERK1/2 induit des anomalies mitotiques menant à la binucléation. Une localisation erronée et une surexpression de la kinase Aurora A, de même que des protéines de passage du complexe chromosomique (CPC), Aurora B, Survivine et INCENP, sont observées. L'inhibition partielle de l'activation de ERK1/2 par de faible dose de PD184352, un inhibiteur de MEK1/2, est suffisante pour renverser la surexpression de ces régulateurs mitotiques, de même que corriger les anomalies de la mitose et réduire la tétra/aneuploïdie engendrée par Ras oncogénique. Ainsi, nous avons démontré, pour la première fois, que la voie des MAP kinases ERK1/2 est impliquée dans la CIN, la tétraploïdie et l'aneuploïdie. Nos résultats suggèrent que la perte de Sef est un événement oncogénique précoce, qui contribue à la localisation nucléaire aberrante de MEK1/2 qui est observée dans les tumeurs colorectales. Cette localisation anormale de MEK1/2 est associée à l'initiation de la transformation, la progression tumorale et la CIN, via l'activité soutenue de ERK1/2. Ces informations sont capitales et démontrent l’importance de la voie de signalisation Ras/Raf/MEK/ERK1/2 dans le processus de tumorigénèse colorectale. / The Ras-dependent Raf/MEK/ERK1/2 signaling pathway is frequently hyperactivated in human cancer as a result of receptor tyrosine kinase overexpression or gain-of-function mutations in RAS or RAF genes. More specificaly, activating mutation in RAS genes are found in ~ 30-50% of colorectal adenomas and phosphorylation of ERK1/2 is frequently observed in human colorectal cancer cells and tumor specimens. In a large TMA analysis, we found that MEK1/MEK2 are aberrantly activated in 44% of human colorectal cancers. In addition, our analysis revealed that 79% of colorectal cancers exhibit aberrant phospho-MEK1/2 staining in the nucleus, as compared to 4% of normal tissue. How dysregulation and mislocalization of MEK1/2 contribute to tumor initiation and progression is not well understood. In order to determine the exact contribution of MEK1 and MEK2 to the pathogenesis of colorectal cancer, wild type and constitutively active forms of MEK1 and MEK2 were ectopically expressed by retroviral gene transfer in the normal intestinal epithelial cell line IEC-6. We found that the expression of activated MEK1 or MEK2 is sufficient to morphologically transform intestinal epithelial cells, dysregulate cell proliferation and induce the formation of high-grade adenocarcinomas after orthotopic transplantation in mice. A large proportion of these intestinal tumors metastasize to the liver and lung. Importantly, we show that silencing of MEK2 expression completely suppresses the proliferation of human colon carcinoma cell lines, whereas inactivation of MEK1 has a much weaker effect. In a second project, we have investigated the impact of the nuclear mislocalization of phosphorylated MEK1/2 observed in colorectal tumors. We show that oncogenic activation of Ras is sufficient to induce the nuclear accumulation of phosphorylated MEK1/2 and ERK1/2 in intestinal epithelial cells. To evaluate the biological impact of the mislocalization of MEK1/2, we have forced the localization of MEK1 in the nucleus of epithelial cells. We found that sustained nuclear MEK1 signaling leads to hyperactivation of ERK1/2 and to enhanced cell proliferation. Nuclear localization of MEK1 also leads to tetraploidization, chromosomal instability (CIN) and tumorigenesis. Importantly, we show that oncogenic Ras downregulates the spatial regulator Sef, concomitant to nuclear accumulation of activated MEK1/2. Moreover, re-expression of Sef is sufficient to restore the normal localization of MEK1/2 and to revert the cell cycle defects and tumorigenesis induced by oncogenic Ras. Another project was initiated to characterize the tetraploidy and CIN observed upon hyperactivation of the Ras-ERK1/2 pathway. Aneuploidy and CIN are observed in the majority of colorectal cancers and are associated with a poorer prognosis. We show that hyperactivation of ERK1/2 by oncogenic Ras or sustained nuclear MEK-ERK1/2 signaling induces mitotic defects that lead to tetraploidy, aneuploidy and CIN. We also found that dysregulation of Ras-ERK1/2 signaling alters the expression and localization of Aurora A and the Chromosomal passenger complex proteins. In conclusion, we show for the first time that the MEK/ERK1/2 signaling pathway is implicated in aneuploidy and CIN. Our results suggest that sustained nuclear ERK1/2 signaling may contribute to the initiation and progression of colorectal cancer by rapidly inducing aneuploidy and CIN. We suggest that loss of Sef is an early oncogenic event that contributes to genetic instability and tumor progression by sustaining nuclear ERK1/2 signaling. These observations are significant and highlight the importance of the Ras-ERK1/2 signaling pathway in colorectal tumorigenesis.

Recent knowledge suggests that the onset of cancer is modulated by the interplay of internal and external environmental factors along with numerous gene variants. Structural chromsomal aberrations in peripheral blood lymphocytes are considered as biomarkers of effect of genotoxic carcinogens and reflect elevated risk of cancer. Incomplete or deficient repair of double-strand breaks in DNA underlie chromosomal aberrations and the measurement of cytogenetic alterations may reflect interindividual differences in the response towards the mutagen. In this study the expected deficiences in the DNA repair capacity have been determined in incident oncological patients with breast, colorectal and urogenital cancers. The determination of chromosomal aberrations have been supplemented by the measurement of variants in genes involved in double-strand breaks repair (XRCC3, rs861539; RAD54L, rs1048771). Methodologically, we employed conventional cytogenetic analysis, cytogenetic analysis following the induction of chromocomal damage by bleomycin ("Challenge assay"), TaqMan discrimination analysis for the detection of allelic variants and statistical analyses. By using these methods we did not observe statistically signifiant differences either in chromosomal breaks (p=0,354) or in a percentage of cells with...

The thesis provides a comprehensive overview of key issues affecting practice, policy and patients, in current efforts for colorectal cancer (CRC) disease control. The global burden of CRC is expected to increase by 60% to more than 2.2 million new cases and 1.1 million deaths by 2030. CRC incidence and mortality rates vary up to 10-fold worldwide, which is thought to reflect variation in lifestyles, especially diet. Better primary prevention, and more effective early detection, in screening and surveillance, are needed to reduce the number of patients with CRC in future1. The risk factors for CRC development include genetic, behavioural, environmental and socio-economic factors. Changes to surveillance, which offer non-invasive testing and provide primary prevention interventions represent promising opportunities to improve outcomes and personalise care in those at risk of CRC. By systematic review of the literature, I highlight the gaps in comparative effectiveness analyses of post-polypectomy surveillance. Using micro-simulation methods I assess the role of non-invasive, faecal immunochemical testing in surveillance programmes, to optimise post-polypectomy surveillance programmes, and in an accompanying sub-study, I explore the value of adding an adjunct diet and lifestyle intervention. The acceptability of such revisions is exposed to patient preference evaluation by discrete choice experiment methods. These preferences are accompanied by evidence generated from the prospective evaluation of the health literacy, numeracy, sedentary behaviour levels, body mass index (BMI) and information provision about cancer risk factors, to highlight the potential opportunities for personalisation and optimisation of surveillance. Additional analysis examines the optimisation of a screening programme facing colonoscopy constraints, highlighting the attendant potential to reduce costs and save lives within current capacity.

Connor O’Hara July 29, 2019 Inhibition of Cancer Stem Cells by Glycosaminoglycan Mimetics In the United States cancer is the second leading cause of death, with colorectal cancer (CRC) being the third deadliest cancer and expected to cause over 51,000 fatalities in 2019 alone.1 The current standard of care for CRC depends largely on the staging, location, and presence of metastasis.2 As the tumor grows and invades nearby lymph tissue and blood vessels, CRC has the opportunity to invade not only nearby tissue but also metastasize into the liver and lung (most commonly).3 The 5-year survival rate for metastasized CRC is <15%, and standard of care chemotherapy regimens utilizing combination treatments only marginally improve survival.3-5 Additionally, patients who have gone into remission from late-stage CRC have a high risk of recurrence despite advances in treatment.6-7 The Cancer Stem-like Cell (CSC) paradigm has grown over the last 20 years to become a unifying hypothesis to support the growth and relapse of tumors previously regressed from chemotherapy (Figure 1).8 The paradigm emphasizes the heterogeneity of a tumor and its microenvironment, proposing that a small subset of cells in the tumor are the source of tumorigenesis with features akin to normal stem cells.9 The CSCs normally in a quiescent state survive this chemotherapy and “seed” tumor redevelopment.10 First observed in acute myeloid lymphoma models, CSCs have since been identified in various other cancers (to include CRC) by their cell surface antigens and unique properties characterizing them from normal cancer cells.11-12 These include tumor initiation, limitless self-renewal capacity to generate clonal daughter cells, as well as phenotypically diverse, mature, and highly differentiated progeny.13-14 Previously our lab has identified a novel molecule called G2.2 (Figure 2) from a unique library of sulfated compounds showing selective and potent inhibition of colorectal CSCs in-vitro.15 G2.2 is a mimetic of glycosaminoglycans (GAGs) and belongs to a class of molecules called non-saccharide GAG mimetics (NSGMs). Using a novel dual-screening platform, comparisons were made on the potency of G2.2 in bulk monolayer cells, primary 3D tumor spheroids of the same cell line, and subsequent generations of tumor spheroids. This work has shown in-vitro the fold-enhancement of CSCs when culturing as 3D tumor spheroids. Spheroid culture serves as a more accurate model for the physiological conditions of a tumor, as well as the functional importance of upregulating CSCs. Evaluation of G2.2 and other NSGMs was performed in only a few cell lines, developing a need to better understand the ability of G2.2 to inhibit spheroids from a more diverse panel of cancer cells to better understand G2.2’s mechanism. The last few decades have seen the advancement in fundamental biological and biochemical knowledge of tumor cell biology and genetics.16 CRC, in particular, has served as a useful preclinical model in recapitulating patient tumor heterogeneity in-vitro.17 Recent work has characterized the molecular phenotypes of CRC cell lines in a multi-omics analysis, stratifying them into 4 clinically robust and relevant consensus molecular subtypes (CMS).18-19 Our work was directed to screen a panel of cells from each of the molecular subtypes and characterize the action of G2.2 and 2nd generation lipid-modified analogs, synthesized to improve the pharmacokinetic properties of the parent compound. Four NSGMs, namely G2.2, G2C, G5C, and G8C (Figure 2) were studied for their ability to inhibit the growth of primary spheroids across a phenotypically diverse panel. Compound HT-29 IC50 (μM) Panel Average IC50 (μM) G2.2 28 ± 1 185 ± 55 G2C 5 ± 2 16 ± 15 G5C 8 ± 2 63 ± 19 G8C 0.7 ± 0.2 6 ± 3 Primary spheroid inhibition assays were performed comparing the potency of new NSGMs to G2.2. Fifteen cell lines were evaluated in a panel of colorectal adenocarcinoma cell lines with several cell lines representing each CMS. Primary spheroid inhibition assays revealed 3 distinct response with regard to G2.2’s ability to inhibit spheroid growth. Cells from CMS 3 and 4, which display poor clinical prognosis, metabolic dysregulation, and enhanced activation of CSC pathways, showed the most sensitivity to G2.2 (mean IC50 = 89 ± 55 μM). Mesenchymal CMS 4 cell lines were over 3-fold more sensitive to treatment with G2.2 when compared to CMS 1 cell lines. Resistant cell lines were composed entirely of CMS 1 and 2 (mean IC50 = 267 ± 105 μM). In contrast, all lipid-modified analogs showed greater potency than the parent NSGM in almost every CRC cell line. Of the three analogs, G8C showed the greatest potency with a mean IC50 of less than 15 μM. Of the CRC spheroids studied, HT-29 (CMS 3) was most sensitive to G8C (IC50 = 0.73 μM). To evaluate the selectivity of NSGMs for CSC spheroid inhibition, MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium) cytotoxicity assays were performed on monolayer cell culture, and the fold-selectivity of NSGM for spheroids was analyzed. Data shows that NSGMs preferentially target CSC-rich spheroids compared with monolayer cellular growth, with G2.2 having over 7-fold selectivity for spheroid conditions. This fold selectivity was enhanced in CMS 3/4, supporting the idea that G2.2 targets a mesenchymal and stem-like phenotype. To further validate this selectivity, limiting dilution assays were performed across the panel to determine the tumor-initiating capacity of each cell line. Cell lines which showed a sensitive response to G2.2 were over 2-fold more likely to develop into spheroids, validating the previous hypothesis. Further characterization was performed analyzing the changes G2.2 induced on CSC markers, as well as the basal expression of a unique pair of cancer cells. Western blots showed a reduction in self-renewal marker across all CMS after treatment with G2.2, and that cell lines sensitive to G2.2-treatment overexpress mesenchymal and stem-like markers. G2.2-resistant cell lines show an epithelial phenotype, lacking this expression. The positive results observed in these studies enhance the understanding of G2.2 and analogs, and further evaluation with additional cell lines of various tissues would improve the knowledge thus far gained. However, all experiments described take valuable time to perform and analyze. Thus, there became a need to develop a high-throughput screening (HTS) platform for our assays that standardized analysis and enhanced productivity. Initial development of the method for this assay are underway, and recent evidence from these evaluations of breast cancer spheroids suggests that G2.2 and analogs may be tissue-specific compounds for the treatment of cancer. Future work entails refining the application of this method for evaluation of the NCI-60 (National Cancer Institute) tumor cell panel. Overall, these results make several suggestions concerning the NSGMs evaluated against the panel. First, G2.2 selectively targets CSCs with limited toxicity to monolayer cells of the same cell line. Further, G2.2 has the greatest potency with CMS 3/4, whose mesenchymal phenotypes are associated with poor clinical prognosis and enrichment of CSCs. 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