Solid cancers often shed (sub)cellular materials into the circulation, such as circulating tumor cells and extracellular microvesicles. Mounting evidence supports that these circulating materials could serve as surrogate cancer markers for classifying primary tumors, stratifying patients for targeted therapies, assessing treatment efficacy, and achieving clinical benefits. A sensor platform capable of sensitive and portable detection of circulating cancer markers would thus be an invaluable tool, that will advance our understanding of tumor biology as well as clinical outcomes. This dissertation describes various systems that we have developed for quantitative analyses of circulating cancer biomarkers. Firstly, we have developed a novel magnetic resonance sensing platform for microvesicle analyses. By using a chip-based platform that combines microfiltration and bioorthogonal nanoparticle targeting, we demonstrate for the first time that magnetic biosensing can be applied for clinical evaluation of circulating microvesicles in blood samples to monitor cancer therapy. Secondly, we have advanced a new plasmonic sensor to achieve label-free detection of microvesicles. Based on periodic nanohole arrays, this platform has been applied for high-throughput protein profiling of microvesicles in native ascites. Finally, we have implemented microfluidic devices to effectively enrich circulating tumor cells from peripheral whole blood, and to enable comprehensive molecular analyses of isolated tumor cells at a single cell resolution. By enabling rapid, sensitive and cost-effective detection of circulating cancer markers, these developed platforms could significantly expand the reach of preclinical and clinical cancer research, in informing therapy selection, rationally directing trials, and improving sequential monitoring to achieve better clinical outcomes.

abstract: Biomarkers find a wide variety of applications in oncology from risk assessment to diagnosis and predicting and monitoring recurrence and response to therapy. Developing clinically useful biomarkers for cancer is faced with several challenges, including cancer heterogeneity and factors related to assay development and biomarker performance. Circulating biomarkers offer a rapid, cost-effective, and minimally-invasive window to disease and are ideal for population-based screening. Circulating immune biomarkers are stable, measurable, and can betray the underlying antigen when present below detection levels or even no longer present. This dissertation aims to investigate potential circulating immune biomarkers with applications in cancer detection and novel therapies. Over 600,000 cancers each year are attributed to the human papillomavirus (HPV), including cervical, anogenital and oropharyngeal cancers. A key challenge in understanding HPV immunobiology and developing immune biomarkers is the diversity of HPV types and the need for multiplexed display of HPV antigens. In Project 1, nucleic acid programmable protein arrays displaying the proteomes of 12 HPV types were developed and used for serum immunoprofiling of women with cervical lesions or invasive cervical cancer. These arrays provide a valuable high-throughput tool for measuring the breadth, specificity, heterogeneity, and cross-reactivity of the serologic response to HPV. Project 2 investigates potential biomarkers of immunity to the bacterial CRISPR/Cas9 system that is currently in clinical trials for cancer. Pre-existing B cell and T cell immune responses to Cas9 were detected in humans and Cas9 was modified to eliminate immunodominant epitopes while preserving its function and specificity. This dissertation broadens our understanding of the immunobiology of cervical cancer and provides insights into the immune profiles that could serve as biomarkers of various applications in cancer. / Dissertation/Thesis / Doctoral Dissertation Molecular and Cellular Biology 2018

Background: Heart damage from cancer therapy is a significant problem for survivors. Some of the most effective treatments, such as anthracyclines, cause heart toxicity that can lead to significant morbidity and mortality. Cardiotoxicity also contributes to the loss of promising cancer drugs in early development and is notoriously difficult to predict. This translational project employs parallel pre-clinical and clinical studies to explore circulating biomarkers and cardiac magnetic resonance imaging (CMR) during development of anthracycline associated cardiotoxicity with the aim of finding biomarkers to aid clinical decision making and enable forward/back translation. Methods: Pre-clinical work: A rat model of chronic anthracycline-induced cardiomyopathy was developed involving 8 weekly intravenous boluses of doxorubicin followed by a 4 week ‘washout’ period. A time course assessment of cardiac function using multiple MRI parameters was performed alongside a panel of circulating biomarkers measured prior to dosing. Clinical work: In parallel following ethical approval, 30 cancer patients receiving standard anthracycline chemotherapy were recruited. Serial CMR scans were performed using standard and new exploratory techniques before, during and after treatment and blood was taken to evaluate a similar panel of cardiotoxicity biomarkers using multiplex ELISA at corresponding time points. Results: Pre-clinical results: Systolic and diastolic function declined progressively, culminating in left ventricular dysfunction (LVEF < 50%) by 12 weeks. Myocardial electron microscopy revealed myofibrillar and mitochondrial damage after one dose and gross histopathological damage after 5 doses. Myocardial contrast enhancement and troponin I increased significantly after eight doses and preceded LV dysfunction. Extensive fibrosis was seen 1 month after drug cessation. Clinical results: LVEF declined progressively in all patients and 7 patients (23%) had persistent LV dysfunction 12 months after therapy. Troponin I elevations were seen towards the end of therapy and peak troponin I corresponded with LVEF decline. None of the other circulating biomarkers correlated strongly with outcome. Lower baseline extracellular volume (ECV) was associated with greater LVEF decline but little change in ECV was seen over time. Baseline dyssynchrony was associated with worse outcome and deteriorated with time alongside LVEF decline. Conclusions: Results suggest that troponin I and cardiac MRI are sensitive translational tools in drug induced cardiotoxicity. However, troponin I is a relatively late marker, peaking after substantial myocardial damage, too late to halt or change reatment. The imaging suggests that fibrosis and inflammation cannot be detected within a year of chemotherapy but baseline ECV and strain analysis may have a role in risk stratification.

Advancements in clinical care have led to a growing cohort of preterm-born individuals now entering adulthood. Before birth, such adults were often exposed to a suboptimal intrauterine environment, and after delivery, key developmental stages that would normally occur in utero during the third trimester had to take place under ex utero physiological conditions. Through detailed cardiovascular phenotyping, this thesis investigates the cardiovascular changes in preterm-born young adults, utilising a cohort of individuals with data collection since recruitment at birth. The detailed perinatal information was first used to design nested case-control studies to investigate the effects of early lipid and glucocorticoid exposure on long-term cardiovascular physiology in individuals born preterm. It was demonstrated that intravenous lipid administration leads to an artificial elevation of total cholesterol levels in immediate postnatal life, which is associated with long-term changes in aortic and left ventricular function proportional to the degree of cholesterol elevation. Additionally, exposure to antenatal glucocorticoids relates to a regional increase in aortic arch stiffness in young adulthood, as well as changes in glucose metabolism. It was then shown that young adults born preterm have increased left ventricular mass, out of proportion to blood pressure, and a unique three-dimensional left ventricular geometry, with reduced systolic and diastolic function compared to term-born controls. Similarly, they also show distinct differences in the right ventricle, with increased right ventricular mass and a proportion having clinically impaired right ventricular systolic function. Finally, it was demonstrated that preterm-born individuals have increased circulating levels of antiangiogenic factors in young adulthood, which relate to capillary rarefaction and blood pressure elevation. These findings are of considerable public health relevance given that nearly 10% of births are now preterm. Understanding whether modification of these variations in cardiovascular structure and function prevent the development of cardiovascular disease in this growing subgroup of the population will be of future interest.

Dans la dysfonction endothéliale, le compartiment endothélial circulant joue simultanément le rôle d’acteur impliqué dans la régénération du tissu lésé et celui d’indicateur de l’état d’altération ou de régénération de l’endothélium. Dans l’artérite oblitérante des membres inférieurs (AOMI), l’un des axes de recherche porte sur le développement d’un produit de thérapie cellulaire capable d’induire la formation de néo-Vaisseaux. Face à la difficulté d’obtenir et d`amplifier des cellules progénitrices endothéliales (CPE) chez l’adulte sain, et a fortiori chez le patient, l’une des hypothèses laisse envisager le recours à d’autres types cellulaires ayant des propriétés vasculogéniques. Chez patients atteints de maladies cardiovasculaires, et d’AOMI en particulier, les cellules mononuclées de moelle osseuse et les CPE montrent des propriétés angiogéniques diminuées. Nous avons mis en évidence la capacité des cellules souches mésenchymateuses (CSM) isolées de patients atteints d’AOMI à induire une reperfusion, par recrutement de cellules endothéliales in situ, avec la même efficacité que celles de donneurs sains. Les CSM ne se différencient pas en cellules endothéliales mais agissent par paracrinie. La seconde hypothèse d’obtention d’un produit de thérapie cellulaire autologue angiogène est de trier des cellules plus immatures que les CPE afin de les différencier secondairement vers la lignée endothéliale à l’image du modèle pathologique de la cellule souche d’hémangiome CD133+ qui laisse envisager les Very Small Embryonic Like stem cells (VSEL), cellules souches multipotentes CD133+, comme un candidat de cellules post-Natales à potentiel vasculaire. Nous avons dérivés, en culture en conditions angiogéniques, des VSEL qui acquièrent un phénotype mésenchymateux mais présentent un profil sécrétoire proche de celui des CPE. Les VSEL favorisent la revascularisation post-Ischémique et acquièrent un phénotype endothélial in vitro et in vivo suggérant que les VSEL peuvent être à l’origine de la lignée endothéliale. Les VSEL se présentent également comme un biomarqueur de la dysfonction endothéliale mobilisé de la moelle osseuse (MO) vers le sang périphérique (PB) chez les patients souffrant d’AOMI. Les biomarqueurs cellulaires circulants représentent non seulement des marqueurs non invasifs de l’endothélium mais peuvent également apporter des informations utiles pour le diagnostic, le pronostic et le suivi thérapeutique des patients souffrant de pathologies associées à une dysfonction endothéliale. Une modification du nombre de CPE et de cellules endothéliales circulantes (CEC) dans la circulation a été rapportée dans différentes situations pathologiques respectivement associées à une régénération et une altération endothéliale telle l’augmentation du taux de CEC chez des patients présentant une hypertension artérielle pulmonaire (HTAP). La technique de référence pour le dénombrement des CEC dans le sang périphérique est l’immunoséparation magnétique (IMS). Cette méthode non automatisée et chronophage, repose sur l’énumération par microscopie à fluorescence des cellules CD146+ préalablement isolées. Bien que reproductible, cette numération est soumise à de nombreux biais de quantification, difficile à mettre en oeuvre et sujette à interprétation. La mise au point d’une méthode de détection automatisée des CEC par cytométrie à focalisation acoustique (AFC) s’est montrée fiable et robuste, dans une cohorte de patients atteints d’HTAP traitée ou non, constituant une alternative pertinente à l’analyse par microscopie. L’ensemble de ces travaux ouvre donc de nouvelles perspectives dans la détection des biomarqueurs cellulaires circulants impliqués dans la dysfonction endothéliale, proposant les VSEL comme nouvel acteur vasculogénique. / In endothelial dysfunction, circulating endothelial compartment simultaneously plays the role of actor involved in the regeneration of injured tissue and reflects endothelium state. In peripheral arterial disease (PAD), one of the research areas is the development of a cellular therapy product capable of inducing the formation of neo-Vessels. Faced with the difficulty to obtain and amplify endothelial progenitor cells (EPC) in adults, one of the assumptions lets consider the use of other cell types with vasculogenic properties. In patients with cardiovascular disease, and PAD in particular, bone marrow mononuclear cells and EPC show reduced angiogenic properties. We have demonstrated the ability of isolated mesenchymal stem cells (MSCs) from PAD patients to induce reperfusion by recruitment of endothelial cells in situ, with the same efficiency as that of healthy donors MSCs. MSCs do not differentiate into endothelial cells but act by paracrine. The second hypothesis of obtaining an autologous angiogenic cell therapy product is to sort cells more immature than the CPE and to differentiate them secondarily into endothelial lineage as the pathological cell model of hemangioma stem cells CD133 + which lets consider the Very Small Embryonic like stem cells (VSEL), CD133 + multipotent stem cells as a potential candidate of postnatal vascular cell. We have derived and cultured in angiogenic conditions VSEL that acquired a mesenchymal phenotype but exhibited a secretory profile similar to that of EPC. VSEL promote post-Ischemic revascularization and acquire an endothelial phenotype in vitro and in vivo suggesting that VSEL may be responsible for the endothelial lineage. VSEL also appear as a biomarker of endothelial dysfunction mobilized from bone marrow (BM) to peripheral blood (PB) in patients with PAD. Cellular circulating biomarkers are not only non-Invasive markers of endothelium but can also provide useful information for the diagnosis, prognosis and therapeutic monitoring of patients with endothelial dysfunction associated pathologies. Changing the number of EPC and circulating endothelial cells (CEC) in the circulation has been reported in different pathological situations respectively associated with endothelial regeneration and alteration such as the increase of CEC in patients with pulmonary arterial hypertension (PAH). The reference technique for the enumeration of CEC in peripheral blood is magnetic immunoseparation (IMS). This non-Automated and time-Consuming method, based on the enumeration by fluorescence microscopy of CD146 + cells isolated. Although reproducible, this count is subject to many through quantification, difficult to implement and subject to interpretation. The development of an acoustic focusing cytometry (AFC) method for automated detection of CEC has proved reliable and robust results, in a cohort of patients with PAH treated or not, constituting a relevant alternative analysis to microscopy. All of this work opens new perspectives in the detection of cellular circulating biomarkers involved in endothelial dysfunction, suggesting VSEL as new vasculogenic actor.