Mortality due to cancer is a global health issue that can be improved through further development of diagnostic and prognostic tools. Recent advancements in technologies aiding cancer research have made significant strides, however a demand for a non-invasive clinically relevant point-of-care tools exists. To accomplish this feat, the desired instrument needs to be low-cost, easy-to-operate, efficient, and have rapid processing and analysis. Microfluidic platforms in cancer research have proven to be advantageous due to its operation at the microscale, which has low costs, favorable physics, high precision, short experimentation time, and requires minimal reagent and sample sizes. Label-free technologies rely on cell biophysical characteristics to identify, evaluate, and study biological samples. Biomechanical probing of cells through deformability assays provides a label-free method of identifying cell health and monitoring response to physical and chemical stimuli. Bioimpedance analysis is an alternative versatile label-free method of evaluating cell characteristics by measuring cell response to electrical signals. Microfluidic technologies can facilitate biomechanical and bioelectrical analysis through deformability assays and impedance spectroscopy. This dissertation demonstrates scientific contributions towards single-cell analysis and liquid biopsy devices focusing on cancer research. First, cell deformability assays were improved through the introduction of multi-constriction channels, which revealed that cells have a non-linear response to deformation. Combining impedance analysis with microfluidic deformability assays provided a large dataset of mechano-electrical information, which improved cell characterization and greatly decreased post-processing times. Next, two unique biosensors demonstrated improved throughput while maintaining sensitivity of single-cell analysis assays through parallelization and incorporating machine learning for data processing. Liquid biopsies involve studying cancer cells in patient vascular systems, called circulating tumor cells (CTCs), through blood samples. CTC tests reveal valuable information on patient prognosis, diagnosis and can aide therapy selection in a minimally invasive manner. This body of work presents two liquid biopsy devices that enrich murine and human blood samples and isolate CTCs to ease detection and analysis. Additionally, a microfluidic CTC detection biosensor is introduced to reliably count and identify cancer cells in murine blood, where an extremely low-cost version of the assay is also validated. Thus, the assays presented in this dissertation show promise of microfluidic technologies towards point-of-care systems for cancer research. / Doctor of Philosophy / Cancer is the second leading cause of death worldwide with approximately 2 million new cases each year in the just United States. Significant research development for diagnostic and prognostic tools have been conducted, however they can be expensive, invasive, time-consuming, unreliable, and not always easily accessible. Thus, a tool that is cheap, minimally invasive, easy-to-use, and robust needs to be developed to combat these issues. Typical cancer studies have primarily focused on biological and biochemical methods for evaluation; however, researchers have begun to leverage small-scale biosensors that utilize biophysical attributes. Recent studies have proven that these lab-on-a-chip technologies can produce meaningful results by exploiting these biophysical characteristics. Microfluidics is a science that consists of sub-millimeter sized channels which show a great deal of promise as they require minimal materials and can quickly and efficiently analyze biological samples. Label-free methods of studying cells rely on their physical properties, such as size, deformability, density, and electrical properties. These biophysical characteristics can be easily obtained at the single-cell level through microfluidic-based assays. Measuring and monitoring these attributes can provide valuable information to help understand cancer cell response to stimuli such as chemotherapeutic drugs or other therapies. A liquid biopsy is a non-invasive method of evaluating cancer patients by studying circulating tumor cells (CTCs) that exist in their blood. This dissertation reports a wide range of label-free microfluidic assays that evaluate and study biological samples at the single-cell level and for liquid biopsies. These assays consist of microfluidic channels with sensors that can rapidly obtain biophysical characteristics and process blood samples for liquid biopsy applications. Uniquely modifying microfluidic channel geometries and sensor configurations improved upon previously developed single-cell and CTC-based tools. The resulting devices were low in cost, easy-to-use, efficient, and reliable methods that alleviates current issues in cancer research while showing clinical utility.

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Ye / Genetic and epigenetic alterations significantly contribute to development of human cancer. Genotyping tumour tissue in search for these actionable genetic and epigenetic changes has become routine practice in oncology. However, sampling tumour tissue has significant inherent limitations. It provides only a single snapshot in time, prone to selection bias due to intra-tumour heterogeneity, and cannot always be performed owing to its invasive nature. Circulating tumour DNA (ctDNA) based liquid biopsy provides an effective alternative to invasive tissue sampling and have emerged as a minimally invasive, real-time biomarker. Recent advancements in DNA sequencing technologies have revealed enormous potential of ctDNA to improve tumour detection and stratification. In this review, we critically appraise the role of ctDNA as a liquid biopsy for cancer and evaluate the role of circulating tumour DNA as a diagnostic, prognostic and predictive biomarker. We also highlight some technical challenges and constraints associated with circulating DNA analysis.

Yes / Purpose: Nipple secretions are protein-rich and a potential source of breast cancer biomarkers for breast cancer screening. Previous studies of specific proteins have shown limited correlation with clinicopatholigical features. Our aim, in this pilot study, was to investigate the intra- and inter-patient protein composition of nipple secretions and the implications for their use as liquid biopsies. Experimental design: Matched pairs of NAF (n=15) were characterised for physicochemical properties and SDS PAGE. Four pairs were selected for semi-quantitative proteomic profiling and trypsin-digested peptides analysed using 2D LC Orbitrap Fusion mass spectrometry. The resulting data was subject to bioinformatics analysis and statistical evaluation for functional significance. Results: A total of 1990 unique proteins were identified many of which are established cancer associated markers. Matched pairs shared the greatest similarity (average Pearson correlation coefficient of 0.94), but significant variations between individuals was observed. Conclusions: This was the most complete proteomic study of NAF to date providing a valuable source for biomarker discovery. The high level of milk proteins in healthy volunteer samples compared to the cancer patients was associated with galactorrhoea. Using matched pairs increased confidence in patient-specific protein levels but changes relating to cancer stage require investigation of a larger cohort. / Proteomics research was supported by Yorkshire Cancer Research projects, BPP047 and B381PA.

Yes / There has been tremendous progress in detection of breast cancer in postmenopausal women, resulting in two-thirds of women surviving more than 20 years after treatment. However, breast cancer remains the leading cause of cancerrelated deaths in premenopausal women. Breast cancer is increasing in younger women due to changes in life-style as well as those at high risk as carriers of mutations in high-penetrance genes. Premenopausal women with breast cancer are more likely to be diagnosed with aggressive tumours and therefore have a lower survival rate. Mammography plays an important role in detecting breast cancer in postmenopausal women, but is considerably less sensitive in younger women. Imaging techniques, such as contrast-enhanced MRI improve sensitivity, but as with all imaging approaches, cannot differentiate between benign and malignant growths. Hence, current well-established detection methods are falling short of providing adequate safety, convenience, sensitivity and specificity for premenopausal women on a global level, necessitating the exploration of new methods. In order to detect and prevent the disease in high risk women as early as possible, methods that require more frequent monitoring need to be developed. The emergence of “omics” strategies over the last 20 years, enabling the characterisation and understanding of breast cancer at the molecular level, are providing the potential for long term, longitudinal monitoring of the disease. Tissue and serum biomarkers for breast cancer stratification, diagnosis and predictive outcome have emerged, but have not successfully translated into clinical screening for early detection of the disease. The use of breast-specific liquid biopsies, such as nipple aspirate fluid (NAF), a natural secretion produced by breast epithelial cells, can be collected non-invasively for biomarker profiling. As we move towards an age of active surveillance, home-based liquid biopsy collection kits are increasingly being applied and these could provide a paradigm shift where NAF biomarker profiling is used for routine breast health monitoring. The current status of established and newly emerging imaging techniques for early detection of breast cancer and the potential for alternative biomarker screening of liquid biopsies, particularly those applied to high-risk, premenopausal women, will be reviewed. / Proteomics research was supported by Yorkshire Cancer Research projects, BPP047 and B381PA, and co-funded by the European Regional Development Fund and the Republic of Cyprus through the Research Promotion Foundation projects ΥΓΕΙΑ/ΒΙΟΣ/0311(ΒΙΕ/07) and NEKYP/0311/17.

京都大学 / 新制・課程博士 / 博士(医学) / 甲第24993号 / 医博第5027号 / 新制||医||1069(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 滝田 順子, 教授 岩田 想, 教授 万代 昌紀 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

Det här examensarbetet består i ett produktutvecklingsprojekt som utfördes i samarbete med Liquid Biopsy AB. Syftet med arbetet var att utveckla ett engångskassettsbaserat produktsystem baserat på företagets patentsökta metod för isolering av cancer celler i suspension, inklusive cirkulerande tumörceller. Liquid Biopsy AB är ett svenskt utvecklingsbolag som baserat på ny och unik teknik, är oberoende av proteinmarkörer, använder cirkulerande tumörceller och andra suspenderade tumörceller för att möjliggöra bättre och billigare cancerdiagnostik. Examensarbetet har fokuserat på utvecklingen av engångskassetten, men parallellt arbete har även utförts med tillhörande basenhet. Ulrich och Eppingers produktutvecklingsprocess har utgjort grunden för den process som följts i arbetet, dock med ökat fokus på testning och utvärdering. För att få en bredare kunskapsbas inleddes arbetet med en marknads- och omvärldsanalys samt informationsinsamling om utmaningar och medicintekniska krav. För att tydligt definiera produktvisionen utfördes även undersökningar med potentiella användarna, om företagets patentsökta metod och befintliga prototyper samt framtida förbättringspotential. Det kassettkoncept som utvecklats bygger på användning av provrör av existerande standard, få tillverkningsprocesser och god användarvänlighet, något som samtliga varit av hög prioritet under arbetet. För att säkerställa att produktens flödessystem fungerar som tänkt utfördes tester under prototypframtagningen. Testningen visade att konceptet fungerar i stort sett som tänkt med avseende på flöden, dock förekom vissa toleransproblem som följd av den valda prototypframtagningsprocessen, och vissa andra viktiga egenskaper återstår att testa. Resultatet av utvecklingsprocessen är en första fysisk prototyp av engångskassetten och en funktionell partiell prototyp av basenheten, motsvarande gränssnittet mot engångkassetten, för att möjliggöra testning av engångskassetten. Slutsatsen av arbetet är att det framtagna produktsystemet har tydliga fördelar gentemot företagets befintliga prototyper: inklusive att en engångskassett framtagits, att denna kan utgöra underlag för en produkt, och att denna bland annat har väsentligt kortare processväg vilken i sin tur borde kunna leda till förkortad processtid. Utförd finansiell analys visar även att framtaget produktsystem kan säljas till konkurrenskraftiga priser och med en betydligt lägre instegskostnad än dagens konkurrerande produkter. / This thesis consists of a product development project conducted in collaboration with Liquid Biopsy AB. The purpose of this work was to develop a disposable cartridge-based product system based on the company’s patent-pending method for isolation of circulating tumor cells and other suspended tumor cells. Liquid Biopsy AB is a Swedish medical technology research company with a unique new rheological technology, that is independent of protein markers, using suspended cancer cells, including circulating tumor cells, allows better and cheaper cancer diagnostics than today. The thesis work has focused on the development of the disposable cassette, but parallel work has also been performed with the associated base unit. Ulrich and Eppingers product development process has made up the basis for the process being followed in the thesis work, with increased focus on testing and evaluation. The work began with a market analysis and information gathering on challenges and medical requirements. Several activities were also carried out in order to clearly define the product vision, including user-surveys, analysis of the company's existing prototypes, as well as potential for future improvements. The developed cartridge concept is based on the use of standard test tubes, few manufacturing processes and user-friendliness which all have been high priorities in this work. The cartridge concept consists essentially of various plastic materials and is adapted for manufacturing by injection molding. To ensure that the product’s flow system was operating as intended, tests were conducted during the prototype phase. Testing showed that the concept design flows largely as intended, yet with some tolerance problems as a result of the selected rapid prototyping process, while other essential properties remain to be tested. The result of the development process is a first physical prototype of the disposable cartridge and a partial functional prototype of the base unit to allow testing with the disposable cartridge. The conclusion of this thesis work is that the developed product system has strong advantages over the company’s existing prototypes, including a first version of a disposable cassette that has potential to form the basis of a mass-producible product, significantly shorter processing route which in turn should allow a reduction of the processing time. Financial analysis also indicates that the designed product systems can be sold at competitive prices and with a significantly lower entry cost than today's rivaling products.

Doctor of Philosophy / Department of Chemistry / Stefan H. Bossmann / Cancer is a group of diseases that are characterized by uncontrolled growth and spread of cells. In order to treat cancer successfully, it is important to diagnose cancers in their early stages, because survival often depends on the stage of cancer detection. For that purpose, highly sensitive and selective methods must be developed, taking advantage of suitable biomarkers. The expression levels of proteases differ from one cancer type to the other, because different cancers arise from different cell types. According to the literature, there are significant differences between the protease expression levels of cancer patients and healthy people, because solid tumors rely on proteases for survival, angiogenesis and metastasis. Development of fluorescence-based nanobiosensors for the early detection of pancreatic cancer and non-small-cell lung cancer is discussed in this thesis. The nanobiosensors are capable of detecting protease/arginase activities in serum samples over a broad range. The functionality of the nanobiosensor is based on Förster resonance energy transfer and surface energy transfer mechanisms. The nanobiosensors for protease detection feature dopamine-coated Fe/Fe₃O₄ nanoparticles, consensus (cleavage) peptide sequences, meso-tetra(4-carboxyphenyl)porphine (TCPP), and cyanine 5.5. The consensus peptide sequences were synthesized by solid-supported peptide synthesis. In this thesis, improved consensus sequences were used, which permit faster synthesis and higher signal intensities. TCPP, which is the fluorophore of the nanoplatform, was connected to the N-terminal end of the oligopeptides while it was still on the resin. After the addition of TCPP, the TCPP-oligopeptide was cleaved off the resin and linked to the primary amine groups of Fe/Fe₃O₄-bound via a stable amide bond. In the presence of a particular protease, the consensus sequences attached to the nanoparticle can be cleaved and release TCPP to the aqueous medium. Upon releasing the dye, the emission intensity increases significantly and can be detected by fluorescence spectroscopy or, similarly, by using a fluorescence plate reader. In sensing of arginase, posttranslational modification of the peptide sequence will occur, transforming arginine to ornithine. This changes the conformational dynamics of the oligopeptide tether, leading to the increase of the TCPP signal. This is a highly selective technology, which has a very low limit of detection (LOD) of 1 x 10⁻¹⁶ molL⁻¹ for proteases and arginase. The potential of this nanobiosensor technology to detect early pancreatic and lung cancer was demonstrated by using serum samples, which were collected from patients who have been diagnosed with pancreatic cancer and non-small cell lung cancer at the South Eastern Nebraska Cancer Center (lung cancer) and the University of Kansas Cancer Center (pancreatic cancer). As controls, serum samples collected from healthy volunteers were analyzed. In pancreatic cancer detection, the protease/arginase signature for the detection of pancreatic adenocarcinomas in serum was identified. It comprises arginase, MMPs -1, - 3, and -9, cathepsins -B and -E, urokinase plasminogen activator, and neutrophil elastase. For lung cancer detection, the specificity and sensitivity of the nanobiosensors permit the accurate measurements of the activities of nine signature proteases in serum samples. Cathepsin -L and MMPs-1, -3, and -7 permit detecting non-small-cell lung-cancer at stage 1.

Survival rates in cancers have improved vastly over the years. However, some survival rates remain extremely low, as is the case for ovarian and lung cancer. The lack of robust and reliable biomarkers is strongly reflected in the absence of pre-screening programs, and as such, most patients in these cancer types are diagnosed only in advanced stages, leaving few treatment options. Moreover, relapse and resistance to therapies adds to the complexities of treating these diseases, even in the era of targeted drug development. Research has shown the presence of cancer material, in the form of circulating cancer cells (CTCs) and genomic material in the blood of patients, opening the possibility of 'liquid biopsies'. Liquid biopsies allow sampling of the disease to provide phenotypic and genomic data on the cancer in real-time and on a routine basis. Moreover, they overcome obstacles currently faced by conventional tissue biopsies. In this work we evaluate the use of a novel CTC imaging flow-cytometry platform, and report the ability to characterise and quantify these cells in blood samples. Moreover, we report significantly higher levels of CTCs in cancer patients compared to controls, and found them to be associated with a poorer prognosis. In particular, in lung cancer we observe these findings even in the early stages, suggesting a potential diagnostic use for this assay. We detect a similar trend in when analysing the ctDNA and suggest the possibility of using this technique with a prognostic value in the advanced setting. We also report on the analysis of existing microarray data by use of unique gene regulatory networks to identify biomarkers of interest. RAD51AP1 was identified by this process. Clinical validation revealed an over-expression of this gene in both tissue and blood of ovarian and lung cancers. Moreover, the gene over-expression was associated with a poor overall survival. Functional analysis in vitro revealed silencing RAD51AP1 suppressed tumour growth, in addition, various tumorigenic proteins were down-regulated, whilst apoptotic and immune genes were up-regulated. These results suggest a role for RAD51AP1 as a potential therapeutic target. In this study, we also demonstrate the ability to further exploit tumour genomic material in the blood by means of RNAseq, cancer panels, and CNI scoring to identify novel markers, that play an important role in disease genesis and evolution. RNAseq analysis identified XIST as a gene up-regulated in the blood and tissue of lung cancers. The ovarian cancer panels revealed 2 unique gene signatures in the ovarian cancer patients. With the CNI analyses also highlighting chromosomal aberrations from plasma analysis of cancer patients. Collectively, the use of all these techniques and exploitation of available blood based biomarkers could see significant improvements to survival rates in these, currently devastating diseases.

Orientador: Adriana Polachini Valle / Resumo: Introdução: O câncer de próstata (CP) é o mais incidente entre os homens em todas as regiões do Brasil. A detecção e caracterização de células tumorais circulantes (CTCs) tem sido apontada como uma alternativa para melhor compreensão da biologia dos tumores, incluindo câncer de próstata. Objetivo: Este estudo tem como objetivo avaliar a detecção de CTCs em pacientes com tumor de próstata localizado e metastático por teste rápido de filtração celular. Metodologia: Foram incluídos pacientes com diagnóstico anatomopatológico de câncer de próstata ou neoplasia intraepitelial prostática. Os dados demográficos, laudos anatomopatológicos e de Cintilografia Óssea e valores do antígeno prostático especifico ( PSA) foram obtidos pelo estudo dos prontuários médicos dos pacientes. Os pacientes foram classificados como portadores de tumor metastático quando apresentavam evidência de imagem metastática pela Cintilografia Óssea. As CTS foram isoladas por teste rápido de filtração celular com posterior imunocitoquímica utilizando-se anticorpos monoclonais anti-PSA para caracterização câncer de próstata específica das células. Resultados: As CTCs foram detectadas em 9 dos 21 pacientes (43%) com positividade de 60% no grupo metastático e 36% no grupo de tumor localizado. Não foram observadas associações entre os valores de PSA e tratamento instituído com a detecção de CTCS. Discussão: A positividade das CTCs no presente estudo mostrou-se semelhante aos dados da literatura, embora possam ser ci... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Introduction: Prostate cancer (PC) is the most frequent among men in all regions of Brazil. The detection and characterization of circulating tumor cells (CTCs) has been pointed out as an alternative for a better understanding of the biology of tumors, including prostate cancer. Objective: This study aims to evaluate the detection of CTCs in patients with localized and metastatic prostate tumor by rapid cell filtration test. Methodology: Patients with anatomopathological diagnosis of prostate cancer or prostatic intraepithelial neoplasia were included. Demographic data, anatomopathological and bone scintigraphy reports and prostate specific antigen (PSA) values were obtained by the study of patients' medical records. Patients were classified as having metastatic tumor when they presented evidence of metastatic image by Bone Scintigraphy. The CTS were isolated by rapid cell filtration test with subsequent immunocytochemistry using anti-PSA monoclonal antibodies for cell-specific prostate cancer characterization. Results: CTCs were detected in 9 of the 21 patients (43%) with 60% positivity in the metastatic group and 36% in the localized tumor group. No associations were observed between PSA values and treatment established with CTCS detection. Discussion: The positivity of the CTCs in the present study was similar to the data in the literature, although some limitations of the study may be cited, such as a small number of patients included, difficulties encountered by research... (Complete abstract click electronic access below) / Mestre