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A dissertation submitted to the Faculty of Health Sciences, University of the Witwatersrand, in fulfilment of the requirements for the degree of Master of Science, Johannesburg 2017 / The high mortality rates of pancreatic ductal adenocarcinoma (PDAC) are largely attributed to a delayed diagnosis, of which in advanced disease, patients are unable to receive surgical resection with curative intent. Clinical presentations and genetic features shared between PDAC and other pancreatic conditions such as chronic pancreatitis (CP) are insufficient to facilitate the disease and often lead to diagnostic uncertainty at an early stage. The purpose of this study was to develop sensitive and specific non-invasive markers to aid in the detection and disease monitoring of PDAC. Here, circulating cell-free DNA (cfDNA) isolated from plasma samples of patients with PDAC (n= 155) and two control groups consisting of patients with either CP (n= 46) or critical limb ischemia (CLI) (n= 88) revealed significant differences in measured concentrations between the three patient groups (p= 0.006-Kruskal-Wallis test).When two groups were compared with each other using the Wilcoxon rank-sum test, observable differences were seen between the two pancreatic diseases: PDAC and CP (p= 0.002), and between the two controls: CP and the CLI groups (p= 0.007). A strong association was also observed in elevated cfDNA levels of CLI patients with HIV (p= 0.03), indicating a poor prognosis for patients. Results from methylationspecific PCR (MSP) in age-matched patient samples showed promoter methylation to account for the loss of Smad4 in late-stage PDAC; with an observed association with overall increasing cfDNA levels (p= 0.03).This study indicates the potential clinical utility of cfDNA as a non-invasive tool to predict disease progression both quantitatively and qualitatively, as well as to trace epigenetic changes in tumour markers associated with PDAC. Further investigation to identify hypermethylated genes in cfDNA for the early detection of PDAC is warranted. / XL2018

L'adénocarcinome canalaire pancréatique (ADKp) possède une architecture compacte, où les cellules tumorales forment des glandes emprisonnées dans un bouclier fibrotique, composé à 50% de collagènes. Ce bouclier empêche la vascularisation, limite l'apport en nutriments et oxygène. Beaucoup de cellules meurent, mais certaines survivent, en reprogrammant en particulier leur métabolisme. Ula plus étudiée est l'utilisation constitutive de la glycolyse, indépendamment de la présence d'oxygène (Effet Warburg). Nous montrons que la population hypoxique de l'ADKp dépend aussi de la dégradation de la glutamine, et que l'activité concomitante de la glycolyse et de la glutaminolyse entraîne la réactivation de la biosynthèse des hexosamines. Ces composés participent à la prolifération tumorale en stabilisant les transporteurs au glucose, ou des oncogènes. L'activité glycolytique intense des cellules hypoxiques permet la synthèse de lactate qui sert de ressource nutritive aux cellules oxygénées adjacentes aux cellules hypoxiques. Nous montrons que certaines cellules oxygénées sont capables de survivre au stress nutritif en dégradant le collagène (écophagie), en utilisant la proline qu'il contient. Les cellules tumorales captent et dégradent les fragments de collagènes pour survivre. Des traçages isotopiques de collagène marqué permettent d'appuyer que la proline internalisée provient du collagène matriciel. Cette proline est transformée en glutamate et fournit le cycle de Krebs pour favoriser la survie tumorale. Ces travaux montrent l'importance de l'étude de la reprogrammation métabolique dans l'ADKp, et le rôle de l'hypoxie ou du collagène dans la progression tumorale. / Pancreatic ductal adenocarcinoma (PDAC) has a compact architecture wherein the tumor cells are organized in glands and trapped in a fibrotic shield (stroma) made of up to 50% of collagen. This shield prevents blood supply, limits nutrients and oxygen intake. Many cells die, but some survive, and proliferate particularly by reprogramming their metabolism. The most studied metabolic reprogramming remains tumor cells addiction to glucose and the constitutive use of glycolysis, regardless of the presence of oxygen (Warburg effect). We show that the hypoxic population of PDAC also depends on glutamine degradation, and the concomitant activity of both glycolysis and glutaminolysis reactivates the hexosamine biosynthetic pathway. These compounds contribute to tumor proliferation by stabilizing glucose transporters, or oncogenes. The intense glycolytic activity of hypoxic cells allows the synthesis of lactate. Excreted in the microenvironment, it serves as a nutritive resource to oxygenic cells adjacent to the hypoxic population and enables their proliferation. We show that some oxygenated cells are also able to survive under nutrient stress by degrading collagen (ecophagy) and use proline it contains. Tumor cells intake and degrade collagen fragments to survive. Isotopic tracer experiments using labeled collagen support the idea that proline comes from the extracellular collagen. This proline is degraded and converted into glutamate, fueling the Krebs cycle for anaplerosis and promotes tumor survival. These studies therefore show the importance to study the metabolic reprogramming of PDAC, and the role of hypoxia or collagen matrix in tumor progression.

Le 17 novembre 2016 a eu lieu la 3ème journée mondiale de lutte contre le cancer du pancréas.Cette prise en considération tardive rend compte de la dualité entre une incidence faible et un pronostic redoutable. Sa réputation de cancer rapidement mortel est attestée par un ratio incidence/mortalité proche de 1. Au 10ème rang en termes de localisations de cancers, il se hisse au 4ème rang en termes de mortalité par cancer et devrait devenir, en 2020, la 2ème cause de décès par cancer devant le cancer du côlon et juste après le cancer du poumon. Le taux de survie à 5 ans, tous stades confondus, est de 5% aux USA et en Europe.L’adénocarcinome canalaire pancréatique représente la tumeur la plus fréquente (80% des tumeurs pancréatiques exocrines). Sa localisation dans la glande pancréatique est céphalique dans 2/3 des cas.A ce jour, le traitement chirurgical reste le seul traitement potentiellement curatif. Celui-ci ne s’adresse qu’à une faible proportion de patients. En effet, seul 20% des patients présentant un adénocarcinome pancréatique céphalique sont effectivement résécables permettant d’obtenir un taux de survie globale à 5 ans d'environ 10 à 20% si la résection est suivie de chimiothérapie adjuvante ou non. Ces résultats modestes sont en outre à pondérer par la morbi-mortalité des résections pancréatiques céphaliques. Dans la série de l’Association Française de Chirurgie, reprenant les résections pancréatiques céphaliques réalisées en France entre 2004 et 2010, la mortalité était de 3,8% et la morbidité de 54%. Parmi les complications post-opératoires, la fistule pancréatique représente la principale complication en termes de mortalité (15 à 25%), génératrice de coût important dans les soins et d’une augmentation significative de la durée de séjour. La fistule pancréatique demeure la pierre angulaire de l’amélioration du pronostic des patients.L’objectif de ce travail sur l’adénocarcinome canalaire pancréatique céphalique traité chirurgicalement était d’analyser certains facteurs influençant la morbi-mortalité au trois temps de sa prise en charge :- Avant l’intervention, avec l’étude d’un facteur pronostic préopératoire, sur une cohorte de patients, pouvant influencer la survenue d’une fistule pancréatique et la mortalité- Pendant l’intervention, avec la réalisation d’une méta-analyse sur le type de reconstruction pancréatique et son influence sur la survenue d’une fistule pancréatique- Après l’intervention, avec l’étude de l’influence de la survenue d’une complication sévère sur la survie et la survie sans récidive.Au cours de cette thèse nous avons vu, que la réduction du taux de fistule pancréatique, par le seul biais de techniques peropératoires semble difficilement réalisable au regard de la multiplicité des techniques et de la difficulté à réaliser des études randomisées contrôlées méthodologiquement satisfaisantes. En revanche, la recherche des facteurs liés aux patients, prédisposant à la survenue d’une fistule pancréatique semble l’approche à privilégier. Ceci est d’autant plus primordial dès lors que nous avons mis en évidence un lien entre la survenue d’une complication sévère et la survie ou la récidive chez les patients réséqués. Ce travail souligne l’importance d’être capable d’identifier, dès la consultation, les patients à haut risque de complications sévères et de fistule post-opératoire d’une part, pour sélectionner les bons candidats à la chirurgie et d’autre part, pour être capable de leur apporter une information franche et loyale indispensable éthiquement au consentement éclairé. / The third World Day on pancreatic cancer took place the 17th November 2016. This late consideration is due to the duality between his relative scarcity and a dreadful prognosis.Its aggressiveness is underlined by a mortality rate equal to its incidence. Ranked 10th on cancer-related localization and 4th on cancer-related mortality, he will become the second cause of cancer-related deaths in 2020 just behind pulmonary cancer and before colorectal cancer. 5-yr survival rate is 5% irrespective of the stage.Pancreatic ductal adenocarcinoma is the most frequent form (80% of exocrine pancreatic tumors). He is localized in cephalic pancreas in 2/3 of cases.Although pancreatic resection provides the only chance of long-term survival, no more than 20% of patients will be eligible for surgery in curative intent leading to a 5-yr survival rate of 10 to 20%. Pancreaticoduodenectomy for pancreatic head, neck and uncinated process is still a challenging procedure. In the study of the French Surgery Association, mortality and morbidity rate were respectively 3.8% and 54%. Postoperative pancreatic fistula is considered as the Achilles’ heel of pancreaticoduodenectomy and is associated with increased post-operative mortality. Postoperative pancreatic fistula generates significant costs and prolonged hospital stay. Thus postoperative pancreatic fistula is the corner stone of patient’s prognosis improvement.The aim of this study on operated pancreatic ductal adenocarcinoma was to analyze several factors influencing morbidity and mortality.- Before surgery, by testing the impact of body surface area in a cohort of patients.- During surgery, by conducting a meta-analysis on reconstruction methods for pancreatic anastomosis.- After surgery, by evaluating the influence of severe complications on survival and recurrence.We show that the use of various surgical refinements, such as type of pancreatic anastomoses, are equivocal to decrease postoperative pancreatic fistula rate and that performing randomized controlled trials will be difficult. In contrast, the search for patient’s factors leading to postoperative pancreatic fistula seems to be the promising approach. This is of major concern as we demonstrated the causal link between the occurrence of severe postoperative complications and survival or recurrence. This work highlights the need for surgeons to distinguish during preoperative consultation high-risk patients in order to select the best candidates suitable for surgery as well as to give them a full and frank information ethically necessary for free and informed consent.

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O adenocarcinoma pancreático ductal representa a quarta causa de morte por câncer, visto que as taxas de incidência são praticamente idênticas às taxas de mortalidade, o que justifica a natureza altamente agressiva do tumor. Em uma análise preliminar realizada por nosso grupo, avaliou-se a expressão do gene homeobox HOXB7 nas linhagens celulares MIA PaCa-2, BxPC-3 e Capan-1, bem como em tecidos pancreáticos normais, detectando-se o aumento significativo da expressão nas células derivadas de adenocarcinoma pancreático. Alterações na expressão de HOXB7 foram relatadas na formação e progressão de outros cânceres. Nessas condições, este estudo visou não somente avaliar a expressão deste gene em uma série de 29 adenocarcinomas pancreáticos ductais, 6 tecidos metastáticos e 24 tecidos peritumorais, comparando-os aos tecidos normais, mas também averiguar o efeito de sua inibição sobre o perfil de expressão das células citadas. A análise da expressão gênica demonstrou a hiperregulação do transcrito do gene HOXB7 nos tecidos tumorais, corroborando os resultados observados nas linhagens celulares MIA PaCa-2, BxPC-3 e Capan-1. A inibição realizada com RNA de interferência promoveu a modulação de diferentes processos biológicos nas três linhagens celulares pesquisadas, bem como a indução de apoptose e diminuição da proliferação das células MIA PaCa-2. Nesse contexto, o homeobox neste estudo investigado representa mais um componente associado à ampla rede de moléculas envolvidas na caracterização do câncer pancreático e um promissor alvo para futuras terapias biológicas / The pancreatic ductal adenocarcinoma is the fourth leading cause of cancer death, whereas the incidence rates are practically identical to mortality rates, which explains the highly aggressive tumor. In a preliminary analysis performed by our group, we evaluated the expression of the homeobox gene HOXB7 in cell lineages MIA PaCa-2, BxPC-3 and Capan-1, as well as in normal pancreatic tissue, detecting a significant increase in expression in cells derived from pancreatic adenocarcinoma. Changes in expression of HOXB7 were reported in the formation and progression of other cancers. Under these conditions, this study aimed to not only evaluate the expression of this gene in a series of 29 pancreatic ductal adenocarcinomas, 6 metastatic tissues and 24 peritumoral tissues, comparing them to normal tissues, but also examined the effect of its inhibition on the expression profile of the cells mentioned. The analysis of gene expression showed the hyper-regulation of HOXB7 gene transcript in the tumor tissues, confirming the results observed in cell lineages MIA PaCa-2, BxPC-3 and Capan-1. The inhibition performed with RNA interference promoted the modulation of different biological processes in all three cell lines investigated, as well as the induction of apoptosis and decreased in proliferation of the MIA PaCa-2 cells. In this context, the homeobox investigated in this study represents another component associated with the extensive network of molecules involved in the characterization of pancreatic cancer and a promising target for future biologic therapies

RNAs não codificadores longos (lncRNAs) compõem uma fração significativa do transcriptoma. Alterações na expressão de lncRNAs já foram observadas em vários cânceres humanos, mas ainda não foram exploradas no adenocarcinoma pancreático ductal (PDAC), uma doença devastadora e agressiva para a qual faltam métodos para diagnóstico precoce e tratamentos efetivos. Utilizando uma plataforma de microarranjo de cDNA com sondas para 984 lncRNAs e 2371 mRNAs, o presente estudo identificou conjuntos de lncRNAs expressos em 38 amostras clínicas pancreáticas. O enriquecimento de (i) elementos regulatórios associados às regiões promotoras (H3K4me3); (ii) possíveis inícios de transcrição (CAGE-tags); (iii) presença de elementos conservados sugere que ao menos uma fração desses RNAs seja originada a partir de unidades transcricionais independentes, reguladas e possivelmente funcionais. Foram identificadas assinaturas de expressão gênica compostas por mRNA e lncRNAs associadas ao tumor primário e à metástase pancreática. A assinatura gIenica associada à metástase apresentou enriquecimento RNAs intrônicos de loci gênicos associados à via MAPK quinase. O aumento de expressão dos transcritos intrônicos dos loci PPP3CB, MAP3K14 e DAPK1 foi confirmado por qPCR em metástases. Em conjunto, este trabalho aponta para a importância de lncRNAs intrônicos no PDAC e para a necessidade de estudos mais aprofundados para uma melhor compreensão do papel dessa classe de transcritos na biologia da doença. / Long noncoding RNAs (lncRNAs) compose a significant fraction of transcriptome. Altered expression of lncRNAs has been observed in diverse human cancers, but has not being investigated in pancreatic ductal adenocarcinoma (PDAC), a devastating and aggressive disease that lack early diagnosis methods and effective treatments. Using a cDNA microarray platform with probes interrogating 984 lncRNAs and 2371 mRNA, the present study identified subsets of lncRNAs expressed in 38 pancreatic clinical samples. Enrichment of (i) regulatory elements associated to promoter region (H3K4me3); (ii) putative transcription start site (CAGEtags) and (iii) conserved elements, suggest that at least a fraction of these RNAs could be independent transcriptional unit, regulated, an possibly functional. Gene expression signatures comprised of mRNAs and lncRNAs and associated to primary or metastatic tumors were found. A gene signature associated to metastasis was enriched in intronic ncRNAs mapping to gene loci associated to the MAPK pathway. Over expression of intronic RNAs from PPP3CB, MAP3K14 and DAPK1 was confirmed by qPCR in metastatic samples. Taken together, this study points to the importance of intronic lncRNAs in PDAC and for the need to study this class of ncRNAs in greater detail to better understand its role in the biology of PDAC.

O adenocarcinoma pancreático (PDAC) é uma neoplasia de difícil diagnóstico precoce e cujo tratamento não tem apresentado avanços expressivos desde a última década. As tecnologias de sequenciamento de nova geração (next generation sequencing - NGS) podem trazer importantes avanços para a busca de novos marcadores para diagnóstico de PDACs, podendo também contribuir para o desenvolvimento de terapias individualizadas. Bancos de dados são ferramentas poderosas para integração, padronização e armazenamento de grandes volumes de informação. O objetivo do presente estudo foi modelar e implementar um banco de dados relacional (CaRDIGAn - Cancer Relational Database for Integration and Genomic Analysis) que integra dados disponíveis publicamente, provenientes de experimentos de NGS de amostras de diferentes tipos histopatológicos de PDAC, com dados gerados por nosso grupo no IQ-USP, facilitando a comparação entre os mesmos. A funcionalidade do CaRDIGAn foi demonstrada através da recuperação de dados clínicos e dados de expressão gênica de pacientes a partir de listas de genes candidatos, associados com mutação no oncogene KRAS ou diferencialmente expressos em tumores identificados em dados de RNAseq gerados em nosso grupo. Os dados recuperados foram utilizados para a análise de curvas de sobrevida que resultou na identificação de 11 genes com potencial prognóstico no câncer de pâncreas, ilustrando o potencial da ferramenta para facilitar a análise, organização e priorização de novos alvos biomarcadores para o diagnóstico molecular do PDAC. / Pancreatic Ductal Adenocarcinoma (PDAC) is a type of cancer difficult to diagnose early on and treatment has not improved over the last decade. Next Generation Sequencing (NGS) technology may contribute to discover new biomarkers, develop diagnose strategies and personalised therapy applications. Databases are powerfull tools for data integration, normalization and storage of large data volumes. The main objective of this study was the design and implementation of a relational database to integrate publicly available data of NGS experiments of PDAC pacients with data generated in by our group at IQ-USP, alowing comparisson between both data sources. The database was called CaRDIGAn (Cancer Relational Database for Integration and Genomic Analysis) and its funcionalities were tested by retrieving clinical and expression data of public data of genes differencially expressed genes in our samples or genes associated with KRAS mutation. The output of those queries were used to fit survival curves of patients, which led to the identification of 11 genes potencially usefull for PDAC prognosis. Thus, CaRDIGAn is a tool for data storage and analysis, with promissing applications to identification and priorization of new biomarkers for molecular diagnosis in PDAC.

L’adénocarcinome canalaire pancréatique (ADKP) est l’une des tumeurs solides avec le pronostic le plus sombre. Le stroma de ces tumeurs, très abondant, est composé de matrice extra cellulaire ainsi que de cellules stromales (incluant des fibroblastes activés associés au cancer ou des cellules immunitaires). Les fibres nerveuses infiltrant ce stroma tumoral sont considérées comme une caractéristique des ADKP, impliquées dans le phénomène de remodelage nerveux, qui participent aux douleurs neuropathiques, à la dissémination des cellules tumorales, ainsi qu’à la rechute de la maladie après chirurgie. Le remodelage nerveux associé aux ADKP est régulé par un réseau fonctionnel, impliquant des interactions physiques et moléculaires entre cellules tumorales, cellules nerveuses dont les cellules de Schwann et les autres cellules stromales. Dans cette étude, nous avons démontré que les cellules de Schwann (cellules gliales, soutient des neurones périphériques) stimulent l’agressivité (migration, invasion, tumorigénicité) des cellules pancréatiques tumorales de façon dépendante du TGFβ (Transforming Growth Factor beta). En effet, nous révélons que le milieu conditionné des cellules de Schwann est enrichi en nombreuses molécules de signalisation, incluant de grandes quantités de TGFβ capable d’activer sa voie de signalisation dépendante des protéines SMAD, au sein des cellules cancéreuses. Des analyses de spectrométrie de masse des sécrétomes des cellules de Schwann et des cellules tumorales pancréatiques, cultivées seules ou ensemble, soulignent le rôle central du TGFβ dans les interactions neuro-épithéliales, comme illustré par la signature protéomique relative aux mécanismes d’adhésion et de motilité cellulaires. Ainsi, ces résultats démontrent que les cellules de Schwann sont une source de TGFβ dans les ADKP, et jouent un rôle crucial dans l’acquisition de propriétés agressives par les cellules tumorales / Pancreatic ductal adenocarcinoma (PDAC) is one of the solid tumors with the poorest prognosis. The stroma of this tumor is abundant and composed of extracellular matrix and stromal cells (including cancer-associated fibroblasts and immune cells). Nerve fibers invading this stroma represent a hallmark of PDAC, involved in neural remodeling, which participates in neuropathic pain, cancer cells dissemination and tumor relapse after surgery. Pancreatic cancer-associated neural remodeling is regulated through functional interplays mediated by physical and molecular interactions between cancer cells, nerve cells and surrounding Schwann cells, and other stromal cells. In the present study, we show that Schwann cells (glial cells supporting peripheral neurons) can enhance aggressiveness (migration, invasion, tumorigenicity) of pancreatic cancer cells in a transforming growth factor beta (TGFβ)-dependent manner. Indeed, we reveal that conditioned medium from Schwann cells contains various signaling cues, including high amounts of TGFβ able to activate the TGFβ-SMAD signaling pathway in cancer cells. Secretome analyses by mass spectrometry of Schwann cells and pancreatic cancer cells cultured alone or in combination highlighted the central role of TGFβ in neuro-epithelial interactions, as illustrated by proteomic signatures related to cell adhesion and motility. Altogether, these results demonstrate that Schwann cells are a meaningful source of TGFβ in PDAC, which plays a crucial role in the acquisition of aggressive properties by pancreatic cancer cells