Intraductal papillary mucinous neoplasms (IPMN) are pancreatic lesions with uncertain biologic behavior. This study sought objective, accurate prediction tools, through the use of quantitative histopathological signatures of nuclear images, for classifying lesions as chronic pancreatitis (CP), IPMN, or pancreatic carcinoma (PC). Forty-four pancreatic resection patients were retrospectively identified for this study (12 CP; 16 IPMN; 16 PC). Regularized multinomial regression quantitatively classified each specimen as CP, IPMN, or PC in an automated, blinded fashion. Classification certainty was determined by subtracting the smallest classification probability from the largest probability (of the three groups). The certainty function varied from 1.0 (perfectly classified) to 0.0 (random). From each lesion, 180 +/- 22 nuclei were imaged. Overall classification accuracy was 89.6% with six unique nuclear features. No CP cases were misclassified, 1/16 IPMN cases were misclassified, and 4/16 PC cases were misclassified. Certainty function was 0.75 +/- 0.16 for correctly classified lesions and 0.47 +/- 0.10 for incorrectly classified lesions (P = 0.0005). Uncertainty was identified in four of the five misclassified lesions. Quantitative histopathology provides a robust, novel method to distinguish among CP, IPMN, and PC with a quantitative measure of uncertainty. This may be useful when there is uncertainty in diagnosis.

It is not known whether pancreatic cancers evolve from a single or multiple cells, or from a particular pancreatic lineage. However, in the Pdx1-Cre; LSL-KrasG12D; LSLTp53R172H mouse model of pancreatic cancer, all pancreatic lineages are susceptible to express mutant KRas and p53. Hence, such mouse model implies a scenario of maximal heterogeneity of cancer cell origins. On this basis, I isolated seven subclones of heterogeneous mouse pancreatic cancer cells from a single tumour; each of them had a distinct morphology and gene expression profile. Notably, they possessed different intrinsic phospho-SMADs downstream of the TGFβ receptor (phospho-SMAD2/3) or the BMP receptor (Phospho-SMAD1/5/8). I discovered that SMAD4, a co-SMAD which is frequently found to be lost in pancreatic caner tissues, upregulated HNF4α via the classical BMP-SMAD1 pathway, when cells were experiencing metabolic stress upon deprivation of serum, or in the presence of excess thymidine. Under serum starvation at a hypoglycemic-like glucose concentration, the HNF4α-expressing sub-clones appeared to be more able to sustain an unstressed morphology than other non-HNF4α-expressing sub-clones. Immunohistochemical staining on pancreatic cancer sections revealed nuclear co-localization of SMAD4 and HNF4α in human (half of the cases) and in mouse samples. As a secondary project conducted during characterization of cells, I also found that three of the subclones more robustly proliferated under anchorage independent conditions, and they relied on the MEK-ERK pathway and the canonical Wnt pathway, to a different degree. Both studies demonstrate for the first time in primary cell culture that pancreatic cancer cells within a tumour could be highly heterogeneous in terms of both morphology and signaling pathways.

Etude à l'aide des outils de transcriptomique de 17 cultures primaires, maintenues à l'état vivant par xénogreffes et cultures cellulaires, et issues de patients ayant présenté un adénocarcinome pancréatique. Par clustering hiérarchique basée sur l'ensemble des gènes du transcriptome tumoral, 5 patients avec dénomination anonyme se sont fortement distingués des autres patients et présentaient de façon similaire des tumeurs peu différenciées sur le plan histologique et une survie péjorative de moins de 8 mois. Dans cette population de « courts survivants », un total de 942 gènes exprimés de façon significativement différentielle a été retrouvé. Parmi ces gènes, 439 gènes sont apparus significativement sous exprimés et 505 gènes significativement surexprimés (fold change ≥2). L'analyse par GO a montré que parmi ces 942 gènes différentiellement exprimés, nous avons retrouvé un enrichissement important chez les courts survivants, des gènes impliqués dans le cycle cellulaire et l'activité mitotique, la réponse cellulaire au stress, le métabolisme cellulaire ainsi que le métabolisme de l'ADN et l'organisation chromosomique. Par ailleurs, nous avons choisi parmi les 17 cultures primaires, les 3 lignées cellulaires les plus sensibles et les 3 les plus résistantes aux drogues selon les résultats des tests de « Chimiogramme ». Plusieurs gènes ont été identifiés comme spécifiquement surexprimés ou sous-exprimés en relation avec une sensibilité ou une résistance particulières des cellules aux drogues utilisées. Nous avons identifié 671 gènes associés à la gemcitabine, 1107 à l'oxaliplatine, 308 au 5-FU et seulement 34 et 46 au docétaxel et au SN38 respectivement. / We developed an efficient strategy in which PDAC samples from 17 consecutive patients were collected by Endoscopic Ultrasound-Guided Fine-Needle Aspiration (EUS-FNA) or surgery and preserved, by an original approach, as breathing tumors by xenografting and as a primary culture of epithelial cells. Transcriptomic analysis was performed from breathing tumors by an Affymetrix approach. We observed a significant heterogeneity in the RNA expression profile of tumors. However, the bioinformatic analysis of this data was able to discriminate between patients with long- and short-term survival corresponding to patients carrying poorly-differentiated PDAC tumors respectively. We identified 942 genes with statically different expression. Among these genes, 439 were under-expressed and 505 genes over-expressed (fold change ≥2) in short survivors. Primary culture of cells allowed us to analyze their relative sensitivity to anticancer drugs in vitro by a "Chemogram", by similarity with the antibiogram for microorganisms, establishing an individual profile of drug sensitivity. As expected, the response was patient-dependent. Interestingly, we also found that the transcriptome analysis predict the sensitivity of cells to the five anticancer drugs the most frequently used to treating patients with PDAC. In conclusion, using this approach, we found that the transcriptomic analysis could predict the sensitivity to anticancer drugs and the clinical outcome of patients with PDAC.

Pancreatic Ductal Adenocarcinoma (PDAC) continues to have a dismally low survival rate due to late diagnosis and poor treatment options. Therefore, there is a need to understand the early stages and progression of the disease. PDAC is known to have two types of cells of origin: ductal cells or acinar cells. Since acinar-derived PDAC is thought to be the more malignant of the two, it was chosen as the focus of this work. Most studies of acinar cells as they relate to PDAC are accomplished by using animal models such as genetically engineered mouse models. While this method yields a large amount of insight into the progression of the disease and the role of specific genes, it has the drawbacks of being very time and resource intensive. The quicker and less costly alternative is <i>in vitro </i>culture. Specifically, here we have developed a microfluidic model which can incorporate a key aspect of the extracellular matrix (ECM), type I collagen, and mimics the 3D geometry of an <i>in vivo </i>acinus. Most attempts at <i>in vitro </i>culture have been limited by the fact that isolated acinar cells show a decrease in the amount of digestive enzymes they secrete as culture continues. For this reason, we are using a reprogrammed cancer cell line. These cells can be induced with doxycycline to express PTF1a, which allows the cells to adapt acinar characteristics, such as the production of digestive enzymes. We were able to successfully culture and induce PTF1a in these cells within our chip. We showed that the cells exhibit no invasion into the collagen matrix once PTF1a is expressed, thus eliminating a key aspect of cancer cell culture. The cells grown in the chip are confirmed to be producing PRSS2, the digestive enzyme trypsinogen. Collectively, this suggests that we have produced healthy acinar cells growing in the same configuration that they would <i>in vivo. </i>This has many applications in the study of pancreatic ductal adenocarcinoma, as we have developed way to culture reprogramed cancer cells as their benign precursors and maintain acinar characteristics <i>in vitro.</i> It will also have applications in the study of many other pancreatic diseases by providing an <i>in vitro</i> model of a healthy, functional acinus.

Este estudo envolve a avaliação retrospectiva, estudo de Coorte, de 138 pacientes que realizaram Ecoendoscopia com punção aspirativa por agulha fina (EEPAAF) no período de maio de 2004 a julho de 2007. Os dados foram coletados por meio de consulta aos prontuários, constantes do arquivo médico do Hospital das Clínicas da Universidade de São Paulo. O critério de inclusão foi a presença de massa pancreática sólida à tomografia computadorizada e o critério de exclusão foi a presença de tumor pancreático não sólido. O objetivo da pesquisa foi verificar o índice de positividade da ecoendoscopia com punção por agulha fina (EE-PAAF) em massa pancreática sólida, baseada na técnica empregada no Serviço de Endoscopia Gastrointestinal do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP), utilizando as variáveis: característica da massa (tamanho, localização, presença de linfonodo peripancreático, presença de linfonodo em tronco celíaco); número de punções para obtenção de microfragmento e citológico; e experiência do profissional executante. O aparelho utilizado foi um ecoendoscópio da marca Olympus, modelo OLYMPUS EUS (EYS) EXERA EU-C60, com transdutor setorial eletrônico e agulhas de 22 gauges da marca Wilson-Cook. Casuística: 138 pacientes realizaram EE-PAAF de massa pancreática sólida no período entre maio de 2004 e julho de 2007. Resultado: 76 (55,4%) deles são do sexo masculino e 61 (44,5%), do sexo feminino. A idade variou de 16 a 87 anos, com média de 59,9 anos. As lesões foram cefálicas em 94 (68,1%) dos casos. Massas maiores que 4 cm tiveram percentual de positividade maior, chegando a 40%, mas as lesões menores que 2 cm obtiveram um percentual de 43% de inconclusivo. A obtenção de microfragmentos foi conseguida em 100% dos casos positivos e apenas 73,1%, quando negativo (p = 0,004). Não houve diferença estatística em relação à experiência do endoscopista. Apenas 80 pacientes tiveram anotado o número de punções e notou-se que existe um melhor desempenho quanto maior for o número delas. O diagnóstico anatomopatológico definitivo de neoplasia pancreática ocorreu em apenas 41 (29,7%) indivíduos. Conclusão: Em relação às características da massa: quanto maior a massa, maior a positividade do método; a localização não correlacionou com maior positividade; há tendência de positividade quando presentes os linfonodos peripancreáticos; em relação ao número de punções: quanto maior o número delas, maior a positividade do método. Em relação à experiência do profissional: não houve diferença no índice de positividade da punção da massa pancreática sólida / This study involves a retrospective evaluation, Cohort study , of 138 patients who were submitted to Echoendoscopy through aspiration puncture with thin needle ( EE PAAF) ( EE APTN) between May 2004 and June 2007. The data were collected through the medical charts present in the medical files of Hospital das Clínicas (Clinical Hospital ) of the University of São Paulo, having as inclusion criterion the presence of solid pancreatic mass in computerized tomography and as exclusion criterion the presence of non solid pancreatic tumor. This study aims to verify the positivity rate of the echoedoscopy with puncture with thin needle (EEPTN) or (EEPAF) in solid pancreatic mass based on the technique used in the Gastro intestinal Endoscopy Unit of Hospital das Clínicas of the Medicine College of the University of São Paulo (HCFMUSP) using the following variables: mass characteristics ( size, location, presence of peripancreatic lymph node, presence of lymph node in celiac trunk); number of punctures to obtain microfragment for cytology, and experience of the professional in charge. The equipment used was an echoendoscopy device model Olympus EUS (EYES) Exera EU C60, with electronic sectorial transductor and 22 gauges Wilson-Cook needles . Methods: 138 patients were submitted to EE APTN of solid pancreatic mass between may 2004 and july 2007. Results: 76 (55,4%) male patients and 61 (44.5%) female patients. Age ranged from 16 to 87 years and means 59,9 years. The lesions were cephalic in 94 (68,1%). Mass larger than 4 cm had a higher percentage of positivity reaching 40%, but lesions smaller than 2 cm had a percentage of 43% of inconclusive. Microfragments were obtained in 100% of the positive cases and only 73,1% when negative (p = 0,004). There was no statistic difference regarding the experience of the endoscopy professional. Only 80 patients had the number of punctures written down and it was noticed that there is better performance as the number of punctures is increased. The definitive histopathologycal diagnosis of pancreatic neoplasia occurred in only 41(29,7%) patients.Conclusion: Regarding mass characteristics: the larger the mass, the larger the positivity of the method; the location didnt correlate with bigger positivity; when the lymph nodes are present, there is a tendency to positivity; concerning the number of punctures: the higher number of punctures, higher positivity of the method. As to the experience of the encoscopy professional: there was no difference in the rate of positivity of the puncture of the solid pancreatic mass

Background: The systemic immune-inflammation index based on peripheral neutrophil, lymphocyte, and platelet counts has shown a prognostic impact in several malignancies. The aim of this study was to determine the prognostic role of systemic immune-inflammation index in patients with pancreatic ductal adenocarcinoma undergoing resection. Methods: Consecutive patients who underwent surgical resection at the department of surgery at the Medical University of Vienna between 1995 and 2014 were included into this study. The systemic immune-inflammation index was calculated by the formula platelet*neutrophil/lymphocyte. Optimal cutoffs were determined using Youden's index. Uni-and multivariate analyses were calculated by the Cox proportional hazard regression model for overall survival. Results Three hundred twenty-one patients were included in this study. Clinical data was achieved from a prospective patient database. In univariate survival analysis, elevated systemic immune-inflammation index was found to be significantly associated with shortened patients' overall survival (p = 0.007). In multivariate survival analysis, systemic immune-inflammation index remained an independent prognostic factor for overall survival (p = 0.004). No statistical significance could be found for platelet to lymphocyte ratio and neutrophil to lymphocyte ratio in multivariate analysis. Furthermore, area under the curve analysis showed a higher prognostic significance for systemic immune-inflammation index, compared to platelet to lymphocyte ratio and neutrophil to lymphocyte ratio. Conclusion A high systemic immune-inflammation index is an independent, preoperative available prognostic factor in patients with resectable pancreatic ductal adenocarcinoma and is superior to platelet to lymphocyte ratio and neutrophil to lymphocyte ratio for predicting overall survival in pancreatic ductal adenocarcinoma patients.

Glicose e oxigênio desempenham um importante papel na regulação do metabolismo celular. Dada a importância de ambos no metabolismo - o primeiro como fonte de carbono preferencial da maior parte das células, e o segundo como aceptor final de elétrons na cadeia respiratória, em diversos organismos desenvolveram-se métodos adequados para detectar sua presença de modo a ajustar o metabolismo em função de sua disponibilidade. Neste trabalho foi realizado o estudo da expressão, no nível transcricional, dos genes envolvidos nas vias metabólicas primárias e genes envolvidos em morte celular, em células humanas, com o intuito de determinar as alterações no metabolismo energético em resposta a condições de hipóxia e anóxia, por meio da técnica de microarrays de cDNA. Utilizamos, inicialmente, células normais de fibroblasto humano ASl98 e células de fibroblasto humano MRC-5 imortalizadas por transfecção por SV40, e por fim células provenientes de ilhotas pancreáticas humanas, para a elaboração de um protocolo de cultura celular em que as mesmas crescessem aderidas a microcarregadores Cytodex I. Numa segunda etapa, células de ilhotas pancreáticas humanas foram cultivadas em suspensão, aderidas aos microcarregadores, num biorreator, sendo então realizada a análise do perfil transcricional dos genes escolhidos, frente às condições de baixa tensão de oxigênio. É apresentada a análise da expressão gênica de aproximadamente 160 genes na qual foram verificados um comportamento de indução daqueles envolvidos no metabolismo de lipídios e alguns na morte celular e um comportamento inicial de indução, e posterior inibição, do metabolismo primário como um todo. Em vista dos dados obtidos é de interesse ressaltar que essas células deveriam ser mantidas em saturações de oxigênio acima de 5% para evitar o efeito deletério observado na baixa concentração de oxigênio sobre a viabilidade celular, em termos da indução de alguns genes envolvidos na morte celular e da repressão geral dos relacionados ao metabolismo energético. Também foi verificado que, em saturações de oxigênio de até 10%, as células adotaram um padrão transcricional que indicou uma resposta ao estresse por falta de oxigênio, este por sua vez reflete-se na viabilidade celular, característica crucial para o sucesso do transplante clínico de ilhotas. / Glucose and oxygen have important roles on the regulation of cellular metabolism. Due to their importance in metabolism, the former as the preferential carbon source and the later as the final electron acceptor of the respiratory chain, many organisms have developed suitable processes to detect their presence in order to adjust the cellular metabolism to their availability. In this work, we have studied, in human cells and at the transcriptional level, the expression of genes involved in primary metabolism pathways and some of those related to cell death, aiming to resolve alterations in the energetic metabolism as a response to hypoxic and anoxic conditions, by means of cDNA microarrays. We initially used AS198 human fibroblastic normal cells and MRC-5 human fibroblastic cells immortalized by SV40, and later on cells from human pancreatic islets, to develop a cell culture protocol in which they would grow on the surface of Cytodex 1 microcarriers. As a second step, cells from human pancreatic islets were cultured on microcarriers in suspension inside a bioreactor. This culture was then used to carry out the transcriptional profile analysis of selected genes in response to low levels of oxygen. This work presents the analysis of gene expression of approximately 160 genes that can be divided into two distinct groups. The first group, the expression of which is induced, comprises genes involved in lipid metabolism and some of those related to cell death. The expression of the second group, consisting of diverse genes of the primary metabolism, suffers an initial induction followed by repression. Given the data acquired it is interesting to note that the human pancreatic islets should be maintained under at least 5% dissolved oxygen to avoid the deleterious effects on cell viability observed at lower oxygen concentrations, resulting in the induction of some genes involved in cell death and the repression of those related to energetic metabolism. It was also verified that, under oxygen saturation of at least 10%, these cells adopted a transcriptional profile that indicated a response to the stress created by the lack of oxygen, which would in turn reflect on cell viability, a crucial characteristic for success in clinical islet transplantation.

Activating mutations of the kras proto-oncogene are found in more than 90% of human pancreatic ductal adenocarcinoma (PDAC) and can result in increased activity of the NF-κB pathway, leading to constitutive production of proinflammatory cytokines such as TNF-α. Pancreatic cancer progression occurs through a series of pre-invasive lesions, pancreatic intraepithelial neoplasias (PanIN lesions), which progress into invasive carcinoma. The aim of this thesis is to understand the autocrine role of TNF-α produced by premalignant epithelial cells in pancreatic tumour progression. This cytokine has already been shown to be involved in the progression of cancer. The major hypothesis therefore tested was that TNF-α secreted by pre-malignant epithelial cells promotes the early stages of pancreatic carcinogenesis by sustaining an inflamed microenvironment. In the spontaneous kras+/LSL-G12D; pdx1-cre mouse model of pancreatic cancer, concomitant genetic deletion of the TNF-α/IKK2 pathway substantially delayed pancreatic cancer progression and resulted in downregulation of the classical Notch target genes hes1 and hey1. Cell lines from the different PanIN bearing mice were established and used to dissect the cooperation between TNF-α/IKK2 and Notch signalling during PanIN progression. Optimal expression of Notch target genes was induced upon TNF-α stimulation of the canonical NF-κB signalling pathway, in cooperation with basal Notch signals. Mechanistically, TNF-α stimulation resulted in phosphorylation of histone H3 at the hes1 promoter and this signal was lost upon ikk2 genetic deletion. HES1 suppressed the expression of pparg, which encodes for the anti-inflammatory nuclear receptor PPAR-γ. Thus, crosstalk between TNF-α/IKK2 and Notch sustained an intrinsic inflammatory profile of the transformed cells. The treatment of PanIN bearing mice with rosiglitazone, a PPAR-γ agonist, also delayed PanIN progression. A malignant cell-autonomous, low-grade inflammatory process was shown to operate from the very early stages of kras-driven pancreatic carcinogenesis, which may cooperate with the Notch signalling pathway to promote pancreatic cancer progression.

It is imperative that the cancer research community has the means with which to effectively locate, access, manage, analyse and interpret the plethora of data values being generated by novel technologies. This thesis addresses this unmet requirement by using pancreatic cancer and breast cancer as prototype malignancies to develop a generic integrative transcriptomic model. The analytical workflow was initially applied to publicly available pancreatic cancer data from multiple experimental types. The transcriptomic landscape of comparative groups was examined both in isolation and relative to each other. The main observations included (i) a clear separation of profiles based on experimental type, (ii) identification of three subgroups within normal tissue samples resected adjacent to pancreatic cancer, each showing disruptions to biofunctions previously associated with pancreatic cancer (iii) and that cell lines and xenograft models are not representative of changes occurring during pancreatic tumourigenesis. Previous studies examined transcriptomic profiles across 306 biological and experimental samples, including breast cancer. The plethora of clinical and survival data readily available for breast cancer, compared to the paucity of publicly available pancreatic cancer data, allowed for expansion of the pipeline’s infrastructure to include functionalities for cross-platform and survival analysis. Application of this enhanced pipeline to multiple cohorts of triple negative and basal-like breast cancers identified differential risk groups within these breast cancer subtypes. All of the main experimental findings of this thesis are being integrated with the Pancreatic Expression Database and the Breast Cancer Campaign Tissue Bank bioinformatics portal, which enhances the sharing capacity of this information and ensures its exposure to a wider audience.

This thesis focuses on the use of data mining techniques to investigate the expected survival time of patients with pancreatic cancer. Clinical patient data have been useful in showing overall population trends in patient treatment and outcomes. Models built on patient level data also have the potential to yield insights into the best course of treatment and the long-term outlook for individual patients. Within the medical community, logistic regression has traditionally been chosen for building predictive models in terms of explanatory variables or features. Our research demonstrates that the use of machine learning algorithms for both feature selection and prediction can significantly increase the accuracy of models of patient survival. We have evaluated the use of Artificial Neural Networks, Bayesian Networks, and Support Vector Machines. We have demonstrated (p<0.05) that data mining techniques are capable of improved prognostic predictions of pancreatic cancer patient survival as compared with logistic regression alone.