Analysis of outcome and cancer stem cells status in patients with resectable pancreatic adenocarcinoma

RESUMO: Actualmente, a única possibilidade de cura para doentes com adenocarcinoma do pâncreas (PDAC) é a ressecção cirúrgica, no início deste estudo, perguntamo-nos se os predictores clínico-patológicos clássicos de prognostico poderiam ser validados em uma grande cohort de doentes com cancro do pâncreas ressecável e se outros predictores clínicos poderiam ter um papel na decisão de que doentes beneficiariam de ressecção cirúrgica. No capítulo 2, observamos que até 30% dos doentes morrem no primeiro ano após a ressecção cirúrgica, pelo que o nosso objectivo foi determinar factores pré-operatórios que se correlacionam com mortalidade precoce após ressecação cirúrgica com recurso a um instrumento estatisticamente validado, o Charlson-Age Comorbidity Index (CACI), determinamos que um CACI score superior a 4 foi preditivo de internamentos prolongados (p <0,001), complicações pós-operatórias (p = 0,042), e mortalidade em 1 ano pós- ressecção cirúrgica (p <0,001). Um CACI superior a 6 triplicou a mortalidade no primeiro ano pós-cirurgia e estes doentes têm menos de 50% de probabilidade de estarem vivos um ano após a cirurgia. No capítulo 3, o nosso objectivo foi identificar uma proteína de superfície que se correlacionasse estatisticamente com o prognostico de doentes com adenocarcinoma do pâncreas e permitisse a distinção de subgrupos de doentes de acordo com as suas diferenças moleculares, perguntamo-nos ainda se essa proteína poderia ser um marcador de células-estaminais. No nosso trabalho anterior observamos que as células tumorais na circulação sanguínea apresentavam genes com características bifenotípica epitelial e mesenquimal, enriquecimento para genes de células estaminais (ALDH1A1 / ALDH1A2 e KLF4), e uma super-expressão de genes da matriz extracelular (colagénios, SPARC, e DCN) normalmente identificados no estroma de PDAC. Após a avaliação dos tumores primários com RNA-ISH, muitos dos genes identificados, foram encontrados co-localizando em uma sub-população de células na região basal dos ductos pancreáticos malignos. Além disso, observamos que estas células expressam o marcador SV2A neuroendócrino, e o marcador de células estaminais ALDH1A1/2. Em comparação com tumores negativos para SV2, os doentes com tumores SV2 positivos apresentaram níveis mais baixos de CA 19-9 (69% vs. 52%, p = 0,012), tumores maiores (> 4 cm, 23% vs. 10%, p = 0,0430), menor invasão de gânglios linfáticos (69% vs. 86%, p = 0,005) e tumores mais diferenciados (69% vs. 57%, p = 0,047). A presença de SV2A foi associada com uma sobrevida livre de doença mais longa (HR: 0,49 p = 0,009) bem como melhor sobrevida global (HR: 0,54 p = 0,018). Em conjunto, esta informação aponta para dois subtipos diferentes de adenocarcinoma do pâncreas, e estes subtipos co-relacionam estatisticamente com o prognostico de doentes, sendo este subgrupo definido pela presença do clone celular SV2A / ALDH1A1/2 positivo com características neuroendócrinas. No Capítulo 4, a expressão de SV2A no cancro do pâncreas foi validado em linhas celulares primárias. Demonstramos a heterogeneidade do adenocarcinoma do pâncreas de acordo com características clonais neuroendócrinas. Ao comparar as linhas celulares expressando SV2 com linhas celulares negativas, verificamos que as linhas celulares SV2+ eram mais diferenciadas, diferindo de linhas celulares SV2 negativas no que respeita a mutação KRAS, proliferação e a resposta à quimioterapia. No capítulo 5, perguntamo-nos se o clone celular SV2 positivo poderia explicar a resistência a quimioterapia observada em doentes. Observamos um aumento absoluto de clones celulares expressando SV2A, em múltiplas linhas de evidência - doentes, linhas de células primárias e xenotransplantes. Embora, tenhamos sido capazes de demonstrar que o adenocarcinoma do pâncreas é uma doença heterogénea, consideramos que a caracterização genética destes clones celulares expressando SV2A é de elevada importância. Pretendemos colmatar esta limitação com as seguintes estratégias: Após o tratamento com quimioterapia neoadjuvante na nossa coorte, realizamos microdissecação a laser das amostras primarias em parafina, de forma a analisar mutações genéticas observadas no adenocarcinoma pancreático; em segundo lugar, pretendemos determinar consequências de knockdown da expressão de SV2A em nossas linhas celulares seguindo-se o tratamento com gemicitabina para determinação do papel funcional de SV2A; finalmente, uma vez que os nossos esforços anteriores com um promotor - repórter e SmartFlare ™ falharam, o próximo passo será realizar RNA-ISH PrimeFlow™ seguido de FACS e RNA-seq para caracterização deste clone celular. Em conjunto, conseguimos provar com várias linhas de evidência, que o adenocarcinoma pancreático é uma doença heterogénea, definido por um clone de células que expressam SV2A, com características neuroendócrinas. A presença deste clone no tecido de doentes correlaciona-se estatisticamente com o prognostico da doença, incluindo sobrevida livre de doença e sobrevida global. Juntamente com padrões de proliferação e co-expressão de ALDH1A1/2, este clone parece apresentar um comportamento de células estaminais e está associado a resistência a quimioterapia, uma vez que a sua expressão aumenta após agressão química, quer em doentes, quer em linhas de células primárias.----------------------------- ABSTRACT: Currently, the only chance of cure for patients with pancreatic adenocarcinoma is surgical resection, at the beginning of my thesis studies, we asked if the classical clinicopathologic predictors of outcome could be validated in a large cohort of patients with early stage pancreatic cancer and if other clinical predictors could have a role on deciding which patients would benefit from surgery. In chapter 2, we found that up to 30% of patients die within the first year after curative intent surgery for pancreatic adenocarcinoma. We aimed at determining pre-operative factors that would correlate with early mortality following resection for pancreatic cancer using a statistically validated tool, the Charlson-Age Comorbidity Index (CACI). We found that a CACI score greater than 4 was predictive of increased length of stay (p<0.001), post-operative complications (p=0.042), and mortality within 1-year of pancreatic resection (p<0.001). A CACI score of 6 or greater increased 3-fold the odds of death within the first year. Patients with a high CACI score have less than 50% likelihood of being alive 1 year after surgery. In chapter 3 we aimed at identifying a surface protein that correlates with patient’s outcome and distinguishes sub-groups of patients according to their molecular differences and if this protein could be a cancer stem cell marker. The most abundant class of circulating tumor cells identified in our previous work was found to have biphenotypic features of epithelial to mesenchymal transition, enrichment for stem-cell associated genes (ALDH1A1/ALDH1A2 and KLF4), and an overexpression of extracellular matrix genes (Collagens, SPARC, and DCN) normally found in the stromal microenvironment of PDAC primary tumors. Upon evaluation of matched primary tumors with RNA-ISH, many of the genes identified were found to co-localize in a sub-population of cells at the basal region of malignant pancreatic ducts. In addition, these cells expressed the neuroendocrine marker SV2A, and the stem cell marker ALDH1A1/2. Compared to SV2 negative tumors, patients with SV2 positive tumors were more likely to present with lower CA 19-9 (69% vs. 52%, p = 0.012), bigger tumors (size > 4 cm, 23% vs. 10%, p= 0.0430), less nodal involvement (69% vs. 86%, p = 0.005) and lower histologic grade (69% vs. 57%, p = 0.047). The presence of SV2A expressing cells was associated with an improved disease free survival (HR: 0.49 p=0.009) and overall survival (HR: 0.54 p=0.018) and correlated linearly with ALDH1A2. Together, this information points to two different sub-types of pancreatic adenocarcinoma, and these sub-types correlated with patients’ outcome and were defined by the presence of a SV2A/ ALDH1A1/2 expressing clone with neuroendocrine features. In Chapter 4, SV2A expression in cancer was validated in primary cell lines. We were able to demonstrate pancreatic adenocarcinoma heterogeneity according to neuroendocrine clonal features. When comparing SV2 expressing cell lines with SV2 negative cell lines, we found that SV2+ cell lines were more differentiated and differ from SV2 negative cell lines regarding KRAS mutation, proliferation and response to chemotherapy. In Chapter 5 we aimed at determining if this SV2 positive clone could explain chemoresistance observed in patients. We found an absolute increase in SV2A expressing cells, with multiple lines of evidence, in patients, primary cell lines and xenografts. Although, we have been able to show evidence that pancreatic adenocarcinoma is a heterogeneous disease, our findings warrant further investigation. To further characterize SV2A expressing clones after treatment with neoadjuvant chemotherapy in our cohort, we have performed laser capture microdissection of the paraffin embedded tissue in this study and will analyze the tissue for known genetic mutations in pancreatic adenocarcinoma; secondly, we want to know what will happen after knocking down SV2A expression in our cell lines followed by treatment with gemcitabine to determine if SV2A is functionally important; finally, since our previous efforts with a promoter – reporter and SmartFlare™ have failed, we will utilize a novel PrimeFlow™ RNA-ISH assay followed by FACS and RNA sequencing to further characterize this cellular clone. Overall our data proves, with multiple lines of evidence, that pancreatic adenocarcinoma is a heterogeneous disease, defined by a clone of SV2A expressing cells, with neuroendocrine features. The presence of this clone in patients’ tissue correlates with patient’s disease free survival and overall survival. Together with patterns of proliferation and ALDH1A1/2 co-expression, this clone seems to present a stem-cell-like behavior and is associated with chemoresistance, since it increases after chemotherapy, both in patients and primary cell lines.

Targeting Heme with Single Domain Antibodies

Heme, i.e. iron (Fe) protoporphyrin IX, functions as a prosthetic group in a variety of hemoproteins that participate in vital biologic functions essential to sustain life. Heme is a highly reactive molecule, participating in redox reactions, and presumably for this reason it must be sequestered within the heme pockets of hemoproteins, controlling its reactivity. However, under biological stress conditions, hemoproteins can release their prosthetic groups, generating “free heme”, which binds loosely to proteins or to other molecules and presumably acquires unfettered redox activity. Moreover, a growing body of evidence supports the notion that “free heme” can act in a vasoactive, pro-inflammatory and cytotoxic manner when released from a subset of these hemoproteins, such as extracellular hemoglobin, generated during hemolytic conditions. (...)

A domain-specific language for ETL patterns specification in Data Warehousing Systems

During the last few years many research efforts have been done to improve the design of ETL (Extract-Transform-Load) systems. ETL systems are considered very time-consuming, error-prone and complex involving several participants from different knowledge domains. ETL processes are one of the most important components of a data warehousing system that are strongly influenced by the complexity of business requirements, their changing and evolution. These aspects influence not only the structure of a data warehouse but also the structures of the data sources involved with. To minimize the negative impact of such variables, we propose the use of ETL patterns to build specific ETL packages. In this paper, we formalize this approach using BPMN (Business Process Modelling Language) for modelling more conceptual ETL workflows, mapping them to real execution primitives through the use of a domain-specific language that allows for the generation of specific instances that can be executed in an ETL commercial tool.

Using a domain-specific language to enrich ETL schemas

Today it is easy to find a lot of tools to define data migration schemas among different types of information systems. Data migration processes use to be implemented on a very diverse range of applications, ranging from conventional operational systems to data warehousing platforms. The implementation of a data migration process often involves a serious planning, considering the development of conceptual migration schemas at early stages. Such schemas help architects and engineers to plan and discuss the most adequate way to migrate data between two different systems. In this paper we present and discuss a way for enriching data migration conceptual schemas in BPMN using a domain-specific language, demonstrating how to convert such enriched schemas to a first correspondent physical representation (a skeleton) in a conventional ETL implementation tool like Kettle.

OPM3® Portugal project: information systems and technologies organizations: outcome analysis

Increasing the maturity in Project Management (PM) has become a goal for many organizations, leading them to adopt maturity models to assess the current state of its PM practices and compare them with the best practices in the industry where the organization is inserted. One of the main PM maturity models is the Organizational Project Management Maturity Model (OPM3®), developed by the Project Management Institute. This paper presents the Information Systems and Technologies organizations outcome analysis, of the assesses made by the OPM3® Portugal Project, identifying the PM processes that are “best” implemented in this particular industry and those in which it is urgent to improve. Additionally, a comparison between the different organizations’ size analyzed is presented.

Self-narrative reconstruction after dilemma-focused therapy for depression: a comparison of good and poor outcome cases

Objective: The aim of this study is to improve the understanding of self-changes after an intervention for depression focused on implicative dilemmas, a type of cognitive conflict related to identity. As recent research has highlighted the relevance of identity-related dilemmas in clients with depression, we sought to assess the way in which clients resolve such inner conflicts after a tailored dilemma-focused intervention and how this is reflected in the clients’ self-narratives. Method: We used three instruments to observe differences between good (n = 5) and poor (n = 5) outcome cases: (i) the Repertory Grid Technique to track the resolution of dilemmas, (ii) the Change Interview to compile clients’ accounts of changes at posttreatment, and (iii) the Innovative Moments Coding System to examine the emergence of clients’ novelties at the Change Interview. Results: Groups did not differ in terms of the number and relevance of client-identified significantly helpful events. However, between-group differences were found for the resolution of dilemmas and for the proportion of high-level innovative moment (IM) types. Furthermore, a greater self-narrative reconstruction was associated with higher levels of symptom improvement. Conclusions: Good outcome cases seem to be associated with the resolution of conflicts and high-level IMs.

Clozapine-induced severe eosinophilia: report of a case with good outcome

INTRODUCTION: Clozapine is the antipsychotic of choice in the treatment of refractory schizophrenia. However, its side effects, such as eosinophilia, may preclude its use. METHODS: Case report and literature review. RESULTS: Young woman, 19 years old, diagnosed with hebefrenic schizophrenia, admitted at Unicamp's psychiatry ward after psychotic symptoms relapse. Clozapine was started after unsuccessful attempts with risperidon and olanzapine. By the fourth week of clozapine use, eosinophils began to increase. Drug titration was stopped, but eosinophils counts continued to rise up, reaching the mark of 5200/mm³. Due to severity of psychotic symptoms and to the good response obtained with clozapine, we decided to investigate organs involvement before withdrawing the medication. As the patient had no organs involvement, clozapine was maintained and one month after eosinophils peak, it was already normalized. CONCLUSION: Eosinophilia should not necessarily lead to clozapine's withdrawal. Patients who present eosinophilia must be at rigorous observation for organs involvement, and if there is no such involvement, clozapine might be maintained, considering the possible benign and transitory nature of the eosinophils count elevation.

Critical aortic stenosis in the neonate. Clinical assessment and surgical outcome in 18 patients

OBJECTIVE - To assess neonates with aortic stenosis with early decompensation operated upon. (LCO) (CHF). METHODS - A and retrospective study analyzing 6 neonates with LCO, group I (GI), and 12 neonates with CHF, group II (GII). Clinical radiographic, electrocardiographic and echocardiographic findings also provided comparative bases for the study, as did surgical and evolutional findings. RESULTS - The mean ages at hospitalization and surgery (p = 0.0031) were 14.3 and 14.8 days in GI and 35.4 and 42.8 days in GII, respectively. Cardiac murmurs were more intense in GII (p = 0.0220). The aortic ring was smaller in GI (8.0 ± 2.5mm) as compared to GII (11.4±1.4mm) (p = 0.2882). Ventricular function was reduced to 18±5.5% and 33.3±7.6% in GI and GII, respectively (p = 0.0162). Aortic atresia, however, was present only in 2 neonates in GI. Five of 6 patients in GI died but all patients in GII survived (p=0.0007). In the latter group, 84.6% of the patients were in functional class I (FC-I) in the long-term follow-up, with moderate residual lesions in 6 neonates, discrete residual lesions in 4, and reoperation in 2. CONCLUSION - Aortic stenosis is a severe anomaly of the neonate, whose immediate evolution depends on the pre-operative anatomic and functional findings, and the late evolution essentially depends on the anatomic features of the valve.

The Brugada syndrome. Outcome of one case

The Brugada syndrome is a rare condition, and due to its mutating manner of presentation it may be difficult to diagnose. We report one case and discuss the diagnostic aspects and the clinical outcome of one patient with characteristic findings of this syndrome. These findings are especially defined by J-ST elevation in the right leads of serial electrocardiographic records, wide oscillations of J points and ST segments during 24-hour Holter monitoring, and nocturnal sudden death. We stress the importance of the Holter monitor findings for diagnostic complementation. Through this method it is possible to establish a correlation between vigil activities and sleep and the variability of the degree of impairment in ventricular repolarization.

Clinical outcome of patients with familial hypercholesterolemia and coronary artery disease undergoing partial ileal bypass surgery

Familial hypercholesterolemia is characterized by high serum levels of total cholesterol and LDL-cholesterol. It may be homozygous or heterozygous. In homozygous patients, LDL-cholesterol levels range from 500 to 1000mg/dL and coronary artery disease is precocious, usually manifesting itself between the 2nd and 3rd decades of life. The diagnosis is often made by the presence of xanthoma tuberosum and tendinous xanthomas that appear between the 1st and 2nd decades of life. The use of high doses of statins or even unusual procedures (apheresis, partial ileal bypass surgery, liver transplantation, gene therapy), or both, is necessary for increasing survival and improving quality of life, because a reduction in cholesterol levels is essential for stabilizing the coronary artery disease and reducing xanthomas. We report our experience with 3 patients with xanthomatous familial hypercholesterolemia and coronary artery disease, who underwent partial ileal bypass surgery. Their follow-up over the years (approximately 8 years) showed a mean 30% reduction in total cholesterol, with a significant reduction in the xanthomas and stabilization of the coronary artery disease.

Outcome of acute renal failure associated with cardiac surgery in infants

OBJECTIVE: To analyze the impact of acute renal failure (ARF) on the evolution of infants undergoing cardiac surgery. METHODS: We assessed 15 infants undergoing cardiac surgery who developed (ARF). Their demographic, clinical and surgical data, and evolution were analyzed. RESULTS: Their mean age was 4.4±4.0 months (8 days to 24 months). Twelve infants were males, and 4 patients already had ARF at surgery. The primary cause of ARF was immediate acute cardiac dysfunction in 10 infants, cardiac dysfunction associated with sepsis in 2 infants, and isolated sepsis in 3 infants. All children depended on mechanical ventilation during their postoperative period, 14 infants used vasoactive drugs, and 11 had an infectious process associated with ARF. Thirteen infants required dialytic treatment. Eleven infants developed oluguric ARF, and all had to undergo peritoneal dialysis; of the 4 patients with non-oliguric, 2 required dialysis, the main indication being hypervolemia. Of these 13 dialyzed infants, 4 died in the first 24 hours because of the severity of the underlying cardiac disease (mean urea level of 49±20 mg/dl). The mortality rate for the entire group was 60% , and it was higher among the patients with oliguria ARF (73% vs 25%, p<0.001). The cause of death was acute cardiac dysfunction in 6 infants (early type-1ARF) and sepsis in the 3 remaining infants (late type-2 ARF). CONCLUSION: The mortality rate of ARF associated with cardiac surgery in infants was hight, being higher among children with oliguria; peritoneal dialysis was indicated due to clinically uncontrolled hypervolemia and not to the uremic hypercatabolic state.

Influence of the echocardiographic score and not of the previous surgical mitral commissurotomy on the outcome of percutaneous mitral balloon valvuloplasty

OBJECTIVE: To evaluate prior mitral surgical commissurotomy and echocardiographic score influence on the outcomes and complications of percutaneous mitral balloon valvuloplasty. METHODS: We performed 459 complete mitral valvuloplasty procedures. Four hundred thirteen were primary valvuloplasty and 46 were in patients who had undergone prior surgical commissurotomy. The prior commissurotomy group was older, had higher echo scores, and a tendency toward a higher percentage of atrial fibrillation. RESULTS: When the groups were compared with each other, no differences were found in pre- and postprocedure mean pulmonary artery pressure, mean mitral gradient, mitral valve area, and mitral regurgitation . Because we found no significant differences, we subdivided the entire group based on echo scores, those with echo scores <=8 and those with echo scores >8 the mitral valve area being higher in the <=8 echo score group 2.06±0.42 versus 1.90±0.40cm² (p=0.0090) in the >8 echo score group. CONCLUSION: Dividing the groups based on echo score revealed that the higher echo score group had smaller mitral valve areas postvalvuloplasty.

BIOMedical search engine framework: lightweight and customized implementation of domain-specific biomedical search engines

The Smart Drug Search is publicly accessible at http://sing.ei.uvigo.es/sds/. The BIOMedical Search Engine Framework is freely available for non-commercial use at https://github.com/agjacome/biomsef

Atrial activation during sinus rhythm in patients with rheumatic and non-rheumatic paroxysmal atrial fibrillation. Frequency-domain analysis using signal-averaged electrocardiography

OBJECTIVE: Using P-wave signal-averaged electrocardiography, we assessed the patterns of atrial electrical activation in patients with idiopathic atrial fibrillation as compared with patterns in patients with atrial fibrillation associated with structural heart disease. METHODS: Eighty patients with recurrent paroxysmal atrial fibrillation were divided into 3 groups as follows: group I - 40 patients with atrial fibrillation associated with non-rheumatic heart disease; group II - 25 patients with rheumatic atrial fibrillation; and group III - 15 patients with idiopathic atrial fibrillation. All patients underwent P-wave signal-averaged electrocardiography for frequency-domain analysis using spectrotemporal mapping and statistical techniques for detecting and quantifying intraatrial conduction disturbances. RESULTS: We observed an important fragmentation in atrial electrical conduction in 27% of the patients in group I, 64% of the patients in group II, and 67% of the patients in group III (p=0.003). CONCLUSION: Idiopathic atrial fibrillation has important intraatrial conduction disturbances. These alterations are similar to those observed in individuals with rheumatic atrial fibrillation, suggesting the existence of some degree of structural involvement of the atrial myocardium that cannot be detected with conventional electrocardiography and echocardiography.

Comorbid depression and anxiety effects on pregnancy and neonatal outcome

The effects of comorbid depression and anxiety were compared to the effects of depression alone and anxiety alone on pregnancy mood states and biochemistry and on neonatal outcomes in a large multi-ethnic sample. At the prenatal period the comorbid and depressed groups had higher scores than the other groups on the depression measure. But, the comorbid group had higher anxiety, anger and daily hassles scores than the other groups, and they had lower dopamine levels. As compared to the non-depressed group, they also reported more sleep disturbances and relationship problems. The comorbid group also experienced a greater incidence of prematurity than the depressed, the high anxiety and the non-depressed groups. Although the comorbid and anxiety groups were lower birthweight than the non-depressed and depressed groups, the comorbid group did not differ from the depressed and anxiety groups on birth length. The neonates of the comorbid and depressed groups had higher cortisol and norepinephrine and lower dopamine and serotonin levels than the neonates of the anxiety and non-depressed groups as well as greater relative right frontal EEG. These data suggest that for some measures comorbidity of depression and anxiety is the worst condition (e.g., incidence of prematurity), while for others, comorbidity is no more impactful than depression alone.