Development of computational tools for the integrated analysis of DNA microarray data with applications in cancer research

The MAP-i Doctoral Program of the Universities of Minho, Aveiro and Porto

Paving the way for predictive diagnostics and personalized treatment of invasive aspergillosis

Invasive aspergillosis (IA) is a life-threatening fungal disease commonly diagnosed among individuals with immunological deficits, namely hematological patients undergoing chemotherapy or allogeneic hematopoietic stem cell transplantation. Vaccines are not available, and despite the improved diagnosis and antifungal therapy, the treatment of IA is associated with a poor outcome. Importantly, the risk of infection and its clinical outcome vary significantly even among patients with similar predisposing clinical factors and microbiological exposure. Recent insights into antifungal immunity have further highlighted the complexity of host-fungus interactions and the multiple pathogen-sensing systems activated to control infection. How to decode this information into clinical practice remains however, a challenging issue in medical mycology. Here, we address recent advances in our understanding of the host-fungus interaction and discuss the application of this knowledge in potential strategies with the aim of moving toward personalized diagnostics and treatment (theranostics) in immunocompromised patients. Ultimately, the integration of individual traits into a clinically applicable process to predict the risk and progression of disease, and the efficacy of antifungal prophylaxis and therapy, holds the promise of a pioneering innovation benefiting patients at risk of IA.

Urothelial bladder cancer progression: lessons learned from the bench

Urothelial bladder carcinoma (UBC) is an intricate malignancy with a variable natural history and clinical behavior. Despite developments in diagnosis/prognosis refinement and treatment modalities, the recurrence rate is high, and progression from non-muscle to muscle invasive UBC commonly leads to metastasis. Moreover, patients with muscle-invasive or extra-vesical disease often fail the standard chemotherapy treatment, and overall survival rates are poor. Thus, UBC remains a challenge in the oncology field, representing an ideal candidate for research on biomarkers that could identify patients at increased risk of recurrence, progression, and chemo-refractoriness. However, progress toward personalized medicine has been hampered by the unique genetic complexity of UBC. Recent genome-wide expression and sequencing studies have brought new insights into its molecular features, pathogenesis and clinical diversity, revealing a landscape where classical pathology is intersected by the novel and heterogeneous molecular groups. Hence, it seems plausible to postulate that only an integrated signature of prognostic/predictive biomarkers inherent in different cancer hallmarks will reach clinical validation. In this review, we have summarized ours and others' research into novel putative biomarkers of progression and chemoresistance that encompass several hallmarks of cancer: tumor neovascularization, invasion and metastasis, and energy metabolism reprogramming of the tumor microenvironment.

Evaluating biomaterial-and microfluidic-based 3D tumor models

Cancer is a major cause of morbidity and mortality worldwide, with a disease burden estimated to increase in the coming decades. Disease heterogeneity and limited information on cancer biology and disease mechanisms are aspects that 2D cell cultures fail to address. We review the current "state-of-the-art" in 3D Tissue Engineering (TE) models developed for and used in cancer research. Scaffold-based TE models and microfluidics, are assessed for their potential to fill the gap between 2D models and clinical application. Recent advances in combining the principles of 3D TE models and microfluidics are discussed, with a special focus on biomaterials and the most promising chip-based 3D models.

Expression of histone methyltransferases as novel biomarkers for renal cell tumor diagnosis and prognostication

Renal cell tumors (RCTs) are the most lethal of the common urological cancers. The widespread use of imaging entailed an increased detection of small renal masses, emphasizing the need for accurate distinction between benign and malignant RCTs, which is critical for adequate therapeutic management. Histone methylation has been implicated in renal tumorigenesis, but its potential clinical value as RCT biomarker remains mostly unexplored. Hence, the main goal of this study was to identify differentially expressed histone methyltransferases (HMTs) and histone demethylases (HDMs) that might prove useful for RCT diagnosis and prognostication, emphasizing the discrimination between oncocytoma (a benign tumor) and renal cell carcinoma (RCC), especially the chromophobe subtype (chRCC). We found that the expression levels of three genes-SMYD2, SETD3, and NO66-was significantly altered in a set of RCTs, which was further validated in a large independent cohort. Higher expression levels were found in RCTs compared to normal renal tissues (RNTs) and in chRCCs comparatively to oncocytomas. SMYD2 and SETD3 mRNA levels correlated with protein expression assessed by immunohistochemistry. SMYD2 transcript levels discriminated RCTs from RNT, with 82.1% sensitivity and 100% specificity (AUC=0.959), and distinguished chRCCs from oncocytomas, with 71.0% sensitivity and 73.3% specificity (AUC: 0.784). Low expression levels of SMYD2, SETD3, and NO66 were significantly associated with shorter disease-specific and disease-free survival, especially in patients with non-organ confined tumors. We conclude that expression of selected HMTs and HDMs might constitute novel biomarkers to assist in RCT diagnosis and assessment of tumor aggressiveness.

Longitudinal analysis of tumor marker CEA of breast cancer patients from Braga's hospital

Allied to an epidemiological study of population of the Senology Unit of Braga’s Hospital that have been diagnosed with malignant breast cancer, we describe the progression in time of repeated measurements of tumor marker Carcinoembryonic antigen (CEA). Our main purpose is to describe the progression of this tumor marker as a function of possible risk factors and, hence, to understand how these risk factors influences that progression. The response variable, values of CEA, was analyzed making use of longitudinal models, testing for different correlation structures. The same covariates used in a previous survival analysis were considered in the longitudinal model. The reference time used was time from diagnose until death from breast cancer. For diagnostic of the models fitted we have used empirical and theoretical variograms. To evaluate the fixed term of the longitudinal model we have tested for a changing point on the effect of time on the tumor marker progression. A longitudinal model was also fitted only to the subset of patients that died from breast cancer, using the reference time as time from date of death until blood test.

Tumor primário de pulmão simulando doença de Alzheimer: relato de caso

RESUMO Retratamos o relato de um homem de 61 anos que apresentava um glioblastoma multiforme em região do giro têmporo-occipital lateral esquerdo que rechaça cranialmente o hipocampo e o corno temporal do ventrículo lateral correspondente. Não havia sinais e sintomas neurológicos e o quadro clínico lembrava a demência de Alzheimer. Havia comprometimento de memória e alterações comportamentais com duração de três meses. Foram afastadas inicialmente outras causas de demência rapidamente progressivas e a ressonância magnética revelou a etiologia tumoral dos sintomas neuropsiquiátricos. Foi submetido à bateria de testes neuropsicométricos com pontuação compatível com doença de Alzheimer (DA). Em razão de extensa área de edema, foi introduzida dexametasona com reversão completa dos sintomas neuropsiquiátricos iniciais e a repetição da bateria neuropsicológica mostrou melhora acentuada em todos os testes. Optou-se por tratamento conservador, após biópsia por agulha, com evolução para óbito em cinco meses.

Stage at presentation of breast cancer in Luanda, Angola - a retrospective study

Background: It is expected that, by 2020, 15 million new cases of cancer will occur every year in the world, one million of them in Africa. Knowledge of cancer trends in African countries is far from adequate, and improvements in cancer prevention efforts are urgently needed. The aim of this study was to characterize breast cancer clinically and pathologically at presentation in Luanda, Angola; we additionally provide quality information that will be useful for breast cancer care planning in the country. Methods: Data on breast cancer cases were retrieved from the Angolan Institute of Cancer Control, from 2006 to 2014. For women diagnosed in 2009 (5-years of follow-up), demographic, clinical and pathological information, at presentation, was collected, namely age at diagnosis, parity, methods used for pathological diagnoses, tumor pathological characteristics, stage of disease and treatment. Descriptive statistics were performed. Results: The median age of women diagnosed with breast cancer in 2009 was 47 years old (range 25–89). The most frequent clinical presentation was breast swelling with axillary lymph nodes metastasis (44.9 %), followed by a mass larger than 5 cm (14.2 %) and lump (12.9 %). Invasive ductal carcinoma was the main histologic type (81.8 %). Only 10.1 % of cancer cases had a well differentiated histological grade. Cancers were diagnosed mostly at advanced stages (66.7 % in stage III and 11.1 % in stage IV). Discussion: In this study, breast cancer was diagnosed at a very advanced stage. Although it reports data from a single cancer center in Luanda, Angola it reinforces the need for early diagnosis and increasing awareness. According to the main challenges related to breast cancer diagnosis and treatment herein presented, we propose a realistic framework that would allow for the implementation of a breast cancer care program, built under a strong network based on cooperation, teaching, audit, good practices and the organization of health services. Conclusion: Angola needs urgently a program for early diagnosis of breast cancer.

Ontological representation of tumor-node-metastasis classification and an ontology-driven classifier: a study on colorectal cancer

Dissertação de mestrado integrado em Engenharia Biomédica (área de especialização em Informática Médica)

Neoplastic pericardial disease. Analysis of 26 patients

PURPOSE: To characterize patients with neoplastic pericardial disease diagnosed by clinical presentation, complementary test findings, and the histological type of tumor. METHODS: Twenty-six patients with neoplastic pericardial disease were retrospectively analyzed. RESULTS: Clinical manifestations and abnormalities in chest roentgenograms and electrocardiograms were frequent, but were not specific. Most patients underwent surgery. There was a high positivity of the pericardial biopsy when associated with the cytological analysis of the pericardial liquid used to determine the histological type of the tumor, particularly when the procedure was performed with the aid of pericardioscopy. CONCLUSION: The correct diagnosis of neoplastic pericardial disease involves suspicious but nonspecific findings during clinical examination and in screen tests. The suspicious findings must be confirmed through more invasive diagnostic approaches, in particular pericardioscopy with biopsy and cytological study.

Invasive hemodynamic monitoring in the postoperative period of cardiac surgery

OBJETIVE: To assess the hemodynamic profile of cardiac surgery patients with circulatory instability in the early postoperative period (POP). METHODS: Over a two-year period, 306 patients underwent cardiac surgery. Thirty had hemodynamic instability in the early POP and were monitored with the Swan-Ganz catheter. The following parameters were evaluated: cardiac index (CI), systemic and pulmonary vascular resistance, pulmonary shunt, central venous pressure (CVP), pulmonary capillary wedge pressure (PCWP), oxygen delivery and consumption, use of vasoactive drugs and of circulatory support. RESULTS: Twenty patients had low cardiac index (CI), and 10 had normal or high CI. Systemic vascular resistance was decreased in 11 patients. There was no correlation between oxygen delivery (DO2) and consumption (VO2), p=0.42, and no correlation between CVP and PCWP, p=0.065. Pulmonary vascular resistance was decreased in 15 patients and the pulmonary shunt was increased in 19. Two patients with CI < 2L/min/m² received circulatory support. CONCLUSION: Patients in the POP of cardiac surgery frequently have a mixed shock due to the systemic inflammatory response syndrome (SIRS). Therefore, invasive hemodynamic monitoring is useful in handling blood volume, choice of vasoactive drugs, and indication for circulatory support.

Tumor metastático espinocelular de cérvix uterino para coração: diagnóstico ante mortem

Mulher de 63 anos com história pregressa de câncer de útero e queixa de fadiga e dispnéia aos pequenos esforços. Ao exame, apresentava-se hipertensa e com estertores de bases pulmonares. O ecocardiograma transtorácico mostrou massa de pouca mobilidade em ventrículo direito. A paciente foi levada para cirurgia, ocasião em que se encontrou uma massa envolvendo a parede anterior da artéria pulmonar, valva tricúspide, átrio direito e parede posterior do ventrículo direito. A artéria pulmonar e o ventrículo direito foram reconstruídos com patch de pericárdio bovino e a valva tricúspide foi substituída por prótese biológica número 31. O exame anatomopatológico demonstrou metástase de células escamosas com áreas bem diferenciadas e infiltrativas. A paciente recebeu alta hospitalar um mês após a cirurgia. Quatro meses após, entretanto, foi readmitida em estado terminal, confirmando o prognóstico reservado da doença neste estágio.

Tumor em ventrículo direito em paciente com melanoma

Os tumores primários cardíacos são infreqüentes; entretanto, as neoplasias metastáticas com acometimento do coração são mais comuns. Alguns tumores apresentam, em estudos post-mortem, implantes secundários cardíacos com freqüências que superam 50%. Esse comprometimento deve ser lembrado em pacientes com história de neoplasia, que apresentem distúrbios de condução, sopro, cardiomegalia ou arritmias. Relatar-se-á, a seguir, o caso de um homem de 39 anos, encaminhado por cansaço e dispnéia aos esforços. Ecocardiograma evidenciou grande massa tumoral em ventrículo direito. A história médica pregressa revelou antecedentes de melanoma e a avaliação complementar mostrou doença metastática para pulmões, coração e cérebro, com evolução a óbito. Os aspectos singulares do caso são a presença de uma grande massa no ventrículo direito de origem metastática, ilustrando um quadro clínico raro e de prognóstico reservado.

USO DE MARCADORES TUMORALES COMO VALORES PREDICTIVOS DE MALIGNIDAD EN EL TUMOR VENEREO TRANSMISIBLE CANINO

Entre los tumores frecuentes en los caninos, se encuentra el denominado Tumor Venéreo Transmisible (TVT). El origen celular exacto del TVT no está claro, aunque estudios inmunohistoquímicos muestran las características de compatibilidad con células histiocíticas. En nuestra región se diagnostican con frecuencia aunque no se tienen datos precisos de su incidencia. El diagnóstico precoz es la mejor herramienta utilizada tanto en medicina veterinaria como humana para el control de tumores. El tumor puede ser muy agresivo localmente, rara vez metastiza. El manejo terapéutico no ha sido sencillo. Se han probado distintos tratamientos como cirugía, radioterapia, bioterapia y quimioterapia- La quimioterapia ha demostrado ser el tratamiento mas efectivo y la droga mas utilizada es el sulfato de vincristina, pero el tiempo del tratamiento hasta la remisión completa varía ampliamente entre individuos. Si bien existen estadificaciones clínicas y diagnósticos citológicos e histológicos que permiten establecer el grado de malignidad, los mismos tienen componentes subjetivos por su naturaleza cualitativa. Los marcadores tumorales se han utilizado especialmente en el establecimiento de un pronóstico acertado. Entre estos están las Regiones Organizadoras Nucleolares (NORs), que pueden colorearse con tinciones argénticas (AgNOR). dichas regiones corresponden a segmentos de cromosomas que contienen genes ribosomales. Por otro lado, existen marcadores de proliferación celular como el anticuerpo monoclonal Ki 67, el cual detecta un antígeno nuclear que se expresa en las células que entran al ciclo celular (fases G1, S, G2 y mitosis), proporcionando una medida directa de la fracción de crecimiento del tejido. El uso de estos marcadores fue eficiente en patología humana, mientras en veterinaria existen escasos reportes La mayoría de los marcadores se han usado sobre muestras histológicas, existiendo escasa información de su uso en muestras citológicas. Conocer el diagnóstico y el pronóstico del tumor relacionándolo con el tratamiento instaurado permitiría predecir las expectativas y calidad de vida del paciente. El contar en Medicina Veterinaria con una herramienta cuantitativa como son los marcadores tumorales que soporte las observaciones subjetivas que aporta el diagnóstico citomorfológico, podría contribuir a establecer de manera confiable el pronóstico del paciente con TVT, así como también definir el modelo terapéutico. Por esto sería importante la búsqueda de técnicas rápidas y seguras que permitan establecer pronósticos cada vez más precisos.