The cyclin D1 (CCND1) rs9344 G>A polymorphism predicts clinical outcome in colon cancer patients treated with adjuvant 5-FU-based chemotherapy

Recent evidence indicates a potential prognostic and predictive value for germline polymorphisms in genes involved in cell cycle control. We investigated the effect of cyclin D1 (CCND1) rs9344 G>A in stage II/III colon cancer patients and validated the findings in an independent study cohort. For evaluation and validation set, a total of 264 and 234 patients were included. Patients treated with 5-fluorouracil-based chemotherapy, carrying the CCND1 rs9344 A/A genotype had significantly decreased time-to-tumor recurrence (TTR) in univariate analysis and multivariate analysis (hazard ratio (HR) 2.47; 95% confidence interval (CI) 1.16-5.29; P=0.019). There was no significant association between CCND1 rs9344 G>A and TTR in patients with curative surgery alone. In the validation set, the A allele of CCND1 rs9344 G>A remained significantly associated with decreased TTR in univariate and multivariate analyses (HR 1.94; 95% CI 1.05-3.58; P=0.035). CCND1 rs9344 G>A may be a predictive and/or prognostic biomarker in stage II/III colon cancer patients, however, prospective trials are warranted to confirm our findings.

Natural Killer Cell-like signature observed in locally advanced rectal cancer after neoadjuvant chemoradiotherapy in a tumour regression grade dependent manner

Background: Around 10-15% of patients with locally advanced rectal cancer (LARC) undergo a pathologically complete response (TRG4) to neoadjuvant chemoradiotherapy; the rest of patients exhibit a spectrum of tumour regression (TRG1-3). Understanding therapy-related genomic alterations may help us to identify underlying biology or novel targets associated with response that could increase the efficacy of therapy in patients that do not benefit from the current standard of care.
Methods: 48 FFPE rectal cancer biopsies and matched resections were analysed using the WG-DASL HumanHT-12_v4 Beadchip array on the illumina iScan. Bioinformatic analysis was conducted in Partek genomics suite and R studio. Limma and glmnet packages were used to identify genes differentially expressed between tumour regression grades. Validation of microarray results will be carried out using IHC, RNAscope and RT-PCR.
Results: Immune response genes were observed from supervised analysis of the biopsies which may have predictive value. Differential gene expression from the resections as well as pre and post therapy analysis revealed induction of genes in a tumour regression dependent manner. Pathway mapping and Gene Ontology analysis of these genes suggested antigen processing and natural killer mediated cytotoxicity respectively. The natural killer-like gene signature was switched off in non-responders and on in the responders. IHC has confirmed the presence of Natural killer cells through CD56+ staining.
Conclusion: Identification of NK cell genes and CD56+ cells in patients responding to neoadjuvant chemoradiotherapy warrants further investigation into their association with tumour regression grade in LARC. NK cells are known to lyse malignant cells and determining whether their presence is a cause or consequence of response is crucial. Interrogation of the cytokines upregulated in our NK-like signature will help guide future in vitro models.

Immunohistochemistry should undergo robust validation equivalent to that of molecular diagnostics

Immunohistochemistry (IHC) is a widely available and highly utilised tool in diagnostic histopathology and is used to guide treatment options as well as provide prognostic information. IHC is subjected to qualitative and subjective assessment, which has been criticised for a lack of stringency, while PCR-based molecular diagnostic validations by comparison are regarded as very rigorous. It is essential that IHC tests are validated through evidence-based procedures. With the move to ISO15189 (2012), not just of the accuracy, specificity and reproducibility of each test need to be determined and managed, but also the degree of uncertainty and the delivery of such tests. The recent update to ISO 15189 (2012) states that it is appropriate to consider the potential uncertainty of measurement of the value obtained in the laboratory and how that may impact on prognostic or predictive thresholds. In order to highlight the problems surrounding IHC validity, we reviewed the measurement of Ki67and p53 in the literature. Both of these biomarkers have been incorporated into clinical care by pathology laboratories worldwide. The variation seen appears excessive even when measuring centrally stained slides from the same cases. We therefore propose in this paper to establish the basis on which IHC laboratories can bring the same level of robust validation seen in the molecular pathology laboratories and the principles applied to all routine IHC tests.

Guidance for laboratories performing molecular pathology for cancer patients

Molecular testing is becoming an important part of the diagnosis of any patient with cancer. The challenge to laboratories is to meet this need, using reliable methods and processes to ensure that patients receive a timely and accurate report on which their treatment will be based. The aim of this paper is to provide minimum requirements for the management of molecular pathology laboratories. This general guidance should be augmented by the specific guidance available for different tumour types and tests. Preanalytical considerations are important, and careful consideration of the way in which specimens are obtained and reach the laboratory is necessary. Sample receipt and handling follow standard operating procedures, but some alterations may be necessary if molecular testing is to be performed, for instance to control tissue fixation. DNA and RNA extraction can be standardised and should be checked for quality and quantity of output on a regular basis. The choice of analytical method(s) depends on clinical requirements, desired turnaround time, and expertise available. Internal quality control, regular internal audit of the whole testing process, laboratory accreditation, and continual participation in external quality assessment schemes are prerequisites for delivery of a reliable service. A molecular pathology report should accurately convey the information the clinician needs to treat the patient with sufficient information to allow for correct interpretation of the result. Molecular pathology is developing rapidly, and further detailed evidence-based recommendations are required for many of the topics covered here.

Validating the accuracy of a model to predict the onset of myopia in children.

PURPOSE: To assess the sensitivity and specificity of models predicting myopia onset among ethnically Chinese children. METHODS: Visual acuity, height, weight, biometry (A-scan, keratometry), and refractive error were assessed at baseline and 3 years later using the same equipment and protocol in primary schools in Xiamen (China) and Singapore. A regression model predicting the onset of myopia < -0.75 diopters (D) after 3 years in either eye among Xiamen children was validated with Singapore data. RESULTS: Baseline data were collected from 236 Xiamen children (mean age, 7.82 ± 0.63 years) and from 1979 predominantly Chinese children in Singapore (7.83 ± 0.84 years). Singapore children were significantly taller and heavier, and had more myopia (31.4% vs. 6.36% < -0.75 D in either eye, P < 0.001) and longer mean axial length. Three-year follow-up was available for 80.0% of Xiamen children and 83.1% in Singapore. For Xiamen, the area under the receiver-operator curve (AUC) in a model including ocular biometry, height, weight, and presenting visual acuity was 0.974 (95% confidence interval [CI], 0.945-0.997). In Singapore, the same model achieved sensitivity, specificity, and positive predictive value of 0.844, 0.650, and 0.669, with an AUC of 0.815 (95% CI, 0.791-0.839). CONCLUSIONS: Accuracy in predicting myopia onset based on simple measurements may be sufficient to make targeted early intervention practical in settings such as Singapore with high myopia prevalence. Models based on cohorts with a greater prevalence of high myopia than that in Xiamen could be used to assess accuracy of models predicting more severe forms of myopia.

Immune-derived PD-L1 gene expression defines a subgroup of stage II/III colorectal cancer patients with favorable prognosis that may be harmed by adjuvant chemotherapy

A recent phase 2 study of metastatic colorectal carcinoma (CRC) patients showed that mismatch repair gene status was predictive of clinical response to PD-1-targeting immune checkpoint blockade. Further examination revealed strong correlation between PD-L1 protein expression and microsatellite instability (MSI) in stage IV CRC, suggesting that the amount of PD-L1 protein expression could identify late stage patients who may benefit from immunotherapy. To assess whether the clinical associations between PD-L1 gene expression and MSI identified in metastatic CRC are also present in stage II/III CRC, we used in silico analysis to elucidate the cell types expressing the PD-L1 gene. We found a significant association of PD-L1 gene expression with MSI in early stage CRC (P < 0.001) and show that unlike in non-CRC tumors, PD-L1 is derived predominantly from the immune infiltrate. We demonstrate that PD-L1 gene expression has positive prognostic value in the adjuvant disease setting (PD-L1low v PD-L1high HR = 9.09; CI, 2.11-39.10). PD-L1 gene expression had predictive value, as patients with high PD-L1 expression appear to be harmed by standard-of-care treatment (HR = 4.95; CI,1.10-22.35). Building on the promising results from the metastatic CRC PD-1-targeting trial, we provide compelling evidence that PD-L1high/MSI/immunehigh stage II/III CRC patients should not receive standard chemotherapy. This conclusion supports the rationale to clinically evaluate this patient subgroup for PD-1 blockade treatment.

Factores preditores do estado de saúde em indivíduos vítimas de AVC

Apesar dos inúmeros avanços ao nível da prevenção e intervenção perante o acidente vascular cerebral, este continua a ser a condição mais prevalente e com grande impacto na sociedade, com alterações significativas no estado de saúde destes indivíduos. Estudar os factores preditores da variabilidade no estado de saúde poderá contribuir para a melhoria da qualidade dos cuidados. Objectivos (i) Analisar o constructo explicativo de factores pessoais, factores relacionados com o AVC e com tratamento realizado (fisioterapia), bem como nível de deficiência, grau de incapacidade e percepção sobre grau de recuperação no estado de saúde dos indivíduos. Material e métodos Efectuou-se um estudo de nível II, tipo descritivo – correlacional, de corte transversal, levado a efeito em 378 indivíduos com diagnóstico de AVC que se encontravam a efectuar tratamento de fisioterapia. A recolha de dados foi efectuada através de um questionário estruturado e elaborado que enquadra as variáveis sócio-demográficas, clínicas e de tratamento, e das medidas: Chedoke-McMaster Stroke Assessment (CMSA) e Questionário de Avaliação do Impacto do Acidente Vascular Cerebral (SIS). Para a identificação dos factores explicativos da variabilidade de resultado (dimensões do estado de saúde) recorreu-se à Regressão Linear Múltipla (RLM) com a aplicação do método de análise stepwise. Resultados (i) os indivíduos encontram-se afectados em múltiplas dimensões do estado de saúde, com piores pontuações ao nível da funcionalidade da mão, força, participação social, actividades de vida diária e mobilidade; (ii) surgem como factores explicativos o sexo, a idade e os anos de escolaridade, sendo que, de entre os factores relacionados com o tratamento de fisioterapia, apenas o número de sessões realizadas aduz valor preditivo na variabilidade para a dimensão comunicação do estado de saúde; (iii) a localização da lesão e as complicações no internamento aduzem capacidade preditora na variação do estado de saúde, em praticamente todos os domínios; (iv) são relevantes em termos preditivos a deficiência e a incapacidade, sendo que quanto maior o seu grau, menor será o perfil de estado de saúde; (v) o valor preditivo observado é sempre mais elevado quando se olha para os domínios físicos do estado de saúde (força, AVD, mobilidade e funcionalidade da mão – R2adj entre 0,516 e 0,742, p<0,001) do que para os restantes domínios. Nestes últimos, releva sobretudo o maior valor explicativo registado para o domínio participação social (R2adj de 0,410) e o menor para o domino emoção (R2adj de 0,124). Conclusão Pelos valores preditivos encontrados para a deficiência e incapacidade, importa no tratamento do doente pós AVC olhar para as limitações de actividade e restrições de participação encontrados (CIF) já que com as alterações neste domínio se conseguem alterações significativas do estado de saúde.

Valor prognóstico cardiovascular da MAPA numa população hipertensa portuguesa

Efectuou-se um estudo prospectivo e observacional em 1200 doentes, maiores de 18 anos, com hipertensão essencial e sem eventos cardiovasculares (CV) prévbs que foram referenciados entre 1991 e 1998 para realização de MAPA no Serviço de Cardiologia do Hospital Infante D. Pedro, Aveiro (HIP), na Unidade de Hipertensão e Risco CV do Hospital Pedro Hispano (HPH), Matosinhos e na Clínica Cross/Moss do Porto. O objectivo principal deste estudo foi avaliar, nesta população, seguida durante 8- 12 anos, o valor preditivo de morbi-mortalidade CV da pressurometria ambulatória de 24 horas (MAPA), nomeadamente de diversos índices e valores dela extraída, tais como: (i) valores médios da pressão arterial (PA) de 24-h, diurna e nocturna; (ii) queda tensional noctuma, (iii) diferentes padrões de queda tensional nocturna em particular do padrão Non Dipper; (iv) PA diferencial de 24h, diurna e nodurna; (v) frequência cardíaca de 24 horas (vi) Ambulatory Arterial Stifness. Foram incluídos registos de MAPA de 1200 doentes, de um total de 2644, dos quais 53,8% eram mulheres e 10,2% eram diabéticos. Ao longo de um follow up médio de 8,2+3,0 anos, verificaram-se 62 óbitos e 152 eventos CV fatais e não fatais compreendendo 79 AVC, 51 eventos coronários e 22 classificados de outros eventos cardiovasculares. O estudo permitiu concluir que: 1- A MAPA foi superior a PA casual como preditor de eventos CV globais e de acidentes cerebrovasculares (AVC). 2 - De entre os valores da MAPA, o valor preditivo dos valores sistólicos (de 24 h, diurnos e nocturnos) foi superior ao dos respectivos valores diastólicos e o dos valores nocturnos foi superior ao dos valores diurnos. 3 - 0s eventos CV totais e os eventos coronários foram mais frequentes nos homens do que nas mulheres, sem diferença relativamente ao AVC. O valor preditivo independente da MAPA (sobretudo da PAS e da PP24h) foi superior nas mulheres vs homens relativamente aos eventos globais e AVC. 4- 0s padrões non-dipper e reverted-dipper de queda tensional nocturna associaram-se a pior prognóstico cardiovascular, relativamente ao padrão dipper. Contudo, dentro do padrão non-dipper, somente os doentes com queda tensional nocturna entre 0-4,9% -non-dippers 1 (mas não os doentes com queda tensional nocturna entre 5,O-9,9% -non-dippers 2) apresentaram risco CV superior ao do padrão dipper e semelhante ao do padrão reverted-dipper. Este achado poderá implicar a reclassificação do padrão non-dipper e do risco CV a ele associado. 5- O índice de rigidez arterial derivado da MAPA (AASI) correlaciona-se com outros índices (ex. a velocidade da onda de pulso) e contribui para estratificar o risco CV (eventos CV e AVC). O valor preditivo CV do AASI não é globalmente superior ao da PP 24h, embora em alguns casos o AASI possa acrescentar informação prognostica adicional a PP.

Pregnancy and newborns disorders followed by urine metabolomics

Chapter 1 introduces the scope of the work by identifying the clinically relevant prenatal disorders and presently available diagnostic methods. The methodology followed in this work is presented, along with a brief account of the principles of the analytical and statistical tools employed. A thorough description of the state of the art of metabolomics in prenatal research concludes the chapter, highlighting the merit of this novel strategy to identify robust disease biomarkers. The scarce use of maternal and newborn urine in previous reports enlightens the relevance of this work. Chapter 2 presents a description of all the experimental details involved in the work performed, comprising sampling, sample collection and preparation issues, data acquisition protocols and data analysis procedures. The proton Nuclear Magnetic Resonance (NMR) characterization of maternal urine composition in healthy pregnancies is presented in Chapter 3. The urinary metabolic profile characteristic of each pregnancy trimester was defined and a 21-metabolite signature found descriptive of the metabolic adaptations occurring throughout pregnancy. 8 metabolites were found, for the first time to our knowledge, to vary in connection to pregnancy, while known metabolic effects were confirmed. This chapter includes a study of the effects of non-fasting (used in this work) as a possible confounder. Chapter 4 describes the metabolomic study of 2nd trimester maternal urine for the diagnosis of fetal disorders and prediction of later-developing complications. This was achieved by applying a novel variable selection method developed in the context of this work. It was found that fetal malformations (FM) (and, specifically those of the central nervous system, CNS) and chromosomal disorders (CD) (and, specifically, trisomy 21, T21) are accompanied by changes in energy, amino acids, lipids and nucleotides metabolic pathways, with CD causing a further deregulation in sugars metabolism, urea cycle and/or creatinine biosynthesis. Multivariate analysis models´ validation revealed classification rates (CR) of 84% for FM (87%, CNS) and 85% for CD (94%, T21). For later-diagnosed preterm delivery (PTD), preeclampsia (PE) and intrauterine growth restriction (IUGR), it is found that urinary NMR profiles have early predictive value, with CRs ranging from 84% for PTD (11-20 gestational weeks, g.w., prior to diagnosis), 94% for PE (18-24 g.w. pre-diagnosis) and 94% for IUGR (2-22 g.w. pre-diagnosis). This chapter includes results obtained for an ultraperformance liquid chromatography-mass spectrometry (UPLC-MS) study of pre-PTD samples and correlation with NMR data. One possible marker was detected, although its identification was not possible. Chapter 5 relates to the NMR metabolomic study of gestational diabetes mellitus (GDM), establishing a potentially predictive urinary metabolic profile for GDM, 2-21 g.w. prior to diagnosis (CR 83%). Furthermore, the NMR spectrum was shown to carry information on individual phenotypes, able to predict future insulin treatment requirement (CR 94%). Chapter 6 describes results that demonstrate the impact of delivery mode (CR 88%) and gender (CR 76%) on newborn urinary profile. It was also found that newborn prematurity, respiratory depression, large for gestational age growth and malformations induce relevant metabolic perturbations (CR 82-92%), as well as maternal conditions, namely GDM (CR 82%) and maternal psychiatric disorders (CR 91%). Finally, the main conclusions of this thesis are presented in Chapter 7, highlighting the value of maternal or newborn urine metabolomics for pregnancy monitoring and disease prediction, towards the development of new early and non-invasive diagnostic methods.

Papel do peptídeo natriurético cerebral de tipo B na classificação do tipo de AVC isquémico

Tese de doutoramento, Medicina Clinica (Neurologia), Universidade de Lisboa, Faculdade de Medicina, 2014

New approaches for the diagnosis of human papillomavirus infection:relevance for clinical practice and cancer prevention

Tese de doutoramento, Biologia (Microbiologia), Universidade de Lisboa, Faculdade de Ciências, 2014

Detecting Adverse Events in Clinical Trial Free Text

Thesis (Master's)--University of Washington, 2013

Detecção do vírus do papiloma humano por PCR em tempo real : relevância para medicina legal

Tese de mestrado, Medicina Legal e Ciências Forenses, Faculdade de Medicina, Universidade de Lisboa, 2014

Risk Modelling Framework for Emergency Hospital Readmission, Using Hospital Episode Statistics Inpatient Data

The objective of this study was to develop, test and benchmark a framework and a predictive risk model for hospital emergency readmission within 12 months. We performed the development using routinely collected Hospital Episode Statistics data covering inpatient hospital admissions in England. Three different timeframes were used for training, testing and benchmarking: 1999 to 2004, 2000 to 2005 and 2004 to 2009 financial years. Each timeframe includes 20% of all inpatients admitted within the trigger year. The comparisons were made using positive predictive value, sensitivity and specificity for different risk cut-offs, risk bands and top risk segments, together with the receiver operating characteristic curve. The constructed Bayes Point Machine using this feature selection framework produces a risk probability for each admitted patient, and it was validated for different timeframes, sub-populations and cut-off points. At risk cut-off of 50%, the positive predictive value was 69.3% to 73.7%, the specificity was 88.0% to 88.9% and sensitivity was 44.5% to 46.3% across different timeframes. Also, the area under the receiver operating characteristic curve was 73.0% to 74.3%. The developed framework and model performed considerably better than existing modelling approaches with high precision and moderate sensitivity.

PET/CT com 18-fluor-fluorodeoxiglucose no seguimento do melanoma maligno cutâneo

Introdução – O melanoma maligno cutâneo (MMC) é considerado uma das mais letais neoplasias e no seu seguimento recorre-se, para além dos exames clínicos e da análise de marcadores tumorais, a diversos métodos imagiológicos, como é o exame Tomografia por Emissão de Positrões/Tomografia Computorizada (PET/CT, do acrónimo inglês Positron Emission Tomography/Computed Tomography) com 18fluor-fluorodeoxiglucose (18F-FDG). O presente estudo tem como objetivo avaliar a utilidade da PET/CT relativamente à análise da extensão e à suspeita de recidiva do MMC, comparando os achados imagiológicos com os descritos em estudos CT. Metodologia – Estudo retrospetivo de 62 estudos PET/CT realizados em 50 pacientes diagnosticados com MMC. Excluiu-se um estudo cujo resultado era duvidoso (nódulo pulmonar). As informações relativas aos resultados dos estudos anatomopatológicos e dos exames imagiológicos foram obtidas através da história clínica e dos relatórios médicos dos estudos CT e PET/CT. Foi criada uma base de dados com os dados recolhidos através do software Excel e foi efetuada uma análise estatística descritiva. Resultados – Dos estudos PET/CT analisados, 31 foram considerados verdadeiros positivos (VP), 28 verdadeiros negativos (VN), um falso positivo (FP) e um falso negativo (FN). A sensibilidade, especificidade, o valor preditivo positivo (VPP), o valor preditivo negativo (VPN) e a exatidão da PET/CT para o estadiamento e avaliação de suspeita de recidiva no MMC são, respetivamente, 96,9%, 96,6%, 96,9%, 96,6% e 96,7%. Dos resultados da CT considerados na análise estatística, 14 corresponderam a VP, 12 a VN, três a FP e cinco a FN. A sensibilidade, especificidade, o VPP e o VPN e a exatidão da CT para o estadiamento e avaliação de suspeita de recidiva no MMC são, respetivamente, 73,7%, 80,0%, 82,4%, 70,6% e 76,5%. Comparativamente aos resultados CT, a PET/CT permitiu uma mudança na atitude terapêutica em 23% dos estudos. Conclusão – A PET/CT é um exame útil na avaliação do MMC, caracterizando-se por uma maior acuidade diagnóstica no estadiamento e na avaliação de suspeita de recidiva do MMC comparativamente à CT isoladamente.