Ankylosing spondylitis: genomic and functional characterization of candidate genes and their repercussion in clinical practice

RESUMO: Introdução: A espondilite anquilosante (EA) é uma doença inflamatória crónica caracterizada pela inflamação das articulações sacroilíacas e da coluna. A anquilose progressiva motiva uma deterioração gradual da função física e da qualidade de vida. O diagnóstico e o tratamento precoces podem contribuir para um melhor prognóstico. Neste contexto, a identificação de biomarcadores, assume-se como sendo muito útil para a prática clínica e representa hoje um grande desafio para a comunidade científica. Objetivos: Este estudo teve como objetivos: 1 - caracterizar a EA em Portugal; 2 - investigar possíveis associações entre genes, MHC e não-MHC, com a suscetibilidade e as características fenotípicas da EA; 3 - identificar genes candidatos associados a EA através da tecnologia de microarray. Material e Métodos: Foram recrutados doentes com EA, de acordo com os critérios modificados de Nova Iorque, nas consultas de Reumatologia dos diferentes hospitais participantes. Colecionaram-se dados demográficos, clínicos e radiológicos e colhidas amostras de sangue periférico. Selecionaram-se de forma aleatória, doentes HLA-B27 positivos, os quais foram tipados em termos de HLA classe I e II por PCR-rSSOP. Os haplótipos HLA estendidos foram estimados pelo algoritmo Expectation Maximization com recurso ao software Arlequin v3.11. As variantes alélicas dos genes IL23R, ERAP1 e ANKH foram estudadas através de ensaios de discriminação alélica TaqMan. A análise de associação foi realizada utilizando testes da Cochrane-Armitage e de regressão linear, tal como implementado pelo PLINK, para variáveis qualitativas e quantitativas, respetivamente. O estudo de expressão génica foi realizado por Illumina HT-12 Whole-Genome Expression BeadChips. Os genes candidatos foram validados usando qPCR-based TaqMan Low Density Arrays (TLDAs). Resultados: Foram incluídos 369 doentes (62,3% do sexo masculino, com idade média de 45,4 ± 13,2 anos, duração média da doença de 11,4 ± 10,5 anos). No momento da avaliação, 49,9% tinham doença axial, 2,4% periférica, 40,9% mista e 7,1% entesopática. A uveíte anterior aguda (33,6%) foi a manifestação extra-articular mais comum. Foram positivos para o HLA-B27, 80,3% dos doentes. Os haplótipo A*02/B*27/Cw*02/DRB1*01/DQB1*05 parece conferir suscetibilidade para a EA, e o A*02/B*27/Cw*01/DRB1*08/DQB1*04 parece conferir proteção em termos de atividade, repercussão funcional e radiológica da doença. Três variantes (2 para IL23R e 1 para ERAP1) mostraram significativa associação com a doença, confirmando a associação destes genes com a EA na população Portuguesa. O mesmo não se verificou com as variantes estudadas do ANKH. Não se verificou associação entre as variantes génicas não-MHC e as manifestações clínicas da EA. Foi identificado um perfil de expressão génica para a EA, tendo sido validados catorze genes - alguns têm um papel bem documentado em termos de inflamação, outros no metabolismo da cartilagem e do osso. Conclusões: Foi estabelecido um perfil demográfico e clínico dos doentes com EA em Portugal. A identificação de variantes génicas e de um perfil de expressão contribuem para uma melhor compreensão da sua fisiopatologia e podem ser úteis para estabelecer modelos com relevância em termos de diagnóstico, prognóstico e orientação terapêutica dos doentes. -----------ABSTRACT: Background: Ankylosing Spondylitis (AS) is a chronic inflammatory disorder characterized by inflammation in the spine and sacroiliac joints leading to progressive joint ankylosis and in progressive deterioration of physical function and quality of life. An early diagnosis and early therapy may contribute to a better prognosis. The identification of biomarkers would be helpful and represents a great challenge for the scientific community. Objectives: The present study had the following aims: 1- to characterize the pattern of AS in Portuguese patients; 2- to investigate MHC and non-MHC gene associations with susceptibility and phenotypic features of AS and; 3- to identify candidate genes associated with AS by means of whole-genome microarray. Material and Methods: AS was defined in accordance to the modified New York criteria and AS cases were recruited from hospital outcares patient clinics. Demographic and clinical data were recorded and blood samples collected. A random group of HLA-B27 positive patients and controls were selected and typed for HLA class I and II by PCR-rSSOP. The extended HLA haplotypes were estimated by Expectation Maximization Algorithm using Arlequin v3.11 software. Genotyping of IL23R, ERAP1 and ANKH allelic variants was carried out with TaqMan allelic discrimination assays. Association analysis was performed using the Cochrane-Armitage and linear regression tests as implemented in PLINK, for dichotomous and quantitative variables, respectively. Gene expression profile was carried out using Illumina HT-12 Whole-Genome Expression BeadChips and candidate genes were validated using qPCR-based TaqMan Low Density Arrays (TLDAs). Results: A total of 369 patients (62.3% male; mean age 45.4±13.2 years; mean disease duration 11.4±10.5 years), were included. Regarding clinical disease pattern, at the time of assessment, 49.9% had axial disease, 2.4% peripheral disease, 40.9% mixed disease and 7.1% isolated enthesopathic disease. Acute anterior uveitis (33.6%) was the most common extra-articular manifestation. 80.3% of AS patients were HLA-B27 positive. The haplotype A*02/B*27/Cw*02/DRB1*01/DQB1*05 seems to confer susceptibility to AS, whereas A*02/B*27/Cw*01/DRB1*08/DQB1*04 seems to provide protection in terms of disease activity, functional and radiological repercussion. Three markers (two for IL23R and one for ERAP1) showed significant single-locus disease associations. Association of these genes with AS in the Portuguese population was confirmed, whereas ANKH markers studied did not show an association with AS. No association was seen between non-MHC genes and clinical manifestations of AS. A gene expression signature for AS was established; among the fourteen validated genes, a number of them have a well-documented inflammatory role or in modulation of cartilage and bone metabolism. Conclusions: A demographic and clinical profile of patients with AS in Portugal was established. Identification of genetic variants of target genes as well as gene expression signatures could provide a better understanding of AS pathophysiology and could be useful to establish models with relevance in terms of susceptibility, prognosis, and potential therapeutic guidance.

Correlation between the mechanical cycling behavior and microstructure in laser welded joints using NiTi memory shape alloys

Dissertação para obtenção do Grau de Mestre em Engenharia de Materiais

The HIF1A Functional Genetic Polymorphism at Locus +1772 Associates with Progression to Metastatic Prostate Cancer and Refractoriness to Hormonal Castration

The hypoxia inducible factor 1 alpha (HIF1a) is a key regulator of tumour cell response to hypoxia, orchestrating mechanisms known to be involved in cancer aggressiveness and metastatic behaviour. In this study we sought to evaluate the association of a functional genetic polymorphism in HIF1A with overall and metastatic prostate cancer (PCa) risk and with response to androgen deprivation therapy (ADT). The HIF1A +1772 C>T (rs11549465) polymorphism was genotyped, using DNA isolated from peripheral blood, in 1490 male subjects (754 with prostate cancer and 736 controls cancer-free) through Real-Time PCR. A nested group of cancer patients who were eligible for androgen deprivation therapy was followed up. Univariate and multivariate models were used to analyse the response to hormonal treatment and the risk for developing distant metastasis. Age-adjusted odds ratios were calculated to evaluate prostate cancer risk. Our results showed that patients under ADT carrying the HIF1A +1772 T-allele have increased risk for developing distant metastasis (OR, 2.0; 95%CI, 1.1-3.9) and an independent 6-fold increased risk for resistance to ADT after multivariate analysis (OR, 6.0; 95%CI, 2.2-16.8). This polymorphism was not associated with increased risk for being diagnosed with prostate cancer (OR, 0.9; 95%CI, 0.7-1.2). The HIF1A +1772 genetic polymorphism predicts a more aggressive prostate cancer behaviour, supporting the involvement of HIF1a in prostate cancer biological progression and ADT resistance. Molecular profiles using hypoxia markers may help predict clinically relevant prostate cancer and response to ADT.

Neuropsychological Abnormalities in Children with the Panayiotopoulos Syndrome Point to Parietal Lobe Dysfunction

Panayiotopoulos syndrome (PS) is a common epilepsy syndrome associated with rare clinical seizures and unknown localization of the epileptogenic area. Despite findings of normal development in patientswith PS, recent neuropsychological studies point to subtle and diverse cognitive impairments. No well-outlined hypothesis about the localization of the brain dysfunction responsible for these impairments has been proposed.We further explored the cognitive dysfunctions in PS andmade inferences on the most likely anatomical localization of brain impairment. A group of 19 patients (aged 6–12) with PS was rated according to spike activity and lateralization. The patients were submitted to a neuropsychological evaluation to assess general intelligence, memory, language, visual–perceptual abilities, attention, and executive functions. Using 35-channel scalp EEG recordings, the N170 face-evoked event-related potential (ERP)was obtained to assess the functional integrity of the ventral pathway. All patientswith PS showed normal IQ but subtle and consistent neurocognitive impairments. Namely, we found abnormalities in the copy task of the Rey–Osterrieth Complex Figure and in theNarrative Memory Test. There was no correlation between neuropsychological impairments with spike activity and hemispheric spike lateralization. The N170 ERP was normal in all patients except for one. Our neuropsychological findings demonstrate impairments in visual–perceptual abilities and in semantic processing. These findings, paired with the absence of occipital lobe dysfunction in all neuropsychological studies of PS performed to this date, support the existence of parietal lobe dysfunction.

Compositional and functional analysis of polycomb target chromatin

Dissertation presented to obtain the Ph.D degree in Molecular Biology

Insights into the biological significance of alternative splicing in Arabidopsis: functional characterization of a dual-targeted E3 ligase and the SCL30a SR protein

Dissertation presented to obtain the Ph.D degree in Molecular Biology

The HIF1A Functional Genetic Polymorphism at Locus +1772 Associates with Progression to Metastatic Prostate Cancer and Refractoriness to Hormonal Castration

The hypoxia inducible factor 1 alpha (HIF1a) is a key regulator of tumour cell response to hypoxia, orchestrating mechanisms known to be involved in cancer aggressiveness and metastatic behaviour. In this study we sought to evaluate the association of a functional genetic polymorphism in HIF1A with overall and metastatic prostate cancer (PCa) risk and with response to androgen deprivation therapy (ADT). The HIF1A +1772 C>T (rs11549465) polymorphism was genotyped, using DNA isolated from peripheral blood, in 1490 male subjects (754 with prostate cancer and 736 controls cancer-free) through Real-Time PCR. A nested group of cancer patients who were eligible for androgen deprivation therapy was followed up. Univariate and multivariate models were used to analyse the response to hormonal treatment and the risk for developing distant metastasis. Age-adjusted odds ratios were calculated to evaluate prostate cancer risk. Our results showed that patients under ADT carrying the HIF1A +1772 T-allele have increased risk for developing distant metastasis (OR, 2.0; 95%CI, 1.1-3.9) and an independent 6-fold increased risk for resistance to ADT after multivariate analysis (OR, 6.0; 95%CI, 2.2-16.8). This polymorphism was not associated with increased risk for being diagnosed with prostate cancer (OR, 0.9; 95%CI, 0.7-1.2). The HIF1A +1772 genetic polymorphism predicts a more aggressive prostate cancer behaviour, supporting the involvement of HIF1a in prostate cancer biological progression and ADT resistance. Molecular profiles using hypoxia markers may help predict clinically relevant prostate cancer and response to ADT.

The Oncological and Functional Risks of the Organ Preservation Experimental Treatment Approach

We increasingly face conservative surgery for rectal cancer and even the so called ‘wait and see’ approach, as far as 10–20% patients can reach a complete pathological response at the time of surgery. But what can we say to our patients about risks? Standard surgery with mesorectal excision gives a <2% local recurrence with a post operative death rate of 2–8% (may reach 30% at 6 months in those over 85), but low AR has some deterioration in bowel function and in low cancer a permanent stoma may be required. Also a long-term impact on urinary and sexual function is possible. Distant metastasis rate seem to be identical in the standard and conservative approach. It is difficult to evaluate conservative approach because a not clear standardization of surgery for low rectal cancer. Rullier et al tried to clarify, and they found identical results for recurrence (5–9%), disease free survival (70%) at 5y for coloanal anastomosis and intersphinteric resection. Other series have found local recurrence higher than with standard approach and functional results may be worse and, in some situations, salvage therapy is compromised or has more complications. In this context, functional outcomes are very important but most studies are incomplete in measuring bowel function in the context of conservative approach. In 2005 Temple et al made a survey of 122/184 patient after sphinter preserving surgery and found a 96.9% of incomplete evacuation, 94.4% clustering, 93.2% food affecting frequency, 91.8% gas incontinence and proposed a systematic evaluation with a specific questionnaire. In which concerns ‘Wait and see’ approach for complete clinical responders, it was first advocated by Habr Gama for tumors up to 7cm, with a low locoregional failure of 4.6%, 5y overall survival 96%, 72% for disease free survival; one fifth of patients failed in the first year; a Dutch trial had identical results but others had worse recurrence rates; in other series 25% of patients could not be salvaged even with APR; 30% have subsequent metastatic disease what seems equal for ‘wait and see’ and operated patients. In a recent review Glynne Jones considers that all the evaluated ‘wait and see’ studies are heterogeneous in staging, inclusion criteria, design and follow up after chemoradiation and that there is the suggestion that patients who progress while under observation fare worse than those resected. He proposes long-term observational studies with more uniform inclusion criteria. We are now facing a moment where we may be more aggressive in early cancer and neoadjuvant treatment to be more conservative in the subsequent treatment but we need a better stratification of patients, better evaluation of results and more clear prognostic markers.

Structural and functional studies of PpcA: a key protein in the electron transfer pathways of Geobacter sulfurreducens

Dissertação para obtenção do Grau de Doutor em Bioquímica, ramo de Biotecnologia

Caracterização dos níveis de atividade física das pessoas com 75 ou mais anos e a sua relação com a auto-perceção de saúde e a dor

RESUMO: A atividade física (AF) surge como uma estratégia constante no combate aos efeitos nefastos do envelhecimento e nesse sentido, surgem recomendações, mundialmente aceites, de que os idosos deverão realizar pelo menos 150 minutos de atividade moderada por semana, aumentar as atividades ligeiras e reduzir os comportamentos sedentários (ACSM, 2010). Contudo não sabemos se os idosos cumprem ou não estas recomendações e ao que corresponde objetivamente aumentar os níveis de atividade ligeira e diminuir os comportamentos sedentários: que proporção ocupam ou deverão ocupar na vida dos idosos? Os benefícios da AF são vastos e amplamente aceites, nomeadamente ao nível da melhoria da autoperceção de saúde (ApS) e redução da dor, no entanto, desconhece-se a relação existente entre o nível de AF e estas variáveis e o estudo desta relação revela-se de extrema importância tendo em conta o seu impacto na funcionalidade, bem-estar e qualidade de vida do idoso. Objetivo: Caracterizar os níveis de AF e os comportamentos sedentários de indivíduos com mais de 75 anos e analisar a sua relação com a auto-perceção de saúde e a dor. Metodologia: Trata-se de um estudo descritivo de correlação, com uma amostra constituída por 66 participantes, com média de idade de 80.1 (±3.83) anos. As variáveis em estudo foram o nível de AF, os comportamentos sedentários, a ApS e a dor. Foi aplicado um protocolo de avaliação, constituído por um questionário de caracterização sociodemográfica e do nível de AF, o Yale Física Activity Survey (YPAS), o MOS Short-Form Health Survey (SF-12) e a Escala Numérica de Dor. Resultados: Os resultados revelaram que os participantes despendiam em média 50% do seu tempo semanal em comportamentos sedentários; 38.5% em atividades ligeiras e 480.23 minutos, ou seja, 11%, em atividades moderadas. Verificou-se uma relação positiva e estatisticamente significativa entre a ApS geral e a quantidade de AF moderada (Rs=0.490,p=0.000), o gasto total energético semanal (Rs=0.231, p=0.031), a pontuação de caminhada (Rs=0.422, p=0.000) e a pontuação de movimento (Rs=0.313, p=0.005); uma associação negativa, estatisticamente significativa, entre a dor e a pontuação de posição de pé (Rs=-0.305,p=0.006); e entre a pontuação de posição de sentado do YPAS e a ApS geral (Rs=-0.342,p=0.003). Conclusões: Os resultados sugerem que os participantes ocupavam metade da sua semana em comportamentos sedentários, contudo em termos da quantidade de AF moderada vão de encontro aos mínimos propostos pelas guidelines internacionais para se obter benefícios de saúde. No entanto, a distribuição, quer em termos de intensidade como de frequência, destas atividades ao longo da semana poderá não ser a mais adequada. O presente estudo aponta ainda para a existência de uma relação positiva entre o nível de AF e a ApS, ou seja, na nossa amostra um maior nível de AF estava associado a uma melhor ApS; uma relação negativa entre o nível de AF e a dor, um maior nível de AF estava também associado a uma menor intensidade de dor; e uma relação negativa entre os comportamentos sedentários e a ApS, ou seja, na amostra de utentes, com mais de 75 anos, em estudo, um score mais elevado de comportamentos sedentários estava associado a uma pior ApS.---------ABSTRACT: Background: Physical activity (PA) has been widely pointed as an answer to overcome aging’s negative impact. In this sense, recommendations have arise supporting that older adults should perform, at least, 150 minutes of moderate intensity PA per week, increase their light intensity PA and decrease sedentary behaviours (ACSM, 2010). Nevertheless, it is unclear whether older adults reach these recommendations or not and, also, what exactly means to increase light intensity PA and to reduce sedentary behaviours: which proportion they fill or should fill in older adults life? PA’s benefits are extensive and widely accepted, namely improvements in self-related health (SRH) and pain reduction, however, the relation between these variables and PA level and sedentary behaviours is still unknown, and we find it extremely important to clarify the nature of this relation considering its impact on older adults functional level, wellbeing and quality of life. Purpose: Characterize older adults, over 75 years old, PA levels and sedentary behaviours and to investigate its relation to self-rated health and pain. Methods: We conducted a descriptive-correlational study, with a geographic convenience sample of 66 participants with a mean age of 80.1 (±3.83) years. Our study variables were PA level, sedentary behaviours, SRH and pain. We applied an assessment protocol, including a socio-demographic and PA level questionnaire, Yale Physical Activity Survey (YPAS), MOS Short-Form Health Survey (SF-12) and Numeric Pain Scale. Results: Revealed that participants spent an average of 50% of their total weekly time in sedentary behaviours; 38.5% in light intensity PA; and 480.23 minutes per week, meaning 11.04%, in moderate intensity PA. We encountered a positive relation, with statistical significance, between global SRH and moderate intensity PA amount (Rs=0.490, p=0.000), total energy expenditure (Rs=0.231, p=0.031), walking score (Rs=0.422, p=0.000) and movement score (Rs=0.313, p=0.005); a negative association, with statistical significance, between pain and standing score (Rs=-0.305, p=0.006); and between sitting score and global SRH (Rs=-0.342,p=0.003). Conclusions: Our results unveil that the subjects in our sample spent half of their week in sedentary behaviours, nonetheless they met moderate intensity PA recommendations to obtain health benefits. However, activities distribution, regarding both its intensity and frequency, throughout the week might not be the most appropriate. This study points towards the existence of a positive relation between PA level and SRH, meaning that, in our sample, a higher PA level was associated to a better SRH; a negative relation between PA level and pain, i.e. a higher PA level was associated to less pain; and a negative relation between sedentary behaviours and SRH, meaning that a higher sitting score was associated to a worse SRH, in the sample of older adults over 75 years in study.

Lack of Spontaneous Venous Pulsation: Possible Risk Indicator in Normal Tension Glaucoma?

PURPOSE: Recently, the absence of spontaneous venous pulsation (SVP) has been suggested as a vascular risk factor for primary open-angle glaucoma (POAG). As the mechanism behind this phenomenon is still unknown, the authors have studied this vascular component using colour Doppler imaging (CDI). METHODS: A total of 236 patients were divided into three diagnostic groups: healthy controls (81), POAG (86) and normal tension glaucoma (NTG; 69). All subjects were submitted to CDI studies of the retrobulbar circulation, intraocular pressure measurements and assessment of SVP existence. Mann-Whitney, chi-square contingency tables and Spearman correlations were used to explore differences and correlations between variables in the diagnostic groups. RESULTS: Eighty-two percent of healthy controls had SVP (66/81), while a smaller numbers were registered in both glaucoma groups: POAG - 50% (43/86); NTG - 51% (35/69). In NTG patients, but not in POAG patients, the prevalence of the SVP phenomenon decreases with increased glaucoma damage (p = 0.04; p = 0.55, respectively). Overall glaucoma patients from both groups had lower central retinal vein (CRV) velocities than the healthy controls (p < 0.05). NTG patients with SVP had less severe visual field defects (mean defect -6.92 versus -11.1, p < 0.05), higher [correction added after online publication 21 September 2012; the word 'higher' has been inserted to replace the word 'lower'] peak systolic and mean flow velocities in the central retinal artery (p < 0.01; p < 0.05, respectively) as well as higher [correction added after online publication 21 September 2012; the word higher has been inserted to replace the word lower] maximal velocities and RI of the CRV (p < 0.02; p < 0.05, respectively). CONCLUSIONS: Glaucoma patients have a decrease in CRV velocities. SVP is less prevalent in glaucoma patients than in healthy individuals. This phenomenon apparently reflects different hemodynamic patterns in the central retinal vessels. This variable may be of particular importance in NTG patients, where it may be associated with more advanced functional damage.

The influence of animation on functional food intake in children

A Work Project, presented as part of the requirements for the Award of a Masters Degree in Management from the NOVA – School of Business and Economics

Structural and functional characterization of the gene products responsible for phototrophic iron oxidation by purple bacteria

Dissertação para a obtenção de grau de doutor em Bioquímica pelo Instituto de Tecnologia Química e Biológica. Universidade Nova de Lisboa

Isolation and functional characterization of mononuclear phagocytes from human lepromatous lesions

In the present study, inflammatory cells from human lepromatous lesions were isolated by enzymatic dissociation of tissue. They were maintained in culture up to five days and their morphologic, cythochemicaland functional characteristics were described.

Regulation of the rice gene OsRMC under salt stress: identification and functional characterization of novel transcription factors

Dissertation presented to obtain the Ph.D degree in Biology