DATA DRIVEN APPROACHES TO IDENTIFY DETERMINANTS OF HEART DISEASES AND CANCER RESISTANCE

Cancer and cardio-vascular diseases are the leading causes of death world-wide. Caused by systemic genetic and molecular disruptions in cells, these disorders are the manifestation of profound disturbance of normal cellular homeostasis. People suffering or at high risk for these disorders need early diagnosis and personalized therapeutic intervention. Successful implementation of such clinical measures can significantly improve global health. However, development of effective therapies is hindered by the challenges in identifying genetic and molecular determinants of the onset of diseases; and in cases where therapies already exist, the main challenge is to identify molecular determinants that drive resistance to the therapies. Due to the progress in sequencing technologies, the access to a large genome-wide biological data is now extended far beyond few experimental labs to the global research community. The unprecedented availability of the data has revolutionized the capabilities of computational researchers, enabling them to collaboratively address the long standing problems from many different perspectives. Likewise, this thesis tackles the two main public health related challenges using data driven approaches. Numerous association studies have been proposed to identify genomic variants that determine disease. However, their clinical utility remains limited due to their inability to distinguish causal variants from associated variants. In the presented thesis, we first propose a simple scheme that improves association studies in supervised fashion and has shown its applicability in identifying genomic regulatory variants associated with hypertension. Next, we propose a coupled Bayesian regression approach -- eQTeL, which leverages epigenetic data to estimate regulatory and gene interaction potential, and identifies combinations of regulatory genomic variants that explain the gene expression variance. On human heart data, eQTeL not only explains a significantly greater proportion of expression variance in samples, but also predicts gene expression more accurately than other methods. We demonstrate that eQTeL accurately detects causal regulatory SNPs by simulation, particularly those with small effect sizes. Using various functional data, we show that SNPs detected by eQTeL are enriched for allele-specific protein binding and histone modifications, which potentially disrupt binding of core cardiac transcription factors and are spatially proximal to their target. eQTeL SNPs capture a substantial proportion of genetic determinants of expression variance and we estimate that 58% of these SNPs are putatively causal. The challenge of identifying molecular determinants of cancer resistance so far could only be dealt with labor intensive and costly experimental studies, and in case of experimental drugs such studies are infeasible. Here we take a fundamentally different data driven approach to understand the evolving landscape of emerging resistance. We introduce a novel class of genetic interactions termed synthetic rescues (SR) in cancer, which denotes a functional interaction between two genes where a change in the activity of one vulnerable gene (which may be a target of a cancer drug) is lethal, but subsequently altered activity of its partner rescuer gene restores cell viability. Next we describe a comprehensive computational framework --termed INCISOR-- for identifying SR underlying cancer resistance. Applying INCISOR to mine The Cancer Genome Atlas (TCGA), a large collection of cancer patient data, we identified the first pan-cancer SR networks, composed of interactions common to many cancer types. We experimentally test and validate a subset of these interactions involving the master regulator gene mTOR. We find that rescuer genes become increasingly activated as breast cancer progresses, testifying to pervasive ongoing rescue processes. We show that SRs can be utilized to successfully predict patients' survival and response to the majority of current cancer drugs, and importantly, for predicting the emergence of drug resistance from the initial tumor biopsy. Our analysis suggests a potential new strategy for enhancing the effectiveness of existing cancer therapies by targeting their rescuer genes to counteract resistance. The thesis provides statistical frameworks that can harness ever increasing high throughput genomic data to address challenges in determining the molecular underpinnings of hypertension, cardiovascular disease and cancer resistance. We discover novel molecular mechanistic insights that will advance the progress in early disease prevention and personalized therapeutics. Our analyses sheds light on the fundamental biological understanding of gene regulation and interaction, and opens up exciting avenues of translational applications in risk prediction and therapeutics.

[Psychophysiologic manifestations, psychological and somatic risk factors and the physician-patient relationship in patients with heart diseases]

In daily medicine we often see patients complaining about thoracic pain. There is little doubt about the etiology in the most cases, but several patients continue posing diagnostic problems. There are different pathophysiological views to understand the situation of those patients, and it is important to determine their mental and psychological conditions. For this purpose, the focus on transference and countertransference phenomena has to be stressed. With these elements it will be possible to determine the diagnostic and therapeutic approach to those patients to reassure them and to justify investigations.

Tecnologia de iplex massarray aplicado ao diagnóstico de miocardiopatia hipertrófica

A miocardiopatia hipertrófica (MH) é a doença cardíaca genética mais comum, afectando 1:500 indivíduos, apresentando um padrão de transmissão autossómico dominante, com mutações associadas a genes sarcoméricos e não sarcoméricos. A MH apresenta uma variedade de manifestações clínicas, desde indivíduosassintomáticos a indivíduos que manifestam uma progressão da severidade dos sintomas, podendo nalguns casos ocorrer morte súbita. O diagnóstico clínico é realizado por Electrocardiograma e Ecocardiograma. O diagnóstico genético baseia-se na Sequenciação Automática (SA) dos 5 principais genes sarcoméricos MYBPC3, MYH7, TNNT2, TNNI3 e MYL2, sendo considerada uma metodologia bastante dispendiosa e demorada e que não permite a identificação de mutações em cerca de 1/3 dos individuos. A Genotipagem por iPLEX MassARRAY revela-se uma boa alternativa à SA no diagnóstico genético de MH, uma vez que permite a análise de várias amostras em simultâneo, para um elevado número de mutações, num único ensaio, com uma maior rentabilidade de tempo e recursos. Este trabalho teve como objectivo a optimização e a validação desta metodologia, na detecção de 541 mutações em 33 genes, tendo-se verificado que 29 % das reacções multiplex necessitam de ser revistas, quer pelo desenho de novos conjuntos de primers, quer pela sua relocalização no chip.

Avaliação da dose de radiação: angiotomografia coronariana - métodos retrospectivo e prospectivo

The aim of this study was to evaluate the effective dose received by patients undergoing CCTA in both acquisition methods in the period June 1st to October 30th, 2013. Data collection was performed at the Clínica Sabedotti in Ponta Grossa/PR, with General Electric Equipment VCT XT, 64 detections lines. The effective dose was measured from the thirty cases randomly selected of Picture Archival and Communication System – PACS, reported by Dose Lenght Product (DLP) equipment for each examination and the conversion factor (EDLP) set by the European Commission for cardiac region (EDLP = 0.014). The results showed significant differences in radiation dose delivered to the patient according to the employee acquisition method, Retrospective or Prospective of ECG.

Early Diagnosis of Myocardial Dysfunction in Patients With Hematological Malignancies Submitted to Chemotherapy. Preliminary Results.

Early Diagnosis of Miocardial Dysfunction in Patients with Hematological Malignancies Submitted to Chemotherapy. Preliminary Background: Considering the current diagnostic improvements and tl1erapeutic approaches, patients witl 1 cancer can now be healed or keep the disease under control, still, the chemotherapy may cause heart damage, evolving to Congestive Heart Failure. Recognition of those changes increases the chances of control the endpoints; hence, new parameters of cardiac and fluid mechanics analysis have been used to assess the myocardial function, pursuing an earlier diagnosis of the cardiac alterations. This study aimed to detect early cardiac dysfunction consequently to chemotherapy in patients with hematological malignancies (HM). Methods: Patients with leukemia and lymphoma, submitted to chemotherapy, without knowing heart diseases were studied. Healthy volunteers served as the control group. Conventional 2DE parameters of myocardial function were analyzed. The peak global longitudinal, circumferential and radial left ventricular (LV) strain were deternined by 2D and 3D speckle tracking (STE); peak area strain measured by 3D STE and LV torsionn, twisting rate, recoil / recoil rate assessed by 2D STE. The LV vortex formation time (VFT) during the rapid diastolic filling was estimated by the 2D mitral valve (MV) planimetry and Pulsed Doppler LV inflow by: VFT- 4(1-β) / π x α3 x LVEF Where 1- β is the E wave contribution to the LV stroke volume and α3 is a volumetric variable related to the MV area. The statistical level was settled on 5%. Results: See Table. Conclusion: Despite the differences between the two groups concerning the LVESV, LVEF and E´, those parameters still are in the normal range when considering the patients submitted to chemotherapy; thus, in the clinical setting, they are not so noticeable. The 3D GLS was smaller among the patients, oppositely to the 2D GLS, suggesting that the former variable is more accurate to assess tlhe LV systolic function. The VFT is a dimensionless measure of the optimal vortex development inside the LV chamber; reflecting the efficiency of the diastolic filling and, consequently, blood ejection. This index showed to be diminished in patients with HM submitted to chemotherapy, indicating an impairment of the in1pulse and thrust, hence appearing to be a very early marker of diastolic and systolic dysfunction in this group.

Prevalence of heart disease in symptomatic cats: an overview from 1998 to 2005

A total of 408 cats with various cardiovascular problems has been presented to two investigational clinics during the last 8 years. The number of yearly examinations has steadily increased during this period. Definitive cardiovascular disease was diagnosed in 287 cats, whereby hypertrophic cardiomyopathy (HCM) was the most common diagnosis with 67.6%. Congenital cardiovascular malformations were found in 11.8% of the cases. Ventricular septal defect (VSD) was the most frequent anomaly, in contrast to previously published studies. The ECG was found to be relatively non-specific and insensitive for the diagnosis of heart disease: Its usefulness lies in the recognition and diagnosis of cardiac arrhythmias. The radiographically recognized changes were also non-specific for certain heart diseases. Radiographs of the thorax are especially useful in the evaluation of cardiomegaly, and secondary signs of congestion.

Diseases of the heart /

Includes index.

Cancer gene signatures in risk stratification: use in personalized medicine

Cancer is a complex disease which arises due to a series of genetic changes related to cell division and growth control. Cancer remains the second leading cause of death in humans next to heart diseases. As a testimony to our progress in understanding the biology of cancer and developments in cancer diagnosis and treatment methods, the overall median survival time of all cancers has increased six fold one year to six years during the last four decades. However, while the median survival time has increased dramatically for some cancers like breast and colon, there has been only little change for other cancers like pancreas and brain. Further, not all patients having a single type of tumour respond to the standard treatment. The differential response is due to genetic heterogeneity which exists not only between tumours, which is called intertumour heterogeneity, but also within individual tumours, which is called intratumoural heterogeneity. Thus it becomes essential to personalize the cancer treatment based on a specific genetic change in a given tumour. It is also possible to stratify cancer patients into low- and high-risk groups based on expression changes or alterations in a group of genes gene signatures and choose a more suitable mode of therapy. It is now possible that each tumour can be analysed using various high-throughput methods like gene expression profiling and next-generation sequencing to identify its unique fingerprint based on which a personalized or tailor-made therapy can be developed. Here, we review the important progress made in the recent years towards personalizing cancer treatment with the use of gene signatures.

Established cardiovascular disease and CVD risk factors in a primary care population of middle-aged Irish men and women

Contemporary Irish data on the prevalence of major cardiovascular disease (CVD) risk factors are sparse. The primary aims of this study were (1) to estimate the prevalence of major cardiovascular disease risk factors, including Type 2 Diabetes Mellitus, in the general population of men and women between the ages of 50 and 69 years; and (2) to estimate the proportion of individuals in this age group at high absolute risk of cardiovascular disease events on the basis of pre-existing cardiovascular disease or as defined by the Framingham equation. Participants were drawn from the practice lists of 17 general practices in Cork and Kerry using stratified random sampling. A total of 1018 people attended for screening (490 men, 48%) from 1473 who were invited, a response rate of 69.1%. Cardiovascular disease risk factors and glucose intolerance are common in the population of men and women aged between 50 and 69 years. Almost half the participants were overweight and a further quarter met current international criteria for obesity, one of the highest recorded prevalence rates for obesity in a European population sample. Forty per cent of the population reported minimal levels of physical activity and 19% were current cigarette smokers. Approximately half the sample had blood pressure readings consistent with international criteria for the diagnosis of hypertension, but only 38% of these individuals were known to be hypertensive. Eighty per cent of the population sample had a cholesterol concentration in excess of 5 mmol/l. Almost 4% of the population had Type 2 Diabetes Mellitus, of whom 30% were previously undiagnosed. A total of 137 participants (13.5%) had a history or ECG findings consistent with established cardiovascular disease. Of the remaining 881 individuals in the primary prevention population, a total of 20 high-risk individuals (19 male) had a risk of a coronary heart disease event 30% over ten years according to the Framingham risk equation, giving an overall population prevalence of 2.0% (95% CI 1.3 - 3.0). At a risk level 20% over ten years, an additional 91 individuals (8.9%) were identified. Thus a total of 24.4% of the population were at risk either through pre-existing CVD (13.5%) or an estimated 10-year risk exceeding 20% according to the Framingham risk equation (10.9%). Thus a substantial proportion of middle-aged men are at high risk of CVD. The findings emphasise the scale of the CVD epidemic in Ireland and the need for ongoing monitoring of risk factors at the population level and the need to develop preventive strategies at both the clinical and societal level.

Resource utilization and cost analyses of home-based palliative care service provision:The Niagara West End-of-Life Shared-Care Project

Background: Increasing emphasis is being placed on the economics of health care service delivery - including home-based palliative care. Aim: This paper analyzes resource utilization and costs of a shared-care demonstration project in rural Ontario (Canada) from the public health care system's perspective. Design: To provide enhanced end-of-life care, the shared-care approach ensured exchange of expertise and knowledge and coordination of services in line with the understood goals of care. Resource utilization and costs were tracked over the 15 month study period from January 2005 to March 2006. Results: Of the 95 study participants (average age 71 years), 83 had a cancer diagnosis (87%); the non-cancer diagnoses (12 patients, 13%) included mainly advanced heart diseases and COPD. Community Care Access Centre and Enhanced Palliative Care Team-based homemaking and specialized nursing services were the most frequented offerings, followed by equipment/transportation services and palliative care consults for pain and symptom management. Total costs for all patient-related services (in 2007 CAN) were 1,625,658.07 - or 17,112.19 per patient/117.95 per patient day. Conclusion: While higher than expenditures previously reported for a cancer-only population in an urban Ontario setting, the costs were still within the parameters of the US Medicare Hospice Benefits, on a par with the per diem funding assigned for long-term care homes and lower than both average alternate level of care and hospital costs within the Province of Ontario. The study results may assist service planners in the appropriate allocation of resources and service packaging to meet the complex needs of palliative care populations. © 2012 The Author(s).

Family-based associations in measures of psychological distress and quality of life in a cardiac screening clinic for inheritable cardiac diseases: a cross-sectional study

BACKGROUND: Family-based cardiac screening programmes for persons at risk for genetic cardiac diseases are now recommended. However, the psychological wellbeing and health related quality of life (QoL) of such screened patients is poorly understood, especially in younger patients. We sought to examine wellbeing and QoL in a representative group of adults aged 16 and over in a dedicated family cardiac screening clinic.

METHODS: Prospective survey of consecutive consenting patients attending a cardiac screening clinic, over a 12 month period. Data were collected using two health measurement tools: the Short Form 12 (version 2) and the Hospital Anxiety and Depression Scale (HADS), along with baseline demographic and screening visit-related data. The HADS and SF-12v.2 outcomes were compared by age group. Associations with a higher HADS score were examined using logistic regression, with multi-level modelling used to account for the family-based structure of the data.

RESULTS: There was a study response rate of 86.6%, with n=334 patients providing valid HADS data (valid response rate 79.5%), and data on n=316 retained for analysis. One-fifth of patients were aged under 25 (n=61). Younger patients were less likely than older to describe significant depression on their HADS scale (p<0.0001), although there were overall no difference between the prevalence of a significant HADS score between the younger and older age groups (18.0% vs 20.0%, p=0.73). Significant positive associates of a higher HADS score were having lower educational attainment, being single or separated, and being closely related to the family proband. Between-family variance in anxiety and depression scores was greater than within-family variance.

CONCLUSIONS: High levels of anxiety were seen amongst patients attending a family-based cardiac screening clinic.Younger patients also had high rates of clinically significant anxiety. Higher levels of anxiety and depression tends to run in families, and this has implications for family screening and intervention programmes.