Genomic Profiling of Gastric Cancer

Gastric cancer is the fourth most common cancer and the second most common cause of cancer-related death worldwide. Due to lack of early symptoms, gastric cancer is characterized by late stage diagnosis and unsatisfactory options for curative treatment. Several genomic alterations have been identified in gastric cancer, but the major factors contributing to initiation and progression of gastric cancer remain poorly known. Gene copy number alterations play a key role in the development of gastric cancer, and a change in gene copy number is one of the fundamental mechanisms for a cancer cell to control the expression of potential oncogenes and tumor suppressor genes. This thesis aims at clarifying the complex genomic alterations of gastric cancer to identify novel molecular biomarkers for diagnostic purposes as well as for targeted treatment. To highlight genes of potential biological and clinical relevance, we carried out a systematic microarray-based survey of gene expression and copy number levels in primary gastric tumors and gastric cancer cell lines. Results were validated using immunohistochemistry, real-time qRT-PCR, and affinity capture-based transcript (TRAC) assay. Altogether 192 clinical gastric tissue samples and 7 gastric cancer cell lines were included in this study. Multiple chromosomal regions with recurrent copy number alterations were detected. The most frequent chromosomal alterations included gains at 7q, 8q, 17q, 19q, and 20q and losses at 9p, 18q, and 21q. Distinctive patterns of copy number alterations were detected for different histological subtypes (intestinal and diffuse) and for cancers located in different parts of the stomach. The impact of copy number alterations on gene expression was significant, as 6-10% of genes located in the regions of gains and losses also showed concomitant alterations in their expression. By combining the information from the DNA- and RNA-level analyses many novel gastric cancer-related genes, such as ALPK2, ENAH, HHIPL2, and OSMR, were identified. Independent genome-wide gene expression analysis of Finnish and Japanese gastric tumors revealed an additional set of genes that was differentially expressed in cancerous gastric tissues compared with normal tissue. Overexpression of one of these genes, CXCL1, was associated with an improved survival of gastric cancer. Thus, using an integrative microarray analysis, several novel genes were identified that may be critically important for gastric carcinogenesis. Further studies of these genes may lead to novel biomarkers for gastric cancer diagnosis and targeted therapy.

Développement et caractérisation de nouveaux modèles du cancer épithélial de l’ovaire

Le cancer épithélial de l’ovaire (EOC) est le plus mortel des cancers gynécologiques. Cette maladie complexe progresse rapidement de façon difficilement décelable aux stades précoces. De plus, malgré une chirurgie cytoréductive et des traitements de chimiothérapie le taux de survie des patientes diagnostiquées aux stades avancées demeurt faible. Dans le but d’étudier l’EOC dans un contexte ex vivo, l’utilisation de modèles cellulaires est indispensable. Les lignées cellulaires d’EOC sont un outil pratique pour la recherche cependant, la façon dont l'expression des gènes est affectée en culture par comparaison à la tumeur d'origine n'est pas encore bien élucidée. Notre objectif était donc de développer et de caractériser de nouveaux modèles de culture in vitro qui réflèteront plus fidèlement la maladie in vivo. Nous avons tout d’abord utiliser des lignées cellulaires disponibles au laboratoire afin de mettre au point un modèle 3D de culture in vitro d’EOC. Des sphéroïdes ont été générés à l’aide de la méthode des gouttelettes inversées, une méthode pionnière pour la culture des cellules tumorales. Nous avons ensuite procédé à une analyse des profils d’expression afin de comparer le modèle sphéroïde au modèle de culture en monocouche et le modèle xénogreffe in vivo. Ainsi, nous avons identifié des gènes stratifiant les modèles tridimensionnels, tant in vivo qu’in vitro, du modèle 2D monocouche. Parmi les meilleurs candidats, nous avons sélectionné S100A6 pour une caractérisation ultérieure. L’expression de ce gène fût modulée afin d’étudier l’impact de son inhibition sur les paramètres de croissance des sphéroïdes. L’inhibition de ce gène a comme effet de réduire la motilité cellulaire mais seulement au niveau du modèle sphéroïde. Finalement, toujours dans l’optique de développer des modèles d’EOC les plus représentatifs de la maladie in vivo, nous avons réussi à développer des lignées cellulaires uniques dérivées de patientes atteintes d’EOC du type séreux, soit le plus commun des EOC. Jusque là, très peu de lignées cellulaires provenant de ce type de cancer et de patientes n’ayant pas reçu de chimiothérapie ont été produites. De plus, nous avons pour la première fois caractérise des lignées d’EOC de type séreux provenant à la fois de l’ascite et de la tumeur solide de la même patiente.

Impact of Epstein-Barr virus load, virus genotype, and frequency of the 30bp deletion in the viral BNLF-1 gene in patients harboring the human immunodeficiency virus

Patients infected with the human immunodeficiency virus (HIV) are at higher risk of developing Epstein-Barr Virus (EBV)-associated lymphomas. The usefulness of monitoring EBV in peripheral blood mononuclear cells (PBMCs) of patients infected with HIV has not been established. The aim of this study was to evaluate the EBV viral load in PBMCs, the frequency of viral genotypes, and the presence of the 30-bp deletion in the BNLF-1 gene. DNA samples from 156 patients attending the HIV/AIDS Day Clinic at Botucatu School of Medicine, Sao Paulo State University were evaluated. The EBV viral load was detectable by real time PCR in 123/156 (78.8%) cases and was higher in patients not receiving antiretroviral treatment or under therapeutic failure than in patients under successful highly active antiretroviral therapy (HAART) (P=0.0076). Overall, the profile of patients with high EBV viral load included elevated HIV viremia (P=0.0005), longer time of HIV diagnosis (P=0.0026), and increased levels of T CD8 + lymphocytes (P=0.0159). The successful amplification of the EBNA-2 gene by nested-PCR was achieved in 95 of 123 (77.2%) cases, of which 75.8% were EBV-1, 9.5% EBV-2, and 14.7% were co-infected with both EBV-1 and -2. The analysis of the BNLF-1 gene was possible in 99 of 123 (80.5%) cases, of which 50.5% had the 30-bp deletion. EBV-1 was more common than EBV-2, which may reflect the fact that the cohort was predominantly Caucasian and heterosexual. J. Med. Virol. 85:2110-2118, 2013. © 2013 Wiley Periodicals, Inc.

Avaliação da efetividade da farinha da casca do maracujá sobre as alterações metabólicas secundárias à terapia antirretroviral em pacientes portadores de síndrome Lipodistrófica

Alterações anatômicas e metabólicas são comuns nos indivíduos portadores de HIV que fazem uso de Terapia Antiretroviral de elevada potência (TARV). Foi realizado um ensaio clínico para avaliar a efetividade da utilização da farinha da casca do maracujá (FCM) associado à orientação dietoterápica sobre as alterações metabólicas secundárias a TARV em pacientes com lipodistrofia do ambulatório de lipodistrofia do Hospital Universitário João de Barros Barreto. Foram avaliados 36 pacientes adultos, de ambos os sexos, portadores de HIV, com síndrome lipodistrófica em uso de TARV. Esses indivíduos foram divididos em dois grupos (n= 18 cada); o grupo 1 recebeu 30 gramas diárias de FCM durante 90 dias associado a orientação dietoterápica; o grupo 2 recebeu apenas orientação dietoterápica. As alterações metabólicas foram analisadas antes e após a intervenção. Os resultados foram analisados através software BioEstat 5.0 e Diet Pro com nível de significância p < 0,05. Observou-se maior prevalência do sexo masculino, faixa etária de 40 a 49 anos, solteiros e renda familiar de 1 a 3 salários mínimos. A maioria apresentava 10 a 15 anos de tempo de diagnóstico do HIV e mesmo tempo de utilização de TARV. O esquema de TARV mais prescrito foi 1 ou 2 INTR + 2 IP. A síndrome lipoatrófica foi mais prevalente e a síndrome metabólica foi detectada em 19,4 % da amostra. A maioria apresentou diagnóstico nutricional de Eutrofia. Não houve diferença significativa entre os 2 grupos em nenhuma dessas variáveis citadas, demonstrando a homogeneidade dos grupos. A utilização da FCM foi efetiva na redução dos valores plasmáticos do colesterol total após 30 dias de utilização, sem, no entanto, alterar a sua classificação; houve melhora nos valores plasmáticos de LDL – c após uso de FCM por 90 dias e melhora de categoria (aumento da classificação LDL – c ótimo); ocorreu um aumento do HDL – c após 90 dias de consumo de FCM sem melhora na classificação desta lipoproteína; houve diminuição dos valores plasmáticos de triglicerídeos após 30 dias de FCM e melhora de categoria. Não houve alterações na glicemia após a utilização da FCM. Os indivíduos que utilizaram a FCM apresentaram um risco inferior de desenvolver doença arterial coronariana após 90 dias de utilização. Não houve diferença entre os dois grupos no que diz respeito ao consumo dos principais componentes da alimentação. A utilização de 30 gramas de FCM durante 90 dias associado à orientação dietoterápica é eficaz na melhora dos níveis plasmáticos de colesterol total, LDL – c, HDL – c e Triglicerídeos sem interferir nos valores de glicemia.

Prior history of sexually transmitted diseases in women living with AIDS in Sao Paulo, Brazil

Objectives: To describe the epidemiological profile, risk behaviors, and the prior history of sexually transmitted diseases (STDs) in women living with acquired immunodeficiency syndrome (AIDS). Methods: Cross-sectional study, performed at the Centro de Referencia e Treinamento em DST/AIDS of Sao Paulo. The social, demographic, behavioral, and clinical data such as age, schooling, marital status, age at first sexual intercourse, number of sexual partners, parity, use of drugs, time of HIV diagnosis, CD4 count, and viral load determination were abstracted from the medical records of women living with AIDS who had gynecological consultation scheduled in the period from June 2008 to May 2009. Results: Out of 710 women who were scheduled to a gynecological consultation during the period of the study, 598 were included. Previous STD was documented for 364 (60.9%; 95% CI: 56.9%-64.8%) women. The associated factors with previous STDs and their respective risks were: human development index (HDI) <0.50 (ORaj = 5.5; 95% CI: 2.8-11.0); non-white race (ORaj = 5.2; 95% CI: 2.5-11.0); first sexual intercourse at or before 15 years of age (ORaj = 4.4; 95% CI: 2.3-8.3); HIV infection follow-up time of nine years or more (ORaj = 4.2; 95% CI: 2.3-7.8)]; number of sexual partners during the entire life between three and five partners (ORaj = 2.2; 95% CI: 1.1-4.6), and six or more sexual partners (ORaj = 3.9; 95% CI: 1.9-8.0%); being a sex worker (ORaj = 1.9; 95% CI: 1.1-3.1). Conclusions: A high prevalence of a prior history of STDs in the studied population was found. It is essential to find better ways to access HIV infection prevention, so that effective interventions can be more widely implemented. (C) 2012 Elsevier Editora Ltda. All rights reserved.

Prior history of sexually transmitted diseases in women living with AIDS in São Paulo, Brazil

OBJECTIVES: To describe the epidemiological profile, risk behaviors, and the prior history of sexually transmitted diseases (STDs) in women living with acquired immunodeficiency syndrome (AIDS). METHODS: Cross-sectional study, performed at the Centro de Referência e Treinamento em DST/AIDS of São Paulo. The social, demographic, behavioral, and clinical data such as age, schooling, marital status, age at first sexual intercourse, number of sexual partners, parity, use of drugs, time of HIV diagnosis, CD4 count, and viral load determination were abstracted from the medical records of women living with AIDS who had gynecological consultation scheduled in the period from June 2008 to May 2009. RESULTS: Out of 710 women who were scheduled to a gynecological consultation during the period of the study, 598 were included. Previous STD was documented for 364 (60.9%; 95% CI: 56.9%-64.8%) women. The associated factors with previous STDs and their respective risks were: human development index (HDI) < 0.50 (ORaj = 5.5; 95% CI: 2.8-11.0); non-white race (ORaj = 5.2; 95% CI: 2.5-11.0); first sexual intercourse at or before 15 years of age (ORaj = 4.4; 95% CI: 2.3-8.3); HIV infection follow-up time of nine years or more (ORaj = 4.2; 95% CI: 2.3-7.8)]; number of sexual partners during the entire life between three and five partners (ORaj = 2.2; 95% CI: 1.1-4.6), and six or more sexual partners (ORaj = 3.9; 95% CI: 1.9-8.0%); being a sex worker (ORaj = 1.9; 95% CI: 1.1-3.1). CONCLUSIONS: A high prevalence of a prior history of STDs in the studied population was found. It is essential to find better ways to access HIV infection prevention, so that effective interventions can be more widely implemented.

Improved antiretroviral treatment outcome in a rural African setting is associated with cART initiation at higher CD4 cell counts and better general health condition

Background Data on combination antiretroviral therapy (cART) in remote rural African regions is increasing. Methods We assessed prospectively initial cART in HIV-infected adults treated from 2005 to 2008 at St. Francis Designated District Hospital, Ifakara, Tanzania. Adherence was assisted by personal adherence supporters. We estimated risk factors of death or loss to follow-up by Cox regression during the first 12 months of cART. Results Overall, 1,463 individuals initiated cART, which was nevirapine-based in 84.6%. The median age was 40 years (IQR 34-47), 35.4% were males, 7.6% had proven tuberculosis. Median CD4 cell count was 131 cells/μl and 24.8% had WHO stage 4. Median CD4 cell count increased by 61 and 130 cells/μl after 6 and 12 months, respectively. 215 (14.7%) patients modified their treatment, mostly due to toxicity (56%), in particular polyneuropathy and anemia. Overall, 129 patients died (8.8%) and 189 (12.9%) were lost to follow-up. In a multivariate analysis, low CD4 cells at starting cART were associated with poorer survival and loss to follow-up (HR 1.77, 95% CI 1.15-2.75, p = 0.009; for CD4 <50 compared to >100 cells/μl). Higher weight was strongly associated with better survival (HR 0.63, 95% CI 0.51-0.76, p < 0.001 per 10 kg increase). Conclusions cART initiation at higher CD4 cell counts and better general health condition reduces HIV related mortality in a rural African setting. Efforts must be made to promote earlier HIV diagnosis to start cART timely. More research is needed to evaluate effective strategies to follow cART at a peripheral level with limited technical possibilities.

Long-term immunologic response to antiretroviral therapy in low-income countries: a collaborative analysis of prospective studies

BACKGROUND: Few data are available on the long-term immunologic response to antiretroviral therapy (ART) in resource-limited settings, where ART is being rapidly scaled up using a public health approach, with a limited repertoire of drugs. OBJECTIVES: To describe immunologic response to ART among ART patients in a network of cohorts from sub-Saharan Africa, Latin America, and Asia. STUDY POPULATION/METHODS: Treatment-naive patients aged 15 and older from 27 treatment programs were eligible. Multilevel, linear mixed models were used to assess associations between predictor variables and CD4 cell count trajectories following ART initiation. RESULTS: Of 29 175 patients initiating ART, 8933 (31%) were excluded due to insufficient follow-up time and early lost to follow-up or death. The remaining 19 967 patients contributed 39 200 person-years on ART and 71 067 CD4 cell count measurements. The median baseline CD4 cell count was 114 cells/microl, with 35% having less than 100 cells/microl. Substantial intersite variation in baseline CD4 cell count was observed (range 61-181 cells/microl). Women had higher median baseline CD4 cell counts than men (121 vs. 104 cells/microl). The median CD4 cell count increased from 114 cells/microl at ART initiation to 230 [interquartile range (IQR) 144-338] at 6 months, 263 (IQR 175-376) at 1 year, 336 (IQR 224-472) at 2 years, 372 (IQR 242-537) at 3 years, 377 (IQR 221-561) at 4 years, and 395 (IQR 240-592) at 5 years. In multivariable models, baseline CD4 cell count was the most important determinant of subsequent CD4 cell count trajectories. CONCLUSION: These data demonstrate robust and sustained CD4 response to ART among patients remaining on therapy. Public health and programmatic interventions leading to earlier HIV diagnosis and initiation of ART could substantially improve patient outcomes in resource-limited settings.

Age in antiretroviral therapy programmes in South Africa: a retrospective, multicentre, observational cohort study.

BACKGROUND As access to antiretroviral therapy (ART) expands, increasing numbers of older patients will start treatment and need specialised long-term care. However, the effect of age in ART programmes in resource-constrained settings is poorly understood. The HIV epidemic is ageing rapidly and South Africa has one of the highest HIV population prevalences worldwide. We explored the effect of age on mortality of patients on ART in South Africa and whether this effect is mediated by baseline immunological status. METHODS In this retrospective cohort analysis, we studied HIV-positive patients aged 16-80 years who started ART for the first time in six large South African cohorts of the International Epidemiologic Databases to Evaluate AIDS-Southern Africa collaboration, in KwaZulu-Natal, Gauteng, and Western Cape (two primary care clinics, three hospitals, and a large rural cohort). The primary outcome was mortality. We ascertained patients' vital status through linkage to the National Population Register. We used inverse probability weighting to correct mortality for loss to follow-up. We estimated mortality using Cox's proportional hazards and competing risks regression. We tested the interaction between baseline CD4 cell count and age. FINDINGS Between Jan 1, 2004, and Dec 31, 2013, 84,078 eligible adults started ART. Of these, we followed up 83,566 patients for 174,640 patient-years. 8% (1817 of 23,258) of patients aged 16-29 years died compared with 19% (93 of 492) of patients aged 65 years or older. The age adjusted mortality hazard ratio was 2·52 (95% CI 2·01-3·17) for people aged 65 years or older compared with those 16-29 years of age. In patients starting ART with a CD4 count of less than 50 cells per μL, the adjusted mortality hazard ratio was 2·52 (2·04-3·11) for people aged 50 years or older compared with those 16-39 years old. Mortality was highest in patients with CD4 counts of less than 50 cells per μL, and 15% (1103 of 7295) of all patients aged 50 years or older starting ART were in this group. The proportion of patients aged 50 years or older enrolling in ART increased with successive years, from 6% (290 of 4999) in 2004 to 10% (961 of 9657) in 2012-13, comprising 9% of total enrolment (7295 of 83 566). At the end of the study, 6304 (14%) of 44,909 patients still alive and in care were aged 50 years or older. INTERPRETATION Health services need reorientation towards HIV diagnosis and starting of ART in older individuals. Policies are needed for long-term care of older people with HIV. FUNDING National Institutes of Health (National Institute of Allergy and Infectious Diseases), US Agency for International Development, and South African Centre for Epidemiological Modelling and Analysis.

Amphibian transcription factor IIIA proteins contain a sequence element functionally equivalent to the nuclear export signal of human immunodeficiency virus type 1 Rev.

The human immunodeficiency virus type 1 (HIV-1) Rev protein is required for nuclear export of late HIV-1 mRNAs. This function is dependent on the mutationally defined Rev activation domain, which also forms a potent nuclear export signal. Transcription factor IIIA (TFIIIA) binds to 5S rRNA transcripts and this interaction has been proposed to play a role in the efficient nuclear export of 5S rRNA in amphibian oocytes. Here it is reported that amphibian TFIIIA proteins contain a sequence element with homology to the Rev activation domain that effectively substitutes for this domain in inducing the nuclear export of late HIV-1 mRNAs. It is further demonstrated that this TFIIIA sequence element functions as a protein nuclear export signal in both human cells and frog oocytes. Thus, this shared protein motif may play an analogous role in mediating the nuclear export of both late HIV-1 RNAs and 5S rRNA transcripts.

A qualitative analysis of health care provider perceptions of depression and suicidality in Mozambique

Thesis (Master's)--University of Washington, 2016-06

Touch of AIDS : A love story

Touch of AIDS: A Love Story is a memoir covering the ten years since my husband, Steven's HIV positive diagnosis in 1987. The story begins when we find our circumstances redefined and our future challenged by the plague of this century. Steven's inability to withstand the toxic effects of the earliest approved antiviral drugs leads us to turn to alternative therapies. After his conversion to AIDS we return to Western medicine but continue on a quest that takes us from Taoist studies at home in Florida to sacred Navajo ceremonies in Arizona. As Steven finds that healing comes in great part from the journey itself and that he is stronger physically, emotionally and spiritually than he was before his HIV diagnosis, I realize that we can live with fear as long as we don't become its victims. Love and hope empower our lives as we live with AIDS.

A Qualitative Assessment of Breast Cancer Advocates in Bolivia, Colombia, Ecuador and Peru

Thesis (Master's)--University of Washington, 2016-06

Prevalencia e incidencia de cáncer en habitantes de Sibaté, y georeferenciación de casos 2010-2014

Introducción: El Cáncer es prevenible en algunos casos, si se evita la exposición a sustancias cancerígenas en el medio ambiente. En Colombia, Cundinamarca es uno de los departamentos con mayores incrementos en la tasa de mortalidad y en el municipio de Sibaté, habitantes han manifestado preocupación por el incremento de la enfermedad. En el campo de la salud ambiental mundial, la georreferenciación aplicada al estudio de fenómenos en salud, ha tenido éxito con resultados válidos. El estudio propuso usar herramientas de información geográfica, para generar análisis de tiempo y espacio que hicieran visible el comportamiento del cáncer en Sibaté y sustentaran hipótesis de influencias ambientales sobre concentraciones de casos. Objetivo: Obtener incidencia y prevalencia de casos de cáncer en habitantes de Sibaté y georreferenciar los casos en un periodo de 5 años, con base en indagación de registros. Metodología: Estudio exploratorio descriptivo de corte transversal,sobre todos los diagnósticos de cáncer entre los años 2010 a 2014, encontrados en los archivos de la Secretaria de Salud municipal. Se incluyeron unicamente quienes tuvieron residencia permanente en el municipio y fueron diagnosticados con cáncer entre los años de 2010 a 2104. Sobre cada caso se obtuvo género, edad, estrato socioeconómico, nivel académico, ocupación y estado civil. Para el análisis de tiempo se usó la fecha de diagnóstico y para el análisis de espacio, la dirección de residencia, tipo de cáncer y coordenada geográfica. Se generaron coordenadas geográficas con un equipo GPS Garmin y se crearon mapas con los puntos de la ubicación de las viviendas de los pacientes. Se proceso la información, con Epi Info 7 Resultados: Se encontraron 107 casos de cáncer registrados en la Secretaria de Salud de Sibaté, 66 mujeres, 41 hombres. Sin división de género, el 30.93% de la población presento cáncer del sistema reproductor, el 18,56% digestivo y el 17,53% tegumentario. Se presentaron 2 grandes casos de agrupaciones espaciales en el territorio estudiado, una en el Barrio Pablo Neruda con 12 (21,05%) casos y en el casco Urbano de Sibaté con 38 (66,67%) casos. Conclusión: Se corroboro que el análisis geográfico con variables espacio temporales y de exposición, puede ser la herramienta para generar hipótesis sobre asociaciones de casos de cáncer con factores ambientales.

Late diagnosis and vulnerabilities of the elderly living with HIV/AIDS

Objective: To identify vulnerabilities of elderly people with HIV/AIDS and the trajectory that they follow until reaching the diagnosis of the disease. Method: Qualitative research conducted in specialized clinics in the state of Sao Paulo, from January to June 2011. Semi-structured interviews were conducted with 11 elderly people who were found to be infected with the virus at the age of 60 years or older. The interviews were analyzed using content analysis. Results: In this process four categories emerged, then analyzed with reference to the theoretical framework of vulnerability. Conclusion: Late diagnosis of HIV infection or AIDS among the elderly happens in the secondary or tertiary service. Issues related to sexual life of the elderly are only questioned by health professionals after the diagnosis, also the time that condom use becomes absolute. It is believed that the investigation of the vulnerability of the elderly to HIV/AIDS allows for carrying out appropriate interventions for this population.