Qatar Foundation Annual Research Forum Volume 2012 Issue 1

Background and Objectives: Posaconazole (PSZ), is an antifungal prophylactic therapy that is used in hematologic cancer patients. It is approved for prophylaxis in hematologic cancer patients ≥13 years in USA, Canada, Australia, and ≥18 years in the European Union. In 2010, PSZ was added to the formulary of Al-Amal Hospital, the only adult cancer hospital in Qatar. The objective of this study is to conduct a drug use evaluation (DUE) study of posaconazole at Al-Amal Hospital. Methods: A retrospective, single centered, observational DUE study was conducted to include a convenient sample of hematologic cancer patients who used PSZ prophylactically during the year 2010. All patients, thirty-one, who received PSZ in 2010 were nominated of which 20 patients' profiles were reviewed, data were collected into a pre-prepared collection sheet and descriptive analysis was performed. Results: In Qatar, PSZ was used prophylactically in hematologic cancer patients >15 years with febrile and afebrile neutropenia. It is also planned to be used prophylactically for the upcoming bone marrow transplantation unit patients. All the 20 patients, 17 males and 3 females, received the PSZ for prophylaxis and were compliant. More than 50% of patients received proton pump inhibitors concurrently with posaconazole. Only 1 case had a recorded recommendation regarding the administration of PSZ with food. Five patients received vincristine-based chemotherapy protocol, one of which received it concurrently with PSZ for two cycles and developed seizure. Two patients developed mild breakthrough fungal infection, oral thrush, while on PSZ prophylactically. Conclusion: The PSZ regulations in Qatar are similar to the worldwide recommendations. The PSZ practice in Al-Amal hospital abides by the regulations. However, three points need to be addressed: PSZ has low bioavailability that can be enhanced by taking it with meals and by dividing the total daily dose. PSZ co-administration with proton pump inhibitors should be stopped as it may result in PSZ sub-therapeutic levels. Possible serious PSZ drug-drug interactions, seizures, in adult hematologic cancer patients should be highlighted and carefully monitored.

Background: Essential thrombocythemia (ET) is a myeloproliferative neoplasm (MPN) marked by a risk of thrombotic and hemorrhagic complications, and by a long-term risk of evolution to myelofibrosis (MF), and acute leukemia (AL). Methods: Inclusion criteria: ET diagnosed as per WHO classification 2008, age 18 to 45 year. Exclusion criteria: (hepatic and renal dysfunction, history of psychiatric disorder, in particular depression, autoimmune hepatitis, severe cardiac dysfunction, known hypersensitivity to IFN. Complete hematologic response (CR) as per ELN guidelines and molecular response (MR) was defined as 'complete' when JAK2V617F became undetectable with the technique used (i.e., V617F <1%), 'partial' when >50% decrease of baseline V617F was obtained, and 'minor' when V617F decrease was between 20% and 49%. After inclusion, Pegasys was started subcutaneously at 50 microgram weekly for 4 weeks then 135 microgramg/week from week 5. Results: Baseline characteristics of the patients are age 19-44 years, 16 males and 24 females. Five patients had a history of major thrombotic events. All the patients responded to Pegasys at the 12-month evaluation including 35 hematologic CRs (94.6%), and 5 PRs (5.4%). Cumulative incidences of hematologic CRs and PRs showed that 100% of responses were achieved within 12 months. After the first year, V617F continued to decrease without evidence of plateau, the proportion of mutant JAK2 being always similar or lower in the last sample compared with the previous one. None of the responding patients experienced an increase of V617F during follow-up. Median V617F was 58% at 12 months (P <0.001). Hematologic response was achieved in all patients within 2 months and were sustained beyond the first year. Toxicities included musculoskeletal pain in 6 patients, skin toxicity in 4, and GI symptoms in 2, none of the toxicity exceeds WHO Grade 2. Conclusion: PEGylated interferon alfa-2a is an effective and promising treatment for ET reducing the vascular risk and preventing evolution to MF, MDS, and AL. With low toxicity profiles and good hematological and molecular responses, percentage of V617F appears to be a good tool to monitor minimal residual disease and to evaluate treatment efficacy. However, further studies are needed to confirm these results.

Background and Objectives: Reference assisted assembly requires the use of a reference sequence, as a model, to assist in the assembly of novel genomes. The standard method for identifying the best reference sequence for the assembly of a novel genome aims at counting the number of reads of the novel genome that align to the reference sequences and then choosing the reference sequence which has the highest number of reads aligning to it. This work explores the use of minimum description length (MDL) principle and its two variants, the two-part MDL and sophisticated MDL, in identifying the optimal reference sequence for genome assembly. Methods: The relevance of MDL to genome assembly can be realized by understanding that genome assembly is an inference problem where the task at hand is to infer the novel genome from read data obtained from sequencing. The task of MDL is to identify the model that best describes the data and within comparative assembly framework the same meaning applies to finding the reference sequences that best describe the set of reads. This work explores the potential of three variants of MDL: two-part MDL, sophisticated MDL and minimax regret for the selection of the optimal reference sequence for comparative assembly. Results: The proposed scheme based on sophisticated MDL has been shown to work successfully for the four possible set of mutations: SNPs, insertions, inversions and deletions. The proposed scheme chooses the reference sequence which has the smaller number of SNPs, insertions and deletions. The MDL scheme is able to detect all inversions and rectify them. Conclusions: The work compared the MDL scheme with the standard method of counting the number of reads that align to the reference sequence, and found that though the standard method is a necessary condition for finding the optimal sequence, it is not the sufficient condition. Therefore, the proposed MDL scheme encompassed within itself the standard method of: counting the number of reads, by defining it in an inverted fashion as counting the number of reads that did not align to the reference sequence.

Objectives: To formulate and evaluate oral dosage forms of metformin hydrochloride (MH) having sustained-release properties that would also increase MH bioavailability and address the shortcomings in the currently marketed sustained-release tablets. Methods: MH micronized powder was dispersed in molten polymeric matrices composed of Gelucire® 50/13 and various proportions of high molecular weight hydrophilic polymers, hydrophobic oily semisolid excipients, and mucoadhesive polymeric materials. The MH loaded matrices were filled in hard gelatin capsules (HGC) each containing 500 mg MH and were subsequently characterized using differential scanning calorimetry (DSC) and X-ray diffraction (XRD) analysis. The prepared HGC were subjected to content uniformity and in vitro dissolution testing according to the USP-35 compendium requirements. The dissolution data were compared to instant and sustained-release marketed tablets. The effect of incorporating various proportions of the semisolid excipients on MH dissolution release rate, were also investigated. Results: MH content of the prepared HGC ranged between 96 to 103%. All the prepared semisolid filled HGC resulted in extended-release profiles of MH that lasted between 5 to 11 hours and demonstrated a release pattern which typically follows the release from mixes of triglycerides with polyethylene glycol esters of fatty acids. The incorporation of mucoadhesive excipients like carbomer to the Gelucire® 50/13-MH semisolid matrices extended the release of MH from 5 hours initially to 9 hours as a result of the formation of a gel layer around the matrix. However, the incorporation of different hydrophilic excipients like PEG35000 and Gelucire® 44/14 along with the mucoadhesive excipients sustained the release of MH up to 11 hours. XRD analysis of the MH prepared matrices demonstrated minor changes in the crystalline nature of MH. Depending on the loading ratios and the nature of the semisolid matrices used, DSC analysis revealed the changes in MH crystallinity to be from 100 to 23%. Conclusion: HGC formulated using semisolid matrices showed promising results in extending the release of MH. However, bioavailability studies to test the ability of such Gelucire based HGC of MH to improve its bioavailability and in vivo residence times are future plans.

Background and Objectives: A pregnant female requested prenatal diagnosis for a congenital and complex eye disease segregating in her family. The three-generation pedigree of Romanian ethnic origin was suggestive of an X-linked inheritance, due to exclusively affected males and no father-to-son transmission. Affected individuals had bilateral optic nerve atrophy, microphthalmia, nystagmus, leukocoria, cataract, retinal detachment, eye tumors reported as retinoblastomas, moderate mental and motor retardation, and seizures. All efforts to obtain the detailed medical records of affected individuals were fruitless. Methods: The disease locus was mapped utilizing 78 microsatellite markers that span the X-chromosome at ~2 Mb intervals, followed by candidate genes analysis and mutations detection by Sanger sequencing. Results: Affected individuals share an ~10 Mb region between DXS1056 and GATA160B08 at Xp11.23-11.4. Candidate genes in this linkage interval included BCOR and NDP. Mutation screening identified a c.267C>A p.F89L mutation in the NPD gene in all affected individuals, previously described in a single unrelated Dutch family and speculated as causing Norrie disease. Conclusions: In retrospect, clinical symptomatology fits the Norrie disease phenotype. The reported retinoblastomas were most likely pseudogliomas characteristic of Norrie disease. Detection of the c.C267A p.F89L mutation in a second unrelated family confirms the pathogenic nature of the mutation for Norrie disease. Utilization of gene mapping through linkage analyses and candidate gene screening previously utilized exclusively for research applications, were applied at a diagnostic setting and were essential in deciphering the offending molecular defect and diagnosing a disease which due to lack of medical records and poor and misleading clinical history would have no chance of being diagnosed correctly. Clinical diagnosis and mutation identification were essential prerequisites for providing proper genetic counseling and prenatal diagnosis in this family.

Background: Metabolic syndrome is associated with the rising incidence of obesity in developed countries, particularly in urban settings and is reaching epidemic proportions. Qatar, a rapidly modernizing country, has witnessed dramatic changes in urbanization and lifestyle. Recent studies demonstrate a significant prevalence of obesity and metabolic syndrome in Qatari population. According to a New York Times article (April 2010), the International Association for the Study of Obesity has ranked Qatar sixth globally for prevalence of obesity. Epidemiological studies suggest that a poor uterine environment elicited by maternal environmental exposure may program fetus susceptibility to develop cardiovascular and metabolic disease in childhood and later in life. Several studies have demonstrated the associations between pre-pregnancy obesity, chronic hypertension and dyslipidemia, and high risk of preterm birth and intrauterine growth restriction. However, there are no studies to examine the metabolic profile of Arabian pregnant women in early pregnancy with birth outcomes. Objectives: The objective of the present proposal is to examine the association between metabolic syndrome and obesity in early pregnancy of Qatari women and the risk of delivery preterm or growth restricted singletons. Methods: Qatari mother-child cohort: a prospective cohort examining a population sample of pregnant women and their children at the prefecture of Doha, Qatar within 1 year. The pregnant mothers, at maternity clinics and hospitals of Doha, were contacted. The consented participants were invited to provide biological samples in two time points of their pregnancy. Participants were interviewed to obtain information on several environmental and dietary factors, together with anthropometric measurements and blood pressure. Biochemical analyses were performed on serum triglycerides, total cholesterol, high and low density lipoprotein cholesterol, glucose, apolipoproteins, leptin, adiponectin and Interleukins. Expected results: At the national level this will be the first mother-child cohort study in Qatar. The study shall provide evidence-based relationship between maternal occupational/environmental exposure, such as sedentary life style, obesity, and other metabolic syndromes, and the subsequent birth outcomes on the Qatari population. Conclusion: Based on the study results, the public health perspective will be addressed by policy makers at the Supreme Council of Health in Qatar.

Background and Objectives: Trauma is the leading cause of death among the young population in the Middle East, including Qatar. A significant number of trauma and injured patients will require sophisticated critical care services and a disproportionately high level of hospital resources are centered within critical care units. The introduction of an advanced ACGME structured Trauma & Critical Care (TCC) Fellowship Program at the Hamad General Hospital (HGH) in Doha, Qatar will improve patient safety and outcomes, medical care and professional satisfaction. Methods: A review of the clinical impact of the TCC Fellowship Program in the trauma service at HGH, the only tertiary and national trauma center in Qatar, was conducted after the second year of implementation to evaluate the healthcare delivery to the severely injured patients, using tools from the ICU resource, evaluation, and patient outcomes rating tool (ICU Report)®. Results: Since the implementation of the TCC Fellowship Program in 2008, structured educational and training curriculum have been implemented for physicians assigned to the trauma service at the HGH. Nine fellows have successfully completed the program and graduated. A 40% decrease of intra-hospital mortality has been observed in our trauma service. Three fellows have been promoted to consultant level and six to critical care teaching staff, enhancing staff satisfaction and the overall score of our trauma ICU. Conclusions: Advanced postgraduate medical education and training program in trauma and critical care medicine have significantly contributed to patient safety and outcome of critically injured patients in Qatar and have enhanced the overall performance of our trauma service and staff satisfaction. The fellowship program is expanding to other disciplines, and is enrolling national and international candidates in emergency medicine and anesthesia in our institution and is impacting healthcare delivery of the complex cases of injured patients in the country.

Background Consanguinity and endogamy are common in the Middle East, resulting in a higher frequency of autosomal recessive (AR) disorders. This consanguinity facilitates discovery of disease causative genes particularly after introduction of the new techniques such as Whole Exome Sequencing (WES). In order to reduce the overall socio-economic burden of such diseases, the development of diagnostic tools and prevention strategies must be a priority. To achieve these goals, the causal genes underlying human genetic diseases should be first discovered. The goal of this study is to identify novel genes causing AR diseases in Qatari population using WES. Methods Genomic DNAs were captured with the Illumina TruSeq library and sequenced with Illumina HiSeq2000. The reads were aligned to the reference genome using BWA. Variants calling and annotation were performed by SAMtools and ANNOVAR, respectively. Novel variants were defined as those having an allele frequency <0.05 in the 1000 Genomes database and predicted to be nonsynonymous substitutions. Results WES was applied on affected individuals of 3 consanguineous families with Mental Retardation (MR: 2 siblings), Peripheral Neuropathy (PN: 2 siblings) and Eye Anomaly (EA: 1 male). The mode of inheritance was assumed to be AR in MR and PN families. This led to identification of 3 and 4 homozygous candidate variants, shared by two siblings, respectively. The mode of inheritance in EA was considered to be AR and/or X-linked that led to the identification of 26 autosomal homozygous and 6 X-linked genes. The function of one of the genes on X-chromosome was related to the patient phenotype. Conclusions These preliminary interesting results highlight the power of WES, to identify potential candidate genes for AR disorders. The identified genes will be considered for functional follow-up investigation and further characterization. However, our results also highlight that the large number of population-specific variants - which may be common polymorphisms in Qatar but are so far absent from public databases - make diagnosis and discovery more difficult than in well-studied Caucasian populations. We urge genetics researchers in Qatar to actively participate in the creation of a local variant database, which will greatly facilitate such future studies.

Background and Objective: Cells exposed to stress conserve energy for the repair of cellular damage by inhibiting translational initiation. The stress stimuli can trigger several stress response pathways leading to global translational attenuation, chiefly by the phosphorylation of eIF2α and disruption of the 43S assembly, which correlates to the compartmentalization of untranslated polyadenylated mRNA in discrete cytoplasmic ribonucleoprotein complexes known as Stress Granules (SGs). In a diabetic milieu, endothelial cells (ECs) that line the lumen of the blood vessels are constantly exposed to high glucose (HG) concentration (stress), which contributes to increased oxidative stress in these cells that in turn is responsible for high rates of cardiovascular complications among diabetic individuals. However, the effect of high glucose as a stress in relation to SG assembly in ECs remains unclear. The central objective of the present study is to evaluate the role of HG-induced oxidative stress in SG assembly in ECs and whether antioxidant treatment could aid in the reversal of these effects. Methods: Mouse microvascular endothelial cells (MMECs) cultured in DMEM were exposed to normal (NG, 11mM) and high (HG, 40mM) glucose for 0-48h. DHE staining was performed to evaluate oxidative stress in ECs upon HG exposure. Fixed cells were probed for SG marker proteins (G3BP and TIAR) followed by immunofluorescence confocal microscopy. Immunoblotting was performed using protein lysate samples and was probed for p-PERK, PERK, p-eIF2α and eIF2a. N-acetyl cysteine was used as the anti-oxidant in order to study the role of oxidative stress in HG induced SG formation. Results: DHE staining indicated that oxidative stress significantly increased in HG exposed MMECs while this effect was reversed upon in NAC treatment. NAC treatment also markedly decreased HG-induced SG assembly. Conclusion: The data suggest that HG-induced oxidative stress plays a major role in SG assembly in ECs. However, more studies are warranted to evaluate the process of assembly and dis-assembly of SGs in ECs upon HG exposure, which may provide a better understanding of the role of SG formation in balancing EC apoptosis and survival in a diabetic milieu. This project was funded by QNRF-NPRP # 08-165-3-054 & 4-910-3-244.

Background & Objectives: Despite the solid foundation on epidemiological evidence and basic science research, nearly 90% of the randomized controlled trials (RCT) designed to measure the efficacy of interventions on HIV incidence failed to measure a statistically significant efficacy against HIV incidence. Here, we propose the use of computer simulations to control trials as a useful tool to overcome the difficulty of effect size estimation and outcome interpretation derived from HIV intervention RCTs. Methods: We simulated the Partners in Prevention HSV/HIV transmission study recently conducted to test the efficacy of herpes simplex virus type 2 (HSV-2) suppressive therapy by acyclovir in reducing HIV transmission. We also simulated different variations of this trial, and the Rakai male circumcision trial. We developed individual-based Monte-Carlo models parameterized by the data of these RCTs and simulated the RCTs 1000 times. To measure the efficacy of the intervention, we conducted a log-rank survival analysis for each RCT realization and estimated the statistical power as the fraction of realizations that rejected the null hypothesis. Results: Our analyses indicated that the partners in prevention RCT had only 14% likelihood to observe a statistically significant efficacy for the intervention. In contrast, a different and more potent regimen for HSV-2 suppression had 87% chance of observing a statistically significant efficacy. For the Rakai male circumcision trial simulation, 94% of the RCT realizations showed statistically significant efficacy for the intervention. Conclusions: The simulations indicate that several unexpected odds have colluded to undermine the statistical power of the partners in prevention study, and therefore it would be premature to discredit the concept of acyclovir therapy for HIV prevention based on the outcome of the partners in prevention trial. Our study highlights how in silico simulations of RCTs can provide powerful tools for optimizing the design of RCTs and predicting their outcome. Observational and biological evidence summarized in computer simulations could help us on the estimation of effect size ranges and a better understanding of the system, which might provide a powerful tool to enhance the success of any HIV intervention RCT.