The significance of eighteen rice genotypes on arsenic accumulation, physiological response and potential health risk.

Rice is an important food crop that is susceptible to arsenic (As) contamination under paddy soil conditions depending on As uptake characteristics of the rice genotypes. Here we unveiled the significance of eighteen (fine and coarse) rice genotypes against As accumulation/tolerance, morphological and physiological response, and antioxidant enzymes-enabled defense pathways. Arsenic significantly affected rice plant morphological and physiological attributes, with relatively more impacts on fine compared to coarse genotypes. Grain, shoot, and root As uptake were lower in fine genotypes (0.002, 0.020, and 0.032 mg pot-1 DW, respectively) than that of coarse (0.031, 0.60, and 1.2 mg pot-1 DW, respectively). Various biochemical (pigment contents, hydrogen peroxide, lipid peroxidation) and defense (antioxidant enzymes) plant parameters indicated that the fine genotypes, notably Kainat and Basmati-385, possessed the highest As tolerance. Arsenic-induced risk indices exhibited greater hazard quotient (up to 1.47) and carcinogenic risk (up to 0.0066) for coarse genotypes compared to the fine ones, with the greatest risk for KSK-282. This study elaborates the pivotal role of genotypic variation among rice plants in As accumulation, which is crucial for mitigating the associated human health risk. Further research is required on molecular aspects, e.g., genetic sequencing, to examine rice genotypes variation in defense mechanisms to As contamination.

3D hotspots of recurrent retroviral insertions reveal long-range interactions with cancer genes.

Genomically distal mutations can contribute to the deregulation of cancer genes by engaging in chromatin interactions. To study this, we overlay viral cancer-causing insertions obtained in a murine retroviral insertional mutagenesis screen with genome-wide chromatin conformation capture data. Here we find that insertions tend to cluster in 3D hotspots within the nucleus. The identified hotspots are significantly enriched for known cancer genes, and bear the expected characteristics of bona fide regulatory interactions, such as enrichment for transcription factor-binding sites. In addition, we observe a striking pattern of mutual exclusive integration. This is an indication that insertions in these loci target the same gene, either in their linear genomic vicinity or in their 3D spatial vicinity. Our findings shed new light on the repertoire of targets obtained from insertional mutagenesis screening and underline the importance of considering the genome as a 3D structure when studying effects of genomic perturbations.

Prolonged Ezh2 Depletion in Glioblastoma Causes a Robust Switch in Cell Fate Resulting in Tumor Progression.

EZH2 is frequently overexpressed in glioblastoma (GBM), suggesting an oncogenic function that could be a target for therapeutic intervention. However, reduced EZH2 activity can also promote tumorigenesis, leading to concerns about the use of EZH2 inhibitors. Here, we provide further insight about the effects of prolonged Ezh2 inhibition in glioblastoma using preclinical mouse models and primary tumor-derived human GBM cell lines. Using doxycycline-inducible shRNAs that mimic the effects of a selective EZH2 inhibitor, we demonstrate that prolonged Ezh2 depletion causes a robust switch in cell fate, including significantly enhanced proliferation, DNA damage repair, and activation of part of the pluripotency network, resulting in altered tumor cell identity and tumor progression. Short-term Ezh2 depletion significantly improved survival without the tumor progression observed upon prolonged Ezh2 depletion, suggesting that precise dosing regiments are very important. These results could be of high clinical relevance with regard to how glioblastomas should be treated with epigenetic therapies.

Chromatin landscapes of retroviral and transposon integration profiles.

The ability of retroviruses and transposons to insert their genetic material into host DNA makes them widely used tools in molecular biology, cancer research and gene therapy. However, these systems have biases that may strongly affect research outcomes. To address this issue, we generated very large datasets consisting of ~ 120,000 to ~ 180,000 unselected integrations in the mouse genome for the Sleeping Beauty (SB) and piggyBac (PB) transposons, and the Mouse Mammary Tumor Virus (MMTV). We analyzed ~ 80 (epi)genomic features to generate bias maps at both local and genome-wide scales. MMTV showed a remarkably uniform distribution of integrations across the genome. More distinct preferences were observed for the two transposons, with PB showing remarkable resemblance to bias profiles of the Murine Leukemia Virus. Furthermore, we present a model where target site selection is directed at multiple scales. At a large scale, target site selection is similar across systems, and defined by domain-oriented features, namely expression of proximal genes, proximity to CpG islands and to genic features, chromatin compaction and replication timing. Notable differences between the systems are mainly observed at smaller scales, and are directed by a diverse range of features. To study the effect of these biases on integration sites occupied under selective pressure, we turned to insertional mutagenesis (IM) screens. In IM screens, putative cancer genes are identified by finding frequently targeted genomic regions, or Common Integration Sites (CISs). Within three recently completed IM screens, we identified 7%-33% putative false positive CISs, which are likely not the result of the oncogenic selection process. Moreover, results indicate that PB, compared to SB, is more suited to tag oncogenes.

Applications of DNA integrating elements: Facing the bias bully.

Retroviruses and DNA transposons are an important part of molecular biologists' toolbox. The applications of these elements range from functional genomics to oncogene discovery and gene therapy. However, these elements do not integrate uniformly across the genome, which is an important limitation to their use. A number of genetic and epigenetic factors have been shown to shape the integration preference of these elements. Insight into integration bias can significantly enhance the analysis and interpretation of results obtained using these elements. For three different applications, we outline how bias can affect results, and can potentially be addressed.

Patient communication in radiology: current status of breaking bad news among radiologists and radiology trainees in Pakistan.

Breaking bad news can be an intimidating task for any physician. The aim of this study was to record the practices of breaking bad news to the patients by Pakistani radiologists and trainees. The radiologists and trainees attending the 26th National Radiological Conference in October 2010 in Karachi, Pakistan, were surveyed. The response rate was 76%. The respondents included residents (51%), private practicing radiologists (28%), academic radiologists (13%), and other trainees (8%). Most of the academic radiologists communicated with their patients. The daily frequency of breaking bad news by residents was noted, which was highest in the public teaching hospitals (71%). For severe abnormalities such as malignancy, 50% residents, 55% of the academic radiologists and 74% of the private practicing radiologists were very uncomfortable in disclosure of results. Differences in frequency of communication with patients were noticed with both different training levels, and different settings of practice in a developing country.

Analysis of tumor heterogeneity and cancer gene networks using deep sequencing of MMTV-induced mouse mammary tumors.

Cancer develops through a multistep process in which normal cells progress to malignant tumors via the evolution of their genomes as a result of the acquisition of mutations in cancer driver genes. The number, identity and mode of action of cancer driver genes, and how they contribute to tumor evolution is largely unknown. This study deployed the Mouse Mammary Tumor Virus (MMTV) as an insertional mutagen to find both the driver genes and the networks in which they function. Using deep insertion site sequencing we identified around 31000 retroviral integration sites in 604 MMTV-induced mammary tumors from mice with mammary gland-specific deletion of Trp53, Pten heterozygous knockout mice, or wildtype strains. We identified 18 known common integration sites (CISs) and 12 previously unknown CISs marking new candidate cancer genes. Members of the Wnt, Fgf, Fgfr, Rspo and Pdgfr gene families were commonly mutated in a mutually exclusive fashion. The sequence data we generated yielded also information on the clonality of insertions in individual tumors, allowing us to develop a data-driven model of MMTV-induced tumor development. Insertional mutations near Wnt and Fgf genes mark the earliest "initiating" events in MMTV induced tumorigenesis, whereas Fgfr genes are targeted later during tumor progression. Our data shows that insertional mutagenesis can be used to discover the mutational networks, the timing of mutations, and the genes that initiate and drive tumor evolution.

Diffusion weighted MR imaging of ring enhancing brain lesions.

OBJECTIVE: To evaluate the role of diffusion weighted imaging in differentiating the cause of ring enhancing brain lesions. STUDY DESIGN: Analytical, descriptive study. PLACE AND DURATION OF STUDY: Department of Radiology, The Aga Khan University Hospital, Karachi, from March 2007 to July 2011. METHODOLOGY: Diffusion weighted imaging (DWI) was performed on 37 patients having ring enhancing lesions on their post-contrast brain MRI scans. These lesions were characterized into neoplastic and abscess cavity on the basis of diffusion restriction. Correlation of all these findings was done with histopathology obtained in all these patients. Sensitivity, specificity, positive and negative predictive values and diagnostic accuracy of DWI were calculated. Comparisons of mean ADC values of abscess and neoplastic lesions were also done using t-test. RESULTS: DWI had a sensitivity of 94.73%, specificity of 94.44%, positive predictive value of 94.73%, and negative predictive value of 94.44% and diagnostic accuracy of 94.5% in differentiating brain abscess from neoplastic brain lesions. Mean ADC value in central cavity and wall of neoplastic lesions and brain abscesses were calculated with significant p-value of 0.001 and 0.025 respectively. CONCLUSION: Diffusion weighted imaging is non-invasive method with high sensitivity and specificity which can help in differentiation of ring enhancing neoplastic lesions and brain abscesses. This modality should be read in conjunction with conventional imaging.

Acute vertebral compression fracture: differentiation of malignant and benign causes by diffusion weighted magnetic resonance imaging.

OBJECTIVE: To evaluate the sensitivity, specificity and accuracy of diffusion weighted (DWI) magnetic resonance imaging (MRI) in the diagnosis and differentiation between benign (osteoporotic/infectious) and malignant vertebral compression fractures in comparison with histology findings and clinical follow up. METHODS: The study was conducted at the Radiology Department, Aga Khan University Hospital (AKUH) Karachi. It was a one year cross-sectional study from 01/01/2009 to 01/01/2010. Forty patients with sixty three vertebral compression fractures were included. Diffusion-weighted sequences and apparent diffusion coefficient (ADC) images on a 1.5 T MR scanner were obtained in all patients to identify the vertebral compression fracture along with benign and malignant causes. Imaging findings were compared with histopathologic results and clinical follow-up. RESULTS: Diffusion-weighted MR imaging found to have, 92% sensitivity, 90% specificity and accuracy of 85% in differentiation of benign and malignant vertebral compression fracture while PPV and NPV were 78 % and 90% respectively. CONCLUSION: Diffusion weighted magnetic resonance imaging offers a safe, accurate and non invasive modality to differentiate between the benign and malignant vertebral compression fracture.

Role of multidetector computed tomography (MDCT) in patients with ovarian masses.

OBJECTIVE: To evaluate the diagnostic accuracy of multidetector 64-slice computed tomography (MDCT) in the diagnosis and differentiation of benign and malignant ovarian masses using histopathology and surgical findings as the gold standard. MATERIAL AND METHODS: This study was conducted in Aga Khan University Hospital, Karachi, Pakistan. Data was reviewed retrospectively from 1 November 2008 to 12 December 2009. One hundred patients found to have ovarian masses on CT scan were included in the study. CT scan was performed in all these patients after administration of oral and IV contrast. Ovarian masses were classified as benign and malignant on scan findings. Imaging findings were compared with histopathologic results and surgical findings. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and diagnostic accuracy of MDCT were calculated. RESULTS: MDCT was found to have 97% sensitivity, 91% specificity, and an accuracy of 96% in the differentiation of benign and malignant ovarian masses, while PPV and NPV were 97% and 91%, respectively. CONCLUSION: MDCT imaging offers a safe, accurate and noninvasive modality to differentiate between benign and malignant ovarian masses.

Accuracy of computed tomography in diagnosing malignancy in solitary pulmonary lesions.

OBJECTIVE: To evaluate accuracy of Computed Tomography (CT) for diagnosing malignancy in solitary pulmonary lesions (SPLs). METHODS: A prospective cross-sectional study was conducted from 20-01-2007 to 30-06-2008 at the Radiology department, Aga Khan University Hospital (AKUH) Karachi. Fifty-three patients with solitary pulmonary lesions (SPLs) seen in prior chest x-rays or chest CT scans were referred to radiology department for CT guided biopsy. CT scan was performed for each patient prior to biopsy and CT evaluation of the SPLs was performed followed by CT guided Biopsy. Histopathological diagnosis of the lesion was taken as the gold standard. RESULTS: CT was found to be 100% sensitive, 30% specific and 87% accurate for diagnosing malignancy in solitary pulmonary lesions while PPV and NPV were 86% and 100% respectively. CONCLUSION: CT scan is highly sensitive yet non-specific and cannot be used as the definitive diagnostic modality for diagnosing malignancy in solitary pulmonary lesions.

Carotid artery disease in patients undergoing elective coronary artery bypass surgery.

OBJECTIVE: To determine frequency of carotid artery disease in patients undergoing elective coronary artery bypass grafting (CABG) using Doppler sonography. STUDY DESIGN: Observational study. PLACE AND DURATION OF STUDY: Radiology Department, The Aga Khan University Hospital, Karachi, from January 2005 to September 2008. METHODOLOGY: Patients with known cardiovascular disease waiting for CABG surgery were enrolled for carotid artery Doppler sonography. A predefined data entry form was used for data collection. Coronary angiography findings, carotid artery findings and other associated factors were noted from medical and radiological records. Frequency and pattern of carotid artery disease along with associated risk factors were evaluated. Data was entered and analyzed in SPSS version 15. Pearson chi-square for categorical and independent "t" test was applied for continuous variables at 95% confidence level. P-value of less than 0.05 were considered significant. RESULTS: A total of 176 patients (85% male, mean age=65 years) undergoing elective coronary artery bypass grafting were evaluated preoperatively for carotid artery disease by neck color Doppler sonography. Twenty percent of patients were found to have advanced carotid artery disease (> 50% stenosis), 6% had critical stenosis (> 75% stenosis) and 3% had complete stenosis. Frequency of atherosclerotic plaques was 50%, more common on right side and more prevalent in common carotid artery. Family background of carotid or coronary artery disease and history of smoking were significantly associated with presence of carotid artery disease (p < 0.05). CONCLUSION: A sizeable proportion of patients undergoing elective coronary artery bypass grafting surgery for coronary artery disease were found to have coexistant carotid artery disease.

Assessment of menisci and ligamentous injuries of the knee on magnetic resonance imaging: correlation with arthroscopy.

OBJECTIVE: To evaluate the validity of MRI, in the assessment of the meniscal and cruciate ligamenteous injuries of the knee joint and comparison with arthroscopic findings. METHODS: A one year prospective cross-sectional study from January 2006 to January 2007, was performed on 50 patients (32 males & 18 females) with knee injury presenting at the orthopedic unit of AKUH. The patients were referred to radiology department for MRI evaluation and arthroscopy. RESULTS: The sensitivity, specificity and accuracy for MRI of the menisci and ligaments were as follows: medial meniscus resulted in 100% sensitivity, 69.27% specificity, 90% PPV, 100% NPV and 92% accuracy: lateral meniscus resulted in 87.5% sensitivity, 88.23% specificity, 77% PPV, 93% NPV and 88% accuracy: anterior cruciate ligament resulted in 86.67% sensitivity, 91.43% specificity, 81% PPV, 94% NPV and 88% accuracy; posterior cruciate ligament resulted in 100% sensitivity, 95.83% specificity,50% PPV, 100 NPV and 96% accuracy. CONCLUSION: Magnetic resonance imaging is a good, accurate and non invasive modality for the assessment of menisci and ligamenteous injuries. It can be used as a first line investigation in patients with soft tissue trauma to knee.

Acute respiratory failure in Pakistani patients: risk factors associated with mortality.

OBJECTIVE: To assess the outcome and risk factors associated with mortality in patients with acute respiratory failure (ARF). DESIGN: Observational study. PLACE AND DURATION OF STUDY: The Aga Khan University Hospital, Karachi, between January 1997 and June 2001. PATIENTS AND METHODS: All adult patients admitted with a medical cause of acute respiratory failure were reviewed. The primary outcome measure was mortality and secondary outcome measures were factors associated with mortality in ARF. Multiple logistic regression analysis was used to identify the independent risk factors for mortality. RESULTS: A total of 270 patients were admitted with ARF. Hypercapnic respiratory failure was seen in 186 (69%) and hypoxemic in 84 (31%) cases. Pneumonia and COPD exacerbation were the most common underlying causes of ARF. Ventilator support was required in 93 (34.4%) patients. Hospital mortality was 28%. Chronic renal failure, malignancy, hypokalemia, severe acidosis (pH <7.25) septicemia and ARDS independently correlated with mortality. Mortality rate increased sharply (84%) with the presence of three or more risk factors. CONCLUSION: Acute respiratory failure has a high mortality rate (28%). Development of ARDS or septicemia was associated with high mortality. Presence of more than one risk factor significantly increased the mortality rate.

Primary lymphoma of the cervix.

A 62-years old female presented with postmenopausal vaginal bleeding for one month. On vaginal examination soft fungated mass was palpated in cervix that bled to touch. Ultrasound, CT scan and MRI showed well-defined mass in cervix. On biopsy it was proved to be a primary non-Hodgkin's lymphoma.