Translocation t(1;19) in acute precursor B-cell lymphoblastic Leukaemia in paediatric patients- Pakistani population.

OBJECTIVE: To determine the impact of translocation t(1;19) in paediatric patients diagnosed with precursor B-cell acute lymphoblastic leukaemia. METHODS: The retrospective study was conducted at the Shaukat Khanum Memorial Cancer Hospital and Research Centre, Lahore, Pakistan, and comprised data from January 2012 to January 2018 of paediatric patients diagnosed with precursor B-cell acute lymphoblastic leukaemia. Data of patients having t(1;19) translocation with or without complex karyotype formed group A, while data of patients without any cytogenetic abnormality formed the control group B. Relapse and event-free survival were calculated and the outcomes were compared between the groups. Data was analysed using SPSS 20. RESULTS: Of the 450 subjects whose data was analysed, 84(18.7%) were included; 25(30%) in group A and 59(70%) were in group B. There were 21(84%) males and 4(16%) females in group A with mean age on presentation 3.68±0.6 years compared to 41(69.4%) males and 18(30.5%) females with mean age on presentation 4.0±0.92 (p>0.05). There were no differences between the groups in terms of baseline markers (p>0.05). The relapse and event-free survival rates were also not significantly different between the groups (p>0.05). CONCLUSIONS: There was no significant difference related to outcomes of precursor B-cell acute lymphoblastic leukaemia patients having t(1;19) translocation with or without complex karyotype and those without any cytogenetic abnormality, indicating that translocation t(1;19)-positive patients do not need treatment intensification.

Evolution of efficacious pangenotypic hepatitis C virus therapies.

Hepatitis C compromises the quality of life of more than 350 million individuals worldwide. Over the last decade, therapeutic regimens for treating hepatitis C virus (HCV) infections have undergone rapid advancements. Initially, structure-based drug design was used to develop molecules that inhibit viral enzymes. Subsequently, establishment of cell-based replicon systems enabled investigations into various stages of HCV life cycle including its entry, replication, translation, and assembly, as well as role of host proteins. Collectively, these approaches have facilitated identification of important molecules that are deemed essential for HCV life cycle. The expanded set of putative virus and host-encoded targets has brought us one step closer to developing robust strategies for efficacious, pangenotypic, and well-tolerated medicines against HCV. Herein, we provide an overview of the development of various classes of virus and host-directed therapies that are currently in use along with others that are undergoing clinical evaluation.

Utilisation Patterns and Treatment Outcomes of EGFR-Tyrosine Kinase Inhibitors in EGFR-mutant Advanced Lung Carcinoma in the Pakistani-Asian Population: A Real-world Data Study.

Introduction: Data on the utilisation of epidermal growth factor receptor (EGFR) tyrosine-kinase inhibitors (TKIs) and their clinical outcomes in a heterogeneous Pakistani-Asian population have not been previously reported. This manuscript presents the first account of the clinical outcomes of EFGR-TKIs in EGFR-mutant lung adenocarcinoma among Pakistani-Asians. Materials and methods: A real-world data study was conducted on all advanced lung cancer patients harbouring EGFR-mutations from the cancer registry of Shaukat Khanum Memorial Cancer Hospital and Research Centre, Lahore, Pakistan. We identified three different patterns of the use of EGFR-TKIs (Groups 1, 2 and 3) that reflect the ground realities of cancer care and delivery in Pakistan. We also noted a significant proportion of patients (Group 4) without access to EGFR TKIs. We compared the objective response rates (ORR), progression-free survival (PFS) and overall survival (OS) of each of the four groups and reported their toxicity profile. Results: Within the limitations of a retrospective analysis, we saw differences in the frequency of EGFR mutations in this population. However, response rates and long-term outcomes of EGFR TKI therapy were comparable with the existing data. The overall use of EGFR TKIs led to a superior outcome in ORR, PFS and OS compared to chemotherapy alone; (77.8% vs. 50.0%, 16.3 vs. 10.7 months; P = 0.099; 85.6 vs. 25.9 months, respectively; P = 0.13). Conclusion: Except for modest differences, EGFR-mutant advanced lung adenocarcinoma outcomes among Pakistani-Asians are comparable to those of other populations.

Significance of CMV reactivation in non-allogeneic stem cell transplant patients with cancers: experience of single tertiary care cancer institute.

CMV reactivation is rare in hematological as well as solid organ malignancies in non-allogeneic stem cell transplant settings. An increasing number of patients undergoing active treatment or follow-up and diagnosed with CMV reactivation in recent years prompted us to investigate the risk factors and outcomes of CMV reactivation or disease. This was a hospital-based retrospective study that included 174 cancer patients suspected of CMV reactivation. Among them, forty-one tested positive for CMV viremia. The risk factors for CMV reactivation included the use of steroids in 78% of patients, active cancer in 43.9%, use of a monoclonal antibody rituximab in 31.7%, a history of radiation in 26.8%, and autologous stem cell transplant in 12% of patients. The median age was 36 years, and the most common clinical feature was fever (58.5%; n = 24), followed by GI symptoms (12.1%; n = 5), respiratory symptoms (14.6%; n = 6), cytopenia (7.3%; n = 3), and visual/neurological symptoms (4.8%; n = 2). The mean CMV viral load was 37,332 copies/ml (range: 75.00-633,000.00 copies/ml). Nineteen patients received CMV treatment with an average treatment duration of 81.5 days. The median overall survival was 2 months, with 12.0% of patients alive at 5 years. CMV reactivation is associated with significant morbidity and mortality. We recommend vigilant monitoring of CMV-related symptoms, with a low threshold for testing and treatment, for patients with multiple risk factors for CMV reactivation.

Diagnostic Utility Of Fish For MDM2 In Adipocytic Neoplasms.

BACKGROUND: The 2013 World Health Organization (WHO) classification of soft tissue and bone tumours recognizes benign entities such as lipoma and four major liposarcoma subtypes: atypical lipomatous tumour/well differentiated liposarcomas (ALT/WDL), dedifferentiated liposarcomas (DDL), myxoid liposarcoma and pleomorphic liposarcoma. This classification of atypical and malignant adipocytic tumours has evolved significantly over the past few decades owing to contributions from cytogenetics, molecular genetics and Immunohistochemical correlates. Most ALT/WDLs can be diagnosed on histology; however, some of the biopsies may be underdiagnosed due to focal atypia or limited nature of tissue for the biopsy. Fluorescence in situ hybridization (FISH) for MDM2 (located at 12q14-15) gene amplification has emerged as gold standard for diagnosis in cases with limiting histological factors. METHODS: We studied MDM2 amplification by FISH in 55 such problematic adipocytic tumours with overlapping morphological features and a retrospective analysis was made against their corresponding histological features. RESULTS: MDM2 amplification correctly identified 11 of 17 ALT/WDLs (64.71% concordance) and 8 of 10 Lipomas (80% concordance). We were able to differentiate liposarcomas from other high grade sarcomatous lesions and sub-classified these lesions into pleomorphic and dedifferentiated types. CONCLUSIONS: FISH for MDM2 amplification should be used as a gold standard in adjunction with morphology and immunohistochemistry for problematic adipocytic neoplasms.

A Personalized Therapeutics Approach Using an In Silico Drosophila Patient Model Reveals Optimal Chemo- and Targeted Therapy Combinations for Colorectal Cancer.

In silico models of biomolecular regulation in cancer, annotated with patient-specific gene expression data, can aid in the development of novel personalized cancer therapeutic strategies. Drosophila melanogaster is a well-established animal model that is increasingly being employed to evaluate such preclinical personalized cancer therapies. Here, we report five Boolean network models of biomolecular regulation in cells lining the Drosophila midgut epithelium and annotate them with colorectal cancer patient-specific mutation data to develop an in silico Drosophila Patient Model (DPM). We employed cell-type-specific RNA-seq gene expression data from the FlyGut-seq database to annotate and then validate these networks. Next, we developed three literature-based colorectal cancer case studies to evaluate cell fate outcomes from the model. Results obtained from analyses of the proposed DPM help: (i) elucidate cell fate evolution in colorectal tumorigenesis, (ii) validate cytotoxicity of nine FDA-approved CRC drugs, and (iii) devise optimal personalized treatment combinations. The personalized network models helped identify synergistic combinations of paclitaxel-regorafenib, paclitaxel-bortezomib, docetaxel-bortezomib, and paclitaxel-imatinib for treating different colorectal cancer patients. Follow-on therapeutic screening of six colorectal cancer patients from cBioPortal using this drug combination demonstrated a 100% increase in apoptosis and a 100% decrease in proliferation. In conclusion, this work outlines a novel roadmap for decoding colorectal tumorigenesis along with the development of personalized combinatorial therapeutics for preclinical translational studies.

Multi-center real-world comparison of the fully automated Idylla™ microsatellite instability assay with routine molecular methods and immunohistochemistry on formalin-fixed paraffin-embedded tissue of colorectal cancer.

Microsatellite instability (MSI) is present in 15-20% of primary colorectal cancers. MSI status is assessed to detect Lynch syndrome, guide adjuvant chemotherapy, determine prognosis, and use as a companion test for checkpoint blockade inhibitors. Traditionally, MSI status is determined by immunohistochemistry or molecular methods. The Idylla™ MSI Assay is a fully automated molecular method (including automated result interpretation), using seven novel MSI biomarkers (ACVR2A, BTBD7, DIDO1, MRE11, RYR3, SEC31A, SULF2) and not requiring matched normal tissue. In this real-world global study, 44 clinical centers performed Idylla™ testing on a total of 1301 archived colorectal cancer formalin-fixed, paraffin-embedded (FFPE) tissue sections and compared Idylla™ results against available results from routine diagnostic testing in those sites. MSI mutations detected with the Idylla™ MSI Assay were equally distributed over the seven biomarkers, and 84.48% of the MSI-high samples had ≥ 5 mutated biomarkers, while 98.25% of the microsatellite-stable samples had zero mutated biomarkers. The concordance level between the Idylla™ MSI Assay and immunohistochemistry was 96.39% (988/1025); 17/37 discordant samples were found to be concordant when a third method was used. Compared with routine molecular methods, the concordance level was 98.01% (789/805); third-method analysis found concordance for 8/16 discordant samples. The failure rate of the Idylla™ MSI Assay (0.23%; 3/1301) was lower than that of referenced immunohistochemistry (4.37%; 47/1075) or molecular assays (0.86%; 7/812). In conclusion, lower failure rates and high concordance levels were found between the Idylla™ MSI Assay and routine tests.

2-Deoxy-D-glucose reduces epilepsy progression by NRSF-CtBP-dependent metabolic regulation of chromatin structure.

Temporal lobe epilepsy is a common form of drug-resistant epilepsy that sometimes responds to dietary manipulation such as the 'ketogenic diet'. Here we have investigated the effects of the glycolytic inhibitor 2-deoxy-D-glucose (2DG) in the rat kindling model of temporal lobe epilepsy. We show that 2DG potently reduces the progression of kindling and blocks seizure-induced increases in the expression of brain-derived neurotrophic factor and its receptor, TrkB. This reduced expression is mediated by the transcription factor NRSF, which recruits the NADH-binding co-repressor CtBP to generate a repressive chromatin environment around the BDNF promoter. Our results show that 2DG has anticonvulsant and antiepileptic properties, suggesting that anti-glycolytic compounds may represent a new class of drugs for treating epilepsy. The metabolic regulation of neuronal genes by CtBP will open avenues of therapy for neurological disorders and cancer.

DNMT1 silencing affects locus specific DNA methylation and increases prostate cancer derived PC3 cell invasiveness.

PURPOSE: DNMT1 maintains genomic DNA methylation at 5'-CpG-3' residues in somatic cells. Recent findings revealed that DNMT1 depletion causes distinct phenotypic changes in colon and gastric cancer cell lines, suggesting that the extent to which DNMT1 influences the expression of its target genes is cell-type specific. We determined the impact of DNMT1 depletion in prostate cancer derived cells on their gene expression profiles and cellular phenotype. MATERIALS AND METHODS: Small interfering RNA was used to silence DNMT1 expression in prostate cancer derived PC3 cells (ATCC). The resulting cell line was validated by reverse transcriptase-polymerase chain reaction and Western blotting. Proliferation, migration and invasion assays were done in engineered cells to asses the effect of DNMT1 silencing on cellular phenotype. DNA microarrays were done to monitor changes in gene expression. RESULTS: Our data showed that DNMT1 loss dramatically decreased cell proliferation but significantly increased cell migratory and invasive potential. Additionally, in the limited set of genes whose expression and DNA methylation status were determined DNMT1 loss was associated with increased CDKN3 and claudin-3 expression, and also culminated in specific demethylation of Rb1 and RAR-beta promoters. CONCLUSIONS: These results show that the genetic and phenotypic consequences of silencing DNMT1 in PC3 cells are markedly different from those in colon and gastric cancers, indicating that DNMT1 preferentially targets certain gene promoters. Our findings also suggest that decreasing DNMT1 levels or activity can potentially enhance prostate cancer cell invasiveness.

Down-regulation of DNMT3b in PC3 cells effects locus-specific DNA methylation, and represses cellular growth and migration.

BACKGROUND: Aberrations in DNA methylation patterns promote changes in gene expression patterns and are invariably associated with neoplasia. DNA methylation is carried out and maintained by several DNA methyltransferases (DNMTs) among which DNMT1 functions as a maintenance methylase while DNMT3a and 3b serve as de novo enzymes. Although DNMT3b has been shown to preferentially target the methylation of DNA sequences residing in pericentric heterochromatin whether it is involved in gene specific methylation remains an open question. To address this issue, we have silenced the expression of DNMT3b in the prostate-derived PC3 cells through RNA interference and subsequently studied the accompanied cellular changes as well as the expression profiles of selected genes. RESULTS: Our results demonstrate that DNMT3b depletion results in increased apoptosis and reduced migration of PC3 cells compared to the untransfected control cells. Reduced DNMT3b expression resulted in hypomethylation of retinoblastoma (Rb), retinoic-acid receptor beta (RAR-beta), and adenomatous polyposis coli (APC) gene promoters, and also culminated in increased expression of CDKN3 and cytochrome b5. Although DNMT3b silenced cells were found to have reduced growth and migratory potential, there was no apparent changes in their invasive ability compared to the parental PC3 cell line. CONCLUSION: Our findings reveal that DNMT3b preferentially targets certain gene promoters in PC3 cells and that its depletion significantly reduces growth and migration of PC3 cells.

Silencing of MBD1 and MeCP2 in prostate-cancer-derived PC3 cells produces differential gene expression profiles and cellular phenotypes.

Alterations in genomic CpG methylation patterns have been found to be associated with cell transformation and neoplasia. Although it is recognized that methylation of CpG residues negatively regulates gene expression, how the various MBPs (methyl-binding proteins) contribute to this process remains elusive. To determine whether the two well characterized proteins MeCP2 (methyl-CpG-binding protein 2) and MBD1 (methyl-CpG-binding domain 1) have distinct or redundant functions, we employed RNAi (RNA interference) to silence their expression in the prostate cancer-derived PC3 cell line, and subsequently compared cell growth, invasion and migration properties of these cell lines in addition to their respective mRNA-expression profiles. Cells devoid of MeCP2 proliferated more poorly compared with MBD1-deficient cells and the parental PC3 cells. Enhanced apoptosis was observed in MeCP2-deficient cells, whereas apoptosis in parental and MBD1-deficient cells appeared to be equivalent. Boyden chamber invasion and wound-healing migration assays showed that MBD1-silenced cells were both more invasive and migratory compared with MeCP2-silenced cells. Finally, gene chip microarray analyses showed striking differences in the mRNA-expression profiles obtained from MeCP2- and MBD1-depleted cells relative to each other as well as when compared with control cells. The results of the present study suggest that MeCP2 and MBD1 silencing appear to affect cellular processes independently in vivo and that discrete sets of genes involved in cellular proliferation, apoptosis, invasion and migration are targeted by each protein.

Fluorescence in Situ Hybridization (FISH) for Differential Diagnosis of Soft Tissue Sarcomas

Introduction:Soft tissue sarcomas are rare tumors comprising 1 percent of solid malignancies. The latest edition of WHO soft tissue pathology lists 94 benign and malignant soft tissue tumors. Many of these show a large degree of morphological overlap. Immunohistochemistry has been shown to be reliable in many cases for differential diagnosis of lesions, although cytogenetic tests are considered the gold standard for many entities.Fluorescence in-situ hybridization (FISH) is a cytogenetic technique that uses fluorescent probes that bind to only those parts of the chromosome which have a high degree of sequence complementarity. Many soft tissue tumors show recurrent genetic mutations that are now being used as diagnostic markers. Knowledge of the molecular identity allows prediction of behavior, prognosis and treatment response. Objective:The aim of this study was to identify genetic mutations in soft tissue sarcomas using FISH testing and to assess correlations with histological diagnosis. Material and methods:A total of 25 cases of different soft tissue sarcomas diagnosed on histology with the help of immunohistochemical staining and for which FISH studies were requested were included in this study. Three pathologists with a special interest in soft tissue sarcomas reviewed the cases. FISH tests for EWS, the X:18 translocation, FOXO1 and MDM2 were respectively applied for 8 cases of Ewing sarcoma, 8 cases of synovial sarcoma, 2 cases of rhabdomyosarcoma and 7 cases of dedifferentiated liposarcoma and atypical lipomatous tumors/well differentiated liposarcomas. Results:EWS gene fusion was detected in 7 out of 8 cases of Ewing sarcoma and the X:18 translocation was positive in 3 of the 8 cases of synovial sarcoma. FOXO1 was not detected in either of the two rhabdomyosarcomas. MDM2 by FISH was detected in only one out of 5 cases of atypical lipomatous tumors and 1 out of 2 dedifferentiated liposarcomas. Conclusion: FISH is a useful adjunct in the diagnostic assessment of different types of soft tissue sarcomas. It is easy to set up, is relatively inexpensive and has the ability to diagnose sarcomas with great accuracy, especially in cases which can not be accurately classified even after thorough histological and immunohistochemical evaluation. It may play a very important role in the accurate diagnosis and correct management of patients.

Ultrastructural features of sprouted mossy fiber synapses in kindled and kainic acid-treated rats.

The mossy fiber pathway in the dentate gyrus undergoes sprouting and synaptic reorganization in response to seizures. The types of new synapses, their location and number, and the identity of their postsynaptic targets determine the functional properties of the reorganized circuitry. The goal of this study was to characterize the types and proportions of sprouted mossy fiber synapses in kindled and kainic acid-treated rats. In normal rats, synapses labeled by Timm histochemistry or dynorphin immunohistochemistry were rarely observed in the supragranular region of the inner molecular layer when examined by electron microscopy. In epileptic rats, sprouted mossy fiber synaptic terminals were frequently observed. The ultrastructural analysis of the types of sprouted synapses revealed that 1) in the supragranular region, labeled synaptic profiles were more frequently axospinous than axodendritic, and many axospinous synapses were perforated; 2) sprouted mossy fiber synaptic terminals formed exclusively asymmetric, putatively excitatory synapses with dendritic spines and shafts in the supragranular region and with the soma of granule cells in the granule cell layer; 3) in contrast to the large sprouted mossy fiber synapses in resected human epileptic hippocampus, the synapses formed by sprouted mossy fibers in rats were smaller; and 4) in several cases, the postsynaptic targets of sprouted synapses were identified as granule cells, but, in one case, a sprouted synaptic terminal formed a synapse with an inhibitory interneuron. The results demonstrate that axospinous asymmetric synapses are the most common type of synapse formed by sprouted mossy fiber terminals, supporting the viewpoint that most sprouted mossy fibers contribute to recurrent excitation in epilepsy.

Population-based surveillance for severe rotavirus gastroenteritis in children in Karachi, Pakistan.

The incidence of rotavirus-associated severe diarrhoea and distribution of rotavirus genotypes in children less than five years of age was determined in two low-income communities in Karachi, Pakistan. Over a two-year period, 717 children met eligibility criteria for severe diarrhoea and stools were obtained from 575 (80%) with 97 (17%) being rotavirus positive. Adjusted annual rates of severe rotavirus diarrhoea in children less than five years and less than one year were respectively 5.7 and 16.9 per 1000 in community A, and 8.1 and 25.4 per 1000 child years of observation in community B. An estimated 1 in 40 infants experience a severe episode of rotavirus gastroenteritis annually in Pakistan. The most common rotavirus strains were G9P[8] (15%), G1P[8] (13%) and G1[P4] (8.4%). This information will inform policy decisions about the introduction of rotavirus vaccines.

Localized domains of G9a-mediated histone methylation are required for silencing of neuronal genes.

Negative regulation of transcription is an important strategy in establishing and maintaining cell-specific gene expression patterns. Many neuronal genes are subject to active transcriptional repression outside the nervous system to establish neuronal specificity. NRSF/REST has been demonstrated to regulate at least 30 genes and contribute to their neuronal targeting by repressing transcription outside the nervous system. Further, human genome database searches reveal that over 800 genes contain an NRSE. Here we report that NRSF recruits the histone methylase G9a to silence NRSF target genes in nonneuronal cells. We show that G9a generates a highly localized domain of dimethylated histone H3-K9 around NRSEs, but H3-K27 remains unmethylated. The NRSEs are also associated with HP1. Finally, we demonstrate that dominant-negative G9a abrogates silencing of chromosomal neuronal genes. These findings implicate a role for histone methylation in targeting neuronal gene expression to the nervous system.