Publications

Computational prediction of disease-associated non-synonymous polymorphism (nsSNP) has provided a significant platform to filter out the pathological mutations from large pool of SNP datasets at a very low cost input. Several methodologies and complementary protocols have been previously implemented and has provided significant prediction results. Although the previously implicated prediction methods were capable of investigating the most likely deleterious nsSNPs, but due to the lack of genotype-phenotype association analysis, the prediction results lacked in accuracy level. In this work we implemented the computational compilation of protein conformational changes as well as the probable disease-associated phenotypic outcomes. Our result suggested E403K mutation in mitotic centromere-associated kinesin protein as highly damaging and showed strong concordance to the previously observed colorectal cancer mutations aggregation tendency and energy value changes. Moreover, the molecular dynamics simulation results showed major loss in conformation and stability of mutant N-terminal kinesin-like domain structure. The result obtained in this study will provide future prospect of computational approaches in determining the SNPs that may affect the native conformation of protein structure and lead to cancer-associated disorders.

Prognostat is an interactive Web-based prognostic tool for estimating hospice patient survival based on a patient's Palliative Performance Scale (PPS) score, age, gender, and cancer status. The tool was developed using data from 5,893 palliative care patients, which was collected at the Victoria Hospice in Victoria, British Columbia, Canada, beginning in 1994. This study externally validates Prognostat with a retrospective cohort of 590 hospice patients at LifePath Hospice and Palliative Care in Florida, USA. The criteria used to evaluate the prognostic performance were the Brier score, area under the receiver operating curve, discrimination slope, and Hosmer-Lemeshow goodness-of-fit test. Though the Kaplan-Meier curves show each PPS level to be distinct and significantly different, the findings reveal low agreement between observed survival in our cohort of patients and survival predicted by the prognostic tool. Before developing a new prognostic model, researchers are encouraged to update survival estimates obtained using Prognostat with the information from their cohort of patients. If it is to be useful to patients and clinicians, Prognostat needs to explicitly report patient risk scores and estimates of baseline survival.

Trial sequential analysis (TSA) has been proposed as a method to assess the risk of random error in cumulative meta-analysis (MA), which increases due to repeated significance testing. The aim of TSA is to assist researchers from wrongly concluding treatment differences in the absence of a benefit (i.e. true versus false positive). Similar to monitoring boundaries applied in individual randomized controlled trials, recent literature has advocated the use of TSA for assessing the conclusiveness of results from MAs to determine the requirement for future studies in case of true positive results. While this may be desirable, we present empirical evidence from a recent systematic review to demonstrate that the use of TSA may lead to a premature declaration of statistically significant treatment difference, when further accumulated evidence suggested otherwise. Using all apparently conclusive MAs in multiple-myeloma, we empirically studied under what thresholds for the risk ratio reduction and power a true positive result becomes false positive. We recommend that the conclusion of significant treatment differences in cumulative MA should be weighed against acceptable thresholds regarding the type I error, power and apriori specified clinically meaningful treatment difference.

Genetic evolution corresponds to various biochemical changes that are vital development of new functional traits. Phylogenetic analysis has provided an important insight into the genetic closeness among species and their evolutionary relationships. Centromere-associated protein-E (CENP-E) protein is vital for maintaining cell cycle and checkpoint signal mechanisms are vital for recruitment process of other essential kinetochore proteins. In this study we have focussed on the evolution driven structural changes in CENP-E motor domain among primate lineage. Through molecular dynamics simulation and computational chemistry approaches we examined the changes in ATP binding affinity and conformational deviations in human CENP-E motor domain as compared to the other primates. Root mean square deviation (RMSD), Root mean square fluctuation (RMSF), Radius of gyration (Rg) and principle component analysis (PCA) results together suggested a gain in stability level as we move from tarsier towards human. This study provides a significant insight into how the cell cycle proteins and their corresponding biochemical activities are evolving and illustrates the potency of a theoretical approach for assessing, in a single study, the structural, functional, and dynamical aspects of protein evolution.

BACKGROUND: AKT1 (v-akt murine thymoma viral oncogene homologue 1) kinase is one of the most frequently activated proliferated and survival pathway of cancer. Recently it has been shown that E17K mutation in the Pleckstrin Homology (PH) domain of AKT1 protein leads to cancer by amplifying the phosphorylation and membrane localization of protein. The mutant has shown resistance to AKT1/2 inhibitor VIII drug molecule. In this study we have demonstrated the detailed structural and molecular consequences associated with the activity regulation of mutant protein.

METHODS: The docking score exhibited significant loss in the interaction affinity to AKT1/2 inhibitor VIII drug molecule. Furthermore, the molecular dynamics simulation studies presented an evidence of rapid conformational drift observed in mutant structure.

RESULTS: There was no stability loss in mutant as compared to native structure and the major cation-π interactions were also shown to be retained. Moreover, the active residues involved in membrane localization of protein exhibited significant rise in NHbonds formation in mutant. The rise in NHbond formation in active residues accounts for the 4-fold increase in the membrane localization potential of protein.

CONCLUSION: The overall result suggested that, although the mutation did not induce any stability loss in structure, the associated pathological consequences might have occurred due to the rapid conformational drifts observed in the mutant AKT1 PH domain.

GENERAL SIGNIFICANCE: The methodology implemented and the results obtained in this work will facilitate in determining the core molecular mechanisms of cancer-associated mutations and in designing their potential drug inhibitors.

BACKGROUND: Limited data have been reported describing the outcome and prognosis of patients with MDS in whom treatment with azanucleosides has failed. We report our single-institutional experience of patients with higher-risk MDS in whom therapy with azacitidine has failed.

PATIENTS AND METHODS: This was a retrospective study of MDS patients treated at the Moffitt Cancer Center in whom azacitidine treatment regimens had failed. Patients were identified through the Moffitt database, and clinical data were extracted. Azacitidine failure was defined as failure to achieve hematologic improvement or better after at least 4 cycles of therapy, loss of response, or disease progression during therapy. The objectives were to characterize response to salvage therapies after azacitidine failure and to estimate the overall survival. All responses were defined according to the International Working Group 2006 criteria, and survival was estimated using the Kaplan-Meier method.

RESULTS: A total of 59 patients in whom azacitidine treatment had failed were identified. The median age at treatment failure was 68 years, and most were Caucasian male patients. Thirteen patients received intensive chemotherapy with an overall response rate of 31%. Six patients were treated with decitabine, and none responded. Median overall survival of the entire cohort after azacitidine failure was 5.8 months (95% confidence interval, 1.3-10.3 months), with an estimated 12-month survival of 17%.

CONCLUSION: Patients with higher-risk MDS in whom azacitidine treatment has failed have a poor prognosis and low probability of response to salvage treatments. The standard of care after azanucleoside failure should be enrollment in clinical trials.

Ras-related C3 botulinum toxin substrate 1 (RAC1) is a plasma membrane-associated small GTPase which cycles between the active GTP-bound and inactive GDP-bound states. There is wide range of evidences indicating its active participation in inducing cancer-associated phenotypes. RAC1 F28L mutation (RAC(F28L)) is a fast recycling mutation which has been implicated in several cancer associated cases. In this work we have performed molecular docking and molecular dynamics simulation ( 0.3 μs) to investigate the conformational changes occurring in the mutant protein. The RMSD, RMSF and NHbonds results strongly suggested that the loss of native conformation in the Switch I region in RAC1 mutant protein could be the reason behind its oncogenic transformation. The overall results suggested that the mutant protein attained compact conformation as compared to the native. The major impact of mutation was observed in the Switch I region which might be the crucial reason behind the loss of interaction between the guanine ring and F28 residue.

AIM: To compare the overall survival (OS) and progression-free survival (PFS) with associated adverse events (AE) in patients with unresectable hepatocellular carcinoma (HCC) treated with transarterial chemoembolization (TACE) + sorafenib vs TACE alone.

METHODS: In this retrospective cohort study we collected data on all consecutive patients with a diagnosis of unresectable HCC between 2007 and 2011 who had been treated with TACE + sorafenib or TACE alone. We hypothesized that the combination therapy is superior to TACE alone in improving the survival in these patients. Data extracted included patient's demographics, etiology of liver disease, histology of HCC, stage of liver disease with respect to model of end stage liver disease score and Child-Turcotte-Pugh (CTP) classification and Barcelona Clinic Liver Cancer (BCLC) staging for HCC. Computed tomography scan findings, alpha fetoprotein levels, number of treatments and related AE were also recorded and analyzed.

RESULTS: Of the 43 patients who met inclusion criteria, 13 were treated with TACE + sorafenib and 30 with TACE alone. There was no significant difference in median survival: 20.6 mo (95%CI: 13.4-38.4) for the TACE + sorafenib and 18.3 mo (95%CI: 11.8-32.9) for the TACE alone (P = 0.72). There were also no statistically significant differences between groups in OS (HR = 0.82, 95%CI: 0.38-1.77; P = 0.61), PFS (HR = 0.93, 95%CI: 0.45-1.89; P = 0.83), and treatment-related toxicities (P = 0.554). CTP classification and BCLC staging for HCC were statistically significant (P = 0.001, P = 0.04 respectively) in predicting the survival in patients with HCC. The common AE observed were abdominal pain, nausea, vomiting and mild elevation of liver enzymes.

CONCLUSION: Combination therapy with TACE + sorafenib is safe and equally effective as TACE alone in patients with unresectable HCC. CTP classification and BCLC staging were the significant predictors of survival. Future trials with large number of patients are needed to further validate this observation.

Determining the deleterious non-synonymous single nucleotide polymorphisms (nsSNPs), that might be involved in inducing disease-associated phenomena, is now among the most important field of computational genomic research. The rapid evolution in sequencing technologies has now outranged the limit of available sequence databases and has out-fledged the amount of SNP data that are yet to be characterized. In this article we have performed a comprehensive analysis of deleterious nsSNPs in MyH7 gene associated with cardiomyopathy cases using a set of computational platforms. We implemented a set of computational SNP analysis platforms along with the Bayesian calculations in order to filter the most likely mutation that might be associated with cardiomyopathy associated disorders. The Bayesian calculation depicted 27 fold rises in the likelihood score for causing cardiomyopathy disorder when MyH7 gene mutations were compiled. Furthermore, we reported E466Q mutation in MyH7 motor domain that showed increase in the amyloid propensity of protein, as well as a significant level of pathogenicity was also observed. The prediction roadmap followed in this article has showed a notable range of accuracy and can be used for determining cardiomyopathy associated nsSNPs for other candidate genes.

BACKGROUND: Aurora kinases belong to the highly conserved kinase family and play a vital role in cell cycle regulation. The structure and function of these kinases are inter-related and sometimes they also act as substitutes in case of knockdown of other aurora kinases.

METHOD: In this work we carried out the evolutionary reconstruction and population genetic studies of aurora kinase proteins. Substitution saturation test, CAI (Codon adaptation index), gene expression and RSCU (Relative synonymous codon usage) values were computed for all the three aurora kinases. Linear regression method was used to check the dependency of gene expression on their CAI values.

RESULTS: The results suggested that aurora-B and aurora-C has shown convergence in their evolutionary pathway. Moreover, the aurora-A I57V mutation showed high penetrance in human population and exist at very high frequency (84.4%) when compared to the native residue (15.6%). The mutation showed notable range of functional gain and seemed to be promising for the evolution of aurora-A function. Mutant allele might also become a challenging prospect for understanding the pattern of evolution followed by cell cycle kinases.

CONCLUSION: The overall result suggested that the aurora-A is currently under the evolutionary transition and to determine the functional significance of the mutation further investigation are required.