AACR Centennial Conference: Translational Cancer Medicine-- Nov 4-8, 2007; Singapore

PL02-05 

All cancers are due to abnormalities in DNA. The availability of the human genome sequence has led to the proposal that resequencing of cancer genomes will reveal the full complement of somatic mutations and hence all the cancer genes. To explore the nature of the information that will be derived from cancer genome sequencing we have sequenced the coding exons of the family of 518 protein kinases, ~1.3Mb DNA per cancer sample, in 210 cancers of diverse histological types. Despite the screen being directed toward the coding regions of a gene family that has previously been strongly implicated in oncogenesis, the results indicate that the majority of somatic mutations detected are “passengers”. There is considerable variation in the number and pattern of these mutations between individual cancers, indicating substantial diversity of processes of molecular evolution between cancers. The imprints of exogenous mutagenic exposures, mutagenic treatment regimes and DNA repair defects can all be seen in the distinctive mutational signatures of individual cancers. This systematic mutation screen and others have previously yielded a number of cancer genes that are frequently mutated in one or more cancer types and which are now anticancer drug targets (for example BRAF , PIK3CA , and EGFR ). However, detailed analyses of the data from our screen additionally suggest that there exist a large number of additional “driver” mutations which are distributed across a substantial number of genes. It therefore appears that cells may be able to utilise mutations in a large repertoire of potential cancer genes to acquire the neoplastic phenotype. However, many of these genes are employed only infrequently. These findings may have implications for future anticancer drug development.

Patterns of Somatic Mutation in Human Cancer Genomes

基礎講座 電気泳動(Electrophoresis)

Context: The interpretation of novel missense variants is a challenge with increasing numbers of such variants being identified and a responsibility to report the findings in the context of all available scientific evidence. Various in silico bioinformatic tools have been developed that predict the likely pathogenicity of missense variants; however, their utility within the diagnostic setting requires further investigation. Aim: The aim of our study was to test the predictive value of two of these tools, sorting intolerant from tolerant (SIFT) and polymorphism phenotyping (PolyPhen), in a set of 141 missense variants (131 pathogenic, 8 benign) identified in the ABCC8, GCK, and KCNJ11 genes. Methods: Sixty-six of the mutations caused a gain of protein function, while 67 were loss-of-function mutations. The evolutionary conservation at each residue was also investigated using multiple sequence alignments from the UCSC genome browser. Results: The sensitivity of SIFT and PolyPhen was reasonably high (69% and...

Using SIFT and PolyPhen to Predict Loss-of-Function and Gain-of-Function Mutations

Lamin A/C proteins are the major components of a thin proteinaceous filamentous meshwork, the lamina, that underlies the inner nuclear membrane. A few specific mutations in the lamin A/C gene cause a disease with remarkably different clinical features: FPLD, or familial partial lipodystrophy (Dunnigan-type), which mainly affects adipose tissue. Lamin A/C mutant R482W is the key variant that causes FPLD. Biomolecular interaction and molecular dynamics (MD) simulation analysis were performed to understand dynamic behavior of native and mutant structures at atomic level. Mutant lamin A/C (R482W) showed more interaction with its biological partners due to its expansion of interaction surface and flexible nature of binding residues than native lamin A/C. MD simulation clearly indicates that the flexibility of interacting residues of mutant are mainly due to less involvement in formation of inter and intramolecular hydrogen bonds. Our analysis of native and Mutant lamin A/C clearly shows that the structural and functional consequences of the mutation R482W causes FPLD. Because of the pivotal role of lamin A/C in maintaining dynamics of nuclear function, these differences likely contribute to or represent novel mechanisms in laminopathy development.

https://link.springer.com/content/pdf/10.1007%2Fs00726-011-1108-7.pdf

In silico investigation of molecular mechanism of laminopathy caused by a point mutation (R482W) in lamin A/C protein

Tuberculosis continues to be a global health threat. Pyrazinamide (PZA) is an important first-line drug in multidrug-resistant tuberculosis treatment. The emergence of strains resistant to PZA represents an important public health problem, as both first- and second-line treatment regimens include PZA. It becomes toxic to Mycobacterium tuberculosis when converted to pyrazinoic acid by the bacterial pyrazinamidase (PncA) enzyme. Resistance to PZA is caused mainly by the loss of enzyme activity by mutation, the mechanism of resistance is not completely understood. In our studies, we analysed three mutations (D8G, S104R and C138Y) of PncA which are involved in resistance towards PZA. Binding pocket analysis solvent accessibility analysis, molecular docking and interaction analysis were performed to understand the interaction behaviour of mutant enzymes with PZA. Molecular dynamics simulations were conducted to understand the three-dimensional (3D) conformational behaviour of native and mutants PncA. Our analy...

Drug resistance mechanism of PncA in Mycobacterium tuberculosis

Mucin 1 is an important tumor marker, and is notable for the autoproteolytic event, a signature of all SEA domain containing proteins. However the isoform MUC1/Y, unlike its closest counterpart MUC1/X, is noted to be uncleavable despite the presence of the catalytic site. Sequence analysis has revealed the presence of an 18 residue segment spliced out from MUC1/Y marking the only difference between uncleavable MUC1/Y and cleavable MUC1/X mucin 1 isoforms. This work was aimed at studying in silico, the structural and functional significance of the 18 residue insert in the cleavage process. 3-Dimensional structures of the isoforms were predicted using a combined threading and ab initio method followed by mutation and normal mode analysis. Our analysis revealed both isoforms to poses an intact SEA domain, nevertheless, an altered functional scaffold around the cleavage site was noted between the structures. Mutation analysis by alanine substitutions at the insert region revealed Ile67 to be more destabilizing, resulting in increased fluctuation of the neighboring residues. Predicted molecular motions of the protein indicated localized motions in the native, rather than the mutated model. Intramolecular interactions between the native and I67A structures showed wide variations in main chain and side chain interactions. Furthermore, the findings suggest the neighboring residues, in particular Ile67 contribute more to the structural and functional properties of the protein and hence it is predicted to be one of the crucial residues for the cleavable nature of MUC1/X.

Computational investigation of theoretical models of cleavable and uncleavable mucin 1 isoforms.

Investigations on the interactions of scorpion neurotoxins with the predicted structure of D1 dopamine receptor by protein-protein docking method. A bioinformatics approach.

The role of aromatase inhibitors in the management of breast cancer has been promising as it markedly suppresses the production of estrogen. The inhibitors are very effective in postmenopausal women and used as the first line therapy for hormone-sensitive breast cancer. The third generation aromatase inhibitors are advantageous having less adverse effects over other breast cancer drugs and they have also been recommended for use with tamoxifen. The aromatase inhibitors are of two different types; steroidal and nonsteroidal. Steroidal inhibitors are mechanism based inhibitors that mimic the natural substrate and are irreversible, unlike non-steroidal inhibitors which are reversible. The expression of aromatase occurs in a tissue specific manner with a set of distinctive transcription factors. In tumorous breast tissue, the enzyme is overexpressed with the help of four different promoters, I.3, I.4, I.7 and II and in turn, the growth stimulatory effects of estrogen is magnified to very high levels. Aromatase inhibition approach is considered as the gold standard and hence, in this review, we have discussed different types of aromatase inhibitors with their advantages.

C. Sudandiradoss

Papers

Computational investigation of theoretical models of cleavable and uncleavable mucin 1 isoforms.

Investigations on the interactions of scorpion neurotoxins with the predicted structure of D1 dopamine receptor by protein-protein docking method. A bioinformatics approach.

Aromatase inhibitors - types and advantages

Analysis of binding residues between scorpion neurotoxins and D2 dopamine receptor: A computational docking study

Computational exploration of polymorphisms in 5-Hydoxytryptamine 5-HT1A and 5-HT2A receptors associated with psychiatric disease