XPG polymorphisms are associated with prognosis of advanced non-small cell lung cancer treated with platinum-based doublet chemotherapy.

We conducted a cohort study to investigate whether 3 potential single nucleotide polymorphisms (SNPs) in the xeroderma pigmentosum complementation group G (XPG) gene could predict the survival of advanced non-small cell lung cancer (NSCLC) patients treated with platinum-based doublet chemotherapy. We enrolled 262 patients with histologically confirmed NSCLC between November 2007 and December 2008 in this study. The 3 SNPs (rs2296147T>C, rs2094258C>T, and rs873601G>A) were genotyped using polymerase chain reaction-restriction fragment length polymorphism analysis. Older age, Eastern Cooperative Oncology Group performance score ≥2 and higher disease stage were associated with shorter survival. In the Cox proportional hazard model, patients carrying the rs2296147 TT genotype and the T allele had a significantly reduced risk of developing progressive disease or dying from NSCLC. The HRs (95%CI) were 0.31 (0.13-0.73) and 0.44 (0.24-0.83) for progression-free survival and 0.32 (0.14-0.71) and 0.54 (0.32-0.98) for overall survival, respectively. Moreover, advanced NSCLC patients carrying the rs2094258 GG and the G allele had a significantly decreased risk of developing progressive disease. The HRs (95%CI) for the rs2094258 GG genotype and the G allele were 0.35 (0.16-0.80) and 0.45 (0.23-0.86) for overall survival, respectively. We suggest that the rs2296147 and rs2094258 polymorphisms could be used as surrogate markers, leading to individualization of NSCLC treatment strategies.

Genetic features of a translation initiation system composed of IRES element, nucleotide context surrounding the initiation codon, and translation initiation region of classical swine fever virus RNA.

Nucleotide and codon usage are typically examined to investigate viral evolution. In this study, we analyzed the genetic information of 46 strains of classical swine fever virus (CSFV) RNA, nucleotide usage in the internal ribosome entry site (IRES), the nucleotide context surrounding the initiation codon, and synonymous codon usage in the translation initiation region. Phylogenetic analysis of the IRES element indicated that the genetic diversity of this element is generally similar to the phylogenetic clusters of CSFV genotypes. Nucleotides surrounding the initiation codon of CSFV RNA were generally more stable (ACAUGGCACAUGGAGUUG) compared to the internal AUG in the CSFV coding sequence. The second codon position after the initiation codon was generally selected to be GAG, which has lower tRNA abundance in pigs than its synonymous member (GAA). Regarding the synonymous codon usage bias in the CSFV translation initiation region, some codons showing low tRNA abundance in pigs are more frequently located in the translation initiation region than in the open reading frame of CSFV. Although CSFV, similarly to other RNA viruses, has a high mutation rate in nature, the regulatory features of nucleotide and synonymous codon usage of the IRES element, the nucleotide context surrounding the initiation codon and the translation initiation region in CSFV RNA have been 'branded' in the system of translation initiation to accommodate gene expression mediated by the cap-independent translation mechanism.

Characteristics of synonymous codon usage bias in the beginning region of West Nile virus.

Adaptation in the overall codon usage pattern of West Nile virus (WNV) to that of two hosts was estimated based on the synonymous codon usage value (RSCU). Synonymous codon usage biases for the beginning coding sequence of this virus were also analyzed by calculating the usage fluctuation for each synonymous codon along the target region (the first 270 codon sites of the whole coding sequence of WNV). Adaptation of WNV to Anopheles gambiae regarding the overall codon usage revealed a mixture of synonymous codon usage patterns between this virus and its vector. Regarding the adaptation of WNV to its dead-end host and codon usage, although a mixture of overall codon usage patterns exists, the number of codons with reversed tendency codon usage is lower than that between the virus and its vector. In addition, some codons with low RSCU values for this virus are highly selected in the beginning translation region of WNV, while codons with low RSCU values in this region tend to pair with tRNAs present in low abundance in the host, suggesting that highly selected codons in a specific region in the beginning region of WNV are, to some degree, influenced by the corresponding low tRNA abundance of hosts to regulate the translation speed of the WNV polyprotein.

Association of miR-149C>T and miR-499A>G polymorphisms with the risk of hepatocellular carcinoma in the Chinese population.

We investigate the potential association of miR-149C>T and miR-499A>G polymorphisms and the risk of hepatocellular carcinoma (HCC). A matched case-control study of 152 cases and 304 controls were conducted. The miR-149C>T and miR-499A>G genotypes were analyzed using duplex polymerase chain reaction with restricted fragment length polymorphism. HCC patients were more likely to be smokers and drinkers, have hepatitis B and C virus infections, and a family history of cancer. The miR-149 CC genotype was associated with a reduced risk of HCC, while the miR-499 GG genotype was associated with an increased risk of HCC. However, we did not find that the miR-149 CC and miR-499 GG genotypes were associated with risk of HCC, and no interaction was found between miR-149C>T and miR-499A>G polymorphisms and hepatitis B virus infection. In conclusion, the miRNA-149C>T and miR-499A>G polymorphisms were found to play an important role for HCC risk in China. This finding could be useful in identifying people at high risk for the disease for early intervention.

Mapping codon usage in sequence regions flanking cleavage positions in the hepatitis A virus polyprotein.

To analyze the synonymous codon usage patterns of sequence regions flanking cleavage sites in the hepatitis A virus (HAV) polyprotein, the codon usage bias at codon positions and the synonymous codon usage in the target contexts of 30 virus strains were estimated by two simple methods that were based on the values for relative synonymous codon usage. In addition, the pattern of synonymous codon usage was compared between the genomic sequences in HAV and those of its human host. Our results indicated that HAV adopts a combination of coincidence and antagonism with the synonymous codon usage in humans. This characteristic may help HAV to efficiently use the translational machinery in its human host. We also observed that codon usage exhibited a strong bias in some specific positions in these contexts, and that the underrepresented synonymous codons, CUA for Leu, ACG for Thr, GUA for Val, and UCG for Ser, are preferentially used in these positions. These underrepresented synonymous codons likely play roles in regulating the rate of protein translation and influencing the secondary structure of the sequence regions flanking the cleavage sites.