TP63-TRIM29 axis regulates enhancer methylation and chromosomal instability in prostate cancer.

BACKGROUND: Prostate adenocarcinoma (PRAD) is the second leading cause of cancer-related deaths in men. High variability in DNA methylation and a high rate of large genomic rearrangements are often observed in PRAD. RESULTS: To investigate the reasons for such high variance, we integrated DNA methylation, RNA-seq, and copy number alterations datasets from The Cancer Genome Atlas (TCGA), focusing on PRAD, and employed weighted gene co-expression network analysis (WGCNA). Our results show that only single cluster of co-expressed genes is associated with genomic and epigenomic instability. Within this cluster, TP63 and TRIM29 are key transcription regulators and are downregulated in PRAD. We discovered that TP63 regulates the level of enhancer methylation in prostate basal epithelial cells. TRIM29 forms a complex with TP63 and together regulates the expression of genes specific to the prostate basal epithelium. In addition, TRIM29 binds DNA repair proteins and prevents the formation of the TMPRSS2:ERG gene fusion typically observed in PRAD. CONCLUSION: Our study demonstrates that TRIM29 and TP63 are important regulators in maintaining the identity of the basal epithelium under physiological conditions. Furthermore, we uncover the role of TRIM29 in PRAD development.

BNIP3 as a Regulator of Cisplatin-Induced Apoptosis.

BNIP3 is a member of Bcl-2 protein family involved in regulation of various forms of cell death. However, its role in these processes remains unclear and varies depending on the type of cancer cells and environmental factors (pH, O2 level, etc.). Here, the role of BNIP3 in apoptosis regulation in lung adenocarcinoma cells was investigated. The suppressed expression of BNIP3 caused inhibition of oxygen consumption and stimulated production of the mitochondrial reactive oxygen species, suggesting the role of BNIP3 in induction of mitochondrial dysfunction and its potential involvement in regulation of cell death. Indeed, cytochrome c release in the cells with BNIP3 knockout and knockdown was higher than in the wild-type (WT) upon apoptosis stimulation by cisplatin. Moreover, suppression of BNIP3 expression led to the increase in the caspase-3 activity and, as a consequence, accumulation of the apoptotic marker - p89 fragment of poly(ADP-ribose)-polymerase (PARP) - as compared to WT cells. Analysis of the SubG1 population by flow cytometry confirmed the elevated level of apoptosis in the BNIP3 knockout cells. Pretreatment with the antioxidant Trolox did not affect cell death, indicating that it was independent on reactive oxygen species. These data show that BNIP3 is involved in maintaining normal functioning of mitochondria and, as a result, can regulate the mitochondrial pathway of cell death.

[Synthesis and properties of a symmetric dimeric bisbenzimidazole, a DNA-specific ligand].

Dimeric bisbenzimidazole DB(5) fluorescing in the blue spectral area (lambda(em) 476 nm) within the DNA complex was synthesized. DB(5) is bound by a double-strand DNA and can differentially stain human and plant (flax) chromosomes. According to preliminary data, it provides considerably more intensely contrasting chromosome staining than DAPI and Hoechst 33258 dyes. It was also found that DB(5) is an in vitro inhibitor of HIV-1 integrase in the reaction of 3'-processing. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2008, vol. 34, no. 2; see also http://www.maik.ru.

[HIV-1 integrase inhibition by modified oligonucleotides: optimization of the inhibitor structure].

Integration of human immunodeficiency virus type 1 DNA into the infected cell genome is one of the key steps of the viral replication cycle. Therefore viral enzyme integrase, which realizes the integration, is of interest as a target for new antiviral drugs. Conjugates of 11-mer single stranded oligonucleotides with hydrophobic molecules are shown to be efficient integrase inhibitors since they induce dissociation of the integrase-viral DNA complex. The effect of the oligonucleotide length and structure as well as the structure of hydrophobic molecules on the conjugate inhibitory activity has been studied. Conjugates with eosin and oleic acid are shown to be the most active. Conjugates of these molecules with 2'-O-methyl-oligonucleotide inhibit integrase at 50-100 nM and have no influence on a number of other DNA-binding enzymes.

[Computer search for novel HIV-1 integrase inhibitors].

HIV-1 integrase is the third enzyme essential for viral replication. It represents an attractive target for new anti-HIV drugs. Diketo acids represent the most prospective class of integrase inhibitors; one of them (S1360) is currently under clinical trials. We prepared the training set containing 90 diketoacid derivatives and performed re-training of computer program PASS. Average accuracy of prediction in LOO cross-validation for HIV-1 integrase inhibitors was shown to be 99%. We selected eight new potential HIV-1 integrase inhibitors among about the 700,000 substances from the databases of commercially available chemicals; anti-integrase activity was found experimentally in two selected compounds.