Biology subjects
Publications and source records attributed to Zatsepin, T..
Nucleic acid aptamers are artificial recognition elements with high potential in biotechnology. Approaches for aptamer affinity optimization and activity regulation are required for aptamer-based nanodevices. Here thrombin aptamer affinity was increased by a single nucleotide modification with 7,8-dihydro-8-oxo-1,N6-ethenoadenine. Whereas a double modification makes the aptamer activity Ag+-dependent.
AbstractThe oncoprotein Gankyrin/PSMD10 is upregulated in various cancers, including glioblastoma multiforme (GBM), the most difficult tumor to treat. The heterogeneity of this type of tumor requires a multi-targeted approach to overcome radio- and chemoresistance. Here we aim to investigate the effects of Gankyrin inhibition on glioma cell proliferation and its impact on sensitivity to chemotherapy both in vitro and in vivo. We have employed the RNA interference approach as a valuable tool to downregulate the expression of target genes. Small interfering RNA (siRNA) were formulated into lipid nanoparticles (LNP) to facilitate delivery and overcome challenges, including RNase activity. We demonstrate that knockdown of Gankyrin promotes cell growth arrest of murine (GL261, CT-2[A]) and human (U87, GBM23, GBM24) glioma cells and induces the generation of reactive oxygen species and apoptosis. Importantly, Gankyrin inhibition enhances the therapeutic effect of temozolomide in murine glioma cell lines and decreases the IC50 of doxorubicin and cisplatin for U87 and GL261 cells. The therapeutic potential of Gankyrin inhibition was shown in patient-derived glioblastoma stem cells, which are responsible for tumor initiation and resistance to therapy. We showed that downregulation of Gankyrin led to decreased cell proliferation in vitro and improved survival in xenograft glioma model mice. Our results suggest that harnessing siRNA against Gankyrin may serve as a novel therapeutic strategy for glioblastoma therapy in a multi-drug approach and address challenges in current treatment by sensitizing glioma cells to chemotherapy. HighlightsO_LIsiRNA-mediated knockdown of Gankyrin reduced cell proliferation of murine and human glioma cells, induced ROS generation and promoted apoptosis. C_LIO_LIInhibition of Gankyrin increased the therapeutic effect of temozolomide in resistant CT- 2A glioma cells and decreased the IC50 concentration of doxorubicin and cisplatin in U87 and GL261 cells. C_LIO_LIDownregulation of Gankyrin inhibited the growth of patient-derived glioma stem cells and increased the survival of NOD/SCID xenograft glioma model mice C_LI
Non-canonical nucleic acid structures possess an ability to interact selectively with proteins, thereby exerting influence over various intracellular processes. Numerous studies indicate that genomic G-quadruplexes and i-motifs are involved in the regulation of transcription. These structures are formed temporarily during the unwinding of the DNA double helix; and their direct determination is a rather difficult task. In addition, i-motif folding is pH-dependent, with most i-motifs having low stability at neutral pH. However, some genomic i-motifs with long cytosine repeats were shown to be stable at pH 7.3, suggesting their functionality within the nucleus. Here we studied pH-dependent behavior of a model i-motif with flanking sequences that forms a duplex motif. Kinetic studies on bimodular structures with cytosine residues replaced with an environment-sensitive fluorescent label reveal the stabilization of the i-motif structure near the i-motif-duplex junction. These results highlight the importance of the natural environment of i-motifs for the correct assessment of their stability.
During liver development, bipotential progenitor cells called hepatoblasts differentiate into hepatocytes or cholangiocytes. Hepatocyte differentiation is uniquely associated with multi-axial polarity, enabling the anisotropic expansion of apical lumina between adjacent cells and formation of a three-dimensional network of bile canaliculi (BC). Cholangiocytes, the cells forming the bile ducts, exhibit the vectorial polarity common to epithelial cells. Whether and how cell polarization feeds back on the gene regulatory pathways governing hepatoblast differentiation is unknown. Here, we used primary hepatoblasts to investigate the contribution of anisotropic apical expansion to hepatocyte differentiation. Silencing of the small GTPase Rab35 caused isotropic lumen expansion and formation of multicellular cysts with the vectorial polarity of cholangiocytes. Gene expression profiling revealed that these cells express reduced levels of hepatocyte markers and upregulate genes associated with cholangiocyte identity. Time-course RNA sequencing demonstrated that loss of lumen anisotropy precedes these transcriptional changes. Independent alterations in apical lumen morphology induced either by modulation of the subapical actomyosin cortex or increased intraluminal pressure caused similar transcriptional changes. These findings suggest that cell polarity and lumen morphogenesis feedback to hepatoblast-to-hepatocyte differentiation. Summary statementDifferentiation of liver progenitors to functional hepatocytes requires anisotropic elongation of their nascent apical surfaces into tubular bile canaliculi.
AO_SCPLOWBSTRACTC_SCPLOWProstate adenocarcinoma (PRAD) is the second most common cause of cancer-related deaths in men. PRAD is often characterized by DNA methylation variability and a high rate of large genomic rearrangements. To elucidate the reasons behind such high variance, we used weighted gene co-expression network analysis for integration RNA-seq, DNA methylation and copy number alterations data from The Cancer Genome Atlas PRAD. Our results show that only a single cluster of co-expressed genes is associated with genomic and epigenomic instability. Within this cluster, TP63 and TRIM29 are key transcription regulators. We revealed that TP63 regulates the level of enhancer methylation in prostate basal epithelium cells. TRIM29 forms a complex with TP63 and together regulate the expression of genes specific to the prostate basal epithelium. Moreover, TRIM29 binds DNA repair proteins and prevents formation of the TMPRSS2:ERG gene fusion typically observed in PRAD. Therefore, the study shows that TRIM29 and TP63 are important regulators maintaining the identity of the basal epithelium under physiological conditions. Finally, we uncover the role of TRIM29 in PRAD development.
Lumen morphogenesis is key to the function of organs and results from the integration of molecular pathways and mechanical forces1-3. The mechanisms governing anisotropic lumen expansion remain elusive4-6. In contrast to epithelial cells which have simple apico-basal polarity and form tubes, hepatocytes are multi-polar and form narrow lumina that grow anisotropically between adjacent cells, collectively generating a complex 3D network of bile canaliculi (BC)7,8. Here, we studied lumen elongation and BC morphogenesis in differentiating primary mouse hepatoblasts in vitro. Remarkably, we discovered a pattern of specific extensions of the apical membrane traversing the lumen between adjacent hepatocytes and sealed by tight junctions, reminiscent of the bulkheads of boats. These structures were also present in the developing liver. A targeted screen revealed that silencing of Rab35 caused loss of the bulkheads, conversion of hepatocyte into simple epithelial polarity and formation of spherical lumina in vitro. Strikingly, we could re-engineer hepatocyte polarity and tissue morphogenesis in vivo in the embryonic liver, converting BC into simple epithelial tubes. Our results suggest that the apical bulkheads of hepatocytes are cell-intrinsic anisotropic mechanical elements that ensure stability of the elongating lumen between two cells, thus determining the structure of BC during liver tissue morphogenesis.