Proximity Utilizing Biotinylation of Nuclear Proteins in vivo

Introduction. The human genome consists of roughly 30,000 genes coding for over 500,000 different proteins, of which more than 10,000 proteins can be produced by the cell at any given time (the cellular “proteome”). It has been estimated that over 80% of proteins do not operate alone, but in complexes. These protein-protein interactions (PPI) are regulated by several mechanisms. For example, post-translational modifications (methylation, acetylation, phosphorylation, or ubiquitination) or metal-binding can lead to conformational changes that alter the affinity and kinetic parameters of the interaction. Many PPIs are part of larger cellular networks of interactions or interactomes. Indeed, these interactions are at the core of the entire interactomics system of any living cell, and so, aberrant PPIs are the basis of multiple diseases, such as neurodegenerative diseases and cancer. The objective of this study was to develop a method of monitoring protein-protein interactions and proximity dependence in vivo.Methods. The biotin ligase BirA was fused to the protein of interest, and the Biotin Acceptor Peptide (BAP) was fused to an interacting partner to make the detection of its biotinylation possible by western blot or mass spectrometry.Results. Using several experimental systems (BirA.A + BAP.B), we showed that the biotinylation is interaction/proximity dependent. Here, A and B are the next nuclear proteins used in the experiments – 3 paralogues of heterochromatin protein HP1a (CBX5), HP1b (CBX1), HP1g (CBX3), wild type and transcription mutant factor Kap1, translesion DNA polymerase PolH and E3, ubiquitin ligase RAD18, Proliferative Cell Nuclear Antigen (PCNA), ubiquitin Ub, SUMO-2/3, different types and isoforms of histones H2A, H2Az, H3.1, H3.3, CenpA, H2A.BBD, and macroH2A. The variant of this approach is termed PUB-NChIP (Proximity Utilizing Biotinylation with Native Chromatin Immuno-precipitation) and is designed to purify and study the protein composition of chromatin in proximity to the nuclear protein of interest. Using the RAD18 protein as a model, we demonstrated that the RAD18-proximal chromatin is enriched in some H4 acetylated species. Moreover, the RAD18-proximal chromatin containing a replacement histone H2Az has a different pattern of H4 acetylation.Conclusion. Progress in the last decade in cancer drug therapy has led us to the conclusion that the nucleus of eukaryotic cells is an active site for many cellular processes important to the development of cancer. These processes include changes in genetic and epigenetic landscape (e. g. methylation of DNA, modification of histones) and the expression levels of transcription factors, which regulates gene products (e.g. hypoxia-inducible factor 1? (HIF-1?) in chronic anemia, etc.) where protein-protein interactions play important role. Understanding the nature of protein-protein interactions may improve design strategies for small-molecule PPI modulators. PPI assay technologies that closely reflect physiological conditions hold the key to developing specific anti-cancer drugs.

Heparin-Conjugated Fibrin Hydrogel with Chondroinductive Growth Factors and Human Synovium-Derived Mesenchymal Stem Cells for the Treatment of Articular Cartilage Defects: Evaluation of Clinical Safety

The purpose of this study was to evaluate the safety of an injectable heparin-conjugated fibrin (HCF) hydrogel containing human synovium-derived mesenchymal stem cells (SDMSCs), TGF-β1, and BMP-4 after implantation into articular cartilage defect in patients with osteoarthritis (OA). The study included 15 OA patients with a mean age of 44.2±18.0 years. The median articular cartilage defect size was 4.9±2.0 cm. HCF hydrogel, containing SDMSCs and growth factors (TGF-β1 and BMP-4), was implanted into the cartilage defect using DUPLOJECT two-syringe device connected with the DUPLOTIP dual lumen cannula. Clinical and radiological outcomes were evaluated with VAS, WOMAC, KOOS, and MOCART. The clinical study results showed that implantation of HCF hydrogel with autologous SDMSCs, TGF-β1, and BMP-4 appeared to be safe and did not show severe adverse events in OA patients. The assessment of clinical outcomes after 6 months showed improvement in VAS, WOMAC, and KOOS scores in all patients. The MOCART evaluation demonstrated an enhancement of cartilage tissue repair in 73.3% of OA patients at 6 months after surgery. Thus, implantation of HCF hydrogel with SDMSCs, TGF-β1, and BMP-4 was safe and demonstrated signs of improvement in articular cartilage repair. The evaluation of the long-term safety and therapeutic efficacy of HCF hydrogel is required in a further clinical study using a larger number of OA patients

RC-4BC cells express nicotinic and muscarinic acetylcholine receptors.

Acetylcholine is one of the most important endogenous neurotransmitters in a range of organisms spanning different animal phyla. Within pituitary gland it acts as autocrine and paracrine signal. In a current study we assessed expression profile of the different subunits of nicotinic as well as muscarinic acetylcholine receptors in RC-4BC cells, which are derived from rat pituitary gland tumor. Our findings indicate that β2, δ, and M2 subunits are expressed by the cells with the lowest Ct values compared to other tested subunits. The detected Ct values were 26.6±0.16, 27.95±0.5, and 28.8±0.25 for β2, δ, and M2 subunits, respectively

Proximity Utilizing Biotinylation of Nuclear Proteins in vivo

Introduction. The human genome consists of roughly 30,000 genes coding for over 500,000 different proteins, of which more than 10,000 proteins can be produced by the cell at any given time (the cellular “proteome”). It has been estimated that over 80% of proteins do not operate alone, but in complexes. These protein-protein interactions (PPI) are regulated by several mechanisms. For example, post-translational modifications (methylation, acetylation, phosphorylation, or ubiquitination) or metal-binding can lead to conformational changes that alter the affinity and kinetic parameters of the interaction. Many PPIs are part of larger cellular networks of interactions or interactomes. Indeed, these interactions are at the core of the entire interactomics system of any living cell, and so, aberrant PPIs are the basis of multiple diseases, such as neurodegenerative diseases and cancer. The objective of this study was to develop a method of monitoring protein-protein interactions and proximity dependence in vivo. Methods. The biotin ligase BirA was fused to the protein of interest, and the Biotin Acceptor Peptide (BAP) was fused to an interacting partner to make the detection of its biotinylation possible by western blot or mass spectrometry. Results. Using several experimental systems (BirA.A + BAP.B), we showed that the biotinylation is interaction/proximity dependent. Here, A and B are the next nuclear proteins used in the experiments – 3 paralogues of heterochromatin protein HP1a (CBX5), HP1b (CBX1), HP1g (CBX3), wild type and transcription mutant factor Kap1, translesion DNA polymerase PolH and E3, ubiquitin ligase RAD18, Proliferative Cell Nuclear Antigen (PCNA), ubiquitin Ub, SUMO-2/3, different types and isoforms of histones H2A, H2Az, H3.1, H3.3, CenpA, H2A.BBD, and macroH2A. The variant of this approach is termed PUB-NChIP (Proximity Utilizing Biotinylation with Native Chromatin Immuno-precipitation) and is designed to purify and study the protein composition of chromatin in proximity to the nuclear protein of interest. Using the RAD18 protein as a model, we demonstrated that the RAD18-proximal chromatin is enriched in some H4 acetylated species. Moreover, the RAD18-proximal chromatin containing a replacement histone H2Az has a different pattern of H4 acetylation. Conclusion. Progress in the last decade in cancer drug therapy has led us to the conclusion that the nucleus of eukaryotic cells is an active site for many cellular processes important to the development of cancer. These processes include changes in genetic and epigenetic landscape (e. g. methylation of DNA, modification of histones) and the expression levels of transcription factors, which regulates gene products (e.g. hypoxia-inducible factor 1α (HIF-1α) in chronic anemia, etc.) where protein-protein interactions play important role. Understanding the nature of protein-protein interactions may improve design strategies for small-molecule PPI modulators. PPI assay technologies that closely reflect physiological conditions hold the key to developing specific anti-cancer drugs