-
Experimental & Molecular Medicine Apr 2022Alzheimer's disease (AD) is caused by synaptic and neuronal loss in the brain. One of the characteristic hallmarks of AD is senile plaques containing amyloid β-peptide... (Review)
Review
Alzheimer's disease (AD) is caused by synaptic and neuronal loss in the brain. One of the characteristic hallmarks of AD is senile plaques containing amyloid β-peptide (Aβ). Aβ is produced from amyloid precursor protein (APP) by sequential proteolytic cleavages by β-secretase and γ-secretase, and the polymerization of Aβ into amyloid plaques is thought to be a key pathogenic event in AD. Since γ-secretase mediates the final cleavage that liberates Aβ, γ-secretase has been widely studied as a potential drug target for the treatment of AD. γ-Secretase is a transmembrane protein complex containing presenilin, nicastrin, Aph-1, and Pen-2, which are sufficient for γ-secretase activity. γ-Secretase cleaves >140 substrates, including APP and Notch. Previously, γ-secretase inhibitors (GSIs) were shown to cause side effects in clinical trials due to the inhibition of Notch signaling. Therefore, more specific regulation or modulation of γ-secretase is needed. In recent years, γ-secretase modulators (GSMs) have been developed. To modulate γ-secretase and to understand its complex biology, finding the binding sites of GSIs and GSMs on γ-secretase as well as identifying transiently binding γ-secretase modulatory proteins have been of great interest. In this review, decades of findings on γ-secretase in AD are discussed.
Topics: Alzheimer Disease; Amyloid Precursor Protein Secretases; Amyloid beta-Peptides; Amyloid beta-Protein Precursor; Humans; Proteolysis; Signal Transduction
PubMed: 35396575
DOI: 10.1038/s12276-022-00754-8 -
Proceedings of the National Academy of... Nov 2022Cell-free DNA (cfDNA) fragmentation patterns contain important molecular information linked to tissues of origin. We explored the possibility of using fragmentation...
Cell-free DNA (cfDNA) fragmentation patterns contain important molecular information linked to tissues of origin. We explored the possibility of using fragmentation patterns to predict cytosine-phosphate-guanine (CpG) methylation of cfDNA, obviating the use of bisulfite treatment and associated risks of DNA degradation. This study investigated the cfDNA cleavage profile surrounding a CpG (i.e., within an 11-nucleotide [nt] window) to analyze cfDNA methylation. The cfDNA cleavage proportion across positions within the window appeared nonrandom and exhibited correlation with methylation status. The mean cleavage proportion was ∼twofold higher at the cytosine of methylated CpGs than unmethylated ones in healthy controls. In contrast, the mean cleavage proportion rapidly decreased at the 1-nt position immediately preceding methylated CpGs. Such differential cleavages resulted in a characteristic change in relative presentations of CGN and NCG motifs at 5' ends, where N represented any nucleotide. CGN/NCG motif ratios were correlated with methylation levels at tissue-specific methylated CpGs (e.g., placenta or liver) (Pearson's absolute > 0.86). cfDNA cleavage profiles were thus informative for cfDNA methylation and tissue-of-origin analyses. Using CG-containing end motifs, we achieved an area under a receiver operating characteristic curve (AUC) of 0.98 in differentiating patients with and without hepatocellular carcinoma and enhanced the positive predictive value of nasopharyngeal carcinoma screening (from 19.6 to 26.8%). Furthermore, we elucidated the feasibility of using cfDNA cleavage patterns to deduce CpG methylation at single CpG resolution using a deep learning algorithm and achieved an AUC of 0.93. FRAGmentomics-based Methylation Analysis (FRAGMA) presents many possibilities for noninvasive prenatal, cancer, and organ transplantation assessment.
Topics: Pregnancy; Female; Humans; Cell-Free Nucleic Acids; Biomarkers, Tumor; DNA Methylation; Liver Neoplasms; Epigenesis, Genetic; DNA; Cytosine; Guanine; Nucleotides; Phosphates
PubMed: 36288287
DOI: 10.1073/pnas.2209852119 -
Cell Mar 2018Human diseases are often caused by loss of somatic cells that are incapable of re-entering the cell cycle for regenerative repair. Here, we report a combination of...
Human diseases are often caused by loss of somatic cells that are incapable of re-entering the cell cycle for regenerative repair. Here, we report a combination of cell-cycle regulators that induce stable cytokinesis in adult post-mitotic cells. We screened cell-cycle regulators expressed in proliferating fetal cardiomyocytes and found that overexpression of cyclin-dependent kinase 1 (CDK1), CDK4, cyclin B1, and cyclin D1 efficiently induced cell division in post-mitotic mouse, rat, and human cardiomyocytes. Overexpression of the cell-cycle regulators was self-limiting through proteasome-mediated degradation of the protein products. In vivo lineage tracing revealed that 15%-20% of adult cardiomyocytes expressing the four factors underwent stable cell division, with significant improvement in cardiac function after acute or subacute myocardial infarction. Chemical inhibition of Tgf-β and Wee1 made CDK1 and cyclin B dispensable. These findings reveal a discrete combination of genes that can efficiently unlock the proliferative potential in cells that have terminally exited the cell cycle.
Topics: Animals; CDC2 Protein Kinase; Cell Cycle Proteins; Cell Proliferation; Cyclin B1; Cyclin D1; Cyclin-Dependent Kinase 4; Cytokinesis; Heart; Humans; Induced Pluripotent Stem Cells; Mice; Mice, Inbred C57BL; Mice, Transgenic; Myocardial Infarction; Myocytes, Cardiac; Myosin Heavy Chains; Nuclear Proteins; Protein-Tyrosine Kinases; Rats; Regeneration; Transforming Growth Factor beta
PubMed: 29502971
DOI: 10.1016/j.cell.2018.02.014 -
Annual Review of Biochemistry Jun 2019Division of amoebas, fungi, and animal cells into two daughter cells at the end of the cell cycle depends on a common set of ancient proteins, principally actin... (Review)
Review
Division of amoebas, fungi, and animal cells into two daughter cells at the end of the cell cycle depends on a common set of ancient proteins, principally actin filaments and myosin-II motors. Anillin, formins, IQGAPs, and many other proteins regulate the assembly of the actin filaments into a contractile ring positioned between the daughter nuclei by different mechanisms in fungi and animal cells. Interactions of myosin-II with actin filaments produce force to assemble and then constrict the contractile ring to form a cleavage furrow. Contractile rings disassemble as they constrict. In some cases, knowledge about the numbers of participating proteins and their biochemical mechanisms has made it possible to formulate molecularly explicit mathematical models that reproduce the observed physical events during cytokinesis by computer simulations.
Topics: Actins; Animals; Cell Cycle; Cytokinesis; Eukaryota; Humans; Models, Biological; Myosins; Signal Transduction; Spindle Apparatus; Yeasts
PubMed: 30649923
DOI: 10.1146/annurev-biochem-062917-012530 -
ChemistryOpen Aug 2020Bioorthogonal reactions including the bioorthogonal ligations and cleavages have become an active field of research in chemical biology, and they play important roles in... (Review)
Review
Bioorthogonal reactions including the bioorthogonal ligations and cleavages have become an active field of research in chemical biology, and they play important roles in chemical modification and functional regulation of biomolecules. This review summarizes the developments and applications of the representative bioorthogonal reactions including the Staudinger reactions, the metal-mediated bioorthogonal reactions, the strain-promoted cycloadditions, the inverse electron demand Diels-Alder reactions, the light-triggered bioorthogonal reactions, and the reactions of chloroquinoxalines and -dithiophenols.
Topics: Alkynes; Azides; Catalysis; Cycloaddition Reaction; Heterocyclic Compounds, 1-Ring; Light; Metals, Heavy; Phosphines; Photolysis; Quinoxalines; Sulfhydryl Compounds
PubMed: 32817809
DOI: 10.1002/open.202000128 -
The Journal of Cell Biology Apr 2018Many biological events, such as the propagation of nerve impulses, the synchronized cell cycles of early embryogenesis, and collective cell migration, must be... (Review)
Review
Many biological events, such as the propagation of nerve impulses, the synchronized cell cycles of early embryogenesis, and collective cell migration, must be coordinated with remarkable speed across very large distances. Such rapid coordination cannot be achieved by simple diffusion of molecules alone and requires specialized mechanisms. Although active transport can provide a directed and efficient way to travel across subcellular structures, it cannot account for the most rapid examples of coordination found in biology. Rather, these appear to be driven by mechanisms involving traveling waves of chemical activities that are able to propagate information rapidly across biological or physical systems. Indeed, recent advances in our ability to probe the dynamics of signaling pathways are revealing many examples of coordination of cellular and developmental processes through traveling chemical waves. Here, we will review the theoretical principles underlying such waves; highlight recent literature on their role in different contexts, ranging from chemotaxis to development; and discuss open questions and future perspectives on the study of chemical waves as an essential feature of cell and tissue physiology.
Topics: Animals; Cell Biology; Cell Cycle Checkpoints; Cell Physiological Phenomena; Chemotaxis; Cytokinesis; Developmental Biology; Diffusion; Gene Expression Regulation, Developmental; Humans; Intracellular Signaling Peptides and Proteins; Kinetics; Models, Biological; Morphogenesis; Protein Transport; Signal Transduction
PubMed: 29317529
DOI: 10.1083/jcb.201701158 -
Molecules (Basel, Switzerland) Nov 2015Deoxyribozymes or DNAzymes are single-stranded catalytic DNA molecules that are obtained by combinatorial in vitro selection methods. Initially conceived to function as... (Review)
Review
Deoxyribozymes or DNAzymes are single-stranded catalytic DNA molecules that are obtained by combinatorial in vitro selection methods. Initially conceived to function as gene silencing agents, the scope of DNAzymes has rapidly expanded into diverse fields, including biosensing, diagnostics, logic gate operations, and the development of novel synthetic and biological tools. In this review, an overview of all the different chemical reactions catalyzed by DNAzymes is given with an emphasis on RNA cleavage and the use of non-nucleosidic substrates. The use of modified nucleoside triphosphates (dN*TPs) to expand the chemical space to be explored in selection experiments and ultimately to generate DNAzymes with an expanded chemical repertoire is also highlighted.
Topics: Animals; Catalysis; DNA; DNA, Catalytic; Humans; Nucleic Acid Conformation; RNA; Substrate Specificity
PubMed: 26610449
DOI: 10.3390/molecules201119730 -
Nature Communications Aug 2020Catalytic cleavage of strong bonds including hydrogen-hydrogen, carbon-oxygen, and carbon-hydrogen bonds is a highly desired yet challenging fundamental transformation...
Catalytic cleavage of strong bonds including hydrogen-hydrogen, carbon-oxygen, and carbon-hydrogen bonds is a highly desired yet challenging fundamental transformation for the production of chemicals and fuels. Transition metal-containing catalysts are employed, although accompanied with poor selectivity in hydrotreatment. Here we report metal-free nitrogen-assembly carbons (NACs) with closely-placed graphitic nitrogen as active sites, achieving dihydrogen dissociation and subsequent transformation of oxygenates. NACs exhibit high selectivity towards alkylarenes for hydrogenolysis of aryl ethers as model bio-oxygenates without over-hydrogeneration of arenes. Activities originate from cooperating graphitic nitrogen dopants induced by the diamine precursors, as demonstrated in mechanistic and computational studies. We further show that the NAC catalyst is versatile for dehydrogenation of ethylbenzene and tetrahydroquinoline as well as for hydrogenation of common unsaturated functionalities, including ketone, alkene, alkyne, and nitro groups. The discovery of nitrogen assembly as active sites can open up broad opportunities for rational design of new metal-free catalysts for challenging chemical reactions.
PubMed: 32796938
DOI: 10.1038/s41467-020-17909-8 -
ChemistryOpen Oct 2020DNAzymes are in vitro selected DNA oligonucleotides with catalytic activities. RNA cleavage is one of the most extensively studied DNAzyme reactions. To expand the... (Review)
Review
DNAzymes are in vitro selected DNA oligonucleotides with catalytic activities. RNA cleavage is one of the most extensively studied DNAzyme reactions. To expand the chemical functionality of DNA, various chemical modifications have been made during and after selection. In this review, we summarize examples of RNA-cleaving DNAzymes and focus on those modifications introduced during in vitro selection. By incorporating various modified nucleotides via polymerase chain reaction (PCR) or primer extension, a few DNAzymes were obtained that can be specifically activated by metal ions such as Zn and Hg. In addition, some modifications were introduced to mimic RNase A that can cleave RNA substrates in the absence of divalent metal ions. In addition, single modifications at the fixed regions of DNA libraries, especially at the cleavage junctions, have been tested, and examples of DNAzymes with phosphorothioate and histidine-glycine modified tertiary amine were successfully obtained specific for Cu, Cd, Zn, and Ni. Labeling fluorophore/quencher pair right next to the cleavage junction was also used to obtain signaling DNAzymes for detecting various metal ions and cells. Furthermore, we reviewed work on the cleavage of 2'-5' linked RNA and L-RNA substrates. Finally, applications of these modified DNAzymes as biosensors, RNases, and biochemical probes are briefly described with a few future research opportunities outlined at the end.
Topics: Amines; Biosensing Techniques; DNA, Catalytic; Drug Design; Metals
PubMed: 33101831
DOI: 10.1002/open.202000134 -
Electrophoresis Mar 2017During the last years there was a substantial increase in the use of antibodies and related proteins as therapeutics. The emphasis of the pharmaceutical industry is on... (Review)
Review
During the last years there was a substantial increase in the use of antibodies and related proteins as therapeutics. The emphasis of the pharmaceutical industry is on IgG1, IgG2, and IgG4 antibodies, which are therefore in the focus of this article. In order to ensure appropriate quality control of such biopharmaceuticals, deep understanding of their chemical degradation pathways and the resulting impact on potency, pharmacokinetics, and safety is required. Criticality of modifications may be specific for individual antibodies and has to be assessed for each molecule. However, some modifications of conserved structure elements occur in all or at least most IgGs. In these cases, criticality assessment may be applicable to related molecules or molecule formats. The relatively low dissociation energy of disulfide bonds and the high flexibility of the hinge region frequently lead to modifications and cleavages. Therefore, the hinge region and disulfide bonds require specific consideration during quality assessment of mAbs. In this review, available literature knowledge on underlying chemical reaction pathways of modifications, analytical methods for quantification and criticality are discussed. The hinge region is prone to cleavage and is involved in pathways that lead to thioether bond formation, cysteine racemization, and iso-Asp (Asp, aspartic acid) formation. Disulfide or sulfhydryl groups were found to be prone to reductive cleavage, trisulfide formation, cysteinylation, glutathionylation, disulfide bridging to further light chains, and disulfide scrambling. With regard to potency, disulfide cleavage, hinge cleavage, disulfide bridging to further light chains, and cysteinylation were found to influence antigen binding and fragment crystallizable (Fc) effector functionalities. Renal clearance of small fragments may be faster, whereas clearance of larger fragments appears to depend on their neonatal Fc receptor (FcRn) functionality, which in turn may be impeded by disulfide bond cleavage. Certain modifications such as disulfide induced aggregation and heterodimers from different antibodies are generally regarded critical with respect to safety. However, the detection of some modifications in endogenous antibodies isolated from human blood and the possibility of in vivo repair mechanisms may reduce some safety concerns.
Topics: Antibodies, Monoclonal; Disulfides; Humans; Immunoglobulin G; Protein Conformation
PubMed: 27982442
DOI: 10.1002/elps.201600425