Photo-Cross-Linking between Br U and Pyrene Residues in an RNA/DNA Hybrid

In this study, we investigated the photoreaction of Br U in a pyrene-labeled DNA duplex, RNA duplex, and DNA/RNA hybrids. We found that the photoreactivity of Br U changed dramatically from hydrogen abstraction to cross-linking by changing the conformation of the duplex from the B-form to the A-form. Among three A-form structures, the largest amount of cross-linked products was observed when Br U was incorporated into the RNA strand and the pyrene was conjugated to the 5' end of the DNA. These results indicate that the contact manner of pyrene was different between A- and B-form duplexes. This is a rare example of the use of the reactivity of bromouracil to analyze the contact between a small molecule with a weak binding affinity and a nucleic acid.

X-ray zooming microscopy with two Fresnel zone plates

We propose a variable-magnification full-field x-ray microscope using two Fresnel zone plates (FZPs). By moving the positions of the two FZPs, the magnification can be continuously changed even if the sample and camera positions are fixed. It was demonstrated that the magnification can be changed in the range of 25-150× using a hard x-ray beam at 14.4 keV. Using the first FZP as a convex lens and the second FZP as a concave lens, high magnification can be achieved at a short camera length. Even under the condition of a camera length of about 7 m, a magnification higher than 300× was achieved, and a line and space pattern with a pitch of 40 nm was observed at 10 keV. By inserting a knife edge at an appropriate position in the optical system, a phase-contrast image can be easily obtained, which is useful for soft-tissue observation of biological samples.

Tumor Accumulation of PIP-Based KRAS Inhibitor KR12 Evaluated by the Use of a Simple, Versatile Chicken Egg Tumor Model

Simple Summary

One of the goals of nanoplatform-based cancer therapy is to achieve tumor accumulation of anticancer agents. We have focused on PIP-based KRAS inhibitor KR12 (pyrrole–imidazole polyamide indole-seco–CBI conjugate), which has been reported to exhibit tumor growth inhibition in a xenograft mouse model. To evaluate the tumor accumulation property of KR12, we have synthesized a fluorescently labeled KR12 derivative (KR12-TAMRA) and employed a chicken egg tumor assay, a simple and versatile assay to examine tumor accumulation. Our results show that KR12-TAMRA accumulates specifically in the tumor when injected into a fertilized chicken egg transplanted with human cancer cells. We also demonstrate nuclear accumulation of KR12-TAMRA. Finally, inhibition of tumor growth in the chorioallantoic membrane (CAM) assay is shown. These results uncover a number of attractive features of PIP-based KR12 for cancer therapy.

Abstract

Background: The KRAS inhibitor KR12, based on pyrrole-imidazole polyamide (PIP), has been developed and shown to exhibit efficacy in mouse experiments. Because some PIP species exhibit tumor accumulation capability, we decided to evaluate whether the PIP portion of KR12 exhibits tumor accumulation. We employed the CAM assay that provides a simple method for tumor accumulation evaluation. Methods: KR12 PIP was synthesized and conjugated to TAMRA to produce a fluorescently labeled reagent (KR12-TAMRA). This reagent was injected into a fertilized chicken egg that has been transplanted with human cancer cells. Distribution of the red fluorescence was examined by cutting out tumor as well as various organs from the embryo. Results: The red fluorescence of KR12-TAMRA was found to overlap with the green fluorescence of the tumor formed with GFP-expressing cancer cells. We also observed nuclear localization of KR12-TAMRA. Treatment of KR12 that contained the alkylating agent CBI in the tumor-bearing chicken egg resulted in tumor growth inhibition. Conclusions: KR12 contains a PIP that has two key features: tumor accumulation and nuclear localization. KR12 conjugated with CBI exhibits inhibition of tumor growth in the CAM model.

Anatomical factors associated with progression of hallux valgus

BACKGROUND

The purpose of this study was to clarify the incidence rate and the risk factors for the progression of the hallux valgus deformity.

METHODS

Patients who had weight-bearing radiographs of the foot taken twice or more, with a ≥2-year interval, were retrospectively analyzed. Progression of the deformity was defined as an increase in the hallux valgus angle of ≥5° during the follow-up. The association of hallux valgus progression with patient characteristics and radiographic measurements at baseline was determined using univariate and multivariate analyses.

RESULTS

Totally, 268 patients (217 women and 51 men; median age, 64 years) were analyzed. An increase in the hallux valgus angle of ≥5° occurred in 44 (17%) patients in a median follow-up of 49 months. Large hallux valgus angle (odds ratio, 1.07) on the dorsoplantar radiograph at baseline were independent risk factors for the progression of the deformity.

CONCLUSION

Progression of the hallux valgus deformity occurred in one of six patients. Furthermore, large hallux valgus angle was the risk factor for subsequent deformity progression. Patients with large hallux valgus angle should be informed about the possible progression of the deformity.

Detecting Distal Radial Fractures from Wrist Radiographs Using a Deep Convolutional Neural Network with an Accuracy Comparable to Hand Orthopedic Surgeons

In recent years, fracture image diagnosis using a convolutional neural network (CNN) has been reported. The purpose of the present study was to evaluate the ability of CNN to diagnose distal radius fractures (DRFs) using frontal and lateral wrist radiographs. We included 503 cases of DRF diagnosed by plain radiographs and 289 cases without fracture. We implemented the CNN model using Keras and Tensorflow. Frontal and lateral views of wrist radiographs were manually cropped and trained separately. Fine-tuning was performed using EfficientNets. The diagnostic ability of CNN was evaluated using 150 images with and without fractures from anteroposterior and lateral radiographs. The CNN model diagnosed DRF based on three views: frontal view, lateral view, and both frontal and lateral view. We determined the sensitivity, specificity, and accuracy of the CNN model, plotted a receiver operating characteristic (ROC) curve, and calculated the area under the ROC curve (AUC). We further compared performances between the CNN and three hand orthopedic surgeons. EfficientNet-B2 in the frontal view and EfficientNet-B4 in the lateral view showed highest accuracy on the validation dataset, and these models were used for combined views. The accuracy, sensitivity, and specificity of the CNN based on both anteroposterior and lateral radiographs were 99.3, 98.7, and 100, respectively. The accuracy of the CNN was equal to or better than that of three orthopedic surgeons. The AUC of the CNN on the combined views was 0.993. The CNN model exhibited high accuracy in the diagnosis of distal radius fracture with a plain radiograph.

A hexameric ribozyme nanostructure formed by double-decker assembly of a pair of triangular ribozyme trimers

The modular architecture of naturally occurring ribozymes makes them a promising class of structural platforms to design and assemble three-dimensional (3D) RNA nanostructures, into which the catalytic ability of the platform ribozyme can be installed. We have constructed and analyzed RNA nanostructures with polygonal-shaped (closed) ribozyme oligomers by assembling unit RNAs derived from the Tetrahymena group I intron with a typical modular architecture. In this study, we dimerized ribozyme trimers with a triangular shape by introducing three pillar units. The resulting double-decker nanostructures containing six ribozyme units were characterized biochemically and their structures were observed by atomic force microscopy. The double-decker hexamers exhibited higher catalytic activity than the parent ribozyme trimers.

Size-dependent growth tactics of a partially migratory fish before migration

In many migratory species, smaller migrants suffer higher mortality rates during the risky migration. To minimize the size-selective mortality, migrants with smaller body sizes would need to accelerate growth rates or delay migration timing to attain a large enough body size prior to migration. To test these predictions, we investigated size-dependent patterns of growth rates and migration timing of juvenile masu salmon (Oncorhynchus masou) before their oceanic migration. We tracked uniquely marked individuals in a study population consisted of oceanic migrants and river-dwelling residents using mark-recapture surveys and PIT-tag antenna-reader system. Data supported our predictions about size-dependent growth rates and migration timing. For approximately 6 months before outmigration (i.e., between the decision of migration and the start of migration), eventual migrants grew more than residents if their initial size was smaller, but such a difference in growth rate diminished for fish with larger initial sizes. In addition, smaller eventual migrants delayed the timing of outmigration compared to larger individuals, to attain a larger body size in the river prior to migration. These results suggest that size-selective mortality during migration has shaped size-dependent patterns of the pre-migration growth in migratory masu salmon. Size-conditional changes in growth rate and duration of pre-migration period may be an adaptive tactic for the migratory animals.

Dissection of nanoconfinement and proximity effects on the binding events in DNA origami nanocavity

Both ligand binding and nanocavity can increase the stability of a biomolecular structure. Using mechanical unfolding in optical tweezers, here we found that a DNA origami nanobowl drastically increased the stability of a human telomeric G-quadruplex bound with a pyridostatin (PDS) ligand. Such a stability change is equivalent to >4 orders of magnitude increase (upper limit) in binding affinity (K_d: 490 nM → 10 pM (lower limit)). Since confined space can assist the binding through a proximity effect between the ligand-receptor pair and a nanoconfinement effect that is mediated by water molecules, we named such a binding as mechanochemical binding. After minimizing the proximity effect by using PDS that can enter or leave the DNA nanobowl freely, we attributed the increased affinity to the nanoconfinement effect (22%) and the proximity effect (78%). This represents the first quantification to dissect the effects of proximity and nanoconfinement on binding events in nanocavities. We anticipate these DNA nanoassemblies can deliver both chemical (i.e. ligand) and mechanical (i.e. nanocavity) milieus to facilitate robust mechanochemical binding in various biological systems.

Predators mitigate the destabilising effects of heatwaves on multitrophic stream communities

Amidst the global extinction crisis, climate change will expose ecosystems to more frequent and intense extreme climatic events, such as heatwaves. Yet, whether predator species loss-a prevailing characteristic of the extinction crisis-will exacerbate the ecological consequences of extreme climatic events remains largely unknown. Here, we show that the loss of predator species can interact with heatwaves to moderate the compositional stability of ecosystems. We exposed multitrophic stream communities, with and without a dominant predator species, to realistic current and future heatwaves and found that heatwaves destabilised algal communities by homogenising them in space. However, this happened only when the predator was absent. Additional heatwave impacts on multiple aspects of stream communities, including changes to the structure of algal and macroinvertebrate communities, as well as total algal biomass and its temporal variability, were not apparent during heatwaves and emerged only after the heatwaves had passed. Taken together, our results suggest that the ecological consequences of heatwaves can amplify over time as their impacts propagate through biological interaction networks, but the presence of predators can help to buffer such impacts. These findings underscore the importance of conserving trophic structure, and highlight the potential for species extinctions to amplify the effects of climate change and extreme events.

Photoswitchable single-stranded DNA-peptide coacervate formation as a dynamic system for reaction control

In cells, segregation allows for diverse biochemical reactions to take place simultaneously. Such intricate regulation of cellular processes is achieved through the dynamic formation and disassembly of membraneless organelles via liquid-liquid phase separation (LLPS). Herein, we demonstrate the light-controlled formation and disassembly of liquid droplets formed from a complex of polylysine (pLys) and arylazopyrazole (AAP)-conjugated single-stranded DNA. Photoswitchablility of droplet formation was also shown to be applicable to the control of chemical reactions; imine formation and a DNAzyme-catalyzed oxidation reaction were accelerated in the presence of droplets. These outcomes were reversed upon droplet disassembly. Our results demonstrate that the photoswitchable droplet formation system is a versatile model for the regulation of reactions through dynamic LLPS.

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Incorporating AAP enabled light-controlled droplet formation with ssDNA and pLys

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Droplets were reversibly formed or disassembled without altering sample composition

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Photoswitchability depended on sequence and ionic interactions but not flexibility

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Photoswitchable droplet formation accelerated uncatalyzed and catalyzed reactions

RUNX1 transactivates BCR-ABL1 expression in Philadelphia chromosome positive acute lymphoblastic leukemia

The emergence of tyrosine kinase inhibitors as part of a front‐line treatment has greatly improved the clinical outcome of the patients with Ph⁺ acute lymphoblastic leukemia (ALL). However, a portion of them still become refractory to the therapy mainly through acquiring mutations in the BCR‐ABL1 gene, necessitating a novel strategy to treat tyrosine kinase inhibitor (TKI)‐resistant Ph⁺ ALL cases. In this report, we show evidence that RUNX1 transcription factor stringently controls the expression of BCR‐ABL1, which can strategically be targeted by our novel RUNX inhibitor, Chb‐M'. Through a series of in vitro experiments, we identified that RUNX1 binds to the promoter of BCR and directly transactivates BCR‐ABL1 expression in Ph⁺ ALL cell lines. These cells showed significantly reduced expression of BCR‐ABL1 with suppressed proliferation upon RUNX1 knockdown. Moreover, treatment with Chb‐M' consistently downregulated the expression of BCR‐ABL1 in these cells and this drug was highly effective even in an imatinib‐resistant Ph⁺ ALL cell line. In good agreement with these findings, forced expression of BCR‐ABL1 in these cells conferred relative resistance to Chb‐M'. In addition, in vivo experiments with the Ph⁺ ALL patient‐derived xenograft cells showed similar results. In summary, targeting RUNX1 therapeutically in Ph⁺ ALL cells may lead to overcoming TKI resistance through the transcriptional regulation of BCR‐ABL1. Chb‐M' could be a novel drug for patients with TKI‐resistant refractory Ph⁺ ALL.

Enhanced Immunostimulatory Activity of Covalent DNA Dendrons

The present study focused on the design and synthesis of covalent DNA dendrons bearing multivalent cytosine-phosphate-guanine oligodeoxynucleotides (CpG ODNs) that can stimulate the immune system through the activation of TLR9. These dendrons were synthesized using branching trebler phosphoramidite containing three identical protecting groups that enabled the simultaneous synthesis of multiple strands on a single molecule. Compared with linear ODNs, covalent DNA dendrons were found to be more resistant to nuclease degradation and were more efficiently taken up by macrophage-like RAW264.7 cells. Cellular uptake was suggested to be mediated by macrophage scavenger receptors. The covalent DNA dendrons composed of multivalent immunostimulatory branches enhanced the secretion of proinflammatory cytokines TNF-α and IL-6 from RAW264.7 cells, and 9-branched DNA dendrons showed the highest enhancement. Given their enhanced efficacy, we expect covalent DNA dendrons to be useful structures of oligonucleotide medicines.

Strong and Specific Recognition of CAG/CTG Repeat DNA (5'-dWGCWGCW-3') by a Cyclic Pyrrole-Imidazole Polyamide

Abnormally expanded CAG/CTG repeat DNA sequences lead to a variety of neurological diseases, such as Huntington's disease. Here, we synthesized a cyclic pyrrole‐imidazole polyamide (cPIP), which can bind to the minor groove of the CAG/CTG DNA sequence. The double‐stranded DNA melting temperature (T_m) and surface plasmon resonance assays revealed the high binding affinity of the cPIP. In addition, next‐generation sequencing showed that the cPIP had high specificity for its target DNA sequence.

Photo-Controllable Phase Transition of Arylazopyrazole-Conjugated Oligonucleotides

Phase transition is a promising aspect of DNA as biopolymers. Anionic DNA oligonucleotides easily form complexes with cationic polypeptides such as polylysine, and duplex formation significantly influences their complexation and resulting microcompartments. In this study, phase transition of microcompartments containing DNA and polylysine was systematically induced by modulating duplex formation of arylazopyrazole-conjugated oligonucleotides with light. We demonstrated that UV irradiation destabilized DNA duplex and generated isotropic coacervates, while duplex stabilization by visible light irradiation caused the formation of liquid crystalline coacervates. This photocontrol of phase transition was highly repeatable, and similar changes were observed even after ten cycles of light irradiation. Our approach would provide a robust control layer to the development of tailor-made microcompartments.

Biomimetic DNA Nanotechnology to Understand and Control Cellular Responses

At the cellular level, numerous nanocues guide the cells to adhere, interact, proliferate, differentiate, etc. Understanding and manipulating the cellular functions in vitro, necessitates the elucidation of these nanocues provided to the cells by the extracellular matrix (ECM), neighbouring cells or in the form of ligands. DNA nanotechnology is a biocompatible, flexible and a promising molecular level toolkit for mimicking cell-cell and cell-matrix interactions. In this review, we summarize various advances in cell-matrix, cell-cell and cell receptor-ligand interactions using DNA nanotechnology as a tool. We also provide a brief outlook on the current challenges and the future potentials of these DNA-based nanostructures so as to inspire novel innovations in the field.

Telomere-specific chromatin capture using a pyrrole-imidazole polyamide probe for the identification of proteins and non-coding RNAs

Background

Knowing chromatin components at a DNA regulatory element at any given time is essential for understanding how the element works during cellular proliferation, differentiation and development. A region-specific chromatin purification is an invaluable approach to dissecting the comprehensive chromatin composition at a particular region. Several methods (e.g., PICh, enChIP, CAPTURE and CLASP) have been developed for isolating and analyzing chromatin components. However, all of them have some shortcomings in identifying non-coding RNA associated with DNA regulatory elements.

Results

We have developed a new approach for affinity purification of specific chromatin segments employing an N-methyl pyrrole (P)-N-methylimidazole (I) (PI) polyamide probe, which binds to a specific sequence in double-stranded DNA via Watson–Crick base pairing as a minor groove binder. This new technique is called proteomics and RNA-omics of isolated chromatin segments (PI-PRICh). Using PI-PRICh to isolate mouse and human telomeric components, we found enrichments of shelterin proteins, the well-known telomerase RNA component (TERC) and telomeric repeat-containing RNA (TERRA). When PI-PRICh was performed for alternative lengthening of telomere (ALT) cells with highly recombinogenic telomeres, in addition to the conventional telomeric chromatin, we obtained chromatin regions containing telomeric repeat insertions scattered in the genome and their associated RNAs.

Conclusion

PI-PRICh reproducibly identified both the protein and RNA components of telomeric chromatin when targeting telomere repeats. PI polyamide is a promising alternative to simultaneously isolate associated proteins and RNAs of sequence-specific chromatin regions under native conditions, allowing better understanding of chromatin organization and functions within the cell.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13072-021-00421-8.

Characterization of a Conformation-Restricted Amyloid β Peptide and Immunoreactivity of Its Antibody in Human AD brain

Characterization of amyloid β (Aβ) oligomers, the transition species present prior to the formation of Aβ fibrils and that have cytotoxicity, has become one of the major topics in the investigations of Alzheimer's disease (AD) pathogenesis. However, studying pathophysiological properties of Aβ oligomers is challenging due to the instability of these protein complexes in vitro. Here, we report that conformation-restricted Aβ42 with an intramolecular disulfide bond at positions 17 and 28 (SS-Aβ42) formed stable Aβ oligomers in vitro. Thioflavin T binding assays, nondenaturing gel electrophoresis, and morphological analyses revealed that SS-Aβ42 maintained oligomeric structure, whereas wild-type Aβ42 and the highly aggregative Aβ42 mutant with E22P substitution (E22P-Aβ42) formed Aβ fibrils. In agreement with these observations, SS-Aβ42 was more cytotoxic compared to the wild-type and E22P-Aβ42 in cell cultures. Furthermore, we developed a monoclonal antibody, designated TxCo-1, using the toxic conformation of SS-Aβ42 as immunogen. X-ray crystallography of the TxCo-1/SS-Aβ42 complex, enzyme immunoassay, and immunohistochemical studies confirmed the recognition site and specificity of TxCo-1 to SS-Aβ42. Immunohistochemistry with TxCo-1 antibody identified structures resembling senile plaques and vascular Aβ in brain samples of AD subjects. However, TxCo-1 immunoreactivity did not colocalize extensively with Aβ plaques identified with conventional Aβ antibodies. Together, these findings indicate that Aβ with a turn at positions 22 and 23, which is prone to form Aβ oligomers, could show strong cytotoxicity and accumulated in brains of AD subjects. The SS-Aβ42 and TxCo-1 antibody should facilitate understanding of the pathological role of Aβ with toxic conformation in AD.

Targeted epigenetic induction of mitochondrial biogenesis enhances antitumor immunity in mouse model

Considering the potential of combinatorial therapies in overcoming existing limitations of cancer immunotherapy, there is an increasing need to identify small-molecule modulators of immune cells capable of augmenting the effect of programmed cell death protein 1 (PD-1) blockade, leading to better cancer treatment. Although epigenetic drugs showed potential in combination therapy, the lack of sequence specificity is a major concern. Here, we identify and develop a DNA-based epigenetic activator with tri-arginine vector called EnPGC-1 that can trigger the targeted induction of the peroxisome proliferator-activated receptor-gamma coactivator 1 alpha/beta (PGC-1α/β), a regulator of mitochondrial biogenesis. EnPGC-1 enhances mitochondrial activation, energy metabolism, proliferation of CD8⁺ T cells in vitro, and, in particular, enhances oxidative phosphorylation, a feature of long-lived memory T cells. Genome-wide gene analysis suggests that EnPGC-1 and not the control compounds can regulate T cell activation as a major biological process. EnPGC-1 also synergizes with PD-1 blockade to enhance antitumor immunity and improved host survival.

Non-invasive Regulation of Cellular Morphology Using a Photoswitchable Mechanical DNA Polymer

The extracellular matrix (ECM) in which the cells reside provides a dynamic and reversible environment. Spatiotemporal cues are essential when cells are undergoing morphogenesis, repair and differentiation. Emulation of such an intricate system with reversible presentation of nanoscale cues can help us better understand cellular processes and can allow the precise manipulation of cell function in vitro. Herein, we formulated a photoswitchable DNA mechanical nanostructure containing azobenzene moieties and dynamically regulated the spatial distance between adhesion peptides using a photoswitchable DNA polymer with photoirradiation. We found that the DNA polymer reversibly forms two different structures, a relaxed linear and shrunken compact form, observed by AFM. Using the mechanical properties of this DNA polymer, UV and visible light irradiation induced a significant morphology change of the cells between a round shape and spindle shape, thus providing a tool to decipher the language of the ECM better.

RUNX inhibitor suppresses graft‐versus‐host disease through targeting RUNX‐NFATC2 axis

Patients with refractory graft‐versus‐host disease (GVHD) have a dismal prognosis. Therefore, novel therapeutic targets are still needed to be identified. Runt‐related transcriptional factor (RUNX) family transcription factors are essential transcription factors that mediate the essential roles in effector T cells. However, whether RUNX targeting can suppress, and GVHD is yet unknown. Here, we showed that RUNX family members have a redundant role in directly transactivating NFATC2 expression in T cells. We also found that our novel RUNX inhibitor, Chb‐M’, which is the inhibitor that switches off the entire RUNX family by alkylating agent–conjugated pyrrole‐imidazole (PI) polyamides, inhibited T‐cell receptor mediated T cell proliferation and allogenic T cell response. These were designed to specifically bind to consensus RUNX‐binding sequences (TGTGGT). Chb‐M’ also suppressed the expression of NFATC2 and pro‐inflammatory cytokine genes in vitro. Using xenogeneic GVHD model, mice injected by Chb‐M’ showed almost no sign of GVHD. Especially, the CD4 T cell was decreased and GVHD‐associated cytokines including tissue necrosis factor‐α and granulocyte‐macrophage colony‐stimulating factor were reduced in the peripheral blood of Chb‐M’ injected mice. Taken together, our data demonstrates that RUNX family transcriptionally upregulates NFATC2 in T cells, and RUNX‐NFATC2 axis can be a novel therapeutic target against GVHD.

Integrated analysis of immune-related gene subtype and immune index for immunotherapy in clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) is the most common type of renal cell carcinoma (RCC) with high immunogenicity. Research on immune-related gene (IRG) is of great significance in ccRCC in identifying new therapeutic targets and improving patient prognosis. In this study, the IRG patterns of ccRCC were investigated and correlated these patterns with tumor microenvironment infiltrating characteristics in immunotherapy. Moreover, an IRG score was constructed to quantify the pattern of individual tumors through the principal component analysis algorithm. Two distinct molecular subtypes (C1 and C2) were identified based on the IRGs expression profile. Subtype C1 was characterized with significantly high level of immune-checkpoint, immune score, stromal score, showed high drug sensitivity in Sorafenib, Sunitinib, Cisplatin, Vinblastine, Vinorelbine, Vorinostat, and Gemcitabine. Cytokine-cytokine receptor pathway, chemokine signaling pathway, and JAK signaling pathways were found enriched in the subtype C1 account for the poor prognosis. Subtype C2 was linked to a better survival outcome. By using the Connective Map database, subtype specific small molecular drugs identified that could facilitate the treatment of ccRCC patients. In addition, A immune index that used to evaluated the immune modification patterns and further validated in the other types RCC dataset, such as papillary renal cell carcinoma (pRCC) and chromophobe renal cell carcinoma (chRCC). Together, this study identified two distinct molecular subtypes with immune index, aid to the treatment of ccRCC and enhancing our cognition of the tumor microenvironment infiltration characterization in ccRCC immunotherapy.