SARS-CoV-2 RNA stabilizes host mRNAs to elicit immunopathogenesis.

SARS-CoV-2 RNA interacts with host factors to suppress interferon responses and simultaneously induces cytokine release to drive the development of severe coronavirus disease 2019 (COVID-19). However, how SARS-CoV-2 hijacks host RNAs to elicit such imbalanced immune responses remains elusive. Here, we analyzed SARS-CoV-2 RNA in situ structures and interactions in infected cells and patient lung samples using RIC-seq. We discovered that SARS-CoV-2 RNA forms 2,095 potential duplexes with the 3' UTRs of 205 host mRNAs to increase their stability by recruiting RNA-binding protein YBX3 in A549 cells. Disrupting the SARS-CoV-2-to-host RNA duplex or knocking down YBX3 decreased host mRNA stability and reduced viral replication. Among SARS-CoV-2-stabilized host targets, NFKBIZ was crucial for promoting cytokine production and reducing interferon responses, probably contributing to cytokine storm induction. Our study uncovers the crucial roles of RNA-RNA interactions in the immunopathogenesis of RNA viruses such as SARS-CoV-2 and provides valuable host targets for drug development.

Complementary Alu sequences mediate enhancer-promoter selectivity.

Enhancers determine spatiotemporal gene expression programs by engaging with long-range promoters1-4. However, it remains unknown how enhancers find their cognate promoters. We recently developed a RNA in situ conformation sequencing technology to identify enhancer-promoter connectivity using pairwise interacting enhancer RNAs and promoter-derived noncoding RNAs5,6. Here we apply this technology to generate high-confidence enhancer-promoter RNA interaction maps in six additional cell lines. Using these maps, we discover that 37.9% of the enhancer-promoter RNA interaction sites are overlapped with Alu sequences. These pairwise interacting Alu and non-Alu RNA sequences tend to be complementary and potentially form duplexes. Knockout of Alu elements compromises enhancer-promoter looping, whereas Alu insertion or CRISPR-dCasRx-mediated Alu tethering to unregulated promoter RNAs can create new loops to homologous enhancers. Mapping 535,404 noncoding risk variants back to the enhancer-promoter RNA interaction maps enabled us to construct variant-to-function maps for interpreting their molecular functions, including 15,318 deletions or insertions in 11,677 Alu elements that affect 6,497 protein-coding genes. We further demonstrate that polymorphic Alu insertion at the PTK2 enhancer can promote tumorigenesis. Our study uncovers a principle for determining enhancer-promoter pairing specificity and provides a framework to link noncoding risk variants to their molecular functions.

RIC-seq for global in situ profiling of RNA-RNA spatial interactions.

Highly structured RNA molecules usually interact with each other, and associate with various RNA-binding proteins, to regulate critical biological processes. However, RNA structures and interactions in intact cells remain largely unknown. Here, by coupling proximity ligation mediated by RNA-binding proteins with deep sequencing, we report an RNA in situ conformation sequencing (RIC-seq) technology for the global profiling of intra- and intermolecular RNA-RNA interactions. This technique not only recapitulates known RNA secondary structures and tertiary interactions, but also facilitates the generation of three-dimensional (3D) interaction maps of RNA in human cells. Using these maps, we identify noncoding RNA targets globally, and discern RNA topological domains and trans-interacting hubs. We reveal that the functional connectivity of enhancers and promoters can be assigned using their pairwise-interacting RNAs. Furthermore, we show that CCAT1-5L-a super-enhancer hub RNA-interacts with the RNA-binding protein hnRNPK, as well as RNA derived from the MYC promoter and enhancer, to boost MYC transcription by modulating chromatin looping. Our study demonstrates the power and applicability of RIC-seq in discovering the 3D structures, interactions and regulatory roles of RNA.

Identification of ICAT as an APC Inhibitor, Revealing Wnt-Dependent Inhibition of APC-Axin Interaction.

Adenomatous polyposis coli (APC) and Axin are core components of the ß-catenin destruction complex. How APC's function is regulated and whether Wnt signaling influences the direct APC-Axin interaction to inhibit the ß-catenin destruction complex is not clear. Through a CRISPR screen of ß-catenin stability, we have identified ICAT, a polypeptide previously known to block ß-catenin-TCF interaction, as a natural inhibitor of APC. ICAT blocks ß-catenin-APC interaction and prevents ß-catenin-mediated APC-Axin interaction, enhancing stabilization of ß-catenin in cells harboring truncated APC or stimulated with Wnt, but not in cells deprived of a Wnt signal. Using ICAT as a tool to disengage ß-catenin-mediated APC-Axin interaction, we demonstrate that Wnt quickly inhibits the direct interaction between APC and Axin. Our study highlights an important scaffolding function of ß-catenin in the assembly of the destruction complex and suggests Wnt-inhibited APC-Axin interaction as a mechanism of Wnt-dependent inhibition of the destruction complex.

Artificial intelligence-enabled microbiome-based diagnosis models for a broad spectrum of cancer types.

Microbiome-based diagnosis of cancer is an increasingly important supplement for the genomics approach in cancer diagnosis, yet current models for microbiome-based diagnosis of cancer face difficulties in generality: not only diagnosis models could not be adapted from one cancer to another, but models built based on microbes from tissues could not be adapted for diagnosis based on microbes from blood. Therefore, a microbiome-based model suitable for a broad spectrum of cancer types is urgently needed. Here we have introduced DeepMicroCancer, a diagnosis model using artificial intelligence techniques for a broad spectrum of cancer types. Built based on the random forest models it has enabled superior performances on more than twenty types of cancers' tissue samples. And by using the transfer learning techniques, improved accuracies could be obtained, especially for cancer types with only a few samples, which could satisfy the requirement in clinical scenarios. Moreover, transfer learning techniques have enabled high diagnosis accuracy that could also be achieved for blood samples. These results indicated that certain sets of microbes could, if excavated using advanced artificial techniques, reveal the intricate differences among cancers and healthy individuals. Collectively, DeepMicroCancer has provided a new venue for accurate diagnosis of cancer based on tissue and blood materials, which could potentially be used in clinics.

The SIAH E3 ubiquitin ligases promote Wnt/ß-catenin signaling through mediating Wnt-induced Axin degradation.

The Wnt/ß-catenin signaling pathway plays essential roles in embryonic development and adult tissue homeostasis. Axin is a concentration-limiting factor responsible for the formation of the ß-catenin destruction complex. Wnt signaling itself promotes the degradation of Axin. However, the underlying molecular mechanism and biological relevance of this targeting of Axin have not been elucidated. Here, we identify SIAH1/2 (SIAH) as the E3 ligase mediating Wnt-induced Axin degradation. SIAH proteins promote the ubiquitination and proteasomal degradation of Axin through interacting with a VxP motif in the GSK3-binding domain of Axin, and this function of SIAH is counteracted by GSK3 binding to Axin. Structural analysis reveals that the Axin segment responsible for SIAH binding is also involved in GSK3 binding but adopts distinct conformations in Axin/SIAH and Axin/GSK3 complexes. Knockout of SIAH1 blocks Wnt-induced Axin ubiquitination and attenuates Wnt-induced ß-catenin stabilization. Our data suggest that Wnt-induced dissociation of the Axin/GSK3 complex allows SIAH to interact with Axin not associated with GSK3 and promote its degradation and that SIAH-mediated Axin degradation represents an important feed-forward mechanism to achieve sustained Wnt/ß-catenin signaling.

Microbiota-induced inflammatory responses in bladder tumors promote epithelial-mesenchymal transition and enhanced immune infiltration.

The intratumoral microbiota can modulate the tumor immune microenvironment (TIME), however, the underlying mechanism by which intratumoral microbiota influences the TIME in urothelial carcinoma of bladder (UCB) remains unclear. To address this, we collected 402 patients with UCB with paired host transcriptome and tumor microbiome samples from The Cancer Genome Atlas (TCGA). We found that the intratumoral microbiome profiles were significantly correlated with the expression pattern of epithelial-mesenchymal transition (EMT)-related genes. Furthermore, we detected that the genus Lachnoclostridiumand Sutterellain tumors could indirectly promote EMT program by inducing an inflammatory response. Moreover, the inflammatory response induced by these two intratumoral bacteria further enhanced intratumoral immune infiltration, affecting patient survival and response to immunotherapy. In addition, an independent immunotherapy cohort of 348 patients with bladder cancer was used to validate our results. Collectively, our study elucidates the potential mechanism by which the intratumoral microbiota influences the TIME of UCB and provides a new guiding strategy for targeted therapy of UCB.

Full Electron Delocalization across the Cluster in 1,12-bisBMes2-p-carborane Radical Anion.

Conjugation between three-dimensional (3D) carboranes and the attached substituents is commonly believed to be very weak. In this paper, we report that reducing 1,12-bis(BMes2)-p-carborane (B2pCab) with one electron gives a radical anion with a centrosymmetric semiquinoidal structure. This radical anion shows extensive electron delocalization between the two boron centers over the p-carborane bridge due to the overlap of carborane lowest unoccupied molecular orbital (LUMO) and the BMes2 LUMO. Unlike dianions of other C2B10H12 carboranes, which rearrange to a nido-form, two-electron reduction of B2pCab leads to a rearrangement into a basket-shaped intermediate.

Self-Limiting Phase Transition Enabling Reversible Overstoichiometric Li Storage in Ni-Rich Cathodes.

Ni-rich cathodes are some of the most promising candidates for advanced lithium-ion batteries, but their available capacities have been stagnant due to the intrinsic Li+ storage sites. Extending the voltage window down can induce the phase transition from O3 to 1T of LiNiO2-derived cathodes to accommodate excess Li+ and dramatically increase the capacity. By setting the discharge cutoff voltage of LiNi0.6Co0.2Mn0.2O2 to 1.4 V, we can reach an extremely high capacity of 393 mAh g-1 and an energy density of 1070 Wh kg-1 here. However, the phase transition causes fast capacity decay and related structural evolution is rarely understood, hindering the utilization of this feature. We find that the overlithiated phase transition is self-limiting, which will transform into solid-solution reaction with cycling and make the cathode degradation slow down. This is attributed to the migration of abundant transition metal ions into lithium layers induced by the overlithiation, allowing the intercalation of overstoichiometric Li+ into the crystal without the O3 framework change. Based on this, the wide-potential cycling stability is further improved via a facile charge-discharge protocol. This work provides deep insight into the overstoichiometric Li+ storage behaviors in conventional layered cathodes and opens a new avenue toward high-energy batteries.

Energy Barriers and Gap Between Two Excited States in a Dual-Emissive Carborane.

A thorough understanding of the internal conversion process between excited states is important for the designing of ideal multiple-emissive materials. However, it is hard to experimentally measure both the energy barriers and gaps between the excited states of a compound. For a long time, it is dubious if what was measured is the energy gap or barrier between two excited states. In this paper, we designed 1-(pyren-2'-yl)-9,12-di(p-tolyl)-o-carborane (2), which shows dual-emission in solution. Temperature-dependent fluorescence measurements show that the two emission bands in hexane are corresponding to two different excited states. The ratio of the emission bands is controlled by thermodynamics at higher temperatures and by kinetics at lower temperatures. Thus, the energy barrier and energy gaps between the two excited states of 2 can be experimentally estimated.

Fluorescence Enhancement of CdS:Ag Quantum Dots Co-Assembled with Au Nanoparticles in a Hollow Nanosphere Form.

Colloidal quantum dots (QDs) have exceptional fluorescence properties. Overcoming aggregation-induced quenching and enhancing the fluorescence of colloidal QDs have remained a challenging issue in this field. In this study, composite hollow nanospheres composed of Au nanoparticles (NPs) and CdS:Ag-doped QDs were successfully constructed through controlled microemulsion-based cooperative assembly. This method harnessed the localized surface plasmon resonance (LSPR) effect of Au NPs nearby doped QDs, resulting in enhanced doped QD fluorescence and the observation of the Purcell effect. The composite hollow nanospheres show a fluorescence enhancement compared to that of the pure CdS:Ag QDs. The enhanced fluorescence was demonstrated to come from the synergetic enhancement of the absorption and emission transition of the doped QDs. This approach provides a feasible technological pathway to address the challenge of improving the fluorescence performance of the doped QDs.

Triple B←N Lewis Pair-Functionalized Triazatruxenes with Large Stokes Shifts.

A novel class of multiple B←N Lewis pair-functionalized polycyclic aromatic hydrocarbons with different BR2 groups (R = Cl or Et) directly attached at positions 1, 6, and 11 of triazatruxene was synthesized. The triazatruxene backbone of 4 displays a bowl shape, and its molecular skeleton shows a highly twisted propeller-like structure with C3 symmetry. The introduction of B←N Lewis pairs not only results in a large decrease in the HOMO-LUMO gap but also lowers the LUMO to -3.00 eV. Both compounds show excellent stability with large Stokes shifts of ≤8234 cm-1 and solvatochromic emission in solvents of different polarities.

Aqueous Topological Synthesis of Au@semiconductor Core-Shell Nanocrystals with Morphology and Composition Engineering.

Core-shell nanocrystals (C-S NCs) are an essential class of materials whose structural engineering has attracted wide attention due to their tunable optical and electrical properties, especially noble metal@semiconductor (NMS) C-S NCs with flexible plasmon-exciton coupling. Due to their diverse critical applications, especially aqueous biological applications, herein we propose an aqueous topological strategy enabled by cation exchange reactions (CER) to synthesize various plasmonic Au@semiconductor C-S NCs, in which environmentally friendly triphenylphosphine (TPP) is used as an initiator instead of inflammable tributyl phosphine (TBP). The introduction of the milder, solid TPP facilitated a new aqueous CER strategy for synthesizing Au@semiconductor NCs with tailored chalcogenide compositions and morphologies. For example, the as-synthesized Au@ZnS C-S NRs had better absorption and biocompatibility and exhibited excellent photodynamic therapy efficacy.

Self-Assembly of Lanthanide-Aluminum Cluster-Organic Frameworks with Magnetocaloric Effect and Luminescence.

The self-assembly of the lanthanide metal-organic frameworks presents a formidable challenge but profound significance. Compared with the metal-organic frameworks based on 4f-3d ions, the chemistry of 4f-3p metal-organic frameworks has not been fully explored so far. In this study, two lanthanide-aluminum-based clusters [Ln6Al(IN)10(µ3-OH)5(µ3-O)3(H2O)8]·xH2O (x = 2, Ln = Gd, abbreviated as Gd6Al; x = 2.5, Ln = Eu, abbreviated as Eu6Al; HIN = isonicotinic acid) have been meticulously designed and obtained by hydrothermal reaction at low pH. The crystallographic study revealed that both Gd6Al and Eu6Al clusters exhibit an unprecedented sandwiched metal-organic framework holding a highly ordered honeycomb network. To our knowledge, it is the first case of Ln-Al-based cluster-organic frameworks. Furthermore, magnetic investigation of Gd6Al manifests a decent magnetic entropy change of -ΔSmmax = 28.8 J kg-1 K-1 at 2 K for ΔH = 7.0 T. Significantly, the introduction of AlIII ions into the lanthanide metal-organic frameworks displays excellent solid-state luminescent capability with a lifetime of 371.6 µs and quantum yield of 6.64%. The construction and investigation of these two Ln-Al clusters represent great progress in the 4f-3p metal-organic framework.

4,9- and 4,10-Substituted pyrenes: synthesis, successful isolation, and optoelectronic properties.

We report herein a way to prepare and purify optoelectronic functional 4,9- and 4,10-substituted pyrene isomers. By tuning the size of substituents, the designed 4,9- and 4,10-isomers can be successfully isolated by recycling preparative size-exclusion chromatography (SEC) and/or repeated recrystallization. The structure and purity of the isolated compounds 1-5 have been confirmed by 1H NMR, 13C NMR, and HRMS. The photophysical and electrochemical properties of compounds 1-5 have been studied in detail both experimentally and theoretically. The lowest transitions of these pyrenes, 1-5, are allowed, with moderate to high fluorescence quantum yields and radiative decay rates around 108 s-1. The differences between the electrochemical and photophysical properties of 4,9-, 4,10-, 1,6-, and 2,7-substituted isomers are compared and concluded.

Fabrication of Nitrogen Based Magnetic Conjugated Microporous Polymer for Efficient Extraction of Neonicotinoids in Water Samples.

Facile and sensitive methods for detecting neonicotinoids (NEOs) in aquatic environments are crucial because they are found in extremely low concentrations in complex matrices. Herein, nitrogen-based magnetic conjugated microporous polymers (Fe3O4@N-CMP) with quaternary ammonium groups were synthesized for efficient magnetic solid-phase extraction (MSPE) of NEOs from tap water, rainwater, and lake water. Fe3O4@N-CMP possessed a suitable specific surface area, extended π-conjugated system, and numerous cationic groups. These properties endow Fe3O4@N-CMP with superior extraction efficiency toward NEOs. The excellent adsorption capacity of Fe3O4@N-CMP toward NEOs was attributed to its π-π stacking, Lewis acid-base, and electrostatic interactions. The proposed MSPE-HPLC-DAD approach based on Fe3O4@N-CMP exhibited a wide linear range (0.1-200 µg/L), low detection limits (0.3-0.5 µg/L), satisfactory precision, and acceptable reproducibility under optimal conditions. In addition, the established method was effectively utilized for the analysis of NEOs in tap water, rainwater, and lake water. Excellent recoveries of NEOs at three spiked levels were in the range of 70.4 to 122.7%, with RSDs less than 10%. This study provides a reliable pretreatment method for monitoring NEOs in environmental water samples.

The specific viral composition in triple-negative breast cancer tissue shapes the specific tumor microenvironment characterized on pathological images.

Numerous studies have shown that different subtypes of breast cancer (BC) have significant differences in terms of the tumor microbiome, host gene expression, and histopathological image, whereas the biological links between these cancer-associated indicators are still unknown. Here, we performed a comprehensive analysis with 610 patients of the four subtypes of BC with matched tissue microbiota, host transcriptome, and histopathological image samples. Correlation analysis showed that the composition of intratumoral viruses shaped the tumor microenvironment (TME) of patients with BC, and the TME was further reflected in the histopathological images. Of the four subtypes, patients with triple-negative breast cancer (TNBC) had unique intratumoral viral community composition, non-cancer cell infiltration in the TME, and histopathological image characteristics. Furthermore, we detected multiple virus-cell-image association axes in TNBC, in which tumor-associated macrophages (TAMs) have clinical prognostic implication. This study provides a comprehensive map of the associations between the intratumoral virome, TME, and histopathological image of TNBC, as well as insights into disease prognosis that can be crucial for precise therapeutic intervention strategies.

A novel heterozygous missense variant of the ARID4A gene identified in Han Chinese families with schizophrenia-diagnosed siblings that interferes with DNA-binding activity.

ARID4A plays an important role in regulating gene expression and cell proliferation. ARID4A belongs to the AT-rich interaction domain (ARID)-containing family, and a PWWP domain immediately precedes its ARID region. The molecular mechanism and structural basis of ARID4A are largely unknown. Whole-exome sequencing (WES) revealed that a novel heterozygous missense variant, ARID4A c.1231 C > G (p.His411Asp), was associated with schizophrenia (SCZ) in this study. We determined the crystal structure of the PWWP-ARID tandem at 2.05 Å, revealing an unexpected mode in which ARID4A assembles with its PWWP and ARID from a structural and functional supramodule. Our results further showed that compared with the wild type, the p.His411Asp ARID mutant protein adopts a less compact conformation and exhibits a weaker dsDNA-binding ability. The p.His411Asp mutation decreased the number of cells that were arrested in the G0-G1 phase and caused more cells to progress to the G2-M phase. In addition, the missense mutation promoted the proliferation of HEK293T cells. In conclusion, our data provide evidence that ARID4A p.His411Asp could cause a conformational change in the ARID4A ARID domain, influence the DNA binding function, and subsequently disturb the cell cycle arrest in the G1 phase. ARID4A is likely a susceptibility gene for SCZ; thus, these findings provide new insight into the role of ARID4A in psychiatric disorders.

Protein Labeling Facilitates the Understanding of Protein Corona Formation via Fluorescence Resonance Energy Transfer and Fluorescence Correlation Spectroscopy.

Once nanoparticles enter into the biological milieu, nanoparticle-biomacromolecule complexes, especially the protein corona, swiftly form, which cause obvious effects on the physicochemical properties of both nanoparticles and proteins. Here, the thermodynamic parameters of the interactions between water-soluble GSH-CdSe/ZnS core/shell quantum dots (GSH-QDs) and human serum albumin (HSA) were investigated with the aid of labeling fluorescence of HSA. It was proved that the labeling fluorescence originating from a fluorophore (BDP-CN for instance) could be used to investigate the interactions between QDs and HSA. Gel electrophoresis displayed that the binding ratio between HSA and QDs was ∼2:1 by direct visualization. Fluorescence resonance energy transfer (FRET) results indicated that the distance between the QDs and the fluorophore BDP-CN in HSA was 7.2 nm, which indicated that the distance from the fluorophore to the surface of the QDs was ∼4.8 nm. Fluorescence correlation spectroscopy (FCS) results showed that HSA formed a monolayer of a protein corona with a thickness of 5.5 nm. According to the spatial structure of HSA, we could speculate that the binding site of QDs was located at the side edge (not the triangular plane) of HSA with an equilateral triangular prism. The elaboration of the thermodynamic parameters, binding ratio, and interaction orientation will highly improve the fundamental understanding of the formation of protein corona. This work has guiding significance for the exploration of the interactions between proteins and nanomaterials.