Computational prediction and experimental validation identify functionally conserved lncRNAs from zebrafish to human.

Functional studies of long noncoding RNAs (lncRNAs) have been hindered by the lack of methods to assess their evolution. Here we present lncRNA Homology Explorer (lncHOME), a computational pipeline that identifies a unique class of long noncoding RNAs (lncRNAs) with conserved genomic locations and patterns of RNA-binding protein (RBP) binding sites (coPARSE-lncRNAs). Remarkably, several hundred human coPARSE-lncRNAs can be evolutionarily traced to zebrafish. Using CRISPR-Cas12a knockout and rescue assays, we found that knocking out many human coPARSE-lncRNAs led to cell proliferation defects, which were subsequently rescued by predicted zebrafish homologs. Knocking down coPARSE-lncRNAs in zebrafish embryos caused severe developmental delays that were rescued by human homologs. Furthermore, we verified that human, mouse and zebrafish coPARSE-lncRNA homologs tend to bind similar RBPs with their conserved functions relying on specific RBP-binding sites. Overall, our study demonstrates a comprehensive approach for studying the functional conservation of lncRNAs and implicates numerous lncRNAs in regulating vertebrate physiology.

From Liquid to Solid-State Batteries: Li-Rich Mn-Based Layered Oxides as Emerging Cathodes with High Energy Density.

Li-rich Mn-based (LRMO) cathode materials have attracted widespread attention due to their high specific capacity, energy density, and cost-effectiveness. However, challenges such as poor cycling stability, voltage deca,y and oxygen escape limit their commercial application in liquid Li-ion batteries. Consequently, there is a growing interest in the development of safe and resilient all-solid-state batteries (ASSBs), driven by their remarkable safety features and superior energy density. ASSBs based on LRMO cathodes offer distinct advantages over conventional liquid Li-ion batteries, including long-term cycle stability, thermal and wider electrochemical windows stability, as well as the prevention of transition metal dissolution. This review aims to recapitulate the challenges and fundamental understanding associated with the application of LRMO cathodes in ASSBs. Additionally, it proposes the mechanisms of interfacial mechanical and chemical instability, introduces noteworthy strategies to enhance oxygen redox reversibility, enhances high-voltage interfacial stability, and optimizes Li+ transfer kinetics. Furthermore, it suggests potential research approaches to facilitate the large-scale implementation of LRMO cathodes in ASSBs.

hsa_circ_0020378 regulating miR-339-3p/COL1A1 promotes osteosarcoma progression.

Osteosarcoma is a malignant orthopedic tumor that is frequently diagnosed in the pediatric population. Several studies have summarized the functions of circular RNAs (circRNAs) in the progression of osteosarcoma. This study aimed to investigate a novel circRNA, hsa_circ_0020378 (circ_0020378), and elucidate its functions and underlying mechanisms during osteosarcoma progression. The expression levels of circ_0020378, miR-339-3p, and COL1A1 in osteosarcoma cells and tissues were determined using RT-qPCR or Western blotting. CCK8, transwell migration, colony formation, and xenograft experiments were performed to assess the malignancy of osteosarcoma cells. Luciferase and RNA immunoprecipitation (RIP) experiments were employed to validate the interactions of miR-339-3p with circ_0020378 and COL1A1 3'UTR. Osteosarcoma cells and tissues showed significant upregulation of circ_0020378 and COL1A1 and downregulation of miR-339-3p. Silencing circ_0020378 in osteosarcoma cells inhibited their proliferation, colony formation, and migration. The inhibitive influence of circ_0020378 silencing during osteosarcoma tumorigenesis in vitro was verified in vivo. Circ_0020378 sponged miR-339-3p which targeted COL1A1 3'UTR. Circ _0020378 silencing disrupted the tumor-promoting effect of the miR-339-3p inhibitor in osteosarcoma cells. Furthermore, miR-339-3p inhibitor attenuated the suppressive effect of COL1A1 downregulation on malignant osteosarcoma cell phenotypes. Circ_0020378 stimulates osteosarcoma progression by downregulating miR-339-3p/COL1A1 expression. These findings provide a theoretical basis for the discovery of novel osteosarcoma targets.

Pervasive downstream RNA hairpins dynamically dictate start-codon selection.

Translational reprogramming allows organisms to adapt to changing conditions. Upstream start codons (uAUGs), which are prevalently present in mRNAs, have crucial roles in regulating translation by providing alternative translation start sites1-4. However, what determines this selective initiation of translation between conditions remains unclear. Here, by integrating transcriptome-wide translational and structural analyses during pattern-triggered immunity in Arabidopsis, we found that transcripts with immune-induced translation are enriched with upstream open reading frames (uORFs). Without infection, these uORFs are selectively translated owing to hairpins immediately downstream of uAUGs, presumably by slowing and engaging the scanning preinitiation complex. Modelling using deep learning provides unbiased support for these recognizable double-stranded RNA structures downstream of uAUGs (which we term uAUG-ds) being responsible for the selective translation of uAUGs, and allows the prediction and rational design of translating uAUG-ds. We found that uAUG-ds-mediated regulation can be generalized to human cells. Moreover, uAUG-ds-mediated start-codon selection is dynamically regulated. After immune challenge in plants, induced RNA helicases that are homologous to Ded1p in yeast and DDX3X in humans resolve these structures, allowing ribosomes to bypass uAUGs to translate downstream defence proteins. This study shows that mRNA structures dynamically regulate start-codon selection. The prevalence of this RNA structural feature and the conservation of RNA helicases across kingdoms suggest that mRNA structural remodelling is a general feature of translational reprogramming.

PrismNet: predicting protein-RNA interaction using in vivo RNA structural information.

Fundamental to post-transcriptional regulation, the in vivo binding of RNA binding proteins (RBPs) on their RNA targets heavily depends on RNA structures. To date, most methods for RBP-RNA interaction prediction are based on RNA structures predicted from sequences, which do not consider the various intracellular environments and thus cannot predict cell type-specific RBP-RNA interactions. Here, we present a web server PrismNet that uses a deep learning tool to integrate in vivo RNA secondary structures measured by icSHAPE experiments with RBP binding site information from UV cross-linking and immunoprecipitation in the same cell lines to predict cell type-specific RBP-RNA interactions. Taking an RBP and an RNA region with sequential and structural information as input ('Sequence & Structure' mode), PrismNet outputs the binding probability of the RBP and this RNA region, together with a saliency map and a sequence-structure integrative motif. The web server is freely available at http://prismnetweb.zhanglab.net.

Prediction of Dynamic RBP-RNA Interactions Using PrismNet.

A capacity to detect the binding profiles of RNA targets for an RNA-binding protein (RBP) under different cellular conditions is essential to understand the functions of the RBP in posttranscriptional regulation. However, the prediction of RBP binding sites in vivo remains challenging. Tools that predict RBP-RNA interactions using sequence and/or predicted structures cannot reflect the exact state of RNA in vivo. PrismNet, which uses both sequences and in vivo RNA structure information from probing experiments, can accurately predict RBP binding under different cellular conditions by deep learning, and can be applied for functional studies of RBPs. Here, we provide a detailed protocol showing how to train a PrismNet model of RBP-RNA interactions for an RBP, and how to apply the model for predictions of the RBP binding under different conditions.

LncRNA-Smad7 mediates cross-talk between Nodal/TGF-ß and BMP signaling to regulate cell fate determination of pluripotent and multipotent cells.

Transforming growth factor ß (TGF-ß) superfamily proteins are potent regulators of cellular development and differentiation. Nodal/Activin/TGF-ß and BMP ligands are both present in the intra- and extracellular milieu during early development, and cross-talk between these two branches of developmental signaling is currently the subject of intense research focus. Here, we show that the Nodal induced lncRNA-Smad7 regulates cell fate determination via repression of BMP signaling in mouse embryonic stem cells (mESCs). Depletion of lncRNA-Smad7 dramatically impairs cardiomyocyte differentiation in mESCs. Moreover, lncRNA-Smad7 represses Bmp2 expression through binding with the Bmp2 promoter region via (CA)12-repeats that forms an R-loop. Importantly, Bmp2 knockdown rescues defects in cardiomyocyte differentiation induced by lncRNA-Smad7 knockdown. Hence, lncRNA-Smad7 antagonizes BMP signaling in mESCs, and similarly regulates cell fate determination between osteocyte and myocyte formation in C2C12 mouse myoblasts. Moreover, lncRNA-Smad7 associates with hnRNPK in mESCs and hnRNPK binds at the Bmp2 promoter, potentially contributing to Bmp2 expression repression. The antagonistic effects between Nodal/TGF-ß and BMP signaling via lncRNA-Smad7 described in this work provides a framework for understanding cell fate determination in early development.

Single-cell transcriptome and translatome dual-omics reveals potential mechanisms of human oocyte maturation.

The combined use of transcriptome and translatome as indicators of gene expression profiles is usually more accurate than the use of transcriptomes alone, especially in cell types governed by translational regulation, such as mammalian oocytes. Here, we developed a dual-omics methodology that includes both transcriptome and translatome sequencing (T&T-seq) of single-cell oocyte samples, and we used it to characterize the transcriptomes and translatomes during mouse and human oocyte maturation. T&T-seq analysis revealed distinct translational expression patterns between mouse and human oocytes and delineated a sequential gene expression regulation from the cytoplasm to the nucleus during human oocyte maturation. By these means, we also identified a functional role of OOSP2 inducing factor in human oocyte maturation, as human recombinant OOSP2 induced in vitro maturation of human oocytes, which was blocked by anti-OOSP2. Single-oocyte T&T-seq analyses further elucidated that OOSP2 induces specific signaling pathways, including small GTPases, through translational regulation.

Anomalously High Ionic Conductivity of Li2SiS3-Type Conductors.

Solid-state electrolytes that exhibit high ionic conductivities at room temperature are key materials for obtaining the next generation of safer, higher-specific-energy solid-state batteries. However, the number of currently available crystal structures for use as superionic conductors remains limited. Here, we report a lithium superionic conductor, Li2SiS3, with tetragonal crystal symmetry, which possesses a new three-dimensional framework structure consisting of isolated edge-sharing tetrahedral dimers. This species exhibits an anomalously high ionic conductivity of 2.4 mS cm-1 at 298 K, which is 3 orders of magnitude higher than the reported ionic conductivity for its orthorhombic polymorph. The framework of this conductor consists mainly of silicon, which is abundant in natural resources, and its further optimization may lead to the development of new solid-state electrolytes for large-scale applications.

Comparison of viral RNA-host protein interactomes across pathogenic RNA viruses informs rapid antiviral drug discovery for SARS-CoV-2.

In contrast to the extensive research about viral protein-host protein interactions that has revealed major insights about how RNA viruses engage with host cells during infection, few studies have examined interactions between host factors and viral RNAs (vRNAs). Here, we profiled vRNA-host protein interactomes for three RNA virus pathogens (SARS-CoV-2, Zika, and Ebola viruses) using ChIRP-MS. Comparative interactome analyses discovered both common and virus-specific host responses and vRNA-associated proteins that variously promote or restrict viral infection. In particular, SARS-CoV-2 binds and hijacks the host factor IGF2BP1 to stabilize vRNA and augment viral translation. Our interactome-informed drug repurposing efforts identified several FDA-approved drugs (e.g., Cepharanthine) as broad-spectrum antivirals in cells and hACE2 transgenic mice. A co-treatment comprising Cepharanthine and Trifluoperazine was highly potent against the newly emerged SARS-CoV-2 B.1.351 variant. Thus, our study illustrates the scientific and medical discovery utility of adopting a comparative vRNA-host protein interactome perspective.

Predicting dynamic cellular protein-RNA interactions by deep learning using in vivo RNA structures.

Interactions with RNA-binding proteins (RBPs) are integral to RNA function and cellular regulation, and dynamically reflect specific cellular conditions. However, presently available tools for predicting RBP-RNA interactions employ RNA sequence and/or predicted RNA structures, and therefore do not capture their condition-dependent nature. Here, after profiling transcriptome-wide in vivo RNA secondary structures in seven cell types, we developed PrismNet, a deep learning tool that integrates experimental in vivo RNA structure data and RBP binding data for matched cells to accurately predict dynamic RBP binding in various cellular conditions. PrismNet results for 168 RBPs support its utility for both understanding CLIP-seq results and largely extending such interaction data to accurately analyze additional cell types. Further, PrismNet employs an "attention" strategy to computationally identify exact RBP-binding nucleotides, and we discovered enrichment among dynamic RBP-binding sites for structure-changing variants (riboSNitches), which can link genetic diseases with dysregulated RBP bindings. Our rich profiling data and deep learning-based prediction tool provide access to a previously inaccessible layer of cell-type-specific RBP-RNA interactions, with clear utility for understanding and treating human diseases.

In vivo structural characterization of the SARS-CoV-2 RNA genome identifies host proteins vulnerable to repurposed drugs.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the ongoing coronavirus disease 2019 (COVID-19) pandemic. Understanding of the RNA virus and its interactions with host proteins could improve therapeutic interventions for COVID-19. By using icSHAPE, we determined the structural landscape of SARS-CoV-2 RNA in infected human cells and from refolded RNAs, as well as the regulatory untranslated regions of SARS-CoV-2 and six other coronaviruses. We validated several structural elements predicted in silico and discovered structural features that affect the translation and abundance of subgenomic viral RNAs in cells. The structural data informed a deep-learning tool to predict 42 host proteins that bind to SARS-CoV-2 RNA. Strikingly, antisense oligonucleotides targeting the structural elements and FDA-approved drugs inhibiting the SARS-CoV-2 RNA binding proteins dramatically reduced SARS-CoV-2 infection in cells derived from human liver and lung tumors. Our findings thus shed light on coronavirus and reveal multiple candidate therapeutics for COVID-19 treatment.

Acupoint Injection for Nonspecific Chronic Low Back Pain: A Systematic Review and Meta-Analysis of Randomized Controlled Studies.

INTRODUCTION: Nonspecific chronic low back pain (NCLBP) became a public health and economic problem. Acupoint injection was used widely for patients with NCLBP. However, there were inconsistent results on the efficacy for these people. Therefore, this review was performed to systematically assess the efficacy and safety of acupoint injection. MATERIALS AND METHODS: The literature sources were collected via EMBASE, Medline, CENTRAL, CINAHL, CNKI, VIP, Wanfang, and Sino-Med Database from their inception to October 13, 2019. Endnote X7, widely used document management software, was used to manage and screen the literature sources. Each record was screened according to the predetermined inclusion criteria by two review authors independently. Quality assessment tool, "Risk of table," was used to assess the quality of the included studies according to the recommendation of the Cochrane Handbook for Systematic Reviews of Interventions. Data extraction was performed by one reviewer and verified by another reviewer. Any disagreement was addressed via consulting with a third reviewer in the abovementioned processes. All procedures were performed according to the Cochrane Handbook for Systematic Reviews of Interventions. RESULTS: This review included 13 studies involving 1381 patients with NCLBP. Quantitative analysis results indicated that there is no sufficient evidence that acupoint injection can improve the pain of patients with low back pain based on two trails: Visual Analogue Scale (VAS: MD = -1.33, 95% confidence interval (95% CI) -3.30 to 0.64, P=0.18, random-effect model). When assessing the effectiveness of acupoint injection therapy, the results indicated that acupoint injection can improve the effective rate for nonspecific chronic low back pain (OR = 3.64, 95% CI 2.4 to 5.21, P < 0.0001, fixed-effect model). CONCLUSION: There is insufficient evidence to indicate that acupoint injection therapy could improve the pain for patients with NCLBP. However, the level of evidence was downgraded to "very low quality" because of the poor methodological quality and clinical heterogeneity. The results should be interpreted with caution. Higher quality RCTs with more appropriate comparison, more objective outcome instruments, and adequate follow-up periods are necessary to assess the efficacy of acupoint injection for NCLBP. The PROSPERO Research registration identifying number is CRD42019119158.

RNA structure maps across mammalian cellular compartments.

RNA structure is intimately connected to each step of gene expression. Recent advances have enabled transcriptome-wide maps of RNA secondary structure, called 'RNA structuromes'. However, previous whole-cell analyses lacked the resolution to unravel the landscape and also the regulatory mechanisms of RNA structural changes across subcellular compartments. Here we reveal the RNA structuromes in three compartments, chromatin, nucleoplasm and cytoplasm, in human and mouse cells. The cytotopic structuromes substantially expand RNA structural information and enable detailed investigation of the central role of RNA structure in linking transcription, translation and RNA decay. We develop a resource with which to visualize the interplay of RNA-protein interactions, RNA modifications and RNA structure and predict both direct and indirect reader proteins of RNA modifications. We also validate a novel role for the RNA-binding protein LIN28A as an N6-methyladenosine modification 'anti-reader'. Our results highlight the dynamic nature of RNA structures and its functional importance in gene regulation.

4,6-Substituted-1H-Indazoles as potent IDO1/TDO dual inhibitors.

Indoleamine 2,3-dioxygenase 1 (IDO1) and tryptophan 2,3-dioxygenase (TDO) are constitutively overexpressed in many types of cancer cells and exert important immunosuppressive functions. In this article, a series of 4,6-substituted-1H-indazole derivatives were synthesized and evaluated the inhibitory activities against IDO1 and TDO, as well as their structure-activity relationships (SARs). Among these, compound 35 displayed the most IDO1 inhibitory potency with an IC50 value of 0.74 µM in an enzymatic assay and 1.37 µM in HeLa cells. Quantitative analysis of the Western blot results indicated that 35 significantly decreased the INFγ-induced IDO1 expression in a concentration-dependent manner. In addition, 35 showed promising TDO inhibition with an IC50 value of 2.93 µM in the enzymatic assay and 7.54 µM in A172 cells. Moreover, compound 35 exhibited in vivo antitumor activity in the CT26 xenograft model. These findings suggest that 1H-indazole derivative 35 is a potent IDO1/TDO dual inhibitor, and has the potential to be developed for IDO1/TDO-related cancer treatment.

Integrative Analysis of Zika Virus Genome RNA Structure Reveals Critical Determinants of Viral Infectivity.

Zika virus (ZIKV) strains can be classified into the ancestral African and contemporary Asian lineages, with the latter responsible for recent epidemics associated with neurological conditions. To understand how Asian strains lead to exacerbated disease, a crucial step is identifying genomic variations that affect infectivity and pathogenicity. Here we use two high-throughput sequencing approaches to assess RNA secondary structures and intramolecular RNA-RNA interactions in vivo for the RNA genomes of Asian and African ZIKV lineages. Our analysis identified functional RNA structural elements and a functional long-range intramolecular interaction specific for the Asian epidemic strains. Mutants that disrupt this extended RNA interaction between the 5' UTR and the E protein coding region reduce virus infectivity, which is partially rescued with compensatory mutants, restoring this RNA-RNA interaction. These findings illuminate the structural basis of ZIKV regulation and provide a resource for the discovery of RNA structural elements important for ZIKV infection.

Widespread of horizontal gene transfer in the human genome.

BACKGROUND: A fundamental concept in biology is that heritable material is passed from parents to offspring, a process called vertical gene transfer. An alternative mechanism of gene acquisition is through horizontal gene transfer (HGT), which involves movement of genetic materials between different species. Horizontal gene transfer has been found prevalent in prokaryotes but very rare in eukaryote. In this paper, we investigate horizontal gene transfer in the human genome. RESULTS: From the pair-wise alignments between human genome and 53 vertebrate genomes, 1,467 human genome regions (2.6 M bases) from all chromosomes were found to be more conserved with non-mammals than with most mammals. These human genome regions involve 642 known genes, which are enriched with ion binding. Compared to known horizontal gene transfer regions in the human genome, there were few overlapping regions, which indicated horizontal gene transfer is more common than we expected in the human genome. CONCLUSIONS: Horizontal gene transfer impacts hundreds of human genes and this study provided insight into potential mechanisms of HGT in the human genome.

Microcrystalline preparation of akebia saponin D for its bioavailability enhancement in rats.

Akebia Saponin D (ASD) or asperosaponin VI is the most abundant constituent of the rhizome of Dipsacus asper, which has been used for the treatment of lower back pain, traumatic hematoma and bone fractures. In recent years, it was reported that ASD was a potential treatment strategy for Alzheimer's disease (AD). However, the low bioavailability of ASD limited its clinical utility. Microcrystalline preparation is one of the effective methods to improve drug absorption. The drugs prepared by different methods can present different solid forms (polymorphs), and different polymorphs have significantly different bioavailabilities. The objective of this study was to prepare ASD polymorphs using the different preparation processes and to evaluate their physicochemical properties and oral absorption. ASD-2 obtained by the antisolvent process was simpler and had higher recovery (78.5%) than that of ASD-1 by a two-step macroporous resin column separation (56.5%). The ASD polymorphs were characterized using differential scanning calorimetry (DSC), thermogravimetry analysis (TGA), powder X-ray diffraction (PXRD) and scanning electron microscopy (SEM). The results revealed that ASD-2 existed in microcrystalline form, while ASD-1 was amorphous. Furthermore, the equilibrium solubility, dissolution in aqueous solution and pharmacokinetic parameters of the samples were determined. ASD-2 showed lower aqueous solubility than that of ASD-1 (p < 0.01). In addition, ASD-2 showed lower dissolution with only 65% of the drug released while ASD-1 had a higher dissolution with 99% of drug released at the end of the 180 min testing period. Although ASD-1 significantly increased solubility and dissolution, the AUC 0-20h of ASD-2 was 4.3 times that of the amorphous ASD-1 in vivo. Data suggest that the microcrystalline preparation of ASD-2 is not only reasonable in economy and suitable for large-scale preparation, but also a promising method to enhance bioavailability of ASD.

Simultaneous quantification of Akebia saponin D and its five metabolites in human intestinal bacteria using ultra-performance liquid chromatography triple quadrupole mass spectrometry.

A rapid and sensitive ultra-performance liquid chromatography triple quadrupole mass spectrometry (UPLC-TQ/MS) method was developed for simultaneous quantification of Akebia saponin D (ASD) and its five metabolites in intestinal mixtures of bacteria from human feces. After protein precipitation, the analytes and internal standard (IS), glycyrrhetinic acid, were determined in selected ion recording (SIR) mode with negative ion ESI source. Chromatographic separation was carried out on an ACQUITY UPLC™ BEH C18 column (100mm×2.1mm, 1.7µm) using gradient elution. The mobile phase consisted of solvents A (acetonitrile) and B (0.1% aqueous formic acid) at the flow rate of 0.4mL/min. Each sample was chromatographed within 10.5min including equilibration time. The linearity ranged from 0.1 to 100µg/mL for ASD, and 2-1000ng/mL for five metabolites, Dipsacus saponin A (M1), HN-saponin F (M2), hederagenin-28-O-ß-d-glucopyranoside (M3), Akebia saponin PA (M4), hederagenin (M5). The limits of detection (LOD) were 0.41, 0.59, 0.61, 0.55, 0.52 and 0.31ng/mL for ASD, M1, M2, M3, M4 and M5, respectively. The intra- and inter-day precision was all within 11.1% and accuracy ranged from -8.33% to 12.47%. The conversion rate of five metabolites was 41.21% in 24h. The method was validated and successfully applied to quantification of ASD and its five metabolites in human intestinal bacteria.