CellTracer: a comprehensive database to dissect the causative multilevel interplay contributing to cell development trajectories.

During the complex process of tumour development, the unique destiny of cells is driven by the fine-tuning of multilevel features such as gene expression, network regulation and pathway activation. The dynamic formation of the tumour microenvironment influences the therapeutic response and clinical outcome. Thus, characterizing the developmental landscape and identifying driver features at multiple levels will help us understand the pathological development of disease in individual cell populations and further contribute to precision medicine. Here, we describe a database, CellTracer (http://bio-bigdata.hrbmu.edu.cn/CellTracer), which aims to dissect the causative multilevel interplay contributing to cell development trajectories. CellTracer consists of the gene expression profiles of 1 941 552 cells from 222 single-cell datasets and provides the development trajectories of different cell populations exhibiting diverse behaviours. By using CellTracer, users can explore the significant alterations in molecular events and causative multilevel crosstalk among genes, biological contexts, cell characteristics and clinical treatments along distinct cell development trajectories. CellTracer also provides 12 flexible tools to retrieve and analyse gene expression, cell cluster distribution, cell development trajectories, cell-state variations and their relationship under different conditions. Collectively, CellTracer will provide comprehensive insights for investigating the causative multilevel interplay contributing to cell development trajectories and serve as a foundational resource for biomarker discovery and therapeutic exploration within the tumour microenvironment.

LncACTdb 3.0: an updated database of experimentally supported ceRNA interactions and personalized networks contributing to precision medicine.

LncACTdb 3.0 is a comprehensive database of experimentally supported interactions among competing endogenous RNA (ceRNA) and the corresponding personalized networks contributing to precision medicine. LncACTdb 3.0 is freely available at http://bio-bigdata.hrbmu.edu.cn/LncACTdb or http://www.bio-bigdata.net/LncACTdb. We have updated the LncACTdb 3.0 database with several new features, including (i) 5669 experimentally validated ceRNA interactions across 25 species and 537 diseases/phenotypes through manual curation of published literature, (ii) personalized ceRNA interactions and networks for 16 228 patients from 62 datasets in TCGA and GEO, (iii) sub-cellular and extracellular vesicle locations of ceRNA manually curated from literature and data sources, (iv) more than 10 000 experimentally supported long noncoding RNA (lncRNA) biomarkers associated with tumor diagnosis and therapy, and (v) lncRNA/mRNA/miRNA expression profiles with clinical and pathological information of thousands of cancer patients. A panel of improved tools has been developed to explore the effects of ceRNA on individuals with specific pathological backgrounds. For example, a network tool provides a comprehensive view of lncRNA-related, patient-specific, and custom-designed ceRNA networks. LncACTdb 3.0 will provide novel insights for further studies of complex diseases at the individual level and will facilitate the development of precision medicine to treat such diseases.

Study on chemical profiling of bailing capsule and its potential mechanism against thyroiditis based on network pharmacology with molecular docking strategy.

Bailing capsule (BLC), a drug that is clinically administered to modulate the autoimmune system, exhibits promising therapeutic potential in the treatment of thyroiditis. This study elucidates the chemical profile of BLC and its potential therapeutic mechanism in thyroiditis, leveraging network pharmacology and molecular docking techniques. Utilizing ultra-high-performance liquid chromatography coupled with linear trap-Orbitrap mass spectrometry (UHPLC-LTQ-Orbitrap MS), 58 compounds were identified, the majority of which were nucleosides and amino acids. Utilizing the ultra-high-performance liquid chromatography coupled with triple quadrupole tandem mass spectrometry (UHPLC QqQ MS/MS) strategy, 16 representative active components from six batches of BLCs were simultaneously determined. Network pharmacology analysis further revealed that the active components included 5'-adenylate, guanosine, adenosine, cordycepin, inosine, 5'-guanylic acid, and l-lysine. Targets with higher connectivity included AKT1, MAPK3, RAC1, and PIK3CA. The signaling pathways primarily focused on thyroid hormone regulation and the Ras, PI3K/AKT, and MAPK pathways, all of which were intricately linked to inflammatory immunity and hormonal regulation. Molecular docking analysis corroborated the findings from network pharmacology, revealing that adenosine, guanosine, and cordycepin exhibited strong affinity toward AKT1, MAPK3, PIK3CA, and RAC1. Overall, this study successfully elucidated the material basis and preliminary mechanism underlying BLC's intervention in thyroiditis, thus laying a solid basis for further exploration of its in-depth mechanisms.

METTL3-mediated m6A modification of SIRT1 mRNA inhibits progression of endometriosis by cellular senescence enhancing.

BACKGROUND: Endometriosis (EMs), the ectopic planting of functional endometrium outside of the uterus, is a leading cause of infertility and pelvic pain. As a fundamental mRNA modification, N6-methyladenosine (m6A) participates in various pathological processes. However, the role of m6A RNA modification in endometriosis remains unclear. The present study explores METTL3-mediated m6A modification and the mechanisms involved in endometriosis. METHODS: The dominant m6A regulators in EMs were analysed using RT‒PCR. Candidate targets and possible mechanisms of METTL3 were assessed by m6A-mRNA epitranscriptomic microarray and RNA sequencing. A primary ESCs model was employed to verify the effect of METTL3 on m6A modification of SIRT1 mRNA, and the mechanism was elucidated by RT‒PCR, Western blotting, MeRIP, and RIP assays. CCK-8 viability assays, Transwell invasion assays, EdU proliferation assays, wound healing migration assays, and senescence-associated ß-galactosidase staining were performed to illuminate the potential biological mechanism of METTL3 and SIRT1 in ESCs in vitro. An in vivo PgrCre/ + METTL3 -/- female homozygous mouse model and a nude mouse xenograft model were employed to further investigate the physiologic consequences of METTL3-mediated m6A alteration on EMs. RESULTS: Our data show that decreased METTL3 expression significantly downregulates m6A RNA methylation levels in ESCs. Silencing m6A modifications mediated by METTL3 accelerates ESCs viability, proliferation, migration, and invasion in vitro. The m6A reader protein YTHDF2 binds to m6A modifications to induce the degradation of SIRT1 mRNA. SIRT1/FOXO3a signalling pathway activation is subsequently inhibited, promoting the cellular senescence of ESCs and inhibiting the ectopic implantation of ESCs in vitro and in vivo. CONCLUSIONS: Our findings demonstrate that METTL3-mediated m6A methylation epigenetically regulates the ectopic implantation of ESCs, resulting in the progression of endometriosis. Our study establishes METTL3-YTHDF2-SIRT1/FOXO3a as a critical axis and potential mechanism in endometriosis.

Design, synthesis and antitumor activity of novel thiophene- triazine derivatives bearing arylurea unit as potent PI3K/mTOR inhibitorss.

In this article, we designed and synthesized a series of novel thiophene-triazine derivatives bearing arylurea unit as potent dual PI3K/mTOR inhibitors. The cytotoxicity of all the target compounds were evaluated against nine cancer cell lines (breast cancer cell line MCF-7, lung cancer cell lines A549, NCI-H460, H2228 and H1975, cervical cancer cell lines Hela and Hela-MDR, ovarian cancer cell lines Ovcar-2 and glioma U87MG) and the kinase inhibitory activity against PI3K/mTOR kinases was also tested. The results demonstrated that most of the target compounds exhibited moderate to excellent activity and high selectivity against one or more cancer cell lines. Among them, seven compounds displayed better activity than lead compound GDC-0941. The inhibitory activity of the most promising compound on nine cancer cell lines was 302.5 times better than that of GDC-0941 with the IC50 values as low as 0.008 ± 0.002 µM, and the inhibitory activity against PI3Kα and mTOR kinase was excellent, with the IC50 values of 177.41 and 12.24 nM, respectively, indicating that it was a potential dual PI3Kα/mTOR inhibitor. The Structure-Activity Relationships (SARs) indicated that the introduction of the arylurea group significantly improved the cellular and kinase activities of the target compounds. Moreover, the results of toxicity and hemolysis experiments demonstrated that the most promising compound had low toxicity and good safety. The results of PCR assay and molecular docking modes showed that it was a potential PI3K/mTOR inhibitor, which was worthy of further study.

Combination of ferroptosis and pyroptosis dual induction by triptolide nano-MOFs for immunotherapy of Melanoma.

Immunotherapy has good potential to eradicate tumors in the long term. However, due to the low immunogenicity of tumor cells, current cancer immunotherapies are not effective. To address this limitation, we constructed a BSA-FA functionalized iron-containing metal-organic framework (TPL@TFBF) that triggers a potent systemic anti-tumor immune response by inducing ferroptosis and pyroptosis in tumor cells and releasing large quantities of damage-associated molecular patterns (DAMPs) to induce immunogenicity, and showing excellent efficacy against melanoma lung metastases in vivo. This nanoplatform forms a metal-organic framework through the coordination between tannic acid (TA) and Fe3+ and is then loaded with triptolide (TPL), which is coated with FA-modified BSA. The nanoparticles target melanoma cells by FA modification, releasing TPL, Fe3+ and TA. Fe3+ is reduced to Fe2+ by TA, triggering the Fenton reaction and resulting in ROS production. Moreover, TPL increases the production of intracellular ROS by inhibiting the expression of nuclear factor erythroid-2 related factor (Nrf2). Such simultaneous amplification of intracellular ROS induces the cells to undergo ferroptosis and pyroptosis, releasing large amounts of DAMPs, which stimulate antigen presentation of dendritic cells (DCs) and the proliferation of cytotoxic T lymphocytes (CD4+/CD8 + T cells) to inhibit tumor and lung metastasis. In addition, combining nanoparticle treatment with immune checkpoint blockade (ICB) further inhibits melanoma growth. This work provides a new strategy for tumor immunotherapy based on various combinations of cell death mechanisms.

LnCeCell: a comprehensive database of predicted lncRNA-associated ceRNA networks at single-cell resolution.

Within the tumour microenvironment, cells exhibit different behaviours driven by fine-tuning of gene regulation. Identification of cellular-specific gene regulatory networks will deepen the understanding of disease pathology at single-cell resolution and contribute to the development of precision medicine. Here, we describe a database, LnCeCell (http://www.bio-bigdata.net/LnCeCell/ or http://bio-bigdata.hrbmu.edu.cn/LnCeCell/), which aims to document cellular-specific long non-coding RNA (lncRNA)-associated competing endogenous RNA (ceRNA) networks for personalised characterisation of diseases based on the 'One Cell, One World' theory. LnCeCell is curated with cellular-specific ceRNA regulations from >94 000 cells across 25 types of cancers and provides >9000 experimentally supported lncRNA biomarkers, associated with tumour metastasis, recurrence, prognosis, circulation, drug resistance, etc. For each cell, LnCeCell illustrates a global map of ceRNA sub-cellular locations, which have been manually curated from the literature and related data sources, and portrays a functional state atlas for a single cancer cell. LnCeCell also provides several flexible tools to infer ceRNA functions based on a specific cellular background. LnCeCell serves as an important resource for investigating the gene regulatory networks within a single cell and can help researchers understand the regulatory mechanisms underlying complex microbial ecosystems and individual phenotypes.

Cross-Talk between N6-Methyladenosine and Their Related RNAs Defined a Signature and Confirmed m6A Regulators for Diagnosis of Endometriosis.

An RNA modification known as N6-methyladenosine (m6A) interacts with a range of coding and non-coding RNAs. The majority of the research has focused on identifying m6A regulators that are differentially expressed in endometriosis, but it has ignored their mechanisms that are derived from the alterations of modifications among RNAs, affecting the disease progression primarily. Here, we aimed to investigate the potential roles of m6A regulators in the diagnostic potency, immune microenvironment, and clinicopathological features of endometriosis through interacting genes. A GEO cohort was incorporated into this study. Variance expression profiling was executed via the "limma" R package. Pearson analysis was performed to investigate the correlations among 767 interacting lncRNAs, 374 interacting mRNAs, and 23 m6A regulators. K-means clustering analysis, based on patterns of mRNA modifications, was applied to perform clinical feature analysis. Infiltrating immune cells and stromal cells were calculated using the Cibersort method. An m6A-related risk model was created and supported by an independent risk assay. LASSO regression analysis and Cox analyses were implemented to determine the diagnostic genes. The diagnostic targets of endometriosis were verified using PCR and the WB method. Results: A thorough investigation of the m6A modification patterns in the GEO database was carried out, based on mRNAs and lncRNAs related to these m6A regulators. Two molecular subtypes were identified using unsupervised clustering analysis, resulting in further complex infiltration levels of immune microenvironment cells in diversified endometriosis pathology types. We identified two m6A regulators, namely METTL3 and YTHDF2, as diagnostic targets of endometriosis following the usage of overlapping genes to construct a diagnostic m6A signature of endometriosis through multivariate logistic regression, and we validated it using independent GSE86534 and GSE105764 cohorts. Finally, we found that m6A alterations might be one of the important reasons for the progression of endometriosis, especially with significant downregulation of the expressions of METTL3 and YTHDF2. Finally, m6A modification patterns have significant effects on the diversity and complexity of the progression and immune microenvironment, and might be key diagnostic markers for endometriosis.

[Mechanism of Mongolian drug Naru-3 in initiation of neuroinflammation of neuropathic pain from MMP9/IL-1ß signaling pathway].

Neuropathic pain(NP) has similar phenotypes but different sequential neuroinflammatory mechanisms in the pathological process. It is of great significance to inhibit the initiation of neuroinflammation, which has become a new direction of NP treatment and drug development in recent years. Mongolian drug Naru-3 is clinically effective in the treatment of trigeminal neuralgia, sciatica, and other NPs in a short time, but its pharmacodynamic characteristics and mechanism of analgesia are still unclear. In this study, a spinal nerve ligation(SNL) model simulating clinical peripheral nerve injury was established and the efficacy and mechanism of Naru-3 in the treatment of NPs was discussed by means of behavioral detection, side effect evaluation, network analysis, and experimental verification. Pharmacodynamic results showed that Naru-3 increased the basic pain sensitivity threshold(mechanical hyperalgesia and thermal radiation hyperalgesia) in the initiation of SNL in animals and relieved spontaneous pain, however, there was no significant effect on the basic pain sensitivity threshold and motor coordination function of normal animals under physiological and pathological conditions. Meanwhile, the results of primary screening of target tissues showed that Naru-3 inhibited the second phase of injury-induced nociceptive response of formalin test in mice and reduced the expression of inflammatory factors in the spinal cord. Network analysis discovered that Naru-3 had synergy in the treatment of NP, and its mechanism was associated with core targets such as matrix metalloproteinase-9(MMP9) and interleukin-1ß(IL-1ß). The experiment further took the dorsal root ganglion(DRG) and the stage of patho-logical spinal cord as the research objects, focusing on the core targets of inducing microglial neuroinflammation. By means of Western blot, immunofluorescence, agonists, antagonists, behavior, etc., the mechanism of Naru-3 in exerting NP analgesia may be related to the negative regulation of the MMP9/IL-1ß signaling pathway-mediated microglia p38/IL-1ß inflammatory loop in the activation phase. The relevant research enriches the biological connotation of Naru-3 in the treatment of NP and provides references for clinical rational drug use.

[Baimai Ointment relieves chronic pain induced by chronic compression of dorsal root ganglion in rats by regulating neuroactive ligand-receptor interaction and HIF-1 signaling pathway].

The Baimai Ointment with the effect of relaxing sinew and activating collaterals demonstrates a definite effect on Baimai disease with pain, spasm, stiffness and other symptoms, while the pharmacodynamic characteristics and mechanism of this agent remain unclear. In this study, a rat model of chronic compression of L4 dorsal root ganglion(CCD) was established by lumbar disc herniation, and the efficacy and mechanism of Baimai Ointment in the treatment of CCD were preliminarily explored by behavioral tests, side effect evaluation, network analysis, antagonist and molecular biology verification. The pharmacodynamic experiment indicated that Baimai Ointment significantly improved the pain thresholds(mechanical pain, thermal pain, and cold pain) and gait behavior of CCD model rats without causing tolerance or obvious toxic and side effects. Baimai Ointment inhibited the second-phase nociceptive response of mice in the formalin test, increased the hot plate threshold of normal mice, and down-regulated the expression of inflammatory cytokines in the spinal cord. Network analysis showed that Baimai Ointment had synergistic effect in the treatment of CCD and was related to descending inhibition/facilitation system and neuroinflammation. Furthermore, behavioral tests, Western blot, and immunofluorescence assay revealed that the pain-relieving effect of Baimai Ointment on CCD may be related to the regulation of the interaction between neuroactive ligand and receptors(neuroligands) such as CHRNA7, ADRA2A, and ADRB2, and the down-regulation of the expression of NOS2/pERK/PI3K, the core regulatory element of HIF-1 signaling pathway in spinal microglia. The findings preliminarily reveal the mechanism of relaxing sinew and activating collaterals of Baimai Ointment in the treatment of Baimai disease, providing a reference for the rational drug use and further research of this agent.

A formal [4 + 2] annulation of diamines and prop-2-ynyl sulfonium salts for the synthesis of tetrahydroquinoxalines.

A formal [4 + 2] annulation of diamines and prop-2-ynyl sulfonium salts was developed. This strategy enables efficient access to tetrahydroquinoxalines in excellent yields.

LnCeVar: a comprehensive database of genomic variations that disturb ceRNA network regulation.

LnCeVar (http://www.bio-bigdata.net/LnCeVar/) is a comprehensive database that aims to provide genomic variations that disturb lncRNA-associated competing endogenous RNA (ceRNA) network regulation curated from the published literature and high-throughput data sets. LnCeVar curated 119 501 variation-ceRNA events from thousands of samples and cell lines, including: (i) more than 2000 experimentally supported circulating, drug-resistant and prognosis-related lncRNA biomarkers; (ii) 11 418 somatic mutation-ceRNA events from TCGA and COSMIC; (iii) 112 674 CNV-ceRNA events from TCGA; (iv) 67 066 SNP-ceRNA events from the 1000 Genomes Project. LnCeVar provides a user-friendly searching and browsing interface. In addition, as an important supplement of the database, several flexible tools have been developed to aid retrieval and analysis of the data. The LnCeVar-BLAST interface is a convenient way for users to search ceRNAs by interesting sequences. LnCeVar-Function is a tool for performing functional enrichment analysis. LnCeVar-Hallmark identifies dysregulated cancer hallmarks of variation-ceRNA events. LnCeVar-Survival performs COX regression analyses and produces survival curves for variation-ceRNA events. LnCeVar-Network identifies and creates a visualization of dysregulated variation-ceRNA networks. Collectively, LnCeVar will serve as an important resource for investigating the functions and mechanisms of personalized genomic variations that disturb ceRNA network regulation in human diseases.

Double Confinement Hydrogel Network Enables Continuously Regenerative Solar-to-Hydrogen Conversion.

Soft matter catalyst system allowing controllable manipulation of the organized nanostructure and surface property holds the potential for renewable energy. Here we demonstrate the construction of a continuously regenerative hydrogel photocatalyst that confines the metal-thiolate coordination induced nanocavity into robust micro-sized spongy network for water splitting. Thanks to low vaporization enthalpy and fast proton mobility of water molecules confining in nanocavities, the composite delivers outstanding photocatalytic H2 production (TOF of 4568 H2 h-1 ), nearly 4.5 times higher than that on the catalyst without confinements. Incorporating with conductive polymers, the TOF is substantially improved to 7819 H2 h-1 . Impressively, continuous regeneration is for the first time achieved with H2 production retention improved from 24 % to 72 % by regulating optically-active catalyst surfaces. This optical regeneration method provides new avenues for sustainable solar energy conversion.

Celastrol exerts a neuroprotective effect by directly binding to HMGB1 protein in cerebral ischemia-reperfusion.

BACKGROUND: Celastrol (cel) was one of the earliest isolated and identified chemical constituents of Tripterygium wilfordii Hook. f. Based on a cel probe (cel-p) that maintained the bioactivity of the parent compound, the targets of cel in cerebral ischemia-reperfusion (I/R) injury were comprehensively analyzed by a quantitative chemical proteomics method. METHODS: We constructed an oxygen-glucose deprivation (OGD) model in primary rat cortical neurons and a middle cerebral artery occlusion (MCAO) model in adult rats to detect the direct binding targets of cel in cerebral I/R. By combining various experimental methods, including tandem mass tag (TMT) labeling, mass spectrometry, and cellular thermal shift assay (CETSA), we revealed the targets to which cel directly bound to exert neuroprotective effects. RESULTS: We found that cel inhibited the proinflammatory activity of high mobility group protein 1 (HMGB1) by directly binding to it and then blocking the binding of HMGB1 to its inflammatory receptors in the microenvironment of ischemia and hypoxia. In addition, cel rescued neurons from OGD injury in vitro and decreased cerebral infarction in vivo by targeting HSP70 and NF-κB p65. CONCLUSION: Cel exhibited neuroprotective and anti-inflammatory effects by targeting HSP70 and NF-κB p65 and directly binding to HMGB1 in cerebral I/R injury.

LncACTdb 2.0: an updated database of experimentally supported ceRNA interactions curated from low- and high-throughput experiments.

We describe LncACTdb 2.0 (http://www.bio-bigdata.net/LncACTdb/), an updated and significantly expanded database which provides comprehensive information of competing endogenous RNAs (ceRNAs) in different species and diseases. We have updated LncACTdb 2.0 with more data and several new features, including (i) manually curating 2663 experimentally supported ceRNA interactions from >5000 published literatures; (ii) expanding the scope of the database up to 23 species and 213 diseases/phenotypes; (iii) curating more ceRNA types such as circular RNAs and pseudogenes; (iv) identifying and scoring candidate lncRNA-associated ceRNA interactions across 33 cancer types from TCGA data; (v) providing illustration of survival, network and cancer hallmark information for ceRNAs. Furthermore, several flexible online tools including LncACT-Get, LncACT-Function, LncACT-Survival, LncACT-Network and LncACTBrowser have been developed to perform customized analysis, functional analysis, survival analysis, network illustration and genomic visualization. LncACTdb 2.0 also provides newly designed, user-friendly web interfaces to search, browse and download all the data. The BLAST interface is convenient for users to query dataset by inputting custom sequences. The Hot points interface provides users the most studied items by others. LncACTdb 2.0 is a continually updated database and will serve as an important resource to explore ceRNAs in physiological and pathological processes.

The clinical application of PIVKA-II in hepatocellular carcinoma and chronic liver diseases: A multi-center study in China.

BACKGROUND: Due to the absence of specific symptoms and low survival rate, efficient biomarkers for hepatocellular carcinoma (HCC) diagnosis are urgently required. The purpose of this study was to evaluate the diagnostic performance of protein induced by vitamin K absence or antagonist-II (PIVKA-II) and to determine the optimal cutoff values for HBV infection-related HCC. METHODS: We conducted a cross-sectional, multi-center study in China to ascertain the cutoff value for HCC patients in the context of CHB- and HBV-related cirrhosis. The receiver operating characteristic curve (ROC) and the area under the curve (AUC) were used to evaluate the diagnostic performance of PIVKA-II. RESULTS: This study enrolled 784 subjects and demonstrated that PIVKA-II had a sensitivity of 84.08% and a specificity of 90.43% in diagnosis HCC from chronic liver diseases. PIVKA-II at a cutoff of 37.5 mAU/mL yielded an AUC of 0.9737 (sensitivity 91.78% and specificity 96.30%) in discriminating HCC from chronic hepatitis B (CHB) patients. PIVKA-II at a cutoff of 45 mAU/mL yielded an AUC of 0.9419 (sensitivity 77.46% and specificity 95.12%) in discriminating HCC- from HBV-related cirrhosis patients. Furthermore, using a cutoff value of 40 mAU/mL for PIVKA-II as an HCC marker, only 4.81% (15/312) was positive in chronic hepatitis and 12.80% (37/289) in cirrhosis patients, revealing the satisfactory specificity of PIVKA-II in chronic liver disease of different etiologies. CONCLUSION: Our data indicated that PIVKA-II had satisfactory diagnostic efficiencies and could be used as a screening or surveillance biomarker in HCC high-risk population.

Correction to: Guizhi-Shaoyao-Zhimu decoction attenuates rheumatoid arthritis partially by reversing inflammation-immune system imbalance.

An amendment to this paper has been published and can be accessed via the original article.

Exploring and characterizing a novel combination of paeoniflorin and talatizidine for the treatment of rheumatoid arthritis.

Wutou Decoction (WTD) achieves favorable therapeutic response in treating rheumatoid arthritis (RA), especially for wind-cold-dampness stimulating RA. However, its material basis and molecular mechanisms remain unclear. To address this problem, the main bioactive compounds (BACs) of WTD against RA and the candidate targets were identified in the current study via transcriptional regulatory network analysis, computational structure-based methods, as well as in vivo and in vitro experimental validations. As a result, we successfully established a RA rat model named AIA-S, which simulated the clinical manifestations and pathological changes of wind-cold-dampness stimulating RA, and also displayed the distinctive characteristics and biological basis of inflammatory-immune system imbalance and abnormal energy metabolism changes. In addition, ALOX15B-PPAR-γ-PTGS2-FGF2-IL-1ß-c-JUN-MMP13-TGF-ß1 signal axis, involved into thermogenesis and energy metabolism, as well as maintaining the balance of inflammation-immune system, was identified as a candidate target of WTD against RA, according to the transcriptional regulatory network analysis on "RA-related gene-WTD-effective gene interaction network". Moreover, Paeoniflorin (PAE) and Talatizidine (TLT) were demonstrated to be the main BACs of WTD against RA for the following reasons: firstly, both PAE and TLT were the BACs of WTD according to ADME analysis in silico and the pharmacokinetics analysis in vivo. Secondly, both PAE and TLT were able to bind with PPAR-γ, c-JUN, MMP13 and TGF-ß1, which were the candidate targets of WTD against RA, with the strong binding affinity. Thirdly, the PAE and TLT combination exerted significant therapeutic effects on AIA-S rats through reversing the imbalance of inflammatory-immune system, and the disturbance of thermogenesis and energy metabolism, which were similar to WTD. More importantly, the administration of TLT or PAE alone didn't exert as prominently therapeutic effects as that of the two-BAC-combination did. Fourthly, the PAE and TLT combination promoted adipogenesis and lipogenesis by upregulating the PPAR-γ-induced lipogenic proteins. In conclusion, this study identified PAE and TLT as the main BACs of WTD in alleviating the severity of RA, and also developed a novel combination of PAE and TLT as a promising candidate drug for RA therapy.

Identification of potential prognostic TF-associated lncRNAs for predicting survival in ovarian cancer.

The pathophysiology of ovarian cancer (OV) is complex and depends on multiple biological processes and pathways. Therefore, there is an urgent need to identify reliable prognostic biomarkers for predicting clinical outcomes and helping personalize treatment of OV. A long non-coding RNA (lncRNA)-based risk score model was constructed to infer the prognostic efficacy of transcription factors (TFs) based on the OV dataset from The Cancer Genome Atlas. The risk score model was further validated in other independent cohorts from Gene Expression Omnibus. Time-dependent receiver operating characteristic curves were used to evaluate the survival prediction performance in comparison with other clinical and molecular variables. Our results revealed that the top-ranked TF-associating lncRNAs were significantly associated with overall survival, progression-free survival and disease-free survival. Stratification analysis according to clinical variables indicated the prognostic independence of POLR2A-associating lncRNAs. In comparison, the signature of POLR2A-associating lncRNAs was more sensitive and specific than existing clinical and molecular signatures. Functional and experimental analysis suggested that POLR2A-associating lncRNAs may be involved in known biological processes and pathways of OV. Our findings revealed that the lncRNA-based risk score model can provide helpful information on OV prognosis stratification and discovery of therapeutic biomarkers.

Theranostic Quercetin Nanoparticle for Treatment of Hepatic Fibrosis.

The progression of hepatic fibrosis can lead to cirrhosis and hepatic failure, but the development of antifibrotic drugs have faced the challenges of poor effectiveness and targeted specificity. Herein, a theranostic strategy was carried to encapsulate a natural medicine (Quercetin, QR) into hepatitis B core (HBc) protein nanocages (NCs) for imaging and targeted treatment of hepatic fibrosis. It was noted that nanoparticles (RGD-HBc/QR) with surface-displayed RGD targeting ligand exhibit a rather high selectivity toward activated HSCs via the binding affinity with integrin αvß3, and an efficient inhibition of proliferation and activation of hepatic stellate cells (HSCs) in vitro and in vivo. Once encapsulated in quercetin-gadolinium complex and/or labeled with the NIR fluorescent probes (Cy5.5), the resulting nanoparticles (RGD-HBc/QGd) show great potential as NIR fluorescent and magnetic resonance imaging contrast agents for hepatic fibrosis in vivo. Therefore, the multifunctional integrin-targeted nanoparticles could selectively deliver QR to the activated HSCs, and may provide an effective antifibrotic theranostic strategy.