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"Shi, Jian"
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Machine learning and bioinformatics approaches for classification and clinical detection of bevacizumab responsive glioblastoma subtypes based on miRNA expression
2022
For the precise treatment of patients with glioblastoma multiforme (GBM), we classified and detected bevacizumab (BVZ)-responsive subtypes of GBM and found their differential expression (DE) of miRNAs and mRNAs, clinical characteristics, and related functional pathways. Based on miR-21 and miR-10b expression z-scores, approximately 30% of GBM patients were classified as having the GBM BVZ-responsive subtype. For this subtype, GBM patients had a significantly shorter survival time than other GBM patients (
p
= 0.014), and vascular endothelial growth factor A (VEGF) methylation was significantly lower than that in other GBM patients (
p
= 0.005). It also revealed 14 DE miRNAs and 7 DE mRNAs and revealed functional characteristics between GBM BVZ subgroups. After comparing several machine learning algorithms, the construction and cross-validation of the SVM classifier were performed. For clinical use, miR-197 was optimized and added to the miRNA panel for better classification. Afterwards, we validated the classifier with several GBM datasets and discovered some key related issues. According to this study, GBM BVZ subtypes can be classified and detected by a combination of SVM classifiers and miRNA panels in existing tissue GBM datasets. With certain modifications, the classifier may be used for the classification and detection of GBM BVZ subtypes for future clinical use.
Journal Article
Tumor Necrosis Factor Receptor-Associated Factor Regulation of Nuclear Factor κB and Mitogen-Activated Protein Kinase Pathways
2018
Tumor necrosis factor receptor (TNFR)-associated factors (TRAFs) are a family of structurally related proteins that transduces signals from members of TNFR superfamily and various other immune receptors. Major downstream signaling events mediated by the TRAF molecules include activation of the transcription factor nuclear factor κB (NF-κB) and the mitogen-activated protein kinases (MAPKs). In addition, some TRAF family members, particularly TRAF2 and TRAF3, serve as negative regulators of specific signaling pathways, such as the noncanonical NF-κB and proinflammatory toll-like receptor pathways. Thus, TRAFs possess important and complex signaling functions in the immune system and play an important role in regulating immune and inflammatory responses. This review will focus on the role of TRAF proteins in the regulation of NF-κB and MAPK signaling pathways.
Journal Article
DPDDI: a deep predictor for drug-drug interactions
2020
Background
The treatment of complex diseases by taking multiple drugs becomes increasingly popular. However, drug-drug interactions (DDIs) may give rise to the risk of unanticipated adverse effects and even unknown toxicity. DDI detection in the wet lab is expensive and time-consuming. Thus, it is highly desired to develop the computational methods for predicting DDIs. Generally, most of the existing computational methods predict DDIs by extracting the chemical and biological features of drugs from diverse drug-related properties, however some drug properties are costly to obtain and not available in many cases.
Results
In this work, we presented a novel method (namely DPDDI) to predict DDIs by extracting the network structure features of drugs from DDI network with graph convolution network (GCN), and the deep neural network (DNN) model as a predictor. GCN learns the low-dimensional feature representations of drugs by capturing the topological relationship of drugs in DDI network. DNN predictor concatenates the latent feature vectors of any two drugs as the feature vector of the corresponding drug pairs to train a DNN for predicting the potential drug-drug interactions. Experiment results show that, the newly proposed DPDDI method outperforms four other state-of-the-art methods; the GCN-derived latent features include more DDI information than other features derived from chemical, biological or anatomical properties of drugs; and the concatenation feature aggregation operator is better than two other feature aggregation operators (i.e., inner product and summation). The results in case studies confirm that DPDDI achieves reasonable performance in predicting new DDIs.
Conclusion
We proposed an effective and robust method DPDDI to predict the potential DDIs by utilizing the DDI network information without considering the drug properties (i.e., drug chemical and biological properties). The method should also be useful in other DDI-related scenarios, such as the detection of unexpected side effects, and the guidance of drug combination.
Journal Article
Considering Exosomal miR-21 as a Biomarker for Cancer
Cancer is a fatal human disease. Early diagnosis of cancer is the most effective method to prevent cancer development and to achieve higher survival rates for patients. Many traditional diagnostic methods for cancer are still not sufficient for early, more convenient and accurate, and noninvasive diagnosis. Recently, the use of microRNAs (miRNAs), such as exosomal microRNA-21(miR-21), as potential biomarkers was widely reported. This initial systematic review analyzes the potential role of exosomal miR-21 as a general biomarker for cancers. A total of 10 studies involving 318 patients and 215 healthy controls have covered 10 types of cancers. The sensitivity and specificity of pooled studies were 75% (0.70–0.80) and 85% (0.81–0.91), with their 95% confidence intervals (CIs), while the area under the summary receiver operating characteristic curve (AUC) was 0.93. Additionally, we examined and evaluated almost all other issues about biomarkers, including cutoff points, internal controls and detection methods, from the literature. This initial meta-analysis indicates that exosomal miR-21 has a strong potential to be used as a universal biomarker to identify cancers, although as a general biomarker the case number for each cancer type is small. Based on the literature, a combination of miRNA panels and other cancer antigens, as well as a selection of appropriate internal controls, has the potential to serve as a more sensitive and accurate cancer diagnosis tool. Additional information on miR-21 would further support its use as a biomarker in cancer.
Journal Article
Regulatory networks between neurotrophins and miRNAs in brain diseases and cancers
2015
Neurotrophins are involved in many physiological and pathological processes in the nervous system. They regulate and modify signal transduction, transcription and translation in neurons. It is recently demonstrated that the neurotrophin expression is regulated by microRNAs (miRNAs), changing our views on neurotrophins and miRNAs. Generally, miRNAs regulate neurotrophins and their receptors in at least two ways: (1) miRNAs bind directly to the 3' untranslated region (UTR) of isoform-specific mRNAs and post-transcriptionally regulate their expression; (2) miRNAs bind to the 3' UTR of the regulatory factors of neurotrophins and regulate their expression. On the other hand, neurotrophins can regulate miRNAs. The results of BNDF research show that neurotrophins regulate miRNAs in at least three ways: (1) ERK stimulation enhances the activation of TRBP (HIV-1 TAR RNA-binding protein) and Dicer, leading to the upregulation of miRNA biogenesis; (2) ERK-dependent upregulation of Lin28a (RNA-binding proteins) blocks select miRNA biogenesis; (3) transcriptional regulation of miRNA expression through activation of transcription factors, including CREB and NF-KB. These regulatory processes integrate positive and negative regulatory loops in neurotrophin and miRNA signaling pathways, and also expand the function of neurotrophins and miRNAs. In this review, we summarize the current knowledge of the regulatory networks between neurotrophins and miRNAs in brain diseases and cancers, for which novel cutting edge therapeutic, delivery and diagnostic approaches are emerging.
Journal Article
Application of the Theory of Planned Behavior in Environmental Science: A Comprehensive Bibliometric Analysis
2019
Since the theory of planned behavior (TPB) was proposed by Ajzen in 1985, it has attracted extensive interest and been widely applied worldwide. Although an increasing number of studies have employed the TPB in the domain of environmental science, there have been no attempts to retrospectively analyze existing articles. The current study aimed to holistically understand the application status of the TPB in environmental science from a knowledge domain visualization perspective. A total of 531 journal articles were obtained through the Scopus database to perform a bibliometric analysis and content analysis. The results showed that waste management, green consumption, climate and environment, saving and conservation, and sustainable transportation are the primary research topics; the United States (U.S.), Mainland China, the United Kingdom (UK), and Malaysia are the most productive countries/regions. Moreover, the cross-disciplinary situations, main source journals, and key articles were revealed. Furthermore, the extended factors, integrated theories, major methods, specific groups, and control variables of environmental science research using the TPB were elaborated and integrated into a comprehensive application framework. Constructive criticisms were ultimately discussed. The findings contribute in several ways to help relevant researchers learn about the application of TPB to environmental science and provide new insights and holistic references for further research on environment-related behavior.
Journal Article
Highly Efficient Purely Organic Phosphorescence Light‐Emitting Diodes Employing a Donor–Acceptor Skeleton with a Phenoxaselenine Donor
by
Zhou, Jiadong
,
Qiu, Weidong
,
Liu, Denghui
in
Lifetime
,
Motion pictures
,
organic light‐emitting diode
2023
Purely organic room‐temperature phosphorescence (RTP) materials generally exhibit low phosphorescence quantum yield (ϕP) and long phosphorescence lifetime (τP) due to the theoretically spin‐forbidden triplet state. Herein, by introducing a donor–acceptor (D–A) skeleton with a phenoxaselenine donor, three nonaromatic amine donor containing compounds with high ϕP and short τP in amorphous films are developed. Besides the enhanced spin–orbit coupling (SOC) by the heavy‐atom effect of selenium, the D–A skeleton which facilitates orbital angular momentum change can further boost SOC, and severe nonradiative energy dissipation is also suppressed by the rigid molecular structure. Consequently, a record‐high external quantum efficiency of 19.5% are achieved for the RTP organic light‐emitting diode (OLED) based on 2‐(phenoxaselenin‐3‐yl)‐4,6‐diphenyl‐1,3,5‐triazine (PXSeDRZ). Moreover, voltage‐dependent color‐tunable emission and single‐molecule white emission are also realized. These results shed light on the broad prospects of purely organic phosphorescence materials as highly efficient OLED emitters especially for potential charming lighting applications. A record‐high external quantum efficiency approaching 20%, voltage‐dependent color‐tunable emissions and single‐molecule white emissions are realized for purely organic electro‐phosphorescence device employing a room‐temperature phosphorescence emitter with a planar donor–acceptor skeleton and a phenoxaselenine donor.
Journal Article
Gefitinib versus vinorelbine plus cisplatin as adjuvant treatment for stage II–IIIA (N1–N2) EGFR-mutant NSCLC (ADJUVANT/CTONG1104): a randomised, open-label, phase 3 study
2018
Cisplatin-based adjuvant chemotherapy is the standard of care for patients with resected stage II–IIIA non-small-cell lung cancer (NSCLC). RADIANT and SELECT trial data suggest patients with EGFR-mutant stage IB–IIIA resected NSCLC could benefit from adjuvant EGFR tyrosine kinase inhibitor treatment. We aimed to compare the efficacy of adjuvant gefitinib versus vinorelbine plus cisplatin in patients with completely resected EGFR-mutant stage II–IIIA (N1–N2) NSCLC.
We did a randomised, open-label, phase 3 trial at 27 centres in China. We enrolled patients aged 18–75 years with completely resected (R0), stage II–IIIA (N1–N2), EGFR-mutant (exon 19 deletion or exon 21 Leu858Arg) NSCLC. Patients were stratified by N stage and EGFR mutation status and randomised (1:1) by Pocock and Simon minimisation with a random element to either gefitinib (250 mg once daily) for 24 months or intravenous vinorelbine (25 mg/m2 on days 1 and 8) plus intravenous cisplatin (75 mg/m2 on day 1) every 3 weeks for four cycles. The primary endpoint was disease-free survival in the intention-to-treat population, which comprised all randomised patients; the safety population included all randomised patients who received at least one dose of study medication. Enrolment to the study is closed but survival follow-up is ongoing. The study is registered with ClinicalTrials.gov, number NCT01405079.
Between Sept 19, 2011, and April 24, 2014, 483 patients were screened and 222 patients were randomised, 111 to gefitinib and 111 to vinorelbine plus cisplatin. Median follow-up was 36·5 months (IQR 23·8–44·8). Median disease-free survival was significantly longer with gefitinib (28·7 months [95% CI 24·9–32·5]) than with vinorelbine plus cisplatin (18·0 months [13·6–22·3]; hazard ratio [HR] 0·60, 95% CI 0·42–0·87; p=0·0054). In the safety population, the most commonly reported grade 3 or worse adverse events in the gefitinib group (n=106) were raised alanine aminotransferase and asparate aminotransferase (two [2%] patients with each event vs none with vinorelbine plus cisplatin). In the vinorelbine plus cisplatin group (n=87), the most frequently reported grade 3 or worse adverse events were neutropenia (30 [34%] patients vs none with gefitinib), leucopenia (14 [16%] vs none), and vomiting (eight [9%] vs none). Serious adverse events were reported for seven (7%) patients who received gefitinib and 20 (23%) patients who received vinorelbine plus cisplatin. No interstitial lung disease was noted with gefitinib. No deaths were treatment related.
Adjuvant gefitinib led to significantly longer disease-free survival compared with that for vinorelbine plus cisplatin in patients with completely resected stage II–IIIA (N1–N2) EGFR-mutant NSCLC. Based on the superior disease-free survival, reduced toxicity, and improved quality of life, adjuvant gefitinib could be a potential treatment option compared with adjuvant chemotherapy in these patients. However, the duration of benefit with gefitinib after 24 months might be limited and overall survival data are not yet mature.
Guangdong Provincial Key Laboratory of Lung Cancer Translational Medicine; National Health and Family Planning Commission of People's Republic of China; Guangzhou Science and Technology Bureau; AstraZeneca China.
Journal Article
Colossal resistance switching and band gap modulation in a perovskite nickelate by electron doping
2014
The electronic properties of correlated oxides are exceptionally sensitive to the orbital occupancy of electrons. Here we report an electron doping strategy via a chemical route, where interstitial dopants (for example, hydrogen) can be reversibly intercalated, realizing a sharp phase transition in a model correlated perovskite nickelate SmNiO
3
. The electron configuration of
e
g
orbital of
in SmNiO
3
is modified by injecting and anchoring an extra electron, forming a strongly correlated
structure leading to the emergence of a new insulating phase. A reversible resistivity modulation greater than eight orders of magnitude is demonstrated at room temperature. A solid-state room temperature non-volatile proton-gated phase-change transistor is demonstrated based on this principle, which may inform new materials design for correlated oxide devices. Electron doping-driven phase transition accompanied by large conductance changes and band gap modulation opens up new directions to explore emerging electronic and photonic devices with correlated oxide systems.
Orbital occupancy by electrons has a large effect on electronic properties of correlated oxides. Here, the authors report a chemical doping strategy of a perovskite nickelate, leading to the observation of a new insulating phase and a reversible resistivity modulation greater than eight orders of magnitude.
Journal Article
Divanillyl sulfone suppresses NLRP3 inflammasome activation via inducing mitophagy to ameliorate chronic neuropathic pain in mice
2021
Background
Chronic neuropathic pain is a frequent sequel to peripheral nerve injury and maladaptive nervous system function. Divanillyl sulfone (DS), a novel structural derivative of 4,4′-dihydroxydibenzyl sulfoxide from a traditional Chinese medicine
Gastrodia elata
with anti-nociceptive effects, significantly alleviated neuropathic pain following intrathecal injection. Here, we aimed to investigate the underlying mechanisms of DS against neuropathic pain.
Methods
A chronic constrictive injury (CCI) mouse model of neuropathic pain induced by sciatic nerve ligation was performed to evaluate the effect of DS by measuring the limb withdrawal using Von Frey filament test. Immunofluorescence staining was used to assess the cell localizations and expressions of Iba-1, ASC, NLRP3, and ROS, the formation of autolysosome. The levels of NLRP3-related proteins (caspase-1, NLRP3, and IL-1β), mitophagy-related proteins (LC3, Beclin-1, and p62), and apoptosis-related proteins (Bcl-XL and Bax) were detected by Western blotting. The apoptosis of BV-2 cell and caspase activity were evaluated by flow cytometry.
Results
DS significantly alleviated the neuropathic pain by increasing the mechanical withdrawal threshold and inhibiting the activation of NLRP3 in CCI-induced model mice. Our findings indicated that DS promoted the mitophagy by increasing the LC3II and Beclin 1 and decreasing the levels of p62 protein in BV-2 cell. This is accompanied by the inhibition of NLRP3 activation, which was shown as inhibited the expression of NLRP3 in lysates as well as the secretion of mature caspase-1 p10 and IL-1β p17 in supernatants in cultured BV-2 microglia. In addition, DS could promote mitophagy-induced improvement of dysfunctional mitochondria by clearing intracellular ROS and restoring mitochondrial membrane potential.
Conclusion
Together, our findings demonstrated that DS ameliorate chronic neuropathic pain in mice by suppressing NLRP3 inflammasome activation induced by mitophagy in microglia. DS may be a promising therapeutic agent for chronic neuropathic pain.
Journal Article