Publications by authors named "Fangyuan Gao"

56 Publications

Nano-scale resolution of native retinal rod disk membranes reveals differences in lipid composition.

J Cell Biol 2021 Aug 16;220(8). Epub 2021 Jun 16.

Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA.

Photoreceptors rely on distinct membrane compartments to support their specialized function. Unlike protein localization, identification of critical differences in membrane content has not yet been expanded to lipids, due to the difficulty of isolating domain-specific samples. We have overcome this by using SMA to coimmunopurify membrane proteins and their native lipids from two regions of photoreceptor ROS disks. Each sample's copurified lipids were subjected to untargeted lipidomic and fatty acid analysis. Extensive differences between center (rhodopsin) and rim (ABCA4 and PRPH2/ROM1) samples included a lower PC to PE ratio and increased LC- and VLC-PUFAs in the center relative to the rim region, which was enriched in shorter, saturated FAs. The comparatively few differences between the two rim samples likely reflect specific protein-lipid interactions. High-resolution profiling of the ROS disk lipid composition gives new insights into how intricate membrane structure and protein activity are balanced within the ROS, and provides a model for future studies of other complex cellular structures.
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http://dx.doi.org/10.1083/jcb.202101063DOI Listing
August 2021

Fuzheng Jiedu Xiaoji formulation inhibits hepatocellular carcinoma progression in patients by targeting the AKT/CyclinD1/p21/p27 pathway.

Phytomedicine 2021 Jul 18;87:153575. Epub 2021 Apr 18.

Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing, China. Electronic address:

Background: Hepatocellular carcinoma (HCC) is a common malignant tumor with limited treatment options. Conventional antitumor therapy combined with traditional Chinese medicine (TCM) to limit tumor progression has gradually become the focus of complementary and alternative therapies for HCC treatment. The Fuzheng Jiedu Xiaoji formulation (FZJDXJ) alleviates the clinical symptoms of patients and inhibits tumor progression, but its curative effect still requires extensive clinical research and mechanistic analysis.

Purpose: To explore the effectiveness of FZJDXJ in HCC patients and investigate its biological function and mechanism underlying anticancer therapy.

Methods: This randomized controlled clinical trial enrolled 291 HCC patients receiving transcatheter arterial chemoembolization (TACE) therapy; patients received either FZJDXJ combined with standard treatment, or standard treatment alone, for 48 weeks. Statistical analyses were performed according to survival time at the end of the trial. The main constituents of the FZJDXJ extracts were identified and evaluated using high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) and molecular docking. The antitumor effects of FZJDXJ and its specific biological mechanism of action were studied.

Results: After 48 weeks of treatment, one-year overall survival (OS) and progression-free survival (PFS) were significantly different between the two groups. Co-administration of FZJDXJ and TACE prolonged the OS of HCC patients, especially in BCLC A or B stage. FZJDXJ and TACE treatment effectively extended the PFS of patients, especially in the BCLC B stage. HPLC-MS/MS identified 1619 active constituents of FZJDXJ, including formononetin, chlorogenic acid (CGA), caffeic acid, luteolin, gallic acid, diosgenin, ergosterol endoperoxide, and lupeol, which may function through the AKT/CyclinD1/p21/p27 pathways. Through molecular docking, CGA and gallic acid could effectively combine with Thr308, an important phosphorylation site of AKT1. FZJDXJ inhibited tumor growth in nude mice. In vitro, FZJDXJ-mediated serum inhibited the proliferation, migration, and invasion of liver cancer cells, and promoted cell apoptosis.

Conclusion: Clinically, FZJDXJ combined with TACE therapy significantly prolonged OS and PFS and reduced the mortality rate of HCC patients. Mechanistically, FZJDXJ effectively inhibited the proliferation and migration of liver cancer cells through the modulation of the AKT/CyclinD1/p21/p27 pathways, and may be a promising TCM drug for anti-HCC therapy.
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http://dx.doi.org/10.1016/j.phymed.2021.153575DOI Listing
July 2021

Metabolomics based comprehensive investigation of Gardeniae Fructus induced hepatotoxicity.

Food Chem Toxicol 2021 Jul 5;153:112250. Epub 2021 May 5.

School of Pharmacy, Second Military Medical University, Shanghai, 200433, China; Shanghai Key Laboratory for Pharmaceutical Metabolite Research, School of Pharmacy, Second Military Medical University, Shanghai, 200433, China. Electronic address:

Gardeniae Fructus (Zhizi in Chinese, ZZ in brief), a commonly used herbal medicine, has aroused wide concern for hepatotoxicity, but the mechanism remains to be investigated. This study was aimed at investigating the mechanism of ZZ-induced liver injury in vivo and in vitro based on metabolomics and evaluating the hepatotoxicity prediction ability of the in vitro model. SD rats were administered with extracted ZZ and HepG2 cells were treated with genipin, the major hepatotoxic metabolite of ZZ. Liver, plasma, intracellular and extracellular samples were obtained for metabolomics analysis. As a result, ZZ caused plasma biochemical and liver histopathological alterations in rats, and induced purine and amino acid metabolism disorder in the liver and pyrimidine, primary bile acids, amino acid metabolism and pantothenate and CoA biosynthesis disorder in the plasma. Pyrimidine, purine, amino acid metabolism and pantothenate and CoA biosynthesis were also found to be disturbed in the genipin-treated HepG2 cells, which exhibited similarity with the result in vivo. This study comprehensively illustrates the underlying mechanism involved in ZZ-related hepatotoxicity from the aspect of metabolome, and provides evidence that identifying hepatotoxicity can be achieved in cells, representing a non-animal alternative for systemic toxicology.
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http://dx.doi.org/10.1016/j.fct.2021.112250DOI Listing
July 2021

Blimp-1 inhibits Th9 cell differentiation and attenuates diabetic coronary heart disease.

Int Immunopharmacol 2021 Jun 8;95:107510. Epub 2021 Mar 8.

Department of Endocrinology, Changzheng Hospital, Naval Medical University, Shanghai 200003, China. Electronic address:

Diabetic coronary heart disease (DM-CHD) poses a major threat to the world. The newly described T cell subset-Th9 cells and related cytokine interleukin (IL)-9 play important roles in the pathogenesis of diabetes and atherosclerosis. B lymphocyte-induced maturation protein 1 (Blimp-1) has been indicated to negatively regulate Th9 development in allergic asthma, but its role in DM-CHD remains unclear. Hence, this study was designed to investigate the role of Blimp-1 in DM-CHD and to elucidate whether the mechanism was associated with regulation of Th9 cell differentiation. Our results showed that serum Blimp-1 mRNA level was decreased whereas proportion of Th9 cells (IL-9 CD4 T cells) and serum level of Th9-related IL-9 were increased in DM-CHD patients. Furthermore, serum Blimp-1 mRNA level was negatively correlated with IL-9 level in DM-CHD patients. Importantly, administration of lentiviruses expressing Blimp-1 (LV-Blimp-1) significantly inhibited Th9 cell differentiation and alleviated the severity of atherosclerotic lesions in the aorta and coronary artery, dyslipidemia, inflammation, vascular endothelial dysfunction, and oxidative stress in DM-CHD model rats. Collectively, Blimp-1 exerts a protective effect in DM-CHD rats and the mechanism might involve inhibition of Th9 cell differentiation.
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http://dx.doi.org/10.1016/j.intimp.2021.107510DOI Listing
June 2021

The application of exogenous PopW increases the tolerance of L. to drought stress through multiple mechanisms.

Physiol Mol Biol Plants 2020 Dec 24;26(12):2521-2535. Epub 2020 Dec 24.

Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 People's Republic of China.

Tomato is a major cultivated vegetable species of great economic importance throughout the world, but its fruit yield is severely impaired by drought stress. PopW, a harpin protein from ZJ3721, plays vital roles in various plant defence responses and growth. In this study, we observed that the foliar application of PopW increased tomato drought tolerance. Our results showed that compared with water-treated plants, PopW-treated plants presented a significantly higher recovery rate and leaf relative water content under drought-stress conditions. PopW decreased the malondialdehyde content and relative electrical conductivity by 40.2% and 21%, respectively. Drought disrupts redox homeostasis through the excessive accumulation of reactive oxygen species (ROS). PopW-treated plants displayed an obvious reduction in ROS accumulation due to enhanced activities of the antioxidant enzyme catalase, superoxide dismutase and peroxidase. Moreover, PopW promoted early stomatal closure, thereby minimizing the water loss rate of plants under drought stress. Further investigation revealed that endogenous abscisic acid (ABA) levels and the transcript levels of drought-responsive genes involved in ABA signal transduction pathways increased in response to PopW. These results confirm that PopW increases drought tolerance through multiple mechanisms involving an enhanced water-retention capacity, balanced redox homeostasis, increased osmotic adjustment, reduced membrane damage and decreased stomatal aperture, suggesting that the application of exogenous PopW may be a potential method to enhance tomato drought tolerance.
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http://dx.doi.org/10.1007/s12298-020-00918-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7772130PMC
December 2020

Serum Clusterin: A Potential Marker for Assessing the Clinical Severity and Short-Term Prognosis of Hepatitis B Virus-Related Acute-on-Chronic Liver Failure.

Dis Markers 2020 12;2020:8814841. Epub 2020 Dec 12.

Center of Integrative Medicine, Beijing Ditan Hospital Affiliated to Capital Medical University, Beijing 100015, China.

Background: Acute-on-chronic liver failure (ACLF) is a clinical syndrome characterized by acute deterioration of liver function and high short-term mortality. Clusterin, with biological functions similar to small heat shock proteins, can protect cells from apoptosis induced by various stressors. The aim of this study was to detect the level of serum clusterin in hepatitis B virus- (HBV-) related ACLF and to assess the predictive value of clusterin for the short-term prognosis of HBV-ACLF.

Methods: We detected serum clusterin by ELISA in 108 HBV-ACLF patients, 63 HBV-non-ACLF patients, and 44 normal controls.

Results: Serum clusterin was markedly lower in HBV-ACLF patients (median, 51.09 g/mL) than in HBV-non-ACLF patients (median, 188.56 g/mL) and normal controls (median, 213.45 g/mL; all < 0.05). Nonsurviving HBV-ACLF patients who died within 90 days had much lower clusterin levels than did surviving patients, especially those who died within 28 days (nonsurvival group vs. survival group: 39.82 ± 19.34 vs. 72.26 ± 43.52, < 0.001; survival time ≤ 28 vs. survival time > 28: median 28.39 vs. 43.22, = 0.013). The results showed that for identifying HBV-ACLF, the sensitivity of clusterin (93.7%) was similar to the sensitivities of the international normalized ratio (INR; 94.4%) and total bilirubin (TBIL; 94.8%), but its specificity (90.7%) was higher than that of prothrombin activity (PTA; 65.8%) and TBIL (69.8%) and was similar to INR (88.9%). As the concentration of clusterin increased, the mortality of HBV-ACLF patients decreased significantly from 59.3% to 7.0%. Clusterin had better ability for predicting the prognosis of HBV-ACLF patients than did the model for end-stage liver disease (MELD) score and the chronic liver failure consortium (CLIF-C) ACLF score (MELD vs. clusterin: = 0.012; CLIF-C ACLF vs. clusterin: = 0.031).

Conclusion: Serum clusterin is a potential biomarker for HBV-ACLF which can be used to assess clinical severity and the short-term prognosis of patients with this disease and may help clinicians identify HBV-ACLF with greater specificity and improved prognostic accuracy than existing prognostic markers.
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http://dx.doi.org/10.1155/2020/8814841DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7755493PMC
December 2020

A facile "one-material" strategy for tandem enrichment of small extracellular vesicles phosphoproteome.

Talanta 2021 Feb 15;223(Pt 2):121776. Epub 2020 Oct 15.

National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China.

Small extracellular vesicles (SEVs), are cell-derived, membrane-enclosed nanometer-sized vesicles that play vital roles in many biological processes. Recent years, more and more evidences proved that small EVs have close relationship with many diseases such as cancers and Alzheimer's disease. The use of phosphoproteins in SEVs as potential biomarkers is a promising new choice for early diagnosis and prognosis of cancer. However, current techniques for SEVs isolation still facing many challenges, such as highly instrument dependent, time consuming and insufficient purity. Furthermore, complex enrichment procedures and low microgram amounts of proteins available from clinical sources largely limit the throughput and the coveage depth of SEVs phosphoproteome mapping. Here, we synthesized Ti-modified magnetic graphene-oxide composites (GFST) and developed a "one-material" strategy for facile and efficient phosphoproteome enrichment and identification in SEVs from human serum. By taking advantage of chelation and electrostatic interactions between metal ions and phosphate groups, GFST shows excellent performance in both SEVs isolation and phosphopeptide enrichment. Close to 85% recovery is achieved within a few minutes by simple incubation with GFST and magnetic separation. Proteome profiling of the isolated serum SEVs without phosphopeptide enrichment results in 515 proteins, which is approximately one-fold more than those otained by ultracentrifugation or coprecipitation kits. Further application of GFST in one-material-based enrichment led to identification of 859 phosphosites in 530 phosphoproteins. Kinase-substrate correlation analysis reveals enriched substrates of CAMK in serum SEVs phosphoproteome. Therefore, we expect that the low instrument dependency and the limited sample requirement of this new strategy may facilitate clinical investigations in SEV-based transportation of abnormal kinases and substrates for drug target discovery and cancer monitoring.
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http://dx.doi.org/10.1016/j.talanta.2020.121776DOI Listing
February 2021

Elovl2 Is Required for Robust Visual Function in Zebrafish.

Cells 2020 12 2;9(12). Epub 2020 Dec 2.

Viterbi Family Department of Ophthalmology, Shiley Eye Institute, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA.

Omega-3 and omega-6 polyunsaturated fatty acids (PUFAs) play critical roles in membrane stability and cell signaling within the retina. ELOVL2 (Elongation of Very Long Chain Fatty Acids-Like 2), an elongase involved in the synthesis of long chain polyunsaturated fatty acids (LC-PUFAs), has recently been implicated in regulating aging in the mammalian retina. In this work, we characterize the expression and function of in the retina development in embryonic zebrafish. Whole mount in situ hybridization shows is expressed in the Muller glia in embryonic and adult zebrafish. Lipidomics analysis of crispants whole embryos at day 2 and eyes at day 7 demonstrated significant changes in lipids composition, especially on the level of lipids containing docosahexaenoic acid (DHA). Histological analysis of zebrafish lacking revealed increased retinal thickness compared to controls at day 7 without gross disruptions of the retinal architecture. Finally, crispants showed differences in the visual motor reflex light off (VMR-OFF) at day 7 compared to controls. In sum, inactivation of in zebrafish embryos caused changes in lipid composition and in visual behavior, further confirming the important role of LC-PUFAs in healthy vision.
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http://dx.doi.org/10.3390/cells9122583DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7761535PMC
December 2020

Selenium ameliorates aflatoxin B1-induced uterine injury in female mice and necrosis of human endometrial microvascular endothelial cells.

J Appl Toxicol 2021 May 25;41(5):799-810. Epub 2020 Nov 25.

Department of Gynecology, Cangzhou Central Hospital, Cangzhou, China.

This study aimed to observe the effects of Selenium (Se) on aflatoxin B1 (AFB1)-induced uterine injury in female mice and necrosis of human endometrial microvascular endothelial cells (HEMECs). Fifty female mice were randomly divided into control group; AFB1 group; Se group (0.2 mg/kg each day); AFB1 + Se group; and positive control group. After continuous treatment for 30 days, uterine tissues were harvested, which were used for hematoxylin and eosin (H&E) staining. Necrosis-related proteins including RIPK1, RIPK3, and MLKL were examined in uterine tissues using western blot and immunohistochemistry. HEMECs were treated with different concentrations of AFB1 or Se, which were used for selecting the optimal concentrations. RIPK1, RIPK3 and MLKL expression was detected in HEMECs exposed to AFB1 and/or Se via western blot and immunofluorescence. H&E staining results showed that AFB1 induced uterine injury of female male, which was ameliorated by Se treatment. According to western blot and immunohistochemistry, RIPK1, RIPK3, and MLKL expression was distinctly increased in uterine tissues of AFB1-treated mice, which was decreased by Se treatment. Cell viability of HEMECs was gradually lowered as the concentrations of AFB1and Se increased. A 10-μM AFB1 exposure significantly increased RIPK1, RIPK3, and MLKL expression in HEMECs, which was improved following co-treatment with 5-μM Se. Thus, our findings revealed that Se may ameliorate AFB1-induced uterine injury in female mice and necrosis of HEMECs.
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http://dx.doi.org/10.1002/jat.4120DOI Listing
May 2021

Transcriptome and genome sequencing elucidates the molecular basis for the high yield and good quality of the hybrid rice variety Chuanyou6203.

Sci Rep 2020 11 17;10(1):19935. Epub 2020 Nov 17.

Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, People's Republic of China.

The yield heterosis of rice is sought by farmers and strong contributes to food safety, but the quality of hybrid rice may be reduced. Therefore, developing new varieties with both high yield and good quality is a heavily researched topic in hybrid rice breeding. However, the molecular mechanism governing yield heterosis and high rice quality has not been elucidated to date. In this study, a comparative transcriptomics and genomic analysis was performed on a hybrid rice variety, Chuanyou6203 (CY6203), and its parents to investigate the molecular mechanism and gene regulation network governing the formation of yield and quality stages. A total of 66,319 SNPs and InDels between CH3203 and C106B were detected in the 5'-UTR, exon, intronic, and 3'-UTR regions according to the reference genome annotation, which involved 7473 genes. A total of 436, 70, 551, 993, and 1216 common DEGs between CY6203 and both of its parents were identified at the same stage in panicles and flag leaves. Of the common DEGs, the numbers of upregulated DEGs between CY6203 and CH3203 were all greater than those of upregulated DEGs between CY6203 and C106B in panicles and flag leaves at the booting, flowering, and middle filling stages. Approximately 40.61% of mRNA editing ratios were between 0.4 and 0.6, and 1.68% of mRNA editing events (editing ratio ≥ 0.8) in CY6203 favored one of its parents at three stages or a particular stage, suggesting that the hypothetical heterosis mechanism of CY6203 might involve dominance or epistasis. Also 15,934 DEGs were classified into 19 distinct modules that were classified into three groups by the weighted gene coexpression network analysis. Through transcriptome analysis of panicles and flag leaves in the yield and quality stages, the DEGs in the green-yellow module primarily contributed to the increase in the source of CY6203 due to an in increase in photosynthetic efficiency and nitrogen utilization efficiency, and a small number of DEGs related to the grain number added spikelet number per panicle amplified its sink. The balanced expression of the major high-quality alleles of C106B and CH3203 in CY6203 contributed to the outstanding quality of CY6203. Our transcriptome and genome analyses offer a new data set that may help to elucidate the molecular mechanism governing the yield heterosis and high quality of a hybrid rice variety.
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http://dx.doi.org/10.1038/s41598-020-76762-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7673993PMC
November 2020

Novel Two-Dimensional MoS-Ti Nanomaterial for Efficient Enrichment of Phosphopeptides and Large-Scale Identification of Histidine Phosphorylation by Mass Spectrometry.

Anal Chem 2020 10 23;92(19):12801-12808. Epub 2020 Sep 23.

State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102200, China.

Due to its key roles in regulating the occurrence and development of cancer, protein histidine phosphorylation has been increasingly recognized as an important form of post-translational modification in recent years. However, large-scale analysis of histidine phosphorylation is much more challenging than that of serine/threonine or tyrosine phosphorylation, mainly because of its acid lability. In this study, MoS-Ti nanomaterials were synthesized using a solvothermal method and taking advantage of the electrostatic adsorption between MoS nanosheets and Ti. The MoS-Ti nanomaterials have the advantage of the combined affinity of Ti and Mo toward phosphorylation under medium acidic conditions (pH = 3), which is crucial for preventing hydrolysis and loss of histidine phosphorylation during enrichment. The feasibility of using the MoS-Ti nanomaterial for phosphopeptide enrichment was demonstrated using mixtures of β-casein and bovine serum albumin (BSA). Further evaluation revealed that the MoS-Ti nanomaterial is capable of enriching synthetic histidine phosphopeptides from 1000 times excess tryptic-digested HeLa cell lysate. Application of the MoS-Ti nanomaterials for large-scale phosphopeptide enrichment results in the identification of 10 345 serine, threonine, and tyrosine phosphosites and the successful mapping of 159 histidine phosphosites in HeLa cell lysates, therefore indicating great potential for deciphering the vital biological roles of protein (histidine) phosphorylation.
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http://dx.doi.org/10.1021/acs.analchem.0c00618DOI Listing
October 2020

Comparison of Transcatheter Arterial Chemoembolization-Radiofrequency Ablation and Transcatheter Arterial Chemoembolization Alone for Advanced Hepatocellular Carcinoma with Macrovascular Invasion Using Propensity Score Analysis: A Retrospective Cohort Study.

J Oncol 2020 20;2020:1341863. Epub 2020 Aug 20.

Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China.

Background: To compare the efficacies of transcatheter arterial chemoembolization (TACE) with radiofrequency ablation (RFA) (TACE + RFA) and TACE alone in patients with hepatocellular carcinoma (HCC) and macrovascular invasion (MVI).

Methods: In total, 664 patients having HCC with MVI were included. Of these patients, 141 were treated with TACE + RFA, 254 with TACE alone, and 269 with supportive therapy (control group). The overall survival (OS) was compared among these groups. Propensity score matching (PSM) was performed for balancing the characteristics of the three groups.

Results: After one-to-one PSM, the 12-month OS rates were higher in the TACE and TACE + RFA groups than in the control group (=0.0009 and =0.0017, respectively). Furthermore, higher 12-month OS rates were observed in the TACE + RFA group than in the TACE group (=0.0192). The 12-month OS rates of patients were remarkably higher in -fetoprotein (AFP) < 400 ng/ml, tumor < 3, tumor diameter < 5 cm, or portal vein tumor thrombosis (PVTT) group who were treated with TACE + RFA than in those who were treated with TACE (=0.0122, =0.0090, =0112, and =0.0071, respectively).

Conclusions: TACE + RFA provides a superior survival outcome than TACE alone in HCC patients, especially in AFP <400 ng/ml, tumor <3, tumor diameter <5 cm, or PVTT group.
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http://dx.doi.org/10.1155/2020/1341863DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7455819PMC
August 2020

Protective Effect of Probiotics against Esophagogastric Variceal Rebleeding in Patients with Liver Cirrhosis after Endoscopic Therapy.

Med Sci Monit 2020 Aug 8;26:e924040. Epub 2020 Aug 8.

Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing, China (mainland).

BACKGROUND Probiotic therapy has been shown to be beneficial against some liver diseases. However, there is still uncertainty regarding the clinical efficacy of probiotics for the treatment of variceal rebleeding. This research explored the efficacy of probiotics in variceal rebleeding. MATERIAL AND METHODS This was a retrospective study of 704 consecutive patients with liver cirrhosis who recovered from esophagogastric variceal bleeding after endoscopic treatment. Patients were subdivided into a probiotics cohort (n=214) and a non-probiotics cohort (n=490) based on the cumulative defined daily dose (cDDD) of probiotics received during follow-up. Propensity score matching was utilized to obtain a relatively balanced cohort of 200 patients per group for the analysis. Patients were monitored for rebleeding during the one-year follow-up. RESULTS Multivariate Cox regression analysis revealed that probiotic therapy (≥28cDDD) was an independent protector against rebleeding (AHR=0.623; 95% CI=0.488-0.795; P<0.001). After propensity score matching, Kaplan-Meier analysis revealed that the rebleeding rate was higher in the non-probiotics cohort (n=200) than in the probiotics cohort (n=200) (56.0% vs. 44.0%, P=0.002). The incidence of rebleeding decreased with increased probiotic dosage (56.0%, 48.5%, 43.3%, and 38.1% in <28 cDDD, 28-60 cDDD, 61-90 cDDD, and >90 cDDD groups, respectively; P=0.011). The median rebleeding interval in the probiotics cohort (n=95) was significantly longer than that in the non-probiotics cohort (n=261) (147.0 vs. 91.0 days; P<0.001). CONCLUSIONS Adjuvant probiotic therapy significantly reduced the incidence of variceal rebleeding and delayed rebleeding after endotherapy in patients with cirrhosis.
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http://dx.doi.org/10.12659/MSM.924040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7433391PMC
August 2020

Biolistic DNA Delivery in Turfgrass Embryonic Callus Initiated from Mature Seeds.

Methods Mol Biol 2020 ;2124:251-261

Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA.

We describe a protocol for the establishment and preparation of creeping bentgrass (Agrostis stolonifera L.) cultivar "Penn A-4" embryonic calli, biolistic transformation, selection, and regeneration of transgenic plants. The embryonic callus is initiated from mature seeds, maintained by visual selection under the dissecting microscope and subjected to bombardment with plasmid DNA containing a bialaphos-resistance (bar) gene. PCR, Southern, and Northern blot analyses are used to confirm the transgene integration and expression.
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http://dx.doi.org/10.1007/978-1-0716-0356-7_13DOI Listing
February 2021

Artificial neural network-based models used for predicting 28- and 90-day mortality of patients with hepatitis B-associated acute-on-chronic liver failure.

BMC Gastroenterol 2020 Mar 13;20(1):75. Epub 2020 Mar 13.

Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, People's Republic of China.

Background: This study aimed to develop prognostic models for predicting 28- and 90-day mortality rates of hepatitis B virus (HBV)-associated acute-on-chronic liver failure (HBV-ACLF) through artificial neural network (ANN) systems.

Methods: Six hundred and eight-four cases of consecutive HBV-ACLF patients were retrospectively reviewed. Four hundred and twenty-three cases were used for training and constructing ANN models, and the remaining 261 cases were for validating the established models. Predictors associated with mortality were determined by univariate analysis and were then included in ANN models for predicting prognosis of mortality. The receiver operating characteristic curve analysis was used to evaluate the predictive performance of the ANN models in comparison with various current prognostic models.

Results: Variables with statistically significant difference or important clinical characteristics were input in the ANN training process, and eight independent risk factors, including age, hepatic encephalopathy, serum sodium, prothrombin activity, γ-glutamyltransferase, hepatitis B e antigen, alkaline phosphatase and total bilirubin, were eventually used to establish ANN models. For 28-day mortality in the training cohort, the model's predictive accuracy (AUR 0.948, 95% CI 0.925-0.970) was significantly higher than that of the Model for End-stage Liver Disease (MELD), MELD-sodium (MELD-Na), Chronic Liver Failure-ACLF (CLIF-ACLF), and Child-Turcotte-Pugh (CTP) (all p < 0.001). In the validation cohorts the predictive accuracy of ANN model (AUR 0.748, 95% CI: 0.673-0.822) was significantly higher than that of MELD (p = 0.0099) and insignificantly higher than that of MELD-Na, CTP and CLIF-ACLF (p > 0.05). For 90-day mortality in the training cohort, the model's predictive accuracy (AUR 0.913, 95% CI 0.887-0.938) was significantly higher than that of MELD, MELD-Na, CTP and CLIF-ACLF (all p < 0.001). In the validation cohorts, the prediction accuracy of the ANN model (AUR 0.754, 95% CI: 0.697-0.812 was significantly higher than that of MELD (p = 0.019) and insignificantly higher than MELD-Na, CTP and CLIF-ACLF (p > 0.05).

Conclusions: The established ANN models can more accurately predict short-term mortality risk in patients with HBV- ACLF. The main content has been postered as an abstract at the AASLD Hepatology Conference (https://doi.org/10.1002/hep.30257).
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http://dx.doi.org/10.1186/s12876-020-01191-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7081680PMC
March 2020

Nomogram for Individualized Prediction of Hepatocellular Carcinoma with Portal Vein Tumor Thrombosis on Conservative Treatment.

Biomed Res Int 2020 17;2020:1473718. Epub 2020 Feb 17.

Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China.

Background: Portal vein tumor thrombosis (PVTT) is one of the major predictive factors for patients with hepatocellular carcinoma (HCC). The objective of this study was to establish a prognostic nomogram for identifying individual survival outcomes in patients with HCC and PVTT on conservative treatment based on specific factors.

Methods: Two hundred and ten patients with HCC and PVTT on conservative treatment in Beijing Ditan Hospital between June 2008 and May 2017 were studied retrospectively as a derivation cohort. We built a nomogram based on independent risk factors for survival prediction. The concordance index (c-index) and a calibration curve were used to evaluate the predictive accuracy. During the study, 102 patients were included at the Putuo Hospital and Third People's Hospital of Changzhou as a validation cohort.

Results: In the derivation cohort, the independent factors for overall survival were identified by multivariate analysis, namely, aspartate aminotransferase ≥119 IU/L, gamma-glutamyl transferase ≥115 IU/L, Child-Pugh class C liver function, creatinine ≥91 moI/L, -fetoprotein ≥400 ng/ml, and largest tumor diameter ≥5 cm. The nomogram had a c-index of 0.737 (95% confidence interval, 0.692-0.782) and the calibration curves fitted well. The median survival time was 4.2 months in the derivation cohort, with an MST of 5 months for BCLC C stage and 1.8 months for BCLC D stage patients. Kaplan-Meier analysis showed significant statistical differences in the 6-month overall survival rates of the primary and validation cohorts after the total scores were divided into three quartiles (low risk: 0-85; intermediate risk: 86-210; high risk: ≥211; < 0.0001 in both cohorts).

Conclusions: The nomogram can be a more accurate and individualized prediction for 6-month overall survival of patients with HCC and PVTT on conservative treatment, and it is possible to consider further active interventions for patients in the low-risk group (0-85 scores) to achieve the aim of prolonging survival.
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http://dx.doi.org/10.1155/2020/1473718DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7049328PMC
December 2020

A novel mass spectrometry method for the absolute quantification of several cytochrome P450 and uridine 5'-diphospho-glucuronosyltransferase enzymes in the human liver.

Anal Bioanal Chem 2020 Mar 6;412(8):1729-1740. Epub 2020 Feb 6.

National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China.

Cytochrome P450 (CYP450) and 5'-diphosphate glucuronosyltransferases (UGT) are the two major families of drug-metabolizing enzymes in the human liver microsome (HLM). As a result of their frequent abundance fluctuation among populations, the accurate quantification of these enzymes in different individuals is important for designing patient-specific dosage regimens in the framework of precision medicine. The preparation and quantification of internal standards is an essential step for the quantitative analysis of enzymes. However, the commonly employed stable isotope labeling-based strategy (QconCAT) suffers from requiring very expensive isotopic reagents, tedious experimental procedures, and long labeling times. Furthermore, arginine-to-proline conversion during metabolic isotopic labeling compromises the quantification accuracy. Therefore, we present a new strategy that replaces stable isotope-labeled amino acids with lanthanide labeling for the preparation and quantification of QconCAT internal standard peptides, which leads to a threefold reduction in the reagent costs and a fivefold reduction in the time consumed. The absolute amount of trypsin-digested QconCAT peptides can be obtained by lanthanide labeling and inductively coupled plasma-optical emission spectrometry (ICP-OES) analysis with a high quantification accuracy (%RE < 20%). By taking advantage of the highly selective and facile ICP-OES procedure and multiplexed large-scale absolute target protein quantification using biological mass spectrometry, this strategy was successfully used for the absolute quantification of drug-metabolizing enzymes. We obtained good linearity (correlation coefficient > 0.95) over concentrations spanning 2.5 orders of magnitude with improved sensitivity (limit of quantification = 2 fmol) in nine HLM samples, indicating the potential of this method for large-scale absolute target protein quantification in clinical samples. Graphical abstract.
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http://dx.doi.org/10.1007/s00216-020-02445-7DOI Listing
March 2020

A GSH Functionalized Magnetic Ultra-thin 2D-MoS nanocomposite for HILIC-based enrichment of N-glycopeptides from urine exosome and serum proteins.

Anal Chim Acta 2020 Feb 13;1098:181-189. Epub 2019 Nov 13.

State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing, 102200, China.

Protein N-glycosylation plays crucial roles in many biological processes and has close association with the occurrence and development of various cancers. Therefore, it is necessary to analyze the abnormal changes of N-glycopeptides in complex biological samples for biomarker discovery. However, due to their low abundance and poor ionization, N-glycopeptides identification in complex samples by mass spectrometry (MS) is still a challenging task. In this work, a novel magnetic hydrophilic material was prepared by serial functionalization of ultra-thin two-dimensional molybdenum disulfide with FeO nanoparticles, gold nanowire and glutathione (MoS-FeO-Au/NWs-GSH) for efficient N-glycopeptides enrichment. The advantage of using the new nanocomposite is threefold. First, the introduction of magnetic FeO nanoparticles efficiently simplifies the enrichment process. Second, the gold nanowire modification enlarges the surface area of the nanocomposites to facilitate interaction with N-glycopeptides. Third, the employment of highly hydrophilic glutathione leads to specific HILIC-based retention of N-glycopeptides. Low femtomolar detection sensitivity and 1:1000 enrichment selectivity can be achieved using MoS-FeO-Au/NWs-GSH enrichment and bio-mass spectrometry analysis. Successful applications in human urine exosome and serum proteins were demonstrated by the enrichment and identification of 1250 and 489 N-glycopeptides, respectively. This remarkable data set of N-glycoproteome indicates the application potential of the novel nanocomposites for N-glycopeptides enrichment in complex biological samples and for related glycoproteome studies.
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http://dx.doi.org/10.1016/j.aca.2019.11.012DOI Listing
February 2020

[Advances in separation techniques for exosomes and their clinical applications].

Se Pu 2019 Oct;37(10):1071-1083

State Key Laboratory of Proteomics, National Center for Protein Sciences(Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102206, China.

Exosomes are vesicles secreted by many types of cells through exocytosis, and their sizes range from 30 to 200 nm. Exosomes consist of a lipid bilayer membrane, containing a number of bioactive molecules, e. g., proteins, ribose nucleic acid (RNA), and deoxyribo nucleic acid (DNA) derived from the cell of origin. As intercellular communication carriers, exosomes participate in many physiological and pathological processes. Because of the complexity of body fluids, as well as the small size and low density of exosomes, the isolation of exosomes is an essential and challenging step before subsequent analysis and functional studies. This review summarizes the advances in the analytical approaches, characterization methods, biological functions and clinical applications of exosomes, with particular emphasis on exosomes isolation techniques.
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http://dx.doi.org/10.3724/SP.J.1123.2019.02007DOI Listing
October 2019

LncRNA SBF2-AS1 promotes the progression of cervical cancer by regulating miR-361-5p/FOXM1 axis.

Artif Cells Nanomed Biotechnol 2019 Dec;47(1):776-782

b Department of Gynecology , The First Affiliated Hospital of Xinxiang Medical University , Weihui , China.

Long non-coding RNAs (lncRNAs) have been identified as critical players in tumorigenesis. Previous studies revealed that lncRNA SBF2-AS1 was involved in tumor progression. However, the role and underlying mechanism of SBF2-AS1 in cervical cancer (CC) remain unknown. In the present study, our data showed that SBF2-AS1 expression was significantly increased in CC. High SBF2-AS1 expression was associated with advanced FIGO stage and lymph node metastasis of CC patients. Function assays showed that SBF2-AS1 inhibition significantly reduced CC cells proliferation both in vitro and in vivo. Mechanistically, we showed that SBF2-AS1 upregulation restrained the activity of miR-361-5p and led to overexpression of FOXM1 in CC cells. Furthermore, we found that miR-361-5p inhibitors could rescue the effects of SBF2-AS1 inhibition on CC cells proliferation. Taken together, we demonstrated that the SBF2-AS1/miR-361-5p/FOXM1 axis might play an important role in CC progression. SBF2-AS1 might serve as a potential therapeutic target for CC treatment.
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http://dx.doi.org/10.1080/21691401.2019.1577883DOI Listing
December 2019

A novel strategy for facile serum exosome isolation based on specific interactions between phospholipid bilayers and TiO.

Chem Sci 2019 Feb 3;10(6):1579-1588. Epub 2018 Dec 3.

State Key Laboratory of Proteomics , National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing Proteome Research Center , China . Email: ; Email: ; Email:

Exosomes are cell-derived, phospholipid bilayer-enclosed vesicles that play important roles in intercellular interactions and regulate many biological processes. Accumulating evidence suggests that serum exosomes are potential biomarkers for the early diagnosis of cancer. To aid the downstream molecular analyses of tumour-secreted exosomes, purified exosomes are highly desirable. However, current techniques for exosome isolation are time-consuming and highly instrument-dependent, with limited specificity and recovery. Thus, rapid and efficient methods are strongly needed for both basic research and clinical applications. Here, we present a novel strategy for facile exosome isolation from human serum by taking advantage of the specific interaction of TiO with the phosphate groups on the lipid bilayer of exosomes. Due to their simplicity and highly affinitive binding, model exosomes can be reversibly isolated with a high recovery (93.4%). Downstream characterization and proteome profiling reveal that high-quality exosomes can be obtained from human serum by this TiO-based isolation method in 5 min, which is a fraction of the time required for the commonly used ultracentrifugation method. We identified 59 significantly up-regulated proteins by comparing the serum exosomes of pancreatic cancer patients and healthy donors. In addition to the 30 proteins that were reported to be closely related to pancreatic cancer, we found an additional 29 proteins that had not previously been shown to be related to pancreatic cancer, indicating the potential of this novel method as a powerful tool for exosome isolation for health monitoring and disease diagnosis.
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http://dx.doi.org/10.1039/c8sc04197kDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6369439PMC
February 2019

A new scoring model predicting macroscopic vascular invasion of early-intermediate hepatocellular carcinoma.

Medicine (Baltimore) 2018 Dec;97(49):e13536

Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University.

Macroscopic vascular invasion cannot be properly predicted in advance in hepatocellular carcinoma patients based on clinical characteristics and imaging features.To develop a predictive scoring model of macroscopic vascular invasion in hepatocellular carcinoma patients after transcatheter arterial chemoembolization combined with radiofrequency ablation based on specific laboratory and tumor indicators.A predictive scoring model, which estimates the incidence of macroscopic vascular invasion at 1-year follow-up, was constructed based on a derivation cohort of 324 patients with hepatocellular carcinoma; a validation cohort of 120 patients was prospectively included. The prognostic value of the scoring model was determined by concordance index, time-dependent receiver operating characteristics, and calibration curves.Cox multivariate analysis of the derivation cohort identified prothrombin time, aspartate aminotransferase, and Barcelona clinic liver cancer (BCLC) staging as independent predictive factors of macroscopic vascular invasion. The areas under the receiver operating characteristic curves of the predictive scoring model were 0.832 and 0.785 in the derivation and validation cohorts, respectively, and the calibration curves fitted well. Kaplan-Meier analysis showed that the incidence of macroscopic vascular invasion was significantly higher in the high-risk group (score 0-2) than in the low-risk group (score 3-4) in both the derivation and validation cohorts (P < .0001 and P = .0008, respectively).The predictive scoring model enables the accurate prediction of macroscopic vascular invasion incidence 1 year in advance in hepatocellular carcinoma patients who undergo transcatheter arterial chemoembolization combined with radiofrequency ablation.
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http://dx.doi.org/10.1097/MD.0000000000013536DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6310496PMC
December 2018

Development and external validation of a prognostic nomogram for acute decompensation of chronic hepatitis B cirrhosis.

BMC Gastroenterol 2018 Dec 3;18(1):179. Epub 2018 Dec 3.

Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing, China.

Background: Acute decompensation (AD) has been shown to be associated with a high mortality rate for cirrhosis patients. This study aimed to develop a prognostic nomogram to evaluating the individual prognosis for AD of cirrhosis in chronic hepatitis B (CHB).

Methods: The nomogram was developed using data from a retrospective study on 509 patients hospitalized for AD of CHB cirrhosis from October 2008 to February 2014 at the Beijing Ditan Hospital, Capital Medical University. The predictive accuracy, discriminative ability, and clinical net benefit were evaluated by concordance index (C-index), calibration curves, and decision curve analysis (DCA). The results were validated on 620 patients consecutively enrolled from January 2005 to December 2010 at the Renji Hospital, Shanghai Jiao Tong University,.

Results: On multivariate analysis of the derivation cohort, independent factors included in the nomogram were age, previous decompensation, bacterial infection, hepatic encephalopathy, and total bilirubin. The calibration curve for the probability of survival showed good agreement between the nomogram and actual observation. The nomogram had a C-index of 0.897, which was statistically higher than the C-index values of CTP (0.793), MELD (0.821), SOFA (0.868), or the Chronic Liver Failure Consortium AD (CLIF-C AD) (0.716) scores (p <  0.001 for all). Using DCA, the nomogram also demonstrated superior net benefits over other score models. The results were confirmed in the validation cohort.

Conclusions: The proposed nomogram enables more-accurate individualized prediction of survival than MELD, CTP, SOFA, or CLIF-C AD scores for AD of CHB cirrhosis patients.
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http://dx.doi.org/10.1186/s12876-018-0911-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6276255PMC
December 2018

Nomogram prediction of individual prognosis of patients with acute-on-chronic hepatitis B liver failure.

Dig Liver Dis 2019 03 31;51(3):425-433. Epub 2018 Aug 31.

Center of Integrative Medicine, Beijing Ditan Hospital Capital Medical University, Beijing, China. Electronic address:

Background: The current definitions and etiologies of acute-on-chronic liver failure (ACLF) are clearly very different between East and West.

Aims: This study aimed to develop an effective prognostic nomogram for acute-on-chronic hepatitis B liver failure (ACHBLF) as defined by the Asia Pacific Association for the Study of the Liver (APASL).

Methods: The nomogram was based on a retrospective study of 573 patients with ACHBLF, defined according to the APASL, at the Beijing Ditan Hospital. The results were validated using a bootstrapped approach to correct for bias in two external cohorts, including an APASL ACHBLF cohort (10 hospitals, N = 329) and an EASL-CLIF ACHBLF cohort (Renji Hospital, N = 300).

Results: Multivariate analysis of the derivation cohort for survival analysis helped identify the independent factors as age, total bilirubin, albumin, international normalized ratio, and hepatic encephalopathy, which were included in the nomogram. The predictive value of nomogram was the strongest compared with CLIF-C ACLF, MELD and MELD-Na and similar to COSSH-ACLF in both the derivation and prospective validation cohorts with APASL ACHBLF, but the CLIF-C ACLF was better in the EASL-CLIF ACHBLF cohort.

Conclusions: The proposed nomogram could accurately estimate individualized risk for the short-term mortality of patients with ACHBLF as defined by APASL.
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http://dx.doi.org/10.1016/j.dld.2018.08.023DOI Listing
March 2019

Influence factors and a predictive scoring model for measuring the biochemical response of primary biliary cholangitis to ursodeoxycholic acid treatment.

Eur J Gastroenterol Hepatol 2018 11;30(11):1352-1360

Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University.

Aims: The biochemical response after ursodeoxycholic acid (UDCA) treatment contributes toward predicting the prognosis for primary biliary cholangitis (PBC) patients. This study aimed to establish a score model that can be used for predicting the biochemical response.

Patients And Methods: A total of 218 patients in the derivation group and 66 patients in the verification group were enrolled. Response endpoints were based on the Barcelona criteria combined with the Paris I criteria. We determined independent factors of the biochemical response by univariate and multivariate analyses. Then, we established a predictive score model on the basis of regression coefficients after adjusted multivariate analyses.

Results: The median follow-up duration in the derivation and the verification group was 12.9 and 12.2 months, respectively. Multivariate logistic regression analysis after adjusting for sex and age indicated that First-UDCA treatment [odds ratio (OR)=2.543, 95% confidence interval (CI): 1.234-5.240, P=0.011], baseline alanine aminotransferase level (OR=1.265, 95% CI: 1.089-1.471, P=0.002), and baseline total bilirubin level (OR=0.571, 95% CI: 0.420-0.776, P<0.001) were independent factors that influenced the biochemical response in PBC patients after 1 year of UDCA treatment. Therefore, the resulting biochemical response prediction score model represented the sum of the points corresponding to these three variables. The area under the receiver operating characteristic curve of the score model in the derivation group and the verification group was 0.763 (95% CI: 0.701-0.817, P<0.001) and 0.798 (95% CI: 0.681-0.887, P<0.001), respectively.

Conclusion: We developed and verified an easy-to-use scoring model for the first time, which showed excellent predictive value for the biochemical response in PBC patients.
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http://dx.doi.org/10.1097/MEG.0000000000001186DOI Listing
November 2018

Two-Dimensional MoS-Based Zwitterionic Hydrophilic Interaction Liquid Chromatography Material for the Specific Enrichment of Glycopeptides.

Anal Chem 2018 06 17;90(11):6651-6659. Epub 2018 May 17.

State Key Laboratory of Proteomics, National Center for Protein Science Beijing , Beijing Institute of Life-omics , Beijing 102206 , China.

Mass spectrometry (MS)-based glycoproteomics research requires highly efficient sample preparation to eliminate interference from non-glycopeptides and to improve the efficiency of glycopeptide detection. In this work, a novel MoS/Au-NP (gold nanoparticle)-L-cysteine nanocomposite was prepared for glycopeptide enrichment. The two-dimensional (2D) structured MoS nanosheets served as a matrix that could provide a large surface area for immobilizing hydrophilic groups (such as L-cysteine) with low steric hindrance between the materials and the glycopeptides. As a result, the novel nanomaterial possessed an excellent ability to capture glycopeptides. Compared to commercial zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC) materials, the novel nanomaterials exhibited excellent enrichment performance with ultrahigh selectivity and sensitivity (approximately 10 fmol), high binding capacity (120 mg g), high enrichment recovery (more than 93%), satisfying batch-to-batch reproducibility, and good universality for glycopeptide enrichment. In addition, its outstanding specificity and efficiency for glycopeptide enrichment was confirmed by the detection of glycopeptides from an human serum immunoglobulin G (IgG) tryptic digest in quantities as low as a 1:1250 molar ratio of IgG tryptic digest to bovine serum albumin tryptic digest. The novel nanocomposites were further used for the analysis of complex samples, and 1920 glycopeptide backbones from 775 glycoproteins were identified in three replicate analyses of 50 μg of proteins extracted from HeLa cell exosomes. The resulting highly informative mass spectra indicated that this multifunctional nanomaterial-based enrichment method could be used as a promising tool for the in-depth and comprehensive characterization of glycoproteomes in MS-based glycoproteomics.
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http://dx.doi.org/10.1021/acs.analchem.8b00461DOI Listing
June 2018

Rational synthesis of MoS-based immobilized trypsin for rapid and effective protein digestion.

Talanta 2018 Mar 21;179:393-400. Epub 2017 Nov 21.

State Key Laboratory of Proteomics, National Center for Protein Science Beijing, Beijing Institute of Radiation Medicine, Beijing 102206, China.

In this work, a novel MoS-based immobilized trypsin reactor was designed and prepared. Pyrene-1-butyric acid was first assembled onto MoS nanosheets via the strong π-π stacking and then trypsin was covalently immobilized onto the nanocomposite supports through amidation reaction. Compared with traditional in-solution digestion, higher sequence coverage (84%) and shorter time (5min) could be achieved by the novel trypsin reactor during the digestion of BSA. The excellent performances of as-prepared trypsin reactor can be mainly attributed to the designed novel structure of the composites with high surface area resulting in high enzyme loading. In addition, strong reusability, good reproducibility and long storage of the trypsin reactor were also obtained. The novel immobilized trypsin reactor was further applied in large-scale proteomics research. The proteins extracted from HeLa cells and Amygdalus Pedunculata Pall. kernels were chosen to evaluate the digestion performance for the novel MoS-based immobilized trypsin reactor, and the experimental results showed that the number of identified proteins from complex real bio-samples with 1h immobilized tryptic digestion was slightly more than that obtained by 12h in-solution digestion. The above results demonstrated that the protein digestion with our novel MoS-based immobilized trypsin reactor is superior to the conventional protein digestion with free trypsin. Moreover, this simple, fast tryptic digestion method can effectively reduce the levels of artifacts in detection of oxidation and deamidation of peptides from proteins of Amygdalus Pedunculata Pall. kernels. Also, results of Gene Ontology analysis give an explanation for the good survival of Amygdalus Pedunculata Pall. in harsh desert environments from proteomics points of view. Therefore, the novel 2D-MoS-based immobilized trypsin is potentially suitable for the high throughput proteome analysis and opening up a new avenue for Molybdenum disulfide in proteomics field.
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http://dx.doi.org/10.1016/j.talanta.2017.11.027DOI Listing
March 2018

A Novel AP2/ERF Transcription Factor CR1 Regulates the Accumulation of Vindoline and Serpentine in .

Front Plant Sci 2017 6;8:2082. Epub 2017 Dec 6.

Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China.

As one type of the most important alkaloids in the world, terpenoid indole alkaloids (TIAs) show a wide range of pharmaceutical activities that are beneficial for clinical treatments. produces approximately 130 identified TIAs and is considered to be a model plant to study TIA biosynthesis. In order to increase the production of high medical value metabolites whose yields are extremely low in , genetic engineering combined with transcriptional regulation has been applied in recent years. By using bioinformatics which is based on RNA sequencing (RNA-seq) data from methyl jasmonate (MeJA)-treated as well as phylogenetic analysis, the present work aims to screen candidate genes that may be involved in the regulation of TIA biosynthesis, resulting in a novel AP2/ERF transcription factor, CR1 (Catharanthus roseus 1). Subsequently, virus-induced gene silencing (VIGS) of was carried out to identify the involvement of CR1 in the accumulations of several TIAs and quantitative real-time PCR (qRT-PCR) was then applied to detect the expression levels of 7 genes in the related biosynthetic pathway in silenced plants. The results show that all the 7 genes were upregulated in -silenced plants. Furthermore, metabolite analyses indicate that silencing could increase the accumulations of vindoline and serpentine in . These results suggest a novel negative regulator which may be involved in the TIAs biosynthetic pathway.
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http://dx.doi.org/10.3389/fpls.2017.02082DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5724233PMC
December 2017

Downregulation of serum RAB27B confers improved prognosis and is associated with hepatocellular carcinoma progression through PI3K-AKT-P21 signaling.

Oncotarget 2017 Sep 19;8(37):61118-61132. Epub 2017 May 19.

Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing, China.

Previous study revealed that elevated expression of RAB27B in tissues is correlated with hepatocellular carcinoma (HCC) progression; however, the mechanisms involved in promoting HCC development are still unclear. Moreover, HCC tissues are not readily obtained during routine diagnosis. Therefore, to further explore its potential value in early diagnosis, we examined RAB27B expression in patient sera. First, the correlation between serum RAB27B expression and survival, as well as TNM and Barcelona Clinic Liver Cancer stages, were evaluated in patients with HCC. Second, lentiviral vector plasmids carrying interference sequences and plasmids harboring the complete open reading frame of RAB27B were designed to knockdown or overexpress RAB27B in BEL7402 or HuH-7 cells to determine its biological function. Compared with healthy controls and patients with chronic hepatitis B infection, serum RAB27B was significantly increased in patients with HCC. After down-regulating expression of RAB27B, the proliferation of BEL7402 cells was remarkably inhibited both and . Additionally, activation of the PI3K/AKT pathway was significantly diminished. Moreover, cell cycle progression of the knockdown cells was notably arrested in the G1/S phase, and upregulation of p21 contributed to this effect. Restoration experiments to recover RAB27B expression revealed opposing results. These findings indicated RAB27B might regulate cell cycle through the PI3K/AKT/p21 pathway by releasing cytokines via exocytosis, thereby modulating the proliferation of HCC cells. RAB27B could potentially be a valuable serum biomarker for the early diagnosis of, and a therapeutic target in, HCC.
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http://dx.doi.org/10.18632/oncotarget.18010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5617411PMC
September 2017

Polymeric hydrophilic ionic liquids used to modify magnetic nanoparticles for the highly selective enrichment of N-linked glycopeptides.

Sci Rep 2017 08 1;7(1):6984. Epub 2017 Aug 1.

National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116011, China.

The low abundance of glycopeptides in biological samples makes it necessary to enrich them before further analysis. In this study, the polymeric hydrophilic ionic liquid-modified magnetic ([email protected]@PMAC) nanoparticles were synthesized via a one-step reflux-precipitation polymerization. Owing to the excellent hydrophilicity and strong electrostatic interaction toward glycopeptides of the polymerized hydrophilic ionic liquid, [2-(methacryloyloxy) ethyl] trimethylammonium chloride (MAC), the synthesized [email protected]@PMAC nanoparticles exhibited outstanding performance in glycopeptide enrichment with high detection sensitivity (10 fmol), large binding capacity (100 μg mg) and satisfied enrichment recovery (approximately 82%). Furthermore, the newly developed [email protected]@PMAC nanoparticles were applied for the glycopeptide enrichment of HeLa exosome proteins. A total of 1274 glycopeptides from 536 glycoproteins were identified in three replicate analyses of 50 μg of HeLa exosome proteins. These results demonstrate the potential of [email protected]@PMAC nanoparticles for both glycoproteomic analysis and exosome research.
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http://dx.doi.org/10.1038/s41598-017-07516-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5539331PMC
August 2017