The OGT-c-Myc-PDK2 axis rewires the TCA cycle and promotes colorectal tumor growth

Deregulated glucose metabolism termed the "Warburg effect" is a fundamental feature of cancers, including the colorectal cancer. This is typically characterized with an increased rate of glycolysis, and a concomitant reduced rate of the tricarboxylic acid (TCA) cycle metabolism as compared to the normal cells. How the TCA cycle is manipulated in cancer cells remains unknown. Here, we show that O-linked N-acetylglucosamine (O-GlcNAc) regulates the TCA cycle in colorectal cancer cells. Depletion of OGT, the sole transferase of O-GlcNAc, significantly increases the TCA cycle metabolism in colorectal cancer cells. Mechanistically, OGT-catalyzed O-GlcNAc modification of c-Myc at serine 415 (S415) increases c-Myc stability, which transcriptionally upregulates the expression of pyruvate dehydrogenase kinase 2 (PDK2). PDK2 phosphorylates pyruvate dehydrogenase (PDH) to inhibit the activity of mitochondrial pyruvate dehydrogenase complex, which reduces mitochondrial pyruvate metabolism, suppresses reactive oxygen species production, and promotes xenograft tumor growth. Furthermore, c-Myc S415 glycosylation levels positively correlate with PDK2 expression levels in clinical colorectal tumor tissues. This study highlights the OGT-c-Myc-PDK2 axis as a key mechanism linking oncoprotein activation with deregulated glucose metabolism in colorectal cancer.

A Computational and Chemical Design Strategy for Manipulating Glycan-Protein Recognition

Glycans are complex biomolecules that encode rich information and regulate various biological processes, such as fertilization, host-pathogen binding, and immune recognition, through interactions with glycan-binding proteins. A key driving force for glycan-protein recognition is the interaction between the π electron density of aromatic amino acid side chains and polarized C─H groups of the pyranose (termed the CH-π interaction). However, the relatively weak binding affinity between glycans and proteins has hindered the application of glycan detection and imaging. Here, computational modeling and molecular dynamics simulations are employed to design a chemical strategy that enhances the CH-π interaction between glycans and proteins by genetically incorporating electron-rich tryptophan derivatives into a lectin PhoSL, which specifically recognizes core fucosylated N-linked glycans. This significantly enhances the binding affinity of PhoSL with the core fucose ligand and enables sensitive detection and imaging of core fucosylated glycans in vitro and in xenograft tumors in mice. Further, the study showed that this strategy is applicable to improve the binding affinity of GafD lectin for N-acetylglucosamine-containing glycans. The approach thus provides a general and effective way to manipulate glycan-protein recognition for glycoscience applications.

Biological Properties of 3D-Printed Zirconia Implants with p-Cell Structures

Research on 3-dimensional (3D) printed porous zirconia-based dental implants is still in its infancy. This study aimed to evaluate the biological responses of novel zirconia implants with p-cell structures fabricated by 3D printing. The solid zirconia samples exhibited comparable density, 3-point flexural strength, and accelerated aging properties compared to specimens prepared previously by conventional methods. Cell-based experiments showed that the p-cell structure promoted cell proliferation, adhesion, and osteogenesis-related protein expression. Mechanical tests showed that both p-cell and control implants could withstand a torque of 35 Ncm without breaking. The mean maximum breaking loads of p-cell and control implants were 1,222.429 ± 115.591 N and 1,903.857 ± 250.673 N, respectively, which were much higher than the human physiological chewing force and human mean maximum occlusal force. An animal experiment showed that the bone trabeculae around the implants were significantly thicker, more numerous, and denser in the p-cell group than in the control group. This work could provide promising guidance for further exploring 3D printing techniques for porous zirconia bionic implants in dentistry.

Nuclear and cytoplasmic specific RNA binding proteome enrichment and its changes upon ferroptosis induction

The key role of RNA-binding proteins (RBPs) in posttranscriptional regulation of gene expression is intimately tied to their subcellular localization. Here, we show a subcellular-specific RNA labeling method for efficient enrichment and deep profiling of nuclear and cytoplasmic RBPs. A total of 1221 nuclear RBPs and 1333 cytoplasmic RBPs were enriched and identified using nuclear/cytoplasm targeting enrichment probes, representing an increase of 54.4% and 85.7% compared with previous reports. The probes were further applied in the omics-level investigation of subcellular-specific RBP-RNA interactions upon ferroptosis induction. Interestingly, large-scale RBPs display enhanced interaction with RNAs in nucleus but reduced association with RNAs in cytoplasm during ferroptosis process. Furthermore, we discovered dozens of nucleoplasmic translocation candidate RBPs upon ferroptosis induction and validated representative ones by immunofluorescence imaging. The enrichment of Tricarboxylic acid cycle in the translocation candidate RBPs may provide insights for investigating their possible roles in ferroptosis induced metabolism dysregulation.

Discovery of highly potent and selective KRASG12C degraders by VHL-recruiting PROTACs for the treatment of tumors with KRASG12C-Mutation

Although several covalent KRASG12C inhibitors have made great progress in the treatment of KRASG12C-mutant cancer, their clinical applications are limited by adaptive resistance, motivating novel therapeutic strategies. Through drug design and structure optimization, a series of highly potent and selective KRASG12C Proteolysis Targeting Chimeras (PROTACs) were developed by incorporating AMG510 and VHL ligand VH032. Among them, degrader YN14 significantly inhibited KRASG12C-dependent cancer cells growth with nanomolar IC50 and DC50 values, and ＞ 95 % maximum degradation (Dmax). Molecular dynamics (MD) simulation showed that YN14 induced a stable KRASG12C: YN14: VHL ternary complex with low binding free energy (ΔG). Notably, YN14 led to tumor regression with tumor growth inhibition (TGI%) rates more than 100 % in the MIA PaCa-2 xenograft model with well-tolerated dose-schedules. We also found that KRASG12C degradation exhibited advantages in overcoming adaptive KRASG12C feedback resistance over KRASG12C inhibition. Furthermore, combination of RTKs, SHP2, or CDK9 inhibitors with YN14 exhibited synergetic efficacy in KRASG12C-mutant cancer cells. Overall, these results demonstrated that YN14 holds exciting prospects for the treatment of tumors with KRASG12C-mutation and boosted efficacy could be achieved for greater clinical applications via drug combination.

SPPUSM: An MS/MS spectra merging strategy for improved low-input and single-cell proteome identification

Single and rare cell analysis provides unique insights into the investigation of biological processes and disease progress by resolving the cellular heterogeneity that is masked by bulk measurements. Although many efforts have been made, the techniques used to measure the proteome in trace amounts of samples or in single cells still lag behind those for DNA and RNA due to the inherent non-amplifiable nature of proteins and the sensitivity limitation of current mass spectrometry. Here, we report an MS/MS spectra merging strategy termed SPPUSM (same precursor-produced unidentified spectra merging) for improved low-input and single-cell proteome data analysis. In this method, all the unidentified MS/MS spectra from multiple test files are first extracted. Then, the corresponding MS/MS spectra produced by the same precursor ion from different files are matched according to their precursor mass and retention time (RT) and are merged into one new spectrum. The newly merged spectra with more fragment ions are next searched against the database to increase the MS/MS spectra identification and proteome coverage. Further improvement can be achieved by increasing the number of test files and spectra to be merged. Up to 18.2% improvement in protein identification was achieved for 1 ng HeLa peptides by SPPUSM. Reliability evaluation by the "entrapment database" strategy using merged spectra from human and E. coli revealed a marginal error rate for the proposed method. For application in single cell proteome (SCP) study, identification enhancement of 28%-61% was achieved for proteins for different SCP data. Furthermore, a lower abundance was found for the SPPUSM-identified peptides, indicating its potential for more sensitive low sample input and SCP studies.

PD-1 Inhibitors and Chemotherapy Combined with or without Radiotherapy for Patients with Oligometastatic Esophageal Cancer

PURPOSE/OBJECTIVE(S)

Oligometastatic esophageal cancer (OMEC) is an intermediate state between local advanced and widespread metastatic disease, which is associated with better prognosis compared to poly-metastatic esophageal cancer (EC). The previous studies demonstrated the survival benefit from local radiotherapy for OMEC patients. But the data of PD-1 inhibitors combined with radiotherapy for OMEC is still scarce. The purpose of the present study was to determine the efficacy and safety of PD-1 inhibitors plus radiotherapy in OMEC.

MATERIALS/METHODS

OMEC was defined as "up to five measurable metastatic lesions and up to three organs involved". Patients with OMEC receiving PD-1 inhibitors plus chemotherapy in a single center were retrospectively analyzed in this study. They were dichotomized according to whether or not they had received radiotherapy. The efficacy and safety of immunochemotherapy combined with radiotherapy (RT group) and immunochemotherapy alone (NRT group) were investigated.

RESULTS

A total of 226 patients were included; 108 patients received PD-1 inhibitors plus chemotherapy and radiotherapy, while other 118 patients were treated with immunochemotherapy alone. Baseline characteristics were well balanced between the groups. The overall response rate (ORR) was 58.3% in the RT group and 41.5% in the NRT group (P = 0.012), respectively. The median PFS was 13.5 months (95% CI, 10.0-17.1) for the RT group and 8.8 months (95% CI, 9.2-12.0) for the NRT group (P = 0.000). The addition of radiotherapy was the major prognostic factor for PFS (hazard ratio, 0.56; 95% CI, 0.406-0.761; P = 0.000) by univariate Cox regression analysis. Patients were well-tolerated, and the overall incidence of adverse events was similar between the RT group and NRT group. In addition, the incidence of treatment-related pneumonitis did not differ between the two groups. Grade 3-5 pneumonitis was observed in 3.7% and 5.1% of patients in the RT and NRT groups, respectively.

CONCLUSION

The additional of radiotherapy to PD-1 inhibitors and chemotherapy improved PFS of patients with OMEC and showed acceptable toxicity. Further prospective studies investigating the combination of immunochemotherapy and radiotherapy are warranted.

Outcome Supervised Deep Learning Model on Pathological Whole Slide Images for Survival Prediction of Immunotherapy in Non-Small Cell Lung Cancer Patients: A Multicenter Study

PURPOSE/OBJECTIVE(S)

Although PD-(L)1 inhibitors were marked by durable efficacy in non-small cell lung cancer patients (NSCLC), about 60% of patients still suffer from recurrence and metastasis after PD-(L)1 inhibitors treatment. And there were no robust biomarkers of the response of PD-(L)1 inhibitors. Whole slide images (WSIs) of H&E-stained specimens have been found to characterize the tumor microenvironment, and might be the potential prognostic predictors of NSCLC patients. To accurately predict the response to PD-(L)1 inhibitors, we presented the deep learning model based on WSI of H&E-stained specimens of NSCLC patients.

MATERIALS/METHODS

Two independent cohorts of NSCLC patients receiving PD-(L)1 inhibitors from two hospitals were enrolled for model training and testing respectively. The WSI images of H&E-stained histological specimens were obtained from these patients, and patched into 1024×1024 pixels. The labels of patched images were determined due to their progression free survival (PFS) with the interval of 4 months. The patch-level model was firstly trained based on Vit to identify the predictive patches in training cohort, and patch-level probability distribution was performed. Then we trained patient-level survival model-based Vit-RNN framework, and tested it in external validation cohort.

RESULTS

A total of 291 WSI images of H&E-stained histological specimens from 198 NSCLC patients in primary cohort and 62 WSI images from 30 NSCLC patients in testing cohort were included for model training and external validation. All patients were divided into 4 groups due to their PFS after PD-(L)1 inhibitors. There were 246,318 patches from 291 images in primary cohort after image pre-processing, and all images were randomly divided into train cohort and validation cohort with the proportion of 7:3. The patch-level Vit model with the highest accuracy was saved and the predictive patches were selected after 50 epochs training. All patches were ranked by the probability of correct prediction, and the first 50 top-ranked patches from each WSI image are sequentially passed to the patient-level Vit-RNN model. The Vit-RNN survival achieved an accuracy of 88.6% in the validation cohort, and an accuracy of 81% in the testing cohort. The multivariate cox analysis also indicated the Vit-RNN survival model remained a statistically independent predictor of survival from PD-(L)1 inhibitors (P = 0.0085).

CONCLUSION

The outcome supervised Vit-RNN survival model based on pathological WSIs could be used to predict the efficacy the PD-(L)1 inhibitors in NSCLC patients, laying the foundation for the deployment of computational pathomics in clinical practice of immunotherapy.

Absolute Quantification of Dynamic Cellular Uptake of Small Extracellular Vesicles via Lanthanide Element Labeling and ICP-MS

Small extracellular vesicles (sEVs) are increasingly reported to play important roles in numerous physiological and pathological processes. Cellular uptake of sEVs is of great significance for functional regulation in recipient cells. Although various sEV quantification, labeling, and tracking methods have been reported, it is still highly challenging to quantify the absolute amount of cellular uptake of sEVs and correlate this information with phenotypic variations in the recipient cell. Therefore, we developed a novel strategy using lanthanide element labeling and inductively coupled plasma-mass spectrometry (ICP-MS) for the absolute and sensitive quantification of sEVs. This strategy utilizes the chelation interaction between Eu3+ and the phosphate groups on the sEV membrane for specific labeling. sEVs internalized by cells can then be quantified by ICP-MS using a previously established linear relationship between the europium content and the particle numbers. High Eu labeling efficiency and stability were demonstrated by various evaluations, and no structural or functional alterations in the sEVs were discovered after Eu labeling. Application of this method revealed that 4020 ± 171 sEV particles/cell were internalized by HeLa cells at 37 °C and 61% uptake inhibition at 4 °C. Further investigation led to the quantitative differential analysis of sEV cellular uptake under the treatment of several chemical endocytosis inhibitors. A 23% strong inhibition indicated that HeLa cells uptake sEVs mainly through the macropinocytosis pathway. This facile labeling and absolute quantification strategy of sEVs with ppb-level high sensitivity is expected to become a potential tool for studying the functions of sEVs in intracellular communication and cargo transportation.

Sensitive N-Glycopeptide Profiling of Single and Rare Cells Using an Isobaric Labeling Strategy without Enrichment

Single-cell omics is critical in revealing population heterogeneity, discovering unique features of individual cells, and identifying minority subpopulations of interest. As one of the major post-translational modifications, protein N-glycosylation plays crucial roles in various important biological processes. Elucidation of the variation in N-glycosylation patterns at single-cell resolution may largely facilitate the understanding of their key roles in the tumor microenvironment and immune therapy. However, comprehensive N-glycoproteome profiling for single cells has not been achieved due to the extremely limited sample amount and incompatibility with the available enrichment strategies. Here, we have developed an isobaric labeling-based carrier strategy for highly sensitive intact N-glycopeptide profiling for single cells or a small number of rare cells without enrichment. Isobaric labeling has unique multiplexing properties, by which the "total" signal from all channels triggers MS/MS fragmentation for N-glycopeptide identification, while the reporter ions provide quantitative information. In our strategy, a carrier channel using N-glycopeptides obtained from bulk-cell samples significantly improved the "total" signal of N-glycopeptides and, therefore, promoted the first quantitative analysis of averagely 260 N-glycopeptides from single HeLa cells. We further applied this strategy to study the regional heterogeneity of N-glycosylation of microglia in mouse brain and discovered region-specific N-glycoproteome patterns and cell subtypes. In conclusion, the glycocarrier strategy provides an attractive solution for sensitive and quantitative N-glycopeptide profiling of single/rare cells that cannot be enriched by traditional workflows.

Assessing the construction of a Healthy City in China: a conceptual framework and evaluation index system

OBJECTIVES

COVID-19 has brought challenges to the health of all mankind. It is particularly important to promote the construction of a 'Healthy China' and build a 'healthy community'. The aims of this study were to construct a reasonable conceptual framework for the Healthy City concept and to assess Healthy City construction in China.

STUDY DESIGN

This study combined qualitative and quantitative research.

METHODS

This study proposes the concept model of 'nature-human body-Healthy City' and accordingly constructs an evaluation index system for the construction of a Healthy City that integrates five dimensions, namely, the medical level, economic basis, cultural development, social services, and ecological environment to explore the spatial and temporal heterogeneity of Healthy City construction in China. Finally, the influencing factors of Healthy City construction patterns are explored using GeoDetector.

RESULTS

(1) The pace of Healthy City construction is generally on the rise; (2) the construction of Healthy Cities exhibits significant global spatial autocorrelation and gradually increasing agglomeration. The spatial distribution of cold hotspot areas was relatively stable; (3) medical and health progress is an important factor; the level of economic development is the leading support; the endowment of resources and environment is the basic condition; public service support provides important support; and scientific and technological innovation capabilities provide technical support for the construction of a Healthy City.

CONCLUSIONS

The spatial heterogeneity of Healthy City construction in China is evident, and the state of spatial distribution is relatively stable. The spatial pattern of Healthy City construction is shaped by a combination of factors. Our research will provide a scientific basis for promoting the construction of Healthy Cities and helping to implement the Health China Strategy.

A three-stage search strategy combining database reduction and retention time filtering to improve the sensitivity of low-input and single-cell proteomic analysis

When performing proteome profiling of low-input and single-cell samples, achieving deep protein coverage is very challenging due to the sensitivity limitation of current proteomic methods. Herein, we introduce a three-stage search strategy that combines the advantages of database reduction and Δ retention time (ΔRT) filtering. The strategy improves peptide/protein identification and reproducibility by retaining more correct identifications and filtering out incorrect identifications. The raw data were first merged and searched against a Uniprot database with a relaxed false discovery rate (FDR) of 40% to identify the possible detectable proteins. The identified proteins were then used as a new database to search the raw data against with a tighter FDR of 10%. After this, the results were filtered using ΔRT (the difference between the measured and predicted RT) to reduce the incorrect identifications and maintain the FDR below 1%. This strategy resulted in over 30% improvement in proteome coverage for single-cells and samples of similar size. The reproducibility of identification and quantification was also enhanced for the low-input samples. Moreover, the 50% higher number of differential proteins found in the two types of single neurons indicates the application potential of this strategy.

Tandem enrichment of serum exosomes and exosomal RNA with titanium dioxide

Exosomes have great potential as biomarker carriers for disease diagnosis and prognosis. In recent years, exosomal RNA (exoRNA) has become a promising candidate for the early diagnosis and prognosis of cancers, and its pathophysiological roles in various diseases have been revealed. For example, exosome-derived mRNAs, miRNAs, circRNAs, and lncRNAs function as signalling molecules to regulate tumour growth, angiogenesis, invasion, metastasis, and the response to chemotherapy. However, the isolation of exosomes and exoRNA with high quality and purity remains challenging due to the relatively small size of exosomes and the limited amount of RNA in exosomes. In this work, we developed a novel tandem enrichment method to isolate exoRNA from serum based on the specific interaction between titanium dioxide (TiO₂) and the phosphate groups on the lipid bilayer of exosomes and of the exoRNA. TiO₂-based RNA isolation was first demonstrated and optimized in HeLa cells. A total of 130.9 ± 8.34 µg of RNA was rapidly enriched from approximately 5 × 10⁶ HeLa cells within 10 min. This was a 41.5% higher yield than that using a commercial Ultrapure RNA Kit. TiO₂-based tandem enrichment of exoRNA was then performed using human serum, obtaining 64.53±3.41 ng of exoRNA from 500 µL of human serum within 30 min. A total of 2,137,902 reads, including seven types of exoRNAs, were identified from the exosomes. This method is compatible with various downstream RNA processing techniques and does not use toxic or irritating reagents, such as phenol or chloroform, providing a simple, economical, rapid, and safe approach for exoRNA extraction from biological samples.

An angled-shape tip-based strategy for highly sensitive proteomic profiling of a low number of cells

Profiling proteins plays an essential role in understanding the functions and dynamic networks in biological systems. Mass spectrometry-based proteomic analysis commonly requires multistep sample processing, which results in severe sample loss. Although the recently developed microproteomic strategies have substantially reduced sample loss via droplet microfluidic technology, specialized equipment and well-trained personnel are needed, which may limit their wide adoption. Here, we report an angled-shape tip-based strategy for rapid sample preparation and sensitive proteomic profiling of small cell populations (<1000 cells). The angled-shape tip provided a 'reactor' for the entire proteomic sample processing workflow, from cell capture and lysis to protein digestion, eliminating the sample transfer-induced protein loss. The angled-shape tip was surface-treated for anti-protein adsorption which further reduced the sample loss. Using this strategy, 1241 ± 38-4110 ± 37 protein groups and 4010 ± 700-34 879 ± 575 peptides were identified from 10-1000 HeLa cells with high quantification reproducibility in only 4.5 h sample processing time, which was superior to the reported methods and commercial kits, especially for <100 cells. This approach was easily accessible, straightforward to operate, and compatible with flow cytometry-based cell sorting. It showed great potential for in-depth proteomic profiling of rare cells (<1000 cells) in both basic biological research and clinical application.

[Clinical characteristics and prognosis of primary and secondary diffuse large B-cell lymphoma of the pancreas]

Objective: To analyze the clinical characteristics and prognosis of primary and secondary pancreatic diffuse large B-cell lymphoma (DLBCL) . Methods: Clinical data of patients with pancreatic DLBCL admitted at Shanghai Rui Jin Hospital affiliated with Shanghai Jiao Tong University School of Medicine from April 2003 to June 2020 were analyzed. Gene mutation profiles were evaluated by targeted sequencing (55 lymphoma-related genes). Univariate and multivariate Cox regression models were used to evaluate the prognostic factors of overall survival (OS) and progression-free survival (PFS) . Results: Overall, 80 patients were included; 12 patients had primary pancreatic DLBCL (PPDLBCL), and 68 patients had secondary pancreatic DLBCL (SPDLBCL). Compared with those with PPDLBCL, patients with SPDLBCL had a higher number of affected extranodal sites (P<0.001) and had higher IPI scores (P=0.013). There was no significant difference in the OS (P=0.120) and PFS (P=0.067) between the two groups. Multivariate analysis indicated that IPI intermediate-high/high risk (P=0.025) and double expressor (DE) (P=0.017) were independent adverse prognostic factors of OS in patients with pancreatic DLBCL. IPI intermediate-high/high risk (P=0.021) was an independent adverse prognostic factor of PFS in patients with pancreatic DLBCL. Targeted sequencing of 29 patients showed that the mutation frequency of PIM1, SGK1, BTG2, FAS, MYC, and MYD88 in patients with pancreatic DLBCL were all >20%. PIM1 (P=0.006 for OS, P=0.032 for PFS) and MYD88 (P=0.001 for OS, P=0.017 for PFS) mutations were associated with poor OS and PFS in patients with SPDLBCL. Conclusion: There was no significant difference in the OS and PFS between patients with PPDLBCL and those with SPDLBCL. IPI intermediate-high/high risk and DE were adverse prognostic factors of pancreatic DLBCL. PIM1, SGK1, BTG2, FAS, MYC, and MYD88 were common mutations in pancreatic DLBCL. PIM1 and MYD88 mutations indicated worse prognosis.

[Quality of life and risk factors in patients with herpes zoster]

Objective: To evaluate the quality of life and influencing factors of patients with herpes zoster (HZ) seen in hospitals. Methods: Based on Zoster Brief Pain Inventory (ZBPI) and Five-level EuroQol Five-dimensional Questionnaire (EQ-5D-5L), a cross-sectional survey was conducted to evaluate the pain severity and quality of life of 332 HZ cases seen in 22 hospitals of Lu'an City (Anhui Province), Zibo City (Shandong Province) and Tongchuan City (Shaanxi Province) from October to December 2021. The censored least absolute deviations (CLAD) model was used to analyze the related factors affecting the changes of patients' health utility values. Results: The 45.5% of 332 HZ cases were male. The median (Q₁,Q₃) age was 59 (50, 68) years. 59.64% of them assessed by ZBPI had moderate to severe pain in the past 24 hours (worst pain score≥5), and that of PHN cases was 84.8%(39/46). 77.7% (258/332), 77.4% (257/332) and 74.1% (246/332) of all patients reported that pain interfered with sleep, mood and general activities, respectively. Aging [β_40-49y (95%CI)=-0.11 (-0.15, -0.08); β_50-59y (95%CI)=-0.03 (-0.05, 0.00); β_60-69y (95%CI)=-0.09 (-0.12, -0.06); β_70-90y(95%CI)=-0.16 (-0.19, -0.12)], working status (unemployed) [β_farmer (95%CI)=0.15 (0.13, 0.18); β_retirees(95%CI)=0.21 (0.18, 0.24); β_employee (95%CI)=0.13 (0.10, 0.16) ], complications[β_PHN (95%CI)=-0.08 (-0.13, -0.04); β_{other complications} (95%CI)=-0.12 (-0.15, -0.08)], within 30 days after onset [β(95%CI)=-0.01 (-0.03, 0.01)] and treatment [β_{other complications} (95%CI)=-0.09 (-0.11, -0.06)] were related factors for the decline of health utility value (all P values <0.05). Conclusions: More than half of the patients with HZ had moderate to severe pain in the past 24 hours, which had a serious negative impact on the physical and mental health of the patients. Elderly patients, acute patients and patients with complications had lower health utility values and worse health status. We suggest that eligible people be vaccinated with HZ vaccine as soon as possible.

A new integrated method for tissue extracellular vesicle enrichment and proteome profiling

Extracellular vesicles (EVs) are membranous vesicles released by cells that carry a number of biologically important components such as lipids, proteins, and mRNAs. EVs can mediate cancer cell migration, invasion, angiogenesis, and cell survival, greatly contributing to cell-to-cell communication in the tumor microenvironment. Additionally, EVs have been found to have diagnostic and prognostic significance in various cancers. However, the direct isolation of pure EVs remains challenging, especially from tissue samples. Currently available EV isolation approaches, e.g., ultracentrifugation, are time-consuming, instrumental dependent, and have a low recovery rate with limited purity. It is urgent to develop rapid and efficient methods for enriching tissue EVs for biological and clinical studies. Here, we developed a novel isolation approach for tissue EVs using an extraction kit combined with TiO2 microspheres (kit-TiO2). The EVs were first precipitated from the tissue fluid using a precipitation agent and then further enriched using microspheres based on the specific interaction between TiO2 and the phosphate groups on the lipid bilayer of the EVs. Kit-TiO2 approach led to improved purity and enrichment efficiency of the isolated EVs, as demonstrated by western blot and proteomic analysis, compared with previously reported methods. A total of 1966 protein groups were identified from the tissue EVs. We compared the proteomic profiles of the liver tissue EVs from healthy and hepatocellular carcinoma (HCC) bearing-mice. Twenty-five significantly upregulated and 75 downregulated protein groups were found in the HCC EVs. Among the differentially expressed proteins, Atic, Copa, Cont3, Me1, Anxa3, Fth1, Anxa5, Phb1, Acaa2, ATPD, and Glud1 were reported to be highly relevant to HCC. This novel isolation strategy has provided a powerful tool for enriching EVs directly from tissues, and may be applied in biomarker discovery and drug screening of HCC.

Synthesis of Surface-Functionalized Molybdenum Disulfide Nanomaterials for Efficient Adsorption and Deep Profiling of the Human Plasma Proteome by Data-Independent Acquisition

Blood is one of the most important clinical samples for protein biomarker discovery, as it provides rich physiological and pathological information and is easy to obtain with low invasiveness. However, the discovery of protein biomarkers in the blood by mass spectrometry (MS)-based proteomic strategies has been shown to be highly challenging due to the particularly large concentration range of proteins and the strong interference by the high-abundant proteins in the blood. Therefore, developing sensitive methods for low-abundant biomarker protein identification is a key issue that has received great attention. Here, we report the synthesis and characterization of surface-functionalized magnetic molybdenum disulfide (MoS₂) for the large-scale adsorption of low-abundant plasma proteins and deep profiling by MS. MoS₂ nanomaterials resulted in the coverage of more than 3400 proteins (including a single-peptide hit) in a single LC-MS analysis without peptide prefractionation using pooled plasma samples, which were five times more than those obtained by the direct analysis of the plasma proteome. A detection limit in the low ng L^-1 range was obtained, which is rare compared with previous reports.

Impacts of international food and feed trade on nitrogen balances and nitrogen use efficiencies of food systems

International trade of agricultural products has greatly increased over time, but its impacts on sustainable development are debated. It may contribute to food security in importing countries, increases the dependency between countries, and has been implicated in displacement of environmental pollution and resource depletion. There is also discussion about the relationships between trade and nitrogen (N) balances and N use efficiencies (NUE). We explored relationships between changes in the trade of food and feed and in N balances and NUE of the food supply systems through simulation modeling and an analysis of empirical data of 115 countries (representing 91% of global population) for the period 1961-2011. In the empirical analysis, 64 main importing countries and 14 main exporting countries, were distinguished. Importing countries had on average a higher population density than exporting countries but rather similar protein intake and GDP per capita. The empirical analysis indicate that main importing countries had on average higher N fertilizer inputs to their food supply systems, and also higher N surpluses and higher NUE than main exporting countries. The overall mean NUE of the food supply system of main importing countries decreased with increasing import, but the relationships between import and NUE were diverse when these countries were grouped according to population density and GDP per capita. We compared N balances and partial N balances, and three methodologies commonly used for estimating NUE. We observed that NUE2 provides an unbiased estimate for both importing and exporting countries. Our study contributes to the understanding of the diverse relationships between international trade, N balances and NUE of food systems.

A New Strategy for High-Efficient Tandem Enrichment and Simultaneous Profiling of N-Glycopeptides and Phosphopeptides in Lung Cancer Tissue

N-glycosylation and phosphorylation, two common posttranslational modifications, play important roles in various biological processes and are extensively studied for biomarker and drug target screening. Because of their low abundance, enrichment of N-glycopeptides and phosphopeptides prior to LC–MS/MS analysis is essential. However, simultaneous characterization of these two types of posttranslational modifications in complex biological samples is still challenging, especially for tiny amount of samples obtained in tissue biopsy. Here, we introduced a new strategy for the highly efficient tandem enrichment of N-glycopeptides and phosphopeptides using HILIC and TiO₂ microparticles. The N-glycopeptides and phosphosites obtained by tandem enrichment were 21%–377% and 22%–263% higher than those obtained by enriching the two PTM peptides separately, respectively, using 160–20 μg tryptic digested peptides as the starting material. Under the optimized conditions, 2798 N-glycopeptides from 434 N-glycoproteins and 5130 phosphosites from 1986 phosphoproteins were confidently identified from three technical replicates of HeLa cells by mass spectrometry analysis. Application of this tandem enrichment strategy in a lung cancer study led to simultaneous characterization of the two PTM peptides and discovery of hundreds of differentially expressed N-glycosylated and phosphorylated proteins between cancer and normal tissues, demonstrating the high sensitivity of this strategy for investigation of dysregulated PTMs using very limited clinical samples.

[Medial border of D3 lymphadenectomy for right colon cancer]

The extent of D3 lymphadenectomy for right colon cancer, especially the medial border of central lymph node dissection remains controversial. D3 lymphadenectomy and complete mesocolon excision (CME) are two standard procedures for locally advanced right colon carcinoma. D3 lymphadenectomy determines the medial border according to the distribution of the lymph nodes. The mainstream medial border should be the left side of superior mesenteric vein (SMV) according to the definition of D3, but there are also some reports that regards the left side of superior mesenteric artery (SMA) as the medial border. In contrast, the CME procedure emphasizes the beginning of the colonic mesentery and the left side of SMA should be considered as the medial border. Combined with the anatomical basis, oncological efficacy and technical feasibility of D3 lymph node dissection, we think that it is safe and feasible to take the left side of SMA as the medial boundary of D3 lymph node dissection. This procedure not only takes into account the integrity of mesangial and regional lymph node dissection, but also dissects more distant lymph nodes at risk of metastasis. It has its anatomical basis and potential oncological advantages. However, at present, this technical concept is still in the exploratory stage in practice, and the related clinical evidence is not sufficient.

[The role and mechanism of lncRNA C9ORF139 targeting miR-24-3P/TAOK1 in regulating the proliferation of acute myeloid leukemia cells]

Objective: To investigate the role and mechanism of long non-coding RNA (lncRNA) C9ORF139 targeting micro RNA(miR)-24-3P/TAOK1 in regulating the proliferation of acute myeloid leukemia (AML) cells. Methods: AML cells HL-60 and THP-1 were purchased from the Chinese Academy of Sciences and divided into 4 groups:group A was negative control group (siNC group), group B was interference C9ORF139 group (siC9ORF139 group), group C was siC9ORF139+miR-24-3p inhibitor group, and group D was miR-24-3P+TAOK1 overexpression group (oe-TAOK1 group). Real-time fluorescence quantitative reverse transcription PCR was used to detect the expression levels of AML cell lines of HL-60 and THP-1 in four groups. Cell Counting Kit-8 assay was performed to measure cell proliferation. Flow cytometry was applied to analyze cell apoptosis. Transwell test was applied to detect cell migration and invasion ability. Western blot was used to detect p-serine/threonine kinase (p-raf) and p-mitogen activation proteinkinase (p-MEK), p-extracellular regulatory protein kinase (p-ERK) expression. The luciferase reporter gene plasmid was constructed to verify the binding ability of C9ORF139,miR-24-3P and TAOK1.Nude mice were inoculated with subcutaneous tumor cells of HL-60 (group A) and HL-60 (group B). Results: After the C9ORF139 gene was knocked down and cultured for 120 h, The cell proliferation ability (0.62±0.02, 0.82±0.02), migration ability (0.22±0.03, 0.05±0.01), invasion ability (0.20±0.02, 0.13±0.03) of group B were all lower than that of group A (1.30±0.02, 1.83±0.07; 0.99±0.02, 0.99±0.02; 1.00±0.01, 1.00±0.01) (all P<0.05). When co-transfected with miR-24-3 inhibitor, cell proliferation ability, migration ability and invasion ability were all higher in group B (all P<0.05). When co-transfected with miR-24-3P and oe-TAOK1 plasmid, cell proliferation ability, migration ability and invasion ability were all higher than group B (all P<0.05).When the C9ORF139 gene in the cells was knocked down, the apoptosis level of group B (28.56±8.07, 17.74±1.91) were higher than those of group A (0.31±0.27, 2.49±0.33)(all P<0.05); when co-transfected with miR-24-3P inhibitor, the apoptosis level (2.34±0.09, 3.06±0.06) were lower than those in group B (all P<0.05); when co-transfected with miR-24-3P and oe-TAOK1 in the plasmid group, the apoptosis level (2.16±1.29, 4.80±0.37) were also lower than those of group B (all P<0.05). In HL-60 and THP-1 cells, when C9ORF139 was not mutated, the luciferase activity of miR-24-3P group was lower than that of the miR-NC group (P<0.05). When the binding site with miR-24-3p in C9ORF139 sequence was mutated, the luciferase activity in miR-24-3p group was equivalent to that in miR-NC group (P>0.05).When TAOK1 was not mutated; the luciferase activity of miR-24-3P group was lower than that of group A (P<0.05). When the binding site with miR-24-3p in TAOK1 sequence was mutated, the luciferase activity in miR-24-3p group was equivalent to that in miR-NC group (P>0.05).When the C9ORF139 gene in HL-60 cells was knocked down and cultured for 72 h, the phosphorylation expression levels of Raf, MEK and ERK molecules in group B were significantly lower than those in group A (all P<0.05). By day 14, the tumor volume in the group A was greater than the tumor cell volume in the group B [(284.49±57.61) vs (125.70±18.64) mm³, P=0.017]. The tumor weight of HL-60 in group A was heavier than that of group B [(847.80±159.36) vs (408.40±113.16) mg, P=0.001]. Conclusions: LncRNA C9ORF139 regulates TAOK1 by sponging miR-24-3P to promote the proliferation, invasion and migration of acute myeloid leukemiacell.In vivo experiments have confirmed that the expression of C9ORF139 can promote the growth of subcutaneous tumors in AML nude mice.

Spatiotemporal Activation of Protein O-GlcNAcylation in Living Cells

O-linked N-acetylglucosamine (O-GlcNAc) is a prevalent protein modification that plays fundamental roles in both cell physiology and pathology. O-GlcNAc is catalyzed solely by O-GlcNAc transferase (OGT). The study of protein O-GlcNAc function is limited by the lack of tools to control OGT activity with spatiotemporal resolution in cells. Here, we report light control of OGT activity in cells by replacing a catalytically essential lysine residue with a genetically encoded photocaged lysine. This enables the expression of a transiently inactivated form of OGT, which can be rapidly reactivated by photo-decaging. We demonstrate the activation of OGT activity by monitoring the time-dependent increase of cellular O-GlcNAc and profile glycoproteins using mass-spectrometry-based quantitative proteomics. We further apply this activation strategy to control the morphological contraction of fibroblasts. Furthermore, we achieved spatial activation of OGT activity predominantly in the cytosol. Thus, our approach provides a valuable chemical tool to control cellular O-GlcNAc with much needed spatiotemporal precision, which aids in a better understanding of O-GlcNAc function.

Synthesis of zwitterionic polymer modified graphene oxide for hydrophilic enrichment of N-glycopeptides from urine of healthy subjects and patients with lung adenocarcinoma

As one of the most common and important post-translational modifications, protein N-glycosylation plays essential roles in many biological processes and have long been considered closely correlated with the occurrence and progression of multiple diseases. Systematic characterization of these disease-related protein N-glycosylation is one of the most convenient ways for new diagnostic biomarker and therapeutic drug target discovering. However, the biological samples are extremely complex and the abundance of N-glycoproteins are especially low, which make highly efficient N-glycoprotein/glycopeptide enrichment before mass spectrometry analysis a prerequisite. In this work, a new type of hydrophilic material (GO-pDMAPS) was prepared by in situ growth of linear zwitterionic polymer chains on the surface of GO and it was successfully applied for N-glycopeptide enrichment from human urine. Due to the excellent hydrophilicity and the facilitate interactions between this GO-pDMAPS and the targets, a total of 1426 N-glycosylated sites corresponding to 766 N-glycoproteins as well as 790 N-glycosylation sites corresponding to 470 N-glycoproteins were enriched and identified from urine of healthy subjects and patients with lung adenocarcinoma, respectively. Among which, 27 N-glycoproteins were expressed exclusively and 4 N-glycoproteins were upregulated at least 3 times comparing with the healthy group, demonstrating the tremendous potential of this new hydrophilic material for large scale and in depth N-glycoproteome research.

Chemically labeled ThUBD permits rapid and super-sensitive imaging of polyubiquitination signals

The ThUBD-HRP probe and the consequential developed TUF-WB+ method can detect polyubiquitination signal through one-step incubation with hypersensitivity, unbiased detection and a shorter operation time compared with the antibody method.

H1-Receptor Antagonist Olopatadine Inhibits MUC5AC Secretion by Conjunctival Goblet Cells

The study examined the effect of H1-receptor antagonist olopatadine on the secretory function of cultured rat conjunctival goblet cells (CGC) assessed by enzyme-linked lectin assay employing UEA-I lectin. The level of mRNA for membrane-bound protein MUC16 in histaminestimulated CGC was assayed by reverse transcription PCR in the control and after preliminary application of olopatadine. The intracellular calcium concentration [Ca²⁺]i was measured by the calcium colorimetric method using GENMED kits. The effects of histamine and olopatadine on p-ERK level were assessed by Western blotting. Histamine up-regulated secretion of mucin MUC5AC and expression of membrane-bound protein MUC16 in CGC. In addition, it increased both [Ca²⁺]i and the level of phosphorylated ERK. These effects were diminished by preliminary application of olopatadine that probably acted via the ERK signaling pathway. Thus, olopatadine reduced [Ca²⁺]i and down-regulated ERK phosphorylation by binding to H1-receptors, thereby inhibiting secretion of mucin from histamine-stimulated CGC.

An Integrated Strategy for Mass Spectrometry-Based Multiomics Analysis of Single Cells

Single-cell-based genomics and transcriptomics analysis have revealed substantial cellular heterogeneity among seemingly identical cells. Knowledge of the cellular heterogeneity at multiomics levels is vital for a better understanding of tumor metastasis and drug resistance, stem cell differentiation, and embryonic development. However, unlike genomics and transcriptomics studies, single-cell characterization of metabolites, proteins, and post-translational modifications at the omics level remains challenging due to the lack of amplification methods and the wide diversity of these biomolecules. Therefore, new tools that are capable of investigating these unamplifiable "omes" from the same single cells are in high demand. In this work, a microwell chip was prepared and the internal surface was modified for hydrophilic interaction liquid chromatography-based tandem extraction of metabolites and proteins and subsequent protein digestion. Next, direct electrospray ionization mass spectrometry was adopted for single-cell metabolome identification, and a data-independent acquisition-mass spectrometry approach was established for simultaneous proteome profiling and phosphoproteome analysis without phosphopeptide enrichment. This integrated strategy resulted in 132 putatively annotated compounds, more than 1200 proteins, and the first large-scale phosphorylation data set from single-cell analysis. Application of this strategy in chemical perturbation studies provides a multiomics view of cellular changes, demonstrating its capability for more comprehensive investigation of cellular heterogeneity.

One-Step Enzymatic Labeling Reveals a Critical Role of O-GlcNAcylation in Cell-Cycle Progression and DNA Damage Response

O-linked N-acetylglucosamine (O-GlcNAcylation) is a ubiquitous post-translational modification of proteins that is essential for cell function. Perturbation of O-GlcNAcylation leads to altered cell-cycle progression and DNA damage response. However, the underlying mechanisms are poorly understood. Here, we develop a highly sensitive one-step enzymatic strategy for capture and profiling O-GlcNAcylated proteins in cells. Using this strategy, we discover that flap endonuclease 1 (FEN1), an essential enzyme in DNA synthesis, is a novel substrate for O-GlcNAcylation. FEN1 O-GlcNAcylation is dynamically regulated during the cell cycle. O-GlcNAcylation at the serine 352 of FEN1 disrupts its interaction with Proliferating Cell Nuclear Antigen (PCNA) at the replication foci, and leads to altered cell cycle, defects in DNA replication, accumulation of DNA damage, and enhanced sensitivity to DNA damage agents. Thus, our study provides a sensitive method for profiling O-GlcNAcylated proteins, and reveals an unknown mechanism of O-GlcNAcylation in regulating cell cycle progression and DNA damage response.

What is an appropriate caesarean delivery rate for China: a multicentre survey

Objective

To assess the current status of caesarean delivery (CD) in China, propose reference CD rates for China overall, and by regions, investigate the main indications for CDs and identify possible areas for safe reduction.

Design

A multicentre cross‐sectional study.

Setting

A total of 94 hospitals across 23 provinces in China.

Population

A total of 73 977 randomly selected deliveries.

Methods

We used a modified Robson classification to characterise CDs in subgroups and by regions, and the World Health Organization (WHO) C‐Model to calculate reference CD rates.

Main outcome measures

CD rates in China.

Results

In 2015–2016, the overall CD rate in China was 38.9% (95% CI 38.6–39.3%). Considering the obstetric characteristics of the population, the multivariable model‐based reference CD rate was estimated at 28.5% (95% CI 28.3–28.8%). Accordingly, an absolute reduction of 10.4% (or 26.7% relative reduction) may be considered. The CD rate varied substantially by region. Previous CD was the most common indication in all regions, accounting for 38.2% of all CDs, followed by maternal request (9.8%), labour dystocia (8.3%), fetal distress (7.7%) and malpresentation (7.6%). Overall, 12.7% of women had prelabour CDs, contributing to 32.8% of the total CDs.

Conclusions

Nearly 39% of births were delivered by caesarean in China but a reduction of this rate by a quarter may be considered attainable. Repeat CD contributed more than one‐third of the total CDs. Given the large variation in maternal characteristics, region‐specific or even hospital‐specific reference CD rates are needed for precision management of CD.

Tweetable abstract

The caesarean rate in 2015–2016 in China was 38.9%, whereas the reference rate was 28.5%.

The caesarean rate in 2015–2016 in China was 38.9%, whereas the reference rate was 28.5%.

Linked article This article is commented on by M Varner, p. 148 in this issue. To view this mini commentary visit https://doi.org/10.1111/1471-0528.16953.

[Advances in technologies for large-scale enrichment and identification of ribonucleic acid-protein complexes]

核糖核酸(RNA)在细胞中并非单独存在,从它们产生到被降解的过程中与大量蛋白质发生相互作用,RNA结合蛋白(RNA-binding proteins, RBPs)能与RNA结合形成RNA-蛋白质复合物(RP复合物),并以这种复合物的形式发挥生理功能。RNAs或RBPs任一组分的异常与缺失都会影响RP复合物的正常生理功能,从而导致疾病的发生,如代谢异常、肌肉萎缩症、自身免疫性疾病和癌症。因此,定性定量分析RBPs及其在正常细胞和肿瘤细胞中与RNAs靶标之间的复杂相互作用网络有助于挖掘RP复合物在肿瘤发生发展中的作用,开发肿瘤生物标志物和新的治疗方式。要深入研究和理解RNAs与RBPs的相互作用网络,须依赖组学技术对RP复合物进行大规模鉴定。而作为在组学层面系统性解析RP复合物组成、含量和功能的第一步,大规模富集RP复合物极具挑战性。为了解决这一难题,研究者们发展了各种富集鉴定策略。该文针对RP复合物富集策略的最新进展进行了综述,包括紫外光交联和免疫沉淀(crosslinking and immunoprecipitation, CLIP)及其衍生技术、基于“点击化学”的富集策略和基于相分离的富集策略,比较分析了它们的技术原理、优缺点,以方便研究者们选择合适的策略来解决感兴趣的生物学问题。该文最后总结了当前的RP复合物富集方法仍然存在富集效率低和操作繁琐等亟需解决的技术挑战,为富集策略的发展提供了研究方向。

An RNA tagging approach for system-wide RNA-binding proteome profiling and dynamics investigation upon transcription inhibition

RNA-protein interactions play key roles in epigenetic, transcriptional and posttranscriptional regulation. To reveal the regulatory mechanisms of these interactions, global investigation of RNA-binding proteins (RBPs) and monitor their changes under various physiological conditions are needed. Herein, we developed a psoralen probe (PP)-based method for RNA tagging and ribonucleic-protein complex (RNP) enrichment. Isolation of both coding and noncoding RNAs and mapping of 2986 RBPs including 782 unknown candidate RBPs from HeLa cells was achieved by PP enrichment, RNA-sequencing and mass spectrometry analysis. The dynamics study of RNPs by PP enrichment after the inhibition of RNA synthesis provides the first large-scale distribution profile of RBPs bound to RNAs with different decay rates. Furthermore, the remarkably greater decreases in the abundance of the RBPs obtained by PP-enrichment than by global proteome profiling suggest that PP enrichment after transcription inhibition offers a valuable way for large-scale evaluation of the candidate RBPs.

A new tandem enrichment strategy for the simultaneous profiling of O-GlcNAcylation and phosphorylation in RNA-binding proteome

RNA-protein interactions play important roles in almost every step of the lifetime of RNAs, such as RNA splicing, transporting, localization, translation and degradation. Post-translational modifications, such as O-GlcNAcylation and phosphorylation, and their "cross-talk" (OPCT) are essential to the activity and function regulation of RNA-binding proteins (RBPs). However, due to the extremely low abundance of O-GlcNAcylation and the lack of RBP-targeted enrichment strategies, large-scale simultaneous profiling of O-GlcNAcylation and phosphorylation on RBPs is still a challenging task. In the present study, we developed a tandem enrichment strategy combining metabolic labeling-based RNA tagging for selective purification of RBPs and HILIC-based enrichment for simultaneous O-GlcNAcylation and phosphorylation profiling. Benefiting from the sequence-independent RNA tagging by ethynyluridine (EU) labeling, 1115 RBPs binding to different types of RNAs were successfully enriched and identified by quantitative mass spectrometry (MS) analysis. Further HILIC enrichment on the tryptic-digested RBPs and MS analysis led to the first large-scale identification of O-GlcNAcylation and phosphorylation in the RNA-binding proteome, with 461 O-GlcNAc peptides corresponding to 300 RBPs and 671 phosphopeptides corresponding to 389 RBPs. Interestingly, ∼25% RBPs modified by two PTMs were found to be related to multiple metabolism pathways. This strategy has the advantage of high compatibility with MS and provides peptide-level evidence for the identification of O-GlcNAcylated RBPs. We expect it will support simultaneous mapping of O-GlcNAcylation and phosphorylation on RBPs and facilitate further elucidation of the crucial roles of OPCT in the function regulation of RBPs.

Posttranscriptional regulation of de novo lipogenesis by glucose-induced O-GlcNAcylation

O-linked β-N-acetyl glucosamine (O-GlcNAc) is attached to proteins under glucose-replete conditions; this posttranslational modification results in molecular and physiological changes that affect cell fate. Here we show that posttranslational modification of serine/arginine-rich protein kinase 2 (SRPK2) by O-GlcNAc regulates de novo lipogenesis by regulating pre-mRNA splicing. We found that O-GlcNAc transferase O-GlcNAcylated SRPK2 at a nuclear localization signal (NLS), which triggers binding of SRPK2 to importin α. Consequently, O-GlcNAcylated SRPK2 was imported into the nucleus, where it phosphorylated serine/arginine-rich proteins and promoted splicing of lipogenic pre-mRNAs. We determined that protein nuclear import by O-GlcNAcylation-dependent binding of cargo protein to importin α might be a general mechanism in cells. This work reveals a role of O-GlcNAc in posttranscriptional regulation of de novo lipogenesis, and our findings indicate that importin α is a "reader" of an O-GlcNAcylated NLS.

Simultaneous metabolomics and proteomics analysis of plasma-derived extracellular vesicles

Extracellular vesicles (EVs) are nanoscale vesicles with a phospholipid bilayer. In the past few decades, EVs have gained more and more attention, which is attributed to their important roles in cell-to-cell communication. They are regarded as promising sources for disease biomarkers and have been explored for applications in early-stage diagnostics, monitoring of disease status, therapeutics and drug delivery. Nevertheless, EVs are a heterogeneous group of vesicles, and include two predominant classes: exosomes and microvesicles. The origins of these vesicles are diverse, which determines their differences in features and functions. To study the diversity of these EV subpopulations, it is essential to elucidate their compositions including proteins, metabolites, etc. Here, we presented a tandem extraction method to obtain metabolites and proteins from the same batch of EVs simultaneously, enabling a multi-omics differential analysis of exosomes and microvesicles in human plasma. As a result, we found 112 different proteins and 50 different metabolites between exosomes and microvesicles, demonstrating the diversity of these EV subpopulations. Furthermore, compared with human plasma, these two major classes of EVs showed distinct metabolome features, which indicated the necessity of analysing the metabolites derived from EVs to obtain a more comprehensive profile of the plasma metabolome, and the potential of EVs as important sources for biomarker screening.

An Ultrafast N-Glycoproteome Analysis Method Using Thermoresponsive Magnetic Fluid-Immobilized Enzymes

N-Glycosylation is one of the most common and important post-translational modification methods, and it plays a vital role in controlling many biological processes. Increasing discovery of abnormal alterations in N-linked glycans associated with many diseases leads to greater demands for rapid and efficient N-glycosylation profiling in large-scale clinical samples. In the workflow of global N-glycosylation analysis, enzymatic digestion is the main rate-limiting step, and it includes both protease digestion and peptide-N4–(N-acetyl-beta-glucosaminyl) asparagine amidase (PNGase) F deglycosylation. Prolonged incubation time is generally required because of the limited digestion efficiency of the conventional in-solution digestion method. Here, we propose novel thermoresponsive magnetic fluid (TMF)-immobilized enzymes (trypsin or PNGase F) for ultrafast and highly efficient proteome digestion and deglycosylation. Unlike other magnetic material-immobilized enzymes, TMF-immobilized enzymes display a unique temperature-triggered magnetic response behavior. At room temperature, a TMF-immobilized enzyme completely dissolves in an aqueous solution and forms a homogeneous system with a protein/peptide sample for efficient digestion but cannot be separated by magnetic force because of its excellent water dispersity. Above its lower critical solution temperature (LCST), thermoflocculation of a TMF-immobilized enzyme allows it to be easily recovered by increasing the temperature and magnetic force. Taking advantage of the unique homogeneous reaction of a TMF-immobilized enzyme, both protein digestion and glycopeptide deglycosylation can be finished within 3 min, and the whole sample processing time can be reduced by more than 20 times. The application of a TMF-immobilized enzyme in large-scale profiling of protein N-glycosylation in urine samples led to the successful identification of 2,197 N-glycopeptides and further demonstrated the potential of this strategy for fast and high-throughput analysis of N-glycoproteome in clinical samples.

A new urinary exosome enrichment method by a combination of ultrafiltration and TiO2 nanoparticles

Exosomes are small membrane-bound vesicles secreted by most cell types and play an important role in cell-to-cell communication. Increasing evidence shows that exosomal proteins in urine may be used as novel biomarkers for certain diseases. Purified urinary exosomes are necessary for downstream studies and application development. However, conventional methods for exosome isolation and enrichment are technically challenging and time-consuming. Poor specificity, low recovery and instrumental dependence also limit the use of these methods. It is particularly urgent to develop a rapid and efficient extraction method for basic research and clinical application. Particularly, urine is a dilute solution system with relatively low abundance of exosomes, due to which the isolation of urinary exosome requires more efficient technology. Here, we propose a new strategy for facile exosome isolation from human urine by utilizing the ultrafiltration technique and the specific interaction of TiO₂ with the phosphate groups on the lipid bilayer of exosomes. Downstream characterization and proteomic analysis indicate that high-quality exosomes can be obtained from human urine by this ultrafiltration-TiO₂ series method in 20 minutes, and 91.5% exosomes with an intact structure are captured from urine by this method. Moreover, 1874 protein groups have been identified through LC-MS. The results show that the protein identification of our method is 23% higher at least than those obtained by conventional strategies. We also identified 30 differential proteins by comparing the urinary exosomes from healthy male and female volunteers. These proteins are related to biological processes, such as lipid metabolism, fatty acid metabolism and nucleotide metabolism. Our analysis reveals that combining conventional ultrafiltration and TiO₂-based isolation is ideal to overcome the inherent limitations of identification of exosome proteins derived from urine, and yield highly pure exosome components for downstream proteomic analysis.

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

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 Ti⁴⁺-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.

Supine Cycling Exercise Enhances Cerebral Oxygenation of Motor-Related Areas in Healthy Male Volunteers

It has been reported that the cardiovascular response in the supine position is different from that in the sitting position. However, there are few reports on the effects of posture on cerebral oxygenation during exercise. Cycling exercises change oxygenated hemoglobin (O₂Hb) and deoxygenated hemoglobin (HHb) levels in motor-related areas. Therefore, this study compared O₂Hb levels at motor-related areas during recumbent versus supine cycling. Eleven healthy young male performed a 30-min cycling exercise protocol at 50% of the maximal oxygen uptake (VO₂ max) in the recumbent and supine positions. Near-infrared spectroscopy (NIRS) was used to measure exercise-induced O₂Hb and HHb changes in the right (R-PMA) and left premotor areas (L-PMA), supplementary motor area (SMA), and primary motor cortex (M1). In R-PMA, L-PMA and SMA, the O₂Hb obtained during supine cycling was significantly higher than that during recumbent cycling (R-PMA, 0.031 ± 0.01 vs. 0.693 ± 0.01; L-PMA, 0.027 ± 0.01 vs. 0.085 ± 0.013; SMA, 0.041 ± 0.011 vs. 0.076 ± 0.008 mM·cm, recumbent vs. supine position; p < 0.05). These results suggest that supine cycling exercise increases R-PMA, L-PMA, and SMA O₂Hb levels in healthy young men.

Proteomic analysis of cisplatin- and oxaliplatin-induced phosphorylation in proteins bound to Pt-DNA adducts

Cisplatin and oxaliplatin are widely used anti-tumour chemotherapeutic agents with different spectra of activity. The therapeutic efficacy of such platinum-based drug is believed to, at least in part, result from formation of Pt-DNA adducts, followed by DNA damage response and ultimately apoptosis. However, it remains unclear whether these DNA lesions caused by cisplatin and oxaliplatin elicit distinct reactions in cellular signaling pathways. Here, a label-free comparative proteomic study was performed to profile the protein phosphorylation patterns using Pt-DNA probes with different ligand identities and geometries. Phosphorylated proteins recognizing different cisplatin- and oxaliplatin-DNA lesions were enriched and analyzed on LC-MS/MS. Proteomic analysis revealed that cisplatin mainly affected proteins involved in mRNA processing, while chromatin organization and rRNA processing are two major biological processes influenced by oxaliplatin. Changes to site-specific phosphorylation levels of two proteins YBX1 and UBF1 were also validated by Western blotting. In particular, platinum drug treatment in colon and liver cancer cell lines down-regulated S484 phosphorylation of UBF1, which is an essential transcription factor responsible for ribosomal DNA transcription activation, implying that inhibition of ribosome biogenesis might be involved in the cytotoxic mechanism of platinum drugs. Collectively, these results directly reflected distinct protein phosphorylation patterns triggered by cisplatin and oxaliplatin, and could also provide valuable resources for future mechanistic studies of platinum-based anti-tumour agents.

Café-au-lait macules overlying segmental macular hyperpigmentation in a pediatric patient: an early sign for mosaic neurofibromatosis type 1

The presentation of multiple café-au-lait macules (CALMs) in children is a common reason for referral to a dermatologist. Segmental CALMs, a subtype of CALMs, is usually limited to a specific part of the body. Mosaic neurofibromatosis type 1 (NF1; OMIM 162200) is a common congenital disorder associated with segmental CALMs with an incidence of about 1 case/40000 patients, which is lower than the prevalence of patients with germline NF1 mutations1,2 .

Novel Two-Dimensional MoS2-Ti4+ Nanomaterial for Efficient Enrichment of Phosphopeptides and Large-Scale Identification of Histidine Phosphorylation by Mass Spectrometry

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, MoS₂-Ti⁴⁺ nanomaterials were synthesized using a solvothermal method and taking advantage of the electrostatic adsorption between MoS₂ nanosheets and Ti⁴⁺. The MoS₂-Ti⁴⁺ nanomaterials have the advantage of the combined affinity of Ti⁴⁺ 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 MoS₂-Ti⁴⁺ nanomaterial for phosphopeptide enrichment was demonstrated using mixtures of β-casein and bovine serum albumin (BSA). Further evaluation revealed that the MoS₂-Ti⁴⁺ nanomaterial is capable of enriching synthetic histidine phosphopeptides from 1000 times excess tryptic-digested HeLa cell lysate. Application of the MoS₂-Ti⁴⁺ 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.

Quality assessment of randomized controlled trial abstracts on drug therapy of periodontal disease from the abstracts published in dental Science Citation Indexed journals in the last ten years

Background

Randomized controlled trials (RCTs) provide the highest level of evidence and are likely to influence clinical decision-making. This study evaluated the reporting quality of RCT abstracts on drug therapy of periodontal disease and assessed the associated factors.

Material and Methods

The Pubmed database was searched for periodontal RCTs published in Science Citation Indexed (SCI) dental journals from 2010/01/01 to 2019/07/17. Information was extracted from the abstracts according to a modified Consolidated Standards of Reporting Trials (CONSORT) guideline checklist. The data was analyzed using descriptive statistical analysis and the statistical associations were examined using the linear regression analysis (P <0.05).

Results

This study retrieved 1715 articles and 249 of them were finally included. The average overall CONSORT score was 15.6 ± 3.4, which represented 40.9% (±0.6) of CONSORT criteria filling. The reporting rate of some items (trial design, numbers analyzed, confidence intervals, intention-to-treat analysis or per-protocol analysis, harms, registration) was less than 30%. The adequate reporting rate of some items (participants, randomization, numbers analyzed, confidence intervals, intention-to-treat analysis or per protocol analysis) was no more than 4%. None of the abstracts reported funding. According to the multivariable linear regression results, number of authors (P=0.030), word count (P <0.001), continent (P=0.003), structured format (P <0.001), type of periodontal disease (P <0.001) and international collaboration (P=0.023) have a significant association with reporting quality.

Conclusions

The quality of RCT abstracts on drug therapy of periodontal disease in SCI dental journals remained suboptimal. More efforts should be made to improve RCT abstracts reporting quality.

Key words:Abstracts, RCT, drug therapy, periodontal disease, CONSORT, reporting quality assessment.

[Clinical characteristics and death risk factors of severe COVID-19]

Objective: To analyze the clinical features and death-related risk factors of COVID-19. Methods: We enrolled 891 COVID-19 patients admitted to the Affiliated Hospital of Jianghan University from December 2019 to February 2020, including 427 men and 464 women. Of the 891 cases, 582 were severe or critical, including 423(73%)severe and 159 (27%) critical cases. We compared the demographics, laboratory findings, clinical characteristics, treatments and prognosis data of the 582 severe patients. Univariate and multivariate logistic regression analysis was conducted to explore the risk factors associated with death in COVID-19 patients. Results: The 582 severe patients included 293 males and 289 females, with a median age of 64(range 24 to 106). Sixty-three patients died, including 45 males and 18 females, with a median age of 71(range 37 to 90). The average onset time of the 582 patients was 8 days, of whom 461 (79%) had fever, 358 (62%) dry cough, 274 (47%) fatigue. There were 206 cases with shortness of breath (35%), 155 cases with expectoration (27%), 83 cases with muscle pain or joint pain (14%), 71 cases with diarrhea (12%), and 29 cases with headache (4%). Underlying diseases were present in 267 (46%) patients, most commonly hypertension (194, 33%), followed by diabetes (69, 12%), coronary atherosclerotic heart disease (37, 6%), tumor (18, 3%), and chronic obstructive pulmonary disease (5, 1%). Chest CT showed bilateral lung involvement in 505 patients (87%). Upon admission, the median lymphocyte count of the 582 patients was 0.8(IQR, 0.6-1.1)×10(9)/L, the median D-dimer was 0.5 (IQR, 0.4- 0.8) mg/L, the median N-terminal brain natriuretic peptide precursor (NT-proBNP) was 433 (IQR, 141- 806) pg/L, and the median creatinine was 70.3 (IQR, 56.9-87.9) μmol/L. The death group had a median lymphocyte count of 0.5 (0.4-0.8)×10(9)/L, D-dimer 1.1 (0.7-10.0)mg/L, N-terminal brain natriuretic peptide precursor 1479(893-5 087) pg/ml, and creatinine 89.9(67.1-125.3) μmol/L. Multivariate logistic analysis showed that increased D-dimer (OR: 1.095, 95% CI: 1.045-1.148, P<0.001), increased NT-proBNP (OR: 4.759, 95% CI: 2.437-9.291, P<0.001), and decreased lymphocyte count (OR: 0.180, 95% CI: 0.059-0.550, P=0.003) were the risk factors of death in COVID-19 patients. Conclusions: The average onset time of severe COVID-19 was 8 days, and the most common symptoms were fever, dry cough and fatigue. Comorbidities such as hypertension were common and mostly accompanied by impaired organ functions on admission. Higher D-dimer, higher NT-proBNP, and lower lymphocyte count were the independent risk factors of death in COVID-19 patients.