Allergic bronchopulmonary mycosis due to Schizophyllum commune in a patient with chronic hepatitis B.

INTRODUCTION: Schizophyllum commune (S. commune) is an opportunistic pathogenic fungus and can cause infection of the respiratory system in immunocompromised hosts. Allergic bronchopulmonary mycosis (ABPM) is the major disease caused by S. commune. However, identification of S. commune using routine mycological diagnostic methods is difficult. It is easy to make mistakes in diagnosis and treatment, resulting in deterioration of the disease. We report the first case of ABPM due to S. commune in a Chinese patient with chronic hepatitis B. CASE PRESENTATION: The patient presented cough, sputum and dyspnea for six months. The pathogen was missed during routine laboratory workup. We performed bronchoscopy examination and bronchoalveolar lavage. S. commune was identified by metagenomic next-generation sequencing (mNGS) of bronchial alveolar lavage fluid (BALF). Hence, the patient was immediately treated with 200 mg voriconazole twice daily (intravenous infusion) and 20 mg prednisone once a day (oral therapy), along with oral entecavir for hepatitis B. There was no recurrence of infection after the medication was discontinued. CONCLUSIONS: S. commune infection should be considered in the diagnosis of patients with refractory cough, sputum and dyspnea, especially in immunocompromised individuals. The mNGS technique is an effective supplementary technique for the diagnosis of S. commune infection, enabling precise clinical decision-making and appropriate treatment. Most patients have good prognosis with a combination of proper antifungal therapy and hormonal therapy.

High-throughput drug target discovery using a fully automated proteomics sample preparation platform.

Drug development is plagued by inefficiency and high costs due to issues such as inadequate drug efficacy and unexpected toxicity. Mass spectrometry (MS)-based proteomics, particularly isobaric quantitative proteomics, offers a solution to unveil resistance mechanisms and unforeseen side effects related to off-targeting pathways. Thermal proteome profiling (TPP) has gained popularity for drug target identification at the proteome scale. However, it involves experiments with multiple temperature points, resulting in numerous samples and considerable variability in large-scale TPP analysis. We propose a high-throughput drug target discovery workflow that integrates single-temperature TPP, a fully automated proteomics sample preparation platform (autoSISPROT), and data independent acquisition (DIA) quantification. The autoSISPROT platform enables the simultaneous processing of 96 samples in less than 2.5 hours, achieving protein digestion, desalting, and optional TMT labeling (requires an additional 1 hour) with 96-channel all-in-tip operations. The results demonstrated excellent sample preparation performance with >94% digestion efficiency, >98% TMT labeling efficiency, and >0.9 intra- and inter-batch Pearson correlation coefficients. By automatically processing 87 samples, we identified both known targets and potential off-targets of 20 kinase inhibitors, affording over a 10-fold improvement in throughput compared to classical TPP. This fully automated workflow offers a high-throughput solution for proteomics sample preparation and drug target/off-target identification.

N-linked glycoproteins and host proteases are involved in swine acute diarrhea syndrome coronavirus entry.

IMPORTANCE: Gaining insight into the cell-entry mechanisms of swine acute diarrhea syndrome coronavirus (SADS-CoV) is critical for investigating potential cross-species infections. Here, we demonstrated that pretreatment of host cells with tunicamycin decreased SADS-CoV attachment efficiency, indicating that N-linked glycosylation of host cells was involved in SADS-CoV entry. Common N-linked sugars Neu5Gc and Neu5Ac did not interact with the SADS-CoV S1 protein, suggesting that these molecules were not involved in SADS-CoV entry. Additionally, various host proteases participated in SADS-CoV entry into diverse cells with different efficiencies. Our findings suggested that SADS-CoV may exploit multiple pathways to enter cells, providing insights into intervention strategies targeting the cell entry of this virus.

Deciphering intercellular signaling complexes by interaction-guided chemical proteomics.

Indirect cell-cell interactions mediated by secreted proteins and their plasma membrane receptors play essential roles for regulating intercellular signaling. However, systematic profiling of the interactions between living cell surface receptors and secretome from neighboring cells remains challenging. Here we develop a chemical proteomics approach, termed interaction-guided crosslinking (IGC), to identify ligand-receptor interactions in situ. By introducing glycan-based ligation and click chemistry, the IGC approach via glycan-to-glycan crosslinking successfully captures receptors from as few as 0.1 million living cells using only 10 ng of secreted ligand. The unparalleled sensitivity and selectivity allow systematic crosslinking and identification of ligand-receptor complexes formed between cell secretome and surfaceome in an unbiased and all-to-all manner, leading to the discovery of a ligand-receptor interaction between pancreatic cancer cell-secreted urokinase (PLAU) and neuropilin 1 (NRP1) on pancreatic cancer-associated fibroblasts. This approach is thus useful for systematic exploring new ligand-receptor pairs and discovering critical intercellular signaling events.

Effect of prone position in patients with acute respiratory distress syndrome supported by venovenous extracorporeal membrane oxygenation: a retrospective cohort study.

BACKGROUND: The application of prone position (PP) in acute respiratory distress syndrome (ARDS) supported by venovenous extracorporeal membrane oxygenation (VV-ECMO) is controversial. OBJECTIVES: To evaluate the safety and efficacy of application of PP during VV-ECMO in patients with ARDS. METHODS: This was a single-center, retrospective study of patients who met the Berlin definition of ARDS, and were supported with VV-ECMO. We divided the patients into two groups. The prone group included patients who were supported by VV-ECMO, and experienced at least one period of PP, while those without PP during VV-ECMO were defined as the supine group. Propensity score matching (PSM) at a ratio of 1:1 was introduced to minimize potential confounders. The primary outcomes were the complications of PP and the change of arterial oxygen pressure/fraction of the inspiration (PaO2/FiO2) ratio after PP. The secondary outcomes were hospital survival, ICU survival, and ECMO weaning rate. RESULTS: From April 2013 to October 2020, a total of 91 patients met the diagnostic criteria of ARDS who were supported with ECMO. 38 patients (41.8%) received at least one period of PP during ECMO, while 53 patients (58.2%) were maintained in supine position during ECMO. 22 minor complications were reported in the prone group and major complications were not found. The other ECMO-related complications were similar between two groups. The PaO2/FiO2 ratio significantly improved after PP compared with before (174.50 (132.40-228.25) mmHg vs. 158.00 (122.93-210.33) mmHg, p < 0.001). PSM selected 25 pairs of patients with similar characteristics. Hospital survival or ICU survival did not differ between the two groups (40% vs. 28%, p = 0.370; 40% vs. 32%, p = 0.556). Significant difference of ECMO weaning rate between two groups was not found (56% vs. 32%, p = 0.087). CONCLUSIONS: PP during VV-ECMO was safe and could improve oxygenation. A large-scale and well-designed RCT is needed in the future.

Simultaneously Identifying and Distinguishing Glycoproteins with O-GlcNAc and O-GalNAc (the Tn Antigen) in Human Cancer Cells.

Glycoproteins with diverse glycans are essential to human cells, and subtle differences in glycan structures may result in entirely different functions. One typical example is proteins modified with O-linked ß-N-acetylglucosamine (O-GlcNAc) and O-linked α-N-acetylgalactosamine (O-GalNAc) (the Tn antigen), in which the two glycans have very similar structures and identical chemical compositions, making them extraordinarily challenging to be distinguished. Here, we developed an effective method benefiting from selective enrichment and the enzymatic specificity to simultaneously identify and distinguish glycoproteins with O-GlcNAc and O-GalNAc. Metabolic labeling was combined with bioorthogonal chemistry for enriching glycoproteins modified with O-GlcNAc and O-GalNAc. Then, the enzymatic reaction with galactose oxidase was utilized to specifically oxidize O-GalNAc, but not O-GlcNAc, generating the different tags between glycopeptides with O-GlcNAc and O-GalNAc that can be easily distinguishable by mass spectrometry (MS). Among O-GlcNAcylated proteins commonly identified in three types of human cells, those related to transcription and RNA binding are highly enriched. Cell-specific features are also revealed. Among glycoproteins exclusively in Jurkat cells, those involved in human T-lymphotropic virus type 1 (HTLV-1) infection are overrepresented, which is consistent with the cell line source and suggests that protein O-GlcNAcylation participated in the response to the virus infection. Furthermore, glycoproteins with the Tn antigen have different subcellular distributions in different cells, which may be attributed to the distinct mechanisms for the formation of protein O-GalNAcylation.

[Comparison of the performance of secretome analysis based on metabolic labeling by three unnatural sugars].

Many secreted proteins, including cytokines, growth factors and hormones, are crucial in processes like intercellular signaling. Dynamic changes in secreted proteins usually reflect the growth and pathological state of the cells. Many drug targets are secretory proteins. The proteins are also important biomarkers. Conditioned cell culture media are important samples for secretory proteomic studies. Biomass spectrometry-based proteomic analysis enables the systematic study of secretory proteins. The main problem in analyzing secretory proteins in conditioned culture media is the low concentration of these proteins and the presence of serum, amino acids, and additives in culture media that may interfere with the protein analysis. Conventional secretory proteome analysis uses serum-free cell culture to reduce sample complexity, and typically involves protein concentration, purification, and desalting using ultrafiltration, dialysis, lyophilization, and trichloroacetic acid (TCA) or acetone precipitation, followed by enzymatic digestion and mass spectrometry analysis. This analytical process does not allow specific enrichment of secreted proteins. Thus, only a few secreted proteins can be identified. In addition, prolonged serum-free incubation of cells also tends to lead to unexpected changes in their activity status. A bioorthogonal-based enrichment approach can effectively avoid this problem. In recent years, unnatural sugars containing bio-orthologous groups, such as azide groups, have been used to metabolically label glycosylated proteins, enabling cellular imaging or selective enrichment of glycoproteins and their use for proteomic analysis. The strategy is a two-step process. First, azide-based sugar analogues are added to the cell culture medium and introduced to glycoproteins via the intracellular glycan biosynthesis pathway. Second, they are specifically covalently labeled with imaging probes or affinity probes via click chemistry. Since secreted proteins are usually glycoproteins, this glycolytic labeling has been used to label and enrich secreted proteins. N-Azidoacetylgalactosamine (GalNAz), N-azidoacetylglucosamine (GlcNAz), and N-azidoacetylmannosamine (ManNAz) are classical azide-based sugar analogues. Their effects on cytoplasmic membrane proteins have been compared. However, only ManNAz has been used for metabolic labeling of secreted proteins. No other glyco-analogues that label secreted proteins have been reported. Here, the bio-orthogonal chemical biology technology achieved highly selective labeling and enriched secreted proteins. In combination with click chemistry, different sugar analogues were evaluated for metabolic labeling of secreted proteins. HeLa cells were metabolically labeled by ManNAz, GalNAz, and GlcNAz (the three most commonly used commercial sugar analogues). These glycolytic markers can selectively label specific types of glycosylation. For example, ManNAz, an analogue of the biosynthetic precursor of sialic acid, N-acetylmannosamine (ManNAc), can label sialylated N- or O-glycoproteins. GalNAz, an analogue of N-acetylgalactosamine (GalNAc), can replace GalNAc as a core residue of mucin-type O-glycans and thus label O-glycoproteins. In addition, the intracellular metabolic intermediate of GalNAz (pyrophosphate) UDP-GalNAz can be interconverted with UDP-GlcNAz catalyzed by UDP-galactose-4-differential isomerase (GALE) and thus can also label N-glycoproteins and O-GlcNAc glycoproteins instead of GlcNAc. The GlcNAz analogue is commonly used to label nuclear and cytoplasmic glycoproteins with β-O-GlcNAc residues, but can also label N-glycoproteins with mucin-type O-glycoproteins by converting GALE to GalNAz, followed by enrichment using a biotin-alkynyl probe. Label-free quantitative proteomic analysis was performed to evaluate their labeling efficiency. ManNAz-based secretory protein labeling identified 282 secretory proteins, 224 plasma membrane proteins, and 846 N-glycosites. Compared with GalNAz and GlcNAz, the enrichment of secreted proteins was increased 130% and 67.2%, respectively, and the enrichment of plasma membrane proteins was increased 273.3% and 148.7%, respectively. This study provides a useful comparative analysis and new strategies for highly selective enrichment and systematic secretome analysis.

The circular RNA NT5E promotes non-small cell lung cancer cell growth via sponging microRNA-134.

The current study tested expression and potential function of circular RNA ecto-5'-nucleotidase (circNT5E) in human non-small cell lung cancer (NSCLC). We show that circNT5E levels are significantly elevated in human NSCLC tissues and cells, correlating with downregulation of its potential targets, miR-134, miR-422a and miR-338. In A549 and primary NSCLC cells, circNT5E shRNA inhibited cancer cell growth, proliferation and migration, whiling inducing apoptosis activation. Conversely, ectopic circNT5E overexpression promoted A549 cell progression in vitro. miR-134 is the primary target of circNT5E in lung cancer cells. RNA-Pull down assay in A549 cells confirmed the direct association between biotinylated-miR-134 and circNT6E. miR-134 levels were significantly increased in circNT5E-silenced A549 cells, but reduced with circNT5E overexpression. Forced overexpression of miR-134 mimicked circNT5E shRNA-induced actions, inhibiting NSCLC cell growth and proliferation. In contrast, miR-134 inhibition largely attenuated circNT5E shRNA-induced anti-NSCLC cell activity. Importantly, circNT5E shRNA was ineffective in miR-134-overexpressed A549 cells. Collectively, circNT5E promotes human NSCLC cell progression possibly by sponging miR-134.

MicroRNA-4651 targets bromodomain-containing protein 4 to inhibit non-small cell lung cancer cell progression.

Bromodomain-containing protein 4 (BRD4) overexpression in non-small cell lung cancer (NSCLC) promotes cancer progression. Here, we show that miR-4651 selectively targets and negatively regulates BRD4 in A549 and primary human NSCLC cells. RNA pull-down experiments confirmed that miR-4651 directly binds to BRD4 mRNA. Further, ectopic overexpression of miR-4651 in A549 cells and primary NSCLC cells decreased BRD4 3'-UTR luciferase reporter activity and its expression, whereas miR-4651 inhibition elevated both. Functional studies demonstrated that NSCLC cell growth, proliferation, and migration were suppressed with ectopic miR-4651 overexpression but enhanced with miR-4651 inhibition. BRD4 re-expression using a 3'-UTR mutant BRD4 reversed A549 cell inhibition induced by miR-4651 overexpression. Further, miR-4651 overexpression or inhibition failed to alter the functions of BRD4-KO A549 cells. In vivo, miR-4651-overexpressing A549 xenografts grew slowly than control A549 xenografts in severe combined immunodeficient mice. Finally, miR-4651 was downregulated in human NSCLC tissues, correlating with BRD4 elevation. Together, miR-4651 targets BRD4 to inhibit NSCLC cell growth in vitro and in vivo.

Specific Identification of Glycoproteins Bearing the Tn Antigen in Human Cells.

Glycoproteins contain a wealth of valuable information regarding the development and disease status of cells. In cancer cells, some glycans (such as the Tn antigen) are highly up-regulated, but this remains largely unknown for glycoproteins with a particular glycan. Herein, an innovative method combining enzymatic and chemical reactions was first designed to enrich glycoproteins with the Tn antigen. Using synthetic glycopeptides with O-GalNAc (the Tn antigen) or O-GlcNAc, we demonstrated that the method is selective for glycopeptides with O-GalNAc and can distinguish between these two modifications. The diagnostic ions from the tagged O-GalNAc further confirmed the effectiveness of the method and confidence in the identification of glycopeptides with the Tn antigen by mass spectrometry. Using this method, we identified 96 glycoproteins with the Tn antigen in Jurkat cells. The method can be extensively applied in biological and biomedical research.

Preparation of phenyl-functionalized magnetic mesoporous silica microspheres for the fast separation and selective enrichment of phenyl-containing peptides.

Peptide enrichment before mass spectrometry analysis is essential for large-scale peptidomic studies, but challenges still remain. Herein, magnetic mesoporous silica microspheres with phenyl group modified interior pore walls were prepared by a facile sol-gel coating strategy, and were successfully applied for selective enrichment of phenyl-containing peptides in complex biological samples. The newly prepared nanomaterials possessed abundant silanol groups in the exterior surface and numerous phenyl groups in the interior pore walls, as well as a large surface area (592.6 m2 /g), large pore volume (0.33 cm3 /g), uniform mesopores (3.8 nm), strong magnetic response (29.3 emu/g), and good dispersibility in aqueous solution. As a result of the unique structural properties and size-exclusion effect, the core-shell phenyl-functionalized magnetic mesoporous silica microspheres exhibited excellent performance in fast separation and selective enrichment of phenyl-containing peptides, and the adsorption capacity for bradykinin reached 22.55 mg/g. In addition, selective enrichment of phenyl-containing peptides from complex samples that are consist of peptides, large proteins, and human serum were achieved by using the as-prepared microspheres, followed by high-performance liquid chromatography with ultraviolet detection and electrospray ionization quadrupole time-of-flight mass spectrometry analysis. These results demonstrated the as-prepared microspheres would be a potential candidate for endogenous phenyl-containing peptides enrichment and biomarkers discovery in peptidome analysis.

Negative Ion Laser Desorption/Ionization Time-of-Flight Mass Spectrometric Analysis of Small Molecules Using Graphitic Carbon Nitride Nanosheet Matrix.

Ultrathin graphitic carbon nitride (g-C3N4) nanosheets served as a novel matrix for the detection of small molecules by negative ion matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was described for the first time. In comparison with conventional organic matrices and graphene matrix, the use of g-C3N4 nanosheet matrix showed free matrix background interference and increased signal intensity in the analysis of amino acids, nucleobases, peptides, bisphenols (BPs), and nitropolycyclic aromatic hydrocarbons (nitro-PAHs). A systematic comparison of g-C3N4 nanosheets with positive and negative ion modes revealed that mass spectra produced by g-C3N4 nanosheets in negative ion mode were featured by singly deprotonated ion without matrix interference, which was rather different from the complicated alkali metal complexes in positive ion mode. Good salt tolerance and reproducibility allowed the determination of 1-nitropyrene (1-NP) in sewage, and its corresponding detection limit was lowered to 1 pmol. In addition, the ionization mechanism of the g-C3N4 nanosheets as matrix was also discussed. The work expands its application scope of g-C3N4 nanosheets and provides an alternative approach for small molecules.

CuFe2O4 magnetic nanocrystal clusters as a matrix for the analysis of small molecules by negative-ion matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

CuFe2O4 magnetic nanocrystal clusters (CuFe2O4 MNCs) were proposed as a new matrix for small molecule analysis by negative ion matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the first time. We demonstrated its advantages over conventional organic matrices in the detection of small molecules such as amino acids, peptides, nucleobases, fatty acids, and steroid hormones. A systematic comparison of CuFe2O4 MNCs with different ionization modes revealed that MS spectra obtained for the CuFe2O4 MNC matrix in the negative ion mode was only featured by deprotonated ion peaks with a free matrix background, which was different from the complicated alkali metal adducts produced in the positive ion mode. The developed method was found relatively tolerant to salt contamination and exhibited good reproducibility. A detection limit down to the subpicomolar level was achieved when testosterone was analyzed. In addition, by comparison of the MS spectra obtained from bare Fe3O4 and MFe2O4 MNC (M = Co, Ni, Cu, Zn) matrices, two main factors of MFe2O4 MNC matrices were revealed to play a vital role in assisting the negative ion desorption/ionization (D/I) process: doping transition metals into ferrite nanocrystals favoring laser absorption and energy transfer and a good match between the UV absorption of MFe2O4 MNCs and the excitation of nitrogen laser source facilitating LDI efficiency. This work creates a new branch of application for MFe2O4 MNCs and provides an alternative solution for small molecule analysis.

Preparation of a poly(3'-azido-3'-deoxythymidine-co-propargyl methacrylate-co-pentaerythritol triacrylate) monolithic column by in situ polymerization and a click reaction for capillary liquid chromatography of small molecules and proteins.

Combining free radical polymerization with click chemistry via a copper-mediated azide/alkyne cycloaddition (CuAAC) reaction in a "one-pot" process, a facile approach was developed for the preparation of a poly(3'-azido-3'-deoxythymidine-co-propargyl methacrylate-co-pentaerythritol triacrylate) (AZT-co-PMA-co-PETA) monolithic column. The resulting poly(AZT-co-PMA-co-PETA) monolith showed a relatively homogeneous monolithic structure, good permeability and mechanical stability. Different ratios of monomers and porogens were used for optimizing the properties of a monolithic column. A series of alkylbenzenes, amides, anilines, and benzoic acids were used to evaluate the chromatographic properties of the polymer monolith in terms of hydrophobic, hydrophilic and cation-exchange interactions, and the results showed that the poly(AZT-co-PMA-co-PETA) monolith exhibited more flexible adjustment in chromatographic selectivity than that of the parent poly(PMA-co-PETA) and AZT-modified poly(PMA-co-PETA) monoliths. Column efficiencies for toluene, DMF, and formamide with 35,000-48,000 theoretical plates per m could be obtained at a linear velocity of 0.17 mm s(-1). The run-to-run, column-to-column, and batch-to-batch repeatabilities of the retention factors were less than 4.2%. In addition, the proposed monolith was also applied to efficient separation of sulfonamides, nucleobases and nucleosides, anesthetics and proteins for demonstrating its potential.

Magnetic metal-organic framework nanocomposites for enrichment and direct detection of small molecules by negative-ion matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

Zeolitic imidazolate framework-8 coated magnetic nanocomposites (Fe3O4@ZIF-8 MNCs) served as an absorbent and a matrix for negative-ion MALDI-TOF MS. The host-guest property and interference-free background made them an ideal dual platform for the sensitive analysis of small molecules.

Preparation of magnetic metal-organic framework nanocomposites for highly specific separation of histidine-rich proteins.

This work reports a novel metal-organic framework (MOF)-based metal affinity platform for the rapid and highly specific separation of histidine-rich proteins using zeolitic imidazolate framework-8 coated magnetic nanocomposites (denoted as Fe3O4@ZIF-8). The coating of the ZIF-8 layer on the Fe3O4 core was performed in aqueous solution at room temperature and merely took 10 minutes. The monodisperse Fe3O4@ZIF-8 has an average diameter of 190 nm, displays superparamagnetism with a saturation magnetization value of 47.9 emu g-1, and possesses a large external surface area of 131.0 m2 g-1. Due to the high density of low-coordinated Zn atoms on the surface of ZIF-8, Fe3O4@ZIF-8 exhibited a large adsorption capacity for model histidine-rich proteins (>6000 mg g-1 for bovine hemoglobin) and relatively low adsorption capacities for other proteins which contain fewer surface-exposed histidine residues. Moreover, Fe3O4@ZIF-8 showed excellent recyclability (more than 10 times) with high recovery (88.4%). In addition, Fe3O4@ZIF-8 can be used to selectively separate hemoglobin from a protein mixture and human blood samples. The good results demonstrate the potential of Fe3O4@ZIF-8 in the separation of histidine-rich proteins.