The mechanism of Pseudomonas aeruginosa outer membrane vesicle biogenesis determines their protein composition

Gram-negative bacteria produce outer membrane vesicles (OMVs) and contain bacterial cargo including nucleic acids and proteins. The proteome of OMVs can be altered by various factors including bacterial growth stage, growth conditions, and environmental factors. However, it is currently unknown if the mechanism of OMV biogenesis can determine their proteome. In this study, we examined whether the mechanisms of OMV biogenesis influenced the production and protein composition of Pseudomonas aeruginosa OMVs. OMVs were isolated from three P. aeruginosa strains that produced OMVs either by budding alone, by explosive cell lysis, or by both budding and explosive cell lysis. We identified that the mechanism of OMV biogenesis dictated OMV quantity. Furthermore, a global proteomic analysis comparing the proteome of OMVs to their parent bacteria showed significant differences in the identification of proteins in bacteria and OMVs. Finally, we determined that the mechanism of OMV biogenesis influenced the protein composition of OMVs, as OMVs released by distinct mechanisms of biogenesis differed significantly from one another in their proteome and functional enrichment analysis. Overall, our findings reveal that the mechanism of OMV biogenesis is a main factor that determines the OMV proteome which may affect their subsequent biological functions.

Reply to the 'Comment on "Realization of the Zn3+ oxidation state"' by Y. Shang, N. Shu, Z. Zhang, P. Yang and J. Xu, Nanoscale, 2022, , DOI: 10.1039/D1NR07031B

In a recent paper (https://doi.org/10.1039/D1NR02816B), we suggested that Zn can assume a +3-oxidation state when interacting with super-electrophilic clusters, BeB₁₁(CN)₁₂ and BeB₂₃(CN)₂₂. In a comment to our paper (https://doi.org/10.1039/D1NR07031B), Shang et al. have questioned this suggestion. Using density functional theory with the TPSSh functional and def2-SVP basis sets in the Gaussian16 software and semiempirical localized orbital bonding analysis (LOBA), the authors have made three major claims: (1) the oxidation state of Zn in Zn[BeB₁₁(CN)₁₂] and Zn[BeB₂₃(CN)₂₂] is +2; (2) electron affinities are not reliable to probe the oxidation states; and (3) our results are "misleading" because these are based on the VASP code. According to these authors, VASP is not suitable for small clusters because it uses projected augmented wave (PAW) pseudopotentials. In the following, we show that these claims are invalid, caused by both misunderstanding and the authors' use of a lower-level theory.

Abstract 3491: New targets and new approaches for multiple myeloma: Extracellular vesicles as functional liquid biomarkers

Background: We have previously demonstrated that stromal cells (HS5) pre-treated with small extracellular vesicles (sEV) enriched from blood plasma of myeloma (MM) patients promoted adhesion of human MM cell lines (HMCL), with preliminary proteomic profiling of MM-sEV (vs healthy donors-HD) revealing enrichment of factors implicated in cell migration and adhesion.

Aims: To demonstrate that plasma-derived MM-sEV induce a microenvironment favoring MM progression and identify the protein content of plasma-sEV that promotes this.

Methods: sEV were enriched from plasma (1mL) using a commercial kit. Proteomic profiling (nLC and high-resolution mass spectrometry, Orbitrap HF-X) of plasma-sEV derived from HD (x10) and patients with MM (x8) or pre-malignant conditions (monoclonal gammopathy of undetermined significance - MGUS x10; smouldering/asymptomatic MM - SMM x4), and functional studies (co-culture system HS5:HMCL) were performed.

Results: Stromal cells pre-treated with MM-sEV induced both HMCL proliferation (p < 0.05) and drug resistance (p < 0.0001) to anti-MM drugs (proteasome inhibitors) when compared to untreated stromal cells.The protein concentrations of MM-sEV positively correlated with tumor burden (r0.77; p=0.024).A total of 412 proteins were detected and quantified by proteomic profiling of plasma-sEV with 13 reported as highly enriched in EV marker databases (ExoCarta top 100) and 8/13 corresponding to universal cancer EV-markers proposed by Hoshino et al, Cell 2020. Gene ontology analysis of identified proteins (G:Profiler; p < 0.05) revealed enrichment for cellular component terms such as “extracellular vesicles/exosomes” and for several biological processes including “cell communication”, “endocytosis”, “cell migration”, “cellular response to stimulus”, “immune response”. Comparative analysis between our dataset and several publicly available datasets revealed sEV-markers with potential discriminatory specificity for MM, MGUS or SMM. Comparative analysis revealed 40, 40 and 41 proteins differentially regulated between HD-sEV and MM-sEV or MGUS-sEV or SMM-sEV (P < 0.05; log2 fold change ≥2). A specific protein signature identified in MM-sEV was found in ≥30% of MM-sEV but <30% HD-sEV. Specific protein signatures were also identified in MGUS-sEV (≥30% of MGUS-sEV but <30% HD-sEV or MM-sEV or SMM-sEV) and SMM-sEV (≥30% of SMM-sEV but <30% HD-sEV or MM-sEV or MGUS-sEV). These proteins were not found in human whole plasma (Lehallier et al, Nat medicine 2019) or solid tumors-derived sEV described by Hoshino et al (Cell 2020) and Vinik et al (Science Advances 2020).

Conclusions: MM-sEV may play an important role in disease progression by re-programming the tumor microenvironment. The characterization and proteomic profiling of disease-specific circulating sEV as a biomarker discovery strategy may provide translational applications in MM.

Citation Format: Antonia Reale, Tiffany Khong, Rong Xu, Irena Carmichael, Haoyun Fang, Nicholas Bingham, Sridurga Mithraprabhu, Maoshan Chen, Malarmathy Ramachandran, David W. Greening, Andrew Spencer. New targets and new approaches for multiple myeloma: Extracellular vesicles as functional liquid biomarkers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3491.

Analysis of an adaptive lead weighted ResNet for multiclass classification of 12-lead ECGs

Background. Twelve lead ECGs are a core diagnostic tool for cardiovascular diseases. Here, we describe and analyse an ensemble deep neural network architecture to classify 24 cardiac abnormalities from 12 lead ECGs.Method. We proposed a squeeze and excite ResNet to automatically learn deep features from 12-lead ECGs, in order to identify 24 cardiac conditions. The deep features were augmented with age and gender features in the final fully connected layers. Output thresholds for each class were set using a constrained grid search. To determine why the model made incorrect predictions, two expert clinicians independently interpreted a random set of 100 misclassified ECGs concerning left axis deviation.Results. Using the bespoke weighted accuracy metric, we achieved a 5-fold cross-validation score of 0.684, and sensitivity and specificity of 0.758 and 0.969, respectively. We scored 0.520 on the full test data, and ranked 2nd out of 41 in the official challenge rankings. On a random set of misclassified ECGs, agreement between two clinicians and training labels was poor (clinician 1:κ= -0.057, clinician 2:κ= -0.159). In contrast, agreement between the clinicians was very high (κ= 0.92).Discussion. The proposed prediction model performed well on the validation and hidden test data in comparison to models trained on the same data. We also discovered considerable inconsistency in training labels, which is likely to hinder development of more accurate models.

[Stereotactic body radiation therapy for patients with lung and liver oligometastases from colorectal cancer: a phase Ⅱ trial]

Objective: To explore the safety and effectiveness of stereotactic body radiation therapy (SBRT) for oligometastases from colorectal cancer (CRC). Methods: This is a prospective, single-arm phase Ⅱ trial. Patients who had histologically proven CRC, 1 to 5 detectable liver or lung metastatic lesions with maximum diameter of any metastases ≤5 cm were eligible. SBRT was delivered to all lesions. The primary endpoint was 3-year local control (LC). The secondary endpoints were treatment-related acute toxicities of grade 3 and above, 1-year and 3-year overall survival (OS) and progression free survival (PFS). Survival analysis was performed using the Kaplan-Meier method and Log rank test. Results: Petients from 2016 to 2019 who were treated in Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College. Forty-eight patients with 60 lesions were enrolled, including 37 liver lesions and 23 lung lesions. Forty-six patients had 1 or 2 lesions, with median diameter of 1.3 cm, the median biologically effective dose (BED(10)) was 100.0 Gy. The median follow-up was 19.5 months for all lesions. Twenty-five lesions developed local failure, the median local progression free survival was 15 months. The 1-year LC, OS and PFS was 70.2% (95% CI, 63.7%~76.7%), 89.0% (95% CI, 84.3%~93.7%) and 40.4% (95%CI, 33.0%~47.8%). The univariate analysis revealed that planning target volume (PTV) and total dose were independent prognostic factors of LC (P<0.05). For liver and lung lesions, the 1-year LC, OS and PFS was 58.7% and 89.4% (P=0.015), 89.3% and 86.5% (P=0.732), 30.5% and 65.6% (P=0.024), respectively. No patients developed acute toxicity of grade 3 and above. Conclusion: SBRT is safe and effective treatment method for oligometastases from CRC under precise respiratory motion management and robust quality assurance.

[Bioinformatics screening and analysis of key differentially expressed genes characteristics in nonalcoholic fatty liver disease]

Objective: To screen and analyze the key differentially expressed genes characteristics in nonalcoholic fatty liver disease (NAFLD) with bioinformatics method. Methods: NAFLD-related expression matrix GSE89632 was downloaded from the GEO database. Limma package was used to screen differentially expressed genes (DEGs) in healthy, steatosis (SS), and nonalcoholic steatohepatitis (NASH) samples. WGCNA was used to analyze the output gene module. The intersection of module genes and differential genes was used to determine the differential genes characteristic, and then GO function and KEGG signaling pathway enrichment analysis were performed. The protein-protein interaction network (PPI) was constructed using the online website STRING and Cytoscape software, and the key (Hub) genes were screened. Finally, R software was used to analyze the receiver operating characteristic curve (ROC) of the Hub gene. Results: 92 differentially expressed genes characteristic were obtained through screening, which were mainly enriched in inflammatory response-related functions of "lipopolysaccharide response and molecular response of bacterial origin", as well as cancer signaling pathways of "proteoglycan in cancer" and "T-cell leukemia virus infection-related". 10 hub genes (FOS, CXCL8, SERPINE1, CYR61, THBS1, FOSL1, CCL2, MYC, SOCS3 and ATF3) had good diagnostic value. Conclusion: The differentially expressed hub genes among the 10 NAFLD disease-related characteristics obtained with bioinformatics analysis may become a diagnostic and prognostic marker and potential therapeutic target for NAFLD. However, further basic and clinical studies are needed to validate.

Effect of 2D and 3D Culture Microenvironments on Mesenchymal Stem Cell-Derived Extracellular Vesicles Potencies

Therapeutic benefits of mesenchymal stem cells (MSCs) are now widely believed to come from their paracrine signalling, i.e. secreted factors such as cytokines, chemokines, and extracellular vesicles (EVs). Cell-free therapy using EVs is an active and emerging field in regenerative medicine. Typical 2D cultures on tissue culture plastic is far removed from the physiological environment of MSCs. The application of 3D cell culture allows MSCs to adapt to their cellular environment which, in turn, influences their paracrine signalling activity. In this study we evaluated the impact of 3D MSCs culture on EVs secretion, cargo proteome composition, and functional assessment in immunomodulatory, anti-inflammatory and anti-fibrotic properties.

MSC-EVs from 2D and 3D cultures expressed classical EV markers CD81, CD63, and CD9 with particle diameter of &lt;100 nm. There were distinct changes in immunomodulatory potencies where 3D cultures exhibited reduced indoleamine 2,3-dioxygenase (IDO) activity and significantly reduced macrophage phagocytosis. Administration of 2D and 3D EVs following double dose bleomycin challenge in aged mice showed a marked increase of bodyweight loss in 3D group throughout days 7–28. Histopathological observations of lung tissues in 3D group showed increased collagen deposition, myofibroblast differentiation and leukocytes infiltrations. Assessment of lung mechanics showed 3D group did not improve lung function and instead exhibited increased resistance and tissue damping. Proteome profiling of MSC-EV composition revealed molecular enrichment of EV markers (compared to parental cells) and differential proteome between EVs from 2D and 3D culture condition associated with immune-based and fibrosis/extracellular matrix/membrane organization associated function.

This study provides insight into distinct variation in EV protein composition dependent on the cellular microenvironment of the parental cells, which could have implications in their therapeutic effect and potency. Overall, this work suggests that EVs produced from 3D MSC cultures did not enhance typical MSC-EV properties expected from 2D cultures (immunomodulation, anti-fibrotic, anti-inflammatory). The outcome highlights critical differences between MSC-EVs obtained from different culture microenvironments, which should be considered when scaling up MSC culture for clinical manufacturing.

[Carbon peak, carbon neutrality: strategic opportunities for China's health system]

Excessive emission of greenhouse gases is the most important reason for global warming. Severe climate change significantly threatens human health. World Health Organization estimated that 12.6 million deaths were attributable to modifiable environmental factors and climate change would lead to 0.25 million deaths annually during 2030-2050. All countries in the world try to reduce greenhouse gas emission to mitigate adverse impacts of climate change by following the Paris Agreement, through setting goals and measures of carbon peak, and carbon neutrality. China plays a very important role in the campaign of global Carbon Peak and Carbon Neutrality. Climate change is also a global health emergency, and Carbon Peak and Carbon Neutrality will be a strategic opportunity for China's health system. The goals of Carbon Peak and Carbon Neutrality are harmonized with those of China's health system, both aiming to provide high-quality health security for all Chinese people. China's health system should try to not only reduce its own carbon footprints, but also make significant contributions to the global Carbon Peak and Carbon Neutrality campaign.

Proteomic dissection of large extracellular vesicle surfaceome unravels interactive surface platform

The extracellular vesicle (EV) surface proteome (surfaceome) acts as a fundamental signalling gateway by bridging intra- and extracellular signalling networks, dictates EVs' capacity to communicate and interact with their environment, and is a source of potential disease biomarkers and therapeutic targets. However, our understanding of surface protein composition of large EVs (L-EVs, 100-800 nm, mean 310 nm, ATP5F1A, ATP5F1B, DHX9, GOT2, HSPA5, HSPD1, MDH2, STOML2), a major EV-subtype that are distinct from small EVs (S-EVs, 30-150 nm, mean 110 nm, CD44, CD63, CD81, CD82, CD9, PDCD6IP, SDCBP, TSG101) remains limited. Using a membrane impermeant derivative of biotin to capture surface proteins coupled to mass spectrometry analysis, we show that out of 4143 proteins identified in density-gradient purified L-EVs (1.07-1.11 g/mL, from multiple cancer cell lines), 961 proteins are surface accessible. The surface molecular diversity of L-EVs include (i) bona fide plasma membrane anchored proteins (cluster of differentiation, transporters, receptors and GPI anchored proteins implicated in cell-cell and cell-ECM interactions); and (ii) membrane surface-associated proteins (that are released by divalent ion chelator EDTA) implicated in actin cytoskeleton regulation, junction organization, glycolysis and platelet activation. Ligand-receptor analysis of L-EV surfaceome (e.g., ITGAV/ITGB1) uncovered interactome spanning 172 experimentally verified cognate binding partners (e.g., ANGPTL3, PLG, and VTN) with highest tissue enrichment for liver. Assessment of biotin inaccessible L-EV proteome revealed enrichment for proteins belonging to COPI/II-coated ER/Golgi-derived vesicles and mitochondria. Additionally, despite common surface proteins identified in L-EVs and S-EVs, our data reveals surfaceome heterogeneity between the two EV-subtype. Collectively, our study provides critical insights into diverse proteins operating at the interactive platform of L-EVs and molecular leads for future studies seeking to decipher L-EV heterogeneity and function.