Identification of immune-related endoplasmic reticulum stress genes in sepsis using bioinformatics and machine learning

Background

Sepsis-induced apoptosis of immune cells leads to widespread depletion of key immune effector cells. Endoplasmic reticulum (ER) stress has been implicated in the apoptotic pathway, although little is known regarding its role in sepsis-related immune cell apoptosis. The aim of this study was to develop an ER stress-related prognostic and diagnostic signature for sepsis through bioinformatics and machine learning algorithms on the basis of the differentially expressed genes (DEGs) between healthy controls and sepsis patients.

Methods

The transcriptomic datasets that include gene expression profiles of sepsis patients and healthy controls were downloaded from the GEO database. The immune-related endoplasmic reticulum stress hub genes associated with sepsis patients were identified using the new comprehensive machine learning algorithm and bioinformatics analysis which includes functional enrichment analyses, consensus clustering, weighted gene coexpression network analysis (WGCNA), and protein-protein interaction (PPI) network construction. Next, the diagnostic model was established by logistic regression and the molecular subtypes of sepsis were obtained based on the significant DEGs. Finally, the potential diagnostic markers of sepsis were screened among the significant DEGs, and validated in multiple datasets.

Results

Significant differences in the type and abundance of infiltrating immune cell populations were observed between the healthy control and sepsis patients. The immune-related ER stress genes achieved strong stability and high accuracy in predicting sepsis patients. 10 genes were screened as potential diagnostic markers for sepsis among the significant DEGs, and were further validated in multiple datasets. In addition, higher expression levels of SCAMP5 mRNA and protein were observed in PBMCs isolated from sepsis patients than healthy donors (n = 5).

Conclusions

We established a stable and accurate signature to evaluate the diagnosis of sepsis based on the machine learning algorithms and bioinformatics. SCAMP5 was preliminarily identified as a diagnostic marker of sepsis that may affect its progression by regulating ER stress.

Optimal dose of tirzepatide for type 2 diabetes mellitus: A meta-analysis and trial sequential analysis

Objective

The purpose of this study is to evaluate the optimal dose of tirzepatide (TZP) for the treatment of type 2 diabetes mellitus (T2DM) by meta-analysis and trial sequential analysis (TSA).

Methods

Clinical trials of TZP for T2DM were obtained by searching 8 databases with a time limit from database creation to May 2022. Mean differences (MD) and 95% confidence intervals (95%CI) were used for continuous variables, and relative risk (RR) and 95%CI were used for dichotomous variables.

Results

Compared with TZP 5 mg, meta-analysis showed that TZP 10 mg significantly reduced glycosylated hemoglobin type A1c (HbA1c) (MD −0.24, 95%CI −0.31~-0.17, P < 0.00001), fasting serum glucose (FSG) (MD −5.82, 95%CI −8.35~-3.28, P < 0.00001) and weight (MD −2.47, 95%CI −2.95~-1.98, P < 0.00001), and TZP 15 mg significantly reduced HbA1c (MD −0.37, 95%CI −0.44~-0.29, P < 0.00001), FSG (MD −8.52, 95%CI −11.07~-5.98, P < 0.00001) and weight (MD −4.63, 95%CI −5.45~-3.81, P < 0.00001). Compared with TZP 10 mg, TZP 15 mg dramatically reduced HbA1c (MD −0.12, 95%CI −0.19~-0.05, P = 0.001), FSG (MD −2.73, 95%CI −5.29~-0.17, P = 0.04) and weight (MD −2.18, 95%CI −2.67~-1.70, P < 0.00001). The TSA indicated that the benefits observed in the current information set were conclusive, except for the FSG of “TZP 15 mg vs. TZP 10 mg”. In terms of safety endpoints, meta-analysis revealed that there was no significant difference in the serious adverse events (AEs), major adverse cardiovascular events-4 (MACE-4), cardiovascular death, hypertension, cancer and hypoglycemic of the three dose groups of TZP. Compared with TZP 5 mg, TZP 10 mg increased total adverse events (RR 1.06, 95%CI 1.01~1.11, P = 0.03) and gastrointestinal (GI) AEs (RR 1.17, 95%CI 1.03~1.33, P = 0.02), and TZP 15 mg increased total AEs (RR 1.10, 95%CI 1.05~1.15, P = 0.0001). There were no significant differences in total AEs and GI AEs for TZP 15 mg compared to TZP 10 mg. The TSA demonstrated that the total AEs of “TZP 15 mg vs. TZP 5 mg” were conclusive.

Conclusions

TZP 15 mg >TZP 10 mg > TZP 5 mg in terms of lowering glycemia and reducing weight. TZP 5 mg > TZP 10 mg = TZP 15 mg in terms of safety. On this basis, we recommend TZP 5 mg as the first-choice dose for patients with T2DM to minimize AEs while reducing glycemia and weight. If patients cannot effectively control their glycemia after taking TZP 5 mg, it is recommended to take TZP 15 mg directly to achieve the best effect of glycemic reduction. However, most of the included studies have the background of basic medication, the independent efficacy and safety of different doses of TZP still need to be tested.

Systematic review registration

Unique Identifier: CRD42022341966.

Comparison of weight loss and adverse events of obesity drugs in children and adolescents: a systematic review and meta-analysis

BACKGROUND

The global incidence of childhood obesity is increasing. Currently, there are only few established drugs for treating adolescent obesity. Randomized clinical trials (RCTs) comparing pharmacological interventions in children with obesity are scarce; therefore, we aimed to analyze the relative efficacy and adverse reactions of these drugs and compare the effects of each drug on body mass index (BMI).

RESEARCH DESIGN AND METHODS

This meta-analysis focused on the slimming effect, safety, and correlation of metformin, orlistat, exenatide, liraglutide, and topiramate in children with obesity. Several international databases were searched and clinical trials on the treatment of obesity in children in which the drug was administered for ≥ 6 months were included. Changes in BMI before and after treatment were analyzed using a Bayes framework, and the surface under the cumulative ranking was calculated.

RESULTS

Of 2102 relevant articles retrieved, 21 RCTs were included in the study. Compared to other drugs, liraglutide reduced BMI the most in children with obesity. However, it was most associated with drug withdrawal due to adverse events while topiramate was least.

CONCLUSIONS

Liraglutide had a higher probability of achieving clinically significant weight loss compared with other drugs while topiramate was superior in safety.

A proteomic atlas of atherosclerosis: regional proteomic signatures for plaque inflammation and calcification

Funding Acknowledgements

Type of funding sources: Foundation. Main funding source(s): This study was mainly supported from the British Heart Foundation (BHF) supporting Prof. Manuel Mayr as a Chair Holder (CH/16/3/32406) with BHF programme grant support (RG/16/14/32397) and Dr. Theofilatos with BHF programm grant support (G/20/10387).

Background

Using proteomics, we strove to reveal novel molecular subtypes of human atherosclerotic lesions, study their associations with histology and imaging and relate them to long-term cardiovascular outcomes.

Methods

219 samples were obtained from 120 patients undergoing carotid endarterectomy. Sequential protein extraction was combined with multiplexed, discovery proteomics. Parallel reaction monitoring for 135 proteins was deployed for targeted validation. A combination of statistical, bioinformatics and machine learning methods was used to perform differential expression, network, pathway enrichment analysis and train and evaluate prognostic models.

Results

Our extensive proteomics analysis from the core and periphery of plaques doubled the coverage of the plaque proteome compared to the largest proteomics study on atherosclerosis thus far. Plaque inflammation and calcification signatures were inversely correlated and validated with targeted proteomics. The inflammation signature was enriched with neutrophil-derived proteins, including calprotectin (S100A8/9) and myeloperoxidase. The calcification signature contained fetuin-A, osteopontin, and gamma-carboxylated proteins. Sex differences in the proteome of atherosclerosis were explained by a higher proportion of calcified plaques in women. Single-cell RNA sequencing data attributed the inflammation signature predominantly to neutrophils and macrophages and the calcification signature to smooth muscle cells, except for certain plasma proteins that were not expressed but retained in the plaque, i.e., fetuin-A. Echogenic lesions reflect the collagen content and calcification of plaque but carotid Duplex ultrasound fails to capture the extent of inflammatory protein changes in symptomatic plaques. Applying dimensionality reduction and machine learning on the proteomics data defined 4 distinct plaque phenotypes and revealed key protein signatures linked to smooth muscle cell content, plaque calcification and structural extracellular matrix, which improved the 9-year prognostic AUC by 25% compared to ultrasound and histology. A biosignature of four proteins (CNN1, PROC, SERPH, and CSPG2) independently predicted the progression of atherosclerosis and cardiovascular mortality with an AUC of 75%

Conclusion

We combined discovery and targeted proteomics with network reconstruction and clustering techniques to provide molecular insights into protein changes in atherosclerotic plaques. The application of proteomics and machine learning techniques revealed distinct clusters of plaques that inform on disease progression and future adverse cardiovascular events.

Macrophage-derived exosomal aminopeptidase N aggravates sepsis-induced acute lung injury by regulating necroptosis of lung epithelial cell

Sepsis-induced acute lung injury (ALI) is a serious sepsis complication and the prevailing cause of death. Circulating plasma exosomes might exert a key role in regulating intercellular communication between immunological and structural cells, as well as contributing to sepsis-related organ damage. However, the molecular mechanisms by which exosome-mediated intercellular signaling exacerbate ALI in septic infection remains undefined. Therefore, we investigated the effect of macrophage-derived exosomal APN/CD13 on the induction of epithelial cell necrosis. Exosomal APN/CD13 levels in the plasma of septic mice and patients with septic ALI were found to be higher. Furthermore, increased plasma exosomal APN/CD13 levels were associated with the severity of ALI and fatality in sepsis patients. We found remarkably high expression of APN/CD13 in exosomes secreted by LPS-stimulated macrophages. Moreover, c-Myc directly induced APN/CD13 expression and was packed into exosomes. Finally, exosomal APN/CD13 from macrophages regulated necroptosis of lung epithelial cells by binding to the cell surface receptor TLR4 to induce ROS generation, mitochondrial dysfunction and NF-κB activation. These results demonstrate that macrophage-secreted exosomal APN/CD13 can trigger epithelial cell necroptosis in an APN/CD13-dependent manner, which provides insight into the mechanism of epithelial cell functional disorder in sepsis-induced ALI.

Necroptosis of lung epithelial cells is regulated by aminopeptidase N levels in circulating plasma exosomes in patients and mice with sepsis-induced acute lung injury.

Cold Spray: Over 30 Years of Development Toward a Hot Future

Cold Spray (CS) is a deposition process, part of the thermal spray family. In this method, powder particles are accelerated at supersonic speed within a nozzle; impacts against a substrate material triggers a complex process, ultimately leading to consolidation and bonding. CS, in its modern form, has been around for approximately 30 years and has undergone through exciting and unprecedented developmental steps. In this article, we have summarized the key inventions and sub-inventions which pioneered the innovation aspect to the process that is known today, and the key breakthroughs related to the processing of materials CS is currently mastering. CS has not followed a liner path since its invention, but an evolution more similar to a hype cycle: high initial growth of expectations, followed by a decrease in interest and a renewed thrust pushed by a number of demonstrated industrial applications. The process interest is expected to continue (gently) to grow, alongside with further development of equipment and feedstock materials specific for CS processing. A number of current applications have been identified the areas that the process is likely to be the most disruptive in the medium-long term future have been laid down.

Clinical effect of unilateral balloon infusion of low dose bone cement in PKP for osteoporotic thoracolumbar compression fractures in the elderly

OBJECTIVE

The study was undertaken to determine the clinical effectiveness of percutaneous kyphoplasty (PKP) with unilateral balloon infusion of low dose of bone cement for treatment of osteoporotic vertebral compression fractures (OVCFs) in the elderly.

PATIENTS AND METHODS

A retrospective study was carried out. A total of 36 patients with OVCFs treated by PKP from August 2019 and August 2020 were included. Patients were divided into two groups according to the amount of bone cement infused into the vertebral body. The amount of cement in conventional-dose group was 3.5-6.0 mL and the amount of cement in small-dose group was 1.8-3.0 mL. Pain relief before and after the operation were evaluated, and the leakage of bone cement in the two groups was also observed.

RESULTS

Two groups of patients have obtained a good clinical efficacy. Pain has significant differences before and after the operation (p < 0.05). More importantly, compared with conventional-dose group, small-dose group has lower bone cement leakage rate (p < 0.05).

CONCLUSIONS

PKP with small-dose bone cement infusion can obtain the same clinical effects of conventional-dose, but the incidence of bone cement leakage is lower and safe.

Curative efficiency and adverse events of alternative therapy and medicine for functional constipation in adults: A protocol for systematic review and meta-analysis

BACKGROUND

The efficacy of alternative therapies and medications for functional constipation (FC) in adults is well established, however, the efficacy and safety of different alternative therapies and medications for FC in adults is not fully clarified. Due to there are many different alternative therapies and medications available for the treatment of febrile FC in adults, the selection of appropriate alternative therapies and medications has become an urgent issue. The purpose of this study was to evaluate the effectiveness and safety of alternative therapy and medicine for FC in adults.

METHODS

PubMed, Web of Science, Scopus, Cochrane Library, Embase, China National Knowledge Infrastructure, China Science and Technology Journal Database and Wanfang Data were searched to identify randomized controlled trials which focused on alternative therapy and medicine for FC in adults from December 15, 2020 to July 1, 2021. Subsequently, 2 researchers will be independently responsible for literature screening, data extraction, and assessment of their quality. This study uses The R Programming Language 4.0.2 based on Bayesian framework for NMA. Odds ratios or standardized mean differences will be modeled using Markov chain Monte Carlo methods, both with 95% confidence intervals.

RESULTS

The results of this meta-analysis will be submitted to a peer-reviewed journal for publication.

CONCLUSIONS

The conclusion of this systematic review will provide evidence for selecting an optimal alternative therapy and medicine for patients with FC in adults.

ETHICS AND DISSEMINATION

The protocol of the systematic review does not require ethical approval because it does not involve humans. This article will be published in peer-reviewed journals and presented at relevant conferences.

SYSTEMATIC REVIEW REGISTRATION

INPLASY202210091.

Mechanical and Fatigue Properties of Diamond-Reinforced Cu and Al Metal Matrix Composites Prepared by Cold Spray

Diamond-reinforced metal matrix composites (DMMC) prepared by cold spray are emerging materials simultaneously featuring outstanding thermal conductivity and wear resistance. In our paper, their mechanical and fatigue properties relevant to perspective engineering applications were investigated using miniature bending specimens. Two different diamond mass concentrations (20 and 50%) embedded in two metal matrices (Al-lighter than diamond, Cu-heavier than diamond) were compared with the respective cold-sprayed pure metals, as well as bulk Al and Cu references. The pure Al, Cu coatings showed properties typical for cold spray deposits, i.e., decreased elastic moduli (50 GPa for Al, 80 GPa for Cu), limited ductility (< 1 × 10-3) and low fracture toughness (3.8 MPa·m0.5 for Al, 5.6 MPa·m0.5 for Cu) when compared to the bulks. Significantly improved properties (strain at fracture, ultimate strength, fatigue crack growth resistance, fracture toughness) were then observed for the produced DMMC. The improvement can be explained by a combination of two factors: changes in the properties of the metallic matrix triggered by the reinforcement particles peening effect and stress redistribution due to the particles presence.

Mechanism Study of Thermally Induced Anti-Tumor Drug Loading to Engineered Human Heavy-Chain Ferritin Nanocages Aided by Computational Analysis

Diverse drug loading approaches for human heavy-chain ferritin (HFn), a promising drug nanocarrier, have been established. However, anti-tumor drug loading ratio and protein carrier recovery yield are bottlenecks for future clinical application. Mechanisms behind drug loading have not been elaborated. In this work, a thermally induced drug loading approach was introduced to load anti-tumor drug doxorubicin hydrochloride (DOX) into HFn, and 2 functionalized HFns, HFn-PAS-RGDK, and HFn-PAS. Optimal conditions were obtained through orthogonal tests. All 3 HFn-based proteins achieved high protein recovery yield and drug loading ratio. Size exclusion chromatography (SEC) and transmission electron microscopy (TEM) results showed the majority of DOX loaded protein (protein/DOX) remained its nanocage conformation. Computational analysis, molecular docking followed by molecular dynamic (MD) simulation, revealed mechanisms of DOX loading and formation of by-product by investigating non-covalent interactions between DOX with HFn subunit and possible binding modes of DOX and HFn after drug loading. In in vitro tests, DOX in protein/DOX entered tumor cell nucleus and inhibited tumor cell growth.

Development of purification process for dual-function recombinant human heavy-chain ferritin by the investigation of genetic modification impact on conformation

Ferritin is a promising drug delivery platform and has been functionalized through genetic modifications. This work has designed and expressed a dual-functional engineered human heavy-chain ferritin (HFn) with the inserted functional peptide PAS and RGDK to extend half-life and improve tumor targeted drug delivery. A facile and cost-effective two-step purification pathway for recombinant HFn was developed. The genetic modification was found to affect HFn conformation, and therefore varied the purification performance. Heat-acid precipitation followed by butyl fast flow hydrophobic interaction chromatography (HIC) has been developed to purify HFn and modified HFns. Nucleic acid removal reached above 99.8% for HFn and modified HFns. However, HFn purity reached above 95% and recovery yield (overall) above 90%, compared with modified HFns purity above 82% and recovery yield (overall) above 58%. It is interesting to find that the inserted functional peptides significantly changed the molecule conformation, where a putative turnover of the E-helix with the inserted functional peptides formed a "flop" conformation, in contrast with the "flip" conformation of HFn. It could be the cause of fragile stability of modified HFns, and therefore less tolerant to heat and acid condition, observed by the lower recovery yield in heat-acid precipitation.