Identification of sepsis-associated mitochondrial genes through RNA and single-cell sequencing approaches.

BACKGROUND: Sepsis ranks among the most formidable clinical challenges, characterized by exorbitant treatment costs and substantial demands on healthcare resources. Mitochondrial dysfunction emerges as a pivotal risk factor in the pathogenesis of sepsis, underscoring the imperative to identify mitochondrial-related biomarkers. Such biomarkers are crucial for enhancing the accuracy of sepsis diagnostics and prognostication. METHODS: In this study, adhering to the SEPSIS 3.0 criteria, we collected peripheral blood within 24 h of admission from 20 sepsis patients at the ICU of the Southwest Medical University Affiliated Hospital and 10 healthy volunteers as a control group for RNA-seq. The RNA-seq data were utilized to identify differentially expressed RNAs. Concurrently, mitochondrial-associated genes (MiAGs) were retrieved from the MitoCarta3.0 database. The differentially expressed genes were intersected with MiAGs. The intersected genes were then subjected to GO (Gene Ontology), and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses and core genes were filtered using the PPI (Protein-Protein Interaction) network. Subsequently, relevant sepsis datasets (GSE65682, GSE28750, GSE54514, GSE67652, GSE69528, GSE95233) were downloaded from the GEO (Gene Expression Omnibus) database to perform bioinformatic validation of these core genes. Survival analysis was conducted to assess the prognostic value of the core genes, while ROC (Receiver Operating Characteristic) curves determined their diagnostic value, and a meta-analysis confirmed the accuracy of the RNA-seq data. Finally, we collected 5 blood samples (2 normal controls (NC); 2 sepsis; 1 SIRS (Systemic Inflammatory Response Syndrome), and used single-cell sequencing to assess the expression levels of the core genes in the different blood cell types. RESULTS: Integrating high-throughput sequencing with bioinformatics, this study identified two mitochondrial genes (COX7B, NDUFA4) closely linked with sepsis prognosis. Survival analysis demonstrated that patients with lower expression levels of COX7B and NDUFA4 exhibited a higher day survival rate over 28 days, inversely correlating with sepsis mortality. ROC curves highlighted the significant sensitivity and specificity of both genes, with AUC values of 0.985 for COX7B and 0.988 for NDUFA4, respectively. Meta-analysis indicated significant overexpression of COX7B and NDUFA4 in the sepsis group in contrast to the normal group (P < 0.01). Additionally, single-cell RNA sequencing revealed predominant expression of these core genes in monocytes-macrophages, T cells, and B cells. CONCLUSION: The mitochondrial-associated genes (MiAGs) COX7B and NDUFA4 are intimately linked with the prognosis of sepsis, offering potential guidance for research into the mechanisms underlying sepsis.

Adaptive sparse attention-based compact transformer for object tracking.

The Transformer-based Siamese networks have excelled in the field of object tracking. Nevertheless, a notable limitation persists in their reliance on ResNet as backbone, which lacks the capacity to effectively capture global information and exhibits constraints in feature representation. Furthermore, these trackers struggle to effectively attend to target-relevant information within the search region using multi-head self-attention (MSA). Additionally, they are prone to robustness challenges during online tracking and tend to exhibit significant model complexity. To address these limitations, We propose a novel tracker named ASACTT, which includes a backbone network, feature fusion network and prediction head. First, we improve the Swin-Transformer-Tiny to enhance its global information extraction capabilities. Second, we propose an adaptive sparse attention (ASA) to focus on target-specific details within the search region. Third, we leverage position encoding and historical candidate data to develop a dynamic template updater (DTU), which ensures the preservation of the initial frame's integrity while gracefully adapting to variations in the target's appearance. Finally, we optimize the network model to maintain accuracy while minimizing complexity. To verify the effectiveness of our proposed tracker, ASACTT, experiments on five benchmark datasets demonstrated that the proposed tracker was highly comparable to other state-of-the-art methods. Notably, in the GOT-10K1 evaluation, our tracker achieved an outstanding success score of 75.3% at 36 FPS, significantly surpassing other trackers with comparable model parameters.

Development of a Human B7-H3-Specific Antibody with Activity against Colorectal Cancer Cells through a Synthetic Nanobody Library.

Nanobodies have emerged as promising tools in biomedicine due to their single-chain structure and inherent stability. They generally have convex paratopes, which potentially prefer different epitope sites in an antigen compared to traditional antibodies. In this study, a synthetic phage display nanobody library was constructed and used to identify nanobodies targeting a tumor-associated antigen, the human B7-H3 protein. Combining next-generation sequencing and single-clone validation, two nanobodies were identified to specifically bind B7-H3 with medium nanomolar affinities. Further characterization revealed that these two clones targeted a different epitope compared to known B7-H3-specific antibodies, which have been explored in clinical trials. Furthermore, one of the clones, dubbed as A6, exhibited potent antibody-dependent cell-mediated cytotoxicity (ADCC) against a colorectal cancer cell line with an EC50 of 0.67 nM, upon conversion to an Fc-enhanced IgG format. These findings underscore a cost-effective strategy that bypasses the lengthy immunization process, offering potential rapid access to nanobodies targeting unexplored antigenic sites.

Suppressing Ion Migration by Synergistic Engineering of Anion and Cation toward High-Performance Inverted Perovskite Solar Cells and Modules.

Ion migration-induced intrinsic instability and large-area fabrication pose a tough challenge for the commercial deployment of perovskite photovoltaics. Herein, an interface heterojunction and metal electrode stabilization strategy is developed by suppressing ion migration via managing lead-based imperfections. After screening a series of cations and nonhalide anions, the ideal organic salt molecule dimethylammonium trifluoroacetate (DMATFA) consisting of dimethylammonium (DMA+) cation and trifluoroacetate (TFA-) anion is selected to manipulate the surface of perovskite films. DMA+ enables the conversion of active excess and/or unreacted PbI2 into stable new phase DMAPbI3, inhibiting photodecomposition of PbI2 and ion migration. Meanwhile, TFA- can suppress iodide ion migration through passivating undercoordinated Pb2+ and/or iodide vacancies. DMA+ and TFA- synergistically stabilize the heterojunction interface and silver electrode. The DMATFA-treated inverted perovskite solar cells and modules achieve a maximum efficiency of 25.03% (certified 24.65%, 0.1 cm2) and 20.58% (63.74 cm2), respectively, which is the record efficiency ever reported for the devices based on vacuum flash evaporation technology. The DMATFA modification results in outstanding operational stability, as evidenced by maintaining 91% of its original efficiency after 1520 h of maximum power point continuous tracking.

Tricarboxylic Acid Cycle Metabolite-Coordinated Biohydrogels Augment Cranial Bone Regeneration Through Neutrophil-Stimulated Mesenchymal Stem Cell Recruitment and Histone Acetylation-Mediated Osteogenesis.

Cranial bone defects remain a major clinical challenge, increasing patients' life burdens. Tricarboxylic acid (TCA) cycle metabolites play crucial roles in facilitating bone tissue regeneration. However, the development of TCA cycle metabolite-modified biomimetic grafts for skull bone regeneration still needs to be improved. The mechanism underlying the release of TCA cycle metabolites from biomaterials in regulating immune responses and mesenchymal stem cell (MSC) fate (migration and differentiation) remains unknown. Herein, this work constructs biomimetic hydrogels composed of gelatin and chitosan networks covalently cross-linked by genipin (CGG hydrogels). A series of TCA cycle metabolite-coordinated CGG hydrogels with strong mechanical and antiswelling performances are subsequently developed. Remarkably, the citrate (Na3Cit, Cit)-coordinated CGG hydrogels (CGG-Cit hydrogels) with the highest mechanical modulus and strength significantly promote skull bone regeneration in rat and murine cranial defects. Mechanistically, using a transgenic mouse model, bulk RNA sequencing, and single-cell RNA sequencing, this work demonstrates that CGG-Cit hydrogels promote Gli1+ MSC migration via neutrophil-secreted oncostatin M. Results also indicate that citrate improves osteogenesis via enhanced histone H3K9 acetylation on osteogenic master genes. Taken together, the immune microenvironment- and MSC fate-regulated CGG-Cit hydrogels represent a highly efficient and facile approach toward skull bone tissue regeneration with great potential for bench-to-bedside translation.

A high-throughput molecular dynamics screening (HTMDS) approach to the design of novel cyclopeptide inhibitors of ATAD2B based on the non-canonical combinatorial library.

Cyclic peptides (CPs) are a promising class of drugs because of their high biological activity and specificity. However, the design of CP remains challenging due to their conformational flexibility and difficulties in designing stable binding conformation. Herein, we present a high-throughput MD screening (HTMDS) process for the iterative design of stable CP binders with a combinatorial CP library composed of canonical and non-canonical amino acids. As a proof of concept, we apply our methods to design CP inhibitors for the bromodomain (BrD) of ATAD2B. 698,800 CP candidates with a total of 25,570 ns MD simulations were performed to study the protein-ligand binding interactions. The binding free energies (ΔGbind) estimated by MM/PBSA approach for eight lead CP designs were found to be low. CP-1st.43 was the best CP candidate with an estimated ΔGbind of -28.48 kcal/mol when compared to the standard inhibitor C-38 which has been experimentally validated and shown to exhibit ΔGbind of -17.11 kcal/mol. The major contribution of binding sites for BrD of ATAD2B involved the hydrogen-bonding anchor within the Aly-binding pocket, salt bridging, and hydrogen-bonding mediated stabilization of the ZA loop and BC loop, and the complementary Van der Waals attraction. Our methods demonstrate encouraging results by yielding conformationally stable and high-potential CP binders that should have potential applicability in future CP drug development.Communicated by Ramaswamy H. Sarma.

A high-throughput MD screening (HTMDS) process for cyclic peptides (CPs) binders designed with canonical and non-canonical amino acids.698,800 CP candidates with a total of 25,570 ns MD simulations were performed to study the protein-ligand binding interactions and CP design.Some potent CP candidates were obtained with high binding free energies (ΔGbind) estimated by the MM/PBSA approach compared with the standard inhibitor C-38 against the bromodomain (BrD) of ATAD2B.

Screening of four lysosome-related genes in sepsis based on RNA sequencing technology.

PURPOSE: Screening of lysosome-related genes in sepsis patients to provide direction for lysosome-targeted therapy. METHODS: Peripheral blood samples were obtained from 22 patients diagnosed with sepsis and 10 normal controls for the purpose of RNA sequencing and subsequent analysis of differential gene expression. Concurrently, lysosome-related genes were acquired from the Gene Ontology database. The intersecting genes between the differential genes and lysosome-related genes were then subjected to PPI, GO and KEGG analyses. Core genes were identified through survival analysis, and their expression trends in different groups were determined using meta-analysis. Single-cell RNA sequencing was used to clarify the cellular localization of core genes. RESULTS: The intersection of 1328 sepsis-differential genes with 878 lysosome-related genes yielded 76 genes. PPI analysis showed that intersecting genes were mainly involved in Cellular process, Response to stimulus, Immune system process, Signal transduction, Lysosome. GO and KEGG analysis showed that intersecting genes were mainly involved in leukocyte mediated immunity, cell activation involved in immune response, lytic vacuole, lysosome. Survival analysis screened four genes positively correlated with sepsis prognosis, namely GNLY, GZMB, PRF1 and RASGRP1. The meta-analysis revealed that the expression levels of these four genes were significantly higher in the normal control group compared to the sepsis group, which aligns with the findings from RNA sequencing data. Furthermore, single-cell RNA sequencing demonstrated that T cells and NK cells exhibited high expression levels of GNLY, GZMB, PRF1, and RASGRP1. CONCLUSION: GNLY, GZMB, PRF1, and RASGRP1, which are lysosome-related genes, are closely linked to the prognosis of sepsis and could potentially serve as novel research targets for sepsis, offering valuable insights for the development of lysosome-targeted therapy. The clinical trial registration number is ChiCTR1900021261, and the registration date is February 4, 2019.

Rationally Tailoring Chiral Molecules to Minimize Interfacial Energy Loss Enables Efficient and Stable Perovskite Solar Cells Using Vacuum Flash Technology.

Facing the defects and energy barrier at the interface of perovskite solar cells, we propose a chiral molecule engineering strategy to simultaneously heal interfacial defects and regulate interfacial energy band alignment. S-ibuprofen (S-IBU), R-ibuprofen (R-IBU), and racemic ibuprofen (rac-IBU) are used to post-treat perovskite films. rac-IBU molecules possess the strongest anchoring on the surface of perovskites among all chiral molecules, translating into the best defect passivation effect. The hydrophobic isobutyl group and benzene ring could increase the film moisture resistance ability. Due to reduced interfacial defects and interfacial energy barrier, rac-IBU enables efficient devices with a maximum efficiency exceeding 24% based on vacuum flash technology without antisolvents. The encapsulated rac-IBU-modified device could maintain 90% of its initial performance after 1040 h of continuous maximum power point tracking. This work provides a feasible route to minimize interfacial nonradiative recombination losses by controlling spatial conformation via rational chiral molecule engineering.

Overburdened ferroptotic stress impairs tooth morphogenesis.

The role of regulated cell death in organ development, particularly the impact of non-apoptotic cell death, remains largely uncharted. Ferroptosis, a non-apoptotic cell death pathway known for its iron dependence and lethal lipid peroxidation, is currently being rigorously investigated for its pathological functions. The balance between ferroptotic stress (iron and iron-dependent lipid peroxidation) and ferroptosis supervising pathways (anti-lipid peroxidation systems) serves as the key mechanism regulating the activation of ferroptosis. Compared with other forms of regulated necrotic cell death, ferroptosis is critically related to the metabolism of lipid and iron which are also important in organ development. In our study, we examined the role of ferroptosis in organogenesis using an ex vivo tooth germ culture model, investigating the presence and impact of ferroptotic stress on tooth germ development. Our findings revealed that ferroptotic stress increased during tooth development, while the expression of glutathione peroxidase 4 (Gpx4), a crucial anti-lipid peroxidation enzyme, also escalated in dental epithelium/mesenchyme cells. The inhibition of ferroptosis was found to partially rescue erastin-impaired tooth morphogenesis. Our results suggest that while ferroptotic stress is present during tooth organogenesis, its effects are efficaciously controlled by the subsequent upregulation of Gpx4. Notably, an overabundance of ferroptotic stress, as induced by erastin, suppresses tooth morphogenesis.

Navigation path extraction for inter-row robots in Panax notoginseng shade house based on Im-YOLOv5s.

Introduction: The accurate extraction of navigation paths is crucial for the automated navigation of agricultural robots. Navigation line extraction in complex environments such as Panax notoginseng shade house can be challenging due to factors including similar colors between the fork rows and soil, and the shadows cast by shade nets. Methods: In this paper, we propose a new method for navigation line extraction based on deep learning and least squares (DL-LS) algorithms. We improve the YOLOv5s algorithm by introducing MobileNetv3 and ECANet. The trained model detects the seven-fork roots in the effective area between rows and uses the root point substitution method to determine the coordinates of the localization base points of the seven-fork root points. The seven-fork column lines on both sides of the plant monopoly are fitted using the least squares method. Results: The experimental results indicate that Im-YOLOv5s achieves higher detection performance than other detection models. Through these improvements, Im-YOLOv5s achieves a mAP (mean Average Precision) of 94.9%. Compared to YOLOv5s, Im-YOLOv5s improves the average accuracy and frame rate by 1.9% and 27.7%, respectively, and the weight size is reduced by 47.9%. The results also reveal the ability of DL-LS to accurately extract seven-fork row lines, with a maximum deviation of the navigation baseline row direction of 1.64°, meeting the requirements of robot navigation line extraction. Discussion: The results shows that compared to existing models, this model is more effective in detecting the seven-fork roots in images, and the computational complexity of the model is smaller. Our proposed method provides a basis for the intelligent mechanization of Panax notoginseng planting.

High-performance multilayer WSe2/SnS2p-n heterojunction photodetectors by two step confined space chemical vapor deposition.

Two-dimensional (2D) p-n heterojunctions have attracted great attention due to their outstanding properties in electronic and optoelectronic devices, especially in photodetectors. Various types of heterojunctions have been constituted by mechanical exfoliation and stacking. However, achieving controlled growth of heterojunction structures remains a tremendous challenge. Here, we employed a two-step KI-assisted confined-space chemical vapor deposition method to prepare multilayer WSe2/SnS2p-n heterojunctions. Optical characterization results revealed that the prepared WSe2/SnS2vertical heterostructures have clear interfaces as well as vertical heterostructures. The electrical and optoelectronic properties were investigated by constructing the corresponding heterojunction devices, which exhibited good rectification characteristics and obtained a high detectivity of 7.85 × 1012Jones and a photoresponse of 227.3 A W-1under visible light irradiation, as well as a fast rise/fall time of 166/440µs. These remarkable performances are likely attributed to the ultra-low dark current generated in the depletion region at the junction and the high direct tunneling current during illumination. This work demonstrates the value of multilayer WSe2/SnS2heterojunctions for applications in high-performance photodetectors.

High-Responsivity and Broadband MoS2 Photodetector Using Interfacial Engineering.

Combining MoS2 with mature silicon technology is an effective method for preparing high-performance photodetectors. However, the previously studied MoS2/silicon-based heterojunction photodetectors cannot simultaneously demonstrate high responsivity, a fast response time, and broad spectral detection. We constructed a broad spectral n-type MoS2/p-type silicon-based heterojunction photodetector. The SiO2 dielectric layer on the silicon substrate was pretreated with soft plasma to change its thickness and surface state. The pretreated SiO2 dielectric layer and the silicon substrate constitute a multilayer heterostructure with a high carrier concentration and responsiveness. Taking silicon-based and n-type MoS2 heterojunction photodetectors as examples, its responsivity can reach 4.05 × 104 A W1- at 637 nm wavelength with a power density of 2 µW mm-2, and the detectable spectral range is measured from 447 to 1600 nm. This pretreated substrate was proven applicable to other n-type TMDCs, such as MoTe2, ReS2, etc., with certain versatility.

[Knot-free anchor repair of anterior talofibular ligament under total ankle arthroscopy].

OBJECTIVE: To explore clinical effect of repairing anterior talofibular ligament with knot-free anchors under total ankle arthroscopy in treating chronic lateral ankle instability. METHODS: From April 2018 to August 2021, 24 patients with chronic lateral ankle instability were treated with knot-free anchors under total ankle arthroscopy to repair anterior talofibular ligament, including 16 males and 8 females, aged from 22 to 42 years old with an average of(28.6±5.8) years old;the time from injury to opertaion ranged from 6 to 10 months with an average of(7.7±1.3) months. Preoperative and postoperative American Orhopaedic Foot and Ankle Society (AOFAS) score, visual analogue scale (VAS), talar tilt, anterior talar translation(ATT) were recorded and compared. RESULTS: All patients were followed up from 10 to 12 months with an average of (10.2±1.14) months. Incision were healed at stageⅠ, and no infection, nerve injury and lateral ankle instability occurred. AOFAS score improved from(52.79±8.96) before opertaion to (93.00± 4.01) at 6 months after operation, 23 patients got excellent result and 1 good;VAS decreased from (5.50±0.98) before opertaion to (1.04±0.80) at 6 months after operation(P<0.05);talar tilt decreased from(9.16±2.09)° to (3.10±1.72)° at 3 months after operation(P<0.05);ATT decreased from(8.80±2.55) mm to (2.98±1.97) mm at 3 months after operation(P<0.05). Twenty-four patients drawer test and varus-valgus rotation wer negative. CONCLUSION: Repairing anterior talofibular ligament with knot-free anchors under total ankle arthroscopy for the treatment of chronic lateral ankle instability has advantages of less trauma, less complications safe and reliable, and good recovery of ankle joint function.

Releasing YAP dysfunction-caused replicative toxicity rejuvenates mesenchymal stem cells.

Hippo-independent YAP dysfunction has been demonstrated to cause chronological aging of stromal cells by impairing the integrity of nuclear envelope (NE). In parallel with this report, we uncover that YAP activity also controls another type of cellular senescence, the replicative senescence in in vitro expansion of mesenchymal stromal cells (MSCs), but this event is Hippo phosphorylation-dependent, and there exist another NE integrity-independent downstream mechanisms of YAP. Specifically, Hippo phosphorylation causes reduced nuclear/active YAP and then decreases the level of YAP protein in the proceeding of replicative senescence. YAP/TEAD governs RRM2 expression to release replicative toxicity (RT) via licensing G1/S transition. Besides, YAP controls the core transcriptomics of RT to delay the onset of genome instability and enhances DNA damage response/repair. Hippo-off mutations of YAP (YAPS127A/S381A ) satisfactorily release RT via maintaining cell cycle and reducing genome instability, finally rejuvenating MSCs and restoring their regenerative capabilities without risks of tumorigenesis.

Divalent Anion-Induced Biohydrogels with High Strength, Anti-swelling, and Bioactive Capability for Enhanced Skull Bone Regeneration.

Increased intracranial pressure after traumatic brain injury (TBI) is an urgent problem in clinical practice. A pliable hydrogel is preferred for cranioplasty applications after TBI since it can protect brain tissue and promote bone healing. Nevertheless, biohydrogels for cranial bone regeneration still face challenges of poor mechanical properties, large swelling ratios, and low osteogenesis activity. Herein, inspired by Hofmeister effects, biopolymer hydrogels composed of protein and polysaccharides were treated with a Hofmeister series including a series of monovalent and divalent anions. Our results reveal that the divalent anion-cross-linked biohydrogels exhibit stronger mechanical properties and lower swelling ratios compared with monovalent-anion treated gels. Intriguingly, the divalent HPO42- anion induced biohybrid hydrogels with excellent mechanical behaviors (3.7 ± 0.58 MPa, 484 ± 76.7 kPa, and 148.3 ± 6.85 kJ/m3), anti-swelling capability (16.7%), and gradual degradation ability, significantly stimulating osteogenic differentiation and in vivo cranial bone regeneration. Overall, this study may provide new insights into the design of biomimetic hydrogels for treating cranial bone defects after TBI.

Managing Interfacial Defects and Carriers by Synergistic Modulation of Functional Groups and Spatial Conformation for High-Performance Perovskite Photovoltaics Based on Vacuum Flash Method.

Interfacial nonradiative recombination loss is a huge barrier to advance the photovoltaic performance. Here, one effective interfacial defect and carrier dynamics management strategy by synergistic modulation of functional groups and spatial conformation of ammonium salt molecules is proposed. The surface treatment with 3-ammonium propionic acid iodide (3-APAI) does not form 2D perovskite passivation layer while the propylammonium ions and 5-aminopentanoic acid hydroiodide post-treatment lead to the formation of 2D perovskite passivation layers. Due to appropriate alkyl chain length, theoretical and experimental results manifest that COOH and NH3 + groups in 3-APAI molecules can form coordination bonding with undercoordinated Pb2+ and ionic bonding and hydrogen bonding with octahedron PbI6 4- , respectively, which makes both groups be simultaneously firmly anchored on the surface of perovskite films. This will strengthen defect passivation effect and improve interfacial carrier transport and transfer. The synergistic effect of functional groups and spatial conformation confers 3-APAI better defect passivation effect than 2D perovskite layers. The 3-APAI-modified device based on vacuum flash technology achieves an alluring peak efficiency of 24.72% (certified 23.68%), which is among highly efficient devices fabricated without antisolvents. Furthermore, the encapsulated 3-APAI-modified device degrades by less than 4% after 1400 h of continuous one sun illumination.

Screening of core genes prognostic for sepsis and construction of a ceRNA regulatory network.

OBJECTIVE: To screen out core genes potentially prognostic for sepsis and construct a competing endogenous RNA (ceRNA) regulatory network. METHODS: Subjects included in this project were 23 sepsis patients and 10 healthy people. RNA-seq for lncRNA, miRNA and mRNA was performed in the peripheral blood samples. Differentially expressed RNAs (DER) were screened out for further analysis. GO annotation and GSEA functional clustering were performed to view the functional enrichment of DEmRNAs. Core genes of prognostic significance were screened out with the weighted correlation network analysis (WGCNA). Meta-analysis and Survival analysis was devised in different microarray datasets. RT-qPCR was conducted to validate these core genes. A ceRNA network was accordingly constructed according to the correlation analysis and molecular interaction prediction. RESULTS: RNA-seq and differential analysis screened out 1,044 DEmRNAs, 66 DEmiRNAs and 155 DElncRNAs. The GO and GSEA analysis revealed that DEmRNAs are mainly involved in inflammatory response, immune regulation, neutrophil activation. WGCNA revealed 4 potential core genes, including CD247, IL-2Rß, TGF-ßR3 and IL-1R2. In vitro cellular experiment showed up-regulated expression of IL-1R2 while down-regulated of CD247, IL-2Rß, TGF-ßR3 in sepsis patients. Correspondingly, a ceRNA regulatory network was build based on the core genes, and multiple lncRNAs and miRNAs were identified to have a potential regulatory role in sepsis. CONCLUSION: This study identified four core genes, including CD247, IL-1R2, IL-2Rß and TGF-ßR3, with potential to be novel biomarkers for the prognosis of sepsis. In the meantime, a ceRNA network was constructed aiming to guide further study on prognostic mechanism in sepsis.

Screening of potential immune-related genes expressed during sepsis using gene sequencing technology.

To screen potential pivotal targets in sepsis through peripheral blood. Septic patients (n = 23) and healthy volunteers (n = 10) were enrolled according to SEPSIS 3.0. Peripheral blood was collected within 24 h of enrollment, RNA-seq was performed on the peripheral blood. The sequencing data was screened for DEGs (p < 0.01; logFC ≥ 2). PPI, WGCNA and survival curve analysis were used to identify potential targets. Then, 5 PBMC samples were conducted by single-cell sequencing for cell lineage location. Finally, mouse sepsis model and clinic samples were performed to verify the targets gene using RNA-seq and RT-PCR, respectively. Compared to the control group, 1007 DEGs were found in septic group. BCL9L, BCL11B, CD247, CD96, MAFG and SAMD3 were in the core of network. These six genes correlated to the survival rate of septic patients and they were mainly expressed in T cells, except that MAFG was located in monocyte cell. The expression levels of six key genes were confirmed by animal and clinical samples. BCL9L, BCL11B, CD247, CD96 and SAMD3 were decreased in sepsis and mainly expressed in the T cell; while MAFG increased in sepsis and localizes to monocytes. These genes may be therapeutic targets for sepsis.

Bioinformatics analysis of differentially expressed genes in diabetic foot ulcer and preliminary experimental verification.

Background: Molecular changes are closely related to the pathogenesis and healing process of diabetic foot ulcers (DFUs), and are crucial for the early prediction and intervention of DFU. Methods: Bioinformatics analysis was performed in this study to identify the key differentially expressed genes (DEGs) in DFU, analyze their functions and function modes, and conduct preliminary experimental verification to determine the potential pivotal genes in the pathogenesis of DFU. Two datasets, GSE68183 and GSE80178, were obtained from the Gene Expression Omnibus (GEO). DEGs were obtained using GEO2R. Six co-expressed DEGs (co-DEGs) were obtained by R language analysis. The co-DEGs were constructed by using STRING and Cytoscape 3.7.2 to construct a protein-protein interaction (PPI) network, and two hub genes, NHLRC3 and BNIP3, were identified. The BNIP3 gene was selected for further analysis. Co-DEGs were used for Gene Ontology (GO) function analysis using the WebGestalt database, and BNIP3-related biological processes focused on mitochondrial protein decomposition. GO function analysis of the BNIP3 gene and its interacting genes was carried out using the cluster profile package and org.hs.eg. db package of the R language and its biological process was enriched in the cell response to external stimuli and autophagy. Results: BNIP3 and its interacting genes were retrieved from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and KEGG pathway enrichment analysis was performed using the WebGestalt database. The results showed that BNIP3 was significantly correlated with mitochondrial autophagy and the FoxO signaling pathway. The miRDB and TargetScan databases were used to identify the relevant microRNAs (miRNAs) regulating the BNIP3 gene, and it was found that miRNA-182 may be involved in the targeted regulation of BNIP3. Western blot analysis was performed to determine the abnormal expression of BNIP3. Conclusions: Our study found that the BNIP3 gene may be a new biomarker and intervention target for DFU.

Epigenetic regulation of embryonic ectoderm development in stem cell differentiation and transformation during ontogenesis.

Dynamic chromatin accessibility regulates stem cell fate determination and tissue homeostasis via controlling gene expression. As a histone-modifying enzyme that predominantly mediates methylation of lysine 27 in histone H3 (H3K27me1/2/3), Polycomb repressive complex 2 (PRC2) plays the canonical role in targeting developmental regulators during stem cell differentiation and transformation. Embryonic ectoderm development (EED), the core scaffold subunit of PRC2 and as an H3K27me3-recognizing protein, has been broadly implicated with PRC2 stabilization and allosterically stimulated PRC2. Accumulating evidences from experimental data indicate that EED-associating epigenetic modifications are indispensable for stem cell maintenance and differentiation into specific cell lineages. In this review, we discuss the most updated advances to summarize the structural architecture of EED and its contributions and underlying mechanisms to mediating lineage differentiation of different stem cells during epigenetic modification to expand our understanding of PRC2.