Bulk RNA Sequencing With Integrated Single-Cell RNA Sequencing Identifies BCL2A1 as a Potential Diagnostic and Prognostic Biomarker for Sepsis

Construction of Diagnostic Model for Regulatory T Cell-Related Genes in Sepsis Based on Machine Learning

Background: Sepsis is a complex syndrome caused by a severe infection that occurs with a severe inflammatory response. Regulatory T cells (Tregs) have immunosuppressive effects and play a crucial role in modulating the immune response. There-fore, the number of Tregs is significantly increased in sepsis patients. Methods and Results: This paper aims to identify Tregs associated with the diagnosis of sepsis. For this purpose, transcriptional data from the GEO database for sepsis and its controls were downloaded and subjected to differential expression analysis. Immuno-infiltration analysis of the obtained DEGs revealed that Tregs were significantly different in sepsis and its controls. To further explore the cellular landscape and interactions in sepsis, single-cell RNA sequencing (scRNA-seq) data were analyzed. We identified key cell types and their interactions, including Tregs, using cell-cell communication analysis tools such as CellChat. This analysis provided in-sights into the dynamic changes in immune cell populations and their communication networks in sepsis. Thus, we utilized multiple machine learning algorithms to screen and extract Treg-related genes associated with sepsis diagnosis. We then performed both in-ternal and external validation tests. The final diagnostic model was constructed with high diagnostic accuracy (accuracy of 0.9615). Furthermore, we verified the diagnostic gene via a qPCR experiment. Conclusions: This paper elucidates the potential diagnostic targets associated with Tregs in sepsis progression and provides comprehensive understanding of the immune cell interactions in sepsis through scRNA-seq analysis.

Multi-omics analysis reveals that low cathepsin S expression aggravates sepsis progression and worse prognosis via inducing monocyte polarization

Background

Monocytes represent a vital cellular subpopulation in the peripheral blood, crucial in the progression of sepsis. Nonetheless, the prognostic role and precise function of monocytes in sepsis are still inadequately understood.

Methods

Single-cell transcriptomic sequencing and bioinformatics analysis were performed on peripheral blood samples from septic patients to identify key molecules in cell subsets. Subsequently, the expression pattern of this molecule was validated through diverse biological experiments, encompassing quantitative RT-PCR, western blotting, and immunofluorescence. Finally, the functionality of this molecule was evaluated using its specific agonist.

Results

A total of 22 monocytes-related biomarkers were identified from single-cell and bulk RNA-seq analyses. Initially, LASSO analysis was performed to derive a prognostic signature composed of 4 key genes, including CD14, CTSS, CXCL8 and THBS1. Subsequently, mendelian randomization and survival analysis demonstrated that only CTSS showed crucially protective role in sepsis development and prognosis. Next, CTSS was confirmed to be lower expressed in peripheral monocytes of septic patients. Inflammatory markers (p < 0.05) and migration ability of LPS-activated monocytes were significantly reduced after CTSS agonist. In addition, CTSS agonist decreased the pulmonary tissue monocyte/macrophages infiltration in septic mice.

Conclusion

Monocyte marker CTSS represent a promising target for the diagnosis and prognosis evaluation of sepsis and plays a critical role in monocytes activation, tissue inflammatory response and macrophages infiltration. Thus, CTSS agonist probably serves as new drug for clinical protection against sepsis.

Single-Cell Landscape of Bronchoalveolar Lavage Fluid Identifies Specific Neutrophils during Septic Immunosuppression

Sepsis-induced immunosuppression is related to increased susceptibility to secondary infections and death. Lung is the most vulnerable target organ in sepsis, but the understanding of the pulmonary immunosuppression state is still limited. Here, single-cell RNA sequencing of bronchoalveolar lavage fluid (BALF) is performed to map the landscape of immune cells, revealing a neutrophil-driven immunosuppressive program in the lungs of patients with immunosuppressive sepsis. Although immunosuppressive genes are upregulated in different immune cells, only neutrophils dramatically increase in the BALF of patients in immunosuppressive phase of sepsis. Five neutrophil subpopulations in BALF are identified, among which CXCR2+ and CD274 (PD-L1 coding gene)+IL1RN+ neutrophil subpopulations increased significantly during septic immunosuppression. Interestingly, a developmental trajectory from CXCR2+ to CD274+IL1RN+ neutrophil subpopulation is disclosed. Moreover, the therapeutic effect of CXCR2 blockade is observed on the survival of septic mice, along with a decreased number of PD-L1+ neutrophils. Taken together, the CXCR2+ neutrophil subpopulation is discovered as a contributor to immunosuppression in sepsis and identified it as a potential therapeutic target in sepsis treatment.

Single-cell analysis reveals the loss of FABP4-positive proliferating valvular endothelial cells relates to functional mitral regurgitation

BACKGROUND

Functional mitral regurgitation (MR) is a common form of mitral valve dysfunction that often persists even after surgical intervention, requiring reoperation in some cases. To advance our understanding of the pathogenesis of functional MR, it is crucial to characterize the cellular composition of the mitral valve leaflet and identify molecular changes in each cell subtype within the mitral valves of MR patients. Therefore, we aimed to comprehensively examine the cellular and molecular components of mitral valves in patients with MR.

METHODS

We conducted a single-cell RNA sequencing (scRNA-seq) analysis of mitral valve leaflets extracted from six patients who underwent heart transplantation. The cohort comprised three individuals with moderate-to-severe functional MR (MR group) and three non-diseased controls (NC group). Bioinformatics was applied to identify cell types, delineate cell functions, and explore cellular developmental trajectories and interactions. Key findings from the scRNA-seq analysis were validated using pathological staining to visualize key markers in the mitral valve leaflets. Additionally, in vitro experiments with human primary valvular endothelial cells were conducted to further support our results.

RESULTS

Our study revealed that valve interstitial cells are critical for adaptive valve remodelling, as they secrete extracellular matrix proteins and promote fibrosis. We discovered an abnormal decrease in a subpopulation of FABP4 (fatty acid binding protein 4)-positive proliferating valvular endothelial cells. The trajectory analysis identifies this subcluster as the origin of VECs. Immunohistochemistry on the expanded cohort showed a reduction of FABP4-positive VECs in patients with functional MR. Intervention experiments with primary cells indicated that FABP4 promotes proliferation and migration in mitral valve VECs and enhances TGFβ-induced differentiation.

CONCLUSIONS

Our study presented a comprehensive assessment of the mitral valve cellular landscape of patients with MR and sheds light on the molecular changes occurring in human mitral valves during functional MR. We found a notable reduction in the proliferating endothelial cell subpopulation of valve leaflets, and FABP4 was identified as one of their markers. Therefore, FABP4 positive VECs served as proliferating endothelial cells relates to functional mitral regurgitation. These VECs exhibited high proliferative and differentiative properties. Their reduction was associated with the occurrence of functional MR.

Single-cell RNA sequencing and transcriptomic analysis reveal key genes and regulatory mechanisms in sepsis

The pathogenesis of sepsis, with a high mortality rate and often poor prognosis, has not been fully elucidated. Therefore, an in-depth study on the pathogenesis of sepsis at the molecular level is essential to identify key sepsis-related genes. The aim of this study was to explore the key genes and potential molecular mechanisms of sepsis using a bioinformatics approach. In addition, key genes with miRNA network correlation analysis and immune infiltration correlation analysis were investigated. The scRNA dataset (GSE167363) and RNA-seq dataset (GSE65682, GSE134347) from GEO database were used for screening out differentially expressed genes using single-cell sequencing and transcriptome sequencing. The analysis of immune infiltration was evaluated by the CIBERSORT method. Key genes and possible mechanisms were identified by WGCNA analysis, GSVA analysis, GSEA enrichment analysis and regulatory network analysis, and miRNA networks associated with key genes were constructed. Nine key genes associated with the development of sepsis, namely IL7R, CD3D, IL32, GPR183, HLA-DPB1, CD81, PEBP1, NCL, and ETS1 were screened, and the specific signaling mechanisms associated with the key genes causing sepsis were predicted. Immune profiling showed immune heterogeneity between control and sepsis samples. A regulatory network of 82 miRNAs, 266 pairs of mRNA-miRNA relationship pairs was also constructed. These nine key genes have the potential to become biomarkers for the diagnosis of sepsis and provide new targets and research directions for the treatment of sepsis.

Acetylation of TIR domains in the TLR4-Mal-MyD88 complex regulates immune responses in sepsis

Activation of the Toll-like receptor 4 (TLR4) by bacterial endotoxins in macrophages plays a crucial role in the pathogenesis of sepsis. However, the mechanism underlying TLR4 activation in macrophages is still not fully understood. Here, we reveal that upon lipopolysaccharide (LPS) stimulation, lysine acetyltransferase CBP is recruited to the TLR4 signalosome complex leading to increased acetylation of the TIR domains of the TLR4 signalosome. Acetylation of the TLR4 signalosome TIR domains significantly enhances signaling activation via NF-κB rather than IRF3 pathways. Induction of NF-κB signaling is responsible for gene expression changes leading to M1 macrophage polarization. In sepsis patients, significantly elevated TLR4-TIR acetylation is observed in CD16+ monocytes combined with elevated expression of M1 macrophage markers. Pharmacological inhibition of HDAC1, which deacetylates the TIR domains, or CBP play opposite roles in sepsis. Our findings highlight the important role of TLR4-TIR domain acetylation in the regulation of the immune responses in sepsis, and we propose this reversible acetylation of TLR4 signalosomes as a potential therapeutic target for M1 macrophages during the progression of sepsis.

Contribution of A1 to macrophage survival in cooperation with MCL-1 and BCL-XL in a murine cell model of myeloid differentiation

Myeloid cells are the first line of defence against pathogens. Mitochondrial apoptosis signalling is a crucial regulator of myeloid cell lifespan and modulates the function of myeloid cells. The anti-apoptotic protein BCL-2-family protein BCL2A1/A1/BFL-1 is strongly upregulated in inflammation in macrophages. We analysed the contribution of A1 to apoptosis regulation in a conditional system of in vitro differentiation of murine macrophages from immortalised progenitors. We disabled the expression of A1 by targeting all murine A1 isoforms in the genome. Specific inhibitors were used to inactivate other anti-apoptotic proteins. Macrophage progenitor survival mainly depended on the anti-apoptotic proteins MCL-1, BCL-XL and A1 but not BCL-2. Deletion of A1 on its own had little effect on progenitor cell survival but was sensitised to cell death induction when BCL-XL or MCL-1 was neutralised. In progenitors, A1 was required for survival in the presence of the inflammatory stimulus LPS. Differentiated macrophages were resistant to inhibition of single anti-apoptotic proteins, but A1 was required to protect macrophages against inhibition of either BCL-XL or MCL-1; BCL-2 only had a minor role in these cells. Cell death by neutralisation of anti-apoptotic proteins completely depended on BAX with a small contribution of BAK only in progenitors in the presence of LPS. A1 and NOXA appeared to stabilise each other at the posttranscriptional level suggesting direct binding. Co-immunoprecipitation experiments showed the binding of A1 to NOXA and BIM. Interaction between A1 and Noxa may indirectly prevent neutralisation and destabilization of MCL-1. Our findings suggest a unique role for A1 as a modulator of survival in the macrophage lineage in concert with MCL-1 and BCL-XL, especially in a pro-inflammatory environment.

Correlation between the gut microbiota characteristics of hosts with severe acute pancreatitis and secondary intra-abdominal infection

Objective

The objective of the study is to investigate the changes in the composition of intestinal microecology in severe acute pancreatitis (SAP) patients with or without intra-abdominal infection and also to analyze the expression of antibiotic resistance genes to provide evidence for early warning of infectious diseases and the rational use of antibiotics.

Methods

Twenty patients with SAP were enrolled in the study. According to whether the enrolled patients had a secondary intra-abdominal infection, they were divided into two groups, each consisting of 10 patients. Stool specimens were collected when the patients were admitted to the emergency intensive care unit (EICU), and nucleic acid extraction was performed. Next-generation gene sequencing was used to compare the differences in intestinal microflora diversity and drug resistance gene expression between the two groups.

Results

The gut microbiota of patients in the infection group exhibited distribution on multiple clustered branches with some intra-group heterogeneity, and their flora diversity was compromised. The infected group showed an enrichment of various opportunistic bacteria in the gut microbiota, along with a high number of metabolic functions, stress functions to external signals, and genes associated with pathogenesis. Drug resistance genes were expressed in the gut microbiota of both groups, but their abundance was significantly lower in the non-infected group.

Conclusion

The intestinal microbiota of patients in the infection group exhibited distribution on multiple clustered branches with some intra-group heterogeneity, and their flora diversity was compromised. Additionally, drug resistance genes were expressed in the gut microbiota of both groups, although their abundance was significantly lower in the non-infected group.

ADAR1 Inhibits Macrophage Apoptosis and Alleviates Sepsis-induced Liver Injury Through miR-122/BCL2A1 Signaling

BACKGROUND AND AIMS

As sepsis progresses, immune cell apoptosis plays regulatory roles in the pathogenesis of immunosuppression and organ failure. We previously reported that adenosine deaminases acting on RNA-1 (ADAR1) reduced intestinal and splenic inflammatory damage during sepsis. However, the roles and mechanism of ADAR1 in sepsis-induced liver injury remain unclear.

METHODS

We performed transcriptome and single-cell RNA sequencing of peripheral blood mononuclear cells (PBMCs) from patients with sepsis to investigate the effects of ADAR1 on immune cell activities. We also employed a cecal ligation and puncture (CLP) sepsis mouse model to evaluate the roles of ADAR1 in sepsis-induced liver injury. Finally, we treated murine RAW 264.7 macrophages with lipopolysaccharide to explore the underlying ADAR1-mediated mechanisms in sepsis.

RESULTS

PBMCs from patients with sepsis had obvious apoptotic morphological features. Single-cell RNA sequencing indicated that apoptosis-related pathways were enriched in monocytes, with significantly elevated ADAR1 and BCL2A1 expression in severe sepsis. CLP-induced septic mice had aggravated liver injury and Kupffer cell apoptosis that were largely alleviated by ADAR1 overexpression. ADAR1 directly bound to pre-miR-122 to modulate miR-122 biosynthesis. miR-122 was an upstream regulator of BCL2A1. Furthermore, ADAR1 also reduced macrophage apoptosis in mice with CLP-induced sepsis through the miR-122/BCL2A1 signaling pathway and protected against sepsis-induced liver injury.

CONCLUSIONS

The findings show that ADAR1 alleviates macrophage apoptosis and sepsis-induced liver damage through the miR-122/BCL2A1 signaling pathway. The study provides novel insights into the development of therapeutic interventions in sepsis.