Identification of key genes and pathways associated with different immune statuses of hepatitis B virus infection

The novel role of LCK and other PcDEGs in the diagnosis and prognosis of sepsis: Insights from bioinformatic identification and experimental validation

BACKGROUND

Programmed cell death (PCD) has emerged as a pivotal progress in pathogenesis of sepsis, but its role in identification of sepsis has not been fully understood.

METHODS

Differentially expressed genes (DEGs) were identified from the GEO database. PCD-related genes were intersected with DEGs, and key PcDEGs were identified through the protein-protein interaction (PPI) network. To pinpoint hub PcDEGs in sepsis, we applied Random Forest (RF), Support Vector Machine (SVM), Extreme Gradient Boosting (XGB), and Generalized Linear Model (GLM) algorithms. Additionally, the expression levels of five hub PcDEGs were validated in single cell RNA sequencing of sepsis patients and peripheral blood mononuclear cells (PBMCs) from a clinical cohort by quantitative real-time PCR (qRT-PCR). LCK expression was further determined by ELISA, and its diagnostic and prognostic value was evaluated using ROC analysis. LCK levels in the cecal ligation and puncture (CLP)-induced sepsis mouse model were assessed by Western blot and Immunofluorescence (IF). Finally, we assessed the regulatory role of LCK in cell apoptosis using flow cytometry and Western blot analysis.

RESULTS

70 PcDEGs were identified by intersecting 690 DEGs and 1254 PCD-related genes. PPI analysis identified top 15 genes based on Degree algorithm. We then identified five hub PcDEGs (LCK, IL10RA, CD3E, CD5 and ITGAM) that could serve as biomarkers through machine learning. As the expressions of LCK, IL10RA, CD3E and CD5 decreased and ITGAM expression was upregulated in septic patients. Consistently, Serum LCK concentration was reduced in septic patients, and the area under the ROC curve (AUC) of LCK was 0.753. Importantly, LCK displayed more pronounced reduction in non-survivors and those with septic shock than survivors and non-shock patients. The AUC for LCK was 0.726 in predicting mortality of septic patients. Moreover, we observed a decrease expression of LCK in the vital organs (liver, lung, spleen, thymus and PBMC) of septic mice model which mirrored observations in septic patients. Finally, we found that inhibiting LCK promoted apoptosis in Jurkat cells.

CONCLUSIONS

Our study reveals that PcDEGs are dysregulated in sepsis, and closely related to disease pathology. Our finding provides new insights into clinical identification and outcome prediction of sepsis. Of note, LCK is a new biomarker for diagnosis and prognosis, which might be a potential therapeutic target for the treatment of sepsis.

RIPK3 activation of CaMKII triggers mitochondrial apoptosis in NIBV-infected renal tubular epithelial cells

The purpose of this study was to investigate whether RIPK3-mediated programmed cell death can promote the replication and transmission of renal infectious bronchitis virus in renal tubular epithelial cells. Primary renal tubular epithelial cells were extracted from 1 to 7 day old Hy-Line Brown chicks, cultured in vitro by type I collagenase digestion, and infected with 1MOI SX9 strain. Cell samples were collected at 12 hpi, 24 hpi, 36 hpi and 48 hpi for experimental exploration. Our results showed that NIBV infection could lead to programmed necrosis and mitochondrial apoptosis, and the expression levels of programmed necrosis-related genes TNFR1, TRADD, FADD, RIPK1, RIPK3 and MLKL increased significantly with the extension of infection time, the expression levels of mitochondrial apoptosis-related genes Cyt-C, APAF-1, Caspase-9 and Csapase-3 were significantly increased at 36 hpi. While, after 36 hpi of virus infection, apoptosis decreased and necrosis increased, and virus replication peaked. In order to further explore the effect of necroptosis on the amplification of renal infectious virus, the RIPK3 was inhibited at 36 hpi. Inhibition of necroptosis could reduce viral replication and cell death, programmed necrosis occurred in the cells, and cell membrane perforation led to virus diffusion and replication. NIBV-induced necroptosis depends on RIPK3, and RIPK3 activates CAMKII and interacts to cause abnormal opening of mitochondrial membrane permeability transition pore, promotes Ca2 + influx into mitochondria, initiates mitochondrial apoptosis. While, inhibition of RIPK3 significantly inhibited the programmed necrosis of cells caused by NIBV infection, making excessive necrosis into moderate necrosis, thereby inhibiting the replication of the virus in cells.

A single-cell atlas of immunocytes in the spleen of a mouse model of Wiskott-Aldrich syndrome

Wiskott-Aldrich syndrome (WAS) is a disorder characterized by rare X-linked genetic immune deficiency with mutations in the Was gene, which is specifically expressed in hematopoietic cells. The spleen plays a major role in hematopoiesis and red blood cell clearance. However, to date, comprehensive analyses of the spleen in wild-type (WT) and WASp-deficient (WAS-KO) mice, especially at the transcriptome level, have not been reported. In this study, single-cell RNA sequencing (scRNA-seq) was adopted to identify various types of immune cells and investigate the mechanisms underlying immune deficiency. We identified 30 clusters and 10 major cell subtypes among 11,269 cells; these cell types included B cells, T cells, dendritic cells (DCs), natural killer (NK) cells, monocytes, macrophages, granulocytes, stem cells and erythrocytes. Moreover, we evaluated gene expression differences among cell subtypes, identified differentially expressed genes (DEGs), and performed enrichment analyses to identify the reasons for the dysfunction in these different cell populations in WAS. Furthermore, some key genes were identified based on a comparison of the DEGs in each cell type involved in specific and nonspecific immune responses, and further analysis showed that these key genes were previously undiscovered pathology-related genes in WAS-KO mice. In summary, we present a landscape of immune cells in the spleen of WAS-KO mice based on detailed data obtained at single-cell resolution. These unprecedented data revealed the transcriptional characteristics of specific and nonspecific immune cells, and the key genes were identified, laying a foundation for future studies of WAS, especially studies into novel and underexplored mechanisms that may improve gene therapies for WAS.

Tenofovir alters the immune microenvironment of pregnant women with hepatitis B virus infection: Evidence from single-cell RNA sequencing

BACKGROUND

Mother-to-child is the main route of the transmission of hepatitis B virus (HBV) infection. Tenofovir fumarate (TDF) antiviral treatment has become the most extensive choice worldwide. However, the effects of TDF treatment on the immune function of pregnant women remains unclear. Here we investigate the effect of TDF treatment on the immune microenvironment of pregnant women with HBV infection using single-cell RNA sequencing (scRNA-seq).

METHODS

Three HBV-infected pregnant women were treated with TDF and six samples were collected before and after the treatment. In total, 68,200 peripheral blood mononuclear cells (PBMCs) were extracted for 10 × scRNA-seq. The cells were clustered using t-distributed stochastic neighbor embedding (t-SNE) and unbiased computational informatics analysis.

RESULTS

The analysis identified four-cell subtypes, including T cells, monocytes, natural killer (NK) cells, and B cells, and unraveled the developmental trajectory and maturation of CD4⁺ T and CD8⁺ T cell subtypes. The cellular state and molecular features of the effector/memory T cells revealed a significant increase in the inflammatory state of CD4⁺ T cells and the cytotoxic characteristics of CD8⁺ T cells. Additionally, after TDF treatment, the monocytes showed a tendency for M1 polarization, and the cytotoxicity of NK cells was enhanced. Furthermore, the analysis of intercellular communication revealed the interaction of various subtypes of cells and the heterogeneous expression of key signal pathways.

CONCLUSIONS

The findings of this study reveal significant differences in cellular subtypes and molecular characteristics of PBMCs of pregnant women with HBV infection before and after TDF treatment and demonstrate the recovery of immune response after treatment. These findings could help develop immune intervention measures to control HBV during pregnancy and the puerperium period.

The CD56-CD16+ NK cell subset in chronic infections

Long-term human diseases can shape the immune system, and natural killer (NK) cells have been documented to differentiate into distinct subsets specifically associated with chronic virus infections. One of these subsets found in large frequencies in HIV-1 are the CD56-CD16+ NK cells, and this population's association with chronic virus infections is the subject of this review. Human NK cells are classically defined by CD56 expression, yet increasing evidence supports the NK cell status of the CD56-CD16+ subset which we discuss herein. We then discuss the evidence linking CD56-CD16+ NK cells to chronic virus infections, and the potential immunological pathways that are altered by long-term infection that could be inducing the population's differentiation. An important aspect of NK cell regulation is their interaction with human leukocyte antigen (HLA) class-I molecules, and we highlight work that indicates both virus and genetic-mediated variations in HLA expression that have been linked to CD56-CD16+ NK cell frequencies. Finally, we offer a perspective on CD56-CD16+ NK cell function, taking into account recent work that implies the subset is comparable to CD56+CD16+ NK cell functionality in antibody-dependent cell cytotoxicity response, and the definition of CD56-CD16+ NK cell subpopulations with varying degranulation capacity against target cells.

The association between Fc gamma RIIb expression levels and chronic hepatitis B virus infection progression

BACKGROUND

Fc gamma receptor IIb (FcγRIIb) is an important inhibitory receptor that plays vital roles in regulating various immune response processes and the pathogenesis of many infectious diseases. The purpose of our research was to evaluate FcγRIIb expression in serum and liver biopsy specimens from hepatitis B virus (HBV)-infected patients and to explore the association of FcγRIIb with chronic HBV infection.

METHODS

Enzyme-linked immunosorbent assay (ELISA) was adopted to measure the serum FcγRIIb levels in 119 HBV-infected patients and 24 healthy controls. An immunohistochemical method was then employed to identify FcγRIIb expression in biopsy specimens from patients with chronic hepatitis B (CHB). The integrated optical density (IOD) value was measured to represent FcγRIIb expression levels.

RESULTS

Serum FcγRIIb levels were decreased in CHB patients compared to controls (P < 0.001). The FcγRIIb levels in the CHB patient group were remarkably lower than those in the HBV carrier group (P < 0.001). In addition, FcγRIIb levels were negatively associated with AST and ALT (r = -0.3936, P = 0.0063; r = -0.3459, P = 0.0097, respectively). The IOD values of FcγRIIb expression in the moderate and severe CHB groups were significantly lower than those in the control group (P = 0.006 and P < 0.001, respectively). The FcγRIIb level tended to be lower with pathological changes related to hepatitis. Furthermore, correlation analysis revealed that FcγRIIb had negative correlations with AST and ALT (r = -0.688, P = 0.0016; r = -0.686, P = 0.0017, respectively) but a positive association with the platelet count (r = 0.6464, P = 0.0038).

CONCLUSIONS

FcγRIIb levels are significantly related to chronic HBV infection and the progression of CHB. Changes in FcγRIIb may affect the progression of liver inflammation and fibrosis in CHB patients.

Mechanisms of DNA Methylation in Virus-Host Interaction in Hepatitis B Infection: Pathogenesis and Oncogenetic Properties

Hepatitis B virus (HBV), the well-studied oncovirus that contributes to the majority of hepatocellular carcinomas (HCC) worldwide, can cause a severe inflammatory microenvironment leading to genetic and epigenetic changes in hepatocyte clones. HBV replication contributes to the regulation of DNA methyltransferase gene expression, particularly by X protein (HBx), and subsequent methylation changes may lead to abnormal transcription activation of adjacent genes and genomic instability. Undoubtedly, the altered expression of these genes has been known to cause diverse aspects of infected hepatocytes, including apoptosis, proliferation, reactive oxygen species (ROS) accumulation, and immune responses. Additionally, pollutant-induced DNA methylation changes and aberrant methylation of imprinted genes in hepatocytes also complicate the process of tumorigenesis. Meanwhile, hepatocytes also contribute to epigenetic modification of the viral genome to affect HBV replication or viral protein production. Meanwhile, methylation levels of HBV integrants and surrounding host regions also play crucial roles in their ability to produce viral proteins in affected hepatocytes. Both host and viral changes can provide novel insights into tumorigenesis, individualized responses to therapeutic intervention, disease progress, and early diagnosis. As such, DNA methylation-mediated epigenetic silencing of cancer-related genes and viral replication is a compelling therapeutic goal to reduce morbidity and mortality from liver cancer caused by chronic HBV infection. In this review, we summarize the most recent research on aberrant DNA methylation associated with HBV infection, which is involved in HCC development, and provide an outlook on the future direction of the research.

Levels of serum IgG subclasses in patients with liver disease: A retrospective study

Viral and alcoholic liver disease, drug induced liver disease (DILD), primary biliary cirrhosis (PBC) and autoimmune hepatitis (AIH) are among the most common liver diseases observed in clinical practice. These diseases lack unique clinical characteristics at the beginning of pathogenesis, which renders specific diagnosis difficult. Immunoglobulin G (IgG) subclasses are the main isoform of antibodies that can be found in the serum that serve important protective roles in immunity. The present study aimed to investigate the serum IgG subclass distribution in patients with the five common liver diseases aforementioned. The present study retrospectively recorded and analyzed the serum IgG subclass levels of different patients, who were grouped according to their clinical diagnosis. Serum IgG subclass levels were measured using immunonephelometric assays. IgG3 levels were found to be significantly increased whereas IgG4 levels were significantly decreased in patients with PBC. In patients with AIH, IgG1 levels were significantly increased. By contrast, IgG1/IgG level ratios in patients with viral liver disease were significantly increased. No clear pattern in the distribution characteristics of IgG subclasses could be observed in cohorts with alcoholic liver disease and DILD in the present study. Additionally, model for end-stage liver disease scores regarding IgG1 in patients with AIH shared a synergistic relationship. Anti-mitochondrial antibody subtype M2 (AMA-M2) and IgG3 in patients with PBC demonstrated a synergistic relationship. These results suggested that IgG subclasses may be used as biomarkers to further the understanding of liver disease, which could allow for early diagnosis.

Identification of key genes and pathways associated with different immune statuses of hepatitis B virus infection

We aimed to identify key genes and pathways associated with different immune statuses of hepatitis B virus (HBV) infection. The gene expression and DNA methylation profiles were analysed in different immune statuses of HBV infection. Differentially expressed genes (DEGs) and differentially methylated genes (DMGs) were identified, followed by their functional and integrative analyses. The differential expression of IgG Fc receptors (FcγRs) in chronic HBV-infected patients and immune cells during different stages of HBV infection was investigated. Toll-like receptor (TLR) signalling pathway (including TLR6) and leucocyte transendothelial migration pathway (including integrin subunit beta 1) were enriched during acute infection. Key DEGs, such as FcγR Ib and FcγR Ia, and interferon-alpha inducible protein 27 showed correlation with alanine aminotransferase levels, and they were differentially expressed between acute and immune-tolerant phases and between immune-tolerant and immune-clearance phases. The integrative analysis of DNA methylation profile showed that lowly methylated and highly expressed genes, including cytotoxic T lymphocyte-associated protein 4 and mitogen-activated protein kinase 3 were enriched in T cell receptor signalling pathway during acute infection. Highly methylated and lowly expressed genes, such as Ras association domain family member 1 and cyclin-dependent kinase inhibitor 2A were identified in chronic infection. Furthermore, differentially expressed FcγR Ia, FcγR IIa and FcγR IIb, CD3- CD56+ CD16+ natural killer cells and CD14high CD16+ monocytes were identified between immune-tolerant and immune-clearance phases by experimental validation. The above genes and pathways may be used to distinguish different immune statuses of HBV infection.