Ribosome-rescuer PELO catalyzes the oligomeric assembly of NOD-like receptor family proteins via activating their ATPase enzymatic activity

Machine Learning and Experiments Revealed Key Genes Related to PANoptosis Linked to Drug Prediction and Immune Landscape in Spinal Cord Injury

Spinal cord injury (SCI) is a severe central nervous system injury without effective therapies. PANoptosis is involved in the development of many diseases, including brain and spinal cord injuries. However, the biological functions and molecular mechanisms of PANoptosis-related genes in spinal cord injury remain unclear. In the bioinformatics analysis of public data of SCI, the differentially expressed genes (DEGs) identified by GSE151371 were hybridized with PANoptosis-related genes (PRGs) to obtain differentially expressed PANoptosis-related genes (DE-PRGs). Through three machine learning algorithms, we obtained the hub genes. Then, we constructed functional analysis, drug prediction, regulatory network construction, and immune infiltrating cell analysis. Finally, the expression of the hub gene was verified in GSE93561, GSE45376, and qRT-PCR analysis. Through the above analysis, 14 DE-PRGs were obtained by intersecting 3582 DEGs with 46 PRGs. Five key hub genes, CASP4, GSDMB, NAIP, NLRC4, and NLRP3, were obtained by 3 machine learning algorithms. All five hub genes were enriched in phagocytosis mediated by FC GAMMA R. The 11 immune cells were significantly different between spinal cord injury (SCI) group and human control (HC) group, such as mast cell and gamma delta T cell. The transcription factor (TF)-hub gene network contained 10-nodes (4 hub genes and 6 TFs) and 8-edges. The miRNA-hub gene network consisting of 5-nodes (3 hub genes and 2 miRNAs) and 3-edges was constructed. Moreover, the CASP4 predicted 1 small molecule drug and NLRP3 predicted 9 small molecule drugs. Finally, the expression of 5 hub genes were significantly different in GSE45376 and GSE93561 (SCI vs. HC) and mice SCI model (Sham vs. SCI). Collectively, we identified 5 hub genes (CASP4, GSDMB, NAIP, NLRC4, and NLRP3) associated with PANoptosis, providing potential directions for treating spinal cord injury.

A novel method for achieving ecological indicator based on vertical soil bacterial communities coupled with machine learning: A case study of a typical tropical site in China

Global industrialization has resulted in severe contamination of soil with heavy metals (HMs). Nevertheless, it is unclear if it affects the depth-resolved bacterial communities. Herein, we collected soil samples at different depths from a typical HM-contaminated site and used amplicon sequencing to determine the differences in depth-resolved bacterial communities and to assess the thresholds and ecological impacts of HMs. Results revealed that HM levels reduced markedly with soil depth. The bacteria in upper soil exhibited higher community diversity and a more complex and stable ecological network structure. As depth increased, the proportion of negative interactions gradually elevated, indicating more competitive interspecies behavior. Threshold analyses based on machine learning revealed that arsenic (As) and copper (Cu) exhibited nonlinear impacts on ecosystems. Cu demonstrated a low-threshold effect, with its ecological consequences manifested at extremely low concentrations. Our results highlighted the utility of microbial monitoring in assessing the adverse effects of HMs on soil health to support environmental management and ecological restoration.

Genetic analysis reveals the shared genetic architecture between breast cancer and atrial fibrillation

Background

Epidemiological studies have observed an association between atrial fibrillation (AF) and breast cancer (BC). However, the underlying mechanisms linking these two conditions remain unclear. This study aims to systematically explore the genetic association between AF and BC.

Methods

We utilized the largest available genome-wide association study (GWAS) datasets for European individuals, including summary data for AF (N = 1,030,836) and BC (N = 247,173). Multiple approaches were employed to systematically investigate the genetic relationship between AF and BC from the perspectives of pleiotropy and causality.

Results

Global genetic analysis using LDSC and HDL revealed a genetic correlation between AF and BC (rg = 0.0435, P = 0.039). Mixer predicted genetic overlap between non-MHC regions of the two conditions (n = 125, rg = 0.05). Local genetic analyses using LAVA and GWAS-PW identified 22 regions with potential genetic sharing. Cross-trait meta-analysis by CPASSOC identified one novel pleiotropic SNP and 14 pleiotropic SNPs, which were subsequently annotated. Eight of these SNPs passed Bayesian colocalization tests, including one novel pleiotropic SNP. Further fine-mapping analysis identified a set of causal SNPs for each significant SNP. TWAS analyses using JTI and FOCUS models jointly identified 10 pleiotropic genes. Phenome-wide association study (PheWAS) of novel pleiotropic SNPs identified two eQTLs (PELO, ITGA1). Gene-based PheWAS results showed strong associations with BMI, height, and educational attainment. PCGA methods combining GTEx V8 tissue data and single-cell RNA data identified 16 co-enriched tissue types (including cardiovascular, reproductive, and digestive systems) and 5 cell types (including macrophages and smooth muscle cells). Finally, univariable and multivariable bidirectional Mendelian randomization analyses excluded a causal relationship between AF and BC.

Conclusion

This study systematically investigated the shared genetic overlap between AF and BC. Several pleiotropic SNPs and genes were identified, and co-enriched tissue and cell types were revealed. The findings highlight common mechanisms from a genetic perspective rather than a causal relationship. This study provides new insights into the AF-BC association and suggests potential experimental targets and directions for future research. Additionally, the results underscore the importance of monitoring the potential risk of one disease in patients diagnosed with the other.

Evolution of Biological Hydroxyapatite Modification Strategy: Anti-Inflammation Approach Rescues the Calcium-NOD-Like Receptor-Inflammation Axis-Mediated Periodontal Redevelopment Failure

Periodontal regenerative medicine is currently undergoing a paradigm shift from dissecting the healing process toward utilization of the developmental program. Biological hydroxyapatite (BHA), a major component of guided tissue regeneration, has long been optimized for inducing multidirectional differentiation of periodontal ligament cells (PDLCs). However, this approach runs counter to the redevelopment strategy. Thus, the conventional BHA should evolve to induce the redevelopment process of periodontal tissue. In this study, histopathological changes and immune microenvironment characteristics of the periodontal developmental process, natural healing process (Blank group), and BHA-mediated healing process (BHA group) were compared to evaluate the main manifestations of BHA-mediated periodontal "developmental engineering" outcome. Our results suggested that neither the Blank nor BHA group could recur key events in periodontal development. The implantation of BHA led to pro-inflammatory immune microenvironment and an unstable blood fibrin clot structure, which facilitated the invasion of outer gingival fibroblasts, consequently disrupting redevelopmental events. High-throughput chip technology was further used to explore the underlying mechanism of immune activation, revealing that the calcium-NOD-like receptor-inflammation axis signaling axis promoted the activation of pro-inflammatory immune response that contributed to redevelopment failure. An immunomodulatory cytokine interleukin 4 (IL4)-modified BHA was used to further validate the efficacy of developmental engineering strategy. IL4 could partially rescued the redevelopment failure through immunosuppression. This study presented an innovative strategy for the development of advanced periodontal regenerative materials and offered a potential approach for the application of development-inspired periodontal tissue engineering strategies. It represented a marked advancement in the development of regenerative medicine and propelled the clinical organ restoration forward.

PRRSV-2 nsp2 Ignites NLRP3 inflammasome through IKKβ-dependent dispersed trans-Golgi network translocation

The NLRP3 inflammasome is a fundamental component of the innate immune system, yet its excessive activation is intricately associated with viral pathogenesis. Porcine reproductive and respiratory syndrome virus type 2 (PRRSV-2), belonging to the family Arteriviridae, triggers dysregulated cytokine release and interstitial pneumonia, which can quickly escalate to acute respiratory distress and death. However, a mechanistic understanding of PRRSV-2 progression remains unclear. Here, we screen that PRRSV-2 nsp2 activates the NLRP3 inflammasome, thereby instigating a state of hyperinflammation. Mechanistically, PRRSV-2 nsp2 interacts with the nucleotide-binding and oligomerization (NACHT) domain of NLRP3, augmenting IKKβ recruitment to driving NLRP3 translocation to the dispersed trans-Golgi network (dTGN) for oligomerization. This process facilitates ASC polymerization, culminating in the activation of the NLRP3 inflammasome. In addition, the IKKβ-dependent NLRP3 translocation to the dTGN is pivotal for pseudorabies virus (PRV) and encephalomyocarditis virus (EMCV)-induced inflammatory responses. Collectively, these results elucidate a novel mechanism of NLRP3 inflammasome activation during PRRSV-2 infection, providing valuable insights into PRRSV-2 pathogenesis.

Knowledge mapping of trained immunity/innate immune memory: Insights from two decades of studies

This study employs knowledge mapping and bibliometric techniques to analyze the research landscape of trained immunity over the past 20 years and to identify current research hotspots and future development directions. The literature related to trained immunity was searched from the Web of Science Core Collection database, spanning 2004 to 2023. VOSViewer, CiteSpace and Bibliometrix were used for the knowledge mapping analysis. The foremost research institutions are Radboud University Nijmegen, University of Bonn, and Harvard University. Professor Netea MG of Radboud University Nijmegen has published the greatest number of articles. The current research focus encompasses immune memory, nonspecific effects, epigenetics, metabolic reprogramming, BCG vaccine, and the development of trained immunity-based vaccines. It is likely that research on trained immunity-based vaccines will become a major focus in the development of new vaccines in the future. It would be advantageous to observe a greater number of prospective clinical studies with robust evidence.

Protection against DSS-induced colitis in mice through FcεRIα deficiency: the role of altered Lactobacillus

The role of mast cells (MCs) in ulcerative colitis (UC) development is controversial. FcεRI, the IgE high-affinity receptor, is known to activate MCs. However, its role in UC remains unclear. In our study, Anti-FcεRI showed highly diagnostic value for UC. FcεRIα knockout in mice ameliorated DSS-induced colitis in a gut microbiota-dependent manner. Increased Lactobacillus abundance in FcεRIα deficient mice showed strongly correlation with the remission of colitis. RNA sequencing indicated activation of the NLRP6 inflammasome pathway in FcεRIα knockout mice. Additionally, Lactobacillus plantarum supplementation protected against inflammatory injury and goblet cell loss, with activation of the NLRP6 inflammasome during colitis. Notably, this effect was absent when the strain is unable to produce lactic acid. In summary, colitis was mitigated in FcεRIα deficient mice, which may be attributed to the increased abundance of Lactobacillus. These findings contribute to a better understanding of the relationship between allergic reactions, microbiota, and colitis.

NOD1 and NOD2: Essential Monitoring Partners in the Innate Immune System

Nucleotide-binding oligomerization domain containing 1 (NOD1) and NOD2 are pivotal cytoplasmic pattern-recognition receptors (PRRs) that exhibit remarkable evolutionary conservation. They possess the ability to discern specific peptidoglycan (PGN) motifs, thereby orchestrating innate immunity and contributing significantly to immune homeostasis maintenance. The comprehensive understanding of both the structure and function of NOD1 and NOD2 has been extensively elucidated. These receptors proficiently recognize an array of damage-associated molecular patterns (DAMPs) as well as pathogen-associated molecular patterns (PAMPs), subsequently mediating inflammatory responses and autophagy. In recent years, emerging evidence has highlighted the crucial roles played by NOD1 and NOD2 in regulating infectious diseases, metabolic disorders, cancer, and autoimmune conditions, among others. Perturbation in either their loss or excessive activation can detrimentally impact immune homeostasis. This review offers a comprehensive overview of the structural characteristics, subcellular localization, activation mechanisms, and significant roles of NOD1 and NOD2 in innate immunity and related disease.

Insect ribosome-rescuer Pelo-Hbs1 complex on sperm surface mediates paternal arbovirus transmission

Arboviruses can be paternally transmitted by male insects to offspring for long-term persistence, but the mechanism remains largely unknown. Here, we use a model system of a destructive rice reovirus and its leafhopper vector to find that insect ribosome-rescuer Pelo-Hbs1 complex expressed on the sperm surface mediates paternal arbovirus transmission. This occurs through targeting virus-containing tubules constituted by viral nonstructural protein Pns11 to sperm surface via Pns11-Pelo interaction. Tubule assembly is dependent on Hsp70 activity, while Pelo-Hbs1 complex inhibits tubule assembly via suppressing Hsp70 activity. However, virus-activated ubiquitin ligase E3 mediates Pelo ubiquitinated degradation, synergistically causing Hbs1 degradation. Importantly, Pns11 effectively competes with Pelo for binding to E3, thus antagonizing E3-mediated Pelo-Hbs1 degradation. These processes cause a slight reduction of Pelo-Hbs1 complex in infected testes, promoting effective tubule assembly. Our findings provide insight into how insect sperm-specific Pelo-Hbs1 complex is modulated to promote paternal virus transmission without disrupting sperm function.

ZAP facilitates NLRP3 inflammasome activation via promoting the oligomerization of NLRP3

The NOD-like receptor family protein 3 (NLRP3) inflammasome is a crucial complex for the host to establish inflammatory immune responses and plays vital roles in a series of disorders, including Alzheimer's disease and acute peritonitis. However, its regulatory mechanism remains largely unclear. Zinc finger antiviral protein (ZAP), also known as zinc finger CCCH-type antiviral protein 1 (ZC3HAV1), promotes viral RNA degradation and plays vital roles in host antiviral immune responses. However, the role of ZAP in inflammation, especially in NLRP3 activation, is unclear. Here, we show that ZAP interacts with NLRP3 and promotes NLRP3 oligomerization, thus facilitating NLRP3 inflammasome activation in peritoneal macrophages of C57BL/6 mice. The shorter isoform of ZAP (ZAPS) appears to play a greater role than the full-length isoform (ZAPL) in HEK293T cells. Congruously, Zap-deficient C57BL/6 mice may be less susceptible to alum-induced peritonitis and lipopolysaccharide-induced sepsis in vivo. Therefore, we propose that ZAP is a positive regulator of NLRP3 activation and a potential therapeutic target for NLRP3-related inflammatory disorders.

Acetylation is required for full activation of the NLRP3 inflammasome

Full activation of the NLRP3 inflammasome needs two sequential signals: a priming signal, followed by a second, assembly signal. Several studies have shown that the two signals trigger post-translational modification (PTM) of NLRP3, affecting activity of the inflammasome, however, the PTMs induced by the second signal are less well characterized. Here, we show that the assembly signal involves acetylation of NLRP3 at lysine 24, which is important for the oligomerization and the actual assembly of NLRP3 without affecting its recruitment to dispersed trans-Golgi network (dTGN). Accordingly, NLRP3 inflammasome activation is impaired in NLRP3-K24R knock-in mice. We identify KAT5 as an acetyltransferase able to acetylate NLRP3. KAT5 deficiency in myeloid cells and pharmacological inhibition of KAT5 enzymatic activity reduce activation of the NLRP3 inflammasome, both in vitro and in vivo. Thus, our study reveals a key mechanism for the oligomerization and full activation of NLRP3 and lays down the proof of principle for therapeutic targeting of the KAT5-NLRP3 axis.

Protocol for reconstitution of oligomeric assembly of NAIP5-NLRC4 inflammasome in vitro

Inflammasomes are multimeric protein complexes that have crucial functions in innate immunity. Here, we present a protocol to reconstitute the PELO-driven assembly of NAIP5-NLRC4 inflammasome in vitro. We describe steps for expression and purification of recombinant PELO and flagellin, preparation of native cell lysate containing NAIP5-NLRC4, and in vitro assembly of NAIP5-NLRC4 inflammasome. We then detail analysis of NAIP5-NLRC4 inflammasome by blue native polyacrylamide gel electrophoresis and immunoblotting. This protocol can be adapted to monitor the oligomeric assembly of other inflammasome types. For complete details on the use and execution of this protocol, please refer to Wu et al. (2023).1.