Immune Signaling Network Research Articles

Transcriptomic and Proteomic Insights into Host Immune Responses in Pediatric Severe Malarial Anemia: Dysregulation in HSP60-70-TLR2/4 Signaling and Altered Glutamine Metabolism.

Severe malarial anemia (SMA, Hb < 6.0 g/dL) is a leading cause of childhood morbidity and mortality in holoendemic Plasmodium falciparum transmission zones. This study explored the entire expressed human transcriptome in whole blood from 66 Kenyan children with non-SMA (Hb ≥ 6.0 g/dL, n = 41) and SMA (n = 25), focusing on host immune response networks. RNA-seq analysis revealed 6862 differentially expressed genes, with equally distributed up-and down-regulated genes, indicating a complex host immune response. Deconvolution analyses uncovered leukocytic immune profiles indicative of a diminished antigenic response, reduced immune priming, and polarization toward cellular repair in SMA. Weighted gene co-expression network analysis revealed that immune-regulated processes are central molecular distinctions between non-SMA and SMA. A top dysregulated immune response signaling network in SMA was the HSP60-HSP70-TLR2/4 signaling pathway, indicating altered pathogen recognition, innate immune activation, stress responses, and antigen recognition. Validation with high-throughput gene expression from a separate cohort of Kenyan children (n = 50) with varying severities of malarial anemia (n = 38 non-SMA and n = 12 SMA) confirmed the RNA-seq findings. Proteomic analyses in 35 children with matched transcript and protein abundance (n = 19 non-SMA and n = 16 SMA) confirmed dysregulation in the HSP60-HSP70-TLR2/4 signaling pathway. Additionally, glutamine transporter and glutamine synthetase genes were differentially expressed, indicating altered glutamine metabolism in SMA. This comprehensive analysis underscores complex immune dysregulation and novel pathogenic features in SMA.

The role of uncertainty and negative feedback loops in the evolution of induced immune defenses.

Organisms use constitutive or induced defenses against pathogens and other external threats. Constitutive defenses are constantly on, whereas induced defenses are activated when needed. Each of these strategies has costs and benefits, which can affect the type of defense that evolves in response to pathogens. In addition, induced defenses are usually regulated by multiple negative feedback mechanisms that prevent overactivation of the immune response. However, it is unclear how negative feedback affects the costs, benefits, and evolution of induced responses. To address this gap, we developed a mechanistic model of the well-characterized Drosophila melanogaster immune signaling network that includes 3 separate mechanisms of negative feedback as a representative of the widespread phenomenon of multilevel regulation of induced responses. We show that, under stochastic fly-bacteria encounters, an induced defense is favored when bacterial encounters are rare or uncertain, but in ways that depend on the bacterial proliferation rate. Our model also predicts that the specific negative regulators that optimize the induced response depend on the bacterial proliferation rate, linking negative feedback mechanisms to the factors that favor induction.

Pleiotropy alleviates the fitness costs associated with resource allocation trade-offs in immune signalling networks.

Many genes and signalling pathways within plant and animal taxa drive the expression of multiple organismal traits. This form of genetic pleiotropy instigates trade-offs among life-history traits if a mutation in the pleiotropic gene improves the fitness contribution of one trait at the expense of another. Whether or not pleiotropy gives rise to conflict among traits, however, likely depends on the resource costs and timing of trait deployment during organismal development. To investigate factors that could influence the evolutionary maintenance of pleiotropy in gene networks, we developed an agent-based model of co-evolution between parasites and hosts. Hosts comprise signalling networks that must faithfully complete a developmental programme while also defending against parasites, and trait signalling networks could be independent or share a pleiotropic component as they evolved to improve host fitness. We found that hosts with independent developmental and immune networks were significantly more fit than hosts with pleiotropic networks when traits were deployed asynchronously during development. When host genotypes directly competed against each other, however, pleiotropic hosts were victorious regardless of trait synchrony because the pleiotropic networks were more robust to parasite manipulation, potentially explaining the abundance of pleiotropy in immune systems despite its contribution to life history trade-offs.

The involvement of RIPK4 in TNF-α-stimulated IL-6 and IL-8 production by melanoma cells

PurposeThe receptor-interacting protein kinase (RIPK4) has an oncogenic function in melanoma, regulates NF-κB and Wnt/β-catenin pathways, and is sensitive to the BRAF inhibitors: vemurafenib and dabrafenib which lead to its decreased level. As its role in melanoma remains not fully understood, we examined the effects of its downregulation on the transcriptomic profile of melanoma.MethodsApplying RNA-seq, we revealed global alterations in the transcriptome of WM266.4 cells with RIPK4 silencing. Functional partners of RIPK4 were evaluated using STRING and GeneMANIA databases. Cells with transient knockdown (via siRNA) and stable knockout (via CRISPR/Cas9) of RIPK4 were stimulated with TNF-α. The expression levels of selected proteins were assessed using Western blot, ELISA, and qPCR.ResultsGlobal analysis of gene expression changes indicates a complex role for RIPK4 in regulating adhesion, migration, proliferation, and inflammatory processes in melanoma cells. Our study highlights potential functional partners of RIPK4 such as BIRC3, TNF-α receptors, and MAP2K6. Data from RIPK4 knockout cells suggest a putative role for RIPK4 in modulating TNF-α-induced production of IL-8 and IL-6 through two distinct signaling pathways—BIRC3/NF-κB and p38/MAPK. Furthermore, increased serum TNF-α levels and the correlation of RIPK4 with NF-κB were revealed in melanoma patients.ConclusionThese data reveal a complex role for RIPK4 in regulating the immune signaling network in melanoma cells and suggest that this kinase may represent an alternative target for melanoma-targeted adjuvant therapy.

Abstract 2546: Identifying co-mutational signatures in STK11 mutated advanced non-small cell lung cancer (aNSCLC) patients that help overcome poor response to immune checkpoint inhibitors (ICI’s)

Abstract Background: ICIs, either alone or in combination with chemotherapy, have become the primary treatment options for aNSCLC patients without any targetable mutations. However, not all patients benefit similarly from these therapies even after selection based on the currently approved biomarker PD-L1 expression. Previous studies have shown that mutations in certain genes like STK11 and KEAP1 may predict non-response to these therapies. Mutations in STK11 occur in 25-30% of aNSCLC patients. We have used a real-world clinico-genomics dataset to investigate how this STK11+ aNSCLC patient population responds to ICIs in the context of other underlying co-mutations and whether some beneficial co-mutations may help patients overcome resistance due to their STK11 status. Methods: The ConcertAI Genome360TM NSCLC dataset (N=14193) was used in this retrospective study. aNSCLC patients who tested positive for STK11 mutations and received ICIs were considered (N=377). Based on their response to ICIs, the patients were divided into responder (N= 192) and non-responder (N=185) cohorts. Other genes with pathogenic mutations, fusions, and copy number changes were identified in both cohorts, and enrichment analysis was performed to identify co-mutations significantly enriched in one cohort vs the other. Once significant co-mutations were identified, pathway analysis was performed, taking into account the immune signaling network to help rationalise and validate the results. Results: One potential mechanism by which STK11 mutations influence the response to ICIs is through downregulation of the cGas-Sting pathway, which has been shown to play an important role in ICI response. Our co-mutational analysis also strongly supported this theory. We found that additional mutations that can nullify the effect of STK11 mutations on the cGas-Sting pathway led to a positive response (p=0.002) within the STK11+ cohort. Two such co-mutational signatures in responder patients identified were co-mutations in STK11/SMARCA4/TP53 (no KEAP1) (p-value = 0.003) and SKT11/KRAS/RBM10 (p-value = 0.04). Additionally, co-mutations in the DNA damage pathway genes (ATM, BRCA1, BRIP1, PALB2, STAG2) (p-value = 0.001) were also predictive of response to ICIs in the STK11+ cohort. Conclusion: By leveraging a real-world clinico-genomics dataset linking the tumor genomic profiles with patient response to ICIs, we have been able to perform a comprehensive co-mutational analysis of STK11+ aNSCLC patients to tease out the interplay of various biomarkers and signaling pathways that determine response to ICIs. Even though 25-30% aNSCLC patients are STK11+, we find that ~23% of these patients could still benefit from ICI treatment due to the presence of other co-mutations. Citation Format: Neeraj Singh, Smita Agrawal. Identifying co-mutational signatures in STK11 mutated advanced non-small cell lung cancer (aNSCLC) patients that help overcome poor response to immune checkpoint inhibitors (ICI’s) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2546.

Decomposition of dynamic transcriptomic responses during effector-triggered immunity reveals conserved responses in two distinct plant cell populations

Rapid plant immune responses in the appropriate cells are needed for effective defense against pathogens. Although transcriptome analysis is often used to describe overall immune responses, collection of transcriptome data with sufficient resolution in both space and time is challenging. We reanalyzed public Arabidopsis time-course transcriptome data obtained after low-dose inoculation with a Pseudomonas syringae strain expressing the effector AvrRpt2, which induces effector-triggered immunity in Arabidopsis. Double-peak time-course patterns are prevalent among thousands of upregulated genes. We implemented a multi-compartment modeling approach to decompose the double-peak pattern into two single-peak patterns for each gene. The decomposed peaks reveal an “echoing” pattern: the peak times of the first and second peaks correlate well across most upregulated genes. We demonstrated that the two peaks likely represent responses of two distinct cell populations that respond either cell autonomously or indirectly to AvrRpt2. Thus, the peak decomposition has extracted spatial information from the time-course data. The echoing pattern also indicates a conserved transcriptome response with different initiation times between the two cell populations despite different elicitor types. A gene set highly overlapping with the conserved gene set is also upregulated with similar kinetics during pattern-triggered immunity. Activation of a WRKY network via different entry-point WRKYs can explain the similar but not identical transcriptome responses elicited by different elicitor types. We discuss potential benefits of the properties of the WRKY activation network as an immune signaling network in light of pressure from rapidly evolving pathogens.

Mapping the functional form of the trade-off between infection resistance and reproductive fitness under dysregulated immune signaling.

Immune responses benefit organismal fitness by clearing parasites but also exact costs associated with immunopathology and energetic investment. Hosts manage these costs by tightly regulating the induction of immune signaling to curtail excessive responses and restore homeostasis. Despite the theoretical importance of turning off the immune response to mitigate these costs, experimentally connecting variation in the negative regulation of immune responses to organismal fitness remains a frontier in evolutionary immunology. In this study, we used a dose-response approach to manipulate the RNAi-mediated knockdown efficiency of cactus (IκBα), a central regulator of Toll pathway signal transduction in flour beetles (Tribolium castaneum). By titrating cactus activity across four distinct levels, we derived the shape of the relationship between immune response investment and traits associated with host fitness, including infection susceptibility, lifespan, fecundity, body mass, and gut homeostasis. Cactus knock-down increased the overall magnitude of inducible immune responses and delayed their resolution in a dsRNA dose-dependent manner, promoting survival and resistance following bacterial infection. However, these benefits were counterbalanced by dsRNA dose-dependent costs to lifespan, fecundity, body mass, and gut integrity. Our results allowed us to move beyond the qualitative identification of a trade-off between immune investment and fitness to actually derive its functional form. This approach paves the way to quantitatively compare the evolution and impact of distinct regulatory elements on life-history trade-offs and fitness, filling a crucial gap in our conceptual and theoretical models of immune signaling network evolution and the maintenance of natural variation in immune systems.

Functional dissection of the PME and PMEI super families in the protection of Populus pectin during Fusarium wilt

Integration of the pectin homogalacturonan (HG) integrity and remodeling into defense immunity facilitates building blocks of stress resilience within the host and pathogen interactions in the forests. Recent advances in apoplastic pectin methylesterases (PMEs) and coordinated PME inhibitors (PMEIs) deployed immune signaling, highlighting their critical roles in regulating biotic stress adaptation. Nevertheless, the PME and PMEI multiple isoenzyme families involved in defense priming in the model tree species are largely unknown. The in silico demonstration of the molecular profile identified 70 PME- (50 type-I proPME and 20 type-II PME) and 49 PMEI-encoding genes in the Populus genome. Evaluation of the transcript abundance verified 20 PtproPMEs and 18 PtPMEIs that showed predominant expression in the root and genetic redundancy for type-II PtPMEs. Dynamic changes in the transcriptome and experimental evaluation revealed a minuscule number of type-I proPMEs and PMEIs that showed marked promotions during a time-course Fusarium solani (Fs) infection. Using GC/LC-mass-based non-targeted metabolomics to inspect structure-related carbohydrates and PME activities suggested a correlation between proPME-PMEI co-expression and deformed pectin HG biosynthesis. Further functional examination of the enzyme inhibitory affinities of recombinant PtPMEI1 and 39 in vitro and apoplastic patterns suggested a clustering of the type-I proPME in the regulation of the innate immunity by maintaining homeostasis of the pectin HG de-methylesterification (DME) in the cell wall. The coherent omics-wide survey of the fungi pathogen-induced PME-PMEIs and disturbed carbohydrate accumulation provide theoretical cues for in-depth mining of the biological significance of the underlying immune signaling networks within an apoplastic niche in trees.

Abstract 15922: Integrative Analysis of Extracellular Vesicles in Heart Transplant Rejection: From Biomarker Discovery to Novel Immune Mechanisms

Introduction: At the forefront of post-heart transplant care is early detection of transplant rejection. However, the current gold standard for detecting acute cellular transplant rejection is recurrent invasive endomyocardial biopsies (EMB). We aimed at developing a non-invasive biomarker for acute cellular heart transplant rejection (ACR) using a plasma extracellular vesicle (EV) platform. Methods: Peripheral and coronary sinus plasma samples were prospectively collected from 183 (31.7% female) patients from 2020 to 2023 during routine surveillance EMB. A discovery cohort comprised five patients who displayed ISHLT 0-1R biopsy followed by an ISHLT 2R grade rejection event. Plasma EVs were isolated from the baseline (0-1R) and rejection (2R) time points. Subsequently, integrative analysis of plasma EV proteomic, miRNomic, and metabolomics was performed pairwise with the samples. Results: The study collected 943 sample time points from 183 patients. Of these sample collections, 43 (4.5%) cases were 2R rejections. Our proteomic analysis of the plasma EVs identified 28 proteins found explicitly during a grade 2R rejection and 87 differentially expressed proteins during a 2R rejection event. An Ingenuity Pathway Analysis (IPA) analysis of the upregulated proteins highlighted EVs mediated mTOR signaling and antigen presentation as central to rejection events. Although all patients in the discovery cohort were negative for antibody-mediated rejection (AMR), the proteomic findings also revealed increased B-cell receptor signaling, implying a mechanistic intersection of ACR and AMR. Conclusions: A distinct set of proteins were found in plasma EVs during ACR events, providing potentially specific and sensitive biomarkers to reduce the need for EMB that could be exploited for ACR diagnosis. The proteins identified formed an immune signaling network that suggests a novel role for EVs in ACR pathogenesis.

Genomic Determinants of Hematopoietic Progenitor Sensitivity to Innate Immune Signaling

Innate immune processes impact diverse hematopoietic stem and progenitor cell (HSPC) functions, yet how innate immune signaling networks are sensed by HSPC genomes and how HSPC genomic activity alters cell responsiveness to innate immune regulators are not fully understood. We demonstrated that E14.5 primary (-77 -/-) and immortalized (hi-77 -/-) GATA2-deficient fetal progenitors from Gata2 -77 enhancer deletion mice upregulate Interferon-gamma (IFNγ) and Toll-like receptor (TLR) signaling components (Johnson et al. JEM 2020) and are hypersensitive to IFNγ and TLR signaling (Tran et al. iScience 2023). Combinatorial signaling involving both pathways regulates genes that are not regulated by individual pathways and amplifies responses beyond that induced by single pathways. Innate immune-activated genes harbor motifs for signal-dependent transcription factors, including the ETS factor PU.1, and GATA2 deficiency elevates PU.1 activity to upregulate B-lineage and myeloid genes (Jung et al. JCI 2023). We hypothesize that PU.1 links innate immune signaling networks and HSPC genome control. In new multi-omic studies, we asked if PU.1 is required to sense exclusively IFNγ or TLR signaling, both pathways independently or combinatorially, or is not essential. We used hi-77 -/- progenitors lacking a PU.1 enhancer ( Spi1URE-/-) with ~2-fold lower PU.1 vs. control hi-77 -/- progenitors. RNA-seq was conducted with hi-77 -/- and hi-77 -/-; Spi1URE-/- progenitors, with or without IFNγ, TLR1/2 agonist Pam 3CSK 4, or both agents for 4 h. hi-77 -/-; Spi1URE-/- progenitors lost the responsiveness of 27 TLR-activated genes and retained the responsiveness of 6 TLR-activated genes. 80% of IFNγ-activated genes (115 of 144) retained IFNγ-responsiveness when PU.1 was reduced. In hi-77 -/-; Spi1URE-/- progenitors, 68.2% (148 of 217 genes) retained their responsiveness to combinatorial signaling. These studies revealed the disproportionate importance of PU.1 for TLR- vs. IFNγ-mediated transcriptional control and a PU.1 requirement for combinatorial signaling at the majority of loci. Elevated IFNγ and TLR1/2 signaling in GATA2-deficient fetal progenitors is associated with increased monocytic and reduced granulocytic progenitors (Johnson et al. JEM 2020; Blood Adv 2022). Ablation of Irf8, encoding an IFNγ pathway component, partially normalizes the granulocytic progenitor deficit (Johnson et al. Blood Adv. 2022). Since GATA2 deficiency creates crosstalk between IFNγ and TLR1/2 pathways to elevate cytokine/chemokine production (Tran et al . iScience 2023), we asked if attenuating TLR signaling reverses the differentiation defect. As MYD88 Innate Immune Signal Transduction Adaptor (MYD88) is crucial for TLR1/2 signaling, we generated -77 +/-; Myd88-/- mice. Timed matings were conducted to obtain -77 +/+, -77 -/-, Myd88-/-, and -77 -/-; Myd88-/- E14.5 embryos. Myd88 ablation in -77 -/- embryos did not reverse the skewed granulocytic vs. monocytic progenitor ratio. To determine if MYD88 loss impacts -77 -/- progenitor function, we analyzed CMP and GMP populations from E14.5 embryos with CFU assays. In comparison with -77 +/+, -77 -/- CMP and Myd88-/- CMP produced fewer CFU-G colonies (1.9-fold decrease, P = 0.0097 and 2.0-fold decrease, P = 0.007, respectively). Surprisingly, -77 -/-; Myd88-/- CMP exhibited a further reduction in CFU-G colonies (5.2-fold decrease, P &amp;lt; 0.0001). The CFU-G colonies produced by -77 +/-; Myd88-/- CMP resembled that of -77 +/+ CMP. Thus, GATA2 and MYD88 synergistically promote CFU-G production from CMP, and a single -77 allele maintains CMP activity to produce CFU-G without Myd88. Myd88 deletion did not affect the reduced CFU-G nor the increased CFU-M with -77 -/- GMP. We are testing if TLR1/2 signaling is not required to maintain balanced fetal liver progenitor populations or if another signaling adapter nullifies the impact of MYD88 loss. Our studies revealed a mechanism underlying the hypersensitivity of GATA2-deficient fetal progenitors to innate immune signaling, and MYD88 loss further decreases the reduced CFU-G generated from -77 -/- CMP. We are testing the hypothesis that GATA2 restricts assembly of PU.1-containing chromatin complexes and analyzing models to unveil functional ramifications of elevated innate immune signaling in single HSPCs.

Ubiquitination and cell-autonomous immunity.

Cell-autonomous immunity is the first line of defense by which cells recognize and contribute to eliminating invasive pathogens. It is composed of immune signaling networks that sense microbial pathogens, promote pathogen restriction, and stimulate their elimination, including host cell death. Ubiquitination is a pivotal orchestrator of these pathways, by changing the activity of signal transducers and effector proteins in an efficient way. In this review, we will focus on how ubiquitin connects the pathways that sense pathogens to the cellular responses to invaders and shed light on how ubiquitination impacts the microenvironment around the infected cell, stimulating the appropriate immune response. Finally, we discuss therapeutic options directed at favoring cell-autonomous immune responses to infection.

Pleiotropy promotes the evolution of inducible immune responses in a model of host-pathogen coevolution.

Components of immune systems face significant selective pressure to efficiently use organismal resources, mitigate infection, and resist parasitic manipulation. A theoretically optimal immune defense balances investment in constitutive and inducible immune components depending on the kinds of parasites encountered, but genetic and dynamic constraints can force deviation away from theoretical optima. One such potential constraint is pleiotropy, the phenomenon where a single gene affects multiple phenotypes. Although pleiotropy can prevent or dramatically slow adaptive evolution, it is prevalent in the signaling networks that compose metazoan immune systems. We hypothesized that pleiotropy is maintained in immune signaling networks despite slowed adaptive evolution because it provides some other advantage, such as forcing network evolution to compensate in ways that increase host fitness during infection. To study the effects of pleiotropy on the evolution of immune signaling networks, we used an agent-based modeling approach to evolve a population of host immune systems infected by simultaneously co-evolving parasites. Four kinds of pleiotropic restrictions on evolvability were incorporated into the networks, and their evolutionary outcomes were compared to, and competed against, non-pleiotropic networks. As the networks evolved, we tracked several metrics of immune network complexity, relative investment in inducible and constitutive defenses, and features associated with the winners and losers of competitive simulations. Our results suggest non-pleiotropic networks evolve to deploy highly constitutive immune responses regardless of parasite prevalence, but some implementations of pleiotropy favor the evolution of highly inducible immunity. These inducible pleiotropic networks are no less fit than non-pleiotropic networks and can out-compete non-pleiotropic networks in competitive simulations. These provide a theoretical explanation for the prevalence of pleiotropic genes in immune systems and highlight a mechanism that could facilitate the evolution of inducible immune responses.

Single-cell RNA sequencing reveals the immune microenvironment and signaling networks in cystitis glandularis.

Cystitis glandularis (CG) is a rare chronic bladder hyperplastic disease that mainly manifests by recurrent frequent urination, dysuria and gross hematuria. The current lack of unified diagnosis and treatment criteria makes it essential to comprehensively describe the inflammatory immune environment in CG research. Here, we performed scRNA-sequencing in CG patients for the first time, in which four inflamed tissues as well as three surrounding normal bladder mucosa tissues were included. Specifically, we isolated 18,869 cells to conduct bioinformatic analysis and performed immunofluorescence experiments. Our genetic results demonstrate that CG does not have the classic chromosomal variation observed in bladder tumors, reveal the specific effects of TNF in KRT15 epithelial cells, and identify a new population of PIGR epithelial cells with high immunogenicity. In addition, we confirmed the activation difference of various kinds of T cells during chronic bladder inflammation and discovered a new group of CD27-Switch memory B cells expressing a variety of immunoglobulins. CG was regarded as a rare disease and its basic study is still weak.Our study reveals, for the first time, the different kinds of cell subgroups in CG and provides the necessary basis for the clinical treatment of cystitis glandularis. Besides, our study significantly advances the research on cystitis glandularis at the cellular level and provides a theoretical basis for the future treatment of cystitis glandularis.

Plant Disease Resistance-Related Signaling Pathways: Recent Progress and Future Prospects.

Plant-pathogen interactions induce a signal transmission series that stimulates the plant's host defense system against pathogens and this, in turn, leads to disease resistance responses. Plant innate immunity mainly includes two lines of the defense system, called pathogen-associated molecular pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). There is extensive signal exchange and recognition in the process of triggering the plant immune signaling network. Plant messenger signaling molecules, such as calcium ions, reactive oxygen species, and nitric oxide, and plant hormone signaling molecules, such as salicylic acid, jasmonic acid, and ethylene, play key roles in inducing plant defense responses. In addition, heterotrimeric G proteins, the mitogen-activated protein kinase cascade, and non-coding RNAs (ncRNAs) play important roles in regulating disease resistance and the defense signal transduction network. This paper summarizes the status and progress in plant disease resistance and disease resistance signal transduction pathway research in recent years; discusses the complexities of, and interactions among, defense signal pathways; and forecasts future research prospects to provide new ideas for the prevention and control of plant diseases.

TRAF trimers form immune signalling networks via RING domain dimerization.

For many inflammatory cytokines, the response elicited is dependent on the recruitment of the tumour necrosis factor receptor-associated factor (TRAF) family of adaptor proteins. All TRAF proteins have a trimeric C-terminal TRAF domain, while at the N-terminus most TRAFs have a RING domain that forms dimers. The symmetry mismatch of the N- and C-terminal halves of TRAF proteins means that when receptors cluster, it is presumed that RING dimers connect TRAF trimers to form a network. Here, using purified TRAF6 proteins, we provide direct evidence in support of this model, and we show that TRAF6 trimers bind Lys63-linked ubiquitin chains to promote their processive assembly. This study provides critical evidence in support of TRAF trimers as key players in signalling.

The Emerging Role of PP2C Phosphatases in Tomato Immunity.

The antagonistic effect of plant immunity on growth likely drove evolution of molecular mechanisms that prevent accidental initiation and prolonged activation of plant immune responses. Signaling networks of pattern-triggered and effector-triggered immunity, the two main layers of plant immunity, are tightly regulated by the activity of protein phosphatases that dephosphorylate their protein substrates and reverse the action of protein kinases. Members of the PP2C class of protein phosphatases have emerged as key negative regulators of plant immunity, primarily from research in the model plant Arabidopsis thaliana, revealing the potential to employ PP2C proteins to enhance plant disease resistance. As a first step towards focusing on the PP2C family for both basic and translational research, we analyzed the tomato genome sequence to ascertain the complement of the tomato PP2C family, identify conserved protein domains and signals in PP2C amino acid sequences, and examine domain combinations in individual proteins. We then identified tomato PP2Cs that are candidate regulators of single or multiple layers of the immune signaling network by in-depth analysis of publicly available RNA-seq datasets. These included expression profiles of plants treated with fungal or bacterial pathogen-associated molecular patterns, with pathogenic, nonpathogenic, and disarmed bacteria, as well as pathogenic fungi and oomycetes. Finally, we discuss the possible use of immunity-associated PP2Cs to better understand the signaling networks of plant immunity and to engineer durable and broad disease resistance in crop plants. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Integrated plasma proteomic and single-cell immune signaling network signatures demarcate mild, moderate, and severe COVID-19

SummaryThe biological determinants underlying the range of coronavirus 2019 (COVID-19) clinical manifestations are not fully understood. Here, over 1,400 plasma proteins and 2,600 single-cell immune features comprising cell phenotype, endogenous signaling activity, and signaling responses to inflammatory ligands are cross-sectionally assessed in peripheral blood from 97 patients with mild, moderate, and severe COVID-19 and 40 uninfected patients. Using an integrated computational approach to analyze the combined plasma and single-cell proteomic data, we identify and independently validate a multi-variate model classifying COVID-19 severity (multi-class area under the curve [AUC]training = 0.799, p = 4.2e-6; multi-class AUCvalidation = 0.773, p = 7.7e-6). Examination of informative model features reveals biological signatures of COVID-19 severity, including the dysregulation of JAK/STAT, MAPK/mTOR, and nuclear factor κB (NF-κB) immune signaling networks in addition to recapitulating known hallmarks of COVID-19. These results provide a set of early determinants of COVID-19 severity that may point to therapeutic targets for prevention and/or treatment of COVID-19 progression.

Regulation of Treg Cell Metabolism and Function in Non-Lymphoid Tissues.

Regulator T cells (Tregs) play pivotal roles in maintaining immune tolerance and regulating immune responses against pathogens and tumors. Reprogramming of cellular metabolism has been determined as a crucial process that connects microenvironmental cues and signaling networks to influence homeostasis and function of tissue Tregs. In adaptation to a variety of non-lymphoid tissues, Tregs coordinate local immune signals and signaling networks to rewire cellular metabolic programs to sustain their suppressive function. Altered Treg metabolism in turn shapes Treg activation and function. In light of the advanced understanding of immunometabolism, manipulation of systemic metabolites has been emerging as an attractive strategy aiming to modulate metabolism and function of tissue Tregs and improve the treatment of immune-related diseases. In this review, we summarize key immune signals and metabolic programs involved in the regulation of tissue Tregs, review the mechanisms underlying the differentiation and function of Tregs in various non-lymphoid tissues, and discuss therapeutic intervention of metabolic modulators of tissue Tregs for the treatment of autoimmune diseases and cancer.

Virulence strategies of an insect herbivore and oomycete plant pathogen converge on host E3 SUMO ligase SIZ1.

Summary Pathogens and pests secrete proteins (effectors) to interfere with plant immunity through modification of host target functions and disruption of immune signalling networks. The extent of convergence between pathogen and herbivorous insect virulence strategies is largely unexplored.We found that effectors from the oomycete pathogen, Phytophthora capsici, and the major aphid pest, Myzus persicae target the host immune regulator SIZ1, an E3 SUMO ligase. We used transient expression assays in Nicotiana benthamiana as well as Arabidopsis mutants to further characterize biological role of effector–SIZ1 interactions in planta. We show that the oomycete and aphid effector, which both contribute to virulence, feature different activities towards SIZ1. While M. persicae effector Mp64 increases SIZ1 protein levels in transient assays, P. capsici effector CRN83_152 enhances SIZ1‐E3 SUMO ligase activity in vivo.SIZ1 contributes to host susceptibility to aphids and an oomycete pathogen. Knockout of SIZ1 in Arabidopsis decreased susceptibility to aphids, independent of SNC1, PAD4 and EDS1. Similarly SIZ1 knockdown in N. benthamiana led to reduced P. capsici infection.Our results suggest convergence of distinct pathogen and pest virulence strategies on an E3 SUMO ligase to enhance host susceptibility.

Protein interaction network analysis reveals genetic enrichment of immune system genes in frontotemporal dementia

Interactors of protein products of known genes for frontotemporal dementia (FTD) are likely to be involved in the molecular pathways towards disease. We therefore applied protein interaction network (PIN) analysis to prioritize candidate genes for rare variant association analysis. We created an FTD-PIN starting from known FTD genes downloading their physical interactors and performed functional enrichment analyses. We identified overrepresented processes in FTD and selected genes (n = 440) belonging to these processes for rare variant analysis in a Belgian cohort of 228 FTD patients and 345 controls. SKAT-O analysis suggested TNFAIP3 as the top gene (p = 0.7 × 10−3) reaching near test-wide significance (p = 2.5 × 10−4). We then analyzed the TNFAIP3-subnetwork within the FTD-PIN which indicated enrichment of several immune signaling networks, suggesting that disrupted immune signaling may be implicated in TNFAIP3-related FTD. Our study demonstrates that integration of PINs with genetic data is a useful approach to increase the power for rare variant association analysis. Furthermore, we present a computational pipeline for identifying potential novel therapeutic targets and risk-modifying variants.