Sphingosine-1-phosphate suppresses TLR-induced CXCL8 secretion from human T cells

T cells produce a number of cytokines and chemokines upon stimulation with TLR agonists in the presence or absence of TCR signals. Here, we show that secretion of neutrophil chemoattractant CXCL8 from human T cell line Jurkat in response to stimulation with TLR agonists is reduced when cell stimulation is carried out in presence of serum. Serum does not, however, inhibit TCR-activated secretion of CXCL8 nor does it down-regulate TLR-costimulated IL-2 secretion from activated T cells. The molecule that can mimic the ability to bring about suppression in CXCL8 from TLR-activated T cells is serum-borne bioactive lipid, S1P. Serum and S1P-mediated inhibition require intracellular calcium. S1P also suppresses CXCL8 secretion from peripheral blood-derived human T cells activated ex vivo with various TLR ligands. Our findings reveal a previously unrecognized role for S1P in regulating TLR-induced CXCL8 secretion from human T cells.

Src kinases central to T-cell receptor signaling regulate TLR-activated innate immune responses from human T cells

TLRs have a fundamental role in immunity. We have recently reported that stimulation of TLR2 and TLR5 in freshly isolated and activated human T cells with microbial ligands without concomitant activation through the TCR brings about secretion of neutrophil chemoattractant, CXCL8, and effector cytokine, IFN-γ, respectively. However, the mechanism of TLR signaling in T cells has not been worked out. Here, we show that the Src family kinases, p56(lck)(Lck) and p59(fyn)(Fyn), which are essential for activation of T cells through the TCR, are also critical for signal transduction through TLRs in human T cells. The secretion of CXCL8 following stimulation of the model human T cell line, Jurkat, with the TLR5 ligand, flagellin, was reduced in presence of the Src-kinase inhibitor, PP2 and specific inhibitors of Lck and Fyn. These inhibitors suppressed generation of activated JNK and p38, which were both required for TLR-induced CXCL8 production. The Lck-deficient derivative of Jurkat, JCam1.6, responded poorly to TLR2, TLR5 and TLR7 agonists, and did not generate active signaling intermediates. Lck and Fyn inhibitors also reduced TLR5-induced IFN-γ secretion from the activated T cell phenotype-representing T cell line, HuT78, without modulating JNK and p38 activation. These results reveal that TCR and TLRs share key proximal signaling regulators in T cells.

Antibody-recruiting protein-catalyzed capture agents to combat antibiotic-resistant bacteria

Antibiotic resistant infections are projected to cause over 10 million deaths by 2050, yet the development of new antibiotics has slowed. This points to an urgent need for methodologies for the rapid development of antibiotics against emerging drug resistant pathogens. We report on a generalizable combined computational and synthetic approach, called antibody-recruiting protein-catalyzed capture agents (AR-PCCs), to address this challenge. We applied the combinatorial protein catalyzed capture agent (PCC) technology to identify macrocyclic peptide ligands against highly conserved surface protein epitopes of carbapenem-resistant Klebsiella pneumoniae, an opportunistic Gram-negative pathogen with drug resistant strains. Multi-omic data combined with bioinformatic analyses identified epitopes of the highly expressed MrkA surface protein of K. pneumoniae for targeting in PCC screens. The top-performing ligand exhibited high-affinity (EC₅₀ ∼50 nM) to full-length MrkA, and selectively bound to MrkA-expressing K. pneumoniae, but not to other pathogenic bacterial species. AR-PCCs that bear a hapten moiety promoted antibody recruitment to K. pneumoniae, leading to enhanced phagocytosis and phagocytic killing by macrophages. The rapid development of this highly targeted antibiotic implies that the integrated computational and synthetic toolkit described here can be used for the accelerated production of antibiotics against drug resistant bacteria.

Type 1 interferon-dependent repression of NLRC4 and iPLA2 licenses down-regulation of Salmonella flagellin inside macrophages

Inflammasomes have been implicated in the detection and clearance of a variety of bacterial pathogens, but little is known about whether this innate sensing mechanism has any regulatory effect on the expression of stimulatory ligands by the pathogen. During infection with Salmonella and many other pathogens, flagellin is a major activator of NLRC4 inflammasome-mediated macrophage pyroptosis and pathogen eradication. Salmonella switches to a flagellin-low phenotype as infection progresses to avoid this mechanism of clearance by the host. However, the host cues that Salmonella perceives to undergo this switch remain unclear. Here, we report an unexpected role of the NLRC4 inflammasome in promoting expression of its microbial ligand, flagellin, and identify a role for type 1 IFN signaling in switching of Salmonella to a flagellin-low phenotype. Early in infection, activation of NLRC4 by flagellin initiates pyroptosis and concomitant release of lysophospholipids which in turn enhance expression of flagellin by Salmonella thereby amplifying its ability to elicit cell death. TRIF-dependent production of type 1 IFN, however, later represses NLRC4 and the lysophospholipid biosynthetic enzyme iPLA2, causing a decline in intracellular lysophospholipids that results in down-regulation of flagellin expression by Salmonella These findings reveal a previously unrecognized immune-modulating regulatory cross-talk between endosomal TLR signaling and cytosolic NLR activation with significant implications for the establishment of infection with Salmonella.

Serum-borne lipids amplify TLR-activated inflammatory responses

TLRs recognize conserved pathogen associated molecular patterns and generate innate immune responses. Several circulating and cell membrane associated proteins have been shown to collaborate with TLRs in sensing microbial ligands and promoting inflammatory responses. Here, we show that serum and serum-borne lipids including lysophosphatidylcholine (LPC) amplify inflammatory responses from intestinal epithelial cells and mononuclear phagocytes primed with microbial TLR ligands. Treatment with the inhibitors of G protein-coupled receptor (GPCR) signaling, suramin, or pertussis toxin (PT), the inhibitor of JNK-MAPK, or knockdown of LPC response-regulating GPCR, G2A, decreases the augmentation brought about by serum or LPC in TLR-induced inflammatory response. In vivo administration of PT or anti-G2A antibody reduces TLR2-activated cytokine secretion. The ability of host lipids to costimulate TLR-generated cellular responses represents a novel pathway for the amplification of innate immunity and inflammation.

A retrospective audit of clinicopathological attributes and treatment outcomes of adolescent and young adult non-Hodgkin lymphomas from a tertiary care center

Background:

The uniqueness of adolescent and young adult (AYA) non-Hodgkin lymphomas (NHL) with respect to biology and treatment have largely remained unanswered due to marked heterogeneity in treatment, paucity of prospective, or retrospective studies and poor representation of AYA in clinical trials. This audit attempts to put forward the clinicopathological attributes and treatment outcomes of AYA NHL treated with both pediatric and adult protocols from a single centre in a developing country.

Patients and Methods:

Hospital records of all consecutive NHL patients registered in lymphoma clinic from January 2007 to May 2010 were reviewed for information on demography, clinical features, histology subtype, staging, treatment regimen, response rates, toxicities, and follow up. Two-year progression-free (PFS) and overall survival (OS) were calculated with Kaplan-Meier method.

Results:

AYA NHL constituted 4% of all lymphomas. Diffuse large B-cell (DLBL) was the most frequent subtype. Following were the 2-year PFS and OS - DLBL 64%, 76.9%, Burkitt's lymphoma: 56%, 56%, lymphoblastic lymphoma: 33.2%, 44%. Our results did not show any improvement in outcome of DLBL with the use of Burkitt's lymphoma like regimen.

Conclusions:

This study highlights some of the key features of AYA NHL occurring in developing world.

A small sustained increase in NOD1 abundance promotes ligand-independent inflammatory and oncogene transcriptional responses

Small, genetically determined differences in transcription [expression quantitative trait loci (eQTLs)] are implicated in complex diseases through unknown molecular mechanisms. Here, we showed that a small, persistent increase in the abundance of the innate pathogen sensor NOD1 precipitated large changes in the transcriptional state of monocytes. A ~1.2- to 1.3-fold increase in NOD1 protein abundance resulting from loss of regulation by the microRNA cluster miR-15b/16 lowered the threshold for ligand-induced activation of the transcription factor NF-κB and the MAPK p38. An additional sustained increase in NOD1 abundance to 1.5-fold over basal amounts bypassed this low ligand concentration requirement, resulting in robust ligand-independent induction of proinflammatory genes and oncogenes. These findings reveal that tight regulation of NOD1 abundance prevents this sensor from exceeding a physiological switching checkpoint that promotes persistent inflammation and oncogene expression. Furthermore, our data provide insight into how a quantitatively small change in protein abundance can produce marked changes in cell state that can serve as the initiator of disease.

MyD88-dependent pro-inflammatory activity in Vi polysaccharide vaccine against typhoid promotes Ab switching to IgG

Vi capsular polysaccharide is currently in use as a vaccine against human typhoid caused by Salmonella Typhi. The vaccine efficacy correlates with IgG anti-Vi Abs. We have recently reported that Vi can generate inflammatory responses through activation of the TLR2/TLR1 complex. In the present study, we show that immunization with Vi produces IgM as well as IgG Abs in wild type mice. This ability is not compromised in mice deficient in T cells. However, immunization of mice lacking the TLR adaptor protein, MyD88, with Vi elicits only IgM Abs. These results suggest that MyD88-dependent pro-inflammatory ability of the Vi vaccine might be vital in generating IgG Abs with this T-independent Ag.

Accessibility of O Antigens Shared between Salmonella Serovars Determines Antibody-Mediated Cross-Protection

Pathogenic Salmonella serovars produce clinical manifestations ranging from systemic infection typhoid to invasive nontyphoidal Salmonella disease in humans. These serovars share a high degree of homology at the genome and the proteome level. However, whether infection or immunization with one serovar provides protection against other serovars has not been well studied. We show in this study that immunization of mice with live typhoidal serovar, Salmonella Typhi, generates cross-reactive immune responses, which provide far greater resistance against challenge with nontyphoidal serovar Salmonella Enteritidis than with another nontyphoidal serovar, Salmonella Typhimurium. Splenic T cells from these immunized mice produced similar levels of IL-2 and IFN-γ upon ex vivo stimulation with Ags prepared from S Enteritidis and S Typhimurium. In contrast, Abs against S Typhi interacted with live intact S Enteritidis but did not bind intact S Typhimurium. These pathogen-reactive Abs were largely directed against oligosaccharide (O)-antigenic determinant of LPS that S Typhi shares with S Enteritidis. Abs against the O determinant, which S Typhi shares with S Typhimurium, were present in the sera of immunized mice but did not bind live intact Salmonella because of surface inaccessibility of this determinant. Similar accessibility-regulated interaction was seen with Abs generated against S Typhimurium and S Enteritidis. Our results suggest that the ability of protective Abs elicited with one Salmonella serovar to engage with and consequently provide protection against another Salmonella serovar is determined by the accessibility of shared O Ags. These findings have significant and broader implications for immunity and vaccine development against pathogenic Salmonellae.

Dual RNA-seq as an effective tool to simultaneously identify transcriptional changes in host macrophages and invading intracellular pathogens

Intracellular pathogens have evolved strategies to subvert the host immune response and establish infection leading to disease. For example, Mycobacterium tuberculosis (MTB) has been recently reported to effectively counteract immunological and anti-tubercular challenges by activating resistance mechanisms that enable the pathogen to attain an immune tolerant state. A systems scale approach using dual RNA Sequencing revealed key transcriptional factors that enabled researchers to discover a drug combination that delivers more effective killing of MTB. On the basis of our preliminary findings we hypothesize that similar to MTB, Salmonella spp. have evolved to escape host macrophage responses by down-regulating the expression of flagellin, a potent activator of the NLRC4 inflammasome, by taking advantage of a natural host negative feedback mechanism that allows the pathogen to reside intracellularly within macrophages. However, how Salmonella and host transcriptional networks rewire over the course of infection to permit development of an immune-evasive phenotype in the pathogen remains unknown. Using dual RNA-Seq and regulatory network analysis, we propose to simultaneously identify the molecular changes that occur in both the host and the pathogen during infection. We aim to conduct a temporal study to find transcriptional changes at different time points post infection that lead to development of a permissive host environment and allow Salmonella to undergo immune escape within macrophages. Our study will help identify the key regulators that shape host-pathogen crosstalk over the course of Salmonella infection with potentially important implications for bacterial pathogenesis and immunity.

Identifying innate immune regulators of Mycobacterium tuberculosis pathogenesis in macrophages

Tuberculosis (TB) is a leading infectious disease that contributes to approximately 1.4 million deaths annually worldwide. In the present situation of the COVID-19 pandemic and disrupted healthcare services, mathematical modelling predicts that there will be an additional 6.3 million new cases and 1.4 million more TB deaths by the end of 2025. Innate immune cells like macrophages are the frontline responders in host defense against Mycobacterium tuberculosis (MTB) and may also play a major role in disease establishment. A major roadblock in developing effective strategies against TB is the inability of current anti-TB drugs to target both replicating and non-replicating bacteria. We have found that lack of specific components of the host innate sensing machinery has a major impact on intracellular bacterial growth and the production of IL-1β and IFN-β during MTB infection of macrophages; the latter cytokines play major roles in host-protective and host-detrimental outcomes of infection respectively. RNA seq reveals that these innate immune modules differentially control the expression of genes implicated in host protein synthesis and MTB dissemination and escape from the granuloma. Ongoing work is utilizing Path-Seq for quantitative profiling of the MTB transcriptome within infected macrophages and investigating macrophage-dependent mechanisms of MTB restriction and persistence in vivo. Our study will potentially identify immune regulators that make the macrophage environment either permissive or restrictive for intracellular replication of MTB with important implications for developing combinatorial targeting approaches for host-directed treatment of TB.

A non-canonical role of caspase-1 in regulating bacterial physiology and antimicrobial resistance

Caspase-1 is a key effector molecule involved in inflammasome activation and has a well-established role in restricting the growth of intracellular pathogens like Salmonella by triggering a form of cell death called pyroptosis. Here we reveal a non-canonical, cell death independent role for caspase-1 in controlling the transcriptional state and drug resistance of intracellular Salmonella. Using Pathogen-sequencing, a method for sensitive transcriptional profiling of miniscule numbers of intracellular bacteria from infected macrophages, we show that that caspase-1 regulates key processes involved in survival and antimicrobial susceptibility of intracellular Salmonella. Host caspase-1 increased susceptibility of Salmonella to endogenous cationic antimicrobial peptides, as well as to a cationic polypeptide antibiotic used as a last-line drug in Gram-negative bacterial infections. These effects of caspase-1 were independent of its enzymatic activity but dependent on its ability to repress activation of a two-component signal transduction system in intracellular bacteria. These effects were also independent of caspase-11. Our data suggest a “backup” role for caspase-1 in dampening antimicrobial resistance of intracellular Salmonella which evade initial innate immune detection and restriction by caspase-1. These findings also reveal the role of a key innate immune effector in altering pathogen physiology, broadening our view of host-pathogen crosstalk with possible implications for targeting caspase-1 in host-directed therapy to combat antimicrobial resistance.

Supported by grant from NIH (R01 AI155685-A1 ) and AAI Careers in Immunology Fellowship (2018-2019)

A modest change in regulation of NOD1 expression has a major impact on inflammation and gastric cancer

Altered protein dosage by defects in single genes leads to haploinsufficiencies and monogenic disorders, but the impact of small changes in gene expression on multifactorial disease is unknown. Here we show that a persistent small (~1.5 fold) increase in expression of NOD1 (Nucleotide-binding oligomerization domain-containing protein 1), a key innate sensor of bacterial infection, precipitates a large physiological effect with dramatically altered cellular function associated with carcinogenesis. Inhibition of miR-15b and miR-16 microRNA function leads to a ~1.2–1.4 fold increase in NOD1 protein concentration, with even slightly greater increases leading to ligand-independent, switch-like NOD1 activation. miRNA regulation of NOD1 plays a crucial role in limiting the development of an inflammatory state is impaired in gastric cancer with a small increase in NOD1 being associated with greater early patient mortality. Overall, our data show that tight control of NOD1 expression by miRNA prevents this sensor from exceeding a physiological switching checkpoint that promotes persistent inflammation and lethal cancer progression, and reveal the impact of a single and modest cellular alteration on cancer. These findings also have broader implications for understanding how small expression changes caused by genetic variation impact development of complex diseases like autoimmunity and cancer.

Lentivirus-mediated Conditional Gene Expression

The ability to identify the role of a particular gene within a system is dependent on control of the expression of that gene. In this protocol, we describe a method for stable, conditional expression of Nod-Like receptors (NLRs) in THP-1 cells using a lentiviral expression system. This system combines all the necessary components for tetracycline-inducible gene expression in a single lentivector with constitutive co-expression of a selection marker, which is an efficient means for controlling gene expression using a single viral infection of cells. This is done in a third generation lentiviral expression platform that improves the safety of lentiviruses and allows for greater gene expression than previous lentiviral platforms. The lentiviral expression plasmid is first engineered to contain the gene of interest driven by a TRE (tetracycline response element) promoter in a simple gateway cloning step and is then co-transfected into HEK293T cells, along with packaging and envelope plasmids to generate the virus. The virus is used to infect a cell type of interest at a low MOI so that the majority of the transduced cells contain a single viral integration. Infected cells are grown under selection, and viral integration is validated by qPCR. Gene expression in stably transduced cells is induced with doxycycline and validated by qPCR, immunoblot, and flow cytometry. This flexible lentiviral expression platform may be used for stable and robust induction of a gene of interest in a range of cells for multiple applications. Graphic abstract: Schematic overview of lentiviral transduction of THP-1 cells.

The NLRC4 inflammasome regulates extra- and intra-macrophage expression of its own pathogen-derived ligand flagellin to impact Salmonella survival

Inflammasomes have been implicated in the detection and clearance of a variety of bacterial pathogens, but whether the process of inflammasome activation per se regulates expression of microbial effectors is unknown. Here we show that inflammasome activation regulates expression of the NLRC4 ligand, flagellin, on Salmonella. Lysophospholipids released upon macrophage pyroptosis increase expression of flagellin on Salmonella and its ability to induce further NLRC4 inflammasome-dependent pyroptosis, establishing a positive feedback loop that potentiates Salmonella detection and clearance. As infection progresses, this positive feedback is checked by inhibition of NLRC4 expression and lysophospholipid biosynthesis, thus switching Salmonella to a flagellin-negative phenotype inside macrophages. While inhibition of inflammasome activation could be a host strategy aimed at preventing overt cell death and enabling generation of a productive adaptive immune response post infection, our study demonstrates that Salmonella hijacks this host response to facilitate its intracellular survival. Our data reveal a host-dependent mechanism by which Salmonella downregulates flagellin within macrophages and identify the modulation of expression of a pathogen-derived inflammasome ligand by the very process of inflammasome activation as a novel mode of host-pathogen cross talk during infection with a bacterial pathogen.

A sustained small increase in NOD1 expression promotes ligand-independent oncogenic activity

Small genetically-determined differences in transcription are implicated in complex disease but the mechanisms by which small changes in gene expression impact the origin of complex disease are unknown. Recent GWAS fine-mapping studies show that many causal alleles for complex immune-related diseases lie in non-coding regions of genes, generating expression quantitative trait loci (eQTLs), with the extent of expression variation between susceptible and resistant genotypes often in the 1.5–3 fold range. Concurrently, systems-level studies across several cancer types suggest a regulatory organization in which disease-promoting genomic mutations lie upstream of functional master regulator proteins, a change in whose expression by 1.5–3 fold is responsible for propagating a tumor cell state. Here we show that a persistent small (~1.5 fold) increase in expression of the innate sensor NOD1 (Nucleotide-binding Oligomerization Domain-containing protein 1) precipitates large cancer-promoting changes in cell state in the absence of ligand-driven activity. A ~1.2–1.4-fold increase in NOD1 protein concentration by loss of microRNA regulation sensitizes cells to ligand-induced inflammation with an additional slight increase leading to ligand-independent NOD1 activation that upregulates the expression of proto-oncogenes and is linked to poor prognosis in gastric cancer. Our data show that tight expression regulation of NOD1 prevents this sensor from exceeding a physiological switching checkpoint that promotes persistent inflammation and oncogene expression and reveal the impact of a single small quantitative change in cell state on cancer.

A host innate immune circuit licenses downregulation of Salmonella flagellin expression inside macrophages

While the effect of bacterial molecules on host immune system is well studied, how host factors affect expression of bacterial molecules is not understood in great detail. Inflammasomes are instrumental in detection and clearance of bacterial pathogens, but little is known about whether there is an active cross-talk between the host sensing mechanism and the expression of stimulatory ligands by the pathogen. We used Salmonella-macrophage infection model to assess the impact of inflammasome activation on the expression of flagellin as a candidate Salmonella protein. We discovered that early during infection, host lysophospholipids released upon rapid NLRC4-mediated pyroptosis of macrophages increase flagellin expression by extracellular bacteria which leads to even greater pyroptosis when these bacteria infect healthy macrophages, thus facilitating NLRC4-mediated detection and clearance of Salmonella. A TLR-dependent host response, however, later inhibits expression of NLRC4 and the lysophospholipid biosynthetic enzyme iPLA2, causing a decline in intracellular lysophospholipids pool that permits downregulation of flagellin by intracellular Salmonella. Our findings reveal a novel mode of host-pathogen cross-talk wherein expression of a bacterium-derived inflammasome ligand is temporally controlled by the very process of inflammasome activation, and identify a host mechanism that controls switching of Salmonella to a flagellin-low phenotype inside macrophages with important implications for bacterial pathogenesis and immunity. Future investigations will utilize dual RNA-Seq studies to understand how Salmonella gene expression networks rewire to adapt to different host intracellular microenvironments.

A host cell-intrinsic innate regulatory circuit limits inflammasome activity and promotes immune escape of Salmonella inside macrophages

Inflammasomes have been implicated in the detection and clearance of a variety of bacterial pathogens, but little is known about whether there is active cross-talk between the host sensing mechanism and the expression of stimulatory ligands by the pathogen. Here we show that inflammasome activation regulates expression of the NLRC4 and TLR5 ligand, flagellin, by Salmonella. Host lysophospholipids released upon NLRC4-mediated pyroptosis increase flagellin expression by extracellular bacteria that enhances pyroptosis upon internalization, establishing a positive feedback loop that potentiates Salmonella detection and clearance. A TLR-dependent host negative feedback response later inhibits inflammasome activation and lysophospholipid biosynthesis within cells, prompting the pathogen to switch to a flagellin-low phenotype and establish an intracellular survival niche inside macrophages. Ablation of this host regulatory circuit prevents downregulation of flagellin by intracellular Salmonella and promotes bacterial clearance in vivo. Our data identify modulation of expression of a bacterium-derived inflammasome ligand by the very process of inflammasome activation as a novel mode of host-pathogen cross-talk and reveal a host mechanism that is adapted by Salmonella for flagellin downregulation and immune escape within macrophages.