Four guiding principles for effective trainee-led STEM community engagement through high school outreach.

To address ongoing academic achievement gap, there is a need for more school-university partnerships promoting early access to STEM education. During summer 2020, members of our institute initiated QBio-EDGE (Quantitative Biology-Empowering Diversity and Growth in Education), an outreach program for high schools in Los Angeles. In the hope of contributing to increasing diversity in academia, QBio-EDGE aims to make STEM education more accessible for students from historically excluded communities by exposing them to scientific research and diverse scientist role models. This program is led by early career researchers (ECRs), i.e., undergraduate, graduate, and postdoctoral researchers. In our first year, the outreach activities took place during virtual learning, presenting challenges and opportunities within the program development. Here, we provide a practical guide outlining our outreach efforts, key factors we considered in the program development, and hurdles we overcame. Specifically, we describe how we assembled our diverse team, how we established trusting partnerships with participating schools, and how we designed engaging student-centered, problem-based classroom modules on quantitative biology and computational methods applications to understand living systems. We also discuss the importance of increased institutional support. We hope that this may inspire researchers at all career stages to engage with local schools by participating in science outreach, specifically in quantitative and computational fields. We challenge institutions to actively strengthen these efforts.

Tonic TNF conditioning of macrophages safeguards stimulus-specific inflammatory responses.

Tumor necrosis factor (TNF) is a key inflammatory cytokine that warns recipient cells of a nearby infection or tissue damage. Acute exposure to TNF activates characteristic oscillatory dynamics of the transcription factor NFκB and induces a characteristic gene expression program; these are distinct from the responses of cells directly exposed to pathogen-associated molecular patterns (PAMPs). Here, we report that tonic TNF exposure is critical for safeguarding TNF's specific functions. In the absence of tonic TNF conditioning, acute exposure to TNF causes (i) NFκB signaling dynamics that are less oscillatory and more like PAMP-responsive NFκB dynamics, (ii) immune gene expression that is more similar to the Pam3CSK4 response program, and (iii) broader epigenomic reprogramming that is characteristic of PAMP-responsive changes. We show that the absence of tonic TNF signaling effects subtle changes to TNF receptor availability and dynamics such that enhanced pathway activity results in non-oscillatory NFκB. Our results reveal tonic TNF as a key tissue determinant of the specific cellular responses to acute paracrine TNF exposure, and their distinction from responses to direct exposure to PAMPs.

Erroneous expression of NKG2D on granulocytes detected by phycoerythrin-conjugated clone 149810 antibody.

BACKGROUND: The activating Natural killer group 2 member D (NKG2D) receptor is typically expressed on NK cells, CD8 T lymphocytes, γδ T cells and small subsets of CD4 T lymphocytes. During the course of an extensive flow cytometry phenotyping of immune cells in the peripheral blood of patients with glioblastoma multiforme (GBM) we noticed an unexpected expression of NKG2D receptor on granulocytes using the phycoerythrin (PE)-conjugated clone 149810 antibody. METHODS: Peripheral blood samples from 35 patients with GBM and 22 age-matched healthy control (HC) donors were analyzed using flow cytometry, imaging cytometry and real-time quantitative reverse transcription PCR to validate the observed expression of NKG2D receptor on myeloid cells. RESULTS: Reactivity with PE-149810 was mostly observed on granulocytes from GBM patients on dexamethasone treatment where it correlated with inferior survival rates. Surprisingly, such NKG2D expression on granulocytes was not observed using the allophycocyanin (APC)-conjugate of the same clone 149810 antibody or an indirect staining procedure with unconjugated clone 149810 antibody. Moreover, the PE-conjugate of a different anti-NKG2D clone (1D11) also did not stain granulocytes. Imaging cytometry indicated cell surface and intracellular localization of PE-149810 but not of PE-1D11 in granulocytes. CONCLUSION: Our results uncover an erroneous and false positive reactivity of PE-labeled (but not of APC-labeled or unconjugated) anti-NKG2D antibody 149810 on granulocytes from dexamethasone-treated GBM patients and raise a note of caution for studies of NKG2D expression on non-lymphoid cells.

Stimulus-specific responses in innate immunity: Multilayered regulatory circuits.

Immune sentinel cells initiate immune responses to pathogens and tissue injury and are capable of producing highly stimulus-specific responses. Insight into the mechanisms underlying such specificity has come from the identification of regulatory factors and biochemical pathways, as well as the definition of signaling circuits that enable combinatorial and temporal coding of information. Here, we review the multi-layered molecular mechanisms that underlie stimulus-specific gene expression in macrophages. We categorize components of inflammatory and anti-pathogenic signaling pathways into five layers of regulatory control and discuss unifying mechanisms determining signaling characteristics at each layer. In this context, we review mechanisms that enable combinatorial and temporal encoding of information, identify recurring regulatory motifs and principles, and present strategies for integrating experimental and computational approaches toward the understanding of signaling specificity in innate immunity.

Characterization of DNA-protein complexes by nanoparticle tracking analysis and their association with systemic lupus erythematosus.

Nanotechnology enables investigations of single biomacromolecules, but technical challenges have limited the application in liquid biopsies, for example, blood plasma. Nonetheless, tools to characterize single molecular species in such samples represent a significant unmet need with the increasing appreciation of the physiological importance of protein structural changes at nanometer scale. Mannose-binding lectin (MBL) is an oligomeric plasma protein and part of the innate immune system through its ability to activate complement. MBL also serves a role as a scavenger for cellular debris, especially DNA. This may link functions of MBL with several inflammatory diseases in which cell-free DNA now appears to play a role, but mechanistic insight has been lacking. By making nanoparticle tracking analysis possible in human plasma, we now show that superoligomeric structures of MBL form nanoparticles with DNA. These oligomers correlate with disease activity in systemic lupus erythematosus patients. With the direct quantification of the hydrodynamic radius, calculations following the principles of Taylor dispersion in the blood stream connect the size of these complexes to endothelial inflammation, which is among the most important morbidities in lupus. Mechanistic insight from an animal model of lupus supported that DNA-stabilized superoligomers stimulate the formation of germinal center B cells and drive loss of immunological tolerance. The formation involves an inverse relationship between the concentration of MBL superoligomers and antibodies to double-stranded DNA. Our approach implicates the structure of DNA-protein nanoparticulates in the pathobiology of autoimmune diseases.

Six distinct NFκB signaling codons convey discrete information to distinguish stimuli and enable appropriate macrophage responses.

Macrophages initiate inflammatory responses via the transcription factor NFκB. The temporal pattern of NFκB activity determines which genes are expressed and thus, the type of response that ensues. Here, we examined how information about the stimulus is encoded in the dynamics of NFκB activity. We generated an mVenus-RelA reporter mouse line to enable high-throughput live-cell analysis of primary macrophages responding to host- and pathogen-derived stimuli. An information-theoretic workflow identified six dynamical features-termed signaling codons-that convey stimulus information to the nucleus. In particular, oscillatory trajectories were a hallmark of responses to cytokine but not pathogen-derived stimuli. Single-cell imaging and RNA sequencing of macrophages from a mouse model of Sjögren's syndrome revealed inappropriate responses to stimuli, suggestive of confusion of two NFκB signaling codons. Thus, the dynamics of NFκB signaling classify immune threats through six signaling codons, and signal confusion based on defective codon deployment may underlie the etiology of some inflammatory diseases.

Cellular Requirements for Sensing and Elimination of Incoming HSV-1 DNA and Capsids.

Incoming viruses challenge the cell with diverse foreign molecules, which need to be sensed quickly to initiate immune responses and to remove the viral components. In this study, we investigate the cellular requirements for sensing and degradation of incoming viral DNA and capsids during herpes simplex virus type 1 (HSV-1) infections. Using click chemistry labeling of the viral genome, we found that HSV-1 DNA was released from a subset of capsids into the cytosol early in infection. By next-generation sequencing of cyclic GMP-AMP (cGAMP) synthase (cGAS)-bound DNA from HSV-1-infected cells, we show that HSV-1 DNA was bound by the cytosolic DNA sensor cGAS. Activation of cGAS enzymatic activity by viral DNA did not require proteasomal activity, indicating that viral DNA release into the cytosol is not proteasome-dependent. However, induction of interferon (IFN)-ß expression was blocked by inhibition of the proteasome, suggesting a contribution of the proteasome to IFN-ß induction through the cGAS-stimulator of interferon genes pathway. Viral DNA was cleared from the cytosol within few hours, in a manner dependent on TREX1 and a cGAS-dependent process. Capsid material in the cytoplasm was also degraded rapidly. This was partially blocked by treatment with a proteasome inhibitor. This treatment led to accumulation of DNA-containing viral capsids near the nucleus and reduced nuclear entry of viral DNA. Thus, cells infected with HSV-1 use a panel of mechanisms to eliminate viral DNA and capsids. This represents a barrier for establishment of infection and potentially enables the host to gear the IFN-ß response to a level required for antiviral defense without causing immunopathology.

Stimulus-specificity in the Responses of Immune Sentinel Cells.

Innate immune sentinel cells must initiate and orchestrate appropriate immune responses for myriad pathogens. These stimulus-specific gene expression responses are mediated by combinatorial and temporal coding within a handful of immune response signaling pathways. We outline the scope of our current understanding and indicate pressing outstanding questions. The innate immune response is a first-line defense against invading pathogens and coordinates the activation and recruitment of specialized immune cells, thereby initiating the adaptive immune response. While the adaptive immune system is capable of highly pathogen-specific immunity through the process of genetic recombination and clonal selection, innate immunity is frequently viewed as a catch-all system that initiates general immune activation. In this review, we are re-examining this view, as we are distinguishing between immune sentinel functions mediated by macrophages and dendritic cells and innate immune effector functions mediated by cells such as neutrophils, NK cells, etc. Given pathogen diversity, including modes of entry, replication cycles, and strategies of immune evasion and spread, all successive waves of the immune response ought to be tailored to the specific immune threat, leading us to postulate that immune sentinel functions by macrophages and dendritic cells ought to be highly stimulus-specific. Here we review the experimental evidence for stimulus-specific responses by immune sentinel cells which initiate and coordinate immune responses, as well as the mechanisms by which this specificity may be achieved.

In-depth immunophenotyping of patients with glioblastoma multiforme: Impact of steroid treatment.

Despite aggressive treatment regimens based on surgery and radiochemotherapy, the prognosis of patients with grade IV glioblastoma multiforme (GBM) remains extremely poor, calling for alternative options such as immunotherapy. Immunological mechanisms including the Natural Killer Group 2 member D (NKG2D) receptor-ligand system play an important role in tumor immune surveillance and targeting the NKG2D system might be beneficial. However, before considering any kind of immunotherapy, a precise characterization of the immune system is important, particularly in GBM patients where conventional therapies with impact on the immune system are frequently co-administered. Here we performed an in-depth immunophenotyping of GBM patients and age-matched healthy controls and analyzed NKG2D ligand expression on primary GBM cells ex vivo. We report that GBM patients have a compromised innate immune system irrespective of steroid (dexamethasone) medication. However, dexamethasone drastically reduced the number of immune cells in the blood of GBM patients. Moreover, higher counts of immune cells influenced by dexamethasone like CD45+ lymphocytes and non-Vδ2 γδ T cells were associated with better overall survival. Higher levels of NKG2D ligands on primary GBM tumor cells were observed in patients who received radiochemotherapy, pointing towards increased immunogenic potential of GBM cells following standard radiochemotherapy. This study sheds light on how steroids and radiochemotherapy affect immune cell parameters of GBM patients, a pre-requisite for the development of new therapeutic strategies targeting the immune system in these patients.

Inborn errors in RNA polymerase III underlie severe varicella zoster virus infections.

Varicella zoster virus (VZV) typically causes chickenpox upon primary infection. In rare cases, VZV can give rise to life-threatening disease in otherwise healthy people, but the immunological basis for this remains unexplained. We report 4 cases of acute severe VZV infection affecting the central nervous system or the lungs in unrelated, otherwise healthy children who are heterozygous for rare missense mutations in POLR3A (one patient), POLR3C (one patient), or both (two patients). POLR3A and POLR3C encode subunits of RNA polymerase III. Leukocytes from all 4 patients tested exhibited poor IFN induction in response to synthetic or VZV-derived DNA. Moreover, leukocytes from 3 of the patients displayed defective IFN production upon VZV infection and reduced control of VZV replication. These phenotypes were rescued by transduction with relevant WT alleles. This work demonstrates that monogenic or digenic POLR3A and POLR3C deficiencies confer increased susceptibility to severe VZV disease in otherwise healthy children, providing evidence for an essential role of a DNA sensor in human immunity.

cGAS is activated by DNA in a length-dependent manner.

Cytosolic DNA stimulates innate immune responses, including type I interferons (IFN), which have antiviral and immunomodulatory activities. Cyclic GMP-AMP synthase (cGAS) recognizes cytoplasmic DNA and signals via STING to induce IFN production. Despite the importance of DNA in innate immunity, the nature of the DNA that stimulates IFN production is not well described. Using low DNA concentrations, we show that dsDNA induces IFN in a length-dependent manner. This is observed over a wide length-span of DNA, ranging from the minimal stimulatory length to several kilobases, and is fully dependent on cGAS irrespective of DNA length. Importantly, in vitro studies reveal that long DNA activates recombinant human cGAS more efficiently than short DNA, showing that length-dependent DNA recognition is an intrinsic property of cGAS independent of accessory proteins. Collectively, this work identifies long DNA as the molecular entity stimulating the cGAS pathway upon cytosolic DNA challenge such as viral infections.

Molecular requirements for sensing of intracellular microbial nucleic acids by the innate immune system.

Nucleic acids sensors of the innate immune system recognize various RNA and DNA structures during infection to induce transcription of interferon and pro-inflammatory cytokines and activation of inflammasomes. Cytosolic RNA is recognized by RIG-I and MDA5, while intracellular DNA is sensed among others by cGAS, AIM2, IFI16 and RNA polymerase III. The diversity of nucleic acid species produced during infection in the cytosol and nucleus and the limited chemical differences between self and non-self nucleic acids challenge the host's innate pattern recognition system to ensure reliable sensing while avoiding immune activation by self nucleic acids. We review the molecular characteristics of intracellular nucleic acid sensor ligands, the structural basis of the binding preferences of the sensors, the identity and origin of immunostimulatory nucleic acid species during infection, the influence of intracellular localization of the sensor on immune activation, and the ability of viruses to use the ligand specificity of the sensors to evade recognition.

HSV-1 ICP27 targets the TBK1-activated STING signalsome to inhibit virus-induced type I IFN expression.

Herpes simplex virus (HSV) 1 stimulates type I IFN expression through the cGAS-STING-TBK1 signaling axis. Macrophages have recently been proposed to be an essential source of IFN during viral infection. However, it is not known how HSV-1 inhibits IFN expression in this cell type. Here, we show that HSV-1 inhibits type I IFN induction through the cGAS-STING-TBK1 pathway in human macrophages, in a manner dependent on the conserved herpesvirus protein ICP27. This viral protein was expressed de novo in macrophages with early nuclear localization followed by later translocation to the cytoplasm where ICP27 prevented activation of IRF3. ICP27 interacted with TBK1 and STING in a manner that was dependent on TBK1 activity and the RGG motif in ICP27. Thus, HSV-1 inhibits expression of type I IFN in human macrophages through ICP27-dependent targeting of the TBK1-activated STING signalsome.

NKG2D- and T-cell receptor-dependent lysis of malignant glioma cell lines by human γδ T cells: Modulation by temozolomide and A disintegrin and metalloproteases 10 and 17 inhibitors.

The interaction of the MHC class I-related chain molecules A and B (MICA and MICB) and UL-16 binding protein (ULBP) family members expressed on tumor cells with the corresponding NKG2D receptor triggers cytotoxic effector functions in NK cells and γδ T cells. However, as a mechanism of tumor immune escape, NKG2D ligands (NKG2DLs) can be released from the cell surface. In this study, we investigated the NKG2DL system in different human glioblastoma (GBM) cell lines, the most lethal brain tumor in adults. Flow cytometric analysis and ELISA revealed that despite the expression of various NKG2DLs only ULBP2 is released as a soluble protein via the proteolytic activity of "a disintegrin and metalloproteases" (ADAM) 10 and 17. Moreover, we report that temozolomide (TMZ), a chemotherapeutic agent in clinical use for the treatment of GBM, increases the cell surface expression of NKG2DLs and sensitizes GBM cells to γδ T cell-mediated lysis. Both NKG2D and the T-cell receptor (TCR) are involved. The cytotoxic activity of γδ T cells toward GBM cells is strongly enhanced in a TCR-dependent manner by stimulation with pyrophosphate antigens. These data clearly demonstrate the complexity of mechanisms regulating NKG2DL expression in GBM cells and further show that treatment with TMZ can increase the immunogenicity of GBM. Thus, TMZ might enhance the potential of the adoptive transfer of ex vivo expanded γδ T cells for the treatment of malignant glioblastoma.

Innate recognition of alphaherpesvirus DNA.

Alphaherpesviruses include human and animal pathogens, such as herpes simplex virus type 1, which establish life-long latent infections with episodes of recurrence. The immunocompetence of the infected host is an important determinant for the outcome of infections with alphaherpesviruses. Recognition of pathogen-associated molecular patterns by pattern recognition receptors is an essential, early step in the innate immune response to pathogens. In recent years, it has been discovered that herpesvirus DNA is a strong inducer of the innate immune system. The viral genome can be recognized in endosomes by TLR9, as well as intracellularly by a variety of DNA sensors, the best documented being cGAS, RNA Pol III, IFI16, and AIM2. These DNA sensors use converging signaling pathways to activate transcription factors, such as IRF3 and NF-κB, which induce the expression of type I interferons and other inflammatory cytokines and activate the inflammasome. This review summarizes the recent literature on the innate sensing of alphaherpesvirus DNA, the mechanisms of activation of the different sensors, their mechanisms of signal transduction, their physiological role in defense against herpesvirus infection, and how alphaherpesviruses seek to evade these responses to allow establishment and maintenance of infection.