Clinton J. Bradfield

Macrophages harness pattern recognition receptors (PRRs) to detect conserved bacterial components and mount effective immune responses. Many Gram-negative bacteria modify their lipid A structures to limit recognition by Toll-like receptor 4 (TLR4) and cytosolic Caspase-11 lipopolysaccharide sensors. One common evasion strategy is to reduce the lipid A acylation state from hexa- to tetra-acylation. This alteration can limit binding to receptors and dampen subsequent immune signaling responses, yet the proteomic alterations associated with this altered immunogenicity remain incompletely understood. Here, we systematically profiled proteomic alterations induced by extracellular or transfected hexa-acylated Kdo2-lipid A (Kdo2) and tetra-acylated lipid-IVa (IVa) to assess TLR4-dependent, TLR4-independent, and non-canonical inflammasome activation pathways. Kdo2 elicited stronger inflammatory responses in immortalized bone-marrow-derived macrophages (iBMDMs), as evidenced by robust TNF production, Caspase-11 cleavage, and IL-1α/IL-1β release. In contrast, IVa elicited minimal TNF secretion and failed to effectively induce non-canonical inflammasome activation. Global label-free quantitative proteomic analysis of iBMDMs stimulated with a low dose of immunogenic LPS displayed route-specific immune signatures: enrichment of TNF signaling, interferon-associated pathways, and mitochondrial metabolic remodeling. Equimolar amounts of low-acylated LPS failed to effectively induce these immune signatures, supporting a threshold-dependent model in which the lipid A structure and route of exposure define inflammatory progression. Collectively, our findings provide mechanistic insight into how lipid A structural variation modulates macrophage immune programming and cytosolic inflammasome activation.

The immunologic consequences of using bactericidal versus bacteriostatic antibiotic treatments are unclear. We observed a bacteriostatic (growth halting) treatment was more protective than a bactericidal (bacteria killing) treatment in a murine peritonitis model. To understand this unexpected difference, we compared macrophage responses to bactericidal treated bacteria or bacteriostatic treated bacteria. We found that Gram-negative bacteria treated with bactericidal drugs induced more proinflammatory cytokines than those treated with bacteriostatic agents. Bacterial DNA – released only by bactericidal treatments – exacerbated inflammatory signaling through TLR9. Without TLR9 signaling, the in vivo efficacy of bactericidal drug treatment was rescued. This demonstrates that antibiotics can act in important ways distinct from bacterial inhibition: like causing treatment failure by releasing DNA that induces excessive inflammation. These data establish a novel link between how an antibiotic affects bacterial physiology and subsequent immune system engagement, which may be relevant for optimizing treatments to simultaneously clear bacteria and modulate inflammation.

Precise and efficient delivery of macromolecules into cells enhances basic biology research and therapeutic applications in cell therapies, drug delivery, and personalized medicine. While pulsed electric field electroporation effectively permeabilizes cell membranes to deliver payloads without the need for toxic chemical or viral transduction agents, conventional bulk electroporation devices face major challenges with cell viability and heterogeneity due to variations in fields generated across cells and electrochemistry at the electrode-electrolyte interface. Here, we introduce the use of microfabricated electrodes based on the conducting polymer poly(3,4-ethylenedioxythiophene) doped with polystyrene sulfonate (PEDOT:PSS), which substantially increases cell viability and transfection efficiency. As a proof of concept, we demonstrate the enhanced delivery of Cas9 protein, guide RNA, and plasmid DNA into cell lines and primary cells. This use of PEDOT:PSS enables rapid modification of difficult-to-transfect cell types to accelerate their study and use as therapeutic platforms.

Macrophages must scale inflammation to the trajectories of infections, escalating as pathogen loads rise, resolving as they fall. The cytokine IL-10 and its chromatin-level effector BCL-3 are critically important anti-inflammatory agents, yet how they avoid muting newly recruited cells before those cells read their own pathogen input has been unclear. Applying systematically varied consecutive TLR4 (Kdo2-Lipid A) stimuli to bone marrow-derived macrophages, we identify two coupled features. First, macrophages retain a quantitative memory of prior stimulation: only when a secondary TLR stimulus matches or exceeds a prior one, IκBα degradation, NF-κB/MAPK activation, and cytokine output increase. Second, IL-10 susceptibility is itself gated by TLR4 history: even a 100-fold IL-10 excess fails to suppress TNF-α in weakly primed cells. Both trace to history- and IL-10-dependent BCL-3 recruitment with p65 displacement at the Tnf κB site. Modeling shows how this licensing logic enables trajectory-aware responses that clear pathogens while limiting tissue damage.

All living organisms deploy cell-autonomous defenses to combat infection. In plants and animals, large supramolecular complexes often activate immune proteins for protection. In this work, we resolved the native structure of a massive host-defense complex that polymerizes 30,000 guanylate-binding proteins (GBPs) over the surface of gram-negative bacteria inside human cells. Construction of this giant nanomachine took several minutes and remained stable for hours, required guanosine triphosphate hydrolysis, and recruited four GBPs plus caspase-4 and Gasdermin D as a cytokine and cell death immune signaling platform. Cryo–electron tomography suggests that GBP1 can adopt an extended conformation for bacterial membrane insertion to establish this platform, triggering lipopolysaccharide release that activated coassembled caspase-4. Our “open conformer” model provides a dynamic view into how the human GBP1 defense complex mobilizes innate immunity to infection.

Checkpoint blockade revolutionized cancer therapy, but we still lack a quantitative, mechanistic understanding of how inhibitory receptors affect diverse signaling pathways. To address this issue, we developed and applied a fluorescent intracellular live multiplex signal transduction activity reporter (FILMSTAR) system to analyze PD-1-induced suppressive effects. These studies identified pathways triggered solely by TCR or requiring both TCR and CD28 inputs. Using presenting cells differing in PD-L1 and CD80 expression while displaying TCR ligands of distinct potency, we found that PD-1-mediated inhibition primarily targets TCR-linked signals in a manner highly sensitive to peptide ligand quality. These findings help resolve discrepancies in existing data about the site(s) of PD-1 inhibition in T cells while emphasizing the importance of neoantigen potency in controlling the effects of checkpoint therapy.

The enzyme NDPK-D promotes changes in mitochondrial function that support inflammasome activation.

Cleansing the cytosol: Most human cells, not just those belonging to the immune system, mount protective responses to infection when activated by the immune cytokine interferon-gamma (IFN-γ). How IFN-γ confers this function in nonimmune cells and tissues is poorly understood. Gaudet et al. used genome-scale CRISPR/Cas9 gene editing to identify apolipoprotein L-3 (APOL3) as an IFN-γ–induced bactericidal protein that protects human epithelium, endothelium, and fibroblasts against infection (see the Perspective by Nathan). APOL3 directly targets bacteria in the host cell cytosol and kills them by dissolving their anionic membranes into lipoprotein complexes. This work reveals a detergent-like mechanism enlisted during human cell-autonomous immunity to combat intracellular pathogens. Science , abf8113, this issue p. eabf8113 ; see also abj5637, p. 276