Immune activation in plants triggers extracellular alkalinization, presumably by inhibiting plasma membrane H+-ATPases. The precise role and underlying mechanisms of this process remain poorly understood. Here, we show that Pseudomonas syringae bacteria induce apoplastic alkalinization not only at the site of infection but also in neighboring distal tissues to prime defenses and disease resistance in Arabidopsis. We show that several calcium-dependent protein kinases phosphorylate Ser899 of two major autoinhibited H+-ATPases to dampen their activity, leading to alkalinization. The distal alkalinization is accompanied by the transcriptional activation of phytocytokines, including plant elicitor peptides, serine-rich endogenous peptides, and their receptors. We show that these phytocytokines promote distal alkalinization and disease resistance, whereas the apoplastic alkalinization sensitizes the phytocytokine perception that further induces phytocytokine genes. Our study suggests that apoplastic alkalinization and phytocytokine gene expression mutually potentiate and act as a combined signal that propagates in local-distal communication and disease resistance priming.

The small interfering RNA (siRNA) pathway directs broad-spectrum antiviral defense through RNA silencing so that virulent infection requires efficient suppression of the defense mechanism. Here, we show that strigolactone (SL) hormone signaling promotes antiviral silencing in rice plants by transcriptional activation of RNA-dependent RNA polymerase 1 (RDR1) and RDR6. We demonstrate that protein P3 of the rice grassy stunt virus (RGSV) blocks SL signaling by directly sequestering the receptor DWARF14 from DWARF3. Structural and functional analyses of the P3-DWARF14 complex reveal that the aspartic acid at position 102 (D102) of DWARF14 is essential for the P3 interaction but not for SL perception. Notably, a single D102N substitution of DWARF14, introduced into two rice cultivars by cytosine base editing (CBE) confers resistance against RGSV by blocking viral suppression of SL signaling-dependent antiviral silencing. Our findings establish a transgene-free strategy for engineering disease resistance by precise genome editing of the SL receptor to escape pathogen suppression of the endogenous defense pathway.

Solid tumors harbor immunosuppressive microenvironments that inhibit tumor-infiltrating lymphocytes (TILs) through the voracious consumption of glucose. We sought to restore TIL function by providing them with an exclusive fuel source. The glucose disaccharide cellobiose, which is the building block of cellulose, contains a β-1,4-glycosidic bond that animals (or their tumors) cannot hydrolyze, but fungi and microbes have evolved enzymes to catabolize cellobiose into useful glucose. We equipped mouse T cells and human chimeric antigen receptor (CAR)-T cells with two proteins derived from fungi that enable import and hydrolysis of cellobiose, and we demonstrated that cellobiose supplementation during glucose withdrawal restores key anti-tumor T-cell functions: viability, proliferation, cytokine production, and cytotoxic killing. Engineered T cells offered cellobiose suppress tumor growth and prolong survival. Offering exclusive access to a natural disaccharide augments cancer immunotherapies. This approach could be used to answer questions about glucose metabolism across many cell types, biological processes, and diseases.

Ferroptosis is a tumor-suppressive mechanism with therapeutic potential. While canonical ferroptosis is usually triggered by inducers, such as erastin and RSL-3, or by glutathione peroxidase (GPX)4 loss, how ferroptosis occurs naturally in vivo without these triggers has been unclear. Building on evidence that p53 can mediate ferroptosis as a natural tumor-suppressive pathway, we describe a noncanonical, in vivo ferroptosis driven by reactive oxygen species (ROS)-induced phosphatidic acid (PA) peroxidation that proceeds without inducers. We identify GPX1 as a key regulator of this ROS-induced ferroptosis by modulating PA peroxidation. GPX1's effects depend on OSBPL8, an endoplasmic reticulum (ER)-membrane-associated oxysterol-binding protein. ROS-driven lipid peroxidation accumulates at the ER before plasma membrane rupture and cell death; GPX1 is recruited to the ER via OSBPL8 and directly reduces oxidized PA. OSBPL8 and GPX1 are overexpressed in cancers; knockdown of either promotes ROS-induced ferroptosis and suppresses tumor growth. Our data link the GPX1-OSBPL8 axis to in vivo ferroptosis and tumor suppression.

In natural and artificial settings, fluid flow and hydrodynamic interactions shape how bacteria attach to surfaces and form biofilms. Tao et al. show that motile E. coli can swim upstream through microstructured environments, revealing how the interplay between geometry and flow governs invasion dynamics and suggesting design principles to prevent bacterial colonization.

In this issue of Cell, Shi and colleagues introduce a urine-based liquid biopsy approach that reshapes how treatment response in NMIBC is assessed. They use urine tumor DNA to detect minimal residual disease and disentangle the contributions of surgery and immunotherapy to disease control, with implications extending beyond bladder cancer.

The tumor microenvironment drives cancer progression, yet neural contributions remain underexplored. Zhang et al. unravel a signaling circuit involving cancer cells, sensory neurons, and cancer-associated fibroblasts that promotes desmoplasia and excludes cytotoxic T cells, positioning the neuron-fibroblast axis as a therapeutic vulnerability and potential predictor of immunotherapy response.

Rooted in place, plants must continuously respond and adapt to their ever-changing environment to survive, especially as climate change intensifies. Calcium ions (Ca²⁺) play a central role in plant responses to both biotic and abiotic challenges. Ca²⁺ signaling involves the coordinated action of channels and transporters that generate specific "Ca²⁺ codes," along with Ca²⁺-binding proteins that act as sensors to decode them. Studies over the past several decades have explored the molecular components that form the toolkit, pathways, and networks for the coding and decoding of Ca²⁺ signals in plants. This review focuses on the emerging mechanisms of calcium signaling in plants, beginning with an overview of the universal conceptual framework that governs the coding and decoding of Ca²⁺ signals, followed by examples of pathways in plant growth and reproduction, responses to abiotic stress and microbes, and systemic signaling in plants.

T cell receptor (TCR)-T cell therapy is effective for solid tumors, yet identifying potent, specific TCRs for tumor antigens is challenging. Conventional affinity maturation may cause fatal off-target toxicity. Catch bonds play a crucial role in mechanosensory receptor signaling, including the TCR, but their formation and potential to mitigate the challenges of TCR-T remain unclear. Here, we demonstrate that histidine scanning can identify TCR hotspots capable of forming additional catch bonds, which can be randomized to create TCR libraries for screening low-affinity, higher-potency variants. Mechanistically, histidine facilitates the formation of hydrogen bonds and salt bridges and fortifies the intracellular signaling cascade. Using this approach, we engineered different TCRs specific for various antigens, without off-target toxicity or on-target toxicity. Our findings introduce a universal method of engineering low-affinity, high-potency TCRs for safe TCR-T cell therapy, without requiring the structure for designing TCR libraries. Additionally, histidine scanning can be broadly applied to other mechanosensory ligand-receptor systems.

Plant growth relies on the activity of key transcription factors. Here, we uncover a mechanism for organ-specific growth driven by opposing electrochemical signals that propagate in a cell-type-specific manner. Using a genetically encoded pH sensor and a pH-sensitive dye, we show that apoplastic pH in epidermal cells oscillates antiphasically relative to phloem pH. The clock component CCA1 lowers apoplastic pH in hypocotyl epidermal cells while increasing it in companion cells. This opposing regulation promotes hypocotyl growth but inhibits root elongation. Mechanistically, CCA1 activates auxin signaling in shoots while repressing sucrose transporter 2 and the electrogenic (H+)-pump ATPase AHA3 by directly binding their promoters. The repression decreases sucrose loading into the phloem and slows transport velocity. Expressing CCA1 in the phloem is sufficient to inhibit root elongation, whereas AHA3 overexpression in CCA1 overexpressing seedlings rescues root growth. Thus, a circadian rheostat orchestrates electrochemical signals to optimize source capacity with sink demand.

Bifidobacterium longum and B. infantis are pioneer colonizers of the neonatal gut and are widely used as probiotics to support infant growth, development, and disease resistance. However, commercial strains derived largely from high-income countries (HICs) may be suboptimal for infants in low- and middle-income countries (LMICs). We assembled a global genomic atlas of more than 4,000 genomes from 48 countries, increasing representation from LMICs by 12- to 17-fold. High-resolution phylogenomic and functional analyses support delineating B. longum and B. infantis as distinct species with divergent functions and epidemiological patterns. B. infantis dominates early-life microbiota in LMICs but is rarely detected in HICs. Natural B. infantis strains show extreme biogeographic stratification and predicted adaptations to local plant-glycan-rich diets and breast-milk-derived substrates, including urea and B vitamins. This genomic resource enables genome-guided selection of geographically matched strains to inform more effective probiotics and precision microbiome therapeutics for diverse infant populations.

We present PocketXMol, an atom-level model that unifies generative tasks related to protein pocket interactions. Using atomic prompts as task specifications, PocketXMol supports various molecular tasks, including structure prediction and de novo design of small molecules and peptides, without task-specific fine-tuning. PocketXMol achieved strong performance on 11 of 13 computational benchmarks and remained competitive on the remaining two, outperforming 55 baseline models. We applied PocketXMol to design caspase-9-inhibiting small molecules, achieving efficacy comparable with commercial pan-caspase inhibitors. We also adopted PocketXMol to generate PD-L1-binding peptides, resulting in a success rate that largely exceeds library screening. Three representative peptides underwent further experiments, which validated their cellular specificity and confirmed their potential for molecular probing and therapeutics. PocketXMol provides a general platform for AI-aided drug discovery and enables a wide range of future applications.

Insulating sheaths of myelin accelerate neuronal communication in the mammalian brain. Oligodendrocytes that produce myelin are generated throughout life to gradually increase myelin coverage, but these dynamics have not been defined brain-wide across the lifespan. We developed a cellular mapping pipeline involving tissue clearing, lightsheet microscopy, and AI-assisted analysis to identify the precise location of millions of oligodendrocytes and assess regional myelin density in the mouse brain. These atlases revealed the diversity of oligodendrocyte patterning, which was consistent between brain hemispheres, individuals, and sexes but displayed both age- and region-specific differences. Integration of these atlases with transcriptomic and ultrastructural datasets highlighted underlying mechanisms that may control this patterning. In models of demyelination and disease, we identified regions of enhanced oligodendrocyte resilience and vulnerability and white matter injury near β-amyloid plaques, demonstrating the utility of this pipeline for defining brain-wide oligodendrocyte dynamics in both health and disease.

Blood factors transfer the benefits of exercise to the aged brain independent of physical activity. Here, we show that the liver-derived exercise factor (exerkine) glycosylphosphatidylinositol (GPI)-specific phospholipase D1 (GPLD1), a GPI-degrading enzyme, reverses aging- and Alzheimer's-related memory loss by targeting the brain vasculature. GPLD1 has the potential to cleave over 100 putative GPI-anchored proteins, necessitating the identification of downstream targets that mediate cognitive rejuvenation for translational application. We identified GPI-anchored tissue-nonspecific alkaline phosphatase (TNAP) on the brain vasculature as a GPLD1 substrate. Mimicking age-related increases in cerebrovascular TNAP impaired blood-brain transport and cognition in young mice and mitigated GPLD1-induced cognitive benefits in aged mice. Inhibiting TNAP recapitulated the benefits of GPLD1 in old age, restoring youthful hippocampal transcriptional signatures and rescuing cognition. In an Alzheimer's disease model, increasing GPLD1 or inhibiting TNAP ameliorated Aβ pathology and improved cognitive deficits. We thus identify brain vasculature as a mediator of the cognitive benefits of a liver-to-brain exercise axis.

In contrast to living organisms, viruses were long thought to lack protein synthesis machinery and instead depend on host factors to translate viral transcripts. Here, we discover that giant DNA viruses encode a distinct and functional IF4F translation-initiation complex to drive protein synthesis, thereby blurring the line between cellular and acellular biology. During infection, eukaryotic IF4F on host ribosomes is replaced by an essential viral IF4F that regulates viral translation, virion formation, and replication plasticity during altered host states. Structural dissection of viral IF4F reveals that the mRNA cap-binding subunit mediates exclusive interactions with viral mRNAs, constituting a molecular switch from translating host to viral proteins. Thus, our study establishes that viruses express a eukaryotic translation-initiation complex for protein synthesis, illuminating a series of evolutionary innovations in a core process of life.

Endothelial cells (ECs) are essential components of the vertebrate circulatory system; however, a comprehensive atlas characterizing how ECs acquire organ-specific transcriptomic heterogeneity has not been established. Here, we generated a time-series endothelial resource covering the entirety of mouse embryonic development, including 26 time points and 8 organs. Time-series multi-organ comparison revealed emergence timing and lineage trajectory of organotypic ECs together with organ-specific genes and pathways. Using these resources, we found that most ECs showed distinguishable organ specificity before late gestation. The organotypic EC-enriched genes were associated with vascular function in the organs. Human and mouse pulmonary ECs underwent an evolutionarily conserved transcriptional transition. Endothelial-specific knockout of Casz1, a pulmonary EC-enriched transcription factor, resulted in impaired vascular growth, disturbed pulmonary endothelial organotypic differentiation, and deficient epithelial-EC crosstalk. Our work provides a powerful endothelial resource that reveals fundamental principles of organ-specific EC differentiation and uncovers previously unknown molecular mechanisms governing lung-specific vascular development.

Autophagy, a programmed self-eating process, underlies the progression of multifactorial diseases like pancreatic ductal adenocarcinoma (PDA). Except for nutrient availability, the contribution of microenvironmental factors to autophagy regulation is not well understood. Through integrating functional genomics and tumor-like 3D cultures, we show that human PDA cells regulate their autophagy levels by sensing the extracellular matrix (ECM) via the integrinα3-Hippo-YAP1 axis. The spatial proximity of PDA cells to the ECM shapes their intracellular autophagy levels, leading to heterogeneous biological responses. Specifically, PDA cells with low autophagy levels are proliferative, whereas those with high autophagy levels display better tolerance to chemotherapies. Targeting the ECM-mediated autophagy regulation reduces autophagic heterogeneity, alters PDA growth, and shapes antitumor responses to FDA-approved therapies. In summary, we have characterized a non-metabolic regulation of autophagy through ECM sensing, opening the possibility to investigate and target ECM-specific outputs in diseases.

The tumor microenvironment (TME) poses a major barrier to effective immunotherapy, yet high-throughput perturbation-mapping approaches to dissect TME spatial complexity and its contextual immune modulators remain lacking. Here, we introduce CRISPR-laser-captured microdissection (LCM) integration mapping of the tumor-immune microenvironment (CLIM-TIME), a scalable platform that integrates CRISPR screening with LCM of metastatic tumors for transcriptomic, deconvolution, and immunofluorescence analyses. CLIM-TIME enables spatially resolved mapping of how tumor suppressor gene (TSG) loss reshapes the TME and modulates immune responses. We identified seven distinct TME subtypes, revealing that DNA repair and Polycomb repressive complex (PRC) TSG loss is linked to immune-infiltrated TMEs sensitive to T cell therapy. In contrast, knockouts of TSGs in the Hippo pathway promoted immune evasion and therapy resistance by fostering myeloid-enriched but T cell-excluded TMEs with elevated extracellular matrix (ECM). Targeting the ECM-crosslinking enzyme LOXL2 effectively remodeled the metastatic TME, enhancing T cell infiltration and improving therapeutic efficacy in lung metastases across multiple cancers.

A recent first-in-human clinical trial demonstrated that survival in glioblastoma (GBM) patients following rQNestin34.5v.2 oncolytic virus treatment was associated with immune activation signatures. This study was registered at ClinicalTrials.gov (NCT03152318). Here, we provide in situ evidence of ongoing T cell-mediated cytotoxicity against tumor cells at late time points following single treatment, with deep and persistent T cell infiltration into tumor regions. Shorter distances between cleaved caspase-3+ tumor cells and granzyme B+ T cells were associated with longer progression-free survival following treatment. Pre-existing tumor-infiltrating T cells expanded locally upon treatment, correlating with longer overall patient survival. T cells with an early activation program closely interacted with tumor cells and were strongly enriched upon treatment. Viral remnants were restricted to necrotic regions, while T cells infiltrated deeply into live tumor regions. These data demonstrate that single oncolytic virus treatment can expand pre-existing T cell clones and trigger persistent T cell-mediated immunity against GBM.

Microbes are ubiquitous on Earth, forming microbiomes that sustain macroscopic life and biogeochemical cycles. Microbial dispersal, driven by natural processes and human activities, interconnects microbiomes across habitats, yet most comparative studies focus on specific ecosystems. To study planetary microbiome structure, function, and inter-habitat interactions, we systematically integrated 85,604 public metagenomes spanning diverse habitats worldwide. Using species-based unsupervised clustering and parameter modeling, we delineated 40 habitat clusters and quantified their ecological similarity. Our framework identified key drivers shaping microbiome structure, such as ocean temperature and host lifestyle. Regardless of biogeography, microbiomes were structured primarily by host-associated or environmental conditions, also reflected in genomic and functional traits inferred from 2,065,975 genomes. Generalists emerged as vehicles thriving and facilitating gene flow across ecologically disparate habitat types, illustrated by generalist-mediated horizontal transfer of an antibiotic resistance island across human gut and wastewater, further dispersing to environmental habitats, exemplifying human impact on the planetary microbiome.