Despite extensive research, molecular differences in human populations and the influence of ancestry, age, geography, and diet are poorly understood. We performed comprehensive multiomics profiling (including genomics, transcriptomics, proteomics, metabolomics, lipidomics, metallomics, glycomics, and microbiomics) on samples from 322 healthy individuals of European, East Asian, and South Asian ancestry across multiple continents. We identified ethnicity-associated molecular features linked to host metabolism, autoimmune disease risk, drug metabolism, and neurodegenerative pathways. We uncovered ancestry- and geography-related molecular changes affecting metabolism, immune function, microbiome composition, and biological aging. Specific genetic variants and gene expression differences were associated with lipid metabolism and immune regulation. Geography influenced biological age: East Asians showed lower biological age in their ancestral regions, whereas individuals of European ancestry exhibited lower biological age in the US/Canada than in Europe. Diet-microbiome metabolism interactions displayed ethnicity-specific patterns, many related to health. This open access resource advances understanding of ethnicity-environment interactions and supports precision medicine.

Antibody-drug conjugates are among the fastest-growing anticancer therapies, delivering potent payloads directly to tumor cells with improved safety across hematologic and solid tumors. This review focuses on their biology and where the field needs to move as they expand into earlier-stage use and combinations that heighten the need for careful patient selection and toxicity management.

Mitochondria generate phosphoenolpyruvate (PEP), although its export mechanism and physiological roles were unknown. In this issue of Cell, Kajimura and colleagues identify SLC25A35 as the mitochondrial PEP exporter and uncover a previously unrecognized role for mitochondrial PEP synthesis in glyceroneogenesis in adipose tissue and upon development of fatty liver disease.

Bacterial viruses can send and receive signals to inform critical decisions. In this issue of Cell, Manley et al. and Gallego-del-Sol et al. independently identify crosstalk between bacterial viruses, leading us to wonder what the information warfare landscape between them looks like.

In this issue of Cell, Gongwer et al.1 and Johnson et al.2 identify the plasticity of intratelencephalic (IT) neuronal projections to anterior insula as a central substrate mediating the antidepressant effects of accelerated intermittent theta burst stimulation. These studies suggest a revolutionary future in which brain stimulation can enable circuit-specific plasticity.

Circadian rhythms are mainly generated by a gene regulatory network (GRN) constituted by transcription factors (TFs). Comparisons between plant and mammalian circadian clock GRNs suggest conservation of the network architecture rather than its components. Therefore, a rhythm-generating capacity is not restricted to canonical circadian clock GRNs. Here, we showed that although the circadian clock GRN was arrhythmic, circadian rhythms were maintained in refrigerated postharvest strawberries. Through systematic dual-luciferase assays and network analysis, we discovered a noncanonical GRN pillared by five uncharacterized TFs. We developed a heterologous reconstitution system and demonstrated the rhythm-generating ability of this GRN. Subsequent systematic evolution of ligands by exponential enrichment followed by high-throughput sequencing (SELEX-seq), electrophoretic mobility shift assay (EMSA), and DNA affinity purification (DAP)-qPCR analyses suggested that this GRN was responsible for the circadian rhythms of downstream genes. Fruit-specific perturbation of this GRN led to enhanced susceptibility to Botrytis cinerea. Collectively, our study identified a noncanonical quasi-circadian GRN, realized the heterologous reconstitution of eukaryotic circadian GRNs, and demonstrated its function in immune regulation.

Genetic variants produce complex phenotypic effects that confound current assays and predictive models. We developed variant in situ sequencing (VIS-seq), a pooled, image-based method measuring variant effects on molecular and cellular phenotypes in diverse cell types. Applying VIS-seq to ∼3,000 LMNA and PTEN variants yielded high-dimensional morphological profiles capturing changes in protein abundance, localization, activity, and cell architecture. VIS-seq identified a subset of linker-subdomain LMNA variants that increase nuclear circularity, in contrast to aggregating or low-abundance rod-subdomain variants that decrease circularity. VIS-seq also identified autism-associated PTEN variants that mislocalize and accurately distinguished autism-linked from tumor syndrome-linked and gnomAD control variants. Most variants impacted a multidimensional phenotypic continuum not recapitulated by any single functional readout. By linking variants to cell images at scale, VIS-seq illuminates how variant effects cascade from molecules to subcellular structures to cells, providing a framework for resolving the complexity of variant function.

Gene regulatory networks modulate the expression of the genome in response to signals and environmental conditions. Reconstructions of such networks can reveal the control principles cells use to maintain homeostasis and execute cell-state transitions. Here, we introduce a computational framework, dimension-scalable single-cell perturbation integration network (D-SPIN), that infers mechanistically interpretable and generative models of gene regulatory networks from single-cell mRNA-seq datasets collected across thousands of perturbation conditions. The models explain how perturbations modulate cell-state proportions by reconfiguring underlying regulatory interactions. Using large Perturb-seq and drug response datasets, D-SPIN models reveal key regulators of cell fate decisions and the coordination of distant cellular pathways in response to gene knockdowns and drug treatments, elucidate how combinations of immunomodulatory drugs induce combinatorial cell states through additive recruitment of gene expression programs, and simulate shifts in immune cell population structures across unobserved drug dosage combinations. D-SPIN provides a computational framework for revealing principles of cellular information processing and physiological control.

Directed migration of immune and epithelial cells is critical for rapid responses to tissue injury or infection. Endogenous electric fields, generated by disruption of the transepithelial potential across the skin, are thought to guide cells to wound sites. However, how single cells detect these electrical cues remains unclear. We identified Galvanin (TMEM154), a poorly characterized single-pass transmembrane protein, as required for electric-field-guided migration of rapidly moving cells. Expression of Galvanin is sufficient to confer electric-field-guided migration on otherwise non-responsive epithelial cells. Upon electric-field exposure, Galvanin rapidly relocalizes to the anodal side of cells, and in human neutrophils, relocalization is immediately followed by changes in spatial patterns of cellular protrusion and retraction. These data suggest Galvanin acts as a direct sensor of the electric field, transducing spatial information about a cell's electrical environment to the intracellular migratory apparatus to support directed cell migration.

Cell fate transitions are driven by regulatory circuitry, yet RNA velocity models cellular dynamics without explicitly accounting for gene regulatory interactions, limiting mechanistic insight. Conversely, gene regulatory network (GRN) inference methods largely neglect the dynamic nature of biological systems. To overcome this conceptual disconnect, we present RegVelo, a bottom-up, actionable, and interpretable deep learning framework that jointly models splicing kinetics and gene regulatory interactions. Across diverse biological systems, RegVelo provides reliable predictive power for terminal states, gene interactions, and perturbation simulations. By applying RegVelo to zebrafish neural crest development using full-length Smart-seq3 and shared gene expression and chromatin accessibility measurements, we delineate regulatory programs underlying fate specification. Guided by in silico perturbations and validated by CRISPR-Cas9 knockout and single-cell Perturb-seq, we establish tfec as an early driver and elf1 as a regulator of pigment cell fate. RegVelo establishes a quantitative framework for bridging gene regulation and cell fate decisions.

Spatial transcriptomics (ST) assays are transforming our understanding of tumor heterogeneity, but their high cost limits their application in large-scale biomarker discovery. Here, we present "Path2Space," a deep-learning model that predicts spatial gene expression directly from histopathology slides. Trained on extensive breast cancer ST data, Path2Space robustly predicts the spatial expression of thousands of genes, outperforming 21 established methods. Charting the tumor microenvironment (TME) of 976 breast cancer TCGA (The Cancer Genome Atlas) tumors, it accurately infers cell-type abundances and identifies three spatially defined breast cancer subgroups with distinct survival outcomes. Notably, the derived low-cost spatial TME landscapes enable more accurate predictions of patient response to chemotherapy and trastuzumab compared with costly conventional bulk-sequencing-based biomarkers. Path2Space thus offers a scalable, fast, and cost-effective alternative to molecular assays. It opens avenues for large cohort treatment biomarker discovery and translationally relevant insights into tumor biology, with potential applicability across many cancer indications.

Ischemia-reperfusion injury (IRI) is a major clinical challenge in transplantation, vascular surgeries, myocardial infarction, and stroke. Disruption of energy and redox homeostasis triggers ferroptosis, a regulated, iron-dependent form of cell death, leading to organ dysfunction. We identify an early and transient increase of lipid peroxidation in human liver transplants and validate it as a therapeutic target. FXT-001, a ferroptosis inhibitor with dual radical and iron-trapping activity, provides robust protection in preclinical models, including ex situ perfusion of porcine liver and lung grafts. In a split ex vivo machine perfusion setting using declined human donors, FXT-001 treatment preserves graft viability, whereas untreated lungs deteriorate. We also develop FXT-002 and FXT-003 with enhanced pharmacokinetic and safety profiles. These findings support the use of ferroptosis inhibitors as a therapeutic strategy in transplantation and other IRI-associated conditions.

Phytoalexins are core components of plant chemical defense against pathogens. However, the genetic basis and regulatory mechanisms governing their biosynthesis remain preliminary. Debneyol is a well-defined, broad-spectrum fungicidal phytoalexin. Here, we elucidate its biosynthetic pathway, key regulators, and activity against multiple pathogens. We show that debneyol is synthesized from farnesyl pyrophosphate (FPP) through three steps catalyzed by 5-epi-aristolochene synthase (EAS), 5-epi-aristolochene epoxidase (EAE), and epoxide hydrolase-1 (EH1). MCD1 (miR1919-targeted cell death-factor-1) interacts with EAS and EAE, enhancing their association and EAE activity and promoting debneyol biosynthesis. Increased MCD1 expression confers plant resistance not only against fungal but also viral and bacterial pathogens. Our work reveals a complete plant phytoalexin-based chemical defense machinery, opening avenues for engineering broad-spectrum plant resistance and industrial-scale debneyol production via synthetic biology.

Drought reshapes the plant root microbiota, yet the mechanistic drivers and consequences of this observation remain unclear. We discovered that suppression of host immunity and iron homeostasis is required for Streptomyces enrichment in roots during drought across diverse soils. Genetic and physiological manipulation of these host pathways confirmed their requirement in modulating Streptomyces root enrichment. Drought-induced suppression of iron uptake was conserved across the ∼160 mya monocot-eudicot divergence. Some Streptomyces strains enhanced plant growth and rescued iron uptake under drought. These benefits were uncoupled from Streptomyces root enrichment. They were instead shaped by intra-Streptomyces antagonism. We propose a two-step model: drought-driven downregulation of host iron and immune pathways enriches Streptomyces, while intra-genus dynamics fine-tune strain-level assembly and functional outcomes. Our data refine the idea that Streptomyces are enriched in roots during drought in response to a plant "cry for help" and consequently contribute to the alleviation of this abiotic stress.

Polyploidy, or whole-genome duplication (WGD), serves as both a significant evolutionary force and a potential evolutionary dead end, particularly among angiosperms. Despite the prevalence of polyploid organisms, instances of ancient polyploidy are surprisingly rare, presenting a paradox that remains poorly understood. In this study, we constructed a comprehensive genomic dataset of 470 angiosperm species and dated 132 ancient WGD events that are non-randomly distributed, revealing a clustering around pivotal periods of environmental upheaval and extinction. Notably, our findings highlight a strong correlation between waves of paleopolyploidization and significant events such as the Middle Miocene Disruption, the Eocene-Oligocene Transition (EOT), the Paleocene-Eocene Thermal Maximum (PETM), the Cretaceous-Paleogene (K-Pg) extinction, and different oceanic anoxic events (OAEs). We propose that polyploid organisms have an increased chance of survival during times of great environmental turmoil, a conclusion with important implications in the context of contemporary climate change and rapid global warming.

Human aging is characterized by complex structural and functional decline, but quantifying its heterogeneity and assessing biological age remain challenges. We present the mCAS (multicentric Chinese aging standardized cohort) developed from 2,019 Chinese individuals aged 18-91 years. Integrating high-dimensional clinical, physiological, and molecular-level data, we constructed a three-tiered aging framework: the core capacity clock (CC-clock) to quantify clinical physiological decline, the multimodal clock (MM-clock) with extensive parameter coverage and enhanced predictive precision, and organ-associated aging clocks. Cross-layer analysis demonstrates that plasma protein clocks not only capture chronological age but also serve as efficient proxies for systemic physiological capacity. Leveraging this framework for discovery, we identified the age-dependent accumulation of coagulation factors as a driver of multi-organ senescence and systemic inflammatory activation. This study provides a foundational framework that bridges molecular signatures with functional decline, identifies new biomarkers for aging assessment, and reveals a novel translational driver of aging.

Transcranial magnetic stimulation (TMS) is a widely used neuromodulation treatment for depression, but its mechanisms are poorly understood. Indirect clinical evidence suggests that TMS enhances plasticity within the prefrontal cortical target site and engages downstream networks. However, establishing causal mechanisms to help optimize the large stimulation parameter space has been challenging. Using an optogenetic model of accelerated intermittent theta burst stimulation (prelimbic [PL]-aiTBS) that drives rapid antidepressant-like effects, we examined cell type-specific effects on synapse-related gene expression, increased spine density, and increased excitatory currents in prefrontal intratelencephalic projection neurons. Whole-brain c-Fos immunolabeling, fiber photometry, chemogenetic, and projection-specific optogenetic manipulations revealed that PL-aiTBS activates a fronto-insular network that is necessary and sufficient for its antidepressant-like behavioral effects. Finally, we validate a key role for fronto-insular connectivity and TMS-evoked responses in the human insula using intracortical stereo-electroencephalogram (EEG) and resting-state fMRI. These results establish a fronto-insular circuit as a critical mediator of the antidepressant effects of aiTBS.

Small cell lung cancer (SCLC), a highly aggressive neuroendocrine malignancy, exhibits poor response to immunotherapy, and the underlying mechanisms remain unclear. Here, we identify a blood-brain barrier-like vascular gate (BVG) in SCLC, distinct from non-SCLC (NSCLC) and other cancers, composed of tightly connected endothelial cells, a thickened basement membrane, and dense pericyte coverage. Functionally, this blood-brain barrier-like vascular gate restricts immune cell infiltration, contributing to SCLC's immunotherapy resistance. Mechanistically, achaete-scute family basic-helix-loop-helix (bHLH) transcription factor 1 (ASCL1), the master transcription factor of SCLC, is essential for BVG formation by regulating insulin-like growth factor-binding protein 5 (IGFBP5), which activates the IGF1 signaling in endothelial cells. IGFBP5 knockout or treatment with the IGF1R inhibitor OSI-906 enhances CD8+ T cell infiltration and synergizes with anti-PD1 therapy. Furthermore, this ASCL1-IGFBP5-IGF1R axis and the BVG are conserved across multiple neuroendocrine cancers (NECs). Our findings reveal a previously unrecognized vascular gate in NECs and propose novel therapeutic strategies to enhance immunotherapy efficacy in these recalcitrant cancers.

Repetitive transcranial magnetic stimulation (rTMS) is an emerging treatment for brain disorders, but its therapeutic mechanism is poorly understood. We developed a mouse model of rTMS with superior clinical face validity and investigated the neural mechanism by which accelerated intermittent theta burst stimulation (aiTBS), the first rapid-acting rTMS antidepressant protocol, reversed chronic stress-induced behavioral deficits. Using fiber photometry, we showed that aiTBS drives distinct patterns of neural activity in intratelencephalic (IT) and pyramidal tract (PT) projection neurons in dorsomedial prefrontal cortex (dmPFC). However, only IT neurons exhibited persistently increased activity during both aiTBS and subsequent depression-related behaviors. aiTBS reversed stress-related loss of dendritic spines on IT, but not PT neurons, further demonstrating cell type-specific effects of stimulation. Chemogenetically inhibiting dmPFC IT, but not PT neurons, during rTMS blocked the antidepressant-like behavioral effects of aiTBS. Thus, we demonstrate a prefrontal mechanism linking rapid aiTBS-driven therapeutic effects to cell type-specific circuit plasticity.