Human genome sequencing typically relies on mapping reads to a reference genome to call variants, but this approach introduces technical biases, excluding duplicated and structurally polymorphic regions of the genome. To overcome this, we present a telomere-to-telomere genome benchmark with near-perfect accuracy across 99.4% of the diploid HG002 genome. This benchmark adds 701.4 Mb of autosomal sequence and both sex chromosomes (216.8 Mb), which were absent from prior benchmarks. We annotated genes and repeats on both haplotypes, including 19,956 protein-coding genes on the maternal haplotype and 19,190 on the paternal haplotype, and developed new methods to measure the accuracy of reads, phased variant call sets, and assemblies against a diploid reference. Genome-wide analyses show that de novo assembly resolves 2%-7% more sequence and outperforms variant calling accuracy by an order of magnitude, expanding the reach of genomic medicine to the entire genome and enabling a new era of personalized genomics.

Classical evolutionary theories of aging, including antagonistic pleiotropy (AP) and the disposable soma theory (DST), explain why aging exists but are often applied without considering how sex-specific reproductive strategies shape the forces of natural selection on survival. They do not explain why females consistently outlive males across taxa, despite their greater reproductive investment, or why in some contexts, such as eusocial queens, extraordinary fecundity is coupled with exceptional longevity. To explain these patterns, we propose the reproductive resilience hypothesis (RRH), which posits that when reproductive success depends on prolonged survival and caregiving, natural selection favors coupling reproduction with enhanced somatic maintenance rather than trading it off. We suggest that reproductive events, including age at sexual maturity, pregnancy, lactation, and menopause, are pivotal life-history transitions and must be explicitly integrated into studies of sex differences that drive aging and susceptibility to age-related diseases. We further propose that loss of reproductive resilience is a sex-specific hallmark of aging that coordinates the emergence of multiple downstream hallmarks, helping explain the acceleration of systemic aging and age-related disease following reproductive decline. We propose that, for these reasons, studying females should be prioritized, as it has unique implications for discovering pathways to slow aging and prevent age-related diseases, ultimately benefiting both women and men.

In this issue of Cell, Wang et al. reveal the mechanism of a bacterial antiphage system that contains two reverse transcriptases. Through an unprecedented process, the enzymes synthesize double-stranded DNA; one uses a noncoding RNA template and the other uses its amino acid residues to template and prime DNA synthesis.

Two decades after the Human Genome Project, we finally have the ability to read the complete genome of any human and (nearly) any species. These sequences provide the ideal foundation for training predictive models of the genome that will accelerate basic research, enable accurate diagnostics, and guide precision medicine.

Immunosuppressed patients with non-melanoma skin cancer experience worse clinical outcomes, yet the tumor immune microenvironment associated with systemic immunosuppression remains incompletely defined. Using integrated single-cell, spatial transcriptomic, multiplex immunofluorescence, and spatial epigenomic profiling across immunocompetent and immunosuppressed tumors, we found that overall immune-cell composition was largely preserved despite differences in immune-cell distribution, spatial organization, and T cell clonality. Immunosuppressed tumors demonstrated reduced intratumoral macrophage densities, decreased T cell clonal diversity, altered antigen-presenting cell and T cell spatial interactions, and distinct fibroblast- and macrophage-associated spatial niches. Multi-cohort validation across complementary spatial and single-cell platforms identified consistent alterations in innate-adaptive immune organization in immunosuppressed tumors. Together, these findings define spatial and functional remodeling of the tumor immune microenvironment under systemic immunosuppression and provide a framework for future therapeutic investigation in high-risk patients.

Three-dimensional (3D) histology provides volumetric insights into tissue microarchitectures across entire specimens, holding great promise for more accurate prognostication. However, existing methods are too slow for intraoperative consultations. We present ULTRA (ultrarapid cleared stimulated Raman with AI), a label-free, stain-free, fixation-free, and section-free platform that leverages the chemical specificity of stimulated Raman scattering (SRS) microscopy for rapid 3D histological analysis. Through the synergistic development of a one-step tissue-clearing protocol and unsupervised learning algorithms, ULTRA delivers high-resolution, formalin-fixed, paraffin-embedded (FFPE)-grade deep 3D virtual histology within 30 min, covering orders of magnitude more tissue than slide-based methods. In human surgical glioma samples, ULTRA accurately resolves key histological features in 3D and delineates depth-dependent tumor infiltration margins at single-cell resolution. By compressing 3D histology from days or hours to an intraoperative timescale, ULTRA addresses a critical clinical gap and enables more informed surgical decision-making in the operating room.

Activation-induced cytidine deaminase (AID) accomplishes somatic hypermutation (SHM) of VH(D)JH genes in germinal center B cells for antibody diversification and affinity maturation. How AID specifically targets VH(D)JH remains unclear. We report the discovery of LINE-1 (L1) retrotransposons upstream to many VH genes in the immunoglobulin locus. These L1s are evolutionarily old, truncated, and retrotransposition dead. Recombined VH promoters generate long, strong antisense RNAs encoding upstream L1s, triggering the human silencing hub (HUSH) complex and AID recruitment, which we term L1-driven SHM. We show that L1-driven SHM occurs in vivo using HUSH conditional knockout mice and engineered mice with VH genes devoid of upstream L1s. Insertion of transcriptionally active L1s at non-immunoglobulin loci endogenously lacking upstream L1s promotes off-target SHM. We demonstrate that old retrotransposons serve physiological roles, and our findings reveal how B cells co-opted an anti-retrotransposon silencing mechanism to promote antibody diversity. In doing so, we established a new link between cell-intrinsic innate and adaptive immunity.

Breastfeeding reduces the risk of severe lower respiratory infections (sLRIs), a leading cause of infant mortality; however, the protective mechanisms remain elusive. Here, we demonstrated that the absence of milk-derived osteopontin (OPN), highly expressed in colostrum, predisposes neonatal mice to viral and bacterial sLRI, consequent to disrupted dendritic cell (DC) hematopoiesis in the developing liver and lung. Amelioration of disease severity by oral OPN supplementation was associated with increased enteric abundance of Lactobacillaceae and elevated levels of serum 3-phenyllactic acid (PLA), a peroxisome proliferator-activated receptor gamma (PPARγ) agonist. Supplementation with PLA or the PPARγ agonist rosiglitazone restored lung DC hematopoiesis via airway epithelium-derived chemokine ligand 25 (CCL25)-mediated recruitment of lymphoid-myeloid primed progenitors and induction of a supportive lung niche. PLA-induced DC hematopoiesis and disease tolerance were attenuated by plasmacytoid DC depletion, immunoneutralization of stem cell factor, or genetic deletion of airway epithelial Flt3L. Our findings elucidate a microbiome-host interaction by which milk OPN confers protection against sLRI.

The brain vasculature comprises diverse specialized cells that are essential for brain function, yet their spatial organization remains poorly understood. Here, we construct a comprehensive cerebrovascular cell atlas encompassing 314,535 transcriptomes that captures the arteriovenous axis and defines consensus cell states. We then perform spatial transcriptomics to map 1,529,740 cells across the human temporal cortex and hippocampus, uncovering stereotyped micro-communities termed vascular cell ensembles. These ensembles comprise specialized subsets of endothelial cells, mural cells, fibroblasts, and perivascular macrophages that align with the arteriovenous architecture to coordinate segment-specific functions, such as neurovascular coupling, blood-brain barrier transport, and immune surveillance. By overlaying genetic risk and pharmacologic reactivity, we identify ensemble-specific susceptibilities and candidate therapeutic targets across neurological diseases, including small vessel disease and stroke. This study provides a resource to dissect the spatial and functional logic underlying human cerebrovascular biology and establishes a blueprint for decoding neurological disease susceptibility and therapeutic response.

Amino acid levels fluctuate across diverse pathological conditions. Whether such amino acid modulations directly shape pathophysiology by regulating host gene expression remains unknown. We found that extracellular arginine restriction, observed in cancer and infection, represses specific arginine tRNAs-directly suppressing translation of major histocompatibility complex I (MHC class I) and antigen presentation. Arginine regulation of MHC class I was codon-usage dependent, as synonymous codon mutations prevented MHC class I modulation. Dietary arginine restriction impaired anti-viral immunity against influenza and SARS-CoV-2 and increased colon tumorigenesis. Conversely, increasing arginine availability via dietary supplementation or myeloid-specific arginase 1 deletion enhanced MHC class I protein levels, suppressed colon tumorigenesis, and improved viral infection outcomes. These disease-modulating effects were abolished in β2-microglobulin (B2m)-deficient mice. Thus, dietary modulation of a single amino acid critically influences codon-biased translation and MHC class I-mediated immunity to respiratory viral infections and cancer, revealing an unexpected mechanism and disease hazard for arginine deficiency and highlighting potential for amino acid-based translation modulation therapy.

The regulation of 3D cell shape is a fundamental problem of life. In multicellular tissues, cell shape emerges through the balance of forces inside and outside the cell. In epithelia, the basement membrane (BM) is the first extracellular barrier that cells sense biochemically and mechanically. Despite this, little is known about how BM mechanical properties are regulated and how they impact cell shape. Through mathematical modeling, we show that the stress relaxation time of the BM can regulate cell shape. Using molecular dynamics simulations, we show that the stress relaxation time of a collagen IV network can be inferred from the lifetime of collagen IV molecules. To measure collagen IV lifetime in vivo, we develop a fluorescent timer reporter for collagen IV and show that perlecan modifies collagen IV lifetime. This cross-disciplinary approach establishes a multiscale framework to probe matrix turnover, and its regulation and function in cell shape control.

Tick-borne orthonairoviruses, including the emerging wetland virus (WELV), pose a growing public health concern as cases increase, yet their pathogenesis remains unclear. Here, we show that WELV infection causes fatal liver dysfunction in patients, characterized by elevated hepatic enzymes, triacylglycerol accumulation, and hyperinflammation. WELV induces gasdermin E (GSDME)-dependent pyroptosis in hepatocytes through mitochondrial and Fas-mediated apoptotic pathways. Viral RNA activates RIG-I/CASP3-mediated GSDME cleavage, while viral nucleoprotein undergoes CASP3-dependent processing, forming a negative regulatory feedback loop. GSDME directly interacts with fatty acid synthase (FASN) and blocks K48-linked ubiquitination to inhibit FASN degradation, driving lipid metabolic reprogramming and lethal hepatic steatosis. GSDME knockout abolishes pyroptosis and metabolic dysregulation, conferring complete protection against WELV infection. Clinically approved caspase and FASN inhibitors mitigate liver pathology and improve survival in WELV-infected mice. These findings establish a pyroptosis-metabolism axis driving orthonairovirus pathogenesis, highlighting GSDME as a critical determinant of liver injury and a promising target for antiviral therapy.

Immune aging impairs T cell-mediated tumor control as well as cancer immunotherapy outcomes. The most important drivers of T cell dysfunction in aged tumors remain unknown. We performed single-cell CRISPR screens to identify Dusp5 and Zfp219 as key regulators of CD8+ T cell persistence and effector differentiation within aged tumors. Loss of Dusp5 increased extracellular signal-regulated kinase (ERK) phosphorylation and globally enhanced T cell proliferation. Conversely, Zfp219 deletion induced epigenetic reprogramming and increased expression of cytotoxic molecules, enhancing antitumor immunity specifically in aging. Levels of the human ortholog ZNF219 were higher within intratumoral CD8+ T cells from older cancer patients, which correlates with worse survival following immunotherapy. Zfp219 ablation synergized with immune checkpoint inhibitors to expand effector-like CD8+ T cells, leading to tumor clearance in aged mice. Our findings highlight Dusp5 and Zfp219 as critical drivers of age-related T cell dysfunction that can be targeted to rejuvenate antitumor immunity in older cancer patients.

Recent advances in AI inspire visions of universal models of biology. Yet living systems are evolved, emergent processes whose behaviors cannot be inferred from their parts alone. We propose grounding AI in canonical biological processes, constructing data-driven world models with explicit mechanistic links across molecules, cells, and their dynamics in space and time.

Defense-associated reverse transcriptase (DRT) systems mediate antiviral immunity through distinct modes of cDNA synthesis: class 1 DRTs catalyze untemplated synthesis, whereas class 2 DRTs polymerize non-coding RNA-templated products. However, how these distinct modes drive defense remains unclear. Here, we report that DRT3 immunity arises when class 1 and class 2 RT activities cooperate to produce self-complementary double-stranded DNA (dsDNA). DRT3a uses a 5'-ACACAC-3' RNA template to synthesize poly-(dTdG) repeats, whereas DRT3b synthesizes poly-(dCdA) repeats without any nucleic acid template. Cryo-electron microscopy reveals that DRT3b forms a hexamer and uses active-site-adjacent residues as deoxyadenosine and deoxycytidine gates to enforce alternating nucleotide addition, representing a unique example of amino-acid-templated DNA polymerization. DRT3 is toxic in cells lacking RecBCD, implicating host recombination machinery in limiting dsDNA accumulation, and the phage-encoded RecBCD inhibitor Gam triggers DRT3-mediated abortive infection. These findings reveal how two polymerases with distinct templating strategies generate complementary DNA for antiviral defense.

Cancer management remains fragmented across its continuum, from late-stage diagnosis and salvage therapies to non-personalized surveillance. Here, we present Oncoformer, a unified multimodal transformer model trained on the China Oncology Multimodal Prediction and Surveillance Study (COMPASS) cohort (3.67 million individuals, 17.7 million clinical visits) and validated on independent external cohorts, including the UK Biobank. Oncoformer integrates longitudinal electronic health records with chest X-ray imaging to address multiple clinical tasks: pan-cancer diagnosis (area under the receiver operating characteristic curve [AUROC] = 0.956), future cancer prediction up to 1 year before diagnosis (AUROC = 0.869), tumor stage inference (mean AUROC > 0.90), patient-specific treatment-response forecasting, and recurrence-free survival stratification across ten cancer types (all p < 0.01). Staging predictions were independently validated against postoperative pathological endpoints and shown to converge on core cancer genomic pathways. By translating routine clinical data into a dynamic view of cancer evolution, Oncoformer provides a framework for risk-informed cancer prediction and treatment stratification using routine clinical data.

Systematically simulating and predicting phenotypic effects of diverse interventions across heterogeneous cellular environments is central to the vision of artificial intelligence virtual cell (AIVC). However, disparities in perturbagen modalities, assay formats, and data production efficiency hinder unified modeling and analysis of genetic and chemical screens. This study presents UniPert-G2CP, a two-stage deep learning framework that bridges genetic and chemical screens by unifying multimodal molecular perturbagen (cause) representations and enabling genetic-to-chemical perturbation phenotype (effect) transfer learning. Validated on large-scale genetic and chemical screening datasets, UniPert-G2CP enables more efficient, accurate, robust, interpretable, and generalizable simulation of multicellular and multidomain perturbation cause-effect spaces. Further joint analysis of these spaces reveals cellular heterogeneity underlying drug responses, providing mechanistic insights into drug action and resistance. Collectively, UniPert-G2CP advances universal biological causal modeling, accelerates AIVC realization, and expands the potential of AI-powered precision medicine.

Mg2+ is essential for all living organisms, yet its transport across mammalian membranes remains poorly understood. Here, we present cryoelectron microscopy (cryo-EM) structures of a full-length mammalian Mg2+ transporter on the plasma membrane, human CNNM4, in outward-facing and occluded states, revealing an unexpected tetrameric assembly organized as a dimer of asymmetric dimers-distinct from the symmetric dimers in prokaryotic homologs and long assumed for eukaryotic CNNMs. We show that Mg2+/ATP binding stabilizes the dynamic intracellular domains and promotes tetramerization, while an acidic patch binds additional Mg2+, potentially acting as a sensor to couple cytoplasmic Mg2+ levels to transport activity. Within the transmembrane domain, a key glutamate flips upon Na+ binding and destabilizes the Mg2+-binding site in the outward-facing state, thereby promoting Mg2+/Na+ exchange. Together, these findings establish a mechanistic framework for CNNM transport and regulation that diverges from prokaryotic models and links CNNM function to human physiology and disease.

Drought threatens crop productivity, yet enhancing tolerance often compromises yield. Abscisic acid (ABA) signaling is central to drought response, but its deep conservation can constrain adaptive flexibility. Here, we identify ROAD1 (rice orphan gene adapted for drought 1), an Oryza-specific orphan gene that confers robust drought tolerance without obvious growth defects under normal conditions. ROAD1 originated from Oryza meridionalis, and its functional allele, ROAD1C, was selected during japonica domestication. In field trials, elite rice lines carrying ROAD1C exhibited up to 34.75% higher grain yield than corresponding controls under drought. Mechanistically, ROAD1 bypasses the canonical ABA receptor-ligand complex by binding the phosphatase OsPP2C68, preventing sucrose non-fermenting 1-related protein kinases 2 (SnRK2) dephosphorylation and activating downstream responses. ROAD1 also interacts with protein phosphatase 2C (PP2C) orthologs from maize, wheat, and Arabidopsis, and heterologous expression of ROAD1C enhances drought tolerance in Arabidopsis, rapeseed, maize, wheat, and poplar. These findings reveal that an Oryza-specific orphan gene can co-opt conserved signaling for potential trans-species drought tolerance.

The beneficial fungus Trichoderma enhances plant growth and stress tolerance through poorly understood mechanisms. Here, we show that Trichoderma harzianum swollenin ThSWO contributes to efficient root colonization and plant growth promotion. ThSWO traverses the plant cell wall and localizes to the plasma membrane, where it interacts with ABC transporter AtABCB5, which we establish as a bona fide auxin efflux carrier. ThSWO binding to NBD2 and R-domain faces of AtABCB5 prosmotes phosphorylation at Ser640 and Ser644, enhancing indole-3-acetic acid (IAA) efflux and triggering auxin-associated responses, including cell wall acidification, membrane potential transitions, and accelerated cytoplasmic streaming. Structure-guided substitutions at the AtABCB5-ThSWO interface differentially affected transporter binding and lateral root promotion, supporting the conclusion that host auxin transport is a primary effector target. These findings reveal a molecular mechanism by which a fungal effector co-opts host auxin transport machinery to promote plant development, with implications for microbe-assisted crop improvement.