Virtual cells are an emerging frontier at the intersection of artificial intelligence and biology. A key goal of these cell state models is predicting cellular responses to perturbations. The Virtual Cell Challenge is being established to catalyze progress toward this goal. This recurring and open benchmark competition from the Arc Institute will provide an evaluation framework, purpose-built datasets, and a venue for accelerating model development.

The reproductive cycle in females influences their social and sexual behaviors. In this issue of Cell, Wang et al. find that the calcium channel Cav3.2 in the brain's prefrontal cortex functions as a hormone-regulated electrophysiological switch. It connects hormonal state to brain activity, enabling the processing of signals from potential male partners and facilitating sexual behavior during the reproductive period.

The SARS-CoV-2 polymerase NiRAN domain initiates RNA capping. Previous results showed that both GTP and GDP can be utilized by NiRAN to yield GpppA together with RNAylated nsp9 (RNA-nsp9); however, the G-pocket substrate selection and the working mechanism of NiRAN remain unclear. Small et al. questioned the binding of the non-hydrolyzable GTP analog GMPPNP in the G-pocket of the RTC:RNA-nsp9:GMPPNP structure (PDB: 8GWE) and proposed that the GTP-mediated RNA-capping mechanism remains unresolved. Here, we show the optimized density derived from the original data to support the modeling of GMPPNP, and we reveal why the alternative data processing method failed to obtain density results. We provide additional biochemical and structural evidence by using GTP, GDP, GMPPNP, and GDP⋅BeF3- as probes to clarify the GTP-mediated RNA-capping mechanism and reconcile the two currently known models by using GTP and GDP as substrates. This Matters Arising Response addresses the Small et al. (2025) Matters Arising paper, published concurrently in Cell.

Exercise has well-established health benefits, yet its molecular underpinnings remain incompletely understood. We conducted an integrated multi-omics analysis to compare the effects of acute vs. long-term exercise in healthy males. Acute exercise induced transient responses, whereas repeated exercise triggered adaptive changes, notably reducing cellular senescence and inflammation and enhancing betaine metabolism. Exercise-driven betaine enrichment, partly mediated by renal biosynthesis, exerts geroprotective effects and rescues age-related health decline in mice. Betaine binds to and inhibits TANK-binding kinase 1 (TBK1), retarding the kinetics of aging. These findings systematically elucidate the molecular benefits of exercise and position betaine as an exercise mimetic for healthy aging.

Eukaryotic life evolved over a billion years ago when ancient cells engulfed and integrated prokaryotes to become modern mitochondria and chloroplasts. Sacoglossan "solar-powered" sea slugs possess the ability to acquire organelles within a single lifetime by selectively retaining consumed chloroplasts that remain photosynthetically active for nearly a year. The mechanism for this "animal photosynthesis" remains unknown. Here, we discovered that foreign chloroplasts are housed within novel, host-derived organelles we term "kleptosomes." Kleptosomes use ATP-sensitive ion channels to maintain a luminal environment that supports chloroplast photosynthesis and longevity. Upon slug starvation, kleptosomes digest stored chloroplasts for additional nutrients, thereby serving as a food source. We leveraged this discovery to find that organellar retention and digestion of photosynthetic cargo has convergently evolved in other photosynthetic animals, including corals and anemones. Thus, our study reveals mechanisms underlying the long-term acquisition and evolutionary incorporation of intracellular symbionts into organelles that support complex cellular function.

The Nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain initiates mRNA capping in coronaviruses through a GDP-polyribonucleotidyltransferase reaction, with RNA covalently linked to nsp9. GDP is the preferred substrate for this reaction, but the NiRAN domain can also utilize GTP to produce an authentic 5' RNA cap structure, though the GTP-mediated mechanism is unclear. Yan and colleagues claimed to have delineated the reaction mechanism from the analysis of a cryoelectron microscopy (cryo-EM) structure of a trapped catalytic intermediate of the SARS-CoV-2 NiRAN domain with a β-γ-non-hydrolyzable GTP analog (GMPPNP) and RNA-nsp9 (PDB: 8GWE). We show that the cryo-EM data used to derive PDB: 8GWE do not support the presence of GMPPNP in the NiRAN active site, and the resulting atomic model is incompatible with fundamental chemical principles. We conclude that Yan and colleagues' conclusions are not experimentally supported and the mechanism for GTP-mediated RNA capping by the SARS-CoV-2 NiRAN domain remains unresolved. This Matters Arising paper is in response to Yan et al. (2022), published in Cell. See also the response by Huang et al. (2025), published in this issue.

This study reports the first-in-human application of iPSC-derived CD19/BCMA dual-targeting chimeric antigen receptor-natural killer (CAR-NK) cells (QN-139b) in a patient with severe, diffuse cutaneous systemic sclerosis. The allogeneic product was genetically edited for reduced alloreactivity and improved in vivo performance, with no structural chromosomal abnormalities detected. The treatment led to significant B cell depletion with minimal toxicity, similar to CAR T cell therapy. The patient showed marked clinical improvements during the 6-month follow-up, including reduced autoantibodies and reversed fibrosis, which are resistant to conventional treatments. Single-cell analysis of peripheral blood revealed that the treatment shifted B cells toward more naive phenotypes and eliminated pathogenic B cells. Proteomic studies demonstrated suppression of inflammation and fibrosis, enhanced tissue regeneration, and improved angiogenesis. Pathological evaluation confirmed the elimination of infiltrated lymphocytes from affected skin along with restored skin and microvascular structure. These findings suggest QN-139b is a promising immune-modulatory treatment for severe autoimmune diseases.

Sleep is known to promote tissue growth and regulate metabolism, partly by enhancing growth hormone (GH) release, but the underlying circuit mechanism is unknown. We demonstrate how GH release, which is enhanced during both rapid eye movement (REM) and non-REM (NREM) sleep, is regulated by sleep-wake-dependent activity of distinct hypothalamic neurons expressing GH-releasing hormone (GHRH) and somatostatin (SST). SST neurons in the arcuate nucleus suppress GH release by inhibiting nearby GHRH neurons that stimulate GH release, whereas periventricular SST neurons inhibit GH release by projecting to the median eminence. GH release is associated with strong surges of both GHRH and SST activity during REM sleep but moderately increased GHRH and decreased SST activity during NREM sleep. Furthermore, we identified a negative feedback pathway in which GH enhances the excitability of locus coeruleus neurons and increases wakefulness. These results elucidate a circuit mechanism underlying bidirectional interactions between sleep and hormone regulation.

Biased agonism of G protein-coupled receptors (GPCRs) offers potential for safer medications. Current efforts have explored the balance between G proteins and β-arrestin; however, other transducers like GPCR kinases (GRKs) remain understudied. GRK2 is essential for β2 adrenergic receptor (β2AR)-mediated glucose uptake, but β2AR agonists are considered poor clinical candidates for glycemic management due to Gs/cyclic AMP (cAMP)-induced cardiac side effects and β-arrestin-dependent desensitization. Using ligand-based virtual screening and chemical evolution, we developed pathway-selective agonists of β2AR that prefer GRK coupling. These compounds perform well in preclinical models of hyperglycemia and obesity and demonstrate a lower potential for cardiac and muscular side effects compared with standard β2-receptor agonists and incretin mimetics, respectively. Furthermore, the lead candidate showed favorable pharmacokinetics and was well tolerated in a placebo-controlled clinical trial. GRK-biased β2AR partial agonists are thus promising oral alternatives to injectable incretin mimetics used in the treatment of type 2 diabetes and obesity.

Next-generation sequencing is pivotal for diagnosing inborn errors of immunity (IEI) but predominantly yields variants of uncertain significance (VUS), creating clinical ambiguity. Activated PI3Kδ syndrome (APDS) is caused by gain-of-function (GOF) variants in PIK3CD or PIK3R1, which encode the PI3Kδ heterodimer. We performed massively parallel base editing of PIK3CD/PIK3R1 in human T cells and mapped thousands of variants to a clinically important readout (phospho-AKT/S6), nominating >100 VUS and unannotated variants for functional classification and validating 27 hits. Leniolisib, an FDA-approved PI3Kδ inhibitor, rescued aberrant signaling and dysfunction in GOF-harboring T cells and revealed partially drug-resistant PIK3R1 hotspots that responded to novel combination therapies of leniolisib with mTORC1/2 inhibition. We confirmed these findings in T cells from APDS patients spanning the functional spectrum discovered in the screen. Integrating our screens with population-level genomic studies revealed that APDS may be more prevalent than previously estimated. This work exemplifies a broadly applicable framework for removing ambiguity from sequencing in IEI.

Glutamatergic neuronal activity promotes proliferation of both oligodendrocyte precursor cells (OPCs) and gliomas, including diffuse midline glioma (DMG). However, the role of neuromodulatory brainstem neurons projecting to midline structures where DMGs arise remains unexplored. Here, we demonstrate that midbrain cholinergic neuronal activity modulates OPC and DMG proliferation in a circuit-dependent manner. Optogenetic stimulation of the cholinergic pedunculopontine nucleus (PPN) promotes glioma growth in pons, while stimulation of the laterodorsal tegmentum nucleus (LDT) drives proliferation in thalamus. DMG-bearing mice exhibit higher acetylcholine release and increased cholinergic neuronal activity over the disease course. In co-culture, cholinergic neurons enhance DMG proliferation, and acetylcholine directly acts on DMG cells. Single-cell RNA sequencing revealed high CHRM1 and CHRM3 expression in primary DMG samples. Pharmacological or genetic blockade of M1/M3 receptors abolished cholinergic activity-driven DMG proliferation. Taken together, these findings demonstrate that midbrain cholinergic long-range projections promote activity-dependent DMG growth, mirroring a parallel proliferative effect on healthy OPCs.

Developmental gene expression is regulated by the dynamic interplay of histone H3 lysine 4 (H3K4) and histone H3 lysine 27 (H3K27) methylation, yet the physiological roles of these epigenetic modifications remain incompletely understood. Here, we show that mice depleted for all forms of H3K4 methylation, using a dominant histone H3-lysine-4-to-methionine (H3K4M) mutation, succumb to a severe loss of all major blood cell types. H3K4M-expressing hematopoietic stem cells (HSCs) and committed progenitors are present at normal numbers, indicating that H3K4 methylation is dispensable for HSC maintenance and commitment but essential for progenitor cell maturation. Mechanistically, we reveal that H3K4 methylation opposes the deposition of repressive H3K27 methylation at differentiation-associated genes enriched for a bivalent (i.e., H3K4/H3K27-methylated) chromatin state in HSCs and progenitors. Indeed, by concomitantly suppressing H3K27 methylation in H3K4-methylation-depleted mice, we rescue the acute lethality, hematopoietic failure, and gene dysregulation. Our results provide functional evidence for the interaction between two crucial chromatin marks in mammalian tissue homeostasis.

Inflammation, aberrant proteostasis, and energy depletion are hallmarks of neurodegenerative diseases such as multiple sclerosis (MS). However, the interplay between inflammation, proteasomal dysfunction in neurons, and its consequences for neuronal integrity remains unclear. Using transcriptional, proteomic, and functional analyses of proteasomal subunits in inflamed neurons, we found that interferon-γ-mediated induction of the immunoproteasome subunit, proteasome 20S beta 8 (PSMB8) impairs the proteasomal balance, resulting in reduced proteasome activity. This reduction causes the accumulation of phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 (PFKFB3), a key metabolic regulator, leading to enhanced neuronal glycolysis, reduced pentose phosphate pathway activity, oxidative injury, and ferroptosis. Neuron-specific genetic and systemic pharmacological targeting of PSMB8 or PFKFB3 protected neurons in vitro and in a mouse model of MS. Our findings provide a unifying explanation for proteasomal dysfunction in MS and possibly other neurodegenerative diseases, linking inflammation to metabolic disruption, and presenting an opportunity for targeted neuroprotective therapies.

Plant nucleotide-binding, leucine-rich repeat (NLR) immune receptors recognize pathogen effectors and activate defense. NLR genes can be non-functional in distantly related plants (restricted taxonomic functionality, RTF). Here, we enable Solanaceae NLR gene function in rice, soybean, and Arabidopsis by co-delivering sensor NLR genes with their cognate NLR required for cell death (NRC)-type helper NLRs. In soybean protoplasts and in Arabidopsis plants, Solanum americanum Rpi-amr1, Rpi-amr3, and pepper Bs2 sensor NLRs confer cognate effector responsiveness if co-expressed with NRC helper NLRs. Rice carrying pepper Bs2 and NRCs recognizes the conserved effector, AvrBs2, and resists an important pathogen, Xanthomonas oryzae pv. oryzicola, for which no resistance gene is available in rice. Rice lines carrying sensor and helper NLR genes otherwise resemble wild type, with unaltered basal resistance or field fitness. Thus, interfamily co-transfer of sensor and helper NLRs can broaden the utility of sensor NLRs, extending the tools available to control diseases of rice, soybean, Brassica, and other crops.

Single-cell RNA sequencing has revolutionized our understanding of cellular diversity but remains constrained by scalability, high costs, and the destruction of cells during analysis. To overcome these challenges, we developed STAMP (single-cell transcriptomics analysis and multimodal profiling), a highly scalable approach for the profiling of single cells. By leveraging transcriptomics and proteomics imaging platforms, STAMP eliminates sequencing costs, enabling cost-efficient single-cell genomics of millions of cells. Immobilizing (stamping) cells in suspension onto imaging slides, STAMP supports multimodal (RNA, protein, and H&E) profiling, while retaining cellular structure and morphology. We demonstrate STAMP's versatility by profiling peripheral blood mononuclear cells, cell lines, and stem cells. We highlight the capability of STAMP to identify ultra-rare cell populations, simulate clinical applications, and show its utility for large-scale perturbation studies. In total, we present data for 10,962,092 high-quality cells/nuclei and 6,030,429,954 transcripts. STAMP makes high-resolution cellular profiling more accessible, scalable, and affordable.

Recent outbreaks of multidrug-resistant fungi infecting human skin emphasize the importance of understanding fungal pathophysiology and spread. In efforts to address health concerns with various Indigenous Peninsular Malaysians (Orang Asli [OA]), tinea imbricata-a Trichophyton concentricum fungal skin infection-emerged as a particular concern. We investigated the etiology and transmission of tinea imbricata by culturing, testing antifungal sensitivities, and sequencing T. concentricum isolates in remote OA villages. Among regionally conserved isolates, we identified the emergence of terbinafine-resistant T. concentricum microbiologically and genomically. Investigating the skin microbiomes of 82 Indigenous OA, we found unique microbiota and lower relative abundances of bacterial commensals (Cutibacterium acnes, Staphylococcus epidermidis) among OA versus Malaysian and US urban populations, emphasizing how understudied populations provide unprecedented knowledge on host-microbiome co-evolution. These findings provide valuable insights into clinical, microbiological, and genomic features of chronic fungal skin infections, offering the potential to inform strategies to address drug resistance and effective therapy.

Microbial communities coat nearly every surface in the environment and have co-existed with animals throughout evolution. Whether animals exploit omnipresent microbial cues to navigate their surroundings is not well understood. Octopuses use "taste-by-touch" chemotactile receptors (CRs) to explore the seafloor, but how they distinguish meaningful surfaces from the rocks and crevices they encounter is unknown. Here, we report that secreted signals from microbiomes of ecologically relevant surfaces activate CRs to guide octopus behavior. Distinct molecules isolated from individual bacterial strains located on prey or eggs bind single CRs in subtly different structural conformations to elicit specific mechanisms of receptor activation, ion permeation and signal transduction, and maternal care and predation behavior. Thus, microbiomes on ecological surfaces act at the level of primary sensory receptors to inform behavior. Our study demonstrates that uncovering interkingdom interactions is essential to understanding how animal sensory systems evolved in a microbe-rich world.

Ants originated over 150 million years ago through an irreversible transition to superorganismal colony life. Comparative analyses of 163 ant genomes, including newly generated whole-genome sequences of 145 ant species, reveal extensive genome rearrangements correlated with speciation rates. Meanwhile, conserved syntenic blocks are enriched with co-expressed genes involved in basal metabolism and caste differentiation. Gene families related to digestion, endocrine signaling, cuticular hydrocarbon synthesis, and chemoreception expanded in the ant ancestor, while many caste-associated genes underwent positive selection in the formicoid ancestor. Elaborations and reductions of queen-worker dimorphism and other social traits left convergent signatures of intensified or relaxed selection in conserved signaling and metabolic pathways, suggesting that a core gene set was used to diversify organizational complexity. Previously uncharacterized genetic regulators of caste development were confirmed by functional experiments. This study reconstructs the genetic underpinning of social traits and their integration within gene-regulatory networks shaping caste phenotypes.

The hippocampus is crucial for memory. Memory consolidation is thought to be subserved by hippocampal "replays" of previously experienced trajectories. However, it is unknown how the brain replays long spatial trajectories in very large, naturalistic environments. Here, we investigated this in the hippocampus of bats that were flying prolonged flights in a 200-m-long tunnel. We found many time-compressed replay sequences during sleep and during awake pauses between flights, similar to rodents exploring small environments. Individual neurons fired multiple times per replay, according to their multiple place fields. Surprisingly, replays were highly fragmented, depicting short trajectory pieces covering only ∼6% of the environment size-unlike replays in small setups, which cover most of the environment. This fragmented replay may reflect biophysical or network constraints on replay distance and may facilitate memory chunking for hippocampal-neocortical communication. Overall, hippocampal replay in very large environments is radically different from classical notions of memory reactivation-carrying important implications for hippocampal network mechanisms in naturalistic, real-world environments.

When a material enters the body, it is immediately attacked by hundreds of proteins, organized into complex networks of binding interactions and reactions. How do such complex systems interact with a material, "deciding" whether to attack? We focus on the complement system of ∼40 blood proteins that bind microbes, nanoparticles, and medical devices, initiating inflammation. We show a sharp threshold for complement activation upon varying a fundamental material parameter, the surface density of potential complement attachment points. This sharp threshold manifests at scales spanning single nanoparticles to macroscale pathologies, shown here for diverse engineered and living materials. Computational models show these behaviors arise from a minimal subnetwork of complement, manifesting percolation-type critical transitions in the complement response. This criticality switch explains the "decision" of a complex signaling network to interact with a material.