Vessel normalization aims to correct the abnormal vasculature in the tumor to improve drug delivery and immune control. In this issue of Cell, Wang et al. identify an immune-excluding vasculature in small-cell lung cance...Vessel normalization aims to correct the abnormal vasculature in the tumor to improve drug delivery and immune control. In this issue of Cell, Wang et al. identify an immune-excluding vasculature in small-cell lung cancer, where excessive vessel integrity drives immune desertification, and propose "reverse normalization" to restore immune access and overcome immunotherapy resistance.
Yan X, Chavez AG, Franch M
… +20 more, Katlowitz KA, Gautam I, Kim B, Krishna A, Shrivastava A, Van Arsdel K, Belanger J, Chericoni A, Ismail T, Mickiewicz EA, Paulo D, Zhu H, Goldman AM, Krishnan V, Maheshwari A, Bartoli E, Provenza NR, Yoo SBM, Hayden BY, Sheth SA
The human brain has the remarkable ability to comprehend and express similar concepts in multiple languages. To understand how it does so, we examined responses of hippocampal neurons during passive listening, directed s...The human brain has the remarkable ability to comprehend and express similar concepts in multiple languages. To understand how it does so, we examined responses of hippocampal neurons during passive listening, directed speaking, and spontaneous conversation in both English and Spanish in a small group of balanced bilinguals. We found a small number of putative "cross-language neurons," whose responses to equivalent words (e.g., "tierra" and "earth") are correlated. However, neurons' semantic tunings differed substantially by language, suggesting language-specific neural implementations. Instead, the crucial driver of translation was a preserved geometric organization of neural responses between the two languages, one that did not depend on neuron-level functional overlap. Indeed, that geometry was implemented by a common set of neurons along distinct readout axes; this difference in readout may help prevent cross-language interference. Together, these results suggest that the hippocampus encodes a language-independent internal model for meaning.
Gastrulation is the fundamental stage of human development, governed by the faithful interaction between embryonic and extra-embryonic tissues. Despite its significance, the role of extra-embryonic lineages in directing...Gastrulation is the fundamental stage of human development, governed by the faithful interaction between embryonic and extra-embryonic tissues. Despite its significance, the role of extra-embryonic lineages in directing embryonic diversification and organization remains elusive. Here, we developed a defined co-culture system where embryonic stem cells (ESCs) are cultured with various extra-embryonic cell types, mimicking in vivo amniotic ectoderm, trophoblast, and extra-embryonic mesoderm, and uncovered the previously unrecognized role of different extra-embryonic cells in regulating embryonic cells. Furthermore, leveraging the advantages of microengineering techniques, we spatially and molecularly reconstructed the interactions among distinct extra-embryonic and embryonic cells, demonstrating that the coordinated regulation of extra-embryonic cells alone can recapitulate the human primitive streak (PS) formation, while also exhibiting extended developmental potential. This advancement may allow for experimental exploration and manipulation of previously inaccessible stages of human early gastrulation, providing an opportunity to glimpse the onset of this crucial developmental process.
The Rising Star cave system excavations resulted in a high number of well-preserved skeletal specimens from multiple individuals of Homo naledi, showing a high degree of morphological homogeneity, including dental variat...The Rising Star cave system excavations resulted in a high number of well-preserved skeletal specimens from multiple individuals of Homo naledi, showing a high degree of morphological homogeneity, including dental variation possibly consistent with a single-sex sample. Here, we report the paleoproteomic analysis of dental enamel proteins extracted via micro-destructive acid etching from 23 H. naledi specimens belonging to a minimum of 20 individuals. After excluding the possibility of technical bias, no convincing evidence supporting the confident identification of male individuals was detected in any of the investigated samples. We also detect no variability in the recovered proteome, and we observe two amino acid substitutions: a derived one in amelogenin X compared with Homo, and an ancestral one in COL17A1, also present in Paranthropus robustus. Our results further support the homogeneity of H. naledi fossils and show how to sustainably investigate extinct hominins.
Gautier O, Blum JA, Nguyen TP
… +23 more, Cao S, Klemm S, Yamakawa M, Huh D, Hurt JA, Sinnott-Armstrong N, Zeng Y, Davis CO, Bombosch J, Liu C, Encarnacion LN, Guttenplan KA, Chen D, Kathiria A, Zhao L, Moore S, Meng A, Ong K, Cleveland DW, Ravits J, Rexach JE, Greenleaf WJ, Gitler AD
To define molecular determinants of motor neuron degeneration in amyotrophic lateral sclerosis (ALS), we generated longitudinal single-nucleus transcriptomes and chromatin accessibility profiles of spinal motor neurons t...To define molecular determinants of motor neuron degeneration in amyotrophic lateral sclerosis (ALS), we generated longitudinal single-nucleus transcriptomes and chromatin accessibility profiles of spinal motor neurons together with spatial transcriptomics from the SOD1-G93A mouse model. Vulnerable alpha motor neurons showed thousands of molecular changes, marking a transition into a distinct cell state we named "disease-associated motor neurons" (DMs). We identified transcription factor networks that govern how healthy cells transition into DMs and those associated with motor neuron subtype-selective vulnerability. Upregulation of DM-associated transcription factors in human motor neurons induced key features of DMs, demonstrating an active regulatory component. Human ALS spinal cord single-nucleus RNA sequencing data demonstrated conservation of the DM signature in alpha motor neurons, and human orthologs of regions differentially accessible in SOD1-G93A mouse motor neurons were enriched for ALS genetic risk variants. Together, these findings establish a conserved, genetically linked motor neuron signature in ALS.
Lei G, Lu Z, Xu Z
… +33 more, Braun C, Huo D, Gao J, Tan L, Hong T, Wu S, Sun M, Zhao X, Li Q, Chen X, Yan Y, Lee H, Mao C, Zhuang L, Ku LT, Puebla N, Barsoumian H, Yao J, Hong L, Zhang J, Tran H, Lee JJ, Gibbons D, Vaporciyan A, Heymach J, Lin C, Gottlieb E, You MJ, Welsh JW, Lin SH, Zang X, Li Z, Gan B
Cuproptosis is a recently identified form of copper-dependent cell death that depends on ferredoxin 1 (FDX1)-mediated protein lipoylation. Here, we reveal that CD8 T cell-mediated antitumor immunity enhances tumor cell s...Cuproptosis is a recently identified form of copper-dependent cell death that depends on ferredoxin 1 (FDX1)-mediated protein lipoylation. Here, we reveal that CD8 T cell-mediated antitumor immunity enhances tumor cell susceptibility to cuproptosis, leading to a more potent tumor-suppressive effect of cuproptosis inducers in immunocompetent hosts compared with immunodeficient ones. Mechanistically, cuproptotic tumor cells act as a form of immunogenic cell death, releasing damage-associated molecular patterns that activate dendritic cells and enhance antitumor immunity. Reciprocally, CD8 T cell-derived interferon (IFN)-γ enhances FDX1 transcription in tumor cells by activating the signal transducer and activator of transcription 1 (STAT1)-IFN regulatory factor-1 (IRF1) signaling axis, resulting in heightened tumor cell sensitivity to cuproptosis. Consequently, combining a cuproptosis inducer with anti-programmed cell death ligand 1 (PD-L1) therapy amplifies tumoral cuproptosis and demonstrates efficacy in overcoming PD-L1 therapy resistance across multiple preclinical models. Our findings unveil a previously unrecognized connection between antitumor immunity and cuproptosis and highlight a potential therapeutic approach to counteract tumor immunotherapy resistance by targeting this unique cell death pathway.
Yue S, Guo Z, Pan C
… +22 more, Jing XA, Tao L, Nguyen T, Tang J, Chan Y, Contreras-Trujillo H, Jiang D, Yan X, Xiang H, Liu X, Bloom C, Ediriwickrema A, Koschade S, Wang X, Wang Z, Shu N, Shi Y, McKim DB, Lu R, Majeti R, Zhang C, Ying QL
Engineered macrophages are promising for tumor immunotherapy but are limited by poor ex vivo expansion, genetic tractability, and biodistribution after transfer. Here, we develop defined culture conditions that enable lo...Engineered macrophages are promising for tumor immunotherapy but are limited by poor ex vivo expansion, genetic tractability, and biodistribution after transfer. Here, we develop defined culture conditions that enable long-term expansion of mouse and human granulocyte-monocyte progenitors (GMPs) while preserving progenitor identity and myeloid potential, establishing GMPs as a renewable engineering platform. Mechanistically, we identify myeloperoxidase as a regulator of GMP proliferation. Expanded GMPs are readily engineered and, after transfer, seed hematopoietic niches and generate donor-derived myelopoiesis that restores antibacterial defense in chronic granulomatous disease mice and yields abundant tumor-infiltrating macrophages. GMPs engineered with chimeric antigen receptors (CARs) suppress CD19-positive leukemia and human epidermal growth factor receptor 2 (HER2)-positive solid tumors. We further introduce a CAR incorporating an immunoglobulin G (IgG) Fc domain that recruits host Fc receptor-expressing phagocytes, enables T cell priming across major histocompatibility complex (MHC) mismatch, and enhances efficacy in immunocompetent allogeneic cancer models. Together, these findings establish expandable GMPs as a scalable platform for engineered immunotherapy.
Elucidating the relationships among in vivo activity, brain-wide projection, and gene expression is critical for understanding neuronal functions, but characterizing these modalities for the same neuron remains technical...Elucidating the relationships among in vivo activity, brain-wide projection, and gene expression is critical for understanding neuronal functions, but characterizing these modalities for the same neuron remains technically challenging. Here, we developed a trimodal platform combining in vivo Ca imaging, morphological reconstruction of single neurons in cleared whole brains, and post hoc imaging-based in situ transcriptomic profiling in thick brain sections. We applied this platform to the mouse primary visual cortex (VISp) and obtained trimodal profiles for 141 intratelencephalic (IT) and pyramidal tract (PT) neurons. We found that regional axonal arborization, soma location, transcriptomic signatures, and subcellular RNA localization emerged as informative predictors for distinguishing neurons preferentially responsive to different visual stimuli. Importantly, morphological and transcriptomic features are complementary and, when integrated, can better predict neuronal function. Thus, this trimodal platform enables a comprehensive understanding of the relationships among gene expression, morphological diversity, and functional properties of single neurons.
Shao N, Chen M, Xu N
… +24 more, Qin Y, Zhao Q, Bock R, Zhou M, Duan G, Yang J, Ji D, Wu D, Wang Y, Lu Y, Lei X, Sun K, Liu K, Liu G, Meng X, Jing Y, Fan X, Zhao Y, Wang B, Yu H, Liu C, Jiang Y, Zhou Z, Li J
Sunlight fuels life but generates singlet oxygen (O), which causes photodamage and triggers signaling and antioxidative defense pathways in chloroplasts where photosynthesis takes place. How cells sense O and instantaneo...Sunlight fuels life but generates singlet oxygen (O), which causes photodamage and triggers signaling and antioxidative defense pathways in chloroplasts where photosynthesis takes place. How cells sense O and instantaneously mount photoprotection remains elusive. Here, we show that a key mediator of O responses, METHYLENE BLUE SENSITIVITY1 (MBS1), is conserved from plants to animals and comprises a zinc-finger (ZnF) domain flanked by intrinsically disordered regions. MBS1 plays a critical role in ¹O₂ sensing through ZnF conformational change and phase transition from liquid-like droplets to lower-dynamic condensates. These chloroplast-associated condensates under high light attenuate light penetration to shield chloroplasts from photodamage. In rice, MBS1-overexpressing lines exhibit enhanced high-light tolerance and yield in 4-year field trials. Our findings uncover a "sunscreening" mechanism via MBS1 condensates that confer chloroplast photoprotection, highlighting its value for improving rice yields in the field under high-light stress exacerbated by climate change.
Li Y, Li Z, Quinton R
… +21 more, Ji Y, Zhang X, Xiang J, Wang X, Yang S, Eweje F, Chen Y, Luo X, Li Y, Mulholland J, Chen S, Bergstrom C, Kim T, Maria Olguin F, Willens S, Lin SH, Nirschl JJ, West R, Neal J, Diehn M, Li R
The tumor microenvironment (TME) critically shapes disease progression and therapeutic resistance. However, a comprehensive understanding of its spatial architecture remains elusive, and clinical translation is challengi...The tumor microenvironment (TME) critically shapes disease progression and therapeutic resistance. However, a comprehensive understanding of its spatial architecture remains elusive, and clinical translation is challenging. Here, we present cellular architecture and neighborhood-informed virtual AI-driven spatial profiling (CANVAS), an artificial intelligence platform that infers tumor ecological habitats from hematoxylin and eosin (H&E) histopathology. Built on an atlas of over 18 million cells profiled by 41-plex spatial proteomics across 457 patients with non-small cell lung cancer, CANVAS establishes 10 reproducible cellular neighborhoods (CNs) capturing conserved spatial organization of the TME. Through multimodal alignment and foundation-model-based morphological encoding, CANVAS predicts CN-anchored habitat structures from H&E slides and enables clinical evaluation in over 5,000 patients spanning 9 cancer types. Across patient cohorts, CANVAS supports prognostic modeling, spatial ecotype stratification, and immunotherapy outcome prediction. These results establish CANVAS as a clinically scalable platform for spatial profiling, bridging single-cell analysis to population-level insight and enabling precision oncology.
Ueki H, Tomita Y, Duong C
… +15 more, Mitake H, Kiso M, Furusawa Y, Zhao D, da Silva Lopes TJ, Wu L, Feng H, Yamayoshi S, Fukuyama S, Yamashita M, Ozawa M, Ikawa M, Yoshida N, Watanabe T, Kawaoka Y
Functional validation of host factors in whole-animal models is a major bottleneck in virology; it hinders the translation of data from in vitro studies into a deeper understanding of the viral life cycle and pathogenesi...Functional validation of host factors in whole-animal models is a major bottleneck in virology; it hinders the translation of data from in vitro studies into a deeper understanding of the viral life cycle and pathogenesis. To address this challenge, we developed a systematic in vivo screening platform for influenza A virus. This platform comprises a library of 84 CRISPR-Cas9-generated gene-modified mouse lines targeting host factors prioritized from the literature and in vitro small interfering RNA (siRNA) screening studies. Using this resource, we identified 17 host factors whose genetic ablation conferred resistance to influenza A virus infection. Further studies of two of these factors, Arhgef28 and Lasp1, revealed distinct protective mechanisms against influenza A virus. We offer this mouse library to the research community as a powerful platform for studying virus-host interactions in a physiologically relevant context.
Freeburg NF, Chafamo D, Konanur Gopikrishna G
… +47 more, Murphy RM, Peng JJ, Parthasarathy S, Dumont S, Estrada EG, Logun MT, Sun Y, Wang X, Grover P, Rodriguez JL, Zhang DL, Park K, Fu Y, Ben Hamouda N, Hernandez-Verdin I, Lamrani L, Hicks KA, Cooper NA, Ekwegbara C, Bawden EG, Waterfall JJ, Fuentealba J, Alcantara M, Seykora JT, Prouty SM, Barrett D, Banerjee E, Cox A, Assenmacher CA, Macia C, Yin M, Carpenter EL, Ming GL, Sautès-Fridman C, Fridman WH, Tartour E, Wherry EJ, Amigorena S, Fraietta JA, Nasrallah MP, Song H, Miller TE, Bagley SJ, O'Rourke DM, Binder ZA, Alanio C, Silverbush D
Glioblastoma (GBM) is the most common primary malignant brain tumor in adults, with a median survival of under 15 months and no effective treatment after recurrence. A recent phase 1 trial of intracerebroventricular biva...Glioblastoma (GBM) is the most common primary malignant brain tumor in adults, with a median survival of under 15 months and no effective treatment after recurrence. A recent phase 1 trial of intracerebroventricular bivalent chimeric antigen receptor (CAR) T cells in recurrent GBM, registered at ClinicalTrials.gov (NCT05168423), showed promising responses, including tumor reduction and prolonged survival. However, relapse remains common. We performed in-depth profiling of longitudinal cerebrospinal fluid (CSF) and tumor samples from responders and non-responders to characterize immune dynamics following infusion. Our study reveals that, although CAR T cells activate post infusion across all patients, outcomes were defined by divergent remodeling of the endogenous immune landscape. Cytotoxic natural killer cell expansion characterized responders, whereas regulatory T cell expansion and abundant baseline immunosuppressive scavenger myeloid cells characterized non-responders. These findings indicate that host immune cells play a critical role in CAR T cell therapy for GBM, suggesting that combinatorial strategies modulating the endogenous immune compartment could improve next-generation treatments.
In eukaryotes, bridge-like lipid-transfer proteins (BLTPs) are central in mediating vesicle-independent lipid transfer between organelles. BLTPs span the cytosolic space between organelles at contact sites, featuring hyd...In eukaryotes, bridge-like lipid-transfer proteins (BLTPs) are central in mediating vesicle-independent lipid transfer between organelles. BLTPs span the cytosolic space between organelles at contact sites, featuring hydrophobic channels for lipids to travel between membranes. How BLTPs cooperate with partner proteins to orchestrate lipid delivery remains a mystery. Here, we used cryo-electron microscopy to visualize a complex comprising the prototypical BLTP VPS13A and the plasma membrane-localized scramblase XK at near-atomic resolution. VPS13A interacts with XK via its pleckstrin homology domain, priming VPS13A's bridge-like lipid-transfer domain to deliver lipids directly to the cytosolic leaflet of the acceptor membrane. In molecular dynamics simulations, this arrangement allows for robust lipid transfer. Newly delivered lipids can then be equilibrated between leaflets of the membrane bilayer by the scramblase, allowing for membrane growth. Mechanistic insights regarding lipid delivery by VPS13A are directly applicable to all VPS13 proteins and, more broadly, to all BLTP family members.
Li Z, Leng L, Zhai J
… +18 more, Wang X, Yang W, Wang S, Wan H, Zhang S, Gong F, Liao X, Li Y, Zeng Q, Chen Y, Xiang Z, Liu F, He F, Yang Y, Wang H, Xu X, Lin G, So C
∼50% of fertilized eggs arrest during human pre-implantation development, representing a major bottleneck for assisted reproductive technology. The underlying causes remain controversial. By imaging ∼150 live human and m...∼50% of fertilized eggs arrest during human pre-implantation development, representing a major bottleneck for assisted reproductive technology. The underlying causes remain controversial. By imaging ∼150 live human and monkey fertilized eggs for up to 5 days, we uncovered that the second mitotic divisions are the most error-prone, accounting for early embryonic arrest. Stochastic centriole overduplication, which could be effectively suppressed by transient treatment with PLK4 inhibitor centrinone, predisposed 2-cell blastomeres to assembling multipolar spindles and missegregating chromosomes. Missegregated chromosomes in turn resulted in the formation of most micronuclei in human embryos and led to the arrest or death of daughter blastomeres. By contrast, late embryonic arrest was largely independent of chromosome missegregations but involved the activation of endoplasmic reticulum stress response, which could impair the expression of subsets of junctional and cell polarity proteins required for blastocyst formation. Thus, two distinct causes contribute to the low efficiency of human pre-implantation development.
Cellular differentiation and morphogenesis require the coordination between cytoskeletal remodeling and transcriptional programs, raising the question of how cytoskeletal information is conveyed to the nucleus. Here, we...Cellular differentiation and morphogenesis require the coordination between cytoskeletal remodeling and transcriptional programs, raising the question of how cytoskeletal information is conveyed to the nucleus. Here, we profile the nuclear and cytosolic proteome of human and murine neural stem cells (NSCs) and uncover abundant cytoskeletal proteins in the nucleus, including the microtubule-associated protein 1B (MAP1B), implicated in disease. We find that MAP1B shuttles to the nucleus where it interacts with the BRG1-containing chromatin remodeling complex. MAP1B's nuclear enrichment promotes NSC fate, as opposed to its cytosolic function promoting neuronal differentiation. In vivo, increasing the nuclear/cytosol ratio disrupts neuronal positioning, reminiscent of patients with MAP1B mutations. Mutant human brain organoids show aberrant MAP1B nuclear enrichment, enhanced BRG1 chromatin binding, and neuronal ectopia formation. Our study uncovers a nuclear pool of cytoskeleton-associated proteins, revealing their role in fate regulation during brain development and reshaping our understanding of neurodevelopmental disease etiology.
Cephalotaxine-type and homoerythrina-type alkaloids are structurally unique and biologically important natural products isolated from endangered species that belong to the genus Cephalotaxus. Among them, homoharringtonin...Cephalotaxine-type and homoerythrina-type alkaloids are structurally unique and biologically important natural products isolated from endangered species that belong to the genus Cephalotaxus. Among them, homoharringtonine (HHT [1]) is a marketed drug used to treat leukemia. However, the scalable production of HHT is significantly hindered by limited natural resources. Despite intensive investigation over half a century, the complete biosynthetic pathways of these alkaloids remain unknown. Here, we applied a comprehensive multi-omics analysis and used a set of chemically synthesized standard compounds to identify the missing enzymes required for the biosynthesis of cephalotaxinone and homoerythratine. We also uncovered a rare case of divergent oxidation catalyzed by two highly homologous cytochrome P450 enzymes, CfCYP2 and CfCYP3, in the biosynthesis of two structurally distinct alkaloids. We further identified the key residues that significantly affect the divergent oxidation outcomes and ultimately reconstituted the complete biosynthetic pathways for producing these two alkaloids in N. benthamiana.
Transposable elements (TEs) comprise nearly half of mammalian genomes and have shaped genome architecture, chromatin organization, and transcriptional landscapes. Thanks to recent advances in long-read sequencing and fun...Transposable elements (TEs) comprise nearly half of mammalian genomes and have shaped genome architecture, chromatin organization, and transcriptional landscapes. Thanks to recent advances in long-read sequencing and functional (epi)genomics, the focus has shifted from TE families to individual TE loci, revealing widespread, locus-specific regulatory roles. While most TEs have lost the capacity to mobilize, they still retain a DNA form and, when transcribed, an RNA form, both of which can affect genome regulation. TEs can serve as alternative promoters, exons, splicing regulators, and 3' end modulators. They can also act as enhancers, drive three-dimensional (3D) genome organization, and give rise to long non-coding RNAs (lncRNAs) that serve as platforms for transcriptional and chromatin regulators. Mechanistically, TE repression involves DNA methylation, histone modification, phase-separated condensates, RNA modifications, RNA degradation, and nuclear compartmentalization, yet this repression can be selectively lifted during development or stress to expand regulatory potential. TEs therefore contribute to cell-type identity, developmental transitions, and responses to environmental stimuli, while their dysregulation is linked to human disorders including neurodegeneration, cancer, and autoimmune disease. TEs also hold translational promise as biomarkers and tools for gene and cell engineering. In summary, the pervasive integration of TEs as mini-genes, structural scaffolds, and regulatory elements redefines our view of the genome: rather than a gene-centric landscape dotted with repetitive "junk," mammalian DNA is a TE-rich ecosystem in which TEs drive gene regulatory networks and evolution.
RNA velocity can predict the direction of cell-state change, but the regulatory programs shaping these changes remain difficult to identify. In this issue of Cell, Wang et al. introduce RegVelo, a framework that integrat...RNA velocity can predict the direction of cell-state change, but the regulatory programs shaping these changes remain difficult to identify. In this issue of Cell, Wang et al. introduce RegVelo, a framework that integrates gene regulatory networks into RNA velocity analysis to nominate candidate regulators that may bias cell fate.
In this issue of Cell, Chen et al. analyze angiosperm genomes to map whole-genome duplication events, revealing non-random waves of polyploidy linked to climatic shifts and periods of low diversity. They suggest polyploi...In this issue of Cell, Chen et al. analyze angiosperm genomes to map whole-genome duplication events, revealing non-random waves of polyploidy linked to climatic shifts and periods of low diversity. They suggest polyploids may have preferentially established during periods of environmental stress, shaping plant evolutionary history across multiple global events.
T cells live or die by their metabolism, yet one nutrient can serve very different ends. In this issue of Cell, Kelly et al. show that cysteine's sulfur is partitioned between glutathione and iron-sulfur cluster synthesi...T cells live or die by their metabolism, yet one nutrient can serve very different ends. In this issue of Cell, Kelly et al. show that cysteine's sulfur is partitioned between glutathione and iron-sulfur cluster synthesis. This routing drives CD8 T cell proliferation, effector function, and anti-tumor immunity.