In this issue of Cell, Jaschke and Luchsinger et al. uncover a gut-to-brain signaling mechanism that dynamically shapes protein intake. During recovery from extreme fasting, ammonia derived from the metabolism of specific dietary amino acids is detected by Trpa1-expressing intestinal epithelial cells, leading to the activation of a protein aversion pathway.

A better understanding of human implantation is essential for improving assisted reproduction outcomes and addressing recurrent implantation failure (RIF). However, ethical constraints and limited access to human embryos make direct studies challenging. To overcome this, we developed a 3D in-chip implantation model using human blastoids or blastocysts co-cultured with a bioengineered human endometrial tissue, termed endometrioid. This system successfully recapitulates key events of human implantation and early post-implantation development. Importantly, when modeling implantation using samples derived from RIF patients, we observed significantly reduced blastoid implantation capability compared with endometrioids from fertile controls. Furthermore, a targeted screen of U.S. Food and Drug Administration (FDA)-approved compounds identified candidates that markedly enhanced implantation efficiency in RIF-derived endometrioids. Together, this 3D platform enables mechanistic investigation of human implantation and implantation failure and offers a scalable approach to evaluate therapeutic strategies for improving embryo-endometrium interaction in a clinical setting.

Implantation of a human embryo into the endometrium is a crucial event in gestation, as it marks the initiation of a pregnancy and is prone to high failure rates. We have limited understanding of these stages because of the inaccessibility of implanting embryos and the lack of suitable model systems. Here, we establish an in vitro model that recapitulates the luminal, glandular, and stromal compartments of the superficial layer of receptive human endometrium. Human embryos and blastoids implant into the endometrial model, achieving post-implantation hallmarks including advanced trophoblast structures that underlie early events in placental development. Single-cell RNA sequencing of the embryo-endometrial interface at day 14 uncovers predicted molecular interactions between conceptus and endometrium. Disrupting signaling interactions between extravillous trophoblast and endometrial stromal cells caused defects in trophoblast outgrowth, demonstrating the importance of crosstalk processes to sustain embryogenesis. This platform opens the opportunity to investigate early stages of human embryo implantation.

As our understanding of biological systems reaches single-cell and high spatial resolutions, it becomes imperative that pharmacological approaches match this precision to understand drug actions. This need is particularly urgent for the targeted covalent inhibitors that are currently re-entering the stage for cancer treatments. By leveraging the unique kinetics of click reactions, we developed volumetric clearing-assisted tissue click chemistry (vCATCH) to enable deep and homogeneous click labeling across the three-dimensional (3D) mammalian body. With simple and passive incubation steps, vCATCH offers cellular-resolution drug imaging in the entire adult mouse. We combined vCATCH with hydrogel-based reinforcement of three-dimensional imaging solvent-cleared organs (HYBRiD) imaging and virtual reality to visualize and quantify in vivo targets of two clinical cancer drugs, afatinib and ibrutinib, which recapitulated their known pharmacological distribution and revealed previously unreported tissue and cell-type engagement potentially linked to off-target effects. vCATCH provides a body-wide, unbiased platform to map covalent drug engagements at unprecedented scale and precision.

During chronic stress, cells must support both tissue function and their own survival. Hepatocytes perform metabolic, synthetic, and detoxification roles, but chronic nutrient imbalances can induce hepatocyte death and precipitate metabolic dysfunction-associated steatohepatitis (MASH, formerly NASH). Despite prior work identifying stress-induced drivers of hepatocyte death, chronic stress' functional impact on surviving cells remains unclear. Through cross-species longitudinal single-cell multi-omics, we show that ongoing stress drives prognostic developmental and cancer-associated programs in non-transformed hepatocytes while reducing their mature functional identity. Creating integrative computational methods, we identify and then experimentally validate master regulators perturbing hepatocyte functional balance, increasing proliferation under stress, and directly priming future tumorigenesis. Through geographic regression on human tissue microarray spatial transcriptomics, we uncover spatially structured multicellular communities and signaling interactions shaping stress responses. Our work reveals how cells' early solutions to chronic stress can prime future tumorigenesis and outcomes, unifying diverse modes of cellular dysfunction around core actionable mechanisms.

Pre-mRNA processing components in nuclear speckles encompass one or more folded RNA recognition motifs (RRMs) and disordered regions with specific sequence grammars. Such proteins include serine/arginine-rich splicing factors (SRSFs) and transactive response DNA binding protein (TDP)-43. The SRSFs and TDP-43 are unique archetypes of block copolymers encoding specific patterns of inter-domain homotypic and heterotypic attractions and repulsions. The interplay of these interactions drives microphase separation and the formation of ordered, size-limited assemblies. Microphases of SRSFs and TDP-43 are 23-45 nm in diameter, each comprising tens of molecules. Sub-micron-scale assemblies of SRSFs in cells are consistent with being clusters of microphases. The speckle-associated regulatory long non-coding RNA (lncRNA) metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) binds specifically and preferentially to SRSF1 microphases, while destabilizing TDP-43 microphases. In protein mixtures, the interactions between microphases drive the formation of micron-scale double-emulsion structures with core-shell organization. Our findings show how interactions involving copolymers featuring folded domains and disordered regions drive the formation of microphases.

Lymph nodes (LNs) enable innate defense to limit pathogen dissemination while also driving adaptive immunity. Yet, certain innate responses can restrict adaptive processes, suggesting that these must be tightly regulated. Here, we report that after infection or immunization, LN architecture is rapidly altered, with large-scale, polarized recruitment of neutrophils and monocytes from inflamed blood vessels and intranodal repositioning of natural killer (NK) cells. Mechanistically, dendritic cells (DCs) promote this through expression of inflammatory chemokines and integrin ligands. While these DC-driven innate responses are necessary for efficient pathogen containment, they paradoxically limit early adaptive immunity, with infiltrating neutrophils displacing lymphocytes and reducing the LN area available for T cell priming. Upon threat cessation, however, DCs and DC-recruited monocytes phagocytose the neutrophils, restoring tissue architecture and generating polarized domains for downstream adaptive immune cell activation. Thus, DCs orchestrate innate cell organization during inflammation, serving as rheostats of innate versus adaptive functions of the LN.

Immune tolerance at the maternal-fetal interface (MFI) is required for fetal development. Excessive maternal interferon-gamma (IFN-γ) and interleukin-17 (IL-17) are linked to pregnancy complications, but the regulation of maternal IFN-γ and IL-17 at the MFI is poorly understood. Here, we demonstrate a gut-placenta immune axis in pregnant mice in which the absence or perturbation of gut microbiota dysregulates maternal IFN-γ and IL-17 responses at the MFI, resulting in fetal resorption. Microbiota-dependent tryptophan derivatives suppress IFN-γ+ and IL-17+ T cells at the MFI by priming myeloid-derived suppressor cells (MDSCs) and gut-derived RORγt+ regulatory T cells (Tregs), respectively. The tryptophan derivative indole-3-carbinol, or tryptophan-metabolizing Lactobacillus murinus, rebalances the T cell response at the MFI and reduces fetal resorption in germ-free mice. Furthermore, MDSCs, RORγt+ Tregs, and microbiota-dependent tryptophan derivatives are dysregulated at the MFI in human recurrent miscarriage cases. Together, our findings identify microbiota-dependent immune tolerance mechanisms that promote fetal development.

Exploring targeted therapies for esophageal squamous cell carcinoma (ESCC) remains challenging. Although investigating the roles and therapeutic applications of liquid-liquid phase separation (LLPS) is increasingly of interest, its relationship with ESCC remains unclear. After improving the assay for transposase-accessible chromatin using sequencing (ATAC-seq) protocol for limited-amount clinical samples, we unravel transcription factor AP-2 beta (TFAP2β) as a key downregulated transcription factor (TF) through combined chromatin accessibility and gene expression analyses with cancerous and paracancerous tissues from early-stage ESCC patients. TFAP2β undergoes condensation in the nucleus to bind the zinc finger protein 131 (ZNF131) promoter, thereby inhibiting ZNF131 expression and ESCC progression. The other two crucial downregulated TFs uncovered are incorporated into TFAP2β condensates to bind their corresponding target, suggesting that LLPS may be a hallmark of ESCC transcription. In addition, we obtained compound A6 that mediates intrinsically disordered region conformational changes to enhance TFAP2β condensation and specific ESCC suppression in cells, mice, and patient-derived organoids. Thus, we indicate an LLPS-mediated transcriptional mechanism and a potential therapeutic approach for ESCC.

The mammalian brain contains diverse neuronal and immune cell types that exhibit dynamic motions in response to distinct extracellular environments. However, technical limitations make it difficult to investigate complex cellular motions in the developing brain in vivo. Here, we establish the intravital imaging of externally immobilized embryos (IMEE) method for long-term, large-field, and deep-depth imaging of mouse embryos, excelling in viewing angle flexibility, procedural simplicity, and functional applicability. Through combining IMEE with in utero retro-orbital injection and topological analysis of vector fields, we characterize distinct neuronal migration patterns and illustrate interactions among neurons, immune cells, and vasculature under physiological conditions and environmental stress during brain development. Our results suggest that neuronal migration guidance and immune surveillance depend on cellular adaptation to the local environment through distinct motion patterns of somata or processes. Our findings provide critical insight into the environmentally adaptive nature of neural cells in the developmental landscape.

Enteric neurons (ENs) are interwoven into the gastrointestinal (GI) tract, where they integrate local and external information to coordinate gut function across diverse cell types. Since EN dysfunction underlies the pathophysiology of multiple GI diseases, targeting relevant EN populations presents a multifaceted therapeutic approach. Despite their importance in essential physiologies, ENs remain underexplored from a transcriptional, circuit-based, and functional perspective. To enable target identification and validation in drug discovery, we leveraged a suite of modern neuroscience tools and profiled ENs. Single-nuclei sequencing, chemogenetics, circuit tracing, and pharmacology resolved how EN populations can modulate GI motility, secretion, food intake, and inflammation. We then determined the extent of conservation between mouse and human EN subsets. This work provides disease-relevant insights into EN cell type- and region-specific functions, lays the methodological groundwork to further probe EN function in vivo, and highlights translational hurdles and opportunities between mouse and human.

Nucleoside-modified messenger RNA (mRNA) vaccines elicit protective antibodies through their ability to promote T follicular helper (Tfh) cell differentiation. The lipid nanoparticles (LNPs) of mRNA vaccines possess inherent adjuvant activity. However, the extent to which the nucleoside-modified mRNA is sensed and contributes to Tfh cell responses remains undefined. Herein, we deconvolute the signals induced by LNPs and mRNA that instruct dendritic cells (DCs) to promote Tfh cell differentiation. We demonstrate that the mRNA drives the production of type I interferons, which act on DCs to enhance their maturation and Tfh cell differentiation, and favors plasma cells and memory B cell responses. In parallel, LNPs, which allow for mRNA uptake by DCs within the draining lymph node, also modulate Tfh cell responses by shaping the localization of CD25+ DCs. Our work unravels distinct adjuvant features of mRNA and LNPs necessary for the induction of Tfh cells, with implications for rational vaccine design.

While melanoma cells often express a high burden of mutated proteins, the infiltration of reactive T cells rarely results in tumor-eradicating immunity. We discovered that large extracellular vesicles, known as melanosomes, secreted by melanoma cells are decorated with major histocompatibility complex (MHC) molecules that stimulate CD8+ T cells through their T cell receptor (TCR), causing T cell dysfunction and apoptosis. Immunopeptidomic and T cell receptor sequencing (TCR-seq) analyses revealed that these melanosomes carry MHC-bound tumor-associated antigens with higher affinity and immunogenicity, which compete with their tumor cell of origin for direct TCR-MHC interactions. Analysis of biopsies from melanoma patients confirmed that melanosomes trap infiltrating lymphocytes, induce partial activation, and decrease CD8+ T cell cytotoxicity. Inhibition of melanosome secretion in vivo significantly reduced tumor immune evasion. These findings suggest that MHC export protects melanoma from the cytotoxic effects of T cells. Our study highlights a novel immune evasion mechanism and proposes a therapeutic avenue to enhance tumor immunity.

More than a century after their discovery, neutrophils continue to puzzle immunologists. Their remarkable migratory, cytotoxic, phagocytic, and degranulating capacities gave rise to the traditional perception that they are dedicated microbe hunters. Yet neutrophils possess an equally exceptional ability to acquire new traits across different environments, and when considered as a lineage collective, they are long-lived, reprogrammable, and retain memory of past insults. Here, we focus on the concept of the collective to make sense of both traditional properties and those that challenge existing dogmas. We model the structure of the collective as the combination of two biologically distinct compartments and discuss the unique properties that emerge beyond the sum of the individual cells. We hope that our review will stimulate discussion and spark new ideas about how neutrophils contribute to and can be exploited to promote health.

Disease recurrence in early-stage non-small cell lung cancer (NSCLC) remains a persistent clinical challenge, underscoring the need for better prognostic biomarkers. In this preview, we highlight the clinical implications of ultrasensitive ctDNA monitoring in lung cancer risk modeling reported by Black et al. in this issue of Cell.

Cell-mediated drug-delivery systems have garnered significant attention for their potential to boost therapeutic efficacy in cancer treatment. Here, we engineered immunoglobulin E (IgE)-sensitized mast cells (IgE-MCs) to achieve antigen-guided delivery of oncolytic adenoviruses (OVs) and local immune activation. By harnessing tumor-specific antigens as allergens, IgE-MCs accumulated at antigen-positive tumors, enabling targeted OV delivery and releasing chemokines and inflammatory mediators that remodeled the tumor microenvironment. IgE-MCs encapsulating OVs induced robust anticancer immune responses and inhibited tumor growth in several murine models. Of note, in a humanized human epidermal growth factor receptor-2 (HER2)-positive patient-derived xenograft model, human MCs armed with anti-HER2 IgE and loaded with OVs increased intratumoral T cell responses and reduced tumor growth, demonstrating feasibility in a clinically relevant setting and supporting patient-specific IgE selection. Together, our study highlights the translational promise of IgE-MCs as an antigen-specific delivery platform for cancer immunotherapy.

The tumor immune microenvironment (TIME) critically impacts cancer progression and immunotherapy response. Multiplex immunofluorescence (mIF) is a powerful imaging modality for deciphering TIME, but its applicability is limited by high cost and low throughput. We propose GigaTIME, a multimodal AI framework for population-scale TIME modeling by bridging cell morphology and states. GigaTIME learns a cross-modal translator to generate virtual mIF images from hematoxylin and eosin (H&E) slides by training on 40 million cells with paired H&E and mIF data across 21 proteins. We applied GigaTIME to 14,256 patients from 51 hospitals and over 1,000 clinics across seven US states in Providence Health, generating 299,376 virtual mIF slides spanning 24 cancer types and 306 subtypes. This virtual population uncovered 1,234 statistically significant associations linking proteins, biomarkers, staging, and survival. Such analyses were previously infeasible due to the scarcity of mIF data. Independent validation on 10,200 TCGA patients further corroborated our findings.

Microtubules have long been recognized as upstream mediators of intracellular signaling, but the mechanisms underlying this fundamental function remain elusive. Here, we identify the structural basis by which microtubules regulate the guanine nucleotide exchange factor H1 (GEFH1), a key activator of the Ras homolog family member A (RhoA) pathway. We show that specific features of the microtubule lattice bind the C1 domain of GEFH1, leading to the sequestration and inactivation of this signaling protein. Targeted mutations in C1 residues disrupt this interaction, triggering GEFH1 release and activation of RhoA-dependent immune responses. Building on this sequestration-and-release mechanism, we identify microtubule-binding C1 domains in additional signaling proteins, including other guanine nucleotide exchange factors (GEFs), kinases, a GTPase-activating protein (GAP), and a tumor suppressor, and show that microtubule-mediated regulation via C1 domains is conserved in the Ras association domain-containing protein 1A (RASSF1A). Our findings establish a structural framework for understanding how microtubules can function as spatiotemporal signal sensors, integrating and processing diverse signaling pathways to control important cellular processes.

Conventional hydrogel-based bioprinting methods often suffer from insufficient cell densities, which may limit crucial cell-cell interactions and impair overall tissue functions. Here, we present an approach that modifies cell membranes with acrylate bonds, allowing living cells at physiological densities (up to ∼109 cells mL-1) to serve directly as bioinks, demonstrating photoactivated bioprinting through digital light processing using purely cellular bioinks. Our cell-dense bioinks (CLINKs) rapidly produce tissue constructs that closely mimic native tissues, characterized by strong structural relevancy and robust functionality. The high cellularity and living nature of CLINKs enable the creation of advanced biological models such as connected neural circuits and rhythmically contracting mini-hearts derived entirely from stem cells, effectively capturing essential native-like behaviors. Implants created through this method showcase the capacity to integrate with the host, thereby promoting regeneration. Our CLINK technology holds substantial promise in tissue biofabrication, opening alternative avenues for biomedical applications.

Psilocybin holds promise as a treatment for mental illnesses. One dose of psilocybin induces structural remodeling of dendritic spines in the medial frontal cortex in mice. The dendritic spines would be innervated by presynaptic neurons, but the sources of these inputs have not been identified. Here, using monosynaptic rabies tracing, we map the brain-wide distribution of inputs to frontal cortical pyramidal neurons. We discover that psilocybin's effect on connectivity is network specific, strengthening the routing of inputs from perceptual and medial regions (homolog of the default mode network) to subcortical targets while weakening inputs that are part of cortico-cortical recurrent loops. The pattern of synaptic reorganization depends on the drug-evoked spiking activity because silencing a presynaptic region during psilocybin administration disrupts the rewiring. Collectively, the results reveal the impact of psilocybin on the connectivity of large-scale cortical networks and demonstrate neural activity modulation as an approach to sculpt the psychedelic-evoked neural plasticity.