He Y, Bae JSH, Nowak E
… +34 more, Outeiral C, Nissley DA, Tumber A, Berridge G, Salah E, Wang Y, He W, Zhang H, Chen T, Tusk S, Mathea S, Wang YJ, Grassam-Rowe A, Kukura P, Schofield CJ, O'Brien DP, Pierangelini A, Churchill GC, Lanyon-Hogg T, Ke Y, Xu C, Ye T, Watkins H, Ying L, Koschinski A, Solaro RJ, Tan X, Bolla JR, Wang X, Knapp S, Deane CM, Zaccolo M, Nowotny M, Lei M
Although kinase activators hold significant therapeutic promise, their development remains challenging and rarely achieved. Here, we report the discovery of direct small-molecule activators of p21-activated kinase-1 (PAK...Although kinase activators hold significant therapeutic promise, their development remains challenging and rarely achieved. Here, we report the discovery of direct small-molecule activators of p21-activated kinase-1 (PAK1), a key regulator of cardiac homeostasis, using a rational peptide-guided strategy. Targeting PAK1 autoinhibitory regulation, we identified a previously unrecognized autoinhibition-release site between the autoregulatory region and the kinase domain. Subsequent high-throughput screening and medicinal chemistry optimization yielded selective allosteric activators that enhance PAK1 activity with micromolar potency and isoform selectivity. Structural and mechanistic analyses indicate that these activators disrupt autoinhibitory regulation and promote local and global conformational transitions to the active state. Enhanced PAK1 signaling was confirmed in cardiac cells, and in vivo studies demonstrated therapeutic efficacy in both inherited and acquired cardiac hypertrophy. Collectively, these findings establish rational modulation of kinase autoinhibitory regulation as a potential strategy for the broader discovery of kinase activators, a largely unexplored area of therapeutic development.
Kelly B, Cha M, Gremelspacher T
… +15 more, Martin JL, Andreis M, Maloo I, Carrizo GE, Gidley M, Stanczak MA, Apostolova P, Longo J, DeCamp LM, Ma EH, Sheldon RD, Jones RG, Sanin DE, Majumdar A, Pearce EL
Delineating how acquired nutrients are partitioned into different intracellular pathways and how these various fates support distinct functions in T cells is limited. We show that CD8 T cells acquire cysteine to serve bo...Delineating how acquired nutrients are partitioned into different intracellular pathways and how these various fates support distinct functions in T cells is limited. We show that CD8 T cells acquire cysteine to serve both as a substrate for glutathione (GSH) production, which modulates effector functions, and to cede its sulfur for NFS1-dependent FeS cluster synthesis, which supports proliferation. NFS1 deletion in activated CD8 T cells promotes exhaustion and dampens anti-cancer immunity, whereas blocking cysteine flux into GSH or enforcing FeS metabolism enhances tumor control. This role for disrupted FeS metabolism in T cell exhaustion is echoed in data from human hepatocellular carcinoma. Elucidating how different intracellular pathways use cysteine enables targeted control of cysteine flux to retain the beneficial effects of cysteine while abolishing those that restrain function. We illustrate this concept for one metabolite, cysteine, but it is likely to apply to other metabolites relevant for immune cell function.
Zhang Z, Ho YJ, Fang X
… +65 more, Kim M, Li M, Luan W, Hinterleitner C, Haubner S, Kogel F, Pratt EC, Ozcelik E, Reyes J, Jiang Q, Yang VW, Chen YJ, Wang T, Liu H, Hu H, Zhuang X, Park J, Paffenholz SV, Chen K, Chang Q, Kulick A, Zhang J, Chan E, Rosiek E, Fan N, Williams RA, Wang AC, Freeman S, Tian S, Gunset G, Garcia Angus A, Lecomte N, Yildirim SY, Ali E, Wu M, Miranda IC, Antonescu CR, Basturk O, Tarcan Z, Rekhtman N, Wilson C, Basar M, Sauter JL, Al-Ahmadie HA, Singer S, Iacobuzio-Donahue C, Rudin C, de Stanchina E, Ganesh K, Romesser PB, Weigelt B, Huh DD, Leibold J, Feucht J, Vázquez-García I, Bott MJ, Zamarin D, Shah SP, Lewis JS, Amor C, Pe'er D, Mansilla-Soto J, Filliol A, Sadelain M, Lowe SW
Chimeric antigen receptor (CAR) T cells have transformed hematologic cancer therapy but remain limited in solid tumors by antigen heterogeneity and a suppressive, pro-fibrotic microenvironment. We previously identified t...Chimeric antigen receptor (CAR) T cells have transformed hematologic cancer therapy but remain limited in solid tumors by antigen heterogeneity and a suppressive, pro-fibrotic microenvironment. We previously identified the urokinase plasminogen activator receptor (uPAR) as upregulated in senescent, pro-fibrotic cells and showed that uPAR-directed CAR T cells could safely reverse fibrosis in mice. Integrative analyses now reveal that uPAR is broadly expressed in solid tumors enriched for TP53 and RAS pathway mutations. These tumors adopt a progenitor-like state supported by a niche of uPAR-positive stromal cells with senescence features. Human uPAR CAR T cells eliminate tumor cells and their stromal support, induce durable regressions across diverse models, eradicate systemic metastases, and are potentiated by senescence-inducing therapies. Importantly, these cells achieve robust antitumor activity without sustained myelosuppression in mice reconstituted with human immune systems. Together, these findings establish uPAR as a broadly applicable CAR T target capable of overcoming major barriers in solid tumor therapy.
The laboratory mouse is a key model system for biomedical research, yet body-wide measurement tools are lacking. Here, we generate spatiotranscriptomics profiles of whole-mouse sections that accurately capture histologic...The laboratory mouse is a key model system for biomedical research, yet body-wide measurement tools are lacking. Here, we generate spatiotranscriptomics profiles of whole-mouse sections that accurately capture histological regions. We spatially assign 379 cell types across whole-mouse section profiles by building a reference dataset of 59M single cells coupled with a scalable computational method for cell-type assignment. Moreover, we exploit these whole-mouse profiles to create a machine learning pipeline, LABEL, which enables pan-body annotation of tissues and cell types on histology images from H&E-stained sections. Lastly, we apply whole-mouse spatial profiling to map systemic inflammation in endotoxemia, which delineates organism-wide changes in gene expression programs across tissues and cell types. Together, our work paves the way for body-wide studies of the molecular and cellular processes that govern the organismal biology of the laboratory mouse across space, time, and conditions.
Linking genetic data with electronic health records in hospital biobanks promises to advance precision medicine, but limited ancestral diversity constrains discovery and generalizability. We analyzed 93,936 participants...Linking genetic data with electronic health records in hospital biobanks promises to advance precision medicine, but limited ancestral diversity constrains discovery and generalizability. We analyzed 93,936 participants from the UCLA ATLAS Community Health Initiative to inform disease prevalence and genetic risk across five continental and 36 fine-scale ancestry groups. We discovered numerous unreported gene-phenotype associations, including FN3K with intestinal disaccharidase deficiency in Europeans and admixed Americans. Polygenic scores (PGS) robustly predicted common diseases, with effects markedly diminished in non-Europeans. Furthermore, we reduced the pronounced European bias in curated clinical variants using computational predictors, uncovering unreported disease-gene associations, including ANKZF1 and peripheral vascular disease in African Americans. Longitudinal data revealed that semaglutide efficacy varies across ancestries, is associated with PGS for type 2 diabetes, and is modulated by genetic variation in PTPRU. These findings illustrate how ancestrally diverse biobanks from a single health system yield robust disease associations and pharmacogenomic insights.
Stimulator of interferon genes (STING) activation requires coat protein complex II (COPII)-mediated endoplasmic reticulum (ER) exit, but the mechanism remains elusive. Here, we identify EEΦxΦ (EEVTV in human STING) as th...Stimulator of interferon genes (STING) activation requires coat protein complex II (COPII)-mediated endoplasmic reticulum (ER) exit, but the mechanism remains elusive. Here, we identify EEΦxΦ (EEVTV in human STING) as the ER-exit motif recognized by SEC24 homolog C (SEC24C). Using AlphaFold3, we present a predicted structure of SEC24C binding to a STING dimer, revealing the EEΦxΦ motif in a previously structurally unresolved region. Mutations in this motif or the SEC24C cargo-binding site disrupt STING trafficking and signaling. Our findings support a STING oligomerization and avidity threshold model that explains regulated ER exit. The EEΦxΦ motif is conserved in vertebrate STING homologs and is sufficient to mediate ER exit of unrelated proteins. Interestingly, the STING ER-exit motif is suboptimal compared with known SEC24C cargos, which is crucial for preventing immune overactivation. An engineered "super-ER-exit" STING is constitutively active and induces potent antitumor immunity. Tandem repeats of this motif competitively inhibit endogenous STING signaling. Collectively, this study elucidates the STING-ER-exit mechanism and presents strategies for modulating STING signaling.
Piaget's theory posits that children develop structured knowledge schemas for inferring and assimilating new information, yet the underlying neural mechanisms remain unclear. In 203 participants aged 8-25 years, we inves...Piaget's theory posits that children develop structured knowledge schemas for inferring and assimilating new information, yet the underlying neural mechanisms remain unclear. In 203 participants aged 8-25 years, we investigated how maturation of a two-dimensional (2D) knowledge map underpins inferential reasoning and knowledge assimilation. Grid-cell-like codes in the entorhinal cortex (EC) strengthened with age, reflecting schema representations in non-spatial conceptual spaces, and predicted improved inferential reasoning. These grid-like codes also supported the medial prefrontal cortex (mPFC) in encoding distance relationships between objects on the 2D map. As participants assimilated new information, they integrated it into existing grid patterns in the EC. Moreover, the maturation of these neural codes tracked real-world intelligence measures, particularly reasoning abilities. Our findings demonstrate that the development of non-spatial grid-like neural codes offers a mechanistic account of cognitive development, bridging psychological theory with a fundamental cellular representation of the cognitive map.
Shrestha HK, Sun H, Yarbro JM
… +44 more, Lee D, Liu D, Wang E, McReynolds M, Zhang N, Xie B, Yang S, Yu K, Poudel S, Li Y, Yuan ZF, Kong D, Wang M, Wang Z, Niu M, Wang H, Zaman M, Wang J, Vanderwall DR, Sun Y, Wu Z, Chen PC, Bai B, High AA, Faura J, Liu C, Bennett DA, Johnson ECB, Seyfried NT, Levey AI, Haroutunian V, Serrano GE, Beach TG, DeTure M, Kanekiyo T, Petersen RC, Bu G, McLean PJ, Dickson DW, Rademakers R, Yu G, Wang X, Zhang B, Peng J
Neurodegenerative diseases (NDs) pose clinical challenges due to their complexity and molecular heterogeneity. Here, we present a pan-neurodegeneration atlas (PanNDA) from multilayer, deep proteomic analysis of 2,279 hum...Neurodegenerative diseases (NDs) pose clinical challenges due to their complexity and molecular heterogeneity. Here, we present a pan-neurodegeneration atlas (PanNDA) from multilayer, deep proteomic analysis of 2,279 human brain samples spanning 6 major NDs: Alzheimer's disease (AD), Lewy body dementia (LBD), frontotemporal lobar degeneration with TDP-43 pathology, progressive supranuclear palsy with tau pathology, vascular dementia, and Parkinson's disease. PanNDA integrates data from whole proteome, detergent-insoluble proteome, and posttranslational modifications (phosphorylation and ubiquitination), enabling intra- and inter-disease comparisons. Intra-disease analyses uncover distinct molecular subtypes (e.g., three in AD and four in LBD), reveal dysregulated pathways, and prioritize top-ranked proteins. Inter-disease comparisons identify shared alterations in NDs, such as GPNMB in microglial and lysosomal activation and NPTX2 in synaptic regulation, alongside disease-specific changes and hub regulators within protein networks. Overall, PanNDA provides a systems-level framework for understanding ND mechanisms and serves as a foundational resource that is accessible via an interactive website: https://penglab.shinyapps.io/pannda.
Some mammalian tissues can replace lost cells within one lineage, but organ-level regeneration-restoring diverse cell types across lineages-remains rare. Here, we show that late embryonic full-thickness skin injuries hea...Some mammalian tissues can replace lost cells within one lineage, but organ-level regeneration-restoring diverse cell types across lineages-remains rare. Here, we show that late embryonic full-thickness skin injuries heal by regenerating epithelial, mesenchymal, neuronal, and vascular tissues with proper connectivity. However, this ability is lost soon after birth, resulting in failure to restore most cell types and hyperinnervation within the wound bed. Single-cell sequencing identified a postnatal wound-specific fibroblast (PWF) population absent after embryonic wounding. Through an in vivo screen, we discovered that three PWF-enriched genes-Timp1, Cxcl12, and Ccl7-inhibit organ-level regeneration and cause hyperinnervation when overexpressed in embryonic wounds. Reducing hyperinnervation in postnatal wounds through the depletion of Cxcl12 in fibroblasts or nerve ablation enables regeneration of diverse lineages after injury. Our study identifies mechanisms that transition an organ from regenerative to non-regenerative, discovers fibroblast-driven hyperinnervation as a key barrier, and demonstrates that removing this barrier unlocks organ-level regeneration.
To define and systematically characterize the human E3 ubiquitin ligase (E3) landscape, we generated the E3-ome, a compendium of E3s encoded by the human genome. The E3-ome integrates experimental data, bioinformatics, a...To define and systematically characterize the human E3 ubiquitin ligase (E3) landscape, we generated the E3-ome, a compendium of E3s encoded by the human genome. The E3-ome integrates experimental data, bioinformatics, and published research, revealing 672 high-confidence E3s. We standardized E3 classifications to create a unified framework for annotation and comparative analysis. The E3-ome identified several previously unrecognized domains, motifs, E3 candidates, and relationships, expanding the diversity of E3s. Furthermore, the E3-ome mapped the spatial and physiological organization of E3s across human tissues and cell types, revealing context-dependent E3s. Genetic analyses identified disease-associated variants across the E3-ome, linking E3s to diverse human pathologies. Together, these analyses define the human E3 landscape at high resolution and deliver a foundational resource to drive mechanistic and therapeutic discovery.
Guo G, Zhao H, Bai K
… +24 more, Lu J, Wu Q, Lu L, Zhang Y, Dong L, Li G, Chen Y, Hou Y, Lu P, Li M, Zhang H, Wang G, Zhu K, Huang B, Cui X, Fu H, Hu C, Chu Z, Lyu X, Kamoun S, Wang C, Liu Z, Selvaraj M, Jones JDG
Nucleotide-binding, leucine-rich repeat (NLR) receptors are widespread intracellular immune sensors across kingdoms. Plant G10-type coiled-coil (CC)-NLRs constitute a distinct phylogenetic clade that remains poorly chara...Nucleotide-binding, leucine-rich repeat (NLR) receptors are widespread intracellular immune sensors across kingdoms. Plant G10-type coiled-coil (CC)-NLRs constitute a distinct phylogenetic clade that remains poorly characterized. Here, we identified a gain-of-function mutant of wheat autoimmunity 3 (WAI3), which encodes a constitutively active CC-NLR resulting from a residue substitution in the leucine-rich repeat (LRR) domain. Cryo-electron microscopy (cryo-EM) analysis reveals that activated WAI3 assembles into a distinctive octameric resistosome. Arabidopsis RPS2, another CC-NLR, also forms an octamer, indicating a conserved structural property across monocot and dicot plants. The WAI3 resistosome induces a prolonged and sustained increase in cytosolic calcium, likely facilitated by a unique channel architecture arising from its divergent coiled-coil (CC) domain configuration. Notably, this domain arrangement may be shared by plant NLRs that lack the conserved EDVID (Glu-Asp-Val-Ile-Asp) motif in their CC domains. Together, our findings uncover a conserved yet previously uncharacterized NLR resistosome structure and provide insights into the plant immune receptor plasticity.
How morphological diversity arises from variations in biomechanical processes remains an open question. Although forces shape tissues, how force-generating systems differ across species to create diverse forms is unclear...How morphological diversity arises from variations in biomechanical processes remains an open question. Although forces shape tissues, how force-generating systems differ across species to create diverse forms is unclear. Here, we combine comparative morphogenesis and active matter theory across six cnidarian species spanning 500 million years of divergence to identify the mechanical basis of larval shape diversity. We define species-specific configurations of mechanical modules-termed mechanotypes-that quantitatively predict larval shapes across taxa. We find that shape elongation is a simple trait at the mesoscale level, as its variation depends on one mechanical module, whereas shape polarity is a complex trait dependent on several modules. Perturbations mimicking interspecies regulatory differences reshape these modules, reprogramming larval morphology into forms resembling sister species. By establishing a mesoscale mechanical framework for cross-species comparison, this work reveals how variations in a limited set of tissue-scale parameters generate morphological diversity.
Influenza virus is transmitted via respiratory expulsions, but detecting infectious virus in expulsions is challenging. Here, we describe quantification and genotyping of infectious virus in respiratory particles using a...Influenza virus is transmitted via respiratory expulsions, but detecting infectious virus in expulsions is challenging. Here, we describe quantification and genotyping of infectious virus in respiratory particles using a modular influenza sampling tunnel (MIST). The particles deposit on cell monolayers, enabling culture, quantification, and sequencing of viruses. Concomitantly, water-sensitive paper and fine particle samplers yield respiratory particle counts over a broad size range. Using the MIST, we captured infectious virus from humans experimentally infected with the influenza virus on multiple days post-inoculation. The recovered respiratory particles varied in quantity over three orders of magnitude and contained viral variants also detected in samples from infected individuals. Expulsion of infectious virus was associated with infectious viral load in saliva and nasopharyngeal swabs and with clinical symptoms. These data reveal maintenance of viral diversity in expelled aerosols and suggest heterogeneity among individuals in the magnitude of infectious expulsions, impacting forward transmission potential.
Song H, Wang W, Mei T
… +19 more, Zheng H, Ning K, Liu X, Cheung S, Cao Z, Sheng D, Mai X, Zhu H, Guo G, Liu S, Wei R, Wang Q, Cao Y, Ding Y, Fei Y, Liu R, Hattori M, Sheng C, Lu B
Targeted protein degradation (TPD) technologies provide huge opportunities for drug discovery, but degrading transmembrane (TM) targets remains challenging. Since TM proteins are canonically folded on the endoplasmic ret...Targeted protein degradation (TPD) technologies provide huge opportunities for drug discovery, but degrading transmembrane (TM) targets remains challenging. Since TM proteins are canonically folded on the endoplasmic reticulum (ER) membrane, we hypothesized that harnessing ER-associated degradation (ERAD) may enable efficient degradation of TM proteins. Here, we established a TPD technology hijacking ERAD and named it ERAD-engaging chimeras (ERADECs), capable of degrading TM targets with high efficacy. We identified desonide as a binder of SYVN1, an ER E3 ligase mediating ERAD. We designed ERADECs targeting programmed death-ligand 1 (PD-L1) by connecting desonide to a known PD-L1 ligand and observed SYVN1- and ERAD-dependent PD-L1 degradation with high efficacy. Functionally, these ERADECs exhibited stronger tumor suppression and PD-L1-lowering effects than a clinically used PD-L1 antibody in vivo. The concept of ERADECs is also expandable to other membrane targets. Collectively, we established a platform technology hijacking ERAD to selectively degrade TM targets with remarkable efficiency.
RNA is frequently chemically modified, with over 170 types of chemical modifications identified to date in cellular RNAs. These modifications, along with their effector proteins, constitute new layers of gene expression...RNA is frequently chemically modified, with over 170 types of chemical modifications identified to date in cellular RNAs. These modifications, along with their effector proteins, constitute new layers of gene expression regulation by controlling either the fate of modified RNAs at nearly every stage of their life cycle or local transcription through modulating the nearby chromatin state and transcriptional complexes. This is especially evident in dynamic biological contexts such as cellular state transitions, signaling, immune responses, and stress adaptation. In this review, we discuss recent breakthroughs and promising avenues for future exploration. Particular attention is given to the functional significance of mRNA modifications, the emerging roles of modifications on chromatin-associated regulatory RNAs in chromatin and transcriptional regulation, and mechanistic insights that will guide future scientific interrogation of RNA modifications in gene expression regulation. We also highlight how these fundamental understandings are beginning to catalyze the development of novel therapeutic strategies.
Despite advances in structure prediction from sequence, predicting cellular activity requires conformational ensembles that capture propensities to form functionally active states. Such ensembles remain difficult to meas...Despite advances in structure prediction from sequence, predicting cellular activity requires conformational ensembles that capture propensities to form functionally active states. Such ensembles remain difficult to measure and even harder to predict. Here, we systematically altered the HIV-1 transactivation response element (TAR) RNA sequence to change its propensity to adopt a functional versus inactive secondary structure and quantified these propensities using proton chemical exchange saturation transfer (H CEST) NMR without isotopic labeling. Minor sequence changes shifted the active-state propensity by ∼500-fold, quantitatively predicting 125- to 300-fold changes in binding to the RNA-binding region of Tat and cellular transactivation. These propensities could be inferred from secondary-structure prediction algorithms and incorporated into a thermodynamic framework to quantitatively predict how sequence changes alter protein-binding affinity and cellular activity in this well-characterized system. Our findings establish a quantitative thermodynamic framework that links the RNA sequence to cellular activity through conformational ensembles, setting the stage for more generalized predictions as computational ensemble modeling continues to advance.
Du S, Long Q, Zhou Y
… +34 more, Fu J, Wu H, Yang L, Xie Y, Ding Y, Zhang M, Guo J, Wang M, Lin J, Hu M, Zhang J, Yao D, Li W, Bao F, Xiang G, Wu Y, Huang Y, Liang H, Wang R, Li H, Chen B, Li C, Wang J, Zhang J, Qin D, Sun J, Zhu Y, Sun F, Wang W, Lu G, Chan WY, Zhao H, Liu C, Liu X
Mitochondrial transplantation holds significant potential for the treatment of mitochondrial diseases. However, how to efficiently deliver exogenous mitochondria to somatic cells or tissues remains unresolved. We present...Mitochondrial transplantation holds significant potential for the treatment of mitochondrial diseases. However, how to efficiently deliver exogenous mitochondria to somatic cells or tissues remains unresolved. We present a mitochondrial transplantation approach to deliver mitochondria into the cells and tissues of mice and monkeys with high efficiency, based on encapsulating mitochondria with vesicles derived from the plasma membrane of erythrocytes. Treatment with encapsulated mitochondria complemented the loss, deletion, or mutation of mitochondrial DNA, thereby rescuing the associated bioenergetic and biochemical defects in patient-derived cells with mitochondrial disorders. Furthermore, mitochondrial capsules rescued the mitochondrial DNA depletion syndrome and Leigh syndrome in Dguok and Ndufs4 mouse models, respectively. Moreover, in a mouse model of Parkinson's disease, mitochondrial capsules rescued neuron loss, improved motor skills, and restored mitochondrial function in the affected brain regions. Our study demonstrates the potential of this mitochondrial capsule as a treatment for mitochondrial disorders and proposes an "organelle therapy" strategy in regenerative medicine.
Westbury MV, Brown SC, Cabrera AA
… +16 more, Morales HE, Parreira B, Ma J, Coll Macià M, Rey-Iglesia A, Dyke A, Scharff-Olsen CH, Scott MB, Wiig Ø, Bachmann L, Kovacs KM, Lydersen C, Ferguson SH, Szpak P, Fordham DA, Lorenzen ED
Bowhead whales were heavily exploited during commercial whaling between the 16th and 20th centuries. Current and near-future climate warming poses a new threat. Assessing bowhead vulnerability to climatic change remains...Bowhead whales were heavily exploited during commercial whaling between the 16th and 20th centuries. Current and near-future climate warming poses a new threat. Assessing bowhead vulnerability to climatic change remains challenging due to insufficient knowledge regarding responses to past climates and pre-whaling population dynamics. We integrate paleogenomics and stable isotopes (δC and δN) from 206 bowhead fossils from the Atlantic Arctic with paleoclimate and ecological modeling based on 823 radiocarbon-dated fossils, including 140 from this study. We find long-term resilience of bowheads to Holocene environmental perturbations, with no detectable changes in genetic diversity or population structure. Simulated commercial-whaling-driven genetic and fitness changes indicate that population subdivision and loss of genetic diversity are unlikely to be fully realized, despite nearly a century since whaling ceased. Furthermore, even in simulated complete population recovery scenarios, overall fitness did not return to pre-whaling levels, potentially compromising the future resilience of bowhead whales.