Cell Discovery最新文献

Gene fusions are becoming critical oncogenic drivers with potential therapeutic relevance across various cancers. However, their roles and clinical implications in breast cancer remain largely unexplored. In this study, we leveraged a large-scale multiomics cohort and a drug screening platform for breast cancer to systematically profile gene fusions. We identified ADK fusion genes as novel and recurrent drivers in hormone receptor-positive (HR+)/human epidermal growth factor receptor 2-negative (HER2‒) breast cancer. Functionally, the most commonly occurring ADK fusion gene, KAT6B::ADK, enhances metastatic potential and confers tamoxifen resistance. Mechanistically, KAT6B::ADK activates ADK kinase activity through liquid‒liquid phase separation, triggering the activation of an integrated stress response signaling pathway. Notably, patient-derived organoids harboring KAT6B::ADK from HR+/HER2‒ breast cancer demonstrate increased sensitivity to ADK inhibitors, underscoring the therapeutic potential of this fusion gene. Our findings establish ADK fusions as therapeutic targets in HR+/HER2‒ breast cancer, offering new avenues for innovative precision treatment strategies in this patient population.

Liver transplantation remains constrained by the scarcity of donor organs and the risks inherent in the procedure, underscoring the urgent need for novel cirrhosis therapies. We developed a protocol to convert human primary hepatocytes into expandable hepatocyte-derived liver progenitor-like cells (HepLPCs), which secrete high levels of matrix metalloproteinases and hepatocyte growth factor. In a thioacetamide-induced rat model of cirrhosis, human HepLPCs demonstrated potent anti-fibrotic properties and promoted liver regeneration. Biodistribution studies revealed that most xenogenic HepLPCs were cleared from the body within one week, suggesting that their therapeutic benefits likely arise from paracrine signaling rather than long-term engraftment. We initiated a first-in-human clinical trial involving nine patients with cirrhosis to evaluate the feasibility and safety of HepLPCs. Preclinical toxicity assessments in 36 crab-eating macaques confirmed the safety of HepLPC treatment. In the clinical trial, nine patients (mean age: 53 years), primarily with HBV-related cirrhosis, received HepLPCs via trans-hepatic arterial infusion without immunosuppressants. No serious adverse event was observed, and the minor adverse events were consistent with those commonly seen in cirrhosis patients. The treatment was well tolerated, with no transfusion reactions or dose-limiting toxicities. While significant changes in Child-Pugh and MELD scores were not observed, some patients showed improvements in liver biochemical parameters, coagulation profiles, and portal hypertension indicators during the six-month follow-up. These findings indicate that HepLPC therapy is safe and feasible, offering a promising new strategy for treating cirrhosis. Further clinical trials are needed to assess its efficacy in patients with decompensated cirrhosis and acute-on-chronic liver failure.

The Tol-Pal system is essential for maintaining outer membrane (OM) stability during cell division in Gram-negative bacteria. The inner membrane complex TolQRA harnesses proton motive force (PMF) to establish transient interactions within the periplasm, thereby coordinating cell envelope remodeling and facilitating OM invagination at division sites. However, the precise mechanism remains unclear. Here, we present cryo-electron microscopy structures of Escherichia coli TolQRA in multiple conformational states at 2.92-3.52 Å resolution, revealing rotary dynamics within the complex. Computational simulations reveal a proton-conductive channel comprising the putative proton-accepting residue Asp23 and the conserved polar residues Thr145 and Thr178, with monitored inter-residue distances providing support for a proton-driven rotary mechanism. Site-directed mutagenesis combined with functional assays validates the AlphaFold-predicted structure of the periplasmic domains of TolR and TolA, and further pinpoints critical residues required for complex function. Together, these findings advance our understanding of TolQRA-mediated proton transduction and offer new avenues for antibiotic drug development.

The role of CD8⁺ tissue-resident memory T (CD8⁺ T_RM) in inflammation is well established. However, the mechanisms by which CD8⁺ T_RM cells are activated in tissues have remained elusive. Here, we show that Leucine zipper-like transcription regulator 1 (LZTR1), a substrate adaptor for cullin3 (CUL3) ubiquitin ligase complex, regulates CD8⁺ T_RM activation and proliferation in cutaneous and colonic epithelia through modulation of major histocompatibility complex class I (MHC-I) expression in an NF-κB1-dependent manner. Mechanistically, LZTR1 modulates MHC-I transcription by regulating co-translational biogenesis of NF-κB1 (p50) in a ubiquitination-independent but proteasome-dependent manner through direct binding with ribosome and proteasome. Loss of LZTR1 leads to suppression of CD8⁺ T_RM activation and proliferation and decreased production of IL-17A with blunting of inflammatory responses in both cutaneous and gut epithelia in vivo. In summary, these data identify LZTR1 as a novel regulator of CD8⁺ T_RM function and provide insights into the mechanisms that drive and maintain CD8⁺ T-cell responses in epithelial-associated autoimmune diseases.

Single-domain antibodies (sdAbs) have emerged as powerful therapeutic agents due to their small size, high stability, and superior tissue penetration. However, unlike conventional monoclonal antibodies (mAbs), sdAbs lack an Fc domain, limiting their functional versatility and manufacturability. To address this challenge, we developed TFDesign-sdAb, a deep learning-based generative-ranking framework that enables rational engineering of sdAbs with tailored functionalities. Our framework integrates a structure-aware diffusion model (IgGM) for large-scale candidate generation and a fine-tuned sorter (A2binder) that evaluates and prioritizes them based on predicted functionality. Unlike traditional CDR-focused approaches, TFDesign-sdAb optimizes both complementarity-determining regions (CDRs) and framework regions (FRs), allowing sdAbs to acquire new functional properties while maintaining antigen specificity. We validated our approach by conferring Protein A binding to human VHs and nanobodies that originally lacked this feature, achieving high expression rates, strong binding affinities, and successful purification via industry-standard Protein A affinity chromatography. High-resolution structural characterization (1.49 Å and 2.0 Å) of the redesigned sdAb-Protein A complexes revealed conserved FR-mediated binding motifs that recapitulate natural Fc-Protein A interactions, validating the accuracy of our model. Furthermore, our pipeline streamlined the antibody engineering process, achieving a 100% success rate in generating Protein A-binding sdAbs while maintaining their original antigen-binding affinity. This work demonstrates the power of AI-driven design in overcoming long-standing limitations in antibody engineering and presents a scalable, generalizable solution for enhancing sdAb functionality.

Bacterial pathogens have evolved multiple mechanisms to modulate host cell death, evade host immunity, and establish persistent infection. Here, we show that an infective endocarditis causative pathogen, Bergeyella cardium, is frequently detected in oral specimens from clinical patients. A variant strain of Bergeyella cardium (BCV) induces unique cytoplasmic vacuolization cell death and minor apoptosis-like cell death in macrophages. The cytoplasmic vacuolization cell death triggered by BCV is characterized by Fused LysosOme-Associated Termination (floatptosis) and is inhibited by the sodium channel inhibitor amiloride. Moreover, outer membrane vesicles (OMVs) or transfection of barrel-like membrane proteins, lipocalin, β-barrel, and PorV, dramatically induce cytoplasmic vacuolization. Endosomal solute carrier family 9 member A9 (SLC9A9) plays important roles in the process of BCV-, OMVs-, and barrel-like proteins-triggered cytoplasmic vacuolization cell death via promoting vacuole fusion. SLC9A9 deficiency or amiloride administration increases host defense against BCV infection. These findings contribute to developing novel approaches to modulate cytoplasmic vacuolization cell death and treat infectious diseases.

Recent advances in single-cell technology enable the simultaneous capture of T cell receptor (TCR) sequences and gene expression (GEX), providing an integrated view of T cell function. However, linking TCRαβ information and T cell phenotypes at the population level to elucidate their disease association remains an unaddressed gap. Here, by constructing a large-scale reference of paired single-cell RNA/TCR sequencing (scRNA/TCR-seq) comprising more than 2 million T cells from 70 studies, 1017 biological samples, 583 individuals, and 46 disease conditions, along with their single-cell transcriptome, full-length paired TCR, and human leukocyte antigen (HLA) genotypes, we revealed the intrinsic features of germline-encoded TCR-major histocompatibility complex (MHC) restriction in CD4⁺/CD8⁺ lineages. We also observed widely existing public TCRαβs across the population, associated with higher clonal expansion levels and shared HLA alleles. The most publicly shared TCRs are likely to target epitopes from common viruses, such as Epstein-Barr virus (EBV), cytomegalovirus (CMV), and influenza A virus (IAV). Furthermore, we introduced TCR-DeepInsight, a computational framework to identify HLA-shared and disease-associated TCRαβ clusters that exhibit similar TCR sequence and GEX profiles, extensible for researchers to incorporate their data with our reference and characterize potentially functional TCRs. In summary, our work presents a panoramic scTCRαβ reference and computational methods for TCR study.

Lactylation, a lactate-mediated post-translational modification, has garnered significant attention for its pivotal role in epigenetic modulation. However, the intricate interplay between lactylation and ferroptosis in lung adenocarcinoma (LUAD) remains to be fully elucidated. Utilizing metabolomic profiling and comprehensive metabolic library screening, our study uncovers that ferroptosis markedly enhances lactic acid accumulation and subsequent protein lactylation, which in turn confers resistance to ferroptosis in LUAD cells. Functional assays, comprising cell viability tests, lipid peroxidation detection, as well as malondialdehyde and glutathione measurements, collectively reveal that SUMO2-K11 lactylation (SUMO2-K11la), the most prominently elevated lactylation in response to ferroptosis induction, serves as a pivotal factor in determining ferroptosis resistance. Sumoylation proteomics and co-immunoprecipitation assays reveal that SUMO2-K11la impairs the interaction between SUMO2 and ACSL4. Consequently, this disruption facilitates the degradation of ACSL4, thereby disrupting lipid metabolism and effectively mitigating ferroptosis. Furthermore, AARS1 is identified as the lactyltransferase and HDAC1 as the delactylase for SUMO2-K11la. Based on these findings, we develop a cell-penetrating peptide that competitively and specifically inhibits SUMO2-K11la. This peptide significantly potentiates ferroptosis and sensitizes LUAD to cisplatin in xenograft models, while enhancing chemoimmunotherapy responses in spontaneous lung cancer models. Overall, our findings imply that SUMO2-K11la is a pivotal regulator of ferroptosis resistance in LUAD, and suggest a promising strategy to potentiate ferroptosis-based cancer therapies via targeting SUMO2-K11la by the cell-penetrating peptide.

Multidrug resistance is a significant barrier in cancer therapy largely due to poorly understood regulatory mechanisms. Here we reveal that certain anticancer drugs can bind to newly synthesized proteins prior to reaching their canonical targets, resulting in various forms of protein damage. This binding disrupts protein functions, particularly those of mitochondrial proteins, resulting in substantial cytotoxicity. The protein damage is further exacerbated by mitochondrial reactive oxygen species generated as a consequence of the initial damage, creating a positive feedback loop. In response, cancer cells rapidly initiate a chain of events, which we term the Protein Damage Response (PDR). This includes damage recognition primarily mediated by protein ubiquitination and subsequent damage clearance via the proteasome system. Notably, patients with advanced, drug-resistant metastatic breast or colon cancers exhibit elevated proteasome activity. In an effort to predict drug resistance, we developed a sensitive kit for detecting proteasome levels, enabling the identification and subtyping of patients with high proteasome activity to support tailored therapeutic strategies. Using a three-dimensional tumor slice culture-based drug sensitivity assay and an investigator-initiated clinical trial, we demonstrate that three clinically approved proteasome inhibitors effectively overcome multidrug resistance in colon and breast cancer patients with elevated proteasome activity.