Cell reports最新文献

Triple-negative breast cancer (TNBC) is a prevalent breast cancer subtype with the lowest 5-year survival. Several factors influence outcomes, but their inherent molecular and cellular heterogeneity are increasingly acknowledged as crucial determinants. Here, we report on the spatio-molecular heterogeneity underlying TNBC tumors in a retrospective, treatment-naive cohort with differential prognoses (17 good prognoses [GPx] >15-year survival and 15 poor prognoses [PPx] <3-year survival]) profiled using GeoMx Digital Spatial Profiler. Analyses reveal that epithelial and microenvironment (TME) states are transcriptionally distinct between groups. Invasive GPx epithelia show an increase in immune transcripts, with a more immune-rich TME (via IF). PPx epithelia, in contrast, are more metabolically and translationally active, with a mesenchymal/fibrotic TME. Pre-cancerous epithelia in PPx exhibit a presence of aggressiveness, marked by increased EMT signaling and complement activity. We identify distinct epithelial gene signatures for PPx and GPx that can accurately classify diagnostic samples and likely inform therapy.

Human liver ductal epithelium is morphologically, functionally, and transcriptionally heterogeneous. Understanding the impact of this heterogeneity has been challenging due to the absence of systems that recapitulate this heterogeneity in vitro. Here, we found that human liver cholangiocyte organoids do not retain the complex cellular heterogeneity of the native ductal epithelium. Inspired by the knowledge of the cellular niche, we refined our previous organoid medium to fully capture the in vivo cellular heterogeneity. We employed this refined system to analyze the relationships between human biliary epithelial cell states. In our refined model, cholangiocytes transition toward hepatocyte-like states through a bipotent state. Additionally, inhibiting WNT signaling enhances the differentiation capacity of the cells toward hepatocyte-like states. By capturing the in vivo cholangiocyte heterogeneity, our improved organoid model represents a platform to investigate the impact of the different liver ductal cell states in cell plasticity, regeneration, and disease.

Remapping is a fundamental feature of hippocampal contextual representations that underlies memory encoding and separation. Recently in Cell Reports, Tarcsay et al¹ have shown that experience determines remapping dynamics in context learning.

We optogenetically mapped the function and spatial organization of inhibitory circuits formed by interneurons (INs) within the claustrum, a highly interconnected but poorly understood brain region. INs expressing parvalbumin or somatostatin attenuate claustrum output by inhibiting projection neurons (PNs), while INs expressing vasoactive intestinal peptide promote claustrum output by disinhibiting PNs. The spatial organization and degree of convergence differ for each interneuronal circuit. A computational model incorporating measured circuit properties predicts that differential inhibition of PNs by INs toggles claustrum output between cortical and subcortical brain regions and that the spatial organization of IN circuits nonlinearly filters claustrum output according to the strength and spatial distribution of excitatory input. Experimental measurements show that the claustrum spatially filters cortical input as predicted by the model. We conclude that the organization of its inhibitory circuits allows the claustrum to serve as a filter that improves the signal-to-noise ratio of signals transmitted to its downstream targets.

RIG-I (DDX58) is typically localized in the cytoplasm and activates innate immunity. However, the mechanisms governing its nuclear translocation and functions remain incompletely understood. Here, we discover that RIG-I undergoes lactylation, which is mediated by the acetyltransferase PCAF. Treatment with the lactate transporter inhibitor syrosingopine blocks the efflux of lactate from cancer cells, increasing intracellular lactate concentration, promoting RIG-I lactylation, and enhancing the nuclear translocation of lactylated RIG-I in an importin 8-dependent manner. The nuclear-localized RIG-I interacts with PARP1 and attenuates its activity, thereby inhibiting DNA damage repair. Moreover, we find that low RIG-I expression is associated with unfavorable prognosis and survival in lung adenocarcinoma (LUAD). Syrosingopine treatment sensitizes LUAD cells to PARP inhibitor (PARPi) and potentiates the therapeutic efficacy of olaparib in a mouse LUAD model. Altogether, our study reveals that lactylation drives RIG-I nuclear function to inhibit DNA damage repair via PARP suppression. This supports the potential co-administration of syrosingopine and PARPi for LUAD treatment.

Applying cryoelectron microscopy (cryo-EM) to small protein complexes is usually challenging due to their lack of features for particle alignment. Here, we characterized antibody responses to 21 kDa human immunodeficiency virus (HIV) membrane-proximal external region germline-targeting (MPER-GT) immunogens through cryo-EM by complexing them with 10E8 or Fabs derived from MPER-GT-immunized animals. Distinct antibody-antigen interactions were analyzed using atomic models generated from cryo-EM maps. Mutagenesis screening revealed that off-target monoclonal antibodies (mAbs), which do not compete with 10E8, bind non-MPER epitopes, and the binding of two most dominant epitopes were verified by cryo-EM. The structures of 10E8-class on-target Fabs showed binding patterns that resemble the YxFW motif in the 10E8 heavy chain complementarity-determining region 3 (HCDR3) loop. Additionally, we demonstrate that high-resolution maps can be generated from heterogeneous samples with pooled competing Fabs. Overall, our findings will facilitate the optimization of MPER-GT antigens and push the size limit for cryo-EM-based epitope mapping with smaller antigens and heterogeneous antibody mixes.

Despite recent advances in cell migration mechanics, the principles governing rapid T cell movement remain unclear. Efficient migration is critical for antitumoral T cells to locate and eliminate cancer cells. To investigate the upper limits of cell speed, we develop a hybrid stochastic-mean field model of bleb-based cell motility. Our model suggests that cell-matrix adhesion-free bleb migration is highly inefficient, challenging the feasibility of adhesion-independent migration as a primary fast mode. Instead, we show that T cells can achieve rapid migration by combining bleb formation with adhesion-based forces. Supporting our predictions, three-dimensional gel experiments confirm that T cells migrate significantly faster under adherent conditions than in adhesion-free environments. These findings highlight the mechanical constraints of T cell motility and suggest that controlled modulation of tissue adhesion could enhance immune cell infiltration into tumors. Our work provides insights into optimizing T cell-based immunotherapies and underscores that indiscriminate antifibrotic treatments may hinder infiltration.

Neuro-glial mitochondrial transfer critically sustains neuronal function in disease. While this transfer reshapes inflammatory microenvironments, its pathological mechanisms in peripheral inflammatory pain remain uncharacterized, impeding targeted interventions. Here, employing primary satellite glial cells (SGCs)-trigeminal ganglion neurons (TGNs) co-culture models, we demonstrate that, during acute inflammation, SGCs transfer functional mitochondria to injured TGNs via tunneling nanotubes and free mitochondrial uptake. Inflammatory stress impairs mitophagy, leading to dysfunctional mitochondrial accumulation and heightened neuronal hyperexcitability. Mitochondria from SGCs restore mitophagic flux and enhance mitochondrial-endoplasmic reticulum (ER) contact sites, thereby facilitating calcium exchange and homeostasis while reducing neuronal hyperexcitability. Critically, Atl1 knockout and overexpression mice models reveal that ATL1-driven ER restructuring initiates autophagosome formation during mitophagy and regulates early-stage autophagic progression. Taken together, our findings uncover a neuroprotective axis wherein glial mitochondrial donation safeguards neurons, directly nominating mitochondrial dynamics for therapeutic intervention in orofacial inflammatory pain.

Oscillations in the levels of second messengers are observed throughout the phylogenetic tree, with signaling information encoded in the frequency of the spikes. Different biological targets respond to different frequencies of oscillation, leading to the concept of frequency counting. The most widely observed and best understood oscillatory second messenger is cytosolic Ca²⁺. Ca²⁺ oscillations are generated in all cell types, are seen throughout the life of a cell, and are indispensable for diverse biological processes ranging from fertilization to cell death and myriad responses in between including excitation-transcription coupling through Ca²⁺-dependent gene expression. The widely expressed Ca²⁺-dependent transcription factors nuclear factor (NF) of activated T cells (NFAT) and NF-κB are recruited by different Ca²⁺ oscillation frequencies, increasing the signaling bandwidth through the universal Ca²⁺ messenger. Here, we show that Ca²⁺ nanodomains near Ca²⁺ channels at the cell surface are central to gene expression. Cytosolic Ca²⁺ oscillations are not necessary for Ca²⁺-dependent gene expression, provided Ca²⁺ nanodomains near Ca²⁺ release-activated Ca²⁺ (CRAC) channels are formed. Our results establish that a fundamental unit of excitation-transcription coupling is the Ca²⁺ channel nanodomain at the cell surface.

Human early development is challenging to study due to limited samples and cell numbers. The emergence of 8-cell-stage (8C) embryo-like cells (8CLCs) offers new opportunities to understand embryonic genome activation (EGA) in humans. Our research compares and characterizes 8CLCs from various stem cell-based systems to determine how well these models reflect human early embryonic development. Using single-cell RNA sequencing datasets from multiple studies, we integrate data to identify key gene co-expression modules, transposable element expression, and biological processes recapitulated in 8CLCs. We identify both mature and intermediate 8CLCs, with the Yoshihara and Mazid datasets best representing 8C embryos. 8CLCs show remodeling in energy and RNA metabolism, regulation of RNA splicing, and ribosome biogenesis, mirroring human 8C embryos. Our findings underscore the importance of distinguishing mature 8CLCs from partially reprogrammed cell states to improve their use as models for human EGA.