【Cell】2025年5月论文导读（188卷，9-11期）
期刊介绍：
Cell是Cell Press细胞出版社旗下的旗舰刊，创办于1974年，由Elsevier公司出版发行。这是一本多学科期刊，包括但不限于细胞生物学、分子生物学、神经科学、免疫学、病毒学和微生物学、癌症、人类遗传学、系统生物学、信号传导和疾病机制和疾病治疗。该期刊为双周刊，最新影响因子为45.5。
本期文献导读将呈现2025年5月的主要刊物内容。
May 01, 2025；Volume 188 Issue 9 p2307-2560
在2025年5月1日，共发表18篇文章，其中包括2篇pre-view，13篇Articles，2篇Resources，1篇Correction。
1.Precision proteogenomics reveals pan-cancer impact of germline variants
精准蛋白质组学揭示生殖系突变的泛癌影响
We investigate the impact of germline variants on cancer patients? proteomes, encompassing 1,064 individuals across 10 cancer types. We introduced an approach, ?precision peptidomics,? mapping 337,469 coding germline variants onto peptides from patients? mass spectrometry data, revealing their potential impact on post-translational modifications, protein stability, allele-specific expression, and protein structure by leveraging the relevant protein databases. We identified rare pathogenic and common germline variants in cancer genes potentially affecting proteomic features, including variants altering protein abundance and structure and variants in kinases (ERBB2 and MAP2K2) impacting phosphorylation. Precision peptidome analysis predicted destabilizing events in signal-regulatory protein alpha (SIRPA) and glial fibrillary acid protein (GFAP), relevant to immunomodulation and glioblastoma diagnostics, respectively. Genome-wide association studies identified quantitative trait loci for gene expression and protein levels, spanning millions of SNPs and thousands of proteins. Polygenic risk scores correlated with distal effects from risk variants. Our findings emphasize the contribution of germline genetics to cancer heterogeneity and high-throughput precision peptidomics.
该研究探索了生殖系突变对癌症患者蛋白质组的影响，研究涉及10种癌症类型的1,064名患者。该研究引入了一种名为“精准肽组学”的方法，将337,469个编码生殖系突变映射到患者质谱数据的肽段上，并利用相关的蛋白质数据库揭示其对翻译后修饰、蛋白质稳定性、等位基因特异性表达和蛋白质结构的潜在影响。该研究鉴定了可能影响蛋白质组学特征的癌症基因中罕见致病性和常见生殖系突变，包括改变蛋白质丰度和结构的变异，以及影响磷酸化的激酶（ERBB2和MAP2K2）变异。精准肽组学分析预测了信号调节蛋白α（SIRPA）和胶质纤维酸性蛋白（GFAP）的稳定性降低事件，这分别与免疫调节和胶质母细胞瘤诊断相关。全基因组关联分析确定了基因表达和蛋白质水平的数量性状位点，涵盖数百万个SNP和数千种蛋白质。多基因风险评分与风险变异的远端效应相关。研究结果强调了生殖系遗传因素对癌症异质性和高通量精准肽组学的影响。
2.icrobiota-derived bile acids antagonize the host androgen receptor and drive anti-tumor immunity
微生物来源的胆汁酸拮抗宿主雄激素受体并驱动抗肿瘤免疫
Microbiota-derived bile acids (BAs) are associated with host biology/disease, yet their causal effects remain largely undefined. Herein, we speculate that characterizing previously undefined microbiota-derived BAs would uncover previously unknown BA-sensing receptors and their biological functions. We integrated BA metabolomics and microbial genetics to functionally profile >200 putative microbiota BA metabolic genes. We identified 56 less-characterized BAs, many of which are detected in humans/mammals. Notably, a subset of these BAs are potent antagonists of the human androgen receptor (hAR). They inhibit AR-related gene expression and are human-relevant. As a proof-of-principle, we demonstrate that one of these BAs suppresses tumor progression and potentiates the efficacy of anti-PD-1 treatment in an AR-dependent manner. Our findings show that an approach combining bioinformatics, BA metabolomics, and microbial genetics can expand our knowledge of the microbiota metabolic potential and reveal an unexpected microbiota BA-AR interaction and its role in regulating host biology.
微生物来源的胆汁酸 (BA) 与宿主生物学/疾病相关，但其具体的因果关系在很大程度上仍不明确。研究团队推测，表征此前未定义的微生物来源的BA 有助于揭示此前未知的BA感受体及其生物学功能。该研究整合了 BA 代谢组学和微生物遗传学，对 200 多个潜在的微生物 BA 代谢基因进行了功能表征。该研究鉴定出56 个尚未充分表征的 BA，其中许多在人类/哺乳动物中可被检测到。值得注意的是，其中一部分BA是人类雄激素受体 (hAR) 的强效拮抗剂。它们抑制 AR 相关基因的表达，并且在人体中具有生理意义。该研究证明其中一种 BA 能够抑制肿瘤进展，并以 AR 依赖的方式增强抗 PD-1 治疗的疗效。该研究的研究结果表明，综合运用生物信息学、BA 代谢组学和微生物遗传学的方法可以拓展对微生物群代谢潜力的认识，并揭示意想不到的微生物群 BA-AR 相互作用及其在调节宿主生物学功能中的作用。
3.Ligand-induced ubiquitination unleashes LAG3 immune checkpoint function by hindering membrane sequestration of signaling motifs
配体诱导的泛素化通过阻碍信号传导基序的膜隔离来释放LAG3免疫检查点功能
Lymphocyte activation gene 3 (LAG3) has emerged as a promising cancer immunotherapy target, but the mechanism underlying LAG3 activation upon ligand engagement remains elusive. Here, LAG3 was found to undergo robust non-K48-linked polyubiquitination upon ligand engagement, which promotes LAG’s inhibitory function instead of causing degradation. This ubiquitination could be triggered by the engagement of major histocompatibility complex class II (MHC class II) and membrane-bound (but not soluble) fibrinogen-like protein 1 (FGL1). LAG3 ubiquitination, mediated redundantly by the E3 ligases c-Cbl and Cbl-b, disrupted the membrane binding of the juxtamembrane basic residue-rich sequence, thereby stabilizing the LAG3 cytoplasmic tail in a membrane-dissociated conformation enabling signaling. Furthermore, LAG3 ubiquitination is crucial for the LAG3-mediated suppression of antitumor immunity in vivo. Consistently, LAG3 therapeutic antibodies repress LAG3 ubiquitination, correlating with their checkpoint blockade effects. Moreover, patient cohort analyses suggest that LAG3/CBL coexpression could serve as a biomarker for response to LAG3 blockade. Collectively, our study reveals an immune-checkpoint-triggering mechanism with translational potential in cancer immunotherapy.
淋巴细胞激活基因3 (LAG3) 已成为一个颇具前景的癌症免疫治疗靶点，但 LAG3在与配体结合后的激活机制仍不清楚。该研究发现，LAG3 在与配体结合后会发生显著的非 K48 连接多泛素化，该修饰增强了LAG3的抑制功能，而非促进其降解。这种泛素化是由与主要组织相容性复合体II类(MHC II类) 以及膜结合型（而非可溶型）纤维蛋白原样蛋白1(FGL1)的结合所触发。由E3连接酶 c-Cbl和Cbl-b协同介导的LAG3泛素化，破坏了富含碱性残基序列近膜区序列与细胞膜的结合，从而使LAG3胞质尾得以稳定在一种膜解离构象状态，并实现信号传导功能。此外，LAG3泛素化对于LAG3介导的体内抗肿瘤免疫抑制至关重要，LAG3治疗性抗体抑制LAG3泛素化，其作用机制与它们所发挥的检查点阻断效应相关。另外，患者队列分析表明，LAG3/CBL的共表达可作为预测对LAG3阻断疗法响应的生物标志物。总之，该研究揭示了一种在癌症免疫治疗中具有转化潜力的免疫检查点激活机制。
4.Engineering TCR-controlled fuzzy logic into CAR T cells enhances therapeutic specificity
将TCR控制的模糊逻辑引入CAR-T细胞可增强治疗特异性
Chimeric antigen receptor (CAR) T cell immunotherapy represents a breakthrough in the treatment of hematological malignancies, but poor specificity has limited its applicability to solid tumors. By contrast, natural T cells harboring T cell receptors (TCRs) can discriminate between neoantigen-expressing cancer cells and self-antigen-expressing healthy tissues but have limited potency against tumors. We used a high-throughput platform to systematically evaluate the impact of co-expressing a TCR and CAR on the same CAR T cell. While strong TCR-antigen interactions enhanced CAR activation, weak TCR-antigen interactions actively antagonized their activation. Mathematical modeling captured this TCR-CAR crosstalk in CAR T cells, allowing us to engineer dual TCR/CAR T cells targeting neoantigens (HHATL8F/p53R175H) and human epithelial growth factor receptor 2 (HER2) ligands, respectively. These T cells exhibited superior anti-cancer activity and minimal toxicity against healthy tissue compared with conventional CAR T cells in a humanized solid tumor mouse model. Harnessing pre-existing inhibitory crosstalk between receptors, therefore, paves the way for the design of more precise cancer immunotherapies.
嵌合抗原受体 (CAR) T 细胞免疫疗法是血液系统恶性肿瘤治疗的一项重大突破，但其相对不足的特异性限制了其在实体瘤中的应用。相比之下，携带T 细胞受体 (TCR)的天然T细胞虽能区分表达肿瘤新抗原的癌细胞和表达自身抗原的健康组织，但其抗肿瘤效力有限。研究人员利用高通量平台系统地评估了 TCR和CAR共表达对同一CAR T细胞所产生的影响。研究发现，虽然强烈的TCR-抗原相互作用能增强CAR的活化，但微弱的TCR-抗原相互作用会显著抑制T细胞的活化。基于数学建模捕捉到的CAR T细胞中的这种TCR-CAR串扰，使该研究成功设计出分别靶向肿瘤新抗原(HHATL8F/p53R175H)和人类上皮生长因子受体2(HER2) 配体的双重TCR/CAR T细胞。与传统的CAR-T细胞相比，这些T细胞在人源化实体瘤小鼠模型中表现出更强的抗癌活性，同时对健康组织的毒性极低。因此，利用受体间预先存在的抑制性串扰，为设计更精准的癌症免疫疗法奠定了基础。
5.Autoimmune mechanisms elucidated through muscle acetylcholine receptor structures
通过肌肉乙酰胆碱受体结构阐明自身免疫机制
Skeletal muscle contraction is triggered by acetylcholine (ACh) binding to its ionotropic receptors (AChRs) at neuromuscular junctions. In myasthenia gravis (MG), autoantibodies target AChRs, disrupting neurotransmission and causing muscle weakness. While treatments exist, variable patient responses suggest pathogenic heterogeneity. Progress in understanding the molecular basis of MG has been limited by the absence of structures of intact human muscle AChRs. Here, we present high-resolution cryoelectron microscopy (cryo-EM) structures of the human adult AChR in different functional states. Using six MG patient-derived monoclonal antibodies, we mapped distinct epitopes involved in diverse pathogenic mechanisms, including receptor blockade, internalization, and complement activation. Electrophysiological and binding assays revealed how these autoantibodies directly inhibit AChR channel activation. These findings provide critical insights into MG immunopathogenesis, uncovering unrecognized antibody epitope diversity and modes of receptor inhibition, and provide a framework for developing personalized therapies targeting antibody-mediated autoimmune disorders.
骨骼肌收缩是由乙酰胆碱 (ACh)与神经肌肉接头处的离子型受体 (AChR) 结合触发的。在重症肌无力 (MG)中，自身抗体靶向AChR，干扰神经传递并导致肌肉无力。虽然存在治疗方法，但患者反应各异，提示存在致病机制的异质性。由于缺乏完整的人体肌肉AChR结构，对MG分子机制的理解进展一直受到限制。该研究展示了不同功能状态下成人AChR的高分辨率冷冻电镜 (cryo-EM) 结构。通过使用六种MG 患者来源的单克隆抗体，研究人员定位了参与多种致病机制（包括受体阻断、内化和补体激活）的不同表位。电生理学和结合分析揭示了这些自身抗体如何直接抑制AChR通道的活化。这些发现为理解MG免疫发病机制提供了关键见解，揭示了未知的抗体表位多样性及其受体抑制模式，并为开发针对抗体介导的自身免疫性疾病的个体化疗法奠定了基础。
6.Genetic protection from type 1 diabetes resulting from accelerated insulin mRNA decay
来自胰岛素mRNA降解加速导致的1型糖尿病遗传保护
Insulin gene (INS) variation and beta-cell stress are associated with the risk of development of type 1 diabetes (T1D) and autoimmunity against insulin. The unfolded protein response alleviating endoplasmic reticulum (ER) stress involves activation of inositol-requiring enzyme 1α (IRE1α) that impedes translation by mRNA decay. We discover that the IRE1α digestion motif is present in insulin mRNA carrying SNP rs3842752 (G>A). This SNP in the 3’ untranslated region of INS associates with protection from T1D (INSP). ER stress in beta cells with INSP led to accelerated insulin mRNA decay compared with the susceptible INS variant (INSS). Human islets with INSP showed improved vitality and function and reversed diabetes more rapidly when transplanted into diabetic mice than islets carrying INSS only. Surrogate beta cells with INSP expressed less ER stress and INS-DRiP neoantigen. This explanation for genetic protection from T1D may act instead of or in concert with the previously proposed mechanism attributed to INS promoter polymorphism.
胰岛素基因 (INS) 变异和β细胞应激与患1型糖尿病 (T1D)及针对胰岛素的自身免疫反应的风险相关。缓解内质网 (ER)应激的未折叠蛋白反应涉及激活肌醇依赖酶1α (IRE1α)，从而通过 mRNA 降解抑制蛋白质翻译。该研究发现 IRE1α的消化基序存在于携带SNP rs3842752(G>A)的胰岛素mRNA中。INS 3’ 非翻译区中的这个SNP赋予对1型糖尿病的保护作用(INSP)。与易感型INS变异(INSS)相比，携带INSP的β细胞内发生内质网应激导致胰岛素mRNA降解加速。当移植到糖尿病小鼠体内时，携带INSP的人类胰岛相比携带INSS的胰岛表现出活力和功能的改善，并且逆转糖尿病的速度更快。携带INSP的模拟β 细胞表现出较低水平的内质网应激和INS-DRiP（缺陷核糖体产物）新抗原。对于1型糖尿病遗传保护机制的这一解释，可能替代或协同先前提出的INS启动子多态性机制发挥作用
7.Enteric neuronal Piezo1 maintains mechanical and immunological homeostasis by sensing force
肠道神经元Piezo1通过感知机械力调控肠道运动和免疫稳态
The gastrointestinal (GI) tract experiences a myriad of mechanical forces while orchestrating digestion and barrier immunity. A central conductor of these processes, the enteric nervous system (ENS), detects luminal pressure to regulate peristalsis independently of extrinsic input from the central and peripheral nervous systems. However, how the ~500 million enteric neurons that reside in the GI tract sense and respond to force remains unknown. Herein, we establish that the mechanosensor Piezo1 is functionally expressed in cholinergic enteric neurons. Optogenetic stimulation of Piezo1+ cholinergic enteric neurons drives colonic motility, while Piezo1 deficiency reduces cholinergic neuronal activity and slows peristalsis. Additionally, Piezo1 deficiency in cholinergic enteric neurons abolishes exercise-induced acceleration of GI motility. Finally, we uncover that enteric neuronal Piezo1 function is required for motility alterations in colitis and acts to prevent aberrant inflammation and tissue damage. This work uncovers how the ENS senses and responds to mechanical force.
胃肠道在协调消化和屏障免疫的同时持续承受着各种机械力。这些过程的核心调控者是肠神经系统 (ENS)，其通过检测腔内压力来调节蠕动，独立于来自中枢和周围神经系统的外部输入。然而，位于胃肠道中的约5亿个肠道神经元如何感知和响应机械力仍不清楚。该研究证实，机械传感器Piezo1在胆碱能肠道神经元中功能性表达。光遗传学刺激Piezo1+胆碱能肠道神经元可驱动结肠运动，而Piezo1缺失则会降低胆碱能神经元活性并减缓蠕动。此外，胆碱能肠道神经元中的Piezo1缺失会消除运动诱导的胃肠道运动加速。最后，该研究发现肠道神经元Piezo1的功能是结肠炎中倡导运动变化所必需的，并有助于预防异常炎症和组织损伤。该研究揭示了ENS如何感知和应答机械力。
8.Global analysis of protein turnover dynamics in single cells
单个细胞中蛋白质周转动力学的全局分析
Single-cell proteomics (SCPs) has advanced significantly, yet it remains largely unidimensional, focusing primarily on protein abundances. In this study, we employed a pulsed stable isotope labeling by amino acids in cell culture (pSILAC) approach to simultaneously analyze protein abundance and turnover in single cells (SC-pSILAC). Using a state-of-the-art SCP workflow, we demonstrated that two SILAC labels are detectable from ~4,000 proteins in single HeLa cells recapitulating known biology. We performed a large-scale time-series SC-pSILAC analysis of undirected differentiation of human induced pluripotent stem cells (iPSCs) encompassing 6 sampling times over 2 months and analyzed >1,000 cells. Protein turnover dynamics highlighted differentiation-specific co-regulation of protein complexes with core histone turnover, discriminating dividing and non-dividing cells. Lastly, correlating cell diameter with the abundance of individual proteins showed that histones and some cell-cycle proteins do not scale with cell size. The SC-pSILAC method provides a multidimensional view of protein dynamics in single-cell biology.
单细胞蛋白质组学 (SCP) 已取得显著进展，但其研究方向仍较为单一，主要关注蛋白质丰度。该研究采用脉冲式氨基酸稳定同位素标记方法(pSILAC)，同时分析单细胞蛋白质丰度和周转 (SC-pSILAC)。该研究采用先进的SCP工作流程，证明在单个HeLa细胞的约4,000种蛋白质中可检测到两种SILAC标记，从而重现了已知的生物学过程。该研究对人类诱导多能干细胞 (iPSC)的非定向分化进行了大规模时间序列SC-pSILAC分析，涵盖2个月内6次采样，分析了超过1,000个细胞。蛋白质周转动力学揭示了蛋白质复合物与核心组蛋白周转在分化特异方面的协同调控，从而区分了分裂细胞和非分裂细胞。最后，将细胞直径与单个蛋白质的丰度关联起来，结果显示组蛋白和一些细胞周期蛋白不随细胞尺度发生比例变化。 SC-pSILAC方法提供了单细胞生物学中蛋白质动力学的多维视角。
9.Microtubules in Asgard archaea
阿斯加德古菌中发现微管结构
Microtubules are a hallmark of eukaryotes. Archaeal and bacterial homologs of tubulins typically form homopolymers and non-tubular superstructures. The origin of heterodimeric tubulins assembling into microtubules remains unclear.Here, we report the discovery of microtubule-forming tubulins in Asgard archaea, the closest known relatives of eukaryotes. These Asgard tubulins (AtubA/B) are closely related to eukaryotic α/β-tubulins and the enigmatic bacterial tubulins BtubA/B. Proteomics of Candidatus Lokiarchaeum ossiferum showed that AtubA/B were highly expressed. Cryoelectron microscopy structures demonstrate that AtubA/B form eukaryote-like heterodimers, which assembled into 5-protofilament bona fide microtubules in vitro. The additional paralog AtubB2 lacks a nucleotide-binding site and competitively displaced AtubB. These AtubA/B2 heterodimers polymerized into 7-protofilament non-canonical microtubules. In a sub-population of Ca. Lokiarchaeum ossiferum cells, cryo-tomography revealed tubular structures, while expansion microscopy identified AtubA/B cytoskeletal assemblies.Our findings suggest a pre-eukaryotic origin of microtubules and provide a framework for understanding the fundamental principles of microtubule assembly.
微管是真核生物的标志。古菌和细菌的微管蛋白同源物通常形成均聚物和非管状超结构。由异二聚体微管蛋白组装成微管的起源尚不清楚。该研究报道了在真核生物已知亲缘关系最近的古菌——阿斯加德古菌中，发现了可形成微管的微管蛋白。这些阿斯加德微管蛋白（AtubA/B）与真核生物的α/β-微管蛋白以及神秘的细菌微管蛋白BtubA/B密切相关。对Candidatus Lokiarchaeum ossiferum进行的蛋白质组学分析表明AtubA/B呈高表达。冷冻电镜结构分析表明AtubA/B形成类似真核生物的异二聚体，并在体外组装成具有5条原纤维的真正微管。额外的旁系同源物AtubB2缺乏核苷酸结合位点，并竞争性地取代了AtubB。这些AtubA/B2异二聚体聚合成7条原丝的非典型微管。在部分Ca. Lokiarchaeum ossiferum细胞中，冷冻电子断层扫描揭示了微管状结构，而膨胀显微镜则发现了AtubA/B组成的细胞骨架结构。该研究的结果表明微管起源于前真核生物时期，并为理解微管组装的基本原理奠定了基础。
10.Mechanism of DNA capture by the MukBEF SMC complex and its inhibition by a viral DNA mimic
MukBEF SMC复合物捕获DNA的机制及病毒DNA模拟物的抑制作用
Ring-like structural maintenance of chromosome (SMC) complexes are crucial for genome organization and operate through mechanisms of DNA entrapment and loop extrusion. Here, we explore the DNA loading process of the bacterial SMC complex MukBEF. Using cryoelectron microscopy (cryo-EM), we demonstrate that ATP binding opens one of MukBEF’s three potential DNA entry gates, exposing a DNA capture site that positions DNA at the open neck gate. We discover that the gp5.9 protein of bacteriophage T7 blocks this capture site by DNA mimicry, thereby preventing DNA loading and inactivating MukBEF. We propose a comprehensive and unidirectional loading mechanism in which DNA is first captured at the complex?s periphery and then ingested through the DNA entry gate, powered by a single cycle of ATP hydrolysis. These findings illuminate a fundamental aspect of how ubiquitous DNA organizers are primed for genome maintenance and demonstrate how this process can be disrupted by viruses.
染色体结构维持（SMC）复合物的环状结构对基因组组织至关重要，其机制包括DNA捕获和环挤压。该研究探究了细菌SMC复合物MukBEF的DNA装载过程。利用冷冻电镜（cryo-EM），该研究证实ATP结合会打开MukBEF三个DNA入口之一，从而暴露出一个DNA捕获位点，该位点将DNA定位于开放的颈部。该研究发现噬菌体T7的gp5.9蛋白通过模拟DNA结构阻断了该捕获位点，从而阻止了DNA装载并使MukBEF失活。该研究提出了一种全面且单向的装载机制，其中DNA首先在复合物的外周被捕获，然后通过DNA入口被内化，这个过程由一次ATP水解循环驱动。这些发现阐明了广泛存在的DNA组织蛋白如何为基因组维护的基本机制，并揭示了病毒如何破坏这一过程。
11.Functional and antigenic landscape of the Nipah virus receptor-binding protein
尼帕病毒受体结合蛋白的功能和抗原图谱
Nipah virus recurrently spills over to humans, causing fatal infections. The viral receptor-binding protein (RBP or G) attaches to host receptors and is a major target of neutralizing antibodies. Here, we use deep mutational scanning to measure how all amino-acid mutations to the RBP affect cell entry, receptor binding, and escape from neutralizing antibodies. We identify functionally constrained regions of the RBP, including sites involved in oligomerization, along with mutations that differentially modulate RBP binding to its two ephrin receptors. We map escape mutations for six anti-RBP antibodies and find that few antigenic mutations are present in natural Nipah strains. Our findings offer insights into the potential for functional and antigenic evolution of the RBP that can inform the development of antibody therapies and vaccines.
尼帕病毒反复波及人类造成致命感染。病毒受体结合蛋白（RBP或G）附着于宿主受体，且是中和抗体的主要靶点。该研究利用深度突变扫描评估了RBP上所有氨基酸突变对细胞进入、受体结合以及中和抗体逃逸能力的影响。该研究确定了RBP的功能保守区域，包括参与寡聚化的位点，以及差异性调节RBP与其两个肾上腺素受体结合的突变。该研究绘制了六种抗RBP抗体的逃逸突变图谱，发现自然流行的尼帕病毒株中几乎不存在抗原突变。这些发现为RBP的功能和抗原进化潜力提供了重要见解，可为抗体疗法和疫苗的开发提供指导。
12.A chemical radar allows bacteria to detect and kill predators
化学雷达系统使细菌感知并杀伤捕食者
Amoebal predation exerts a strong evolutionary selection pressure on bacteria, thus driving the development of effective predator-defense strategies. However, little is known about the molecular interplay between bacteria and predators, particularly how bacteria can sense and kill their microbial predators. We show how the ubiquitous bacterium Pseudomonas syringae detects and kills the social amoeba Polysphondylium pallidum. Combining comparative genomics, molecular biology, and chemical analyses, we identified a chemical radar system. The system relies on P. syringae secreting the lipopeptide syringafactin, which is deacylated by the amoeba. The resulting peptides are sensed via the bacterial sensor protein chemical radar regulator (CraR) that activates genes for converting the predator-derived signal into the amoebicide pyrofactin. This system is widespread in P. syringae and enables bacteria to infect A. thaliana in the presence of amoebae. Our study advances the understanding of microbial sensing and opens new avenues for the discovery of natural products.
变形虫的捕食行为对细菌施加了强大的进化选择压力，从而促使有效的捕食者防御策略演化。然而，人们对细菌与捕食者之间的分子相互作用知之甚少，尤其是细菌如何感知并杀死其微生物捕食者。该研究展示了普遍存在的细菌丁香假单胞菌（Pseudomonas syringae）如何感知并杀死社会性变形虫苍白多核变形虫（Polysphondylium pallidum）。结合比较基因组学、分子生物学和化学分析，该研究鉴定出一种化学雷达系统。该系统依赖于丁香假单胞菌分泌的脂肽丁香脂肽（syringafactin），该脂肽会被变形虫脱酰基化，脱酰基化产生的肽通过细菌的传感蛋白“化学雷达调节器”（CraR）感知，该蛋白激活将捕食者衍生信号转化为杀变形虫剂焦脂肽的基因。该系统在丁香假单胞菌中广泛存在，使细菌能够在变形虫存在的情况下感染拟南芥。该研究深化了对微生物感知机制的理解，并为发现天然产物拓展了新的途径。
13.Conserved genetic basis for microbial colonization of the gut
肠道微生物定植的保守遗传基础
Despite the fundamental importance of gut microbes, the genetic basis of their colonization remains largely unexplored. Here, by applying cross-species genotype-habitat association at the tree-of-life scale, we identify conserved microbial gene modules associated with gut colonization. Across thousands of species, we discovered 79 taxonomically diverse putative colonization factors organized into operonic and non-operonic modules. They include previously characterized colonization pathways such as autoinducer-2 biosynthesis and novel processes including tRNA modification and translation. In vivo functional validation revealed YigZ (IMPACT family) and tRNA hydroxylation protein-P (TrhP) are required for E. coli intestinal colonization. Overexpressing YigZ alone is sufficient to enhance colonization of the poorly colonizing MG1655 E. coli by >100-fold. Moreover, natural allelic variations in YigZ impact inter-strain colonization efficiency. Our findings highlight the power of large-scale comparative genomics in revealing the genetic basis of microbial adaptations. These broadly conserved colonization factors may prove critical for understanding gastrointestinal (GI) dysbiosis and developing therapeutics.
尽管肠道微生物至关重要，但它们定植的遗传基础仍未被深入探究。该研究通过在生命树的尺度上应用跨物种基因型-栖息地关联分析，鉴定出与肠道定植相关的保守微生物基因模块。在数千个物种中，该研究发现了79个分类学上不同的推定定植因子，这些因子被组织成操纵子模块和非操纵子模块。它们包括先前表征的定植途径，例如自诱导物-2的生物合成，以及包括tRNA修饰和翻译在内的新过程。体内功能验证表明，YigZ（IMPACT家族）和tRNA羟基化蛋白-P（TrhP）是大肠杆菌肠道定植所必需的。仅过表达YigZ就足以使定植能力较差的MG1655大肠杆菌的定植率提高100倍以上。此外，YigZ的天然等位基因变异会影响菌株间的定植效率。该研究的结果凸显了大规模比较基因组学在揭示微生物适应性遗传基础方面的能力。这些广泛保守的定植因子可能对理解胃肠道菌群失调和开发治疗方法至关重要。
14.Crop root bacterial and viral genomes reveal unexplored species and microbiome patterns
作物根系细菌和病毒基因组揭示了未知物种和微生物组模式
Reference genomes of root microbes are essential for metagenomic analyses and mechanistic studies of crop root microbiomes. By combining high-throughput bacterial cultivation with metagenomic sequencing, we constructed comprehensive bacterial and viral genome collections from the roots of wheat, rice, maize, and Medicago. The crop root bacterial genome collection (CRBC) significantly expands the quantity and phylogenetic diversity of publicly available crop root bacterial genomes, with 6,699 bacterial genomes (68.9% from isolates) and 1,817 undefined species, expanding crop root bacterial diversity by 290.6%. The crop root viral genome collection (CRVC) contains 9,736 non-redundant viral genomes, with 1,572 previously unreported genus-level clusters in crop root microbiomes. From these, we identified conserved bacterial functions enriched in root microbiomes across soils and host species and uncovered previously unexplored bacteria-virus connections in crop root ecosystems. Together, the CRBC and CRVC serve as valuable resources for investigating microbial mechanisms and applications, supporting sustainable agriculture.
根系微生物参考基因组对于作物根系微生物组的宏基因组分析和机制研究至关重要。通过高通量细菌培养与宏基因组测序相结合，该研究构建了小麦、水稻、玉米和蒺藜苜蓿根系的全面细菌和病毒基因组集合。作物根系细菌基因组集合 (CRBC)显著扩展了公开可用的作物根系细菌基因组的数量和系统发育多样性，包含6,699个细菌基因组（68.9% 来自分离株）和1,817个未定义物种，使作物根系细菌多样性提高了290.6%。作物根系病毒基因组集合 (CRVC)包含 9,736个非冗余病毒基因组，以及1,572个此前未在作物根系微生物组中报告的属级簇。由此，该研究鉴定了跨土壤和宿主物种在根系微生物组中富集的保守细菌功能，并揭示了作物根系生态系统中此前未探索的细菌-病毒关联。CRBC 和CRVC共同构成了研究微生物机制和应用的宝贵资源，支持可持续发展农业。
15.Genetically encoded reporters of actin filament organization in living cells and tissues
活细胞和组织中肌动蛋白丝排布的遗传编码报告基因
The cytoskeletal protein actin is crucial for cell shape and integrity throughout eukaryotes. Actin filaments perform essential biological functions, including muscle contraction, cell division, and tissue morphogenesis. These diverse activities are achieved through the ability of actin filaments to be arranged into precise architectures. Much progress has been made in defining the proteome of the actin cytoskeleton, but a detailed appreciation of the dynamic organizational state of the actin filaments themselves has been hindered by available tools. Fluorescence polarization microscopy is uniquely placed for measuring actin filament organization by exploiting the sensitivity of polarized light excitation to the orientation of fluorophores attached to actin filaments. By engineering fusions of five widely used actin localization reporters to fluorescent proteins with constrained mobility, we have succeeded in developing genetically encoded, green- and red-fluorescent-protein-based reporters for non-invasive, quantitative measurements of actin filament organization in living cells and tissues by fluorescence polarization microscopy.
细胞骨架蛋白肌动蛋白在真核生物中对细胞形状和完整性至关重要。肌动蛋白丝发挥着重要的生物学功能，包括肌肉收缩、细胞分裂和组织形态发生。这些多样化的活动是通过肌动蛋白丝能够排列成精确结构的能力来实现的。在定义肌动蛋白细胞骨架的蛋白质组方面已经取得了很大进展，但现有技术手段的限制使得对肌动蛋白丝自身动态排布状态的深入认识受阻。荧光偏振显微镜利用偏振光激发对附着在肌动蛋白丝上的荧光团方向的敏感性，在测量肌动蛋白丝排布方面具有独特的优势。通过将五种广泛使用的肌动蛋白定位报告基因与具有受限运动性的荧光蛋白进行融合，该研究成功开发了基于绿色和红色荧光蛋白的遗传编码报告基因，用于通过荧光偏振显微镜对活细胞和组织中的肌动蛋白丝排布进行非侵入性定量测量。
May 15, 2025；Volume 188 Issue 10 p2561-2828
在2025年5月15日，共发表19篇文章，其中包括1篇pre-view，1篇Commentary，12篇Articles，3篇Resources，2篇Correction。
1.ALDH7A1 protects against ferroptosis by generating membrane NADH and regulating FSP1
ALDH7A1通过产生膜NADH和调节FSP1抑制铁死亡
Ferroptosis is a form of cell death due to iron-induced lipid peroxidation. Ferroptosis suppressor protein 1 (FSP1) protects against this death by generating antioxidants, which requires nicotinamide adenine dinucleotide, reduced form (NADH) as a cofactor. We initially uncover that NADH exists at significant levels on cellular membranes and then find that this form of NADH is generated by aldehyde dehydrogenase 7A1 (ALDH7A1) to support FSP1 activity. ALDH7A1 activity also acts directly to decrease lipid peroxidation by consuming reactive aldehydes. Furthermore, ALDH7A1 promotes the membrane recruitment of FSP1, which is instigated by ferroptotic stress activating AMP-activated protein kinase (AMPK) to promote the membrane localization of ALDH7A1 that stabilizes FSP1 on membranes. These findings advance a fundamental understanding of NADH by revealing a previously unappreciated pool on cellular membranes, with the elucidation of its function providing a major understanding of how FSP1 acts and how an aldehyde dehydrogenase protects against ferroptosis.
铁死亡是一种由于铁诱导的脂质过氧化而导致的细胞死亡形式。铁死亡抑制蛋白1 (FSP1) 通过产生抗氧化剂来抑制这种死亡，而抗氧化剂的产生需要还原型烟酰胺腺嘌呤二核苷酸 (NADH) 作为辅因子。该研究首先发现NADH显著富集于细胞膜上，随后发现这种形式的NADH是由醛脱氢酶7A1(ALDH7A1)产生的，以支持FSP1活性。ALDH7A1的活性还通过消耗活性醛类直接降低脂质过氧化水平。此外，ALDH7A1促进FSP1的膜募集，这一过程起始于铁死亡应激激活腺苷酸活化蛋白激酶(AMPK)进而促进ALDH7A1的膜定位，从而稳定FSP1在膜上。这些发现通过揭示细胞膜上存在一个先前未被重视的NADH库，从而深化了对 NADH的基本理解，其功能的阐明为理解FSP1如何发挥作用以及醛脱氢酶如何抑制铁死亡提供了重要的见解。
2.Cell membranes sustain phospholipid imbalance via cholesterol asymmetry
细胞膜通过胆固醇不对称性维持磷脂失衡
Membranes are molecular interfaces that compartmentalize cells to control the flow of nutrients and information. These functions are facilitated by diverse collections of lipids, nearly all of which are distributed asymmetrically between the two bilayer leaflets. Most models of biomembrane structure and function include the implicit assumption that these leaflets have similar abundances of phospholipids. Here, we show that this assumption is generally invalid and investigate the consequences of lipid abundance imbalances in mammalian plasma membranes (PMs). Using lipidomics, we report that cytoplasmic leaflets of human erythrocyte membranes have >50% overabundance of phospholipids compared with exoplasmic leaflets. This imbalance is enabled by an asymmetric interleaflet distribution of cholesterol, which regulates cellular cholesterol homeostasis. These features produce unique functional characteristics, including low PM permeability and resting tension in the cytoplasmic leaflet that regulates protein localization.
膜是将细胞区隔开以控制营养物质和信息流动的分子界面。这些功能的实现依赖于多种脂质集合，它们几乎都非对称地分布在双层膜的两个小叶之间。大多数生物膜结构和功能模型都包含一个隐含的假设，即这些小叶具有相似的磷脂含量。该研究证明了这一假设普遍不成立，并研究了哺乳动物质膜(PM)中脂质含量失衡的后果。基于脂质组学的分析，该研究报道了人类红细胞膜的胞内小叶的磷脂含量比胞外小叶高出50%以上。这种不平衡是由胆固醇在小叶间的非对称分布造成的，而胆固醇本身调节细胞胆固醇稳态。这些特征产生了独特的功能特性，包括低质膜通透性和胞质侧小叶的静息张力，从而调节蛋白质定位。
3.Therapeutic potential of allosteric HECT E3 ligase inhibition
变构HECT E3连接酶抑制的治疗潜力
Targeting ubiquitin E3 ligases is therapeutically attractive; however, the absence of an active-site pocket impedes computational approaches for identifying inhibitors. In a large, unbiased biochemical screen, we discover inhibitors that bind a cryptic cavity distant from the catalytic cysteine of the homologous to E6-associated protein C terminus domain (HECT) E3 ligase, SMAD ubiquitin regulatory factor 1 (SMURF1). Structural and biochemical analyses and engineered escape mutants revealed that these inhibitors restrict an essential catalytic motion by extending an α helix over a conserved glycine hinge. SMURF1 levels are increased in pulmonary arterial hypertension (PAH), a disease caused by mutation of bone morphogenetic protein receptor-2 (BMPR2). We demonstrated that SMURF1 inhibition prevented BMPR2 ubiquitylation, normalized bone morphogenetic protein (BMP) signaling, restored pulmonary vascular cell homeostasis, and reversed pathology in established experimental PAH. Leveraging this deep mechanistic understanding, we undertook an in silico machine-learning-based screen to identify inhibitors of the prototypic HECT E6AP and confirmed glycine-hinge-dependent allosteric activity in vitro. Inhibiting HECTs and other glycine-hinge proteins opens a new druggable space.
靶向泛素E3连接酶具有治疗潜力；然而，由于缺乏活性位点口袋，无法通过计算方法识别抑制剂。该研究利用大规模、无偏倚的生化筛选发现了一些抑制剂，它们可以结合一个隐蔽的腔体，该腔体远离与E6相关蛋白C末端结构域(HECT) E3连接酶同源的SMAD泛素调节因子1 (SMURF1)的催化半胱氨酸位点。基于结构和生化分析以及工程化的耐药突变体，该研究发现这些抑制剂通过将α螺旋延伸覆盖在一个保守的甘氨酸铰链上，从而限制了一个重要的催化功能。在肺动脉高压(PAH，一种由骨形态发生蛋白受体2 [BMPR2]突变引起的疾病)中，SMURF1水平升高。该研究证实，抑制SMURF1可有效阻止BMPR2泛素化，使骨形态发生蛋白(BMP)信号转导恢复正常，恢复肺血管细胞稳态，并逆转已建立的肺动脉高压(PAH)实验模型的病理变化。基于这一深入的机制理解，该研究进行了基于机器学习筛选，以鉴定原型HECT E6AP的抑制剂，并在体外验证了其甘氨酸铰链依赖性的变构活性。抑制HECT连接酶和其他甘氨酸铰链蛋白开辟了一个新的药物应用空间。
4.Engineering sonogenetic EchoBack-CAR T cells
声遗传学EchoBack-CAR T细胞的工程化构建
Chimeric antigen receptor (CAR) T cell therapy for solid tumors encounters challenges such as on-target off-tumor toxicity, exhaustion, and limited T cell persistence. Here, we engineer sonogenetic EchoBack-CAR T cells using an ultrasensitive heat-shock promoter screened from a library and integrated with a positive feedback loop from CAR signaling, enabling long-lasting CAR expression upon focused-ultrasound (FUS) stimulation. EchoBack-hGD2CAR T cells, targeting disialoganglioside GD2, exhibited potent cytotoxicity and persistence in 3D glioblastoma (GBM) models. In mice, EchoBack-hGD2CAR T cells suppressed GBM without off-tumor toxicity and outperformed their constitutive counterparts. Single-cell RNA sequencing revealed enhanced cytotoxicity and reduced exhaustion in EchoBack-CAR T cells compared with the standard CAR T cells. This EchoBack design was further adapted to target prostate-specific membrane antigen (EchoBack-PSMACAR) for prostate cancer treatment, demonstrating long-lasting tumor suppression with minimal off-tumor toxicity. Thus, the sonogenetic EchoBack-CAR T cells can serve as a versatile, efficient, and safe strategy for solid tumor treatment.
嵌合抗原受体 (CAR) T 细胞疗法在实体瘤治疗中面临诸多挑战，例如靶向非肿瘤组织（脱靶）毒性、细胞耗竭以及T细胞持久性有限。该研究利用从启动子库中筛选出的超敏感热休克启动子（HSP），并将其与源自CAR信号的自维持正反馈回路整合，构建了声遗传学EchoBack-CAR T细胞，使其在聚焦超声(FUS)刺激下能够实现持久的CAR蛋白表达。靶向二唾液酸神经节苷脂GD2的EchoBack-hGD2CAR T细胞在3D胶质母细胞瘤(GBM)模型中表现出强大的细胞毒性和持久性。在荷瘤小鼠体内，EchoBack-hGD2CAR T细胞能够抑制GBM生长，无脱靶毒性，且其疗效显著优于其组成型表达的对照CAR T细胞。单细胞RNA测序显示，与标准CAR T细胞相比，EchoBack-CAR T细胞具有更强的细胞毒性和更低的耗竭程度。研究人员进一步改进将这种EchoBack设计应用于靶向前列腺特异性膜抗原（EchoBack-PSMACAR）的CAR，用于治疗前列腺癌，结果展现出持久的肿瘤抑制效果，且脱靶毒性极小。因此，声遗传学EchoBack-CAR T细胞可作为一种通用型、高效且安全的实体瘤治疗新策略。
5.Engineered nucleocytosolic vehicles for loading of programmable editors
构建核质载体用于装载可编程编辑器
Advanced gene editing methods have accelerated biomedical discovery and hold great therapeutic promise, but safe and efficient delivery of gene editors remains challenging. In this study, we present a virus-like particle (VLP) system featuring nucleocytosolic shuttling vehicles that retrieve pre-assembled Cas-effectors via aptamer-tagged guide RNAs. This approach ensures preferential loading of fully assembled editor ribonucleoproteins (RNPs) and enhances the efficacy of prime editing, base editing, trans-activators, and nuclease activity coupled to homology-directed repair in multiple immortalized, primary, stem cell, and stem-cell-derived cell types. We also achieve additional protection of inherently unstable prime editing guide RNAs (pegRNAs) by shielding the 3’-exposed end with Csy4/Cas6f, further enhancing editing performance. Furthermore, we identify a minimal set of packaging and budding modules that can serve as a platform for bottom-up engineering of enveloped delivery vehicles. Notably, our system demonstrates superior per-VLP editing efficiency in primary T lymphocytes and two mouse models of inherited retinal disease, highlighting its therapeutic potential.
先进的基因编辑方法加速了生物医学发现，并带来了巨大的治疗前景，但基因编辑器的安全高效递送仍具挑战性。该研究提出了一种病毒样颗粒 (VLP) 系统，该系统以核质穿梭载体为特征，这些载体可通过适配体标记的向导RNA（gRNA）捕获并转运预先组装的Cas效应蛋白复合物。该方法确保了完全组装的编辑器核糖核蛋白 (RNP)的优先装载，并显著提升了多种永生化细胞、原代细胞、干细胞和干细胞衍生细胞类型中与同源性定向修复偶联的初代编辑、碱基编辑、反式激活因子和核酸酶活性的效率。该研究还通过使用Csy4/Cas6f蛋白屏蔽 3’末端暴露区，为具有固有不稳定性的初代编辑引导RNA(pegRNA)提供了额外的保护，从而进一步提高了编辑性能。此外，该研究还确定了一组最简化的包装和出芽模块，可作为自下而上工程化改造包膜递送载体的平台。值得注意的是，该研究的系统在原代T淋巴细胞和两种遗传性视网膜疾病小鼠模型中表现出单位VLP编辑效率的优异，凸显了其治疗潜力。
6.Nanoscale DNA tracing reveals the self-organization mechanism of mitotic chromosomes
纳米尺度DNA示踪揭示有丝分裂染色体的自组织机制
How genomic DNA is folded during cell division to form the characteristic rod-shaped mitotic chromosomes essential for faithful genome inheritance is a long-standing open question in biology. Here, we use nanoscale DNA tracing in single dividing cells to directly visualize how the 3D fold of genomic DNA changes during mitosis at scales from single loops to entire chromosomes. Our structural analysis reveals a characteristic genome scaling minimum of 6-8 megabases in mitosis. Combined with data-driven modeling and molecular perturbations, we can show that very large and strongly overlapping loops formed by condensins are the fundamental structuring principle of mitotic chromosomes. These loops compact chromosomes locally and globally to the limit set by chromatin self-repulsion. The characteristic length, density, and increasingly overlapping structure of mitotic loops we observe in 3D fully explain how the rod-shaped mitotic chromosome structure emerges by self-organization during cell division.
在细胞分裂过程中，基因组DNA如何折叠形成特征性的杆状有丝分裂染色体（这对于基因组的可靠遗传至关重要），这在生物学中是一个长期悬而未决的问题。该研究利用纳米级DNA示踪技术，在单个分裂细胞中直接观测基因组DNA三维构象在有丝分裂过程中的动态变化，其尺度从单个环状结构到整条染色体。该研究的结构分析表明，有丝分裂过程中基因组折叠存在一个特征性的最小值（6-8兆碱基对）。结合数据驱动建模和分子扰动，该研究证实，由凝聚素形成的超大且高度重叠的环状结构是构成有丝分裂染色体的基本结构原理。这些环状结构在染色质自身排斥力的限制下，将染色体在局部和整体上压缩至极限。该研究在三维空间中观察到的有丝分裂环状结构的特征性长度、密度和逐渐重叠的结构，完整地阐释了杆状有丝分裂染色体结构如何在细胞分裂过程中通过自组织形。
7.Quiescent cell re-entry is limited by macroautophagy-induced lysosomal damage
巨自噬诱导的溶酶体损伤限制了静止细胞重新进入细胞周期
To maintain tissue homeostasis, many cells reside in a quiescent state until prompted to divide. The reactivation of quiescent cells is perturbed with aging and may underlie declining tissue homeostasis and resiliency. The unfolded protein response regulators IRE-1 and XBP-1 are required for the reactivation of quiescent cells in developmentally L1-arrested C. elegans. Utilizing a forward genetic screen in C. elegans, we discovered that macroautophagy targets protein aggregates to lysosomes in quiescent cells, leading to lysosome damage. Genetic inhibition of macroautophagy and stimulation of lysosomes via the overexpression of HLH-30 (TFEB/TFE3) synergistically reduces lysosome damage. Damaged lysosomes require IRE-1/XBP-1 for their repair following prolonged L1 arrest. Protein aggregates are also targeted to lysosomes by macroautophagy in quiescent cultured mammalian cells and are associated with lysosome damage. Thus, lysosome damage is a hallmark of quiescent cells, and limiting lysosome damage by restraining macroautophagy can stimulate their reactivation.
为维持组织稳态，许多细胞处于静止状态，直至被诱导分裂。静止细胞的再激活会随着衰老而受到干扰，并可能是组织稳态和修复能力下降的基础。在发育过程中L1期停滞的秀丽隐杆线虫中，未折叠蛋白反应调节因子IRE-1和XBP-1是静止细胞再激活所必需的。通过对秀丽隐杆线虫进行正向遗传筛选，该研究发现巨自噬将静止细胞中的蛋白质聚集体靶向递送至溶酶体，进而导致溶酶体损伤。通过基因抑制巨自噬作用并通过过表达HLH-30（TFEB/TFE3）激活溶酶体，可以协同减轻溶酶体损伤。受损的溶酶体在L1停滞较长时间后需要IRE-1/XBP-1通路介导其修复。在静止培养的哺乳动物细胞中，蛋白质聚集体也会通过巨自噬被靶向递送至溶酶体，并与溶酶体损伤相关。因此，溶酶体损伤是静止细胞的一个标志性特征，而通过抑制巨自噬来减轻溶酶体损伤可以刺激静止细胞的再激活。
8.Channel synapse mediates neurotransmission of airway protective chemoreflexes
通道突触介导气道保护性化学反射的神经传递
Neural reflexes to chemicals in the throat protect the airway from aspiration and infection. Mechanistic understanding of these reflexes remains premature, exemplified by chronic cough-a sensitized cough reflex-being a prevalent unmet clinical need. Here, in mice, a whole-body search for channel synapses-featuring CALHM1/3 channel-mediated neurotransmitter release-and single-cell transcriptomics uncovered subclasses of the Pou2f3+ chemosensory cell family in the throat communicating with vagal neurons via this synapse. They express G protein-coupled receptors (GPCRs) for noxious chemicals, T2Rs, which upon stimulation trigger swallow and cough-like expulsive reflexes in the hypopharynx and larynx, respectively. These reflexes were abolished by Calhm3 and Pou2f3 knockout and could be triggered by targeted optogenetic stimulation. Furthermore, aeroallergen exposure augmented CALHM3-dependent expulsive reflex. This study identifies Pou2f3+ epithelial cells with channel synapses as chemosensory end organs of airway protective reflexes and sites of their hyperresponsiveness, advancing mechanistic understanding of airway defense programs with distinct therapeutic potential.
咽喉对化学物质的神经反射保护呼吸道免于误吸和感染。对这些反射机制的理解尚不成熟，例如慢性咳嗽——一种敏化咳嗽反射——是一种普遍存在的未满足的临床需求。该研究在小鼠体内通过全身心搜寻，以CALHM1/3通道介导的神经递质释放为特征的通道突触，并结合单细胞转录组学分析，揭示了咽喉中通过该突触与迷走神经元进行通讯的Pou2f3+化学感受细胞家族的亚类。它们表达针对有害化学物质的G蛋白偶联受体(GPCR)——苦味受体（T2Rs），其在受到刺激后分别在下咽部和喉部触发吞咽和咳嗽驱除反射。这些反射可通过敲除Calhm3和Pou2f3消除，而靶向光遗传学刺激则能触发这些反射。此外，空气过敏原暴露增强了CALHM3依赖性的驱除反射。该研究确定了具有通道突触的Pou2f3+上皮细胞是气道保护性反射的化学感受终末器官及其高反应性位点，从而推进了对气道防御程序机制的理解，并具有独特的治疗潜力。
9.Meningeal lymphatics-microglia axis regulates synaptic physiology
脑膜淋巴管-小胶质细胞轴调控突触生理
Meningeal lymphatics serve as an outlet for cerebrospinal fluid, and their dysfunction is associated with various neurodegenerative conditions. Previous studies have demonstrated that dysfunctional meningeal lymphatics evoke behavioral changes, but the neural mechanisms underlying these changes have remained elusive. Here, we show that prolonged impairment of meningeal lymphatics alters the balance of cortical excitatory and inhibitory synaptic inputs, accompanied by deficits in memory tasks. These synaptic and behavioral alterations induced by lymphatic dysfunction are mediated by microglia, leading to increased expression of the interleukin 6 gene (Il6). IL-6 drives inhibitory synapse phenotypes via a combination of trans- and classical IL-6 signaling. Restoring meningeal lymphatic function in aged mice reverses age-associated synaptic and behavioral alterations. Our findings suggest that dysfunctional meningeal lymphatics adversely impact cortical circuitry through an IL-6-dependent mechanism and identify a potential target for treating aging-associated cognitive decline.
脑膜淋巴管是脑脊液的出口，其功能障碍与多种神经退行性疾病相关。先前的研究表明，脑膜淋巴管功能障碍可引发行为改变，但这些改变背后的神经机制仍不清楚。该研究表明，脑膜淋巴管的长期损伤会改变皮质兴奋性和抑制性突触输入的平衡，并伴随出现记忆任务能力缺陷。这些由淋巴管功能障碍引起的突触和行为改变是由小胶质细胞介导的，导致白细胞介素6 (Il-6) 表达上调。IL-6 通过反式和经典信号传导的协同来驱动抑制性突触表型。在老年小鼠中恢复脑膜淋巴管功能，可逆转与年龄相关的突触和行为改变。该研究的结果表明，功能失调的脑膜淋巴系统通过IL-6依赖性机制对皮质神经回路产生不利影响，并确定了治疗衰老相关认知能力下降的潜在靶点。
10.Rorγt-positive dendritic cells are required for the induction of peripheral regulatory T cells in response to oral antigens
Rorγt阳性树突状细胞是诱导外周调节性T细胞应答口服抗原所必需的
The intestinal immune system maintains tolerance to harmless food proteins and gut microbiota through peripherally derived RORγt+ Tregs (pTregs), which prevent food intolerance and inflammatory bowel disease. Recent studies suggested that RORγt+ antigen-presenting cells (APCs), which encompass rare dendritic cell (DC) subsets and type 3 innate lymphoid cells (ILC3s), are key to pTreg induction. Here, we developed a mouse with reduced RORγt+ APCs by deleting a specific cis-regulatory element of Rorc encoding RORγt. Single-cell RNA sequencing and flow cytometry analyses confirmed the depletion of a RORγt+ DC subset and ILC3s. These mice showed a secondary reduction in pTregs, impaired tolerance to oral antigens, and an increase in T helper (Th)2 cells. Conversely, ILC3-deficient mice showed no pTregs or Th2 cell abnormalities. Lineage tracing revealed that RORγt+ DCs share a lymphoid origin with ILC3s, consistent with their similar phenotypic traits. These findings highlight the role of lymphoid RORγt+ DCs in maintaining intestinal immune balance and preventing conditions like food allergies.
肠道免疫系统通过外周来源的RORγt+调节性T细胞（pTregs）维持对无害食物蛋白和肠道菌群的耐受性，从而预防食物不耐受和炎症性肠病。近期研究表明，RORγt+ 抗原呈递细胞 (APC)，包括稀有的树突状细胞 (DC) 亚群和3型先天淋巴细胞 (ILC3)，是诱导pTregs的关键。该研究通过删除编码 RORγt的 Rorc基因中一个特定的顺式调控元件，构建了RORγt+ APC数量减少的小鼠模型。单细胞RNA测序和流式细胞术分析证实了RORγt+ DC亚群和ILC3的缺失。这些小鼠表现出pTregs的继发性减少、对口服抗原的耐受性受损以及辅助性T (Th)2细胞增多。相反，ILC3缺陷小鼠未出现pTregs数量减少或Th2细胞增多等异常。谱系追踪显示，RORγt+树突状细胞(DCs)与ILC3具有共同的淋巴系来源，这与它们相似的表型特征相符。这些发现凸显了淋巴系来源的RORγt+树突状细胞在维持肠道免疫稳态和预防食物过敏等疾病中的作用。
11.Growth of the maternal intestine during reproduction
生殖过程中母体肠道的生长
The organs of many female animals are remodeled by reproduction. Using the mouse intestine, a striking and tractable model of organ resizing, we find that reproductive remodeling is anticipatory and distinct from diet- or microbiota-induced resizing. Reproductive remodeling involves partially irreversible elongation of the small intestine and fully reversible growth of its epithelial villi, associated with an expansion of isthmus progenitors and accelerated enterocyte migration. We identify induction of the SGLT3a transporter in a subset of enterocytes as an early reproductive hallmark. Electrophysiological and genetic interrogations indicate that SGLT3a does not sustain digestive functions or enterocyte health; rather, it detects protons and sodium to extrinsically support the expansion of adjacent Fgfbp1-positive isthmus progenitors, promoting villus growth. Our findings reveal unanticipated specificity to physiological organ remodeling. We suggest that organ- and state-specific growth programs could be leveraged to improve pregnancy outcomes or prevent maladaptive consequences of such growth.
许多雌性动物的器官会因生殖而重塑。利用小鼠肠道（一个引人注目且易于处理的器官大小调整模型），该研究发现生殖重塑具有预见性，且不同于饮食或微生物群诱导的大小调整。生殖重塑涉及小肠部分不可逆的伸长和其上皮绒毛完全可逆的生长，这与峡部祖细胞的扩增和肠上皮细胞迁移的加速有关。该研究发现，部分肠上皮细胞中SGLT3a转运蛋白的表达上调是生殖早期的标志性事件。电生理学和遗传学证据表明，SGLT3a的功能并不在于维持消化功能或肠上皮细胞健康；相反，它检测质子和钠信号，从而从外部支持邻近表达Fgfbp1的峡部祖细胞的扩增，促进绒毛生长。该研究的研究结果揭示了生理性器官重塑中令人意外的特异性。该研究建议可以利用针对器官和局部的特定生长程序来改善妊娠结果或规避此类生长可能导致的适应不良后果。
12.PAX translocations remodel mitochondrial metabolism through altered leucine usage in rhabdomyosarcoma
PAX易位通过改变横纹肌肉瘤中的亮氨酸使用来重塑线粒体代谢
Alveolar rhabdomyosarcoma (ARMS) patients harboring paired-box fusion proteins (PAX3/7-FOXO1) exhibit a greater incidence of tumor relapse, metastasis, and poor survival outcome, thereby underscoring the urgent need to develop effective therapies to treat this subtype of childhood cancer. To uncover mechanisms that contribute to tumor initiation, we develop a muscle progenitor model and use epigenomic approaches to unravel genome rewiring events mediated by PAX3/7 fusion proteins. Among the key targets of PAX3/7 fusion proteins, we identify a cohort of oncogenes, fibroblast growth factor (FGF) receptors, tRNA-modifying enzymes, and genes essential for mitochondrial metabolism and protein translation, which we successfully targeted in preclinical trials. We identify leucine usage as a key factor driving the growth of aggressive PAX-fusion tumors, as limiting its bioavailability impaired oxidative phosphorylation and mitochondrial metabolism, delaying tumor progression and improving survival in vivo. Our data provide a compelling list of actionable targets and suggest promising new strategies to treat this tumor.
携带配对盒融合蛋白 (PAX3/7-FOXO1)的肺泡横纹肌肉瘤 (ARMS)患者表现出更高的肿瘤复发率、转移率和不良的生存结局，因此迫切需要开发有效的疗法来治疗此类儿童癌症亚型。为了揭示肿瘤发生的机制，该研究构建了一个肌肉祖细胞模型，并利用表观基因组学方法解析了PAX3/7 融合蛋白介导的基因组重塑事件。在PAX3/7融合蛋白的关键靶点中，该研究鉴定出一系列致癌基因、成纤维细胞生长因子 (FGF)受体、tRNA修饰酶以及线粒体代谢和蛋白翻译所必需的基因，并在临床前试验中成功靶向这些靶点。该研究发现亮氨酸的利用是驱动侵袭性PAX融合肿瘤生长的关键因素，因为限制其生物利用度会损害氧化磷酸化和线粒体代谢，从而延缓肿瘤进展并提高体内生存率。该研究的数据提供了一系列令人信服的可行靶点，为治疗此类肿瘤提出了前景广阔的新策略。
13.Engineering mtDNA deletions by reconstituting end joining in human mitochondria
通过重建人类线粒体末端连接来设计线粒体DNA缺失
Recent breakthroughs in the genetic manipulation of mitochondrial DNA (mtDNA) have enabled precise base substitutions and the efficient elimination of genomes carrying pathogenic mutations. However, reconstituting mtDNA deletions linked to mitochondrial myopathies remains challenging. Here, we engineered mtDNA deletions in human cells by co-expressing end-joining (EJ) machinery and targeted endonucleases. Using mitochondrial EJ (mito-EJ) and mito-ScaI, we generated a panel of clonal cell lines harboring a ~3.5 kb mtDNA deletion across the full spectrum of heteroplasmy. Investigating these cells revealed a critical threshold of ~75% deleted genomes, beyond which oxidative phosphorylation (OXPHOS) protein depletion, metabolic disruption, and impaired growth in galactose-containing media were observed. Single-cell multiomic profiling identified two distinct nuclear gene deregulation responses: one triggered at the deletion threshold and another progressively responding to heteroplasmy. Ultimately, we show that our method enables the modeling of disease-associated mtDNA deletions across cell types and could inform the development of targeted therapies.
线粒体DNA (mtDNA) 基因操作的最新突破使得精确的碱基替换和携带致病突变的基因组的有效消除成为可能。然而，构建与线粒体肌病相关的mtDNA缺失片段仍然具有挑战性。该研究通过共表达末端连接(EJ)机器和靶向核酸内切酶，在人类细胞中构建了mtDNA缺失。利用线粒体EJ (mito-EJ)和mito-ScaI，该研究构建了一组包含约3.5 kb mtDNA缺失的克隆细胞系，该缺失覆盖了从低到高的全部异质性水平范围。分析这些细胞发现了一个约75%缺失基因组的关键阈值，超过该阈值后，细胞将出现氧化磷酸化(OXPHOS)蛋白水平下降、代谢紊乱以及在含半乳糖培养基中的生长受损的现象。单细胞多组学分析鉴定出了两种不同的核基因表达失调反应：一种在缺失阈值处被触发，另一种则随异质性水平升高而渐进发生。最终，该研究表明，该方法能够在多种细胞类型中模拟疾病相关的线粒体DNA缺失，并可能为靶向治疗的开发提供参考。
14.Fast, accurate, and versatile data analysis platform for the quantification of molecular spatiotemporal signals
快速、准确、多功能的分子时空信号量化数据分析平台
Optical recording of intricate molecular dynamics is becoming an indispensable technique for biological studies, accelerated by the development of new or improved biosensors and microscopy technology. This creates major computational challenges to extract and quantify biologically meaningful spatiotemporal patterns embedded within complex and rich data sources, many of which cannot be captured with existing methods. Here, we introduce activity quantification and analysis (AQuA2), a fast, accurate, and versatile data analysis platform built upon advanced machine-learning techniques. It decomposes complex live-imaging-based datasets into elementary signaling events, allowing accurate and unbiased quantification of molecular activities and identification of consensus functional units. We demonstrate applications across a wide range of biosensors, cell types, organs, animal models, microscopy techniques, and imaging approaches. As exemplar findings, we show how AQuA2 identified drug-dependent interactions between neurons and astroglia, as well as distinct sensorimotor signal propagation patterns in the mouse spinal cord.
随着新型或改进的生物传感器和显微镜技术的发展，分子动力学光学记录正成为生物学研究中不可或缺的手段。这也带来了巨大的计算挑战：如何从复杂丰富的数据源中提取并量化具有生物学意义的时空模式，其中许多模式无法通过现有方法捕捉。该研究介绍了活动量化与分析 (AQuA2)，这是一个基于先进机器学习技术的快速、准确且多功能的数据分析平台。它能将基于活细胞成像的复杂数据集分解为基本信号事件，从而实现分子活动的准确、无偏量化，并识别出具有共识性的功能单元功能单元。该研究展示了该平台在各种生物传感器、细胞类型、器官、动物模型、显微镜技术和成像方法中的适用性。作为示例研究结果，该研究展示了AQuA2如何识别神经元和星形胶质细胞之间的药物依赖性相互作用，以及小鼠脊髓中独特的感觉运动信号传播模式。
15.Human proteome distribution atlas for tissue-specific plasma proteome dynamics
用于组织特异性血浆蛋白质组动力学的人类蛋白质组分布图谱
The plasma proteome is maintained by the influx and efflux of proteins from surrounding organs and cells. To quantify the extent to which different organs and cells impact the plasma proteome in healthy and diseased conditions, we developed a mass-spectrometry-based proteomics strategy to infer the tissue origin of proteins detected in human plasma. We first constructed an extensive human proteome atlas from 18 vascularized organs and the 8 most abundant cell types in blood. The atlas was interfaced with previous RNA and protein atlases to objectively define proteome-wide protein-organ associations to infer the origin and enable the reproducible quantification of organ-specific proteins in plasma. We demonstrate that the resource can determine disease-specific quantitative changes of organ-enriched protein panels in six separate patient cohorts, including sepsis, pancreatitis, and myocardial injury. The strategy can be extended to other diseases to advance our understanding of the processes contributing to plasma proteome dynamics.
血浆蛋白质组源于周围器官和细胞中蛋白质的流入和流出。为了量化不同器官和细胞在健康和疾病状态下对血浆蛋白质组的影响程度，该研究开发了一种基于质谱的蛋白质组学策略，用于推断人体血浆中检测到的蛋白质的组织来源。该研究首先构建了一个广泛的人类蛋白质组图谱，涵盖了18个血管化器官和血液中丰度最高的8种细胞类型。该图谱与之前的RNA和蛋白质图谱相结合，客观地定义了蛋白质组水平的蛋白质-器官关联，从而推断其来源，并实现了血浆中器官特异性蛋白质的可重复精确定量。该研究证明该资源能在六个独立患者队列（包括脓毒症、胰腺炎和心肌损伤）中精确定量疾病特异性的器官腹肌蛋白组合变化。该策略可以扩展到其他疾病，增进对血浆蛋白质组动态变化机制的理解。
May 29, 2025；Volume 188 Issue 11 p2829-3096
在2025年5月29日，共发表19篇文章，其中包括3篇pre-view，1篇persectives，1篇short article，13篇Articles，1篇Resources。
1.An Arabidopsissingle-nucleus atlas decodes leaf senescence and nutrient allocation
拟南芥单核转录组图谱解析叶片衰老和营养分配
With rapid advancements in single-cell RNA sequencing (scRNA-seq) technologies, exploration of the systemic coordination of critical physiological processes has entered a new era. Here, we generated a comprehensive Arabidopsis single-nucleus transcriptomic atlas using over 1 million nuclei from 20 tissues encompassing multiple developmental stages. Our analyses identified cell types that have not been characterized in previous single-protoplast studies and revealed cell-type conservation and specificity across different organs. Through time-resolved sampling, we revealed highly coordinated onset and progression of senescence among the major leaf cell types. We originally formulated two molecular indexes to quantify the aging state of leaf cells at single-cell resolution. Additionally, facilitated by weighted gene co-expression network analysis, we identified hundreds of promising hub genes that may integratively regulate leaf senescence. Inspired by the functional validation of identified hub genes, we built a systemic scenario of carbon and nitrogen allocation among different cell types from source leaves to sink organs.
随着单细胞RNA测序（scRNA-seq）技术的快速发展，对关键生理过程系统性协调的探索进入了一个新时代。该研究利用涵盖多个发育阶段的20个组织来源的超过100万个细胞核样本，构建了全面的拟南芥单核转录组图谱。该研究鉴定了此前单原生质体研究中未曾表征的细胞类型，并揭示了不同器官间细胞类型的保守性和特异性。通过时间分辨采样，该研究揭示了叶片主要细胞类型之间衰老的启动和进展高度协调。该研究首次构建了两个分子指标，用于在单细胞分辨率量化叶片细胞的衰老状态。此外，通过加权基因共表达网络分析，该研究鉴定了数百个可能协同调控叶片衰老的核心基因。基于所鉴定核心基因功能验证结果，该研究构建了从源叶到库器官不同细胞类型之间碳氮分配的动态模型。
2.Synthetic deconvolution of an auxin-dependent transcriptional code
生长素依赖性转录编码的合成解卷积
How developmental signals program gene expression in space and time is still poorly understood. Here, we addressed this question for the plant master regulator, auxin. Transcriptional responses to auxin rely on a large multigenic transcription factor family, the auxin response factors (ARFs). We deconvoluted the complexity of ARF-regulated transcription using auxin-inducible synthetic promoters built from cis-element pair configurations differentially bound by ARFs. We demonstrate using cellular systems that ARF transcriptional properties are not only intrinsic but also depend on the cis-element pair configurations they bind to, thus identifying a bi-layer ARF/cis-element transcriptional code. Auxin-inducible synthetic promoters were expressed differentially in planta showing at single-cell resolution how this bi-layer code patterns transcriptional responses to auxin. Combining cis-element pair configurations in synthetic promoters created distinct patterns, demonstrating the combinatorial power of the auxin bi-layer code in generating diverse gene expression patterns that are not simply a direct translation of auxin distribution.
发育信号如何编程基因的时空表达目前仍知之甚少。在此，该研究以植物主调控因子——生长素为例来探讨这个问题。对生长素的转录应答依赖于一个庞大的多基因转录因子家族，即生长素响应因子（ARFs）。该研究利用基于被不同 ARF 差异结合的顺式元件对（cis-element pair）构型构建的生长素诱导型合成启动子来解卷积ARF调控转录的复杂性。该研究在细胞系统中证明，ARF 的转录特性不仅是内在的，也取决于它们所结合的顺式元件对构型，从而鉴定出一个双层（bi-layer）的 ARF/顺式元件转录编码。这些生长素诱导型合成启动子在植物体内呈现差异性表达，以单细胞分辨率展示了这一双层编码如何塑造对生长素的转录应答。在合成启动子中组合不同的顺式元件对构型，可创建出独特的表达模式，这证明了生长素双层编码能够生成并非仅仅是生长素分布直接转译结果的多样化基因表达模式。
3.Extensive N4 cytosine methylation is essential for Marchantia sperm function
广泛存在的N4胞嘧啶甲基化对地钱精子功能至关重要
N4-methylcytosine (4mC) is an important DNA modification in prokaryotes, but its relevance and even its presence in eukaryotes have been mysterious. Here we show that spermatogenesis in the liverwort Marchantia polymorpha involves two waves of extensive DNA methylation reprogramming. First, 5-methylcytosine (5mC) expands from transposons to the entire genome. Notably, the second wave installs 4mC throughout genic regions, covering over 50% of CG sites in sperm. 4mC requires a methyltransferase (MpDN4MT1a) that is specifically expressed during late spermiogenesis. Deletion of MpDN4MT1a alters the sperm transcriptome, causes sperm swimming and fertility defects, and impairs post-fertilization development. Our results reveal extensive 4mC in a eukaryote, identify a family of eukaryotic methyltransferases, and elucidate the biological functions of 4mC in reproductive development, thereby expanding the repertoire of functional eukaryotic DNA modifications.
N4-甲基胞嘧啶（4mC）是原核生物中一种重要的 DNA 修饰，但其在真核生物中的相关性甚至存在性一直是个谜。该研究证明地钱（Marchantia polymorpha）的精子发生涉及两给阶段的广泛的DNA甲基化重编程。第一波是5-甲基胞嘧啶（5mC）从转座子扩展到整个基因组。值得注意的是，第二波则在基因区域广泛沉积4mC，覆盖了精子中超过50%的CG位点。4mC的形成需要一种在精子发生晚期特异性表达的甲基转移酶（MpDN4MT1a）。敲除MpDN4MT1a会改变精子的转录组，导致精子游动能力和受精能力缺陷，并损害受精后的发育。该研究揭示了真核生物中广泛的4mC存在，鉴定了一个真核生物甲基转移酶家族，并阐明了4mC在生殖发育中的生物学功能，从而扩展了功能性真核生物 DNA修饰的种类。
4.Extracellular respiration is a latent energy metabolism in Escherichia coli
胞外呼吸是大肠杆菌中的一种潜在的能量代谢
Diverse microbes utilize redox shuttles to exchange electrons with their environment through mediated extracellular electron transfer (EET), supporting anaerobic survival. Although mediated EET has been leveraged for bioelectrocatalysis for decades, fundamental questions remain about how these redox shuttles are reduced within cells and their role in cellular bioenergetics. Here, we integrate genome editing, electrochemistry, and systems biology to investigate the mechanism and bioenergetics of mediated EET in Escherichia coli, elusive for over two decades. In the absence of alternative electron sinks, the redox cycling of 2-hydroxy-1,4-naphthoquinone (HNQ) via the cytoplasmic nitroreductases NfsB and NfsA enables E. coli respiration on an extracellular electrode. E. coli also exhibits rapid genetic adaptation in the outer membrane porin OmpC, enhancing HNQ-mediated EET levels coupled to growth. This work demonstrates that E. coli can grow independently of classic electron transport chains and fermentation, unveiling a potentially widespread new type of anaerobic energy metabolism.
多种微生物利用氧化还原穿梭分子（redox shuttles）通过介导的胞外电子转移（mediated extracellular electron transfer, EET）与其环境交换电子，以维持厌氧生存。尽管介导的EET被用于生物电催化已有数十年，但关于这些氧化还原穿梭分子如何在细胞内被还原及其在细胞生物能学中的作用等基本问题仍然存在。该研究整合应用基因组编辑、电化学和系统生物学方法以探索困扰学界二十多年的大肠杆菌中介导EET的机制和生物能学。在缺乏其他电子受体的情况下，2-羟基-1,4-萘醌（HNQ）通过细胞质硝基还原酶 NfsB 和 NfsA 进行的氧化还原循环，使得大肠杆菌能够在胞外电极上进行呼吸。大肠杆菌外膜孔蛋白OmpC还表现出快速的遗传适应，从而提升了与生长相耦合的HNQ 介导的EET水平。这项工作证明了大肠杆菌可以不依赖于经典电子传递链和发酵而生长，揭示了一种可能普遍存在的新型厌氧能量代谢方式。
5.Structure and infection dynamics of mycobacteriophage Bxb1
分枝杆菌噬菌体Bxb1的结构与侵染动力学
Mycobacteriophage Bxb1 is a well-characterized virus of Mycobacterium smegmatis with double-stranded DNA and a long, flexible tail. Mycobacteriophages show considerable potential as therapies for Mycobacterium infections, but little is known about the structural details of these phages or how they bind to and traverse the complex Mycobacterium cell wall. Here, we report the complete structure and atomic model of phage Bxb1, including the arrangement of immunodominant domains of both the capsid and tail tube subunits, as well as the assembly of the protein subunits in the tail-tip complex. The structure contains protein assemblies with 3-, 5-, 6-, and 12-fold symmetries, which interact to satisfy several symmetry mismatches. Cryoelectron tomography of phage particles bound to M. smegmatis reveals the structural transitions that occur for free phage particles to bind to the cell surface and navigate through the cell wall to enable DNA transfer into the cytoplasm.
分枝杆菌噬菌Bxb1是一种表征明确的耻垢分枝杆菌（Mycobacterium smegmatis）的病毒，具有双链DNA和长而柔韧的尾部。分枝杆菌噬菌体作为治疗分枝杆菌感染的疗法潜力巨大，但其精细结构及如何结合并穿越分枝杆菌复杂细胞壁的机制尚不清楚。该研究报道了Bxb1噬菌体的完整结构和原子模型，包括衣壳与尾管亚基上免疫显性结构域的排布，以及尾尖复合体中蛋白质亚基的组装方式。该结构包含具有3重、5重、6重及12重对称性的蛋白质组装体，通过相互作用来解决多重对称性失配。对结合到耻垢分枝杆菌的噬菌体颗粒的冷冻电镜断层扫描结果显示，游离的噬菌体颗粒发生结构转变，从而实现与细胞表面的结合并穿越细胞壁，最终将DNA转移到细胞质。
6.Structural basis for plasticity in receptor engagement by an encephalitic alphavirus
甲型脑炎病毒受体结合可塑性的结构基础
The structural basis for shifts in receptor usage remains poorly understood despite the implications for virus adaptation and emergence. Western equine encephalitis virus (WEEV) strains exhibit different patterns of engagement for two of their entry receptors: very-low-density lipoprotein receptor (VLDLR) and protocadherin 10 (PCDH10). Using structural and functional studies, we show that while all WEEV strains have a lipoprotein class A (LA) domain binding site near the E1 fusion loop, VLDLR engagement requires a second binding site in E2 that can vary with single nucleotide substitutions. We also resolve a structure of PCDH10 bound to WEEV, which reveals interactions near the E1 fusion loop with residues that also mediate LA domain binding. Evolutionary analysis enabled the generation of a PCDH10 decoy that protects in vivo against all WEEV strains tested. Our experiments demonstrate how viruses can engage multiple receptors using shared determinants, which likely impacts cellular tropism and virulence.
病毒受体使用的转变机制及其对病毒适应与新发的影响仍不明确。西方马脑炎病毒（WEEV）不同毒株对其两种进入受体——极低密度脂蛋白受体（VLDLR）和原钙粘蛋白10（PCDH10）的结合模式存在差异。通过结构与功能研究，该研究发现尽管所有WEEV毒株在E1融合环附近均存在脂蛋白A类（LA）结构域结合位点，但VLDLR的结合还需要E2上的第二结合位点，后者可通过单核苷酸替换发生改变。同时，该研究解析了PCDH10与WEEV的结合结构，揭示其在E1融合环附近的相互作用由某些残基介导，而这些残基同时也参与LA结构域的结合。进化分析支持开发出一种PCDH10诱饵受体，该诱饵能在体内保护机体抵御所有测试的WEEV毒株。这些实验证明病毒如何利用共享的决定因子结合多种受体，进而影响细胞嗜性与毒力。
7.Molecular basis for shifted receptor recognition by an encephalitic arbovirus
脑炎虫媒病毒受体识别变化的分子基础
Western equine encephalitis virus (WEEV) is an arbovirus that historically caused large outbreaks of encephalitis throughout the Americas. WEEV binds protocadherin 10 (PCDH10) as a receptor, and highly virulent ancestral WEEV strains also bind low-density lipoprotein receptor (LDLR)-related proteins. As WEEV declined as a human pathogen in North America over the past century, isolates have lost the ability to bind mammalian receptors while still recognizing avian receptors. To explain shifts in receptor dependencies and assess the risk of WEEV re-emergence, we determined cryoelectron microscopy structures of WEEV bound to human PCDH10, avian PCDH10, and human very-low-density lipoprotein receptor (VLDLR). We show that one to three E2 glycoprotein substitutions are sufficient for a nonpathogenic strain to regain the ability to bind mammalian receptors. A soluble VLDLR fragment protects mice from lethal challenge by a virulent ancestral WEEV strain. Because WEEV recently re-emerged in South America after decades of inactivity, our findings have important implications for outbreak preparedness.
西方马脑炎病毒（WEEV）是一种虫媒病毒，历史上曾在美洲引发大规模脑炎疫情。WEEV以原钙粘蛋白10（PCDH10）为受体，高毒力祖先毒株还能结合低密度脂蛋白受体（LDLR）相关蛋白。近一个世纪以来，随着WEEV在北美作为人类病原体的消退，其分离株逐渐丧失结合哺乳动物受体的能力，但仍保留对鸟类受体的识别。为阐明受体依赖性转变机制并评估WEEV再度暴发的风险，该研究通过冷冻电镜解析了WEEV与人类PCDH10、鸟类PCDH10及人类极低密度脂蛋白受体（VLDLR）的结合结构。研究表明，1-3个E2糖蛋白替换足以使非致病毒株恢复结合哺乳动物受体的能力。可溶性VLDLR片段可保护小鼠免受致死性祖先毒株攻击。鉴于WEEV沉寂数十年后近期在南美洲再度活跃，本研究对疫情防范具有重要意义。
8.DNA binding and mitotic phosphorylation protect polyglutamine proteins from assembly formation
DNA结合和有丝分裂磷酸化保护聚谷氨酰胺蛋白免受聚集体形成
Polyglutamine (polyQ) expansion is associated with pathogenic protein aggregation in neurodegenerative disorders. However, long polyQ tracts are also found in many transcription factors (TFs), such as FOXP2, a TF implicated in human speech. Here, we explore how FOXP2 and other glutamine-rich TFs avoid unscheduled assembly. Throughout interphase, DNA binding, irrespective of sequence specificity, has a solubilizing effect. During mitosis, multiple phosphorylation events promote FOXP2’s eviction from chromatin and supplant the solubilizing function of DNA. Further, human-specific amino acid substitutions linked to the evolution of speech map to a mitotic phospho-patch, the “EVO patch,” and reduce the propensity of the human FOXP2 to assemble. Fusing the pathogenic form of Huntingtin to either a DNA-binding domain, a phosphomimetic variant of this EVO patch, or a negatively charged peptide is sufficient to diminish assembly formation, suggesting that hijacking mechanisms governing solubility of glutamine-rich TFs may offer new strategies for treatment of polyQ expansion diseases.
多聚谷氨酰胺（polyQ）扩展与神经退行性疾病中的致病性蛋白聚集相关。然而，许多转录因子（如与人类语言功能相关的FOXP2）也含有长polyQ序列。该研究探索了FOXP2等富含谷氨酰胺的转录因子如何避免异常聚集。在整个间期，DNA结合（无论序列特异性如何）均具有溶解作用。有丝分裂期间，多重磷酸化事件促使FOXP2脱离染色质，替代了DNA结合的溶解功能。此外，与人类语言进化相关的人类特异性氨基酸替换定位至一个称为“EVO patch”的有丝分裂磷酸化区域，降低了人类FOXP2的聚集倾向。将致病型亨廷顿蛋白与DNA结合域、EVO patch的磷酸模拟变体或带负电荷多肽融合，均可抑制聚集形成，表明模拟调控富含谷氨酰胺转录因子溶解性的机制或可为polyQ扩展疾病提供新的治疗策略。
9.Long-term histone lactylation connects metabolic and epigenetic rewiring in innate immune memory
长期组蛋白乳酸化连接先天免疫记忆中的代谢与表观遗传重编程
Trained immunity, a de facto innate immune memory characterized by enhanced responsiveness to future challenges, is underpinned by epigenetic and metabolic rewiring. In individuals vaccinated with Bacille Calmette-Guérin (BCG), lactate release was associated with enhanced cytokine responsiveness upon restimulation. Trained monocytes/macrophages are characterized by lactylation of histone H3 at lysine residue 18(H3K18la), mainly at distal regulatory regions. Histone lactylation was positively associated with active chromatin and gene transcription, persisted after the elimination of the training stimulus, and was strongly associated with “trained” gene transcription in response to a secondary stimulus. Increased lactate production upon induction of trained immunity led to enhanced production of proinflammatory cytokines, a process associated with histone lactylation. Pharmacological inhibition of lactate production or histone lactylation blocked trained immunity responses, while polymorphisms of LDHA and EP300 genes modulated trained immunity. Long-term histone lactylation persisted in vivo 90 days after vaccination with BCG, highlighting H3K18la as an epigenetic mark of innate immune memory.
训练免疫（trained immunity）是一种通过表观遗传与代谢重编程增强后续应答能力的先天免疫记忆。在卡介苗（BCG）接种者中，乳酸释放与再刺激后细胞因子应答的增强相关。训练的单核/巨噬细胞表现出组蛋白H3第18位赖氨酸的乳酸化（H3K18la），且该修饰主要富集于远端调控区。组蛋白乳酸化与活性染色质及基因转录呈正相关，且在训练刺激消除后持续存在，并与二次刺激下的“训练”基因转录强关联。训练免疫诱导的乳酸生成增加通过组蛋白乳酸化修饰促进促炎细胞因子的产生。药物抑制乳酸生成或组蛋白乳酸化修饰可阻断训练免疫应答，而LDHA和EP300基因的多态性可调控训练免疫强度。BCG接种后90天，体内仍可长期检测到组蛋白乳酸化修饰的持续存在，凸显H3K18la作为先天免疫记忆的表观遗传标记。
10.Red blood cells undergo lytic programmed cell death involving NLRP3
红细胞经历依赖NLRP3的裂解式程序性死亡
The canonical complement-mediated lysis of mature red blood cells (RBCs) leads to severe pathogenesis. However, inhibition strategies targeting complement are not always as efficient as expected, indicating that unknown mechanisms are awaiting elucidation. In this study, we investigate the intracellular events in mature RBCs following complement activation. The collected evidence demonstrates that complement-induced hemolysis is a caspase-8-dependent programmed RBC death. Furthermore, short NLRP3 (miniNLRP3) fragments in RBCs are identified to engage in the assembly of NLRP3-apoptosis-associated speck-like protein containing a CARD (ASC)-caspase-8 complex. Activated caspase-8 directly induces the proteolysis of β-spectrin, thereby disrupting the skeletal network of the RBC membrane, a process we refer to as spectosis. Spectosis signaling is also activated in autoimmune hemolytic anemia or paroxysmal nocturnal hemoglobinuria, and the inhibition of spectosis significantly reduced complement-induced hemolysis. These findings reveal a programmed death cascade in mature RBCs, which may have important implications for the treatment of hemolytic disorders.
经典补体介导的成熟红细胞裂解可导致严重病理过程。然而，靶向补体的抑制策略效果有限，表明未知机制尚待阐明。该研究探究了补体激活后成熟红细胞内的级联事件。研究表明，补体诱导的溶血是依赖caspase-8的程序性红细胞死亡。此外，红细胞中的短NLRP3片段（miniNLRP3）参与组装NLRP3-凋亡相关斑点样蛋白（ASC）-caspase-8复合体。激活的caspase-8直接导致β-血影蛋白（β-spectrin）的酶解，破坏红细胞膜骨架网络（该过程称为“骨架降解症” ）。自身免疫性溶血性贫血或阵发性睡眠性血红蛋白尿中同样激活此通路，抑制骨架降解可显著减少补体诱导的溶血。这些发现揭示了成熟红细胞的一种程序性死亡级联通路，为溶血性疾病的治疗提供了重要启示。
11.Optimizing stem cell infusion timing in the prevention of acute graft-versus-host disease
优化干细胞输注时机以预防急性移植物抗宿主病
Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is a cornerstone treatment for a broad spectrum of malignant and nonmalignant hematological disorders. However, the success of allo-HSCT is often overshadowed by acute graft-versus-host disease (aGVHD), a life-threatening complication. Here, we show in patients and murine models that the circadian timing of stem cell infusion dictates the development of aGVHD. Early-infused patients exhibit a significantly lower incidence and severity of aGVHD, as well as improved survival. We observed time-of-day variations in the levels of cytokines, especially IL-1α, which controls donor T cell responses after transplantation. The levels of IL-1α in patients were strongly associated with the development of aGVHD. Furthermore, preclinical results showed that the administration of IL-1α neutralizing antibodies markedly alleviated aGVHD and increased survival. Our study suggests that scheduling stem cell infusions early in the day could be a simple yet transformative intervention for preventing aGVHD.
异基因造血干细胞移植（allo-HSCT）是多种恶性/非恶性血液病的核心疗法，但其成功率常受限于急性移植物抗宿主病（aGVHD）这一致命并发症。该研究在患者及小鼠模型中发现，干细胞输注的昼夜节律时相决定aGVHD发生。在日间较早时段输注的患者aGVHD发生率和严重度显著降低，生存率提升。患者细胞因子水平存在昼夜波动，尤其是调控移植后供体T细胞应答的IL-1α。患者体内IL-1α水平与aGVHD的发生显著相关，此外，临床前研究结果显示输注IL-1α中和抗体可显著缓解aGVHD并提高生存率。该研究提示，将干细胞输注安排在日间较早时段可能是预防aGVHD的一种简单却具有变革意义的策略。
12.A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types
用于皮层细胞类型遗传操作的增强子AAV载体与转基因小鼠工具库
The mammalian cortex is comprised of cells classified into types according to shared properties. Defining the contribution of each cell type to the processes guided by the cortex is essential for understanding its function in health and disease. We use transcriptomic and epigenomic cortical cell-type taxonomies from mouse and human to define marker genes and putative enhancers and create a large toolkit of transgenic lines and enhancer adeno-associated viruses (AAVs) for selective targeting of cortical cell populations. We report creation and evaluation of fifteen transgenic driver lines, two reporter lines, and >1,000 different enhancer AAV vectors covering most subclasses of cortical cells. The tools reported here have been made publicly available, and along with the scaled process of tool creation, evaluation, and modification, they will enable diverse experimental strategies toward understanding mammalian cortex and brain function.
哺乳动物皮层由具有共享特征的细胞类型构成。阐明各细胞类型对皮层功能的贡献是理解其在健康与疾病状态下功能的关键。该研究基于小鼠和人类皮层细胞的转录组与表观基因组分类，鉴定标志基因和预测增强子，创建了用于特异性靶向皮层细胞类型的转基因品系和增强子AAV载体。该研究报道了15种转基因驱动系、2种报告系及>1000种增强子AAV载体的构建与评估，这些工具覆盖了大多数皮层细胞亚类，构成了一个综合性工具集。这些工具已公开提供，其规模化构建、评估与优化流程将助力理解哺乳动物皮层及脑功能的多样化实验策略。
13.Microbiome metabolism of dietary phytochemicals controls the anticancer activity of PI3K inhibitors
膳食植物化学物质的微生物组代谢调控PI3K抑制剂的抗癌活性
Phosphatidylinositol 3-kinase (PI3K) signaling is both the effector pathway of insulin and among the most frequently activated pathways in human cancer. In murine cancer models, the efficacy of PI3K inhibitors is dramatically enhanced by a ketogenic diet, with a proposed mechanism involving dietary suppression of insulin. Here, we confirm profound diet-PI3K anticancer synergy but show that it is, surprisingly, unrelated to diet macronutrient composition. Instead, the diet-PI3K interaction involves microbiome metabolism of ingested phytochemicals. Specifically, murine ketogenic diet lacks the complex spectrum of phytochemicals found in standard chow, including the soy phytochemicals soyasaponins. We find that soyasaponins are converted by the microbiome into inducers of hepatic cytochrome P450 enzymes, and thereby lower PI3K inhibitor blood levels and anticancer activity. A high-carbohydrate, low-phytochemical diet synergizes with PI3K inhibition to treat cancer in mice, as do antibiotics that curtail the gut microbiome. Thus, diet impacts anticancer drug activity through phytochemical-microbiome-liver interactions.
磷脂酰肌醇3-激酶（PI3K）信号既是胰岛素效应通路，又是人类癌症中最常激活的通路之一。在鼠类癌症模型中，PI3K抑制剂疗效可因生酮饮食显著增强，其既往提出的机制认为饮食通过抑制胰岛素信号发挥作用。该研究证实了显著的饮食-PI3K抗癌协同作用，但意外地发现其与饮食宏量营养素组成无关。相反，该协同作用源于微生物组对膳食植物化学物质的代谢：鼠类生酮饮食缺乏标准饲料中的复杂植物化学谱（如大豆皂苷）。大豆皂苷被微生物组转化为肝脏细胞色素P450酶的诱导剂，从而导致PI3K抑制剂血药浓度降低与抗癌活性减弱。高碳水化合物、低植物化学饮食可与PI3K抑制协同抗癌，抑制肠道微生物组的抗生素也能产生类似的协同治疗效果。综上，饮食通过“植物化学物质-微生物组-肝脏”相互作用影响抗癌药物活性。
14.A single-cell atlas reveals immune heterogeneity in anti-PD-1-treated non-small cell lung cancer
单细胞图谱揭示抗PD-1治疗下非小细胞肺癌的免疫异质性
Anti-PD-(L)1 treatment is standard for non-small cell lung cancer (NSCLC), but patients show variable responses to the same regimen. The tumor immune microenvironment (TIME) is associated with immunotherapy response, yet the heterogeneous underlying therapeutic outcomes remain underexplored. We applied single-cell RNA and TCR sequencing (scRNA/TCR-seq) to analyze surgical tumor samples from 234 NSCLC patients post-neoadjuvant chemo-immunotherapy. Analyses revealed five distinct TIME subtypes with varying major pathological response (MPR) rates. MPR patients had elevated levels of FGFBP2+ NK/NK-like T cells, memory B cells, or effector T cells, while non-MPR patients showed higher CCR8+ Tregs. T cell clonal expansion analyses unveiled heterogeneity in non-MPR patients, marked by varying expansions of Tex-relevant cells and CCR8+ Tregs. Precursor exhausted T cells (Texp cells) correlated with recurrence-free survival, identifying a patient subgroup with reduced recurrence risk despite lack of MPR. Our study dissects TIME heterogeneity in response to chemoimmunotherapy, offering insights for NSCLC management.
抗PD-(L)1治疗是非小细胞肺癌（NSCLC）的标准疗法，但患者对相同方案的应答存在差异。肿瘤免疫微环境（TIME）与免疫治疗反应相关，但其导致治疗应答异质性的潜在机制尚未被充分阐明。该研究通过单细胞RNA/TCR测序（scRNA/TCR-seq）分析了234例接受新辅助化疗联合免疫治疗的NSCLC患者的术后肿瘤样本。分析鉴定出具有不同的主要病理缓解（MPR）率的五种TIME亚型：MPR患者的FGFBP2⁺ NK/NK样T细胞、记忆B细胞或效应T细胞水平升高，而非MPR患者则表现出更高的CCR8⁺ Treg水平。T细胞克隆扩增分析显示非MPR患者存在异质性，表现为肿瘤抗原特异性耗竭T细胞（Tex）及相关细胞与CCR8⁺ Treg的克隆扩增程度存在差异。前体耗竭T细胞（Texp）与无复发生存期显著相关，据此可识别出一类未达到MPR但复发风险较低的患者亚群。该研究解析了对化疗免疫治疗应答的TIME异质性，为NSCLC的临床管理提供关键见解。
汇报人：李俊虹
导师：赵宇
审核：毛敏姿、任建君
