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2025年8月-9月 CELL（188卷：16-18期）导读 期刊介绍： Cell是Cell Press细胞出版社旗下的旗舰刊，创办于1974年，由爱思唯尔（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，2025年影响因子为42.5。 Aug 07, 2025；Volume 188, Issue 16；p4173-4474 Cell共发表21篇，其中包括2篇Previews; 1篇Review; 2篇Short Articles; 9篇Articles; 3篇Resources; 1篇Matters Arising; 1篇Matters Arising Response; 2篇Corrections。 On the cover: Fluorescent genetically encoded voltage indicators report transmembrane potentials of targeted cell types. In this issue of Cell, Haziza et al. image high-frequency voltage dynamics in multiple neuron classes of behaving mammals, highlighting the brain's hidden, millisecond-scale electrical code underlying perception, thoughts, and emotions. The cover image showcases cell-type-specific membrane voltage signals from a green fluorescent voltage indicator expressed in layer 2/3 pyramidal neurons of the mouse neocortex. This artwork evokes the iconic aesthetic of the famous 1999 movie “The Matrix,” directed by the Wachowskis. 封面内容：荧光蛋白基因编码电压指示剂可记录目标细胞类型的跨膜电位。在本期《Cell》杂志中，哈齐扎（Haziza）等人对行为状态下哺乳动物不同类别神经元的高频电压动态变化进行了成像研究，揭示了大脑中潜藏的、以毫秒为时间尺度的电信号编码——正是这一编码构成了感知、思维与情绪的基础。封面图像展示了小鼠新皮层2/3层锥体细胞中表达的绿色荧光电压指示剂所产生的细胞类型特异性膜电压信号。该图像设计借鉴了沃卓斯基姐妹（Wachowskis）于1999年执导的经典电影《黑客帝国》（TheMatrix）的标志性视觉风格。 1. Microbiota-derived inosine programs protective CD8+ T cell responses against influenza in newborns 微生物来源的肌苷程序化调控新生儿抗流感病毒的保护性CD8+T细胞应答 Early-life susceptibility to respiratory viral infections remains a major public health concern, yet the underlying mechanisms are poorly understood. We demonstrate that antibiotic-induced dysbiosis impairs influenza-specific CD8+ T cell immunity in infant mice and humans through the disruption of nuclear factor interleukin 3 (NFIL3)-dependent T cell programming. Mechanistically, we show that dysbiosis reduces intestinal and circulating inosine levels, disrupting NFIL3’s epigenetic regulation of T cell factor 1 (TCF1) expression. This leads to intrinsic defects in CD8+ T cell proliferation and differentiation, diminished effector responses, and impaired formation of tissue-resident memory cells. Bifidobacterium colonization restores intestinal and pulmonary inosine levels, establishing a specific pathway of gut-lung metabolic communication. Notably, inosine supplementation rescues NFIL3-dependent regulation of TCF1, enhancing CD8+ T cell responses and protection against influenza infection in dysbiotic infants. Our findings reveal how early-life microbial communities shape antiviral immunity and identify inosine as a therapeutic target for enhancing respiratory defenses in infants. 生命早期对呼吸道病毒感染的易感性仍是重大公共卫生问题，但其潜在机制尚未明确。本研究证实，抗生素诱导的肠道菌群失调会通过干扰核因子白细胞介素3（NFIL3）依赖的T细胞编程，损害幼鼠和人类婴幼儿的流感特异性CD8+T细胞免疫功能。从机制上看，研究发现菌群失调会降低肠道和循环系统中的肌苷水平，进而干扰NFIL3对T细胞因子1（TCF1）表达的表观遗传调控。这会导致CD8+T细胞出现增殖与分化的内在缺陷，效应应答减弱，且会造成组织驻留记忆细胞的形成受损。双歧杆菌定植可恢复肠道和肺部的肌苷水平，从而建立起肠道-肺部代谢通讯的特异性通路。值得注意的是，补充肌苷可恢复NFIL3对TCF1的依赖性调控，增强菌群失调婴幼儿的CD8+T细胞应答，并增强其对流感感染的抵抗力。本研究揭示了生命早期微生物群落调控抗病毒免疫的机制，并证实肌苷可作为增强婴幼儿呼吸道防御功能的治疗靶点。 2. Trichophyton concentricum fungal infections and skin microbiomes of Indigenous Peninsular Malaysians 马来半岛原住民的同心毛癣菌感染与皮肤微生物组 Recent outbreaks of multidrug-resistant fungi infecting human skin emphasize the importance of understanding fungal pathophysiology and spread. In efforts to address health concerns with various Indigenous Peninsular Malaysians (Orang Asli [OA]), tinea imbricata—a Trichophyton concentricum fungal skin infection—emerged as a particular concern. We investigated the etiology and transmission of tinea imbricata by culturing, testing antifungal sensitivities, and sequencing T. concentricum isolates in remote OA villages. Among regionally conserved isolates, we identified the emergence of terbinafine-resistant T. concentricum microbiologically and genomically. Investigating the skin microbiomes of 82 Indigenous OA, we found unique microbiota and lower relative abundances of bacterial commensals (Cutibacterium acnes, Staphylococcus epidermidis) among OA versus Malaysian and US urban populations, emphasizing how understudied populations provide unprecedented knowledge on host-microbiome co-evolution. These findings provide valuable insights into clinical, microbiological, and genomic features of chronic fungal skin infections, offering the potential to inform strategies to address drug resistance and effective therapy. 近期多重耐药真菌引发的人类皮肤感染疾病暴发，凸显了深入理解真菌病理生理机制与传播规律的重要性。在针对马来西亚半岛原住民（OrangAsli，简称OA族群）各类健康问题的调研中，叠瓦癣—一种由同心毛癣菌（Trichophytonconcentricum）引起的真菌性皮肤感染成为重点关注对象。本研究通过对偏远OA村落的同心毛癣菌菌株进行培养、抗真菌药敏测试及测序分析，探究了叠瓦癣的病因与传播机制。在区域内保守的菌株中，研究人员从微生物学和基因组学层面均检测到了耐特比萘芬同心毛癣菌的出现。对82名OA族群原住民的皮肤微生物组分析显示，与马来西亚城市人群及美国城市人群相比，OA族群拥有独特的皮肤微生物群，且皮肤共生菌（如痤疮丙酸杆菌Cutibacteriumacnes、表皮葡萄球菌Staphylococcusepidermidis）的相对丰度更低。这一发现表明，对研究不足的人群开展研究，能为宿主-微生物组共进化提供前所未有的认知。本研究结果为慢性真菌皮肤感染的临床特征、微生物学特征及基因组特征提供了宝贵见解，有望为制定耐药性应对策略及有效治疗方案提供参考。 3. In vivo prime editing rescues alternating hemiplegia of childhood in mice 体内原位编辑疗法可治疗幼鼠的交替性偏瘫 Alternating hemiplegia of childhood (AHC) is a neurodevelopmental disorder with no disease-modifying treatment. Mutations in ATP1A3, encoding an Na+/K+ ATPase subunit, cause 70% of AHC cases. Here, we present prime editing (PE) and base editing (BE) strategies to correct ATP1A3 and Atp1a3 mutations in human cells and in two AHC mouse models. We used PE and BE to correct five prevalent ATP1A3 mutations with 43%–90% efficiency. AAV9-mediated in vivo PE corrects Atp1a3 D801N and E815K in the CNS of two AHC mouse models, yielding up to 48% DNA correction and 73% mRNA correction in bulk brain cortex. In vivo PE rescued clinically relevant phenotypes, including restoration of ATPase activity; amelioration of paroxysmal spells, motor defects, and cognition deficits; and dramatic extension of animal lifespan. This work suggests a potential one-time PE treatment for AHC and establishes the ability of PE to rescue a neurological disease in animals. 儿童交替性偏瘫（AlternatingHemiplegiaofChildhood,AHC）是一种尚无疾病修饰治疗手段的神经发育障碍性疾病。编码钠钾ATP酶（Na+/K+ATPase）亚基的ATP1A3基因突变是70%AHC病例的原因。本研究提出了利用引导编辑（primeediting,PE）和碱基编辑（baseediting,BE）技术的治疗策略，在人类细胞及两种AHC小鼠模型中纠正ATP1A3（人源基因）与Atp1a3（鼠源基因）突变。研究人员通过PE和BE技术，以43%–90%的效率成功纠正了5种常见的ATP1A3突变。在两种AHC小鼠模型中，经AAV9（腺相关病毒9型）介导的体内引导编辑，可纠正中枢神经系统（CNS）内Atp1a3基因的D801N与E815K突变；在大脑皮层整体组织中，DNA水平的纠正效率最高达48%，mRNA水平的纠正效率最高达73%。体内引导编辑可改善具有临床相关性的表型，具体包括：恢复钠钾ATP酶活性；改善阵发性发作、运动功能缺陷与认知障碍；显著延长动物寿命。本研究表明，引导编辑有望成为AHC的潜在治疗手段，同时证实了引导编辑技术治疗动物神经系统疾病的能力。 4. Co-development of mesoderm and endoderm enables organotypic vascularization in lung and gut organoids 中胚层和内胚层的共同发育使肺和肠道类器官能够生成器官型血管 The vasculature and mesenchyme exhibit distinct organ-specific characteristics adapted to local physiological needs, shaped by microenvironmental and cell-cell interactions from early development. To recapitulate this entire process, we co-differentiated mesoderm and endoderm within the same spheroid to vascularize lung and intestinal organoids from induced pluripotent stem cells (iPSCs). Bone morphogenetic protein (BMP) signaling fine-tuned the endoderm-to-mesoderm ratio, a critical step in generating appropriate proportions of endothelial and epithelial progenitors with tissue specificity. Single-cell RNA sequencing (scRNA-seq) revealed organ-specific gene signatures of endothelium and mesenchyme and identified key ligands driving endothelial specification. The endothelium exhibited tissue-specific barrier function, enhanced organoid maturation, cellular diversity, and alveolar formation on the engineered lung scaffold. Upon transplantation into mice, the organoid vasculature integrated with the host circulation while preserving organ specificity, further promoting organoid maturation. Leveraging these vascularized organoids, we uncovered abnormal endothelial-epithelial crosstalk in patients with forkhead box F1 (FOXF1) mutations. Multilineage organoids provide an advanced platform to study intricate cell-to-cell communications in human organogenesis and disease. 脉管系统与间充质具有显著的器官特异性，这些特性是在早期发育过程中通过微环境及细胞间相互作用形成的，以适应局部生理需求。为重现这一完整过程，本研究在同一球体结构内共分化中胚层与内胚层，从而实现诱导多能干细胞（iPSCs）来源的肺类器官与肠道类器官血管化。骨形态发生蛋白（BMP）信号通路可精细调控内胚层与中胚层的比例，这是生成比例适宜且具有组织特异性的内皮祖细胞与上皮祖细胞的关键步骤。单细胞RNA测序（scRNA-seq）结果揭示了内皮细胞与间充质细胞的器官特异性基因特征，并筛选出驱动内皮细胞定向分化的关键配体。研究发现，内皮细胞不仅表现出组织特异性屏障功能，还能促进类器官成熟、增加细胞多样性，并在工程化肺支架上推动肺泡形成。将类器官移植到小鼠体内后，类器官中的脉管系统可与宿主循环系统整合，同时保留自身器官特异性，进一步促进类器官成熟。利用这些血管化类器官，研究人员发现叉头框蛋白F1（FOXF1）突变患者存在内皮-上皮细胞间通讯异常。该研究表明，多谱系类器官为研究人类器官发生及疾病中的复杂细胞间通讯提供了先进平台。 5. Bivalent chromatin instructs lineage specification during hematopoiesis 双价染色质指导造血过程中的谱系分化 Developmental gene expression is regulated by the dynamic interplay of histone H3 lysine 4 (H3K4) and histone H3 lysine 27 (H3K27) methylation, yet the physiological roles of these epigenetic modifications remain incompletely understood. Here, we show that mice depleted for all forms of H3K4 methylation, using a dominant histone H3-lysine-4-to-methionine (H3K4M) mutation, succumb to a severe loss of all major blood cell types. H3K4M-expressing hematopoietic stem cells (HSCs) and committed progenitors are present at normal numbers, indicating that H3K4 methylation is dispensable for HSC maintenance and commitment but essential for progenitor cell maturation. Mechanistically, we reveal that H3K4 methylation opposes the deposition of repressive H3K27 methylation at differentiation-associated genes enriched for a bivalent (i.e., H3K4/H3K27-methylated) chromatin state in HSCs and progenitors. Indeed, by concomitantly suppressing H3K27 methylation in H3K4-methylation-depleted mice, we rescue the acute lethality, hematopoietic failure, and gene dysregulation. Our results provide functional evidence for the interaction between two crucial chromatin marks in mammalian tissue homeostasis. 发育过程中的基因表达受组蛋白H3赖氨酸4（H3K4）与组蛋白H3赖氨酸27（H3K27）甲基化的动态互作调控，然而这些表观遗传修饰的生理功能尚未完全明确。本研究通过构建组蛋白H3赖氨酸4突变为蛋氨酸（H3K4M）的显性突变小鼠模型，导致小鼠体内所有形式H3K4甲基化的缺失，结果表明该模型小鼠会出现所有主要血细胞类型的严重缺失并最终死亡。表达H3K4M的造血干细胞（HSCs）及定向祖细胞数量维持正常，这表明H3K4甲基化对造血干细胞的维持与定向分化并非必需，但对祖细胞的成熟至关重要。机制层面研究显示，在造血干细胞和祖细胞中，分化相关基因的染色质多处于二价状态（即同时存在H3K4甲基化与H3K27甲基化），而H3K4甲基化可通过拮抗该类基因上抑制性H3K27甲基化的沉积发挥作用。事实上，在H3K4甲基化缺失的小鼠中同时抑制H3K27甲基化，可改善小鼠急性致死表型、造血功能衰竭及基因表达失调问题。本研究结果为两种关键染色质修饰标记在哺乳动物组织稳态中的相互作用提供了功能性证据。 6. Arrestin-biased allosteric modulator of neurotensin receptor 1 alleviates acute and chronic pain 抑制蛋白偏向性的神经降压素受体1变构调节剂可以缓解急性和慢性疼痛 G-protein-biased agonists have been shown to enhance opioid analgesia by circumventing β-arrestin-2 (βarr2) signaling. We previously reported that SBI-553, a neurotensin receptor 1 (NTSR1)-positive allosteric modulator biased toward βarr2 signaling, attenuates psychostimulant effects in mice. Here, we demonstrate that its analog, SBI-810, exhibits potent antinociceptive properties in rodent models of postoperative pain, inflammatory pain, and neuropathic pain via systemic and local administration. SBI-810’s analgesic effects require NTSR1 and βarr2 but not NTSR2 or βarr1. Mechanistically, SBI-810 suppresses excitatory synaptic transmission, inhibits NMDA receptor and extracellular-regulated signal kinase (ERK) signaling in spinal cord nociceptive neurons, reduces Nav1.7 surface expression and action potential firing in primary sensory neurons, and dampens C-fiber responses. Behaviorally, it reduces opioid-induced conditioned place preference, alleviates constipation, and mitigates chronic opioid withdrawal symptoms. These findings highlight NTSR1-biased allosteric modulators as a promising, non-addictive therapeutic strategy for acute and chronic pain management, acting through both peripheral and central mechanisms. G蛋白偏向性激动剂可避开β-抑制蛋白2（βarr2）信号通路，增强阿片类药物的镇痛效果。此前研究发现，SBI-553作为一种偏向βarr2信号通路的神经降压素受体1（NTSR1）阳性变构调节剂，可减弱小鼠体内精神兴奋剂的作用。本研究进一步证实，其类似物SBI-810通过全身给药或局部给药，在啮齿动物术后疼痛、炎症性疼痛及神经病理性疼痛模型中均表现出强效镇痛作用。SBI-810的镇痛效果依赖于NTSR1与βarr2，而不依赖于NTSR2（神经降压素受体2）或βarr1（β-抑制蛋白1）。机制层面研究显示，SBI-810可通过以下途径发挥作用：抑制脊髓伤害感受神经元中的兴奋性突触传递，下调NMDA受体（N-甲基-D-天冬氨酸受体）与细胞外调节信号激酶（ERK）信号通路活性；降低初级感觉神经元中Nav1.7（电压门控钠通道1.7）的表面表达水平及动作电位发放频率；减弱C纤维（传递伤害性感觉的外周神经纤维）的反应。行为学实验表明，SBI-810可减少阿片类药物诱导的条件性位置偏爱（反映药物成瘾性的关键指标），缓解便秘（阿片类药物常见副作用），并减轻慢性阿片类药物戒断症状。这些研究结果表明，偏向NTSR1的变构调节剂可通过外周与中枢双重机制发挥作用，是一种极具潜力的非成瘾性急性与慢性疼痛管理治疗策略。 7. Repeat-element RNAs integrate a neuronal growth circuit 重复元件 RNA 整合了一个神经元生长回路 Neuronal growth and regeneration are regulated by local translation of mRNAs in axons. We examined RNA polyadenylation changes upon sensory neuron injury and found upregulation of a subset of polyadenylated B2-SINE repeat elements, hereby termed GI-SINEs (growth-inducing B2-SINEs). GI-SINEs are induced from ATF3 and other AP-1 promoter-associated extragenic loci in injured sensory neurons but are not upregulated in lesioned retinal ganglion neurons. Exogenous GI-SINE expression elicited axonal growth in injured sensory, retinal, and corticospinal tract neurons. GI-SINEs interact with ribosomal proteins and nucleolin, an axon-growth-regulating RNA-binding protein, to regulate translation in neuronal cytoplasm. Finally, antisense oligos against GI-SINEs perturb sensory neuron outgrowth and nucleolin-ribosome interactions. Thus, a specific subfamily of transposable elements is integral to a physiological circuit linking AP-1 transcription with localized RNA translation. 神经元的生长与再生受轴突中mRNA局部翻译的调控。本研究检测了感觉神经元损伤后RNA多聚腺苷酸化（polyadenylation）的变化，发现一类多聚腺苷酸化的B2短散在核元件（B2-SINE）重复序列亚群表达上调（研究者将其命名为GI-SINEs—生长诱导型B2-SINEs（growth-inducingB2-SINEs）。GI-SINEs由受损感觉神经元中ATF3（激活转录因子3）及其他AP-1（激活蛋白-1）启动子相关的基因外位点诱导产生，而在受损的视网膜神经节细胞中并未出现上调。外源性GI-SINEs表达可诱导受损感觉神经元、视网膜神经元及皮质脊髓束神经元的轴突生长。机制上，GI-SINEs可与核糖体蛋白及核仁素（nucleolin，一种调控轴突生长的RNA结合蛋白）相互作用，进而调控神经元胞质中的翻译过程。最后，针对GI-SINEs的反义寡核苷酸（antisenseoligos）可干扰感觉神经元的轴突延伸，并破坏核仁素与核糖体的相互作用。综上，该研究表明转座元件的一个特定亚家族是连接AP-1转录与局部RNA翻译的生理通路中不可或缺的组成部分。 8. Infrequent strong connections constrain connectomic predictions of neuronal function 不频繁的强连接限制了对神经元功能的连接组学预测 How does circuit wiring constrain neural computation? Recent work has leveraged connectomic datasets to predict the functions of cells and circuits in the brains of multiple species. However, many of these hypotheses have not been compared with physiological measurements, obscuring the limits of connectome-based functional predictions. To explore these limits, we characterized the visual responses of 43 cell types in the fruit fly and quantitatively compared them with connectomic predictions. We show that these predictions are accurate for some response properties, such as orientation tuning, but are surprisingly poor for other properties, such as receptive field size. Importantly, strong synaptic inputs are more functionally homogeneous than expected by chance and exert a disproportionately large influence on postsynaptic responses. Finally, we quantitatively define the subset of connections that best describe the functional differences between cell types. Our results establish a powerful set of constraints for improving the accuracy of connectomic predictions. 神经环路的连接方式如何约束神经计算功能？近期研究利用连接组学数据集（connectomicdatasets）预测了多个物种大脑中细胞与环路的功能。然而，这些假说中许多尚未与生理测量结果进行对比，导致基于连接组的功能预测存在局限性，而这些局限性尚未明确。为探究上述局限性，本研究对果蝇体内43种细胞类型的视觉反应进行了表征，并将其与连接组学预测结果进行定量对比。研究发现，这些预测对部分反应特性（如朝向选择性，orientationtuning）的预测准确度较高，但对另一些特性（如感受野大小，receptivefieldsize）的预测效果却显著低于预期。重要的是，强突触输入的功能同质性（functionalhomogeneity）显著高于随机水平，且对突触后反应的影响远大于其他输入。最后，研究通过定量分析确定了最能解释不同细胞类型功能差异的特定连接子集。本研究结果为提高连接组学预测准确性提供了一系列重要的约束条件。 9. Identification and application of cell-type-specific enhancers for the macaque brain 猕猴大脑细胞特异性增强子的鉴定及应用 Genetic targeting methods for monitoring and manipulating neuronal activity are not widely used for studying the primate brain, largely owing to the lack of a cell-type-specific targeting method. Using single-cell RNA and ATAC sequencing of macaque brains combined with in vivo screening, we identified a large set of enhancers capable of driving targeted gene expression in specific cell types. AAV vectors driven by these enhancers successfully targeted layer-specific glutamatergic neurons, GABAergic interneuron subtypes, astrocytes, and oligodendrocytes with high specificity. Cross-species comparison revealed that some macaque enhancers are conserved and functional across species, but enhancers with layer-specific targeting in macaques did not label neurons in mice, highlighting evolutionary differences in cortical CREs. Targeting precision was further improved using a FLPo-dependent intersectional approach with two enhancers. These enhancer-AAVs were validated by monitoring and manipulating activity in macaque visual cortex, providing valuable tools to dissect primate neural circuit functions. 用于监测和调控神经元活动的基因靶向技术尚未广泛应用于灵长类动物脑研究，这在很大程度上是由于缺乏细胞类型特异性靶向方法。本研究通过对猕猴大脑进行单细胞RNA测序（scRNA-seq）与单细胞转座酶可及性染色质测序（scATAC-seq），并结合体内筛选，鉴定出大量可驱动特定细胞类型中靶向基因表达的增强子（enhancer）。由这些增强子驱动的腺相关病毒（AAV）载体，能以高特异性靶向分层特异性谷氨酸能神经元、γ-氨基丁酸能（GABAergic）中间神经元亚型、星形胶质细胞及少突胶质细胞。跨物种对比研究发现，部分猕猴增强子在不同物种间具有保守性且功能可跨物种发挥，但在猕猴中具有分层特异性靶向能力的增强子无法标记小鼠神经元，这凸显了皮质顺式调控元件（CREs）在进化过程中的差异。通过采用依赖FLPo重组酶的双增强子交叉靶向策略（FLPo-dependentintersectionalapproach），进一步提升了靶向精准度。研究人员在猕猴视觉皮层中通过监测和调控神经元活动，验证了这些增强子-AAV载体的有效性，为解析灵长类动物神经环路功能提供了极具价值的工具。 Aug 21, 2025；Volume 188, Issue 17；p4475-4810 Cell共发表21篇，其中包括2篇Previews; 1篇Review; 1篇Short Article; 11篇Articles; 1篇Theory；4篇Resources; 1篇Correction。 On the cover: Synonymous mutations, once known as “silent” mutations, are increasingly attracting the interest of biologists. In this issue of Cell, Xin et al. provide an organismal example of synonymous mutation controlling domesticated traits through m6A modification and RNA structure-mediated epitranscriptomic regulations. The cover image depicts coiled cucumber tendrils transitioning into RNA strands, with a tendril of wild cucumber adorned by a bee to symbolize m6A modifications, illustrating how a synonymous mutation alters m6A modification and RNA structure during domestication. Image source: Coloring Dayu. 封面内容：同义突变曾被称为“沉默突变”，如今正日益引发生物学家的关注。在本期《Cell》杂志中，Xin等人以生物体为研究对象，揭示了同义突变通过m6A修饰及RNA结构介导的表观转录组调控，实现对驯化性状的调控作用。封面图像将卷曲的黄瓜卷须转化为RNA链，其中野生黄瓜的卷须上附着一只蜜蜂，以此象征m6A修饰，形象地展现了驯化过程中同义突变如何改变m6A修饰与RNA结构。 1. Recessive epistasis of a synonymous mutation confers cucumber domestication through epitranscriptomic regulation 一个同义突变的隐性交互作用通过表观转录调控促进了黄瓜的栽培过程 Synonymous mutations, once known as “silent” mutations, are increasingly attracting the interest of biologists. Although they may affect transcriptional or post-transcriptional processes, their impact on biological traits remains under-investigated, particularly at the organismal level. Here, we identified two closely linked, epistatically interacting genes: YTH1, an RNA N6-methyladenosine (m6A) reader, and ACS2, an aminocyclopropane-1-carboxylic acid (ACC) synthase, which contribute to cucumber fruit length domestication. The causative mutation in ACS2 is a synonymous substitution at 1287C>T. In wild cucumber, ACS21287C results in m6A modification on nearby adenosine residues and the formation of loose RNA structural conformations. YTH1 recognizes the m6A modification, alters the folding equilibrium toward the weakest RNA structural conformation, and increases the ACS2 protein level, resulting in shorter fruit. In cultivated cucumber, ACS21287T disrupts m6A methylation and forms compact RNA structural conformations, leading to attenuated protein production and fruit elongation. This study provides genetic evidence of synonymous variation shaping a biological trait through epitranscriptomic regulations. 同义突变曾被称为“沉默”突变，如今正日益引起生物学家的关注。尽管同义突变可能影响转录或转录后过程，但其对生物性状的影响仍有待深入研究，尤其是在生物个体层面。本文鉴定出两个紧密连锁且存在上位性互作的基因：一个是RNAN6-甲基腺苷（m6A）读取蛋白编码基因YTH1，另一个是1-氨基环丙烷-1-羧酸（ACC）合酶编码基因ACS2，这两个基因均参与黄瓜果实长度的驯化过程。ACS2基因中的致病突变为1287位碱基的同义替换（1287C>T）。在野生黄瓜中，ACS2基因1287位为胞嘧啶（ACS21287ᴄ）时，会导致其附近腺苷残基发生m6A修饰，并形成松散的RNA二级构象。YTH1蛋白可识别该m6A修饰位点，使RNA折叠平衡向最松散的构象转变，进而提高ACS2蛋白的表达水平，最终导致果实变短。而在栽培黄瓜中，ACS2基因1287位为胸腺嘧啶（ACS21287ᵀ）时，会破坏m6A甲基化修饰，使RNA形成紧密的二级结构构象，从而导致ACS2蛋白合成减少，果实变长。本研究为同义突变通过表观转录组调控塑造生物性状提供了遗传学证据。 2. A microbial amino-acid-conjugated bile acid, tryptophan-cholic acid, improves glucose homeostasis via the orphan receptor MRGPRE 一种由微生物产生的氨基酸与胆酸的结合物——色氨酸-胆酸可通过“孤儿受体”MRGPRE 改善血糖平衡 Recently, microbial amino-acid-conjugated bile acids (MABAs) have been found to be prevalent in human samples. However, their physiological significance is still unclear. Here, we identify tryptophan-conjugated cholic acid (Trp-CA) as the most significantly decreased MABA in patients with type 2 diabetes (T2D), and its abundance is negatively correlated with clinical glycemic markers. We further demonstrate that Trp-CA improves glucose tolerance in diabetic mice. Mechanistically, we find that Trp-CA is a ligand of the orphan G protein-coupled receptor (GPCR) Mas-related G protein-coupled receptor family member E (MRGPRE) and determine the binding mode between the two. Both MRGPRE-Gs-cyclic AMP (cAMP) and MRGPRE-β-arrestin-1-aldolase A (ALDOA) signaling pathways contribute to the metabolic benefits of Trp-CA. Additionally, we find that the bacterial bile salt hydrolase/transferase of Bifidobacterium is responsible for the production of Trp-CA. Together, our findings pave the way for further research on MABAs and offer additional therapeutic targets for the treatment of T2D. 近期研究显示，微生物氨基酸结合胆汁酸（MABAs）普遍存在于人体样本中。然而其生理学意义仍不明确。本研究发现，色氨酸结合胆酸（Trp-CA）是2型糖尿病（T2D）患者体内含量显著降低的MABA，且其丰度与临床血糖指标呈负相关。本文进一步证明，Trp-CA可改善糖尿病小鼠的葡萄糖耐量。在机制上，本文发现Trp-CA是孤儿G蛋白偶联受体（GPCR）Mas相关G蛋白偶联受体家族成员E（MRGPRE）的配体，并确定了两者之间的结合方式。MRGPRE-Gs-环磷酸腺苷（cAMP）和MRGPRE-β-抑制蛋白-1-醛缩酶A（ALDOA）信号通路都有助于Trp-CA的代谢益处。此外，本文发现双歧杆菌的细菌胆盐水解酶/转移酶负责Trp-CA的合成。总之，本研究为进一步研究MABAs铺平了道路，并为T2D的治疗提供了额外的治疗靶点。 3. Functional liver genomics identifies hepatokines promoting wasting in cancer cachexia 功能肝脏基因组学鉴定出在癌症恶病质中促进消瘦的细胞因子 In cancer cachexia, the presence of a tumor triggers systemic metabolic disruption that leads to involuntary body weight loss and accelerated mortality in affected patients. Here, we conducted transcriptomic and epigenomic profiling of the liver in various weight-stable cancer and cancer cachexia models. An integrative multilevel analysis approach identified a distinct gene expression signature that included hepatocyte-secreted factors and the circadian clock component REV-ERBα as key modulator of hepatic transcriptional reprogramming in cancer cachexia. Notably, hepatocyte-specific genetic reconstitution of REV-ERBα in cachexia ameliorated peripheral tissue wasting. This improvement was associated with decreased levels of specific cachexia-controlled hepatocyte-secreted factors. These hepatokines promoted catabolism in multiple cell types and were elevated in cachectic cancer patients. Our findings reveal a mechanism by which the liver contributes to peripheral tissue wasting in cancer cachexia, offering perspectives for future therapeutic interventions. 在癌症恶病质状态下，肿瘤的存在会引发全身性代谢紊乱，导致患者出现非自主性体重下降，并加速其死亡进程。本研究对多种体重稳定的癌症模型及癌症恶病质模型的肝脏组织进行了转录组学与表观基因组学分析。通过多水平整合分析方法，本文鉴定出一组独特的基因表达特征，其中包括肝细胞分泌因子，以及生物钟的组份REV-ERBα——该组份是癌症恶病质状态下肝脏转录重编程的关键调控因子。值得注意的是，在恶病质模型中，通过肝细胞特异性基因重建恢复REV-ERBα的表达后，外周组织消瘦症状得到了改善。这种改善与恶病质状态下受调控的特定肝细胞分泌因子水平降低相关。这些肝因子可促进多种细胞类型的分解代谢，且在恶病质癌症患者体内呈高表达状态。本研究揭示了肝脏在癌症恶病质中推动外周组织消瘦的具体机制，为未来开展针对性治疗提供了思路。 4. The immunoproteasome disturbs neuronal metabolism and drives neurodegeneration in multiple sclerosis 多发性硬化症中，免疫蛋白酶体干扰神经元代谢并驱动神经退行性病变 Inflammation, aberrant proteostasis, and energy depletion are hallmarks of neurodegenerative diseases such as multiple sclerosis (MS). However, the interplay between inflammation, proteasomal dysfunction in neurons, and its consequences for neuronal integrity remains unclear. Using transcriptional, proteomic, and functional analyses of proteasomal subunits in inflamed neurons, we found that interferon-γ-mediated induction of the immunoproteasome subunit, proteasome 20S beta 8 (PSMB8) impairs the proteasomal balance, resulting in reduced proteasome activity. This reduction causes the accumulation of phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 (PFKFB3), a key metabolic regulator, leading to enhanced neuronal glycolysis, reduced pentose phosphate pathway activity, oxidative injury, and ferroptosis. Neuron-specific genetic and systemic pharmacological targeting of PSMB8 or PFKFB3 protected neurons in vitro and in a mouse model of MS. Our findings provide a unifying explanation for proteasomal dysfunction in MS and possibly other neurodegenerative diseases, linking inflammation to metabolic disruption, and presenting an opportunity for targeted neuroprotective therapies. 炎症反应、异常蛋白质稳态及能量耗竭是多发性硬化症（MS）等神经退行性疾病的典型特征。然而，炎症状态下神经元内蛋白酶体功能异常的发生机制，及其与神经元完整性受损之间的相互作用仍不明确。本研究通过对炎症状态下神经元中蛋白酶体亚基的转录组学、蛋白质组学及功能学分析发现：γ-干扰素（interferon-γ）介导的免疫蛋白酶体亚基——蛋白酶体20Sβ8亚基（PSMB8）诱导表达，会破坏蛋白酶体的平衡状态，导致蛋白酶体活性降低。这种活性降低会引发关键代谢调控因子——磷酸果糖-2-激酶/果糖-2,6-二磷酸酶3（PFKFB3）的蓄积，进而导致神经元糖酵解增强、磷酸戊糖途径活性下降、氧化损伤加剧，并最终诱发铁死亡。进一步研究表明，在体外实验及MS小鼠模型中，通过神经元特异性基因调控或全身性药物干预靶向抑制PSMB8或PFKFB3，均可实现神经元保护。本研究为MS及其他潜在神经退行性疾病中蛋白酶体功能异常的机制提供了统一解释，揭示了炎症反应与代谢紊乱之间的关联，同时为开发靶向性神经保护治疗策略提供了新方向。 5. De novo assembly of nuclear stress bodies rearranges and enhances NFIL3 to restrain acute inflammatory responses 核应激体的从头组装能重新排列并增强 NFIL3 的功能，从而抑制急性炎症反应 The membrane-less nuclear stress bodies (nSBs), with satellite III (SatIII) RNAs as the hallmark, are present in primates upon sensing stresses. We report that SatⅢ DNAs, SatⅢ RNAs, and 30 nSB proteins assemble into well-organized structures shortly after stresses. The activated SatⅢ heterochromatin loci rapidly expand, resulting in reduced spatial distance and enhanced expression of adjacent genes, including the transcription suppressor NFIL3, which is known to dampen proinflammatory cytokine production. Rearranging NFIL3 loci within the nSB territory enhances NFIL3 chromatin accessibility and makes NFIL3 promoters more accessible to transcription factors heat shock transcription factor 1 (HSF1) and bromodomain containing 4 (BRD4), which are also recruited to nSBs upon stresses. Human peripheral blood mononuclear cell (PBMC)-derived macrophages under heat shock plus pathogen-associated molecular pattern treatments exhibit increased SatⅢ and NFIL3 expression, the latter of which suppresses key inflammatory cytokines. Importantly, NFIL3 expression positively correlates with SatⅢ activation in septic patients, a process positively correlated to patient survival, highlighting a role of nSBs in restraining inflammatory responses. 以卫星III（SatIII）RNA为标志的无膜核应激小体（nSBs），是灵长类动物细胞感知应激后形成的特异性结构。本研究发现，应激发生后短时间内，SatIIIDNA、SatIIIRNA及30种nSB相关蛋白会组装成结构有序的复合物。其中，被激活的SatIII异染色质位点会快速扩张，导致其与邻近基因的空间距离缩短，进而促进这些基因的表达——这其中包括转录抑制因子NFIL3（已知可抑制促炎细胞因子的产生）。将NFIL3基因座重排至nSB区域内，可提高NFIL3染色质的可及性，同时使NFIL3启动子更易与转录因子热休克转录因子1（HSF1）和含溴结构域蛋白4（BRD4）结合；而应激状态下，HSF1与BRD4也会被招募至nSBs中。在热休克联合病原体相关分子模式（PAMP）处理的人外周血单个核细胞（PBMC）来源巨噬细胞中，SatIII与NFIL3的表达水平显著升高，且NFIL3的高表达可抑制关键促炎细胞因子的产生。更重要的是，在脓毒症患者中，NFIL3的表达水平与SatIII的激活程度呈正相关，而这一过程又与患者生存率呈正相关。上述结果表明，nSBs在抑制过度炎症反应中发挥关键作用。 6. Development of clinically viable non-muscle myosin II small molecule inhibitors 具有临床应用价值的非肌性肌球蛋白II小分子抑制剂的开发 Non-muscle myosin II (NMII), a molecular motor that regulates critical processes such as cytokinesis and neuronal plasticity, has substantial therapeutic potential. However, translating this potential to in vivo use has been hampered by a lack of selective tools. The most prototypical non-selective inhibitor inactivates both NMII and cardiac muscle myosin II (CMII), a key regulator of heart function. Using rational drug design, we developed a series of NMII inhibitors that markedly improve tolerability by selectively targeting NMII over CMII, including MT-228 and clinical candidate MT-110. MT-228 and MT-110 have excellent properties, including high brain penetration and efficacy in preclinical models of methamphetamine use disorder (MUD), which has no current FDA-approved therapies. The structure of MT-228 bound to myosin II provides insight into its selectivity for NMII over CMII. The broad therapeutic windows of these NMII inhibitors provide valuable tools for the scientific community and a promising clinical candidate for the treatment of MUD. 非肌肉肌球蛋白II（non-musclemyosinII,NMII）是一类分子马达蛋白，可调控胞质分裂、神经元可塑性等关键生理过程，具有巨大的治疗潜力。然而，由于缺乏具有选择性的研究工具，其治疗潜力向体内应用的转化一直受到阻碍。最典型的问题是，非选择性抑制剂会同时使NMII与心脏功能关键调控因子——心肌肌球蛋白II（cardiacmusclemyosinII,CMII）失活。本研究通过合理药物设计，开发出一系列NMII抑制剂（包括MT-228及临床候选药物MT-110）。这类抑制剂可优先选择性靶向NMII而非CMII，从而显著提升药物耐受性。研究显示，MT-228与MT-110具备优异特性，不仅血脑屏障穿透能力强，还在甲基苯丙胺使用障碍（methamphetamineusedisorder,MUD）的临床前模型中展现出疗效——目前美国食品药品监督管理局（FDA）尚未批准任何针对MUD的治疗药物。此外，MT-228与肌球蛋白II的结合结构，为其对NMII而非CMII的选择性作用机制提供了分子层面的解释。这些NMII抑制剂具有较宽的治疗窗口，不仅为科学界研究NMII功能提供了宝贵工具，也为MUD的临床治疗提供了极具潜力的候选药物。 7. MT-125 inhibits non-muscle myosin IIA and IIB and prolongs survival in glioblastoma MT—125抑制非肌性肌球蛋白IIA和IIB，延长胶质母细胞瘤的生存期 Glioblastoma (GBM) is the most lethal of primary brain tumors. Here, we report our studies of MT-125, a small-molecule inhibitor of non-muscle myosin II. MT-125 has high brain penetrance and an excellent safety profile, blocks GBM invasion and cytokinesis, and prolongs survival in murine GBM models. By impairing mitochondrial fission, MT-125 increases redox stress and consequent DNA damage, and it synergizes with radiotherapy. MT-125 also induces oncogene addiction to PDGFR signaling through a mechanism that is driven by redox stress, and it synergizes with FDA-approved PDGFR and mTOR inhibitors in vitro. Consistent with this, we find that combining MT-125 with sunitinib, a PDGFR inhibitor, or paxalisib, a combined phosphatidylinositol 3-kinase (PI3K)/mTOR inhibitor, significantly improves survival in orthotopic GBM models over either drug alone. Our results demonstrate that MT-125 is a first-in-class therapeutic that has strong clinical potential for the treatment of GBM. 胶质母细胞瘤（glioblastoma,GBM）是最致命的原发性脑肿瘤。本研究对非肌肉肌球蛋白II小分子抑制剂MT-125展开了相关研究，结果显示，MT-125具有较高的血脑屏障穿透能力和良好的安全性，能够抑制GBM的侵袭与胞质分裂，并延长GBM小鼠模型的生存期。机制层面，MT-125通过抑制线粒体分裂，增加氧化还原应激，进而导致DNA损伤；同时，该药物与放射治疗具有协同作用。此外，MT-125还可通过氧化还原应激驱动的机制，诱导GBM细胞对血小板衍生生长因子受体（PDGFR）信号产生癌基因成瘾性，且在体外实验中，其与美国食品药品监督管理局（FDA）已批准的PDGFR抑制剂及雷帕霉素靶蛋白（mTOR）抑制剂均表现出协同效应。与此机制一致的是，本研究发现，在原位GBM模型中，将MT-125与PDGFR抑制剂舒尼替尼（sunitinib）或磷脂酰肌醇3-激酶（PI3K）/mTOR双靶点抑制剂帕沙利西布（paxalisib）联合使用时，相比单独使用任意一种药物，可显著提高模型小鼠的生存期。本研究结果表明，MT-125作为一款首创新药（first-in-classtherapeutic），在GBM治疗领域具有广阔的临床应用潜力。 8. Cholinergic neuronal activity promotes diffuse midline glioma growth through muscarinic signaling 胆碱能神经元活动通过毒蕈碱信号促进弥漫性中线胶质瘤生长 Glutamatergic neuronal activity promotes proliferation of both oligodendrocyte precursor cells (OPCs) and gliomas, including diffuse midline glioma (DMG). However, the role of neuromodulatory brainstem neurons projecting to midline structures where DMGs arise remains unexplored. Here, we demonstrate that midbrain cholinergic neuronal activity modulates OPC and DMG proliferation in a circuit-dependent manner. Optogenetic stimulation of the cholinergic pedunculopontine nucleus (PPN) promotes glioma growth in pons, while stimulation of the laterodorsal tegmentum nucleus (LDT) drives proliferation in thalamus. DMG-bearing mice exhibit higher acetylcholine release and increased cholinergic neuronal activity over the disease course. In co-culture, cholinergic neurons enhance DMG proliferation, and acetylcholine directly acts on DMG cells. Single-cell RNA sequencing revealed high CHRM1 and CHRM3 expression in primary DMG samples. Pharmacological or genetic blockade of M1/M3 receptors abolished cholinergic activity-driven DMG proliferation. Taken together, these findings demonstrate that midbrain cholinergic long-range projections promote activity-dependent DMG growth, mirroring a parallel proliferative effect on healthy OPCs. 谷氨酸能神经元活动可促进少突胶质前体细胞（oligodendrocyteprecursorcells,OPCs）及胶质瘤（包括弥漫性中线胶质瘤，diffusemidlineglioma,DMG）的增殖。然而，投射至DMG发生部位的中线结构的脑干神经调节神经元在DMG发展中的作用尚未明确。本研究证实，中脑胆碱能神经元活动通过环路依赖性方式调控OPCs与DMG的增殖：光遗传学刺激胆碱能脚桥核（pedunculopontinenucleus,PPN）可促进脑桥部位胶质瘤生长，而刺激外侧背盖核（laterodorsaltegmentumnucleus,LDT）则会驱动丘脑部位肿瘤增殖。在疾病进展过程中，荷DMG小鼠表现出更高的乙酰胆碱释放水平及胆碱能神经元活动增强。共培养实验显示，胆碱能神经元可促进DMG增殖，且乙酰胆碱可直接作用于DMG细胞。单细胞RNA测序结果表明，原发性DMG样本中胆碱能受体M1亚型（CHRM1）与M3亚型（CHRM3）表达水平较高。通过药物或基因手段阻断M1/M3受体后，胆碱能神经元活动介导的DMG增殖效应被完全消除。综上，本研究结果表明，中脑胆碱能神经元的长距离投射可通过活动依赖性方式促进DMG生长，这一作用模式与其对健康OPCs的增殖调控效应具有相似性。 9. Inner speech in motor cortex and implications for speech neuroprostheses 运动皮层中的内部语言及其对语言神经假体的影响 Speech brain-computer interfaces (BCIs) show promise in restoring communication to people with paralysis but have also prompted discussions regarding their potential to decode private inner speech. Separately, inner speech may be a way to bypass the current approach of requiring speech BCI users to physically attempt speech, which is fatiguing and can slow communication. Using multi-unit recordings from four participants, we found that inner speech is robustly represented in the motor cortex and that imagined sentences can be decoded in real time. The representation of inner speech was highly correlated with attempted speech, though we also identified a neural “motor-intent” dimension that differentiates the two. We investigated the possibility of decoding private inner speech and found that some aspects of free-form inner speech could be decoded during sequence recall and counting tasks. Finally, we demonstrate high-fidelity strategies that prevent speech BCIs from unintentionally decoding private inner speech. 语言脑机接口（speechbrain-computerinterfaces,BCIs）在帮助瘫痪患者恢复沟通能力方面展现出良好前景，但同时也引发了关于其可能解码个体私密内心语言的相关讨论。此外，内心语言或许能为现有言语脑机接口的应用提供新路径——当前该技术要求使用者通过身体动作尝试发声，这种方式不仅易产生疲劳，还会降低沟通效率。本研究通过对4名受试者进行多单元神经记录发现，内心语言在运动皮层中存在稳定的神经表征，且可实时解码想象中的语句。研究证实，内心语言与尝试发声（attemptedspeech）的神经表征高度相关，但同时也识别出一个能区分二者的神经“运动意图”维度。针对私密内心语言的解码可能性，本研究进一步探索发现，在序列回忆与计数任务中，自由形式内心语言的部分信息可被解码。最后，本文还提出了高保真度的调控策略，能够有效防止语言脑机接口在非预期情况下解码私密内心语言。 10. Advancing protein evolution with inverse folding models integrating structural and evolutionary constraints 利用结合结构和进化约束的反向折叠模型推进蛋白质进化 Protein engineering enables artificial protein evolution through iterative sequence changes, but current methods often suffer from low success rates and limited cost effectiveness. Here, we present AI-informed constraints for protein engineering (AiCE), an approach that facilitates efficient protein evolution using generic protein inverse folding models, reducing dependence on human heuristics and task-specific models. By sampling sequences from inverse folding models and integrating structural and evolutionary constraints, AiCE identifies high-fitness single and multi-mutations. We applied AiCE to eight protein engineering tasks, including deaminases, a nuclear localization sequence, nucleases, and a reverse transcriptase, spanning proteins from tens to thousands of residues, with success rates of 11%–88%. We also developed base editors for precision medicine and agriculture, including enABE8e (5-bp window), enSdd6-CBE (1.3-fold improved fidelity), and enDdd1-DdCBE (up to 14.3-fold enhanced mitochondrial activity). These results demonstrate that AiCE is a versatile, user-friendly mutation-design method that outperforms conventional approaches in efficiency, scalability, and generalizability. 蛋白质工程通过迭代序列改变实现人工蛋白质进化，但现有方法通常存在成功率低和成本效益有限的问题。本文提出了人工智能驱动的蛋白质工程约束方法（AI-informedconstraintsforproteinengineering,AiCE），这是一种利用通用蛋白质反向折叠模型促进高效蛋白质进化的方法，减少了对人类经验和任务特异性模型的依赖。通过从反向折叠模型中采样序列，并整合结构和进化约束，AiCE能够识别出高适应性的单突变和多突变。本文将AiCE应用于八项蛋白质工程任务，包括脱氨酶、核定位序列、核酸酶和逆转录酶，涉及从数十到数千个残基的蛋白质，成功率达到11%–88%。此外，本文还开发了用于精准医学和农业的碱基编辑器，包括enABE8e（5-bp编辑窗口）、enSdd6-CBE（保真度提高1.3倍）和enDdd1-DdCBE（线粒体活性最高增强14.3倍）。这些结果表明，AiCE是一种多功能、用户友好的突变设计方法，在效率、可扩展性和通用性方面均优于传统方法。 11. Iterative recombinase technologies for efficient and precise genome engineering across kilobase to megabase scales 用于在千碱基至百万碱基范围内实现高效且精确的基因组工程的迭代重组酶技术 Genome editing technologies face challenges in achieving precise, large-scale DNA manipulations in higher organisms, including inefficiency, limited editing scales and types, and the retention of undesired sequences such as recombination sites (“scars”). Here, we present programmable chromosome engineering (PCE) and RePCE, two programmable chromosome editing systems enabling scarless kilobase-to-megabase DNA manipulations in plants and human cells. Through high-throughput engineering, we obtained Lox sites with a 10-fold reduced reversibility and applied an AI-assisted recombinase engineering method (AiCErec) to generate Cre variants with 3.5 times the recombination efficiency of the wild type. Incorporation of a Re-pegRNA-mediated scar-free strategy further enhanced editing precision, allowing scarless insertions, deletions, replacements, inversions, and translocations at the chromosomal level. Key applications include a 315-kb inversion in rice conferring herbicide resistance, scarless chromosome fusions, and a 12-Mb inversion at human disease-related sites. These advances significantly broaden the scope of genome editing applications in molecular breeding, therapeutic development, and synthetic biology. 基因组编辑技术在高等生物中实现精准、大规模DNA操作时面临诸多挑战，包括效率低下、编辑规模和类型有限，以及可能残留重组位点等非预期序列（即“疤痕”）。本文提出了两种可编程染色体编辑系统——可编程染色体工程（PCE）和RePCE，可在植物和人类细胞中实现无疤痕的千碱基至兆碱基级DNA操作。通过高通量工程改造，本文获得了可逆性降低10倍的Lox位点，并应用人工智能辅助的重组酶工程方法（AiCErec），生成了重组效率为野生型3.5倍的Cre变体。整合Re-pegRNA介导的无疤痕策略进一步提高了编辑精度，可在染色体水平实现无疤痕的插入、缺失、替换、倒位和易位。该系统的关键应用包括：在水稻中实现315kb片段倒位以赋予除草剂抗性，无疤痕染色体融合，以及在人类疾病相关位点实现12Mb片段倒位。这些进展显著拓宽了基因组编辑在分子育种、治疗开发和合成生物学领域的应用范围。 Sep 04, 2025；Volume 188，Issue 18；p4811-5120 Cell共发表20篇，其中包括1篇Review; 13篇Articles; 4篇Resources; 2篇Corrections。 On the cover: While essential roles for microbiome-host interactions are becoming clear, whether animals exploit omnipresent external microbial cues to navigate their surroundings is not well understood. In this issue of Cell, Sepela et al. find that octopuses use “taste by touch” chemotactile receptors to explore environmental microbiomes and distinguish prey or progeny from seafloor rocks and crevices. These distinct microbiome signals differentially activate receptors to drive predation and parental behavior, respectively. This research uncovers broad principles for how animals use environmental microbiomes to inform behavior. Artist credit: Lily Soucy. 封面内容：尽管微生物组与宿主间相互作用的重要性已逐渐明确，但动物是否会利用无处不在的外界微生物信号来导航周围环境，目前尚不清楚。在本期《Cell》杂志中，Sepela等人研究发现，章鱼可通过“触觉味觉”（tastebytouch）化学触觉受体探测环境微生物组，从而区分猎物或后代与海底岩石及岩缝。这些不同的微生物组信号会差异性激活受体，分别调控章鱼的捕食行为与亲代抚育行为。该研究揭示了动物利用环境微生物组指导自身行为的普遍规律。 1. Adaptive radiation and social evolution of the ants 蚂蚁的适应性辐射和社会性进化 Ants originated over 150 million years ago through an irreversible transition to superorganismal colony life. Comparative analyses of 163 ant genomes, including newly generated whole-genome sequences of 145 ant species, reveal extensive genome rearrangements correlated with speciation rates. Meanwhile, conserved syntenic blocks are enriched with co-expressed genes involved in basal metabolism and caste differentiation. Gene families related to digestion, endocrine signaling, cuticular hydrocarbon synthesis, and chemoreception expanded in the ant ancestor, while many caste-associated genes underwent positive selection in the formicoid ancestor. Elaborations and reductions of queen-worker dimorphism and other social traits left convergent signatures of intensified or relaxed selection in conserved signaling and metabolic pathways, suggesting that a core gene set was used to diversify organizational complexity. Previously uncharacterized genetic regulators of caste development were confirmed by functional experiments. This study reconstructs the genetic underpinning of social traits and their integration within gene-regulatory networks shaping caste phenotypes. 蚂蚁起源于1.5亿多年前，通过向超有机体群体生活的不可逆转变实现物种演化。本研究对163个蚂蚁基因组进行比较分析（含145个蚂蚁物种新测定的全基因组序列），结果发现，广泛存在的基因组重排与物种形成速率具有相关性；同时，保守的同线性区块中，富集了参与基础代谢和品级分化的共表达基因。在蚂蚁祖先中，与消化、内分泌信号、表皮碳氢化合物合成及化学感受相关的基因家族发生扩张；而在蚁科（formicoid）祖先中，许多品级相关基因以正选择形式演化。蚁后-工蚁二态性及其他社会性状的强化或弱化，在保守信号通路与代谢通路中留下了选择增强或选择放松的趋同特征，这表明蚂蚁可能通过核心基因集实现群体组织复杂性的多样化。此外，本研究还通过功能实验验证了此前未被鉴定的品级发育遗传调控因子。本研究重新构建了社会性特征的遗传基础，并探讨了这些特征在基因调控网络中的整合情况，从而影响了种群的表型特征。 2. Environmental microbiomes drive chemotactile sensation in octopus 环境微生物群驱动章鱼的化学触觉受体 Microbial communities coat nearly every surface in the environment and have co-existed with animals throughout evolution. Whether animals exploit omnipresent microbial cues to navigate their surroundings is not well understood. Octopuses use “taste-by-touch” chemotactile receptors (CRs) to explore the seafloor, but how they distinguish meaningful surfaces from the rocks and crevices they encounter is unknown. Here, we report that secreted signals from microbiomes of ecologically relevant surfaces activate CRs to guide octopus behavior. Distinct molecules isolated from individual bacterial strains located on prey or eggs bind single CRs in subtly different structural conformations to elicit specific mechanisms of receptor activation, ion permeation and signal transduction, and maternal care and predation behavior. Thus, microbiomes on ecological surfaces act at the level of primary sensory receptors to inform behavior. Our study demonstrates that uncovering interkingdom interactions is essential to understanding how animal sensory systems evolved in a microbe-rich world. 微生物群落几乎覆盖了环境中的所有表面，且在整个进化过程中与动物共存。然而，动物是否会利用这些无处不在的微生物信号来导航周围环境，目前尚不清楚。章鱼通过“触觉味觉”（taste-by-touch）化学触觉受体（chemotactilereceptors,CRs）探索海底，但它们如何从所接触的岩石和岩缝中区分出具有意义的表面，这一机制仍不明确。本研究发现，来自生态相关表面微生物组的分泌信号可激活章鱼的CRs，从而指导其行为。从猎物或卵表面的单一菌株中分离出的特定分子，能以细微不同的结构构象结合单个CRs，进而触发受体激活、离子渗透、信号转导的特定机制，并分别调控章鱼的亲代抚育行为与捕食行为。由此可见，生态表面的微生物组可在初级感觉受体层面发挥作用，为动物行为提供信息。本研究表明，揭示跨生物界（微生物与动物）的相互作用，对于理解动物感觉系统在富含微生物的世界中如何演化至关重要。 3. Scalable generation and functional classification of genetic variants in inborn errors of immunity to accelerate clinical diagnosis and treatment 可扩展的免疫遗传缺陷基因变异生成与功能分类加速临床诊断与治疗 Next-generation sequencing is pivotal for diagnosing inborn errors of immunity (IEI) but predominantly yields variants of uncertain significance (VUS), creating clinical ambiguity. Activated PI3Kδ syndrome (APDS) is caused by gain-of-function (GOF) variants in PIK3CD or PIK3R1, which encode the PI3Kδ heterodimer. We performed massively parallel base editing of PIK3CD/PIK3R1 in human T cells and mapped thousands of variants to a clinically important readout (phospho-AKT/S6), nominating >100 VUS and unannotated variants for functional classification and validating 27 hits. Leniolisib, an FDA-approved PI3Kδ inhibitor, rescued aberrant signaling and dysfunction in GOF-harboring T cells and revealed partially drug-resistant PIK3R1 hotspots that responded to novel combination therapies of leniolisib with mTORC1/2 inhibition. We confirmed these findings in T cells from APDS patients spanning the functional spectrum discovered in the screen. Integrating our screens with population-level genomic studies revealed that APDS may be more prevalent than previously estimated. This work exemplifies a broadly applicable framework for removing ambiguity from sequencing in IEI. 下一代测序技术在原发性免疫缺陷病（inbornerrorsofimmunity,IEI）诊断中具有关键作用，但该技术主要产生意义未明变异（variantsofuncertainsignificance,VUS），导致临床诊断存在不确定性。PI3Kδ激活综合征（activatedPI3Kδsyndrome,APDS）由PIK3CD或PIK3R1基因的功能获得性（gain-of-function,GOF）变异引起，这两个基因分别编码PI3Kδ异二聚体的亚基。本研究在人类T细胞中对PIK3CD/PIK3R1基因进行大规模平行碱基编辑，并将数千种变异与具有临床意义的检测指标（磷酸化AKT/S6，phospho-AKT/S6）相关联，筛选出100多种可用于功能分类的VUS及未注释变异，且验证了其中27种具有功能影响的变异。美国食品药品监督管理局（FDA）已批准的PI3Kδ抑制剂来奥利西布（leniolisib），可纠正携带GOF变异T细胞的异常信号传导与功能缺陷；同时，研究还发现PIK3R1基因中存在部分对药物耐药的热点变异，这些变异可通过来奥利西布与mTORC1/2抑制剂联合使用的新型治疗方案得到改善。本研究在涵盖筛选中发现的全功能谱APDS患者T细胞中，验证了上述结果。将筛选数据与人群水平基因组研究相结合后发现，APDS的患病率可能高于此前预估。该研究建立了一套具有广泛适用性的研究框架，为解决IEI测序诊断中的变异意义不确定性问题提供了重要参考。 4. Pseudouridine RNA avoids immune detection through impaired endolysosomal processing and TLR engagement 假尿嘧啶 RNA 通过抑制内溶酶体加工和 Toll 样受体结合来躲避免疫检测 Recognition of exogenous RNA by Toll-like receptors (TLRs) is central to pathogen defense. Using two distinct binding pockets, TLR7 and TLR8 recognize RNA degradation products generated by endolysosomal nucleases. RNA modifications present in endogenous RNA prevent TLR activation; notably, pseudouridine-containing RNA lacks immunostimulatory activity. Indeed, this property has been critical to the successful implementation of mRNA technology for medical purposes. However, the molecular mechanism for this immune evasion has remained elusive. Here, we report that RNase T2 and PLD exonucleases do not adequately process pseudouridine-containing RNA to generate TLR-agonistic ligands. As a second safety mechanism, TLR8 neglects pseudouridine as a ligand for its first binding pocket and TLR7 neglects pseudouridine-containing RNA as a ligand for its second pocket. Interestingly, the medically used N1-methylpseudouridine also evades RNase T2, PLD3, and PLD4 processing but is able to directly activate TLR8. Taken together, our findings provide a molecular basis for self-avoidance by RNA-sensing TLRs. Toll样受体（Toll-likereceptors,TLRs）对外源RNA的识别是机体抵御病原体的核心环节。TLR7与TLR8通过两个不同的结合口袋，识别内体溶酶体核酸酶产生的RNA降解产物。内源性RNA中存在的修饰可抑制TLR激活，其中值得注意的是，含假尿苷（pseudouridine）的RNA不具备免疫刺激活性。事实上，这一特性对mRNA技术在医学领域的成功应用至关重要。然而，含假尿苷RNA实现免疫规避的分子机制至今尚未明确。本研究发现，核酸酶RNaseT2与PLD外切核酸酶无法充分加工含假尿苷的RNA，因而无法生成可激活TLR的配体。作为第二重安全机制，TLR8不会将假尿苷视为其第一个结合口袋的配体，而TLR7也不会将含假尿苷的RNA视为其第二个结合口袋的配体。有趣的是，医学上常用的N1-甲基假尿苷（N1-methylpseudouridine）同样能规避RNaseT2、PLD3及PLD4的加工，但可直接激活TLR8。综上，本研究结果为RNA感知TLRs如何实现自身免疫规避（避免激活针对内源性RNA的免疫反应）提供了分子层面的解释。 5. Combination antiretroviral therapy and MCL-1 inhibition mitigate HTLV-1 infection in vivo 联合抗逆转录病毒疗法与 MCL-1 抑制可减轻体内 HTLV-1 感染 This study investigated preventative and therapeutic agents against human T cell lymphotropic virus type-1 subtype-C (HTLV-1c) infection. We established and characterized a humanized mouse model of HTLV-1c infection and identified that HTLV-1c disease appears slightly more aggressive than the prevalent HTLV-1 subtype-A (HTLV-1a), which may underpin increased risk for infection-associated pulmonary complications in HTLV-1c. Combination antiretroviral therapy with tenofovir and dolutegravir at clinically relevant doses significantly reduced HTLV-1c transmission and disease progression in vivo. Single-cell RNA sequencing (scRNA-seq) and intracellular flow cytometry identified that HTLV-1c infection leads to dysregulated intrinsic apoptosis in infected cells in vivo. Pharmacological inhibition using BH3 mimetic compounds against MCL-1, but not BCL-2, BCL-XL, or BCL-w, killed HTLV-1c-infected cells in vitro and in vivo and significantly delayed disease progression when combined with tenofovir and dolutegravir in mice. Our data suggest that combination antiretroviral therapy with MCL-1 antagonism may represent an effective, clinically relevant, and potentially curative strategy against HTLV-1c. 本研究针对人T细胞白血病病毒1型C亚型（humanTcelllymphotropicvirustype-1subtype-C,HTLV-1c）感染，开展了预防与治疗药物的相关研究。研究团队建立并鉴定了HTLV-1c感染的人源化小鼠模型，发现HTLV-1c相关疾病的侵袭性略高于流行的HTLV-1A亚型（HTLV-1a），这可能是HTLV-1c感染者发生感染相关肺部并发症风险更高的潜在原因。在体内实验中，采用临床相关剂量的替诺福韦（tenofovir）与多替拉韦（dolutegravir）进行抗逆转录病毒联合治疗，可显著降低HTLV-1c的传播效率并延缓疾病进展。通过单细胞RNA测序（single-cellRNAsequencing,scRNA-seq）与细胞内流式细胞术分析发现，HTLV-1c感染会导致体内受感染细胞的内源性凋亡通路调控异常。进一步研究表明，在体外和体内实验中，使用BH3模拟化合物对髓系细胞白血病1蛋白（MCL-1）进行药物抑制（对BCL-2、BCL-XL或BCL-w无抑制作用），可有效杀伤HTLV-1c感染细胞；且在小鼠模型中，将该抑制方案与替诺福韦、多替拉韦联合使用时，能显著延缓疾病进展。本研究数据提示，抗逆转录病毒联合治疗联合MCL-1拮抗，或可成为针对HTLV-1c的有效、具有临床应用价值且潜在治愈性的治疗策略。 6. Structures of the measles virus polymerase complex with non-nucleoside inhibitors and mechanism of inhibition 麻疹病毒聚合酶复合物与非核苷类抑制剂结合的结构及其抑制机制 The measles virus (MeV), a highly contagious non-segmented negative-sense RNA virus in the Paramyxoviridae family, causes millions of infections annually, with no approved antivirals available. The viral polymerase complex, comprising the large (L) protein and the tetrameric phosphoprotein (P), is a key antiviral target. We determined the cryo-electron microscopy structures of the MeV polymerase complex alone and bound to two non-nucleoside inhibitors, ERDRP-0519 and AS-136A. Inhibitor binding induces a conformational change in the catalytic loop, allosterically locking the polymerase in an inactive “GDN-out” state. These findings led to the proposal that ERDRP-0519 would also be effective against Nipah virus (NiV), a highly pathogenic virus with no available antivirals. This proposal was confirmed by structure determination of the NiV polymerase complex and by inhibition of transcription. 麻疹病毒（measlesvirus,MeV）属于副黏病毒科，是一种具有高度传染性的非分节段负链RNA病毒，每年可导致数百万例感染，目前尚无获批的抗病毒药物。由大蛋白（L蛋白）和四聚体磷蛋白（P蛋白）组成的病毒聚合酶复合物是重要的抗病毒药物靶点。本研究解析了麻疹病毒聚合酶复合物单独存在时，以及与两种非核苷抑制剂（ERDRP-0519和AS-136A）结合后的冷冻电镜结构。结果显示，抑制剂结合会诱导聚合酶催化环发生构象变化，通过别构作用将聚合酶锁定在“GDN-out”的失活状态。基于上述发现，本文推测ERDRP-0519对尼帕病毒（Nipahvirus,NiV）也可能具有抑制效果——尼帕病毒是一种致病性极强且同样无获批抗病毒药物的病毒。这一推测通过两项实验得到证实：一是解析了尼帕病毒聚合酶复合物的结构，二是验证了ERDRP-0519对尼帕病毒转录过程的抑制作用。 7. An alternate receptor for adeno-associated viruses 腺相关病毒的替代受体 Systemic gene therapy using adeno-associated virus (AAV) vectors is approved for the treatment of several genetic disorders, but challenges and toxicities associated with high vector doses remain. We report an alternate receptor for AAV (AAVR2, carboxypeptidase D [CPD]), which is distinct from the multi-serotype AAV receptor (AAVR). AAVR2 enables the transduction of clade E AAVs, including AAV8, and determines an exclusive AAVR-independent transduction pathway for AAV11 and AAV12. We characterized direct binding between the AAV8 capsid and AAVR2 by cryo-electron microscopy (cryo-EM) and identified contact residues. We observed that AAV8 directly binds to the carboxypeptidase-like domain 1 of AAVR2 via its variable region VIII and demonstrated that AAV capsids that lack AAVR2 binding can be bioengineered to engage with AAVR2. Finally, we overexpressed a minimal functional AAVR2 to enhance AAV transduction in vivo. Our study provides insights into AAV biology and clinically deployable solutions to reduce dose-related toxicities associated with AAV vectors. 使用腺相关病毒（adeno-associatedvirus,AAV）载体的全身性基因治疗已获批用于治疗多种遗传性疾病，但高载体剂量相关的挑战与毒性问题仍未解决。本研究报道了一种新的AAV替代受体——AAVR2（即羧肽酶D，carboxypeptidaseD,CPD），该受体与多血清型AAV通用受体（AAVR）完全不同。AAVR2可介导E进化枝AAV（包括AAV8）的转导，并为AAV11和AAV12确定了一条不依赖AAVR的特异性转导通路。通过冷冻电镜（cryo-electronmicroscopy,cryo-EM）技术，本研究明确了AAV8衣壳与AAVR2之间的直接结合，并鉴定出二者结合的关键氨基酸残基。研究发现，AAV8通过其可变区VIII（variableregionVIII）直接结合AAVR2的羧肽酶样结构域1（carboxypeptidase-likedomain1）；同时证实，可通过生物工程改造使原本不结合AAVR2的AAV衣壳获得与AAVR2结合的能力。最后，本研究通过在体内过表达具有最小功能的AAVR2片段，成功增强了AAV的体内转导效率。该研究不仅深化了对AAV生物学机制的理解，更为开发可临床应用的解决方案、降低AAV载体剂量相关毒性提供了重要思路。 8. Engineering yeast multicellular behaviors via synthetic adhesion and contact signaling 通过合成粘附和接触信号调控酵母多细胞行为 Multicellular coordination enhances biological complexity, yet the widely used yeast Saccharomyces cerevisiae possesses limited multicellular capabilities. Here, we expand the possibilities for engineering multicellular behaviors in yeast by developing modular toolkits for two key mechanisms in multicellularity, contact-dependent signaling and specific cell-cell adhesion. MARS (mating-peptide anchored response system) enables contact-dependent signaling via surface-displayed peptides and G protein-coupled receptors, mimicking juxtacrine communication, while Saccharomyces SATURN (adhesion toolkit for multicellular patterning) uses adhesion-protein pairs for the creation of programmable cell aggregation patterns. Combining these allows the construction of multicellular logic circuits, equivalent to developmental programs that lead to cell differentiation based on local population. We further created JUPITER (juxtacrine sensor for protein-protein interaction), a genetic sensor based on MARS and SATURN, for assaying protein-protein interactions and selecting high-affinity nanobody binders. Collectively, these toolkits present versatile building blocks for constructing complex, user-defined multicellular yeast systems and expand the scope of its biotechnological applications. 多细胞协同作用可提高生物复杂性，但广泛应用的酿酒酵母（Saccharomycescerevisiae）的多细胞能力有限。为此，本文针对多细胞生物中的两种关键机制（接触依赖性信号传导和特异性细胞间黏附）开发了模块化工具包，以此拓展酿酒酵母多细胞行为工程改造的可能性。其中，MARS（交配肽锚定响应系统，mating-peptideanchoredresponsesystem）可通过表面展示肽与G蛋白偶联受体实现接触依赖性信号传导，模拟邻分泌通讯；而酿酒酵母SATURN（多细胞模式化黏附工具包，adhesiontoolkitformulticellularpatterning）则利用黏附蛋白对构建可编程的细胞聚集模式。将这两种工具包结合，可构建多细胞逻辑电路，该电路相当于一种发育程序，能根据局部细胞群诱导细胞分化。此外，本文还基于MARS和SATURN构建了JUPITER（蛋白质相互作用邻分泌传感器，juxtacrinesensorforprotein-proteininteraction——这是一种用于检测蛋白质相互作用及筛选高亲和力纳米抗体结合物的遗传传感器。综上，这些工具包为构建复杂的、用户定制化的多细胞酵母系统提供了多功能构建模块，并拓展了酿酒酵母在生物技术领域的应用范围。 9. Optogenetics-enabled discovery of integrated stress response modulators 利用光遗传学技术发现整合应激反应的调节因子 The integrated stress response (ISR) is a conserved stress response that maintains homeostasis in eukaryotic cells. Modulating the ISR holds therapeutic potential for diseases including viral infection, cancer, and neurodegeneration, but few known compounds can do so without toxicity. Here, we present an optogenetic platform for the discovery of compounds that selectively modulate the ISR. Optogenetic clustering of PKR induces ISR-mediated cell death, enabling the high-throughput screening of 370,830 compounds. We identify compounds that potentiate cell death without cytotoxicity across diverse cell types and stressors. Mechanistic studies reveal that these compounds upregulate activating transcription factor 4 (ATF4), sensitizing cells to stress and apoptosis, and identify GCN2 as a molecular target. Additionally, these compounds exhibit antiviral activity, and one compound reduced viral titers in a mouse model of herpesvirus infection. Structure-activity and toxicology studies highlight opportunities to optimize therapeutic efficacy. This work demonstrates an optogenetic approach to drug discovery and introduces ISR potentiators with therapeutic potential. 综合应激反应（ISR）是一种保守的应激反应，可维持真核细胞内稳态。调控ISR对病毒感染、癌症、神经退行性疾病等多种疾病具有治疗潜力，但目前已知的可实现该调控的化合物中，少有化合物能在发挥作用的同时不产生毒性。为此，本文构建了一个光遗传学平台，用于筛选可选择性调控ISR的化合物。通过光遗传学手段诱导蛋白激酶R（PKR）聚集，可引发ISR介导的细胞死亡，这一机制为对370,830种化合物进行高通量筛选提供了可能。本研究筛选出了能增强细胞死亡、且在不同细胞类型及应激源下均无细胞毒性的化合物。机制研究表明，这些化合物可上调活化转录因子4（ATF4），增强细胞对压力及凋亡的敏感性，并证实一般性控制非抑制性蛋白激酶2（GCN2）是其分子靶点。此外，这些化合物还具有抗病毒活性，其中一种化合物在疱疹病毒感染小鼠模型中降低了病毒滴度。构效关系及毒理学研究为优化化合物的治疗效果提供了方向。本研究证实了光遗传学方法在药物研发中的应用价值，并发现了具有治疗潜力的ISR增强剂。 10. Neuroendocrine circuit for sleep-dependent growth hormone release 睡眠调控生长激素释放的神经内分泌回路机制 Sleep is known to promote tissue growth and regulate metabolism, partly by enhancing growth hormone (GH) release, but the underlying circuit mechanism is unknown. We demonstrate how GH release, which is enhanced during both rapid eye movement (REM) and non-REM (NREM) sleep, is regulated by sleep-wake-dependent activity of distinct hypothalamic neurons expressing GH-releasing hormone (GHRH) and somatostatin (SST). SST neurons in the arcuate nucleus suppress GH release by inhibiting nearby GHRH neurons that stimulate GH release, whereas periventricular SST neurons inhibit GH release by projecting to the median eminence. GH release is associated with strong surges of both GHRH and SST activity during REM sleep but moderately increased GHRH and decreased SST activity during NREM sleep. Furthermore, we identified a negative feedback pathway in which GH enhances the excitability of locus coeruleus neurons and increases wakefulness. These results elucidate a circuit mechanism underlying bidirectional interactions between sleep and hormone regulation. 已知睡眠可促进组织生长并调节代谢，其部分机制与睡眠增强生长激素（GH）释放有关，但该过程背后的神经环路机制尚未明确。本研究阐明了在快速眼动（REM）睡眠和非快速眼动（NREM）睡眠期间均会增强的GH释放，是如何受表达生长激素释放激素（GHRH）和生长抑素（SST）的不同下丘脑神经元的“睡眠-觉醒”依赖性活动调控的。具体而言，弓状核中的SST神经元通过抑制邻近的、可刺激GH释放的GHRH神经元，从而抑制GH释放；而室周区的SST神经元则通过投射至正中隆起发挥GH释放抑制作用。在REM睡眠期间，GH释放与GHRH和SST神经元的强烈活动峰相关；而在NREM睡眠期间，GH释放则与GHRH神经元活动中度增强、SST神经元活动减弱相关。此外，本研究还发现了一条负反馈通路：GH可增强蓝斑核神经元的兴奋性，并延长觉醒状态。这些结果揭示了睡眠与激素调控之间双向互作的潜在神经环路机制。 11. Single-cell multiregion epigenomic rewiring in Alzheimer’s disease progression and cognitive resilience 单细胞多区域表观基因组重塑在阿尔茨海默病进展与认知恢复中的作用 Alzheimer’s disease (AD) is a neurodegenerative disorder characterized by progressive cognitive decline, yet its epigenetic underpinnings remain elusive. Here, we generate and integrate single-cell epigenomic and transcriptomic profiles of 3.5 million cells from 384 postmortem brain samples across 6 regions in 111 AD and control individuals. We identify over 1 million candidate cis-regulatory elements (cCREs), organized into 123 regulatory modules across 67 cell subtypes. We define large-scale epigenomic compartments and single-cell epigenomic information and delineate their dynamics in AD, revealing widespread epigenome relaxation and brain-region-specific and cell-type-specific epigenomic erosion signatures during AD progression. These epigenomic stability dynamics are closely associated with cell-type proportion changes, glial cell-state transitions, and coordinated epigenomic and transcriptomic dysregulation linked to AD pathology, cognitive impairment, and cognitive resilience. This study provides critical insights into AD progression and cognitive resilience, presenting a comprehensive single-cell multiomic atlas to advance the understanding of AD. 阿尔茨海默病（AD）是一种以进行性认知功能下降为特征的神经退行性疾病，但其表观遗传基础仍不明确。本研究对111名AD患者和健康对照者的384份死后脑组织样本（涵盖6个脑区）进行分析，生成并整合了350万个细胞的单细胞表观基因组图谱与转录组图谱。研究鉴定出超过100万个候选顺式调控元件（cCRE），这些元件在67种细胞亚型中可归类为123个调控模块。通过明确大规模表观基因组区室及单细胞表观基因组信息，并描述其在AD中的动态变化，本研究发现：在AD进展过程中，表观基因组出现广泛松弛现象，且存在脑区特异性和细胞类型特异性的表观基因组侵蚀特征。这些表观基因组稳定性动态变化与以下因素密切相关：细胞类型比例改变、神经胶质细胞状态转换，以及与AD病理特征、认知障碍和认知韧性相关的表观基因组与转录组协同失调。本研究为理解AD进展机制和认知韧性提供了关键见解，同时构建了全面的单细胞多组学图谱，助力深化对AD的认知。 12. Brain endothelial gap junction coupling enables rapid vasodilation propagation during neurovascular coupling 脑血管内皮细胞间隙连接的耦合作用促进了神经血管耦合过程中血管舒张信号的快速传播 To meet the brain’s moment-to-moment energy demand, neural activation rapidly increases local blood flow. This process, known as neurovascular coupling, involves rapid, coordinated vasodilation of the brain’s arterial network. Here, we demonstrate that endothelial gap junction coupling enables long-range propagation of vasodilation signals through the vasculature during neurovascular coupling. The molecular composition of these gap junctions is zonated along the arterio-venous axis, with arteries being the most strongly coupled segment. Using optogenetics and visual stimuli in awake mice, we found that acute, arterial endothelial cell type-specific deletion of Cx37 and Cx40 abolishes arterial gap junction coupling and results in impaired vasodilation. Specifically, we demonstrated that arterial endothelial gap junction coupling determines both the speed and the spatial extent of vasodilation propagation elicited by neural activity. These findings indicate that endothelial gap junctions serve as a signaling highway for neurovascular coupling, enabling flexible and efficient distribution of limited energetic resources. 为满足大脑实时的能量需求，神经激活会迅速增加局部血流。这一被称为“神经血管耦合”的过程，涉及大脑动脉网络快速且协同的舒张。本研究证实，在神经血管耦合过程中，内皮缝隙连接可通过血管系统实现血管舒张信号的长距离传导。这些缝隙连接的分子组成沿动静脉轴呈分区分布，其中动脉是耦合最强的区段。在清醒小鼠模型中，本研究结合光遗传学技术与视觉刺激实验发现：对动脉内皮细胞特异性敲除连接蛋白37（Cx37）和连接蛋白40（Cx40），会完全破坏动脉缝隙连接耦合，并导致血管舒张功能受损。具体而言，研究证实动脉内皮缝隙连接耦合不仅决定了神经活动引发的血管舒张传导速度，还决定了其空间范围。这些发现表明，内皮缝隙连接可作为神经血管耦合的“信号通路”，为大脑灵活且高效分配有限能量资源提供支持。 13. Neuroendocrine cells orchestrate regeneration through Desert hedgehog signaling 神经内分泌细胞通过Desert hedgehog信号通路调控再生过程 Understanding the mechanisms underlying mammalian regeneration may enable development of novel regenerative therapies. We present a mechanism wherein Desert hedgehog (Dhh), secreted from epithelial neuroendocrine cells, elicits a regenerative/protective response from mesenchymal cells. In mammalian airway, this mesenchymal response strikingly amplifies the initial signal from rare neuroendocrine cells to activate the entire tissue for survival and regeneration upon injury from SO2 gas inhalation or following influenza or SARS-CoV-2 infection. Similar epithelial-mesenchymal feedback (EMF) signaling directed by Dhh from neuroendocrine β cells likewise protects mouse pancreatic islets from streptozotocin (STZ) injury. A role for EMF signaling in human pancreatic islets is suggested by higher incidence of diabetes in patients treated with Hedgehog pathway inhibitors. Remarkably, EMF augmentation by small-molecule Hedgehog pathway agonism protects against STZ injury of pancreatic β cells and shields against airway injury from SO2 and influenza infection, with potential protective/therapeutic utility in chemical or infectious airway injury and in diabetes. 深入理解哺乳动物再生的潜在机制，有望推动新型再生疗法的研发。本研究提出一种机制：由上皮神经内分泌细胞分泌的Deserthedgehog（Dhh），可诱导间质细胞产生再生/保护反应。在哺乳动物气道中，这种间质反应能显著放大来自少量神经内分泌细胞的初始信号，从而激活整个气道组织，使其在二氧化硫（SO2）吸入损伤、流感病毒感染或新型冠状病毒（SARS-CoV-2）感染后实现存活与再生。类似地，由神经内分泌β细胞分泌的Dhh所介导的上皮-间质反馈（EMF）信号，也能保护小鼠胰岛免受链脲佐菌素（STZ）损伤。Hedgehog通路抑制剂治疗患者的糖尿病发病率更高这一现象，提示EMF信号在人胰岛中可能同样发挥作用。值得注意的是，通过小分子激动剂激活Hedgehog通路以增强EMF信号，不仅能保护胰腺β细胞免受STZ损伤，还能抵御SO2及流感病毒所致的气道损伤。这一机制在化学性或感染性气道损伤及糖尿病的防治中，具有潜在的保护/治疗价值。 14. Senescence-resistant human mesenchymal progenitor cells counter aging in primates 抗衰老的人间充质祖细胞在灵长类动物中对抗衰老 Aging is characterized by a deterioration of stem cell function, but the feasibility of replenishing these cells to counteract aging remains poorly defined. Our study addresses this gap by developing senescence (seno)-resistant human mesenchymal progenitor cells (SRCs), genetically fortified to enhance cellular resilience. In a 44-week trial, we intravenously delivered SRCs to aged macaques, noting a systemic reduction in aging indicators, such as cellular senescence, chronic inflammation, and tissue degeneration, without any detected adverse effects. Notably, SRC treatment enhanced brain architecture and cognitive function and alleviated the reproductive system decline. The restorative effects of SRCs are partly attributed to their exosomes, which combat cellular senescence. This study provides initial evidence that genetically modified human mesenchymal progenitors can slow primate aging, highlighting the therapeutic potential of regenerative approaches in combating age-related health decline. 衰老的特征之一是干细胞功能衰退，但通过补充此类细胞来对抗衰老的可行性仍不明确。为填补这一研究空白，本研究通过基因修饰增强人间充质祖细胞（SRCs）的抗逆能力构建了抗衰老（seno-resistant）人间充质祖细胞（SRCs）。在一项为期44周的试验中，本研究向老年猕猴静脉输注SRCs，结果显示其体内衰老指标（如细胞衰老、慢性炎症及组织退化）呈全身性降低，且未检测到任何不良反应。值得注意的是，SRCs治疗可改善老年猕猴的脑结构与认知功能，并缓解其生殖系统衰退。SRCs的修复作用部分源于其分泌的外泌体，该外泌体具有对抗细胞衰老的功能。本研究提供了初步证据，证实经基因修饰的人间充质祖细胞可延缓灵长类动物衰老，同时凸显了再生医学手段在对抗年龄相关健康衰退方面的治疗潜力。 汇报人：吴桂儀 导师：赵宇 审核：李向东  任建君  END        阅读最新文献，紧跟前沿进展，这是一名研究者必须具备的习惯和要求。我们华西医院耳鼻咽喉头颈外科的硕士、博士研究生和博士后们自2019年以来，每周开展一次文献泛读和文献精读分享会，至今已累计开展了200多次。2023年9月13日开始，本科室陆续将其进行整理，同步推出在线前沿速递和文献解读板块。通过这种学习和分享的方式，使汇报者和大家都能对近期权威期刊发表的高质量研究有所了解，同时也是学习其他优秀研究者思路、方法和理论的良好手段。希望通过这种形式，把科内的分享扩大到所有的读者，一起学习，共同进步！ 华西医院耳鼻咽喉头颈外科  2023年9月13日

Leiden, the Netherlands, October 20, 2025: Pharming Group N.V. (“Pharming” or “the Company”) (Euronext: PHARM; Nasdaq: PHAR) today announced that 12 abstracts have been accepted for presentation at the American College of Allergy, Asthma & Immunology (ACAAI) 2025 Annual Scientific Meeting taking place in Orlando, Florida on November 6-10. Five posters will present positive new clinical, economic, and comparative data for RUCONEST® (recombinant C1 esterase inhibitor) and its role in on-demand hereditary angioedema (HAE) treatment. Seven posters will highlight new evidence on the real-world effectiveness of Joenja® (leniolisib), including additional results from the Phase III pediatric trial, as well as advancing understanding of the pediatric and caregiver burden in activated phosphoinositide 3-kinase delta (PI3Kδ) syndrome (APDS). Anurag Relan, Chief Medical Officer of Pharming, commented:“We are proud that our scientific contributions in both hereditary angioedema (HAE) and activated phosphoinositide 3-kinase delta (PI3Kδ) syndrome (APDS) have been recognized with a significant number of abstract acceptances at this year’s ACAAI. The work underscores the rigor of our research and our commitment to advancing patient care. We look forward to the new data being presented to the medical community during the meeting in November.” Presentation Details: RUCONEST® Study Title: Indirect Treatment Comparison (ITC) of Recombinant C1 Inhibitor and Sebetralstat for HAE On-Demand Therapy Presenting Author: Dr John Anderson, MD, AllerVie Health, Birmingham, AL, USA and University of Alabama at Birmingham, Birmingham, AL, USAPoster Date/Time: Friday, November 7, 2025, 4:05 pm (EST)Monitor: 14 Study Title: Cost-Effectiveness of rhC1-INH Versus Sebetralstat for Treatment of HAE Attacks Presenting Author: Dr Jonathan A. Bernstein, MD, Advanced Allergy Services, LLC, Cincinnati, OH, USA and Bernstein Clinical Research Center, LLC, Cincinnati, OH, USAPoster Date/Time: Friday, November 7, 2025, 4:05 pm (EST)Monitor: 16 Study Title: Re-Analysis of rhC1-INH Clinical Data With Contemporary Time-to-Event Endpoint DefinitionsPresenting Author: Joseph R. Harper, PharmD, Pharming Healthcare, Inc. Warren, NJ, USAPoster Date/Time: Friday, November 7, 2025, 5:05 pm (EST)Monitor: 15 Study Title: Mapping Patient-Reported Outcome Measures Across Clinical Trials in HAE Presenting Author: Dr Michael Manning, MD, Allergy Asthma & Immunology Associates, LTD, Scottsdale, AZ, USA and University of Arizona College of Medicine-Phoenix, Phoenix, AZ, USA Poster Date/Time: Sunday, November 9, 2025, 11:45 am (EST)Monitor: 13 Study Title: Clinician Perspectives on Modifiers of Observed Treatment Effect in On- Demand HAE Therapy TrialsPresenting Author: Dr Raffi Tachdjian, MD, MPH, Division of Allergy and Clinical Immunology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA, and Division of Allergy & Immunology, Providence Saint John’s Health Center, Santa Monica, CA, USAPoster Date/Time: Saturday, November 8, 2025, 12:15 pm (EST)Monitor: 13 Joenja® (leniolisib)Study Title: Effectiveness of Leniolisib in Reducing Infections Among Patients With APDS Presenting Author: Dr Niraj C. Patel, MD, MS, Division of Pediatric Allergy and Immunology, Duke University, Durham, NC, USAPoster Date/Time: Friday, November 7, 3:50 pm (EST)Monitor: 20 Study Title: Impact of Leniolisib on Healthcare Utilization in Patients With APDSPresenting Author: Ami Claxton, PhD, MS, Pharming Healthcare, Inc., Warren, NJ, USA Poster Date/Time: Friday, November 7, 2025, 4:05 pm (EST) Monitor: 20 Study Title: Symptoms/Quality of Life in Pediatric Patients With APDS Receiving LeniolisibPresenting Author: Jason Bradt, MD , Pharming Healthcare, Inc., Warren, NJ, USA Poster Date/Time: Friday, November 7, 2025, 4:35 pm (EST) Monitor: 20 Study Title: Adult/Pediatric Perspectives and Experiences With APDS and Leniolisib: APPEAL Presenting Author: Amanda Harrington, PhD, Pharming Healthcare Inc., Warren, NJ, USAPoster Date/Time: Friday, November 7, 2025, 2:35 pm (EST) Monitor: 20 Study Title: APDS Burden of Illness: Pediatric and Adolescent Caregiver PerspectivesPresenting Author: Dr Joud Hajjar, MD, PhD, MS, Section of Immunology, Allergy and Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USAPoster Date/Time: Friday, November 7, 2025, 4:20 pm (EST) Monitor: 20 Study Title: Real-World Adherence and Persistence With Leniolisib in Patients With APDSPresenting Author: Jessica Kuivinen, PharmD, PANTHERx Rare Pharmacy, Pittsburgh, PA, USAPoster Date/Time: Saturday, November 8, 2025, 12:15 pm (EST)Monitor: 17 Study Title: Characterization of Activated Phosphoinositide 3-Kinase Delta Syndrome in the APDS-CHOIR Clinical Outcomes RegistryPresenting Author: Kelli Williams, MD, Department of Pediatrics, Medical University of South Carolina, Charleston, SC, USAPoster Date/Time: Friday, November 7, 2025, 14:50 pm (EST)Monitor: 20 In addition to displaying in the exhibit hall at the noted times, ePosters will be accessible online and on demand to registered attendees on Thursday, November 6, 2025, beginning at 08:00 EST on ACAAI’s website. About Hereditary Angioedema (HAE)Hereditary Angioedema (HAE) is a rare genetic disorder.1 The condition is caused by a deficiency of the C1 esterase inhibitor protein, which is normally present in blood and helps control inflammation (swelling) and parts of the immune system. Because defective C1-Inhibitor does not adequately perform its regulatory function, a biochemical imbalance can occur and produce unwanted peptides that induce the capillaries to release fluids into surrounding tissue, thereby causing swelling or edema.2 HAE is characterized by spontaneous and recurrent episodes of swelling (edema attacks) of the skin in different parts of the body, as well as in the airways and internal organs. Edema of the skin usually affects the extremities, the face, and the genitals. Almost all HAE patients suffer from bouts of severe abdominal pain, nausea, vomiting and diarrhea caused by swelling of the intestinal wall.3 Edema of the throat, nose or tongue is particularly dangerous and potentially life-threatening and can lead to obstruction of the airway passages.4 Although there is currently no known cure for HAE, it is possible to treat the symptoms associated with angioedema attacks.5 HAE affects about 1 in 10,000 to 1 in 50,000 people worldwide.6 HAE is often misdiagnosed as the symptoms are similar to many other common conditions such as allergies or appendicitis resulting in diagnostic delay.7 About RUCONEST®RUCONEST® is a recombinant C1 esterase inhibitor (rhC1INH) protein replacement therapy indicated for the treatment of acute attacks in adult and adolescent patients with hereditary angioedema (HAE). RUCONEST® is approved in the U.S., Europe and the UK and is the only recombinant C1 esterase inhibitor worldwide. RUCONEST® is delivered intravenously and is immediately and completely bioavailable enabling rapid intervention at the onset of an HAE attack. At the recommended dose of 50 U/kg, RUCONEST® has been shown to normalize C1INH activity levels, which are clinically relevant in the treatment of HAE. By irreversibly binding to and deactivating key mediators such as coagulation factor FXII and kallikrein, RUCONEST® halts the production of bradykinin and other inflammatory peptides, thereby stopping the progression of the attack. RUCONEST® is not indicated for the treatment of laryngeal attacks, as effectiveness in this subset of patients was not established in clinical studies. 8 Please see Full Prescribing Information and Patient Product Information here About Activated Phosphoinositide 3-Kinase δ Syndrome (APDS) APDS is a rare primary immunodeficiency that was first characterized in 2013. APDS is caused by variants in either one of two identified genes known as PIK3CD or PIK3R1, which are vital to the development and function of immune cells in the body. Variants of these genes lead to hyperactivity of the PI3Kδ (phosphoinositide 3-kinase delta) pathway, which causes immune cells to fail to mature and function properly, leading to immunodeficiency and dysregulation9,10,11 APDS is characterized by a variety of symptoms, including severe, recurrent sinopulmonary infections, lymphoproliferation, autoimmunity, and enteropathy.12,13 Because these symptoms can be associated with a variety of conditions, including other primary immunodeficiencies, it has been reported that people with APDS are frequently misdiagnosed and suffer a median 7-year diagnostic delay.14 As APDS is a progressive disease, this delay may lead to an accumulation of damage over time, including permanent lung damage and lymphoma.12-15 A definitive diagnosis can be made through genetic testing. APDS affects approximately 1 to 2 people per million worldwide. About leniolisibLeniolisib is an oral small molecule phosphoinositide 3-kinase delta (PI3Kẟ) inhibitor approved in the U.S., U.K., Australia and Israel as the first and only targeted treatment of activated phosphoinositide 3-kinase delta (PI3Kδ) syndrome (APDS) in adult and pediatric patients 12 years of age and older. Leniolisib inhibits the production of phosphatidylinositol-3-4-5-trisphosphate, which serves as an important cellular messenger and regulates a multitude of cell functions such as proliferation, differentiation, cytokine production, cell survival, angiogenesis, and metabolism. Results from a randomized, placebo-controlled Phase III clinical trial demonstrated statistically significant improvement in the coprimary endpoints, reflecting a favorable impact on the immune dysregulation and deficiency seen in these patients, and interim open label extension data has supported the safety and tolerability of long-term leniolisib administration.16,17 Leniolisib is currently under regulatory review in the European Economic Area, Japan, Canada and several other countries for APDS. Leniolisib is also being evaluated in two Phase III clinical trials in children with APDS and in two Phase II clinical trials in primary immunodeficiencies (PIDs) with immune dysregulation. The safety and efficacy of leniolisib has not been established for PIDs with immune dysregulation beyond APDS. About Pharming Group N.V. Pharming Group is a global biopharmaceutical company dedicated to transforming the lives of patients with rare, debilitating, and life-threatening diseases. We are developing and commercializing a portfolio of innovative medicines, including small molecules and biologics. Pharming is headquartered in Leiden, the Netherlands, with a significant proportion of its employees based in the U.S. For more information, visit www.pharming.com and find us on LinkedIn. Forward-Looking Statements   This press release may contain forward-looking statements. Forward-looking statements are statements of future expectations that are based on management’s current expectations and assumptions and involve known and unknown risks and uncertainties that could cause actual results, performance, or events to differ materially from those expressed or implied in these statements. These forward-looking statements are identified by their use of terms and phrases such as “aim”, “ambition”, ‘‘anticipate’’, ‘‘believe’’, ‘‘could’’, ‘‘estimate’’, ‘‘expect’’, ‘‘goals’’, ‘‘intend’’, ‘‘may’’, “milestones”, ‘‘objectives’’, ‘‘outlook’’, ‘‘plan’’, ‘‘probably’’, ‘‘project’’, ‘‘risks’’, “schedule”, ‘‘seek’’, ‘‘should’’, ‘‘target’’, ‘‘will’’ and similar terms and phrases. Examples of forward-looking statements may include statements with respect to timing and progress of Pharming's preclinical studies and clinical trials of its product candidates, Pharming's clinical and commercial prospects, and Pharming's expectations regarding its projected working capital requirements and cash resources, which statements are subject to a number of risks, uncertainties and assumptions, including, but not limited to the scope, progress and expansion of Pharming's clinical trials and ramifications for the cost thereof; and clinical, scientific, regulatory, commercial, competitive and technical developments. In light of these risks and uncertainties, and other risks and uncertainties that are described in Pharming's 2024 Annual Report and the Annual Report on Form 20-F for the year ended December 31, 2024, filed with the U.S. Securities and Exchange Commission, the events and circumstances discussed in such forward-looking statements may not occur, and Pharming's actual results could differ materially and adversely from those anticipated or implied thereby. All forward-looking statements contained in this press release are expressly qualified in their entirety by the cautionary statements contained or referred to in this section. Readers should not place undue reliance on forward-looking statements. Any forward-looking statements speak only as of the date of this press release and are based on information available to Pharming as of the date of this release. Pharming does not undertake any obligation to publicly update or revise any forward-looking statement as a result of new information, future events or other information. References Busse PJ, et al. J Allergy Clin Immunol Pract 2021;9:132-50.Nature Reviews Drug Discovery. (2025). Targeting plasma kallikrein in hereditary angioedema. Nature Portfolio. https://www.nature.com/articles/d41573-025-00114-xGARD – Genetic and Rare Diseases Information Center. (n.d.). Hereditary angioneurotic edema. U.S. National Institutes of Health. https://rarediseases.info.nih.gov/diseases/5979/hereditary-angioneurotic-edemaMedlinePlus Genetics. (n.d.). Hereditary angioedema type 3. U.S. National Library of Medicine. https://www.ncbi.nlm.nih.gov/medgen/346653Beard, N., Frese, M., Smertina, E., Mere, P., Katelaris, C., & Mills, K. (2022). Interventions for the long-term prevention of hereditary angioedema attacks. Cochrane Database of Systematic Reviews, 11, CD013403. https://doi.org/10.1002/14651858.CD013403.pub2Nature Reviews Drug Discovery. (2025). Hereditary angioedema: A rare disease with unmet needs. Nature Portfolio. https://www.nature.com/articles/d41573-025-00151-6Nature Reviews Drug Discovery. (2024). Improving diagnosis of hereditary angioedema. Nature Portfolio. https://www.nature.com/articles/d41573-024-00101-8RUCONEST. Prescribing Information. Pharming Healthcare, Inc. 2020.Lucas CL, et al. Nat Immunol. 2014;15(1):88-97.Elkaim E, et al. J Allergy Clin Immunol. 2016;138(1):210-218.Nunes-Santos C, Uzel G, Rosenzweig SD. J Allergy Clin Immunol. 2019;143(5):1676-1687. Coulter TI, et al. J Allergy Clin Immunol. 2017;139(2):597-606.Maccari ME, et al. Front Immunol. 2018;9:543.Jamee M, et al. Clin Rev Allergy Immunol. 2020 Dec;59(3):323-333.Condliffe AM, Chandra A. Front Immunol. 2018;9:338.Rao VK, et al Blood. 2023 Mar 2;141(9):971-983.Rao VK, et al. J Allergy Clin Immunol 2024;153:265-74. For further public information, contact:Pharming Group, Leiden, the NetherlandsMichael Levitan, VP Investor Relations & Corporate CommunicationsT: +1 (908) 705 1696 Saskia Mehring, Corporate Communications ManagerT: +31 6 28 32 60 41 E: investor@pharming.com LifeSpring Life Sciences Communication, Amsterdam, the NetherlandsLeon MelensT: +31 6 53 81 64 27E: pharming@lifespring.nl US PREthan MetelenisT: +1 (917) 882-9038E: Ethan.Metelenis@precisionaq.com Attachment Pharming Group announces presentations at ACAAI_EN_20OCT2025