原创 张玉忠 华西医院耳鼻喉科

华西耳鼻喉前沿学术速递——文献导读（第60期）

2024年9月-11月，CELL（187卷：18-24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，2023年影响因子为45.5。

Sep 05, 2024；Volume 187, Issue 18；p4813-5118

Cell共发表21篇，其中包括1篇Stories; 4篇Previews; 1篇Review; 14篇Articles; 1篇Resources。

On the cover: In this issue of Cell, Wang, Cooper, Farrell et al. discover rare but potent neutralizing antibodies generated during malaria infection that target the key merozoite invasion protein RH5 and block invasion of erythrocytes. Also in this issue, Barrett et al. perform a deep analysis of the landscape of vaccine-induced antibody responses to RH5 and identify an IgG gene signature used by the most potent antibodies. The cover image shows a Plasmodium falciparum merozoite invading an erythrocyte, with the merozoite apex reoriented towards the surface of the erythrocyte. Image resources: Elizabeth Fischer, Andrew Cooper, Ababacar Diouf, and Alan Hoofring.

在本期《Cell》杂志中，Wang、Cooper、Farrell等人发现了在疟疾感染过程中产生的稀有但强效的中和抗体，这些抗体靶向关键的疟原虫裂殖子侵袭蛋白RH5，并阻止对红细胞的侵袭。本期杂志中，Barrett等人深入分析了疫苗诱导的RH5抗体反应图谱，并鉴定出最强效抗体使用的IgG基因特征。封面图像展示了疟原虫裂殖子侵袭红细胞的过程，其中裂殖子的顶端重新定位朝向红细胞表面。图像来源：Elizabeth Fischer、Andrew Cooper、Ababacar Diouf和Alan Hoofring。

1.Allogeneic CD19-targeted CAR-T therapy in patients with severe myositis and systemic sclerosis

同种异体的靶向CD19的CAR-T疗法治疗严重肌炎和系统性硬化症患者

Allogeneic chimeric antigen receptor (CAR)-T cells hold great promise for expanding the accessibility of CAR-T therapy, whereas the risks of allograft rejection have hampered its application. Here, we genetically engineered healthy-donor-derived, CD19-targeting CAR-T cells using CRISPR-Cas9 to address the issue of immune rejection and treated one patient with refractory immune-mediated necrotizing myopathy and two patients with diffuse cutaneous systemic sclerosis with these cells. This study was registered at ClinicalTrials.gov (NCT05859997). The infused cells persisted for over 3 months, achieving complete B cell depletion within 2 weeks of treatment. During the 6-month follow-up, we observed deep remission without cytokine release syndrome or other serious adverse events in all three patients, primarily shown by the significant improvement in the clinical response index scores for the two diseases, respectively, and supported by the observations of reversal of inflammation and fibrosis. Our results demonstrate the high safety and promising immune modulatory effect of the off-the-shelf CAR-T cells in treating severe refractory autoimmune diseases.

同种异体嵌合抗原受体（CAR-T）细胞在扩大CAR-T治疗的可及性方面具有巨大的前景，然而同种异体排斥反应阻碍了其应用。研究人员使用CRISPR-Cas9对健康供体来源的靶向CD19的CAR-T细胞进行基因工程改造，以解决免疫排斥问题，并用这些细胞治疗了一名难治性免疫介导的坏死性肌病患者和两名弥漫性皮肤系统性硬化症患者。注入的细胞持续了3个多月，在治疗2周内实现了B细胞的完全耗竭。在6个月的随访期间，研究人员观察到所有三名患者均出现深度缓解，没有细胞因子释放综合征或其他严重不良事件，主要表现为两种疾病的临床反应指数评分分别显著改善，并观察到炎症和纤维化的逆转。总之，这一研究结果表明，改造后的CAR-T细胞在治疗严重难治性自身免疫性疾病方面具有很高的安全性和有前景的免疫调节作用。

2. Neoadjuvant PARPi or chemotherapy in ovarian cancer informs targeting effector Treg cells for homologous-recombination-deficient tumors

卵巢癌新辅助PARPi或化疗为靶向效应Treg细胞治疗同源重组缺陷肿瘤提供依据

Homologous recombination deficiency (HRD) is prevalent in cancer, sensitizing tumor cells to poly (ADP-ribose) polymerase (PARP) inhibition. However, the impact of HRD and related therapies on the tumor microenvironment (TME) remains elusive. Our study generates single-cell gene expression and T cell receptor profiles, along with validatory multimodal datasets from >100 high-grade serous ovarian cancer (HGSOC) samples, primarily from a phase II clinical trial (NCT04507841). Neoadjuvant monotherapy with the PARP inhibitor (PARPi) niraparib achieves impressive 62.5% and 73.6% response rates per RECIST v.1.1 and GCIG CA125, respectively. We identify effector regulatory T cells (eTregs) as key responders to HRD and neoadjuvant therapies, co-occurring with other tumor-reactive T cells, particularly terminally exhausted CD8+ T cells (Tex). TME-wide interferon signaling correlates with cancer cells upregulating MHC class II and co-inhibitory ligands, potentially driving Treg and Tex fates. Depleting eTregs in HRD mouse models, with or without PARP inhibition, significantly suppresses tumor growth without observable toxicities, underscoring the potential of eTreg-focused therapeutics for HGSOC and other HRD-related tumors.

同源重组缺陷（HRD）在癌症中普遍存在，使肿瘤细胞对多聚ADP-核糖聚合酶（PARP）抑制敏感。然而，HRD及相关疗法对肿瘤微环境（TME）的影响尚不清楚。研究人员分析了单细胞基因表达和T细胞受体谱，并使用了来自超过100个高级别浆液性卵巢癌样本的多模式数据集进行验证，这些样本主要来自一项II期临床试验。新辅助单药治疗使用PARP抑制剂（PARPi）尼拉帕利，在RECIST v.1.1（Response Evaluation Criteria in Solid Tumors, 实体瘤疗效评价标准 v1.1）和GCIG CA125（Gynecologic Cancer InterGroup CA125 标准）中，分别实现了62.5%和73.6%的显著效率。效应调节性T细胞（eTreg）是对HRD和新辅助疗法的关键响应者，伴随着其他肿瘤反应性T细胞，特别是终末衰竭的CD8+ T细胞（Tex）。整个TME中的干扰素信号与癌细胞上调MHC II类分子和共抑制配体相关，可能驱动Treg和Tex的命运。总之，在HRD小鼠模型中，无论是否伴随使用PARP抑制，耗竭eTreg都显著抑制了肿瘤生长且无明显毒性，这突显了以eTreg为靶点的疗法具有治疗高级别浆液性卵巢癌及其他HRD相关肿瘤的潜力。

3.TULIPs decorate the three-dimensional genome of PFA ependymoma

TULIPs修饰了PFA室管膜瘤的三维基因组

Posterior fossa group A (PFA) ependymoma is a lethal brain cancer diagnosed in infants and young children. The lack of driver events in the PFA linear genome led us to search its 3D genome for characteristic features. Here, we reconstructed 3D genomes from diverse childhood tumor types and uncovered a global topology in PFA that is highly reminiscent of stem and progenitor cells in a variety of human tissues. A remarkable feature exclusively present in PFA are type B ultra long-range interactions in PFAs (TULIPs), regions separated by great distances along the linear genome that interact with each other in the 3D nuclear space with surprising strength. TULIPs occur in all PFA samples and recur at predictable genomic coordinates, and their formation is induced by expression of EZHIP. The universality of TULIPs across PFA samples suggests a conservation of molecular principles that could be exploited therapeutically.

颅后窝A组室管膜瘤（PFA）是一种婴幼儿致命的癌症。由于PFA线性基因组中缺乏驱动因素事件，研究人员只能通过搜索其3D基因组以寻找特征。该篇研究中，作者重建了不同儿童肿瘤类型的3D基因组，并揭示了PFA的全局拓扑结构，这与各种人类组织中的干细胞和祖细胞高度相似。PFA独有的一个显著特征是PFA中的B型超远程相互作用（TULIPs），这些区域沿着线性基因组相距很远，在3D核空间中存在强烈的相互作用。TULIPs发生在所有PFA样本中，并在可预测的基因组坐标上重复出现，表明它们的形成是由EZHIP的表达诱导的。总之，TULIPs在PFA样本中的普遍性表明了一种分子原理的保守性，可以在治疗中加以利用。

4.The choroid plexus synergizes with immune cells during neuroinflammation

脉络丛在神经炎症期间与免疫细胞协同作用

The choroid plexus (ChP) is a vital brain barrier and source of cerebrospinal fluid (CSF). Here, we use longitudinal two-photon imaging in awake mice and single-cell transcriptomics to elucidate the mechanisms of ChP regulation of brain inflammation. We used intracerebroventricular injections of lipopolysaccharides (LPS) to model meningitis in mice and observed that neutrophils and monocytes accumulated in the ChP stroma and surged across the epithelial barrier into the CSF. Bi-directional recruitment of monocytes from the periphery and, unexpectedly, macrophages from the CSF to the ChP helped eliminate neutrophils and repair the barrier. Transcriptomic analyses detailed the molecular steps accompanying this process and revealed that ChP epithelial cells transiently specialize to nurture immune cells, coordinating their recruitment, survival, and differentiation as well as regulation of the tight junctions that control the permeability of the ChP brain barrier. Collectively, we provide a mechanistic understanding and a comprehensive roadmap of neuroinflammation at the ChP brain barrier.

脉络丛（ChP）是重要的脑屏障和脑脊液（CSF）的来源。研究人员使用清醒小鼠的纵向双光子成像和单细胞转录组学，来阐明脉络丛调节脑炎症的机制。研究人员通过在侧脑室注射脂多糖来模拟小鼠脑膜炎，并观察到中性粒细胞和单核细胞在脉络丛基质中积聚，并穿过上皮屏障涌入CSF。来自外周的单核细胞被双向募集到脉络丛，并且和来自脑脊液的巨噬细胞也被募集到脉络丛，这种双向募集有助于消除中性粒细胞并修复屏障。转录组学分析详细描述了这一过程的分子步骤，并揭示了脉络丛上皮细胞短暂地发生功能特化以培养免疫细胞，协调它们的募集、存活和分化，以及调节控制ChP脑屏障通透性的紧密连接的作用。总之，这一研究提供了对脉络丛脑屏障神经炎症的机制理解和全面的路线图。

5. Analysis of the diverse antigenic landscape of the malaria protein RH5 identifies a potent vaccine-induced human public antibody clonotype

对疟疾蛋白RH5多样化抗原谱的分析鉴定出一种强效疫苗诱导的人类公共抗体克隆型

The highly conserved and essential Plasmodium falciparum reticulocyte-binding protein homolog 5 (PfRH5) has emerged as the leading target for vaccines against the disease-causing blood stage of malaria. However, the features of the human vaccine-induced antibody response that confer highly potent inhibition of malaria parasite invasion into red blood cells are not well defined. Here, we characterize 236 human IgG monoclonal antibodies, derived from 15 donors, induced by the most advanced PfRH5 vaccine. We define the antigenic landscape of this molecule and establish that epitope specificity, antibody association rate, and intra-PfRH5 antibody interactions are key determinants of functional anti-parasitic potency. In addition, we identify a germline IgG gene combination that results in an exceptionally potent class of antibody and demonstrate its prophylactic potential to protect against P. falciparum parasite challenge in vivo. This comprehensive dataset provides a framework to guide rational design of next-generation vaccines and prophylactic antibodies to protect against blood-stage malaria.

高度保守且必需的恶性疟原虫网织红细胞结合蛋白同源物5（PfRH5）已成为针对疟疾致病血期的疫苗的主要目标。然而，人类疫苗诱导的抗体反应能否有效抑制疟原虫入侵红细胞尚未明确。研究人员对来自15名供体的236个人类IgG单克隆抗体进行了表征，这些抗体是由最先进的PfRH5疫苗诱导产生的。研究人员确定了该分子的抗原性图谱，并确定了表位特异性、抗体结合速率和PfRH5抗体内部相互作用是功能性抗寄生虫效力的关键决定因素。此外，研究人员鉴定出一种能够产生异常强效抗体的种系IgG基因组合，并展示了其在体内对抗恶性疟原虫的潜力。这一综合数据集提供了一个框架，以指导下一代疫苗和预防性抗体的设计，从而保护血期疟疾。

6.Natural malaria infection elicits rare but potent neutralizing antibodies to the blood-stage antigen RH5

自然疟疾感染引发罕见但有效的针对血期抗原RH5的中和抗体

Plasmodium falciparum reticulocyte-binding protein homolog 5 (RH5) is the most advanced blood-stage malaria vaccine candidate and is being evaluated for efficacy in endemic regions, emphasizing the need to study the underlying antibody response to RH5 during natural infection, which could augment or counteract responses to vaccination. Here, we found that RH5-reactive B cells were rare, and circulating immunoglobulin G (IgG) responses to RH5 were short-lived in malaria-exposed Malian individuals, despite repeated infections over multiple years. RH5-specific monoclonal antibodies isolated from eight malaria-exposed individuals mostly targeted non-neutralizing epitopes, in contrast to antibodies isolated from five RH5-vaccinated, malaria-naive UK individuals. However, MAD8–151 and MAD8–502, isolated from two malaria-exposed Malian individuals, were among the most potent neutralizers out of 186 antibodies from both cohorts and targeted the same epitopes as the most potent vaccine-induced antibodies. These results suggest that natural malaria infection may boost RH5-vaccine-induced responses and provide a clear strategy for the development of next-generation RH5 vaccines.

恶性疟原虫网织红细胞结合蛋白同源物5（RH5）是最先进的血期疟疾候选疫苗蛋白，正在疟疾流行地区进行疗效评估，因此，有必要研究自然感染过程中是否增强或抵消机体对RH5的抗体反应。研究人员发现RH5反应性B细胞很少，尽管多年来多次感染，马里的疟疾患者对RH5的循环免疫球蛋白G（IgG）反应是短暂的。从八名疟疾暴露个体中分离的RH5特异性单克隆抗体主要针对非中和表位，这与从五名RH5接种疫苗且未曾感染疟疾的英国个体中分离的抗体形成鲜明对比。然而，从两名疟疾暴露的马里患者中分离的MAD8-151和MAD8-502抗体是两个队列186种抗体中最强的中和抗体之一，且与最有效的疫苗诱导抗体针对相同的表位。这些结果表明，自然疟疾感染可能会增强RH5疫苗诱导的反应，并为开发下一代RH5疫苗提供了明确的策略。

7. Assembly and activation of EBV latent membrane protein 1

EBV潜伏膜蛋白1的组装与激活

Latent membrane protein 1 (LMP1) is the primary oncoprotein of Epstein-Barr virus (EBV) and plays versatile roles in the EBV life cycle and pathogenesis. Despite decades of extensive research, the molecular basis for LMP1 folding, assembly, and activation remains unclear. Here, we report cryo-electron microscopy structures of LMP1 in two unexpected assemblies: a symmetric homodimer and a higher-order filamentous oligomer. LMP1 adopts a non-canonical and unpredicted fold that supports the formation of a stable homodimer through tight and antiparallel intermolecular packing. LMP1 dimers further assemble side-by-side into higher-order filamentous oligomers, thereby allowing the accumulation and specific organization of the flexible cytoplasmic tails for efficient recruitment of downstream factors. Super-resolution microscopy and cellular functional assays demonstrate that mutations at both dimeric and oligomeric interfaces disrupt LMP1 higher-order assembly and block multiple LMP1-mediated signaling pathways. Our research provides a framework for understanding the mechanism of LMP1 and for developing potential therapies targeting EBV-associated diseases.

潜伏膜蛋白1 (Latent membrane protein 1, LMP1)是EB病毒的主要致癌蛋白，在EBV的生命周期和发病机制中发挥多种作用。但LMP1折叠、组装和激活的分子基础仍不清楚。研究人员报道了LMP1在两种组装中的低温电子显微镜结构：对称的同型二聚体和高阶的丝状低聚体。潜伏膜蛋白1采用非经典和不可预测的折叠，支持通过紧密和反平行的分子间包装形成稳定的同型二聚体。LMP1二聚体进一步并排组装成高阶丝状低聚物，从而允许灵活的细胞质尾部的积累和特定组织，以有效地招募下游因子。超高分辨率显微镜和细胞功能分析表明，二聚体和寡聚体界面的突变都会破坏LMP1的高阶组装，并阻断多种LMP1介导的信号通路。该研究为理解LMP1的机制，和开发针对EB病毒相关疾病的潜在疗法提供了一个框架。

8.A replisome-associated histone H3-H4 chaperone required for epigenetic inheritance

表观遗传继承需要复制体相关组蛋白H3-H4分子伴侣

Faithful transfer of parental histones to newly replicated daughter DNA strands is critical for inheritance of epigenetic states. Although replication proteins that facilitate parental histone transfer have been identified, how intact histone H3-H4 tetramers travel from the front to the back of the replication fork remains unknown. Here, we use AlphaFold-Multimer structural predictions combined with biochemical and genetic approaches to identify the Mrc1/CLASPIN subunit of the replisome as a histone chaperone. Mrc1 contains a conserved histone-binding domain that forms a brace around the H3-H4 tetramer mimicking nucleosomal DNA and H2A-H2B histones, is required for heterochromatin inheritance, and promotes parental histone recycling during replication. We further identify binding sites for the FACT histone chaperone in Swi1/TIMELESS and DNA polymerase α that are required for heterochromatin inheritance. We propose that Mrc1, in concert with FACT acting as a mobile co-chaperone, coordinates the distribution of parental histones to newly replicated DNA.

将亲代组蛋白准确地转移到新复制的子代DNA链上对于表观遗传状态的遗传至关重要。尽管已识别出促进亲代组蛋白转移的复制蛋白，但完整的H3-H4四聚体如何从复制叉的前端移动到后端仍不清楚。研究人员结合使用AlphaFold-Multimer结构预测与生化和遗传学方法，确定了复制体中的Mrc1/CLASPIN亚基作为组蛋白伴侣。Mrc1含有一个保守的组蛋白结合结构域，该结构域围绕H3-H4四聚体形成支撑，模拟了核小体DNA和H2A-H2B组蛋白，且对异染色质遗传必不可少，并在复制过程中促进亲代组蛋白的回收。研究人员进一步识别出FACT组蛋白伴侣在Swi1/TIMELESS和DNA聚合酶α中的结合位点，这些位点对异染色质遗传同样重要。研究人员提出Mrc1与FACT作为流动伴侣共同协调亲代组蛋白向新复制的DNA的分配。

9. The fork protection complex promotes parental histone recycling and epigenetic memory

复制叉保护复合体促进亲本组蛋白的回收和表观遗传记忆

The inheritance of parental histones across the replication fork is thought to mediate epigenetic memory. Here, we reveal that fission yeast Mrc1 (CLASPIN in humans) binds H3-H4 tetramers and operates as a central coordinator of symmetric parental histone inheritance. Mrc1 mutants in a key connector domain disrupted segregation of parental histones to the lagging strand comparable to Mcm2 histone-binding mutants. Both mutants showed clonal and asymmetric loss of H3K9me-mediated gene silencing. AlphaFold predicted co-chaperoning of H3-H4 tetramers by Mrc1 and Mcm2, with the Mrc1 connector domain bridging histone and Mcm2 binding. Biochemical and functional analysis validated this model and revealed a duality in Mrc1 function: disabling histone binding in the connector domain disrupted lagging-strand recycling while another histone-binding mutation impaired leading strand recycling. We propose that Mrc1 toggles histones between the lagging and leading strand recycling pathways, in part by intra-replisome co-chaperoning, to ensure epigenetic transmission to both daughter cells.

亲本组蛋白在复制叉的遗传被认为是表观遗传记忆的介导机制。研究人员揭示了裂殖酵母的Mrc1（人类中的CLASPIN）与H3-H4四聚体结合，并作为对称亲本组蛋白继承的中央协调因子发挥作用。Mrc1在关键连接域的突变破坏了亲本组蛋白向滞后链的分配，这与Mcm2组蛋白结合突变体类似。两者突变体均导致H3K9me介导的基因沉默的克隆性和不对称丧失。AlphaFold预测了Mrc1和Mcm2共同伴随H3-H4四聚体，其中Mrc1连接域桥接了组蛋白和Mcm2的结合。生化和功能分析验证了这一模型，并揭示了Mrc1功能的双重性：在连接域组蛋白结合失效破坏了滞后链的回收，而另一组蛋白结合突变则影响了前导链的回收。研究人员提出Mrc1在滞后链和前导链回收途径之间切换组蛋白，部分是通过复制体内共伴侣，以确保表观遗传信息传递给两个子细胞。

10.The FXR1 network acts as a signaling scaffold for actomyosin remodeling

FXR1网络可作为肌动蛋白-肌球蛋白重塑的信号支架

It is currently not known whether mRNAs fulfill structural roles in the cytoplasm. Here, we report the fragile X-related protein 1 (FXR1) network, an mRNA-protein (mRNP) network present throughout the cytoplasm, formed by FXR1-mediated packaging of exceptionally long mRNAs. These mRNAs serve as an underlying condensate scaffold and concentrate FXR1 molecules. The FXR1 network contains multiple protein binding sites and functions as a signaling scaffold for interacting proteins. We show that it is necessary for RhoA signaling-induced actomyosin reorganization to provide spatial proximity between kinases and their substrates. Point mutations in FXR1, found in its homolog FMR1, where they cause fragile X syndrome, disrupt the network. FXR1 network disruption prevents actomyosin remodeling—an essential and ubiquitous process for the regulation of cell shape, migration, and synaptic function. Our findings uncover a structural role for cytoplasmic mRNA and show how the FXR1 RNA-binding protein as part of the FXR1 network acts as an organizer of signaling reactions.

目前尚不清楚mRNA是否在细胞质中具有结构作用。研究人员发现了名为脆性X相关蛋白1（FXR1）的mRNA-蛋白质（mRNP）网络，该网络通过FXR1介导的极长mRNA的包装形成，遍布整个细胞质。这些mRNA作为基础凝聚体支架，聚集FXR1分子。FXR1网络包含多个蛋白质结合位点，并作为与其他蛋白质相互作用的信号平台。研究人员展示了该网络对RhoA信号诱导的肌动蛋白-肌球蛋白重塑的必要性，并提供了激酶及其底物之间的空间接近性。研究人员发现FXR1的点突变（见于其同源基因FMR1，引发脆性X综合症）会破坏该网络，进而阻止肌动蛋白-肌                                                                                                                                                                                                                                              球蛋白重塑——这一过程对细胞形状、迁移和突触功能的调控至关重要。该研究揭示了细胞质mRNA的结构性作用，并展示了FXR1 RNA结合蛋白如何作为FXR1网络一部分充当信号反应的组织者。

11.Multi-layered computational gene networks by engineered tristate logics

基于工程三态逻辑的多层计算基因网络

So far, biocomputation strictly follows traditional design principles of digital electronics, which could reach their limits when assembling gene circuits of higher complexity. Here, by creating genetic variants of tristate buffers instead of using conventional logic gates as basic signal processing units, we introduce a tristate-based logic synthesis (TriLoS) framework for resource-efficient design of multi-layered gene networks capable of performing complex Boolean calculus within single-cell populations. This sets the stage for simple, modular, and low-interference mapping of various arithmetic logics of interest and an effectively enlarged engineering space within single cells. We not only construct computational gene networks running full adder and full subtractor operations at a cellular level but also describe a treatment paradigm building on programmable cell-based therapeutics, allowing for adjustable and disease-specific drug secretion logics in vivo. This work could foster the evolution of modern biocomputers to progress toward unexplored applications in precision medicine.

目前，生物计算严格遵循数字电子学的传统设计原则，在组装更高复杂性的基因电路时可能会达到极限。通过创建三态缓冲区的遗传变体，而不是使用传统的逻辑门作为基本的信号处理单元，研究人员引入了一种基于三态的逻辑综合（TriLoS）框架，用于高效设计能够在单细胞群体内执行复杂布尔演算的多层基因网络。这为各种感兴趣的算术逻辑的简单、模块化和低干扰映射以及有效扩大单细胞的工程空间奠定了基础。研究人员不仅在细胞水平上构建了运行全加全减运算的计算基因网络，还描述了一种基于可编程细胞疗法的治疗范式，允许在体内进行可调节和针对特定疾病的药物分泌逻辑。总之，这项工作促进了现代生物计算机的发展，使其朝着精准医学中未开发的应用方向发展。

12. Molecular and cellular mechanisms of teneurin signaling in synaptic partner matching

突触配对中teneurin信号传导的分子和细胞机制

In developing brains, axons exhibit remarkable precision in selecting synaptic partners among many non-partner cells. Evolutionarily conserved teneurins are transmembrane proteins that instruct synaptic partner matching. However, how intracellular signaling pathways execute teneurins’ functions is unclear. Here, we use in situ proximity labeling to obtain the intracellular interactome of a teneurin (Ten-m) in the Drosophila brain. Genetic interaction studies using quantitative partner matching assays in both olfactory receptor neurons (ORNs) and projection neurons (PNs) reveal a common pathway: Ten-m binds to and negatively regulates a RhoGAP, thus activating the Rac1 small GTPases to promote synaptic partner matching. Developmental analyses with single-axon resolution identify the cellular mechanism of synaptic partner matching: Ten-m signaling promotes local F-actin levels and stabilizes ORN axon branches that contact partner PN dendrites. Combining spatial proteomics and high-resolution phenotypic analyses, this study advanced our understanding of both cellular and molecular mechanisms of synaptic partner matching.

在发育中的大脑中，轴突在许多非伴侣细胞中选择突触伴侣时表现出非凡的精确性。进化上保守的teneurins是一类跨膜蛋白，指导突触伴侣匹配。然而，细胞内信号通路如何介导teneurins的功能尚不清楚。研究人员通过原位邻近标记法获得果蝇大脑中Teneurin（Ten-m）的细胞内互作组；利用定量伴侣匹配测定的基因互作研究，在嗅觉受体神经元（ORN）和投射神经元（PN）中揭示了一个共同的途径：Ten-m结合并负调控RhoGAP，从而激活Rac1小GTP酶以促进突触伴侣匹配。通过单轴突分辨率的发育分析，确定了突触伙伴匹配的细胞机制：Ten-m信号传导促进了局部F-肌动蛋白水平，并稳定了接触到伴侣投射神经元树突的ORN轴突分支。结合空间蛋白质组学和高分辨率表型分析，本研究推进了对突触伴侣匹配的细胞和分子机制的理解。

Sep 19, 2024; Volume 187; Issue 19; p5119-5482

Cell共发表26，其中包括8篇50th Anniversary; 3篇Previews; 1篇Short Articles ; 14篇Articles。

On the cover: As part of Cell's 50th Anniversary, this issue celebrates the world of microbes and the field of microbiology. In their Review, Eren and Banfield discuss the modern era of microbiology that brings together everyone from molecular biologists to computer scientists, statisticians, modelers, and chemists to understand our microbial planet across many scales of inquiry. From laboratory cultures to natural habitats and complex datasets, diverse approaches to microbe-focused research forge solutions for our most pressing needs, from medicine to agriculture to bioremediation. The cover image honors many disciplines that contribute to contemporary microbiology as well as the past 50 years of intense research and discovery. Image credit: Charlotte Hintzmann (https://charlotte-hintzmann.de/).

封面：作为《Cell》50周年纪念的一部分，本期特别庆祝微生物世界和微生物学领域的发展。Eren和Banfield的综述中讨论了现代微生物学时代的到来，汇集了分子生物学家、计算机科学家、统计学家、模型构建学家和化学家等各界专家，共同努力理解微生物星球。从实验室培养物到自然栖息地，再到复杂的数据集，微生物研究的多种方法为我们最迫切的需求提供了解决方案，涵盖医学、农业到生物修复等领域。封面图像向许多学科致敬，这些学科为当代微生物学以及过去50年深入的研究和发现做出了贡献。图像来源：Charlotte Hintzmann (https://charlotte-hintzmann.d)。

1. Structural insights into the diversity and DNA cleavage mechanism of Fanzor

从结构上揭示Fanzor的多样性和DNA裂解机制

Fanzor (Fz) is an ωRNA-guided endonuclease extensively found throughout the eukaryotic domain with unique gene editing potential. Here, we describe the structures of Fzs from three different organisms. We find that Fzs share a common ωRNA interaction interface, regardless of the length of the ωRNA, which varies considerably across species. The analysis also reveals Fz’s mode of DNA recognition and unwinding capabilities as well as the presence of a non-canonical catalytic site. The structures demonstrate how protein conformations of Fz shift to allow the binding of double-stranded DNA to the active site within the R-loop. Mechanistically, examination of structures in different states shows that the conformation of the lid loop on the RuvC domain is controlled by the formation of the guide/DNA heteroduplex, regulating the activation of nuclease and DNA double-stranded displacement at the single cleavage site. Our findings clarify the mechanism of Fz, establishing a foundation for engineering efforts.

Fz是一种由ωRNA引导的核酸内切酶，广泛存在于真核生物中，展示出独特的基因编辑潜力。研究人员解析了来自三种不同生物的Fanzor（Fz）结构。研究发现，尽管不同物种的ωRNA长度差异显著，但Fz共享一个保守的ωRNA相互作用界面。分析还揭示了Fz的DNA识别和解旋能力以及非典型催化位点的存在。结构展示了Fz蛋白构象的变化如何使双链DNA在R环内结合到活性位点。对不同状态下的结构进行检查显示，RuvC结构域上的盖环构象受向导/DNA异源双链形成的控制，从而调节核酸酶的活化以及DNA双链在单个裂解位点的位移。这些研究结果阐明了Fz的机制，为工程应用奠定了基础。

2. DdmDE eliminates plasmid invasion by DNA-guided DNA targeting

DdmDE通过DNA引导的DNA靶向消除质粒入侵

Horizontal gene transfer is a key driver of bacterial evolution, but it also presents severe risks to bacteria by introducing invasive mobile genetic elements. To counter these threats, bacteria have developed various defense systems, including prokaryotic Argonautes (pAgos) and the DNA defense module DdmDE system. Through biochemical analysis, structural determination, and in vivo plasmid clearance assays, we elucidate the assembly and activation mechanisms of DdmDE, which eliminates small, multicopy plasmids. We demonstrate that DdmE, a pAgo-like protein, acts as a catalytically inactive, DNA-guided, DNA-targeting defense module. In the presence of guide DNA, DdmE targets plasmids and recruits a dimeric DdmD, which contains nuclease and helicase domains. Upon binding to DNA substrates, DdmD transitions from an autoinhibited dimer to an active monomer, which then translocates along and cleaves the plasmids. Together, our findings reveal the intricate mechanisms underlying DdmDE-mediated plasmid clearance, offering fundamental insights into bacterial defense systems against plasmid invasions.

水平基因转移是细菌演化的关键驱动因素，但同时也通过引入具有侵入性的移动遗传因子对细菌构成严重威胁。为了抵御这些威胁，细菌发展出多种防御系统，包括原核 Argonautes（pAgo）和DNA防御模块DdmDE系统。通过生化分析、结构解析和体内质粒清除实验，研究人员揭示了DdmDE的组装和激活机制，该机制可消除小型、多拷贝质粒。研究表明，DdmE是一种类似原核生物Argonaute（pAgo）的蛋白，是一种催化不活跃的DNA引导、DNA靶向防御模块。在向导DNA存在的情况下，DdmE靶向质粒并招募含有核酸酶和解旋酶结构域的二聚体蛋白DdmD。当与DNA底物结合时，DdmD从自我抑制状态的二聚体转变为活化的单体，然后沿着质粒移动并进行切割。总之，该研究揭示了DdmDE介导的质粒清除的复杂机制，为细菌防御系统如何抵御质粒入侵提供了基本的见解。

3. Condensate interfacial forces reposition DNA loci and probe chromatin viscoelasticity

凝聚体界面力重新定位DNA位点并探测染色质的粘弹性

Biomolecular condensates assemble in living cells through phase separation and related phase transitions. An underappreciated feature of these dynamic molecular assemblies is that they form interfaces with other cellular structures, including membranes, cytoskeleton, DNA and RNA, and other membraneless compartments. These interfaces are expected to give rise to capillary forces, but there are few ways of quantifying and harnessing these forces in living cells. Here, we introduce viscoelastic chromatin tethering and organization (VECTOR), which uses light-inducible biomolecular condensates to generate capillary forces at targeted DNA loci. VECTOR can be utilized to programmably reposition genomic loci on a timescale of seconds to minutes, quantitatively revealing local heterogeneity in the viscoelastic material properties of chromatin. These synthetic condensates are built from components that naturally form liquid-like structures in living cells, highlighting the potential role for native condensates to generate forces and do work to reorganize the genome and impact chromatin architecture.

生物分子凝聚体通过相分离和相关的相变在活细胞中组装。这些动态分子组装体的一个被低估的特征是它们与其他细胞结构（包括膜、细胞骨架、DNA和RNA以及其他无膜细胞器）形成界面。这些界面预计会产生毛细力，但在活细胞中定量和利用这些力的方法还不多。研究人员介绍了粘弹性染色质栓系和组织（VECTOR）技术，该技术利用光诱导生物分子凝聚体在目标DNA位点生成毛细力。VECTOR可以用于在秒到分钟的时间尺度上可编程地重新定位基因组位点，定量揭示染色质粘弹性材料性质的局部异质性。这些合成凝聚体由天然形成液态结构的组件构建，突显了原生凝聚体在生成力、重组基因组以及影响染色质结构方面的潜在作用。

4. Dynamic regulation of tissue fluidity controls skin repair during wound healing

创面愈合过程中组织流动性的动态调节控制着皮肤的修复

During wound healing, different pools of stem cells (SCs) contribute to skin repair. However, how SCs become activated and drive the tissue remodeling essential for skin repair is still poorly understood. Here, by developing a mouse model allowing lineage tracing and basal cell lineage ablation, we monitor SC fate and tissue dynamics during regeneration using confocal and intravital imaging. Analysis of basal cell rearrangements shows dynamic transitions from a solid-like homeostatic state to a fluid-like state allowing tissue remodeling during repair, as predicted by a minimal mathematical modeling of the spatiotemporal dynamics and fate behavior of basal cells. The basal cell layer progressively returns to a solid-like state with re-epithelialization. Bulk, single-cell RNA, and epigenetic profiling of SCs, together with functional experiments, uncover a common regenerative state regulated by the EGFR/AP1 axis activated during tissue fluidization that is essential for skin SC activation and tissue repair.

在伤口愈合过程中，不同的干细胞群体对皮肤修复作出贡献。然而，干细胞如何被激活以及如何推动对皮肤修复至关重要的组织重塑，仍然知之甚少。通过开发一种允许谱系追踪和基底细胞系消融的小鼠模型，研究人员使用共聚焦和活体成像技术监测干细胞的命运和组织动态。对基底细胞重排的分析表明，基底细胞从固态稳态状态向流体状态动态过渡，使组织在修复过程中得以重塑，这一过程由基底细胞的时空动态和命运行为的最简数学模型预测。随着上皮化的进行，基底细胞层逐渐恢复到固态状态。对干细胞的大规模、单细胞RNA和表观遗传学分析，以及功能实验，揭示了一个由EGFR/AP1轴在组织流体化过程中激活的共同再生状态，该状态对皮肤干细胞激活和组织修复至关重要。

5. Neutrophil trapping and nexocytosis, mast cell-mediated processes for inflammatory signal relay

中性粒细胞捕获和胞吐，肥大细胞介导的炎症信号传递过程

Neutrophils are sentinel immune cells with essential roles for antimicrobial defense. Most of our knowledge on neutrophil tissue navigation derived from wounding and infection models, whereas allergic conditions remained largely neglected. Here, we analyzed allergen-challenged mouse tissues and discovered that degranulating mast cells (MCs) trap living neutrophils inside them. MCs release the attractant leukotriene B4 to re-route neutrophils toward them, thus exploiting a chemotactic system that neutrophils normally use for intercellular communication. After MC intracellular trap (MIT) formation, neutrophils die, but their undigested material remains inside MC vacuoles over days. MCs benefit from MIT formation, increasing their functional and metabolic fitness. Additionally, they are more pro-inflammatory and can exocytose active neutrophilic compounds with a time delay (nexocytosis), eliciting a type 1 interferon response in surrounding macrophages. Together, our study highlights neutrophil trapping and nexocytosis as MC-mediated processes, which may relay neutrophilic features over the course of chronic allergic inflammation.

中性粒细胞是具有重要抗微生物防御作用的哨兵免疫细胞。目前对中性粒细胞在组织中的导航的了解主要来源于创伤和感染模型，而对过敏性疾病的研究则相对较少。本研究分析了过敏原作用小鼠的组织，发现脱颗粒的肥大细胞（MCs）能够将活跃的中性粒细胞困在其内部。肥大细胞释放趋化因子白三烯B4，重新引导中性粒细胞向其聚集，从而利用中性粒细胞用于细胞间通讯的趋化系统。肥大细胞内捕获（MIT）形成后，中性粒细胞死亡，但其未被消化的物质在肥大细胞的空泡内持续存在数日。肥大细胞可从MIT的形成中获益，增强其功能和新陈代谢能力。此外，中性粒细胞更具促炎作用，并能延迟外排活跃的中性粒细胞化合物，从而在周围的巨噬细胞中引发1型干扰素反应。总的来说，该研究强调了中性粒细胞的困捕和中性粒细胞化合物是肥大细胞介导的过程，这些过程可能在慢性过敏性炎症过程中传递中性粒细胞的特征。

6. Macrophage-mediated myelin recycling fuels brain cancer malignancy

巨噬细胞介导的髓鞘回收推动脑癌恶性进展

Tumors growing in metabolically challenged environments, such as glioblastoma in the brain, are particularly reliant on crosstalk with their tumor microenvironment (TME) to satisfy their high energetic needs. To study the intricacies of this metabolic interplay, we interrogated the heterogeneity of the glioblastoma TME using single-cell and multi-omics analyses and identified metabolically rewired tumor-associated macrophage (TAM) subpopulations with pro-tumorigenic properties. These TAM subsets, termed lipid-laden macrophages (LLMs) to reflect their cholesterol accumulation, are epigenetically rewired, display immunosuppressive features, and are enriched in the aggressive mesenchymal glioblastoma subtype. Engulfment of cholesterol-rich myelin debris endows subsets of TAMs to acquire an LLM phenotype. Subsequently, LLMs directly transfer myelin-derived lipids to cancer cells in an LXR/Abca1-dependent manner, thereby fueling the heightened metabolic demands of mesenchymal glioblastoma. Our work provides an in-depth understanding of the immune-metabolic interplay during glioblastoma progression, thereby laying a framework to unveil targetable metabolic vulnerabilities in glioblastoma.

研究人员表示，在新陈代谢受到挑战的环境中生长的肿瘤，如脑中的胶质母细胞瘤，特别依赖于与肿瘤微环境（TME）的相互作用，以满足其高能量需求。为了研究这种代谢相互作用的复杂性，研究人员使用单细胞和多组学分析调查了胶质母细胞瘤TME的异质性，发现了具有促肿瘤特性的代谢重编程的肿瘤相关巨噬细胞（TAM）亚群。这些TAM亚群被称为脂质丰富的巨噬细胞（LLM），其特点是胆固醇积累，表观遗传重编程和免疫抑制，并在侵袭性间质性胶质母细胞瘤亚型中富集。吞噬富含胆固醇的髓鞘碎片使得部分TAM获得LLM表型。随后，LLMs通过LXR/Abca1依赖的方式将来源于髓鞘的脂质直接转移到癌细胞，从而推动间质性胶质母细胞瘤的高度代谢需求。该研究深入理解了胶质母细胞瘤进展中的免疫-代谢相互作用，并为揭示胶质母细胞瘤中可靶向的代谢弱点奠定了基础。

7. Safe and effective in vivo delivery of DNA and RNA using proteolipid vehicles

使用蛋白脂质载体实现安全且有效的体内DNA和RNA递送

Genetic medicines show promise for treating various diseases, yet clinical success has been limited by tolerability, scalability, and immunogenicity issues of current delivery platforms. To overcome these, we developed a proteolipid vehicle (PLV) by combining features from viral and non-viral approaches. PLVs incorporate fusion-associated small transmembrane (FAST) proteins isolated from fusogenic orthoreoviruses into a well-tolerated lipid formulation, using scalable microfluidic mixing. Screening a FAST protein library, we identified a chimeric FAST protein with enhanced membrane fusion activity that improved gene expression from an optimized lipid formulation. Systemically administered FAST-PLVs showed broad biodistribution and effective mRNA and DNA delivery in mouse and non-human primate models. FAST-PLVs show low immunogenicity and maintain activity upon repeat dosing. Systemic administration of follistatin DNA gene therapy with FAST-PLVs raised circulating follistatin levels and significantly increased muscle mass and grip strength. These results demonstrate the promising potential of FAST-PLVs for redosable gene therapies and genetic medicines.

研究人员表示，基因药物在治疗多种疾病方面展现出巨大潜力，但现有递送平台的耐受性、可扩展性和免疫原性问题限制了其临床成功率。为克服这些挑战，研究人员开发了一种蛋白脂质载体（PLV），结合了病毒和非病毒方法的特点。PLV通过可扩展的微流控混合技术，将从融合性正黏病毒中分离的融合相关小跨膜蛋白（FAST蛋白）整合到良好耐受的脂质配方中。通过筛选FAST蛋白库，研究人员鉴定出一种具有增强膜融合活性的嵌合FAST蛋白，并用过优化的脂质配方显著提高了基因表达。系统性给药的FAST-PLV在小鼠和非人灵长类模型中显示出广泛的生物分布，并有效递送mRNA和DNA。FAST-PLV的免疫原性低，且在多次给药后仍能保持活性。使用FAST-PLV递送抑制素DNA基因疗法后，循环抑制素水平升高，肌肉质量和握力显著增加。这些研究结果表明，FAST-PLV在可重复使用的基因疗法和基因药物领域具有广阔的应用前景。

8. Opposing GPCR signaling programs protein intake setpoint in Drosophila

对抗 GPCR 信号程序在果蝇中设定蛋白质摄入量

Animals defend a target level for their fundamental needs, including food, water, and sleep. Deviation from the target range, or “setpoint,” triggers motivated behaviors to eliminate that difference. Whether and how the setpoint itself is encoded remains enigmatic for all motivated behaviors. Employing a high-throughput feeding assay in Drosophila, we demonstrate that the protein intake setpoint is set to different values in male, virgin female, and mated female flies to meet their varying protein demands. Leveraging this setpoint variability, we found, remarkably, that the information on the intake setpoint is stored within the protein hunger neurons as the resting membrane potential. Two RFamide G protein-coupled receptor (GPCR) pathways, by tuning the resting membrane potential in opposite directions, coordinately program and adjust the protein intake setpoint. Together, our studies map the protein intake setpoint to a single trackable physiological parameter and elucidate the cellular and molecular mechanisms underlying setpoint determination and modulation.

动物通过设定目标水平来维持基本需求，如食物、水和睡眠。如果偏离该目标范围或“设定点”，动物会通过激励行为来消除这种差异。然而，设定点本身是如何编码的，仍然是所有动机行为中的一个谜团。通过在果蝇中进行高通量喂食实验，研究人员证明了蛋白质摄入设定点在雄性、未交配雌性和交配雌性果蝇中设定为不同的值，以满足它们的不同蛋白质需求。利用这种设定点的变异性，研究人员发现摄取设定点的信息存储在蛋白质饥饿神经元的静息膜电位中。两条RFamide G蛋白偶联受体（GPCR）通路通过以相反的方向调节静息膜电位，共同程序化和调整蛋白质摄入设定点。总的来说，该研究将蛋白质摄入设定点映射到一个可以追踪的生理参数，并阐明了设定点确定和调节的细胞及分子机制。

9.Stress-sensitive neural circuits change the gut microbiome via duodenal glands

压力敏感的神经回路通过十二指肠腺改变肠道微生物群

Negative psychological states impact immunity by altering the gut microbiome. However, the relationship between brain states and microbiome composition remains unclear. We show that Brunner’s glands in the duodenum couple stress-sensitive brain circuits to bacterial homeostasis. Brunner’s glands mediated the enrichment of gut Lactobacillus species in response to vagus nerve stimulation. Cell-specific ablation of the glands markedly suppressed Lactobacilli counts and heightened vulnerability to infection. In the forebrain, we mapped a vagally mediated, polysynaptic circuit connecting the central nucleus of the amygdala to Brunner’s glands. Chronic stress suppressed central amygdala activity and phenocopied the effects of gland lesions. Conversely, excitation of either the central amygdala or parasympathetic vagal neurons activated Brunner’s glands and reversed the effects of stress on the gut microbiome and immunity. The findings revealed a tractable brain-body mechanism linking psychological states to host defense.

研究人员表示，负面心理状态通过改变肠道微生物群影响免疫力。然而，大脑状态与微生物群组成之间的关系尚不明确。研究人员发现，十二指肠的Brunner’s腺将对压力敏感的大脑回路与细菌稳态相连接。Brunner’s腺介导了对迷走神经刺激的反应，从而促进肠道中的乳酸菌物种富集。特定细胞的腺切除显著减少了乳酸菌的数量，并增加了感染的易感性。在前脑中，研究人员绘制了一个由迷走神经介导的多突触回路，该回路连接杏仁核中枢与Brunner’s腺。慢性压力抑制了中央杏仁核的活动，并模拟了腺损伤的效果。相反，激活杏仁核中枢或副交感迷走神经的神经元能够激活Brunner’s腺，并逆转压力对肠道微生物群和免疫的影响。这些发现揭示了一种可操作的脑-体机制，将心理状态与宿主防御联系起来。

10.Vaginal Lactobacillus fatty acid response mechanisms reveal a metabolite-targeted strategy for bacterial vaginosis treatment

阴道乳酸杆菌脂肪酸反应机制揭示针对代谢物的细菌性阴道病治疗策略

Bacterial vaginosis (BV), a common syndrome characterized by Lactobacillus-deficient vaginal microbiota, is associated with adverse health outcomes. BV often recurs after standard antibiotic therapy in part because antibiotics promote microbiota dominance by Lactobacillus iners instead of Lactobacillus crispatus, which has more beneficial health associations. Strategies to promote L. crispatus and inhibit L. iners are thus needed. We show that oleic acid (OA) and similar long-chain fatty acids simultaneously inhibit L. iners and enhance L. crispatus growth. These phenotypes require OA-inducible genes conserved in L. crispatus and related lactobacilli, including an oleate hydratase (ohyA) and putative fatty acid efflux pump (farE). FarE mediates OA resistance, while OhyA is robustly active in the vaginal microbiota and enhances bacterial fitness by biochemically sequestering OA in a derivative form only ohyA-harboring organisms can exploit. OA promotes L. crispatus dominance more effectively than antibiotics in an in vitro BV model, suggesting a metabolite-based treatment approach.

研究人员表示，细菌性阴道病（BV），一种以乳酸杆菌缺乏为特征的常见综合征，与不良健康结果相关。BV在标准抗生素治疗后经常复发，部分原因是抗生素促进了乳杆菌Lactobacillus iners的微生物群主导地位，而不是具有更有利的健康弯曲乳杆菌Lactobacillus crispatus菌株。因此，需要开发促进L. crispatus和抑制L. iners的治疗策略。研究人员发现，油酸（OA）和类似的长链脂肪酸能够同时抑制L. iners和增强L. crispatus的生长。这些表型需要OA诱导的基因，这些基因在L. crispatus和相关的乳酸杆菌中保守，包括油酸水合酶（ohyA）和推测的脂肪酸外排泵（farE）。FarE介导了对OA的耐药性，而OhyA在阴道微生物群中活性强，通过生化方式将OA隔离为仅携带了ohyA的生物体可以利用的衍生物形式，从而提高了细菌的适应性。OA在体外BV模型中比抗生素更有效地促进了L. crispatus的主导地位，表明基于代谢物的治疗方法可能是一种有效的干预策略。

11. Microbial colonization programs are structured by breastfeeding and guide healthy respiratory development

微生物定植程序受到母乳喂养的影响并能指导健康的呼吸发育

Breastfeeding and microbial colonization during infancy occur within a critical time window for development, and both are thought to influence the risk of respiratory illness. However, the mechanisms underlying the protective effects of breastfeeding and the regulation of microbial colonization are poorly understood. Here, we profiled the nasal and gut microbiomes, breastfeeding characteristics, and maternal milk composition of 2,227 children from the CHILD Cohort Study. We identified robust colonization patterns that, together with milk components, predict preschool asthma and mediate the protective effects of breastfeeding. We found that early cessation of breastfeeding (before 3 months) leads to the premature acquisition of microbial species and functions, including Ruminococcus gnavus and tryptophan biosynthesis, which were previously linked to immune modulation and asthma. Conversely, longer exclusive breastfeeding supports a paced microbial development, protecting against asthma. These findings underscore the importance of extended breastfeeding for respiratory health and highlight potential microbial targets for intervention.

婴儿期的母乳喂养和微生物定植发生在发育的关键时间窗口内，两者都被认为会影响呼吸道疾病的发生风险。然而，母乳喂养和微生物定植的的保护作用调节机制尚不清楚。研究人员分析了来自儿童队列研究的2227名儿童的鼻腔和肠道微生物群、母乳喂养特征和母乳成分。研究发现了强有力的定植模式，与牛奶成分一起，可预测学龄前哮喘和介导母乳喂养的保护作用。研究人员发现，过早停止母乳喂养（3个月前）会导致微生物种类和功能的过早获得，包括瘤胃球菌和色氨酸的生物合成，这在以前被认为与免疫调节和哮喘有关。相反，更长时间的纯母乳喂养有助于促进微生物的有序发育，从而预防哮喘。总之，这一研究强调了延长母乳喂养对呼吸系统健康的重要性，并强调了潜在的微生物干预靶点。

12.Mining human microbiomes reveals an untapped source of peptide antibiotics

人类微生物组的挖掘揭示一个未被开发的肽类抗生素来源

Drug-resistant bacteria are outpacing traditional antibiotic discovery efforts. Here, we computationally screened 444,054 previously reported putative small protein families from 1,773 human metagenomes for antimicrobial properties, identifying 323 candidates encoded in small open reading frames (smORFs). To test our computational predictions, 78 peptides were synthesized and screened for antimicrobial activity in vitro, with 70.5% displaying antimicrobial activity. As these compounds were different compared with previously reported antimicrobial peptides, we termed them smORF-encoded peptides (SEPs). SEPs killed bacteria by targeting their membrane, synergizing with each other, and modulating gut commensals, indicating a potential role in reconfiguring microbiome communities in addition to counteracting pathogens. The lead candidates were anti-infective in both murine skin abscess and deep thigh infection models. Notably, prevotellin-2 from Prevotella copri presented activity comparable to the commonly used antibiotic polymyxin B. Our report supports the existence of hundreds of antimicrobials in the human microbiome amenable to clinical translation.

耐药菌的发展速度超过了传统抗生素的发现进展。研究人员通过计算筛选了1773个人类宏基因组中报告的444054个潜在小蛋白家族，以寻找抗微生物特性，并识别出323个编码在小开放阅读框（smORF）中的候选肽。为了验证计算预测，研究人员合成了78种肽，并在体外筛选其抗微生物活性，其中70.5%显示出抗微生物活性。由于这些化合物与先前报告的抗微生物肽不同，研究人员将其称为smORF编码肽（SEP）。SEP通过靶向细菌膜、相互协同作用和调节肠道共生菌来杀死细菌，这表明它们不仅能对抗病原体，还有可能在重组微生物组群落中发挥作用。主要候选肽在小鼠皮肤脓肿和深部大腿感染模型中表现出抗感染活性。值得注意的是，来自Prevotella copri的prevotellin-2表现出与常用抗生素多黏菌素B相当的抗菌活性。该报告说明在人类微生物组中存在数百种适合临床转化的抗微生物物质。

13. Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic

新冠肺炎疫情中心市场野生动物和病毒的基因追踪

Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Seafood Wholesale Market. Here, we analyze environmental qPCR and sequencing data collected in the Huanan market in early 2020. We demonstrate that market-linked severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic diversity is consistent with market emergence and find increased SARS-CoV-2 positivity near and within a wildlife stall. We identify wildlife DNA in all SARS-CoV-2-positive samples from this stall, including species such as civets, bamboo rats, and raccoon dogs, previously identified as possible intermediate hosts. We also detect animal viruses that infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches, we recover genotypes of market animals and compare them with those from farms and other markets. This analysis provides the genetic basis for a shortlist of potential intermediate hosts of SARS-CoV-2 to prioritize for serological and viral sampling.

病毒通过动物贸易在全球范围内发生了人畜共患病的外溢。COVID-19大流行的起始点通过流行病学追踪与华南海鲜批发市场有关。作者分析了2020年初在华南市场收集的环境样本的qPCR和测序数据，证明了与市场相关的SARS-CoV-2的遗传多样性与市场的出现一致，并发现野生动物摊位附近及摊位内的SARS-CoV-2的阳性率较高。在该摊位所有SARS-CoV-2阳性样本中识别出野生动物DNA，包括麝猫、竹鼠和浣熊犬等物种，这些物种此前已被认为是可能的中间宿主。作者还检测到了感染浣熊犬、果子狸和竹鼠的动物病毒。通过结合宏基因组学和系统发育学方法，研究恢复了市场动物的基因型，并将其与农场和其他市场的动物基因型进行比较。这一分析为优先对SARS-CoV-2潜在中间宿主进行血清学和病毒采样提供了遗传学依据。

Oct 03, 2024; Volume 187; Issue 20; p5483-5796

Cell共发表20篇，其中包括2篇Commentaries；1篇Preview；1篇Review; 2篇Short Articles; 13篇Articles; 1篇Resources。

On the cover: In this issue of Cell, Achom, Sadagopan, Bao et al. analyze whole-genome sequences of a female-predominant kidney cancer driven by rearrangements of the X chromosome. This study lends insight into the differential consequences of somatic X chromosome rearrangements in males and females and illustrates how translocations of the inactive X chromosome can contribute to cancer sex differences. The cover image shows a stylized representation of a rearrangement of the inactive X chromosome that causes activation of X-linked oncogenes (colored region). Image credit: Hans Haag Studios.

在本期《Cell》杂志中，Achom、Sadagopan、Bao等人分析了一种由X染色体重排引起的女性为主的肾癌全基因组序列。本研究提供了关于体细胞X染色体重排在男性和女性中不同后果的见解，并展示了失活X染色体的易位如何促成癌症的性别差异。封面图像展示了失活X染色体重排的样式，导致X连锁癌基因（着色区域）的激活。图像来源：Hans Haag Studios。

1. Mosaic sarbecovirus nanoparticles elicit cross-reactive responses in pre-vaccinated animals

马赛克沙贝病毒纳米颗粒在动物模型中引起交叉反应

Immunization with mosaic-8b (nanoparticles presenting 8 SARS-like betacoronavirus [sarbecovirus] receptor-binding domains [RBDs]) elicits more broadly cross-reactive antibodies than homotypic SARS-CoV-2 RBD-only nanoparticles and protects against sarbecoviruses. To investigate original antigenic sin (OAS) effects on mosaic-8b efficacy, we evaluated the effects of prior COVID-19 vaccinations in non-human primates and mice on anti-sarbecovirus responses elicited by mosaic-8b, admix-8b (8 homotypics), or homotypic SARS-CoV-2 immunizations, finding the greatest cross-reactivity for mosaic-8b. As demonstrated by molecular fate mapping, in which antibodies from specific cohorts of B cells are differentially detected, B cells primed by WA1 spike mRNA-LNP dominated antibody responses after RBD-nanoparticle boosting. While mosaic-8b- and homotypic-nanoparticles boosted cross-reactive antibodies, de novo antibodies were predominantly induced by mosaic-8b, and these were specific for variant RBDs with increased identity to RBDs on mosaic-8b. These results inform OAS mechanisms and support using mosaic-8b to protect COVID-19-vaccinated/infected humans against as-yet-unknown SARS-CoV-2 variants and animal sarbecoviruses with human spillover potential.

为了对抗未来的SARS-CoV-2变种和威胁全球健康的SARS样β-冠状病毒属（沙贝病毒），研究人员设计了马赛克纳米颗粒，其呈现随机排列的沙贝病毒突刺受体结合域（RBD），用于激发更广泛的交叉反应的抗体，而不是可变、免疫优势和暴露的表位。为了研究原始抗原sin（original antigenic sin，OAS），研究人员比较了小鼠和猕猴由马赛克-8（SARS-CoV-2和七种动物沙贝病毒）和同型（仅SARS-CoV-2）RBD纳米颗粒引起的免疫反应，观察到马赛克-8对不匹配（不在纳米颗粒上）的毒株，包括SARS-CoV和动物沙贝病毒引起的反应更强烈。马赛克-8免疫显示了对SARS-CoV-2变体（包括Omicron）的同等中和作用，并保护其免受SARS-CoV-2和SARS-CoV的挑战，而同型的SARS-CoV-2免疫仅保护其免受SARS-CoV-2的感染。分子命运图谱显示，马赛克-8免疫后保守表位的靶向性增加。这些结果共同表明，马赛克-8 RBD纳米颗粒可以保护人们免受SARS-CoV-2变体和未来沙贝病毒的传染。

2. Viral DNA polymerase structures reveal mechanisms of antiviral drug resistance

病毒DNA聚合酶结构揭示抗病毒药物耐药机制

DNA polymerases are important drug targets, and many structural studies have captured them in distinct conformations. However, a detailed understanding of the impact of polymerase conformational dynamics on drug resistance is lacking. We determined cryoelectron microscopy (cryo-EM) structures of DNA-bound herpes simplex virus polymerase holoenzyme in multiple conformations and interacting with antivirals in clinical use. These structures reveal how the catalytic subunit Pol and the processivity factor UL42 bind DNA to promote processive DNA synthesis. Unexpectedly, in the absence of an incoming nucleotide, we observed Pol in multiple conformations with the closed state sampled by the fingers domain. Drug-bound structures reveal how antivirals may selectively bind enzymes that more readily adopt the closed conformation. Molecular dynamics simulations and the cryo-EM structure of a drug-resistant mutant indicate that some resistance mutations modulate conformational dynamics rather than directly impacting drug binding, thus clarifying mechanisms that drive drug selectivity.

DNA聚合酶是重要的药物靶点，许多结构研究捕捉到了它们的不同构象。然而，关于聚合酶构象动力学对药物耐药性影响仍然缺乏详细理解。作者通过冷冻电子显微镜确定了DNA结合的单纯疱疹病毒聚合酶全酶复合物的多种构象，并探究了其与临床使用的抗病毒药物的相互作用。这些结构揭示了催化亚单位Pol和过程因子UL42如何结合DNA以促进过程性的DNA合成。出乎意料的是，在没有进入核苷酸的情况下，研究人员观察到Pol呈现出多种构象，其中指状结构域采样了闭合态。药物结合的结构揭示了抗病毒药物如何选择性地结合更容易采纳闭合构象的酶。分子动力学模拟和耐药突变体的冷冻电子显微镜结构表明，一些耐药突变通过调节构象动力学而非直接影响药物结合，从而阐明了驱动药物选择性的机制。

3. Intracellular Ebola virus nucleocapsid assembly revealed by in situ cryo-electron tomography

原位冷冻电镜断层扫描揭示细胞内埃博拉病毒核衣壳的组装过程

Filoviruses, including the Ebola and Marburg viruses, cause hemorrhagic fevers with up to 90% lethality. The viral nucleocapsid is assembled by polymerization of the nucleoprotein (NP) along the viral genome, together with the viral proteins VP24 and VP35. We employed cryo-electron tomography of cells transfected with viral proteins and infected with model Ebola virus to illuminate assembly intermediates, as well as a 9 Å map of the complete intracellular assembly. This structure reveals a previously unresolved third and outer layer of NP complexed with VP35. The intrinsically disordered region, together with the C-terminal domain of this outer layer of NP, provides the constant width between intracellular nucleocapsid bundles and likely functions as a flexible tether to the viral matrix protein in the virion. A comparison of intracellular nucleocapsids with prior in-virion nucleocapsid structures reveals that the nucleocapsid further condenses vertically in the virion. The interfaces responsible for nucleocapsid assembly are highly conserved and offer targets for broadly effective antivirals.

丝状病毒，包括埃博拉和马尔堡病毒，引发的出血热具有高达90%的致死率。病毒核衣壳的组装依赖于核蛋白（NP）沿病毒基因组的聚合，以及病毒蛋白VP24和VP35的共同组装。研究人员利用冷冻电镜断层扫描技术，对转染了病毒蛋白并感染了模型埃博拉病毒的细胞进行研究，以揭示组装中间体，并获得了完整的细胞内组装的9Å分辨率图谱。该结构显示了之前尚未阐明的与VP35复合的NP的第三层和外层结构。内源性无序区域及其外层NP的C端结构，提供了细胞内核衣壳束之间的恒定宽度，并可能作为病毒基质蛋白的柔性连接区域。将细胞内核衣壳与之前在病毒体内的核衣壳结构进行比较发现，核衣壳在病毒体内进一步垂直凝聚。负责核衣壳组装的界面高度保守，为广谱抗病毒药物提供了靶点。

4. Molecular insights into human phosphatidylserine synthase 1 reveal its inhibition promotes LDL uptake

对人类磷脂酰丝氨酸合成酶1的分子研究显示其抑制可促进LDL的摄取

In mammalian cells, two phosphatidylserine (PS) synthases drive PS synthesis. Gain-of-function mutations in the Ptdss1 gene lead to heightened PS production, causing Lenz-Majewski syndrome (LMS). Recently, pharmacological inhibition of PSS1 has been shown to suppress tumorigenesis. Here, we report the cryo-EM structures of wild-type human PSS1 (PSS1WT), the LMS-causing Pro269Ser mutant (PSS1P269S), and PSS1WT in complex with its inhibitor DS55980254. PSS1 contains 10 transmembrane helices (TMs), with TMs 4–8 forming a catalytic core in the luminal leaflet. These structures revealed a working mechanism of PSS1 akin to the postulated mechanisms of the membrane-bound O-acyltransferase family. Additionally, we showed that both PS and DS55980254 can allosterically inhibit PSS1 and that inhibition by DS55980254 activates the SREBP pathways, thus enhancing the expression of LDL receptors and increasing cellular LDL uptake. This work uncovers a mechanism of mammalian PS synthesis and suggests that selective PSS1 inhibitors have the potential to lower blood cholesterol levels.

研究人员表示，在哺乳动物细胞中，两个磷脂酰丝氨酸（PS）合成酶驱动PS的合成。Ptdss1基因的功能获得性突变会导致PS合成增加，进而引发Lenz-Majewski综合征（LMS）。研究人员通过冷冻电镜解析了野生型人类PSS1（PSS1WT）、导致LMS的Pro269Ser突变体（PSS1P269S）以及与其抑制剂DS55980254结合的PSS1WT的冷冻电镜结构。PSS1包含10个跨膜螺旋（TM），其中TM 4-8形成了位于膜内叶的催化核心。这些结构揭示了PSS1的工作机制，类似于膜结合O-酰基转移酶家族的推测机制。此外，研究人员展示了PS和DS55980254均可以变构抑制PSS1，而DS55980254的抑制作用还可以激活SREBP途径，从而增强低密度脂蛋白受体的表达并增加细胞的LDL摄取。这项研究揭示了哺乳动物PS合成的机制，并表明选择性PSS1抑制剂具有降低血液胆固醇水平的潜力。

5. Thyroid hormone remodels cortex to coordinate body-wide metabolism and exploration

甲状腺激素重塑大脑皮层以协调全身代谢和探索行为

Animals adapt to environmental conditions by modifying the function of their internal organs, including the brain. To be adaptive, alterations in behavior must be coordinated with the functional state of organs throughout the body. Here, we find that thyroid hormone—a regulator of metabolism in many peripheral organs—directly activates cell-type-specific transcriptional programs in the frontal cortex of adult male mice. These programs are enriched for axon-guidance genes in glutamatergic projection neurons, synaptic regulatory genes in both astrocytes and neurons, and pro-myelination factors in oligodendrocytes, suggesting widespread plasticity of cortical circuits. Indeed, whole-cell electrophysiology revealed that thyroid hormone alters excitatory and inhibitory synaptic transmission, an effect that requires thyroid hormone-induced gene regulatory programs in presynaptic neurons. Furthermore, thyroid hormone action in the frontal cortex regulates innate exploratory behaviors and causally promotes exploratory decision-making. Thus, thyroid hormone acts directly on the cerebral cortex in males to coordinate exploratory behaviors with whole-body metabolic state.

动物通过改变内部器官（包括大脑）的功能来适应环境条件。为了适应环境，行为的变化必须与全身器官的功能状态协调。研究人员发现甲状腺激素直接激活成年雄性小鼠前额叶皮层中特定细胞类型的转录程序。这些程序在谷氨酸能投射神经元中富含轴突引导基因，在星形胶质细胞和神经元中富含突触调节基因，并在少突胶质细胞中富含促髓鞘形成因子，这表明皮层回路具有广泛的可塑性。实际上，全细胞电生理学揭示甲状腺激素改变了兴奋性和抑制性突触传递，这一效应需要甲状腺激素诱导的突触前神经元基因调控程序。此外，甲状腺激素在前额叶皮层的作用调节了先天的探索行为，并因此促进了探索决策。因此，甲状腺激素直接作用于雄性大脑皮层，以协调探索行为与全身代谢状态。

6. TEX264 drives selective autophagy of DNA lesions to promote DNA repair and cell survival

TEX264驱动DNA损伤的选择性自噬以促进DNA修复和细胞存活

DNA repair and autophagy are distinct biological processes vital for cell survival. Although autophagy helps maintain genome stability, there is no evidence of its direct role in the repair of DNA lesions. We discovered that lysosomes process topoisomerase 1 cleavage complexes (TOP1cc) DNA lesions in vertebrates. Selective degradation of TOP1cc by autophagy directs DNA damage repair and cell survival at clinically relevant doses of topoisomerase 1 inhibitors. TOP1cc are exported from the nucleus to lysosomes through a transient alteration of the nuclear envelope and independent of the proteasome. Mechanistically, the autophagy receptor TEX264 acts as a TOP1cc sensor at DNA replication forks, triggering TOP1cc processing by the p97 ATPase and mediating the delivery of TOP1cc to lysosomes in an MRE11-nuclease- and ATR-kinase-dependent manner. We found an evolutionarily conserved role for selective autophagy in DNA repair that enables cell survival, protects genome stability, and is clinically relevant for colorectal cancer patients.

DNA修复和自噬是两个对细胞存活至关重要的不同生物过程。尽管自噬有助于维持基因组稳定性，但此前尚无证据表明它在DNA损伤修复中的直接作用。研究人员发现，在脊椎动物中，溶酶体通过自噬选择性降解拓扑异构酶1切割复合物（TOP1cc），从而处理DNA损伤。在临床相关剂量的拓扑异构酶1抑制剂下，通过自噬选择性降解TOP1cc指导DNA损伤修复和细胞存活。TOP1cc通过核膜的瞬时改变被从细胞核排出到溶酶体，并且这一过程与蛋白酶体无关。在机制上，自噬受体TEX264作为DNA复制叉处的TOP1cc传感器，触发TOP1cc由p97 ATP酶处理，并介导TOP1cc通过MRE11核酸酶和ATR激酶依赖的方式输送到溶酶体。研究人员发现选择性自噬在DNA修复中的演化保守作用能够支持细胞存活，保护基因组稳定性，并且在结直肠癌患者中具有临床相关性。

7. High-resolution functional mapping of RAD51C by saturation genome editing

饱和基因组编辑可对RAD51C进行高分辨率功能定位

Pathogenic variants in RAD51C confer an elevated risk of breast and ovarian cancer, while individuals homozygous for specific RAD51C alleles may develop Fanconi anemia. Using saturation genome editing (SGE), we functionally assess 9,188 unique variants, including >99.5% of all possible coding sequence single-nucleotide alterations. By computing changes in variant abundance and Gaussian mixture modeling (GMM), we functionally classify 3,094 variants to be disruptive and use clinical truth sets to reveal an accuracy/concordance of variant classification >99.9%. Cell fitness was the primary assay readout allowing us to observe a phenomenon where specific missense variants exhibit distinct depletion kinetics potentially suggesting that they represent hypomorphic alleles. We further explored our exhaustive functional map, revealing critical residues on the RAD51C structure and resolving variants found in cancer-segregating kindred. Furthermore, through interrogation of UK Biobank and a large multi-center ovarian cancer cohort, we find significant associations between SGE-depleted variants and cancer diagnoses.

RAD51C基因中的致病变异会显著增加乳腺癌和卵巢癌的风险，而特定RAD51C等位基因的纯合个体可能发展为Fanconi贫血。通过饱和基因组编辑（SGE），研究人员功能性地评估了9188种独特变异，包括超过99.5%的所有可能的编码序列单核苷酸变化。通过计算变异丰度的变化和高斯混合建模（GMM），研究人员将3094种变异功能性地分类为破坏性变异，并使用临床真实数据集验证了变异分类的准确性/一致性超过99.9%。细胞适应性是主要的检测指标，使研究人员观察到一种现象，即特定的错义变异表现出不同的耗竭动力学，可能表明它们代表低活性等位基因。研究人员进一步探索了全面的功能图谱，发现了RAD51C结构上的关键残基，并解析了在癌症家族中发现的变异。此外，通过对UK Biobank和大型多中心卵巢癌队列的调查，研究人员发现SGE耗竭的变异与癌症诊断之间存在显著关联。

8. A genetic basis for sex differences in Xp11 translocation renal cell carcinoma

Xp11易位性肾癌性别差异的遗传学基础

Xp11 translocation renal cell carcinoma (tRCC) is a rare, female-predominant cancer driven by a fusion between the transcription factor binding to IGHM enhancer 3 (TFE3) gene on chromosome Xp11.2 and a partner gene on either chromosome X (chrX) or an autosome. It remains unknown what types of rearrangements underlie TFE3 fusions, whether fusions can arise from both the active (chrXa) and inactive X (chrXi) chromosomes, and whether TFE3 fusions from chrXi translocations account for the female predominance of tRCC. To address these questions, we performed haplotype-specific analyses of chrX rearrangements in tRCC whole genomes. We show that TFE3 fusions universally arise as reciprocal translocations and that oncogenic TFE3 fusions can arise from chrXi:autosomal translocations. Female-specific chrXi:autosomal translocations result in a 2:1 female-to-male ratio of TFE3 fusions involving autosomal partner genes and account for the female predominance of tRCC. Our results highlight how X chromosome genetics constrains somatic chrX alterations and underlies cancer sex differences.

研究人员表示，Xp11易位肾细胞癌（tRCC）是一种罕见的以女性多发的癌症，其驱动因素是X染色体Xp11.2上转录因子结合IGMH增强子3（TFE3）基因与X染色体（chrX）或常染色体上的配对基因融合。尚不清楚TFE3融合的底层重排类型，是否融合可以源自有活性的X染色体（chrXa）和无活性的X染色体（chrXi），以及chrXi易位引起的TFE3融合是否导致了tRCC的女性多发特征。为了解决这些问题，研究人员对tRCC全基因组中的chrX重排进行了单倍型特异性分析。研究人员发现TFE3融合普遍通过互易转位的方式产生，且致癌性TFE3融合可以源自chrXi:常染色体转位。配对基因的TFE3融合中，女性与男性的比例为2:1，这解释了tRCC的女性多发特征。这些结果突显了X染色体遗传学如何限制体细胞chrX改变，并且是导致癌症性别差异的基础。

9. Cross-disorder and disease-specific pathways in dementia revealed by single-cell genomics

单细胞基因组学揭示痴呆中的跨疾病和特异性疾病通路

The development of successful therapeutics for dementias requires an understanding of their shared and distinct molecular features in the human brain. We performed single-nuclear RNA-seq and ATAC-seq in Alzheimer’s disease (AD), frontotemporal dementia (FTD), and progressive supranuclear palsy (PSP), analyzing 41 participants and ∼1 million cells (RNA + ATAC) from three brain regions varying in vulnerability and pathological burden. We identify 32 shared, disease-associated cell types and 14 that are disease specific. Disease-specific cell states represent glial-immune mechanisms and selective neuronal vulnerability impacting layer 5 intratelencephalic neurons in AD, layer 2/3 intratelencephalic neurons in FTD, and layer 5/6 near-projection neurons in PSP. We identify disease-associated gene regulatory networks and cells impacted by causal genetic risk, which differ by disorder. These data illustrate the heterogeneous spectrum of glial and neuronal compositional and gene expression alterations in different dementias and identify therapeutic targets by revealing shared and disease-specific cell states.

成功治疗痴呆症需要了解其在人体大脑中的共享和独特分子特征。研究人员在阿尔茨海默病（AD）、额叶颞叶痴呆（FTD）和进行性核上性麻痹（PSP）中进行了单核RNA测序和ATAC测序，分析了41名参与者和约100万个细胞（RNA+ATAC），涵盖了三个在易感性和病理负担上不同的大脑区域。研究人员识别了32种共享的疾病相关细胞类型和14种疾病特异性细胞状态。疾病特异性细胞状态代表了胶质-免疫机制和选择性神经元易感性，这些特征影响了AD中的第5层端脑内侧束神经元、FTD中的2/3层端脑内侧束神经元，以及PSP中的5/6层近投射神经元。研究人员识别了与疾病相关的基因调控网络以及受致病遗传风险影响的细胞，这些在不同疾病中有所不同。这些数据展示了不同痴呆症中胶质和神经元组成及基因表达的异质谱，并通过揭示共享和疾病特异性细胞状态来确定治疗靶点。

Oct 17, 2024; Volume 187; Issue 21; p5797-6124;

Cell共发表24篇，其中包括9篇50th Anniversary; 13篇Articles; 1篇Resources; 1篇Correction。

On the cover: In this issue of Cell, Mathis et al. condense the progress in decoding the brain over the last 50 years. This Perspective explores the mathematical foundations, the current machine learning approaches, and the future of connecting cellular mechanisms to neural representations. The artwork shows a scientist analyzing behavior, large-scale recordings, and BMI data to decode the brain. Artist: Julia Kuhl.

封面：在本期《Cell》杂志中，Mathis等人总结了过去50年解码大脑的进展。这一视角探讨了连接细胞机制与神经表征的数学基础、当前的机器学习方法及其未来的发展方向。图像展示了一位科学家分析行为、大规模记录和脑机接口（BMI）数据以解码大脑。艺术家：Julia Kuhl。

1.Bronze Age cheese reveals human-Lactobacillus interactions over evolutionary history

青铜时代的奶酪揭示人类与乳酸菌在进化历史上的相互作用

Despite the long history of consumption of fermented dairy, little is known about how the fermented microbes were utilized and evolved over human history. Here, by retrieving ancient DNA of Bronze Age kefir cheese (∼3,500 years ago) from the Xiaohe cemetery, we explored past human-microbial interactions. Although it was previously suggested that kefir was spread from the Northern Caucasus to Europe and other regions, we found an additional spreading route of kefir from Xinjiang to inland East Asia. Over evolutionary history, the East Asian strains gained multiple gene clusters with defensive roles against environmental stressors, which can be a result of the adaptation of Lactobacillus strains to various environmental niches and human selection. Overall, our results highlight the role of past human activities in shaping the evolution of human-related microbes, and such insights can, in turn, provide a better understanding of past human behaviors.

尽管发酵乳制品的食用历史悠久，但对于人类历史上如何利用和演化这些发酵微生物仍知之甚少。通过从小河墓地提取青铜时代（约3500年前）开菲尔奶酪的古DNA，研究人员探讨了过去的人类-微生物相互作用。虽然之前有研究表明开菲尔奶酪是从从北高加索传播到欧洲和其他地区，但研究人员发现了开菲尔奶酪从新疆向东亚内陆传播的另一条路线。在历史中，东亚菌株获得了多个具有防御作用的基因簇，这可能是乳酸菌菌株适应不同环境生态位和人类选择的结果。总体而言，这些结果突显了过去人类活动在塑造人类相关微生物进化中的作用，而这些见解反过来可以更好地理解过去的人类行为。

2. Genomic surveillance as a scalable framework for precision phage therapy against antibiotic-resistant pathogens

基因组监测可作为一种可扩展框架用于靶向抗生素耐药病原体的精准噬菌体治疗

Phage therapy is gaining increasing interest in the fight against critically antibiotic-resistant nosocomial pathogens. However, the narrow host range of bacteriophages hampers the development of broadly effective phage therapeutics and demands precision approaches. Here, we combine large-scale phylogeographic analysis with high-throughput phage typing to guide the development of precision phage cocktails targeting carbapenem-resistant Acinetobacter baumannii, a top-priority pathogen. Our analysis reveals that a few strain types dominate infections in each world region, with their geographical distribution remaining stable within 6 years. As we demonstrate in Eastern Europe, this spatiotemporal distribution enables preemptive preparation of region-specific phage collections that target most local infections. Finally, we showcase the efficacy of phage cocktails against prevalent strain types using in vitro and animal infection models. Ultimately, genomic surveillance identifies patients benefiting from the same phages across geographical scales, thus providing a scalable framework for precision phage therapy.

噬菌体治疗在对抗严重抗生素耐药的院感病原体的斗争中受到越来越多的关注。然而，噬菌体狭窄的宿主范围限制了广泛有效的噬菌体治疗的发展。研究人员结合大规模的系统地理分析和高通量噬菌体分型，以指导针对碳青霉烯类耐药鲍曼不动杆菌这种优先考虑的病原体的精准噬菌体鸡尾酒疗法的研发。分析显示，少数菌株类型主导了各个世界地区的感染，其地理分布在6年内保持稳定。正如研究人员在东欧所展示，这种时空分布使得研究人员能够提前准备针对大多数地方感染的区域的特定噬菌体库。最后，研究人员通过体外和动物感染模型展示了噬菌体鸡尾酒疗法对流行菌株类型的有效性。因此，基因组监测识别出在不同地理范围内受益于相同噬菌体的患者，从而提供了一种可扩展的噬菌体精准治疗框架。

3.Biomolecular condensates regulate cellular electrochemical equilibria

生物大分子凝聚体调节细胞电化学平衡

Control of the electrochemical environment in living cells is typically attributed to ion channels. Here, we show that the formation of biomolecular condensates can modulate the electrochemical environment in bacterial cells, which affects cellular processes globally. Condensate formation generates an electric potential gradient, which directly affects the electrochemical properties of a cell, including cytoplasmic pH and membrane potential. Condensate formation also amplifies cell-cell variability of their electrochemical properties due to passive environmental effect. The modulation of the electrochemical equilibria further controls cell-environment interactions, thus directly influencing bacterial survival under antibiotic stress. The condensate-mediated shift in intracellular electrochemical equilibria drives a change of the global gene expression profile. Our work reveals the biochemical functions of condensates, which extend beyond the functions of biomolecules driving and participating in condensate formation, and uncovers a role of condensates in regulating global cellular physiology.

活细胞中电化学环境的控制通常由离子通道介导。研究人员展示了生物大分子凝聚体的形成可以调节细菌细胞的电化学环境，从而广泛影响细胞过程。凝聚体的形成产生电位梯度，直接影响细胞的电化学特性，例如细胞质pH值和膜电位。凝聚体的形成还通过放大被动的环境效应导致细胞间电化学特性的变异性。电化学平衡的调节进一步控制了细胞与环境的相互作用，进而直接影响细菌在抗生素压力下的存活。凝聚体介导的细胞内电化学平衡变化引发了全局基因表达谱的改变。该研究揭示了凝聚体的生化功能，其作用不仅限于驱动和参与凝聚体形成生物分子的功能，还发现了凝聚体在调节细胞全局生理中的作用。

4. Co-opting templated aggregation to degrade pathogenic tau assemblies and improve motor function

通过簇激活降解剂选择性去除病理性tau蛋白，改善运动功能

Protein aggregation causes a wide range of neurodegenerative diseases. Targeting and removing aggregates, but not the functional protein, is a considerable therapeutic challenge. Here, we describe a therapeutic strategy called “RING-Bait,” which employs an aggregating protein sequence combined with an E3 ubiquitin ligase. RING-Bait is recruited into aggregates, whereupon clustering dimerizes the RING domain and activates its E3 function, resulting in the degradation of the aggregate complex. We exemplify this concept by demonstrating the specific degradation of tau aggregates while sparing soluble tau. Unlike immunotherapy, RING-Bait is effective against both seeded and cell-autonomous aggregation. RING-Bait removed tau aggregates seeded from Alzheimer’s disease (AD) and progressive supranuclear palsy (PSP) brain extracts and was also effective in primary neurons. We used a brain-penetrant adeno-associated virus (AAV) to treat P301S tau transgenic mice, reducing tau pathology and improving motor function. A RING-Bait strategy could be applied to other neurodegenerative proteinopathies by replacing the Bait sequence to match the target aggregate.

蛋白质聚集是多种神经退行性疾病的共同特征。选择性降解病理蛋白聚集体，同时保留单体形式是主要的治疗挑战。由于TRIM21 RING结构域的簇集对于激活至关重要，因此TRIM21激酶在特定的装配状态下特异性地降解与抗体结合的蛋白质，然而有效地靶向细胞内装配体仍然是一个挑战。该课题组研究人员将TRIM21的RING结构域定位为目标特异性纳米体，以创建能够选择性降解聚集蛋白的细胞内表达构建体。研究组针对绿色荧光蛋白标记的组蛋白2B (H2B-GFP)和tau(一种在阿尔茨海默氏症和其他神经退行性疾病中病理聚集的蛋白质)评估了这种方法。RING纳米体降解剂在细胞培养和体内实验中均能阻止或逆转tau聚集，同时对单体tau的影响最小。这种方法可能对许多由细胞内蛋白聚集引起的疾病具有治疗潜力。

5. Divergent sensory pathways of sneezing and coughing

打喷嚏和咳嗽的不同感觉通路

Sneezing and coughing are primary symptoms of many respiratory viral infections and allergies. It is generally assumed that sneezing and coughing involve common sensory receptors and molecular neurotransmission mechanisms. Here, we show that the nasal mucosa is innervated by several discrete populations of sensory neurons, but only one population (MrgprC11+MrgprA3−) mediates sneezing responses to a multitude of nasal irritants, allergens, and viruses. Although this population also innervates the trachea, it does not mediate coughing, as revealed by our newly established cough model. Instead, a distinct sensory population (somatostatin [SST+]) mediates coughing but not sneezing, unraveling an unforeseen sensory difference between sneezing and coughing. At the circuit level, sneeze and cough signals are transmitted and modulated by divergent neuropathways. Together, our study reveals the difference in sensory receptors and neurotransmission/modulation mechanisms between sneezing and coughing, offering neuronal drug targets for symptom management in respiratory viral infections and allergies.

打喷嚏和咳嗽是许多呼吸道病毒感染和过敏的主要症状。人们通常认为打喷嚏和咳嗽涉及相同的感官受体和分子神经传递机制。本研究发现鼻粘膜由几种不同的感觉神经元群体支配，但只有一种神经元群体（MrgprC11+MrgprA3−）介导对多种鼻腔刺激物、过敏原和病毒的打喷嚏反应。尽管这个神经元群体也支配气管，但它并不参与咳嗽的调控。相反，另一个独特的感觉神经元群体（生长抑素[SST+]）介导咳嗽而非打喷嚏，揭示了打喷嚏和咳嗽之间一个未曾预料到的感觉机制的差异。在神经回路层面，打喷嚏和咳嗽信号通过不同的神经通路传递和调节。总之，研究揭示了打喷嚏和咳嗽之间在感官受体和神经传递/调节机制上的差异，为呼吸道病毒感染和过敏症状管理提供了神经药物靶点。

6. A line attractor encoding a persistent internal state requires neuropeptide signaling

编码持久内在状态的线性吸引子需要神经肽信号传递

Internal states drive survival behaviors, but their neural implementation is poorly understood. Recently, we identified a line attractor in the ventromedial hypothalamus (VMH) that represents a state of aggressiveness. Line attractors can be implemented by recurrent connectivity or neuromodulatory signaling, but evidence for the latter is scant. Here, we demonstrate that neuropeptidergic signaling is necessary for line attractor dynamics in this system by using cell-type-specific CRISPR-Cas9-based gene editing combined with single-cell calcium imaging. Co-disruption of receptors for oxytocin and vasopressin in adult VMH Esr1+ neurons that control aggression diminished attack, reduced persistent neural activity, and eliminated line attractor dynamics while only slightly reducing overall neural activity and sex- or behavior-specific tuning. These data identify a requisite role for neuropeptidergic signaling in implementing a behaviorally relevant line attractor in mammals. Our approach should facilitate mechanistic studies in neuroscience that bridge different levels of biological function and abstraction.

研究人员表示，内在状态驱动生存行为，但其神经实现机制尚未完全阐明。研究人员在腹内侧下丘脑（VMH）中发现了一个线性吸引子，它代表了攻击状态。线性吸引子可以通过递归连接或神经调节信号来实现，但后者的证据很少。研究人员通过使用细胞类型特异性的CRISPR-Cas9基因编辑结合单细胞钙成像，展示了神经肽信号传递对该系统中线性吸引子动态变化的必要性。在控制攻击行为的成体VMH Esr1+神经元中，同时破坏催产素和抗利尿激素受体减少了攻击行为，降低了持久的神经活动，并消除了线性吸引子动态，而整体神经活动和性别或行为特异性调节仅稍有减少。这些数据确定了神经肽信号传递在实现哺乳动物行为相关的线性吸引子中的必要作用。。这些方法应有助于联通神经科学中不同生物功能和抽象概念层次的机制研究。

7. Sex-dependent effects in the aged melanoma tumor microenvironment influence invasion and resistance to targeted therapy

老年黑色素瘤肿瘤微环境中的性别依赖性效应影响肿瘤侵袭性和对靶向治疗的抵抗力

There is documented sex disparity in cutaneous melanoma incidence and mortality, increasing disproportionately with age and in the male sex. However, the underlying mechanisms remain unclear. While biological sex differences and inherent immune response variability have been assessed in tumor cells, the role of the tumor-surrounding microenvironment, contextually in aging, has been overlooked. Here, we show that skin fibroblasts undergo age-mediated, sex-dependent changes in their proliferation, senescence, ROS levels, and stress response. We find that aged male fibroblasts selectively drive an invasive, therapy-resistant phenotype in melanoma cells and promote metastasis in aged male mice by increasing AXL expression. Intrinsic aging in male fibroblasts mediated by EZH2 decline increases BMP2 secretion, which in turn drives the slower-cycling, highly invasive, and therapy-resistant melanoma cell phenotype, characteristic of the aged male TME. Inhibition of BMP2 activity blocks the emergence of invasive phenotypes and sensitizes melanoma cells to BRAF/MEK inhibition.

皮肤黑色素瘤的发生率和死亡率存在性别差异，并随着年龄的增长，男性群体的发生率和死亡率不成比例地增加。然而，其潜在机制仍不清楚。尽管在肿瘤细胞中已经评估了生物性别差异和固有的免疫反应变异性，但肿瘤周围微环境在衰老背景下的作用却未被充分关注。本研究发现皮肤成纤维细胞在增殖、衰老、活性氧（ROS）水平和应激反应方面经历了年龄介导的性别依赖性变化。研究发现衰老的男性成纤维细胞通过增加AXL的表达选择性地驱动黑色素瘤细胞的侵袭、治疗抵抗表型，并促进老年雄性小鼠的肿瘤转移。由EZH2减少介导的男性成纤维细胞的内源性衰老增加了BMP2的分泌，这反过来促进了较慢周期、高度侵袭性且耐药的黑色素瘤细胞表型，这种表型是衰老男性肿瘤微环境（TME）的特征。抑制BMP2活性能够阻止侵袭性表型的出现，并使黑色素瘤细胞对BRAF/MEK抑制敏感。

8. m6A-modified cenRNA stabilizes CENPA to ensure centromere integrity in cancer cells

m⁶A修饰的cenRNA稳定CENPA，调控癌细胞着丝粒稳态

m6A modification is best known for its critical role in controlling multiple post-transcriptional processes of the mRNAs. Here, we discovered elevated levels of m6A modification on centromeric RNA (cenRNA) in cancerous cells compared with non-cancerous cells. We then identified CENPA, an H3 variant, as an m6A reader of cenRNA. CENPA is localized at centromeres and is essential in preserving centromere integrity and function during mitosis. The m6A-modified cenRNA stabilizes centromeric localization of CENPA in cancer cells during the S phase of the cell cycle. Mutations of CENPA at the Leu61 and the Arg63 or removal of cenRNA m6A modification lead to loss of centromere-bound CENPA during S phase. This in turn results in compromised centromere integrity and abnormal chromosome separation and hinders cancer cell proliferation and tumor growth. Our findings unveil an m6A reading mechanism by CENPA that epigenetically governs centromere integrity in cancer cells, providing potential targets for cancer therapy.

m6A修饰因其在调控mRNA的多种转录后过程中的关键作用而广为人知。本研究发现癌细胞中的着丝粒RNA（cenRNA）相较于非癌细胞中具有较高水平的m6A修饰。随后，作者鉴定出CENPA（一种H3变体）定位于着丝粒，并在有丝分裂过程中对维持着丝粒的完整性和功能至关重要。m6A修饰的cenRNA在癌细胞的S期能够稳定CENPA在着丝粒的定位。CENPA在Leu61和Arg63位点的突变或cenRNA的m6A修饰去除导致S期期间失去着丝粒结合的CENPA，进而导致着丝粒完整性受损、染色体分离异常，并抑制癌细胞增殖和肿瘤生长。该研究揭示了CENPA通过m6A阅读机制表观遗传性地调控癌细胞中的着丝粒完整性，为癌症治疗提供了潜在的靶点。

9.The Fanconi anemia pathway induces chromothripsis and ecDNA-driven cancer drug resistance

范康尼贫血通路诱导染色体碎裂和 ecDNA 驱动的癌症药物耐药性

Chromothripsis describes the catastrophic shattering of mis-segregated chromosomes trapped within micronuclei. Although micronuclei accumulate DNA double-strand breaks and replication defects throughout interphase, how chromosomes undergo shattering remains unresolved. Using CRISPR-Cas9 screens, we identify a non-canonical role of the Fanconi anemia (FA) pathway as a driver of chromothripsis. Inactivation of the FA pathway suppresses chromosome shattering during mitosis without impacting interphase-associated defects within micronuclei. Mono-ubiquitination of FANCI-FANCD2 by the FA core complex promotes its mitotic engagement with under-replicated micronuclear chromosomes. The structure-selective SLX4-XPF-ERCC1 endonuclease subsequently induces large-scale nucleolytic cleavage of persistent DNA replication intermediates, which stimulates POLD3-dependent mitotic DNA synthesis to prime shattered fragments for reassembly in the ensuing cell cycle. Notably, FA-pathway-induced chromothripsis generates complex genomic rearrangements and extrachromosomal DNA that confer acquired resistance to anti-cancer therapies. Our findings demonstrate how pathological activation of a central DNA repair mechanism paradoxically triggers cancer genome evolution through chromothripsis.

染色体碎裂（Chromothripsis）是指错位分离的染色体在微核中被捕获后发生的灾难性破裂。尽管微核在间期积累DNA双链断裂和复制缺陷，但染色体如何发生碎裂仍未阐明。通过CRISPR-Cas9筛选,作者发现了范康尼贫血（FA）通路作为染色体碎裂驱动因子的非典型作用。FA通路的失活抑制了有丝分裂期间的染色体碎裂，而不会影响微核内与间期相关的缺陷。FA核心复合物通过单泛素化FANCI-FANCD2，促进其在有丝分裂期间与未完全复制的微核染色体相互作用。结构选择性的SLX4-XPF-ERCC1内切酶随后诱导持久DNA复制中间体的大规模核酸裂解，从而刺激依赖POLD3的有丝分裂DNA合成，为接下来的细胞周期中碎裂的片段重新组装做准备。值得注意的是，FA通路诱导的染色体碎裂会产生复杂的基因组重排和染色体外DNA，这些都赋予癌细胞对抗癌疗法产生获得性耐药性。该研究揭示了如何通过染色体碎裂，中心DNA修复机制的病理性激活悖论性地触发癌症基因组的进化。

10. Neoself-antigens are the primary target for autoreactive T cells in human lupus

新自体抗原通过激活自体反应性T细胞促进系统性红斑狼疮的发展

Major histocompatibility complex class II (MHC-II) is the most significant genetic risk factor for systemic lupus erythematosus (SLE), but the nature of the self-antigens that trigger autoimmunity remains unclear. Unusual self-antigens, termed neoself-antigens, are presented on MHC-II in the absence of the invariant chain essential for peptide presentation. Here, we demonstrate that neoself-antigens are the primary target for autoreactive T cells clonally expanded in SLE. When neoself-antigen presentation was induced by deleting the invariant chain in adult mice, neoself-reactive T cells were clonally expanded, leading to the development of lupus-like disease. Furthermore, we found that neoself-reactive CD4+ T cells were significantly expanded in SLE patients. A high frequency of Epstein-Barr virus reactivation is a risk factor for SLE. Neoself-reactive lupus T cells were activated by Epstein-Barr-virus-reactivated cells through downregulation of the invariant chain. Together, our findings imply that neoself-antigen presentation by MHC-II plays a crucial role in the pathogenesis of SLE.

主要组织相容性复合体II类（MHC-II）是系统性红斑狼疮（SLE）最重要的遗传风险因素，但引发自体免疫的自体抗原的性质尚不明确。异常的自体抗原，称为新自体抗原，在缺乏肽呈递所必需的恒定链的情况下呈递于MHC-II上。本研究证明了新自体抗原是SLE中克隆扩增的自身反应性T细胞的主要靶标。当通过删除恒定链在成年小鼠中诱导新自我抗原呈递时，新自体反应性T细胞发生克隆扩增，导致类似狼疮的疾病发展。此外，该研究发现SLE患者中新自体反应性CD4+ T细胞显著扩增。EB病毒活化的高频率是SLE的风险因素。新自体反应性狼疮T细胞通过下调恒定链被EB病毒活化的细胞激活。综上所述，MHC-II呈递新自体抗原在SLE发病机制中发挥了至关重要的作用。

11.5-Formylcytosine is an activating epigenetic mark for RNA Pol III during zygotic reprogramming

5-甲酰基胞嘧啶是子代重编程过程中RNA Pol III激活的表观遗传标记

5-Methylcytosine (5mC) is an established epigenetic mark in vertebrate genomic DNA, but whether its oxidation intermediates formed during TET-mediated DNA demethylation possess an instructive role of their own that is also physiologically relevant remains unresolved. Here, we reveal a 5-formylcytosine (5fC) nuclear chromocenter, which transiently forms during zygotic genome activation (ZGA) in Xenopus and mouse embryos. We identify this chromocenter as the perinucleolar compartment, a structure associated with RNA Pol III transcription. In Xenopus embryos, 5fC is highly enriched on Pol III target genes activated at ZGA, notably at oocyte-type tandem arrayed tRNA genes. By manipulating Tet and Tdg enzymes, we show that 5fC is required as a regulatory mark to promote Pol III recruitment as well as tRNA expression. Concordantly, 5fC modification of a tRNA transgene enhances its expression in vivo. The results establish 5fC as an activating epigenetic mark during zygotic reprogramming of Pol III gene expression.

5-甲基胞嘧啶（5mC）是脊椎动物基因组DNA中一个公认的表观遗传标记，但其在TET介导的DNA去甲基化过程中形成的氧化中间产物是否具有生理功能尚不清楚。研究人员发现了一个5-甲酰基胞嘧啶（5fc）核染色中心，它在章鱼和小鼠胚胎的子代基因组激活（ZGA）过程中瞬时形成。研究确定该染色中心为核周区室，这是一种与RNA Pol III 转录相关的结构。在章鱼胚胎中，5fC在ZGA激活的Pol III目标基因上高度富集，尤其是在卵母细胞的串联排列tRNA基因上。通过干扰Tet和Tdg酶，研究发现5fC是促进Pol III招募和tRNA表达所必需的调控标记。此外，对tRNA转基因进行5fC修饰可增强其在体内的表达。该研究结果表明5fC是在Pol III基因表达的合子重编程过程发挥激活功能的表观遗传标记。

Oct 31, 2024; Volume 187; Issue 22; p6125-6414;

Cell共发表18篇，其中包括1篇50th Anniversary; 12篇Articles; 3篇Resources; 1篇Correction; 1篇Retraction。

On the cover: In this issue of Cell, Kashiwagi et al. identify a brainstem circuit that acts as the switch for inducing REM sleep. The identified circuit sends output to areas that regulate forebrain activity, which is responsible for dreaming during REM sleep in humans. Defects in this circuit underlie REM sleep behavior disorder, an early prodromal symptom of Parkinson’s disease, in which patients physically act out their dreams. In the cover illustration, a mouse in REM sleep is dreaming of holding a grape, but in reality, it is holding a walnut that resembles a human brain. This image, in the Nihonga style of painting, symbolizes how the mechanisms of REM sleep uncovered in mice have contributed to the understanding of a human brain disorder. Image credit: Otama-shimai.

封面：在本期《Cell》杂志中，Kashiwagi等人识别出一个脑干回路，作为诱发快速眼动（REM）睡眠的开关。这个回路向调节前脑活动的区域发送输出，前脑活动负责REM睡眠中的梦境生成。该回路的缺陷是REM睡眠行为障碍的根本原因，这是帕金森病的早期前驱症状，患者在梦中会表现出身体动作。封面插图中，一只小鼠在REM睡眠梦中拿着一颗葡萄，但实际上它手里拿着一颗类似人脑的胡桃。这幅画采用日本传统的“日本画”风格，象征着通过揭示小鼠中的REM睡眠机制，促进了对人类脑部疾病的理解。图片来源：Otama-shimai。

1. Transplantation of chemically induced pluripotent stem-cell-derived islets under abdominal anterior rectus sheath in a type 1 diabetes patient

1型糖尿病患者的腹部前直肌鞘下移植化学诱导的多能干细胞来源的胰岛

We report the 1-year results from one patient as the preliminary analysis of a first-in-human phase I clinical trial (ChiCTR2300072200) assessing the feasibility of autologous transplantation of chemically induced pluripotent stem-cell-derived islets (CiPSC islets) beneath the abdominal anterior rectus sheath for type 1 diabetes treatment. The patient achieved sustained insulin independence starting 75 days post-transplantation. The patient’s time-in-target glycemic range increased from a baseline value of 43.18% to 96.21% by month 4 post-transplantation, accompanied by a decrease in glycated hemoglobin, an indicator of long-term systemic glucose levels at a non-diabetic level. Thereafter, the patient presented a state of stable glycemic control, with time-in-target glycemic range at >98% and glycated hemoglobin at around 5%. At 1 year, the clinical data met all study endpoints with no indication of transplant-related abnormalities. Promising results from this patient suggest that further clinical studies assessing CiPSC-islet transplantation in type 1 diabetes are warranted.

研究人员报告了一名1型糖尿病患者，在腹部前直肌鞘下自体移植化学诱导的多能干细胞来源的胰岛（CiPSC胰岛）治疗1年的结果。患者在移植后75天开始实现持续的胰岛素独立。患者的目标血糖范围时间从基线的43.18%增加到移植后第4个月的96.21%，同时伴随糖化血红蛋白的下降，后者是全身血糖水平长期处于非糖尿病水平的指标。此后，患者的血糖控制稳定，目标血糖范围时间超过98%，糖化血红蛋白维持在约5%。在1年时，临床数据达到所有研究终点，且未出现移植相关异常。这名患者的良好结果表明，进一步评估1型糖尿病中CiPSC胰岛移植的临床研究是有必要的。

2. Small-molecule GSDMD agonism in tumors stimulates antitumor immunity without toxicity

激活抗肿瘤免疫且无毒的GSDMD小分子激动剂

Gasdermin-mediated inflammatory cell death (pyroptosis) can activate protective immunity in immunologically cold tumors. Here, we performed a high-throughput screen for compounds that could activate gasdermin D (GSDMD), which is expressed widely in tumors. We identified 6,7-dichloro-2-methylsulfonyl-3-N-tert-butylaminoquinoxaline (DMB) as a direct and selective GSDMD agonist that activates GSDMD pore formation and pyroptosis without cleaving GSDMD. In mouse tumor models, pulsed and low-level pyroptosis induced by DMB suppresses tumor growth without harming GSDMD-expressing immune cells. Protection is immune-mediated and abrogated in mice lacking lymphocytes. Vaccination with DMB-treated cancer cells protects mice from secondary tumor challenge, indicating that immunogenic cell death is induced. DMB treatment synergizes with anti-PD-1. DMB treatment does not alter circulating proinflammatory cytokine or leukocyte numbers or cause weight loss. Thus, our studies reveal a strategy that relies on a low level of tumor cell pyroptosis to induce antitumor immunity and raise the possibility of exploiting pyroptosis without causing overt toxicity.

焦亡能够激活免疫冷肿瘤中的保护性免疫反应。该研究通过高通量筛选，寻找能够激活Gasdermin D（GSDMD）的小分子化合物。研究者筛选出6,7-二氯-2-甲基磺酰基-3-N-叔丁基氨基喹啉（DMB）作为一种直接且选择性的GSDMD激动剂，能够激活GSDMD孔道形成并引发焦亡，而不裂解GSDMD。在小鼠肿瘤模型中，由DMB诱导的脉冲性低水平焦亡抑制肿瘤生长，但不损害表达GSDMD的免疫细胞。使用DMB处理的癌细胞进行疫苗接种，能够保护小鼠免受二次肿瘤发生，表明已诱导免疫源性细胞死亡。DMB治疗与抗PD-1联合使用具有协同效应。DMB治疗不会改变循环中的促炎性细胞因子或白细胞数量，也不会引起体重下降。因此，研究揭示了通过低水平的肿瘤细胞焦亡来诱导抗肿瘤免疫的疗法，并提出了在不引起明显毒性的情况下利用焦亡的可能性。

3. TGF-β and RAS jointly unmask primed enhancers to drive metastasis

TGF-β 和 RAS 联合启动增强子以驱动转移

Epithelial-to-mesenchymal transitions (EMTs) and extracellular matrix (ECM) remodeling are distinct yet important processes during carcinoma invasion and metastasis. Transforming growth factor β (TGF-β) and RAS, signaling through SMAD and RAS-responsive element-binding protein 1 (RREB1), jointly trigger expression of EMT and fibrogenic factors as two discrete arms of a common transcriptional response in carcinoma cells. Here, we demonstrate that both arms come together to form a program for lung adenocarcinoma metastasis and identify chromatin determinants tying the expression of the constituent genes to TGF-β and RAS inputs. RREB1 localizes to H4K16acK20ac marks in histone H2A.Z-loaded nucleosomes at enhancers in the fibrogenic genes interleukin-11 (IL11), platelet-derived growth factor-B (PDGFB), and hyaluronan synthase 2 (HAS2), as well as the EMT transcription factor SNAI1, priming these enhancers for activation by a SMAD4-INO80 nucleosome remodeling complex in response to TGF-β. These regulatory properties segregate the fibrogenic EMT program from RAS-independent TGF-β gene responses and illuminate the operation and vulnerabilities of a bifunctional program that promotes metastatic outgrowth.

上皮-间充质转化（EMTs）和细胞外基质（ECM）重塑是癌症侵袭和转移过程中不同但至关重要的过程。转化生长因子β（TGF-β）和RAS通过SMAD和RAS反应元件结合蛋白1（RREB1）共同触发EMT和纤维形成因子的表达，构成癌细胞中共同转录反应的两个独立部分。该研究展示了这两个部分如何结合形成一个针对肺腺癌转移的程序，并识别了将组成基因的表达与TGF-β和RAS输入联系起来的染色质决定因素。RREB1定位于组蛋白H2A.Z负载的核小体中的H4K16acK20ac标记，这些核小体位于白介素-11（IL11）、血小板衍生生长因子-B（PDGFB）和透明质酸合成酶2（HAS2），以及EMT转录因子SNAI1的增强子上，为这些增强子通过SMAD4-INO80核小体重塑复合体响应TGF-β而激活做准备。这些调控特性将纤维增生性EMT程序与RAS独立的TGF-β基因反应区分开来，并阐明了一个促进转移生长的双功能程序的运作和脆弱性。

4. In vivo DNA replication dynamics unveil aging-dependent replication stress

体内DNA复制动力学揭示与衰老相关的复制压力

The genome duplication program is affected by multiple factors in vivo, including developmental cues, genotoxic stress, and aging. Here, we monitored DNA replication initiation dynamics in regenerating livers of young and old mice after partial hepatectomy to investigate the impact of aging. In young mice, the origin firing sites were well defined; the majority were located 10–50 kb upstream or downstream of expressed genes, and their position on the genome was conserved in human cells. Old mice displayed the same replication initiation sites, but origin firing was inefficient and accompanied by a replication stress response. Inhibitors of the ATR checkpoint kinase fully restored origin firing efficiency in the old mice but at the expense of an inflammatory response and without significantly enhancing the fraction of hepatocytes entering the cell cycle. These findings unveil aging-dependent replication stress and a crucial role of ATR in mitigating the stress-associated inflammation, a hallmark of aging.

体内的基因组复制程序受到多种因素的影响，包括发育信号、基因毒性应激和衰老。研究人员通过监测了年轻和年老小鼠部分肝切除术后再生肝脏中的DNA复制起始动力学，以探讨衰老的影响。在年轻小鼠中，复制起始位点明确，大多数位于表达基因上下游10–50kb的位置，并且它们在基因组中的位置在人类细胞中保持一致。老年小鼠表现出相同的复制起始位点，但起始效率低下，并伴随复制压力反应。ATR检查点激酶抑制剂在老年小鼠中完全恢复了起始效率，但代价是引发了炎症反应，并且未显著提高进入细胞周期的肝细胞比例。这些发现揭示了与衰老相关的复制压力，以及ATR在缓解与压力相关的炎症中的关键作用，这也是衰老的一个标志。

5. A pontine-medullary loop crucial for REM sleep and its deficit in Parkinson’s disease

对快速眼动睡眠至关重要的脑桥-髓质回路缺失与帕金森疾病相关

Identifying the properties of the rapid eye movement (REM) sleep circuitry and its relation to diseases has been challenging due to the neuronal heterogeneity of the brainstem. Here, we show in mice that neurons in the pontine sublaterodorsal tegmentum (SubLDT) that express corticotropin-releasing hormone-binding protein (Crhbp+ neurons) and project to the medulla promote REM sleep. Within the medullary area receiving projections from Crhbp+ neurons, neurons expressing nitric oxide synthase 1 (Nos1+ neurons) project to the SubLDT and promote REM sleep, suggesting a positively interacting loop between the pons and the medulla operating as a core REM sleep circuit. Nos1+ neurons also project to areas that control wide forebrain activity. Ablating Crhbp+ neurons reduces sleep and impairs REM sleep atonia. In Parkinson’s disease patients with REM sleep behavior disorders, CRHBP-immunoreactive neurons are largely reduced and contain pathologic α-synuclein, providing insight into the mechanisms underlying the sleep deficits characterizing this disease.

由于脑干神经元的异质性，识别快速眼动（REM）睡眠回路的特性及其与疾病的关系一直面临挑战。研究人员在小鼠中发现，脑桥嗅觉下被盖（SubLDT）中的神经元表达促肾上腺皮质激素释放激素结合蛋白（Crhbp+神经元）并投射到髓质，促进REM睡眠。在接受Crhbp+神经元投射的髓质区域内，表达一氧化氮合酶1的神经元（Nos1+神经元）投射到SubLDT并促进REM睡眠，这表明桥脑和髓质之间存在一个正反馈的回路，作为核心的REM睡眠回路。Nos1+神经元也投射到控制广泛前脑活动的区域。清除Crhbp+神经元会减少睡眠并损害REM睡眠的维持能力。在患有REM睡眠行为障碍的帕金森病患者中，CRHBP免疫反应神经元大量减少，并含有病理性α-突触核蛋白，这为深入了解该疾病睡眠缺陷的机制提供了线索。

6.CSF proteomics identifies early changes in autosomal dominant Alzheimer’s disease

脑脊液蛋白组学识别出常染色体显性阿尔茨海默病的早期变化

In this high-throughput proteomic study of autosomal dominant Alzheimer’s disease (ADAD), we sought to identify early biomarkers in cerebrospinal fluid (CSF) for disease monitoring and treatment strategies. We examined CSF proteins in 286 mutation carriers (MCs) and 177 non-carriers (NCs). The developed multi-layer regression model distinguished proteins with different pseudo-trajectories between these groups. We validated our findings with independent ADAD as well as sporadic AD datasets and employed machine learning to develop and validate predictive models. Our study identified 137 proteins with distinct trajectories between MCs and NCs, including eight that changed before traditional AD biomarkers. These proteins are grouped into three stages: early stage (stress response, glutamate metabolism, neuron mitochondrial damage), middle stage (neuronal death, apoptosis), and late presymptomatic stage (microglial changes, cell communication). The predictive model revealed a six-protein subset that more effectively differentiated MCs from NCs, compared with conventional biomarkers.

在这项关于常染色体显性阿尔茨海默病（ADAD）的高通量蛋白组学研究中，研究人员旨在识别脑脊液中的早期生物标志物，以便进行疾病监测和治疗策略。研究人员对286名突变携带者（MC）和177名非携带者（NC）的脑脊液蛋白进行了分析。所开发的多层回归模型区分了这两个组之间具有不同伪轨迹的蛋白质。研究人员使用独立的ADAD和散发性AD数据集验证了这些发现，并采用机器学习开发和验证预测模型。该究识别出137种在MC和NC之间具有不同轨迹的蛋白质，其中八种在传统AD生物标志物之前发生变化。这些蛋白质分为三个阶段：早期阶段（应激反应、谷氨酸代谢、神经元线粒体损伤）、中期阶段（神经元死亡、凋亡）和晚期无症状阶段（小胶质细胞变化、细胞通信）。预测模型识别出六种蛋白质，能够比传统生物标志物更有效地区分MC和NC。

7. Emergence of community behaviors in the gut microbiota upon drug treatment

药物治疗下肠道微生物群体行为的出现

Pharmaceuticals can directly inhibit the growth of gut bacteria, but the degree to which such interactions manifest in complex community settings is an open question. Here, we compared the effects of 30 drugs on a 32-species synthetic community with their effects on each community member in isolation. While most individual drug-species interactions remained the same in the community context, communal behaviors emerged in 26% of all tested cases. Cross-protection during which drug-sensitive species were protected in community was 6 times more frequent than cross-sensitization, the converse phenomenon. Cross-protection decreased and cross-sensitization increased at higher drug concentrations, suggesting that the resilience of microbial communities can collapse when perturbations get stronger. By metabolically profiling drug-treated communities, we showed that both drug biotransformation and bioaccumulation contribute mechanistically to communal protection. As a proof of principle, we molecularly dissected a prominent case: species expressing specific nitroreductases degraded niclosamide, thereby protecting both themselves and sensitive community members.

药物可以直接抑制肠道细菌的生长，但这种相互作用在复杂群体环境中的表现程度仍然未知。研究人员比较了30种药物对32种合成群体的整体影响与其对每个群体成员单独作用的影响。尽管大多数单个药物-物种相互作用在群体环境中保持不变，但在所有测试案例中，有26%出现了群体行为。在群体中，药物敏感物种受到交叉保护的现象发生的频率是交叉敏感的6倍，反之亦然。随着药物浓度升高，交叉保护减少而交叉敏感增加，这表明当干扰增强时，微生物群落的恢复能力可能会崩溃。通过对药物处理的群落进行代谢特征分析，研究人员表明药物的生物转化和生物累积在机制上均有助于群体保护。作为原理验证，研究人员在分子层面解析了一个突出案例：表达特定硝基还原酶的物种降解了氯硝柳胺，从而保护了自身和敏感的群体成员。

Nov 14, 2024; Volume 187; Issue 23; p6415-6784;

Cell共发表25篇，其中包括4篇50th Anniversary; 3篇Featured Articles；1篇Preview；8篇Articles; 6篇Resources; 2篇Correction; 1篇Snapshot。

On the cover: In this issue of Cell, Bai et al. develop a pathology-compatible deterministic barcoding in tissue (Patho-DBiT) technology for spatial sequencing of diverse RNA species in clinically archived formalin-fixed paraffin-embedded (FFPE) tissue samples. Patho-DBiT permits spatial co-profiling of large and small non-coding RNAs, splicing isoforms, genome-scale single nucleotide variants, and RNA dynamics from a single run. The cover image features the super-resolved tissue architecture of a human lymphoma FFPE section, along with multiple layers of spatial RNA maps revealed by Patho-DBiT. Image credit: Hannah Wang and Zhiliang Bai.

封面：在本期《Cell》杂志中，Bai等人开发了一种病理学兼容的组织决定性条形码技术（Patho-DBiT），用于对临床存档的福尔马林固定石蜡包埋（FFPE）组织样本进行空间RNA物种测序。Patho-DBiT允许在一次实验中对大小非编码RNA、剪接异构体、基因组规模的单核苷酸变异（SNVs）以及RNA动力学的进行空间共谱分析。封面图展示了人类淋巴瘤FFPE切片的超分辨率组织结构，以及Patho-DBiT揭示的多层空间RNA图谱。图片来源：Hannah Wang 和 Zhiliang Bai。

1. A core microbiome signature as an indicator of health

核心微生物组特征可作为健康指标

The gut microbiota is crucial for human health, functioning as a complex adaptive system akin to a vital organ. To identify core health-relevant gut microbes, we followed the systems biology tenet that stable relationships signify core components. By analyzing metagenomic datasets from a high-fiber dietary intervention in type 2 diabetes and 26 case-control studies across 15 diseases, we identified a set of stably correlated genome pairs within co-abundance networks perturbed by dietary interventions and diseases. These genomes formed a “two competing guilds” (TCGs) model, with one guild specialized in fiber fermentation and butyrate production and the other characterized by virulence and antibiotic resistance. Our random forest models successfully distinguished cases from controls across multiple diseases and predicted immunotherapy outcomes through the use of these genomes. Our guild-based approach, which is genome specific, database independent, and interaction focused, identifies a core microbiome signature that serves as a holistic health indicator and a potential common target for health enhancement.

肠道微生物群对人类健康至关重要，作为一种复杂的适应系统，其功能类似于一个重要器官。为了确定与健康相关的核心肠道微生物，研究人员遵循了系统生物学的原则，即稳定的关系标志着核心组成部分。通过分析来自2型糖尿病高纤维饮食干预的宏基因组数据集以及15种疾病的26项病例对照研究，研究人员在受饮食干预和疾病影响的共同丰度网络中识别出一组稳定相关的基因组对。这些基因组形成了一个“两竞争行会”（TCG）模型，其中一个行会专门负责纤维发酵和丁酸盐产生，另一个行会则以毒性和抗生素耐药性为特征。随机森林模型成功地区分了多种疾病中的病例与对照组，并通过使用这些基因组预测了免疫治疗的结果。研究人员基于微生物群体的策略，专注于基因组、独立于数据库和交互作用，进而识别出一个核心微生物组特征，作为整体健康指标和潜在健康促进的目标。

2.Structural basis of respiratory complex adaptation to cold temperatures

呼吸系统复合物适应寒冷温度的结构基础

In response to cold, mammals activate brown fat for respiratory-dependent thermogenesis reliant on the electron transport chain. Yet, the structural basis of respiratory complex adaptation upon cold exposure remains elusive. Herein, we combined thermoregulatory physiology and cryoelectron microscopy (cryo-EM) to study endogenous respiratory supercomplexes from mice exposed to different temperatures. A cold-induced conformation of CI:III2 (termed type 2) supercomplex was identified with a ∼25° rotation of CIII2 around its inter-dimer axis, shortening inter-complex Q exchange space, and exhibiting catalytic states that favor electron transfer. Large-scale supercomplex simulations in mitochondrial membranes reveal how lipid-protein arrangements stabilize type 2 complexes to enhance catalytic activity. Together, our cryo-EM studies, multiscale simulations, and biochemical analyses unveil the thermoregulatory mechanisms and dynamics of increased respiratory capacity in brown fat at the structural and energetic level.

为了应对寒冷，哺乳动物激活棕色脂肪，通过依赖于电子传递链的呼吸作用产热。然而，寒冷暴露下呼吸复合体适应的结构基础仍不清楚。该研究者结合了体温调节生理学和冷冻电子显微镜（cryo-EM）来研究暴露于不同温度下的小鼠的内源性呼吸超复合物。研究人员鉴定了一种冷诱导的CI:III2（称为2型）超复合物构象，其中CIII2围绕其二聚体间轴旋转了约25°，缩短了复合体间Q交换空间，并展现出有利于电子转移的催化状态。在线粒体膜中的大规模超复合物模拟揭示了脂质-蛋白质排列如何稳定2型复合物，以增强催化活性。该研究的冷冻电镜、多尺度模拟和生化分析共同揭示了棕色脂肪在结构和能量水平上呼吸能力增强的体温调节机制和动力学。

3. A transmitochondrial sodium gradient controls membrane potential in mammalian mitochondria

跨线粒体钠梯度控制哺乳动物线粒体的膜电位

Eukaryotic cell function and survival rely on the use of a mitochondrial H+ electrochemical gradient (Δp), which is composed of an inner mitochondrial membrane (IMM) potential (ΔΨmt) and a pH gradient (ΔpH). So far, ΔΨmt has been assumed to be composed exclusively of H+. Here, using a rainbow of mitochondrial and nuclear genetic models, we have discovered that a Na+ gradient equates with the H+ gradient and controls half of ΔΨmt in coupled-respiring mammalian mitochondria. This parallelism is controlled by the activity of the long-sought Na+-specific Na+/H+ exchanger (mNHE), which we have identified as the P-module of complex I (CI). Deregulation of this mNHE function, without affecting the canonical enzymatic activity or the assembly of CI, occurs in Leber’s hereditary optic neuropathy (LHON), which has profound consequences in ΔΨmt and mitochondrial Ca2+ homeostasis and explains the previously unknown molecular pathogenesis of this neurodegenerative disease.

真核细胞的功能和存活依赖于线粒体H+电化学梯度（Δp），该梯度由线粒体内膜电位（ΔΨmt）和pH梯度（ΔpH）组成。此前，线粒体内膜电位被假设为完全由H+组成。使用一系列线粒体和核遗传模型，研究人员发现Na+梯度等同于H+梯度，并控制着耦合呼吸哺乳动物线粒体中线粒体内膜电位的一半。这种平行性是由长期寻找的Na+特异性Na+/H+交换器（mNHE）的活性控制的，研究人员将其确定为复合物I（CI）的P模块。Leber遗传性视神经病变（LHON）中，mNHE功能失调，但不影响典型酶活性或CI的组装。这种失调对线粒体内膜电位和线粒体Ca2+稳态具有深远的影响，并解释了这种神经退行性疾病以前未知的分子发病机制。

4. Intercellular nanotube-mediated mitochondrial transfer enhances T cell metabolic fitness and antitumor efficacy

细胞间纳米管介导的线粒体转移增强 T 细胞代谢适应性和抗肿瘤功效

Mitochondrial loss and dysfunction drive T cell exhaustion, representing major barriers to successful T cell-based immunotherapies. Here, we describe an innovative platform to supply exogenous mitochondria to T cells, overcoming these limitations. We found that bone marrow stromal cells establish nanotubular connections with T cells and leverage these intercellular highways to transplant stromal cell mitochondria into CD8+ T cells. Optimal mitochondrial transfer required Talin 2 on both donor and recipient cells. CD8+ T cells with donated mitochondria displayed enhanced mitochondrial respiration and spare respiratory capacity. When transferred into tumor-bearing hosts, these supercharged T cells expanded more robustly, infiltrated the tumor more efficiently, and exhibited fewer signs of exhaustion compared with T cells that did not take up mitochondria. As a result, mitochondria-boosted CD8+ T cells mediated superior antitumor responses, prolonging animal survival. These findings establish intercellular mitochondrial transfer as a prototype of organelle medicine, opening avenues to next-generation cell therapies.

线粒体丢失和功能障碍是驱动T细胞衰竭的关键因素，也是基于 T 细胞的免疫疗法取得成功的主要障碍。在该研究中，研究者描述了通过向T细胞提供外源性线粒体，克服这些限制的创新性平台。研究发现，骨髓间质细胞与T细胞建立了纳米管连接，并利用这些细胞间的通道将间质细胞的线粒体转移到CD8+T细胞中。最佳的线粒体转移需要供体和受体细胞上的Talin2。接受供体线粒体的CD8+T细胞表现出增强的线粒体呼吸功能和剩余呼吸能力。当转移到肿瘤携带小鼠中时，这些“超充电”的T细胞比未接受线粒体的T细胞更强烈地扩增，更有效地渗透肿瘤，并表现出较少的衰竭迹象。因此，线粒体增强的CD8+T细胞介导了更优的抗肿瘤反应，延长了动物的生存期。这些发现确立了细胞间线粒体转移作为一种细胞器医学的原型，为下一代细胞疗法开辟了新途径。

5. Lung-resident alveolar macrophages regulate the timing of breast cancer metastasis

肺驻留肺泡巨噬细胞调节乳腺癌转移的时机

Breast disseminated cancer cells (DCCs) can remain dormant in the lungs for extended periods, but the mechanisms limiting their expansion are not well understood. Research indicates that tissue-resident alveolar macrophages suppress breast cancer metastasis in lung alveoli by inducing dormancy. Through ligand-receptor mapping and intravital imaging, it was found that alveolar macrophages express transforming growth factor (TGF)-β2. This expression, along with persistent macrophage-cancer cell interactions via the TGF-βRIII receptor, maintains cancer cells in a dormant state. Depleting alveolar macrophages or losing the TGF-β2 receptor in cancer cells triggers metastatic awakening. Aggressive breast cancer cells are either suppressed by alveolar macrophages or evade this suppression by avoiding interaction and downregulating the TGF-β2 receptor. Restoring TGF-βRIII in aggressive cells reinstates TGF-β2-mediated macrophage growth suppression. Thus, alveolar macrophages act as a metastasis immune barrier, and downregulation of TGF-β2 signaling allows cancer cells to overcome macrophage-mediated growth suppression.

乳腺转移癌细胞可以在肺部保持很长时间的休眠状态，但限制它们扩增的机制尚不清楚。研究人员表明，组织驻留的肺泡巨噬细胞通过诱导休眠来抑制乳腺癌在肺泡中的转移。通过配体-受体定位和活体成像，发现肺泡巨噬细胞表达转化生长因子（TGF）-β2。这种表达以及通过TGF-βRIII受体与癌细胞的持续相互作用使癌细胞保持在休眠状态。去除肺泡巨噬细胞或在癌细胞中失去TGF-β2受体会触发转移细胞觉醒。侵袭性乳腺癌细胞要么被肺泡巨噬细胞抑制，要么通过避免相互作用和下调TGF-β2受体来逃避这种抑制。在侵袭性细胞中恢复TGF-βRIII，会重新建立TGF-β2介导的巨噬细胞生长抑制。因此，肺泡巨噬细胞作为转移的免疫屏障，而TGF-β2信号的下调使癌细胞能够克服巨噬细胞介导的生长抑制。

Nov 27, 2024；Volume 187；Issue 24；p6785-7044

Cell共发表16篇，其中包括9篇Articles; 6篇Featured Article；1篇Resources。

On the cover: The cover, related to Hou et al., uses intricate geometric patterns and biological details to showcase various RNA virus structures, symbolizing the diversity and complexity of the viral world. The virus shapes in the image subtly resemble the digits 0 and 1, alluding to the binary system used in computers and indirectly reflecting the exploration of new viruses through artificial intelligence and computational technology. Image source: Jianye Li, Wan Wang, and Zan Xu.

封面：与Hou等人相关的封面使用复杂的几何图案和生物细节来展示各种 RNA 病毒结构，象征着病毒世界的多样性和复杂性。图像中的病毒形状巧妙地类似于数字0和1，暗示了计算机中使用的二进制系统，并间接反映了通过人工智能和计算技术对新病毒的探索。图片来源：李建业、王婉和徐赞。

1. The multi-stage plasticity in the aggression circuit underlying the winner effect

研究揭示胜利效应背后的攻击性回路中的多阶段可塑性

Winning increases the readiness to attack and the probability of winning, a widespread phenomenon known as the “winner effect.” Here, we reveal a transition from target-specific to generalized aggression enhancement over 10 days of winning in male mice. This behavioral change is supported by three causally linked plasticity events in the ventrolateral part of the ventromedial hypothalamus (VMHvl), a critical node for aggression. Over 10 days of winning, VMHvl cells experience monotonic potentiation of long-range excitatory inputs, transient local connectivity strengthening, and a delayed excitability increase. Optogenetically coactivating the posterior amygdala (PA) terminals and VMHvl cells potentiates the PA-VMHvl pathway and triggers the same cascade of plasticity events observed during repeated winning. Optogenetically blocking PA-VMHvl synaptic potentiation eliminates all winning-induced plasticity. These results reveal the complex Hebbian synaptic and excitability plasticity in the aggression circuit during winning, ultimately leading to increased “aggressiveness” in repeated winners.

胜利增强了攻击的准备性和获胜的概率，这一现象被称为“胜利效应”。研究人员揭示了在雄性小鼠获胜后的10天中，从目标特异性的攻击过渡到普遍性攻击增强的转变。这一行为变化由位于腹内侧下丘脑（VMHvl）的攻击性关键节点中的三个因果相关的可塑性事件所支持。在获胜的10天内，腹内侧下丘脑细胞经历了长距离兴奋性输入的单调增强、瞬时局部连接的增强以及延迟的兴奋性增强。光遗传学共激活后杏仁核末梢和腹内侧下丘脑细胞增强了杏仁核-腹内侧下丘脑通路，并触发了在反复胜利中观察到的相同可塑性事件级联。光遗传学阻断杏仁核-腹内侧下丘脑突触增强则消除了所有由胜利引发的可塑性变化。这些结果揭示了在胜利期间攻击性回路中的复杂Hebbian突触和兴奋性可塑性，最终导致重复获胜者的“攻击性”增加。

2. Mechanisms of memory-supporting neuronal dynamics in hippocampal area

海马区支持记忆的神经元动力学机制

Hippocampal CA3 is central to memory formation and retrieval. Although various network mechanisms have been proposed, direct evidence is lacking. Using intracellular Vm recordings and optogenetic manipulations in behaving mice, we found that CA3 place-field activity is produced by a symmetric form of behavioral timescale synaptic plasticity (BTSP) at recurrent synapses among CA3 pyramidal neurons but not at synapses from the dentate gyrus (DG). Additional manipulations revealed that excitatory input from the entorhinal cortex (EC) but not the DG was required to update place cell activity based on the animal’s movement. These data were captured by a computational model that used BTSP and an external updating input to produce attractor dynamics under online learning conditions. Theoretical analyses further highlight the superior memory storage capacity of such networks, especially when dealing with correlated input patterns. This evidence elucidates the cellular and circuit mechanisms of learning and memory formation in the hippocampus.

海马CA3区在记忆的形成和检索中至关重要。尽管提出了各种网络机制，但缺乏直接的实验证据。通过对行为小鼠进行细胞内膜电位记录和光遗传学操作，研究人员发现CA3区的位置场活动是由CA3锥体神经元间的递归突触的行为时间标度突触可塑性（BTSP）对称形式产生的，而在齿状回（DG）突触中并不存在。进一步的操作揭示，从内嗅皮层（EC）而非DG的兴奋性输入需要根据动物运动来更新位置细胞的活动。这些数据通过一个计算模型得以捕捉，该模型使用BTSP和外部更新输入在在线学习条件下产生吸引子动力学。理论分析进一步强调了此类网络的优越记忆存储能力，特别是在处理相关输入模式时。这些发现阐明了海马中学习和记忆形成的细胞和回路机制。

3. PLD3 and PLD4 synthesize S, S-BMP, a key phospholipid enabling lipid degradation in lysosomes

PLD3和PLD4合成S,S-BMP来促进溶酶体中的脂质降解

Bis(monoacylglycero)phosphate (BMP) is an abundant lysosomal phospholipid required for degradation of lipids, particularly gangliosides. Alterations in BMP levels are associated with neurodegenerative diseases. Unlike typical glycerophospholipids, lysosomal BMP has two chiral glycerol carbons in the S (rather than the R) stereo-conformation, protecting it from lysosomal degradation. How this unusual and yet crucial S,S-stereochemistry is achieved is unknown. Here, we report that phospholipases D3 and D4 (PLD3 and PLD4) synthesize lysosomal S,S-BMP, with either enzyme catalyzing the critical glycerol stereo-inversion reaction in vitro. Deletion of PLD3 or PLD4 markedly reduced BMP levels in cells or in murine tissues where either enzyme is highly expressed (brain for PLD3; spleen for PLD4), leading to gangliosidosis and lysosomal abnormalities. PLD3 mutants associated with neurodegenerative diseases, including risk of Alzheimer’s disease, diminished PLD3 catalytic activity. We conclude that PLD3/4 enzymes synthesize lysosomal S,S-BMP, a crucial lipid for maintaining brain health.

双甘油单酰基磷酸酯（BMP）是一种丰富的溶酶体磷脂，在神经节苷脂的降解过程中起着重要作用。BMP水平的改变与神经退行性疾病的发生密切相关。与典型的甘油磷脂不同，溶酶体中的BMP具有两个S构型（而非R构型）的手性甘油碳，这种独特的构型使其免受溶酶体降解。然而，这种独特但至关重要的S,S立体化学是如何形成的，尚不清楚。在本研究中，作者发现磷脂酶D3和D4（PLD3和PLD4）负责合成溶酶体中的S,S-BMP，其中任一酶在体外均可催化关键的甘油立体翻转反应。删除PLD3或PLD4基因会显著降低细胞或特定小鼠组织中BMP的水平（PLD3在脑部高度表达，PLD4在脾脏高度表达），导致神经节苷脂积累和溶酶体异常。此外，与神经退行性疾病相关（包括阿尔茨海默病风险）的PLD3突变体会削弱PLD3的催化活性。作者认为，PLD3/4酶通过合成溶酶体中的S,S-BMP，提供了一种维持大脑健康所必需的关键脂质。

4. RNA G-quadruplexes form scaffolds that promote neuropathological α-synuclein aggregation

RNA G-四链体形成支架促进神经病理性α-突触核蛋白聚集

Synucleinopathies, including Parkinson’s disease, dementia with Lewy bodies, and multiple system atrophy, are triggered by α-synuclein aggregation, triggering progressive neurodegeneration. However, the intracellular α-synuclein aggregation mechanism remains unclear. Herein, we demonstrate that RNA G-quadruplex assembly forms scaffolds for α-synuclein aggregation, contributing to neurodegeneration. Purified α-synuclein binds RNA G-quadruplexes directly through the N terminus. RNA G-quadruplexes undergo Ca2+-induced phase separation and assembly, accelerating α-synuclein sol-gel phase transition. In α-synuclein preformed fibril-treated neurons, RNA G-quadruplex assembly comprising synaptic mRNAs co-aggregates with α-synuclein upon excess cytoplasmic Ca2+ influx, eliciting synaptic dysfunction. Forced RNA G-quadruplex assembly using an optogenetic approach evokes α-synuclein aggregation, causing neuronal dysfunction and neurodegeneration. The administration of 5-aminolevulinic acid, a protoporphyrin IX prodrug, prevents RNA G-quadruplex phase separation, thereby attenuating α-synuclein aggregation, neurodegeneration, and progressive motor deficits in α-synuclein preformed fibril-injected synucleinopathic mice. Therefore, Ca2+ influx-induced RNA G-quadruplex assembly accelerates α-synuclein phase transition and aggregation, potentially contributing to synucleinopathies.

突触核蛋白病，包括帕金森病、路易体痴呆和多系统萎缩，是由α-突触核蛋白异常聚集引发的，并导致渐进性神经退行性病变。然而，细胞内α-突触核蛋白聚集的具体分子机制尚不明确。本研究作者发现RNA G-四链体的组装形成了α-突触核蛋白聚集的支架，从而促进神经退行性病变。纯化的α-突触核蛋白通过N末端直接结合RNA G-四链体。RNA G-四链体在Ca²⁺诱导下发生相分离和组装，加速了α-突触核蛋白从溶胶到凝胶的相变。在经α-突触核蛋白预形成纤维（preformed fibril, PFF）处理的神经元中，包含突触mRNA的RNA G-四链体组装在过量胞质Ca²⁺内流的条件下与α-突触核蛋白共同聚集，导致突触功能障碍。通过光遗传学方法强制RNA G-四链体组装，能够诱导α-突触核蛋白聚集，造成神经元功能障碍和神经退行性病变。应用5-氨基乙酰丙酸（一种原卟啉IX的前体药物）可以阻止RNA G-四链体的相分离，从而减轻α-突触核蛋白的聚集、神经退行性病变以及在α-突触核蛋白预形成纤维注射的突触核蛋白病小鼠模型中观察到的渐进性运动障碍。因此，Ca²⁺内流诱导的RNA G-四链体组装加速了α-突触核蛋白的相变和聚集，这可能是突触核蛋白病的致病机制之一。

5. Molecular basis of global promoter sensing and nucleosome capture by the SWR1 chromatin remodeler

SWR1染色质重塑复合物对全局启动子感应和核小体捕获的分子基础

The SWR1 chromatin remodeling complex is recruited to +1 nucleosomes downstream of transcription start sites of eukaryotic promoters, where it exchanges histone H2A for the specialized variant H2A.Z. Here, we use cryoelectron microscopy (cryo-EM) to resolve the structural basis of the SWR1 interaction with free DNA, revealing a distinct open conformation of the Swr1 ATPase that enables sliding from accessible DNA to nucleosomes. A complete structural model of the SWR1-nucleosome complex illustrates critical roles for Swc2 and Swc3 subunits in oriented nucleosome engagement by SWR1. Moreover, an extended DNA-binding α helix within the Swc3 subunit enables sensing of nucleosome linker length and is essential for SWR1-promoter-specific recruitment and activity. The previously unresolved N-SWR1 subcomplex forms a flexible extended structure, enabling multivalent recognition of acetylated histone tails by reader domains to further direct SWR1 toward the +1 nucleosome. Altogether, our findings provide a generalizable mechanism for promoter-specific targeting of chromatin and transcription complexes.

SWR1染色质重塑复合物被招募至真核生物启动子转录起始位点下游的+1核小体，并在此位置将组蛋白H2A替换为特殊变体H2A.Z。本研究中，作者利用冷冻电子显微镜（cryo-EM）解析了SWR1与游离DNA相互作用的结构基础，揭示了Swr1 ATP酶的独特开放构象，使其能够从可接近的DNA滑动至核小体。SWR1-核小体复合物的完整结构模型表明，Swc2和Swc3亚基在SWR1定向结合核小体的过程中起着关键作用。此外，Swc3亚基中的一个延长的DNA结合α螺旋能够感应核小体连接区长度，这对于SWR1的启动子特异性招募和活性至关重要。此前未解析的N-SWR1亚复合物形成了一个灵活的扩展结构，通过识别乙酰化组蛋白尾的多价结合域进一步引导SWR1定位于+1核小体。总之，研究揭示了染色质和转录复合物启动子特异性靶向的一种通用的机制。

6.Structure of TnsABCD transpososome reveals mechanisms of targeted DNA transposition TnsABCD转座子的结构揭示靶向DNA转座的机制

Tn7-like transposons are characterized by their ability to insert specifically into host chromosomes. Recognition of the attachment (att) site by TnsD recruits the TnsABC proteins to form the transpososome and facilitate transposition. Although this pathway is well established, atomic-level structural insights of this process remain largely elusive. Here, we present the cryo-electron microscopy (cryo-EM) structures of the TnsC-TnsD-att DNA complex and the TnsABCD transpososome from the Tn7-like transposon in Peltigera membranacea cyanobiont 210A, a type I-B CRISPR-associated transposon. Our structures reveal a striking bending of the att DNA, featured by the intercalation of an arginine side chain of TnsD into a CC/GG dinucleotide step. The TnsABCD transpososome structure reveals TnsA-TnsB interactions and demonstrates that TnsC not only recruits TnsAB but also directly participates in the transpososome assembly. These findings provide mechanistic insights into targeted DNA insertion by Tn7-like transposons, with implications for improving the precision and efficiency of their genome-editing applications.

Tn7类转座子的特点是能够特异性插入宿主染色体。TnsD通过识别att位点招募TnsABC蛋白形成转座复合物，从而促进转座过程。尽管这一通路已得到充分研究，但关于该过程的原子级结构信息仍然鲜为人知。研究人员展示了在Peltigera membranacea蓝藻共生体210A中的Tn7类转座子（一种I-B型CRISPR相关转座子）中TnsC-TnsD-att DNA复合物和TnsABCD转座复合物的冷冻电镜（cryo-EM）结构。该结构揭示了结合位点（att）DNA的显著弯曲，特点是TnsD的精氨酸侧链插入CC/GG二核苷酸阶梯。TnsABCD转座复合物的结构显示了TnsA-TnsB的相互作用，并表明TnsC不仅招募TnsAB，还直接参与了转座复合物的组装。这些发现为Tn7类转座子的靶向插入DNA的机制提供了见解，并对提高其应用于基因编辑的精准性和效率具有重要意义。

7. Mechanistic study of a low-power bacterial maintenance state using high-throughput electrochemistry

通过高通量电化学对低能耗细菌维持状态的机制研究

Mechanistic studies of life’s lower metabolic limits have been limited due to a paucity of tractable experimental systems. Here, we show that redox-cycling of phenazine-1-carboxamide (PCN) by Pseudomonas aeruginosa supports cellular maintenance in the absence of growth with a low mass-specific metabolic rate of 8.7 × 10−4 W (g C)−1 at 25°C. Leveraging a high-throughput electrochemical culturing device, we find that non-growing cells cycling PCN tolerate conventional antibiotics but are susceptible to those that target membrane components. Under these conditions, cells conserve energy via a noncanonical, facilitated fermentation that is dependent on acetate kinase and NADH dehydrogenases. Across PCN concentrations that limit cell survival, the cell-specific metabolic rate is constant, indicating the cells are operating near their bioenergetic limit. This quantitative platform opens the door to further mechanistic investigations of maintenance, a physiological state that underpins microbial survival in nature and disease.

由于缺乏可操作的实验系统，研究生命最低代谢极限的机制一直受到限制。研究人员展示了铜绿假单胞菌通过对吩嗪-1-甲酰胺（PCN）的氧化还原循环支持细胞在无生长状态下的生命维持，其质量特异性代谢率在25°C下为8.7 × 10−4 W (g C)−1。利用高通量电化学培养设备，研究人员发现循环PCN的非生长细胞对传统抗生素具有耐受性，但对那些靶向膜成分的抗生素则易感。在这些条件下，细胞通过一种非经典的、依赖于乙酸激酶和NADH脱氢酶的促进发酵方式来节能。在的不同PCN浓度下，尽管限制细胞存活受到限制，其特定代谢率保持恒定，表明细胞的生物能量极限接近。这一定量平台为进一步研究维持机制提供了可能，这种生理状态为微生物在自然界和疾病中的生存奠定了基础。

8. Rift Valley fever virus coordinates the assembly of a programmable E3 ligase to promote viral replication

裂谷热病毒协调组装一个可编程的E3连接酶以促进病毒复制

Viruses encode strategies to degrade cellular proteins to promote infection and pathogenesis. Here, we revealed that the non-structural protein NSs of Rift Valley fever virus forms a filamentous E3 ligase to trigger efficient degradation of targeted proteins. Reconstitution in vitro and cryoelectron microscopy analysis with the 2.9-Å resolution revealed that NSs forms right-handed helical fibrils. The NSs filamentous oligomers associate with the cellular FBXO3 to form a remodeled E3 ligase. The NSs-FBXO3 E3 ligase targets the cellular TFIIH complex through the NSs-P62 interaction, leading to ubiquitination and proteasome-dependent degradation of the TFIIH complex. NSs-FBXO3-triggered TFIIH complex degradation resulted in robust inhibition of antiviral immunity and promoted viral pathogenesis in vivo. Furthermore, it is demonstrated that NSs can be programmed to target additional proteins for proteasome-dependent degradation, serving as a versatile targeted protein degrader. These results showed that a virulence factor forms a filamentous and programmable degradation machinery to induce organized degradation of cellular proteins to promote viral infection.

病毒通过编码策略降解细胞蛋白以促进感染和致病。在本研究发现裂谷热病毒的非结构蛋白NSs会形成一种丝状E3连接酶，触发目标蛋白的高效降解。通过体外重建和2.9 Å分辨率的冷冻电子显微镜分析表明，NSs形成右手螺旋纤维状聚合物。NSs丝状寡聚物与细胞FBXO3结合，形成重塑的E3连接酶。NSs-FBXO3 E3连接酶通过NSs与P62的相互作用靶向细胞TFIIH复合物，导致其泛素化，并通过蛋白酶体途径降解。NSs-FBXO3触发的TFIIH复合物降解显著抑制了抗病毒免疫，并在体内促进了病毒致病性。此外，研究表明，NSs可以被编程以靶向其他蛋白进行蛋白酶体依赖性降解，充当一种多功能的靶向蛋白降解工具。上述研究结果表明，一种毒力因子能够形成丝状且可编程的降解机制，以组织化方式降解细胞蛋白，从而促进病毒感染。

9. Genome integrity sensing by the broad-spectrum Hachiman antiphage defense complex

广谱Hachiman抗噬菌体防御复合物的基因组完整性感应机制

Hachiman is a broad-spectrum antiphage defense system of unknown function. We show here that Hachiman is a heterodimeric nuclease-helicase complex, HamAB. HamA, previously a protein of unknown function, is the effector nuclease. HamB is the sensor helicase. HamB constrains HamA activity during surveillance of intact double-stranded DNA (dsDNA). When the HamAB complex detects DNA damage, HamB helicase activity activates HamA, unleashing nuclease activity. Hachiman activation degrades all DNA in the cell, creating “phantom” cells devoid of both phage and host DNA. We demonstrate Hachiman activation in the absence of phage by treatment with DNA-damaging agents, suggesting that Hachiman responds to aberrant DNA states. Phylogenetic similarities between the Hachiman helicase and enzymes from eukaryotes and archaea suggest deep functional symmetries with other important helicases across domains of life.

Hachiman是一种功能未知的广谱抗噬菌体防御系统。本研究表明，Hachiman是一个由核酸酶（HamA）和解旋酶（HamB）组成的异源二聚体复合物，称为HamAB。HamA曾被认为是功能未知的蛋白质，现被鉴定为效应核酸酶；HamB则是感应解旋酶。在监测完整的双链DNA（dsDNA）过程中，HamB限制了HamA的活性。当HamAB复合物检测到DNA损伤时，HamB的解旋酶活性被激活，进而释放出HamA的核酸酶活性。Hachiman的激活会降解细胞内的所有DNA，产生既无噬菌体DNA又无宿主DNA的“幻影”细胞。该研究通过DNA损伤剂处理细胞，在没有噬菌体的情况下观察到Hachiman的激活，这表明Hachiman对异常DNA状态做出反应。Hachiman解旋酶与真核生物和古细菌中相关酶的系统发育相似性表明，它与其他生命领域的重要解旋酶在功能上可能存在深层对称性。

汇报人：张玉忠

博后合作导师：赵宇教授

审核：王肖宇、吴桂儀