【Nature】2024年8月4周刊论文导读

期刊介绍：

《Nature》是一本国际性周刊，致力于发表各领域科学和技术中最优质的经同行评审的研究，基于其原创性、重要性、跨学科兴趣、时效性和可读性的结论。《Nature》还提供快速、权威、深刻且引人注目的新闻报道与解读，涵盖影响科学、科学家和更广泛公众的热门趋势和未来趋势。最新影响因子为50.5。

Volume 632 Issue 8026, 22 August 2024

在2024年8月632卷8026期，Nature共发表文章56篇，其中包括1篇Editorial，1篇World View，4篇Research Highlights，7篇News in Focus，2篇Books & Arts，7篇Opinion，3篇Work，6篇News & Views，25篇Article。

1. Single-cell multiregion dissection of Alzheimer’s disease

阿尔茨海默病的单细胞多区域解剖

麻省理工学院计算机科学与人工智能实验室，美国

麻省理工学院和哈佛大学博德研究所，美国

Abstract

Alzheimer’s disease is the leading cause of dementia worldwide, but the cellular pathways that underlie its pathological progression across brain regions remain poorly understood^1-3. Here we report a single-cell transcriptomic atlas of six different brain regions in the aged human brain, covering 1.3 million cells from 283 post-mortem human brain samples across 48 individuals with and without Alzheimer’s disease. We identify 76 cell types, including region-specific subtypes of astrocytes and excitatory neurons and an inhibitory interneuron population unique to the thalamus and distinct from canonical inhibitory subclasses. We identify vulnerable populations of excitatory and inhibitory neurons that are depleted in specific brain regions in Alzheimer’s disease, and provide evidence that the Reelin signalling pathway is involved in modulating the vulnerability of these neurons. We develop a scalable method for discovering gene modules, which we use to identify cell-type-specific and region-specific modules that are altered in Alzheimer’s disease and to annotate transcriptomic differences associated with diverse pathological variables. We identify an astrocyte program that is associated with cognitive resilience to Alzheimer’s disease pathology, tying choline metabolism and polyamine biosynthesis in astrocytes to preserved cognitive function late in life. Together, our study develops a regional atlas of the ageing human brain and provides insights into cellular vulnerability, response and resilience to Alzheimer’s disease pathology.

摘要

阿尔茨海默病是全球范围内导致痴呆症的主要原因，但其在大脑各个区域的病理进展背后的细胞通路仍不清楚。本研究构建了一个涵盖老年人类大脑六个不同区域的单细胞转录组图谱，分析了来自48名患有和未患有阿尔茨海默病的个体的283份死亡后大脑样本，共计130万个细胞。研究鉴定出76种细胞类型，包括特定脑区的星形胶质细胞和兴奋性神经元亚型，以及一种仅存在于丘脑中、不同于经典抑制性亚类的特有抑制性中间神经元亚群。在阿尔茨海默病患者中，研究发现了一些易受影响的兴奋性和抑制性神经元亚群，这些亚群在特定脑区中表现出耗竭现象，并揭示了Reelin信号通路在调控这些神经元易感性中的作用。研究开发了一种可扩展的基因模块鉴定方法，并利用该方法识别出在阿尔茨海默病中发生变化的细胞类型特异性和脑区特异性模块，进而注释了与多种病理变量相关的转录组差异。此外，研究鉴定出一个与阿尔茨海默病相关的星形胶质细胞模块，该模块与胆碱代谢和多胺生物合成相关，可能有助于晚年认知功能的维持。总体而言，本研究绘制了老年人类大脑的区域图谱，并为理解阿尔茨海默病病理中的细胞易感性、反应以及病理认知恢复力提供了新的见解。

2. Histone serotonylation regulates ependymoma tumorigenesis

组蛋白5-羟色胺化调节室管膜瘤的发生

田纳西州孟菲斯市圣犹大儿童研究医院神经肿瘤科学中心，美国

休斯敦贝勒医学院神经外科，美国

Abstract

Bidirectional communication between tumours and neurons has emerged as a key facet of the tumour microenvironment that drives malignancy^1,2. Another hallmark feature of cancer is epigenomic dysregulation, in which alterations in gene expression influence cell states and interactions with the tumour microenvironment³. Ependymoma (EPN) is a paediatric brain tumour that relies on epigenomic remodelling to engender malignancy^4,5; however, how these epigenetic mechanisms intersect with extrinsic neuronal signalling during EPN tumour progression is unknown. Here we show that the activity of serotonergic neurons regulates EPN tumorigenesis, and that serotonin itself also serves as an activating modification on histones. We found that inhibiting histone serotonylation blocks EPN tumorigenesis and regulates the expression of a core set of developmental transcription factors. High-throughput, in vivo screening of these transcription factors revealed that ETV5 promotes EPN tumorigenesis and functions by enhancing repressive chromatin states. Neuropeptide Y (NPY) is one of the genes repressed by ETV5, and its overexpression suppresses EPN tumour progression and tumour-associated network hyperactivity through synaptic remodelling. Collectively, this study identifies histone serotonylation as a key driver of EPN tumorigenesis, and also reveals how neuronal signalling, neuro-epigenomics and developmental programs are intertwined to drive malignancy in brain cancer.

摘要

肿瘤与神经元之间的双向通信已成为推动恶性肿瘤发展的关键肿瘤微环境因素之一。癌症的另一个显著特征是表观基因组的失调，其中基因表达的改变影响了细胞状态及其与肿瘤微环境的相互作用。室管膜瘤（EPN）是一种依赖表观基因组重塑的恶性儿童脑肿瘤；然而，这些表观遗传机制如何在EPN肿瘤进展中与外源性神经元信号相互作用尚不明确。本研究表明，5-羟色胺能神经元的活动可以调控EPN的肿瘤发生，并且5-羟色胺本身作为一种组蛋白活化修饰元件参与其中。抑制组蛋白5-羟色胺化能够阻止EPN肿瘤的发生，并调控一组核心发育转录因子的表达。通过对这些转录因子的高通量体内筛选表明，ETV5通过增强抑制性染色质状态来促进EPN肿瘤的发展。神经肽Y（NPY）是ETV5抑制的基因之一，其过表达通过突触重塑抑制EPN肿瘤的进展以及与肿瘤相关的网络过度活跃性。总之，本研究确定了组蛋白5-羟色胺化是EPN肿瘤发生的关键驱动因素，并揭示了神经信号、神经表观基因组与发育程序如何交织，一起推动脑癌的恶性进展。

3. Molecular basis of human noradrenaline transporter reuptake and inhibition

人去甲肾上腺素转运体再摄取和抑制的分子基础

北京生物结构前沿研究中心，膜生物学国家重点实验室，清华-北京联合生命科学中心，生命科学学院，清华大学，北京

Abstract

Noradrenaline, also known as norepinephrine, has a wide range of activities and effects on most brain cell types¹. Its reuptake from the synaptic cleft heavily relies on the noradrenaline transporter (NET) located in the presynaptic membrane². Here we report the cryo-electron microscopy (cryo-EM) structures of the human NET in both its apo state and when bound to substrates or antidepressant drugs, with resolutions ranging from 2.5 Å to 3.5 Å. The two substrates, noradrenaline and dopamine, display a similar binding mode within the central substrate binding site (S1) and within a newly identified extracellular allosteric site (S2). Four distinct antidepressants, namely, atomoxetine, desipramine, bupropion and escitalopram, occupy the S1 site to obstruct substrate transport in distinct conformations. Moreover, a potassium ion was observed within sodium-binding site 1 in the structure of the NET bound to desipramine under the KCl condition. Complemented by structural-guided biochemical analyses, our studies reveal the mechanism of substrate recognition, the alternating access of NET, and elucidate the mode of action of the four antidepressants.

摘要

去甲肾上腺素（又称去甲基肾上腺素）对大多数脑细胞类型具有广泛的作用，其在突触间隙中的再摄取主要依赖于突触前膜中的去甲肾上腺素转运体（NET）。本研究报道了人类NET在空载状态下以及与底物或抗抑郁药结合时的冷冻电子显微镜（cryo-EM）结构，分辨率范围为2.5Å到3.5Å。两种底物，去甲肾上腺素和多巴胺，在中央底物结合位点（S1）和新发现的胞外变构位点（S2）上显示出相似的结合模式。四种不同的抗抑郁药——西酞普兰、地昔帕明、安非他酮和艾司西酞普兰——占据了S1位点，并以不同的构象阻碍了底物的转运。此外，在NET与地昔帕明结合的结构中，在KCl条件下，观察到钾离子占据了钠结合位点1。通过基于结构的生化分析，研究揭示了底物识别的机制、NET的交替访问机制，并阐明了这四种抗抑郁药的作用模式。

Volume 632 Issue 8025, 15 August 2024

在2024年8月632卷8025期，Nature共发表文章49篇，其中包括1篇Editorial，1篇World View，4篇Research Highlights，9篇News in Focus，1篇Books & Arts，4篇Opinion，2篇Work，4篇News & Views，23篇Article。

1. Single-cell atlas of the human brain vasculature across development, adulthood and disease

人脑脉管系统发育、成年和疾病的单细胞图谱

加拿大安大略省多伦多市多伦多大学神经外科系

苏黎世神经科学中心，苏黎世大学和瑞士苏黎世大学医院

瑞士苏黎世大学医院神经外科

Abstract

A broad range of brain pathologies critically relies on the vasculature, and cerebrovascular disease is a leading cause of death worldwide. However, the cellular and molecular architecture of the human brain vasculature remains incompletely understood1. Here we performed single-cell RNA sequencing analysis of 606,380 freshly isolated endothelial cells, perivascular cells and other tissue-derived cells from 117 samples, from 68 human fetuses and adult patients to construct a molecular atlas of the developing fetal, adult control and diseased human brain vasculature. We identify extensive molecular heterogeneity of the vasculature of healthy fetal and adult human brains and across five vascular-dependent central nervous system (CNS) pathologies, including brain tumours and brain vascular malformations. We identify alteration of arteriovenous differentiation and reactivated fetal as well as conserved dysregulated genes and pathways in the diseased vasculature. Pathological endothelial cells display a loss of CNS-specific properties and reveal an upregulation of MHC class II molecules, indicating atypical features of CNS endothelial cells. Cell–cell interaction analyses predict substantial endothelial-to-perivascular cell ligand–receptor cross-talk, including immune-related and angiogenic pathways, thereby revealing a central role for the endothelium within brain neurovascular unit signalling networks. Our single-cell brain atlas provides insights into the molecular architecture and heterogeneity of the developing, adult/control and diseased human brain vasculature and serves as a powerful reference for future studies.

摘要

多种脑部病变与血管系统密切相关，脑血管疾病是全球范围内主要的死亡原因之一。然而，人类脑血管的细胞和分子结构仍未被完全解析。本研究对来自68名人类胎儿和成年患者的117个样本中的606,380个新鲜分离的内皮细胞、血管周围细胞和其他组织来源的细胞进行了单细胞RNA测序分析，构建了发育中胎儿、正常成人和疾病状态下成人的脑血管分子图谱。研究发现，健康胎儿和成人大脑血管，以及五种依赖血管的中枢神经系统（CNS）疾病（包括脑肿瘤和脑血管畸形）之间存在广泛的分子异质性。研究识别出在患病血管中，动静脉分化的改变、重新激活的胎儿基因以及失调的基因和通路。在病理性内皮细胞中，CNS特异性特性消失，并伴随MHC II类分子的上调，表现出CNS内皮细胞的非典型特征。细胞间相互作用分析预测了内皮细胞与血管周围细胞之间丰富的配体-受体相互作用，包括与免疫和血管生成通路相关的交互，揭示了内皮细胞在脑神经血管单元信号网络中的核心作用。该单细胞脑图谱为理解人类脑血管在发育中的胎儿、成人对照组和病变人脑的分子结构和异质性提供了新的见解，并为未来的研究奠定了重要基础。

2. Immunological memory diversity in the human upper airway

人类上呼吸道的免疫记忆多样性

加利福尼亚州拉荷亚免疫学研究所疫苗创新中心，美国

加州大学圣地亚哥分校传染病与全球公共卫生系医学系，美国

Abstract

The upper airway is an important site of infection, but immune memory in the human upper airway is poorly understood, with implications for COVID-19 and many other human diseases^1,2,3,4. Here we demonstrate that nasal and nasopharyngeal swabs can be used to obtain insights into these challenging problems, and define distinct immune cell populations, including antigen-specific memory B cells and T cells, in two adjacent anatomical sites in the upper airway. Upper airway immune cell populations seemed stable over time in healthy adults undergoing monthly swabs for more than 1 year, and prominent tissue resident memory T (TRM) cell and B (BRM) cell populations were defined. Unexpectedly, germinal centre cells were identified consistently in many nasopharyngeal swabs. In subjects with SARS-CoV-2 breakthrough infections, local virus-specific BRM cells, plasma cells and germinal centre B cells were identified, with evidence of local priming and an enrichment of IgA+ memory B cells in upper airway compartments compared with blood. Local plasma cell populations were identified with transcriptional profiles of longevity. Local virus-specific memory CD4+ TRM cells and CD8+ TRM cells were identified, with diverse additional virus-specific T cells. Age-dependent upper airway immunological shifts were observed. These findings provide new understanding of immune memory at a principal mucosal barrier tissue in humans.

摘要

上呼吸道是一个关键的感染部位，但目前对其免疫记忆特征了解甚少，而这些特征对COVID-19及许多其他人类疾病具有重要影响。本研究证明了可以通过鼻拭子和鼻咽拭子来研究这些具有挑战性的问题，并在上呼吸道的两个相邻解剖部位中识别了不同的免疫细胞亚群，包括抗原特异性记忆B细胞和T细胞。在接受1年以上每月一次的咽拭子检测的健康成人中，研究发现上呼吸道的免疫细胞亚群似乎在时间上保持相对稳定，并且确定了显著的组织驻留记忆T细胞（TRM）和B细胞（BRM）亚群。令人意外的是，在许多鼻咽拭子中一致地识别出了生发中心细胞。在SARS-CoV-2突破性感染的受试者中，研究发现局部存在的病毒特异性BRM细胞、浆细胞和生发中心B细胞，并发现上呼吸道的局部初次免疫刺激和IgA⁺记忆B细胞的富集比血液中更为显著。此外，研究通过长寿的转录谱鉴定了局部的浆细胞亚群。鉴定出局部病毒特异性记忆CD4⁺ TRM细胞和CD8⁺ TRM细胞，以及其他不同的病毒特异性T细胞。研究还观察到与年龄相关的上呼吸道免疫变化。这些发现为理解人类主要黏膜屏障组织中的免疫记忆提供了新的见解。

3. Molecular mimicry in multisystem inflammatory syndrome in children

儿童多系统炎症综合征的分子拟态研究

加州大学旧金山分校医学院糖尿病中心，美国

加州大学旧金山分校内分泌与新陈代谢系医学系，美国

加州大学旧金山分校生物化学与生物物理系，美国

陈 · 扎克伯格生物中心，旧金山，加利福尼亚州，美国

Abstract

Multisystem inflammatory syndrome in children (MIS-C) is a severe, post-infectious sequela of SARS-CoV-2 infection1,2, yet the pathophysiological mechanism connecting the infection to the broad inflammatory syndrome remains unknown. Here we leveraged a large set of samples from patients with MIS-C to identify a distinct set of host proteins targeted by patient autoantibodies including a particular autoreactive epitope within SNX8, a protein involved in regulating an antiviral pathway associated with MIS-C pathogenesis. In parallel, we also probed antibody responses from patients with MIS-C to the complete SARS-CoV-2 proteome and found enriched reactivity against a distinct domain of the SARS-CoV-2 nucleocapsid protein. The immunogenic regions of the viral nucleocapsid and host SNX8 proteins bear remarkable sequence similarity. Consequently, we found that many children with anti-SNX8 autoantibodies also have cross-reactive T cells engaging both the SNX8 and the SARS-CoV-2 nucleocapsid protein epitopes. Together, these findings suggest that patients with MIS-C develop a characteristic immune response to the SARS-CoV-2 nucleocapsid protein that is associated with cross-reactivity to the self-protein SNX8, demonstrating a mechanistic link between the infection and the inflammatory syndrome, with implications for better understanding a range of post-infectious autoinflammatory diseases.

摘要

儿童多系统炎症综合征（MIS-C）是SARS-CoV-2感染后的一种严重后遗症，但将感染与广泛的炎症综合征联系起来的病理生理机制仍然不清楚。在本研究中，通过对大量MIS-C患者样本的分析，识别出一组特定的宿主蛋白，这些蛋白会被患者自身抗体所靶向，其中包括SNX8中的一个特异性自反应表位。SNX8是一种参与调节与MIS-C发病机制相关的抗病毒通路的蛋白质。此外，本研究探索了MIS-C患者对SARS-CoV-2蛋白质组的抗体反应，发现他们对SARS-CoV-2核衣壳蛋白的特定结构域表现出高度反应性。值得注意的是，病毒核衣壳蛋白和宿主SNX8蛋白的免疫原性区域在序列上具有显著相似性。研究发现，许多具有抗SNX8自身抗体的儿童也拥有交叉反应的T细胞，这些T细胞能够同时识别SNX8和SARS-CoV-2核衣壳蛋白的表位。这些发现表明，MIS-C患者对SARS-CoV-2核衣壳蛋白产生了一种特异性的免疫反应，并且这种反应与对自体蛋白SNX8的交叉反应有关。这揭示了感染与炎症综合征之间的机制联系，对于理解一系列感染后自身炎症性疾病具有重要意义。

4. Turbinate-homing IgA-secreting cells originate in the nasal lymphoid tissues

归巢于鼻甲的IgA分泌细胞起源于鼻部淋巴组织

系统免疫学部，魏茨曼科学研究所，以色列

Abstract

Nasal vaccination elicits a humoral immune response that provides protection from airborne pathogens¹, yet the origins and specific immune niches of antigen-specific IgA-secreting cells in the upper airways are unclear². Here we define nasal glandular acinar structures and the turbinates as immunological niches that recruit IgA-secreting plasma cells from the nasal-associated lymphoid tissues (NALTs)3. Using intact organ imaging, we demonstrate that nasal vaccination induces B cell expansion in the subepithelial dome of the NALT, followed by invasion into commensal-bacteria-driven chronic germinal centres in a T cell-dependent manner. Initiation of the germinal centre response in the NALT requires pre-expansion of antigen-specific T cells, which interact with cognate B cells in interfollicular regions. NALT ablation and blockade of PSGL-1, which mediates interactions with endothelial cell selectins, demonstrated that NALT-derived IgA-expressing B cells home to the turbinate region through the circulation, where they are positioned primarily around glandular acinar structures. CCL28 expression was increased in the turbinates in response to vaccination and promoted homing of IgA+ B cells to this site. Thus, in response to nasal vaccination, the glandular acini and turbinates provide immunological niches that host NALT-derived IgA-secreting cells. These cellular events could be manipulated in vaccine design or in the treatment of upper airway allergic responses.

摘要

经鼻接种疫苗可引起体液免疫应答，从而保护集体免受空气传播的病原体感染。然而，上呼吸道中抗原特异性IgA分泌细胞的来源及其所处的特定免疫环境尚不明确。在本研究中，确定了鼻腺泡状结构和鼻甲可作为关键免疫环境，从鼻相关淋巴组织（NALTs）中招募分泌IgA的浆细胞。利用完整器官成像技术，研究展示了经鼻接种疫苗如何诱导NALTs中上皮下圆顶区B细胞的扩增，随后这些B细胞以T细胞依赖的方式侵入由共生菌驱动的慢性生发中心。NALTs中的生发中心反应的启动需要依赖于抗原特异性T细胞的预扩增，而这些T细胞在滤泡间区域与对应的B细胞相互作用。通过NALTs切除和PSGL-1阻断实验（PSGL-1介导与内皮细胞选择素的相互作用），研究发现NALTs来源的IgA表达B细胞通过循环系统归巢至鼻甲区域，主要聚集在腺泡结构周围。疫苗接种后，鼻甲中的CCL28表达增加，进一步促进IgA⁺ B细胞向该部位归巢。因此，鼻腔疫苗接种引发的免疫反应中，鼻腺泡状结构和鼻甲提供了容纳NALTs来源IgA分泌细胞的关键免疫环境。这些细胞事件可为疫苗设计或上呼吸道过敏反应的治疗提供调控手段。

5. SMYD5 methylation of rpL40 links ribosomal output to gastric cancer

rpL40 的 SMYD5 甲基化表明核糖体输出与胃癌相关

斯坦福大学生物系，加利福尼亚州，美国

实验放射肿瘤学系，德州大学安德森癌症中心，休斯顿，美国

Abstract

Dysregulated transcription due to disruption in histone lysine methylation dynamics is an established contributor to tumorigenesis^1,2. However, whether analogous pathologic epigenetic mechanisms act directly on the ribosome to advance oncogenesis is unclear. Here we find that trimethylation of the core ribosomal protein L40 (rpL40) at lysine 22 (rpL40K22me3) by the lysine methyltransferase SMYD5 regulates mRNA translation output to promote malignant progression of gastric adenocarcinoma (GAC) with lethal peritoneal ascites. A biochemical–proteomics strategy identifies the monoubiquitin fusion protein partner rpL40 (ref. 3) as the principal physiological substrate of SMYD5 across diverse samples. Inhibiting the SMYD5–rpL40K22me3 axis in GAC cell lines reprogrammes protein synthesis to attenuate oncogenic gene expression signatures. SMYD5 and rpL40K22me3 are upregulated in samples from patients with GAC and negatively correlate with clinical outcomes. SMYD5 ablation in vivo in familial and sporadic mouse models of malignant GAC blocks metastatic disease, including peritoneal carcinomatosis. Suppressing SMYD5 methylation of rpL40 inhibits human cancer cell and patient-derived GAC xenograft growth and renders them hypersensitive to inhibitors of PI3K and mTOR. Finally, combining SMYD5 depletion with PI3K–mTOR inhibition and chimeric antigen receptor T cell administration cures an otherwise lethal in vivo mouse model of aggressive GAC-derived peritoneal carcinomatosis. Together, our work uncovers a ribosome-based epigenetic mechanism that facilitates the evolution of malignant GAC and proposes SMYD5 targeting as part of a potential combination therapy to treat this cancer.

摘要

组蛋白赖氨酸甲基化的动态失调已被确认为是一个促进肿瘤发生的因素。然而，类似的病理性表观遗传机制是否直接作用于核糖体以促进肿瘤发展仍不清楚。本研究发现赖氨酸甲基转移酶SMYD5通过调节mRNA翻译产量，促使核心核糖体蛋白L40（rpL40）在赖氨酸22位三甲基化（rpL40K22me3），从而加速伴有致死性腹水的胃腺癌（GAC）的恶性进展。通过生化和蛋白质组学策略，研究鉴定出单泛素融合蛋白伙伴rpL40是SMYD5在多种样本中的主要生理底物。在GAC细胞系中，抑制SMYD5-rpL40K22me3轴可重新编程蛋白质合成，从而削弱致癌基因的表达特征。SMYD5和rpL40K22me3在GAC患者样本中表达上调，并与临床预后呈负相关。在恶性GAC的家族性和散发性小鼠模型中，体内敲除SMYD5阻止了转移性疾病的发展，包括腹膜癌。抑制SMYD5对rpL40的甲基化阻碍了人类癌细胞和患者衍生的GAC异种移植瘤的生长，并使它们对PI3K和mTOR抑制剂表现出超敏感性。最后，联合清除SMYD5、抑制PI3K-mTOR和嵌合抗原受体T细胞治疗，可成功治愈一种原本致命的侵袭性GAC衍生的腹膜癌小鼠模型。总之，研究揭示了一种基于核糖体的表观遗传机制，推动了恶性GAC的演变，并提出了靶向SMYD5可作为治疗这种癌症的潜在联合疗法的一部分。

Volume 632 Issue 8024, 8 August 2024

在2024年8月632卷8024期，Nature共发表文章54篇，其中包括1篇Editorial，1篇World View，4篇Research Highlights，9篇News in Focus，1篇Books & Arts，6篇Opinion，3篇Work，5篇News & Views，24篇Article。

1. A human autoimmune organoid model reveals IL-7 function in coeliac disease

人类自身免疫类器官模型揭示了 IL-7在乳糜泻中的作用

斯坦福大学医学院血液系，加利福尼亚州，美国

Abstract

In vitro models of autoimmunity are constrained by an inability to culture affected epithelium alongside the complex tissue-resident immune microenvironment. Coeliac disease (CeD) is an autoimmune disease in which dietary gluten-derived peptides bind to the major histocompatibility complex (MHC) class II human leukocyte antigen molecules (HLA)-DQ2 or HLA-DQ8 to initiate immune-mediated duodenal mucosal injury^1,2,3,4. Here, we generated air–liquid interface (ALI) duodenal organoids from intact fragments of endoscopic biopsies that preserve epithelium alongside native mesenchyme and tissue-resident immune cells as a unit without requiring reconstitution. The immune diversity of ALI organoids spanned T cells, B and plasma cells, natural killer (NK) cells and myeloid cells, with extensive T-cell and B-cell receptor repertoires. HLA-DQ2.5-restricted gluten peptides selectively instigated epithelial destruction in HLA-DQ2.5-expressing organoids derived from CeD patients, and this was antagonized by blocking MHC-II or NKG2C/D. Gluten epitopes stimulated a CeD organoid immune network response in lymphoid and myeloid subsets alongside anti-transglutaminase 2 (TG2) autoantibody production. Functional studies in CeD organoids revealed that interleukin-7 (IL-7) is a gluten-inducible pathogenic modulator that regulates CD8+ T-cell NKG2C/D expression and is necessary and sufficient for epithelial destruction. Furthermore, endogenous IL-7 was markedly upregulated in patient biopsies from active CeD compared with remission disease from gluten-free diets, predominantly in lamina propria mesenchyme. By preserving the epithelium alongside diverse immune populations, this human in vitro CeD model recapitulates gluten-dependent pathology, enables mechanistic investigation and establishes a proof of principle for the organoid modelling of autoimmunity.

摘要

体外模型在研究自身免疫性疾病时，因无法将受影响的上皮与复杂的组织驻留免疫微环境共同培养而受到限制。乳糜泻（CeD）是一种自身免疫性疾病，其中饮食中的谷蛋白衍生肽与主要组织相容性复合体（MHC）II类人类白细胞抗原分子（HLA）-DQ2或HLA-DQ8结合，启动免疫介导的十二指肠黏膜损伤。研究利用内镜活检的完整片段制备了气-液界面（ALI）十二指肠类器官，保留了上皮层以及天然间充质和组织驻留的免疫细胞作为一个完整单元。这些ALI类器官的免疫多样性包括T细胞、B细胞和浆细胞、自然杀伤（NK）细胞和髓系细胞，并且具有广泛的T细胞和B细胞受体库。在来自CeD患者的表达HLA-DQ2.5的类器官中，HLA-DQ2.5限制性谷蛋白肽选择性地诱发了上皮损伤，而阻断MHC-II或NKG2C/D可以抑制这一过程。谷蛋白表位在淋巴细胞和髓系细胞群中引发了CeD类器官的免疫网络反应，并伴随着抗转谷氨酰胺酶2（TG2）自身抗体的产生。CeD类器官的功能研究表明，白介素-7（IL-7）是一种谷蛋白诱导的致病调节因子，可调节CD8⁺ T细胞的NKG2C/D表达，并且是上皮破坏所必需和充分的。此外，活跃期CeD患者的活检样本中内源性IL-7显著上调，主要集中在固有层间充质中，而无谷蛋白饮食的缓解期患者中则未见此现象。通过保留上皮层及多样的免疫细胞群体，这种人类体外CeD模型成功再现了依赖谷蛋白的病理过程，不仅为机制研究提供了新工具，还为类器官模拟自身免疫性疾病建立了重要的概念验证。

2. In vivo interaction screening reveals liver-derived constraints to metastasis

体内相互作用筛选揭示肝源性转移的限制因素

苏黎世联邦理工学院生物系统科学与工程系，巴塞尔，瑞士

Abstract

It is estimated that only 0.02% of disseminated tumour cells are able to seed overt metastases¹. While this suggests the presence of environmental constraints to metastatic seeding, the landscape of host factors controlling this process remains largely unclear. Here, combining transposon technology² and fluorescence niche labelling³, we developed an in vivo CRISPR activation screen to systematically investigate the interactions between hepatocytes and metastatic cells. We identify plexin B2 as a critical host-derived regulator of liver colonization in colorectal and pancreatic cancer and melanoma syngeneic mouse models. We dissect a mechanism through which plexin B2 interacts with class IV semaphorins on tumour cells, leading to KLF4 upregulation and thereby promoting the acquisition of epithelial traits. Our results highlight the essential role of signals from the liver parenchyma for the seeding of disseminated tumour cells before the establishment of a growth-promoting niche. Our findings further suggest that epithelialization is required for the adaptation of CRC metastases to their new tissue environment. Blocking the plexin-B2–semaphorin axis abolishes metastatic colonization of the liver and therefore represents a therapeutic strategy for the prevention of hepatic metastases. Finally, our screening approach, which evaluates host-derived extrinsic signals rather than tumour-intrinsic factors for their ability to promote metastatic seeding, is broadly applicable and lays a framework for the screening of environmental constraints to metastasis in other organs and cancer types.

摘要

据估计，只有约0.02%的播散性肿瘤细胞能够形成显著的转移灶，这表明转移过程可能受到环境的限制。然而，控制这一过程的宿主因子仍不明确。为此，研究结合转座子技术和荧光微环境标记，开发了一种体内CRISPR激活筛选方法，系统性地研究肝细胞与转移细胞之间的相互作用。研究确定了Plexin B2是结直肠癌、胰腺癌和黑色素瘤同系小鼠模型中肝脏转移的关键宿主调节因子。通过解析Plexin B2与肿瘤细胞表面的IV类信号素Semaphorins之间的相互作用，研究发现这会导致KLF4的上调，从而促进上皮特征的获得。研究强调了肝实质信号在播散性肿瘤细胞播种前，建立有利于生长的微环境中的关键作用。进一步的研究显示，上皮化是结直肠癌转移适应其新的组织环境所必需的。阻断Plexin B2–Semaphorin轴可以阻止肿瘤在肝脏的转移定植，因此是一种预防肝转移的潜在治疗策略。最后，该筛选方法评估了宿主来源的外在信号，而非肿瘤内在因素促进转移播种的能力。这种方法具有广泛的适用性，并为其他器官和癌症类型的转移环境限制因素的筛选奠定了基础。

3. In vivo single-cell CRISPR uncovers distinct TNF programmes in tumour evolution

体内单细胞 CRISPR 揭示了肿瘤进化中不同的 TNF 程序

苏黎世联邦理工学院生物系统科学与工程系，巴塞尔，瑞士

苏黎世大学再生医学研究所(IREM) ，苏黎世，瑞士

Abstract

The tumour evolution model posits that malignant transformation is preceded by randomly distributed driver mutations in cancer genes, which cause clonal expansions in phenotypically normal tissues. Although clonal expansions can remodel entire tissues^1,2,3, the mechanisms that result in only a small number of clones transforming into malignant tumours remain unknown. Here we develop an in vivo single-cell CRISPR strategy to systematically investigate tissue-wide clonal dynamics of the 150 most frequently mutated squamous cell carcinoma genes. We couple ultrasound-guided in utero lentiviral microinjections, single-cell RNA sequencing and guide capture to longitudinally monitor clonal expansions and document their underlying gene programmes at single-cell transcriptomic resolution. We uncover a tumour necrosis factor (TNF) signalling module, which is dependent on TNF receptor 1 and involving macrophages, that acts as a generalizable driver of clonal expansions in epithelial tissues. Conversely, during tumorigenesis, the TNF signalling module is downregulated. Instead, we identify a subpopulation of invasive cancer cells that switch to an autocrine TNF gene programme associated with epithelial–mesenchymal transition. Finally, we provide in vivo evidence that the autocrine TNF gene programme is sufficient to mediate invasive properties and show that the TNF signature correlates with shorter overall survival of patients with squamous cell carcinoma. Collectively, our study demonstrates the power of applying in vivo single-cell CRISPR screening to mammalian tissues, unveils distinct TNF programmes in tumour evolution and highlights the importance of understanding the relationship between clonal expansions in epithelia and tumorigenesis.

摘要

肿瘤进化模型指出，在恶性转化之前，癌基因中会出现随机分布的驱动突变，导致正常组织中的克隆扩增。尽管克隆扩增可以重塑整个组织，但少数克隆转化为恶性肿瘤的机制仍不明确。为此，研究开发了一种体内单细胞CRISPR策略，系统性研究了150个最常见的鳞状细胞癌基因在组织内的克隆动态。研究结合了超声引导下的子宫内慢病毒微注射、单细胞RNA测序和导向捕获技术，以纵向监测克隆扩增，并在单细胞转录组水平记录其基因程序。研究发现了一个依赖于TNF受体1且涉及巨噬细胞的肿瘤坏死因子（TNF）信号模块，该模块是上皮组织克隆扩增的普遍驱动因子。相反的是，在肿瘤发生过程中，这一TNF信号模块被下调。而研究识别出一群具有侵袭性的癌细胞，这些细胞展示了与上皮-间质转化相关的自分泌TNF基因程序。最后，体内实验证明自分泌TNF基因程序足以介导侵袭性特性，并显示TNF特征与鳞状细胞癌患者较短的总体生存期相关。总体而言，研究展示了将体内单细胞CRISPR筛选应用于哺乳动物组织的强大能力，揭示了肿瘤进化中不同的TNF程序，并强调了理解上皮中的克隆扩增与肿瘤发生之间关系的重要性。

4. Tumour vasculature at single-cell resolution

单细胞分辨率的肿瘤脉管系统

重庆大学三峡医院，重庆大学，重庆

重庆大学医学院，重庆

湖南省皮肤健康与疾病工程研究中心皮肤科，中南大学湘雅医院，长沙

Abstract

Tumours can obtain nutrients and oxygen required to progress and metastasize through the blood supply¹. Inducing angiogenesis involves the sprouting of established vessel beds and their maturation into an organized network^2,3. Here we generate a comprehensive atlas of tumour vasculature at single-cell resolution, encompassing approximately 200,000 cells from 372 donors representing 31 cancer types. Trajectory inference suggested that tumour angiogenesis was initiated from venous endothelial cells and extended towards arterial endothelial cells. As neovascularization elongates (through angiogenic stages SI, SII and SIII), APLN+ tip cells at the SI stage (APLN+ TipSI) advanced to TipSIII cells with increased Notch signalling. Meanwhile, stalk cells, following tip cells, transitioned from high chemokine expression to elevated TEK (also known as Tie2) expression. Moreover, APLN+ TipSI cells not only were associated with disease progression and poor prognosis but also hold promise for predicting response to anti-VEGF therapy. Lymphatic endothelial cells demonstrated two distinct differentiation lineages: one responsible for lymphangiogenesis and the other involved in antigen presentation. In pericytes, endoplasmic reticulum stress was associated with the proangiogenic BASP1+ matrix-producing pericytes. Furthermore, intercellular communication analysis showed that neovascular endothelial cells could shape an immunosuppressive microenvironment conducive to angiogenesis. This study depicts the complexity of tumour vasculature and has potential clinical significance for anti-angiogenic therapy.

摘要

肿瘤通过血液供应获得进展和转移所需的营养和氧气。诱导血管生成涉及已建立的血管床发芽并成熟为一个有组织的网络。本研究构建了一个单细胞分辨率的肿瘤血管系统综合图谱，涵盖了来自372名供体的约20万个细胞，代表了31种癌症类型。轨迹推断表明，肿瘤血管生成从静脉内皮细胞开始，并逐渐延伸至动脉内皮细胞。随着新生血管化的进展（包括血管生成阶段SI、SII和SIII），在SI阶段的APLN+尖端细胞（APLN+ TipSI）转变为具有增强Notch信号的TipSIII细胞。同时，紧随尖端细胞的茎干细胞从高表达趋化因子过渡到高表达TEK（也称为Tie2）。此外，APLN+ TipSI细胞不仅与疾病进展和不良预后相关，还有望预测抗VEGF治疗的疗效。淋巴内皮细胞表现出两种不同的分化谱系：一种负责淋巴管生成，另一种参与抗原呈递。在周细胞中，内质网应激与促血管生成的BASP1+基质产生周细胞相关。细胞间通讯分析还表明，新生血管内皮细胞能够形成有利于血管生成的免疫抑制微环境。本研究揭示了肿瘤血管系统的复杂性，并对抗血管生成治疗具有潜在的临床意义。

Volume 632 Issue 8023, 8 August 2024

在2024年8月632卷8023期，Nature共发表文章48篇，其中包括1篇Editorial，1篇World View，4篇Research Highlights，7篇News in Focus，0篇Books & Arts，5篇Opinion，2篇Work，6篇News & Views，22篇Article。

1. Sources of gene expression variation in a globally diverse human cohort

全球不同人群队列中基因表达变异的来源

约翰·霍普金斯大学生物系，巴尔的摩市，马里兰州，美国

Abstract

Genetic variation that influences gene expression and splicing is a key source of phenotypic diversity^1,2,3,4,5. Although invaluable, studies investigating these links in humans have been strongly biased towards participants of European ancestries, which constrains generalizability and hinders evolutionary research. Here to address these limitations, we developed MAGE, an open-access RNA sequencing dataset of lymphoblastoid cell lines from 731 individuals from the 1000 Genomes Project⁶, spread across 5 continental groups and 26 populations. Most variation in gene expression (92%) and splicing (95%) was distributed within versus between populations, which mirrored the variation in DNA sequence. We mapped associations between genetic variants and expression and splicing of nearby genes (cis-expression quantitative trait loci (eQTLs) and cis-splicing QTLs (sQTLs), respectively). We identified more than 15,000 putatively causal eQTLs and more than 16,000 putatively causal sQTLs that are enriched for relevant epigenomic signatures. These include 1,310 eQTLs and 1,657 sQTLs that are largely private to underrepresented populations. Our data further indicate that the magnitude and direction of causal eQTL effects are highly consistent across populations. Moreover, the apparent ‘population-specific’ effects observed in previous studies were largely driven by low resolution or additional independent eQTLs of the same genes that were not detected. Together, our study expands our understanding of human gene expression diversity and provides an inclusive resource for studying the evolution and function of human genomes.

摘要

影响基因表达和剪接的遗传变异是表型多样性的重要来源。尽管这些研究非常有价值，但在人类中进行的相关研究往往主要涉及欧洲血统的参与者，这限制了研究结果的普遍性并阻碍了进化研究。为了解决这些局限性，研究开发了MAGE，一个包含731个来自千人基因组计划的个体的开放获取的淋巴母细胞系RNA测序数据集，覆盖了5个大陆的26个人群。研究发现，大部分基因表达（92%）和剪接（95%）的变异在种群内和种群间分布，这反映了DNA序列的变异。该研究进一步探索了遗传变异与附近基因的表达和剪接之间的关联，分别称为顺式表达数量性状位点（eQTLs）和顺式剪接QTLs（sQTLs），鉴定出了超过15,000个潜在的因果eQTLs和超过16,000个潜在的因果sQTLs，这些变异富集了相关的表观基因组特征。其中包括1,310个主要存在于少数群体中的eQTLs和1,657个sQTLs。研究数据进一步表明，因果eQTL效应的大小和方向在不同种群中高度一致。此外，先前研究中观察到的“种群特异性”效应主要是由低分辨率或同一基因的其他独立eQTLs驱动的，而这些eQTLs在以往研究中未被检测到。总之，研究扩展了对人类基因表达多样性的理解，并为研究人类基因组的进化和功能提供了一个包容性资源。

2. Neoantigen-specific cytotoxic Tr1 CD4 T cells suppress cancer immunotherapy

新抗原特异性细胞毒性 Tr1 CD4 T 细胞抑制癌症免疫治疗

华盛顿大学医学院人类免疫学和免疫疗法研究中心，密苏里州圣路易斯市，美国

旧金山帕克癌症免疫治疗研究所，加州，美国

Abstract

CD4⁺ T cells can either enhance or inhibit tumour immunity. Although regulatory T cells have long been known to impede antitumour responses^1,2,3,4,5, other CD4+ T cells have recently been implicated in inhibiting this response^6,7. Yet, the nature and function of the latter remain unclear. Here, using vaccines containing MHC class I (MHC-I) neoantigens (neoAgs) and different doses of tumour-derived MHC-II neoAgs, we discovered that whereas the inclusion of vaccines with low doses of MHC-II-restricted peptides (LDVax) promoted tumour rejection, vaccines containing high doses of the same MHC-II neoAgs (HDVax) inhibited rejection. Characterization of the inhibitory cells induced by HDVax identified them as type 1 regulatory T (Tr1) cells expressing IL-10, granzyme B, perforin, CCL5 and LILRB4. Tumour-specific Tr1 cells suppressed tumour rejection induced by anti-PD1, LDVax or adoptively transferred tumour-specific effector T cells. Mechanistically, HDVax-induced Tr1 cells selectively killed MHC-II tumour antigen-presenting type 1 conventional dendritic cells (cDC1s), leading to low numbers of cDC1s in tumours. We then documented modalities to overcome this inhibition, specifically via anti-LILRB4 blockade, using a CD8-directed IL-2 mutein, or targeted loss of cDC2/monocytes. Collectively, these data show that cytotoxic Tr1 cells, which maintain peripheral tolerance, also inhibit antitumour responses and thereby function to impede immune control of cancer.

摘要

CD4⁺ T细胞可以增强也可抑制肿瘤免疫反应。虽然调节性T细胞（Tregs）早已被认为会阻碍抗肿瘤反应，但近期研究表明，其他类型的CD4⁺ T细胞也可能参与抑制这种反应。然而，这些细胞的性质和功能仍不完全清楚。这项研究使用了含有MHC-I类（MHC-I）新抗原（neoAgs）以及不同剂量的肿瘤来源MHC-II类新抗原的疫苗。研究发现，低剂量MHC-II限制性肽（LDVax）疫苗能够促进肿瘤清除，而含有高剂量的同一MHC-II新抗原（HDVax）疫苗则抑制了肿瘤清除。对HDVax诱导的抑制性T细胞的特性分析表明，这些细胞是表达IL-10、颗粒酶B、穿孔素、CCL5和LILRB4的1型调节性T细胞（Tr1）。肿瘤特异性Tr1细胞抑制了抗PD1、LDVax或过继转移的肿瘤特异性效应T细胞诱导的抗肿瘤反应。在机制上，HDVax诱导的Tr1细胞选择性地杀死MHC-II肿瘤抗原呈递的1型常规树突状细胞（cDC1s），导致肿瘤中cDC1s数量减少。研究还确定了克服这一抑制的方法，包括抗LILRB4阻断、使用CD8导向的IL-2变异体，或有针对性地去除cDC2/单核细胞。总体而言，这些数据表明，维持外周耐受性的细胞毒性Tr1细胞也会抑制抗肿瘤反应，从而阻碍免疫对癌症的控制。

3. An enterococcal phage-derived enzyme suppresses graft-versus-host disease

一种肠球菌噬菌体衍生酶可抑制移植物抗宿主病

东京大学医学科学研究所人类基因组中心健康医学智能部，日本

大阪都市大学医学研究生院免疫学和基因组学系，日本

Abstract

Changes in the gut microbiome have pivotal roles in the pathogenesis of acute graft-versus-host disease (aGVHD) after allogenic haematopoietic cell transplantation (allo-HCT)^1,2,3,4,5,6. However, effective methods for safely resolving gut dysbiosis have not yet been established. An expansion of the pathogen Enterococcus faecalis in the intestine, associated with dysbiosis, has been shown to be a risk factor for aGVHD^7,8,9,10. Here we analyse the intestinal microbiome of patients with allo-HCT, and find that E. faecalis escapes elimination and proliferates in the intestine by forming biofilms, rather than by acquiring drug-resistance genes. We isolated cytolysin-positive highly pathogenic E. faecalis from faecal samples and identified an anti-E. faecalis enzyme derived from E. faecalis-specific bacteriophages by analysing bacterial whole-genome sequencing data. The antibacterial enzyme had lytic activity against the biofilm of E. faecalis in vitro and in vivo. Furthermore, in aGVHD-induced gnotobiotic mice that were colonized with E. faecalis or with patient faecal samples characterized by the domination of Enterococcus, levels of intestinal cytolysin-positive E. faecalis were decreased and survival was significantly increased in the group that was treated with the E. faecalis-specific enzyme, compared with controls. Thus, administration of a phage-derived antibacterial enzyme that is specific to biofilm-forming pathogenic E. faecalis—which is difficult to eliminate with existing antibiotics—might provide an approach to protect against aGVHD.

摘要

肠道微生物组的变化在异基因造血细胞移植（allo-HCT）后急性移植物抗宿主病（aGVHD）的发病机制中发挥着关键作用。然而，目前尚未建立有效且安全的方法来解决肠道菌群失调的问题。研究表明，与菌群失调相关的病原菌粪肠球菌（Enterococcus faecalis）在肠道内的扩增被证明是aGVHD的危险因素。本研究分析了allo-HCT患者的肠道微生物组，发现E. faecalis是通过形成生物膜，而不是通过获得耐药基因来逃避清除并在肠道中增殖。研究者从粪便样本中分离出高致病性的E. faecalis，并通过分析其全基因组测序数据，鉴定出一种源自E. faecalis特异性噬菌体的抗E. faecalis酶。该抗菌酶在体外和体内均显示对E. faecalis的生物膜具有裂解活性。此外，在用E. faecalis或以Enterococcus为主的患者粪便样本定殖的aGVHD诱导无菌小鼠中，与对照组相比，接受E. faecalis特异性酶治疗的组肠道内细胞溶素阳性E. faecalis水平显著降低，生存率显著提高。因此，针对现有抗生素难以清除的生物膜形成的致病性E. faecalis的噬菌体衍生抗菌酶的应用，可能为防护aGVHD提供一种新方法。

汇报人：程丹妮

导师：赵宇

审核：毛敏姿、任建君