·Nature系列期刊导读·

通过声学报告基因对哺乳动物宿主体内微生物进行无创成像

哺乳动物体内的微生物对其健康和疾病具有重要影响，而基因工程可促进微生物的诊疗的发展。决定体内自然微生物和工程菌的活性的一个关键因素是其在宿主体内的位置。然而，基于光学的成像技术难以对哺乳动物深层组织中的微生物进行定位。本研究在细菌中导入声学报告基因，使其表达纳米级的充气蛋白质，利用超声波，实现了可穿透深层组织并具有高空间分辨率的无创成像。经实验证实，该基因可在大肠杆菌和伤寒沙门氏菌中表达，并在胃肠道和肿瘤内部准确定位。这一技术将促进哺乳动物微生物的研究，以及细胞水平的诊断和治疗手段的开发。

论文链接: Bourdeau R W,etal.. Acoustic reporter genes for noninvasive imaging of microorganisms in mammalian hosts.

对肠道菌群的精确控制可改善结肠炎

胃肠道感染性疾病常与肠道菌群失调有关。本研究发现钨酸盐可用于治疗肠道感染时肠杆菌科的异常扩增。钨酸盐在炎症时选择性地抑制钼辅因子依赖的微生物的呼吸通路，但在稳态下对肠道菌群组成的影响很小。小鼠结肠炎模型中，钨酸盐介导的菌群调控降低了肠炎的严重程度。由此证明，通过钨酸盐对微生物菌群成分的精确编辑，改善了肠道菌群失调的不利影响，即钨酸盐可用于减少治疗过程中因肠道菌群失调而产生的副作用。

论文链接: Zhu W,etal.. Precision editing of the gut microbiota ameliorates colitis.

Nature, 2018, 553(7687): 208-211. DOI:10.1038/nature25172.

Abstract: Inflammatory diseases of the gastrointestinal tract are frequently associated with dysbiosis, characterized by changes in gut microbial communities that include an expansion of facultative anaerobic bacteria of the Enterobacteriaceae family (phylum Proteobacteria). Here we show that a dysbiotic expansion of Enterobacteriaceae during gut inflammation could be prevented by tungstate treatment, which selectively inhibited molybdenum-cofactor-dependent microbial respiratory pathways that are operational only during episodes of inflammation. By contrast, we found that tungstate treatment caused minimal changes in the microbiota composition under homeostatic conditions. Notably, tungstate-mediated microbiota editing reduced the severity of intestinal inflammation in mouse models of colitis. We conclude that precision editing of the microbiota composition by tungstate treatment ameliorates the adverse effects of dysbiosis in the inflamed gut.

天然造血系统中谱系的克隆分析

造血作用是生产成熟的红细胞和免疫细胞的过程，从功能上来说，其可作为一个层级结构，而自我更新的造血干细胞和多功能祖细胞位于造血体系的最顶层。本研究使用转座子标签，追踪造血过程中未受干扰情况下的祖细胞和干细胞。结果显示，传统定义的长期造血干细胞是巨核细胞限制性祖细胞的重要来源，这暗示巨核细胞谱系是长期造血干细胞演变的主要方向。该研究为无干扰情况下造血通路图的重新修订提供了理论基础。

论文链接: Rodriguez-Fraticelli A E,etal.. Clonal analysis of lineage fate in native haematopoiesis.

Nature, 2018, 553(7687): 212-216. DOI:10.1038/nature25168.

Abstract: Haematopoiesis, the process of mature blood and immune cell production, is functionally organized as a hierarchy, with self-renewing haematopoietic stem cells and multipotent progenitor cells sitting at the very top. Multiple models have been proposed as to what the earliest lineage choices are in these primitive haematopoietic compartments, the cellular intermediates, and the resulting lineage trees that emerge from them. Given that the bulk of studies addressing lineage outcomes have been performed in the context of haematopoietic transplantation, current models of lineage branching are more likely to represent roadmaps of lineage potential than native fate. Here we use transposon tagging to clonally trace the fates of progenitors and stem cells in unperturbed haematopoiesis. Our results describe a distinct clonal roadmap in which the megakaryocyte lineage arises largely independently of other haematopoietic fates. Our data, combined with single-cell RNA sequencing, identify a functional hierarchy of unilineage- and oligolineage-producing clones within the multipotent progenitor population. Finally, our results demonstrate that traditionally defined long-term haematopoietic stem cells are a significant source of megakaryocyte-restricted progenitors, suggesting that the megakaryocyte lineage is the predominant native fate of long-term haematopoietic stem cells. Our study provides evidence for a substantially revised roadmap for unperturbed haematopoiesis, and highlights unique properties of multipotent progenitors and haematopoietic stem cellsinsitu.

通过体内输送基因组编辑药物来治疗常染色体显性遗传性听力丧失

几乎一半的听力丧失是遗传因素导致的，但目前治疗手段非常有限。本研究开发了一种基因组编辑方法，向新生的人类遗传性耳聋小鼠模型的耳蜗中注射由阳离子脂质包裹的Cas9-gRNA复合物，特异地靶向定位小鼠的Tmc1Bth等位基因，使毛细胞生存率提高，降低听觉脑干反应阈值，从而显著降低进行性听力丧失。这一方法为遗传性听力丧失的治疗提供了新策略。

论文链接: Gao X,etal.. Treatment of autosomal dominant hearing loss byinvivodelivery of genome editing agents.

Nature, 2018, 553(7687): 217-221. DOI:10.1038/nature25164.

Abstract: Although genetic factors contribute to almost half of all cases of deafness, treatment options for genetic deafness are limited. We developed a genome-editing approach to target a dominantly inherited form of genetic deafness. Here we show that cationic lipid-mediatedinvivodelivery of Cas9-guide RNA complexes can ameliorate hearing loss in a mouse model of human genetic deafness. We designed and validated, bothinvitroand in primary fibroblasts, genome editing agents that preferentially disrupt the dominant deafness-associated allele in theTmc1 (transmembrane channel-like gene family 1) Beethoven (Bth) mouse model, even though the mutantTmc1Bthallele differs from the wild-type allele at only a single base pair. Injection of Cas9-guide RNA-lipid complexes targeting theTmc1Bthallele into the cochlea of neonatalTmc1Bth/+mice substantially reduced progressive hearing loss. We observed higher hair cell survival rates and lower auditory brainstem response thresholds in injected ears than in uninjected ears or ears injected with control complexes that targeted an unrelated gene. Enhanced acoustic startle responses were observed among injected compared to uninjectedTmc1Bth/+mice. These findings suggest that protein-RNA complex delivery of target gene-disrupting agentsinvivois a potential strategy for the treatment of some types of autosomal-dominant hearing loss.

增强子的冗余保证了哺乳动物发育表型的稳健性

哺乳动物基因组中存在大量可远距离作用的增强子，但其功能调节的复杂性尚不清楚。本研究通过基因组编辑手段对小鼠7个影响肢体发育的增强子位点进行删除，发现单个删除并不会造成肢体形态异常，但成对删除同一基因的增强子会出现明显表型，并且冗余的增强子可通过加成作用影响基因表达水平。此外，小鼠肢体、大脑和心脏中均发现同一基因附近存在多个增强子的现象。结果表明，增强子的冗余是哺乳动物基因组的一个非常普遍的特征，其可提供有效的调节缓冲，以防止对个体增强子的丧失而产生有害表型的后果。

论文链接: Osterwalder M,etal.. Enhancer redundancy provides phenotypic robustness in mammalian development.

Nature, 2018, 554(7691): 239-243. DOI:10.1038/nature25461.

Abstract: Distant-acting tissue-specific enhancers, which regulate gene expression, vastly outnumber protein-coding genes in mammalian genomes, but the functional importance of this regulatory complexity remains unclear. Here we show that the pervasive presence of multiple enhancers with similar activities near the same gene confers phenotypic robustness to loss-of-function mutations in individual enhancers. We used genome editing to create 23 mouse deletion lines and inter-crosses, including both single and combinatorial enhancer deletions at seven distinct loci required for limb development. Unexpectedly, none of the ten deletions of individual enhancers caused noticeable changes in limb morphology. By contrast, the removal of pairs of limb enhancers near the same gene resulted in discernible phenotypes, indicating that enhancers function redundantly in establishing normal morphology. In a genetic background sensitized by reduced baseline expression of the target gene, even single enhancer deletions caused limb abnormalities, suggesting that functional redundancy is conferred by additive effects of enhancers on gene expression levels. A genome-wide analysis integrating epigenomic and transcriptomic data from 29 developmental mouse tissues revealed that mammalian genes are very commonly associated with multiple enhancers that have similar spatiotemporal activity. Systematic exploration of three representative developmental structures (limb, brain and heart) uncovered more than one thousand cases in which five or more enhancers with redundant activity patterns were found near the same gene. Together, our data indicate that enhancer redundancy is a remarkably widespread feature of mammalian genomes that provides an effective regulatory buffer to prevent deleterious phenotypic consequences upon the loss of individual enhancers.

脑血管系统中细胞类型和空间分区的分子图谱

在发达国家，脑血管疾病是导致死亡的第三大常见原因，但目前对组成大脑血管系统的细胞类型还不甚了解。本研究利用单细胞转录组学技术解析了沿小鼠脑血管轴向不同种细胞的分区情况，发现其中的上皮细胞连续分布，而血管壁细胞则间断分布。研究还鉴定出了一类特别的周细胞：血管周围成纤维细胞。该研究拓展了单细胞转录组学的应用范畴，并为构建哺乳动物血管分子图谱奠定了理论基础。

论文链接: Vanlandewijck M,etal.. A molecular atlas of cell types and zonation in the brain vasculature.

Nature, 2018, 554: 475-480. DOI:10.1038/nature25739.

Abstract: Cerebrovascular disease is the third most common cause of death in developed countries, but our understanding of the cells that compose the cerebral vasculature is limited. Here, using vascular single-cell transcriptomics, we provide molecular definitions for the principal types of blood vascular and vessel-associated cells in the adult mouse brain. We uncover the transcriptional basis of the gradual phenotypic change (zonation) along the arteriovenous axis and reveal unexpected cell type differences: a seamless continuum for endothelial cells versus a punctuated continuum for mural cells. We also provide insight into pericyte organotypicity and define a population of perivascular fibroblast-like cells that are present on all vessel types except capillaries. Our work illustrates the power of single-cell transcriptomics to decode the higher organizational principles of a tissue and may provide the initial chapter in a molecular encyclopaedia of the mammalian vasculature.