通過聲學報告基因?qū)Σ溉閯游锼拗黧w內(nèi)微生物進行無創(chuàng)成像

哺乳動物體內(nèi)的微生物對其健康和疾病具有重要影響，而基因工程可促進微生物的診療的發(fā)展。決定體內(nèi)自然微生物和工程菌的活性的一個關鍵因素是其在宿主體內(nèi)的位置。然而，基于光學的成像技術難以對哺乳動物深層組織中的微生物進行定位。本研究在細菌中導入聲學報告基因，使其表達納米級的充氣蛋白質(zhì)，利用超聲波，實現(xiàn)了可穿透深層組織并具有高空間分辨率的無創(chuàng)成像。經(jīng)實驗證實，該基因可在大腸桿菌和傷寒沙門氏菌中表達，并在胃腸道和腫瘤內(nèi)部準確定位。這一技術將促進哺乳動物微生物的研究，以及細胞水平的診斷和治療手段的開發(fā)。

論文鏈接: Bourdeau R W,etal.. Acoustic reporter genes for noninvasive imaging of microorganisms in mammalian hosts.

對腸道菌群的精確控制可改善結(jié)腸炎

胃腸道感染性疾病常與腸道菌群失調(diào)有關。本研究發(fā)現(xiàn)鎢酸鹽可用于治療腸道感染時腸桿菌科的異常擴增。鎢酸鹽在炎癥時選擇性地抑制鉬輔因子依賴的微生物的呼吸通路，但在穩(wěn)態(tài)下對腸道菌群組成的影響很小。小鼠結(jié)腸炎模型中，鎢酸鹽介導的菌群調(diào)控降低了腸炎的嚴重程度。由此證明，通過鎢酸鹽對微生物菌群成分的精確編輯，改善了腸道菌群失調(diào)的不利影響，即鎢酸鹽可用于減少治療過程中因腸道菌群失調(diào)而產(chǎn)生的副作用。

論文鏈接: 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.

天然造血系統(tǒng)中譜系的克隆分析

造血作用是生產(chǎn)成熟的紅細胞和免疫細胞的過程，從功能上來說，其可作為一個層級結(jié)構，而自我更新的造血干細胞和多功能祖細胞位于造血體系的最頂層。本研究使用轉(zhuǎn)座子標簽，追蹤造血過程中未受干擾情況下的祖細胞和干細胞。結(jié)果顯示，傳統(tǒng)定義的長期造血干細胞是巨核細胞限制性祖細胞的重要來源，這暗示巨核細胞譜系是長期造血干細胞演變的主要方向。該研究為無干擾情況下造血通路圖的重新修訂提供了理論基礎。

論文鏈接: 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.

通過體內(nèi)輸送基因組編輯藥物來治療常染色體顯性遺傳性聽力喪失

幾乎一半的聽力喪失是遺傳因素導致的，但目前治療手段非常有限。本研究開發(fā)了一種基因組編輯方法，向新生的人類遺傳性耳聾小鼠模型的耳蝸中注射由陽離子脂質(zhì)包裹的Cas9-gRNA復合物，特異地靶向定位小鼠的Tmc1Bth等位基因，使毛細胞生存率提高，降低聽覺腦干反應閾值，從而顯著降低進行性聽力喪失。這一方法為遺傳性聽力喪失的治療提供了新策略。

論文鏈接: 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.

增強子的冗余保證了哺乳動物發(fā)育表型的穩(wěn)健性

哺乳動物基因組中存在大量可遠距離作用的增強子，但其功能調(diào)節(jié)的復雜性尚不清楚。本研究通過基因組編輯手段對小鼠7個影響肢體發(fā)育的增強子位點進行刪除，發(fā)現(xiàn)單個刪除并不會造成肢體形態(tài)異常，但成對刪除同一基因的增強子會出現(xiàn)明顯表型，并且冗余的增強子可通過加成作用影響基因表達水平。此外，小鼠肢體、大腦和心臟中均發(fā)現(xiàn)同一基因附近存在多個增強子的現(xiàn)象。結(jié)果表明，增強子的冗余是哺乳動物基因組的一個非常普遍的特征，其可提供有效的調(diào)節(jié)緩沖，以防止對個體增強子的喪失而產(chǎn)生有害表型的后果。

論文鏈接: 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.

腦血管系統(tǒng)中細胞類型和空間分區(qū)的分子圖譜

在發(fā)達國家，腦血管疾病是導致死亡的第三大常見原因，但目前對組成大腦血管系統(tǒng)的細胞類型還不甚了解。本研究利用單細胞轉(zhuǎn)錄組學技術解析了沿小鼠腦血管軸向不同種細胞的分區(qū)情況，發(fā)現(xiàn)其中的上皮細胞連續(xù)分布，而血管壁細胞則間斷分布。研究還鑒定出了一類特別的周細胞：血管周圍成纖維細胞。該研究拓展了單細胞轉(zhuǎn)錄組學的應用范疇，并為構建哺乳動物血管分子圖譜奠定了理論基礎。

論文鏈接: 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.