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TCR cell therapies vanquish solid tumors — finally TCR 细胞疗法终于战胜了实体瘤
IF 33.1 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-02 DOI: 10.1038/s41587-024-02435-5
Charlotte Harrison
The FDA’s approval of the first genetically modified T cell therapy for treating a rare sarcoma is paving the way for next-generation therapies that tackle other types of solid tumors.
美国食品和药物管理局(FDA)批准了首个用于治疗一种罕见肉瘤的转基因 T 细胞疗法,这为治疗其他类型实体瘤的下一代疗法铺平了道路。
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引用次数: 0
Rapid generation of long, chemically modified pegRNAs for prime editing 快速生成用于素材编辑的化学修饰长 pegRNA
IF 46.9 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-30 DOI: 10.1038/s41587-024-02394-x
Xinlin Lei, Anhui Huang, Didi Chen, Xuebin Wang, Ruijin Ji, Jinlin Wang, Yizhou Zhang, Yuming Zhang, Shuhan Lu, Kun Zhang, Qiubing Chen, Ying Zhang, Hao Yin

The editing efficiencies of prime editing (PE) using ribonucleoprotein (RNP) and RNA delivery are not optimal due to the challenges in solid-phase synthesis of long PE guide RNA (pegRNA) (>125 nt). Here, we develop an efficient, rapid and cost-effective method for generating chemically modified pegRNA (125–145 nt) and engineered pegRNA (epegRNA) (170–190 nt). We use an optimized splint ligation approach and achieve approximately 90% production efficiency for these RNAs, referred to as L-pegRNA and L-epegRNA. L-epegRNA demonstrates enhanced editing efficiencies across various cell lines and human primary cells with improvements of up to more than tenfold when using RNP delivery and several hundredfold with RNA delivery of PE, compared to epegRNA produced by in vitro transcription. L-epegRNA-mediated RNP delivery also outperforms plasmid-encoded PE in most comparisons. Our study provides a solution to obtaining high-quality pegRNA and epegRNA with desired chemical modifications, paving the way for the use of PE in therapeutics and various other fields.

由于固相合成长PE引导RNA(pegRNA)(125 nt)的难题,使用核糖核蛋白(RNP)和RNA递送的质粒编辑(prime editing,PE)的编辑效率并不理想。在此,我们开发了一种高效、快速、经济的方法,用于生成化学修饰的 pegRNA(125-145 nt)和工程化的 pegRNA(epegRNA)(170-190 nt)。我们采用优化的夹板连接方法,这些 RNA 的生产效率约为 90%,分别称为 L-pegRNA 和 L-epegRNA。与体外转录产生的 epegRNA 相比,L-epegRNA 在各种细胞系和人类原代细胞中的编辑效率都有所提高,使用 RNP 运送时可提高 10 倍以上,使用 PE 的 RNA 运送时可提高几百倍。在大多数比较中,L-epegRNA介导的RNP递送也优于质粒编码的PE。我们的研究为获得具有所需化学修饰的高质量 pegRNA 和 epegRNA 提供了一种解决方案,为 PE 在治疗学和其他各种领域的应用铺平了道路。
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引用次数: 0
Increasing intracellular dNTP levels improves prime editing efficiency 增加细胞内 dNTP 水平可提高素材编辑效率
IF 46.9 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-25 DOI: 10.1038/s41587-024-02405-x
Pengpeng Liu, Karthikeyan Ponnienselvan, Thomas Nyalile, Sarah Oikemus, Anya T. Joynt, Sukanya Iyer, Karen Kelly, Dongsheng Guo, Pyae P. Kyawe, Emma Vanderleeden, Sambra D. Redick, Lei Huang, Zexiang Chen, Jeong Min Lee, Celia A. Schiffer, David M. Harlan, Jennifer P. Wang, Charles P. Emerson, Nathan D. Lawson, Jonathan K. Watts, Erik J. Sontheimer, Jeremy Luban, Scot A. Wolfe

In primary cell types, intracellular deoxynucleotide triphosphate (dNTP) levels are tightly regulated in a cell cycle-dependent manner. We report that prime editing efficiency is increased by mutations that improve the enzymatic properties of Moloney murine leukemia virus reverse transcriptase and treatments that increase intracellular dNTP levels. In combination, these modifications produce substantial increases in precise editing rates.

在原代细胞类型中,细胞内脱氧核苷酸三磷酸酯(dNTP)水平以依赖细胞周期的方式受到严格调控。我们报告说,通过突变改善莫罗尼小鼠白血病病毒反转录酶的酶学特性,以及增加细胞内 dNTP 水平的处理方法,可提高质粒编辑效率。将这些修饰结合在一起,可大幅提高精确编辑率。
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引用次数: 0
Multistate and functional protein design using RoseTTAFold sequence space diffusion 利用 RoseTTAFold 序列空间扩散进行多态和功能蛋白质设计
IF 46.9 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-25 DOI: 10.1038/s41587-024-02395-w
Sidney Lyayuga Lisanza, Jacob Merle Gershon, Samuel W. K. Tipps, Jeremiah Nelson Sims, Lucas Arnoldt, Samuel J. Hendel, Miriam K. Simma, Ge Liu, Muna Yase, Hongwei Wu, Claire D. Tharp, Xinting Li, Alex Kang, Evans Brackenbrough, Asim K. Bera, Stacey Gerben, Bruce J. Wittmann, Andrew C. McShan, David Baker

Protein denoising diffusion probabilistic models are used for the de novo generation of protein backbones but are limited in their ability to guide generation of proteins with sequence-specific attributes and functional properties. To overcome this limitation, we developed ProteinGenerator (PG), a sequence space diffusion model based on RoseTTAFold that simultaneously generates protein sequences and structures. Beginning from a noised sequence representation, PG generates sequence and structure pairs by iterative denoising, guided by desired sequence and structural protein attributes. We designed thermostable proteins with varying amino acid compositions and internal sequence repeats and cage bioactive peptides, such as melittin. By averaging sequence logits between diffusion trajectories with distinct structural constraints, we designed multistate parent–child protein triples in which the same sequence folds to different supersecondary structures when intact in the parent versus split into two child domains. PG design trajectories can be guided by experimental sequence–activity data, providing a general approach for integrated computational and experimental optimization of protein function.

蛋白质去噪扩散概率模型可用于从头生成蛋白质骨架,但在指导生成具有特定序列属性和功能特性的蛋白质方面能力有限。为了克服这一局限,我们开发了 ProteinGenerator (PG),这是一种基于 RoseTTAFold 的序列空间扩散模型,可同时生成蛋白质序列和结构。PG 从噪声序列表示开始,在所需序列和结构蛋白质属性的指导下,通过迭代去噪生成序列和结构对。我们设计了具有不同氨基酸组成和内部序列重复的恒温蛋白质和笼状生物活性肽,如 Melittin。通过平均具有不同结构约束的扩散轨迹之间的序列对数,我们设计出了多态父子蛋白质三元组,其中相同的序列在完整的父域和分裂成两个子域时会折叠成不同的超二级结构。PG 设计轨迹可以由实验序列-活性数据指导,为蛋白质功能的综合计算和实验优化提供了一种通用方法。
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引用次数: 0
Plastic-eating bacteria boost growing business of bioremediation 吃塑料的细菌促进了生物修复业务的增长
IF 33.1 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-23 DOI: 10.1038/s41587-024-02401-1
Ben Johnson
Bacteria, fungi and plants can be grown and engineered to remove plastics, chemicals and pollutants from contaminated soil and water.
细菌、真菌和植物可以通过培养和工程设计,从受污染的土壤和水中清除塑料、化学品和污染物。
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引用次数: 0
Scalable and unsupervised discovery from raw sequencing reads using SPLASH2 利用 SPLASH2 从原始测序读数中进行可扩展的无监督发现
IF 46.9 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-23 DOI: 10.1038/s41587-024-02381-2
Marek Kokot, Roozbeh Dehghannasiri, Tavor Baharav, Julia Salzman, Sebastian Deorowicz

We introduce SPLASH2, a fast, scalable implementation of SPLASH based on an efficient k-mer counting approach for regulated sequence variation detection in massive datasets from a wide range of sequencing technologies and biological contexts. We demonstrate biological discovery by SPLASH2 in single-cell RNA sequencing (RNA-seq) data and in bulk RNA-seq data from the Cancer Cell Line Encyclopedia, including unannotated alternative splicing in cancer transcriptomes and sensitive detection of circular RNA.

我们介绍了 SPLASH2,它是 SPLASH 的一种快速、可扩展的实现方法,基于一种高效的 k-mer 计数方法,用于检测来自各种测序技术和生物环境的海量数据集中的调节序列变异。我们展示了 SPLASH2 在单细胞 RNA 测序(RNA-seq)数据和癌症细胞系百科全书(Cancer Cell Line Encyclopedia)的大量 RNA-seq 数据中的生物学发现,包括癌症转录组中未标注的替代剪接和环状 RNA 的灵敏检测。
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引用次数: 0
Coordinated, multicellular patterns of transcriptional variation that stratify patient cohorts are revealed by tensor decomposition 张量分解法揭示了使患者群体分层的多细胞转录变异协调模式
IF 46.9 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-23 DOI: 10.1038/s41587-024-02411-z
Jonathan Mitchel, M. Grace Gordon, Richard K. Perez, Evan Biederstedt, Raymund Bueno, Chun Jimmie Ye, Peter V. Kharchenko

Tissue-level and organism-level biological processes often involve the coordinated action of multiple distinct cell types. The recent application of single-cell assays to many individuals should enable the study of how donor-level variation in one cell type is linked to that in other cell types. Here we introduce a computational approach called single-cell interpretable tensor decomposition (scITD) to identify common axes of interindividual variation by considering joint expression variation across multiple cell types. scITD combines expression matrices from each cell type into a higher-order matrix and factorizes the result using the Tucker tensor decomposition. Applying scITD to single-cell RNA-sequencing data on 115 persons with lupus and 83 persons with coronavirus disease 2019, we identify patterns of coordinated cellular activity linked to disease severity and specific phenotypes, such as lupus nephritis. scITD results also implicate specific signaling pathways likely mediating coordination between cell types. Overall, scITD offers a tool for understanding the covariation of cell states across individuals, which can yield insights into the complex processes that define and stratify disease.

组织层面和生物体层面的生物过程往往涉及多种不同细胞类型的协调作用。最近对许多个体进行的单细胞检测有助于研究一种细胞类型的供体水平变异与其他细胞类型的供体水平变异之间的联系。在这里,我们介绍了一种名为单细胞可解释张量分解(scITD)的计算方法,通过考虑多种细胞类型的联合表达变异来确定个体间变异的共同轴线。scITD将每种细胞类型的表达矩阵组合成一个高阶矩阵,并使用塔克张量分解法对结果进行因子化。将 scITD 应用于 115 名红斑狼疮患者和 83 名冠状病毒患者的单细胞 RNA 序列数据,我们确定了与疾病严重程度和特定表型(如狼疮肾炎)相关的细胞协调活动模式。总之,scITD 为了解不同个体细胞状态的共变性提供了一种工具,它可以帮助我们深入了解定义和分层疾病的复杂过程。
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引用次数: 0
Chemical and topological design of multicapped mRNA and capped circular RNA to augment translation 多封端 mRNA 和封端环形 RNA 的化学和拓扑设计,以增强翻译能力
IF 46.9 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-23 DOI: 10.1038/s41587-024-02393-y
Hongyu Chen, Dangliang Liu, Abhishek Aditham, Jianting Guo, Jiahao Huang, Franklin Kostas, Kamal Maher, Mirco J. Friedrich, Ramnik J. Xavier, Feng Zhang, Xiao Wang

Protein and vaccine therapies based on mRNA would benefit from an increase in translation capacity. Here, we report a method to augment translation named ligation-enabled mRNA–oligonucleotide assembly (LEGO). We systematically screen different chemotopological motifs and find that a branched mRNA cap effectively initiates translation on linear or circular mRNAs without internal ribosome entry sites. Two types of chemical modification, locked nucleic acid (LNA) N7-methylguanosine modifications on the cap and LNA + 5 × 2′ O-methyl on the 5′ untranslated region, enhance RNA–eukaryotic translation initiation factor (eIF4E–eIF4G) binding and RNA stability against decapping in vitro. Through multidimensional chemotopological engineering of dual-capped mRNA and capped circular RNA, we enhanced mRNA protein production by up to tenfold in vivo, resulting in 17-fold and 3.7-fold higher antibody production after prime and boost doses in a severe acute respiratory syndrome coronavirus 2 vaccine setting, respectively. The LEGO platform opens possibilities to design unnatural RNA structures and topologies beyond canonical linear and circular RNAs for both basic research and therapeutic applications.

基于 mRNA 的蛋白质和疫苗疗法将受益于翻译能力的提高。在这里,我们报告了一种增强翻译的方法,名为 "连接启用 mRNA-配体核苷酸组装(LEGO)"。我们系统地筛选了不同的化学图案,发现分枝mRNA帽能有效地启动没有内部核糖体进入位点的线性或环形mRNA的翻译。两种类型的化学修饰--帽上的锁定核酸(LNA)N7-甲基鸟苷修饰和 5′非翻译区上的 LNA + 5 × 2′ O-甲基--增强了 RNA 与真核翻译起始因子(eIF4E-eIF4G)的结合,并提高了 RNA 在体外抗脱帽的稳定性。通过对双封顶 mRNA 和封顶环状 RNA 进行多维化学拓扑工程设计,我们将 mRNA 蛋白在体内的生成量提高了 10 倍之多,在严重急性呼吸系统综合征冠状病毒 2 疫苗接种中,初次接种和加强接种后的抗体生成量分别提高了 17 倍和 3.7 倍。乐高平台为基础研究和治疗应用提供了设计非天然 RNA 结构和拓扑结构的可能性,而不是传统的线性和环形 RNA。
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引用次数: 0
Building better mRNA for therapeutics 构建更好的 mRNA 用于治疗
IF 46.9 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-23 DOI: 10.1038/s41587-024-02424-8
Bei Liu, Tao Pan
Redesigning mRNA with chemo-topological strategies improves its stability and translation efficiency, paving the way for more effective mRNA therapeutics.
利用化学拓扑策略重新设计 mRNA 可提高其稳定性和翻译效率,从而为更有效的 mRNA 疗法铺平道路。
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引用次数: 0
Targeting double-stranded nucleic acids using the λExo–pDNA system 利用 λExo-pDNA 系统靶向双链核酸
IF 46.9 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-18 DOI: 10.1038/s41587-024-02409-7
λ exonuclease (λExo) binds 5′-phosphorylated single-stranded DNA (pDNA) at complementary regions on double-stranded DNA and DNA–RNA duplexes under ambient conditions without a PAM-like motif. In the presence of Mg2+, λExo then digests the pDNA into nucleotides.
λ外切酶(λExo)能在环境条件下与双链 DNA 和 DNA-RNA 双链上互补区的 5′-磷酸化单链 DNA(pDNA)结合,但不含类似 PAM 的基团。在 Mg2+ 存在的情况下,λExo 会将 pDNA 消化成核苷酸。
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引用次数: 0
期刊
Nature biotechnology
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