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Using artificial intelligence to develop gene therapy for the lungs 利用人工智能开发肺部基因疗法
IF 46.9 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-12-11 DOI: 10.1038/s41587-024-02491-x
Gene therapy in the lungs could treat a range of devastating illnesses, but lack of safe and efficient delivery has held back the field. Here, in silico screening of millions of lipid nanoparticles (LNPs) yielded several chemically novel and highly potent LNPs for pulmonary gene therapy.
肺部基因疗法可以治疗一系列毁灭性的疾病,但缺乏安全有效的治疗方法阻碍了这一领域的发展。在这里,对数百万脂质纳米颗粒(LNPs)的硅筛选产生了几种化学上新颖且高效的用于肺部基因治疗的LNPs。
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引用次数: 0
Leveraging machine learning and big data techniques to map the global patent landscape of phage therapy 利用机器学习和大数据技术绘制噬菌体治疗的全球专利版图
IF 33.1 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-12-11 DOI: 10.1038/s41587-024-02493-9
Maxime Descartes Mbogning Fonkou, Jude Dzevela Kong
A patent analysis of the phage therapy field underscores a dynamic, evolving landscape marked by regional disparities and a shift in research focus towards broad-spectrum medical applications and treatments for bacterial infections.
噬菌体治疗领域的专利分析强调了一个动态的、不断发展的景观,其特征是区域差异和研究重点向广谱医学应用和细菌感染治疗的转变。
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引用次数: 0
Intestinal mucosal barrier repair and immune regulation with an AI-developed gut-restricted PHD inhibitor ai开发的肠道限制性PHD抑制剂的肠黏膜屏障修复和免疫调节
IF 46.9 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-12-11 DOI: 10.1038/s41587-024-02503-w
Yanyun Fu, Xiao Ding, Man Zhang, Chunlei Feng, Ziqi Yan, Feng Wang, Jianyu Xu, Xiaoxia Lin, Xiaoyu Ding, Ling Wang, Yaya Fan, Taotao Li, Yushu Yin, Xing Liang, Chenxi Xu, Shan Chen, Fadi E. Pulous, David Gennert, Frank W. Pun, Petrina Kamya, Feng Ren, Alex Aliper, Alex Zhavoronkov

Hypoxia-inducible factor prolyl hydroxylase (PHD) inhibitors have been approved for treating renal anemia yet have failed clinical testing for inflammatory bowel disease because of a lack of efficacy. Here we used a multimodel multimodal generative artificial intelligence platform to design an orally gut-restricted selective PHD1 and PHD2 inhibitor that exhibits favorable safety and pharmacokinetic profiles in preclinical studies. ISM012-042 restores intestinal barrier function and alleviates gut inflammation in multiple experimental colitis models.

缺氧诱导因子脯氨酸羟化酶(PHD)抑制剂已被批准用于治疗肾性贫血,但由于缺乏疗效,在炎症性肠病的临床试验中失败。在这里,我们使用多模型多模式生成人工智能平台设计了一种口服肠道限制性选择性PHD1和PHD2抑制剂,在临床前研究中表现出良好的安全性和药代动力学特征。ISM012-042在多种实验性结肠炎模型中恢复肠道屏障功能,减轻肠道炎症。
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引用次数: 0
Artificial intelligence-guided design of lipid nanoparticles for pulmonary gene therapy 基于人工智能的肺基因治疗脂质纳米颗粒设计
IF 46.9 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-12-10 DOI: 10.1038/s41587-024-02490-y
Jacob Witten, Idris Raji, Rajith S. Manan, Emily Beyer, Sandra Bartlett, Yinghua Tang, Mehrnoosh Ebadi, Junying Lei, Dien Nguyen, Favour Oladimeji, Allen Yujie Jiang, Elise MacDonald, Yizong Hu, Haseeb Mughal, Ava Self, Evan Collins, Ziying Yan, John F. Engelhardt, Robert Langer, Daniel G. Anderson

Ionizable lipids are a key component of lipid nanoparticles, the leading nonviral messenger RNA delivery technology. Here, to advance the identification of ionizable lipids beyond current methods, which rely on experimental screening and/or rational design, we introduce lipid optimization using neural networks, a deep-learning strategy for ionizable lipid design. We created a dataset of >9,000 lipid nanoparticle activity measurements and used it to train a directed message-passing neural network for prediction of nucleic acid delivery with diverse lipid structures. Lipid optimization using neural networks predicted RNA delivery in vitro and in vivo and extrapolated to structures divergent from the training set. We evaluated 1.6 million lipids in silico and identified two structures, FO-32 and FO-35, with local mRNA delivery to the mouse muscle and nasal mucosa. FO-32 matched the state of the art for nebulized mRNA delivery to the mouse lung, and both FO-32 and FO-35 efficiently delivered mRNA to ferret lungs. Overall, this work shows the utility of deep learning for improving nanoparticle delivery.

可电离脂质是脂质纳米颗粒的关键组成部分,是领先的非病毒信使RNA传递技术。在这里,为了超越目前依赖于实验筛选和/或合理设计的方法来推进可电离脂质的鉴定,我们引入了使用神经网络的脂质优化,这是一种用于可电离脂质设计的深度学习策略。我们创建了一个9000个脂质纳米颗粒活性测量数据集,并用它来训练一个定向信息传递神经网络,用于预测不同脂质结构的核酸传递。脂质优化使用神经网络预测体外和体内的RNA传递,并推断出与训练集不同的结构。我们用硅评估了160万个脂质,并确定了FO-32和FO-35两种结构,它们的mRNA可以局部传递到小鼠肌肉和鼻黏膜。FO-32与目前最先进的雾化mRNA递送到小鼠肺的技术相匹配,FO-32和FO-35都能有效地将mRNA递送到雪貂肺。总的来说,这项工作显示了深度学习在改善纳米粒子传递方面的效用。
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引用次数: 0
Ovarian tumor cells gain competitive advantage by actively reducing the cellular fitness of microenvironment cells 卵巢肿瘤细胞通过主动降低微环境细胞的适应度来获得竞争优势
IF 46.9 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-12-09 DOI: 10.1038/s41587-024-02453-3
Esha Madan, António M. Palma, Vignesh Vudatha, Amit Kumar, Praveen Bhoopathi, Jochen Wilhelm, Tytus Bernas, Patrick C. Martin, Gaurav Bilolikar, Aenya Gogna, Maria Leonor Peixoto, Isabelle Dreier, Thais Fenz Araujo, Elena Garre, Anna Gustafsson, Kalpana Deepa Priya Dorayappan, Narsimha Mamidi, Zhaoyu Sun, Michail Yekelchyk, Davide Accardi, Amalie Lykke Olsen, Lin Lin, Asaf Ashkenazy Titelman, Michael Bianchi, Phil Jessmon, Elnaz Abbasi Farid, Anjan K. Pradhan, Lena Neufeld, Eilam Yeini, Santanu Maji, Christopher J. Pelham, Hyobin Kim, Daniel Oh, Hans Olav Rolfsnes, Rita C. Marques, Amy Lu, Masaki Nagane, Sahil Chaudhary, Kartik Gupta, Keshav C. Gogna, Ana Bigio, Karthikeya Bhoopathi, Padmanabhan Mannangatti, K. Gopinath Achary, Javed Akhtar, Sara Belião, Swadesh Das, Isabel Correia, Cláudia L. da Silva, Arsénio M. Fialho, Michael J. Poellmann, Kaila Javius-Jones, Adam M. Hawkridge, Sanya Pal, Kumari S. Shree, Emad A. Rakha, Sambhav Khurana, Gaoping Xiao, Dongyu Zhang, Arjun Rijal, Charles Lyons, Steven R. Grossman, David P. Turner, Raghavendra Pillappa, Karanvir Prakash, Gaurav Gupta, Gary L. W. G. Robinson, Jennifer Koblinski, Hongjun Wang, Gita Singh, Sujay Singh, Sagar Rayamajhi, Manny D. Bacolod, Hope Richards, Sadia Sayeed, Katherine P. Klein, David Chelmow, Ronit Satchi-Fainaro, Karuppaiyah Selvendiran, Denise Connolly, Frits Alan Thorsen, Rolf Bjerkvig, Kenneth P. Nephew, Michael O. Idowu, Mark P. Kühnel, Christopher Moskaluk, Seungpyo Hong, William L. Redmond, Göran Landberg, Antonio Lopez-Beltran, Andrew S. Poklepovic, Arun Sanyal, Paul B. Fisher, George M. Church, Usha Menon, Ronny Drapkin, Andrew K. Godwin, Yonglun Luo, Maximilian Ackermann, Alexandar Tzankov, Kirsten D. Mertz, Danny Jonigk, Allan Tsung, David Sidransky, Jose Trevino, Arturo P. Saavedra, Robert Winn, Kyoung Jae Won, Eduardo Moreno, Rajan Gogna

Cell competition and fitness comparison between cancer and tumor microenvironment (TME) cells determine oncogenic fate. Our previous study established a role for human Flower isoforms as fitness fingerprints, where the expression of Flower Win isoforms in tumor cells leads to growth advantage over TME cells expressing Lose isoforms. Here we demonstrate that the expression of Flower Lose and reduced microenvironment fitness is not a pre-existing condition but, rather, a cancer-induced phenomenon. Cancer cells actively reduce TME fitness by the exosome-mediated release of a cancer-specific long non-coding RNA, Tu-Stroma, which controls the splicing of the Flower gene in the TME cells and expression of Flower Lose isoform, which leads to reduced fitness status. This mechanism controls cancer growth, metastasis and host survival in ovarian cancer. Targeting Flower protein with humanized monoclonal antibody (mAb) in mice significantly reduces cancer growth and metastasis and improves survival. Pre-treatment with Flower mAb protects intraperitoneal organs from developing lesions despite the presence of aggressive tumor cells.

肿瘤细胞和肿瘤微环境(TME)细胞之间的竞争和适应性比较决定了肿瘤的命运。我们之前的研究确定了人类Flower亚型作为适应度指纹的作用,在肿瘤细胞中表达Flower Win亚型导致比表达Lose亚型的TME细胞具有生长优势。在这里,我们证明了Flower Lose的表达和微环境适应度的降低不是预先存在的条件,而是一种癌症诱导的现象。癌细胞通过外泌体介导的癌症特异性长链非编码RNA Tu-Stroma的释放来主动降低TME适应度,该RNA控制了TME细胞中Flower基因的剪接和Flower Lose亚型的表达,从而导致适应度降低。这一机制控制着卵巢癌的生长、转移和宿主生存。人源化单克隆抗体(mAb)靶向Flower蛋白可显著降低小鼠肿瘤的生长和转移,提高生存率。尽管存在侵袭性肿瘤细胞,Flower mAb预处理可保护腹膜内器官免受病变的影响。
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引用次数: 0
Challenges for developing broad-based mucosal vaccines for respiratory viruses 开发基础广泛的呼吸道病毒粘膜疫苗面临的挑战
IF 33.1 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-12-06 DOI: 10.1038/s41587-024-02486-8
Junghwa Seo, Jordan Polster, Benjamin Israelow, Kizzmekia S. Corbett-Helaire, David R. Martinez
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引用次数: 0
Biology and applications of CRISPR–Cas12 and transposon-associated homologs CRISPR-Cas12和转座子相关同源物的生物学和应用
IF 33.1 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-12-04 DOI: 10.1038/s41587-024-02485-9
Wen Y. Wu, Belén Adiego-Pérez, John van der Oost
CRISPR-associated Cas12 proteins are a highly variable collection of nucleic acid-targeting proteins. All Cas12 variants use RNA guides and a single nuclease domain to target complementary DNA or, in rare cases, RNA. The high variability of Cas12 effectors can be explained by a series of independent evolution events from different transposon-associated TnpB-like ancestors. Despite basic structural and functional similarities, this has resulted in unprecedented variation of the Cas12 effector proteins in terms of size, domain composition, guide structure, target identity and interference strategy. In this Review, we compare the unique molecular features of natural and engineered Cas12 and TnpB variants. Furthermore, we provide an overview of established genome editing and diagnostic applications and discuss potential future directions. Natural and engineered Cas12 and TnpB variants offer diverse applications in genome editing and diagnostics.
crispr相关的Cas12蛋白是一种高度可变的核酸靶向蛋白。所有Cas12变体都使用RNA向导和单个核酸酶结构域来靶向互补DNA,或者在极少数情况下靶向RNA。Cas12效应子的高变异性可以用来自不同转座子相关的tnpb样祖先的一系列独立进化事件来解释。尽管基本的结构和功能相似,但这导致Cas12效应蛋白在大小、结构域组成、引导结构、靶标身份和干扰策略方面发生了前所未有的变化。在这篇综述中,我们比较了天然和工程Cas12和TnpB变体的独特分子特征。此外,我们还概述了已建立的基因组编辑和诊断应用,并讨论了潜在的未来方向。
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引用次数: 0
Top ten news stories in 2024 2024年十大新闻
IF 33.1 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-12-04 DOI: 10.1038/s41587-024-02500-z
Lisa Melton
From mRNA drugs and the Achilles heel of obesity drugs, to single-cell biology and foundation models for drug discovery, these are some of the big stories most viewed by our readers.
从mRNA药物和肥胖药物的致命弱点,到单细胞生物学和药物发现的基础模型,这些是我们的读者最关注的一些大故事。
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引用次数: 0
2024: research in review 2024年:研究回顾
IF 33.1 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-12-04 DOI: 10.1038/s41587-024-02508-5
Nature Biotechnology editors pick their favorite research articles from 2024.
《自然生物技术》的编辑们从2024年挑选了他们最喜欢的研究文章。
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引用次数: 0
Proteolytic platelets as targeted protein degraders 蛋白水解血小板作为靶向蛋白降解剂
IF 46.9 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-12-03 DOI: 10.1038/s41587-024-02495-7
Proteolytic chimeras constructed from various bioactive modules can degrade either cytoplasmic or extracellular proteins, but their pharmacology faces challenges. Now, a protein degradation platform built with engineered platelets enables the targeted depletion of intracellular and extracellular proteins at hemorrhagic sites, addressing several limitations associated with proteolytic chimeras.
由多种生物活性模块构建的蛋白水解嵌合体可以降解细胞质或细胞外蛋白质,但其药理学面临挑战。现在,用工程血小板构建的蛋白质降解平台能够在出血部位靶向消耗细胞内和细胞外蛋白质,解决与蛋白水解嵌合体相关的几个限制。
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引用次数: 0
期刊
Nature biotechnology
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