MALAT1

Under the terms of the deal, the companies will develop small molecule therapeutics targeting lncRNAs in oncology. PeopleImages.com – Yuri A via Shutterstock. Bayer has teamed up with startup biotech NextRNA Therapeutics to develop small molecules targeting long non-coding RNAs (lncRNAs) in oncology. Under the terms of the deal, NextRNA can get up to $547m if all the milestones are reached, and the deal also included an undisclosed upfront payment. The companies will collaborate on two oncology programmes, the first involving a lncRNA-targeting small molecule in early preclinical development at NextRNA. For the second, NextRNA will pursue lncRNA targets identified by its platform, with Bayer having the option to choose one target for joint development. In 2022, Dana-Farber spinout NextRNA came out of stealth with $9.3m from a seed financing round and $46.8m from a Series A. This is the first high-profile pharma deal for the startup, which focuses on lncRNA-driven diseases. lncRNAs are RNA molecules over 200 nucleotides long that regulate gene expression without coding for proteins. They play key roles in various cellular processes, including those linked to cancer, such as tumour growth, metastasis, drug resistance and angiogenesis. See Also: Shortages improve for Lilly’s GLP-1 weight loss drugs, bumping sales forecast by $3bn Annexon gets grant for anti-c1q antibody fab fragments for inhibiting synapse loss A few companies have hopped on the lncRNA space, with strategies like antisense oligonucleotides, siRNAs, CRISPR/Cas9, small molecules and RNA aptamers being explored to modulate their function. In June 2023, Flamingo Therapeutics secured a €1.7m grant from Flanders Innovation & Entrepreneurship (VLAIO) to advance its lncRNA programme, FTX-001, that targets MALAT-1. The preclinical candidate is being developed in collaboration with Ionis Pharmaceuticals for a Phase I trial in solid tumours. The NextRNA deal comes weeks after Bayer announced that it has cut 3,200 jobs since the beginning of the year, in its Q2 2024 earnings call. At the start of this year, the German pharma giant said that it will roll out a new operating model, one designed to cut bureaucracy and speed up decision-making following which it is aiming to make savings of €2bn a year from 2026. In the announcement accompanying the deal, head of business development and licensing at Bayer’s pharmaceutical division Juergen Eckhardt said: “With NextRNA’s exceptional expertise and lncRNA platform, we aim to advance novel small molecule therapeutics against a new class of targets in oncology. This partnership further adds to our mission to build one of the most transformative and diversified oncology pipelines in the industry.” mRNA vaccine coverage on Pharmaceutical Technology (Or Clinical Trials Arena) is supported by Trilink . Editorial content is independently produced and follows the highest standards of journalistic integrity. Topic sponsors are not involved in the creation of editorial content. Free Whitepaper mRNA capping: low cost, high reward Are you aware of the latest mRNA capping techniques? The success of mRNA-based Covid vaccines has seen the technology boom in popularity – but capping is an essential part of the manufacturing process, and pharmaceutical firms face a range of choices on how to do it. This free whitepaper assesses differences in price, time, complexity and availability for the methods on offer – and provides essential insights on TriLink’s trailblazing CleanCap® approach. Fill in your details to find out more. Thank you. You will receive an email shortly. Please check your inbox to download the Whitepaper. By Trilink Thematic By downloading this Whitepaper, you acknowledge that GlobalData may share your information with Trilink Thematic and that your personal data will be used as described in their Privacy Policy

The blood-brain barrier protects gray matter from unwanted intruders, but its stinginess means it excludes helpful drugs from reaching the brain, too. Antisense oligonucleotides (ASOs), which bind to RNA and prevent them from being translated into proteins, have gained popularity in recent years as a way to treat neurodegenerative diseases. However, getting these drugs into the brain has been challenging, currently requiring invasive infusion directly into the cerebrospinal fluid.Now, Denali Therapeutics has developed a way to deliver these drugs to the brain more easily—by smuggling them across the blood-brain barrier. In studies with mice and macaques, the California-based biotech combined ASOs with their transferrin-targeting transport vehicle platform and successfully knocks down certain gene activity across the brain.“Not only could we get brain uptake, but we could get it into the cell, we could get knock down of the genes that we're interested in,” Denali Chief Scientific Officer Joe Lewcock, Ph.D., told Fierce Biotech in an interview. “Really demonstrating that this platform can be effective for this class of drugs as well.” The results appeared in Science Translational Medicine on Aug. 14. The blood-brain barrier protects precious gray matter from unwanted intruders, but its stinginess means it excludes helpful drugs from reaching the brain too. Denali’s transport vehicle platform is an engineered antibody that targets transferrin receptor 1, which normally shuttles iron—essential for brain function—across the barrier.This technology is the basis for the biotech’s lead drug candidate, DNL310, where iduronate 2-sulfatase enzyme is bound to the transport vehicle and shepherded into cells to treat Hunter syndrome. Individuals with the disease have mutations in the gene that codes for the iduronate 2-sulfatase enzyme, making it not work properly. DNL310 is currently in phase 3 trials.To test the approach with ASOs, Denali scientists chose to focus on a gene called malat1. “It's a commonly used target in the field for proof-of-concept,” according to Lewcock, and is expressed in all cell types of the central nervous system. Binding an ASO targeting malat1 to Denali's transport vehicle forms an oligonucleotide transport vehicle (OTV), which allows the ASO to be shuttled into diverse cells and can successfully reduce expression of the gene in both mice and cynomolgus macaques.Lewcock sees three advantages to OTVs. First is the intravenous delivery, which is less invasive than intrathecal infusion directly into the central nervous system. Another benefit is the even distribution of the drug throughout the brain, hitting all cell types, which could mean greater efficacy and—the third advantage—an improved safety profile.With intrathecal delivery, “to get up to the brain, you have to have very high concentrations in the lumbar spinal cord, and that could cause safety issues,” Lewcock explained. “Even biodistribution allows you to get adequate [amounts of] drug to the right places and avoid that.” With OTVs having proven their mettle in animal studies, Lewcock said Denali is now pursuing two lead OTV candidates in neurodegenerative disease. “One's targeting the MAPT gene, or tau, in the context of Alzheimer's disease, and the second is targeting the alpha-synuclein gene in the context of Parkinson's disease,” he explained. “We've done a lot of work on those targets and optimizing molecules for each of those targets.”The plan is for OTVs to join the broader transport vehicle family, which in addition to enzyme carriers also includes antibody transporters. “We're really building a foundation with the enzyme transport vehicle franchise,” Denali's vice president of investor relations Laura Hansen, Ph.D., said in a joint interview with Fierce Biotech. “Those near- to mid-term revenues expected from those indications will enable us to really continue to expand the transport vehicle platform opportunities into the antibodies and oligonucleotides.”Denali intends to seek accelerated approval for DNL310, the company's enzyme-based lead candidate for Hunter syndrome, Hansen added.

引言 核旁斑组装转录本1 (NEAT1)是一种高度丰富且保守的长链非编码 RNA (lncRNA)，从多发性内分泌肿瘤 (MEN) 基因座转录，编码 NEAT1-1（或 MEN-ε，~3.7 kb）和 NEAT1-2（或 MEN-β，~22.7 kb）。NEAT1-2 lncRNA是核旁斑 (paraspeckles)的主要结构支架。它招募多种 RNA 结合蛋白 (RBP)，包括 NONO、SFPQ、FUS 和 TDP43，驱动液-液相分离 (LLPS) 并塑造这种动态、无膜、和分层的核体。通过组织和调控核内多种重要RBP的定位和富集，NEAT1 在调节染色质状态、转录、剪接、RNA 加工和稳定性【1, 2】，以及在器官发育、神经变性、抗病毒免疫和癌症中发挥多种功能【3, 4】。 NEAT1，MALAT1，以及其他至少130个后生动物的lncRNA 缺失稳定多数mRNA的 3′ poly(A) 尾。这些lncRNA则利用它们3′ 末端的稳定RNA三螺旋（triplex）结构以免受外切核酸酶快速降解【5, 6】。NEAT1 和 MALAT1的前体均通过模仿tRNA结构以招募RNase P切割其5′ 引导序列，产生成熟lncRNA。与此同时，被RNase P切割后的tRNA类似结构生成两个新的小非编码RNA，被分别命名为mascRNA （来自MALAT1）和menRNA（来自NEAT1）【7】。随后，ELAC2（ElaC同源蛋白2，或RNase Z）去除menRNA 的3′ 尾部，然后CCA-添加酶对mascRNA 和menRNA添加3′ CCA尾。这里，有趣的是mascRNA仅接收一次CCA 添加，形成类似tRNA的正常3′ CCA末端尾。然而menRNA 连续接受两次CCA加尾，形成较长的CCACCA尾，造成了核酸外切酶的a招募而在胞内快速降解【8】。目前为止menRNA 的三维结构仍然未知。关于menRNA重复加尾的分子机制，一个从蛋白质角度出发的“分子台虎钳 （molecular vise）”模型提出，在第一次添加 CCA 时，CCA添加酶的“头部”区域通过自身的螺旋运动并协同在远端静态固着在menRNA臂肘（elbow）的“尾部”区域对menRNA或者有结构缺陷的tRNA进行旋转性的机械压缩，造成menRNA局部构象变化，产生一个三个碱基长的侧面凸起，剩余的碱基重新配对，从而实现RNA底物重置，可以重复添加 CCA【9】。然而，目前尚不清楚menRNA是否只是被动地被蛋白酶操控，或者通过调控其自身构象从而指导蛋白酶的功能，以决定其自身的命运。并且，上述模型中蛋白机械做功的能量来源，以及此酶需要对RNA施加多大的扭矩来驱动其构象改变，并不明确。2024年7月18日，美国国立卫生研究院（NIH）资深研究员张金伟研究组在Nature Structural & Molecular Biology杂志上再次发表题为Structural basis of NEAT1 lncRNA maturation and menRNA instability的文章解析首个menRNA晶体结构。menRNA结构和张金伟研究组最近报道的mascRNA结构整体相当类似【10】，但是在氨基酸接受茎环区域有序列上，结构上和稳定性上的差异, 为menRNA之后发生构象变化奠定了基础。 a. NEAT1 lncRNA 末端成熟和menRNA产生的流程图。b. 人源menRNA的整体结构 c. 对比menRNA， mascRNA， 和tRNA的结构相似性和差异。（Credit: Nature Structural & Molecular Biology） 作者而后通过酶动力学、时间相关单光子计数 (TCSPC)、圆二色性 (CD)、实时荧光定量PCR等多种生物化学和生物物理手段揭示了menRNA招募RNase P， ELAC2， 和CCA-添加酶等多个tRNA加工酶的分子机理。利用高精度时间相关单光子计数 (TCSPC) 和圆二色性 (CD) 分析，文章作者发现3’端带有一个CCA尾的menRNA在没有蛋白酶结合或者作用的情况下自身发生了显著构象变化，自主产生了三碱基的侧凸并重组了附近的碱基配对，以此指示CCA添加酶进行第二轮的CCA添加。然后，文章作者去除了CCA添加酶的尾部或者与尾部直接接触menRNA的臂肘区域，发现第二轮CCA添加仍然可以正常进行。这些实验结果与之前提出的分子台虎钳模型明显不符【9】，并且与menRNA驱动自身构象转变的新机理模型完全一致。 a. RNase P和ELAC2 加工NEAT1产生menRNA的前体。b. menRNA和CCA添加酶的结合体结构模型。c. menRNA通过自发构象转变指示CCA添加酶重复CCA 添加，产生CCACCA尾，促进胞内迅速降解。（Credit: Nature Structural & Molecular Biology） 综上，一大类后生动物内以NEAT1 和MALAT1为例的lncRNA采用一种新颖的、异常精简的准tRNA结构来招募指定的tRNA加工酶，同时避免被其他不利的tRNA酶识别，以驱动精准定制的RNA生成、加工和成熟。在核内实现NEAT1 成熟和稳定化之后，menRNA 氨基酸接受茎环区域特异的的序列和结构造成热力学驱动的自主构象转变和茎区配对重组，从而操控CCA添加酶实现两轮CCA添加，促进其自身的快速降解。因此，menRNA的这种作用模式类似于原核生物里广泛存在的转录衰减子和核糖开关。后期出现的下游RNA序列改变了整体RNA的最稳定构象，通过热力学过程驱动预先指定的自身构象转变。这种趋同机制赋予了多种非编码RNA实质性的构象自控能力，并通过自主构象变化来指导RNA聚合酶、核糖体和RNA加工酶发挥RNA预先制定的功能，最终自身决定这些RNA在转录、翻译和降解过程的命运。 参考文献 1. Butler, A.A., et al., Long noncoding RNA NEAT1 mediates neuronal histone methylation and age-related memory impairment. Sci Signal, 2019. 12(588). 2. Hirose, T., et al., NEAT1 long noncoding RNA regulates transcription via protein sequestration within subnuclear bodies. Mol Biol Cell, 2014. 25(1): p. 169-83. 3. Adriaens, C., et al., p53 induces formation of NEAT1 lncRNA-containing paraspeckles that modulate replication stress response and chemosensitivity. Nat Med, 2016. 22(8): p. 861-8. 4. Imamura, K., et al., Long noncoding RNA NEAT1-dependent SFPQ relocation from promoter region to paraspeckle mediates IL8 expression upon immune stimuli. Mol Cell, 2014. 53(3): p. 393-406. 5. Zhang, B., et al., Identification and Characterization of a Class of MALAT1-like Genomic Loci. Cell Rep, 2017. 19(8): p. 1723-1738. 6. Brown, J.A., et al., Formation of triple-helical structures by the 3'-end sequences of MALAT1 and MENbeta noncoding RNAs. Proc Natl Acad Sci U S A, 2012. 109(47): p. 19202-7. 7. Wilusz, J.E., S.M. Freier, and D.L. Spector, 3' end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA. Cell, 2008. 135(5): p. 919-32. 8. Wilusz, J.E., et al., tRNAs marked with CCACCA are targeted for degradation. Science, 2011. 334(6057): p. 817-21. 9. Kuhn, C.D., et al., On-enzyme refolding permits small RNA and tRNA surveillance by the CCA-adding enzyme. Cell, 2015. 160(4): p. 644-658. 10. Skeparnias, I., et al., Structural basis of MALAT1 RNA maturation and mascRNA biogenesis. Nat Struct Mol Biol, 2024. https://www-nature-com.libproxy1.nus.edu.sg/articles/s41594-024-01361-z 责编|探索君 排版|探索君 文章来源|“BioArt” End 往期精选 围观 一文读透细胞死亡(Cell Death) | 24年Cell重磅综述（长文收藏版） 热文 Cell | 是什么决定了细胞的大小？ 热文 Nature | 2024年值得关注的七项技术 热文 Nature | 自身免疫性疾病能被治愈吗？科学家们终于看到了希望 热文 CRISPR技术进化史 | 24年Cell综述