More Like this

1. Charge-altering releasable transporters enhance mRNA delivery in vitro and exhibit in vivo tropism

   https://doi.org/10.1038/s41467-023-42672-x  

   Li, Zhijian; Amaya, Laura; Pi, Ruoxi; Wang, Sean K; Ranjan, Alok; Waymouth, Robert M; Blish, Catherine A; Chang, Howard Y; Wender, Paul A (December 2023, Nature Communications)

   Abstract The introduction of more effective and selective mRNA delivery systems is required for the advancement of many emerging biomedical technologies including the development of prophylactic and therapeutic vaccines, immunotherapies for cancer and strategies for genome editing. While polymers and oligomers have served as promising mRNA delivery systems, their efficacy in hard-to-transfect cells such as primary T lymphocytes is often limited as is their cell and organ tropism. To address these problems, considerable attention has been placed on structural screening of various lipid and cation components of mRNA delivery systems. Here, we disclose a class of charge-altering releasable transporters (CARTs) that differ from previous CARTs based on their beta-amido carbonate backbone (bAC) and side chain spacing. These bAC-CARTs exhibit enhanced mRNA transfection in primary T lymphocytes in vitro and enhanced protein expression in vivo with highly selective spleen tropism, supporting their broader therapeutic use as effective polyanionic delivery systems. 

   more » « less
2. mRNA lipid nanoparticle-mediated pyroptosis sensitizes immunologically cold tumors to checkpoint immunotherapy

   https://doi.org/10.1038/s41467-023-39938-9  

   Li, Fengqiao; Zhang, Xue-Qing; Ho, William; Tang, Maoping; Li, Zhongyu; Bu, Lei; Xu, Xiaoyang (July 2023, Nature Communications)

   Abstract Synergistically improving T-cell responsiveness is promising for favorable therapeutic outcomes in immunologically cold tumors, yet current treatments often fail to induce a cascade of cancer-immunity cycle for effective antitumor immunity. Gasdermin-mediated pyroptosis is a newly discovered mechanism in cancer immunotherapy; however, cleavage in the N terminus is required to activate pyroptosis. Here, we report a single-agent mRNA nanomedicine-based strategy that utilizes mRNA lipid nanoparticles (LNPs) encoding only the N-terminus of gasdermin to trigger pyroptosis, eliciting robust antitumor immunity. In multiple female mouse models, we show that pyroptosis-triggering mRNA/LNPs turn cold tumors into hot ones and create a positive feedback loop to promote antitumor immunity. Additionally, mRNA/LNP-induced pyroptosis sensitizes tumors to anti-PD-1 immunotherapy, facilitating tumor growth inhibition. Antitumor activity extends beyond the treated lesions and suppresses the growth of distant tumors. We implement a strategy for inducing potent antitumor immunity, enhancing immunotherapy responses in immunologically cold tumors. 

   more » « less
3. A deep learning method to integrate extracelluar miRNA with mRNA for cancer studies

   https://doi.org/10.1093/bioinformatics/btae653  

   Athaya, Tasbiraha; Li, Xiaoman; Hu, Haiyan; Mathelier, ed., Anthony (November 2024, Bioinformatics)

   Abstract MotivationExtracellular miRNAs (exmiRs) and intracellular mRNAs both can serve as promising biomarkers and therapeutic targets for various diseases. However, exmiR expression data is often noisy, and obtaining intracellular mRNA expression data usually involves intrusive procedures. To gain valuable insights into disease mechanisms, it is thus essential to improve the quality of exmiR expression data and develop noninvasive methods for assessing intracellular mRNA expression. ResultsWe developed CrossPred, a deep-learning multi-encoder model for the cross-prediction of exmiRs and mRNAs. Utilizing contrastive learning, we created a shared embedding space to integrate exmiRs and mRNAs. This shared embedding was then used to predict intracellular mRNA expression from noisy exmiR data and to predict exmiR expression from intracellular mRNA data. We evaluated CrossPred on three types of cancers and assessed its effectiveness in predicting the expression levels of exmiRs and mRNAs. CrossPred outperformed the baseline encoder-decoder model, exmiR or mRNA-based models, and variational autoencoder models. Moreover, the integration of exmiR and mRNA data uncovered important exmiRs and mRNAs associated with cancer. Our study offers new insights into the bidirectional relationship between mRNAs and exmiRs. Availability and implementationThe datasets and tool are available at https://doi.org/10.5281/zenodo.13891508. 

   more » « less
4. Quantitative profiling of human translation initiation reveals elements that potently regulate endogenous and therapeutically modified mRNAs

   https://doi.org/10.1016/j.molcel.2024.11.030  

   Lewis, Cole JT; Xie, Li H; Bhandarkar, Shivani Milind; Jin, Danni; Abdallah, Kyrillos; Draycott, Austin S; Chen, Yixuan; Thoreen, Carson C; Gilbert, Wendy V (December 2024, Molecular Cell)

   mRNA therapeutics offer a potentially universal strategy for the efficient development and delivery of therapeutic proteins. Current mRNA vaccines include chemically modified nucleotides to reduce cellular immunogenicity. Here, we develop an efficient, high-throughput method to measure human translation initiation on therapeutically modified as well as endogenous RNAs. Using systems-level biochemistry, we quantify ribosome recruitment to tens of thousands of human 5′ untranslated regions (UTRs) including alternative isoforms and identify sequences that mediate 200-fold effects. We observe widespread effects of coding sequences on translation initiation and identify small regulatory elements of 3–6 nucleotides that are sufficient to potently affect translational output. Incorporation of N1-methylpseudouridine (m1Ψ) selectively enhances translation by specific 5′ UTRs that we demonstrate surpass those of current mRNA vaccines. Our approach is broadly applicable to dissecting mechanisms of human translation initiation and engineering more potent therapeutic mRNAs. 

   more » « less
5. High-throughput barcoding of nanoparticles identifies cationic, degradable lipid-like materials for mRNA delivery to the lungs in female preclinical models

   https://doi.org/10.1038/s41467-024-45422-9  

   Xue, Lulu; Hamilton, Alex G; Zhao, Gan; Xiao, Zebin; El-Mayta, Rakan; Han, Xuexiang; Gong, Ningqiang; Xiong, Xinhong; Xu, Junchao; Figueroa-Espada, Christian G; et al (December 2024, Nature Communications)

   Abstract Lipid nanoparticles for delivering mRNA therapeutics hold immense promise for the treatment of a wide range of lung-associated diseases. However, the lack of effective methodologies capable of identifying the pulmonary delivery profile of chemically distinct lipid libraries poses a significant obstacle to the advancement of mRNA therapeutics. Here we report the implementation of a barcoded high-throughput screening system as a means to identify the lung-targeting efficacy of cationic, degradable lipid-like materials. We combinatorially synthesize 180 cationic, degradable lipids which are initially screened in vitro. We then use barcoding technology to quantify how the selected 96 distinct lipid nanoparticles deliver DNA barcodes in vivo. The top-performing nanoparticle formulation delivering Cas9-based genetic editors exhibits therapeutic potential for antiangiogenic cancer therapy within a lung tumor model in female mice. These data demonstrate that employing high-throughput barcoding technology as a screening tool for identifying nanoparticles with lung tropism holds potential for the development of next-generation extrahepatic delivery platforms. 

   more » « less