{ "abstract": "The design of gene therapies with drug-regulatable expression of therapeutic payloads is of interest for diverse applications. We hypothesized that a regulated expression system based on alphavirus-derived self-amplifying RNAs (saRNAs), which encode 4 non-structural proteins (nsPs) that copy the RNA backbone to enable sustained expression, would have advantages in safety and simplicity of delivery. Here we designed saRNAs where payload expression is regulated by the FDA-approved drug trimethoprim (TMP), by fusing TMP-responsive degradation domains (DDs) to nsPs to regulate RNA self-amplification. Screening a library of nsP-DD fusions, we identified an optimal design with DDs fused to nsP2, nsP3, and the payload, achieving a high fold-change in expression level in response to TMP and low expression in the off state. In mice, this saRNA circuit enabled diverse dynamic expression patterns in response to oral TMP. Implementing this circuit for controlled expression of an HIV antigen, an escalating TMP regimen significantly enhanced germinal center responses critical for B cell affinity maturation. This drug-regulated RNA technology holds potential for vaccines, immunotherapies, and gene therapies.", "abstract_shown": true, "affiliations": [ "Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA", "Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA", "Bioinformatics Graduate Program, Boston University, Boston, MA, USA", "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA", "Howard Hughes Medical Institute, Chevy Chase, MD, USA", "Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA", "Division of Pharmaceutics and Pharmacology, College of Pharmacy, Ohio State University, Columbus, OH, USA", "Icahn Genomics Institute, Precision Immunology Institute, Department of Immunology and Immunotherapy, Department of Oncological Sciences, Tisch Cancer Institute, Friedman Brain Institute, Biomedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA", "Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. rweiss@mit.edu", "Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. rweiss@mit.edu", "Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA. djirvine@scripps.edu", "Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. djirvine@scripps.edu", "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA. djirvine@scripps.edu", "Howard Hughes Medical Institute, Chevy Chase, MD, USA. djirvine@scripps.edu", "Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. djirvine@scripps.edu" ], "article_type": null, "arxiv": null, "author_total": 21, "authors": [ { "affs": [ 0 ], "name": "Parisa Yousefpour", "orcid": "0000-0003-0431-8131" }, { "affs": [ 0 ], "name": "Justin R. Gregory", "orcid": "0000-0003-4526-3229" }, { "affs": [ 1, 0 ], "name": "Kristen Si" }, { "affs": [ 1 ], "name": "Jan Lonzarić", "orcid": "0000-0002-1507-2184" }, { "affs": [ 1, 0 ], "name": "Yingzhong Li", "orcid": "0000-0002-4213-2496" }, { "affs": [ 2 ], "name": "Junmin Wang", "orcid": "0009-0004-3728-9538" }, { "affs": [ 0 ], "name": "Kashif Qureshi", "orcid": "0009-0002-7734-0567" }, { "affs": [ 0 ], "name": "Amir Ledbetter", "orcid": "0009-0009-8226-0749" }, { "affs": [ 3, 4, 0 ], "name": "Mariane B. Melo", "orcid": "0000-0002-0409-2454" }, { "affs": [ 1, 0 ], "name": "Alexander Hostetler", "orcid": "0000-0001-6260-8765" }, { "affs": [ 3, 0 ], "name": "Ashley A. Lemnios", "orcid": "0009-0007-5088-2389" }, { "affs": [ 0 ], "name": "Jonathan Dye", "orcid": "0000-0003-2801-8053" }, { "affs": [ 3, 0 ], "name": "Linette Rodriguez" }, { "affs": [ 0 ], "name": "Tanaka K. Remba", "orcid": "0000-0001-9531-4341" }, { "affs": [ 0 ], "name": "Rachel Yeung" }, { "affs": [ 5 ], "name": "Melissa Güereca" }, { "affs": [ 6 ], "name": "Yuebao Zhang", "orcid": "0009-0000-7883-1937" }, { "affs": [ 0 ], "name": "Shengwei Wu", "orcid": "0000-0001-8175-3490" }, { "affs": [ 7 ], "name": "Yizhou Dong", "orcid": "0000-0001-5786-0659" }, { "affs": [ 8, 9 ], "name": "Ron Weiss", "orcid": "0000-0003-0396-2443" }, { "affs": [ 10, 11, 12, 13, 14 ], "name": "Darrell J. Irvine", "orcid": "0000-0002-8637-1405" } ], "bibtex": "https://research.draconitic.com/paper/fcz73t6b3ghq2.bib", "cited_by": 12, "doi": "10.1038/s41551-026-01723-6", "fulltext_url": null, "id": "fcz73t6b3ghq2", "issns": [ "2157-846X" ], "landing_url": "https://doi.org/10.1038/s41551-026-01723-6", "language": "en", "licence": "CC-BY", "licence_label": "CC BY", "licence_source": "journal", "licence_url": "https://creativecommons.org/licenses/by/4.0/", "metadata_licence": null, "native_subjects": [ [ "openalex", "1312|RNA Interference and Gene Delivery" ] ], "openalex": "W7165622488", "pdf_url": "https://www.nature.com/articles/s41551-026-01723-6.pdf", "pmcid": "PMC12157543", "pmid": "40501866", "published": "2026-06-23", "publisher": "Nature Portfolio", "ris": "https://research.draconitic.com/paper/fcz73t6b3ghq2.ris", "sources": [ { "first_seen": "2026-11-04T13:21:06Z", "native_id": "W7165622488", "source": "openalex", "url": "https://doi.org/10.1038/s41551-026-01723-6" } ], "subjects": [ { "field": "biochemistry", "origin": "openalex:1312|RNA Interference and Gene Delivery", "subfield": "molecular-biology" } ], "title": "Engineering drug-responsive replication machinery for precise control of self-amplifying RNA", "title_text": "Engineering drug-responsive replication machinery for precise control of self-amplifying RNA", "type": "peer-reviewed", "updated_at": "2026-11-08T13:20:43Z", "url": "https://research.draconitic.com/paper/fcz73t6b3ghq2", "venue": "Nature Biomedical Engineering", "versions": [] }