Evidence map›Paper›PMID 42337061›Full record

ArticleNature biomedical engineering2026

Engineering drug-responsive replication machinery for precise control of self-amplifying RNA.

Parisa Yousefpour, Justin R Gregory, Kristen Si, Jan Lonzaric, Yingzhong Li, Junmin Wang, Kashif Qureshi, Amir Ledbetter, Mariane B Melo, Alexander Hostetler and 11 more

Abstract read
In one paragraph

Article in Nature biomedical engineering, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed.

  1. Review
  2. Review
  3. Article
  4. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

21 authors.

Parisa YousefpourKoch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
Justin R Gregory *Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
Kristen Si *Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
Jan LonzaricDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-1507-2184
Yingzhong LiKoch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
Junmin WangBioinformatics Graduate Program, Boston University, Boston, MA, USA.
Kashif QureshiKoch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID http://orcid.org/0009-0002-7734-0567
Amir LedbetterKoch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
Mariane B MeloKoch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-0409-2454
Alexander HostetlerKoch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
Ashley A LemniosKoch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID http://orcid.org/0009-0007-5088-2389
Jonathan DyeKoch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID http://orcid.org/0000-0003-2801-8053
Linette RodriguezKoch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
Tanaka K RembaKoch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
Rachel YeungKoch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
Melissa GüerecaDivision of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
Yuebao ZhangDivision of Pharmaceutics and Pharmacology, College of Pharmacy, Ohio State University, Columbus, OH, USA.ORCID http://orcid.org/0009-0000-7883-1937
Shengwei WuKoch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-8175-3490
Yizhou DongIcahn 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.ORCID http://orcid.org/0000-0001-5786-0659
Ron WeissKoch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. rweiss@mit.edu.ORCID http://orcid.org/0000-0003-0396-2443
Darrell J IrvineKoch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. djirvine@scripps.edu.ORCID http://orcid.org/0000-0002-8637-1405

Funding

Identification of neutralizing epitopes on SARS-CoV-2 spike for design of vaccines and small-molecule antiviralsUM1AI144462 · NIAID · SCRIPPS RESEARCH INSTITUTE, THE · PI BURTON, DENNIS R. · 2019 to 2025
$201.6M
VIRUS PRODUCTION COREP30CA014051 · NCI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI Jacqueline A. Lees · 1985 to 2026
$93.9M
Maximizing germinal centers and somatic hypermutation to HIV Env immunogensR37AI125068 · NIAID · LA JOLLA INSTITUTE FOR IMMUNOLOGY · PI Shane P Crotty, Darrell J Irvine · 2021 to 2026
$5.4M
Maximizing germinal centers and somatic hypermutation to HIV Env immunogensR01AI125068 · NIAID · LA JOLLA INSTITUTE FOR IMMUNOLOGY · PI CROTTY, SHANE P, IRVINE, DARRELL J · 2016 to 2020
$4.3M
Immunotherapy via engineered therapeutic programs in tumors using RNAU01CA265706 · NCI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI DONG, YIZHOU, IRVINE, DARRELL J · 2021 to 2025
$3.2M
"Extended dosing" immunization to enhance humoral immunity to next-generation vaccinesR01AI175489 · NIAID · SCRIPPS RESEARCH INSTITUTE, THE · PI Darrell J Irvine · 2023 to 2026
$1.9M
Controlling Vaccine Kinetics with Small Molecule DrugsF32AI164829 · NIAID · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI YOUSEFPOUR, PARISA · 2022 to 2024
$184k
NCI NIH HHS P30 CA014051NCI NIH HHS U01 CA265706NIAID NIH HHS F32 AI164829NIAID NIH HHS R01 AI125068NIAID NIH HHS R01 AI175489NIAID NIH HHS R37 AI125068NIAID NIH HHS UM1 AI144462U.S. Department of Health and Human Services (U.S. Department of Health & Human Services) CA265706U.S. Department of Health & Human Services | National Institutes of Health (NIH) AI164829U.S. Department of Health & Human Services | National Institutes of Health (NIH) AI175489U.S. Department of Health & Human Services | National Institutes of Health (NIH) CA265706U.S. Department of Health & Human Services | National Institutes of Health (NIH) UM1AI144462U.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (OER) AI125068
6 · The paper itself

Abstract

Precise, reversible control of gene expression from self‑amplifying RNA (saRNA) remains difficult, limiting the therapeutic flexibility of this otherwise potent platform. Although alphavirus‑derived saRNAs encode non‑structural proteins that drive RNA replication and offer an intrinsic regulatory point, no existing approach has enabled direct, drug‑dependent control of this machinery for high‑fidelity modulation of expression. Here we engineer saRNA constructs whose replication is activated by the approved small‑molecule drug trimethoprim, using drug‑responsive degradation domains fused to individual non‑structural proteins to regulate self‑amplification. As each replication protein contributes differently to RNA copying, we systematically screened fusion configurations and identified an optimal design combining modified replication proteins with a regulated payload. This construct achieved more than a 10

Identifiers

PMID42337061
PMCPMC13445569

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.