Evidence map›Paper›PMID 40583274›Full record

ArticleMolecular therapy : the journal of the American Society of Gene Therapy2025

3AIM-seq: Quality assessment of mRNA therapeutics using sequencing for 3' poly(A) tails of in vitro-transcribed mRNA.

Jina Seo, Hyo-Jung Park, Ayoung Oh, Chang Beom Jeong, Sohee Kim, Sojeong Lee, Chuna Kim, Hyeshik Chang, Jae-Hwan Nam, Daechan Park

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In one paragraph

Article in Molecular therapy : the journal of the American Society of Gene Therapy, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

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0cells of the map it votes in
2citing 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

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3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
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4 · The record

Corrections and comments

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5 · Who and what money

Authors and funding

10 authors.

Jina SeoDepartment of Molecular Science and Technology, Ajou University, Suwon 16499, South Korea; Ajou Energy Science Research Center, Ajou University, Suwon 16499, South Korea.
Hyo-Jung ParkDepartment of Medical and Biological Sciences, The Catholic University of Korea, Bucheon 14662, South Korea; BK21 Four Department of Biotechnology, The Catholic University of Korea, Bucheon 14662, South Korea.
Ayoung OhDepartment of Medical and Biological Sciences, The Catholic University of Korea, Bucheon 14662, South Korea; BK21 Four Department of Biotechnology, The Catholic University of Korea, Bucheon 14662, South Korea.
Chang Beom JeongDepartment of Molecular Science and Technology, Ajou University, Suwon 16499, South Korea.
Sohee KimAging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, South Korea; Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34141, South Korea.
Sojeong LeeCenter for RNA Research, Institute for Basic Science, Seoul National University, Seoul 08826, South Korea; School of Biological Sciences, Seoul National University, Seoul 08826, South Korea.
Chuna KimAging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, South Korea; Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34141, South Korea.
Hyeshik ChangCenter for RNA Research, Institute for Basic Science, Seoul National University, Seoul 08826, South Korea; School of Biological Sciences, Seoul National University, Seoul 08826, South Korea.
Jae-Hwan NamDepartment of Medical and Biological Sciences, The Catholic University of Korea, Bucheon 14662, South Korea; BK21 Four Department of Biotechnology, The Catholic University of Korea, Bucheon 14662, South Korea. Electronic address: jhnam@catholic.ac.kr.
Daechan ParkDepartment of Molecular Science and Technology, Ajou University, Suwon 16499, South Korea; Advanced College of Bio-Convergence Engineering, Ajou University, Suwon 16499, South Korea. Electronic address: dpark@ajou.ac.kr.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

In vitro-transcribed (IVT) mRNA therapeutics are promising for preventing and treating diseases, including infectious diseases and cancer, by delivering nucleic acid sequences. Assessing the stability of mRNA sequences and poly(A) tail length is crucial to minimize adverse effects and ensure drug efficacy. However, accurately measuring long homopolymeric nucleotides remains technically challenging, and a specialized method for IVT mRNAs is lacking. We introduce 3AIM-seq, a technique optimized experimentally and analytically for sequencing 3' poly(A) tails in IVT mRNAs. To generate high-quality data, we used a ligation-free adapter followed by 3' end amplification to prepare high-throughput sequencing libraries. The 3AIM-seq algorithm employed a sliding window approach to base quality scores, providing higher resolution and accuracy than the base-calling method and distinguishing poly(A) length differences as small as ±5 bp. Using in silico synthetic standard spike-in experiments, the method estimated the homogeneity of poly(A) tail lengths at the individual DNA molecule level in IVT mRNAs with various poly(A) tail structures. Although poly(A) tails of up to 70 bases were accurately measured, stretches exceeding 100 bases exhibited high heterogeneity for length, highlighting the importance of thorough assessments. Therefore, 3AIM-seq is a reliable method for evaluating the structural integrity of IVT mRNA products before clinical use.

Indexed as

High-Throughput Nucleotide SequencingPoly ARNA, MessengerSequence Analysis, RNATranscription, GeneticAlgorithmsHumansPoly ARNA, Messenger3AIM-seqbioinformaticsin vitro-transcribed mRNAmRNA therapeuticsnext-generation sequencingpoly(A) tail measurementRNA stability

Identifiers

PMID40583274
PMCPMC12848163

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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.