Intrinsic targeting of host RNA by Cas13 constrains its utility
Abstract
Cas13 can be used for the knockdown, editing, imaging or detection of RNA and for RNA-based gene therapy. Here by using RNA immunoprecipitation sequencing, transcriptome profiling, biochemical analysis, high-throughput screening and machine learning, we show that Cas13 can intrinsically target host RNA in mammalian cells through previously unappreciated mechanisms. Different from its known cis/trans RNA-cleavage activity, Cas13 can also cleave host RNA via mechanisms that are transcript-specific, independent of the sequence of CRISPR RNA and dynamically dependent on the conformational state of Cas13, as we show for several Cas13-family effectors encoded in one-vector and two-vector lentiviral systems. Moreover, host genes involved in viral processes and whose transcripts are intrinsically targeted by Cas13 contribute to constraining the lentiviral delivery and expression of Cas13. Our findings offer guidance for the appropriate use of lentiviral Cas13 systems and highlight the need for caution regarding intrinsic RNA targeting in Cas13-based applications.
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The highest number of DEGs was from the Cas13bt3-NT sgRNA group compared to Cas13bt3 only or Cas13bt3-VEGFA sgRNA (81 vs 27 and 23).
“Interestingly, we noted the highest number of differentially expressed genes (DEGs) from the Cas13bt3-NT sgRNA group compared to Cas13bt3 only or Cas13bt3-VEGFA sgRNA (81 vs 27 and 23, respectively; Fig. 1I), a finding that corresponds with recent studies (16, 22).”
From Characterization of RNA editing and gene therapy with a compact CRISPR-Cas13 in the retina (2024) · cites this paper as [22]
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Self-citation
- Authors
- Li, Z., Li, Z., Cheng, X., Wang, S., Wang, X., Ma, S., Lu, Z., Zhang, H., Zhao, W., Chen, Z., Yao, Y., Zhang, C., Chao, L., Li, W., & Fei, T.
- Affiliations
- Northeastern University (CN)
- Children's National (US)
- Corresponding author
- Li, Wei
- ORCID
- Venue
- Nature Biomedical Engineering
- Published
- 2023-10-23
- Volume
- 8
- Issue
- 2
- Pages
- 177-192
- ISSN
- 2157-846X (ISSN-L)
- OpenAlex
- W4387874003
- Cited by
- 31
- References
- 51
- Citations by year
- 2026: 11 · 2025: 12 · 2024: 7 · 2023: 1
- FWCI
- 2.75
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- Locations
- Nature Biomedical Engineering (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Natural Science Foundation of China (32071441)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Interference and Gene Delivery
- Keywords
- Cas13, RNA cleavage, lentiviral delivery, viral gene expression, RNA editing, RNA imaging, RNA detection, RNA knockdown
- MeSH terms
- Animals, Mammals, RNA, Genetic Therapy, Lentivirus, Gene Expression Profiling, CRISPR-Cas Systems
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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