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Predicting prime editing efficiency and product purity by deep learning

Nature Biotechnology volume 41, pages 1151–1159 (2023)Cite this article

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Abstract

Prime editing is a versatile genome editing tool but requires experimental optimization of the prime editing guide RNA (pegRNA) to achieve high editing efficiency. Here we conducted a high-throughput screen to analyze prime editing outcomes of 92,423 pegRNAs on a highly diverse set of 13,349 human pathogenic mutations that include base substitutions, insertions and deletions. Based on this dataset, we identified sequence context features that influence prime editing and trained PRIDICT (prime editing guide prediction), an attention-based bidirectional recurrent neural network. PRIDICT reliably predicts editing rates for all small-sized genetic changes with a Spearman’s R of 0.85 and 0.78 for intended and unintended edits, respectively. We validated PRIDICT on endogenous editing sites as well as an external dataset and showed that pegRNAs with high (>70) versus low (<70) PRIDICT scores showed substantially increased prime editing efficiencies in different cell types in vitro (12-fold) and in hepatocytes in vivo (tenfold), highlighting the value of PRIDICT for basic and for translational research applications.

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Fig. 1: High-throughput screen for determinants of prime editing efficiency.
Fig. 2: Prediction of pegRNA editing rates by an attention-based bidirectional RNN.
Fig. 3: Feature importance overview for editing prediction.
Fig. 4: Validation of PRIDICT on endogenous loci and external datasets.
Fig. 5: Evaluation of MLH1dn and tevopreQ1 effect on PE2 editing efficiency and PRIDICT performance in library 2.

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Data availability

Measured editing rates used for analysis and figures in this study are provided as Supplementary Tables and on GitHub (https://github.com/uzh-dqbm-cmi/PRIDICT). DNA-sequencing data is available via the National Center for Biotechnology Information Sequence Read Archive (PRJNA825584). Target sequences of pathogenic mutations were based on the ClinVar database (accessed December 2019), and corresponding genomic sequences (flanking the edit) were acquired via UCSC Genome Browser (Table Browser, hg38). Plasmid encoding for pCMV-PE2-tagRFP-BleoR is available from Addgene (no. 192508).

Code availability

Custom Python code used in this study is provided on GitHub (https://github.com/uzh-dqbm-cmi/PRIDICT). Additional information on the PRIDICT algorithm can be found in Supplementary Methods 1.

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Acknowledgements

We thank the Functional Genomics Center Zurich for their help and support in next-generation sequencing; the Flow Cytometry Facility of the University of Zurich and especially M. Wickert for performing liver hepatocyte sorting experiments; the Science IT team at the University of Zurich for providing infrastructure used for data analysis and especially P. Shemella for helpful discussions about code performance optimizations; R. Schep for discussions about chromatin marks; G. Affentranger for support in the design of figures; the members of the Schwank laboratory for fruitful discussions. This work was supported by the SNF (grant nos. 310030_185293 and 201184), the University Research Priority Program ‘Human Reproduction Reloaded’ and ‘ITINERARE’ of the University of Zurich. K.F.M. holds a PHRT iDoc Fellowship (PHRT_324).

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Author notes

  1. These authors contributed equally: Nicolas Mathis, Ahmed Allam.

Authors and Affiliations

  1. Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland

    Nicolas Mathis, Lucas Kissling, Kim Fabiano Marquart, Lukas Schmidheini, Cristina Solari & Gerald Schwank

  2. Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland

    Ahmed Allam, Zsolt Balázs & Michael Krauthammer

  3. Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland

    Kim Fabiano Marquart & Lukas Schmidheini

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Contributions

N.M. designed the study, performed experiments and analyzed data. A.A. designed and generated attention-based bidirectional RNNs (PRIDICT) and implemented feature extraction strategies. A.A. and N.M. built linear regression and tree-based machine learning models and performed feature extraction analysis. L.K. performed in vivo experiments. K.F.M. and C.S. contributed to arrayed validation experiments. L.S. performed pegRNA and AdV cloning experiments. Z.B. performed the analysis of chromatin characteristics of endogenous loci. N.M., A.A. and G.S. wrote the manuscript. M.K. and G.S. designed and supervised the research. All authors revised the manuscript.

Corresponding authors

Correspondence to Michael Krauthammer or Gerald Schwank.

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Nature Biotechnology thanks Sangsu Bae and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Extended data

Extended Data Fig. 1 Self-targeting screen characteristics.

a, Visualization of library design (library 1) and numbers before and after filtering results. b, Distribution of edit positions for single base replacement edits in library 1. c, Distribution of edit positions for insertion edits in library 1. d, Distribution of edit positions for deletion edits in library 1. e, Distribution of insertion lengths in library 1. f, Distribution of deletion lengths in library 1. g, Distribution of edit types in library 1 (number of design variants and percentage of the total library). h,i, Editing rates of a test self-targeting locus with a forward (Fw) or reverse (Rv) orientation of the target sequence. Either on plasmid level or integrated by lentiviral transduction in HEK293T cells. Data points for bars (from left) 2,3 and 5,6 correspond to two technical replicates (simultaneous transfection of two separate wells). Only one data point was used for the plasmid controls (bar 1 and 4). h, pegRNA with TAG to TGG edit. i, pegRNA with TAG to TAC edit. The observed editing in the forward direction in the absence of PE2 could be caused by lentiviral reshuffling or ADAR-mediated A to I (G) RNA editing. The latter could occur during lentiviral packaging in HEK293T cells: HEK293T cells endogenously express ADAR and the target site is present as RNA on the lentiviral vector and targeted by the complementary pegRNA with a mismatch, providing an ideal template for ADAR-dependent RNA editing. The observation that primarily TAG to TGG (but not TAG to TAC) showed background editing is in line with this hypothesis, as previous studies showed ADAR preference for UAG sequences52.

Extended Data Fig. 2 Additional validation of the DeepPE model.

a, Predicted (PRIDICT) and measured intended editing efficiency for GtoC edits at position 5 of RTT in the dataset from this study. Data from all five test sets (fivefold cross-validation) were combined for this visualization. n = 540. b, Evaluation of attention-based bidirectional RNN (PRIDICT-AttnBiRNN; trained on the dataset from this study) by testing on pegRNAs from Kim et al. 2021 HT dataset (only G to C at Position 5). n = 4,457. c, Evaluation of DeepPE model (original, trained on Kim et al. 2021 HT dataset) by testing on the dataset from this study (only G to C at Position 5). n = 540. d,e, SHAP analysis of XGBoost models trained and tested on DeepPE dataset (n = 43,149) (d) or on G-to-C Position 5 edits from library 1 (e). Feature descriptions are listed in Supplementary Table 1. f, Editing efficiency with different RTT overhang lengths (5, 7, 10, 15 bp) in DeepPE (Kim et al.) dataset. n for each bar (left to right) = 10,746, 10,828, 10,921, 10,654. Error bars = mean ±s.d. g, Editing efficiency with different RTT overhang lengths (3, 7, 10, 15 bp) in GtoC Pos. 5 edits of library 1 for a direct comparison to identical edits in the DeepPE dataset. n for each bar (left to right) = 135, 135, 137, 133. (f,g) Error bars = mean ±s.d. h,i, Evaluation of DeepPE model (n = 18) on 18/45 endogenous edits from this study in HEK293T (h) and K562 (i).

Extended Data Fig. 3 Additional validation of the Easy-Prime PE2 model.

a, Edit type count distribution in the original Easy-Prime test dataset. b, Evaluation of Easy-Prime PE2 model by testing this XGBoost model on the original Easy-Prime test dataset5, filtered against 1 bp edits at position 5 of the RTT to eliminate the bias towards this edit type. n = 585. c–g, Evaluation of Easy-Prime PE2 by testing the model on datasets generated in this study. c, Library 1 in HEK293T, n = 92,423. d, Library 2 (editing with PE2 and pegRNAs without tevopreQ1) in HEK293T, n = 915. e, Library 2 (editing with PE2 and pegRNAs without tevopreQ1) in K562, n = 876. f,g, Endogenous loci from Fig. 4a, b in HEK293T (f) and K562 (g), n = 45. h, Intended editing efficiency rank of the best-predicted pegRNA for each pathogenic locus in library 1 (PRIDICT and Easy-Prime). Pathogenic loci with multiple pegRNAs on rank 1 (identical efficiency) and loci with less than three pegRNAs were excluded from this analysis. Predictions from PRIDICT were taken from five different cross-validations to ensure none of the predictions are included in the training set. n = 12,189. i, Intended editing efficiency rank of the best-predicted pegRNA for each endogenous locus (PRIDICT and Easy-Prime). n = 15.

Extended Data Fig. 4 Additional library 2 evaluation with PEmax.

a, Mean editing efficiencies of each replicate, including all pegRNAs in library 2 with different experimental conditions in U2OS and K562 cells. Error bars indicate the mean ±s.d. of three biologically independent replicates. n = 3. Mean editing of library 2 for each of the three replicates is based on the following number of pegRNAs for each data point (bars left to right) = 916, 922, 917, 924, 879, 869, 877, 866. Note that absolute levels of editing efficiency for PEmax cannot be directly compared to PE2 in this study due to the use of different selection agents (Blasticidin for PEmax screens compared to Zeocin for PE2 screens). Previous studies showed that in identical setups, PEmax surpasses the performance of PE216. b, Spearman correlation for PEmax editing efficiencies in library 2 between different experimental conditions (MLH1dn, tevopreQ1) and cell lines (K562, U2OS). c, Editing efficiency rank correlations (Spearman) in library 2 between editing performed with PE2 versus editing performed with PEmax.

Supplementary information

Supplementary Information

Supplementary Notes 1–3, Tables 1–3, Figs. 1–19 and Methods 1.

Reporting Summary

Supplementary Table 4

List of library sequences used in this study.

Supplementary Table 5

List of oligo sequences used for cloning and PCR.

Supplementary Table 6

Tables containing information about pegRNAs used in library 1, library 2 and endogenous editing experiments and their associated editing efficiencies.

Supplementary Table 7

Table containing Spearman correlations between every pair of features listed in Supplementary Table 1.

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Mathis, N., Allam, A., Kissling, L. et al. Predicting prime editing efficiency and product purity by deep learning. Nat Biotechnol 41, 1151–1159 (2023). https://doi.org/10.1038/s41587-022-01613-7

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