Predicting the effect of CRISPR-Cas9-based epigenome editing

Reviewer #1 (Public Review):

Batra, Cabrera, Spence et al. present a model which integrates histone posttranslational modification (PTM) data across cell models to predict gene expression with the goal of using this model to better understand epigenetic editing. This gene expression prediction model approach is useful if a) it predicts gene expression in specific cell lines b) it predicts expression values rather than a rank or bin, c) it helps us to better understand the biology of gene expression, or d) it helps us to understand epigenome editing activity. Problematically for points a) and b) it is easier to directly measure gene expression than to measure multiple PTMs and so the real usefulness of this approach mostly relates to c) and d).

Other approaches have been published that use histone PTM to predict expression (e.g. 27587684, 36588793). Is this model better in some way? No comparisons are made. The paper does not seem to have substantial novel insights into understanding the biology of gene expression. The approach of using this model to predict epigenetic editor activity on transcription is interesting and to my knowledge novel but I doubt given the variability of the predictions (Figures 6 and S7&8) that many people will be interested in using this in a practical sense. As the authors point out, the interpretation of the epigenetic editing data is convoluted by things like sgRNA activity scoring and to fully understand the results likely would require histone PTM profiling and maybe dCas9 ChIP-seq for each sgRNA which would be a substantial amount of work.

Furthermore from the model evaluation of H3K9me3 it seems the model is not performing well for epigenetic or transcriptional editing- e.g. we know for the best studied transcriptional editor which is CRISPRi (dCas9-KRAB) that recruitment to a locus is associated with robust gene repression across the genome and is associated with H3K9me3 deposition by recruitment of KAP1/HP1/SETDB1 (PMID: 35688146, 31980609, 27980086, 26501517). However, it seems from Figures 2&4 that the model wouldn't be able to evaluate or predict this.

The model seems to predict gene expression for endogenous genes quite well although the authors sometimes use expression and sometimes use rank (e.g. Figure 6) - being clearer with how the model predicts expression rather than using rank or fold change would be very useful.

One concern overall with this approach is that dCas9-p300 has been observed to induce sgRNA-independent off-target H3K27Ac (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8349887/ see Figure S5D) which could convolute interpretation of this type of experiment for the model.

Figure 2
It seems this figure presents known rather than novel findings from the authors' description. Please comment on whether there are any new findings in this figure. Please comment on differences in patterns of repressive and activating histone PTMs between cell lines (e.g. H1-Esc H3K27me3 green 25-50% is more enriched than red 0-25%).

Figure 3&4
There are a number of approaches including DeepChrome and TransferChrome that predict endogenous gene expression from histone PTMs. I appreciate that the authors have not used the histone PTM data to predict gene expression levels of an "average cell" but rather that they are predicting expression within specific cell types or for unseen cell types. But from what is presented it isn't clear that the author's model is better or enabling beyond other approaches. The authors should show their model is better than other approaches or make clear why this is a significant advance that will be enabling for the field. For example is it that in this approach they are actually predicting expression levels whereas previous approaches have only predicted expressed or not expressed or a rank order or bin-based ranking?

Figure 5
From the methods, it seems gene activation is measured by qpcr in hek293 transfected with individual sgRNAs and dCas9-p300. The cells aren't selected or sorted before qPCR so how are we sure that some of the variability isn't due to transfection efficiency associated with variable DNA quality or with variable transfection efficiency?

Figure 6
The use of rank in 6D and 6E is confusing. In 6D a higher rank is associated with higher expression while in 6E a higher rank seems to mean a lower fold change e.g. CYP17A1 has a low predicted fold-change rank and qPCR fold-change rank but in Figure 5 a very high qPCR fold change. Labeling this more clearly or explaining it in the text further would be useful.

Reviewer #2 (Public Review):

Summary:
The authors build a gene expression model based on histone post-translational modifications and find that H3K27ac is correlated with gene expression. They proceed to perturb H3K27ac at 8 gene promoters, and measure gene expression changes to test their model.

Strengths:
The combination of multiple methods to model expression, along with utilizing 6 histone datasets in 13 cell types allowed the authors to build a model that correlates between 0.7-0.79 with gene expression. This group also utilized a tool they are experts in, dCas9-p300 fusions to perturb H3K27ac and monitor gene expression to test their model. Ranked correlations showed some support for the predictions after the perturbation of H3K27ac.

Weaknesses:
The perturbation of only 8 genes, and the only readout being qPCR-based gene expression, as opposed to including H3K27ac, weakened their validation of the computational model. Likewise, the use of six genes that were not expressed being most activated by dCas9-p300 might weaken the correlations vs. looking at a broad range of different gene expressions as the original model was trained on.