Ribosome subunit attrition and activation of the p53–MDM4 axis dominate the response of MLL-rearranged cancer cells to WDR5 WIN site inhibition

Reviewer #1 (Public Review):

Building on previous work from the Tansey lab, here Howard et al. characterize transcriptional and translational changes upon WIN site inhibition of WDR5 in MLL-rearranged cancer cells. They first analyze whether C16, a newer generation compound, has the same cellular effects as C6, an early generation compound. Both compounds reduce the expression of WDR5-bound RPGs in addition to the unbound RPG RPL22L1. They then investigate differential translation by ribo-seq and observe that WIN site inhibition reduces the translational RPGs and other proteins related to biomass accumulation (spliceosome, proteasome, mitochondrial ribosome). Interestingly, this reduction adds to the transcriptional changes and is not limited to RPGs whose promoters are bound by WDR5. Quantitative proteomics at two-time points confirmed the downregulation of RPGs. Interestingly, the overall effects are modest, but RPL22LA is strongly affected. Unexpectedly, most differentially abundant proteins seem to be upregulated 24 h after C6 (see below). A genetic screen showed that loss of p53 rescues the effect of C6 and C16 and helped the authors to identify pathways that can be targeted by compounds together with WIN site inhibitors in a synergistic way. Finally, the authors elucidated the underlying mechanisms and analyzed the functional relevance of the RPL22, RPL22L1, p53, and MDM4 axis.

While this work is not conceptually new, it is an important extension of the observations of Aho et al. The results are clearly described and, in my view, very meaningful overall.

Major points:
1. The authors make statements about the globality/selectivity of the responses in RNA-seq, ribo-seq, and quantitative proteomics. However, as far as I can see, none of these analyses have spike-in controls. I recommend either repeating the experiments with a spike-in control or carefully measuring transcription and translation rates upon WIN site inhibition and normalizing the omics experiments with this factor.

2. Why are the majority of proteins upregulated in the proteomics experiment after 24 h in C6 (if really true after normalization with general protein amount per cell)? This is surprising and needs further explanation.

3. The description of the two CRISPR screens (GECKO and targeted) is a bit confusing. Do I understand correctly that in the GECKO screen, the treated cells are not compared with non-treated cells of the same time point, but with a time point 0? If so, this screen is not very meaningful and perhaps should be omitted. Also, it is unclear to me what the advantages of the targeted screen are since the targets were not covered with more sgRNAs (data contradictory: 4 or 10 sgRNAs per target?) than in Gecko. Also, genome-wide screens are feasible in culture for multiple conditions. Overall, I find the presentation of the screening results not favorable.

4. Can Re-expression of RPL22 rescue the growth arrest of C6?.

Reviewer #2 (Public Review):

Summary:
The manuscript by Howard et al reports the development of high-affinity WDR5-interaction site inhibitors (WINi) that engage the protein to block the arginine-dependent engagement with its partners. Treatment of MLL-rearranged leukemia cells with high-affinity WINi (C16) decreases the expression of genes encoding most ribosomal proteins and other proteins required for translation. Notably, although these targets are enriched for WDR5-ChIP-seq peaks, such peaks are not universally present in the target genes. High concordance was found between the alterations in gene expression due to C16 treatment and the changes resulting from treatment with an earlier, lower affinity WINi (C6). Besides protein synthesis, genes involved in DNA replication or MYC responses are downregulated, while p53 targets and apoptosis genes are upregulated. Ribosome profiling reveals a global decrease in translational efficiency due to WINi with overall ribosome occupancies of mRNAs ~50% of control samples. The magnitude of the decrements of translation for most individual mRNAs exceeds the respective changes in mRNA levels genome-wide. From these results and other considerations, the authors hypothesize that WINi results in ribosome depletion. Quantitative mass spec documents the decrement in ribosomal proteins following WINi treatment along with increases in p53 targets and proteins involved in apoptosis occurring over 3 days. Notably, RPL22L1 is essentially completely lost upon WINi treatment. The investigators next conduct a CRISPR screen to find moderators and cooperators with WINi. They identify components of p53 and DNA repair pathways as mediators of WINi-inflicted cell death (so gRNAs against these genes permit cell survival). Next, WINi are tested in combination with a variety of other agents to explore synergistic killing to improve their expected therapeutic efficacy. The authors document the loss of the p53 antagonist MDM4 (in combination with splicing alterations of RPL22L1), an observation that supports the notion that WINi killing is p53-mediated.

Strengths:
This is a scientifically very strong and well-written manuscript that applies a variety of state-of-the art molecular approaches to interrogate the role of the WDR5 interaction site and WINi. They reveal that the effects of WINi seem to be focused on the overall synthesis of protein components of the translation apparatus, especially ribosomal proteins-even those that do not bind WDR5 by ChIP (a question left unanswered is how much the WDR5-less genes are nevertheless WINi targeted). They convincingly show that disruption of the synthesis of these proteins is accompanied by DNA damage inferred by H2AX-activation, activation of the p53-pathway, and apoptosis. Pathways of possible WINi resistance and synergies with other anti-neoplastic approaches are explored. These experiments are all well-executed and strongly invite more extensive pre-clinical and translational studies of WINi in animal studies. The studies also may anticipate the use of WINi as probes of nucleolar function and ribosome synthesis though this was not really explored in the current manuscript.

Weaknesses:
A mild deficiency in the current manuscript is the absence of cell biological methods to complement the molecular biological and biochemical approaches so ably employed. Some microscopic observations and confirmation of nucleolar dysfunction and DNA damage would be reassuring.