CRISPR Activation Screen for HDAC Inhibitor Resistance

Panobinostat is an oral broad-spectrum histone deacetylase inhibitor that alters gene expression via epigenetic mechanisms and function of key proteins through changes in their protein acetylation state. Panobinostate was approved a few years ago by the FDA and EMA for use in combination with bortezomib and dexamethasone in patients with multiple myeloma (MM) who have received ≥2 prior regimens, including bortezomib and an immunomodulatory drug. To study the mechanisms which regulate the response vs. resistance of MM cells to panobinostat, we performed genome-scale CRISPR activation screen of MM1S cells. MM1S cells were transduced with dCas9 and pooled lentiviral particles of the Calabrese P65-HSF CRISPR activation library consisting of 2 pooled sgRNA sub-libraries. After selection for viral transduction, cells were continuously cultured with (2 different concentration of 12.5 and 20 nM) or without panobinostat for 5 weeks, before being harvested. At that time point, dose-response curves for panobinostat treatment confirmed that the drug-exposed MM.1S cell populations of our study had become significantly less sensitive to panobinostat than treatment- naive MM.1S cells. Genomic DNA was extracted and next generation sequencing was performed to quantify the abundance of the sgRNA "barcodes" within the tumor cell populations of our study, while rank aggregation algorithms were performed to rank genes according to the magnitude and concordance of enrichment for its different sgRNAs. In MM.1S cells which had developed resistance to the lower dose (12.5 nM) of panobinostat, we observed major sgRNA enrichment (at least 4 of 6 sgRNAs, enrichment p-value <0.05, average log2 fold change of enrichment >1.5) for sgRNAs for a variety of genes, of which the most prominently enriched ones encode for the cell surface ABC transporters ABCB1 (MDR1/p-glycoprotein), to a lesser extent ABCC4 (MRP4) and even less so for ABCG2. In addition, we observed sgRNA enrichment for transcription factors, such as IRF4, POU2AF1, AFF2, IKZF3, AFF3, and RELA, or the transcriptional coregulator MTA1; Bcl2 family members such as BCL2 and BCL2L1; and chromatin remodeling genes such as KAT6A. However, in MM.1S cells which had survived the treatment with higher concentration (25 nM) of panobinostat, the genes with significant and concordant sgRNA enrichment were restricted to ABCB1, ABCC4, and IRF4. These observations indicate that the most efficient mechanism for MM cells to develop resistance to both low and higher concentrations of panobinostat is by increasing its export from the cells, with ABCB1 as the primary, but not sole, transporter which can assume this role. When we transduced MM.1S cells, which already express high levels of IRF4 transcript and protein, with lentiviral construct for IRF4 cDNA, we observed a shift to the right for the panobinostat dose-response curve, further supporting the observation that modulation of IRF4 levels in MM cells can alter the degree of MM cell sensitivity to panobinostat. Proteasome inhibitors suppress the activity of RELA and NFkappaB more broadly, while thalidomide derivatives cause degradation of IKZF3 and can decrease the IRF4 transcript levels: these results may respectively explain, at least in part, the mechanistic basis for the enhanced combined effect of panobinostat with proteasome inhibitors and the favorable clinical results obtained with panobinostat and other broad spectrum HDAC inhibitors in combination with thalidomide derivatives. Our study provides unbiased genome-scale systematic characterization of the mechanisms regulating MM cell response vs. resistance to panobinostat and identify the pronounced and dose-dependent enrichment of these resistance mechanisms for genes contributing to panobinostat export from MM cells, as well as a role for IRF4 and (primarily at lower panobinostat concentrations) for other transcription factors, chromatin remodeling genes and anti-apoptotic BCL-2 family members. These observations also support the need for a more systematic characterization of the regulation of expression of ABC transporters in MM cells; and for development of novel strategies to disrupt more comprehensively IRF4 and other transcription factors for which gain-of-function is associated with decreased responsiveness to panobinostat, with the goal of improving the impact of this agent and potentially other broad spectrum HDAC inhibitors in MM.