gene dysregulation is a common feature of acute myeloid leukemia (AML). The molecular mechanisms underlying aberrant gene expression and associated AML pathogenesis remain unclear. The nuclear protein CCCTC-binding factor (CTCF), when bound to insulator sequences, constrains temporal gene-expression patterns within confined chromatin domains for normal development. Here, we used targeted pooled CRISPR-Cas9-knockout library screening to interrogate the function of CTCF boundaries in the gene loci. We discovered that the CTCF binding site located between and genes (CBS7/9) is critical for establishing and maintaining aberrant gene expression in AML. Disruption of the CBS7/9 boundary resulted in spreading of repressive H3K27me3 into the posterior active chromatin domain that subsequently impaired enhancer/promoter chromatin accessibility and disrupted ectopic long-range interactions among the posterior genes. Consistent with the role of the CBS7/9 boundary in locus chromatin organization, attenuation of the CBS7/9 boundary function reduced posterior gene expression and altered myeloid-specific transcriptome profiles important for pathogenesis of myeloid malignancies. Furthermore, heterozygous deletion of the CBS7/9 chromatin boundary in the locus reduced human leukemic blast burden and enhanced survival of transplanted AML cell xenograft and patient-derived xenograft mouse models. Thus, the CTCF boundary constrains the normal gene-expression program, as well as plays a role in maintaining the oncogenic transcription program for leukemic transformation. The CTCF boundaries may serve as novel therapeutic targets for the treatment of myeloid malignancies.

Abbreviations: ammonium acetate (AmAc); background electrolyte (BGE); conductive liquid (CL); capillary zone electrophoresis (CZE); designer Nucleosome (dNuc); extracted ion electropherogram (EIE); endogenous nucleosomes (endoNucs); electrospray ionization (ESI); full-width at half maximum (FWHM); acetic acid (HAc), higher-energy collisional dissociation (HCD), hydrochloric acid (HCl); limit of detection (LOD); methylation equivalents (ME); micrococcal nuclease (MNase); molecular weight cut-off (MWCO); native capillary zone electrophoresis (nCZE); native mass spectrometry (nMS), mononucleosome (Nuc), orbitrap (OT); post-translational modification (PTM); Q Exactive HF MS with Extended Mass Range (QE-EMR); recombinant Nucleosome (rNuc); separation line (SL); signal-to-noise ratio (SNR); total ion electropherogram (TIE); top-down mass spectrometry (TDMS); Ultra High Mass Range (UHMR).

and D.Z. are inventors of two pending patent applications for use of BCL-X L PROTACs as senolytic and antitumor agents. R.H., G.Z., and D.Z. are co-founders of and have equity in Dialectic Therapeutics, which develops BCL-X L /2 PROTACs to treat cancer.

PROteolysis Targeting Chimeras (PROTACs) are bifunctional molecules that degrade target proteins through recruiting E3 ligases. However, their application is limited in part because few E3 ligases can be recruited by known E3 ligase ligands. Through competitive activity-based protein profiling, we found that piperlongumine (PL), a natural product, binds multiple E3 ligases. To evaluate whether PL can be used as an E3 ligase ligand, we generated a series of PL and SNS-032 (a selective CDK9 inhibitor) conjugates and found that the lead conjugate 955 can potently degrade CDK9 in a ubiquitin-proteasome dependent manner. In addition, 955 is more potent than SNS-032 against various tumor cells in vitro. Through TurboID-based proteomics and mechanistic studies, we identified KEAP1 as the E3 ligase recruited by PL to degrade CDK9. These findings demonstrate that PL is a novel E3 ligase ligand that can be used to generate potent anticancer PROTACs.

Background The COVID-19 pandemic has resulted in 275 million infections and 5.4 million deaths as of December 2021. While effective vaccines are being administered globally, there is still a great need for antiviral therapies as antigenically novel SARS-CoV-2 variants continue to emerge across the globe. Viruses require host factors at every step in their life cycle, representing a rich pool of candidate targets for antiviral drug design. Methods To identify host factors that promote SARS-CoV-2 infection with potential for broad-spectrum activity across the coronavirus family, we performed genome-scale CRISPR knockout screens in two cell lines (Vero E6 and HEK293T ectopically expressing ACE2) with SARS-CoV-2 and the common cold-causing human coronavirus OC43. Gene knockdown, CRISPR knockout, and small molecule testing in Vero, HEK293, and human small airway epithelial cells were used to verify our findings. Results While we identified multiple genes and functional pathways that have been previously reported to promote human coronavirus replication, we also identified a substantial number of novel genes and pathways. The website https://sarscrisprscreens.epi.ufl.edu/ was created to allow visualization and comparison of SARS-CoV2 CRISPR screens in a uniformly analyzed way. Of note, host factors involved in cell cycle regulation were enriched in our screens as were several key components of the programmed mRNA decay pathway. The role of EDC4 and XRN1 in coronavirus replication in human small airway epithelial cells was verified. Finally, we identified novel candidate antiviral compounds targeting a number of factors revealed by our screens. Conclusions Overall, our studies substantiate and expand the growing body of literature focused on understanding key human coronavirus-host cell interactions and exploit that knowledge for rational antiviral drug development.