Modeling and targeting of erythroleukemia by hematopoietic genome editing.

Acute erythroid leukemia (AEL) is characterized by a distinct morphology, mutational spectrum, lack of preclinical models, and poor prognosis. Here, using multiplexed genome editing of mouse hematopoietic stem and progenitor cells and transplant assays, we developed preclinical models of AEL and non-erythroid acute leukemia and describe the central role of mutational cooperativity in determining leukemia lineage. Different combination of mutations in Trp53, Bcor, Dnmt3a, Rb1, and Nfix resulted in the development of leukemia with an erythroid phenotype, accompanied by the acquisition of alterations in signaling and transcription factor genes that recapitulate human AEL by cross-species genomic analysis. Clonal expansion during tumor evolution was driven by mutational cooccurrence, with clones harboring a higher number of founder and secondary lesions (eg, mutations in signaling genes) showing greater evolutionary fitness. Mouse and human AEL exhibited deregulation of genes regulating erythroid development, notably Gata1, Klf1, and Nfe2, driven by the interaction of mutations of the epigenetic modifiers Dnmt3a and Tet2 that perturbed methylation and thus expression of lineage-specific transcription factors. The established mouse leukemias were used as a platform for drug screening. Drug sensitivity was associated with the leukemia genotype, with the poly (ADP-ribose) polymerase inhibitor talazoparib and the demethylating agent decitabine efficacious in Trp53/Bcor-mutant AEL, CDK7/9 inhibitors in Trp53/Bcor/Dnmt3a-mutant AEL, and gemcitabine and bromodomain inhibitors in NUP98-KDM5A leukemia. In conclusion, combinatorial genome editing has shown the interplay of founding and secondary genetic alterations in phenotype and clonal evolution, epigenetic regulation of lineage-specific transcription factors, and therapeutic tractability in erythroid leukemogenesis.

PBRM1 bromodomains variably influence nucleosome interactions and cellular function.

Chromatin remodelers use bromodomains (BDs) to recognize histones. Polybromo 1 (PBRM1 or BAF180) is hypothesized to function as the nucleosome-recognition subunit of the PBAF chromatin-remodeling complex and is frequently mutated in clear cell renal cell carcinoma (ccRCC). Previous studies have applied in vitro methods to explore the binding specificities of the six individual PBRM1 BDs. However, BD targeting to histones and the influence of neighboring BD on nucleosome recognition have not been well characterized. Here, using histone microarrays and intact nucleosomes to investigate the histone-binding characteristics of the six PBRM1 BDs individually and combined, we demonstrate that BD2 and BD4 of PBRM1 mediate binding to acetylated histone peptides and to modified recombinant and cellular nucleosomes. Moreover, we show that neighboring BDs variably modulate these chromatin interactions, with BD1 and BD5 enhancing nucleosome interactions of BD2 and BD4, respectively, whereas BD3 attenuated these interactions. We also found that binding pocket missense mutations in BD4 observed in ccRCC disrupt PBRM1-chromatin interactions and that these mutations in BD4, but not similar mutations in BD2, in the context of full-length PBRM1, accelerate ccRCC cell proliferation. Taken together, our biochemical and mutational analyses have identified BD4 as being critically important for maintaining proper PBRM1 function and demonstrate that BD4 mutations increase ccRCC cell growth. Because of the link between PBRM1 status and sensitivity to immune checkpoint inhibitor treatment, these data also suggest the relevance of BD4 as a potential clinical target.

Initial Hearing Preservation Is Correlated With Cochlear Duct Length in Fully-inserted Long Flexible Lateral Wall Arrays.

OBJECTIVES: To characterize the relationship between cochlear duct length (CDL) and initial hearing preservation among cochlear implant recipients of a fully inserted 31.5 mm flexible lateral wall electrode array. STUDY DESIGN: Retrospective review. SETTING: Tertiary academic referral center. PATIENTS: Adult cochlear implant recipients who presented preoperatively with unaided hearing detection thresholds of ≤ 65 dB HL at 125 Hz and underwent cochlear implantation with a 31.5 mm flexible lateral wall array. INTERVENTION: Cochlear implantation with a hearing preservation surgical approach. MAIN OUTCOME MEASURES: Computed tomography was reviewed to determine CDL. Hearing preservation was characterized by the shift in low-frequency pure-tone average (LFPTA; 125, 250, and 500 Hz), and shift in individual unaided hearing detection thresholds at 125, 250, and 500 Hz. RESULTS: Nineteen patients met the criteria for inclusion. The mean CDL was 34.2 mm (range: 30.8-36.5 mm). Recipients experienced a mean LFPTA shift of 27.6 dB HL (range: 10-50 dB HL). Significant, negative correlations were observed between CDL and smaller threshold shifts at individual frequencies and LFPTA (p ≤ 0.048). CONCLUSION: A longer CDL is associated with greater likelihood of preserving low-frequency hearing with long arrays. Low-frequency hearing preservation is feasible with fully inserted long flexible arrays within the initial months after cochlear implantation. Preoperative measurement of CDL may facilitate a more individualized approach in array selection to permit optimal cochlear coverage while enhancing hearing preservation outcomes.