Cooperation of chromatin remodeling SWI/SNF complex and pioneer factor AP-1 shapes 3D enhancer landscapes.

The mechanism controlling the dynamic targeting of SWI/SNF has long been postulated to be coordinated by transcription factors (TFs), yet demonstrating a specific TF influence has proven difficult. Here we take a multi-omics approach to interrogate transient SWI/SNF interactors, chromatin targeting and the resulting three-dimensional epigenetic landscape. We utilize the labeling technique TurboID to map the SWI/SNF interactome and identify the activator protein-1 (AP-1) family members as critical interacting partners for SWI/SNF complexes. CUT&RUN profiling demonstrates SWI/SNF targeting enrichment at AP-1 bound loci, as well as SWI/SNF-AP-1 cooperation in chromatin targeting. HiChIP reveals AP-1-SWI/SNF-dependent restructuring of the three-dimensional promoter-enhancer architecture and generation of enhancer hubs. Through interrogation of the SWI/SNF-AP-1 interaction, we demonstrate an SWI/SNF dependency on AP-1-mediated chromatin localization. We propose that pioneer factors, such as AP-1, bind and target SWI/SNF to inactive chromatin, where it restructures the genomic landscape into an active state through epigenetic rewiring spanning multiple dimensions.

Author Correction: BRD9 defines a SWI/SNF sub-complex and constitutes a specific vulnerability in malignant rhabdoid tumors.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

BRD9 defines a SWI/SNF sub-complex and constitutes a specific vulnerability in malignant rhabdoid tumors.

Bromodomain-containing protein 9 (BRD9) is a recently identified subunit of SWI/SNF(BAF) chromatin remodeling complexes, yet its function is poorly understood. Here, using a genome-wide CRISPR-Cas9 screen, we show that BRD9 is a specific vulnerability in pediatric malignant rhabdoid tumors (RTs), which are driven by inactivation of the SMARCB1 subunit of SWI/SNF. We find that BRD9 exists in a unique SWI/SNF sub-complex that lacks SMARCB1, which has been considered a core subunit. While SMARCB1-containing SWI/SNF complexes are bound preferentially at enhancers, we show that BRD9-containing complexes exist at both promoters and enhancers. Mechanistically, we show that SMARCB1 loss causes increased BRD9 incorporation into SWI/SNF thus providing insight into BRD9 vulnerability in RTs. Underlying the dependency, while its bromodomain is dispensable, the DUF3512 domain of BRD9 is essential for SWI/SNF integrity in the absence of SMARCB1. Collectively, our results reveal a BRD9-containing SWI/SNF subcomplex is required for the survival of SMARCB1-mutant RTs.

Adoptive transfer of murine T cells expressing a chimeric-PD1-Dap10 receptor as an immunotherapy for lymphoma.

Adoptive transfer of T cells is a promising cancer therapy and expression of chimeric antigen receptors can enhance tumour recognition and T-cell effector functions. The programmed death protein 1 (PD1) receptor is a prospective target for a chimeric antigen receptor because PD1 ligands are expressed on many cancer types, including lymphoma. Therefore, we developed a murine chimeric PD1 receptor (chPD1) consisting of the PD1 extracellular domain fused to the cytoplasmic domain of CD3ζ. Additionally, chimeric antigen receptor therapies use various co-stimulatory domains to enhance efficacy. Hence, the inclusion of a Dap10 or CD28 co-stimulatory domain in the chPD1 receptor was compared to determine which domain induced optimal anti-tumour immunity in a mouse model of lymphoma. The chPD1 T cells secreted pro-inflammatory cytokines and lysed RMA lymphoma cells. Adoptive transfer of chPD1 T cells significantly reduced established tumours and led to tumour-free survival in lymphoma-bearing mice. When comparing chPD1 receptors containing a Dap10 or CD28 domain, both receptors induced secretion of pro-inflammatory cytokines; however, chPD1-CD28 T cells also secreted anti-inflammatory cytokines whereas chPD1-Dap10 T cells did not. Additionally, chPD1-Dap10 induced a central memory T-cell phenotype compared with chPD1-CD28, which induced an effector memory phenotype. The chPD1-Dap10 T cells also had enhanced in vivo persistence and anti-tumour efficacy compared with chPD1-CD28 T cells. Therefore, adoptive transfer of chPD1 T cells could be a novel therapy for lymphoma and inclusion of the Dap10 co-stimulatory domain in chimeric antigen receptors may induce a preferential cytokine profile and T-cell differentiation phenotype for anti-tumour therapies.

Randomized controlled trial of a breath-actuated nebulizer in pediatric asthma patients in the emergency department.

BACKGROUND: Bronchodilator treatment for asthma can be provided with various aerosol-generating devices and methods. There have been no randomized trials of a breath-actuated nebulizer versus continuous 1-hour nebulization and/or small-volume constant-output nebulizer in pediatric asthma patients. METHODS: We conducted a randomized study of one-time albuterol treatment with the AeroEclipse breath-actuated nebulizer versus standard therapy (single treatment via small-volume nebulizer or 1-hour of continuous nebulized albuterol) in pediatric asthma patients in the emergency department. Eligible patients were those admitted to the emergency department, 0 months to 18 years of age, who presented with asthma or wheezing. We assessed all the patients with our clinical asthma scoring system and peak-flow measurement if possible. We stratified the patients by clinical asthma score and weight, and then randomized them to receive their initial albuterol treatment in the emergency department via either AeroEclipse or standard therapy. We recorded time in the emergency department, change in clinical asthma score, need for additional bronchodilator treatments, need for admission, patient response, ability to actuate the AeroEclipse, and adverse effects. RESULTS: We enrolled 149 patients between October 14, 2004 and November 11, 2005, and we randomized 84 patients to AeroEclipse and 65 to standard therapy. The cohort's average age was 5.5 years. There were no significant differences in demographics. The initial mean clinical asthma scores were 5.1 ± 2.4 in the AeroEclipse group, and 5.1 ± 2.1 in the standard-therapy group. Time in the emergency department was not different (AeroEclipse 102 min, standard therapy 125 min, P = .10), but the AeroEclipse group had a significantly greater improvement in clinical asthma score (1.9 ± 1.2 vs 1.2 ± 1.4, P = .001) and respiratory rate (P = .002), and significantly lower admission rate (38% vs 57%, P = .03). There was no difference in adverse effects. CONCLUSIONS: Although AeroEclipse did not reduce the time in the ED, it significantly improved clinical asthma score, decreased admissions, and decreased respiratory rate.