Ripley, R. T. | Search bioRxiv

bioRxiv2021

SMARCA4 regulates spatially restricted metabolic plasticity in 3D multicellular tissue

SWI/SNF and related chromatin remodeling complexes act as tissue-specific tumor suppressors and are frequently inactivated in different cancers. Although many regulatory activities of SWI/SNF have been identified using 2D cell culture, the effects of SWI/SNF alterations in more complex 3D tissues have remained poorly understood. Here we employed 3D cell culture conditions that yield transcriptomic states mirroring primary lung adenocarcinoma (LUAD) specimens better than 2D culture. By analyzing spatial patterns of gene expression and DNA accessibility in 3D spheroids using single-cell RNA-seq and ATAC-seq, we find that the SWI/SNF ATPase SMARCA4 (BRG1) induces state-specific changes to DNA accessibility that influence spatially heterogeneous expression patterns and metabolism. In 3D conditions, SMARCA4 promotes accessibility for AP-1 transcription factors, including ATF3, a regulator of metabolism and repressor of NRF2 antioxidant signaling. These changes reduce expression of SLC7A11 in a distinct portion of cells, which sensitizes A549 spheroids to cell death via ferroptosis under oxidizing conditions. Consistent with these results, we find that SMARCA4 alterations are associated with derepression of NRF2 targets in human tumors independently of NRF2/KEAP1 status. Our work reveals new 3D-specific features and unanticipated spatial complexity associated with chromatin remodeling in multicellular tissues.

systems biology↗

bioRxiv2021

Inhibition of CDK4/6 Overcomes Primary Resistance to PD-1 Blockade in Malignant Mesothelioma

BackgroundDespite the profound number of malignant pleural mesothelioma (MPM) patients now treated with PD-1 blockade, insight into the underpinnings of rational therapeutic strategies to treat resistance to checkpoint immunotherapy remain unrealized. Our objective was to develop a novel therapeutic approach to overcome primary resistance to PD-1 blockade in MPM. MethodsWe generated a transcriptome signature of resistance to PD-1 blockade in MPM patients treated with nivolumab (4 responders and 4 non-responders). We used the TCGA MPM cohort (N=73) to determine what genomic alterations were associated with the resistance signature. We tested whether regulation of identified molecules could overcome resistance to PD-1 blockade in an immunocompetent mouse malignant mesothelioma model. ResultsImmunogenomic analysis by applying our anti-PD-1 resistance signature to the TCGA cohort revealed that deletion of CDKN2A was highly associated with primary resistance to PD-1 blockade. Under the hypothesis that resistance to PD-1 blockade can be overcome by CDK4/6 inhibition, we tested whether CDK4/6 inhibitors could overcome resistance to PD-1 blockade in subcutaneous tumors derived from Cdkn2a(-/-) AB1 malignant mesothelioma cells, which were resistant to PD-1 blockade. The combination of daily oral administration of CDK4/6 inhibitors (abemaciclib or palbociclib) and intraperitoneal anti-PD-1 treatment markedly suppressed tumor growth, compared with anti-PD-1 or CDK4/6 inhibitor alone. ConclusionsWe identified a novel therapeutic target, CDK4/6, to overcome primary resistance to PD-1 blockade through comprehensive immunogenomic approaches. These data provide a rationale for undertaking clinical trials of CDK4/6 inhibitors in the more than 40% of patients with MPM who demonstrate loss of CDKN2A.

immunology↗