Regulating epithelial-mesenchymal plasticity from 3D genome organization.

Epithelial-mesenchymal transition (EMT) is a dynamic process enabling polarized epithelial cells to acquire mesenchymal features implicated in development and carcinoma progression. As our understanding evolves, it is clear the reversible execution of EMT arises from complex epigenomic regulation involving histone modifications and 3-dimensional (3D) genome structural changes, leading to a cascade of transcriptional events. This review summarizes current knowledge on chromatin organization in EMT, with a focus on hierarchical structures of the 3D genome and chromatin accessibility changes.

The effect of inhibition of receptor tyrosine kinase AXL on DNA damage response in ovarian cancer.

AXL is a receptor tyrosine kinase that is often overexpressed in cancers. It contributes to pathophysiology in cancer progression and therapeutic resistance, making it an emerging therapeutic target. The first-in-class AXL inhibitor bemcentinib (R428/BGB324) has been granted fast track designation by the U.S. Food and Drug Administration (FDA) in STK11-mutated advanced metastatic non-small cell lung cancer and was also reported to show selective sensitivity towards ovarian cancers (OC) with a Mesenchymal molecular subtype. In this study, we further explored AXL's role in mediating DNA damage responses by using OC as a disease model. AXL inhibition using R428 resulted in the increase of DNA damage with the concurrent upregulation of DNA damage response signalling molecules. Furthermore, AXL inhibition rendered cells more sensitive to the inhibition of ATR, a crucial mediator for replication stress. Combinatory use of AXL and ATR inhibitors showed additive effects in OC. Through SILAC co-immunoprecipitation mass spectrometry, we identified a novel binding partner of AXL, SAM68, whose loss in OC cells harboured phenotypes in DNA damage responses similar to AXL inhibition. In addition, AXL- and SAM68-deficiency or R428 treatment induced elevated levels of cholesterol and upregulated genes in the cholesterol biosynthesis pathway. There might be a protective role of cholesterol in shielding cancer cells against DNA damage induced by AXL inhibition or SMA68 deficiency.

Comparison of long-term outcomes of spinal fusion surgeries supplemented with "topping-off" implants in lumbar degenerative diseases: A systematic review and network meta-analysis.

Background Context: Spinal fusion surgery is a common treatment for lumbar degenerative diseases and has been associated with the long-term complication of adjacent segment disease (ASD). In recent years, the "topping-off" technique has emerged as a new surgical method, combining spinal fusion with a hybrid stabilization device (HSD) or interspinous process device (IPD) proximal to the fused vertebrae. Methods: A literature search using the PubMed, Cochrane Central Register of Controlled Trials, EMBASE, and Web of Science databases identified eligible studies comparing topping-off implant(s) with spinal fusion surgery for lumbar degenerative diseases. Risk of bias was assessed using the Cochrane RoB 2.0 tool for randomized controlled trials and the Newcastle-Ottawa scale for retrospective studies. Each outcome was analyzed using the statistical Confidence in NMA (CINeMA) 1.9.0 software. Results: 17 RCTs and retrospective studies that included 1255 participants and five interventions were identified. The topping-off implants device for intervertebral assisted motion (DIAM; OR = 0.235, p < 0.001), Dynesys (OR = 0.413, p < 0.001), and Coflex (OR = 0.417, p < 0.01) significantly lowered the incidence of radiographic adjacent segment degeneration (RASDeg) compared with spinal fusion surgery alone. Spinal fusion supplemented with DIAM significantly reduced the incidence of clinical adjacent segment disease (CASD) (OR = 0.358, p = 0.032). Conclusions: Spinal fusion supplemented with DIAM substantially reduced the incidence of radiographic and clinical adjacent segment disease. No significant difference was observed between the treatment comparators for reoperation due to ASD and back pain relief score.

3D genome organization in the epithelial-mesenchymal transition spectrum.

BACKGROUND: The plasticity along the epithelial-mesenchymal transition (EMT) spectrum has been shown to be regulated by various epigenetic repertoires. Emerging evidence of local chromatin conformation changes suggests that regulation of EMT may occur at a higher order of three-dimensional genome level. RESULTS: We perform Hi-C analysis and combine ChIP-seq data across cancer cell lines representing different EMT states. We demonstrate that the epithelial and mesenchymal genes are regulated distinctively. We find that EMT genes are regulated within their topologically associated domains (TADs), with only a subset of mesenchymal genes being influenced by A/B compartment switches, indicating topological remodeling is required in the transcriptional regulation of these genes. At the TAD level, epithelial and mesenchymal genes are associated with different regulatory trajectories. The epithelial gene-residing TADs are enriched with H3K27me3 marks in the mesenchymal-like states. The mesenchymal gene-residing TADs, which do not show enrichment of H3K27me3 in epithelial-like states, exhibit increased interaction frequencies with regulatory elements in the mesenchymal-like states. CONCLUSIONS: We propose a novel workflow coupling immunofluorescence and dielectrophoresis to unravel EMT heterogeneity at single-cell resolution. The predicted three-dimensional structures of chromosome 10, harboring Vimentin, identify cell clusters of different states. Our results pioneer a novel avenue to decipher the complexities underlying the regulation of EMT and may infer the barriers of plasticity in the 3D genome context.