PUBLICATIONS
Work from Jon Brown Lab has recently been published in Nature, JCI Insight, JACC:Basic to Translational Science
Proceedings of the National Academy of Sciences and iScience
TRANSCRIPTIONAL SYNERGY IN HUMAN AORTIC ENDOTHELIAL CELLS IS VULNERABLE TO COMBINATION P300/CBP AND BET BROMODOMAIN INHIBITION
iScience, May, 2024
Combinatorial signaling by proinflammatory cytokines synergizes to exacerbate toxicity to cells and tissue injury during acute infections. To explore synergism at the gene regulatory level we investigated the dynamics of transcription and chromatin signaling in response to dual cytokines by integrating nascent RNA imaging mass spectrometry, RNA-sequencing, amplification-independent mRNA quantification, ATAC-sequencing and transcription factor profiling. Costimulation with interferon-gamma and tumor necrosis-alpha synergistically induced a small subset of genes, including the chemokines CXCL9, -10, -11. Gene induction coincided with increased chromatin accessibility at non-coding regions enriched for p65 and STAT1 binding sites. To discover coactivator dependencies, we conducted a targeted chemogenomic screen of transcriptional inhibitors followed by modelling of inhibitor dose-response curves. These results identified high efficacy of either p300/CBP or BET bromodomain inhibitors to disrupt induction of synergy genes. Combination p300/CBP and BET bromodomain inhibition at subIC50 concentrations synergistically abrogated IFN/TNF-induced chemokine gene and protein levels.
IN VIVO BASE EDITING RESCUES HUTCHINSON-GILFORD PROGERIA SYNDROME
Nature, January 6, 2021
Hutchinson-Gilford progeria syndrome (HGPS) is typically caused by a dominant-negative C•G-to-T•A mutation (c.1824 C>T, G608G) in LMNA, the nuclear lamin A gene. This mutation causes RNA mis-splicing that produces progerin, a toxic protein that induces rapid aging and shortens lifespan to ~14 years1-4. Adenine base editors (ABEs) perform targeted A•T-to-G•C base pair conversion with minimal byproducts and without requiring double-strand DNA breaks or donor DNA templates5,6. Here, we describe the use of an ABE to directly correct the pathogenic HGPS mutation in cultured progeria patient-derived fibroblasts and in a mouse model of HGPS. Lentiviral delivery of ABE to patient-derived fibroblasts results in ~90% correction of the pathogenic allele, mitigation of RNA mis-splicing, reduced progerin levels, and correction of nuclear abnormalities. Unbiased off-target DNA and RNA analysis did not detect off-target editing activity in treated patient-derived fibroblasts. In transgenic mice homozygous for the human LMNA c.1824 C>T allele, a single retro-orbital injection of adeno-associated virus 9 (AAV9) encoding the ABE resulted in substantial, durable correction of the pathogenic mutation (~20-60% across various organs 6 months post-injection), restoration of normal RNA splicing, and reduction of progerin protein. In vivo base editing rescued vascular pathology, preserving vascular smooth muscle cell counts and preventing adventitial fibrosis. A single ABE AAV9 injection at P14 improved animal vitality and greatly extended median lifespan from 215 to 510 days. These findings support the potential of in vivo base editing to treat HGPS, and other genetic diseases, by directly correcting the root cause of disease.
COMPARATIVE TRANSCRIPTOMICS OF EX VIVO, PATIENT-DERIVED ENDOTHELIAL CELLS REVEALS NOVEL PATHWAYS ASSOCIATED WITH TYPE 2 DIABETES MELLITUS
JACC: Basic to Translational Science, September 23, 2019
In this study we used low-input RNA-sequencing to annotate the molecular identity of human endothelial cells (ECs) isolated and immunopurified with CD144 microbeads. After validating this technique, comparative gene expression profiling of ECs from healthy subjects and patients with type 2 diabetes mellitus identified both known and novel pathways linked with EC dysfunction. Modeling of diabetes by treating cultured ECs with high glucose identified shared changes in gene expression in diabetic cells. Overall, the data demonstrate how purified ECs from patients can be used to generate new hypotheses about mechanisms of human vascular disease.
IMAGING MASS SPECTROMETRY REVEALS HETEROGENEITY OF PROLIFERATION AND METABOLISM IN ATHEROSCLEROSIS
JCI Insight, June 6th, 2019
Atherosclerotic plaques feature local proliferation of leukocytes and vascular smooth muscle cells (VSMCs) and changes in cellular metabolism. We used Multi-isotope Imaging Mass spectrometry (MIMS), a quantitative imaging platform, to measure coincident cell division and glucose utilization at suborganelle resolution in atherosclerotic plaques. In established plaques, 65% of intimal foam cells but only 4% of medial VSMCs were labeled with 15N-thymidine after 1 week of isotope treatment. Dividing cells demonstrated heightened glucose labeling. MIMS detected 2H-glucose label in multiple subcellular compartments within foam cells including lipid droplets, the cytosol and chromatin. Unexpectedly, we identified an intensely focal region of 2H-label in VSMCs underlying plaques. This signal diminished in regions of aorta without atherosclerosis. In advanced plaques, 15N-thymidine and 2H-glucose labeling in foam cells and VSMCs significantly decreased. These data demonstrate marked heterogeneity in VSMC glucose metabolism that was dependent on both proliferative status and proximity of VSMCs to plaques. These results reveal how quantitative mass spectrometry coupled with isotope imaging can complement other methods used to study cell biology directly in the growing atherosclerotic plaque in vivo.
BET BROMODOMAIN PROTEINS REGULATE ENHANCER FUNCTION DURING ADIPOGENESIS
PNAS, February 14th, 2018
Transcriptional cascades orchestrate activation of the adipocyte gene expression program during adipogenesis. However, the coactivators controlling expression of PPARg and C/EBPa are less well characterized. In this work we demonstrated that BRD4 regulates transcription of PPARg and C/EBPa. During adipogenesis in 3T3L1 cells BRD4 dynamically redistributes to de novo super enhancers that are in close proximity to key genes controlling adipocyte differentiation. BET bromodomain inhibition impedes BRD4 occupancy at these new enhancer regions and thereby disrupts transcription of Pparg and Cebpa,. As a result, adipogenesis is blocked. Furthermore, silencing of super enhancer sites at the Pparg locus by CRISPR-interference inhibits gene expression, demonstrating a functional role for these enhancers in Pparg gene expression and adipogenesis. Together, these data establish BETs and BRD4 as time- and context-dependent coactivators of the adipocyte cell state transition.
Jon Brown Lab | VUMC