Casey E Romanoski
- Assistant Professor, Cellular and Molecular Medicine
- Research Fellow, BIO5 Institute
- Assistant Professor, Clinical Translational Sciences
- Assistant Professor, Genetics - GIDP
The overarching goal of the Romanoski Lab is to better understand the mechanisms by which DNA sequence instructs molecular programs that underlie human biology. We are particularly interested in complex diseases such as atherosclerosis and hypertension, which are caused by combinations of environmental and genetic risk factors. While these diseases involve many cell types, our research is focused on endothelial cells, which line blood vessels and form the barrier between blood and tissue.
Our laboratory is both experimental and computational. We use next-generation sequencing technologies to measure genome-wide molecular phenotypes. By leveraging the interconnected relationships between DNA sequence, transcription factor binding, chromatin modification, and gene expression, we study how cells achieve context-appropriate expression patterns and signal responsiveness.
Ongoing projects in the lab include systems genetics of endothelial cells, transcriptional network determination in different endothelial beds, and functional genetics of GWAS loci.
- Postdoctoral Fellow
- University of California San Diego, La Jolla, US
- PhD Human Genetics
- University of California Los Angeles, Los Angeles, US
- Ph.D. Human Genetics
- University of California, Los Angeles, Los Angeles, California, United States
- Systems Genetics of Endothelial Cell Activation by Oxidized Phospholipids
- B.A. Science and Mathematics
- University of Arizona, Tucson, Arizona, United States
- BA Math and Science
- University of Arizona, Tucson, US
- University of Arizona, Tucson (2016 - Ongoing)
- University of California, San Diego, La Jolla, California (2010 - 2016)
- University of California, Los Angeles, Los Angeles, California (2006 - 2010)
- University of California, Los Angeles, Los Angeles, California (2006 - 2007)
- University of Arizona, Tucson, Arizona (2003 - 2004)
- Poster Award
- Gordon Research Conference on Atherosclerosis, Summer 2017
- Irvine H. Page Young Investigator Research Award Finalist
- Council on Arteriosclerosis, Thrombosis and Vascular Biology, American Heart Association, Spring 2017 (Award Finalist)
Genetics, Genomics, Gene Regulation, Functional Genetics, Transcription, Non-Coding Functional Genetic Variation, Endothelial Cells, Atherosclerosis, Inflammation, Complex Disease Genetics, Gene-by-Environment Interactions, High-Throughput Sequencing Technologies, Bioinformatics, Regulatory Networks, Transcription Factors, Enhancers, Macrophages
I am interested in teaching students about the underpinnings of molecular genetics, high-throughput 'omics', and computational approaches as they are being applied to better understand complex disease biology. I am dedicated to mentoring students to excel in both written and oral scientific communication. I am particularly interested in bolstering success of women and other underrepresented groups in the sciences.
DissertationCMM 920 (Fall 2020)
DissertationGENE 920 (Fall 2020)
Honors Independent StudyPSIO 399H (Fall 2020)
Individualized Science WritingCTS 585 (Fall 2020)
Journal ClubCMM 595A (Fall 2020)
Prin of Cell BiologyCMM 577 (Fall 2020)
Prin of Cell BiologyMCB 577 (Fall 2020)
Student SeminarCMM 696B (Fall 2020)
Art of Scientific CommCMM 603 (Spring 2020)
DissertationCMM 920 (Spring 2020)
Honors Independent StudyPSIO 399H (Spring 2020)
Individualized Science WritingCTS 585 (Spring 2020)
Journal ClubCMM 595A (Spring 2020)
ResearchCTS 900 (Spring 2020)
ResearchGENE 900 (Spring 2020)
Senior CapstoneMCB 498 (Spring 2020)
Student SeminarCMM 696B (Spring 2020)
DissertationCMM 920 (Fall 2019)
DissertationGENE 920 (Fall 2019)
Honors Independent StudyPSIO 399H (Fall 2019)
Introduction to ResearchMCB 795A (Fall 2019)
Prin of Cell BiologyCMM 577 (Fall 2019)
Prin of Cell BiologyMCB 577 (Fall 2019)
ResearchCMM 900 (Fall 2019)
ResearchCTS 900 (Fall 2019)
Senior CapstoneMCB 498 (Fall 2019)
Student SeminarCMM 696B (Fall 2019)
Art of Scientific CommCMM 603 (Spring 2019)
Departmental SeminarCMM 696A (Spring 2019)
Directed RsrchMCB 392 (Spring 2019)
DissertationGENE 920 (Spring 2019)
ResearchCMM 900 (Spring 2019)
Departmental SeminarCMM 696A (Fall 2018)
Directed RsrchMCB 392 (Fall 2018)
Introduction to ResearchMCB 795A (Fall 2018)
Prin of Cell BiologyCMM 577 (Fall 2018)
Prin of Cell BiologyMCB 577 (Fall 2018)
ResearchCMM 900 (Fall 2018)
ResearchGENE 900 (Fall 2018)
Current Tops in Biomedical SciCMM 603 (Spring 2018)
Departmental SeminarCMM 696A (Spring 2018)
Introduction to ResearchMCB 795A (Spring 2018)
ResearchGENE 900 (Spring 2018)
Departmental SeminarCMM 696A (Fall 2017)
Introduction to ResearchMCB 795A (Fall 2017)
Prin of Cell BiologyCMM 577 (Fall 2017)
Prin of Cell BiologyMCB 577 (Fall 2017)
ResearchGENE 900 (Fall 2017)
Current Tops in Biomedical SciCMM 603 (Spring 2017)
Introduction to ResearchMCB 795A (Spring 2017)
Lab Research RotationGENE 795A (Spring 2017)
Introduction to ResearchMCB 795A (Fall 2016)
- Romanoski, C. E. (2010). Systems genetics of endothelial cell activation by oxidized phospholipids.
- Romanoski, C. E. (2016). Genome-Wide Assessment Reveals Marked Differences In The Transcriptomes Of Mononuclear Phagocytes In The Developing Lung. In C21. APPLYING'OMICS TECHNOLOGIES TO REVEAL GENE REGULATORS AND BIOMARKERS IN LUNG DEVELOPMENT AND DISEASE.
- Sajti, E., Link, V. M., Ouyang, Z., Spann, N. J., Westin, E., Romanoski, C. E., Fonseca, G. J., Prince, L. S., & Glass, C. K. (2020). Transcriptomic and epigenetic mechanisms underlying myeloid diversity in the lung. Nature immunology.More infoThe lung is inhabited by resident alveolar and interstitial macrophages as well as monocytic cells that survey lung tissues. Each cell type plays distinct functional roles under homeostatic and inflammatory conditions, but mechanisms establishing their molecular identities and functional potential remain poorly understood. In the present study, systematic evaluation of transcriptomes and open chromatin of alveolar macrophages (AMs), interstitial macrophages (IMs) and lung monocytes from two mouse strains enabled inference of common and cell-specific transcriptional regulators. We provide evidence that these factors drive selection of regulatory landscapes that specify distinct phenotypes of AMs and IMs and entrain qualitatively different responses to toll-like receptor 4 signaling in vivo. These studies reveal a striking divergence in a fundamental innate immune response pathway in AMs and establish a framework for further understanding macrophage diversity in the lung.
- Allan, C. M., Heizer, P. J., Tu, Y., Sandoval, N. P., Jung, R. S., Morales, J. E., Sajti, E., Troutman, T. D., Saunders, T. L., Cusanovich, D. A., Beigneux, A. P., Romanoski, C. E., Fong, L. G., & Young, S. G. (2019). An upstream enhancer regulates expression in a tissue-specific manner. Journal of lipid research, 60(4), 869-879.More infoGlycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1 (GPIHBP1), the protein that shuttles LPL to the capillary lumen, is essential for plasma triglyceride metabolism. When GPIHBP1 is absent, LPL remains stranded within the interstitial spaces and plasma triglyceride hydrolysis is impaired, resulting in severe hypertriglyceridemia. While the functions of GPIHBP1 in intravascular lipolysis are reasonably well understood, no one has yet identified DNA sequences regulating GPIHBP1 expression. In the current studies, we identified an enhancer element located ∼3.6 kb upstream from exon 1 of mouse To examine the importance of the enhancer, we used CRISPR/Cas9 genome editing to create mice lacking the enhancer (). Removing the enhancer reduced expression by >90% in the liver and by ∼50% in heart and brown adipose tissue. The reduced expression of GPIHBP1 was insufficient to prevent LPL from reaching the capillary lumen, and it did not lead to hypertriglyceridemia-even when mice were fed a high-fat diet. Compound heterozygotes ( mice) displayed further reductions in expression and exhibited partial mislocalization of LPL (increased amounts of LPL within the interstitial spaces of the heart), but the plasma triglyceride levels were not perturbed. The enhancer element that we identified represents the first insight into DNA sequences controlling expression.
- Hitzel, J., Lee, E., Zhang, Y., Bibli, S. I., Li, X., Zukunft, S., Pflüger, B., Hu, J., Schürmann, C., Vasconez, A. E., Oo, J. A., Kratzer, A., Kumar, S., Rezende, F., Josipovic, I., Thomas, D., Giral, H., Schreiber, Y., Geisslinger, G., , Fork, C., et al. (2018). Oxidized phospholipids regulate amino acid metabolism through MTHFD2 to facilitate nucleotide release in endothelial cells. Nature communications, 9(1), 2292.More infoOxidized phospholipids (oxPAPC) induce endothelial dysfunction and atherosclerosis. Here we show that oxPAPC induce a gene network regulating serine-glycine metabolism with the mitochondrial methylenetetrahydrofolate dehydrogenase/cyclohydrolase (MTHFD2) as a causal regulator using integrative network modeling and Bayesian network analysis in human aortic endothelial cells. The cluster is activated in human plaque material and by atherogenic lipoproteins isolated from plasma of patients with coronary artery disease (CAD). Single nucleotide polymorphisms (SNPs) within the MTHFD2-controlled cluster associate with CAD. The MTHFD2-controlled cluster redirects metabolism to glycine synthesis to replenish purine nucleotides. Since endothelial cells secrete purines in response to oxPAPC, the MTHFD2-controlled response maintains endothelial ATP. Accordingly, MTHFD2-dependent glycine synthesis is a prerequisite for angiogenesis. Thus, we propose that endothelial cells undergo MTHFD2-mediated reprogramming toward serine-glycine and mitochondrial one-carbon metabolism to compensate for the loss of ATP in response to oxPAPC during atherosclerosis.
- Krause, M. D., Huang, R. T., Wu, D., Shentu, T. P., Harrison, D. L., Whalen, M. B., Stolze, L. K., Di Rienzo, A., Moskowitz, I. P., Civelek, M., Romanoski, C. E., & Fang, Y. (2018). Genetic variant at coronary artery disease and ischemic stroke locus 1p32.2 regulates endothelial responses to hemodynamics. Proceedings of the National Academy of Sciences of the United States of America, 115(48), E11349-E11358.More infoBiomechanical cues dynamically control major cellular processes, but whether genetic variants actively participate in mechanosensing mechanisms remains unexplored. Vascular homeostasis is tightly regulated by hemodynamics. Exposure to disturbed blood flow at arterial sites of branching and bifurcation causes constitutive activation of vascular endothelium contributing to atherosclerosis, the major cause of coronary artery disease (CAD) and ischemic stroke (IS). Conversely, unidirectional flow promotes quiescent endothelium. Genome-wide association studies (GWAS) have identified chromosome 1p32.2 as strongly associated with CAD/IS; however, the causal mechanism related to this locus remains unknown. Using statistical analyses, assay of transposase accessible chromatin with whole-genome sequencing (ATAC-seq), H3K27ac/H3K4me2 ChIP with whole-genome sequencing (ChIP-seq), and CRISPR interference in human aortic endothelial cells (HAECs), our results demonstrate that rs17114036, a common noncoding polymorphism at 1p32.2, is located in an endothelial enhancer dynamically regulated by hemodynamics. CRISPR-Cas9-based genome editing shows that rs17114036-containing region promotes endothelial quiescence under unidirectional shear stress by regulating phospholipid phosphatase 3 (PLPP3). Chromatin accessibility quantitative trait locus (caQTL) mapping using HAECs from 56 donors, allelic imbalance assay from 7 donors, and luciferase assays demonstrate that CAD/IS-protective allele at rs17114036 in PLPP3 intron 5 confers increased endothelial enhancer activity. ChIP-PCR and luciferase assays show that CAD/IS-protective allele at rs17114036 creates a binding site for transcription factor Krüppel-like factor 2 (KLF2), which increases the enhancer activity under unidirectional flow. These results demonstrate that a human SNP contributes to critical endothelial mechanotransduction mechanisms and suggest that human haplotypes and related -regulatory elements provide a previously unappreciated layer of regulatory control in cellular mechanosensing mechanisms.
- Link, V. M., Duttke, S. H., Chun, H. B., Holtman, I. R., Westin, E., Hoeksema, M. A., Abe, Y., Skola, D., Romanoski, C. E., Tao, J., Fonseca, G. J., Troutman, T. D., Spann, N. J., Strid, T., Sakai, M., Yu, M., Hu, R., Fang, R., Metzler, D., , Ren, B., et al. (2018). Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function. Cell.More infoNon-coding genetic variation is a major driver of phenotypic diversity and allows the investigation of mechanisms that control gene expression. Here, we systematically investigated the effects of >50 million variations from five strains of mice on mRNA, nascent transcription, transcription start sites, and transcription factor binding in resting and activated macrophages. We observed substantial differences associated with distinct molecular pathways. Evaluating genetic variation provided evidence for roles of ∼100 TFs in shaping lineage-determining factor binding. Unexpectedly, a substantial fraction of strain-specific factor binding could not be explained by local mutations. Integration of genomic features with chromatin interaction data provided evidence for hundreds of connected cis-regulatory domains associated with differences in transcription factor binding and gene expression. This system and the >250 datasets establish a substantial new resource for investigation of how genetic variation affects cellular phenotypes.
- Link, V. M., Romanoski, C. E., Metzler, D., & Glass, C. K. (2018). MMARGE: Motif Mutation Analysis for Regulatory Genomic Elements. Nucleic acids research, 46(14), 7006-7021.More infoCell-specific patterns of gene expression are determined by combinatorial actions of sequence-specific transcription factors at cis-regulatory elements. Studies indicate that relatively simple combinations of lineage-determining transcription factors (LDTFs) play dominant roles in the selection of enhancers that establish cell identities and functions. LDTFs require collaborative interactions with additional transcription factors to mediate enhancer function, but the identities of these factors are often unknown. We have shown that natural genetic variation between individuals has great utility for discovering collaborative transcription factors. Here, we introduce MMARGE (Motif Mutation Analysis of Regulatory Genomic Elements), the first publicly available suite of software tools that integrates genome-wide genetic variation with epigenetic data to identify collaborative transcription factor pairs. MMARGE is optimized to work with chromatin accessibility assays (such as ATAC-seq or DNase I hypersensitivity), as well as transcription factor binding data collected by ChIP-seq. Herein, we provide investigators with rationale for each step in the MMARGE pipeline and key differences for analysis of datasets with different experimental designs. We demonstrate the utility of MMARGE using mouse peritoneal macrophages, liver cells, and human lymphoblastoid cells. MMARGE provides a powerful tool to identify combinations of cell type-specific transcription factors while simultaneously interpreting functional effects of non-coding genetic variation.
- Hogan, N. T., Whalen, M. B., Stolze, L. K., Hadeli, N. K., Lam, M. T., Springstead, J. R., Glass, C. K., & Romanoski, C. E. (2017). Transcriptional networks specifying homeostatic and inflammatory programs of gene expression in human aortic endothelial cells. eLife, 6.More infoEndothelial cells (ECs) are critical determinants of vascular homeostasis and inflammation, but transcriptional mechanisms specifying their identities and functional states remain poorly understood. Here, we report a genome-wide assessment of regulatory landscapes of primary human aortic endothelial cells (HAECs) under basal and activated conditions, enabling inference of transcription factor networks that direct homeostatic and pro-inflammatory programs. We demonstrate that 43% of detected enhancers are EC-specific and contain SNPs associated to cardiovascular disease and hypertension. We provide evidence that AP1, ETS, and GATA transcription factors play key roles in HAEC transcription by co-binding enhancers associated with EC-specific genes. We further demonstrate that exposure of HAECs to oxidized phospholipids or pro-inflammatory cytokines results in signal-specific alterations in enhancer landscapes and associate with coordinated binding of CEBPD, IRF1, and NFκB. Collectively, these findings identify cis-regulatory elements and corresponding trans-acting factors that contribute to EC identity and their specific responses to pro-inflammatory stimuli.
- Romanoski, C. E. (2017). Transcriptional networks specifying homeostatic and inflammatory programs of gene expression in human aortic endothelial cells. eLIFE.
- Romanoski, C. E. (2016). Deleting an Nr4a1 Super-Enhancer Subdomain Ablates Ly6C low Monocytes while Preserving Macrophage Gene Function. Immunity.
- Romanoski, C. E. (2016). Enhancer Transcription And Enhancer Function. The FASEB Journal.
- Romanoski, C. E. (2016). MAFG Is a Transcriptional Repressor of Bile Acid Synthesis and Metabolism (vol 21, pg 298, 2015). CELL METABOLISM.
- Romanoski, C. E. (2016). MAFG Is a Transcriptional Repressor of Bile Acid Synthesis and Metabolism. Cell Metabolism.
- Thomas, G. D., Hanna, R. N., Vasudevan, N. T., Hamers, A. A., Romanoski, C. E., McArdle, S., Ross, K. D., Blatchley, A., Yoakum, D., Hamilton, B. A., Mikulski, Z., Jain, M. K., Glass, C. K., & Hedrick, C. C. (2016). Deleting an Nr4a1 Super-Enhancer Subdomain Ablates Ly6C(low) Monocytes while Preserving Macrophage Gene Function. Immunity, 45(5), 975-987.More infoMononuclear phagocytes are a heterogeneous family that occupy all tissues and assume numerous roles to support tissue function and systemic homeostasis. Our ability to dissect the roles of individual subsets is limited by a lack of technologies that ablate gene function within specific mononuclear phagocyte sub-populations. Using Nr4a1-dependent Ly6C(low) monocytes, we present a proof-of-principle approach that addresses these limitations. Combining ChIP-seq and molecular approaches we identified a single, conserved, sub-domain within the Nr4a1 enhancer that was essential for Ly6C(low) monocyte development. Mice lacking this enhancer lacked Ly6C(low) monocytes but retained Nr4a1 gene expression in macrophages during steady state and in response to LPS. Because Nr4a1 regulates inflammatory gene expression and differentiation of Ly6C(low) monocytes, decoupling these processes allows Ly6C(low) monocytes to be studied independently.
- Heinz, S., Romanoski, C. E., Benner, C., & Glass, C. K. (2015). The selection and function of cell type-specific enhancers. Nature reviews. Molecular cell biology, 16(3), 144-54.More infoThe human body contains several hundred cell types, all of which share the same genome. In metazoans, much of the regulatory code that drives cell type-specific gene expression is located in distal elements called enhancers. Although mammalian genomes contain millions of potential enhancers, only a small subset of them is active in a given cell type. Cell type-specific enhancer selection involves the binding of lineage-determining transcription factors that prime enhancers. Signal-dependent transcription factors bind to primed enhancers, which enables these broadly expressed factors to regulate gene expression in a cell type-specific manner. The expression of genes that specify cell type identity and function is associated with densely spaced clusters of active enhancers known as super-enhancers. The functions of enhancers and super-enhancers are influenced by, and affect, higher-order genomic organization.
- Romanoski, C. E. (2015). AP-1 and ETS Family Transcription Factors Co-localize at Enhancers in Human Aortic Endothelial Cells. Arteriosclerosis, Thrombosis, and Vascular Biology.
- Romanoski, C. E. (2015). Differentiation enhanced. Nature.
- Romanoski, C. E. (2015). Environment drives selection and function of enhancers controlling tissue-specific macrophage identities. Cell.
- Romanoski, C. E. (2015). Epigenomics: Roadmap for regulation. Nature.
- Romanoski, C. E. (2015). Exploiting genomics and natural genetic variation to decode macrophage enhancers. Trends in immunology.
- Romanoski, C. E. (2015). Siglec receptors impact mammalian lifespan by modulating oxidative stress. Elife.
- Romanoski, C. E. (2015). The Transcriptional Repressor MafG Regulates Cholesterol Catabolism. Arteriosclerosis, Thrombosis, and Vascular Biology.
- Romanoski, C. E. (2015). The selection and function of cell type-specific enhancers. Nature Reviews Molecular Cell Biology.
- Romanoski, C. E., Glass, C. K., Stunnenberg, H. G., Wilson, L., & Almouzni, G. (2015). Epigenomics: Roadmap for regulation. Nature, 518(7539), 314-6.
- Romanoski, C. E., Link, V. M., Heinz, S., & Glass, C. K. (2015). Exploiting genomics and natural genetic variation to decode macrophage enhancers. Trends in immunology, 36(9), 507-18.More infoThe mammalian genome contains on the order of a million enhancer-like regions that are required to establish the identities and functions of specific cell types. Here, we review recent studies in immune cells that have provided insight into the mechanisms that selectively activate certain enhancers in response to cell lineage and environmental signals. We describe a working model wherein distinct classes of transcription factors define the repertoire of active enhancers in macrophages through collaborative and hierarchical interactions, and discuss important challenges to this model, specifically providing examples from T cells. We conclude by discussing the use of natural genetic variation as a powerful approach for decoding transcription factor combinations that play dominant roles in establishing the enhancer landscapes, and the potential that these insights have for advancing our understanding of the molecular causes of human disease.
- Schwarz, F., Pearce, O. M., Wang, X., Samraj, A. N., Läubli, H., Garcia, J. O., Lin, H., Fu, X., Garcia-Bingman, A., Secrest, P., Romanoski, C. E., Heyser, C., Glass, C. K., Hazen, S. L., Varki, N., Varki, A., & Gagneux, P. (2015). Siglec receptors impact mammalian lifespan by modulating oxidative stress. eLife, 4.More infoAging is a multifactorial process that includes the lifelong accumulation of molecular damage, leading to age-related frailty, disability and disease, and eventually death. In this study, we report evidence of a significant correlation between the number of genes encoding the immunomodulatory CD33-related sialic acid-binding immunoglobulin-like receptors (CD33rSiglecs) and maximum lifespan in mammals. In keeping with this, we show that mice lacking Siglec-E, the main member of the CD33rSiglec family, exhibit reduced survival. Removal of Siglec-E causes the development of exaggerated signs of aging at the molecular, structural, and cognitive level. We found that accelerated aging was related both to an unbalanced ROS metabolism, and to a secondary impairment in detoxification of reactive molecules, ultimately leading to increased damage to cellular DNA, proteins, and lipids. Taken together, our data suggest that CD33rSiglecs co-evolved in mammals to achieve a better management of oxidative stress during inflammation, which in turn reduces molecular damage and extends lifespan.
- de Aguiar Vallim, T. Q., Tarling, E. J., Ahn, H., Hagey, L. R., Romanoski, C. E., Lee, R. G., Graham, M. J., Motohashi, H., Yamamoto, M., & Edwards, P. A. (2015). MAFG is a transcriptional repressor of bile acid synthesis and metabolism. Cell metabolism, 21(2), 298-310.More infoSpecific bile acids are potent signaling molecules that modulate metabolic pathways affecting lipid, glucose and bile acid homeostasis, and the microbiota. Bile acids are synthesized from cholesterol in the liver, and the key enzymes involved in bile acid synthesis (Cyp7a1, Cyp8b1) are regulated transcriptionally by the nuclear receptor FXR. We have identified an FXR-regulated pathway upstream of a transcriptional repressor that controls multiple bile acid metabolism genes. We identify MafG as an FXR target gene and show that hepatic MAFG overexpression represses genes of the bile acid synthetic pathway and modifies the biliary bile acid composition. In contrast, loss-of-function studies using MafG(+/-) mice causes de-repression of the same genes with concordant changes in biliary bile acid levels. Finally, we identify functional MafG response elements in bile acid metabolism genes using ChIP-seq analysis. Our studies identify a molecular mechanism for the complex feedback regulation of bile acid synthesis controlled by FXR.
- Gosselin, D., Link, V. M., Romanoski, C. E., Fonseca, G. J., Eichenfield, D. Z., Spann, N. J., Stender, J. D., Chun, H. B., Garner, H., Geissmann, F., & Glass, C. K. (2014). Environment drives selection and function of enhancers controlling tissue-specific macrophage identities. Cell, 159(6), 1327-40.More infoMacrophages reside in essentially all tissues of the body and play key roles in innate and adaptive immune responses. Distinct populations of tissue macrophages also acquire context-specific functions that are important for normal tissue homeostasis. To investigate mechanisms responsible for tissue-specific functions, we analyzed the transcriptomes and enhancer landscapes of brain microglia and resident macrophages of the peritoneal cavity. In addition, we exploited natural genetic variation as a genome-wide "mutagenesis" strategy to identify DNA recognition motifs for transcription factors that promote common or subset-specific binding of the macrophage lineage-determining factor PU.1. We find that distinct tissue environments drive divergent programs of gene expression by differentially activating a common enhancer repertoire and by inducing the expression of divergent secondary transcription factors that collaborate with PU.1 to establish tissue-specific enhancers. These findings provide insights into molecular mechanisms by which tissue environment influences macrophage phenotypes that are likely to be broadly applicable to other cell types.
- Kaikkonen, M. U., Niskanen, H., Romanoski, C. E., Kansanen, E., Kivelä, A. M., Laitalainen, J., Heinz, S., Benner, C., Glass, C. K., & Ylä-Herttuala, S. (2014). Control of VEGF-A transcriptional programs by pausing and genomic compartmentalization. Nucleic acids research, 42(20), 12570-84.More infoVascular endothelial growth factor A (VEGF-A) is a master regulator of angiogenesis, vascular development and function. In this study we investigated the transcriptional regulation of VEGF-A-responsive genes in primary human aortic endothelial cells (HAECs) and human umbilical vein endothelial cells (HUVECs) using genome-wide global run-on sequencing (GRO-Seq). We demonstrate that half of VEGF-A-regulated gene promoters are characterized by a transcriptionally competent paused RNA polymerase II (Pol II). We show that transition into productive elongation is a major mechanism of gene activation of virtually all VEGF-regulated genes, whereas only ∼40% of the genes are induced at the level of initiation. In addition, we report a comprehensive chromatin interaction map generated in HUVECs using tethered conformation capture (TCC) and characterize chromatin interactions in relation to transcriptional activity. We demonstrate that sites of active transcription are more likely to engage in chromatin looping and cell type-specific transcriptional activity reflects the boundaries of chromatin interactions. Furthermore, we identify large chromatin compartments with a tendency to be coordinately transcribed upon VEGF-A stimulation. We provide evidence that these compartments are enriched for clusters of regulatory regions such as super-enhancers and for disease-associated single nucleotide polymorphisms (SNPs). Collectively, these findings provide new insights into mechanisms behind VEGF-A-regulated transcriptional programs in endothelial cells.
- Romanoski, C. E. (2014). Control of VEGF-A transcriptional programs by pausing and genomic compartmentalization. Nucleic acids research.
- Erbilgin, A., Civelek, M., Romanoski, C. E., Pan, C., Hagopian, R., Berliner, J. A., & Lusis, A. J. (2013). Identification of CAD candidate genes in GWAS loci and their expression in vascular cells. Journal of lipid research, 54(7), 1894-905.More infoRecent genome-wide association studies (GWAS) have identified 35 loci that significantly associate with coronary artery disease (CAD) susceptibility. The majority of the genes represented in these loci have not previously been studied in the context of atherosclerosis. To characterize the roles of these candidate genes in the vessel wall, we determined their expression levels in endothelial, smooth muscle, and macrophage cells isolated from healthy, prelesioned, and lesioned mouse aortas. We also performed expression quantitative locus (eQTL) mapping of these genes in human endothelial cells under control and proatherogenic conditions. Of the 57 genes studied, 31 were differentially expressed in one or more cell types in disease state in mice, and the expression levels of 8 were significantly associated with the CAD SNPs in human cells, 7 of which were also differentially expressed in mice. By integrating human and mouse results, we predict that PPAP2B, GALNT4, MAPKAPK5, TCTN1, SRR, SNF8, and ICAM1 play a causal role in the susceptibility to atherosclerosis through a role in the vasculature. Additionally, we highlight the genetic complexity of a subset of CAD loci through the differential expression of multiple candidate genes per locus and the involvement of genes that lie outside linkage disequilibrium blocks.
- Heinz, S., Romanoski, C. E., Benner, C., Allison, K. A., Kaikkonen, M. U., Orozco, L. D., & Glass, C. K. (2013). Effect of natural genetic variation on enhancer selection and function. Nature, 503(7477), 487-92.More infoThe mechanisms by which genetic variation affects transcription regulation and phenotypes at the nucleotide level are incompletely understood. Here we use natural genetic variation as an in vivo mutagenesis screen to assess the genome-wide effects of sequence variation on lineage-determining and signal-specific transcription factor binding, epigenomics and transcriptional outcomes in primary macrophages from different mouse strains. We find substantial genetic evidence to support the concept that lineage-determining transcription factors define epigenetic and transcriptomic states by selecting enhancer-like regions in the genome in a collaborative fashion and facilitating binding of signal-dependent factors. This hierarchical model of transcription factor function suggests that limited sets of genomic data for lineage-determining transcription factors and informative histone modifications can be used for the prioritization of disease-associated regulatory variants.
- Kaikkonen, M. U., Spann, N. J., Heinz, S., Romanoski, C. E., Allison, K. A., Stender, J. D., Chun, H. B., Tough, D. F., Prinjha, R. K., Benner, C., & Glass, C. K. (2013). Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. Molecular cell, 51(3), 310-25.More infoRecent studies suggest a hierarchical model in which lineage-determining factors act in a collaborative manner to select and prime cell-specific enhancers, thereby enabling signal-dependent transcription factors to bind and function in a cell-type-specific manner. Consistent with this model, TLR4 signaling primarily regulates macrophage gene expression through a pre-existing enhancer landscape. However, TLR4 signaling also induces priming of ∼3,000 enhancer-like regions de novo, enabling visualization of intermediates in enhancer selection and activation. Unexpectedly, we find that enhancer transcription precedes local mono- and dimethylation of histone H3 lysine 4 (H3K4me1/2). H3K4 methylation at de novo enhancers is primarily dependent on the histone methyltransferases Mll1, Mll2/4, and Mll3 and is significantly reduced by inhibition of RNA polymerase II elongation. Collectively, these findings suggest an essential role of enhancer transcription in H3K4me1/2 deposition at de novo enhancers that is independent of potential functions of the resulting eRNA transcripts.
- Maubaret, C. G., Salpea, K. D., Romanoski, C. E., Folkersen, L., Cooper, J. A., Stephanou, C., Li, K. W., Palmen, J., Hamsten, A., Neil, A., Stephens, J. W., Lusis, A. J., Eriksson, P., Talmud, P. J., Humphries, S. E., , S. B., & , E. c. (2013). Association of TERC and OBFC1 haplotypes with mean leukocyte telomere length and risk for coronary heart disease. PloS one, 8(12), e83122.More infoTo replicate the associations of leukocyte telomere length (LTL) with variants at four loci and to investigate their associations with coronary heart disease (CHD) and type II diabetes (T2D), in order to examine possible causal effects of telomere maintenance machinery on disease aetiology.
- Romanoski, C. E. (2013). 25-Hydroxycholesterol activates the integrated stress response to reprogram transcription and translation in macrophages. Journal of Biological Chemistry.
- Romanoski, C. E. (2013). Association of TERC and OBFC1 haplotypes with mean leukocyte telomere length and risk for coronary heart disease. PloS one.
- Romanoski, C. E. (2013). Effect of natural genetic variation on enhancer selection and function. Nature.
- Romanoski, C. E. (2013). Identification of CAD candidate genes in GWAS loci and their expression in vascular cells. Journal of lipid research.
- Romanoski, C. E. (2013). Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. Molecular cell.
- Shibata, N., Carlin, A. F., Spann, N. J., Saijo, K., Morello, C. S., McDonald, J. G., Romanoski, C. E., Maurya, M. R., Kaikkonen, M. U., Lam, M. T., Crotti, A., Reichart, D., Fox, J. N., Quehenberger, O., Raetz, C. R., Sullards, M. C., Murphy, R. C., Merrill, A. H., Brown, H. A., , Dennis, E. A., et al. (2013). 25-Hydroxycholesterol activates the integrated stress response to reprogram transcription and translation in macrophages. The Journal of biological chemistry, 288(50), 35812-23.More info25-Hydroxycholesterol (25OHC) is an enzymatically derived oxidation product of cholesterol that modulates lipid metabolism and immunity. 25OHC is synthesized in response to interferons and exerts broad antiviral activity by as yet poorly characterized mechanisms. To gain further insights into the basis for antiviral activity, we evaluated time-dependent responses of the macrophage lipidome and transcriptome to 25OHC treatment. In addition to altering specific aspects of cholesterol and sphingolipid metabolism, we found that 25OHC activates integrated stress response (ISR) genes and reprograms protein translation. Effects of 25OHC on ISR gene expression were independent of liver X receptors and sterol-response element-binding proteins and instead primarily resulted from activation of the GCN2/eIF2α/ATF4 branch of the ISR pathway. These studies reveal that 25OHC activates the integrated stress response, which may contribute to its antiviral activity.
- Lee, S., Birukov, K. G., Romanoski, C. E., Springstead, J. R., Lusis, A. J., & Berliner, J. A. (2012). Role of phospholipid oxidation products in atherosclerosis. Circulation research, 111(6), 778-99.More infoThere is increasing clinical evidence that phospholipid oxidation products (Ox-PL) play a role in atherosclerosis. This review focuses on the mechanisms by which Ox-PL interact with endothelial cells, monocyte/macrophages, platelets, smooth muscle cells, and HDL to promote atherogenesis. In the past few years major progress has been made in identifying these mechanisms. It has been recognized that Ox-PL promote phenotypic changes in these cell types that have long-term consequences for the vessel wall. Individual Ox-PL responsible for specific cellular effects have been identified. A model of the configuration of bioactive truncated Ox-PL within membranes has been developed that demonstrates that the oxidized fatty acid moiety protrudes into the aqueous phase, rendering it accessible for receptor recognition. Receptors and signaling pathways for individual Ox-PL species are now determined and receptor independent signaling pathways identified. The effects of Ox-PL are mediated both by gene regulation and transcription independent processes. It has now become apparent that Ox-PL affects multiple genes and pathways, some of which are proatherogenic and some are protective. However, at concentrations that are likely present in the vessel wall in atherosclerotic lesions, the effects promote atherogenesis. There have also been new insights on enzymes that metabolize Ox-PL and the significance of these enzymes for atherosclerosis. With the knowledge we now have of the regulation and effects of Ox-PL in different vascular cell types, it should be possible to design experiments to test the role of specific Ox-PL on the development of atherosclerosis.
- Lee, S., Springstead, J. R., Parks, B. W., Romanoski, C. E., Palvolgyi, R., Ho, T., Nguyen, P., Lusis, A. J., & Berliner, J. A. (2012). Metalloproteinase processing of HBEGF is a proximal event in the response of human aortic endothelial cells to oxidized phospholipids. Arteriosclerosis, thrombosis, and vascular biology, 32(5), 1246-54.More infoAtherosclerosis is a chronic inflammatory disease initiated by monocyte recruitment and retention in the vessel wall. An important mediator of monocyte endothelial interaction is the chemokine interleukin (IL)-8. The oxidation products of phospholipids, including oxidized 1-palmitoyl-2-arachidonyl-sn-glycerol-3-phosphocholine (Ox-PAPC), accumulate in atherosclerotic lesions and strongly induce IL-8 in human aortic endothelial cells (HAECs). The goal of this study was to identify the proximal events leading to induction of IL-8 by Ox-PAPC in vascular endothelial cells.
- Romanoski, C. E. (2012). Metalloproteinase processing of HBEGF is a proximal event in the response of human aortic endothelial cells to oxidized phospholipids. Arteriosclerosis, thrombosis, and vascular biology.
- Romanoski, C. E. (2012). Role of phospholipid oxidation products in atherosclerosis. Circulation research.
- Kim, J. B., Xia, Y., Romanoski, C. E., Lee, S., Meng, Y., Shi, Y., Bourquard, N., Gong, K. W., Port, Z., Grijalva, V., Reddy, S. T., Berliner, J. A., Lusis, A. J., & Shih, D. M. (2011). Paraoxonase-2 modulates stress response of endothelial cells to oxidized phospholipids and a bacterial quorum-sensing molecule. Arteriosclerosis, thrombosis, and vascular biology, 31(11), 2624-33.More infoChronic infection has long been postulated as a stimulus for atherogenesis. Pseudomonas aeruginosa infection has been associated with increased atherosclerosis in rats, and these bacteria produce a quorum-sensing molecule 3-oxo-dodecynoyl-homoserine lactone (3OC12-HSL) that is critical for colonization and virulence. Paraoxonase 2 (PON2) hydrolyzes 3OC12-HSL and also protects against the effects of oxidized phospholipids thought to contribute to atherosclerosis. We now report the response of human aortic endothelial cells (HAECs) to 3OC12-HSL and oxidized 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (Ox-PAPC) in relation to PON2 expression.
- Romanoski, C. E. (2011). Network for Activation of Human Endothelial Cells by Oxidized Phospholipids A Critical Role of Heme Oxygenase 1. Circulation research.
- Romanoski, C. E. (2011). Paraoxonase-2 Modulates Stress Response of Endothelial Cells to Oxidized Phospholipids and a Bacterial Quorum--Sensing Molecule. Arteriosclerosis, thrombosis, and vascular biology.
- Romanoski, C. E., Che, N., Yin, F., Mai, N., Pouldar, D., Civelek, M., Pan, C., Lee, S., Vakili, L., Yang, W., Kayne, P., Mungrue, I. N., Araujo, J. A., Berliner, J. A., & Lusis, A. J. (2011). Network for activation of human endothelial cells by oxidized phospholipids: a critical role of heme oxygenase 1. Circulation research, 109(5), e27-41.More infoOxidized palmitoyl arachidonyl phosphatidylcholine (Ox-PAPC) accumulates in atherosclerotic lesions, is proatherogenic, and influences the expression of more than 1000 genes in endothelial cells.
- Romanoski, C. E. (2010). Systems genetics analysis of gene-by-environment interactions in human cells. The American Journal of Human Genetics.
- Romanoski, C. E., Lee, S., Kim, M. J., Ingram-Drake, L., Plaisier, C. L., Yordanova, R., Tilford, C., Guan, B., He, A., Gargalovic, P. S., Kirchgessner, T. G., Berliner, J. A., & Lusis, A. J. (2010). Systems genetics analysis of gene-by-environment interactions in human cells. American journal of human genetics, 86(3), 399-410.More infoGene by environment (GxE) interactions are clearly important in many human diseases, but they have proven to be difficult to study on a molecular level. We report genetic analysis of thousands of transcript abundance traits in human primary endothelial cell (EC) lines in response to proinflammatory oxidized phospholipids implicated in cardiovascular disease. Of the 59 most regulated transcripts, approximately one-third showed evidence of GxE interactions. The interactions resulted primarily from effects of distal-, trans-acting loci, but a striking example of a local-GxE interaction was also observed for FGD6. Some of the distal interactions were validated by siRNA knockdown experiments, including a locus involved in the regulation of multiple transcripts involved in the ER stress pathway. Our findings add to the understanding of the overall architecture of complex human traits and are consistent with the possibility that GxE interactions are responsible, in part, for the failure of association studies to more fully explain common disease variation.
- Park, M. S., Romanoski, C. E., & Pryor, B. M. (2008). A re-examination of the phylogenetic relationship between the causal agents of carrot black rot, Alternaria radicina and A. carotiincultae. Mycologia, 100(3), 511-27.More infoThe phylogenetic relationship between Alternaria radicina and A. carotiincultae was reexamined based on morphology, sequence analysis of rDNA (ITS and mitochondrial small subunit [mtSSU]), protein coding genes (actin [ACT], beta-tubulin, chitin synthase [CHS], translation elongation factor [EF-1a], Alternaria allergen a1 [Alt a1], and glyceraldehyde-3-phosphate dehydrogenase [gpd]), and RAPD and ISSR analysis of total genomic DNA. Although some morphological characters overlapped to a degree, with A. radicina isolates expressing moderate variation and A. carotiincultae isolates being highly uniform, A. carotiincultae could be differentiated from A. radicina based on significantly greater growth rate on potato dextrose agar (PDA) or acidified PDA (APDA) and average number of transverse septa per conidium. Sequence of rDNA and two protein coding genes, ACT and CHS, were invariant between species. However polymorphism with the EF-1a, beta-tubulin, and Alt a1 gene strictly separated the population of A. radicina and A. carotiincultae as distinct lineages, as did RAPD and ISSR analysis. The polymorphic gpd gene did not strictly separate the two species. However isolates of A. radicina encompassed several haplotypes, one of which was the exclusive haplotype possessed by A. carotiincultae isolates, suggesting evidence of incomplete lineage sorting. The results suggest that A. carotiincultae is closely related to A. radicina but is a recently divergent and distinct lineage, which supports its status as a separate species.
- Bennett, B. J., Romanoski, C. E., & Lusis, A. J. (2007). Network-centered view of coronary artery disease. Expert review of cardiovascular therapy, 5(6), 1095-103.More infoSystems biology is an emerging field that attempts to examine multiple elements of a biologic system using techniques such as expression microarrays or proteomics. The goal of systems biology is to detect all the elements of a system and create an interaction network between these so that the system can be explained under specified conditions. In this review we discuss how systems-based approaches are being applied to cardiovascular disease, illustrating concepts, such as the integration of orthogonal datasets, coexpression networks and emergent properties.
- Romanoski, C. E. (2007). Network-centered view of coronary artery disease. Expert review of cardiovascular therapy.
- Romanoski, C. E. (2013). 'Enhancer Therapy': emerging strategy targeting cell-specific enhancer RNAs. In HUMAN GENE THERAPY.
- Romanoski, C. E. (2013). Examination of the roles of cholesterol depletion and thiol interactions in gene regulation by Ox-PAPC in endothelial cells using systems approaches. In ANGIOGENESIS.
- Romanoski, C. E. (2013). Systems genetics analyses of human aortic endothelial cell transcript expression predict causal genes associated with complex disorders of the vascular wall. In ANGIOGENESIS.
- Romanoski, C. E. (2010). What Molecules Regulate the Response to Oxidized Phospholipids?. In ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY.
- Romanoski, C. E. (2018, March). Identification of Transcriptional Networks for Vascular Disease. University of Virginia Cardiovascular Research Center Seminar Series. Charlottesville, VA.
- Romanoski, C. E. (2018, March). Systems genetics of human aortic endothelial cells. Cleveland Clinic Annual Page Lecture Series. Cleveland, OH *note: cancelled at last minute due to 'Nor'easter' weather*.
- Hartiala, J. A., Han, Y., Jia, Q., Huang, P., Woodward, N. C., Gukasyan, H., Kurt, Z., Stolze, L. K., Tregouet, D., Smith, N. L., Seldin, M., Mehrabian, M., Lusis, A. J., Wilson, W. H., Hazen, S. L., Yang, X., Romanoski, C. E., & Allayee, H. (2018, October). Genome-Wide Association Studies in >500,000 Individuals Identify Novel Loci for Coronary Artery Disease and Myocardial Infarction. American Society of Human Genetics Annual Conference. San Diego, CA: American Society of Human Genetics.
- Selvarajan, I., Ravindran, A., Polonen, P., Toropainen, A., Laakso, M., Heinaniemi, M., Romanoski, C. E., Civelek, M., & Kaikkonen, M. U. (2018, October). CAD susceptibility enhancers: From association to mechanism. American Society of Human Genetics Annual Conference. San Diego, CA: American Society of Human Genetics.
- Stolze, L. K., Whalen, M. B., Hadeli, N. K., Eshghi, A., Conklin, A., Victor, R., & Romanoski, C. E. (2018, October). Using endothelial cell molecular QTLs to dissect coronary artery disease risk. American Society of Human Genetics Annual Conference. San Diego, CA: American Society of Human Genetics.
- Romanoski, C. E. (2018, February). MARGE: Mutation Analysis for Regulatory Genomic Elements. https://doi.org/10.1101/268839