Casey E. Romanoski, PhD

Associate Professor, Cellular and Molecular Medicine
Associate Professor, Clinical Translational Sciences
Associate Professor, Genetics GIDP
Associate Professor, BIO5 Institute
Research Interests: 

The overarching goal of my research program is to better understand the interaction between DNA variation and gene regulation. I study this interaction in settings of inflammation with application to complex diseases like atherosclerosis and hypertension. My research is predominantly focused on endothelial cells, which line blood vessels and are mediators of inflammation in the vessel wall. Using next-generation sequencing technologies, and a combination of experimental and computational approaches, we study how endothelial cells achieve context-appropriate expression patterns in healthy and inflammatory settings. By leveraging the interconnected relationship between DNA sequence, epigenetics, gene expression, and disease loci from genome-wide association studies, we aim to identify and interpret complex disease mechanisms.

Molecular Medicine Grad Program: 
Yes

Bibliography

2024

Adelus, M. L., J. Ding, B. T. Tran, A. C. Conklin, A. K. Golebiewski, L. K. Stolze, M. B. Whalen, D. A. Cusanovich, and C. E. Romanoski, "Single cell 'omic profiles of human aortic endothelial cells and human atherosclerotic lesions reveals heterogeneity of endothelial subtype and response to activating perturbations.", bioRxiv, 2024 Jan 17. PMCID: PMC10104082  PMID: 37066416

2022

Shen, Z., R. Z. Li, T. A. Prohaska, M. A. Hoeksema, N. J. Spann, J. Tao, G. J. Fonseca, T. Le, L. K. Stolze, M. Sakai, et al., "Systematic analysis of naturally occurring insertions and deletions that alter transcription factor spacing identifies tolerant and sensitive transcription factor pairs.", Elife, vol. 11, 2022 Jan 20. PMID: 35049498
Toropainen, A., L. K. Stolze, T. Örd, M. B. Whalen, P. Martí Torrell, V. M. Link, M. U. Kaikkonen, and C. E. Romanoski, "Functional noncoding SNPs in human endothelial cells fine-map vascular trait associations.", Genome Res, vol. 32, issue 3, pp. 409-424, 2022 03. PMCID: PMC8896458  PMID: 35193936

2021

Watson, A. W., A. D. Grant, S. S. Parker, S. Hill, M. B. Whalen, J. Chakrabarti, M. W. Harman, M. R. Roman, B. L. Forte, C. C. Gowan, et al., "Breast tumor stiffness instructs bone metastasis via maintenance of mechanical conditioning.", Cell Rep, vol. 35, issue 13, pp. 109293, 2021 Jun 29. PMID: 34192535
Selvarajan, I., A. Toropainen, K. M. Garske, M. López Rodríguez, A. Ko, Z. Miao, D. Kaminska, K. Õunap, T. Örd, A. Ravindran, et al., "Integrative analysis of liver-specific non-coding regulatory SNPs associated with the risk of coronary artery disease.", Am J Hum Genet, vol. 108, issue 3, pp. 411-430, 2021 03 04. PMCID: PMC8008493  PMID: 33626337
Conklin, A. C., H. Nishi, F. Schlamp, T. Örd, K. Õunap, M. U. Kaikkonen, E. A. Fisher, and C. E. Romanoski, "Meta-Analysis of Smooth Muscle Lineage Transcriptomes in Atherosclerosis and Their Relationships to In Vitro Models.", Immunometabolism, vol. 3, issue 3, 2021. PMCID: PMC8232871  PMID: 34178388
Hartiala, J. A., Y. Han, Q. Jia, J. R. Hilser, P. Huang, J. Gukasyan, W. S. Schwartzman, Z. Cai, S. Biswas, D-A. Trégouët, et al., "Genome-wide analysis identifies novel susceptibility loci for myocardial infarction.", Eur Heart J, vol. 42, issue 9, pp. 919-933, 2021 Mar 01. PMCID: PMC7936531  PMID: 33532862
Krishnan, K. Chella, L. Vergnes, R. Acín-Pérez, L. Stiles, M. Shum, L. Ma, E. Mouisel, C. Pan, T. M. Moore, M. Péterfy, et al., "Sex-specific genetic regulation of adipose mitochondria and metabolic syndrome by Ndufv2.", Nat Metab, 2021 Oct 25. PMID: 34697471
Örd, T., K. Õunap, L. Stolze, R. Aherrahrou, V. Nurminen, I. Selvarajan, A. Toropainen, T. Lönnberg, E. Aavik, S. Ylä-Herttuala, et al., "Single-Cell Epigenomics and Functional Fine-Mapping of Atherosclerosis GWAS Loci.", Circ Res, 2021 May 24. PMID: 34024118

2020

Johnson, M. D., U. S. Younis, S. V. Menghani, K. J. Addison, M. Whalen, A. L. Pilon, A. E. Cress, F. Polverino, C. Romanoski, M. Kraft, et al., "CC16 Binding to α4β1 Integrin (VLA-4) Protects Against Infection.", Am J Respir Crit Care Med, 2020 Dec 16. PMID: 33326355
Romanoski, C. E., X. Qi, S. Sangam, R. R. Vanderpool, R. S. Stearman, A. Conklin, M. Gonzalez-Garay, F. Rischard, R. J. Ayon, J. Wang, et al., "Transcriptomic profiles in pulmonary arterial hypertension associate with disease severity and identify novel candidate genes.", Pulm Circ, vol. 10, issue 4, pp. 2045894020968531, 2020 Oct-Dec. PMCID: PMC7727059  PMID: 33343881
Sajti, E., V. M. Link, Z. Ouyang, N. J. Spann, E. Westin, C. E. Romanoski, G. J. Fonseca, L. S. Prince, and C. K. Glass, "Transcriptomic and epigenetic mechanisms underlying myeloid diversity in the lung.", Nat Immunol, vol. 21, issue 2, pp. 221-231, 2020 02. PMCID: PMC7667722  PMID: 31959980
Stolze, L. K., A. C. Conklin, M. B. Whalen, M. López Rodríguez, K. Õunap, I. Selvarajan, A. Toropainen, T. Örd, J. Li, A. Eshghi, et al., "Systems Genetics in Human Endothelial Cells Identifies Non-coding Variants Modifying Enhancers, Expression, and Complex Disease Traits.", Am J Hum Genet, 2020 May 16. PMID: 32442411
Chang, E. H., A. L. Willis, C. E. Romanoski, D. A. Cusanovich, N. Pouladi, J. Li, Y. A. Lussier, and F. D. Martinez, "RV Infections in Asthmatics Increase ACE2 Expression and Cytokine Pathways Implicated in COVID-19.", Am J Respir Crit Care Med, 2020 Jul 10. PMID: 32649217
Merritt, E. F., H. J. Johnson, Z. Sheen Wong, A. S. Buntzman, A. C. Conklin, C. M. Cabral, C. E. Romanoski, J. P. Boyle, and A. A. Koshy, "Transcriptional Profiling Suggests T Cells Cluster around Neurons Injected with Toxoplasma gondii Proteins.", mSphere, vol. 5, issue 5, 2020 09 02. PMCID: PMC7471001  PMID: 32878927

2019

Allan, C. M., P. J. Heizer, Y. Tu, N. P. Sandoval, R. S. Jung, J. E. Morales, E. Sajti, T. D. Troutman, T. L. Saunders, D. A. Cusanovich, et al., "An upstream enhancer regulates expression in a tissue-specific manner.", J Lipid Res, vol. 60, issue 4, pp. 869-879, 2019 04 01. PMCID: PMC6446700  PMID: 30598475

2018

Krause, M. D., R-T. Huang, D. Wu, T-P. Shentu, D. L. Harrison, M. B. Whalen, L. K. Stolze, A. Di Rienzo, I. P. Moskowitz, M. Civelek, et al., "Genetic variant at coronary artery disease and ischemic stroke locus 1p32.2 regulates endothelial responses to hemodynamics.", Proc Natl Acad Sci U S A, vol. 115, issue 48, pp. E11349-E11358, 2018 11 27. PMCID: PMC6275533  PMID: 30429326
Hitzel, J., E. Lee, Y. Zhang, S. Iris Bibli, X. Li, S. Zukunft, B. Pflüger, J. Hu, C. Schürmann, A. Estefania Vasconez, et al., "Oxidized phospholipids regulate amino acid metabolism through MTHFD2 to facilitate nucleotide release in endothelial cells.", Nat Commun, vol. 9, issue 1, pp. 2292, 2018 06 12. PMCID: PMC5997752  PMID: 29895827
Link, V. M., C. E. Romanoski, D. Metzler, and C. K. Glass, "MMARGE: Motif Mutation Analysis for Regulatory Genomic Elements.", Nucleic Acids Res, vol. 46, issue 14, pp. 7006-7021, 2018 08 21. PMCID: PMC6101580  PMID: 29893919
Link, V. M., S. H. Duttke, H. B. Chun, I. R. Holtman, E. Westin, M. A. Hoeksema, Y. Abe, D. Skola, C. E. Romanoski, J. Tao, et al., "Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function.", Cell, vol. 173, issue 7, pp. 1796-1809.e17, 2018 06 14. PMCID: PMC6003872  PMID: 29779944

2017

Hogan, N. T., M. B. Whalen, L. K. Stolze, N. K. Hadeli, M. T. Lam, J. R. Springstead, C. K. Glass, and C. E. Romanoski, "Transcriptional networks specifying homeostatic and inflammatory programs of gene expression in human aortic endothelial cells.", Elife, vol. 6, 2017 Jun 06. PMCID: PMC5461113  PMID: 28585919

2016

Thomas, G. D., R. N. Hanna, N. T. Vasudevan, A. A. Hamers, C. E. Romanoski, S. McArdle, K. D. Ross, A. Blatchley, D. Yoakum, B. A. Hamilton, et al., "Deleting an Nr4a1 Super-Enhancer Subdomain Ablates Ly6C(low) Monocytes while Preserving Macrophage Gene Function.", Immunity, vol. 45, issue 5, pp. 975-987, 2016 Nov 15. PMID: 27814941

2015

Romanoski, C. E., V. M. Link, S. Heinz, and C. K. Glass, "Exploiting genomics and natural genetic variation to decode macrophage enhancers.", Trends Immunol, vol. 36, issue 9, pp. 507-18, 2015 Sep. PMCID: PMC4548828  PMID: 26298065
Schwarz, F., O. M. T. Pearce, X. Wang, A. N. Samraj, H. Läubli, J. O. Garcia, H. Lin, X. Fu, A. Garcia-Bingman, P. Secrest, et al., "Siglec receptors impact mammalian lifespan by modulating oxidative stress.", Elife, vol. 4, 2015 Apr 07. PMCID: PMC4384638  PMID: 25846707
Romanoski, C. E., C. K. Glass, H. G. Stunnenberg, L. Wilson, and G. Almouzni, "Epigenomics: Roadmap for regulation.", Nature, vol. 518, issue 7539, pp. 314-6, 2015 Feb 19. PMID: 25693562
Vallim, T. Q. de Aguia, E. J. Tarling, H. Ahn, L. R. Hagey, C. E. Romanoski, R. G. Lee, M. J. Graham, H. Motohashi, M. Yamamoto, and P. A. Edwards, "MAFG is a transcriptional repressor of bile acid synthesis and metabolism.", Cell Metab, vol. 21, issue 2, pp. 298-310, 2015 Feb 03. PMCID: PMC4317590  PMID: 25651182
Heinz, S., C. E. Romanoski, C. Benner, and C. K. Glass, "The selection and function of cell type-specific enhancers.", Nat Rev Mol Cell Biol, vol. 16, issue 3, pp. 144-54, 2015 Mar. PMCID: PMC4517609  PMID: 25650801

2014

Gosselin, D. *, V. M. * Link, C. E. * Romanoski, G. J. Fonseca, D. Z. Eichenfield, N. J. Spann, J. D. Stender, H. B. Chun, H. Garner, F. Geissmann, et al., "Environment drives selection and function of enhancers controlling tissue-specific macrophage identities.", Cell, vol. 159, issue 6, pp. 1327-40, 2014 Dec 4. PMCID: PMC4364385  PMID: 25480297
Kaikkonen, M. U., H. Niskanen, C. E. Romanoski, E. Kansanen, A. M. Kivelä, J. Laitalainen, S. Heinz, C. Benner, C. K. Glass, and S. Ylä-Herttuala, "Control of VEGF-A transcriptional programs by pausing and genomic compartmentalization.", Nucleic Acids Res, vol. 42, issue 20, pp. 12570-84, 2014 Nov 10. PMCID: PMC4227755  PMID: 25352550

2013

Kaikkonen, M. U., N. J. Spann, S. Heinz, C. E. Romanoski, K. A. Allison, J. D. Stender, H. B. Chun, D. F. Tough, R. K. Prinjha, C. Benner, et al., "Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription.", Mol Cell, vol. 51, issue 3, pp. 310-25, 2013 Aug 08. PMCID: PMC3779836  PMID: 23932714
Erbilgin, A., M. Civelek, C. E. Romanoski, C. Pan, R. Hagopian, J. A. Berliner, and A. J. Lusis, "Identification of CAD candidate genes in GWAS loci and their expression in vascular cells.", J Lipid Res, vol. 54, issue 7, pp. 1894-905, 2013 Jul. PMCID: PMC3679391  PMID: 23667179
Maubaret, C. G., K. D. Salpea, C. E. Romanoski, L. Folkersen, J. A. Cooper, C. Stephanou, K. Wah Li, J. Palmen, A. Hamsten, A. Neil, et al., "Association of TERC and OBFC1 haplotypes with mean leukocyte telomere length and risk for coronary heart disease.", PLoS One, vol. 8, issue 12, pp. e83122, 2013. PMCID: PMC3861448  PMID: 24349443
Shibata, N., A. F. Carlin, N. J. Spann, K. Saijo, C. S. Morello, J. G. McDonald, C. E. Romanoski, M. R. Maurya, M. U. Kaikkonen, M. T. Lam, et al., "25-Hydroxycholesterol activates the integrated stress response to reprogram transcription and translation in macrophages.", J Biol Chem, vol. 288, issue 50, pp. 35812-23, 2013 Dec 13. PMCID: PMC3861632  PMID: 24189069
Heinz, S. *, C. E. * Romanoski, C. Benner, K. A. Allison, M. U. Kaikkonen, L. D. Orozco, and C. K. Glass, "Effect of natural genetic variation on enhancer selection and function.", Nature, vol. 503, issue 7477, pp. 487-92, 2013 Nov 28. PMCID: PMC3994126  PMID: 24121437

2012

Lee, S., K. G. Birukov, C. E. Romanoski, J. R. Springstead, A. J. Lusis, and J. A. Berliner, "Role of phospholipid oxidation products in atherosclerosis.", Circ Res, vol. 111, issue 6, pp. 778-99, 2012 Aug 31. PMCID: PMC3563283  PMID: 22935534
Lee, S., J. R. Springstead, B. W. Parks, C. E. Romanoski, R. Palvolgyi, T. Ho, P. Nguyen, A. J. Lusis, and J. A. Berliner, "Metalloproteinase processing of HBEGF is a proximal event in the response of human aortic endothelial cells to oxidized phospholipids.", Arterioscler Thromb Vasc Biol, vol. 32, issue 5, pp. 1246-54, 2012 May. PMCID: PMC3357069  PMID: 22402363

2011

Kim, J. Brian, Y-R. Xia, C. E. Romanoski, S. Lee, YH. Meng, Y-S. Shi, N. Bourquard, K. Wei Gong, Z. Port, V. Grijalva, et al., "Paraoxonase-2 modulates stress response of endothelial cells to oxidized phospholipids and a bacterial quorum-sensing molecule.", Arterioscler Thromb Vasc Biol, vol. 31, issue 11, pp. 2624-33, 2011 Nov. PMCID: PMC3244174  PMID: 21836061
Romanoski, C. E., N. Che, F. Yin, N. Mai, D. Pouldar, M. Civelek, C. Pan, S. Lee, L. Vakili, W-P. Yang, et al., "Network for activation of human endothelial cells by oxidized phospholipids: a critical role of heme oxygenase 1.", Circ Res, vol. 109, issue 5, pp. e27-41, 2011 Aug 19. PMCID: PMC3163234  PMID: 21737788

2010

Romanoski, C. E., S. Lee, M. J. Kim, L. Ingram-Drake, C. L. Plaisier, R. Yordanova, C. Tilford, B. Guan, A. He, P. S. Gargalovic, et al., "Systems genetics analysis of gene-by-environment interactions in human cells.", Am J Hum Genet, vol. 86, issue 3, pp. 399-410, 2010 Mar 12. PMCID: PMC2833388  PMID: 20170901

2008

Park, M. Soo, C. E. Romanoski, and B. M. Pryor, "A re-examination of the phylogenetic relationship between the causal agents of carrot black rot, Alternaria radicina and A. carotiincultae.", Mycologia, vol. 100, issue 3, pp. 511-27, 2008 May-Jun. PMID: 18751557

2007

Bennett, B. J., C. E. Romanoski, and A. J. Lusis, "Network-centered view of coronary artery disease.", Expert Rev Cardiovasc Ther, vol. 5, issue 6, pp. 1095-103, 2007 Nov. PMID: 18035925