Systemic lupus erythematosus (SLE) is a chronic systemic autoimmune disease. African American women are disproportionately affected and the etiology is believed to be a combination of genetic and environmental factors. The natural history typically includes diverse organ system involvement and a chronic course punctuated by flares. Multiple studies have demonstrated that monocyte function is aberrant in SLE and this is significant because monocytes can persist in tissues as differentiated macrophages and mold adaptive responses, thus producing a cascade of effects as a consequence of their aberrant function. Macrophages form the initial lesion in atheromatous disease, associated with the major cause of death in SLE and macrophage infiltration into the kidney is specifically associated with increased morbidity and mortality. These form the rationale for the study of SLE monocytes. We specifically hypothesize that the SLE disease process drives an altered epigenome in monocytes and this contributes to disease perpetuation and end organ manifestations. An altered potential for expression could lead to aberrant monocyte migration or inflammatory mediator expression. Pathologic responses to common innocuous stimuli, such as viruses could ensue as a result of an altered epigenome. This proposal will examine the epigenetic landscape of SLE monocytes and begin to identify pathways that are associated with altered histone modifications. Two opposing histone marks will be examined by ChIP-Seq, H3K4me2 and H3K27me3. We have preliminary data demonstrating altered H4 acetylation in SLE patient monocytes compared to controls. Network analysis of the gene set with altered histone modifications demonstrated nodes of biological relevance, including known inflammatory pathways. A second epigenetic feature, non-coding RNAs, will be examined on an exploratory basis. Preliminary data demonstrate tissue-specific antisense RNA upstream of the TNF1 gene which is associated with binding of a transcriptional repressor. Long mRNA-like non-coding RNAs will be examined and a novel ChIP-Seq approach, using S9.6, used to explore the structure of the potential regulatory RNAs. The S9.6 antibody will be used to identify DNA:RNA hybrid structures and this will be used to filter the non-coding RNAs identified bioinformatically. One of the major goals of this application is to begin to transition to a mechanistic examination of the alterations to the epigenome. We hypothesize that the disease itself drives most of the alterations to the epigenome, however, an existing SNP database on the same SLE cohort will be used to examine potential SNP associations with altered histone modifications. SNP analysis on RNA-Seq and ChIP- Seq data will allow allele-specific quantitation on controls, as a foundation for the SLE samples. This proposal will examine the epigenome in SLE and begin to examine potential causes and consequences. Collectively, these approaches will further our understanding of SLE and may develop a new paradigm for the understanding of the chronicity of autoimmune disease in general.

Public Health Relevance

This application seeks to understand how white cells, monocytes, develop new functions as a result of disease effects in systemic lupus erythematosus (SLE). This project will define changes in the status of the genome as a result of SLE and characterize the physiologic processes that led to the changes. These studies have broad implications for how our immune system could be molded by prior experiences and could lead to novel therapies for SLE.

Agency
National Institute of Health (NIH)
Institute
National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)
Type
Research Project (R01)
Project #
5R01AR058547-04
Application #
8318805
Study Section
Special Emphasis Panel (ZRG1-GGG-M (53))
Program Officer
Wang, Yan Z
Project Start
2009-09-18
Project End
2014-08-31
Budget Start
2012-09-01
Budget End
2013-08-31
Support Year
4
Fiscal Year
2012
Total Cost
$363,760
Indirect Cost
$122,116
Name
Children's Hospital of Philadelphia
Department
Type
DUNS #
073757627
City
Philadelphia
State
PA
Country
United States
Zip Code
19104
Zhang, Zhe; Shi, Lihua; Song, Li et al. (2015) Interferon regulatory factor 1 marks activated genes and can induce target gene expression in systemic lupus erythematosus. Arthritis Rheumatol 67:785-96
Shi, Lihua; Song, Li; Fitzgerald, Michael et al. (2014) Noncoding RNAs and LRRFIP1 regulate TNF expression. J Immunol 192:3057-67
Shi, Lihua; Zhang, Zhe; Yu, Angela M et al. (2014) The SLE transcriptome exhibits evidence of chronic endotoxin exposure and has widespread dysregulation of non-coding and coding RNAs. PLoS One 9:e93846
Shi, Lihua; Perin, Juan C; Leipzig, Jeremy et al. (2011) Genome-wide analysis of interferon regulatory factor I binding in primary human monocytes. Gene 487:21-8