“If you sequence and detail this LD block area, you’ll find variations that are nonfunctional, some that are potentially functional, and some that are potentially causal. Multiple SNPs that impact a gene and possibly, a separate gene, by doing this, generate an endophenotype or multiple endophenotypes that mediate an increase in disease risk,” said Dr. Wakeland. “If we look at these haplotypes rather than individual SNPs, we find an increase in disease associations. So these haplotypes that we identify through sequencing actually represent a risk allele. It is not necessarily a single variant, but a segment of the genome that is segregating within our population as a unit. In some cases, multiple variations within that region may impact phenotypes, or multiple phenotypes are mediated by changes in regulation. The most effective approach to try to understand genetics of this complicated disease is to begin to look at risk alleles as being a haplotype.”
Researchers are now identifying alleles associated with both lupus risk and disease protection at many loci, “so we need to think also about alternative alleles that may have many differences with the risk allele, and may be expressed at a lower level, that may have an impact and even be protective of the disease. Those particular haplotypes are more common in controls than are the risk haplotypes,” said Dr. Wakeland. Risk characteristics of heterozygotes are not yet understood.
Researchers are also studying genomic characteristics of systemic autoimmunity by looking at benign autoimmunity in healthy populations, said Dr. Wakeland.
“Anti-nuclear antibody (ANA) is a common strategy to identify systemic autoimmunity, but is actually a common phenotype. About 25% of normal population will be ANA positive. And about 8% of normal population will have a very high ANA titer—indistinguishable from what we see in many SLE patients,” he said. Newly diagnosed SLE patients who have not started any therapy are almost always ANA positive. But why do so many healthy individuals also have high ANA levels?
“This may not simply be a production of autoantibody against one particular antigen. Rather, it may be a broad spectrum of autoantibody production against many different antigens,” he said. Genetics and genome-wide association study data are helping researchers map the impact of genes related to ANA positivity in both healthy and SLE populations. While SLE patients make a lot of antibody, healthy individuals do as well, usually IgG, but not nearly at the same levels of seen in lupus patients, he said. Comparative heat maps used in these studies show much lower distribution of antigens in healthy individuals than those with SLE. “Typically, most are non-nuclear antigens. If you look at chromatin or any self-antigens—and look across the map from those who are healthy but ANA positive to those with preclinical or incomplete lupus to those with lupus—there is a transition into a lot of nuclear antigens. Chromatin levels among lupus patients are much stronger than you would see in a healthy individual.”