After the completion of the Human Genome Project, one thing became abundantly clear to scientists: that they had only begun to scratch the surface of how genetic information was processed within cells. In the years since, advances in sequencing techniques have allowed scientists to uncover the underlying regulatory mechanisms that take place from gene expression to protein metabolite end products—the regulome, as it is often referred, encompasses all of these processes.
Now, researchers from Stanford University have turned their attention to the regulome of the immune system and utilized a newly developed sequencing technique to study how immune genes are toggled on and off and how they are fundamentally different between men and women. Their results revealed some intriguing surprises and may offer new insight into autoimmune disorders.
"Part of why this is possible is a new technology that was invented at Stanford for measuring the accessibility of the genome to regulatory elements," explained the study's senior author Howard Chang, M.D., Ph.D., professor of dermatology at Stanford University.
The findings from this study were published recently in Cell Systems through an article entitled “Individuality and Variation of Personal Regulomes in Primary Human T Cells.”
Interestingly, the Stanford investigators found that some genes are virtually always on while others seemingly sit unused for quite some time. Moreover, they discovered that the genes which switch on and off differently from person to person are more likely to be associated with autoimmune diseases and that men and women use different regulatory elements to turn on many of the immune system genes. These findings led the team to hypothesize that the difference in activity may explain the much greater incidence of autoimmune diseases such as lupus, scleroderma, and rheumatoid arthritis among women.
"We were interested in exploring the landscape of gene regulation directly from live people and look at differences," said Dr. Chang. "We asked, 'How different or similar are people?' This is different from asking if they have the same genes. I would say the majority of the difference is likely from a nongenetic source.”
Dr. Chang continued, stating "but the single greatest predictor for genes' tendency to turn on and off was the sex of the person. In terms of significance, sex was far more important than all the other things we looked at, perhaps even combined."
The Stanford scientists took advantage of a new sequencing technique that Dr. Change helped developed, publishing the initial paper describing the methodology in January, which maps genome-wide chromatin accessibility and was aptly named Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq). This method allowed the researchers to sample living cells in real time in order to follow their regulatory patterns.
"In the past, people needed a huge number of cells to do this kind of measurement. You'd actually need a pound of flesh to get certain rare cell types,” stated Dr. Chang. “So you can't get that out of a live person—and certainly not more than once, right?"
"But now," continued Dr. Chang, "you are studying copies of copies; you aren't studying the original cells anymore. Those months of being grown in the lab completely changes how the cells are behaving and so you are no longer looking at the personal. How the laboratory cells behave has nothing to do with what the person just ate, whether they had a fight with their girlfriend or whether they had an infection."
The study looked at T cells from 12 healthy volunteers, measuring the genetic regulatory switches within the immune system of each. Across the 12 healthy volunteers, 7% of the genes were switched on in different patterns from person to person. For each person, these patterns persisted over time, like a unique fingerprint. When the team measured gene activity levels from 30 of the top 500 genes the researchers expected would show gender-influenced activity, they found that 20 of the 30 genes showed significant differential activity between men and women.
Dr. Chang and his colleagues hope that their data will help provide the baseline for future studies that look to determine gene regulatory differences among patients affected with autoimmune diseases.