Black Death Selected for Immune-Related Genes, Affecting Disease Susceptibility Today

The Black Death was the single greatest mortality event in recorded history. Caused by the bacterium Yersinia pestis, the bubonic plague pandemic swept through North Africa, Europe, and Asia nearly 700 years ago, wiping out up to 30-60% of the population. Newly reported research now suggests that the pandemic placed a a significant selective pressure on the human population, changing the frequency of certain immune-related genetic variants and affecting our susceptibility to disease today.

Scientists headed by teams at the University of Chicago (UChicago), McMaster University, and the Institut Pasteur, analyzed centuries-old DNA from victims and survivors of the bubonic plague, and identified key genetic differences that determined who lived and who died, and how those aspects of our immune systems have continued to evolve since that time. The results indicated that the same genes that once conferred protection against the infection are today associated with an increased susceptibility to autoimmune diseases such as Crohn’s and rheumatoid arthritis.

“This is, to my knowledge, the first demonstration that indeed, the Black Death was an important selective pressure to the evolution of the human immune system,” said Luis Barreiro, PhD, Professor of Genetic Medicine at UChicago and co-senior author of the team’s published paper in Nature. “There is a lot of talk about how pathogens have shaped human evolution, so being able to formally demonstrate which pathways and genes have been targeted really helps us understand what allowed humans to adapt and exist today. This tells us about the mechanisms that allowed us to survive throughout history and why we’re still here today.”

The findings are the result of seven years of work by first authors, graduate student Jennifer Klunk, formerly of McMaster’s Ancient DNA Centre, and postdoctoral fellow Tauras Vigylas, PhD, and are reported in a paper titled, “Evolution of immune genes is associated with the Black Death.”  In their paper the authors say the studies provide “empirical evidence for the role played by past pandemics in shaping present-day susceptibility to disease.”

Infectious diseases have presented one of the strongest selective pressures in the evolution of humans and other animals, the authors wrote. “Not surprisingly, many candidates for population-specific positive selection in humans involve immune response genes, consistent with the hypothesis that exposure to new and/or re-emerging pathogens has driven adaptation. Clarifying the dynamics that have shaped the human immune system is key to understanding how historical diseases contributed to disease susceptibility today.”

The Black Death killed up to 50% of the Europeans, who likely represented “immunologically naïve populations with little or no prior adaptation to Y. pestis,” the authors continued. “The high mortality rate suggests that genetic variants that conferred protection against Y. pestis infection might have been under strong selection during this time.”

For their research Barreiro and colleagues aimed to identify genetic signatures of natural selection imposed by the plague. To do this they searched for signs of genetic adaptation related to the plague, and focused on a 100-year window before, during and after the Black Death, which reached London in the mid-1300s. “This was a very direct way to evaluate the impact that a single pathogen had on human evolution,” said  Barreiro. “People have speculated for a long time that the Black Death might be a strong cause of selection, but it’s hard to demonstrate that when looking at modern populations, because humans had to face many other selective pressures between then and now. The only way to address the question is to narrow the time window we’re looking at.”

For their study the scientists extracted and screened more than 500 DNA samples from the remains of individuals who had died before the plague, died from it or survived the Black Death in London, including individuals buried in the East Smithfield plague pits used for mass burials in 1348-9.  Additional samples were taken from remains buried in five other locations across Denmark. “To identify loci that may have been under selection during the Black Death, we characterized genetic variation around immune-related genes from 206 ancient DNA extracts, stemming from two different European populations before, during and after the Black Death,” the investigators noted.

 

Using targeted sequencing for a set of 300 immune-related genes, the investigators identified four genes that, depending on the variant, either protected against or increased susceptibility to Y. pestis. They homed in one gene in particular, ERAP2, which demonstrated a particularly strong association to susceptibility. Individuals who possessed two copies of one specific genetic variant, dubbed rs2549794, were able to produce full length copies of the ERAP2 transcript, producing more of the functional protein, when compared with another variant that led to a truncated and non-functional version of the transcript.

Functional ERAP2 plays a role in helping the immune system to recognize the presence of an infection. Individuals who carried two copies of the beneficial ERAP2 variant survived the pandemic at a much higher rates than those with the opposing set of copies, because the rs2549749 variant allowed for more efficient neutralization of Y. pestis by immune cells.

The team even went so far as to test how the rs2549794 variant affected the ability of living human cells to help fight the plague, determining that macrophages expressing two copies of the variant were more efficient at neutralizing Y. pestis compared to those without it. “We suggest that this protein increases the presentation of Yersinia-derived antigens to CD8+ T cells, stimulating a protective immune response against Y. pestis,” they wrote in their paper. “Furthermore, we show that macrophages from individuals possessing the selected ERAP2 allele engage in a unique cytokine response to Y. pestis infection and are better able to limit Y. pestis replication in vitro.”

“When a macrophage encounters a bacterium, it chops it into pieces for them to be presented to other immune cells signaling that there’s an infection,” said Barreiro. “Having the functional version of the gene, appears to create an advantage, likely by enhancing the ability of our immune system to sense the invading pathogen. By our estimate, possessing two copies of the rs2549794 variant would have make a person about 40% more likely to survive the Black Death than those who had two copies of the non-functional variant.” And while Europeans living at the time of the Black Death were initially very vulnerable because they had had no recent exposure to Yersinia pestis, as waves of the pandemic occurred again and again over the following centuries, mortality rates decreased.

 

“Examining the effects of the ERAP2 variants in vitro allows us to functionally test how the different variants affect the behavior of immune cells from modern humans when challenged with living Yersinia pestis,” said Javier Pizarro-Cerda, PhD, head of the Yersinia Research Unit and director of the World Health Organization Collaborating Centre for Plague at Institut Pasteur. “The results support the ancient DNA evidence that rs2549794 is protective against the plague … “This highly original work has been possible only through a successful collaboration between very complementary teams working on ancient DNA, on human population genetics and the interaction between live virulent Yersinia pestis and immune cells, Pizarro-Cerda stated.

Barreiro continued, “The selective advantage associated with the selected loci are among the strongest ever reported in humans showing how a single pathogen can have such a strong impact to the evolution of the immune system.”

The team further suggested that the selection for rs2549794 represented part of the balancing act that evolution places upon our genome. While this ERAP2 variant identified is protective against the Black Death, in modern populations, the same variant is associated with an increased susceptibility to autoimmune diseases, including acting as a known risk factor for Crohn’s disease.

 

“More broadly, our results highlight the contribution of natural selection to present-day susceptibility towards chronic inflammatory and autoimmune disease,” they wrote. “… the selectively advantageous ERAP2 variant is also a known risk factor for Crohn’s disease, and ERAP2 variation has also been associated with other infectious diseases … Likewise, another of our top candidate loci (rs11571319 near CTLA4) is associated with an increased risk of rheumatoid arthritis and systemic lupus erythematosus, such that retaining the putatively advantageous allele during the Black Death confers increased risk for autoimmune disease in present-day populations.”

 

Understanding the dynamics that have shaped the human immune system is key to understanding how past pandemics, like the plague, contribute to our susceptibility to disease in modern times, noted Hendrik Poinar, PhD, Professor of Anthropology at McMaster University and co-senior author on the study. “Diseases and epidemics like the Black Death leave impacts on our genomes, like archeology projects to detect. This is a first look at how pandemics can modify our genomes but go undetected in modern populations. … Even a slight advantage means the difference between surviving or passing. Of course, those survivors who are of breeding age will pass on their genes.”

Such genes are thus under balancing selection, and what provided tremendous protection during hundreds of years of plague epidemics has turned out to be autoimmune related now, continued Poinar, who is director of McMaster’s Ancient DNA Centre, and a principal investigator with the Michael G. DeGroote Institute for Infectious Disease Research and McMaster’s Global Nexus for Pandemics & Biological Threats. “A hyperactive immune system may have been great in the past but in the environment today it might not be as helpful.”

The authors further concluded, “To date, most of the evidence for an association between autoimmune risk alleles and adaptation to past infectious diseases remains indirect, primarily because the aetiological agents driving selection remain hidden. Our ancient genomic and functional analyses suggest that Y. pestis has been one such agent, representing empirical evidence connecting the selective force of past pandemics to present-day susceptibility to disease.”

Future research will scale the project to examine the entire genome, not just a selected set of immune related genes; and the team hopes to explore genetic variants that affect susceptibility to bacteria in modern humans and compare them to these ancient DNA samples to determine if those variants were also a result of natural selection.

Commenting on the newly released research in an accompanying News & Views, David Enard, PhD, at the University of Arizona, said, “it is worth noting that such rapid and strong selection is highly unlikely to occur for human traits other than immune defense. No other set of traits is under such strong evolutionary pressure … Going forward, more studies of ancient DNA could also enable a better understanding of the evolutionary origins of autoimmune diseases.”