Immunity’s Double-Edged Sword
Finding the perfect samples to understand epidemics and pandemics, past and present
By: Geoffrey Feld, Ph.D.; Geocyte
“The best prophet of the future is the past.” – Lord Byron
Covid-19 has upended and ended millions of lives worldwide. But it is not the first, or even the most destructive, pandemic humanity has faced. The Black Death, history’s most infamous pandemic, swept across Eurasia and North Africa in the mid-14th century. It claimed the lives of up to half the local population, killing as many as 50 million of our ancestors. [Green 2020] Deadly diseases like this, which strike people of reproductive age, put huge evolutionary pressure on those infected to adapt and survive. To find these adaptations, researchers need to find the “perfect” samples — in the right place, at the right time, and in the right condition. Only samples like these can confirm historical accounts and reveal how a few different DNA letters could mean the difference between life and death.
Short History of the Black Death
Medieval cosplayers who miss the Middle Ages should be thankful for modern antibiotics and sanitation, which have mostly kept the Black Death in the history books. Also called plague, the Black Death is caused by the bacterium Yersinia pestis, which has likely infected humans (pun intended) for thousands of years. At least 6,000 years ago, an environmental pathogen called Y. pseudotuberculosis — harmless to humans — picked up the virulence factors that let it kill millions, often within a week of exposure. This bacterium lives quietly in black Oriental rats and spreads to humans through infected rat flea bites. That kind of transmission causes the deadlier bubonic plague, marked by swollen lymph nodes or “buboes.” Person-to-person spread through the air causes pneumonic plague, which is less deadly but spreads to more people.
Just like in our current pandemic, trade was likely what spread plague across the globe. A study published in Nature this summer settled a century-old debate over the origins of the 1347-1352 Black Death. It traced the outbreak to a 1338-1339 epidemic of plague in modern-day Kyrgyzstan, a diverse Central Asian community that depended on the Silk Road for its livelihood. [Spyrou 2022] The Oriental rats that carried Y. pestis mainly fed on grain, so researchers believe contaminated grain shipments by sea spread the plague rapidly and over long distances — across the Mediterranean, over the Black Sea to Italy, and onward. Pneumonic plague likely carried the Black Death further inland.
Ancient Samples Tell a Tale
Even though plague has clearly left its mark on human history, it wasn’t until 2011 that researchers had definitive proof that Y. pestis caused it. Despite being chemically fragile, DNA from long-dead organisms can still be extracted and sequenced. Swedish scientist Svante Pääbo pioneered these paleogenetic methods and won the 2022 Nobel Prize in Medicine or Physiology for his work earlier this month. [Advanced Information 2022] Paleogenetics has taught us a great deal about the human condition — from the extinct Neanderthals and Denisovans that Dr. Pääbo studied, to the domestication of dogs, to how humans first settled North and South America.
To understand ancient infections like plague, paleogeneticists extract DNA from inside the teeth of likely victims, where most intact bacterial DNA survives. They then combine the resulting sequencing data with other archeological evidence — historical records, gravestone markings, stratigraphy (the layering of sedimentary and volcanic rock), and radiocarbon dating. Together, this builds a phylogenetic tree showing how the disease organism evolved and spread from outbreak to outbreak. Spyrou and colleagues used these careful methods to identify the epidemic near Lake Issyk-Kul as the likely origin of Europe’s Black Death.
That’s interesting for history buffs and dog lovers, but what can ancient DNA tell us about our lives today? Another group, publishing in Nature earlier this month, asked this same question and took a different approach. Instead of stopping at Y. pestis DNA, they studied human DNA from remains found in gravesites in London and Denmark. By sampling people who died before, during, and after the Black Death, the team tested a hypothesis: a disease deadly enough to wipe out half a local population should leave clear evidence of “human genetic adaptation” in the genomes of survivors, since later plague outbreaks killed a smaller share of people. [Klunk 2022]
Acutely Alive to Chronically Ill
The ancient DNA that Klunk and colleagues extracted was too damaged, and the sample size too small, for whole genome sequencing. They reasoned that the immune system would show the strongest signs of protection against Y. pestis infection. So they used targeted hybridization capture to measure a subset of genes tied to immune response and immune disorders, plus “immune neutral” genes as controls. The larger London sample set served as the discovery cohort, while the smaller Danish cohort was used for testing. They selected variants with a minor allele frequency above 5%, and dropped any whose frequency didn’t clearly explain Black Death susceptibility (higher frequency before exposure) or protection (higher frequency after exposure). This left four candidate variants of interest. Since none sat in protein-coding regions, the researchers assumed they influenced gene expression instead.
Macrophages are the bacteria-eating immune cells that respond first to Y. pestis infection. The researchers ran several lab experiments, exposing virulent and heat-inactivated Y. pestis to donor-derived macrophages (including cells from people with active plague infections), and measured differences in gene expression tied to the four candidate variants. One gene stood out clearly: ERAP2. Macrophages carrying the protective allele against Y. pestis expressed this gene at five times the level of macrophages carrying the harmful allele.
ERAP2 codes for an enzyme involved in presenting antigens to CD8+ T cells through MHC class 1, so it made sense as a player in the immune response to infections like Y. pestis. But the researchers were surprised to find that this ERAP2 variant also had protective effects in macrophages directly. Macrophages from donors who carried two copies of the protective allele showed a distinct cytokine response, and — most importantly — a stronger ability to stop Y. pestis from replicating inside cells.
Stopping the bacteria from multiplying inside infected cells would clearly help a person survive. In fact, the protective allele had a selection coefficient of 0.4 — among the highest ever measured — meaning someone with two copies of that mutation would have been 40% more likely to survive the Black Death than someone with two copies of the harmful variant.
Unfortunately, the same gene that helped people survive the plague seems to cause problems for people today. Modern genome-wide association studies (GWAS) have linked the protective ERAP2 variant to a higher risk of Crohn’s disease. [Fierabracci 2012] Another candidate allele that protected against Y. pestis is linked to CTLA4 (known for its role in cancer immunotherapy), which raises the risk of rheumatoid arthritis and systemic lupus erythematosus. In other words, surviving the Black Death in the 14th century seems to have raised the risk of autoimmune disease in people today, as the study authors conclude in Nature.
Sampling living humans
Today, researchers don’t need to drill into centuries-old teeth to study living people. But just as Klunk and colleagues needed to find the “perfect” human remains, modern therapeutic research depends on finding the right patients — with confirmed disease, clear inclusion and exclusion criteria, and well-annotated medical records. To meet this “needle in a haystack” challenge, Sanguine Bioscience has built relationships with patients and advocacy groups, creating a network of over 60,000 research-ready study participants. We collect samples noninvasively — including whole blood, PBMCs, serum, plasma, skin tapes, stool, and urine — prospectively in patients’ homes, then process them further at Sanguine’s lab. In fact, Sanguine’s database includes hundreds of patients with the same autoimmune diseases that our plague-surviving ancestors unknowingly passed on to modern society, including Crohn’s disease, lupus, rheumatoid arthritis, and others.
Find out whether Sanguine’s approach can accelerate your research into preventing the next pandemic, or easing the burden of autoimmune disease on our ever-evolving civilization.
References:
Green. (2020) The Four Black Deaths. The American Historical Review. 125(5): 1601-1631.
Spyrou et al. (2022) The source of the Black Death in fourteenth-century central Eurasia. Nature. 606: 718-724.
Advanced Information. NobelPrize.org. Nobel Prize Outreach AB 2022. Fri. 21 Oct 2022. https://www.nobelprize.org/prizes/medicine/2022/advanced-information
Klunk et al. (2022) Evolution of immune genes is associated with the Black Death. Nature. Evolution of immune genes is associated with the Black Death
Fierabracci et al. (2012) The putative role of endoplasmic reticulum aminopeptidases in autoimmunity: Insights from genomic-wide association studies. Autoimmunity Reviews. 12:281-288.
