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, nor 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, claiming the lives of up to half the local population and killing as many as 50 million of our ancestors. [Green 2020] Such deadly diseases affecting humans of reproductive age place enormous evolutionary pressure on infected individuals to adapt and survive. Pinpointing these adaptations requires researchers to identify essentially the perfect samples—in the right place, at the right time, and in the right condition—that corroborate historical accounts and serendipitously tell a story of how a few different DNA letters could mean the difference between life and death.
Short History of the Black Death
Medieval cosplayers yearning for the Middle Ages should be thankful for modern antibiotics and sanitation that have relegated the Black Death largely to history books. Also called plague, the Black Death is caused by the bacterium Yersinia pestis, which has likely plagued humans (pun intended) for thousands of years. At least 6,000 years ago, an environmental pathogen called Y. pseudotuberculosis, which is harmless to humans, acquired the virulence factors that enabled the little bugger to kill millions, often within a week of exposure. Living innocuously in black Oriental rats, Y. pestis is transmitted to humans via infected rat flea bites. Such transmission results in the more deadly bubonic plague, causing swollen lymph nodes or “buboes” on infected individuals, while person-to-person aerosol spread of pneumonic plague produces lower mortality but higher infection rates.
Just like our current pandemic, trade was the likely culprit for spreading plague across the globe. A study published in Nature this summer ended a century-old debate on the origins of the 1347-1352 Black Death, pinpointing a 1338-1339 epidemic of Plague in modern-day Kyrgyzstan, a diverse Central Asian community dependent on the Silk Road for livelihood. [Spyrou 2022] Given that the Oriental rats harboring Y. pestis primarily feed on grain, the rapid and long-distance spread of plague across the Mediterranean is attributed to contaminated grain maritime shipments, across the Black Sea to Italy and onward. Pneumonic plague likely spread the Black Death to inland communities.
Ancient Samples Tell a Tale
Even though plague has remarkably made its mark on human history, it wasn’t until 2011 that definitive proof implicated Y. pestis as the causative agent. Despite its labile chemical nature, DNA from long-dead organisms can still be extracted and sequenced using paleogenetic methods pioneered by Swedish scientist Svante Pääbo, who was awarded the 2022 Nobel Prize in Medicine or Physiology for his discoveries earlier this month. [Advanced Information 2022] Paleogenetics has shed enormous light on the human condition, from the extinct hominids Neanderthals and Denisovans that Dr. Pääbo investigated, to the domestication of dogs and the populating of North and South America.
To understand ancient infections like plague, paleogeneticists extract DNA from inside the teeth of plausible victims, where most intact bacterial DNA specimens reside. The resulting sequencing data is then combined with other archeological information like historical records, gravestone markings, stratigraphy (i.e., sedimentary and volcanic rock layers), and radiocarbon dating to generate a phylogenetic tree of the disease organism’s evolution, tracing its origins across sites of outbreak. Spyrou and colleagues used such meticulous methods to identify the epidemic near Lake Issyk-Kul as the likely origin of Europe’s Black Death.
That’s all well and good 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 question and took a slightly different approach. Instead of stopping at Y. pestis DNA, they looked at the human sequences from remains across gravesites in London and Denmark. In uniquely sampling the dead from the years before, during, and after the Black Death, the team hypothesized that a disease capable of wiping out half a local population would impose enough selective pressure such that “human genetic adaptation” would be evident from the genomes, given that subsequent plague outbreaks resulted in lower mortality rates. [Klunk 2022]
Acutely Alive to Chronically Ill
The ancient DNA Klunk and colleagues extracted was too damaged and the sample size too small to conduct whole genome sequencing. Reasoning that the immune system would provide the strongest signatures of protection against Y. pestis infection, they used targeted hybridization capture to measure a subset of both immune response and immune disorder related gene variants, as well as “immune neutral” variants as controls. The larger London sample set served as the variant discovery cohort, while the smaller Danish cohort was used for testing. Selecting for variants using a conservative minor allele frequency of >5% and eliminating variants whose frequency failed to explain either Black Death susceptibility (i.e., higher frequency before exposure) or protection (i.e., higher frequency after exposure), they whittled down the dataset to four candidate variants of interest. Since none overlapped with protein coding regions, they were assumed to influence gene expression.
Macrophages are the bacteria-eating phagocytic immune cells that represent the first responders to Y. pestis infection. The researchers conducted several experiments in vitro, incubating virulent and heat-inactivated Y. pestis with donor-derived differentiated macrophages (including those from individuals infected with active plague), and measured differences in macrophage gene expression, looking for genes associated with the four identified variants. One association stood out above the rest: a gene called ERAP2, for which the protective allele against Y. pestis infection was expressed at fivefold higher levels than the deleterious allele.
ERAP2 codes for an aminopeptidase involved in MHC class 1-dependent presentation of antigens to CD8+ T cells, making it a logical participant in the immune response to infectious agents like Y. pestis. But the researchers were intrigued that the identified ERAP2 variant also resulted in protective effects in macrophages. They found that macrophages derived from donors who were homozygous for the protective allele possessed a unique cytokine response signature, and most importantly, an increased ability to restrict intracellular replication of Y. pestis.
Clearly, preventing the bacteria from replicating within infected cells would increase the survival of humans possessing the variant allele. In fact, the protective allele yielded a selective coefficient of 0.4—among the highest ever calculated—meaning an individual homozygous for that mutation would be 40% more likely to survive the Black Death than those homozygous for the deleterious variant.
Unfortunately, surviving plague due to increased expression of an immune response gene seems to have consequences for individuals today. Modern genome-wide associated studies (GWAS) have implicated the ERAP2 protective variant as a risk factor for Crohn’s disease. [Fierabracci 2012] Furthermore, another candidate protective allele against Y. pestis infection correlated with CTLA4 (of cancer immunotherapy fame), which is a known risk factor for rheumatoid arthritis and systemic lupus erythematosus. Thus, evolutionary pressures from surviving the Black Death in the 14th Century, “confers increased risk for autoimmune disease in present-day populations,” as the authors conclude in Nature.
Sampling living humans
Today, collecting samples from the living does not require drilling into ancient teeth from centuries-old burial sites. But just as identifying the “perfect” human remains was key for Klunk and colleagues, so too is finding the right patients with confirmed disease, inclusion/exclusion criteria, and annotated medical records for modern therapeutic research. To facilitate this “needle in a haystack” challenge, Sanguine Bioscience has been building relationships with patients and advocacy groups to build a network of over 60,000 research-ready study participants. Noninvasively-collected samples–including whole blood, PBMCs, serum, plasma, skin tapes, stool, and urine—can be concurrently collected prospectively in patient’s homes and further processed at Sanguine’s lab. In fact, Sanguine’s database includes hundreds of patients with the same autoimmune diseases our plague-surviving ancestors unknowingly inflicted upon 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. https://doi.org/10.1038/s41586-022-05349-x
Fierabracci et al. (2012) The putative role of endoplasmic reticulum aminopeptidases in autoimmunity: Insights from genomic-wide association studies. Autoimmunity Reviews. 12:281-288.