The Black Death may have influenced the evolution of genes involved in immune responses against pathogens

The Black Death may have influenced the evolution of genes involved in immune responses against pathogens

In a recent study published in Nature Researchers have gathered empirical evidence that past pandemics caused by infectious pathogens have shaped today's human susceptibility to diseases such as autoimmune diseases.

Lernen: Die Entwicklung von Immungenen wird mit dem Schwarzen Tod in Verbindung gebracht. Bildquelle: Marcin Osman/Shutterstock

background

The plague pandemic, commonly referred to as the Black Death, was caused by a species of bacteria, Yersinia pestis, which wiped out 30 to 50% of the Afro-Eurasian population and became the largest mortality event in human history. Such unprecedented mortality rates suggested that allelic variants of immune genes that triggered an immune response against Y. pestis infection may have been under strong selection during this period. In all subsequent plague pandemics in Europe, mortality rates declined significantly, probably due to pathogen evolution, changing cultural practices, or human genetic adaptation to Y. pestis.

Because they had no recent exposure to plague, the Europeans who experienced the Black Death appear to represent an immunologically naïve population with minimal or no adaptation to Y. pestis. However, to date, the immune targets of Y. pestis selected during the Black Death are not yet known. Most evidence for a link between risk alleles associated with autoimmune diseases and adaptation to previous infectious diseases remains indirect, as the etiological factors driving this selection remain hidden.

About the study

In the present study, researchers dug up ancient genomic data from people who died just before, during or after the Black Death pandemic in London and Denmark to characterize their genetic variations. The study's unique sampling design helped researchers distinguish genetic signatures due to Y. pestis from other selective processes, including other infectious diseases such as tuberculosis. In addition, the extent to which other historical events, such as famine, could have influenced the conclusion of positive selection was minimized.

The team visited three London cemeteries to collect deoxyribonucleic acid (DNA) samples from people who died before, during and after the Black Death. In London they also collected samples of all Black Death victims who died between 1348 and 1349 and were buried in East Smithfield. Radiocarbon, stratigraphy and historical data confirmed how these people died. Burials in London were more accurately dated and geographically better controlled than those in Denmark. Next, the team surveyed Danes from five locations across the country. They grouped these people into those who lived in the period before and after the Black Death. In this way, the researchers ensured that they only identified European mitogenomic haplotypes.

The researchers examined 516 samples, including 318 from London and 198 from Denmark. They discovered human DNA using a modified polymerase chain reaction (PCR) test for the cellular myelocytomatosis oncogene gene (c-myc). In addition, they identified 360 nuclear loci with sufficient endogenous DNA for subsequent enrichment and sequencing.

The researchers ensured that deamination and other ancient DNA damage did not manifest as falsified genotype information. Therefore, they trimmed four base pairs (bp) from the start and end of each sequencing read. The final study dataset included 33,110 biallelic variants with an average coverage of 4.6-fold reads per site per individual. They filtered out missing genotype calls at over 50% of the target sites. Next, the team calculated the minor allele frequency (MAF) per population. Finally, they only retained the sites whose average MAF averaged more than 5% in London and Denmark.

In addition, researchers looked for allelic variants within immune genes and genome-wide association study (GWAS) loci that showed unexpected changes in frequency between samples before and after the Black Death to identify gene variants for which the degree of differentiation (FST) was more than expected by chance.

Initially, the team identified 245 common variants with a MAF greater than 10%. These variant alleles were also highly differentiated, as indicated by their FST, which was >95. percentile was. The researchers defined FST using neutral locations when comparing samples from London before and after the Black Death. Next, they argued that alleles that confer increased susceptibility to or protection against Y. pestis should increase or decrease in frequency in people who died during the Black Death or in those sampled after the Black Death, respectively. This narrowed the list of supposedly selected loci from 245 to 35. Finally, they examined whether these loci were as highly differentiated and in the same direction as their London counterparts.

In addition, the team examined whether the four candidate loci identified in the study or genes near them were involved in the transcriptional response to Y. pestis. Therefore, they incubated macrophages from 33 samples with heat-killed Y. pestis. Next, they used ribonucleic acid (RNA) sequencing to compare the gene expression profiles of these samples with those of control samples.

Study results

Functional data from in vitro infection experiments confirmed that the strongest candidates for positive selection were directly involved in the immune response to Y. pestis. The researchers identified four genetic loci that were highly differentiated before and after the Black Death outbreak in London. Therefore, they calculated the selection coefficients for each of these variants using a hidden Markov model (HMM). The same was repeated in the Danish cohort as the strongest selection candidates. Due to the small sample size, replication power was limited. Therefore, some of the 245 highly differentiated loci in London were probably also affected by natural selection, although they did not survive the conservative filtering criteria. Future studies examining the evolutionary role of these variants in the immune response to Y. pestis should use larger sample sizes in conjunction with additional functional data.

Seven genes within 100 kilobases of four candidate loci showed a transcriptional response to Y. pestis in macrophages, with the exception of the leucyl and cysteinyl aminopeptidase gene (LNPEP). In vivo, Toll-like receptor 4 (TLR4) recognized Y. pestis by recognizing its lipopolysaccharide membrane (LPS). To avoid this detection, bacteria deacetylate surface LPS, thereby reducing the binding affinity for TLR4. Toll-like receptor adapter molecule 2 (TICAM2) helped LPS-bound TLR4 enter endosomes and activate type I interferon (IFN) responses. It is therefore possible that increased TICAM2 expression conferred protection against Y. pestis.

The researchers found that the endoplasmic reticulum aminopeptidase 2 (ERAP2) locus had two haplotypes (A and B). In macrophages, reduced ERAP2 expression in individuals carrying the deleterious rs2248374-G haplotype B allele was associated with higher expression of the truncated isoform. Subjects with the beneficial haplotype were able to resist cell death caused by Y. pestis more effectively than subjects with the lethal haplotype. For example, levels of IL-1β, a key proinflammatory cytokine associated with pyroptotic cell death, were three times lower in individuals homozygous for the beneficial ERAP2 genotype than in individuals homozygous for the putatively lethal genotype. However, the results could not be confirmed by in vitro experiments.

Conclusions

The current study used ancient genomic data and functional analysis to gather empirical evidence that Y. pestis infection affected genetic diversity around some immune loci. Four loci that differentiated strongly before and after the Black Death caused by Y. pestis emerged as the strongest candidates for selection. ERAP2 showed the most convincing evidence for selection, with a selection coefficient of 0.4.

This finding suggests that individuals homozygous for the beneficial allele are approximately 40% more likely to survive the Black Death than individuals homozygous for the deadly allele. It is possible that the ERAP2 protein increased the presentation of Y. pestis-specific antigens to CD8+ T cells, thereby stimulating a protective immune response.

ERAP2 was transcriptionally responsive to multiple pathogens, supporting its key role in regulating the immune response. Therefore, selection exerted on ERAP2 by Y. pestis affected the immune response to other pathogens and disease traits. For example, the selectively advantageous ERAP2 allele is a known risk factor for Crohn's disease, and its allelic variation has been linked to other infectious diseases.

Likewise, studies have shown the association of another locus, rs11571319, close to cytotoxic T lymphocyte-associated protein 4 (CTLA4), with an increased risk of rheumatoid arthritis and systemic lupus erythematosus. In fact, the retention of supposedly beneficial alleles of some immune genes during the Black Death led to an increased risk of autoimmune diseases in today's population.

Reference:

• Klunk, J., Vilgalys, T., Demeure, C., Cheng, X., Shiratori, M. & Madej, J. et al. (2022). Die Entwicklung von Immungenen wird mit dem Schwarzen Tod in Verbindung gebracht. Natur. doi: 10.1038/s41586-022-05349-x https://www.nature.com/articles/s41586-022-05349-x

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