Denisovan DNA Shaped the Modern Papuan’s Immune System

The immune system of modern Papuans was likely shaped by genetic influences from an ancient human ancestor, suggests a new study published in PLOS Genetics.

Denisovan DNA contributions to the modern genome

In recent years, advances in DNA sequencing technologies have enabled scientists to explore the genome of our ancient ancestors and compare it to that of a modern-day human. The indigenous peoples of Papua and Papua New Guinea – known as “Papuans” – owe five percent of their genetic code to an extinct species of archaic humans, called the Denisovans. The existence of Denisovans was uncovered in 2010, when DNA extracted from a finger bone found in a Siberian cave was sequenced; work that would later earn Professor Svante Pääbo the 2022 Nobel Prize in Physiology or Medicine. 

“The interactions between Denisovans, Neanderthals and Homo sapiens 50–60,000 years ago are just fascinating,” says evolutionary geneticist Dr. Irene Gallego Romero from the University of Melbourne.

Questioning what role(s) our ancestor’s DNA serves in the modern genome is a popular research focus in ancient DNA analysis. Last year, researchers demonstrated a protective function of Neanderthal DNA against HIV. However, the same gene variants also appeared to confer an increased susceptibility to severe SARS-CoV-2 infection.

In the current study, Romero and colleagues focused on the five percent of the Papuans’ DNA that came from Denisovans. “We know very little about Denisovans, so this was a way of getting a bit of a sideways look at them,” she explains. “However – and more importantly – we wanted to understand the biological consequences of Denisovan DNA for the people who actually carry it. We know Neanderthal DNA contributes to present-day individuals (and all individuals of non-African descent have some in their genome), but the role of Denisovan DNA is a lot more poorly understood.”

Denisovan DNA variants exist in regulatory regions

The research team sequenced the genomes of 56 Papuan individuals that had submitted their DNA for a previous research project conducted by some of the researchers involved in the PLOS Genetics study. “The samples were collected in a couple of different sites of New Guinea Island, both on the Indonesian side and the Papua New Guinea side. They represent a couple of different populations within New Guinea Island,” Romero explains.

Papuans also carry Neanderthal DNA in their genome, so the researchers scoured for regions of DNA that were distinctly “non-human”. They found that Denisovan DNA – but not Neanderthal DNA –occurs in regions known as “cis-regulatory” areas of the genome. “What people think of when they think of genes actually makes up a very small fraction of the human genome – around 2%. Instead, a large fraction of the genome is ‘non-coding’ (it does not encode proteins), but rather ‘regulatory’,” Romero describes. The role of these regulatory regions is to control whether a gene is turned “on” or “off” in specific cells – such as a heart, liver or kidney cell – in addition to how long the gene is active for and under what circumstances.

“Evolutionarily, we see a lot of changes to these regulatory bits of the genome because they're actually less risky – a mutation in a gene that is essential to the function of multiple cell types will have consequences for all of those cell types, but a mutation to the regulatory sequences of that same gene is very likely to have a less severe effect. It's like the difference between turning music on and off completely (mutating the gene) and simply adjusting the volume (mutating the regulatory region),” Romero adds.

In Papuans, the Denisovan gene variants fall in the regulatory regions of genes that are important to immune cells. “We don’t see this in other cell types, which suggests that Denisovan DNA is really making specific contributions to the immune system,” Romero says. This work was supported using computer analysis software. To move beyond prediction and experimentally validate their findings, the researchers turned to cell cultures.

“This is often the bottleneck for all kinds of genetics studies,” Romero says. “The validation is pretty straightforward, using a technique that is well established. We synthesized small segments of DNA (170 bases long) that contained the Denisovan sequence we wanted to test and the equivalent sequence from H. sapiens, and put it directly before the DNA sequence for a protein called green fluorescent protein, or GFP.” If the segments selected by the team are in fact able to regulate genes (i.e., turn them “on” and “off”), the cells would start to produce copies of GFP, turning the cells green, or no GFP would be produced, and they would remain colorless.

“The best thing about this method is that we can measure things with more detail than simply on/off, so we can also say the Denisovan version of this sequence was more effective at turning on GFP than the H. sapiens sequence, or vice versa,” Romero adds. Indeed, the Denisovan DNA was found to regulate the nearby genes in the cell culture, suggesting they play an active role in the immune function of modern-day Papuans. The research team suggest that the Denisovan DNA might have supported the adaptation of early humans living in New Guinea to their environment.

Testing more variants in the presence of infection

In this study, only a handful of the variants identified by computer analysis were validated experimentally, a limitation Romero acknowledges and emphasizes as a focus for future work. “We are definitely working on expanding the number of Denisovan sequences we experimentally test for function! Ideally, we would have tested 1000s or 10,000s of these, not just the 8 we did in the paper (and two of those failed for technical reasons, so really, we only tested 6),” she says.

“It's also important to know that the amount of depth to which we can go is very much limited by the resources we have access to,” Romero adds. “People of non-European ancestry are dramatically under-represented in human genetics and biomedical databases, and these omissions impact health outcomes, by, for example, making it harder to predict the consequences of a specific DNA variant, or by failing to predict adverse drug effects and things like that. But that's a broader limitation of the field.”

While the data suggests the Denisovan variants are impacting the immune system, an interesting next step – in Romero’s words – would be to test what these DNA sequences do in the presence of infection. “That’s something we would definitely love to do in the future,” Romero concludes.

Reference: Vespasiani D, Jacobs G, Cook L, et al. Denisovan introgression has shaped the immune system of present-day Papuans. PLOS Genetics. 2022. doi: 10.1371/journal.pgen.1010470.

Dr. Irene Gallego Romero was speaking to Molly Campbell, Senior Science Writer for Technology Networks.