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A team of scientists from the University of Maryland School of Medicine has found the strongest evidence yet that bacteria occasionally transfer their genes into human genomes, finding bacterial DNA sequences in about a third of healthy human genomes and in a far greater percentage of cancer cells. The results, published today (20 June) in PLOS Computational Biology, suggest that gene transfer from bacteria to humans is not only possible, but also somehow linked to over-proliferation: either cancer cells are prone to these intrusions or the incoming bacterial genes help to kick-start the transformation from healthy cells into cancerous ones.

“It really does seem that human genome sequence data from somatic cells show signs of LGT events from bacteria, and so do cancer cells,” said Jonathan Eisen from University of California, Davis, who coordinated the peer review of the new study but was not involved in the work. “Wild stuff does happen.”

The trillions of bacteria in our bodies regularly exchange DNA with each other, but the idea that their genes could end up in human DNA has been very controversial. In 2001, the team that sequenced the first human genome claimed to have found 113 cases of such lateral gene transfers (LGT), but their conclusion was later refuted.

This high-profile error “had a chilling effect on the field,” according to Julie Dunning Hotopp who led the new study. Although her team has since found several cases of LGT between bacteria and invertebrates, “it’s still difficult to convince people that it may be happening in the human genome,” she said.

Rather than looking for bacterial genes that had become permanent parts of the human genome, Dunning Hotopp’s team searched for traces of microbial DNA in somatic cells—the cells of the body that do not form gametes.

Lab members David Riley and Karsten Sieber scanned publicly available data from the 1000 Genomes Project and found more than 7,000 instances of LGT from bacteria, affecting around a third of the people they studied. When they analyzed sequences from the Cancer Genome Atlas, they discovered 691,000 more instances of LGT 99.9 percent of these came from tumor samples rather than normal tissues.

Acute myeloid leukaemia cells were particularly rife with bacterial sequences. A third of the microbial genes came from a genus called Acinetobacter, and had been inserted into the mitochondrial genome.

Stomach cancer cells also contained lots of bacterial DNA, especially from Pseudomonas. Most of this DNA had been inserted into five genes, four of which were already known to be proto-oncogenes that can give rise to cancer, emphasizing a possible link between LGT and cancerous growth. “Finding these integrations in multiple individuals, as well as in the proto-oncogenes, really spoke to how significant this might be,” said Dunning Hotopp.

“We know already that a significant proportion of cancers are due to insertion of genetic material from viruses,” said Etienne Danchin from the French National Institute for Agricultural Research, who reviewed the paper. “But this is the first time, as far as I know, that HGT from bacteria could be suspected as a cause of cancer.”

However, Dunning Hotopp is very clear that her results tell us nothing about whether the inserted bacterial DNA contributed to causing the cancers, or were just along for the ride. To get at the question of causation, researchers could deliberately add bacterial DNA into the same sites within human cell lines to see if they turn cancerous, she said. But even if the bacterial LGT can initiate over-proliferation, it would be hard to prevent such transfers with antibiotics. “You don’t know when these transfers occur, and you can’t give people antibiotics their entire life,” said Dunning Hotopp. “A vaccine would be nice, but that is assuming these are causative.”

“LGT is incredibly important in evolution but many claims of specific cases of LGT have been seriously flawed,” said Eisen. “I came into this as a serious skeptic. It just seemed so improbable.”

But the team won him over. They ran an extensive set of checks to make sure that these bacterial sequences were not laboratory artifacts and had not come from contaminating microbes.

For example, they showed that LGT was more common in cancer cells than healthy tissue, and two out of ten cancer types were particularly hard hit. If the bacterial integrations were artifacts of the methodology, it should be equally common in any tissue sample. The team also focused on sequences with high coverage—that is, those which had been read many times over. When the team found evidence of LGT, it was consistent across all of these reads. “In the end, the authors addressed every single question that I and the reviewers raised,” said Eisen.

Hank Seifert from Northwestern University, who was not involved in the study, remains cautious. “This paper is very interesting and potentially important,” he said. “However, until the direct analysis of specific tumor cells can be performed to validate that these are real events, this work [is] still speculative.”

But Dunning Hotopp’s team cannot do these validation studies herself. For privacy reasons, they cannot access the original tumor samples that their data came from. “People with access to the samples need to validate that the integrations are correct,” she said.

Danchin agrees that the results need to be validated but said, “I am personally convinced what they have found by screening the different databases is true. I think LGT happens much more frequently than we imagine but, most of the time, is just not detectable.”

D.R. Riley et al., “Bacteria-human somatic cell lateral gene transfer is enriched in cancer samples,” PLOS Computational Biology, 2013.

Many animal genomes include bacterial and fungal genes acquired by horizontal gene transfer (HGT) during evolution, according to a study published today (March 12) in Genome Biology. Scanning the genomes of fruit flies, nematodes, primates, and humans, among other animals, researchers found evidence to suggest that some of these horizontally acquired genes may even be functional.

When the human genome was first published, the suggestion that it contained bacterial genes was controversial. Subsequent studies questioned the possibility of HGT, offering alternate explanations for the presence of genes that resembled bacterial sequences, such as gene loss, or convergent or divergent evolution.

“There were methodological issues with both sides of the argument, and the main problem was that we just didn’t have the data back then that we do now,” said Alastair Crisp of the University of Cambridge, an author on the new study.

More recently, several researchers have reported the lateral transfer of bacterial genes into metazoans under specific circumstances. Examples include the interaction of insect hosts with the obligate intracellular parasite Wolbachia, or the transfer of subsets of bacterial genes into specific kinds of cells, such as cancer cells.

But this latest study is the first to extend across a breadth of species and types of genes. “The study makes a compelling case presenting more evidence of lateral gene transfer from bacteria into eukaryotes,” said microbiologist Julie Hotopp of the University of Maryland who was not involved with the work. “Redoing this type of analysis has been needed for quite some time. People continue to cite the papers from 2000 and 2001 as examples that there is no lateral gene transfer, particularly in humans.”

To re-evaluate the extent of bacterial gene transfer into animals, Crisp and his colleagues analyzed 40 animal genomes, including 10 primates, 12 Drosophila species, and four Caenorhabditis genomes. The researchers computed a score to quantitate how closely a gene aligned to a non-metazoan sequence compared to a metazoan, or animal, sequence. Based on this score, they considered genes that strongly resembled non-animal sequences to be horizontally transferred. Depending on the scores, between 55 percent and 88 percent of the sequences analyzed strongly resembled prokaryotic sequences, suggesting they had been introduced into animal genomes by lateral transfer.

“We had an idea that HGT was much broader than people had previously suspected,” said Crisp. “What surprised us particularly was that there seemed to be a broadly similar amount in both vertebrates and invertebrates.”

The results supported analyses from previous studies that suggested human genes—such as FTO, the fat mass and obesity-associated gene—may have been horizontally acquired. Phylogenetic comparisons also found that some genes, such as hyaluronan synthases (HAS) in the human genome, which were originally thought to be horizontally transferred from bacteria but later rejected, may in fact be of fungal origin.

A large proportion of the “foreign” genes analyzed were found on the same genomic scaffolds as native animal genes. The strong linkage suggested to Crisp and his colleagues that contamination of sequenced samples was unlikely to be the source of these non-native genes.

However, the validity of these results hinge upon the quality of the assembled genomes that were analyzed. “Some genomes, such as C. elegans, D. melanogaster, and the human genome, are very well put-together. But in others, the assemblies may not be as good, and poor assemblies will result in something that looks like gene transfer,” said Hotopp. “It just means that in some organisms they may have overestimated it.”

Crisp’s team found that several of the foreign genes in metazoan genomes encoded enzymes and likely had active biochemical functions. In three nematode and all the primate genomes analyzed, the researchers found that 95 percent of foreign genes contained introns, suggesting that these genes have been “domesticated” over time.

“Since HGT events are not incredibly common, it seems likely that the mechanisms [operating] are very similar to the ones that would insert introns into any genes,” said Crisp. “Looking at recent HGT events can tell us how introns were inserted into other eukaryotic genes, or how transcriptional regulation of new genes evolves.”

The process of lateral gene transfer appears to be both ancient and active today. In human and other primate genomes, foreign genes appear to have entered the genome only in their last common ancestors. But in some Drosophila species and nematodes, the process appears to have occurred much more recently.

The results suggest that “if we use the same yardstick to measure a variety of model organisms, it’s possible to say that mammalian genomes have also been subjected to low levels of HGT, although it happened only on very rare occasions at the early stages of evolution,” said molecular geneticist Irina Arkhipova of the Marine Biological Laboratory in Woods Hole, Massachusetts who was not involved with the study. “Some species are more susceptible than others. But it definitely can happen and has happened during evolution, and has played a role in shaping functional diversity of the gene repertoire in metazoans.”

Microbiologist Jonathan Eisen of the University of California, Davis, who also did not participate in the work noted that the study’s results don’t conclusively exclude gene loss as an alternate explanation of their data.

“This is pretty typical of claims of HGT,” Eisen told The Scientist in an e-mail. “Many researchers show evidence that is consistent with the occurence of HGT (which they did here) but few actually explicitly test alternative hypotheses such as gene loss, bad alignments, convergence, divergence, contamination, random noise, and more.”

“I suspect that [these results] won’t be universally accepted,” said Crisp. “But I think it takes a good shot at settling the controversy.”

A. Crisp et al., “Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes,” doi:10.1186/s13059-015-0607-3, Genome Biology, 2015.