Gut Bacteria can Secrete Carcinogen: Study

Common bacteria inhabiting the gut of healthy individuals can cause DNA (deoxyribonucleic acid) mutations that can lead to cancer, reveals a new study jointly conducted by the Hubrecht Institute for Developmental Biology and Stem Cell Research and the Princess Máxima Center for Pediatric Oncology in Utrecht, The Netherlands. The research team found that when mini gut organoids were exposed to a particular strain of the bacterium Escherichia coli (pks⁺ E. coli), it induced unique mutational signatures in the DNA of human intestinal cells. Surprisingly, these exact same mutational signatures were also found in the DNA of patients with colon cancer, which indicates that the DNA mutations were caused by the same harmful E. coli strain residing in the human gut.

This is the very first time that a bacterium residing in the human body has been implicated in carcinogenesis. Importantly, these findings could lead to the development of novel therapeutic strategies for colon cancer by eradicating these harmful gut bacteria. The research findings have been published in the latest issue of the prestigious British journal, Nature.

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Study Team

The study was jointly led by Dr. Hans Clevers, MSc, MD, PhD and Dr. Ruben van Boxtel, PhD. Dr. Hans Clevers is a Group Leader at the Hubrecht Institute for Developmental Biology and Stem Cell Research and at the Princess Máxima Center for Pediatric Oncology. He is also a Professor of Molecular Genetics at the Utrecht University Medical Center and an Oncode Investigator. Dr. Ruben van Boxtel is a Group Leader at the Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.

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Harmful Effects of Escherichia coli - A Notorious Gut Bacterium

The human body contains almost the same number of bacterial and human cells. Although the majority of these bacteria don’t harm the body, there are some that can cause disease. One of these bacteria is notorious and potentially harmful for the body. This is E. coli, which is so-called because it was discovered by the German-Austrian Pediatrician Dr. Theodor Escherich in 1885. This is the best-known and most extensively studied gut bacterium.

The particular strain of E. coli (pks⁺ E. coli) used in the present study is genotoxic, meaning that it is toxic to genes. The toxicity is brought about by the toxin colibactin present in pks⁺ E. coli, which produces mutations (alternations) in DNA. The mutations are caused by colibactin-induced breaks in the double-helical structure of the DNA. Importantly, it has been suspected for a long time that genotoxic E. coli, which resides in the gut of 1 in 5 people, could be harmful to the human hosts.

“There are probiotics currently on the market that contain genotoxic strains of E. coli. Some of these probiotics are also used in clinical trials,” explains Hans Clevers. “These E. coli strains should be critically re-evaluated in the lab. Though they may provide relief for some bodily discomfort in the short-term, these probiotics could lead to cancer, decades after the treatment”.

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Gut Organoids to Study Colibactin-induced DNA Mutations

Mutations in the double-stranded DNA molecules lead to uncontrolled proliferation of cells, giving rise to cancer. Carcinogens, such as tobacco smoke or ultraviolet (UV) radiation, can damage DNA by causing mutations, which can lead to the development of cancer. However, it was previously unknown that bacteria inhabiting the human gut could also induce carcinogenic mutations in intestinal cells through DNA damage.

In order to study the DNA-damaging effect of colibactin, the researchers used miniature cell-cultured intestines, known as gut organoids. This Gut Organoid Model was originally developed by Hans Clevers and his team. The research team exposed these human intestinal organoids to colibactin-secreting genotoxic E. coli. Following five months of exposure to colibactin secreted by the bacteria, the DNA of the human intestinal cells present in the organoids was sequenced to find the number and types of mutations induced by colibactin.

Carcinogens Exhibit Specific DNA Mutational Signatures

Any and all carcinogens causing DNA mutations leave behind a unique mutational signature. These specific signatures have already been identified for various types of carcinogens, including tobacco smoke and UV rays. Identification and analysis of these mutational signatures in the DNA help to determine any past exposures to carcinogenic agents that may contribute to disease initiation.

“These signatures can have great value in determining causes of cancer and may even direct treatment strategies”, explains Ruben van Boxtel. “We can identify such mutational signatures in several forms of cancer, including pediatric cancer. This time we wondered if the genotoxic bacteria also leave their unique distinguishing mark in the DNA.”

Mechanism of DNA Damage Induced by Colibactin

The mechanism of colibactin-induced DNA damage involved the simultaneous occurrence of two mutational patterns in the DNA present in the cells of the organoids. These involved the nucleotide adenine (A). It should be noted that adenine (A) is one of four nucleotides. The others include guanine (G), cytosine (C) and thymine (T), which pair with each other to form the rungs of the ladder that constitute the DNA double-helix. The mutational patterns involved the following changes in the adenine (A) nucleotide:

• Change of an A to any of the other three nucleotides (G, C or T)
• Loss of a single A in long stretches of A’s
• In both of the above cases, another A was present on the opposite strand of the DNA double-helix, approximately 3 to 4 nucleotide bases away from the site of mutation

Meanwhile, other research groups deciphered the structure of colibactin and its mechanism of interaction with the DNA. Their research revealed colibactin’s ability to simultaneously bind and cross-link two adenine nucleotides located on either side of the two strands of the DNA double-helix.

In this regard, Cayetano Pleguezuelos-Manzano, a PhD student in Hans Clever’s Group, says: “It was like a puzzle falling into place. The mutational patterns that we saw in our experiments could very well be explained by colibactin’s chemical structure”.

Moving from Gut Organoids to Cancer Patients

After identifying the mutational signatures left behind by the genotoxic E. coli in the DNA of cells populating the organoids, the research team decided to move to cancer patients in the next stage of their research. They analyzed more than 5,000 tumors from dozens of types of cancer in a bid to identify any mutational signatures. Of all the cancers investigated, only one type stood out prominently from the rest. This was colon cancer.

“More than 5% of colon cancers had high levels of the signature, while we only saw it in less than 0.1% of all other cancers,” says Jens Puschhof, a PhD student in Hans Clever’s Group. He adds excitedly: “Imagine studying a gut bacterium’s signature for months in a dish, and then finding back the same signature in the DNA of patients.”

Future Prospects

The study findings could have important applications in cancer diagnostics. Screening people for the presence of genotoxic E. coli in their intestines will help to diagnose colon cancer at a very early stage, allowing ample time to initiate treatment and possibly even prevent cancer development. Moreover, in the near future, it may be possible to eradicate these genotoxic gut bacteria altogether, through targeted antibiotic therapy.

Funding Source

The study was funded by Cancer Research UK, Netherlands Organization for Scientific Research, European Research Council, CancerGenomiCs.nl, and the Oncode Institute.

Reference:

1. Mutational Signature in Colorectal Cancer Caused by Genotoxic pks+ E. coli - (https://www.nature.com/articles/s41586-020-2080-8)

Source-Medindia