Using bacterial signatures to screen for colorectal cancers

Colorectal cancer does not manifest as specific symptoms of its own, but rather, the observable symptoms are generally related to non-neoplastic diseases, not CRC. Colonoscopies are the main diagnostic resource, an invasive procedure that can lead to severe complications, even death, and should only be done if absolutely necessary. Although screening tests have a high sensitivity for colorectal cancer, they often yield high percentages of false positives. For example, 30% of patients undergoing immunochemical fecal occult blood tests (FIT) are, in fact negative, and the sensitivity for pre-cancerous lesion of current tests is 29%.

Patients may also go through the fecal immunochemical test (FIT) test, which screens for colon cancer by detecting blood in stool samples originating from the lower intestines, and can serve as a precursor to determine whether an individual should in fact undergo a colonoscopy. However, waiting until the cancerous mass has started to bleed means that it is often too late for the patient. On the other side, blood is also not a clinical indicator of colorectal cancer which presents another serious problem of FIT testing. The diagnostic procedure for detecting and treating colorectal cancer generally involves a cumbersome process with limited diagnostic accuracy – and the team at GoodGut is aiming to change that.

Following her gut

After discovering a biomarker for colorectal cancer as a postdoctoral fellow in 2012, Dr. Mariona Serra, a PhD in pharmacology, knew she wanted to start a company based on her scientific findings. After taking courses in business management in 2014, she founded GoodGut with Xavier Aldeguer and Jesus Garcia-Gil the same year. All three founders shared the same vision: to transform Serra’s discovery into a meaningful application, by developing a non-invasive screening test for early detection of colorectal cancer. GoodGut’s Risk Assessment for Intestinal Disease Colorectal Cancer (RAID-CRC) is a pioneering test, using biomarkers in stool samples to pre-diagnose colon cancer fast and cost-efficiently.

The microbial species colonizing the human body varies from person to person: each individual possesses their own specific microbial fingerprint that changes over time, for example, in response to environmental changes. The research conducted by Serra and her team showed that particular bacteria found in biopsies of patients affected by colorectal cancer could not be found in healthy people.

Detecting cancer risks based on bacteria

The principle on which GoodGut develops their tests is that the detection of these bacteria is associated to cancer risk. “The microbiome is like a garden in our digestive system that we have to look after, one that changes. We have developed a tool that can indicate certain changes in its composition – in this case, six specific bacteria – which we can use to reduce a risk of cancer or to assess the success of a treatment,” says Serra. “We look for imbalances. When the composition of the microbiome changes, the population of certain microorganisms increases or decreases at the expense of others. If such a mechanism is detected and significantly determines it in diseased and healthy individuals, we have a quasi-microbiological profile for bacteria that indicates a disease. However, this finding is not easy – neither the cause nor the effect are always easy to recognize. The same applies to the question of where the bacteria come from; sometimes it can be found in the stool, but also in the air. In the meantime, we have carried out three medical studies and analyzed more than 3,000 samples. Currently, asymptomatic patients are in the final validation stage,” she says.

Saving lives with early diagnoses

Sara Ramió, the technical director of this startup, believes that the technological aspect at a research company like GoodGut is extremely important. “A small company like ours must work in a very cost-efficient manner, for example, by screening large numbers of samples automatically,” Ramió says. “To achieve this, we use QIASymphony, which can process up to 500 qPCR samples per day. To prepare the samples, we use the QIAGEN Multiplex PCR Kit because of its high sensitivity to detect even the smallest amounts of DNA. Our samples may contain less than 10 micrograms of the bacterial DNA we want to detect. The QIAGEN Multiplex Kit also has the advantage of simultaneously displaying different biomarkers and quantify them. For DNA extraction, we use the DNeasy PowerSoil Kit* which, to me, is the best extraction kit on the market since it allows us to obtained a good yield for both gram-negative and gram-positive bacteria. We also use the QuantiNova Kit with excellent results,” says Ramió enthusiastically. Serra adds: “Our screening test is 98% sensitive, and 92% specific, compared with a sensitivity of 75% for a fecal blood test. We estimate that RAID-CRC will eliminate the need for 32% of colonoscopies and detect 59% of pre-cancerous lesions.”

We have the chance to save human lives by making accurate and early diagnoses. We can also reduce the number of unneeded intestinal biopsies, therefore preventing unnecessary diagnostic tests and potentially risky medical procedures,” says Serra. Going forward, the team at GoodGut is also looking beyond diagnostics to develop bacterial treatments in the future to avoid colorectal cancer from developing in the first place.