The Microbiome at SABCS (Part 2)

 Part 2: The microbiome & breast cancer radiation response

With permission from Dr. Shiao

Welcome to Part Two of the microbiome at SABCS! Here we will look at Dr. Shiao's presentation focusing on the effects of the microbiome on radiation therapy. You can find the related publication here.

Most microbiome research in the past has focused primarily or exclusively on bacteria, but the microbiome is more than just the bacteria and their genes! It is also composed of viruses, protists, archaea (like bacteria, but weirder), and fungi. The last is Dr. Shiao’s interest. He and his team want to know if fungi in the gut affect the response of breast tumors to radiation therapy. And if so, how?

First, why would fungi play a part in response to radiation therapy? My understanding is that radiation therapy, like other therapies that kill cells (eg. chemotherapy) are at least partially dependent on an appropriate immune response also occurring. And, as discussed in part 1, we know the gut microbiome (including fungi) can absolutely play a role in immune response.

There is currently good evidence that bacteria regulate response to chemotherapy; specifically, that a diverse microbiome leads to better response. Some of this data has come from antibiotic studies. Antibiotics deplete bacteria, both in number and in diversity. However, it doesn’t reduce bacteria to zero, and different antibiotics have different effects. It’s essential to only take antibiotics when necessary, both from a cancer and an antibiotic resistance standpoint.  But what about radiation? I swear I’m getting there…

Antibiotics & Radiation Therapy

Let’s take a look at the mouse model of breast cancer where some mice were treated with antibiotics and some were not (the control group).  Just reminder that antibiotics kill only bacteria. The takeaway from these experiments is: treatment with antibiotics decreases the effectiveness of radiation therapy, similar to what we see in chemotherapy. See details below or skip to the next section :-)

Methods & Results Details

Below is the experimental design. Blue mice had a “normal” microbiome and green mice were treated with antibiotics. ABX= antibiotics and RT=radiation therapy. Multiple mice were in each group. The antibiotics used were a mix that target a broad range of bacteria, trying to wipe out as many as possible.

In panel A below we see two groups of these mice, a control group (black lines, where each line is a mouse) and the group treated with radiation therapy (green). As expected those treated with radiation therapy have smaller tumors. Panel B is only looking at antibiotic treated mice- blue is no radiation therapy and orange is with radiation therapy. No separation! 

 

In Panel D we see that average survival was also affected by antibiotics- no antibiotics, radiation treated mice (green) survived the longest, antibiotic treated +/- radiation therapy were in the middle, and those with no antibiotics and no radiation survived the shortest time.

 

Additionally, Dr. Shiao’s group found that antibiotic treatment + radiation therapy limited cell death and promoted tumor growth. Again- this is a mouse model, but the results are intriguing.

Fungi & Radiation Therapy

Antibiotic use doesn’t get rid of all bacteria in the gut and may allow other organisms to grow. This is exactly what the team saw- while bacteria were reduced the fungi were increased by over 2500 times! That’s HUGE!

What might these fungi be doing? Are they affecting the radiation response in antibiotic treated mice? As Dr. Shiao pointed out- there are many more bacteria in the gut (fungi only make up about 0.01-0.1% of the gut microbiota), but they are 100x physically larger than bacteria. (I’ll also point out that the bacterial community as a whole has greater genetic/metabolic capabilities, but I don’t think this is a competition? 🙂)

So in the next experiment, the team treated mice with an anti-fungal, fluconazole (anyone else familiar with that one?). The experimental design is the same as above, except instead of antibiotics, an anti-fungal was used. Results: treatment with anti-fungals increased the effectiveness of radiation therapy by enhancing the effect of radiation therapy on cell death! Love to see that!

More Details

But, what exactly is going on here? Digging deeper, Dr. Shiao’s team found that antibiotic treatment decreased bacterial numbers and increased fungal numbers (specifically, Candida and Saccharomyces species), while anti-fungal treatment had little effect on bacterial numbers but decreased all fungi (though not to zero). They explored this latter finding more extensively by asking, what does a mouse model with normal bacterial numbers but lower fungal numbers mean in terms of radiation therapy? It seems to have a beneficial effect on the immune system enhancing immune activation after radiation therapy AND decreasing immune suppression after radiation therapy. And why do we care? Because an appropriately active immune system should lead to decreased tumor and cancer cells and hopefully increased survival.

But all mouse microbiomes are not created equally- lab mice have different gut microbiomes than wild mice, and you can even raise mice with a known microbiome of your choice, or no microbiome at all (sterile or gnotobiotic mice).

Dr. Shiao’s team created a known/standardized mouse gut microbiome by starting with  microbiome-free mice and adding back only a known bacterial community to the gut (no fungi). They then compared this to a mouse with normal bacteria and fungi. Would the results be similar to their previous studies? Yes! Mice with no fungi and a known bacterial community respond BETTER to radiation therapy in both tumor volume (panel N) and percent survival (panel O). (ASF=a standardized bacterial community; RT=radiation treatment). 

 

Additionally, these tumors are less immunosuppressed and exhibit increased immune activation. Weirdly those two things can co-exist and be beneficial from a cancer standpoint because the immune system is complex with many different cells and cell signals.

Breast Cancer Patients?

But hey, mice aren’t human. We have a lot in common, but there are also clear differences (besides the cute ears). Would patients with breast cancer see a benefit to decreasing the fungal microbiota? Dr. Shiao’s team did find that human breast tumors with more fungal receptors have worse survival, but clearly a LOT more work needs to be done. And I for one am here for it, as both a microbe loving scientist and MBC patient.

 

Finally, I really appreciated Dr. Shiao’s slide on why it took so long to get to where we are understanding the microbiota. It’s not because microbes in and on the body were unknown, but because we didn’t have the tools previously to study these microbes. Basic research into new technologies, techniques, and underlying biology are all important to advancing our knowledge of breast cancer and ultimately life saving treatments.

Questions? Comments? Please feel free to post on the blog or Twitter @amybeumer.

 

Shiao, S. L., Kershaw, K. M., Limon, J. J., You, S., Yoon, J., Ko, E. Y., Guarnerio, J., Potdar, A. A., McGovern, D. P. B., Bose, S., Dar, T. B., Noe, P., Lee, J., Kubota, Y., Maymi, V. I., Davis, M. J., Henson, R. M., Choi, R. Y., Yang, W., … Underhill, D. M. (2021). Commensal bacteria and fungi differentially regulate tumor responses to radiation therapy. Cancer Cell, 39(9), 1202-1213.e6. https://doi.org/10.1016/j.ccell.2021.07.002