Bugs in your gut and cancer immunotherapy

Hello, hello!  Do I still have any readers?  I took a bit of a long hiatus, but I’m back and hopefully I will be posting more regularly.  And I have some news!  As of a few weeks ago, I am one of the newest cohosts for the immunology podcast “Audiommunity” (www.emmunity.org)!  I am pretty excited to have this opportunity to discuss all the latest innovations in immunology with a team of Harvard-trained immunologists.  Of course, I am not a Harvard-trained immunologist, but I’m hoping I can add some value to the podcast by being willing to ask the “stupid” questions (there are no stupid questions, amirite?).  I am also hoping to use my blog space to distill some of the high-level research we will be discussing into slightly more accessible summaries.  So if you don’t know one single thing about cancer immunology or immunotherapy, I want you to be able to come away from my page with some new knowledge.

So, without further ado… On the latest episode of “Audiommunity” (episode 26- Lies and Magic), we discussed a recent research article that looked at how the human gut microbiome might play a role in how well a patient with metastatic melanoma responds to immune checkpoint blockade therapy (check out the paper here).  Okay, lots of big terms in that last sentence, so let’s break it all down slowly:

"So, Doc, see anything in there?"

First, let’s talk about the microbiome.  The microbiome is a collection of genes from all the microbes (ie bacteria, fungi and viruses) that live in and on us.  As you have probably heard, human beings are absolutely covered, head-to-toe and inside-out, with bacteria.  They are on our skin, in our mouths, and, yes, in our guts.  At one time, it was commonly believed that there are more bacterial cells on and in our bodies than human cells, although the most recent estimates put that number closer to one-to-one (read more here).  Still, that’s a lot of bacteria (something like 30 trillion cells!).  We call these communities of bacteria the human microbiota, or the normal “flora” (or as I like to call it, your “gut garden”, heh).

Metastatic melanoma, or stage IV melanoma, is a truly horrible diagnosis to receive.  It is melanoma (skin cancer) that has spread through the lymph nodes to other areas of the body, most frequently the brain, bones, lungs and liver.  The 5-year survival rate, which is the percentage of patients likely to be alive 5-years after diagnosis, is very low, hovering around 15 to 20% (see stats here).  But recent, exciting developments in cancer treatment are beginning to improve those odds, for melanoma and other cancers.  These new treatments are called immune checkpoint blockade, or simply immunotherapy.

Seems legit.

Cancer cells and tumors are very tricky things.  Since they are just our own cells, gone wild, they can hold up signs that tell the cells of your immune system not to attack.  Normally, this is a mechanism that healthy cells use to prevent things like autoimmune reactions or to ramp down an immune response after an infection has been cleared. But when used by cancer cells, this trick becomes a dangerous weapon in a tumor’s arsenal.  

The way this works is the cancer cells express proteins on their surface that bind to proteins on the surface of things like T cells, for example, and these binding events cause the T cells to “shut down”. One of the proteins that these cancers can express is called PD-L1 (for “Programmed cell death ligand-1), and this binds to a protein called PD-1 (“Programmed cell death-1) on the surface of T cells (click here for a brief overview from the American Cancer Society).  

The idea behind immunotherapy is to block this binding event, so that the immune cells can raise the alarm against the cancer and attack it.  Scientists like to refer to this as “taking the brakes off the immune system”.  There are now antibody therapies that can block both PD-L1 and PD-1 (for example, you may have seen TV ads for Merck’s Keytruda®, also called pembrolizumab, a PD-1 inhibitor, and made famous by Jimmy Carter), and these are turning out to be remarkably effective against many different types of cancers (2012 NEJM article).

Top: Tumor expresses PD-L1, binds to PD-1 on T cell, and T cell is shut down.  Bottom: anti-PD-1 antibody binds to PD-1 on T-cell and blocks its interaction with PD-L1 on tumor.  T cells are now able to recognize tumor and attack (and they look pissed).

But despite these advances, sometimes immunotherapies don’t work well in some patients or for some types of cancers, or the improvements don’t last, and no one really understands why.  So in the paper we discussed on Audiommunity this week, the authors set out to try and discover whether the gut bacteria in melanoma patients receiving anti-PD-1 treatments had an effect on how well they responded to the treatments.

 

Outline of the study:

The researchers assembled a group of patients with metastatic melanoma (they started with 112), and they collected blood samples and tumor biopsies, and mouth swabs and stool samples to compare the collections of bacteria in the guts of these patients.  They used a technique called 16S rRNA sequencing to determine which bacteria were present in the samples.  16S rRNA is a gene that all bacteria have (we say that it is “well-conserved”), but it differs just a bit between different species of bacteria, so it can act as a sort of molecular nametag for each of the bugs that are present. The patients then received anti-PD-1 immunotherapy.  And 6 months later, the researchers collected samples again, determined whether patients had any improvement in their disease (whether they responded to treatment), and repeated bacterial sequencing.

Results of the study:

What they found was that patients that had a higher diversity of bacteria in their guts (more species, or different types, of bacteria) did better with the treatment than patients with less diversity.  This isn’t a surprising result, since it is pretty well known that loss of microbial diversity, a condition called dysbiosis, results from, or causes, many types of chronic diseases, including cancer (reviewed here).  They also found that patients with specific types of bacteria had different treatment outcomes.  Patients with higher levels of a genus of bacterium called Faecalibacterium responded better, whereas patients with higher levels of members of the order Bacteroidales did worse.

Left gut: highly diverse, lots of multi-colored "sprinkles" (bacteria). Right gut: less diverse, fewer "sprinkles".

Looking at the data a different way, they found that they could predict which patients responded well to the therapy just by looking at the composition of their gut bacteria.  This is a potentially very useful tool for the clinic, because being able to quickly and easily predict how well a patient will do on a specific type of therapy before even beginning the treatment may save critical time in the course of the cancer.

The researchers also compared the types and numbers of immune cells and markers of immune system activation both around the tumors themselves (the tumor microenvironment), and within the gut.  They found that in general there were higher levels of things like tumor-killing T cells and inflammatory markers in the patients that responded well to treatment, and higher levels of suppressive immune cells in the patients that responded poorly.  However, it is unclear whether the gut bacteria directly led to these particular immune conditions or if this is just an association.

Now this is where the study gets really interesting (in my humble opinion).  They took stool samples from the patients, post-treatment, and transferred them into “germ-free mice”.  These are mice that are born and raised in a sterile environment so that they are not colonized by any microbes; this allows researchers to introduce selected bugs into these mice to study their influence on things like the immune system.  After the transplant the mice now mirrored their human patient counterparts (bacterially speaking).  The mice were then injected with melanoma and given immunotherapy.  The mice that received stool from patients that saw improvement in their disease in the initial study wound up with much smaller tumors and higher levels of tumor-fighting immune cells than the mice that received transplants from the patients who didn’t improve.  To put it more plainly, the bacteria in the poop from patients that had a good response to treatment seemed to help the mice respond well to treatment, too.  Pretty cool, if you ask me!

The take-home message:

The long and short of it is this; specific gut bacteria can affect the way a cancer patient responds to immunotherapy.  What is exciting about this is that you can alter your gut microbiota through diet and exercise, probiotics and antibiotics, and through stool transplants (which are already in use in some diseases like Clostridium difficile infection (CDI), to good effect).  This means that it's possible that just some simple tweaks to the bacterial composition of your gut may make immunotherapy even more effective, and the authors of this study are already designing a clinical trial that combines immunotherapy with microbiome alteration (according to this press release).  However, it is important to be clear that despite these promising results, patients should not try to treat themselves with things like probiotics without the express permission of their doctor (***I am not that kind of "doctor”, and nothing in this article or on my blog should be taken as medical advice!!).

So that's all for now, folks.  Please feel free to send me questions, and check back in about a week for my next summary!

Additional Note: the images featured in this post are my own, hand-drawn, mixed-media creations!

Paper reference: 

V. Gopalakrishnan, C. N. Spencer, L. Nezi, A. Reuben, M. C. Andrews, T. V. Karpinets, P. A. Prieto, D. Vicente, K. Hoffman, S. C. Wei, A. P. Cogdill, L. Zhao, C. W. Hudgens, D. S. Hutchinson, T. Manzo, M. Petaccia de Macedo, T. Cotechini, T. Kumar, W. S. Chen, S. M. Reddy, R. Szczepaniak Sloane, J. Galloway-Pena, H. Jiang, P. L. Chen, E. J. Shpall, K. Rezvani, A. M. Alousi, R. F. Chemaly, S. Shelburne, L. M. Vence, P. C. Okhuysen, V. B. Jensen, A. G. Swennes, F. McAllister, E. Marcelo Riquelme Sanchez, Y. Zhang, E. Le Chatelier, L. Zitvogel, N. Pons, J. L. Austin-Breneman, L. E. Haydu, E. M. Burton, J. M. Gardner, E. Sirmans, J. Hu, A. J. Lazar, T. Tsujikawa, A. Diab, H. Tawbi, I. C. Glitza, W. J. Hwu, S. P. Patel, S. E. Woodman, R. N. Amaria, M. A. Davies, J. E. Gershenwald, P. Hwu, J. E. Lee, J. Zhang, L. M. Coussens, Z. A. Cooper, P. A. Futreal, C. R. Daniel, N. J. Ajami, J. F. Petrosino, M. T. Tetzlaff, P. Sharma, J. P. Allison, R. R. Jenq, J. A. Wargo Gut microbiome modulates response to anti–PD-1 immunotherapy in melanoma patients. Science, 2017 DOI: 10.1126/science.aan4236