By Neil Canavan
“This whole thing is right out of left field –
no one expected it.”
– Immunologist, Thomas Gajewski, MD, PhD, University of Chicago
What no one expected was that the community of commensal microbes that live in and on all of us – collectively referred to as the microbiome – all those billions of bugs – are in direct, beneficial communication with the mammalian immune system, and further, that if a cancer patient is missing some of these bugs, otherwise highly effective cancer treatments won’t work.
Describing this phenomenon are not one, but three papers in the January 5th issue of Science, as well as a multitude of recent scientific presentations. Sparking the idea that the microbiome could work in concert with the human immune system was a pair of observations: first, the finding of immune cells where they should not be, and second, the failure of chemotherapy in patients where typically it should have worked. “That was seven years ago,” says Laurence Zitvogel, MD, PhD, Department of Immuno-Oncology, Institut Gustave Roussy, Villejuif, France, who authored one of the three Science articles (the other two being Tom Gajewski, and Jennifer Wargo, of M.D. Anderson Cancer Center). “Very few people at that time believed in the clinical relevance of the microbiome composition in pathophysiology.”
Yet, Zitvogel had seen some odd things. First, she detected Th17 cells, a type of T lymphocyte of the immune system, in the spleens of mice treated with chemotherapy. “I was surprised by this because these cells normally are originating, or at least residing in the gut,” says Zitvogel. “As an oncologist I thought, since most chemotherapies are provoking some kind of intestinal side effect, anorexia, vomiting, diarrhea, maybe there is a link between the two.” The accumulation of Th17 cells in the spleen – a staging area for the immune system – in the context of chemotherapy suggested a nexus between the gut, and T cell-mediated anti-cancer immuno-surveillance (more on this in a moment).
The second observation: while most of Zitvogel’s patients responded to the standard-of-care chemotherapy agent, cyclophosphamide, other patients who were very similar to the responders, did not. The only difference Zitvogel could find between the two groups was the use of antibiotics by the non-responders.
“We started to talk to other people around us, and we ran into Giorgio Trinchieri, at the NIH,” says Zitvogel, “And he had similar data (with the drug, oxaloplatin) and he said, ‘How bizarre, we both have stumbled on the same realization that antibiotics blunt the efficacy of chemotherapy.’”
And so, the effect was validated, via anecdote, and the hunt was on – Zitvogel went looking for bugs.
“We were helped by the microbiology department, they gave us blood agar plates,” and with them Zitvogel cultured bugs from lymph nodes and spleen. The method was crude – it did not support the growth of important anaerobic bacteria – but it was efficient enough for a reasonable comparison between the microbial populations of mice treated with cyclophosphamide, and with those untreated. Subtracting one from the other, a suite of obvious microbial differences emerged: an abundance of Lactobacillus murinus, and johnsonii, and Enterococcus hirae were found in the spleen and lymph nodes (where theoretically they should not be) in tumor-bearing mice that received chemo (and the chemo worked).
Following up on this, Zitvogel used antibiotics to wipe out the microbiome in her tumor bearing mice, and thereafter, the chemo failed.
So, yes. Bugs affect drugs. This astonishing conclusion was published in Science in 2013.
Zitvogel expanded on this work in the recent 2018 Science article by examining the microbiome of patients treated with immunotherapy, specifically, anti-PD-1, in the setting of non-small cell lung cancer.
The results were striking. As with the observations in mice, patients with a “dysbiosis” an imbalance of certain bugs, did very poorly on treatment. The bug in question this time around was Akkermansia muciniphila, and when reintroduced into a mouse model that mirrored her patients, the effect of the drug was restored.
The implications were immediately obvious. “It’s pretty straight forward,” says Zitvogel. “If patients are now diagnosed with intestinal dysbiosis (using methods soon to be standardized) we will be able to correct, or try to correct the dysbiosis by transferring natural product.” Meaning, bugs. “So indeed, this opens up a therapeutic avenue to use allogeneic fecal transplantation from healthy donors.” It’s simply a matter of finding the right combination of bugs.
Like any transplant, compatibility will be an issue, as Zitvogel casually states in her elegant French accent. “It will take a while to figure out how to choose the good shit (GS) from the bad shit (BS) and then to put that in the right patient.”
And to that end (all BS aside), Zitvogel recently founded a new company, Everimmune, to exploit her microbiome findings.
Microbiome research to date, while already extensive, is still unable to answer the basic question: Which came first – the dysbiosis, or the disease? Jennifer Wargo, MD, associate professor of Surgical Oncology and Genomic Medicine, MD Anderson Cancer Center,author of the third paper in Science, has some ideas.
“My hunch? The microbiome contributes (rather than merely being acted upon).” In further explanation, Wargo invokes the landmark, cancer immunosurveillance hypothesis, as put forth by Robert Schreiber. “Look, from infants to adults, we are all developing these mutations in our normal cells that have the ability to flip a little switch and turn into a cancer. Now, what controls that? Our immune system.” The immune system is on constant patrol for both invaders (infectious agents) and rogues (cancer cells).
But how does it know what to look for?
“Think about it,” says Wargo, “The majority of the bacteria in our body is in your gut. The surface area is huge. And all along that interface where the bacteria are, there’s your intestine, and just on the other side of the intestinal wall there’s immune cells – so there’s a constant interaction between gut bacteria and the immune cells.”
Now, if you did not have all these bugs in your gut – and their related digestive activities – you would die, and the immune system knows that, having been trained to leave the bugs alone. But that education goes beyond the bug’s need for self-preservation. “These bugs, in turn, are going to educate my immune system to better recognize things that (are out of place).” Like cancer cells.
With that understanding, the clinical challenge then becomes trying to determine what bugs are required for this life-saving education. In Wargo’s Science paper, where she investigated the microbiomes of melanoma patients treated with anti-PD-1 agents, the bug of greatest discordance between patients who responded to treatment and those who did not belonged to the Ruminococcaceae family – different from the bugs identified in Zitvogel’s work.
Which is not to say that the two investigators came to different conclusions. According to epidemiologist, Carrie Daniel-McDougall, PhD, MPH,Assistant Professor, Division of Cancer Prevention and Population Sciences, MD Anderson Cancer Center, who is working with Wargo to determine what exactly constitutes a “healthy” microbiome – it turns out that it’s not about the specific bug, it’s about the bug’s generalized metabolic activities. “If you look at what (they) found,” says Daniel, “there’s not much functional difference – they are categorically quite similar.” In general, Wargo’s bugs perform certain anabolic activities – and so do Zitvogel’s. “If you look at correlations between all these bacteria, they are co-occurring under different conditions but performing the same function.”
So again, what to do when you, the cancer patient, lack that microbial metabolic function because of an antibiotic-induced dysbiosis? “Taking a broad-spectrum antibiotic is like burning down your garden,” says Daniel. “Some things might be able to sprout back up again, but other things may not – so leading to lower (unhealthy) diversity, and maybe even letting weeds take over.” Thus far, microbiome research strongly suggests that how the garden grows back is going to be unique to the individual.
“So you have to know what’s there,” says Daniel, because by its very nature, a microbiome therapy is going to be a highly personalized. This reality calls into question the use of probiotics, which oncologists often recommend. “How do you know what probiotic to take if you don’t know what you already have?” asks Daniel. “Without realizing, you could screw up the all the good things that were starting to return.”
As quickly as the mysteries of the microbiome are revealed, so are companies coming into being to commercially develop the field. Zitvogel has her Everimmune, and Wargo is working with the Houston-based, MicrobiomeDX.
“Actually, the idea for the company was partially hatched at a preschool birthday party,” says Katherine Burton, who hails from the genetic testing world, and is now Chief Operating Officer of MicrobiomeDX since its inception in April of 2017.
“I knew Jen through our daughters who go to school together,” says Burton. “And one day we were chatting at a birthday party and struck up a conversation about genetics, and um… poop.” From there, the idea was an easy sell. Burton, and her business partner, Thinh Phan, started looking at the published data on the microbiome as it relates to immunotherapy (IO) response, and quickly realized the potential impact on patient outcomes. “So we thought that, with Jen’s clinical expertise, and our CLEA lab background, it was an opportunity to deliver a succinct tool to help analyze and predict IO responses based on the microbiome.”
The business: A CLEA certified lab that offers 16S next-generation sequencing and analysis of gut microbiome, by way of fecal sampling. The clients: “Pharma and biotech companies that are running clinical trials in which the microbiome might associate with outcome,” says Burton. “And academic researchers of course – and even some practitioners who are attuned to a lot of this data who want to monitor their patients while undergoing treatment.”
Burton is even fielding requests from patients themselves, which can be empowering, because the results are increasingly actionable.
Eat Something (Anything)
Consider the study reported at ASH 2017, a retrospective analysis performed at Memorial Sloan Kettering Cancer Center of patients who underwent an allogeneic stem cell transplant (allo-HSCT, an immunotherapy).
“The causes of mortality after allo-HSCT are relapse and GvHD (graft vs. host disease), infection, and organ toxicity,” says Sloan’s, Jonathan Peled, MD, PhD, who serves as an Assistant Attending in the Adult Bone Marrow Transplantation Service at Memorial Sloan Kettering Cancer Center. “Our group and others have reported associations between intestinal microbiota composition and all of these outcomes, including overall survival.”
Using, a machine learning algorithm to gauge a patient’s microbial diversity, Peled and his team determined that domination of the Enterococcus species is associated with acute, gastrointestinal GvHD – in fact, Enterococcus overgrowth resulted in a 30% greater risk for this deadly, treatment-related complication.
As with the Science studies, microbial dysbiosis was related to antibiotic use in general, and broad-spectrum antibiotics in particular. “But I would point out that almost everybody has a drop (of microbial diversity) regardless of antibiotic, we therefore hypothesize that dietary intake could also be a relevant determinant of microbiota composition,” says Peled. This idea is not mere conjecture. “At our institution, those samples collected on days on which (an antibiotic) was not administered, there was a positive correlation between alpha diversity, and caloric intake for that day.” And there was a reduction in mortality.
In general, these results suggest the need to deploy strategies to repair transplant-induced microbiota injury at the time antibiotics are discontinued.
In particular, Peled encourages his post-transplant patients to hit the cafeteria as soon as they can, especially given his preclinical observations. “You can alter the gut microbiota of a mouse within 24 hours if you alter its diet,” says Peled.
Proving once again that you – and your bugs – are what you eat after all.
About the Contributor
Neil Canavan is the author of the recently published book, A Cure Within: Scientists Unleashing the Immune System to Kill Cancer (Cold Spring Harbor Laboratory Press) available on Amazon.