Faecal Microbiota Transplant

Cancer patients who have run out of options for immunotherapy may have a new possibility. It’s the gut microbiome. By changing the gut microbiome in advanced melanoma patients, who had previously failed to respond to treatment, the body responded to anti-PD-1 immunotherapy. Though the research is in phase II trials, it’s very positive news for those who have little hope.

Researchers at UPMC Hillman Cancer Center and the National Cancer Institute (NCI) demonstrated that changing the gut microbiome can transform patients with advanced melanoma who never responded to immunotherapy, which has a failure rate of 40% for this type of cancer, into patients who do.

The results of this proof-of-principle phase II clinical trial were published online in Science. In this study, a team of researchers from UPMC Hillman administered faecal microbiota transplants (FMT) and anti-PD-1 immunotherapy to melanoma patients who had failed all available therapies, including anti-PD-1, and then tracked clinical and immunological outcomes. Collaborators at NCI analysed microbiome samples from these patients to understand why FMT seems to boost their response to immunotherapy.

Diwakar Davar, M.D., a medical oncologist and member of the Cancer Immunology and Immunotherapy Program (CIIP) at UPMC Hillman and colleagues collected faecal samples from patients who responded extraordinarily well to anti-PD-1 immunotherapy and tested for infectious pathogens before giving the samples, through colonoscopy, to advanced melanoma patients who had never previously responded to immunotherapy. The patients were then given the anti-PD-1 drug pembrolizumab. And it worked.

Out of 15 advanced melanoma patients who received the combined FMT and anti-PD-1 treatment, six showed either tumour reduction or disease stabilisation lasting more than a year.

Study Findings:

• Anti–programmed cell death protein 1 (PD-1) therapy provides long-term clinical benefits to patients with advanced melanoma.
• The composition of the gut microbiota correlates with anti–PD-1 efficacy in preclinical models and cancer patients.
• To investigate whether resistance to anti–PD-1 can be overcome by changing the gut microbiota, this clinical trial evaluated the safety and efficacy of responder-derived faecal microbiota transplantation (FMT) together with anti–PD-1 in patients with PD-1–refractory melanoma.
• This combination was well tolerated, provided clinical benefit in 6 of 15 patients, and induced rapid and durable microbiota perturbation. Responders exhibited increased abundance of taxa that were previously associated with response to anti–PD-1, increased CD8⁺ T cell activation, and decreased frequency of interleukin-8–expressing myeloid cells.
• Responders had distinct proteomic and metabolomic signatures, and trans-kingdom network analyses confirmed that the gut microbiome regulated these changes.

“FMT is just a means to an end,” said study co-lead author Dr. Davar, M.D. “We know the composition of the intestinal microbiome–gut bacteria–can change the likelihood of responding to immunotherapy. But what are ‘good’ bacteria? There are about 100 trillion gut bacteria, and 200 times more bacterial genes in an individual’s microbiome than in all of their cells put together.”

Faecal transplant offers a way to capture a wide array of candidate microbes, testing trillions at once, to see whether having the “good” bacteria on board could make more people sensitive to PD-1 inhibitors. This study is among the first to test that idea in humans.

“The likelihood that the patients treated in this trial would spontaneously respond to a second administration of anti-PD-1 immunotherapy is very low,” said study co-senior author Hassane Zarour, M.D., a cancer immunologist and co-leader of the CIIP at UPMC Hillman as well as a professor of medicine at Pitt. “So, any positive response should be attributable to the administration of faecal transplant.”

Analysis of samples taken from FMT recipients in this study revealed immunologic changes in the blood and at tumour sites, suggesting increased immune cell activation in responders as well as increased immunosuppression in non-responders. Artificial intelligence linked these changes to the gut microbiome, likely caused by FMT.

“Even if much work remains to be done, our study raises hope for microbiome-based therapies of cancers,” said Zarour, who holds the James W. and Frances G. McGlothlin Chair in Melanoma Immunotherapy Research at UPMC Hillman.

Collectively, the findings show that FMT and anti–PD-1 changed the gut microbiome and reprogrammed the tumour microenvironment to overcome resistance to anti–PD-1 in a subset of PD-1 advanced melanoma. Ultimately, the goal is to replace FMT with pills containing a cocktail of the most beneficial microbes for boosting immunotherapy–but that’s still several years away.

Reference:

Davar D, Dzutsev AK, McCulloch JA, Rodrigues RR, Chauvin JM, Morrison RM, Deblasio RN, Menna C, Ding Q, Pagliano O, Zidi B, Zhang S, Badger JH, Vetizou M, Cole AM, Fernandes MR, Prescott S, Costa RGF, Balaji AK, Morgun A, Vujkovic-Cvijin I, Wang H, Borhani AA, Schwartz MB, Dubner HM, Ernst SJ, Rose A, Najjar YG, Belkaid Y, Kirkwood JM, Trinchieri G, Zarour HM. Fecal microbiota transplant overcomes resistance to anti-PD-1 therapy in melanoma patients. Science. 2021 Feb 5;371(6529):595-602. doi: 10.1126/science.abf3363. PMID: 33542131; PMCID: PMC8097968.