529

news

Fecal microbiota potentiate checkpoint inhibitors, unleash microbiome startupsMicrobiome companies are scrambling for a piece of the action as checkpoint inhibitors combined with fecal microbiome transplants enhance patient responses to immunotherapy.

Two papers published in Science provide the first clinical evidence that fecal microbial transplants

(FMTs) can boost the anti-cancer efficacy of immune checkpoint inhibitors. At least eight microbiome companies have launched first-in-human trials pairing their microbiome agents with approved immunotherapies (Table 1) to satisfy the growing need to increase the proportion of patients responding to checkpoint inhibitors.

“Immune checkpoint inhibitors are terrific,” says Danny Bar-Zohar, global head of development at Merck KGaA in Darmstadt, Germany. “But the vast majority of people still don’t respond.” Various mechanisms may be at play, some related to patient genomics or proteomics, but new data reinforce a role for the gut microbiome in modulating patient response.

The two early-stage clinical studies cross-validate each other, says Gal Markel, an immuno-oncologist at Tel Aviv University and a coauthor on the first paper. “It’s very powerful that two independent groups show exactly the same thing.” Both studies took gut microbes from patients with metastatic melanoma who had responded to anti–programmed cell death protein 1 (PD-1) therapy and transplanted them into patients who had never responded or had stopped responding to these drugs. Of ten patients studied in the first paper, three of five patients receiving an FMT from one donor had an objective response, including one complete response. Of the five who received a FMT from the other donor, two responded and two had stable disease.

In the second paper, a group led by researchers from University of Pittsburgh and the US National Cancer Institute (NCI) describe a two-stage, single-center study of concurrent FMT with a checkpoint inhibitor in patients with melanoma refractory to

PD-1 inhibitor treatment. They report that 3 of 16 individuals treated with FMT experienced an objective response, including 1 complete response, and 3 more had durable stable disease.

Small differences between the trials make it difficult to draw specific conclusions. In the first trial, with Bristol Myers Squibb’s (BMS’s) Opdivo (nivolumab)—a fully human IgG4 monoclonal antibody (mAb) that targets the PD-1 receptor—patients

were treated with antibiotics to clear their existing gut microbiome before receiving FMT both via colonoscopy and in oral capsules. In the second study, in which patients were treated with Merck’s checkpoint inhibitor Keytruda (pembrolizumab)—a fully human Ig4κ mAb that targets PD-1 receptor ligand 1 (PD-L1) and PD-L2—the researchers avoided antibiotics owing to mounting evidence that antimicrobial drugs can negatively impact

Gut bacteria influence patients’ responses to cancer immunotherapy, a finding that has brought a flurry of studies to test them as combinations. Credit: Steve Gschmeissner/Science Photo Library

Biotech news from around the globe p535

T-cell-immunity COVID-19 test p533

GM moth as pest control p532

IN this section

NaTure BIOTeChNOlOGy | VOL 39 | May 2021 | 529–539 | www.nature.com/naturebiotechnology

530

news

cancer patients’ survival. The FMT was from a single donor and delivered by colonoscopy.

Nonetheless, there are similarities. Hassane Zarour, a medical researcher at the University of Pittsburgh Medical Center Hillman Cancer Center and coauthor of the second paper, notes that typically fewer than 10% of patients who fail to respond initially to anti-PD-1 therapies can become responders. Whereas in his trial 44% of patients responded with at least stable disease, and half did so in the other study. “It’s not statistical proof, but it’s clearly much more than expected.”

The notion that gut microbes might influence cancer patients’ responses to immunotherapy came to light soon after the first checkpoint inhibitor, Keytruda, was approved in 2015. At the time, Laurence Zitvogel, an immunologist and oncologist at Institut Gustave Roussy, used a mouse model to link the commensal bacterial strain Bacteroides fragilis with the antitumor immune response seen with cytotoxic T lymphocyte (CTL) antigen 4 (CTLA-4)-blocking antibodies, and connected the strain’s presence in the gut to a clinical response to Yervoy (ipilimumab), an IgG1κ mAb against CTLA-4, in patients with

melanoma. Subsequently, a team at the University of Chicago led by oncologist Thomas Gajewski showed that bacteria from a distinct genus, Bifidobacterium, improved the efficacy of an anti-PD-L1 agent in mouse models of melanoma. Another landmark paper came in 2018, when researchers led by oncologist Jennifer Wargo at the University of Texas MD Anderson Cancer Center identified the Ruminococcaceae family of bacteria as key to a clinical response to anti-PD-1 therapies in humans.

Gajewski’s research led to a partnership with Evelo Therapeutics, a company that launched one of the earliest microbiome–checkpoint inhibitor combination clinical trials, in 2019, testing a single strain of Bifidobacterium animalis lactis both as a monotherapy and in partnership with Merck’s Keytruda. Evelo, which is developing therapeutics based on both single bacterial strains and extracellular vesicles derived from them, presented interim trial data with Merck in December 2020 showing the B. animalis lactis–Keytruda therapy was safe and well tolerated. Even so, it has since shelved the program in favor of EDP1908, an extracellular vesicle therapy derived from an undisclosed Oscillospiraceae species

that has shown potent activation of effector lymphocyte populations in the tumor microenvironment.

Single strains have certain practical advantages over FMTs: they are simpler to characterize and manufacture. As a result, several drug developers are pursuing this route. 4D Pharma, for example, located in Leeds, UK, is testing MRx0518, an orally delivered strain of Enterococcus gallinarum that functions as a Toll-like receptor (TLR)-5 agonist, in phase 1/2 trials combined with Keytruda. Interim data announced last year showed the therapy was well tolerated in 12 patients with renal cell carcinoma and non-small-cell lung cancer that previously had been refractory to immune checkpoint inhibitors. “We’re seeing very similar biology in the tumor post-treatment” compared with what was reported in the recent FMT studies, says Alex Stevenson, CSO of 4D. Merck and 4D plan to expand the cohort to include up 120 patients with renal cell carcinoma, non-small-cell lung cancer or other solid tumors that had been unresponsive to immunotherapy.

In February, 4D announced a partnership with two other companies, Merck KGaA and Pfizer, to launch a phase 1 trial for MRx0518

Table 1 | Selected companies with microbiome or microbiome-derived product–checkpoint inhibitor combinations in the clinic

Companies Microbiome-based therapy

Checkpoint inhibitor

Indication Type of microbiome-based intervention

Clinical stage

4D Pharma, Merck MRx0518 Keytruda Solid tumors not responding to Keytruda

E. gallinarum strain Phase 2

4D Pharma, Merck KGaa, Pfizer

MRx0518 Bavencio Locally advanced or metastatic urothelial carcinoma

E. gallinarum strain Phase 1

Enterome EO2401 Opdivo Recurrent glioblastoma Cocktail of microbiome-derived derived peptides with homology to tumor-associated antigens

Phase 1b/2a

Enterome EO2401 Opdivo adrenal tumors Cocktail of microbiome-derived derived peptides with homology to tumor-associated antigens

Phase 1/2

Genome & Company, Merck KGaa and Pfizer

GEN-001 Bavencio Solid tumor Enteric-coated capsule encapsulating Lactococcus lactis

Phase 1

Synlogic, Roche SyNB1891 Tecentriq advanced solid tumors and lymphoma

E. coli Nissle engineered with diadenylate cyclase gene and dual dapA and thyA auxotrophies

Phase 1

Vedanta Biosciences, BMS

VE800 Opdivo advanced or metastatic cancers

11-strain consortium of non-pathogenic, non-toxigenic, commensal bacterial strains functionally identified as activating CTLs in mice

Open-label phase 1

Osel CBM588 yervoy and Opdivo

Stage IV or advanced renal cell carcinoma

Clostridium butyricum Phase 1

NuBiyota MET-4 Unnamed anti-PD-1 or -PD-L1 mab

advanced or metastatic solid tumors

Bacterial consortium possibly selected by culturing to form a stable community

Open-label phase 1

NaTure BIOTeChNOlOGy | VOL 39 | May 2021 | 529–539 | www.nature.com/naturebiotechnology

531

news

in combination with the latter’s Bavencio (avelumab), a human IgG1λ mAb against PD-L1. Bavencio is the only immunotherapy approved for locally advanced or metastatic urothelial carcinoma, and the trial will test the combination as first-line maintenance therapy in patients with that cancer. The South Korean microbiome outfit Genome & Company of Seongnam is also testing Bavencio with GEN-001, an enteric-coated capsule containing ≥1×1011 colony-forming units of Lactococcus lactis, identified by 16S ribosomal RNA profiling of microbiota from lung cancer patients who responded to immunotherapy. The investigators dosed their first patients in a phase 1/1b trial in solid tumors last year.

Transferring whole microbiota—communities present in stool—to a new recipient, however, has a much longer clinical track record than the use of single microbial strains or live microbial biotherapeutic products (LBPs) consisting of defined consortia to intervene in disease. FMTs are generally safe; they are delivered by colonoscopy or oral formulation and are performed regularly as part of the standard of care in other disease areas, like recurrent Clostridioides difficile infection.

Thus far, the latest guidance from the FDA on FMT development is a 2016 document specific to use in the treatment of C. difficile infections. In 2019, when two immunocompromised FMT recipients developed invasive infections of antibiotic-resistant Escherichia coli, it prompted the FDA to require FMT developers to perform additional screening for multi-drug-resistant bacteria in their products. This was again updated last April to address an infection risk from SARS-CoV-2 in FMTs. As FMTs are developed for use in cancer immunotherapy, these products would likely follow along similar lines.

According to Giorgio Trinchieri, chief of the Laboratory of Integrative Cancer Immunology at NCI, “They cannot regulate [FMTs] as strictly in terms of composition as they would with any normal biologic.” And, he says, the variability in product composition and additional screening procedures now required to remove potential of pathogens from FMT donor samples is likely to make the development of these products more challenging.

Trinchieri, who is a coauthor on the FMT paper that eschewed antibiotics, also notes that the question of colonization adds complexity. Adding a FMT to a preexisting microbiome creates a new ecology. “When you give 1 species or 10 or 20 species, you have to be sure that those species colonize in the patient, and

what you get in the end is change that is stable and favorable.”

The search for simpler more defined products is prompting microbiome companies to use FMT as a starting point to discover specific microbial strains for incorporation into a LBP. Ella Therapeutics, of which Markel is scientific cofounder and chief medical officer, is taking this approach by studying the gut microbiomes of checkpoint responders. Meanwhile, Microbiotica of Cambridge, UK, has screened patients whose disease did respond to immunotherapy and has identified nine strains that can predict a patient’s response. The resulting microbial signature can be used as a biomarker by other companies to predict immunotherapy response. The defined consortium of nine strains is also the basis for an LBP, with different bacteria in the mixture promoting specific steps in tumor immunity, such as the maturation of dendritic cells, CTL priming via interleukin-12, CTL activation via TLR-3, and CTL tumor cell killing via a T helper 1 (TH1)-directed response.

Vedanta Biosciences is also pursuing defined consortia of bacterial strains to achieve good colonization in the gut while avoiding the inherent unpredictability of FMT. The company’s lead agent, VE800—an 11-strain combination—is in a phase 1 trial with BMS’s Opdivo. (BMS made an equity investment in Vedanta in conjunction with the trial.) “We can shape response and get better colonization, but with a known product,” says Bernat Olle, CEO of Vedanta.

Not all defined bacterial formulations have met with success. Earlier this month, Seres Therapeutics announced it will be discontinuing a phase 1 trial with BMS at the Parker Institute for Cancer Immunotherapy and MD Anderson for SER-401, a defined consortium of bacterial spores, in metastatic melanoma with Opdivo. Although the company announced SER-401 was safe and well-tolerated, it decided to “deprioritize further development of SER-401” and pursue other programs.

Rather than rely on consortia of defined unmodified strains, yet another approach is to create LBPs using molecular engineering. Synlogic’s engineered Escherichia coli Nissle strain (SYN1891) is designed to be injected straight into tumors in a similar fashion to that pioneered by William Bradley Coley more than 130 years ago. SYNB1891 contain a diadenylate cyclase gene from Listeria monocytogenes and two other genes—dapA (encoding dihydrodipicolinate synthase, involved in lysine biosynthesis) and thyA (encoding thymidylate synthase, involved in thymidine biosynthesis)—under the control of a promoter that switches on only

NaTure BIOTeChNOlOGy | VOL 39 | May 2021 | 529–539 | www.nature.com/naturebiotechnology

First Car-T therapy to target BCMa gets FDa nodThe US Food and Drug Administration (FDA) has approved a chimeric antigen receptor (CAR)-T cell immunotherapy for the treatment of multiple myeloma. The first-in-class BCMA-directed CAR-T therapy received the agency’s go-ahead on 26 March for treating adults with relapsed or refractory multiple myeloma, a hematologic neoplastic disease. The results from the pivotal phase 2 studies with Abecma (idecabtagene vicleucel) were published in the New England Journal of Medicine. The approval was based on the KarMMa trial of 127 patients, 100 of whom received Abecma, a genetically modified autologous T cell immunotherapy. Their overall response rate was 72%, and 28% saw a stringent complete response. Abecma is a personalized one-time treatment with 300–460 × 106 CAR-T cells and comes with a boxed warning that includes toxic hematologic effects and cytokine release syndrome.

The CAR-T cell therapy, developed by partners Bristol Myers Squibb and bluebird bio, recognizes and binds BCMA (B cell maturation antigen), a cell surface protein that is almost always expressed on cancer B cells in multiple myeloma. This restricted pattern of expression on plasma cells has made BCMA the antigen of choice for many myeloma immunotherapies in development, including other CAR-T cells and bispecific antibodies. In 2020, an antibody–drug conjugate made by GlaxoSmithKline, Blenrep (belantamab mafodotin), was approved by the FDA and the European Commission. Blenrep combines a humanized monoclonal antibody specific for BCMA with a cytotoxic agent that inhibits microtubule polymerization: monomethyl auristatin. For Bristol Myers Squibb, this is the second CAR-T cell therapy approval. The first was the CD19-directed agent Breyanzi (lisocabtagene maraleucel). BMS and bluebird will jointly market the drug at a list price of $419,500.

Published online: 12 May 2021 https://doi.org/10.1038/s41587-021-00929-0

532

news

in the hypoxic tumor microenvironment. This conditional auxotrophy seeks to limit replication of SYN1891 to the desired malignant tissue. Needless to say, such engineered LBPs—which have never been encountered by the human body—are likely to be given the highest level of scrutiny by the FDA.

According to Richard Riese, Synlogic’s chief medical officer, the heterologous diadenylate cyclase increases levels of cyclic dinucleotide 2′,3′ guanosine monophosphate–adenosine monophosphate (cGAMP), a signaling molecule in the STING (stimulator of interferon genes) protein pathway that is taken up preferentially by antigen-presenting cells, stimulating CD4+ and CD8+ T cell responses. Riese says that other investigators have shown gastrointestinal activation of antitumor immunity, but the effect is indirect compared with that of tumor-site injection; as yet, no one has been able to tap gut mechanisms with a successful

drug or LBP. Synlogic is testing SYNB1891 in phase 1 trials with the anti-PD-L1 Tecentriq (atezolizumab), an Fc-engineered, humanized, non-glycosylated IgG1κ mAb from Roche targeting PD-L1, and as a monotherapy in solid tumors and lymphoma.

A final approach is to focus instead on peptides derived from the microbiota. Enterome, headquartered in Paris and Cambridge, Massachusetts, is testing microbiome-derived peptide antigens, which the company says stimulate an immune response to the tumors, in two phase 1/2 trials combining Opdivo with EO2401, in collaboration with BMS.

For now, companies and researchers still have more questions than answers. NCI’s Trinchieri says it remains unclear which bacteria are responsible for therapeutic responses in which patients, for which tumors, and on which checkpoint inhibitors. “It’s not so clear that what’s good for CTLA-4 is good for PD-1,” he

says. Bacteroides, for one, seem to have a positive effect with anti-CTLA-4 therapies but negative effects with anti-PD-1 ones. “Right now, I won’t say that you can just extrapolate from one immune checkpoint inhibitor or one type of tumor to another.” Of five published clinical microbiome studies on checkpoint inhibitor response, each report associates different species with response: the 2017 paper from Arthur Frankel associates Bacteroides caccae; the Zitvogel 2018 paper, Akkermansia muciniphila; the Gajewski 2018 paper, Bifidobacterium longum; the Wargo 2018 paper, Faecalibacterium sp. and Faecalibacterium prausnitzii; and the Markel 2021 paper, Enterococcaceae, Enterococcus and Streptococcus australis. ❐

Mark ZipkinHaddon Township, NJ, USA

Published online: 16 April 2021 https://doi.org/10.1038/d41587-021-00002-w

NaTure BIOTeChNOlOGy | VOL 39 | May 2021 | 529–539 | www.nature.com/naturebiotechnology

AGBIOTECH

Armyworm meets Friendly mothThe fall armyworm moth, a pest so named for its caterpillar’s invasive and destructive behavior, may now have to contend with a ‘Friendly’ foe. UK-based Oxitec and agbiotech giant Bayer have jointly developed a genetically modified variety to combat the fall armyworm (Spodoptera frugiperda), an insect pest causing severe destruction to corn, rice and sorghum crops in more than 100 countries. Brazil has approved field trials of the GM ‘Friendly’ fall armyworm moths. The technology, originally developed at Oxford University, uses male self-limiting fall armyworm moths. When males are released into infested areas, the moths mate with wild females, but as they produce no female offspring in the next generation, this reduces the population of crop-eating caterpillars. The approach is species specific, is self-limiting in the environment, and has no impact on beneficial insects such as bees. Oxitec has successfully used the technology with mosquitoes to control dengue and Zika in Brazil, and is currently releasing Friendly mosquitoes in the Florida Keys as part of a US Environmental Protection Agency trial. Though some groups remain opposed to the technology, most experts agree that GMOs must be part of an integrated pest management solution,

in addition to rotating crops, encouraging the growth of a pest’s natural predators, and using pesticides selectively to mitigate resistance buildup. ❐

Michael Francisco

Published online: 12 May 2021 https://doi.org/10.1038/s41587-021-00932-5

Natural History Collection / alamy Stock Photo