Recent News 13 : First Cancer Patient Dosed in Groundbreaking CRISPR-Engineered Phage Therapy: SNIPR Biome Advances SNIPR001 into Phase 1b Trial

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First Cancer Patient Dosed in Groundbreaking CRISPR-Engineered Phage Therapy: SNIPR Biome Advances SNIPR001 into Phase 1b Trial

Copenhagen-based biotech SNIPR Biome has reached a major milestone, today the 12th of June, in the development of precision antimicrobials by dosing the first cancer patient in its Phase 1b clinical trial of SNIPR001, a next-generation therapy that harnesses the power of CRISPR-Cas systems combined with bacteriophage technology. This innovative approach marks a significant advancement in the fight against antimicrobial resistance, particularly in vulnerable haematological cancer patients undergoing stem cell transplantation—a population at heightened risk of life-threatening bacterial infections.

Trial Overview and Patient Population

The Phase 1b study is a randomized, double-blind, placebo-controlled trial involving 24 patients with haematological malignancies across eight leading clinical centers in the United States. These patients are undergoing allogeneic or autologous hematopoietic stem cell transplantation (HSCT), a life-saving but immunosuppressive procedure that significantly elevates the risk of systemic infections.

Among this immunocompromised group, Escherichia coli is a major clinical threat, accounting for 25–30% of bacteremia (bloodstream infection) cases, particularly during the neutropenic phase following chemotherapy or conditioning regimens. Alarmingly, up to 65% of E. coli bloodstream isolates in this setting are resistant to fluoroquinolones, a class of antibiotics often used prophylactically.

Why This Matters: The Problem with Current Treatments

Current prophylactic approaches rely heavily on broad-spectrum antibiotics such as ciprofloxacin, which are becoming increasingly ineffective due to resistance. Moreover, these antibiotics indiscriminately disrupt the gut microbiota, leading to collateral damage such as Clostridioides difficile infections, fungal overgrowth, or the emergence of multi-drug resistant (MDR) organisms. The World Health Organization (WHO) and Centers for Disease Control and Prevention (CDC) have both emphasized the urgent need for alternatives to conventional antibiotics, especially in high-risk patient groups.

SNIPR001: A Precision-Engineered Solution

SNIPR001 represents a radical shift from traditional antibiotics. It is composed of four complementary CRISPR-Cas armed bacteriophages (CAPs), each specifically designed to target and eliminate fluoroquinolone-resistant E. coli strains in the gut without affecting beneficial microbial populations.

The therapy was developed through the screening of 162 wild-type bacteriophages against 429 phylogenetically diverse E. coli strains collected from global clinical isolates. From this process, SNIPR Biome identified and genetically engineered the most effective phages, enhancing their specificity through two key innovations:

  1. Tail fiber modification – enables phages to better recognize and bind to specific bacterial surface structures.

  2. CRISPR-Cas integration – equips each phage with a programmable system to precisely degrade bacterial DNA, thereby increasing killing efficiency and reducing the risk of phage resistance.

This combination allows SNIPR001 to act surgically within the microbiome, targeting only the pathogenic, drug-resistant E. coli strains while preserving commensal species that support immune function, metabolism, and intestinal barrier integrity.


Figure 1. An overview of the SNIPR001 creation process. Wild-type phages screened against diverse E. coli strains, then engineered with tail fibers and CRISPR-CAS systems to create four complementary CAPs targeting fluoroquinolone-resistant E. coli in neutropenic cancer patients. Reproduced under the Creative Commons License from Gencay et al. (2023) https://doi.org/10.1038/s41587-023-01759-y

Phase 1a Safety Data: Strong Foundations

This new Phase 1b study builds on robust safety and pharmacodynamic data from the preceding Phase 1a trial, which was conducted in healthy human volunteers and co-funded by CARB-X (Combating Antibiotic-Resistant Bacteria Biopharmaceutical Accelerator). In that trial, SNIPR001 showed:

  • No serious adverse events

  • Effective colonization and targeted engagement of E. coli in the gut

  • Minimal disruption to the overall microbiota composition

  • Favorable pharmacokinetic and pharmacodynamic profiles

Dr. Christian Grøndahl, Co-founder and CEO of SNIPR Biome, commented:

“This milestone builds upon the highly encouraging data from our CARB-X funded Phase 1a trial in healthy volunteers, where SNIPR001 demonstrated promising safety and target engagement. We are proud to be advancing a highly differentiated and precision-based antimicrobial approach into a vulnerable patient population where current therapies are increasingly failing.”

A Novel Therapeutic Modality with Broad Implications

SNIPR001 represents more than a new drug—it exemplifies a paradigm shift in infectious disease treatment, where programmable antimicrobials can be tailored to specific pathogens, resistance genes, or patient microbiomes.

Dr. Erin Duffy, Chief of R&D at CARB-X, added:

“SNIPR001 represents a scientifically innovative strategy that could contribute to addressing an urgent clinical challenge in preventing drug-resistant infections in vulnerable cancer patients. It’s also an important validation of the potential of CRISPR-armed phage therapy.”

This clinical advancement also highlights the synergistic power of synthetic biology, genomics, and microbiome science to create next-generation therapeutics that could circumvent the global antibiotic resistance crisis.

Next Steps and Broader Vision

Pending the outcomes of the Phase 1b trial, SNIPR Biome plans to expand the development of SNIPR001 into larger Phase 2 studies and explore similar CRISPR-armed phage constructs for other pathogens, including Klebsiella pneumoniae, Pseudomonas aeruginosa, and Clostridioides difficile.

The company’s broader platform has the potential to custom-engineer phages against virtually any bacterial pathogen, with ongoing research into applications for oncology, inflammatory bowel disease (IBD), and surgical infection prevention.



References:

https://crisprmedicinenews.com/news/first-cancer-patient-dosed-in-crispr-armed-phage-therapy/

SNIPR Biome Press Release

Gencay et al., Nature Biotechnology (2023): https://doi.org/10.1038/s41587-023-01759-y

WHO & CDC reports on antimicrobial resistance

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