Enhancing CRISPR: Utilizing Single-Cell Multiomics for CRISPR-based Drug Product Analysis

Contributed Commentary By Matthew H. Cato, Mission Bio 

April 5, 2024 | The pace at which CRISPR has transitioned from a research tool to a therapeutic modality is remarkable. Initially targeting genetic diseases, CRISPR holds tremendous promise across various indications, rapidly expanding into oncology and infectious diseases, indicating CRISPR's vast and continual evolution as a modality. The recent approval of the first drug utilizing CRISPR-Cas9 systems for gene editing marks the beginning of a wave of similar approvals expected in the near future.  

Today, drug developers are focusing on enhancing CRISPR by developing simpler editing systems with higher specificity and improved targeting capabilities. However, while this technology is poised to profoundly influence how the biopharma industry discovers and develops the next generation of CRISPR-based medicines, innovators must leverage tools that can evaluate editing outcomes to ensure these therapies are safe and effective for patients throughout the entire drug development, clinical, and commercial timeline. 

Ultra-Deep Characterization With Single-Cell Multiomics 

We are now witnessing the proliferation of CRISPR editing tools and more complex editing systems for therapies and modeling disease, rapidly increasing the pace at which we can now edit multiple targets within the same cell.  

To ensure the safety and efficacy of CRISPR-based products we need to determine how these modifications occur within individual cells, discerning whether an edit has affected one or both alleles. Traditional bulk PCR analysis with next-generation sequencing does not accurately identify whether one or multiple target sites are modified within an individual cell or a population of cells (co-occurrence of edits), or the zygosity of edits (whether the edit is mono- or bi-allelic). 

Single-cell multiomics, which enables the analysis of DNA and protein simultaneously from the same cell, provides the means to deeply characterize heterogeneous cell populations post-editing, including unintended modifications that may occur despite the specificity of the gene editing tool. This single-cell approach is vital for ensuring the safety and efficacy of CRISPR-based therapeutics, particularly in detecting potential unintended outcomes. These events may arise from off-target editing at the wrong site or significant genomic alterations, such as large deletions. Low-throughput methods or traditional bulk detection technologies may miss these events, causing them to increase undetected over the patient's lifetime. Single-cell multiomic methods, which are highly specific and sensitive, can detect these rare or low-occurrence events, offering drug developers a more comprehensive data package to provide to regulatory bodies, and providing a more precise and reproducible picture of the safety and efficiency of edits. 

Navigating the Path: From Discovery to Market 

Beyond initial safety and efficacy evaluation, the depth of single-cell multiomics extends into the drug manufacturing processes and development parameters. Identifying subtle changes becomes imperative as products progress from small batches to large-scale, clinical production for broader patient populations. By adopting a holistic approach and leveraging single-cell analysis across various stages of drug development, companies can mitigate risks and gain comprehensive insights, enhancing the likelihood of successful drug approval and market entry. 

Single-cell multiomics can be used in pre-clinical and IND-enabling studies to help establish safety, bio-distribution, and mechanisms of action of drug products in animal models. Additionally, as part of the chemistry manufacturing and control (CMC) and process development, single-cell multiomics aids in establishing assays for characterization and creating tests essential for utilization in clinical trials.  

Further down the drug development timeline, single-cell approaches can extend to regulated laboratory settings, such as GMP facilities, where they assist in characterization and release testing, and then later for patient monitoring, capturing responses to the drug and any phenotypic changes occurring over time. Given the prolonged follow-up required after patients receive the therapy, single-cell tools have the potential to be invaluable across the lifetime of the patient. 

Single-cell multiomics has versatile applications across various stages of research and development and commercialization. Whether in early animal studies assessing safety, late-stage research for process development in drug manufacturing, or after-market analysis, its utility is evident.  

The Future of Single-Cell Multiomics 

There is a huge need to shift from bulk next-generation sequencing to single-cell multiomics across various domains, such as advancing gene therapies and elucidating CRISPR genome editing and gene delivery systems for comprehensive drug product characterization, development, and patient evaluation. Single-cell multiomics offers incredible insights into the heterogeneity inherent in biological samples, whether in drug products, tissue biopsies, or patient specimens.  

With single-cell multiomics, we have the opportunity to usher in a new era of precision and depth finding better cures for hard-to-treat diseases by building safer, more effective therapeutics and ultimately, saving more patient lives. 

Matthew H. Cato is Vice President Business and Strategic Market Development at Mission Bio, a leader in single-cell multiomic solutions for precision medicine. With a background in immunology and biotechnology, he focuses on strategic commercial development for single-cell technology to advance cell and gene therapeutic solutions. He can be reached at cato@missionbio.com.