Guest Column | November 1, 2021

How Single-Cell Multi-Omics Will Accelerate Cell And Gene Therapy Development

By Yan Zhang, Ph.D., CEO, Mission Bio


For those of us working in the cell and gene therapies space, the mounting enthusiasm is palpable. We’ve seen the first therapies breakthrough, some curative medicines for intractable disease, and we also see skyrocketing investment and bustling pipelines. But outside our bubble, much of the focus is on lingering concerns around several remaining obstacles — notably, characterizing therapies sufficiently and early enough in development to avoid costly surprises and preventable complications later in clinical stages.

Cell and gene therapies are a growing target for those critics. The start of this year was the strongest financing half on record for regenerative medicines, and there are now over a thousand advanced therapy developers in the world, with more than half in North America. The efforts of these companies have led to 2,600 clinical trials so far, and the space is expected to triple over the next five years.

That should all be unmitigated good news. But several recent clinical delays highlight that the pathway for cell and gene therapy approval won’t be smooth. Cell-based therapeutics are inherently heterogeneous due to their biological nature as a “living drug.” And when patient safety concerns arise, the need for thorough characterization becomes all the more pressing, as regulators need to understand the product in all of its complexity.

Several elements drive this complexity. There may be variation in cell lineage or state — for instance, hematopoietic stem cells may differentiate into different cell types. And when a cell therapy is engineered using viral vectors or gene-editing tools, cells are likely to vary in the alterations they contain, potentially affecting safety or efficacy. Cells transduced with a lentiviral vector will differ in transduction efficiency and the number of copies incorporated into the genome. Cells edited by a gene-editing tool, like CRISPR, may be variable in on- and off-target editing, as well as other aspects like zygosity and aberrant translocations. When a therapy requires multiple edits, we should expect heterogeneity of edits across the cells, including edit co-occurrence and zygosity.

As all the recent news headlines remind us, we need better analytical methods to understand the therapeutics that are being produced more comprehensively. Regulators require high-quality Chemistry, Manufacturing and Controls (CMC) and analytics, assessing multiple attributes to ensure safety and efficacy. The rapid development of new cell and gene therapies is, in many ways, outpacing our ability to adequately characterize them. But that pace is driven by the urgent medical need these therapies are addressing, and the high impact we know they can have.

If thorough cell and gene characterization were easy, everyone would already be doing it. Conventional methods are often complex, utilizing multiple platforms and instruments, and the data outputs from each must be harmonized to gain meaningful insights. Making cells available for all these platforms in parallel can be a challenge, and bulk analytic methods that output averages will by definition fail to capture cell-to-cell variation. Additionally, cell and gene therapy samples are limited — every sample taken from a product is less therapeutic available for a patient. Add it all together and conventional characterization is a cumbersome, expensive, imprecise, and time-consuming process that may still fail to fully capture the detail that companies and regulators need.

This is where single-cell multi-omics shines. Workflows that capture and assess genotype and phenotype from the same cell at scale are already established as research tools, leading to insights that are changing our understanding of diseases and how they’re treated. Much of the work so far has been in the cancer space, but increasingly, researchers are utilizing single-cell multi-omics tools to analyze engineered cells, and we expect this number to grow rapidly in the next few years. But until recently, no commercial tools were available to bring this approach to bear on characterizing cell and gene therapies.

Mission Bio’s Tapestri Cell & Gene Therapy Solutions is the first and only such tool on the market today. Our workflow starts with antibody-oligo conjugates, used to tag each cell-surface marker with an oligonucleotide. The sample is deposited in a Tapestri cartridge, where individual cells are encapsulated in oil droplets with a protease, which releases the DNA. Next, targeted DNA and protein-specific oligos are tagged with a cell-specific barcode during target amplification. Because DNA and cells-surface proteins are measured simultaneously, data outputs include genotype and immunophenotype from thousands of individual cells. Data readouts are compiled in a comprehensive report detailing custom aspects of an engineered cell product, reflecting both genotypic data and immunophenotypic data from the same sets of cells.

Now that the tools are available, the possibilities are intriguing. For cells genetically altered using viral editing tools, single-cell characterization allows for measuring vector copy number and transduction efficiency. For cells edited using CRISPR or other gene-editing tools, it can quantify on-target CRISPR editing alongside off-target and translocation events. And in all events, the measurements can be paired with immunophenotypic markers to further enrich the dataset, providing information about each cell type and state.

Measuring all these parameters in a single assay is much quicker than conventional workflows. Traditionally, following successful transduction or transfection, cells first need to be enriched prior to analysis. To identify cell-specific edits, individual cells must be separated and clonally outgrown, which often takes weeks. Once clones have been expanded, genomic analysis is typically accomplished through sequencing or PCR. This places limitations both in terms of timelines and the ability to feasibly pursue multiple simultaneous edits.

By contrast, a single-cell multi-omics assay allows for bypassing cell enrichment and clonal outgrowth, meaning thousands of individual engineered cells can be analyzed in parallel in days, instead of weeks.

This has implications for the entire cell and gene therapy developmental pipeline. Mission Bio’s approach is to help develop custom single-cell assays through our internal Pharma Assay Development (PAD) team for analytical characterization and IND-enabling studies, and after validating the assays, transfer them to companies’ lab or to a CRO/CDMO for the clinical trial and manufacturing stages of development. By enabling critical therapies to be well-characterized early on, they are likely to succeed, getting to the people who need them quickly.

Take the instance of a potentially dangerous clone detected in a patient reporting an adverse event in a clinical trial. A regulatory pause to determine the source of the clone and its relative danger could cost companies — and patients — months of delay. But these sorts of complications could be prevented by thorough and continuous characterization starting as early as IND-enabling studies.

This latest effort to alleviate the issues with cell and gene therapy product characterization through strategic partnership fits directly into the context of our mission: to help researchers and clinicians unlock single-cell biology to accelerate discovery, development, and delivery of advanced therapeutics.

Yan is the Chief Executive Officer of Mission Bio. As a veteran of the genomics industry, Yan is passionate about empowering teams to deliver highly differentiated innovative solutions realizing the mission of accelerating their application to improve human health. Before Mission Bio, Yan served executive roles at Thermo Fisher Scientific, where she led commercial teams in China for rapid market success and general management roles for Reproductive Health and Microarray businesses. She also led product management and commercialization efforts for genetic analysis solutions at Affymetrix, NuGEN Technologies, and Molecular Devices. Yan holds a Ph.D. in Biochemistry from the Medical College of Wisconsin.