Q² Solutions

Quality FFPE analysis at single cell resolution: elevating single cell RNA sequencing innovation to the next level for optimized drug discovery and development

Authors: Joseph Modarelli, Adam Black and Douglas Wilson 


Creating a successful pathway from drug discovery to effective immune cell therapies for patients is no easy feat, especially in a complicated research and development landscape. Innovations that allow experienced researchers to dive deep into biological complexities at a cellular level are expanding what these experts can uncover regarding therapeutic efficacy and toxicity of novel treatments. Evaluating granular patterns of insights can provide a holistic view of how novel treatments may work in the body.


Single cell RNA sequencing is one such innovation. From rare disease detection to tumor heterogeneity insights, lineage tracing, discovering drug-resistant cells and more, this next-generation sequencing method enables in-depth characterization of biomolecules by uncovering gene expression at high resolution within individual cells within a tissue.


As advancements evolve to better meet the intricate needs of complex R&D, it is now possible to interrogate formalin-fixed paraffin embedded (FFPE) tissue sections at single cell resolution, opening opportunities for pharmaceutical and biotech companies to further drive research outcomes with speed and quality insights. Leveraging 10x Genomics Single Cell Flex assay, Q2 Solutions is the first Certified Service Provider of this transformative solution, which is guided by skilled genomics experts.  


This is a critical advancement toward optimizing single cell gene expression from collection to storage and analysis processes for the reasons noted below.


Absolving limitations of single cell analysis for fixed tissue

Historically, for quality single cell analysis, fresh or cryopreserved (fresh frozen) cell suspensions or tissue material was needed, not fixed samples. However, when isolating cells from fixed tissue for evaluation, it is important to keep in mind that these samples are typically fixed in formalin and preserved in paraffin blocks for long-term tissue preservation, and fragmented genetic material is expected. Therefore, these samples are not traditionally compatible with single cell analysis. This can present a challenge as most clinical trial protocols collect and evaluate FFPE tissues.


Optimized operationalization of single cell analysis for FFPE samples

It is now possible to perform gene expression analysis from fixed cells at single cell resolution whether it be from archived or actively created FFPE tissues as a part of a clinical protocol. Equally important, the incorporation of fully optimized workflows allows experts to reduce variability during sample handling to more reliably maintain high quality samples throughout upstream and downstream processing within an operational environment—a high throughput and time efficient workflow.


Enhanced sample input 
With the Single Cell Flex assay, isolated RNA materials from FFPE blocks of varying tissue types, ages and quality can be deemed clinically relevant for evaluation. The assay can detect and replicate between 14,000 to 18,000 genes per tissue type in a highly reproducible manner.


Beyond quantity, it is vital for quality single cell examination within fixed tissue. With use of this advanced assay, data depicts that scoring for immune cell activity from bulk RNA sequencing and single cell RNA sequencing of fixed tissue provide comparable and consistent insights into immune cell presence, emphasizing the high quality cell and RNA capture from the Single Cell Flex assay for downstream analysis.


Automated dissociation and quality control of FFPE tissue samples 
Obtaining high quality single cell data from FFPE tissues requires a robust and standardized tissue dissociation strategy, especially when handling projects featuring many samples.


Q2 Solutions uses automated dissociation and quality control (QC) instrumentation to ensure that high quality sample inputs are maintained throughout all stages of analysis. Automated dissociation helps to remove operator and environmental variability, helping to diminish batch effects across study samples. Also, automated sample QC via automated cell counting further decreases variability while enhancing accuracy. This automated sample processing strategy ensures high throughput and high quality data for downstream bioinformatic analysis.


Deep dive analysis 
The opportunity to fine-tune and explore meaningful gene expression data, produced by multiple tissue types and flexible input amounts, is the true strength of these tech-enabled single cell sequencing workflows.


Experts can gain a better understanding of:

  • How representative cells are of the whole sample population.
  • Differential gene expression across cell types and/or conditions.
  • Changes in the expressions or relative abundances of immune cell populations.
  • New areas of transcriptome analysis.
  • Analysis of gene expression in fixed cells, a historically incompatible sample type for single cell analysis.


Incorporating experienced bioinformatics specialists into clinical trial programs can take single cell data analysis insights a few steps further. Trial sponsors can further customize what insights they are especially interested in, such as differential expression and time series examinations, where cellular changes are monitored over time. 

This level of granular and tailored insights can be critical to clinical trial sponsors who are increasing investments in therapies that modulate immune system responses to fight cancers, immunological disorders and infectious diseases, especially in a competitive market. The breadth of data generated by leveraging optimized workflows for single-cell analysis of fixed tissue can be beneficial to enhancing and accelerating evidence-driven decision-making in drug development while an automated operational workflow can help key stakeholders focus on upholding high quality sample collection, storage and analysis throughout the entire process. 

Click here to learn more about Q2 Solution’s genomics expertise and innovative capabilities in advanced single cell sequencing in FFPE tissue using 10x Genomics Single Cell Gene Expression Flex assay.