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Gaining Single Cell Fluency 

NOVEMBER 2022 – 

Single cell RNA sequencing offers incredible opportunities to catalog cell heterogeneity and gain new insights into cancer, the immune system, cell therapies, and many other areas. However, most current approaches cannot combine high performance, flexibility, and scale.  


Fluent BioSciences is working to solve these challenges by making single cell sequencing more efficient and accessible. The company has developed a novel technology called PIPseq. The technology uses pre-templated instant partitions (PIPs), which segregate complex cell samples into uniform reaction partitions that can be easily sequenced – in large or small samples – on high-throughput platforms. 


“Fluent’s technology eliminates the need for complex, expensive instrumentation and microfluidic consumables,” said Wouter Meuleman, Partner at Illumina Ventures. “PIPseq is a simple, scalable workflow that can enable single cell sequencing in every lab for many applications while reducing costs and increasing accessibility.” 

Simplifying Single Cell Studies

Commercial single cell technologies can be expensive, difficult to scale, and quite complex. These issues limit researchers’ abilities to detect rare events, such as mutated cancer cells, CRISPR-modified cells, specific memory immune cells, and other needles-in-a-haystack. 


“The current tools on the market are extremely limited and quite expensive,” said Sepehr Kiani, Ph.D., Fluent’s president and CEO. “Large-scale experiments have revolutionized our understanding of the immune system but can cost tens to hundreds of thousands of dollars. Translational researchers need to study thousands of patients and test hundreds to millions of cells, they need better tools.” 


PIPseq solves this problem by eliminating microfluidic devices, expensive instruments, and laborious workflows. As a result, labs can perform cost-effective experiments using kit sizes that range from hundreds to millions of cells on simple lab equipment. 


From there, it’s a matter of sequencing and crunching data. Fluent’s cloud-based platform, PIPseeker, translates these data into a user-friendly report containing cell identification, clustering, and differential expression information.


Single Cell Transcriptomics Without the Core 

PIPseq also increases access to single cell analysis. Currently, labs often rely on core facilities to process delicate, live cells, generating logistical and experimental challenges. 

“Even putting your cell sample in an ice bucket and walking it across campus to the core can be difficult,” said Kiani. “You have to schedule when to harvest that sample, and the instrument must be ready when you arrive.” 


Cell fragility is also problematic. Sometimes labs cryopreserve their cells before sending them out for processing. Unfortunately, there’s no guarantee that the cells will be viable or express the same transcripts once they are thawed. Researchers can lose crucial information during these sometimes-lengthy cell preparation processes. 


With PIPseq, labs can now process their fresh samples at the point of cell preparation, opening up many applications for single cell studies. 


“We have a group at the CDC that is processing virus-exposed cells,” said Kiani. “Another group at Boston University is looking to port PIPseq into a BSL-4 lab. These are high containment facilities, and you can't easily bring in complex instrumentation. PIPseq gives them capabilities they never had before.” 


In addition, some samples do not function well in microfluidic channels. Neurons tend to be sticky and clog the chip. PIPseq eliminates this issue, allowing brain researchers to produce high quality results.  


PIPseq is also easy to use. It requires no special equipment, and most scientists can pick up the workflow through a simple instructional video. 


Fluent will soon expand to proteomics and is also working to make PIPseq more accessible for clinical researchers. Currently, there are no appropriate single cell tools for the clinical market, and PIPseq could be a game-changer, particularly in oncology and immunology. 


“We are talking to many people who are itching for a viable path to a clinical solution, but they need that accessibility and scalability to make it work,” said Kiani. “You can’t schedule patients based on core availability; you need a solution at the ready.” 

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