Deployable, Single-use Device for Single Cell Genomics in Clinical Research

Project Summary Single cell RNA-seq (scRNA-seq) has emerged as a potent tool for delineating cell states in heterogeneous cell populations. However, leveraging this potent technology in clinical research and care is challenging due to the logistics of stabilizing the transcriptional profiles soon after sample collection. We have demonstrated feasibility of a single use cassette that integrates sample collection, storage and processing of clinical samples to scRNA-seq libraries. The cassette leverages a picoliter-well array pre-loaded with barcoded transcript capture beads to collect and isolate single cells. A cell preservation reagent is added to the cassette to stabilize the transcript profiles in their native state. An elastomeric plunger is used to seal the array with a semipermeable membrane using a simple snapping mechanism. The sealed cassette can be sent to a central facility for batch processing to sequencing libraries. No specialized equipment is required for collection and storing cells at clinical sites, enabling facile deployment of the technology to multiple clinical sites. We propose to finish development and validate the manufacturing and user workflows for the cassette. Specifically we will 1) harden the manufacturing protocols for generating the cassettes and perform a multi-lot validation campaign, 2) develop and validate a simple workflow for processing and loading clinical samples into the cassette and 3) validate central processing of samples collected and stored in the cassettes by distributed labs. To achieve these goals, we have created a strong consortium including the core Honeycomb team, advisors Dr. Alex Shalek and Dr. Christopher Love, two experts in single cell analysis and co-developers of the underlying technology, and two large pharma partners who have significant experience in the requirements for clinical research and will be extensively validating the technology.