Parse Biosciences is a life sciences company focused on advancing human health and scientific research through single-cell sequencing. This powerful technique examines the genetic material of individual cells. Parse Biosciences aims to make single-cell sequencing more accessible and scalable, supporting discoveries in areas like cancer treatment, tissue repair, stem cell therapy, and understanding the immune system.
The Challenge of Single-Cell Analysis
Traditional “bulk” sequencing pools genetic material from thousands or millions of cells, providing an average genetic profile. However, this obscures the unique characteristics of individual cells within a sample. Tissues are complex, with diverse cell types playing distinct roles, which bulk sequencing cannot differentiate.
Analyzing individual cells presents hurdles like high costs, complex sample preparation, and limited throughput. Early single-cell sequencing technologies, often relying on microfluidics, required specialized and expensive equipment, creating barriers for many laboratories. Extensive sample handling, including centrifugation and washing, could compromise fragile cell populations. Researchers often compromised between the number of cells analyzed and data depth. Achieving sufficient sequencing depth (50,000 to 150,000 reads per cell) also escalated costs.
Parse Bio’s Evercode Technology
Parse Bio addresses these challenges with its Evercode technology, utilizing a unique “split-pool combinatorial barcoding” system. Unlike droplet-based methods that physically isolate cells, Evercode uses cells as individual reaction vessels. This approach removes the need for specialized instruments, requiring only standard lab equipment like a centrifuge, thermal cycler, and pipettes.
The process begins by fixing and permeabilizing cells, allowing unique DNA barcodes and enzymes to enter and act on the RNA. Cells are then distributed across multiple wells, where a distinct oligonucleotide barcode is added to transcripts. After this initial round, cells are pooled and re-distributed into new wells for subsequent barcoding rounds.
This sequential splitting and pooling ensures each cell accumulates a unique barcode combination, creating a distinct “signature” for its transcripts. For instance, four barcoding rounds can generate millions of unique combinations, allowing processing of up to one million cells simultaneously. This combinatorial indexing increases scalability while minimizing “doublets” (two cells accidentally barcoded as one). The Evercode system also allows sample fixation and storage, providing flexibility for researchers to collect and process samples later.
Applications of Parse Bio Technology
Parse Bio’s Evercode technology provides high-resolution insights into cellular heterogeneity across diverse scientific fields. In cancer research, it enables analysis of individual cancer cells, mapping the cellular landscape within tumors. This detailed view reveals how genetic profiles contribute to cancer progression and drug resistance, accelerating biomarker discovery for diagnosis and treatment.
The technology is also applied in immunology to study the immune repertoire with high resolution and scale. For example, Evercode BCR allows capture of B cell receptor sequences alongside gene expression from the same cells, even measuring paired heavy and light chains in up to one million cells. This helps assign B-cell clonotypes to specific subtypes and activation states, advancing antibody discovery. Similarly, Evercode TCR supports detection of mouse and human T-cell receptors, enhancing immune profiling.
Beyond cancer and immunology, Parse Bio’s technology maps neuronal pathways in neuroscience, with implications for neurodegenerative disease research. It also supports developmental biology by tracking cell differentiation and development at a single-cell level. Its ability to analyze large numbers of cells and samples makes it suitable for large-scale drug and perturbation screens, and for generating comprehensive datasets for AI models and population studies.
Benefits and Impact
Evercode technology offers several advantages over previous single-cell sequencing methods. Its instrument-free workflow simplifies the process, making advanced single-cell analysis accessible to more laboratories. This ease of use, combined with sample fixation and storage, offers researchers flexibility in experimental design, allowing for time-course studies and multi-site collaborations.
The combinatorial barcoding approach increases scalability, enabling analysis of hundreds of thousands to millions of cells in a single experiment. For instance, the Evercode Penta kit can profile up to 5 million cells and 384 samples in one run. This high throughput translates to reduced costs per cell, as fewer sequencing reads are needed for robust data, and reagent costs are minimized by pooling samples. The technology also provides high-quality data, with improved gene detection and reduced noise from ambient RNA, common in droplet-based systems. These benefits accelerate scientific discovery by allowing researchers to explore biological questions at greater scale and resolution.