Background
The ability to track, characterize and manipulate live, individual cell lineages within large heterologous populations is crucial for the study of tissue growth and development as well as for characterizing complex disease states and drug response. Current technologies allow for either labeling of highly diverse populations or characterization of lineages from extremely restricted populations but cannot do both. Given these opposing limitations, advancement of the field requires a way to bridge the inherent power of high diversity clonal labeling with technology that enables live isolation and further characterization of single lineages.
Technology
Investigators at The University of Texas at Austin have designed a system called Barcode Assisted Ancestral Specific Expression (BAASE) that allows for targeted isolation and genetic manipulation of live, single lineages present in massively diverse cell populations. BAASE couples a DNA barcode library that has a theoretical capability of labeling >500 million cells with genetic tools that allow recall of a lineage of interest for live isolation and characterization.
The Barcode system is shown to be readable in single cell RNA-seq applications, giving the researcher the ability to decipher both the identity and phenotypic distribution of lineages across highly diverse populations. This system can also be used to drive selective expression of any gene within a single targeted lineage (see figure). Dr. Brock’s group has demonstrated the proof of concept of this system by uniquely labeling ~1 million cells in a mixed population followed by induction of gene expression in a single lineage within that population. They have integrated their system with existing single cell and population based RNA-seq workflows and shown this system to work in diverse cell lines including five cancer lines and primary tumor cells.
Unlike any of the current lineage tracking technologies, BAASE gives the researcher the capability to follow, cell-sort, characterize and genetically manipulate individual lineages in many applications including cancer and developmental biology as well as lineage specific Next-Gen sequencing workflows.
Features and benefits
- Highly diversified and heritable barcode library with a theoretical capability of uniquely labeling >500 million cells within highly heterologous populations
- Uses barcodes to modulate expression of any gene with lineage-specific resolution
- Allows both identification and live isolation of subpopulations that respond to pharmacological treatment or differentiation signals
- Barcodes are demonstrated to be readable in population based or single cell RNA-seq applications, and system works seamlessly into Next-gen sequencing workflows and analysis pipelines.
- Library can be used to generate commercial cell lines to combine with the BAASE expression vectors for the study of differentiation, development, and cancer.
- Demonstrated to be highly tractable for use across a wide variety of cell types
Figure 1
