Optical in situ nucleotide sequence detection using combinatorial hybridization
This technology is a method for optical in situ nucleotide sequence detection using combinatorial hybridization.
Unmet Need: Scalable, high-resolution genetic screens linking genotypes to complex phenotypes
Genetic screens enable the study of various genes underlying specific cellular phenotypes. However, screening is often limited due to issues with scalability, cost, and acquiring correct and adequate resolution and readout, as well as the lack of methods that simultaneously read out transcriptomic, proteomic and perturbation identity in single cells. One approach to circumvent these limitations is the use of optical pooled screening techniques; however, even these approaches are limited by difficulties in imaging complex cellular phenotypes.
The Technology: Scalable, cost-efficient optical CRISPR screening with spatial phenotyping
This technology is a method for CRISPR screening that employs cyclic hybridization-based barcode readout, enabling high specificity and transcript detection efficiency, along with improved signal-to-noise. Instead of in situ sequencing, this method utilizes paired primer and padlock detection oligos that require hybridization to their respective target sequences, allowing the primer to serve as a template for the circularization of the padlock probe. Together, these features improve barcode recovery per cell and enable robust analysis of cell cultures, primary and stem cells, and tissue sections. This pooled approach can be used to study hundreds to thousands of targets simultaneously, enabling larger-scale studies and patient cohorts while reducing costs and permitting higher throughput screening and resolution. This technology has been validated with human breast cancer cell lines, fibroblasts, hESCs, iPSCs and motor neurons, as well as in a tumor xenograft tissue.
Applications:
- Profiling cell behavior in native tissue context
- Large-scale high-throughput genome-wide genetic screening
- Transcriptome profiling
- Research model to generate libraries of primer and padlock oligos encoding various cellular barcodes
- Multi-omic readout of barcode readout, as well as transcriptomic and cyclic IF readout, to study various cell states and behavior pertaining to native contexts and with CRISPR perturbations
Advantages:
- Enables large-scale studies and patient cohorts
- Cost-effective
- High throughput
- High specificity and resolution
- Compatible with multiplexed FISH and immunofluorescence
Lead Inventor:
Related Publications:
Tech Ventures Reference:
IR CU24118
Licensing Contact: Joan Martinez