Maria Contreras

Maria Contreras

Maria, a junior bioengineering student at Rice University, who developed plasmid-based Barcoding System for Pooled Optical Phenotyping of Mixed Cell Populations that will be used to aid the research of genetic disorders

Recently, the development of in situ sequencing (ISS) has facilitated the systematic analysis of the factors that contribute to a wide range of spatially and temporally defined optical phenotypes. This summer made me grow in more ways than I could have ever imagined. I became a better scientist by working alongside incredibly intelligent and hardworking researchers; a more skilled speaker by attending weekly workshops taught by talented communicators, but most importantly, I became a better person by learning from the experiences of the broad staff and fellow BSRP students. Their careers and stories inspired me to become the best version of myself that I can be. BSRP made me believe that it is possible to achieve all the goals I have set up for myself. This technology enables researchers to distinguish tens of thousands of distinct populations of cells directly on the microscope in a pooled context, by sequencing a population-specific barcode. Optical pooled screening (OPS) is an emerging technology that uses ISS to link barcodes to genetic perturbations, allowing the simultaneous analysis of the phenotypic effect of the perturbation of tens of thousands of different genetic components within a target cell line. However, investigating phenotypic variations associated with specific disorders often requires the analysis of multiple cell lines. Currently, screening multiple cell lines for extensive arrayed cell libraries is challenging because it requires meticulous attention to minimize plate-position effects and inter-plate statistical biases. Here, we introduce a plasmid-based barcoding system that enables the simultaneous screening of multiple cell lines in a pooled context using in situ sequencing to read out the cell-line-specific barcode in individual cells. We barcoded and pooled two distinct cell lines and used this system to generate two distinct cell-line-specific phenotypic profiles. The plasmid-based barcoding system presented accelerates and enhances the efficiency of optical pooled screenings, reducing batch effect variability and delivering more accurate results. In a genomics context, this technique facilitates the investigation of phenotypic and genotypic variations associated with numerous genetic diseases, and thus advances the development of potential genetic therapies for these disorders.

 

Project: Development of a Plasmid-Based Barcoding System for Pooled Optical Phenotyping of Mixed Cell Populations

Mentor: Owen Andrews, Blainey Lab