Optimization, RNAi, and Lessons Learned from the Summer

I had met Milan Chheda at an outreach event a few weeks earlier, and my final day at the Broad started with a tour of his workspace. Milan, a neurologist, works in William Hahn's Lab, which focuses on how human cells transform into cancer cells. Milan's work is to optimize a technique that is currently applied to study the development of glioblastomas, a particularly virulent type of brain tumor.

The technique in question uses RNA interference to knock down the expression of certain genes. Using a lentivirus, the researcher introduces a hairpin structure to candidate nerve cells to reduce the expression of a specific gene in vitro. After culturing the nerve cells that have received this structure, the researcher typically uses a microscope to check for glioblastomas or other types of cells that may form.

What does it mean to optimize this technique? Milan is part of an effort to create methods that would enable RNAi experiments to scale up the way the Broad's sequencing center has industrialized gene sequencing. In one example, members of his group are working to use software that automatically checks microscope images for glioblastomas and other features. By identifying trouble spots in the experimental pipeline, the hope is that these experiments can be conducted at a larger scale, resulting in reliable and larger quantities of data to analyze.

I left the Broad with a greater appreciation of the interplay between data gathering and data analysis. Writing about my discussions with other researchers greatly enhanced my ability to gain this appreciation. With this in mind, expect further updates to this blog once I return to Berkeley.