Our novel imaging system lets us see what’s happening inside a cell
The tools of my trade include a sieve, a hole-puncher, and a highly-advanced microscope (one of only three in the Netherlands). With these, we can look inside thousands of fluorescently-tagged cells and simultaneously capture information about their behavior at any given time point. Our unique imaging system allows us to first narrow down and select only the cells that display relevant characteristics before we dive into sequencing their RNA, which gives us a gene expression profile for those cells.
We’re currently looking for new mechanisms that cause the development of therapy resistance. Cancer cells adapt to stress during DNA replication, and gain mutations that benefit their survival. Therefore, we focus on identifying mutations and other molecular alterations that are important for cancer cells to tolerate and escape drug-induced stress. Identifying genes that are critical for the cancer cell will hopefully help us tell which molecular pathways to block to in order to more effectively stop the development of cancer.
Imaging is sharpened by sequencing and bioinformatics
For those of you who are techies, we use a sieve that separates and dispenses single cells into individual wells of a grid on a 2 cm x 2 cm black chip. This is placed under our microscope where each cell is imaged, and cells that are interesting for further analysis are noted. The chip slides over to the left side of the microscope and hovers over a multi-well plate. An ultra-fine needle acts as a hole-puncher and physically pokes a hole through the chip’s floor, releasing that particular cell from the chip into the multi-well plate. Once we’ve collected the cells we want, the micro-well plate is prepared for sequencing by Alexander van Oudenaarden’s lab at the Hubrecht, and then brought to Edwin Cuppen’s sequencing facility at the UMCU. The plate and data then returns home to us, where we perform the bioinformatics analysis, and combine our experimental data with images.