As technology continues to evolve, the potential of gene-expression profiling continues to grow. The field is now expanding to focus on single cells, which many believe have unlimited potential for molecular biologists. A number of companies and academicians presented their latest single-cell related advances at the recent BioEPS “qPCR” meeting in Vienna.
Fluidigm’s Biomark™ System has a relatively new dynamic array biochip (96.96 array) that tests 96 cells against 96 genes in one experiment. “One can assay single cells with a classic PCR microtiter plate, but it’s difficult to run more than an experiment or two off the material from a single cell,” explained Howard High, company spokesman.
“Fluidigm’s platform can run 96 experiments off the contents of a single cell, as well as run several plates. We’ve had customers run up to 1,000 experiments from one cell.” The array assembles cDNA material from individual cells with reagents to create individual qPCR reactions.
This provides significant savings, added Ken Livak, Ph.D., senior scientific fellow. Using standard 384-well plates, it would take about 8 days for a single instrument to run 96 samples against 96 assays. A single run with the chip provides the same throughput as 24 384-well plates, but in only 4 hours, while using 1/200th the amount of reagent, Dr. Livak said. The application to single-cell analysis provides insight into developmental signals such as stem cell differentiation. “When you look at the average gene expression from a large number of cells, you can obscure signal. You’re looking at an average of 10,000 cells, so it doesn’t really tell you what’s occurring among individual cells.”
According to Dr. Livak, analysis of single cells is complex because there are fluctuations in gene expression within single cells. This makes it important to look at enough individual cells to understand the temporal fluctuation and variation that is occurring.
Current applications of the Fluidigm technology include analysis of stem cells and cancer, both of which require single-cell gene-expression profiling to understand, Dr. Livak noted. In addition, the platform is being used in immunology, T-cell studies, and neurological research. “This may be useful for individualized medicine for a specific tumor and to assess the stage of cancer and how aggressive it has to be treated.”
“As people dive into the single-cell arena, the opportunities are limitless. There are so many questions to be answered and so many people trying to figure out the right questions. This is exploding on a global scale,” summarized High.