Express yourself, hey, hey, hey, hey

Eukaryotic Cell. click for source.

Individual mammalian cells are almost always too small to be seen by the naked eye – most require at least a light microscope [this interactive shows relative sizes]. But now, as unbelievable as it sounds, it is possible to characterize and compare the gene expression going on inside of individual cells using next generation sequencing and a technique called Smart-Seq. The technique is sensitive enough to show expression levels of about 8,000 genes! There’s a lot going on in that little speck.

The Central Dogma of molecular biology. DNA is transcribed to RNA, which is translated to proteins. In my project, I’m looking at what is happening at the level of RNA. Click for source.

 

In my research I use a few hundred milligrams of coral tissue, containing millions of cells, to generate gene expression profiles. Doing this we can see what genes are turned on and off in different parts of the coral or in different species of coral.This works pretty well, and we are able to distinguish hundreds of genes that are being used differently within different parts of the coral colony. However, being able to see gene expression at the level of an individual cell opens a new world of research possibilities.

PC3 (dark blue), T24 (light blue), and LNCaP (purple) cancer cell lines show distinctive gene expression profiles in clustering analysis. From Ramsköld et al. 2012.

In the recent paper published in Nature Biotechnology (reference below), Ramsköld et al. profile a number of individual mouse and human cells, including cancer cells, revealing characteristic gene expression patterns. They were able to identify increased production by the cancer cells of RNAs that code for cell surface proteins. These proteins may help cancer cells evade detection by the immune system. Here they are starting with about 20 picograms of RNA (I’m usually starting with a couple hundred nanograms – meaning a couple hundred thousand picograms of RNA). To be able to generate data with so little starting material is an exciting prospect. But one must keep in mind, as every molecular biologist is aware, there is always a bit of luck and magic involved.

Reference: Daniel Ramsköld, Shujun Luo, Yu-Chieh Wang, Robin Li, Qiaolin Deng, Omid R Faridani, Gregory A Daniels, Irina Khrebtukova, Jeanne F Loring, Louise C Laurent, Gary P Schroth, Rickard Sandberg. Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cellsNature Biotechnology, 2012; DOI:10.1038/nbt.2282

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