Journey of a cancer sample, part III

Today, the cancer samples we have been following will go from tangible pieces of tissue to something a bit more abstract: invisible strands of pure DNA. In the process, the samples will be whirled and spun through laboratory machinery, incubated over night, and washed repeatedly with different chemical substances. The final product of all of this will be large droplets of clear liquid at the bottom of tiny, plastic Eppendorf tubes.

We are back in the Biological Samples Platform with research associates Clint Chalk and Cara Fisher. A few weeks ago, Clint sliced lung tissue to prepare slides from the 164 samples of lung cancer and normal tissue that he had received (video and story here). Clinical pathologist Chin-Lee Wu has finished examining all of these slides to confirm their designation as cancerous or not (video and story here), and today, Cara and Clint will be isolating DNA from 40 of these lung cancer tissue samples, for further analysis by other Broad teams.

Clint opens a Styrofoam box filled with dry ice (the samples need to be kept cold) and I can see the white, plastic cassettes inside, each containing a pencil-eraser sized tissue sample. On a carefully cleaned surface, Clint cuts off one minute piece of tissue from each sample with a razor and places it in an Eppendorf tube. He weighs each cut piece as he goes along, aiming to make them all between 25 and 30 milligrams.

The goal of DNA isolation is fairly simple: get the DNA out of cells and then get rid of everything that is not DNA. To help break open the cells to spill out the DNA, Clint places a tiny, metal bead in each tube and then places the tubes in a machine called a tissue lyser, which shakes them vigorously, turning the samples from solid into pulp. He also adds a substance to break up the protein. The tubes will incubate over night and then sit in the freezer until Cara can finish processing them.

Cara and Clint work closely together to prepare samples for a number of ongoing projects. While I watch them work on these cancer samples, boxes of samples for another project arrive. Each of these boxes represents many hours of work, although Clint and Cara work quickly. They have the protocols for processing all kinds of samples memorized; adding the right reagents in the right order is second nature for them.

After the samples have incubated, Cara gets ready to pull out everything in the Eppendorf tubes that is not DNA – this includes chewed-up protein, RNA, and anything else in the broken-apart cells. She “washes” the sample in various chemicals and places the tubes in a centrifuge in between each wash. The centrifuge spins the tubes so fast that gravity pulls down any unwanted material, leaving only DNA in the collection tube. Finally, Cara elutes this pure DNA into an Eppendorf tube that she seals up and places in the freezer.

Next week, Clint and Cara’s colleagues in BSP will check the quality and concentration of the DNA from each sample, and then it will be up to the Project Management team to decide what will happen to this batch of samples. In the meantime, the tubes of DNA will wait in the freezer.