Journey of a cancer sample: A first glimpse

Last week, I visited research associate Clint Chalk in the laboratory of Broad’s Biological Samples Platform (BSP). Clint had just received a collection of tumor tissue samples from patients with lung cancer, which arrived in small, circular containers called cassettes. (Most of the time, samples are shipped to the Broad in pre-barcoded vials so these samples were a little unusual.) Clint slid the edge of a forceps under the cassette’s lid to pop it open and reveal a piece of pink tissue within, about the size of a pencil eraser. I’m not sure what I was expecting to see inside the container – maybe I had thought there would be microscopic threads of DNA, invisible to the naked eye, or cells dissolved in an amorphous liquid, anonymous and impassive. But seeing this sample, a real piece of tissue from a real human being, was deeply moving. It made me think about the patients who donate the samples Clint receives, and the patients who are waiting for discoveries to be made and translated, one day, into better treatments.

BSP receives a variety of cancer samples throughout the year. Ultimately, researchers want to look across the genome of these cancer samples for clues about cancer’s root cause, how it thrives and spreads, and how to stop it. But long before a cancer genome is analyzed, researchers in several Broad platforms collect and track information about these tissues and carefully prepare selected samples for sequencing. In the coming weeks, I plan to follow a sample as it journeys through BSP, the Genetic Analysis Platform, and the Genome Sequencing Platform and share the experience here on the blog (you can watch a video of Clint below).

Clint’s role today is to create an “H&E slide” for each of the samples. In this kind of slide, the tissue is stained with hematoxylin and eosin dyes that reveal the tissue’s cellular structure when viewed beneath a microscope. A pathologist can then examine the slide and determine how many cancer cells are present and confirm that the sample is indeed from a person with lung cancer.

Before he begins work, Clint dons goggles and a mismatched pair of gloves, one purple and one black; one glove gives him the dexterity he needs to slice and mount a sliver of sample while the other protects his fingers from the blade. He gently places the lung tissue sample on a disc covered in glue. He lines up the blade of the cryostat, a laboratory machine that can deftly slice delicate pieces of tissue, and uses it to shave off 5-micrometer-thick slivers (a single human hair can be 100 micrometers thick).

Clint places this slip of a sample on a microscope slide, which he then dips in the hematoxylin and eosin, chemicals that stain the nuclei, cytoplasm, and other components of the cells. He repeats the process for the dozens of samples that have come in. In the end, Clint lays out rows of microscope slides, dotted with pinks and blues from the cellular stains. Once they dry, the slides are ready for BSP’s consultant pathologist to view. I’ll have to come back another day to see this next step.

In the meantime, Clint offers me a sneak peek at the cells – we place one of the dried slides under the microscope and peer at the results. I’m not sure what the swirls and clusters of cells mean – maybe I will find out on my next visit to BSP. For now, all I can see in the specimen from some generous patient with lung cancer, anonymous to me, is an eerie whorl of color, abstract and mysterious.

Update: Check out "part II" here. We will have more installments in this series, so check back soon or subscribe to our RSS feed.