To investigate cellular shrapnel, the team acquired blood samples from 15 breast cancer patients that spanned cancer stages from I to III. They combined all 15 samples to increase the odds of finding useful information. They also collected blood from 15 control healthy volunteers and treated the samples in the same way.
To examine just the smallest-sized cast-off protein remnants, the researchers removed the blood cells and the dozen most abundant proteins from the blood. Then they collected only the smallest protein pieces, many of which are about a tenth the size of common human proteins. The researchers called this collection of degraded pieces the plasma degradome.
Using proteomics methods at EMSL, DOE's Environmental Molecular Sciences Laboratory on the PNNL campus, the team identified the protein fragments in the cancer and healthy degradomes. The fragments between samples differed significantly. For example, cancer blood held fragments from more than 70 different proteins that were chopped into more than 800 pieces. Healthy blood only held 50 different proteins cut up into more than 400 pieces. In addition, the complement of fragments overlapped some between the cancerous and healthy, but not entirely.
Different sets of fragments could indicate that cancers found new ways to cut old proteins, but an analysis showed that this was not the case. The key distinction the researchers found was in how often certain proteins were cut at individual sites -- these differed tremendously. In addition, the proteins most likely to be chopped-up in the cancer samples seemed to fall into known cancer-related protein families.
"We were surprised because we expected random changes to the degradome," said lead author, PNNL biologist Yufeng Shen. "But instead we found a cluster
|Contact: Mary Beckman|
DOE/Pacific Northwest National Laboratory