New insights from old blood

Holstege: “I did my PhD in cancer research, so I knew that DNA damage that accumulates during life is mostly associated with cancer. Mrs van Andel-Schipper eventually died at the extreme age of 115, and with her donation to science she offered scientists a unique chance to learn about the genetic damage, or ‘genetic mutations’ that accumulates in a healthy tissue during life. Our goal was to quantify these mutations and to find out how they differ from cancer-causing mutations.”

Holstege realized that by comparing the genome from blood and brain cells from the same individual, she might be able to detect the mutations that occurred during a lifetime. The reasoning behind this is that brain cells only occasionally divide once the brain is formed and thus the genome remains largely unchanged. In contrast, many blood cells live only 6-10 days and therefore need to be constantly renewed to provide the body with new, healthy blood cells. These new blood cells are produced by blood stem cells, which may accumulate mutations during these divisions. In other words: blood cells carry all the mutations that have occurred in a blood stem cell over a lifetime – ‘somatic mutations’ as these are called.

She then quickly found out that her research project would involve serious big data, which led her to TU’s bioinformatics Professor Marcel Reinders and researcher Marc Hulsman MSc. at EEMCS faculty. An individual’s genome has 3 billion base pairs, which equals 3 gigabyte of data. But if, as the researchers did, you decide you want to sequence different tissues and repeat that up to sixty times to reach sufficient statistical reliability, you easily end up with 10 terabyte of data. 

“The data storage and computing infrastructure in Delft has been instrumental to make this project possible.” says Holstege. “Also, the knowledge to query and interpret large datasets, that is available in the Reinders lab, has been absolutely essential to make this project successful.”

When the article Somatic mutations found in the healthy blood compartment of a 115-yr-old woman demonstrate oligoclonal hematopoiesis came out in Genome Research (24 April 2014), people were most surprised by the finding that the majority of the peripheral blood cells were derived from only two blood stem cells, which were also related to each other.

“We were totally surprised” says Holstege. “We went to visit Professor Frank Staal, who researches blood stem cells at the LUMC, to ask him whether it is possible that someone lives with one or two blood stem cells. He told us that mouse studies have previously shown that the amount of stem cells decreases substantially during a lifetime and that there is a limit to the number of times they can divide. With us, he was thrilled to see that apparently, this is also true for humans.”

The analysis also showed that in the blood cells the chromosome endings, called telomeres, where 17 times shorter than in brain cells. It is known that telomeres shorten at each cell division, and it is also suspected that cell division stops when telomere length reaches a lower limit. When blood stem cells become inactive or die, then the production of new blood cells will cease, which is not compatible with life. 

In other words: however healthy you may be, eventually your blood stem cells may reach an upper limit of cell divisions which may pose a limit to human life. These data suggest that this moment may come well before the 150 years some people strive to reach.

The other amazing thing about the 450 mutations that the team found was the way the genetic damage is spread over the genome. It’s important to know that only 1-2 percent of the DNA contains information that is directly translated into proteins. These parts are called ‘coding’ regions. The other 98-99 percent contains DNA stretches that may have regulatory functions or functions that are currently unknown.

The team found that the mutations are overrepresented in non-coding repetitive sequences or in sequences that are on the outside of the coiled DNA and hence more exposed to external influences. 

What causes vital parts of the genome to be less affected by mutations is currently unclear. Stem cells with serious genetic damage might die and clear themselves from the stem cell pool. Coding regions might also be shielded from external influences or repair mechanisms might be more active on coding regions. As of yet, no one can tell.