New tool for tracing blood cells’ ancestry might one day help predict disease risk

The human blood system is in a constant state of turnover. First-line immune defenders, like neutrophils, need to be replaced after just four to eight hours, platelets can last a week, red blood cells up to four months, and some white blood cells, like memory B cells, live for decades.

The heroic task of constantly replenishing these ranks, and making sure the balance of different types of blood cells is right, falls to a primitive reserve of stem cells that reside deep in the bone marrow. Humans have anywhere between 20,000 and 200,000 hematopoietic stem cells, or HSCs, but just 1,000 of them are active at any given time, giving rise to about 500 billion blood cells every day.

As you can imagine, there are a lot of ways for this complex process to go sideways. Too few red blood cells and a person develops anemia, for example, and too many white blood cells can lead to leukemia. But by the time these conditions are discovered in a patient, the key evolutionary moment when an HSC lost its way has come and gone unobserved. Now, researchers have come up with a way to monitor these changes in human blood cells in real time, raising hopes that it might one day be used to predict disease risk years before symptoms show up.

“Our technology lets us reconstruct this history, like a detective story, and track down who was the bad actor that would eventually cause all these problems,” said Jonathan Weissman, a biologist at the Whitehead Institute in Cambridge, Mass.

In a paper published Monday in Nature, Weissman’s lab, in collaboration with Vijay Sankaran of Boston Children’s Hospital and the Broad Institute of MIT and Harvard, used this technique to trace the ancestries of single blood cells back to the HSC of its birth, building out different branches of the blood system family tree with unprecedented resolution.

“From there we can start to ask, do the different stem cells produce different amounts of blood or different types of blood cells and how does this output deteriorate as people age?” Weissman added.

HSCs can become any type of blood cell. But not all HSCs are the same. Over time, these slow-dividing cells acquire subtle differences — mutations in their DNA, epigenetic markers, or other structural changes that alter how genes are expressed. Scientists refer to these different HSCs and all the blood cells that descend from each one as “clonal groups.”

Using whole genome sequencing, a group of researchers in the U.K. showed recently that clonal diversity shrinks with age. Going into their 40s, most people have lots of clonal groups, but by the age of 70, the majority of their blood cells are being produced by fewer than two dozen clones.

To better understand what changes are happening in HSCs to cause this loss of diversity, some researchers have turned to single-cell sequencing, a tantalizing technology that peels back an individual cell’s operating instructions. A few years ago, Sankaran’s lab at Boston Children’s Hospital used single cell sequencing to look at the dynamic output of HSCs over time. They realized that they could use mitochondrial DNA — which acquires mutations much quicker than nuclear DNA — as a genetic barcode, to trace cells across divisions and differentiation. When two cells share the same mutations in the same place, that’s because it happened in an ancestor.

The method worked but wasn’t very efficient. Meanwhile, Weissman’s lab had developed its own mutation-tracing methods for mapping family trees of cells — using an engineered-mouse approach — to shed light on how tumors spread. The two groups began collaborating, and Chen Weng, a postdoc who split time between both labs, eventually cracked the DNA efficiency issue.

The new system, called ReDeeM, for Regulatory multi-omics with Deep Mitochondrial mutation profiling, improved the detection of mitochondrial DNA mutations 10-fold. It allows scientists to detect around 10 mutations in the mitochondrial genome of a given blood cell, enough to string together a unique identifying genetic barcode. Once the researchers validated that this method worked as well as Weissman’s engineered one in mice, they applied it to human blood samples, creating family trees of the thousands of individual blood cells found in each, along with information about the cell’s gene expression levels.

“What we really want to do is to relate the current state of the cell to its past state,” Weissman said. In healthy, young individuals, he and his colleagues found that most HSCs produce every kind of blood cell, but certain clonal groups were more biased toward producing one type of cell over another. That cell-state information is now helping them figure out which genes and pathways push some HSCs to make more white blood cells while others produce mostly red blood cells and platelets.

In healthy older individuals, they observed the same thing other research groups have previously reported with whole genome sequencing; certain clonal groups began to outcompete others, and their expansion drove down the overall clonal diversity, increasing the risks of certain blood cancers. There are some well-characterized mutations long believed to be responsible for this, including the loss of the Y chromosome.

“What we’ve seen now is that there’s much more expansion going on than can be explained by the known driver genes,” Weissman said. “We think a lot is actually going to be driven by epigenetic changes as well. So an immediate goal for us now is to identify all the drivers responsible for clonal expansion. We believe there are many more to be found.”

For now, ReDeeM is most likely to remain a lab tool to help researchers answer these types of questions. The technique has been patented, but Weissman said it’s too early for company-building. Still, the technology paves the way for a day in the not too distant future where it is conceivable that from a simple blood draw, a doctor could get a sense of what’s going on in that patient’s bone marrow — picking up perturbations there that could help predict a diverse range of diseases.