Barcoding leaves its mark on cells
Dr. Zon and Fernando Camargo, PhD, are pioneering a groundbreaking technology—barcoding—in which they "fingerprint" each stem cell—in zebrafish and mice—with a unique DNA sequence. Because each barcode gets passed on to all the stem cell's progeny, researchers can use it to trace each cell's lineage and study how some blood cancers, such as leukemia, may arise.
Vijay Sankaran, MD, PhD, uses a similar barcoding approach in humans that takes advantage of naturally occurring mutations in the DNA of mitochondria—the cell's energy source.
When scientists evaluate the barcoded cells, they apply a separate technology—single-cell RNA sequencing—that tells them the gene expression patterns in each cell. This information provides vital clues for identifying which genes are driving the cancers, putting the researchers on the path for finding effective therapies.
This work is funded by a $5M grant from Alex's Lemonade Stand Foundation.
Cellular barcoding to thwart pediatric leukemia
Dr. Zon is using the gene-editing technique, CRISPR, to barcode stem cells in a zebrafish model of pediatric leukemia, while Dr. Camargo is employing it in mice. "By tracing the cancer back to its origins, we can determine when the disease initiated and zero in on the cells causing the expansion," says Dr. Zon.
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Once the team identifies the group of cells—or clones—causing the disease, they will uncover the key genes and pathways that trigger leukemia, verify that these genes disrupt stem cell function and screen potential therapies that can specifically target them.
"There may be several disease-driving clones each driven by a different mutation. Therefore, clone-specific treatments may be required to block cancer growth. Barcoding combined with sequencing helps to narrow our search," explains Dr. Camargo. Another benefit of this technology: It can track cancer as it evolves, allowing therapies to be implemented early before the cancer gains momentum.
Our body's natural barcodes
Like DNA in a cell's nucleus, mitochondrial DNA acquires mutations over time, but because they carry only a handful of genes, they are much simpler and cheaper to sequence than nuclear DNA. "Let's say your blood-forming stem cell has a certain mitochondrial mutation," says Dr. Sankaran. "All the daughter cells will have the same barcode, so you can tell which cells are most related to each other."
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If a cell undergoes an error in cell division or differentiation, that can spur cancer. Using mitochondrial barcoding, researchers can find that cell and sequence it to identify the genes driving the cancer. "The approach can also be used to identify the properties of cells that resist treatment. By surveying those cells, we can learn which ones survive and why they are different," says Dr. Sankaran.
Once we understand which properties the cell has that help it respond well to treatment, we can incorporate these winning features into therapies.
Barcoding comes full circle
Success in finding new cancer treatments relies on drug discovery, high throughput drug screening and preclinical and clinical testing.
"Beginning with a blood sample from a leukemia patient, we can use mitochondrial barcoding to isolate the responsible clone, and test drugs that can kill it," says Dr. Zon. Next, the researchers can use cellular barcoding in animals to verify that the drug works and is safe, and then move to humans.
"The beauty of this approach is that each patient has their own unique barcode for their cancer that we can use to fine-tune therapies. If the patient relapses, we may realize that a different clone is causing the problem and so start again, finding a therapy for that clone instead," he adds.