When B-cells turn cancerous may decide fate of childhood leukemia treatment

A new study shows that the stage of normal cell development at which B cells transform into leukemic cells impacts treatment outcomes for pediatric patients with B-cell acute lymphoblastic leukemia (B-ALL).

Scientists at St. Jude Children’s Research Hospital and University Health Network’s Princess Margaret Cancer Center, Toronto, developed a robust single-cell reference atlas of normal human B-cell development and cross-referenced single-cell B-ALL data with it, as well as outcomes data.

The study, which has implications for understanding drug resistance and stratifying patient treatment based on risk, was published today in Nature Cancer.

“At St. Jude, we have large acute lymphoblastic leukemia cohorts that have been genomically profiled with very rich underlying metadata, including outcomes,” said corresponding author Charles Mullighan, MBBS (Hons), MSc, MD, deputy director of the St. Jude Comprehensive Cancer Center, Department of Pathology. “So, not only could we get the biological information from single-cell sequencing, but we could then take that further and look at some of those associated features, clinical or otherwise.”

Finding the off-ramps on the hematopoiesis highway

To determine the cell state at which St. Jude B-ALL samples transformed, Mullighan’s scientists needed to map normal hematopoiesis (blood cell development) at the single-cell level. For this, they collaborated with John Dick, Ph.D., Senior Scientist at University Health Network’s Princess Margaret Cancer Center.

“We have long sought to unravel how human blood stem cells create the blood lineage,” said Dick. “For this study, we were particularly interested in filling in the pathway stem cells take when they create normal human B cells because there was no detailed information for this in humans.”

Using this map, the researchers pinpointed the cell states in hematopoiesis from which B-cells are diverted to become leukemia cells in patient samples. “B-cell leukemia was assumed to arise from cells arrested within a specific window of development, the pro- to pre-B cell stage, and we showed that was true for many of the cases, but also that there was much more diversity than that,” Mullighan said.

“The origin of some cases was more mature and further along in B-cell development,” said co-first author of the study Ilaria Iacobucci, Ph.D., St. Jude Department of Pathology, “but some also involved less mature cells that were mapping to early hematopoietic progenitor states for a substantial proportion of subtypes.”

While the stage of differentiation arrest does not necessarily correlate with the leukemia cell of origin, identifying it allowed the researchers to better grasp how this impacts therapeutic effectiveness.

One of the main ways a cancer cell can evade therapy is by changing its lineage. The data showed that less mature arrested cells retain features allowing lineage changes to occur. The researchers confirmed this by growing non-leukemic common lymphoid progenitor cells, which should be committed to the lymphoid lineage, and observing them differentiate into a myeloid lineage.

“This showed us that a leukemic cell of that stage can actually differentiate into a non-B-cell lineage, essentially doing what we may see patient leukemias doing in the context of treatment,” Mullighan said.

To better grasp the impact the cell developmental state has on clinical outcomes, the researchers developed a “multipotency score.” This score accurately measured the enrichment of multipotent leukemic populations in B-ALL and predicted outcomes on a tested cohort of independent samples. This predictive tool has potential as a novel biomarker for pediatric B-ALL.

“This study fills a critical gap in our understanding of B-cell development,” said Dick. “Moreover, linking these progenitors to clinically relevant leukemia subtypes provide valuable insights that could drive advancements in both diagnostics and therapeutics.”

“With the genomic data that we are generating on every patient, we now have a much more nuanced understanding of subtypes that are prone to developing drug resistance or failing therapy,” Mullighan said. “It provides an additional layer of information that could be used for risk stratification.”