New findings show 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 Centre, 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, PhD, Senior Scientist at University Health Network’s Princess Margaret Cancer Centre.
“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, PhD, 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.”
Authors and funding
The study’s other first authors are Qingsong Gao, St. Jude; Andy Zeng, University Health Network’s Princess Margaret Cancer Centre and University of Toronto; and Laura Garcia-Pratt, University of Toronto. The study’s other co-corresponding author is John Dick, University Health Network’s Princess Margaret Cancer Centre and University of Toronto. The study’s other authors are Sayyam Shah, Alex Murison, Veronique Voisin and Michelle Chan-Seng-Yue, University Health Network’s Princess Margaret Cancer Centre; Matthew Witkowski, University of Colorado Anschutz Medical Campus; Anjali Advani, Cleveland Clinic; Selina Luger, University of Pennsylvania; Mark Litzow, Mayo Clinic; Jacob Rowe, Israel Institute of Technology and Shaare Zedek Medical Center; Elisabeth Paietta, Montefiore Medical Center; Wendy Stock, University of Chicago; and Pradyumna Baviskar, Cheng Cheng, Chunxu Qu, Colin Bailey, Matthew Lear, Xin Zhou, Airen Zaldivar Preaza, and Karishma Gangwani, St. Jude.
The study was supported by grants from Alex’s Lemonade Stand Foundation for Childhood Cancer; the National Cancer Institute (P30 CA021765, R35 CA197695, U10 CA180888, U10 CA180820 and UG1 CA189859); St. Baldrick’s Foundation Robert J. Arceci Innovation Award; the Henry Schueler 41&9 Foundation; University of Toronto MD/PhD studentship award; Princess Margaret Cancer Foundation; Ontario Institute for Cancer Research; Canadian Institutes for Health Research (RN380110-409786); International Development Research Centre Ottawa Canada; Canadian Cancer Society (703212); Terry Fox New Frontiers Program project grant (1106); University of Toronto’s Medicine by Design initiative with funding from the Canada First Research Excellence Fund; The Ontario Ministry of Health; Canada Research Chair; and the American Lebanese Syrian Associated Charities (ALSAC), the fundraising and awareness organization of St. Jude.
St. Jude Children's Research Hospital
St. Jude Children's Research Hospital is leading the way the world understands, treats and cures childhood cancer, sickle cell disease, and other life-threatening disorders. It is the only National Cancer Institute-designated Comprehensive Cancer Center devoted solely to children. Treatments developed at St. Jude have helped push the overall childhood cancer survival rate from 20% to 80% since the hospital opened more than 60 years ago. St. Jude shares the breakthroughs it makes to help doctors and researchers at local hospitals and cancer centers around the world improve the quality of treatment and care for even more children. To learn more, visit stjude.org, read St. Jude Progress, a digital magazine, and follow St. Jude on social media at @stjuderesearch.
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