Newly Defined Subtypes of B-Cell Acute Lymphoblastic Leukemia
Investigators have identified multiple new subtypes of the most common childhood cancer, B-cell acute lymphoblastic leukemia (ALL)—research that has the potential to improve the diagnosis and treatment of high-risk patients. Researchers used integrated genomic analysis, including RNA sequencing, to define the genomic landscape of B-cell ALL in almost 2,000 children and adults. These findings were published by Gu et al in Nature Genetics.
B-cell ALL is the most common form of ALL and the most common cancer in children. It remains the leading cause of pediatric cancer death.
Investigators identified 23 subtypes of B-cell ALL with distinct genomic and clinical features as well as outcomes, including eight new subtypes. Subtype prevalence often varies with age. More than 90% of B-cell ALL cases can now be categorized by subtype compared with 70% a few years ago.
“B-[cell] ALL has remarkable molecular diversity, which we and others have used to refine classification and drive the development of precision medicines to improve B-[cell] ALL treatment and outcomes,” said corresponding author Charles Mullighan, MBBS, MD, a member of the St. Jude Children’s Research Hospital Department of Pathology. “Part of precision medicine is an accurate molecular diagnosis, which this study provides to more patients.”
Discovered Subtypes
Alterations of the transcription factor gene PAX5 defined two new subtypes, including PAX5 P80R, as the first lymphoblastic leukemia initiated by a point mutation. “While secondary mutations are necessary and often involve kinase signaling, we show this point mutation impairs development of B lymphoid cells and promotes development of B-[cell] ALL in mice,” said Dr. Mullighan.
The other PAX5 subtype, PAX5-altered, was defined by diverse alterations in the gene, including sequence mutations or rearrangements with one of 24 other genes. Together, the PAX5 subtypes accounted for almost 10% of the previously uncategorized cases of B-cell ALL.
The new subtypes include a high-risk variety of B-cell ALL that occurs primarily in adults. It is defined by rearrangement of the transcription factors BCL2 with MYC or BCL6. “This subtype has a dismal diagnosis,” Dr. Mullighan said. “Recognition of this subtype-defining rearrangement may lead to alternative therapy for patients.”
In contrast, a subtype defined by rearrangement of the gene DUX4 was associated with a good prognosis in adults as had previously been observed in children.
The study also demonstrated the capability of RNA sequencing to identify multiple types of genomic alterations, highlighting the utility of this technique for leukemia diagnosis, particularly when whole-genome sequencing is not available. Examples in this study included chromosomal rearrangements resulting in fusion genes, gene-expression profiles, and other alterations.
“Through this study, two-thirds of the previous uncharacterized [patients with] B-[cell] ALL could be classified into different subtypes with distinct genetic alteration profiles and clinical features,” said co-first author Zhaohui Gu, PhD, a postdoctoral fellow in the Mullighan laboratory. “That may substantially speed up the development of customized treatments for these patients.
“We also established a robust B-[cell] ALL classification pipeline based mainly on RNA sequencing data that may be integrated into clinical diagnosis of ALL,” Dr. Gu said.
The other newly identified subtypes include:
- NUTM1 gene rearrangement with different partner genes that researchers believe may be vulnerable to treatment;
- HLF gene rearrangement to multiple genes, including TCF4 as well as the previously recognized partner TCF3;
- Three subtypes that share patterns of gene expression similar to those of established B-cell ALL subtypes. The classification suggests that the new subtypes, ETV6-RUNX1–like, KMT2A-like and ZNF384-like, have risk profiles and prognoses similar to the established subtype for which they are named;
- Additional subtypes driven by sequence mutations, including IKZF1 N159Y. Previous work from St. Jude and the Children’s Oncology Group TARGET initiative have shown IKZF1 mutations to be a marker of high risk B-ALL.
“As a clinician, these data describing the diversity of subtypes of B-[cell] ALL will allow us to refine our prognostic abilities for individual patients, and ultimately, will lead to the development of new targeted therapies that will more effectively treat the leukemia with fewer side effects,” said co-author Mark Litzow, MD, Professor of Medicine at the Mayo Clinic and Chair of the Leukemia Committee, ECOG-ACRIN.
Disclosure: The research was funded in part by the American Society of Hematology Scholar Award; the Leukemia and Lymphoma Society’s Career Development Program; St. Baldrick’s Foundation Robert J. Arceci Innovation Award; the National Cancer Institute; the National Institutes of Health; and ALSAC. The study authors’ full disclosures can be found at nature.com.
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