Zhaohui Gu, PhD
Postdoctoral Research Associate
St. Jude Children's Research Hospital, TN
MedicalResearch.com: What is the background for this study? What are the main findings?
Response:B-progenitor acute lymphoblastic leukemia (B-ALL) is the most common pediatric malignancy and the leading cause of childhood cancer death. B-ALL includes multiple subtypes that are defined by distinct genetic alterations and that play an important role in diagnosis, prognosis and therapy of patients. Advances in transcriptome sequencing (RNA-seq)have helped researchers discover additional subtypes and driver mutations inB-ALL and identify possible new therapeutic targets. Still, up to 30% of B-ALL cases do not fit into established subtypes. These patients lack targeted therapeutic approaches and commonly relapse.
Fort his study, we used integrated genomic analysis of 1,988 childhood and adult cases to revise the classification system of B-ALL. The system includes eight new subtypes and a total of 23 B-ALL subtypes. The subtypes are defined by chromosomal rearrangements, sequence mutations, or heterogeneous genomic alterations. Many show a marked variation in prevalence according to age.
The newly identified subtypes included one (n=18) defined by rearrangements of gene BCL2, MYC and/or BCL6 anda distinctive gene expression profile (GEP). Patients in this subtype were mostly adults (n=16) with very poor outcomes.
Another novel subtype was defined by IKZF1 N159Y missense mutation. N159Y is in the DNA-binding domain of IKZF1, and is known to disrupt IKZF1 function, with distinct nuclear mis-localization and induction of aberrant intercellular adhesion. There were eight cases in this subtype that shared highly similar GEPs.
We also identified two subtypes with distinct GEP and characterized by PAX5 alterations. One, PAX5 altered (PAX5alt), included 148 cases. PAX5alt was characterized by diverse PAX5 alterations including rearrangements (n=57), sequence mutations (n=46) and/or focal intragenic amplifications (n=8). These PAX5 alterations were found in 73.6% of PAX5alt cases. The second distinct subtype comprised 44 cases, all with PAX5 P80R missense mutations. Bi-allelic PAX5 alterations were commonly seen in this subtype in the form of PAX5 P80R coupled with a second sequence mutation or deletion of the wild-type PAX5 allele.
Adult PAX5 P80R cases showed better 5-year OS (61.9±13.4%) than those in PAX5alt subtype (42.1±10.2%). In addition, Pax5 P80R heterozygous and homozygous mice developed B lineage leukemia with a median latency of 166 and 87 days, respectively. The heterozygous mice acquired alterations on the second allele, which faithfully recapitulated the condition of the patient leukemia.
MedicalResearch.com: What should readers take away from your report?
Response: Identification of subtypes accurately is very important for diagnosis, intensity-tailored therapy, and to identify targetable lesions. In this large scale genomic study, we demonstrated the power of using RNA-seq to classifying B-ALL and established a revised B-ALL taxonomy with 23 distinct subtypes. We identified 8 novel subtypes, including two defined by PAX5 alterations. Through in vitro and in vivo experiments, we demonstrated that PAX5 P80R could impair B cell differentiation and initiate leukemia.
Together with the subtype defined by IKZF1 N159Y mutation, we showed for the first time that transcription factor missense mutations could be a subtype defining genetic lesions.