RNA sequencing analysis may be the key to accurate diagnosis and treatment of pediatric B-acute lymphoblastic leukemia

A study conducted by Children’s Hospital Los Angeles and City of Hope proposes a promising global genomic assay that can be clinically applied for the diagnosis and treatment of this heterogeneous leukemia, as reported by The Journal of Molecular Diagnostics

Acute lymphoblastic leukemia (ALL) is the most common type of cancer in children and accounts for over 30% of all pediatric cases. A pilot study published in The Journal of Molecular Diagnostics has confirmed that an RNA sequencing analysis (RNA-Seq) workflow can be used for clinical diagnosis of molecular subtypes in pediatric B-acute lymphoblastic leukemia (B-ALL). This promising and cost-efficient global genomic assay for B-ALL could lead to more effective diagnosis and targeted treatment options.

ALL has various molecular subtypes, each with unique drug sensitivity patterns, treatment responses, and prognoses. It’s crucial to identify specific subtypes, particularly in the era of personalized medicine. However, this identification requires an array of profiling tools, which makes the process laborious and expensive.

The co-lead investigator of the study, Gordana Raca, MD, PhD, Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, explains that the goal of the study was to overcome the limitations of current standard-of-care (SOC) testing for pediatric B-ALL, which cannot identify multiple recently discovered subtypes of the disease. They also wanted to determine whether additional data analyses could help determine subtype classification in addition to fusion information for their B-ALL cases, using expression data generated by the enrichment-based RNA-Sequence assay clinically validated in their laboratory for detection of oncogenic fusions in cancer.

Investigators reviewed clinical, morphologic, immune phenotypic, and molecular data, as well as residual DNA, RNA, and frozen bone marrow aspirate and/or leukemic peripheral blood samples from previous clinical testing, in a group of 76 pediatric patients. Results were analyzed from 61 newly diagnosed patients and 25 patients who had relapsed/refractory B-ALL who underwent cytogenetic and molecular characterization as part of their standard clinical care at the Center for Personalized Medicine at Children’s Hospital Los Angeles between March 2016 and September 2020. They hypothesized that RNA-Sequence, which has been used in the discovery of novel molecular subtypes of B-ALL, could also be a clinically useful tool for diagnostic classification of B-ALL cases.

To test this hypothesis, investigators analyzed RNA-Sequencing data in 28 cases of B-ALL with known subtype and 48 with undetermined subtype following clinical karyotype analysis, fluorescence in situ hybridization, chromosomal microarray, and next-generation sequencing DNA and RNA fusion panel testing (OncoKids®). RNA-Sequencing analysis accurately identified the subtypes in all 28 known cases and determined the genetic subtype in 38 of the 48 previously unknown cases (79%). RNA-Sequencing analysis was also able to detect oncogenic fusions, large copy number abnormalities, oncogenic hot-spot sequence variants, and intragenic IKZF1 deletions.

Co-Lead investigator Zhaohui Gu, PhD, Department of Computational and Quantitative Medicine & Systems Biology, Beckman Research Institute of City of Hope, Duarte, says, “The study showed that B-ALL cases with known subtypes by SOC testing were fully concordant with the RNA-Seq–based classification. In addition, RNA-Sequencing analysis allowed us to successfully classify a large proportion of cases that remained unknown upon comprehensive SOC testing. RNA-Seq–based classification was relatively easy to implement in a medium-size academic laboratory using data from a clinically validated fusion assay.”

Dr. Raca adds, “RNA-Seq analysis enables accurate determination of the genetic subtype for an increased proportion of pediatric B-ALL cases, which will allow more accurate risk stratification and optimization of patient management. Accurate subtype determination at diagnosis will also grow our knowledge about morphologic, immunophenotypic, and clinical characteristics of novel B-ALL subtypes. We were surprised by a relatively high frequency of some novel B-ALL subtypes (like PAX5Alt and DUX4) in our patient cohort, which remain undiagnosed by SOC testing. The study also resulted in discovery of several previously unreported fusions.”

Dr. Raca says, “The study showed that expression-profile–based classification, which to date has been mostly used in research, can also be a very powerful clinical assay for pediatric B-ALL. As a single test, it allows subtype determination in a higher proportion of cases than comprehensive multi-modal SOC testing performed at our institution. Therefore, it has the potential to increase both diagnostic yield and efficiency of B-ALL testing.”

In a related editorial, Dr. Shawn H.R. Lee, who works at the Khoo Teck Puat–National University Children’s Medical Institute, National University Health System in Singapore, and also at the Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, agrees that RNA-seq is probably one of the most, if not the most, powerful tool for somatic profiling in pediatric B-ALL. However, he notes that it is still a matter of debate whether RNA-Seq is recommended for all cases as the sole means of classification due to some inherent limitations, particularly in areas where analytical pipelines may not be as robust.

Dr Lee comments, “Overall, RNA-seq as a single somatic genomic ALL diagnostic platform holds immense promise, although still with associated gaps. In some cases, validation of positive cases by an alternative method (such as oncogene fusion test and DNA sequencing) may still be arguably a sounder approach. The test needs further refining to comprehensively obtain mutation information beyond that of molecular subtyping to make it globally accessible. As we move further into the era of precision medicine, the information provided by this test holds excellent promise in guiding relevant and risk-stratified treatment in this childhood cancer.”

This news is a creative derivative product from articles published in famous peer-reviewed journals and Govt reports:

1. Gu Z.,Churchman M.L., Roberts K.G., Moore I.,Zhou X., Nakitandwe J., PAX5-driven subtypes of B-progenitor acute lymphoblastic leukemia. Nat Genet. 2019; 51296-307

2. Yasuda T., Sanada M., Kawazu M., Kojima S., Tsuzuki S., Ueno H., Two novel high-risk adult B-cell acute lymphoblastic leukemia subtypes with high expression of CDX2 and IDH1/2 mutations. Blood. 2022; 1391850-1862

3. Kimura S., Montefiori L., Iacobucci I., Zhao Y., Gao Q., Paietta E.M., Enhancer retargeting of CDX2 and UBTF::ATXN7L3 define a subtype of high-risk B-progenitor acute lymphoblastic leukemia.Blood. 2022; 1393519-3531

4. Brady S.W., Roberts K.G., Gu Z., Shi L., Pounds S., Pei D., The genomic landscape of pediatric acute lymphoblastic leukemia. Nat Genet. 2022; 541376-1389

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