Molecular Classification and Clinical Correlation Utilizing Next-Generation Sequencing in Adult B-Cell Acute Lymphoblastic Leukemia
Authors: Bandikatla Sudeepthi , Shahzad Moazzam , Shah Bijal D , Knepper Todd C 
Published: December 2024

Background:
Molecular characterization is vital for diagnosing, stratifying risk, and treating adult B-cell acute lymphoblastic leukemia (B-ALL). Guidelines, classification systems, and genomic studies increasingly use molecular data, but gaps remain. International Consensus Classification (ICC) introduced 9 new categories, mostly based on distinguishing genomic alterations. NCCN Guidelines classify risk into 2 categories based on cytogenetic and molecular changes. A prior study by Paietta et al. defined 3 molecular risk categories based on adolescent/adult data (median age 30). Large studies on genomic landscape, including entity-defining molecular entities and their extended spectrum of mutations, and treatment outcomes in adult patients with B-ALL are limited.
Methods:
This retrospective, descriptive study of 206 adult B-ALL patients (pts) at our institution analyzed next-generation sequencing (NGS) using a commercial DNA/RNA assay over 8 years. We correlate molecular findings with clinical outcomes and describe additional genomic alterations beyond those defining specific entities.
Intensive treatment was hyperCVAD or asparaginase-based regimens (for BCR:ABL1 (Ph)-negative B-ALL) or tyrosine kinase inhibitors with chemotherapy/immunotherapy (for Ph-positive B-ALL). Event-free survival (EFS) was the time from diagnosis to treatment change (for MRD+ status or relapse) or until the last contact or 7/1/2024 if no progression.
Results:
Median age was 52 years (range: 18-82), with 55% male. Treatment details were available for 97% of pts, 90% of whom received intensive therapy. Among Ph-like pts, 33% were Hispanic.
Using ICC, 58% (n=120) of pts were able to be classified into 10 molecularly defined B-ALL categories. Most (56.7%) were Ph-positive B-ALL, followed by Ph-like (22.5%) and B-ALL with KMT2A rearrangement (6.7%). NCCN risk stratification captured 75% of pts. The 35 pts without an ICC molecular category were classified by NCCN based on mutations in TP53 (97.1%) or IKZF1 (2.9%).
Pts deemed poor risk by NCCN who received intensive treatment (n=82) had mEFS of 32 weeks and mOS (median overall survival) of 141 weeks. Pts deemed standard (std) risk by NCCN who received intensive treatment (n=54) experienced mEFS of 73 weeks and mOS of 148 weeks.
Among Ph-negative pts, using Paietta et al. classification, std-risk pts (n=8) with mEFS of 23 weeks and mOS of 110 weeks, high-risk pts (n=33) with mEFS of 22 weeks and mOS of 106 weeks, and intermediate-risk pts (n=5) with mEFS of 63 weeks and mOS of 318 weeks. NCCN classification had std-risk pts (n=8) with mEFS of 37 weeks and mOS of 120 weeks, and high-risk pts (n=76) had mEFS of 26 weeks and mOS of 106 weeks.
TP53 mutations were found in 20% (n=42) of the study population, mostly in pts not defined by other ICC categories (n=33). Among the remaining 9 patients, TP53 mutations were seen in 37% of KMT2A-rearranged pts, 25% of ETV::RUNX1-like pts, 3% of Ph-like pts, and 3% of Ph-positive pts. Both MYC-rearranged pts had TP53 mutations. Common co-occurring mutations with TP53 were RAS pathway alterations (31%) and CDKN2A/B loss (29%). RAS pathway mutations were found in 48 pts. CDKN2A/B loss co-occurred in 89% of RAS-mutated pts. RAS mutations were present in 28% of Ph-like pts.
IKZF1 alterations (excluding N159Y) were found in 16% of study pts. Of these, 39% were IKZF1 plus (with CDKN2A/B, PAX5, or PAR1). IKZF1 plus was seen in 24% of Ph-like pts and 7% of Ph-positive pts. PAX5alt were found in 5% of study pts. 14% of Ph-like pts and 4% of Ph-positive pts had PAX5 alterations. Whereas, mutated PAX5 P80R were found in 0.8% of all pts. CDKN2A/B loss was seen in 34% of pts across various ICC categories. Of these, 84% had co-occurring mutations, including TP53, NRAS, IKZF1, KRAS, PTPN11, IGH-R, FLT3-ITD, FLT3-TKD, PAX5, MYD88, NCOR2, and RUNX1-R.
Conclusion:
Our study underscores the complexity of B-ALL and importance of comprehensive molecular characterization for risk stratification. ICC captured 58% of our patients, while NCCN captured 75%. Paietta et al. shows similar mEFS and mOS for high-risk pts compared to NCCN but identifies poorer outcomes for std-risk pts and notably higher survival for intermediate-risk pts, though with a limited sample. Notably, B-ALL, NOS comprises 42% of pts, with significant proportion (40%) classified as poor risk. Discrepancies in capturing high-risk pts between classification systems underscore the need for ongoing updates.