Prognostic Impact of Copy Number Alterations’ Profile and AID/RAG Signatures in Acute Lymphoblastic Leukemia (ALL) with BCR::ABL and without Recurrent Genetic Aberrations (NEG ALL) Treated with Intensive Chemotherapy

SIMPLE SUMMARY: Adult ALL is a highly aggressive blood cancer. Two classes of genetic aberrations are responsible for ALL: primary aberrations followed by secondary aberrations. Currently, primary aberrations are used for estimating patients’ risk in adult ALL. In this study, we reassessed the importance of primary and secondary copy number alterations (CNA) aberrations in intensively treated adult ALL patients in correlation to RAG/AID mutator enzyme expression. Primary aberrations alone specified the risk of 30% of patients. To define the prognosis of the remaining 70%, we identified high-risk and low-risk CNA profiles. We found the CNA profiles correlated with differential RAG/AID expression profiles. Furthermore, the outcome of CNA(neg) adult ALL was stratified by AID expression. Thus, we suggested mechanisms linking secondary aberrations with patients’ outcomes and mutator enzymes. Finally, we propose a revised version of risk stratification in adult ALL patients which incorporates primary and secondary genetic lesions. ABSTRACT: Adult acute lymphoblastic leukemia (ALL) is associated with poor outcomes. ALL is initiated by primary aberrations, but secondary genetic lesions are necessary for overt ALL. In this study, we reassessed the value of primary and secondary aberrations in intensively treated ALL patients in relation to mutator enzyme expression. RT-PCR, genomic PCR, and sequencing were applied to evaluate primary aberrations, while qPCR was used to measure the expression of RAG and AID mutator enzymes in 166 adult ALL patients. Secondary copy number alterations (CNA) were studied in 94 cases by MLPA assay. Primary aberrations alone stratified 30% of the patients (27% high-risk, 3% low-risk cases). The remaining 70% intermediate-risk patients included BCR::ABL1(pos) subgroup and ALL lacking identified genetic markers (NEG ALL). We identified three CNA profiles: high-risk bad-CNA (CNA(high)/IKZF1(pos)), low-risk good-CNA (all other CNAs), and intermediate-risk CNA(neg). Furthermore, based on RAG/AID expression, we report possible mechanisms underlying the CNA profiles associated with poor outcome: AID stratified outcome in CNA(neg), which accompanied most likely a particular profile of single nucleotide variations, while RAG in CNA(pos) increased the odds for CNA(high)/IKZF1(pos) development. Finally, we integrated primary genetic aberrations with CNA to propose a revised risk stratification code, which allowed us to stratify 75% of BCR::ABL1(pos) and NEG patients.