Transcriptome-Based Molecular Subtypes Improve the Classification of B Cell Acute Lymphoblastic Leukemia with JAK2 Translocation

Background: Hematological malignancy with JAK2 rearrangement have been mainly found in B cell acute lymphoblastic leukemia (B-ALL) and myeloproliferative neoplasm (such as MPN , CML and M/L-Eo). WHO and ICC guide that B-ALL with JAK2 fusions induced JAK-STAT-activating alterations is classified as BCR::ABL1-like (ph-like) ALL. However, whether all B-ALL carrying JAK2 fusion present ph-like type, and the genetic and molecular mechanism of which is still not clear. Material and Methods: 4540 patients' bone marrow or peripheral blood samples (between 2020 and 2024) from single-center and nineteen healthy donors' bone marrow were screened for hematological malignancy-related fusion genes and gene expression profiles using whole transcriptome sequencing (RNA-seq), and for gene mutations and copy number variation (CNV) using target DNA sequencing (364 genes). All patients underwent routine testing and risk assessment: age, WBC count, cytogenetic/molecular classification, immunophenotyping, MRD, etc. Results: Utilizing RNA-seq and fluorescence in situ hybridization (FISH), we confirmed 23 patients with JAK2 fusions, which involved 11 fusion partner genes (6×PAX5, 4×BCR, 3×PCM1, 2×ATF7IP, 2×TERF2, and one CEP128, PIK3AP1, PPFIBP1, TRIM38, ZBTB44, and ZSCAN16 each). Flow cytometry analysis showed that the most of the patients have an immunophenotype of common B-ALL or pre B-ALL, except one CEP128::JAK2 positive patient with medullary T-ALL, and two PCM1::JAK2 positive patient with elevated eosinophils. Therefore, the incidence of these twenty B-ALL carrying JAK2 fusion accounts for 1.3% of all B-ALL cases. To identify whether these twenty patients with B-ALL phenotype are ph-like or not, we compared gene expression profile of whole transcriptome data between this twenty patients and twenty paired BCR::ABL1 positive B-ALL patients, and nineteen healthy donors, and found that fifteen patients have a gene expression profile highly consistent with BCR:: ABL1 positive B-ALL patients, which means that these patients can be defined as ph-like type B-ALL with JAK2 fusions. Moreover, GO and KEGG analysis showed that BCR:: ABL1 and JAK2 fusions with ph-like type both prominently activate PI3K-AKT and MAPK signaling pathway. Interestingly, We further found that all of the ph-like type B-ALL with JAK2 fusions have IKZF1, or CDKN2A/B gene deletion or mutations, but these 3 genes abnormalities closely related to B cell development or cell cycle did not found in the other five non-ph-like type B-ALL patients with JAK2 fusions. Four out of five non-ph-like type B-ALL patients were PAX5::JAK2 fusion positive without IKZF1, or CDKN2A/B gene abnormalities, which indicated that the probability of B-ALL with PAX5::JAK2 being ph-like type is relatively low that other fusion partner genes. Conclusion: Our primary data showed that most patients carrying JAK2 fusion are diagnosed with B-ALL, but not all B-ALL with JAK2 fusions are ph-like type. B-ALL carrying JAK2 fusions accompanied with IKZF1, or CDKN2A/B gene abnormalities can be diagnosed as ph-like type, which activate PI3K-AKT and MAPK signaling pathway. Disclosures No relevant conflicts of interest to declare.