Background: PAX5 is an essential transcription factor required for B cell differentiation. It is known that PAX5 aberrations confer the occurrence of B cell lymphoblastic leukemia (B-ALL) in various forms of abnormality. However, due to the complexity of the structural variation of PAX5, comprehensive examination and analysis remain challenging.
Aims: To decipher the structural aberrations of the PAX5 gene to investigate their correlation with diagnostic classification and treatment outcome in B-ALL.
Methods: Optical genome mapping (OGM) and transcriptome sequencing (RNA-seq) were performed on the bone marrow samples of 21 newly diagnosed or relapsed/refractory B-ALL cases to decipher PAX5 structure variations including the formation of fusion genes, exon deletion, and exon duplication. Other pathological fusion genes and gene mutations in B-ALL were also analyzed, and patients were followed up for treatment outcomes.
Results: A total of 11 of 21 cases (52.4%) were detected with PAX5 structural variations, including 5 children (age < 14 years) and 6 adults (2.5 ~ 55 years, median = 20), with a male: female = 4.5:1 (9/2). Of them, 5 cases (45.4%) carried PAX5 in-frame fusion genes, and the partner genes RNF38, BCL2, and NSD1 have not been reported. Four cases (36.3%) carried the concatenation of PAX5::ZCCHC7 fusion transcript due to 510Kb 9p focal deletion, which functionally resulted in the truncation of PAX5. The other 2 cases (18.3%) carried PAX5 focal deletions (exon6, exon6-7, respectively). IKZF1 alterations were observed in 8 of the 11 (72.7%) cases, with IK10 being the most common (4 cases).
Eight of the 11 cases carried other genetic abnormalities that define B-ALL subtypes, including 2 BCR::ABL1, 3 BCR::ABL1-like (NUP214::ABL1, EBF1::PDGFRB, and RCSD1::ABL2, respectively), one E2A::PBX1, one ETV6::RUNX1, and one hyperdiploid case. Two cases were positive for CRLF2@IGH, but without genetic abnormalities that define B-ALL subtypes.
Six cases evaluated as high-risk received chimeric antigen receptor T cell (CAR-T) treatment, 5 of which were bridged to allogeneic hematopoietic stem cell transplantation (all0-HSCT), and these 5 cases maintained remission until the last follow-up (21-63m). The patient who was not bridged to allo-HSCT died of relapse 13 months after the disease onset.
Summary/Conclusion: PAX5 structural aberrations are common and important genetic events in B-ALL with various forms, including in-frame gene fusions, 3’ deletion (PAX5::ZCCHC7), and focal exon deletions. OGM combined with RNA-seq helps to decipher pathological PAX5 structural abnormalities. PAX5 structural abnormalities mostly occur in BCR::ABL1-positive and BCR::ABL1-like patients and are often associated with IK10. CART bridging allo-HSCT therapy helps improve these patients’ prognosis and survival rates.
Keywords: Acute lymphoblastic leukemia, PAX5