Recurrent Focal Mkks-SLX4IP Deletion in ETV6::RUNX1 and Ph/Ph-like B-ALL

Introduction

SLX4IP is a regulator involved in alternative lengthening of telomeres (ALT) telomere maintenance, and interstrand crosslinks repair (ICL). Previous studies identified SLX4IP deletion as a result of illegitimate V(D)J-mediated recombination events. SLX4IP depletion sensitized cells to treatment with ICL-inducing agents and has been noted inactivated in a subset of ALT-positive osteosarcomas. Androgen receptor-independent castration-resistant prostate cancer also uniquely relies on SLX4IP-mediated ALT, exhibiting elevated SLX4IP levels. However, the role of SLX4IP deletion in leukemia remains unclear. This study investigates a recurrent structural variant, specifically the focal MKKS-SLX4IP deletion (abbreviated as del), and assess their clinical relevance and pathogenic mechanism using Optical Genome Mapping (OGM) and RNA-seq.

Methods

An unselected cohort of 73 B-ALL patients (21 newly diagnosed, 52 relapsed/refractory) was studied. The cohort included 44 males and 29 females, with 29 pediatric (<14y) and 44 adolescent and adult (≥14y) patients, aged 4-64y (median 17y). Bone marrow samples were analyzed using both OGM and RNA-seq. Structural variants were detected by OGM, while gene expression was analyzed using RNA-seq.

Results

A recurrent focal MKK-SLX4IP deletion was identified in 15 cases (15/73, 20.5%), encompassing partial 5’UTR of the MKKS gene and 5’UTR and coding exon 2 of the SLX4IP gene. This deletion was clustered at a specific breakpoint in the OGM analysis, with a median VAF of 0.43 (range: 0.05-0.93). Among this subset of patients, 80% (12/15) were male and 86.7% (13/15) had relapsed/refractory disease. Notable, 93.3% (14/15) of them enriched in patients with ETV6::RUNX1 (4/15), BCR::ABL1 (3/1), and Ph-like (7/15).

We analyzed the correlation between this del and clinical characteristics, expression of genes within 1Mb of the deletion breakpoint, RAG1/2, FLT3, 16 genes related to hormone metabolism, and 34 genes related to telomeres and DNA repair. All patients with ETV6::RUNX1 were positive for this del in this cohort, and all were young boys (median age 6.5y). In contrast, all patients with Ph-like+del were adolescents or adults (median age 25y; P=0.010). No significant differences in age or gender distribution were found in Ph+del patients.

The expression of MKKS and SLX4IP was significantly reduced in both Ph+Del (MKKS: P=0.017, logFC=3.45; SLX4IP: P =0.053, logFC=3.47) and Ph-like+Del (MKKS: P=0.011, logFC=1.21; SLX4IP: P=0.045, logFC=1.25) groups, with no significant difference in ETV6::RUNX1+Del group. JAG1 expression was significantly increased in the ETV6::RUNX1+Del group (logFC=1.53) while decreased in the other two groups. RAG1 repression was significantly increased in ETV6::RUNX1+Del group (P=0.007, logFC=3.48), while RAG2 and RAG1 expression were increased in Ph+Del (logFC=2.16) and Ph-like+Del (logFC=2.28) groups, respectively. FLT3 expression was significantly elevated in both Ph+del (P=0.030, logFC=5.06) and Ph-like+del (P=0.018, logFC=3.92) groups, while it decreased in ETV6::RUNX1+del patients. TERT expression was upregulated in both Ph+del (logFC=1.72) and Ph-like+del (P=0.006, logFC=2.14) groups. In contrast, in the ETV6::RUNX1+del group, TERT expression decreased, while TERF2 expression significantly increased (P=0.034, logFC=1.85).

Conclusion

Our results indicated the recurrency of focal MKKS-SLX4IP deletion and its correlation with ETV6::RUNX1, Ph, and Ph-like B-ALL subgroup. This deletion is significantly associated with male patients and is linked to increased expression of RAG1 and TERF2, but not to a significant decrease in MKKS and SLX4IP expression in ETV6::RUNX1+del patients. In contrast, Ph and Ph-like patients exhibited decreased expression of MKKS and SLX4IP and increased FLT3 and TERT expression. These findings suggest that the deletion is related to RAG-mediated illegitimate V(D)J recombination. The male predominance in ETV6::RUNX1+del patients may be related to hormone regulation. Given that SLX4IP loss alone is insufficient to induce ALT-like phenotypes in ALT-negative cells but enhances telomere recombination in ALT-positive cells, ETV6::RUNX1+del and Ph/Ph-like+del B-ALL patients may exhibit distinct telomere maintenance mechanisms. Further exploration is needed to determine whether this subset of SLX4IP-deficient leukemias is ALT-positive.