CO49 | Combined nf1/suz12 haploinsufficiency drives aberrant activation of the RAS signaling cascade in immature hoxa-positive T-ALL

Abstract

Introduction. Deletions of the long arm of chromosome 17 (I-17q) in immature T-cell acute lymphoblastic leukemia (T-ALL) of adults encompass NF1 and SUZ12. NF1 encodes a negative regulator of the RAS pathway while SUZ12, a member of the PRC2 complex, is an epigenetic modulator that mediates the methylation of H3K27. Inactivation of NF1 and SUZ12 has been reported to synergistically enhance RAS/MAPK signaling in JMML and solid tumors (Zhang M, Nat Genet 2014; Caye A, Nat Genet 2015; de Raedt T, Nature 2014).
Aim. To elucidate the biological and functional impact of NF1 and SUZ12 haploinsufficiency in T-ALL.
Methods. The I-17q abnormality was detected in 39 out of 447 genomically characterized T-ALL cases (288 adults and 159 children) using a multimodal approach combining FISH, SNP array, and targeted custom NGS analyses. SUZ12 knock down (SUZ12-KD) in the PF382-Cas9 cell line, which harbors an NF1 loss-of-function mutation, was used to model concurrent NF1 and SUZ12 haploinsufficiency. Gene expression analysis was performed by Whole Transcriptome Expression array (WTEa) (Bardelli V, J Mol Diagn 2025) and qRT-PCR, while MAPK pathway activation was assessed by Western blot analysis of phosphorylated ERK (pERK).
Results. I-17q correlated with NF1 and SUZ12 haploinsufficiency and was restricted to the leukemic clone, disappearing upon hematologic and cytogenetic remission. It was significantly linked to adulthood (Chi-square, p = 0.002) and an immature phenotype (p < 0.001), and was enriched in cases with high HOXA expression levels (present in >40% of I-17q–positive cases), which in 68% of cases were driven by known genomic alterations (3 HOXA, 3 NUP214, 2 MLLT10, 2 ZFP36L2, and 1 KMT2A). According to the immature phenotype, upregulation of IGFBP7, MN1, CD34, MEF2C, RUNX2, and BAALC, typically expressed in hematopoietic/progenitor cells, was observed. In addition, GSEA demonstrated enrichment of MAPK pathway signature. In vitro studies showed that the NF1-mutant PF382 cell line exhibited increased ERK phosphorylation after SUZ12 knockdown. Furthermore, enhanced ERK phosphorylation was observed in primary I-17q samples, supporting a cooperative role of NF1 and SUZ12 loss.
Conclusion. I-17q marks immature T-ALL of adults with high levels of HOXA expression. Reflecting a model of concurrent NF1/SUZ12 loss observed in other human tumors, our data indicate that NF1 loss drives activation of the RAS/RAF/MEK/ERK pathway, which is further enhanced by SUZ12 haploinsufficiency, highlighting this signaling cascade as a potential therapeutic target.