Poster Presentation 38th Lorne Cancer Conference 2026

RUNX1 and beyond: genetic mechanisms of resistance to tyrosine kinase inhibitors in chronic myeloid leukaemia (#224)

Zuhal ZN Naderi 1 , Susan SB Branford 2 , Naranie NS Shanmuganathan 3 , Timothy P TPH Hughes 1 3 4 , Teresa TS Sadras 5 , Ilaria Stefania ISP Pagani 1 4
  1. South Australian Health and Medical Research Institute, Adelaide, SA, Australia
  2. Centre for Cancer Biology , SA Pathology, The University of South Australia , Adelaide, SA, Australia
  3. Haematology and Bone Marrow Transplantation, Royal Adelaide Hospital and SA Pathology, Adelaide, SA, Australia
  4. Adelaide Medical School, Faculty of Health and Medical Sciences, Adelaide, SA, Australia
  5. Olivia Newton-John Cancer Research Institute, Melbourne , Victoria , Australia

Intro/Aims:

Despite the success of tyrosine kinase inhibitors (TKIs) in chronic myeloid leukaemia (CML), ~20% of patients develop resistance. Mechanisms include BCR::ABL1 kinase domain mutations, BCR::ABL1 overexpression and epigenetic or transcriptional alterations (e.g. RUNX1, ASXL1, TET2 mutations).

Asciminib, an allosteric inhibitor targeting the ABL1 myristoyl pocket, is active against many BCR::ABL1 mutations, including T315I, and demonstrates efficacy after TKI failure. However, patients with high-risk genetic features remain prone to resistance. Combination approaches, such as asciminib plus dasatinib, are under investigation, including in the ASCENDANCE (CML14, #ACTRN1262300133865) trial.

RUNX1 mutations are frequent in blast-phase CML and associate with poor prognosis, yet their role in resistance to asciminib-based combinations is unknown. This study models dual resistance to asciminib and dasatinib and evaluates the contribution of RUNX1 using patient-derived and functional models.

Results and Methods:

Resistant K562 intermediates were generated through exposure to escalating concentrations of asciminib (ASC) and dasatinib (DAS) in combination at a ratio of 35 to 1. Drug transporter expression was measured by flow cytometry. Early intermediates (3.5 nM ASC + 0.1 nM DAS; 35 nM + 1 nM) did not upregulate ABCG2 or ABCB1. In contrast, late intermediates (350 nM + 10 nM; 525 nM + 15 nM) demonstrated significantly increased ABCG2 expression (p<0.0001, n=3), while ABCB1 remained low. No BCR::ABL1 mutations were detected.

In a retrospective cohort of 575 CML patients, RUNX1 mutations were identified in 31 patients (6.1%) and followed three patterns: (1) present at diagnosis (median variant allele frequency, VAF ~10%) in patients with optimal TKI response; (2) acquired during TKI therapy in myeloid blast phase (n=6; median VAF ~39%), frequently co-occurring with ASXL1, TET2, or SETD1B mutations; and (3) present in lymphoid blast phase (n=6; median VAF 46%), often co-occurring with BCR::ABL1 mutations.

To assess function, CRISPR-Cas9 knockout of RUNX1 was performed in K562 cells and patient-derived variants (p.Arg166Leu, p.Arg107Leu) reintroduced to test TKI sensitivity. Functional work is ongoing.

Conclusions

This stepwise K562 model of dual ASC/DAS resistance identified ABCG2 overexpression as a mediator of acquired resistance. RUNX1 mutations were characterised in patients, and functional studies are ongoing. These models provide a platform to define mutation-informed strategies to overcome resistance in high-risk CML.