Poster Presentation 38th Lorne Cancer Conference 2026

Genomic complexity and adaptive alterations underpin drug resistance in myeloid blast crisis chronic myeloid leukaemia cell lines (#234)

Adelina Fernandes 1 , Verity Saunders 2 , Elyse Page 2 , Muneeza Maqsood 3 , Nur Hezrin Shahrin 3 , Carol Wadham 3 , Ming Lin 3 , John Toubia 3 , Chung Kok 1 3 , Joe McConnell 3 , Dominik Kaczorowski3 3 , Dariusz Ladon 3 , Christopher Hahn 1 3 , Timothy Hughes 2 , Ilaria Stefania Pagani 2 , Susan Branford 3
  1. The University of Adelaide, Adelaide, SOUTH AUSTRALIA, Australia
  2. Leukaemia Research Group, SAHMRI, Adelaide, South Australia, Australia
  3. Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia

Introduction

Blast crisis chronic myeloid leukaemia (BC-CML) is often fatal, mostly due to tyrosine kinase inhibitor (TKI) resistance. While kinase domain mutations in the causal BCR::ABL1 gene explain 50% of resistance cases, alternative genomic drivers remain underexplored. This study aimed to identify such mechanisms and test their functional impact.

 

Methods

Five BC-CML cell lines (K562, KCL22, MYL, LAMA84, AR230) and their imatinib-resistant sublines were profiled with targeted RNA sequencing, whole genome sequencing (WGS), and optical genome mapping. TKI resistance was assessed via Annexin-V/7-AAD apoptosis assays and western blotting-based BCR::ABL1 inhibition. SETD1B loss-of-function was validated using CRISPR/Cas9 knockout in BCR::ABL1+ Ba/F3 cells.

 

Results

All cell lines had chromosomal changes, copy number variations and cancer-gene variants, including novel alterations in tumour suppressors FHIT, WWOX and ANKRD11. Variants were lost and gained between sublines, consistent with clonal competition. Mutations were gained in the resistant subclones. The K562 imatinib-resistant subclone showed BCR::ABL1-independent resistance and had acquired a KRAS Gly12Ala variant and lost a KDM6A deletion.

 

Variants were also associated with sensitivity; KCL22 harbours a BIM deletion polymorphism, conferring intrinsic TKI resistance, but a SETD1B Pro694Thrfs*148 variant was found exclusively in the imatinib-sensitive subclone. SETD1B knockout in BCR::ABL1+ Ba/F3 cells increased sensitivity to TKI (p=0.002 vs wildtype SETD1B with 200nM imatinib) suggesting SETD1B loss could be overcoming BIM-driven resistance.

 

Where no variants were exclusively associated with the resistant subclone by targeted sequencing, e.g. AR230 and LAMA84, WGS revealed complex structural rearrangements on chromosomes 9 and 22, consistent with Philadelphia chromosome evolution. These resistant subclones were sensitive to higher doses of most higher-potency TKIs.

 

 

Conclusion

This study identified diverse genomic alterations associated with imatinib resistance across multiple cell lines. These demonstrate the heterogeneity of TKI resistance in BC-CML and support the need for integrated genomic characterisation of BC-CML cells to guide personalised therapeutic strategies in BC-CML.