Poster Presentation Australasian RNA Biology and Biotechnology Association 2024 Conference

Revealing the therapeutic potential of the epitranscriptome and translational regulation at the onset of Leukemia drug resistance (#163)

Agin Ravindran 1 2 3 , Merin Joy 1 , Alice Cleynen 1 2 3 4 , Nimeree Muntasir 1 , Stefan Prodric 1 2 3 , Akanksha Srivastava 1 2 3 , Madhu Kanchi 1 , Dipti Talaulikar 5 6 , Eduardo Eyras 1 2 3 , Nikolay Shirokikh 1
  1. The Shine-Dalgarno Centre for RNA Innovation, , The John Curtin School of Medical Research, Canberra city, Australian Capital Territory, Australia
  2. The Centre for Computational Biomedical Sciences, The John Curtin School of Medical Research, Canberra city, Australian Capital Territory, Australia
  3. EMBL Australia Partner Laboratory Network, The Australian National University, Canberra City, ACT, Australia
  4. Institut Montpellierain Alexander Grothendieck, CNRS, University of Montpellier, Montpellier, France
  5. Canberra Hospital, Canberra, ACT, Australia
  6. Australian National University Medical School, ACTON, ACT, Australia

B-cell acute lymphoblastic Leukemia (B-ALL) is characterised by prevalent chromosomal translocations leading to the expression of gene fusions. Distinct B-ALL fusions are linked to diverse responses to chemotherapy, leading to different proliferative and survival capacity of the malignant cells under treatment. Previously, we uncovered characteristic gene expression patterns in B-ALL patients with two of the most common fusion types, ETV6-RUNX1 and KMT2A-MLLT1.

The KMT2A-MLLT1 fusion, almost invariably associated with bad prognosis, carried transcriptomic signatures of dysregulated translation machinery, including altered gene expression of IGF2BP2, EIF3B, EIF2AK3, and CTIF. The ETV6-RUNX1 fusion, associated with good prognosis, presented a transcriptome-wide redefinition of translation start sites opposing those of the KMT2A type. Furthermore, recent works point to the dynamic involvement of the epitranscriptome in cancer drug resistance.

Thus, we set out to directly investigate RNA-level signatures of resistance to a common chemotherapeutic, vincristine, in REH (ETV6-RUNX1) and KOPN-8 (KMT2A-MLLT1) B-ALL cell-lines. We employed multiple successive rounds of vincristine treatment to progress B-ALL cells to resistance. Then, using a combination of inhibitor-based translational complex stabilisation1, polysome profiling, direct RNA sequencing and machine learning modification detection2, we investigated fusion-specific translational and epitranscriptomic landscapes in drug resistance.

At the epitranscriptome level, both subtypes displayed an increase in global m6A incidence with prominent and specific modification alterations between resistant and naive cells that may be linked to translational control. From a translational standpoint, we discovered highly specific buffering and synergistic transcription-translation control across a range of distinct mRNAs in both B-ALL cell-lines.

Overall, our work provides the first deep data combining accurate and quantitative isoform-resolved transcriptomics, RNA modification quantification, and assessment of translational control at the onset of chemotherapeutic drug resistance. These results reveal many new fusion-specific pathways associated with the drug resistance potential and will aid in the development of complementary therapeutic approaches for B-ALL subtypes.

  1. Shirokikh, N.E., 2022. Translation complex stabilization on messenger RNA and footprint profiling to study the RNA responses and dynamics of protein biosynthesis in the cells. Critical reviews in biochemistry and molecular biology, 57(3), pp.261-304.
  2. Acera Mateos, P., J Sethi, A., Ravindran, A., Srivastava, A., Woodward, K., Mahmud, S., Kanchi, M., Guarnacci, M., Xu, J., WS Yuen, Z. and Zhou, Y., 2024. Prediction of m6A and m5C at single-molecule resolution reveals a transcriptome-wide co-occurrence of RNA modifications. Nature Communications, 15(1), p.3899.