Oral Presentation 50 Years Shine-Dalgarno Symposium 2023

Dissecting the impacts of gene fusion-mediated translational dysregulation in B-cell lymphoblastic leukemia to highlight novel therapeutic targets (#34)

Agin Ravindran 1 2 , Alice Cleynen 1 3 , Katrina Woodward 1 , Nimeree Muntasir 1 , Shafi Mahmud 1 , Madhu Kanchi 1 , Stanton Tam 1 , Dipti Talaulikar 1 4 5 , Eduardo Eyras 1 2 6 7 , 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. EMBL Australia Partner Laboratory Network, The Australian National University, Canberra City, ACT, Australia
  3. Institut Montpellierain Alexander Grothendieck, CNRS, University of Montpellier, Montpellier, France
  4. Canberra Hospital, Canberra, ACT, Australia
  5. Australian National University Medical School, ACTON, ACT, Australia
  6. Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Australia
  7. Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain

Dysregulation of messenger (m)RNA translation into proteins (protein biosynthesis) is one of the hallmarks of malignant transformation. Translational dysregulation can originate in tumours from direct somatic mutations of the translation machinery, or through the alteration of epistasis during malignant transformation. 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 responses to chemotherapy, proliferation, and malignant survival. Previously we uncovered two characteristic 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, is associated with dysregulation of translational control components (such as IGF2BP2, CPEB2, EIF3B, EIF2AK3, CTIF). The ETV6-RUNX1 fusion, often associated with good prognosis, presented a transcriptome-wide redefinition of translation start sites and effects on translational control components opposing those of the KMT2A-type. We thus proposed that the ETV6-RUNX1 and KMT2A-MLLT1 fusions define a functionally distinct translational landscape and pathophysiology in B-ALL. Here, we set out to directly investigate the translational landscape in REH (ETV6-RUNX1) and KOPN-8 (KMT2A-MLLT1) B-ALL cell lines and GM12878 non-malignant immortalised B-cell control. Using a combination of inhibitor-based translational complex stabilisation, polysome profiling and direct nanopore RNA sequencing, we investigated isoform-resolved translational patterns of mRNA across the cell models and identified fusion-specific epitranscriptomic landscapes. We observed differentially abundant and modified transcripts related to mitochondrial function, cell cycle regulation, DNA binding and repair in both malignant cell lines relative to the control, implying different survival and adaptation strategies. As B-ALL presents a general lack of mutations in gene regulators that commonly serve as therapeutic targets in other leukemias and solid tumours, we aim to highlight new fusion-specific strategies of drug resistance emergence and enable complementary therapeutic approaches for each B-ALL subtype.