Oral Presentation Australasian RNA Biology and Biotechnology Association 2025 Conference

PUS7-mediated pseudouridylation drives vincristine resistance in B-cell acute lymphoblastic leukaemia through epitranscriptomic reprogramming    (127440)

Agin Ravindran 1 2 3 , Alice Cleynen 2 4 , Merin Joy 1 , Amna Chowdhery 1 , Nimeree Muntasir 1 , Stefan Prodic 1 2 3 , Akanksha Srivastava 1 2 3 , Madhu Kanchi 1 , Dipti Talaulikar 5 , 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

B-cell acute lymphoblastic leukemia (B-ALL) subtypes exhibit diverse chemotherapy responses linked to specific chromosomal translocations. Despite the clinical significance of drug resistance in B-ALL, the underlying RNA-level mechanisms remain unexplored. Here, we present the first comprehensive investigation of how epitranscriptomic modifications and translational control drive chemotherapy resistance in B-ALL.

 

We identify PUS7 and DKC1 as the first RNA-modifying enzymes directly linked to chemotherapy resistance acquisition in B-cell acute lymphoblastic leukemia (B-ALL). Using innovative RNA multi-omic technologies, we reveal an unexpected epitranscriptomic switch: while METTL3-dependent m⁶A modifications mark B-ALL malignancy, PUS7-dependent pseudouridylation (Ψ) specifically drives vincristine resistance.

 

We established vincristine-resistant models using REH (ETV6-RUNX1; favorable prognosis) and KOPN-8 (KMT2A-MLLT1; relapse-prone) cell lines through successive treatment rounds. Direct RNA long-read sequencing revealed striking resistance-specific changes: PUS7 expression increased 3-fold with 12-35-fold enrichment of PUS7-motif Ψ sites in differentially modified transcripts. This Ψ surge coincided with dramatic translational reprogramming—polysome:monosome ratios dropped from 1.72 to 0.85 (KOPN-8) and 1.55 to 0.63 (REH), indicating global translation suppression.

 

Critically, PUS7 and DKC1 transcripts escaped this repression, shifting from light to heavy polysomes (PSF>0.75) exclusively in resistant cells. This establishes a positive feedback loop amplifying pseudouridylation capacity precisely when global translation is suppressed—a novel resistance mechanism.

 

Our multi-omic integration reveals coordinated adaptations: epitranscriptomic alterations (increased Ψ), selective translational rewiring (PUS7/DKC1 escape), and metabolic reprogramming (mitochondrial transcripts shift to heavy polysomes). Combined with reduced RNA stability (DTI<6.5) and Ψ-associated alternative splicing near exon junctions, this epitranscriptomic plasticity enables rapid phenotypic adaptation under drug pressure.

 

These findings establish epitranscriptomic reprogramming as a primary, reversible resistance mechanism—distinct from genetic mutations. Unlike genetic markers, PUS7 upregulation occurs early in resistance development, offering a therapeutic window. PUS7 inhibition could restore chemosensitivity by disrupting the Ψ-mediated resistance program.

 

This work transforms our understanding of drug resistance from a genetic to an epitranscriptomic phenomenon. By revealing how cancer cells hijack RNA modification systems to evade therapy, we provide a framework for developing precision therapies targeting the epitranscriptomic machinery in treatment of resistant leukemia. This discovery positions PUS7 and DKC1 as both biomarkers for early resistance detection and novel therapeutic vulnerabilities in B-ALL.