Genome-scale clustered regularly interspaced short palindromic repeats screen identifies nucleotide metabolism as an actionable therapeutic vulnerability in diffuse large B-cell lymphoma

Haematologica. 2024 Dec 1;109(12):3989-4006. doi: 10.3324/haematol.2023.284404.

Abstract

Diffuse large B-cell lymphoma (DLBCL) is the most common malignancy that develops in patients with ataxia-telangiectasia, a cancer-predisposing inherited syndrome characterized by inactivating germline ATM mutations. ATM is also frequently mutated in sporadic DLBCL. To investigate lymphomagenic mechanisms and lymphoma-specific dependencies underlying defective ATM, we applied RNA sequencing and genome-scale loss-of-function clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 screens to systematically interrogate B-cell lymphomas arising in a novel murine model (Atm-/-nu-/-) with constitutional Atm loss, thymic aplasia but residual T-cell populations. Atm-/-nu-/- lymphomas, which phenotypically resemble either activated B-cell-like or germinal center B-cell-like DLBCL, harbor a complex karyotype, and are characterized by MYC pathway activation. In Atm-/-nu-/- lymphomas, we discovered nucleotide biosynthesis as a MYC-dependent cellular vulnerability that can be targeted through the synergistic nucleotide-depleting actions of mycophenolate mofetil (MMF) and the WEE1 inhibitor, adavosertib (AZD1775). The latter is mediated through a synthetically lethal interaction between RRM2 suppression and MYC dysregulation that results in replication stress overload in Atm-/-nu-/- lymphoma cells. Validation in cell line models of human DLBCL confirmed the broad applicability of nucleotide depletion as a therapeutic strategy for MYC-driven DLBCL independent of ATM mutation status. Our findings extend current understanding of lymphomagenic mechanisms underpinning ATM loss and highlight nucleotide metabolism as a targetable therapeutic vulnerability in MYC-driven DLBCL.

MeSH terms

  • Animals
  • Ataxia Telangiectasia Mutated Proteins* / genetics
  • Ataxia Telangiectasia Mutated Proteins* / metabolism
  • CRISPR-Cas Systems
  • Cell Line, Tumor
  • Clustered Regularly Interspaced Short Palindromic Repeats
  • Disease Models, Animal
  • Humans
  • Lymphoma, Large B-Cell, Diffuse* / genetics
  • Lymphoma, Large B-Cell, Diffuse* / metabolism
  • Lymphoma, Large B-Cell, Diffuse* / pathology
  • Mice
  • Mice, Knockout
  • Nucleotides / metabolism

Substances

  • Ataxia Telangiectasia Mutated Proteins
  • Nucleotides

Grants and funding

Funding: This work was supported by grants from CRUK (ref: C20807/ A2864 and C17183/A23303), Bloodwise UK (program grant 11045) and Action for A-T (Ref: 17-1192). CB was supported by grants from MRC and BCUK. PM was also supported in part by a European Regional Development Fund Project (ENOCH: CZ.02.1.01/0.0/0.0/16_019/0000868). MK is a Cancer Research UK Clinicial Scientist.