Nature Communications (Jun 2023)

Tumour mutations in long noncoding RNAs enhance cell fitness

  • Roberta Esposito,
  • Andrés Lanzós,
  • Tina Uroda,
  • Sunandini Ramnarayanan,
  • Isabel Büchi,
  • Taisia Polidori,
  • Hugo Guillen-Ramirez,
  • Ante Mihaljevic,
  • Bernard Mefi Merlin,
  • Lia Mela,
  • Eugenio Zoni,
  • Lusine Hovhannisyan,
  • Finn McCluggage,
  • Matúš Medo,
  • Giulia Basile,
  • Dominik F. Meise,
  • Sandra Zwyssig,
  • Corina Wenger,
  • Kyriakos Schwarz,
  • Adrienne Vancura,
  • Núria Bosch-Guiteras,
  • Álvaro Andrades,
  • Ai Ming Tham,
  • Michaela Roemmele,
  • Pedro P. Medina,
  • Adrian F. Ochsenbein,
  • Carsten Riether,
  • Marianna Kruithof-de Julio,
  • Yitzhak Zimmer,
  • Michaela Medová,
  • Deborah Stroka,
  • Archa Fox,
  • Rory Johnson

DOI
https://doi.org/10.1038/s41467-023-39160-7
Journal volume & issue
Vol. 14, no. 1
pp. 1 – 21

Abstract

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Abstract Long noncoding RNAs (lncRNAs) are linked to cancer via pathogenic changes in their expression levels. Yet, it remains unclear whether lncRNAs can also impact tumour cell fitness via function-altering somatic “driver” mutations. To search for such driver-lncRNAs, we here perform a genome-wide analysis of fitness-altering single nucleotide variants (SNVs) across a cohort of 2583 primary and 3527 metastatic tumours. The resulting 54 mutated and positively-selected lncRNAs are significantly enriched for previously-reported cancer genes and a range of clinical and genomic features. A number of these lncRNAs promote tumour cell proliferation when overexpressed in in vitro models. Our results also highlight a dense SNV hotspot in the widely-studied NEAT1 oncogene. To directly evaluate the functional significance of NEAT1 SNVs, we use in cellulo mutagenesis to introduce tumour-like mutations in the gene and observe a significant and reproducible increase in cell fitness, both in vitro and in a mouse model. Mechanistic studies reveal that SNVs remodel the NEAT1 ribonucleoprotein and boost subnuclear paraspeckles. In summary, this work demonstrates the utility of driver analysis for mapping cancer-promoting lncRNAs, and provides experimental evidence that somatic mutations can act through lncRNAs to enhance pathological cancer cell fitness.