The relationship between the integrity of ribosomal DNA and RNA compartments in cancer

Genetic information is encoded in DNA as an ordered sequence of nucleotide units. Cells can retrieve this information by transcribing DNA into protein-coding messenger and noncoding RNAs. We have previously identified the pyrimidine-rich noncoding transcript PNCTR and showed that it is widely expressed in cancer cells. This RNA originates from an intergenic spacer between repeated genes encoding 47S precursors of ribosomal RNAs in genomic regions called ribosomal DNA (rDNA) arrays. PNCTR can promote cancer cell survival, at least in part, by sequestering multiple copies of the RNA-binding protein PTBP1 in a membraneless perinucleolar compartment (PNC).

Cancers cells tend to accumulate mutations, which often make cancers more challenging to treat. Such genetic instability is commonly observed, for example, in breast cancers, the most common cancer type in the UK. Notably, many breast cancers produce the PNC through yet-to-be-understood mechanisms. Our new data suggest that cancer cells may transcribe PNCTR from genetically rearranged rDNA sequences, emerging as a result of error-prone repair of DNA double-strand breaks (DSBs). We also hypothesize that the assembly of the PNC around nascent PNCTR molecules segregates genetically compromised rDNA loci away from the nucleolus. Finally, we propose that PNCTR plays a key part in the breast cancer biology, and that its knockdown may reduce the ability of cancer cells to thrive and metastasize.

We will explore these intriguing possibilities by pursuing three distinct but interrelated objectives.

1. Elucidating the role of rDNA rearrangements in PNCTR expression: We will test if PNCTR is commonly produced from genetically rearranged rDNA by sequencing PNCTR-enriched RNA fractions from breast cancer cell lines and patient samples and mining publicly available sequencing datasets. The proposed analyses will also illuminate the role of recurrent rDNA DSBs and different DSB repair pathways in the emergence of PNCTR-encoding...