circPCMTD1: a protein-coding circular RNA that regulates DNA damage response in BCR/ABL1-positive leukemias

Circular RNAs (circRNAs) are a novel class of RNA transcripts that regulate important cellular functions in health and disease. In this study, we report on the functional relevance of a protein-coding circRNA, circPCMTD1, in breakpoint cluster region protein-ABL proto-oncogene 1 (BCR/ABL1)-positive myeloid leukemias. In screening experiments, we found that circPCMTD1 depletion strongly inhibited the proliferative capacity of leukemic cells with BCR/ABL1 translocations. RNA sequencing and mass cytometry experiments identified aberrant activation of the DNA damage response (DDR) pathway as a downstream effect of circPCMTD1 depletion. DNA fiber assays, Comet assays, and profiling of DDR markers (such as phospho-H2AX, phospho-CHK1, etc) further underscored the pronounced effect of circPCMTD1 depletion in increasing genotoxic stress and inhibiting leukemic cell growth. circPCMTD1 targeting also led to aberrant DDR activation in blasts from patients with leukemia, with BCR/ABL1 translocations. In in vivo experiments, circPCMTD1 knockdown prolonged the survival of mice engrafted with BCR/ABL1-positive leukemic cells. Mechanistically, we found that circPCMTD1 is enriched in the cytoplasm and associates with the ribosomes of leukemic blasts. We detected a cryptic open reading frame within the circPCMTD1 sequence and found that circPCMTD1 generates a 127 amino-acid peptide product (cPCMTD1-127aa). Using a custom-produced antibody, we found that the cPCMTD1-127aa interacts with the BCR/ABL1 oncoprotein, as well as with the Bloom syndrome protein, TOP3A and RMI1 proteins, which form the BTR complex and regulate DNA repair and genome stability. cPCMTD1-127aa enhanced BTR complex formation, thereby increasing cellular tolerance to genotoxic stress. In summary, we identified and characterized circPCMTD1 as a molecular vulnerability and potential therapeutic target in BCR/ABL1-positive leukemias.