Elucidating the Functional and Mechanistic Roles of LINE-1 Retrotransposons in Myeloid Leukemia

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PROJECT SUMMARY The role of retrotransposons in human cancer has been historically underappreciated both because they have been dismissed as unimportant ‘junk’ DNA, and because their high repetition and variation pose significant technical challenges. There are ~500,000 copies of LINE-1 (or L1) retrotransposons occupying 17% of the human genome, but only ~100 full-length human-specific L1 elements (L1Hs) are capable of active retrotransposition. L1-encoded proteins also mobilize non-autonomous retrotransposons, noncoding RNAs and mRNAs, leading to the generation of a third of human DNA. As such, L1s have been considered mostly deleterious because their activity can lead to genetic mutations and chromosomal alterations that contribute to human disorders including cancer. By domain-based CRISPR screens of human chromatin regulators, we identified MPP8, a component of the HUSH complex responsible for the silencing of L1 retrotransposons, as a selective epigenetic dependency of acute myeloid leukemia (AML) cells. While dispensable for normal hematopoiesis, MPP8 loss impaired AML initiation and maintenance by reactivating L1s. Ectopic L1 activation phenocopied MPP8 loss, whereas blocking L1 retrotransposition abrogated the phenotypes. L1 suppression is associated with therapy resistance and poor prognosis in human AML patients. Hence, while retrotransposons are historically recognized for their cancer-promoting roles as sources of genetic instability and somatic mutations, our findings support an unexpected ‘tumor-suppressive’ function for retrotransposons as a selective dependency for myeloid leukemia. The goal of this project is to elucidate the functional and mechanistic roles of L1 retrotransposons as a new regulatory pathway in AML pathophysiology. The central hypotheses are that L1 retrotransposons function to modulate DNA damage response and/or inflammatory signaling in AML-initiating cells, and that L1 activity controls therapeutic response to DNA damage-inducing agents in myeloid leukemia. Our hypotheses have been formulated on the basis of extensive preliminary studies using orthogonal approaches to modulate L1 function in physiologically relevant AML models and a newly discovered molecular link between suppression of retrotransposons and propagation of cancer-initiating cells. Guided by these findings, these hypotheses will be tested by three specific aims: 1) Establish the functional roles of L1 retrotransposons in the clonal evolution of myeloid leukemia. 2) Elucidate the mechanistic roles of L1 retrotransposons in AML pathogenesis. 3) Determine the effects of modulating retrotransposon activity on therapeutic response to DNA damage-inducing agents in myeloid leukemia. Taken together, these studies will not only elucidate the mechanistic basis for the unexpected ‘tumor-suppressive’ function for retrotransposon activity in myeloid leukemia, but also establish a new paradigm for mobile DNA elements as a previously uncharted regulatory pathway in leukemia biology, whose intervention may lead to improved anti-leukemia therapies.