A non-canonical enzymatic function of PIWIL4 maintains genomic integrity and leukemic growth in AML

Abstract

RNA-binding proteins (RBPs) form a large and diverse class of factors many members of which are overexpressed in hematological malignancies. RBPs participate in various processes of mRNA metabolism and prevent harmful DNA:RNA hybrids or R-loops. Here we report that PIWIL4, a germ stem cell-associated RBP belonging to the RNase H-like superfamily, is overexpressed in acute myeloid leukemia patients and is essential for leukemic stem cell function and AML growth, but dispensable for healthy human hematopoietic stem cells. In AML cells, PIWIL4 binds to a small number of known piwi-interacting RNA. It instead largely interacts with mRNA annotated to protein-coding genic regions and enhancers that are enriched for genes associated with cancer and human myeloid progenitor gene signatures. PIWIL4 depletion in AML cells downregulates human myeloid progenitor signature and LSC-associated genes and upregulates DNA damage signalling. We demonstrate that PIWIL4 is an R-loop resolving enzyme that prevents R-loop accumulation on a subset of AML and LSC-associated genes, and maintains their expression. It also prevents DNA damage, replication stress, and activation of the ATR pathway in AML cells. PIWIL4 depletion potentiates sensitivity to pharmacological inhibition of the ATR pathway and creates a pharmacologically actionable dependency in AML cells.

R-loops in normal and malignant hematopoiesis

“…Since PIWIL4 belongs to the RNase H superfamily, and the binding sites of PIWIL4 contain guanine-rich sequences, the relationship between PIWIL4 and R-loops was also examined. It was found that PIWIL4 has R-loop digestion activity and that this action is required for the maintenance of the proliferative activity of AML cells (Figure 7) (101). AML progression via R-loop regulation by PIWIL4.…”

“…Although piRNAs are expressed specifically in germ cells, PIWIL proteins are known to be upregulated in various malignancies (99,100). PIWIL4 was recently found to be overexpressed in AML, possibly in a MYCdependent manner (101).…”

“…Intriguingly, PIWIL4, a PIWIL protein, appears to have a function distinct from piRNA regulation. This observation stems from the fact that only 6% of PIWIL4 protein overexpressed in AML binds to piRNAs, whereas 48% interacts with proteinencoding RNAs, especially those involved in cancer-related pathways (101). In addition, the inhibition of PIWIL4 expression reduces the stem cell activity of AML cells and, along with increased DNA replication stress, results in increased DNA damage, leading to activation of ataxia telangiectasia and the Rad3-related (ATR) pathway.…”

Epstein-Barr virus reactivation induces divergent abortive, reprogrammed, and host shutoff states by lytic progression

“…Related to YAP1 expression, we identified distinct Hedgehog 127 , Notch 128 , and Wnt 129,130 signaling pathway signatures in E2 and E3 lytic phenotypes as well as Hippo-independent YAP pathway 131 components reported in cancer. E3 cells also expressed genes encoding several PIWI-like family proteins, which protect germline cell genomes from transposable element insertion, maintain stemness, and are upregulated in some cancers [132][133][134][135] .…”