The Non-Canonical, R-Loop Regulatory Function of PIWIL4 Maintains Genomic Integrity and Leukemic Potential of AML Cells

During DNA replication and transcription, RNA:DNA hybrids are formed as part of three stranded nucleic acid structures known as R-loops. R-loops occur frequently in the genome at highly transcribed regions, ribosomal genes, mitochondria and intergenic regions, and are predominantly resolved by Ribonuclease (RNase) H family of enzymes. However, unscheduled and unresolved R-loops represent a potent source of DNA damage, especially in rapidly dividing cells such as cancer cells. It is imperative for cancer cells to prevent accumulation of unresolved R-loops in order to limit DNA damage. So far, the mechanism how leukemic cells prevent accumulation of R-loops is not well understood. In this study, we show that an RNase H-like protein, PIWIL4, is aberrantly and highly expressed in AML patients, prevents R-loop accumulation via its RNase H activity and thereby acts as important regulator of leukemic growth. In our initial analysis, we observed that the recombinant human PIWIL4 protein digested radiolabeled-RNA-containing R-loops in vitro, exhibiting an RNase H-like activity with increasing efficiency, in incremental concentrations and time durations. Moreover, immunoprecipitation of PIWIL4 followed by liquid chromatography mass spectrometry (LC/MS) in HEK cells showed that PIWIL4 was bound with multiple nuclear and nucleolar RNA processing factors that are associated with formation of R-loops. Published RNA-seq and microarray datasets revealed that, among all cancers, PIWIL4 was significantly highest expressed in myeloid leukemia. Quantitative real time PCR (qRT-PCR) of acute myeloid leukemia (AML) patients revealed that PIWIL4 showed an average of 21.6 ± 5.0-fold higher expression in AML patients (n=68; p<0.0001), compared to healthy CD34⁺ bone marrow (BM) and BM mononuclear cells (n=3). Western blot of AML patient samples and intracellular (IC) staining confirmed higher PIWIL4 protein expression levels in AML cells compared to cord blood CD34⁺ HSPCs. Piwil4 expression increased by 6-8 fold in murine BM healthy HPSCs within 48h after transduction with MLL-AF9, AML1-ETO9A and CDX2 oncogenes compared to empty vector (n=3, p<0.0001). Stable knockdown of PIWIL4 in AML cell lines and primary AML samples using shRNA, followed by IC staining and confocal microscopy using an antibody against R-loops (S9.6) revealed a marked increase in accumulation of R-loops within 72h post-transduction in PIWIL4 depleted cells, in contrast to healthy cord blood HSPCs which remained unaffected (n=3). PIWIL4 depleted AML cells exhibited an accumulation of DNA damage associated gH2AX foci, replication stress associated BrdU foci, higher levels of phosphorylated ATR (p-ATR), a marked increase in apoptosis and block in the G2M phase of the cell cycle. Depletion of PIWIL4 significantly impaired clonogenic potential of AML patient samples in vitro (avg. 4.9 ± 0.9-fold reduction, p<0.0001, n=3). In vivo, PIWIL4 depletion in cell lines delayed onset of leukemia (n=8, p<0.001) and in AML patient cells reduced leukemic engraftment in xenografts 12 weeks post-transplantation (avg. scr - 50.6±21% vs avg. shRNA-14.6±10, n=6). Of note, PIWIL4 depletion in cord blood CD34⁺ HSPCs had no impact on colony formation or differentiation in vitro. RNA-seq of PIWIL4 depleted THP-1 cell line followed by GSEA revealed a significant reduction in expression of ribosomal genes and increased expression of G2M checkpoint repair pathway (n=2, p<0.05, FDR<0.05). qRT-PCR of pre-rRNA (45S rRNA) showed a significant reduction in rRNA transcription in shRNA transduced cell lines (avg. 2.5 ± 0.3-fold reduction, n=3, p<0.01). Overexpression of PIWIL4 or RNase H1 in PIWIL4 depleted AML cell lines rescued R-loop and gH2AX signals, induced a decrease in p-ATR and gH2AX protein levels, and rescued the impact on apoptosis and growth phenotype in colony assays. RNA polymerase I inhibitor CX-5461, known to stabilize R-loop associated secondary structures, acted synergistically with PIWIL4 depletion and induced complete cell death of PIWIL4 depleted AML cells compared to scrambled control at IC₅₀ concentrations. Thus, collectively, we could show for the first time that PIWIL4 is a functional RNase H like enzyme in AML cells, suppresses formation of R-loops, thereby preventing DNA damage and apoptosis of AML cells. Our data also suggest that impairing resolution of R-loops is a powerful therapeutic tool in AML.