Decoding the RNA Editome of Normal Versus Malignant Progenitor Cell Aging Short Title: RNA Editing in Normal Aging and MDS/AML Stem Cells

Introduction

Human bone marrow aging is typified by decreased cellularity, stem cell exhaustion and myeloid lineage bias that may set the stage for development of myeloid malignancies. Secondary AML (sAML) arises from prior myelodysplastic syndromes (MDS) or myeloproliferative neoplasms (MPN), and occurs in patients with an average age of >65. Because of the typically advanced age of this population, patients currently have few effective treatment options available after leukemic transformation. We and others have recently identified a key role for enzymatic RNA editing activity in cancer progression, and in particular in leukemia stem cell (LSC) generation. In hematopoietic stem and progenitor cells, adenosine deaminase acting on dsRNA-1 (ADAR1) is the most abundantly expressed RNA editing gene. However, the role of abnormal RNA editing activity has not been elucidated in healthy human bone marrow aging and age-related MDS with a high risk of transforming to sAML. Therefore, we established whole transcriptome-based RNA editing signatures of benign versus malignant bone marrow progenitor cell aging, which provides novel RNA-based functionally relevant biomarkers of aging, MDS and progression to sAML.

Methods

Whole transcriptome sequencing (RNA-Seq) was performed on FACS-purified hematopoietic stem (CD34⁺CD38^-Lin^- HSC) and progenitor cells (CD34⁺CD38⁺Lin^- HPC) from aged (average age = 65.9 y/o) versus young (average age = 25.8 y/o) adult healthy bone marrow samples, and in leukemia stem cells (LSC) from patients with sAML (average age = 71.4 y/o) and MDS (average age = 63.8 y/o). Comparative gene set enrichment analyses (GSEA) and RNA editing profiles were identified for normal and malignant progenitor cell aging.

Results

Aberrant RNA editing activity has recently been shown to be induced in multiple cancers, and has been implicated as a malignant reprogramming factor. Comparative whole transcriptome RNA sequencing (RNA-seq) and single nucleotide variant analyses revealed widespread increases in RNA editing rates in aged versus young HPC, and in human sAML LSC compared with age-matched normal progenitors. Moreover, RNA editing rates, represented as adenosine (A) to inosine/guanosine (G) changes at known RNA editing loci, were increased in sAML compared with MDS progenitors. The differential expression of certain sites is as high as 70%, which can be readily detected by RESS-qPCR. These data suggest that during aging niche-dependent RNA editing deregulation contributes to MDS progression to sAML. Interestingly, the highly edited loci in sAML LSC were distinct from loci that were differentially edited in aged versus young HPC, suggesting that pro-inflammatory conditions in sAML may trigger RNA editing of a unique set of transcripts, including predominantly RNA processing-related gene products and transcription factors. Notably, several loci in transcripts of APOBEC3C/D that we previously found were associated with blast crisis transformation of chronic myeloid leukemia also displayed enhanced editing in sAML LSC, but not aged versus young HPC.

Conclusions

Detection of aberrant RNA processing provides novel biomarkers as well as potential therapeutic targets for sAML LSC eradication with implications for treatment of a variety of human malignancies and other age-related disorders. We have identified commonly RNA-edited transcripts in multiple hematologic malignancies, which could be developed clinically and as companion diagnostic targets for LSC-targeted therapeutics.