AML-749 Regulation of Autophagy and Oxidative Phosphorylation Is Predominantly Altered at the Transcription Level in Leukemic Stem Cells (LSCs) in Relapsed AML

Abstract

Aim Acute myeloid leukemia (AML) is a highly aggressive malignancy of uncontrolled myeloid progenitor cell proliferation and has a dismal survival rate. Despite the availability of standard and targeted therapeutic regimens, the rate of relapse is high in patients when leukemic stem cells (LSCs) are present. LSCs can self-renew and reinitiate leukemia in patients at any time point. Altered gene expression patterns in LSCs at diagnosis and relapse might help elucidate the factors responsible for relapse in AML. Methodology To identify and characterize various factors responsible for tumorigenesis and chemoresistance in AML, transcriptomic profiling of LSCs was done using diagnostic and relapse samples (n=18) collected from the same patient. LSCs predominantly reside in CD34+ CD38- fractions. We sorted LSCs from bone marrow aspirate (BMA) samples obtained from all 18 patients at diagnosis and relapse based on the presence of aberrant markers using BD FACSAria™ III. Bulk RNA sequencing was performed, and the differentially expressed genes identified by DESeq2 were used for pathway enrichment analysis via ShinyGO. Additionally, we employed the rMATS tool to identify altered splicing patterns between relapse and diagnostic LSCs, along with rMAPS to pinpoint significant RNA-binding proteins instrumental in regulating alternative splicing events. Results The most significantly altered pathways were those involved in autophagy and oxidative phosphorylation processes. The identified genes ULK1, ATG13, GABARAPL1, ATP5F1D, UQCRC2, and UQQCR10 were significantly downregulated at relapse in AML LSCs, pointing to the altered metabolic profiles compared to diagnosis. We also identified substantial splicing aberrations in genes that play pivotal roles in autophagy. Conclusion Autophagy and oxidative phosphorylation pathways are significantly altered in AML patients at relapse. These alterations occur at levels of transcription and its regulation during splicing. Our study's future scope is identifying RNA-binding proteins that regulate these processes. This will help decipher the regulatory networks to better understand LSC biology and unveil novel therapeutic targets to improve patient survival outcomes.