Genomic and epigenomic landscapes to predict response to hypomethylating agent therapy in patients with acute myeloid leukemia

Abstract

Acute myeloid leukemia (AML) is a cancer of blood and bone marrow. AML is characterized by the rapid growth of abnormal cells and immature blast cells in the bone marrow and peripheral blood. Recently, it has been discovered that aberrant methylation interferes with normal hematopoiesis and is involved in tumor development and progression. As hypomethylating agents (HMAs) can inhibit DNA methylation, they have been used as an alternative treatment in AML. However, only a subset of AML patients respond to HMAs. Furthermore, patients who were sensitive to HMA in primary treatment develop secondary resistance because of repeated chemotherapy. Thus, understanding the drug resistance mechanism is essential for developing therapeutic strategies to overcome development of resistance. However, little is known about the associated predictive biomarkers or molecular markers. To establish novel resistance mechanisms of HMA therapy, this study provides insight into their epigenetic and genomic characteristics. Furthermore, transcriptional analysis reveals the gene expression environment status. A total of 28 acute myeloid patient samples before HMA treatment were obtained to analyze whole genome bisulfite sequencing (WGBS), whole exome sequencing (WES), and total RNA sequencing. Several putative biological pathways related to drug resistance were identified, including cell differentiation and immune response. The HMA-sensitive group had genes that show low promoter methylation and high expression level associated with myeloid cell differentiation, erythrocyte development, and T cell activation. Furthermore, the responder group indicated relatively hypomethylated transcription factor binding sites around differentially methylated regions compared to the non-responder group. Patients who were resistant to HMA have substantial methylation increases on the hematopoiesis gene promoter and decreased expression. Indeed, inflammatory response was upregulated in the non-responder group. Based on the results, this study suggests that integrated next generation sequencing (NGS) studies such as WGBS, WES, and RNA-sequencing effectively identify biomarkers or biological responses for drug resistance. 급성골수성 백혈병은 골수성 백혈구가 분화 단계 중 전구 세포 혹은 줄기세포에 변이가 발생하여 과도한 분열과 골수 내부에 축적으로인해 말초혈액을 따라 전신으로 퍼지는 질병이다. 결국 정상적인 골수 기능의 마비로 인해 조혈작용의 저하가 발생한다. 최근 DNA 저메틸화제를 사용하여 생존율 개선 효과를 입증하는 연구를 기반으로 해당 약물을 치료에 이용하고 있다. 하지만 DNA 저메틸화제에 대한 저항성이 초기에 발생하거나, 연속된 치료에 의해 발생한다. 이와 같은 이유로 인해 치료반응을 예측할 수 있는 생물학적인 지표를 정립하는 것이 중요한 문제로 떠오르고 있다. 본 연구에서는 DNA 저메틸화제를 이용해 치료를 진행한 급성골수성 백혈병 환자들에게서 약물 투여 이전 골수에 존재하는 DNA와 RNA를 통해 유전정보를 분석하였다. 구체적으로 후성유전학적 분석, 유전자변이 분석, 유전자발현 분석법을 통해 저항성을 예측할 수 있는 기전과 유전자를 확인하였다. 결과적으로 차세대 염기서열 분석법을 통해 저항성을 갖는 환자들의 특성과 기전을 정립하였다.