Targeted nanopore sequencing for the identification of ABCB1 promoter translocations in cancer

BMC Cancer

Stephen S. Taylor¹  Louisa Nelson¹  Daniel H. Wiseman²  Tim C. P. Somervaille³  Fabio M. R. Amaral³  Naseer J. Basma³  Mark S. Williams³  Wolfgang Breitwieser⁴  Gillian Williams⁴  John P. Weightman⁴ 

[1] Division of Cancer Sciences, Faculty of Biology, Medicine and Health, Oglesby Cancer Research Building, The University of Manchester, M20 4GJ, Manchester, UK;Epigenetics of Haematopoiesis Group, Oglesby Cancer Research Building, The University of Manchester, M20 4GJ, Manchester, UK;Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, Oglesby Cancer Research Building, The University of Manchester, M20 4GJ, Manchester, UK;Molecular Biology Core Facility, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, SK10 4TG, Cheshire, UK;

关键词: Acute myeloid leukemia;    ABCB1;    Drug resistance;    Promoter translocation;    HGSC;    Ovarian cancer;   

DOI  :  10.1186/s12885-020-07571-0

来源: Springer

【 摘 要 】

BackgroundResistance to chemotherapy is the most common cause of treatment failure in acute myeloid leukemia (AML) and the drug efflux pump ABCB1 is a critical mediator. Recent studies have identified promoter translocations as common drivers of high ABCB1 expression in recurrent, chemotherapy-treated high-grade serous ovarian cancer (HGSC) and breast cancer. These fusions place ABCB1 under the control of a strong promoter while leaving its open reading frame intact. The mechanisms controlling high ABCB1 expression in AML are largely unknown. We therefore established an experimental system and analysis pipeline to determine whether promoter translocations account for high ABCB1 expression in cases of relapsed human AML.MethodsThe human AML cell line THP-1 was used to create a model of chemotherapy resistance in which ABCB1 expression was driven by a promoter fusion. The THP-1 model was used to establish a targeted nanopore long-read sequencing approach that was then applied to cases of ABCB1high HGSC and AML. H3K27Ac ChIP sequencing was used to assess the activity of native promoters in cases of ABCB1high AML.ResultsProlonged in vitro daunorubicin exposure induced activating ABCB1 promoter translocations in human THP-1 AML cells, similar to those recently described in recurrent high-grade serous ovarian and breast cancers. Targeted nanopore sequencing proved an efficient method for identifying ABCB1 structural variants in THP-1 AML cells and HGSC; the promoter translocations identified in HGSC were both previously described and novel. In contrast, activating ABCB1 promoter translocations were not identified in ABCB1high AML; instead H3K27Ac ChIP sequencing demonstrated active native promoters in all cases studied.ConclusionsDespite frequent high level expression of ABCB1 in relapsed primary AML we found no evidence of ABCB1 translocations and instead confirmed high-level activity of native ABCB1 promoters, consistent with endogenous regulation.

【 授权许可】

CC BY