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

BACKGROUND: Resistance 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-tre...

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Autores principales: Williams, Mark S., Basma, Naseer J., Amaral, Fabio M. R., Williams, Gillian, Weightman, John P., Breitwieser, Wolfgang, Nelson, Louisa, Taylor, Stephen S., Wiseman, Daniel H., Somervaille, Tim C. P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7654162/
https://www.ncbi.nlm.nih.gov/pubmed/33167906
http://dx.doi.org/10.1186/s12885-020-07571-0
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author Williams, Mark S.
Basma, Naseer J.
Amaral, Fabio M. R.
Williams, Gillian
Weightman, John P.
Breitwieser, Wolfgang
Nelson, Louisa
Taylor, Stephen S.
Wiseman, Daniel H.
Somervaille, Tim C. P.
author_facet Williams, Mark S.
Basma, Naseer J.
Amaral, Fabio M. R.
Williams, Gillian
Weightman, John P.
Breitwieser, Wolfgang
Nelson, Louisa
Taylor, Stephen S.
Wiseman, Daniel H.
Somervaille, Tim C. P.
author_sort Williams, Mark S.
collection PubMed
description BACKGROUND: Resistance 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. METHODS: The 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 ABCB1(high) HGSC and AML. H3K27Ac ChIP sequencing was used to assess the activity of native promoters in cases of ABCB1(high) AML. RESULTS: Prolonged 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 ABCB1(high) AML; instead H3K27Ac ChIP sequencing demonstrated active native promoters in all cases studied. CONCLUSIONS: Despite 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12885-020-07571-0.
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spelling pubmed-76541622020-11-12 Targeted nanopore sequencing for the identification of ABCB1 promoter translocations in cancer Williams, Mark S. Basma, Naseer J. Amaral, Fabio M. R. Williams, Gillian Weightman, John P. Breitwieser, Wolfgang Nelson, Louisa Taylor, Stephen S. Wiseman, Daniel H. Somervaille, Tim C. P. BMC Cancer Research Article BACKGROUND: Resistance 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. METHODS: The 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 ABCB1(high) HGSC and AML. H3K27Ac ChIP sequencing was used to assess the activity of native promoters in cases of ABCB1(high) AML. RESULTS: Prolonged 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 ABCB1(high) AML; instead H3K27Ac ChIP sequencing demonstrated active native promoters in all cases studied. CONCLUSIONS: Despite 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12885-020-07571-0. BioMed Central 2020-11-10 /pmc/articles/PMC7654162/ /pubmed/33167906 http://dx.doi.org/10.1186/s12885-020-07571-0 Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research Article
Williams, Mark S.
Basma, Naseer J.
Amaral, Fabio M. R.
Williams, Gillian
Weightman, John P.
Breitwieser, Wolfgang
Nelson, Louisa
Taylor, Stephen S.
Wiseman, Daniel H.
Somervaille, Tim C. P.
Targeted nanopore sequencing for the identification of ABCB1 promoter translocations in cancer
title Targeted nanopore sequencing for the identification of ABCB1 promoter translocations in cancer
title_full Targeted nanopore sequencing for the identification of ABCB1 promoter translocations in cancer
title_fullStr Targeted nanopore sequencing for the identification of ABCB1 promoter translocations in cancer
title_full_unstemmed Targeted nanopore sequencing for the identification of ABCB1 promoter translocations in cancer
title_short Targeted nanopore sequencing for the identification of ABCB1 promoter translocations in cancer
title_sort targeted nanopore sequencing for the identification of abcb1 promoter translocations in cancer
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7654162/
https://www.ncbi.nlm.nih.gov/pubmed/33167906
http://dx.doi.org/10.1186/s12885-020-07571-0
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