Targeting BCR-ABL-independent TKI resistance in chronic myeloid leukemia by mTOR and autophagy inhibition

Rebecca Mitchell, Lisa E.M. Hopcroft, Pablo Baquero, Elaine K. Allan, Kay Hewit, Daniel James, Graham Hamilton, Arunima Mukhopadhyay, Jim O'Prey, Alan Hair, Junia V. Melo, Edmond Chan, Kevin M. Ryan, Véronique Maguer-Satta, Brian Druker, Richard E. Clark, Subir Mitra, Pawel Herzyk, Franck E. Nicolini, Paolo Salomoni & 4 others Emma Shanks, Bruno Calabretta, Tessa L. Holyoake, G. Vignir Helgason

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

Background: Imatinib and second-generation tyrosine kinase inhibitors (TKIs) nilotinib and dasatinib have statistically significantly improved the life expectancy of chronic myeloid leukemia (CML) patients; however, resistance to TKIs remains a major clinical challenge. Although ponatinib, a third-generation TKI, improves outcomes for patients with BCR-ABL-dependent mechanisms of resistance, including the T315I mutation, a proportion of patients may have or develop BCR-ABL-independent resistance and fail ponatinib treatment. By modeling ponatinib resistance and testing samples from these CML patients, it is hoped that an alternative drug target can be identified and inhibited with a novel compound. Methods: Two CML cell lines with acquired BCR-ABL-independent resistance were generated following culture in ponatinib. RNA sequencing and gene ontology (GO) enrichment were used to detect aberrant transcriptional response in ponatinib-resistant cells. A validated oncogene drug library was used to identify US Food and Drug Administration-approved drugs with activity against TKI-resistant cells. Validation was performed using bone marrow (BM)-derived cells from TKI-resistant patients (n = 4) and a human xenograft mouse model (n = 4-6 mice per group). All statistical tests were two-sided. Results: We show that ponatinib-resistant CML cells can acquire BCR-ABL-independent resistance mediated through alternative activation of mTOR. Following transcriptomic analysis and drug screening, we highlight mTOR inhibition as an alternative therapeutic approach in TKI-resistant CML cells. Additionally, we show that catalytic mTOR inhibitors induce autophagy and demonstrate that genetic or pharmacological inhibition of autophagy sensitizes ponatinib-resistant CML cells to death induced by mTOR inhibition in vitro (% number of colonies of control[SD], NVP-BEZ235 vs NVP-BEZ235+HCQ: 45.0[17.9]% vs 24.0[8.4]%, P = 002) and in vivo (median survival of NVP-BEZ235-vs NVP-BEZ235+HCQ-treated mice: 38.5 days vs 47.0 days, P = 04). Conclusion: Combined mTOR and autophagy inhibition may provide an attractive approach to target BCR-ABL-independent mechanism of resistance.

Original languageEnglish (US)
Pages (from-to)467-478
Number of pages12
JournalJournal of the National Cancer Institute
Volume110
Issue number5
DOIs
StatePublished - Jan 1 2018

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Autophagy
Leukemia, Myelogenous, Chronic, BCR-ABL Positive
Protein-Tyrosine Kinases
Myeloid Cells
Pharmaceutical Preparations
RNA Sequence Analysis
Preclinical Drug Evaluations
Gene Ontology
United States Food and Drug Administration
Life Expectancy
ponatinib
Oncogenes
Heterografts
Bone Marrow Cells
Cell Death
Pharmacology
Cell Line
Mutation
Survival
dactolisib

ASJC Scopus subject areas

  • Oncology
  • Cancer Research

Cite this

Mitchell, R., Hopcroft, L. E. M., Baquero, P., Allan, E. K., Hewit, K., James, D., ... Helgason, G. V. (2018). Targeting BCR-ABL-independent TKI resistance in chronic myeloid leukemia by mTOR and autophagy inhibition. Journal of the National Cancer Institute, 110(5), 467-478. https://doi.org/10.1093/jnci/djx236

Targeting BCR-ABL-independent TKI resistance in chronic myeloid leukemia by mTOR and autophagy inhibition. / Mitchell, Rebecca; Hopcroft, Lisa E.M.; Baquero, Pablo; Allan, Elaine K.; Hewit, Kay; James, Daniel; Hamilton, Graham; Mukhopadhyay, Arunima; O'Prey, Jim; Hair, Alan; Melo, Junia V.; Chan, Edmond; Ryan, Kevin M.; Maguer-Satta, Véronique; Druker, Brian; Clark, Richard E.; Mitra, Subir; Herzyk, Pawel; Nicolini, Franck E.; Salomoni, Paolo; Shanks, Emma; Calabretta, Bruno; Holyoake, Tessa L.; Helgason, G. Vignir.

In: Journal of the National Cancer Institute, Vol. 110, No. 5, 01.01.2018, p. 467-478.

Research output: Contribution to journalArticle

Mitchell, R, Hopcroft, LEM, Baquero, P, Allan, EK, Hewit, K, James, D, Hamilton, G, Mukhopadhyay, A, O'Prey, J, Hair, A, Melo, JV, Chan, E, Ryan, KM, Maguer-Satta, V, Druker, B, Clark, RE, Mitra, S, Herzyk, P, Nicolini, FE, Salomoni, P, Shanks, E, Calabretta, B, Holyoake, TL & Helgason, GV 2018, 'Targeting BCR-ABL-independent TKI resistance in chronic myeloid leukemia by mTOR and autophagy inhibition', Journal of the National Cancer Institute, vol. 110, no. 5, pp. 467-478. https://doi.org/10.1093/jnci/djx236
Mitchell, Rebecca ; Hopcroft, Lisa E.M. ; Baquero, Pablo ; Allan, Elaine K. ; Hewit, Kay ; James, Daniel ; Hamilton, Graham ; Mukhopadhyay, Arunima ; O'Prey, Jim ; Hair, Alan ; Melo, Junia V. ; Chan, Edmond ; Ryan, Kevin M. ; Maguer-Satta, Véronique ; Druker, Brian ; Clark, Richard E. ; Mitra, Subir ; Herzyk, Pawel ; Nicolini, Franck E. ; Salomoni, Paolo ; Shanks, Emma ; Calabretta, Bruno ; Holyoake, Tessa L. ; Helgason, G. Vignir. / Targeting BCR-ABL-independent TKI resistance in chronic myeloid leukemia by mTOR and autophagy inhibition. In: Journal of the National Cancer Institute. 2018 ; Vol. 110, No. 5. pp. 467-478.
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abstract = "Background: Imatinib and second-generation tyrosine kinase inhibitors (TKIs) nilotinib and dasatinib have statistically significantly improved the life expectancy of chronic myeloid leukemia (CML) patients; however, resistance to TKIs remains a major clinical challenge. Although ponatinib, a third-generation TKI, improves outcomes for patients with BCR-ABL-dependent mechanisms of resistance, including the T315I mutation, a proportion of patients may have or develop BCR-ABL-independent resistance and fail ponatinib treatment. By modeling ponatinib resistance and testing samples from these CML patients, it is hoped that an alternative drug target can be identified and inhibited with a novel compound. Methods: Two CML cell lines with acquired BCR-ABL-independent resistance were generated following culture in ponatinib. RNA sequencing and gene ontology (GO) enrichment were used to detect aberrant transcriptional response in ponatinib-resistant cells. A validated oncogene drug library was used to identify US Food and Drug Administration-approved drugs with activity against TKI-resistant cells. Validation was performed using bone marrow (BM)-derived cells from TKI-resistant patients (n = 4) and a human xenograft mouse model (n = 4-6 mice per group). All statistical tests were two-sided. Results: We show that ponatinib-resistant CML cells can acquire BCR-ABL-independent resistance mediated through alternative activation of mTOR. Following transcriptomic analysis and drug screening, we highlight mTOR inhibition as an alternative therapeutic approach in TKI-resistant CML cells. Additionally, we show that catalytic mTOR inhibitors induce autophagy and demonstrate that genetic or pharmacological inhibition of autophagy sensitizes ponatinib-resistant CML cells to death induced by mTOR inhibition in vitro ({\%} number of colonies of control[SD], NVP-BEZ235 vs NVP-BEZ235+HCQ: 45.0[17.9]{\%} vs 24.0[8.4]{\%}, P = 002) and in vivo (median survival of NVP-BEZ235-vs NVP-BEZ235+HCQ-treated mice: 38.5 days vs 47.0 days, P = 04). Conclusion: Combined mTOR and autophagy inhibition may provide an attractive approach to target BCR-ABL-independent mechanism of resistance.",
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T1 - Targeting BCR-ABL-independent TKI resistance in chronic myeloid leukemia by mTOR and autophagy inhibition

AU - Mitchell, Rebecca

AU - Hopcroft, Lisa E.M.

AU - Baquero, Pablo

AU - Allan, Elaine K.

AU - Hewit, Kay

AU - James, Daniel

AU - Hamilton, Graham

AU - Mukhopadhyay, Arunima

AU - O'Prey, Jim

AU - Hair, Alan

AU - Melo, Junia V.

AU - Chan, Edmond

AU - Ryan, Kevin M.

AU - Maguer-Satta, Véronique

AU - Druker, Brian

AU - Clark, Richard E.

AU - Mitra, Subir

AU - Herzyk, Pawel

AU - Nicolini, Franck E.

AU - Salomoni, Paolo

AU - Shanks, Emma

AU - Calabretta, Bruno

AU - Holyoake, Tessa L.

AU - Helgason, G. Vignir

PY - 2018/1/1

Y1 - 2018/1/1

N2 - Background: Imatinib and second-generation tyrosine kinase inhibitors (TKIs) nilotinib and dasatinib have statistically significantly improved the life expectancy of chronic myeloid leukemia (CML) patients; however, resistance to TKIs remains a major clinical challenge. Although ponatinib, a third-generation TKI, improves outcomes for patients with BCR-ABL-dependent mechanisms of resistance, including the T315I mutation, a proportion of patients may have or develop BCR-ABL-independent resistance and fail ponatinib treatment. By modeling ponatinib resistance and testing samples from these CML patients, it is hoped that an alternative drug target can be identified and inhibited with a novel compound. Methods: Two CML cell lines with acquired BCR-ABL-independent resistance were generated following culture in ponatinib. RNA sequencing and gene ontology (GO) enrichment were used to detect aberrant transcriptional response in ponatinib-resistant cells. A validated oncogene drug library was used to identify US Food and Drug Administration-approved drugs with activity against TKI-resistant cells. Validation was performed using bone marrow (BM)-derived cells from TKI-resistant patients (n = 4) and a human xenograft mouse model (n = 4-6 mice per group). All statistical tests were two-sided. Results: We show that ponatinib-resistant CML cells can acquire BCR-ABL-independent resistance mediated through alternative activation of mTOR. Following transcriptomic analysis and drug screening, we highlight mTOR inhibition as an alternative therapeutic approach in TKI-resistant CML cells. Additionally, we show that catalytic mTOR inhibitors induce autophagy and demonstrate that genetic or pharmacological inhibition of autophagy sensitizes ponatinib-resistant CML cells to death induced by mTOR inhibition in vitro (% number of colonies of control[SD], NVP-BEZ235 vs NVP-BEZ235+HCQ: 45.0[17.9]% vs 24.0[8.4]%, P = 002) and in vivo (median survival of NVP-BEZ235-vs NVP-BEZ235+HCQ-treated mice: 38.5 days vs 47.0 days, P = 04). Conclusion: Combined mTOR and autophagy inhibition may provide an attractive approach to target BCR-ABL-independent mechanism of resistance.

AB - Background: Imatinib and second-generation tyrosine kinase inhibitors (TKIs) nilotinib and dasatinib have statistically significantly improved the life expectancy of chronic myeloid leukemia (CML) patients; however, resistance to TKIs remains a major clinical challenge. Although ponatinib, a third-generation TKI, improves outcomes for patients with BCR-ABL-dependent mechanisms of resistance, including the T315I mutation, a proportion of patients may have or develop BCR-ABL-independent resistance and fail ponatinib treatment. By modeling ponatinib resistance and testing samples from these CML patients, it is hoped that an alternative drug target can be identified and inhibited with a novel compound. Methods: Two CML cell lines with acquired BCR-ABL-independent resistance were generated following culture in ponatinib. RNA sequencing and gene ontology (GO) enrichment were used to detect aberrant transcriptional response in ponatinib-resistant cells. A validated oncogene drug library was used to identify US Food and Drug Administration-approved drugs with activity against TKI-resistant cells. Validation was performed using bone marrow (BM)-derived cells from TKI-resistant patients (n = 4) and a human xenograft mouse model (n = 4-6 mice per group). All statistical tests were two-sided. Results: We show that ponatinib-resistant CML cells can acquire BCR-ABL-independent resistance mediated through alternative activation of mTOR. Following transcriptomic analysis and drug screening, we highlight mTOR inhibition as an alternative therapeutic approach in TKI-resistant CML cells. Additionally, we show that catalytic mTOR inhibitors induce autophagy and demonstrate that genetic or pharmacological inhibition of autophagy sensitizes ponatinib-resistant CML cells to death induced by mTOR inhibition in vitro (% number of colonies of control[SD], NVP-BEZ235 vs NVP-BEZ235+HCQ: 45.0[17.9]% vs 24.0[8.4]%, P = 002) and in vivo (median survival of NVP-BEZ235-vs NVP-BEZ235+HCQ-treated mice: 38.5 days vs 47.0 days, P = 04). Conclusion: Combined mTOR and autophagy inhibition may provide an attractive approach to target BCR-ABL-independent mechanism of resistance.

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