MITOCHONDRIAL DNA MUTATIONS ARE ASSOCIATED WITH RESPONSE TO IMATINIB IN CHRONIC MYELOID LEUKAEMIA PATIENTS
Author(s): ,
Ilaria Stefania Pagani
Affiliations:
Cancer Program, Precision Medicine Theme,South Australian Health and Medical Research Institute, SAHMRI,Adelaide,Australia;School of Medicine, Faculty of Health Sciences,The University of Adelaide,Adelaide,Australia;Australasian Leukaemia and Lymphoma Group,Melbourne,Australia
,
Chung H Kok
Affiliations:
Cancer Program, Precision Medicine Theme,South Australian Health and Medical Research Institute, SAHMRI,Adelaide,Australia
,
Phuong Dang
Affiliations:
Cancer Program, Precision Medicine Theme,South Australian Health and Medical Research Institute, SAHMRI,Adelaide,Australia
,
Kelly Lim
Affiliations:
School of Medicine, Faculty of Health Sciences,The University of Adelaide,Adelaide,Australia
,
Verity A Saunders
Affiliations:
Cancer Program, Precision Medicine Theme,South Australian Health and Medical Research Institute, SAHMRI,Adelaide,Australia
,
Madeleine Hughes
Affiliations:
Cancer Program, Precision Medicine Theme,South Australian Health and Medical Research Institute, SAHMRI,Adelaide,Australia
,
Monika M Kutyna
Affiliations:
Cancer Program, Precision Medicine Theme,South Australian Health and Medical Research Institute, SAHMRI,Adelaide,Australia
,
Devendra K Hiwase
Affiliations:
Department of Haematology and Bone Marrow Transplantation,Royal Adelaide Hospital and SA Pathology,Adelaide,Australia
,
David T Yeung
Affiliations:
Department of Haematology and Bone Marrow Transplantation,Royal Adelaide Hospital and SA Pathology,Adelaide,Australia
,
Daniel Thomas
Affiliations:
School of Medicine, Faculty of Health Sciences,The University of Adelaide,Adelaide,Australia
,
Timothy P Hughes
Affiliations:
Cancer Program, Precision Medicine Theme,South Australian Health and Medical Research Institute, SAHMRI,Adelaide,Australia
David M Ross
Affiliations:
Department of Haematology and Bone Marrow Transplantation,Royal Adelaide Hospital and SA Pathology,Adelaide,Australia
EHA Library. Stefania Pagani I. 06/09/21; 324559; S151
Dr. Ilaria Stefania Pagani
Dr. Ilaria Stefania Pagani
Contributions
Abstract
Presentation during EHA2021: All Oral presentations will be made available as of Friday, June 11, 2021 (09:00 CEST) and will be accessible for on-demand viewing until August 15, 2021 on the Virtual Congress platform.

Abstract: S151

Type: Oral Presentation

Session title: Response, resistance and treatment-free remission in CML

Background

More than 20% of chronic myeloid leukaemia (CML) patients are resistant to first-line therapy with tyrosine kinase inhibitors (TKIs), with some of them developing fatal blast crisis. Even when treatment is effective most patients require lifelong TKI therapy. New therapies are therefore needed. Metabolic reprogramming is one of the earliest hallmarks of cancer and the identification of deregulated metabolic pathways offers new approaches to target cancer cells. Mitochondrial (mt) metabolism, in particular, may play a key role in controlling survival and proliferation of cancer stem cells and conferring resistance to apoptosis.

Aims

We hypothesize that mtDNA mutations could affect mt function, leading to reduced respiration (oxidative phosphorylation, OXPHOS) and increased sensitivity to TKIs. The role of mutations in mitochondrial-encoded electron transport chain genes has not been elucidated in CML. Therefore, the aim of our work was to investigate the genomic landscape of mtDNA mutations in CML and their association with response to TKIs.

Methods

We sequenced the mt genome of 80 CML patients from the ALLG Tidel I and II trials. Follow-up samples after 12 months of imatinib therapy were used as the inferred germline to identify mtDNA somatic mutations at diagnosis (Pagani IS, et al 2016). Patients not achieving major molecular response (BCR-ABL1 <= 0.1% IS) at 12 months were defined as poor responders (PR). The oxygen consumption rate of primary CML CD34+ cells was measured using the Seahorse XF96 analyser to evaluate OXPHOS function. 

Results

We identified 142 mtDNA somatic point mutations in 31/41 (78%) good responders (GR) at diagnosis (median 3 per patient, range 1-21), and 49 mutations in 30/39 (77%) PR (median 1 per patient, range 1-3) (P=0.041). Interestingly, 4 GR patients showed hypermutated sites with a larger number of mtDNA somatic mutations (>11) than expected from the background distribution. The median variant allele frequency (VAF) was 96.6% (range 3.5-100%), with 2 patients carrying 29 homoplasmic mutations (VAF>98%). The remaining GR patients had mutations with a median VAF of 8% (range 2.1-90.8%). All mtDNA somatic point mutations found in PR were heteroplasmic (median 6.6%, range 2-87.2%). Patients with 3 or more mtDNA somatic point mutations more often achieved MMR (90% vs 68%, P=0.0038) and MR4.5 (BCR-ABL1<0.0032% IS; 63% vs 37%, P=0.011) at 24 months of therapy than did patients with <3 mutations. There was no correlation between Sokal or EUTOS score and the number of mutations.


A limited number of patients had cryovials available for analysis of the mt respiration in CD34+ cells. Four GR had a range of 1-12 mtDNA mutations per patient with median VAF 61.8% (range 5.8-97.1%), and 5 PR had 0-2 mtDNA mutations per patient with median VAF of 5.5% (range 4.2-6.1%). GR had lower maximal respiration (median 115.9 pmol/min, range 76.6-149.7) than PR (median 199.7 pmol/min, range 170.9-222.4; P=0.0055).

Conclusion

A greater number of mtDNA mutations was associated with a better molecular response in imatinib-treated patients. In a small number of patients we found that mtDNA mutations with a higher VAF were associated  with impaired OXPHOS in CD34+ cells at diagnosis. We hypothesize that reduced OXPHOS may sensitize the leukemic cells to imatinib. Functional studies are ongoing.


 

Keyword(s): Chronic myeloid leukemia, Leukemic stem cell, Mitochondria, Mutation analysis

Presentation during EHA2021: All Oral presentations will be made available as of Friday, June 11, 2021 (09:00 CEST) and will be accessible for on-demand viewing until August 15, 2021 on the Virtual Congress platform.

Abstract: S151

Type: Oral Presentation

Session title: Response, resistance and treatment-free remission in CML

Background

More than 20% of chronic myeloid leukaemia (CML) patients are resistant to first-line therapy with tyrosine kinase inhibitors (TKIs), with some of them developing fatal blast crisis. Even when treatment is effective most patients require lifelong TKI therapy. New therapies are therefore needed. Metabolic reprogramming is one of the earliest hallmarks of cancer and the identification of deregulated metabolic pathways offers new approaches to target cancer cells. Mitochondrial (mt) metabolism, in particular, may play a key role in controlling survival and proliferation of cancer stem cells and conferring resistance to apoptosis.

Aims

We hypothesize that mtDNA mutations could affect mt function, leading to reduced respiration (oxidative phosphorylation, OXPHOS) and increased sensitivity to TKIs. The role of mutations in mitochondrial-encoded electron transport chain genes has not been elucidated in CML. Therefore, the aim of our work was to investigate the genomic landscape of mtDNA mutations in CML and their association with response to TKIs.

Methods

We sequenced the mt genome of 80 CML patients from the ALLG Tidel I and II trials. Follow-up samples after 12 months of imatinib therapy were used as the inferred germline to identify mtDNA somatic mutations at diagnosis (Pagani IS, et al 2016). Patients not achieving major molecular response (BCR-ABL1 <= 0.1% IS) at 12 months were defined as poor responders (PR). The oxygen consumption rate of primary CML CD34+ cells was measured using the Seahorse XF96 analyser to evaluate OXPHOS function. 

Results

We identified 142 mtDNA somatic point mutations in 31/41 (78%) good responders (GR) at diagnosis (median 3 per patient, range 1-21), and 49 mutations in 30/39 (77%) PR (median 1 per patient, range 1-3) (P=0.041). Interestingly, 4 GR patients showed hypermutated sites with a larger number of mtDNA somatic mutations (>11) than expected from the background distribution. The median variant allele frequency (VAF) was 96.6% (range 3.5-100%), with 2 patients carrying 29 homoplasmic mutations (VAF>98%). The remaining GR patients had mutations with a median VAF of 8% (range 2.1-90.8%). All mtDNA somatic point mutations found in PR were heteroplasmic (median 6.6%, range 2-87.2%). Patients with 3 or more mtDNA somatic point mutations more often achieved MMR (90% vs 68%, P=0.0038) and MR4.5 (BCR-ABL1<0.0032% IS; 63% vs 37%, P=0.011) at 24 months of therapy than did patients with <3 mutations. There was no correlation between Sokal or EUTOS score and the number of mutations.


A limited number of patients had cryovials available for analysis of the mt respiration in CD34+ cells. Four GR had a range of 1-12 mtDNA mutations per patient with median VAF 61.8% (range 5.8-97.1%), and 5 PR had 0-2 mtDNA mutations per patient with median VAF of 5.5% (range 4.2-6.1%). GR had lower maximal respiration (median 115.9 pmol/min, range 76.6-149.7) than PR (median 199.7 pmol/min, range 170.9-222.4; P=0.0055).

Conclusion

A greater number of mtDNA mutations was associated with a better molecular response in imatinib-treated patients. In a small number of patients we found that mtDNA mutations with a higher VAF were associated  with impaired OXPHOS in CD34+ cells at diagnosis. We hypothesize that reduced OXPHOS may sensitize the leukemic cells to imatinib. Functional studies are ongoing.


 

Keyword(s): Chronic myeloid leukemia, Leukemic stem cell, Mitochondria, Mutation analysis

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