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Acute myeloid leukemia

Monitoring therapy responses at the leukemic subclone level by ultra-deep amplicon resequencing in acute myeloid leukemia

Leukemia volume 31, pages 1048–1058 (2017)Cite this article

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Abstract

In our individualized systems medicine program, personalized treatment options are identified and administered to chemorefractory acute myeloid leukemia (AML) patients based on exome sequencing and ex vivo drug sensitivity and resistance testing data. Here, we analyzed how clonal heterogeneity affects the responses of 13 AML patients to chemotherapy or targeted treatments using ultra-deep (average 68 000 × coverage) amplicon resequencing. Using amplicon resequencing, we identified 16 variants from 4 patients (frequency 0.54–2%) that were not detected previously by exome sequencing. A correlation-based method was developed to detect mutation-specific responses in serial samples across multiple time points. Significant subclone-specific responses were observed for both chemotherapy and targeted therapy. We detected subclonal responses in patients where clinical European LeukemiaNet (ELN) criteria showed no response. Subclonal responses also helped to identify putative mechanisms underlying drug sensitivities, such as sensitivity to azacitidine in DNMT3A mutated cell clones and resistance to cytarabine in a subclone with loss of NF1 gene. In summary, ultra-deep amplicon resequencing method enables sensitive quantification of subclonal variants and their responses to therapies. This approach provides new opportunities for designing combinatorial therapies blocking multiple subclones as well as for real-time assessment of such treatments.

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Acknowledgements

We are grateful to all the patients for donating their samples for research. Kirsi Autio (HUSLAB, Helsinki, Finland) and Tuija Lundan (TYKSLAB, Turku, Finland) are thanked for providing sample materials from clinical specimens. Alun Parsons and Minna Suvela are acknowledged for their efforts to process the samples and staff of the FIMM Sequencing Lab (Maija Lepistö, Tiina Hannunen Aino Palva and Sari Hannula) are thanked for exome sequencing. Jani Saarela, Laura Turunen, Katja Suomi and staff of FIMM High Throughput Biomedicine Unit are thanked for drug sensitivity and resistance testing (DSRT) experiments and analysis. Disha Malani is thanked for her help in retrieving DSRT data. The research leading to these results was supported by Academy of Finland (Center of Excellence for Translational Cancer Biology), Cancer Society of Finland, Sigrid Juselius Foundation, EU-Systems Microscopy (FP7) and TEKES. PNO is supported by the Doctoral Program in Biomedicine (DPBM) from the University of Helsinki. MK is supported by Doctoral Programme in Clinical Research, University of Helsinki. DT is supported by the People Programme (Marie Curie Actions) and Agency of Competitiveness for Companies of the Government of Catalonia, ACCIO.

Author contributions

PNO, HE, MW and OK designed the study and provided critical inputs; MK and KP coordinated clinical sample collection and administered therapies, obtained ethical permits and provided key biological and clinical insights; PNO, HE and SE performed data analysis and interpretation of sequencing data; PE, SL, TM, PNO and HA performed amplicon resequencing experiments, analysis and data interpretation; DT performed driver gene analysis and cancer cell fraction estimation; CH collected samples, coordinated sample management, preparation, processing and analysis; PNO, MW and OK wrote the paper; KW, HE, DT MK, KP and CH provided critical insights into the paper.

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Authors and Affiliations

  1. Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland

    P N Ojamies, P Ellonen, S Lagström, H Almusa, T Miettinen, S Eldfors, K Wennerberg, C Heckman, M Wolf & O Kallioniemi

  2. Department of Hematology, Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland

    M Kontro & K Porkka

  3. MediSapiens Ltd, Helsinki, Finland

    H Edgren

  4. Biomedical Genomics Lab, Research Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu Fabra, Barcelona, Catalonia, Spain

    D Tamborero

  5. Department of Oncology and Pathology, Science for Life Laboratory, Karolinska Institutet, Solna, Sweden

    O Kallioniemi

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Correspondence to O Kallioniemi.

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Competing interests

The authors declare no conflict of interest. The senior authors have received collaborative research grants for other projects as listed. OK has received research funding from Pfizer, Roche and the IMI Predect consortium and is a board member and co-founder of bioinformatics company Medisapiens Ltd, Helsinki, Finland. KP received honoraria and research funding from Bristol-Myers Squibb, Celgene, Novartis and Pfizer. MW received research funding from Pfizer and Bayer Pharma.

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Ojamies, P., Kontro, M., Edgren, H. et al. Monitoring therapy responses at the leukemic subclone level by ultra-deep amplicon resequencing in acute myeloid leukemia. Leukemia 31, 1048–1058 (2017). https://doi.org/10.1038/leu.2016.286

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