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Bipartite network models to design combination therapies in acute myeloid leukaemia

Author

Listed:
  • Mohieddin Jafari

    (University of Helsinki)

  • Mehdi Mirzaie

    (University of Helsinki)

  • Jie Bao

    (University of Helsinki)

  • Farnaz Barneh

    (Prinses Maxima Center for Pediatric Oncology)

  • Shuyu Zheng

    (University of Helsinki)

  • Johanna Eriksson

    (University of Helsinki)

  • Caroline A. Heckman

    (University of Helsinki)

  • Jing Tang

    (University of Helsinki)

Abstract

Combination therapy is preferred over single-targeted monotherapies for cancer treatment due to its efficiency and safety. However, identifying effective drug combinations costs time and resources. We propose a method for identifying potential drug combinations by bipartite network modelling of patient-related drug response data, specifically the Beat AML dataset. The median of cell viability is used as a drug potency measurement to reconstruct a weighted bipartite network, model drug-biological sample interactions, and find the clusters of nodes inside two projected networks. Then, the clustering results are leveraged to discover effective multi-targeted drug combinations, which are also supported by more evidence using GDSC and ALMANAC databases. The potency and synergy levels of selective drug combinations are corroborated against monotherapy in three cell lines for acute myeloid leukaemia in vitro. In this study, we introduce a nominal data mining approach to improving acute myeloid leukaemia treatment through combinatorial therapy.

Suggested Citation

  • Mohieddin Jafari & Mehdi Mirzaie & Jie Bao & Farnaz Barneh & Shuyu Zheng & Johanna Eriksson & Caroline A. Heckman & Jing Tang, 2022. "Bipartite network models to design combination therapies in acute myeloid leukaemia," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-29793-5
    DOI: 10.1038/s41467-022-29793-5
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    1. Ravi S. Narayan & Piet Molenaar & Jian Teng & Fleur M. G. Cornelissen & Irene Roelofs & Renee Menezes & Rogier Dik & Tonny Lagerweij & Yoran Broersma & Naomi Petersen & Jhon Alexander Marin Soto & Eel, 2020. "A cancer drug atlas enables synergistic targeting of independent drug vulnerabilities," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
    2. Paul Geeleher & Eric R. Gamazon & Cathal Seoighe & Nancy J. Cox & R. Stephanie Huang, 2016. "Consistency in large pharmacogenomic studies," Nature, Nature, vol. 540(7631), pages 1-2, December.
    3. Jeffrey W. Tyner & Cristina E. Tognon & Daniel Bottomly & Beth Wilmot & Stephen E. Kurtz & Samantha L. Savage & Nicola Long & Anna Reister Schultz & Elie Traer & Melissa Abel & Anupriya Agarwal & Auro, 2018. "Functional genomic landscape of acute myeloid leukaemia," Nature, Nature, vol. 562(7728), pages 526-531, October.
    4. Zichen Wang & Caroline D. Monteiro & Kathleen M. Jagodnik & Nicolas F. Fernandez & Gregory W. Gundersen & Andrew D. Rouillard & Sherry L. Jenkins & Axel S. Feldmann & Kevin S. Hu & Michael G. McDermot, 2016. "Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd," Nature Communications, Nature, vol. 7(1), pages 1-11, November.
    5. Heli Julkunen & Anna Cichonska & Prson Gautam & Sandor Szedmak & Jane Douat & Tapio Pahikkala & Tero Aittokallio & Juho Rousu, 2020. "Leveraging multi-way interactions for systematic prediction of pre-clinical drug combination effects," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
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