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Integrated multi-omic profiling of azacitidine-venetoclax in AML reveals additional targetable pathways to improve the treatment
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Haematology.ORCID iD: 0000-0001-8749-7299
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Haematology.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Haematology.ORCID iD: 0000-0001-5873-9797
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

The combination of venetoclax and azacitidine constitutes the first-line option for patients with acute myeloid leukemia (AML) who are ineligible for intensive chemotherapy. Azacitidine-venetoclax has shown pronounced clinical and preclinical ecacy but the molecular mechanisms causing this synergy remain to be clarified. We applied an integrative multi-omic approach with focus in epigenetics on two AML cell lines to characterize the effects of azacitidine-venetoclax in vitro on chromatin accessibility, DNA methylation and gene expression patterns.

We report distinct epigenetic and transcriptomic eects when combining azacitidine and venetoclax as compared to either substance alone. With the application of ATAC-seq, we delineate combination-unique gained pathways including the activation of mRNA splicing and NOTCH-HSF1 signaling but also more widespread heterochromatin compared to azacitidine or venetoclax alone. When assessing methylation status, we observed combination-unique hypermethylation of Rac1- and Rho-associated signaling. We integrate the epigenetic alterations of azacitidine-venetoclax with RNA-seq data and report activation of genes involved in the serine synthesis pathway and NTRK signaling that represent potentially upregulated survival pathways upon azacitidine-venetoclax exposure.

We also propose potential synergistic triplet therapies based on in silico drug predictions using condition-wise weighted co-expression networks including inhibitors of proteaseomes, MCL-1 and histone deacetylase. Future studies are needed to investigate whether the inhibition of the mentioned pro-survival pathways or proposed triplets may enhance the effects of azacitidine-venetoclax in AML.

Keywords [en]
Azacitidine, Venetoclax, Acute myeloid leukemia, ATAC-seq, RNA-seq, Methylation, Multi-omics, In silico drug predictions
National Category
Hematology
Research subject
Medical Science
Identifiers
URN: urn:nbn:se:uu:diva-501510OAI: oai:DiVA.org:uu-501510DiVA, id: diva2:1755786
Available from: 2023-05-09 Created: 2023-05-09 Last updated: 2023-05-10Bibliographically approved
In thesis
1. Improving prognostication and treatment choices for patients with AML
Open this publication in new window or tab >>Improving prognostication and treatment choices for patients with AML
2023 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The treatment landscape of the aggressive haematological malignancy acute myeloid leukaemia (AML) has expanded but the prognosis is still unsatisfactory poor. Here, we aimed at improving prognostication and treatment choices in AML by addressing current clinical obstacles to successful AML treatment.

Acute promyelocytic leukaemia (APL) is an AML subset characterised by a high rate of early death (ED). In Paper I, we developed a novel risk score for ED in APL. We identified three risk groups for ED based on regression analyses on first a training cohort from the population-based Swedish AML Registry (n=301) and later an external validation cohort from a hospital-based registry (n=129). The presented risk score included age, platelets and white blood cell (WBC) count. Importantly, already sub-normal to normal WBC counts conferred higher risks of ED.

Molecular studies of elderly AML patients are sparse. In Paper II, we focused on patients ≥65 years to investigate the prognostic effect of molecular markers and to propose an algorithm for response to intensive chemotherapy (IC) in this patient group. We combined clinical data with targeted DNA- and RNA-sequencing of 182 patients. Notably, we identified and externally validated three risk categories for complete remission achievement after IC based on mutational status of TP53 and gene expression levels of ZBTB7A and EEPD1.

Hypomethylating agents (HMAs) constitute a backbone for AML patients ineligible for IC. There are limited studies on their effectiveness in the real-world setting. In Paper III, we compared the utility of HMAs against IC and palliative care in all AML patients ≥60 years in Sweden (n=3135) during 2008-2018. Propensity score matching in this population-based cohort showed that HMAs are as effective as IC upfront when patient characteristics were balanced. Additionally, predictive factors for overall survival in HMA treated patients were different to IC treated patients.

The HMA azacitidine combined with venetoclax is the current frontline option to AML patients unfit for IC. Few studies have addressed how this synergism arises. In Paper IV, we characterised the epigenetic and transcriptomic effects of azacitidine-venetoclax in vitro and elucidated potential survival/resistance mechanisms in AML blasts including the serine synthesis pathway and NTRK signaling. Furthermore, we utilised obtained RNA-seq data and in silico predictions to propose add-ons to azacitidine-venetoclax to further strengthen the synergy.

In summary, the research presented herein contributes to improved personalised medicine in AML via real-world data, risk stratification algorithms and insights into potential novel therapeutic approaches.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2023. p. 69
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 1954
Keywords
Acute myeloid leukaemia, Acute promyelocytic leukaemia, Prognostication, Personalised medicine, Risk stratification, Real-world data, Next-generation sequencing, Azacitidine, Venetoclax
National Category
Hematology
Research subject
Medical Science
Identifiers
urn:nbn:se:uu:diva-501512 (URN)978-91-513-1829-5 (ISBN)
Public defence
2023-09-01, H:son Holmdahlsalen, Uppsala University Hospital, Entrance 100, Uppsala, 13:00 (English)
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Supervisors
Available from: 2023-06-08 Created: 2023-05-09 Last updated: 2023-06-08

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Österroos, AlbinGamboa Cedeno, AngelicaJunkunlo, KingkamonEriksson, AnnaLehmann, Sören

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