Patients samples and clinical data:
The investigator will study samples from 120 patients with a post-MPN acute myeloid leukemia. These samples and the corresponding clinical data are available through FIMBANK, a national network of biological resources for myeloproliferative neoplasms (grant INCa, BCB 2013, Pr Valérie Ugo) and through the prospective phase II clinical trial CPX351-TA-SMP testing CPX351 monotherapy in post-MPN AML (NCT04992949, inclusions started in 01-2022).
WP1: Deciphering the heterogeneity of post-MPN AML (primary objective) To answer these objectives, the investigator will conduct a multi-omics approach including targeted-NGS with a 400-genes panel, RNA-seq and methylome in a total of 120 post-MPN AML samples. All the genomic libraries will be constructed at the genomic facility of Angers University Hospital and the sequencing will be performed on a NovaSeq6000 in the GenoBIRD Platform in Nantes. Bioinformatic analysis will be performed by teams #1 and #3 and will derive for each sample: SNV/Indel and CNV from DNA sequencing, expression of mRNA and lncRNA, genes fusion and splicing events from RNA-seq, and methylation beta-values from methylome.
In order to identify homogeneous subgroups from the genomic data, the investigator will perform unsupervised clustering analyses of each layer of genomic data. Then, all layers will be combined for integration of clusters using the Cluster Of Clusters Analysis (COCA) method (Wilkerson and Hayes, 2010).
WP2: Identify the mechanisms of transformation and putative targets for therapy For this purpose, the investigator will analyze omics data generated in WP1 to identify the main molecular mechanisms driving the leukemic transformation of MPN. The investigator will perform a 2-step procedure: first by analyzing each genomic dataset separately and then, by analyzing all datasets together in an integrated multiblock analysis using the MOGSA method (Integrative Single Sample Gene-set).
A total of 60 samples originating from a subset of patients classified in WP1 will be tested for ex vivo drug screening. The investigator will design a custom-made drug panel including standards of care, several drugs in clinical development in AML and, more importantly, a selection of drugs specifically targeting potential leukemic vulnerabilities identified.
WP3: Confirm the efficacy of selected best drugs and their impact on clonal architecture To further validate the translational relevance of post-MPN AML deregulated pathways, the three most promising drug candidates will then be evaluated in a set of five post-MPN PDX models including at least 2 TP53-mutated post-MPN AML. The investigator will also evaluate how the drugs identified in WP2 may impact clonal evolution of the disease which is a key step towards understanding and improving the treatment of post-MPN AML. The 3 best candidate drugs or combinations identified in WP2 will be studied in cells from 5 selected patients with a complex molecular profile to evaluate the response of various subclones.
