Leukemic initiation in Jam-C-deficient HSPC reveals AP-1/TNF-? gene expression signature as a biomarker for AML

The leukemic stem cell score 17 (LSC-17) based on stemness gene expression signature is recognized as indicator of poor disease outcome in acute myeloid leukemia (AML). However, our understanding of the relationships between LSC and pre-leukemic cells is still incomplete. In particular, it is not known whether “niche-anchoring” of pre-leukemic cell affects disease evolution. To address this issue, we conditionally inactivated the adhesion molecule Jam-C expressed by haematopoietic stem cells (HSC) and LSC in an inducible iMLL-AF9-driven AML mouse model. Deletion of Jam-C in HSC before activation of the leukemia-initiating iMLL-AF9 fusion resulted in a shift from long term (LT-HSC) to short term-HSC (ST-HSC) expansion, suggesting that transcriptional programs of leukemic HSC were altered. RNA sequencing performed on leukemic HSC and GMP isolated from diseased mice revealed that genes upregulated in Jam-C-deficient animals belonged to Activation Protein-1 (AP-1) and TNF-?/NF?B signalling pathways. Using three publicly available datasets of AML gene expression, we further showed that human orthologs of dysregulated genes belonged to a gene regulon distinct from the LSC-17 signature. A prognosis 14-genes score from the AP-1/TNF-?/NF?B gene expression signature was established and called ATIC for “AP-1/TNF-? initiating cell”. ATIC was independent of the LSC-17 score and improved the stratification of AML patients obtained with the LSC-17 score suggesting that the ATIC score reflected the presence of ST-HSC-initiating AML cells at diagnosis. Collectively we provide a novel tool for understanding AML disease heterogeneity through the identification of specific transcriptional programs for leukemic stem and progenitor cells. Overall design: BM cells were recovered from femur and tibia, red blood cells were lysed using 1X RBC lysing buffer (eBioscience) and stained with a cocktail containing Live/dead marker, Sca-1, CD150, CD16/32, CD34, CD117, CD135, CD48, and a biotinylated lineage cocktail containing: CD4, CD8, CD3, CD19, CD11c, DX5, Ter119, CD11b, B220 and Gr1.