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. 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.