Effects of YBX1 on gene expression and translation in acute myeloid leukemia (AML)

• Applicant: Professor Dr. Florian Heidel
• Subject Area: Hematology, Oncology
• Term: since 2020
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 453491106

Persistence of malignant cells following cytotoxic or targeted therapy is a major determinant of adverse outcome in patients with hematologic cancers. Despite the fact that the majority of patients with acute myeloid leukemia (AML) achieve complete remission after chemotherapy, a large proportion of them relapse as a result of residual malignant cells. After discontinuation of treatment, these persistent clones have a competitive advantage over normal cells in the bone marrow niche leading to re-establishment of the disease. Targeting strategies that specifically reduce competitivity of malignant cells while leaving normal cells unaffected are highly needed. Recently, our group identified the splicing factor YBX1 as a downstream effector of JAK2-kinase and uncovered its function in stabilizing cell signaling. Of note, JAK2-mutated cells are not primarily dependent on YBX1, as indicated by an RNAi-screen. However, inactivation of YBX1 sensitized JAK2-mutated cells to JAK-inhibitor treatment.In contrast, analysis of publicly available CRISPR-Cas9 dependency screening datasets on human cancer cell lines of the Achilles Project (Broad Institute) indicated a pan-cancer dependency for YBX1 which was even more significant in hematopoietic cancers and most pronounced in AML cell lines. These findings indicate a relevant dependency and distinct mechanism in AML. We have validated the dependency of AML cells using an arrayed CRISPR-Cas9 based negative selection screen, which showed a strong dependency on Ybx1 following infection with 4 different sgRNAs. This effect could be confirmed in several AML cell lines and in different in vivo models of AML. Transcriptome analysis following YBX1 inactivation revealed deregulation of genes involved in translation and elongation.According to our proposed working program we will confirm the functional relevance of YBX1 for leukemia stem cells in conditional mouse models. In pre-clinical models of human AML (patient-derived xenograft; PDX) we will specifically assess for cell competition against normal hematopoietic cells, a therapeutically relevant setting in a minimal residual disease situation. This approach will be complemented by testing of pharmacologic compounds which may interfere with YBX1 function. Moreover, we will investigate the mechanistic consequences of YBX1-mediated (post-) transcriptional regulation by polysome profiling and global proteome analysis. Using genome editing approaches in human AML cells, we aim to identify relevant molecules that depend on YBX1 function.In summary, we aim to confirm the relevant dependency of AML cells on YBX1 in pre-clinical models followed by investigation of mechanistic aspects to identify relevant effector molecules. Our experimental approach may therefore facilitate therapeutic targeting of frequently persisting leukemic cells, the source of relapse in AML.

• DFG Programme: Research Grants