Developmental-specific proteomic vulnerabilities of Leukemia

Introduction:

The distinct development of fetal and adult blood cells, governed by unique molecular networks and extracellular signals, contributes to the separate onset of acute leukemia in children and adults. Both infant and adult MLL rearranged (MLLr) acute leukemia have poor prognoses due to limited treatment options. To develop age-tailored targeted therapies, a better understanding of the regulatory networks and their responses to external signals is needed. Previously, we identified age-specific proteomic features of normal and MLLr leukemia-initiating cells1-2. Here, we establish an in vitro approach to perturb these age-specific features in infant and adult leukemic cells by stimulating with IFNa or HDAC3 inhibitor, aiming to induce an age-specific proteomic response. The long-term goal is to identify proteins for age-tailored immune therapies targeting immunopeptides on pre-leukemic and leukemic cells.

Methods:

Hematopoietic progenitors were FACS-sorted from fetal and adult MLL-ENL-inducible mice, cultured for 3 days, treated with IFNa, and collected at 17, 40, and 64 hours. Infant (THP1, KOPN8) and adult (NOMO-1, MONO-MAC-6) human leukemic cell lines were treated with IFNa or HDAC3 inhibitor (HDAC3i) and collected after 17 hours. The cellular proteome was analyzed using in-depth data-independent acquisition-based proteomics.

Results:

We found that IFNa stimulation rapidly induces protein expression in both healthy and pre-leukemic cells, and this effect persists longer in wild-type cells than in pre-leukemic cells. IFNa induces upregulation of potential age and lineage-specific targets in both mice pre-leukemic and human leukemic cells. Conversely, HDAC3 inhibition reduces viability in infant leukemia cells harboring MLL-ENL fusion by reprogramming metabolic pathways. In addition, HDAC3 inhibition impacts regulators of proteasomal degradation and induces differential expressions of proteasomal units, predominantly in infant leukemia, which may cause indirect immunomodulatory effects through modulating antigen processing and presentation.

Conclusions:

Our study comprehensively describes IFNa-regulated proteome changes in healthy and MLLr hematopoietic progenitor cells, as well as IFNa- and HDAC3i-regulated proteomic changes in infant and adult human leukemic cells, highlighting age-specific vulnerabilities in MLLr leukemia. Combined with ongoing efforts to identify development-specific immunopeptides, this work contributes to future developments of combinatorial leukemia treatments utilizing proteomic perturbation and targeted immunotherapy.

References

Jassinskaja, M., et al. (2017). Cell Reports, 21(11), 3285–3297.Jassinskaja, M., Ghosh, S. et al. (2024) Leukemia, 38, 1115-1130.