Transcriptional Immunoediting of AML Cells after Allogeneic Hematopoietic Stem Cell Transplantation

Relapse of AML after allogeneic hematopoietic stem cell transplantation (alloSCT) has been linked to reduced expression of major histocompatibility complex type II proteins (MHC-II), which appears to have a regulatory basis. To understand the mechanism of immune evasion in AML, we developed CORENODE, a computational algorithm for genome-wide transcription network decomposition. CORENODE identified the transcription factors (TFs) IRF8 and MEF2C as positive regulators and MYB and MEIS1 as negative regulators of the MHC-II expression in AML. We validated this prediction using several approaches. First, inactivation of IRF8 and MEF2C in AML cell lines by CRISPR-Cas9 resulted in decreased MHC-II expression, while inactivation of MYB and MEIS1 led to MHC-II induction. Second, decreased levels of IRF8 and MEF2C, and increased levels of MYB and MEIS1 were seen in patients with AML relapse after alloSCT, correlating with reduced expression of MHC-II. Finally, MHC-II expression in various patient-derived datasets could be accurately predicted by CORENODE from the combinatorial levels of the 4 TFs. Although immune evasion in AML has been linked to the transcriptional coactivator CIITA, CORENODE predicted that members of the TF tetrad regulate MHC-II genes independently from CIITA. Indeed, inactivation of MYB and MEIS1 in a CIITA knockout AML cell line was able to cause MHC-II induction. Beyond MHC-II, CORENODE identified a module of 58 genes that were up-regulated by IRF8 and down-regulated by MYB. The module was highly enriched for genes participating in graft-versus-leukemia (GvL) reactivity and we found it to be downregulated in 5 of 6 patients with a post-alloSCT AML relapse. Thus, the post-alloSCT changes in MHC-II expression are part of a broader transcriptional program of GvL response in AML, antagonistically regulated by MYB and IRF8. However, reduced expression of MHC-II and other GvL response genes at relapse does not correlate with the myeloid differentiation state, indicating that it is regulated independently. To understand the clonal basis of MHC-II expression loss at the time of relapse, we analyzed MHC-II expression at the single-cell level. Analysis of previously published paired scRNA data at the time of initial diagnosis and after alloSCT demonstrated a small number of cells with reduced MHC-II expression driven by altered MYB and IRF8 levels present at the time of initial diagnosis. These MHC-II-low cells appear to be selected by the immune pressure, resulting in eventual relapse. In summary, our findings reveal an adaptive transcriptional mechanism of AML immunoediting after allogenic transplantation whereby combinatorial fluctuations of TF levels under immune pressure result in selection of cells with a silenced T-cell stimulation program.

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