Acute myeloid leukemia cells can evade immune detection at post-transplant relapse

Allogeneic hematopoietic stem cell transplantation (HSCT), a consolidation therapy strategy in acute myeloid leukemia (AML), is thought to act via an immune-mediated graft-versus-leukemia (GvL) effect. A group of researchers from the McDonnell Genome Institute, Washington, US, hypothesized that immune-mediated mechanisms induced by allogeneic HSCT may cause distinct patterns of tumor evolution in relapsed AML. This theory was investigated and the results of the study were published in the New England Journal of Medicine.

In order to identify genetic and epigenetic alterations that allow leukemia cells to escape the GvL effect, the researchers performed a comprehensive analysis of samples from patients who had relapse of AML after transplantation. Exome sequencing was performed on paired samples obtained from 15 patients at initial presentation and relapse after allogeneic HSCT. For comparison, samples from 20 patients who had relapse after chemotherapy alone were also analyzed.

Key findings:

• The recurrent mutations that were found at relapse after transplantation were similar to those seen at initial presentation and at relapse after chemotherapy
  • No driver mutations were found to be associated with relapse after transplantation
• Among the 15 patients with post-transplant relapse, there were no relapse specific mutation genes involved in antigen presentation, cytokine signaling or immune checkpoint modulation

In order to investigate whether epigenetic changes might be contributing to disease evolution post-transplant, total RNA sequencing was performed on enriched AML blasts from paired samples from seven patients at initial presentation and at post-transplant relapse. Samples from nine patients who relapsed after chemotherapy were also analyzed.

• Among patients with post-transplantation relapse, 221 genes showed significant differential expression between initial presentation and relapse
• Significantly dysregulated pathways in immune-response genes, cell adhesion & motility, and in the innate immune response were observed in relapsed samples from patients with post-transplant relapse
  • Significant downregulation of four major histocompatibility complex (MHC) class II genes including HLA-DPA1, HLA-DPB1, HLA-DQB1, and HLA-DQA1 was observed in six of seven patients

To determine the prevalence of the down-regulation of MHC class II genes, 10 additional patients with post-transplant relapse were analyzed using flow cytometry, yielding a total of 16 patients with post-transplant relapse.

• In 5/16 post-transplantation relapse samples, MHC class II protein levels were at least 60 times lower than levels in the paired presentation samples
• In three patients with post-transplantation relapse, MHC class II protein levels were 4–22 times lower than levels in the paired presentation samples
• Immunohistochemical analysis was performed to identify HLA-DR positive myeloblasts on an additional 18 patients with post-transplant relapse
  • Nine patients had a decrease in HLA-DR
• Decreased expression of MHC class II proteins was observed in post-transplantation relapse samples in a total of 17 of 34 patients using flow cytometry or immunohistochemistry
• In vitro culture of AML blast samples from patients with post-transplant relapse associated with complete down-regulation MHC class II proteins with interferon-y led to a rapid induction of MHC class II protein expression on leukemic blasts

Furthermore, single-cell RNA sequencing in one patient with post-transplant relapse revealed a high expression of MHC class II genes in the vast majority of AML cells at presentation. In addition, no subclone with low MHC class II genes was detected. This indicates, according to the researchers, that clones evolved in response to immune-mediated selective pressure and ultimately escape, thus leading to relapse.

In summary, AML cells at post-transplant relapse associated with a downregulated MHC class II gene expression, which allows the cells to escape immune detection which eventually leads to relapse. The researchers concluded by stating that “AML cells that escaped the immune surveillance provided by allogeneic T cells after allogeneic hematopoietic stem-cell transplantation frequently had dysregulation of a number of pathways that regulate immune function. These changes appeared to be epigenetic in nature in at least some cases, which suggests that therapeutic strategies to resensitize AML cells to the graft-versus-leukemia effect may be feasible”.