Preventing Acute Myeloid Leukaemia Relapse following Allogeneic Stem Cell Transplantation

Stem cell transplantation is the only curative therapy for many patients with acute myeloid leukaemia (AML) and other cancers of the blood and bone marrow. However, cancer recurrence remains the most common cause of death, and is due to failure of the donor immune system to eliminate residual disease. The immune cells most responsible for clearing leukaemia are T cells. T cells are often dysfunctional at relapse, and leukaemia is frequently able to evade them. Understanding why T cells become dysfunctional, and how AML escapes them, is critical to the development of new treatments that re-establish successful immune responses to treat or prevent relapse. Identifying patients with early immune dysfunction is also necessary to allow appropriate targeting of novel therapies.

T-cell dysfunction occurs in many cancers and treatments that re-invigorate T cells have revolutionised cancer care. However, these therapies cause significant toxicity when given to transplant patients. Because there are many potential causes of T-cell dysfunction, it is important to identify those most relevant to the T cells that fight leukaemia, in order to target them without causing unacceptable side effects. To understand how donor T cells become dysfunctional, we will study the expression of genes and the structure of DNA in thousands of individual T cells from patients with AML relapse after transplant. This will allow us to explore in detail the changes that occur as T cells become dysfunctional and identify the major drivers of dysfunction in patients. Targeting these processes will then form the basis of novel therapeutic strategies to treat or prevent post-transplant relapse.

AML frequently displays proteins that are involved in the activation of T cells, called MHCII. Expression is often lost at post-transplant relapse and this reduces the ability of leukaemia to activate T cells, providing a mechanism of immune evasion. How MHCII proteins are regulated in AML is not known. AML is a cancer of the blood-forming cells of the bone marrow. Through a process termed differentiation these cells normally give rise to the mature cells found in blood, some of which strongly express MHCII. This process becomes blocked in AML, but can be re-established by a recently developed class of drugs called LSD1 inhibitors. Using leukaemia and T cells isolated from patient samples, we will investigate the ability of these drugs to drive MHCII expression in AML and promote T-cell activation. LSD1 inhibitors are currently in clinical trials for AML, providing a clear pathway to clinical application, should our results support their use for post-transplant relapse.

Before novel preventative therapies can be given to patients, those at risk of relapse must be identified. Recent studies suggest that early detection of dysfunctional T cells may predict relapse. Changes in the protein content of blood have also been observed that reflect the activity of T cells against leukaemia. Manchester is home to the Stoller Centre, Europe's largest clinical proteomic facility. We are able to analyse thousands of patient samples and track small changes in the concentration of hundreds of plasma proteins. We have established a study to collect blood samples at multiple time points from 300 transplant recipients. We will use these samples to identify changes in the protein content of blood and the properties of T cells that precede AML relapse, in order to develop new predictive blood tests.

Overall, this study will identify the major drivers of immune dysfunction and leukaemic immune evasion that lead to AML relapse after stem cell transplantation. Our results will inform new therapeutic strategies for treating or preventing disease recurrence. We will also develop new blood tests that predict AML relapse, allowing therapeutic targeting of at-risk individuals and improving transplant outcomes.

Allogeneic haematopoietic stem cell transplantation is the only curative therapy for many patients with acute myeloid leukaemia (AML). Relapse remains the most common cause of death and is due to failure of donor T cells to eliminate residual disease. Donor T cells are frequently exhausted at relapse, and AML often exhibits reduced immunogenicity. Determining the major drivers of T-cell exhaustion and leukaemic immunogenicity is critical to inform strategies that re-establish anti-leukaemic T-cell responses and prevent relapse.

Objective 1: Single-cell RNA and ATAC sequencing will be applied to T cells from post-transplant relapse bone marrow to map enhancer activity and transcription factor binding at exhaustion-associated genes. Using patient samples to dissect the regulation of exhaustion will identify the drivers most relevant to post-transplant relapse, these can then be targeted to prevent disease recurrence.

Objective 2: Reduced leukaemic MHC class II (MHCII) expression is common at post-transplant relapse and AML lacking MHCII elicits weaker donor T-cell responses. Our analysis suggests that leukaemic MHCII expression reflects differentiation towards a monocyte-macrophage lineage. Using primary AML and donor T cells in functional co-culture experiments we will determine the immunological consequences of leukaemic differentiation. We will also investigate the ability of differentiation-inducing compounds to augment T-cell activation and promote successful disease clearance.

Objective 3: Before novel therapies can be applied, an at-risk population must be identified. Plasma proteomics (SWATH-MS) and mass cytometry will be applied to serial blood samples from multiple transplant patients to identify signatures of immune dysfunction that predict relapse. The development of predictive biomarkers would represent a significant advance, allowing therapeutic targeting of at-risk individuals, for example using donor T-cell administration.