A compass for those with relapsed leukemia after transplant

ABSTRACT Relapse of leukemia occurs in nearly half of patients after hematopoietic cell transplantation (HCT). While there are a growing number of therapeutic options for leukemic relapse after HCT, we lack a clinical assay capable of simultaneously detecting disease and triaging patients to treatment which will most likely benefit them. In this application, we propose to rigorously evaluate and employ novel single-cell genomic methods and their accompanying computational approaches to detect disease at low levels, inform mechanisms of relapse, and direct future therapy. In Aim 1, we will optimize computational methods for detecting natural genetic variation between donor and recipient, a diagnostic maneuver we believe will improve the sensitivity of detecting malignant cells after HCT. We will then validate these methods using samples from patients in a retrospective fashion. To provide insight into mechanisms of relapse, we have developed a novel molecular approach for identifying perturbations in HLA and related genes, a common means by which leukemia evades the immune system after HCT. In Aim 2, we will validate this method in a manner that explores the lower limit of detection for HLA- perturbed cells. Finally, in Aim 3, we will build on decades of work using flow cytometry to assess the heterogeneity of myeloid neoplasms by integrating our single-cell molecular measures with cell-surface immunophenotype. Using this approach, we seek to define common molecular signatures in leukemia-initiating cells (LICs), a subset of cells in myeloid neoplasms thought to be a chemo-resistant reservoir of leukemia. The proposed studies will establish a new method for surveillance of residual disease after HCT, which we believe will provide a deeper level of confidence and insight into leukemic relapse post-transplant. We expect these studies to form the foundational preclinical data for a single-cell genomics clinical assay capable of risk-stratifying patients with early evidence of leukemic relapse after HCT.