Aplastic Anemia is a disease that results in the destruction of hematopoietic stem cells in the bone marrow by the immune system. Although the exact mechanism of this pathology is not fully understood, the prevailing model proposes that the immune system and specifically T cells are responsible for this destruction. Pediatric and adult aplastic anemia, while clinically similar in their presentation may in fact be representative of different subsets of a spectrum of aplastic anemia. Our group and others have shown that adult patients with aplastic anemia have a tendency to develop cell populations that are predisposed to myelodysplastic syndrome and leukemia. In the pediatric population however, we found that patients tend to develop cell populations that have mutations in certain genes (i.e. PIGA and HLA) which we believe are necessary for the immune system to recognize and kill the stem cells. In this way pediatric patients have a mechanism through which they can evade destruction by the immune system, and regenerate their stem cell population. We propose extending these studies in a bigger pediatric patient cohort to show which specific genetic mutations are protective to the patient. We also want to further our studies to show that pediatric patients that develop these immune escape variants, do not have an increased probability of progressing to myelodysplastic syndrome or leukemia. Furthermore, we aim to show that in patients with both immune escape variants and myelodysplastic changes, these mutations occurred independently of one another. These data can help determine which pediatric patients are most suitable for treatment with immune suppressive therapy versus bone marrow transplantation. They will also open new avenues for development of precision based targeted therapeutics in the future.
Recently our lab and others have discovered that loss of a copy of chromosome 6p from one parent with replacement by duplicating the other parent’s chromosome (termed loss of heterozygosity) is one of the most common genetic changes in pediatric-onset aplastic anemia. This area of chromosome 6p codes for the human leukocyte antigens (HLA), which assist in presenting proteins to the immune system. We also describe other genetic changes in this area termed inactivating somatic mutations, which cause dysfunction of these same HLA proteins in pediatric acquired aplastic anemia. These two changes along with genetic changes in the PIGA gene (causing Paroxysmal Nocturnal Hemoglobinuria) comprise the most common genetic alterations arising in patients with pediatric-onset aplastic anemia. We hypothesize that unlike adultonset acquired aplastic anemia in which genetic changes usually involve genes that are associated with leukemia or myelodysplastic syndrome, these pediatric genetic changes represent a method for stem cells to escape the autoreactive T cells that are trying to destroy them. Therefore these genetic changes in pediatric patients may actually be beneficial and protective from acquiring the leukemia and/or myelodysplastic associated genetic changes. In order to test this hypothesis we have undertaken comprehensive genomic profiling of: copy number variants using SNP-arrays, inactivating somatic mutations of HLA using next generation sequencing and analysis of mutations (genetic changes) in leukemia/myelodysplastic associated genes using our verified somatic heme panel (consisting of 99 known leukemia/myelodysplastic associated genes). We aim to analyze the data of 100 patients (70 pediatric and 30 adult) in order to have a large enough sample size to deduce if genetic HLA changes/loss of heterozygosity and/or genetic PIGA changes represent a distinct pool of alterations that are driven by immune escape pressures. Should this be the case, it would provide useful biomarkers that will help inform treatment options for pediatric patients with acquired aplastic anemia. In this progress report we present the data from 44 patients that have undergone sequencing (26 pediatric onset acquired aplastic anemia and 18 adult acquired aplastic anemia). We have an additional 18 pediatric patients that have been sequenced and are currently
being analyzed using our bioinformatics pipeline. Thus far, our data have been consistent with our hypothesis in the pediatric cohort in that patients with genetic changes in known leukemia/myelodysplastic associated genes do not have concurrent genetic changes in their HLA and/or PIGA regions. The same has not been true for adult patients with aplastic anemia. In the second year of this project we will continue our comprehensive genomic analysis so that we have enough statistical information to definitively decide if HLA and/or PIGA mutations represent distinct and independent mechanisms for immune escape and if so do they offer prognostic and therapeutic information for the pediatric patient population.