Clonal Hematopoiesis By HLA Class I Allele-Lacking Hematopoietic Stem Cells and Concomitant Aberrant Stem Cells Is Rarely Associated with Clonal Evolution to Secondary Myelodysplastic Syndrome and Acute Myeloid Leukemia in Patients with Acquired Aplastic Anemia

[Background] HLA-class I allele-lacking (HLA[-]) leukocytes are detected in approximately 30% of patients with acquired aplastic anemia (AA), and are thought to represent the involvement of cytotoxic T lymphocyte attack against hematopoietic stem cells (HSCs) in the development of AA, based on the high response rate to immunosuppressive therapy (IST) in patients with such aberrant leukocytes. Similar to glycosylphosphatidylinositol-anchored protein (GPI-AP)-deficient (GPI[-]) leukocytes in patients with paroxysmal nocturnal hemoglobinuria (PNH), HLA(-) leukocytes in AA patients are often clonal or oligoclonal and expand to account for more than 50% of the total leukocytes. Despite such overwhelming proliferation, somatic mutations in driver genes as well as telomere shortening that portend clonal evolution are rarely detected in HLA(-) granulocytes, suggesting the genetic stability of HLA(-) HSCs and the persistence of the immune pressure on HSCs that favors expansion of HLA(-) HSCs (Imi, et al. Blood Adv). However, recent studies from the United States have shown a higher incidence of clonal evolution to secondary myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) in AA patients with HLA(-) leukocytes than in those without such leukocytes, a finding inconsistent with the results of our previous study. Given the high prevalence of HLA(-) leukocytes in AA patients, it is critical to determine whether or not the presence of the aberrant leukocytes is associated with clonal evolution. We therefore addressed this issue by studying the prognosis of a large number of AA patients with or without HLA(-) leukocytes who had been followed for a long term period. We also studied the clonal composition of granulocytes in AA patients with HLA(-) cells, wherein aberrant clones other than HLA(-) cells might be responsible for clonal evolution to MDS/AML.

[Methods] We retrospectively analyzed the clinical characteristics of 633 AA patients and peripheral blood samples were examined for the presence of HLA(-) leukocytes using a high-sensitivity flow cytometry (FCM) assay, droplet digital PCR, single-nucleotide polymorphism arrays, or next generation sequencing (NGS) between 2010 and 2020. GPI(-) cells were detected using a high-sensitivity FCM assay as previously described.

[Results] HLA(-) granulocytes were detected in 127 (20.1%) of the 633 patients with a median clone size of 16.9% (range, 0.04%-100%); the aberrant granulocytes accounted for greater than 50% of the total granulocytes in 29 (22.8%) of 127 patients. Eighty-nine (70.0%) of the 127 patients possessed aberrant clones other than HLA(-) clones, which included 0.005% to 91.6% GPI(-) cells (n=86), del(13q) cells (n=3), t(1;10) cells (n=1), t(9;13) cells (n=1), inv12 cells (n=1), and trisomy 8 cells (n=1). The prevalence of GPI(-) cells was not significantly different between patients with and without HLA(-) cells (67.7% vs 65.4%). Eighty-five of 102 (83.3%) patients with HLA(-) cells responded to IST, whereas 231 of 318 (72.6%) without HLA(-) cells responded (p<0.05). In 13 patients who had been in hematological remission for more than 7 years, HLA(-) cells and other concomitant aberrant cells accounted for >90% of granulocytes, suggesting that these few escape clones were enough to sustain the hematopoietic function of the patients. The prognosis survey revealed no clonal evolution to MDS/AML in any of the 127 AA patients with HLA(-) leukocytes after a follow-up period of the median 5 years. In contrast, 15 of 234 (6.4%) patients without HLA(-) cells who were trackable evolved to MDS/AML during a median 5 year follow-up.

[Conclusions] The presence of HLA(-) leukocytes and concomitant aberrant clones was not associated with clonal evolution to MDS/AML in Japanese AA patients, even in those possessing a large (>50% of the total granulocyte) HLA(-) cell population. The discrepancy between our results and the data from the United States may be due to the difference in the race and mechanism underlying HLA loss. These data suggest that HSC clones that escape immune attack, such as HLA(-) and GPI(-) clones, are healthy enough to support hematopoiesis for a long term in AA patients.