Somatic HLA mutations expose the role of class I–mediated autoimmunity in aplastic anemia and its clonal complications

Abstract

Acquired aplastic anemia (aAA) is an acquired deficiency of early hematopoietic cells, characterized by inadequate blood production, and a predisposition to myelodysplastic syndrome (MDS) and leukemia. Although its exact pathogenesis is unknown, aAA is thought to be driven by Human Leukocyte Antigen (HLA)-restricted T cell immunity, with earlier studies favoring HLA class II-mediated pathways. Using whole exome sequencing (WES), we recently identified two aAA patients with somatic mutations in HLA class I genes. We hypothesized that HLA class I mutations are pathognomonic for autoimmunity in aAA, but were previously underappreciated because the Major Histocompatibility Complex (MHC) region is notoriously difficult to analyze by WES. Using a combination of targeted deep sequencing of HLA class I genes and single nucleotide polymorphism array (SNP-A) genotyping we screened 66 aAA patients for somatic HLA class I loss. We found somatic HLA loss in eleven patients (17%), with thirteen loss-of-function mutations in HLA-A*33:03, HLA-A*68:01, HLA-B*14:02 and HLA-B*40:02 alleles. Three patients had more than one mutation targeting the same HLA allele. Interestingly, HLA-B*14:02 and HLA-B*40:02 were significantly overrepresented in aAA patients, compared to ethnicity-matched controls. Patients who inherited the targeted HLA alleles, regardless of HLA mutation status, had a more severe disease course with more frequent clonal complications as assessed by WES, SNP-A, and metaphase cytogenetics, and more frequent secondary MDS. The finding of recurrent HLA class I mutations provides compelling evidence for a predominant HLA class I-driven autoimmunity in aAA, and establishes a novel link between aAA patients’ immunogenetics and clonal evolution.

Somatic mutation of HLA‐DRB1*04:03 in a patient with myelodysplastic syndrome at diagnosis

“…In one study, about 3% to 4% of LOH in the HLA region has been reported among AML patients at diagnosis . In contrast, a somatic HLA loss caused by chromosome 6p LOH or HLA gene mutation was found in 17% of aplastic anemia . As a result of the search for HLA mutations in hematologic malignancies, in addition to LOH for all or part of one HLA haplotype on chromosome 6p, we identified 11 published cases with HLA somatic mutation: 3 acute myelogenous leukemia (AML) with A*02:01 , 1 AML with B*15:01 , 1 acute lymphoblastic leukemia (ALL) with A*03:01 , 1 ALL with A*24:02 , 1 ALL with B*39:01 , 1 chronic lymphocytic leukemia with B*07:02 , 1 non‐Hodgkin lymphoma (NHL) with B*35:01 , 1 NHL with DRB1*13:01 , 1 NHL with DQB1*03:01.…”

Molecular pathogenesis of acquired aplastic anemia

“…Somatic HLA class 1 loss was correlated with a more severe disease course and more frequent evolution to MDS. In contrast to the findings in this report, previous other studies employing WES did not identify HLA class mutations probably due to lower‐sensitivity detection strategies employed in the latter . These recent findings further strengthen the role of HLA class I‐mediated autoimmunity in AA pathogenesis.…”

“…These recent findings further strengthen the role of HLA class I‐mediated autoimmunity in AA pathogenesis. Among the many identified HLA risk alleles, a version of the HLA‐B gene called HLA‐B*‐ 40:02 plays a critical role in AA pathogenesis . Lack of allele expression of HLA‐B* 40:02, either by loss of heterozygosity of 6p chromosome (6pLOH) or due to various SMs, allows for the escape of HSCs from the attack of cytotoxic T cells that are specific to autoantigens presented by the lacked HLA class I alleles.…”

Diagnosis and Treatment of Aplastic Anemia

“…The presence of even a subclinical PNH clone has been found to correlate with an improved response to IST [75–79, 70]. In contrast to PNH, the prognostic impact of somatic HLA loss is less clear [71, 72], with emerging data suggesting that HLA loss may be best viewed as a marker of a higher immune pathogenicity of a patient’s inherited HLA alleles [74, 73]. …”