Genetic Disparities in Killer Cell Immunoglobulin-Like Receptors (KIR) and MHC Class I in Bone Marrow Failure Syndromes
Authors: Epling-Burnette P.K. , Painter Jeffrey S. , Lee H.-S. , Park Jong , Clemente Michael , O’Keefe Christine , Wei Tie-Ying , Wei Sheng , Maciejewski Jaroslaw , Loughran Thomas P. , Paquette Ron , List Alan F. , Djeu Julie Y 
Published: April 2020

Abstract
BACKGROUND: Activating (KIRDS) natural killer cell receptors (NKR) containing an intracellular ITAM activation domain are expressed on NK and some T-cells to invoke effector responses against MHC class I-deficient tumor cells and virus-infected cells. Effector cell activation is abrogated by inhibitory forms (KIRDL) of killer cell immunoglobulin-like receptors (KIR) that bind specific epitopes of MHC class I and prevent reaction against normal cells. Since HLA class I and KIR genes are not linked, KIR gene inheritance may occur in the absence of self HLA-class I alleles (i.e., KIR/HLA-class I mismatch) and thus increase the potential for generation of autoreactive T-cells in autoimmune-mediated bone marrow failure (BMF) syndromes such as LGL leukemia, aplastic anemia (AA), and myelodysplastic syndromes (MDS).
METHODS: Genotypic KIR analysis and HLA typing was performed on peripheral blood from 157 cases recruited by the Bone Marrow Failure Rare Disease Clinical Research Network and compared to 93 healthy controls. T-LGL leukemia was defined as increased numbers of CD3+, CD8+, or CD57+ lymphocytes with T-cell receptor clonality (N=35). The diagnosis of AA (N=47) and MDS (N=53) was established by bone marrow biopsy and 22 patients displayed BMF syndromes with overlapping characteristics or presence of paroxysmal nocturnal hemaglobuinuria (PNH).
RESULTS: Individual KIR gene content was similar in BMF cases and healthy controls although patients with 2–3 activating KIR genes were more common among cases compared to controls (33% in cases vs. 23% in controls, p=0.1). Antigens at the HLA-C locus were divided into two groups, HLA C1 Group with alleles encoding Ser-77-Asn80 (consisting of Cw01, 03, 07, 08, 12, 14 and 16) and HLA C2 alleles encoding Asn-77-Lys-80 (Cw02, 04, 05, 06, 15, 17, and 18). The frequency of a KIR2DL2 or KIR2DL3 positive haplotype in the absence of the corresponding C1 allele in BMF patients (C1 inhibitory mismatch) in marrow failure cases was 20% compared to 8% in controls (p=0.05). There was no difference in the frequency of KIR-C1 mismatch by disease diagnosis (20% BMF vs 21% AA, 16% MDS, and 19% LGL) but all were greater than controls. The presence of KIR2DL1 and the absence of the C2 allele was not statistically different between cases and controls. The activating counterparts of these inhibitory KIRs bind their putative HLA ligands but may also bind alternative activating ligands with similar structural determinants and/or immunoglobulin domains. We compared the frequencies of mismatches in the activating KIR genes and their ligands and found that the combined the presence of KIR2DS2 or KIR2DS3 and absence of the appropriate HLA C1 allele (KIR-C1 mismatch) was more frequent in BMF patients (12%) compared to that of healthy controls (0%) (p=0.007). The disease types of AA, MDS, and LGL leukemia displayed similar frequencies in KIR-C1 activating mismatches with 16%, 13%, and 6%, respectively (p=0.005 AA, p=0.01 MDS, and p=0.14 LGL leukemia). BMF syndromes have been linked to a T-cell dominant autoimmune process. KIR expression and other NKR expression in T-cells occurs after rearrangement of the TCR and thymic education suggesting that the KIR repertoire develops in memory T-cells. Since we have identified that clonal T-cells in LGL leukemia express a unique memory phenotype characterized by expression of CD45RA in the absence of the lymphoid homing receptor L-selectin (CD62L), we examined the phenotype of T-cells that express NK proteins including NKG2A, KIR2DL2/2DS2 (CD158b), KIR2DL1/DS1 (CD158a), and KIR3DL1 (NKB1). For all NKRs, only 0.5% ± .5 of naïve CD4+ T-cells expressed NKRs compared to 3% (p=0.01) and 6% (p=0.0003) of CD4+ effector and terminal effector memory cells, respectively. CD8+ T-cells with a naïve phenotype displayed higher NKR expression (2.6%±2.8) compared to CD4+ T-cells (0.006). The highest overall NKR expression compared to all other T cell types was present in CD8+ terminal effector memory cells (15.5%±15, p=0.006). Terminal effector memory cells (CD8+) are dramatically overrepresented in BMF syndromes particularly in association with bone marrow infiltration.
CONCLUSIONS: KIR expression in the absence of HLA interactions may skew the memory T-cell compartment favoring autoreactivity and impaired peripheral self-tolerance due to expansion of NKR positive T-cells in patients with BMF syndromes. Infiltration of KIR+ T-cells in tissues has been linked to organ dysfunction in several autoimmune diseases including rheumatoid arthritis and diabetes.