Use of killer cell immunoglobulin-like receptor genes as early markers of hematopoietic chimerism after double-umbilical cord blood transplantation.

It has been established that hematopoietic chimerism after double umbilical cord blood transplantation (dUCBT) can predict disease relapse and detect potential engraftment failure. The use of a precise method to evaluate residual host hematopoiesis is imperative because it has been reported that the risk of relapse is higher in patients with mixed chimerism. Up to now, real-time quantitative polymerase chain reaction (PCR) of single nucleotide polymorphism (SNP) markers remains the best method to accurately assess and quantify chimerism. However, this method may be limited by the lack of available in-house SNP discriminant markers between both umbilical cord blood (UCB) units and patients and may not be reliable to assess early chimerism status after dUCBT. In this context, additional approaches are needed. Natural killer (NK) cells are the first population to reconstitute the patient’s hematopoietic system following hematopoietic stem cell transplantation, before T lymphocytes, and we previously reported that cord blood NK cells express killer cell immunoglobulin-like receptors (KIR). Here, we investigated KIR genes as additional markers for early chimerism assessment after dUCBT. KIR gene content varies between individuals who can exhibit seven to fourteen inhibitory and activating KIR genes, defining multiple KIR genotypes. This broad KIR gene polymorphism should be useful as chimerism markers in the context of dUCBT. In order to determine which UCB unit dominates engraftment, KIR genotyping was performed on 40 patients who underwent dUCBT at Nantes CHU, using a multiplex sequence-specific primer-PCR method on day 90 after dUCBT and was compared to KIR genotyping in patients and in UCB units prior to dUCBT. The presence or absence of each KIR gene among 14 studied in patients, UCB units and recipients led us to determine the identity of cells reconstituting recipient hematopoiesis. As illustrated in Figure 1A, recipient #11 was characterized by the absence of KIR2DL2 and KIR2DS2 genes, which were present in this patient before dUCBT. Interestingly, KIR2DL2 and KIR2DS2 were absent in UCB1, but present in UCB2, highlighting that hematopoietic reconstitution resulted from only one UCB unit (unit 1) in this patient (Figure 1A). Phenotypic analysis of cord blood KIR NK cells before dUCBT and recipient KIR NK cells at day 60 after dUCBT using available anti-KIR monoclonal antibodies allowed discrimination of inhibitory and activating KIR expression between the two UCB units (Figure 1B) and confirmed KIR genotyping results. In particular, UCB1 NK cells did not express KIR2DS1 and KIR2DL2, unlike NK cells from UCB2. Moreover, KIR3DL1 was only expressed on NK cells from UCB1. We observed that the recipient’s KIR NK cells on day 60 after dUCBT had the same KIR expression profile as NK cells from UCB1, with expression of KIR3DL1 and absence of KIR2DS1 and KIR2DL2, confirming engraftment of patient #11 with one full dominant UCB1. Analysis of KIR genotyping also allows mixed chimerism to be detected, as illustrated in Figure 1C for patient #13 who presented the KIR2DL5A allele and the deleted non-expressed KIR2DS4 allele (i.e. 1D) before dUCBT. Both UCB units had the KIR2DL5B allele and expressed KIR2DS4. Recipient #13 had both A and B KIR2DL5 alleles and KIR2DS4, in particular, highlighting a mixed chimerism between the patient and one UCB unit. Although rare, mixed chimerism between both UCB units may also be detected using KIR genotyping (Online Supplementary Figure S1). In several other cases, analysis of KIR genotype after dUCBT highlighted engraftment failure and autologous patient reconstitution, as illustrated in recipient #33 (Figure 1D). KIR genotyping was performed in all recipients and was focused on discriminating KIR genes that allowed us to assess hematopoietic chimerism status by their presence or absence (Online Supplementary Table S1). Based on the calculated frequencies of each discriminating KIR gene, we highlight the major implication of three inhibitory and all activating KIR genes (Figure 2A). Overall, qualitative chimerism analysis at day 90 after dUCBT using KIR markers indicated full UCB unit reconstitution (60%), mixed patient/UCB unit reconstitution (20%) and autologous recovery (7.5%) in the recipients included in this study (Figure 2B). However, KIR genotyping did not allow chimerism status to be assigned in the five remaining dUCBT, which were therefore called “indeterminate” (Figure 2B). Although KIR genotyping is a reproducible and reliable method as initially reported, even using a small amount of cord blood DNA (Online Supplementary Figure S2), the patients, UCB units and recipients had the same KIR genotype in these five cases, thus preventing any chimerism assessment using KIR markers. Moreover, KIR genotyping analysis of five other dUCBT revealed mixed chimerism, which was discordant with the conventional SNP analysis, being evaluated as “full donor chimerism” (n=4) or “patient reconstitution” (n=1) as illustrated for patient #15 (Figure 2C). Overall, 31 out of 40 dUCBT (3 dUCBT with patient reconstitution, 3 dUCBT with mixed chimerism and 25 dUCBT with full donor engraftment) had concordant results with the conventional SNP-based analysis (Figure 2D). For some dUCBT with available DNA (n=6), we complemented the KIR genotyping with HLA class I allele typing to provide additional information since numerous HLA class I incompatibilities between UCB units and patients are frequently encountered in the context of dUCBT. Of note, HLA class I genes presenting large allelic polymorphisms are useful markers to re-assess the “indeterminate” dUCBT and the few discordant results between KIR genotyping and the SNP–based method. Our analysis based on KIR genotyping, with secondary complementary HLA class I allele typing, applied in a few cases, allowed chimerism status to be accurately determined in 100% of patients in full concordance with conventional approaches (Figure 2E). Indeed, as illustrated in Figure 2F, KIR genotyping of recipient #39 on day 90 did not allow chimerism status to be assigned. However, using HLA-B typing on day 90 this recipient was typed as HLA-B*35:03, thus demonstrating full UCB1 engraftment, which correlated with the data from the conventional SNP method. In our dUCBT cohort, HLA class I typing was not appropriate as a single method for assessing chimerism because there was often only one discriminating HLA class I allele between both UCB units and the patient (Online Supplementary Table S2). Importantly, HLA class I DNA typing combined with other techniques has already been reported in haploidentical hematopoietic stem cell transplantation to determine chimerism status. More broadly, allelic KIR typing could also be a complementary tool to compare both UCB units and the recipient’s genotypes. Indeed, inhibitory KIR present high allelic polymorphism, such as KIR3DL1, which also affects KIR3DL1 expression. The study of allele poly-