Disease Monitoring in Acute Myeloid Leukemia with CLEC2A qRT-PCR

CLEC2A, C-Type Lectin Domain Family 2 Member A, is a newly discovered AML-restricted antigen. Detailed characteristics, clinical correlations, and therapeutic potential of CLEC2A in AML is presented by Kirkey et. Al. (ASH 2023). CLEC2A is entirely silent in normal hematopoiesis and uniquely expressed in patients with KMT2A rearrangements, providing an ideal therapeutic target in this high-risk subtype of AML. To date, CLEC2A has not been implicated in hematologic malignancies and expression of CLEC2A is entirely absent from normal tissues other than minimal expression in the skin. In addition to its utility as a therapeutic target, CLEC2A provides a unique target for disease monitoring given its lack of expression in normal hematopoietic cells. Here we present a highly sensitive quantitative molecular assay for CLEC2A, establishing its utility for disease monitoring in patients with KMT2A-r AML.

In our efforts to evaluate CLEC2A expression and demonstrate the utility of using CLEC2A for disease monitoring in KMT2A-r, we developed a qRT-PCR assay using probes directed at exon 3 of the CLEC2A gene. The assay was optimized with RNA from the OCI-AML2 cells, validated to be CLEC2A-positive by flow cytometry and RNA from Kasumi-1 and K562 cells, both CLEC2A-negative by flow cytometry. We established the sensitivity of the assay through serial dilution of OCI-AML2 in a background of CLEC2A-negative Kasumi-1 or K562 cell RNA with concentrations ranging from 100% to 0.0001% OCI-AML2 RNA. The sensitivity assay demonstrated CLEC2A was detected at a level of 0.001% in both Kasumi-1 and K562.

Given the association of CLEC2A with KMT2A-r AML, we evaluated the prevalence of CLEC2A as assessed by qRT-PCR. We screened diagnostic specimens from a large cohort of patients enrolled on recent COG Phase III clinical trials (ages 0-29) with and without KMT2A fusions to establish prevalence of CLEC2A expression. Using our CLEC2A qRT-PCR assay we evaluated diagnostic specimens from 122 patients with (N=76) and without (N=46) KMT2A-r, in addition to RNA from 8 normal bone marrow (NBM) samples, as controls and validated CLEC2A was entirely absent in NBM with median expression 0.13 copies per 1e ⁴ GUSB, figure 1A. Of evaluable samples, CLEC2A was detected in 65 of 76 (85%) KMT2A-r cases with a median expression of 317.45 copies per 1e ⁴ GUSB (range 0.03 - 21134.21 copies per 1e ⁴ GUSB). CLEC2A was detected in 21 of 46 (45%) non-KMT2A-r cases tested with a median expression of 1.37 copies per 1e ⁴ GUSB (range 0 - 1204.84 copies per 1e ⁴ GUSB). Further evaluation of KMT2A fusion partner showed that CLEC2A was detected in 100% of MLLT4 (N=6/6), 83.3% in MLLT10 (N=20/24), 72.7% of ELL (N=8/11), and 42.9% in MLLT3 (N=21/49). While CLEC2A expression was seen in both KMT2A-r and non-KMT2A-r AML patients, CLEC2A levels were significantly higher in KMT2A-r patients compared to non-KMT2A-r and NBM samples (p < 0.0001).

Since CLEC2A is expressed in AML with no expression in normal hematopoietic cells, we hypothesized that monitoring CLEC2A via qRT-PCR throughout treatment (i.e., at diagnosis, at end of induction [EOI], at relapse) would provide added specificity to traditional flow cytometric disease monitoring. Using paired RNA samples from patients across multiple timepoints, we evaluated the change in CLEC2A expression throughout treatment, figure 1B. Patients with high CLEC2A expression at diagnosis (mean 1670 copies per 1e ⁴ GUSB, n=39) had decreased expression at EOI (mean 199 copies per 1e ⁴ GUSB, n=45) indicating treatment response, however high CLEC2A expression was seen at time of relapse (mean 1849 copies per 1e ⁴ GUSB, n=13) with CLEC2A expression preserved at relapse for all patients. qRT-PCR was able to detect CLEC2A expression in 7 patients at EOI who were in a morphologic CR with 6/7 (86%) patients being MRD-negative, further highlighting the increased sensitivity of CLEC2A qRT-PCR.

Here we describe qRT-PCR monitoring of CLEC2A, a novel AML-restricted antigen highly enriched in KMT2A-r AML, provides added specificity and sensitivity to traditional flow cytometric MRD analysis. CLEC2A monitoring via qRT-PCR can be used to assess disease response throughout treatment and evaluate impending relapse as CLEC2A expression is retained at relapse. Additionally, qRT-PCR monitoring of CLEC2A can be incorporated in to pre- and post-HSCT disease evaluations similarly to qRT-PCR analysis of other known high-risk fusions such as NUP98-NSD1 fusions.