Enhanced ctDNA Profiling Reveals Molecular Determinants of Response and Resistance in Relapsed and Refractory Mantle Cell Lymphoma (NLG‐MCL7‐VALERIA)

Abstract

Introduction: Deciphering molecular determinants of response to targeted treatments and early detection of refractoriness in patients with relapsed and refractory (R/R) mantle cell lymphoma (MCL) could individualize treatment, improve outcomes and limit unnecessary toxicities. Circulating tumor DNA (ctDNA) allows non-invasive profiling and measurement of treatment responses. Yet, increased sensitivity for detection and distinction from confounding biological signals are warranted. Enhanced ctDNA detection can be achieved using duplex sequencing or tracing of phased variants. Poor recovery of complementary strands and low number of phased variants limit the feasibility of these approaches separately in MCL. Methods: Thus, we developed and optimized a hybrid ctDNA sequencing platform, which combines strand- and phasing-aware error correction methods for improved specificity and sensitivity of non-invasive B-cell lymphoma profiling, quantification and detection (Figure 1A). We applied this platform to profile ctDNA in serial plasma samples from 59 patients with R/R MCL treated with lenalidomide, venetoclax and rituximab in the Nordic phase II trial (NLG-MCL7; VALERIA). We compared the results with outcomes and real-time quantified PCR (RQ-PCR, ‘Euro-Minimal Residual Disease (MRD’)) data from bone marrow (BM) and peripheral blood (PB) samples that guided therapy in the trial (Figure 1B). Results: Joint analysis of targeted sequences from pretreatment tumor, PB, BM, and plasma samples revealed MCL genotypes for ctDNA tracing even in the patients who failed primer designs for Euro-MRD (Figure 1C). Comparison between genotyping of samples from different compartments from individual patients mitigated confounding clonal hematopoiesis background and revealed spatially-confined MCL mutations. TP53 mutated MCL conferred resistance to therapy, whereas SMARCA4 mutations translated into durable molecular remission (Figure 1D-E). Elevated pretreatment ctDNA concentration was associated with multiple clinical risk factors, leukemic disease, and poor outcome (Figure 1F). After six months of therapy, ctDNA levels dropped in all studied patients. The responses in the ctDNA were highly concordant with concomitant Euro-MRD and extended to patients not evaluable by RQ-PCR. Notably, contrasting ctDNA clearance, the analysis of the post-therapy cell-free DNA revealed positive selection of clonal hematopoiesis drivers following therapy exposure, such as TP53 mutations in 77% of the patients. The research was funded by: Academy of Finland, iCAN Flagship, University of Helsinki, Helsinki University Hospital, Finnish Cancer Organisation, Sigrid Juselius Foundation and Abbvie. Keywords: diagnostic and prognostic biomarkers, liquid biopsy, molecular targeted therapies No conflicts of interests pertinent to the abstract.