Deep MRD profiling defines outcome and unveils different modes of treatment resistance in standard- and high-risk myeloma

Abstract

Patients with multiple myeloma (MM) carrying high-risk cytogenetic abnormalities (CA) have inferior outcome despite achieving similar complete response (CR) rates when compared to cases with standard-risk CA. This questions the legitimacy of CR as treatment endpoint for high-risk MM, and represents a biological conundrum regarding the nature of tumor reservoirs persisting after therapy in patients with standard- and high-risk CA. Here, we used next-generation flow (NGF) to evaluate measurable residual disease (MRD) in MM patients with standard- (N=300) vs high-risk CA (N=90) enrolled in the PETHEMA/GEM2012MENOS65 trial (NCT01916252), and to identify mechanisms determining MRD resistance in both patient subgroups (N=40). The 36-month progression-free and overall survival rates were higher than 90% in patients with undetectable MRD, with no significant differences (P≥0.202) between cases having standard- vs high-risk CA. Persistent MRD resulted in median progression-free survival of approximately three and two years in patients with standard- and high-risk CA, respectively (P<0.001). Further use of NGF to isolate MRD followed by whole-exome sequencing of paired diagnostic and MRD tumor cells, revealed greater clonal selection in patients with standard-risk CA, higher genomic instability with acquisition of new mutations in high-risk MM, and no unifying lost or acquired genetic abnormalities driving MRD resistance. Conversely, RNA sequencing of diagnostic and MRD tumor cells uncovered the selection of MRD clones with singular transcriptional programs and ROS-mediated MRD resistance in high-risk MM. Our study supports undetectable MRD as treatment endpoint for MM patients with high-risk CA and proposes characterizing MRD clones to understand and overcome MRD resistance.

Multiple Myeloma: Heterogeneous in Every Way

“…Single-cell RNA-seq confirmed an intratumor transcriptional and copy number alteration heterogeneity, which can be roughly deduced from the transcriptome [26]. Additionally, scRNA-seq can be theoretically applied to the MRD endpoint and provide information about clonal evolution and resistance to treatment mechanisms [23,28]. For patients with detectable residual disease, driver genes (such as CCND1, NSD2 and FRZB) were often found expressed equivalently before and after treatment.…”

“…MM is a clonal disease with a genomic landscape which differs between patients but also in the same tumor. Mutational analysis confirmed the diversity in MM; whole-exome sequencing highlighted an average number of subclones in the same patient of five [23]. This mean value is probably underestimated because the threshold for the subclones' detection was at least 10%.…”

“…A recent study showed that MRD can overcome the initial risk stratification. Despite lower rates of undetectable MRD in high-risk patients, those who achieved it had the same outcomes than standard risk patients with an undetectable MRD [23]. However, for patients with a persistent MRD, high-risk patients had poorer outcomes than standard risk ones.…”

“…As with many cancers, clonal PCs under selection pressure can escape the treatment by selecting fitter subclones and/or acquiring new mutations. Genomic instability seems to be higher for high-risk patients [23]. Hypothetically, we could imagine a therapy adapted based on the risk assessed at the beginning, essentially based on CAs, and during the follow-up, with an adjustment according to the MRD status, to avoid the persistence of these cells that could be responsible for early relapse.…”

Risk and Response-Adapted Treatment in Multiple Myeloma

“…In addition to its prognostic impact, MRD highlighted the notion of dynamic risk in MM. Indeed, achieving undetectable MRD may also abrogate some adverse risk factors, such as high-risk cytogenetics and ISS, as shown by Perrot et al [65], or R-ISS, as shown by [66]. Patients displaying these adverse factors and who achieve undetectable MRD, although it is less likely (in particular in the del(17p) subgroup), have similar outcomes than standard-risk patients with undetectable MRD.…”