Clonal phylogeny and evolution of critical cytogenetic aberrations in multiple myeloma at single-cell level by QM-FISH

Abstract

Single-cell analysis is of significant importance in delineating the exact phylogeny of the subclonal population and in discovering subtle diversification. So far, studies of intratumor heterogeneity and clonal evolution in multiple myeloma (MM) were largely focused on the bulk tumor population level. We performed quantitative multigene fluorescence in situ hybridization (QM-FISH) in 129 longitudinal samples of 57 MM patients. All the patients had newly diagnosed and relapsed paired samples. An expanded cohort of 188 MM patients underwent conventional FISH (cFISH) to validate the cytogenetic evolution in bulk tumor level. Forty-three of 57 patients (75.4%) harbored 3 or 4 cytogenetic clones at diagnosis. We delineated the phylogeny of the subclonal tumor population and derived the evolutionary architecture in each patient. Patients with clonal stabilization had a significantly improved overall survival (OS) than those with other evolutionary patterns (median OS, 71.2 months vs 39.7 months vs 35.2 months vs 25.5 months, for stable, differential, branching, and linear patterns, respectively; P = .001). A high degree of consistency and complementarity across QM-FISH and cFISH was observed in the evaluation of cytogenetic evolution patterns in MM. Survival after relapse was greater influenced by the presence of high-risk aberrations at relapse (hazard ratio = 2.07) rather than present at diagnosis (hazard ratio = 1.55). This study shows that QM-FISH is a valuable tool to elucidate the clonal architecture at the single-cell level. Clonal evolution pattern is of prognostic significance, highlighting the need for repeated cytogenetic evaluation in relapsed MM.

Amp(1q) and tetraploidy are commonly acquired chromosomal abnormalities in relapsed multiple myeloma

“…Consistent with previous findings, 19,21 we found an increase in 1q copy number from diagnosis to relapse in a significant proportion of gain(1q)-positive tumors. A progression from 3 copies to ≥4 copies of 1q21, which has been recently associated with poor outcome, 19 was observed in 16/148 (11%) cases (Table S4). Additionally, an amp (1q) clone was acquired in seven patients who had 2 copies of 1q at first presentation.…”

“…In our cohort, similar to other reports, 35,36 we observed an increase in high‐risk CAs from presentation to relapse. The most commonly gained CAs at relapse were del(17p) and gain/amp(1q) in 13% and 12% of cases, respectively, in agreement with the literature (8–23% and 13–19% of cases, respectively) 19,21,28,37 . However, if only the first relapse is considered, the percentages might be lower.…”

“…This approach identified different evolution patterns after therapy: linear increase of abnormalities, losses and gains of abnormalities indicative of branching evolution, and clonal stability 15,17 . Longitudinal analyses by FISH provided evidence that clonal instability may be associated with an adverse outcome 18,19 . In particular, gain/amp(1q) and del(17p), which are among the most commonly acquired chromosomal abnormalities (CAs) at relapse, have been associated with an adverse prognosis, 19–22 underscoring the utility of repeated FISH testing during the disease course 23 .…”

Aberrant metabolic processes promote the immunosuppressive microenvironment in multiple myeloma

“…The development of MM has been classically viewed as a multistage process ( 4 ). However, the common initiating events, including multiple cytogenetic aberrant, with immunoglobulin heavy chain translocation and hyperdiploidy are insufficient to cause MM occurrence, as MGUS/SMM patients commonly harbor these abnormalities and show no clinical symptoms of MM ( 5 , 6 ). Intra-clonal heterogeneity has been observed at all stages of MM.…”

Tracking Clonal Evolution of Multiple Myeloma Using Targeted Next-Generation DNA Sequencing

“…We and others have previously shown that the evolution of cytogenetic aberrations over time has prognostic significance in MM [ 51 , 52 , 53 ]. Recently, Yan et al performed a single-cell analysis using quantitative multi-gene FISH on 129 longitudinally sampled specimens from 57 MM patients confirming that patients with stable cytogenetic structure achieve significantly longer survival than patients with evolutionary dynamics [ 54 ]. In our dataset, we identified only two patients (7%) with a stable CNV profile ( Table S1 ).…”