Secondary Cytogenetic and Molecular Genetic Abnormalities in Newly Diagnosed Multiple Myeloma Patients

Background: Multiple myeloma (MM) is subdivided into groups based on recurrent cytogenetic abnormalities (CA). In addition, secondary CA and mutations (MUT) have been described that are associated with disease progression.

Aim: To comprehensively evaluate secondary alterations in MM subgroups.

Methods: Bone marrow samples (collected from 06/22 to 01/24) of 807 newly diagnosed multiple myeloma (NDMM) patients (females: 45%, median age 70 years, range 30-94) were analyzed. Plasma cells were enriched (CD138+ MACS) and interphase FISH as well as targeted NGS assessing 66 genes and copy number alterations were performed. Statistical significance was set to p<0.05 and was analyzed with Fisher’s exact or binomial test followed by Benjamini-Hochberg procedure as appropriate.

Results: According to the 2022 international consensus classification patients were hierarchically assigned to 4 groups: Group 1 (n=338, 41%): IGH translocation (t(11;14) (n=195), t(4;14) (n=84), t(14;16) (n=32), t(6;14) (n=19), t(14;20) (n=8)); group 2 (n=377, 46%): hyperdiploidy (≥47 chromosomes (chr) with ≥1 trisomy of 3, 5, 7, 9, 11, 15, 19, 21); group 3 (n=60, 7%): hypodiploidy (≤45 chr with ≥1 monosomy of 13, 14, 16, 22); group 4 (n=32, 4%): not otherwise specified.

In the total cohort, del(1p) was detected in 10.4% of cases. A higher frequency was found in group 3 (40.7%; p<0.001) and a lower frequency in group 1 (4%; p<0.001). However, within group 1 the frequency of del(1p) was heterogeneous ranging from 0.5% in t(11;14) to 10% in t(4;14) (0.5% vs. 10%; p<0.001). The frequency of +1q in the overall cohort was 42% with a significantly higher frequency observed in group 3 (63%; p<0.01). Within group 1, the frequency was lower in t(11;14) patients (26%; p<0.001) and higher in patients with t(4;14) and t(14;16) (66% and 72%; for both p<0.01). Patients in group 3 had a higher frequency of del(17p) (25%; p<0.05) than the total cohort with 11.7% (group 1: 10%, group 2: 11%, group 4: 9%). The frequency of MYC rearrangements (MYC-R) in the entire cohort was 13%. MYC-R were more frequent in group 2 (20.4%; p<0.001) and less frequent in group 1 (7%; p<0.001).

At least 1 MUT was found in 560/807 (70%) patients (median number of MUT/patient: 1 [range: 1-8]). A total of 981 MUT were detected affecting 51 of 66 analyzed genes. Typically MM-related MUT affected KRAS (n=227, 23%; median VAF (mV) 17%), NRAS (n=183, 19%; mV 17%), TP53 (n=80, 8%; mV 22%) and BRAF (n=58, 6%; mV 8%). Further frequently mutated genes with a MUT frequency of ≥1% were DNMT3A (n=85, 9%; mV 5%), DIS3 (n=78, 8%; mV 18%), TET2 (n=68, 7%; mV 7%), IRF4 (n=25, 3%; mV 23%), ATM (n=24, 3%; mV 30%), KLHL6 (n=14, 1%; mV 25%), CREBBP (n=13, 1%; mV 12%) and SF3B1 (n=10, 1%; mV 9%). None of the mutated genes was significantly associated with any of the cytogenetically defined MM groups. DNMT3A, TET2 and SF3B1 are known to be mutated in myeloid malignancies. In subsets of patients we showed that these mutations either occur within the MM clone or in independent probably myeloid clones.

Significant associations were observed between MUT and secondary CA regardless of MM groups: DIS3 MUT were more frequent in patients with +1q than without (14% vs. 5%; p<0.01). More TP53 MUT were detected in patients with del(1p) than in patients without (21% vs. 6%; p<0.01), in patients with del(17p) compared to patients without (43% vs. 3%; p<0.001) and in patients with del(13q) than in patients without (11% vs. 4%; p<0.05). In contrast, less NRAS MUT were found in patients with del(13q) than in patients without (15% vs. 25%; p<0.05).

A total of 80 TP53 MUT were detected in 60 patients. 40 of these patients had a del(17p) and one had a 17p CN-LOH (biallelic TP53 inactivation). Of the remaining 19 patients, 3 patients had 2 to 4 TP53 MUT.

Conclusions: MM group-defining CA were found to be associated with distinct secondary CA but not with distinct MUT. High-risk secondary CA del(1p) and +1q occurred more frequently in patients with CA associated with a poor prognosis such as t(4;14) and t(14;16). Furthermore, all of the investigated secondary CA occurred more frequently in hypodiploid patients. MUT in TP53, NRAS and DIS3 were associated with distinct secondary CA. Our data suggest that future studies should undertake a comprehensive analysis of cytogenetic and molecular genetic features to decipher which of these features are actually associated with poor prognosis – the primary or the secondary lesions – to allow to tailor treatment accordingly.