Multiple Myeloma with a Deletion of Chromosome 17p: TP53 Mutations Are Highly Prevalent and Negatively Affect Prognosis

Background

Deletion of chromosome 17p (del17p) is detected in 10% of multiple myeloma (MM) patients at diagnosis and is associated with both a dismal prognosis and increased prevalence after treatment. Even though this suggests that it might be a driver of disease progression, relatively little is known about the genomic landscape of these tumors. With this study, we aimed to identify recurrent aberrations in a large cohort of del17p MM patients and to assess their prognostic value within this patient group.

Methods

The study design consisted of a discovery phase and a validation phase. For the discovery phase, 44 newly diagnosed MM (NDMM) patients were included with a del17p in at least 50% of plasma cells, as detected with fluorescent in situ hybridization (FISH). From 12 del17p patients, 2 or 3 tumor samples were available to analyze clonal evolution during disease progression. DNA was isolated from peripheral blood and CD138+ enriched bone marrow mononuclear cells, followed by a custom capture of the whole exome, Chr17p and the IgH, Igk, IgL and MYC regions (SeqCap EZ Exome Plus, Nimblegen) and paired-end sequencing. Significantly mutated genes were determined with MutSigCV and significantly deleted or amplified genomic regions with GISTIC2. Single nucleotide variants (SNVs) in TP53, FAM46C, KRAS, NRAS, DIS3 and BRAF were validated using a custom amplicon panel (TruSeq Custom Amplicon Assay v1.5, Illumina), followed by deep sequencing on a MiSeq System.

Findings were validated in a cohort of 463 NDMM patients of the UK Myeloma XI trial, from which whole exome sequencing data were available for paired tumor and germline DNA (Walker et al. - J Clin Oncol 2015). All samples in both the discovery and the validation cohort were reanalyzed with one bioinformatic pipeline, from alignment to variant calling. The copy number status of TP53 was determined with Sequenza, followed by selection of del17p samples after manual inspection of the results.

From a third cohort of 233 MM patients with progressive disease (PDMM) treated at the University of Arkansas for Medical Sciences (UAMS), 406 cancer-related genes were paired-end sequenced from tumor DNA with the FoundationOne Heme assay (He et al. - Blood 2016).

Results

In the discovery cohort, we identified a commonly deleted region (CDR) on Chr17p of 235 kb, in which one or more somatic, nonsilent aberrations (SNSA) in TP53 were detected in 25/44 (57%) patients (adj. p<1x10e-10; n=18 missense, n=8 nonsense, n=2 splicing). Other genes in the CDR on Chr17p lacked any SNSAs. Besides TP53, we found FAM46C and KRAS to be significantly mutated. RB1, TRAF3 and FAM46C were significantly deleted. Del17p MM patients from whom sequential tumor samples were analyzed, showed a stable pattern for TP53 mutational status once a del17p had been acquired.

In the UK Myeloma XI cohort, we detected a del17p in 32/463 (7%) of patients. Of these, 15/32 (47%) had an SNSA in the remaining allele.

Follow-up data were available of 73/76 del17p NDMM patients from both cohorts (n=46 transplant-eligible (TE), n=27 nontransplant-eligible (NTE)), with a median follow-up time of 17 months. TP53 mutated patients had a worse overall survival (OS) than TP53 wildtype patients (p=0.02), of which the strongest effect on OS was seen of TP53 missense mutations (p<0.001). Of note, stratifying patients between TE and NTE resulted in a highly significant effect of TP53 missense mutations on both OS (p<0.0001, median OS 18 months versus not reached) and progression free survival (PFS) (p<0.001, median PFS 12 months versus not reached) in the TE cohort, whereas there was no significant effect on PFS and OS in the NTE cohort.

We went on to look in the FoundationOne cohort of PDMM patients and detected a del17p in 37/233 (16%) of patients and an SNSA in TP53 in 25/37 (68%) of del17p PDMM patients, which is a higher rate than in the 2 NDMM cohorts.

Conclusions

(1) TP53 is somatically mutated in half of del17p MM patients at diagnosis, validated in 2 independent cohorts, and this percentage is higher in del17p MM patients at progression.

(2) Particularly TP53 missense mutations have a significant, negative impact on both PFS and OS in del17p MM patients.

(3) The rest of the genomic landscape of del17p MM is characterized by significant mutations in FAM46C and KRAS, as well as deletions of RB1, TRAF3 and FAM46C.