A high-risk signature for patients with multiple myeloma established from the molecular classification of human myeloma cell lines

Abstract

Background: Multiple myeloma is a plasma-cell tumor with heterogeneity in molecular abnormalities and treatment response.

Design and methods: We have assessed whether human myeloma cell lines have kept patients' heterogeneity using Affymetrix gene expression profiling of 40 human myeloma cell lines obtained with or without IL6 addition and could provide a signature for stratification of patient risk.

Results: Human myeloma cell lines, especially those derived in the presence of IL6, displayed a heterogeneity that overlaps that of the patients with multiple myeloma. Human myeloma cell lines segregated into 6 groups marked by overexpression of MAF, MMSET, CCND1, FRZB with or without overexpression of cancer testis antigens (CTA). Cell lines of CTA/MAF and MAF groups have a translocation involving C-MAF or MAFB, cell lines of groups CCND1-1 and CCND1-2like have a t(11;14) and cell lines of group MMSET have a t(4;14). The CTA/FRZB group comprises cell lines that had no or no recurrent 14q32 translocation. Expression of 248 genes accounted for human myeloma cell line molecular heterogeneity. Human myeloma cell line heterogeneity genes comprise genes with prognostic value for survival of patients making it possible to build a powerful prognostic score involving a total of 13 genes.

Conclusions: Human myeloma cell lines derived in the presence of IL6 recapitulate the molecular diversity of multiple myeloma that made it possible to design, using human myeloma cell line heterogeneity genes, a high-risk signature for patients at diagnosis. We propose this classification to be used when addressing the physiopathology of multiple myeloma with human myeloma cell lines.

Figure 1.

Hierarchical clustering of the 40 HMCLs using the 248 HMCL heterogeneity genes. (A) The 248 genes were identified using SAM multiclass supervised analysis of the 6 molecular groups identified in Online Supplementary Figure S1 (1,000 permutations, P≤0.05). Red and green indicate over-expressed and under-expressed genes, respectively. The expression of some genes is indicated on the right of the dendrogram. HMCLs were clustered into 2 major clusters. One cluster is split into 2 clusters and 4 groups named CTA/MF, CTA/FRZB, CD-1 and CD-2L. The other one is split into 2 groups termed as MF and MS. Name of groups was chosen by analogy with the ACRC molecular classification. (B) The Affymetrix signal for each gene is proportional to the height of each bar (representing a single HMCL). Note that spiked expression of CCND1, MAF and MAFB, and FGFR3 and MMSET is strongly correlated with specific subgroup designations.

Figure 2.

Unsupervised clustering of the gene expression profiling of primary myeloma cells of newly diagnosed patients using the 248 HMCL heterogeneity genes. The Affymetrix gene expression profiles of purified myeloma cells from 345 newly diagnosed patients were publicly available from the ACRC. An unsupervised clustering of the 345 samples (columns) using the 248 HMCL heterogeneity genes (lines) makes it possible to cluster samples into 6 major groups defined by the different gray color scale horizontal histograms and arrows. The percentages above the horizontal histograms indicate the overlap of this clustering with the previously published ACRC 7 molecular group classification. MS:MMSET, LB: low bone disease, MF: MAF, PR:proliferation, HY:hyperdiploid, CD1/2: CD-1 + CD-2

Figure 3.

Seven gene prognostic score. (A) Distribution of the patients from the HM and ACRC-TT2 cohorts according to the 7-gene HMCL score. (B) Kaplan-Meier estimates of overall survival and event-free survival (C) of low risk patients (blue), intermediate risk patients (green) and high risk patients (red) according to our 7-gene HMCL score.

Figure 4.

Kaplan-Meier estimates of overall survival and event-free survival of patients without t(4;14) according to a 6-HMCL gene score in the HM (A) or ACRC-TT2 cohort (B).