Identification of pluripotent and adult stem cell genes unrelated to cell cycle and associated with poor prognosis in multiple myeloma

Abstract

Gene expression-based scores used to predict risk in cancer frequently include genes coding for DNA replication, repair or recombination. Using two independent cohorts of 206 and 345 previously-untreated patients with Multiple Myeloma (MM), we identified 50 cell cycle-unrelated genes overexpressed in multiple myeloma cells (MMCs) compared to normal human proliferating plasmablasts and non-proliferating bone marrow plasma cells and which have prognostic value for overall survival. Thirty-seven of these 50 myeloma genes (74%) were enriched in genes overexpressed in one of 3 normal human stem cell populations--pluripotent (18), hematopoietic (10) or mesenchymal stem cells (9)--and only three genes were enriched in one of 5 populations of differentiated cells (memory B lymphocytes, T lymphocytes, polymorphonuclear cells, monocytes, osteoclasts). These 37 genes shared by MMCs and adult or pluripotent stem cells were used to build a stem cell score ((SC)score), which proved to be strongly prognostic in the 2 independent cohorts of patients compared to other gene expression-based risk scores or usual clinical scores using multivariate Cox analysis. This finding highlights cell cycle-unrelated prognostic genes shared by myeloma cells and normal stem cells, whose products might be important for normal and malignant stem cell biology.

Figure 1. identification of genes overexpressed in primary myeloma cells and/or myeloma cell lines compared to normal plasmablasts or plasma cells and associated with patients’ prognostic value.

281 and 702 probe sets were overexpressed in MMCs and HMCLs compared to normal counterparts, respectively. These probe sets correspond to 678 unique genes/ESTs among which 332 genes/ESTs were associated to bad or good prognostic using HM cohort of patients. The prognostic value of 50 out of the 332 genes/ESTs is validated using an independent UAMS-TT2 cohort. Among these 50 genes, 37 were stem cell genes, 3 were differentiated cell genes and 10 genes were unclassified.

Figure 2. Expression profile of the 37 genes shared by multiple myeloma cells, adult or pluripotent stem cells.

A heatmap of the expression of these genes is shown for normal bone marrow plasma cells, primary multiple myeloma cells from patients, myeloma cell lines, 5 populations of differentiated cells (B cells, T cells, neutrophils, monocytes and osteoclasts) and 3 human stem cell populations (pluripotent stem cells, hematopoietic stem cells and mesenchymal stem cells). Each value represents the difference from the gene median across normal and malignant samples and is depicted according to the color scale shown at the bottom (−5.2 to 4.9 on a log base 2 scale).

Figure 3. Building a myeloma-stem cell score (^SCscore) for predicting overall survival.

A. The prognostic information provided by the 37 stem cell myeloma genes was summed within a ^SCscore as defined in the Materials and Methods. Patients of HM cohort were ranked according to increased ^SCscore and a maximum difference in OS was obtained with ^SCscore  = −2.7 splitting patients in a high risk (10%) and low risk (90%) groups. B. Validation of ^SCscore using UAMS-TT2 cohort.