A Gene Expression Based Centrosome Index Is a Powerful Prognostic Factor in Myeloma.
Authors: Chng Wee-Joo , Fonseca Rafael 
Published: October 2019

Previously, we have shown that centrosome amplification is common in multiple myeloma and is already present in monoclonal gammopathy of undetermined significance (MGUS), suggesting an early role in myelomagenesis. In addition, we derived a gene expression based centrosome index (CI) that correlated closely with centrosome amplification detected by immunofluorescence. We also showed in a heterogeneously treated and relatively small cohort of patients that the CI is an independent prognostic factor. In this study, we validated the prognostic significance of a gene expression based centrosome index (CI) in 2 large cohorts of homogenously treated myeloma patients entered into clinical trials. Cohort 1 consisted of newly diagnosed patients from the University of Arkansas for Medical Science (UAMS) entered treated with total therapy II. These patients have gene expression profiling performed on purified CD138+ plasma cells from pre-treatment bone marrow cells using the Affymetrix U133plus chip (data available from Gene Expression Omnibus). Cohort 2 consisted of relapsed or refractory patients entered into bortezomib trials. These patients have GEP performed on purified CD138+ PCs using the Affymetrix U133A and B chip as part of a pharmacogenomics study (data kindly provided by Millenium Pharmaceuticals). Expression values extracted using the MAS 5.0 software are log-transformed, median centered and analyzed using Genespring 7.0 (Agilent Technologies). Survival is calculated from date of entry into trial till death in both cohorts. In the UAMS dataset, a high CI is significantly associated with shorter survival and emerged as an independent prognostic factor with t(4;14) (detected by spike FGFR3/MMSET expression) when entered into a multivariate Cox proportional hazard analysis (other variables entered included CKS1B expression above median and elevated gene expression based proliferation index, both of which were significantly associated with shorter survival on univariate but not multivariate analysis). In the bortezomib cohort, a high CI is again significantly associated with shorter survival, and this effect is independent of response to bortezomib. Therefore, a high CI is a powerful independent prognostic factor in both newly diagnosed and relapsed patients even in patients treated by intensive therapy (total therapy II) and novel agents (bortezomib). We next compared the gene expression profiles of tumors with high and low CI, to define the molecular phenotype of these aggressive tumors and identify possible novel therapeutic targets. Tumors with high CI over-expressed genes coding for proteins associated with the centrosome (TUBG1, CETN2, TACC3, NEK2, PRKRA, STK6, AURKB and PLK4), cell cycle (CCNB1, CCNB2, CCND2, E2F2, CDC gene family, CDK5, CDK6, CDKN2C), proliferation (RAN, CKS1B, TOP2A, TTK, TYMS, MCM gene family, ASPM), involve in DNA repair / G2 cell cycle checkpoints (BRCA1, CHEK1, CHEK2, MAD2L1, BUB1, BUB1B, FANCD2, REV1L), kinetochore and microtubule attachment (AURKB, BIRC5, CENPA, CENPE, CENPH, ZWINT), genes coding for cancer testis antigens (GAGE and MAGE family) and implicated in other cancer (PTP4A3, EZH2). Consistent with this, the most significantly associated Gene Ontology biological process are cell cycle, mitosis, proliferation, DNA repair, microtubule related In particular, aurora kinases are significantly over-expressed in patients with high CI and may represent novel therapeutic targets in these patients with very poor prognosis.