Development of a Three-Gene-Based Proliferation Score (3GPS) to Predict Proliferation Index in Newly Diagnosed Multiple Myeloma
Authors: Bohra Arwa , Dasari Surendra , Gonsalves Wilson I. , Kapoor Prashant , Zanwar Saurabh , Binder Moritz , Dispenzieri Angela , Timm Michael M , Jevremovic Dragan , Rajkumar S. Vincent , Kumar Shaji 
Published: December 2024

Background: Multiple myeloma (MM) involves the proliferation of monoclonal plasma cells (PCs) in the bone marrow. The plasma cell labeling index (PCLI), indicating the percentage of PCs in the S-phase, is a key prognostic factor in newly diagnosed multiple myeloma (NDMM) patients.
Methods: A retrospective study at Mayo Clinic analyzed bone marrow Affymetrix microarray datasets from 136 NDMM patients (2001-2012). Data normalization and quality assessment were followed by differential gene expression analysis using limma-voom, adjusted for age, BMPC percentage, and disease stage (RISS). Selected genes were dichotomized by median and subjected to logistic regression for high/low PCLI. Data from 594 patients with a Proliferation Index at baseline was pooled from the MMRF (CoMMpass) dataset for validation after normalization across assays.
Results: The baseline characteristics of the patients are as follows: 62 (46%) were female and 74 (54%) were male, with a mean age at diagnosis of 61.6 ± 11.5 years. RISS staging included 36 patients (26.5%) at stage 1, 32 (23.5%) at stage 2, 29 (21.32%) at stage 3, and 39 patients (28.67%) with unknown stage. PCLI distribution showed 113 patients (83.7%) with &lt;2%, and 23 (16.3%) ≥2%.
Differential Analysis: The differential analyses reveal several critical insights. In the primary continuous differential analysis, 21,367 genes were analyzed, identifying 654 as differentially expressed with an FDR-adjusted p-value ≤0.05. Of these, 481 genes were upregulated (top 5: SPC25, TRAT1, PBK, E2F8, ASPM) and 173 were downregulated (top 5: SPARC, CD24, MYOF, CXCL12, VCAM1). Univariate and multivariate stratified analyses showed significant findings: 668 genes in age stratification, 395 genes in BMPC% stratification, and 536 genes in RISS stratification. In multivariate analysis, 408 genes were significant with an FDR-adjusted p-value &lt;0.05 for PCLI and ≥0.05 for BMPC%, age, and RISS.
3-Fold Internal Validation: 240 significant genes were identified in fold 1, 25 in fold 2, and 167 in fold 3, with 21 genes common across all folds (e.g., MCM10, GTSE1, UBE2S, NCAPG, FOXM1, STMN1, NEK2, CENPF, MND1, HJURP, E2F8, TOP2A, SKA1, CCNB2, CCNF, CHAF1A, PBK, EXO1, AURKB, CDCA2, DHFR). 19 genes were common in the sensitivity analysis by excluding RISS 3. 20 genes were common in categorical analysis (Categories &lt;1%, 1-2%, 2-3%, 3-4%, &gt;4%).
3 Gene-Based Proliferation Score (3GPS): On univariate logistic regression analysis of 21 genes for high/low PCLI, 17 significant genes were identified. In the step-wise multivariate analysis, CDCA2 (OR=11.56), DHFR (OR=9.6), and CENPF (OR=6.11) were significant. Log-odds were used as weights. For the high expression(median and above) of gene as 1 and low expression as 0:
3GPS=2.4*CDCA2+ 2.3*DHFR +1.8*CENPF
A cut-off of 2.4 was chosen as CDCA2 had the highest positive concordance rate (90.91%) versus DHFR (86.36%) and CENPF (77.27%).
External Validation: In the CoMMpass dataset, the sensitivity and specificity for the presence of high expression of any of the 3 genes with ≥2 Proliferation Index (PI) were 92.4% and 73.8%, respectively (AUC=83.1%). The median 3GPS was 0 for &lt;2 PI (n=238) and 6.5 for ≥2 PI (n=356). The sensitivity and specificity for the 3GPS in predicting ≥2 PI were 82.6% and 93.6%, respectively (AUC=88.1%).
Pathway Analysis: Significant pathways using Reactome include polo-like kinase mediated events in G2/M transition, condensation of prometaphase chromosomes in metaphase, resolution of sister chromatid cohesion in anaphase, and APC-Cdc20 mediated degradation of Nek2A for regulation of the cell cycle. p53 signaling, cancer pathways, and microtubule regulation were also mapped.
Survival Analysis: In our cohort, for CDCA2 quartiles (Q)3 and Q4, for CENPF Q3 and Q4, and for DHFR Q4 were associated with inferior overall survival. 3GPS ≥2.4 was associated with inferior survival of 60.28 months versus 111.5 months for &lt;2.4 (p&lt;0.01). In the validation dataset, median survival was not reached at 100 months (vs. high 79.7, p&lt;0.01). The multivariate Cox model found 3GPS score ≥2.4 as an independent predictor (HR=1.64, 95% CI: 1.23 - 2.19), along with ECOG status, ISS stage, gender, age, and whether the patient underwent Stem Cell Transplant.
Conclusion: CDCA2, DHFR, and CENPF are associated with ≥ 2% PCLI. The 3GPS score can serve as a measure of gene-based proliferation index. Prospective validation is needed for clinical practice.