Proteomic Analysis of Bone Marrow CD138+ Cells to Identify Proteins Associated With the Response of Multiple Myeloma Patients to Commonly Used Therapeutic Regimens

Abstract

Multiple myeloma (MM) remains incurable; gaps in our understanding of MM molecular pathogenesis and drugs' resistance mechanisms are involved in the failure of therapies. This study aims to identify proteins significantly impacting MM patients' response to commonly used therapeutic regimens. Bone marrow CD138+ selected plasma cells were isolated from patients who had achieved Response (Responders, R) and those who were Non-Responders (NR) to their primary MM therapy. We used LC-MS/MS to investigate the proteomic profile of MM samples, followed by bioinformatics analysis. We identified 1190 proteins, of which 230 showed a statistically significant difference between R and NR, with 27 proteins being upregulated and 203 downregulated in R compared to NR. Pathway enrichment analysis identified pathways related to the immune response and protein synthesis regulation, closely associated with MM progression and response to therapy. The results were validated through individual RNA dataset analysis, corroborating the differential expression of several proteins, including proteins associated with MM (e.g., MIF, ILF3) as well as novel findings (e.g., DCPS and SET). Collectively, proteomics data obtained from R and NR to MM therapy displayed significant changes in the immune system and protein synthesis regulation, supporting their potential role in progression and therapeutic response of MM.

Keywords: biomarkers; cancer; multiple myeloma; proteomics; therapy.

FIGURE 1

(A) PCA plot depicting the distribution of R and NR based on the 230 DEPs. The x‐axis (PC1) and y‐axis (PC2) represent the top two principal components, explaining a percentage of the total variance in protein expression. Each point represents an individual sample, colored according to its respective group (blue for R, green for NR). Ellipses indicate 95% confidence intervals for each group. The separation of clusters suggests differences in the global proteomic profiles between R and NR. (B) Volcano plot illustrating DEPs between R and NR. The x‐axis represents Log₂FC of protein expression (R vs. NR), while the y‐axis represents the –log₁₀(p value) from the Mann–Whitney U test. Proteins with significant upregulation in R versus NR (Log₂FC ≥ 0.58, p value < 0.05) are shown in red, while those significantly downregulated in R versus NR (Log₂FC ≤ −0.58, p value < 0.05) are in green. Non‐significant proteins (p value ≥ 0.05) are displayed in grey. DEP indicates differentially expressed protein; MM, multiple myeloma; NR, non‐responders; R, responders.

FIGURE 2

Selected enriched biological processes and pathways associated with the 230 DEPs in the comparison between R versus NR, identified using Metascape. Pathways related to translation and protein synthesis are indicated in pink, while those associated with the immune system are indicated in red. DEP indicates differentially expressed protein; NR, non‐responders; R, responders.

FIGURE 3

Selected enriched pathways and processes associated with the 55 DEPs in the R versus NR comparison (Metascape), which were also identified with a p value < 0.05 and the same expression trend in at least one of the three available transcriptomic datasets related to MM treatment response. Pathways related to translation and protein synthesis are indicated in pink, while those associated with the immune system are indicated in red.