Comprehensive Translatomic Analysis of Multiple Myeloma Unveils Novel Insights into Disease Pathogenesis

Background: Genomic, transcriptomic, and proteomic studies have significantly advanced our understanding of multiple myeloma (MM) and facilitated the development of targeted therapies. However, a challenge has been the limited correlation between transcriptome and proteome data, leaving gaps in our understanding of how gene expression relates to protein functionality. In-depth characterization of the MM translatome will provide a foundation for elucidating complex molecular mechanisms and developing translational-targeted therapeutic approaches.

Methods: We collected bone marrow samples from 50 newly diagnosed MM (NDMM) patients and 9 healthy donors, and performed gene panel sequencing, RNA-seq, Ribo-seq and MHC-I immunopeptide sequencing on CD138⁺ cells.

Results: We elucidated a coordinated regulation of cancer pathways and genes at both transcriptional and translational levels, correlated with immune function loss and heightened DNA repair processes. Additionally, certain genes were exclusively regulated at the translational level, resulting in the suppression of pathways associated with mitochondrial oxidative respiration. These findings enhance our understanding of immune function disruption and alterations in glycolytic energy metabolism in malignant plasma cells. Furthermore, the specificity of NDMM's translational regulation in response to ER stress suggests that existing transcripts are translated into proteins more rapidly than those induced de novo, indicating a potential initial adaptive response to stress. This underscores a potential therapeutic strategy that targets the essential ER stress response at the translational level, which is crucial for MM cell survival.

Moreover, we discovered novel translatomic subtypes, among them, TE-C2 was associated with R-ISS III. This finding represents the initial indication that high-risk NDMM patients demonstrate distinctive translational characteristics. The TE-C2 group exhibited the worst clinical outcomes, independently providing prognostic information beyond R-ISS III. No significant difference in overall survival or progression-free survival between R-ISS III and non-R-ISS III patients suggested translational features-based grouping enhances prognostic precision. Another subtype associated with SF3B1 genomic mutations. Further integrating ChIP-seq and alternative splicing analyses of SF3B1-mutant cell lines’ Ribo-seq data elucidated a mechanism for splicing-driven translational control. We observed that SF3B1 mutations lead to an increased number of exons with m6A modification sites, potentially regulating translational initiation of target mRNA transcripts through the recruitment of m6A reader proteins. This could be a potential regulatory mechanism to promote the translation of DNA damage response mRNAs.

Translatomic analysis of NDMM also uncovers novel open reading frames (ORFs) with the potential to serve as cancer neoantigens.These noncanonical ORFs may play a crucial role in maintaining protein homeostasis and cell proliferation. The translation patterns of specific lncRNAs with well-established roles in cancer invasion or metastasis and those recognized as prognostic biomarkers strongly suggest their potential as promising targets. Additionally, MHC-I immunopeptidome mass spectrometry further validates the potential of noncanonical ORFs as cancer neoantigens. For instance, micropeptides derived from the LY9 dORF hold promising potential for NDMM immunotherapy.

Conclusion: Our comprehensive analysis of the NDMM translatome not only expands our understanding of the molecular intricacies of NDMM but also paves the way for action toward personalized therapeutic strategies. By elucidating these translational features, we hope to contribute to developing more effective treatment approaches and a paradigm shift toward precision medicine in the management of NDMM.