Sex-Based Differences in Multiple Myeloma: The Critical Role of Exosomal ncRNAs

Findings from a study on the role of exosomal non-coding RNAs (ncRNAs) in the progression of multiple myeloma (MM), with a specific focus on sex-based differences, show that while male and female patients may exhibit perturbations in the same biological pathways, these disruptions are driven by distinct ncRNA-mRNA regulatory networks. ^1,2

The analysis revealed a greater number and variability of dysregulated ncRNAs in male patients. Critical pathways, such as TNF-α signaling via NF-κB, were recurrently enriched in both sexes but were modulated by sex-specific sets of ncRNAs and target genes. The study established a panel of sex-specific ncRNAs with significant effects on gene regulation in MM-associated pathways, underscoring the necessity of developing sex-tailored therapeutic strategies for a more personalized approach to treating MM.

The research demonstrates that analyzing exosomes provides a significantly higher resolution for detecting ncRNA dysregulation compared with traditional bone marrow tissue sampling. The study identifies distinct, sex-specific expression signatures for microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) across various clinical contexts, including patients with newly diagnosed, relapsed, and treated MM.

The majority of prominently dysregulated ncRNAs identified in exosomes were not found to be significantly altered in whole bone marrow samples.

Female patients displayed a higher proportion of exosomal lncRNAs with unchanged expression patterns in corresponding bone marrow tissue compared with males.

The lncRNA CAHM, one of the most influential regulators identified, controlled approximately 2500 mRNAs in both sexes but showed no significant dysregulation in female bone marrow samples.

The miRNA hsa-miR-335-5p, which regulated the highest number of mRNAs in both sexes, was among 29 shared dysregulated miRNAs that were not significantly altered in bone marrow samples.

Analytical Workflow

Exosomes were isolated from patient samples and cell line media, characterized for size and concentration, and their RNA cargo was extracted. RNA sequencing was performed on an Illumina NovaSeq X Plus platform to profile ncRNAs.

Raw sequencing data was processed for quality control. lncRNA and miRNA data were aligned to the GRCh38 (hg38) reference genome to quantify transcript abundance.

A 4-stage filtering process was established to identify the most significant ncRNAs:

1. Filter 1: Identified dysregulated RNAs with an adjusted P-value <.01 and an absolute log2(fold change) >2.
2. Filter 2: Correlated patient data with cell line data to retain significantly dysregulated RNAs.
3. Filter 3: Integrated ncRNA data with mRNA data, identifying interactions validated by the LncSEAv2 (for lncRNA-mRNA) and miRTarBase (for miRNA-mRNA) databases.
4. Filter 4: Isolated dysregulated RNAs detected exclusively in either male or female patients.

Functional analysis of dysregulated mRNAs was performed using the KEGG PATHWAY and MSigDB Hallmark databases to identify perturbed biological pathways.

This methodology resulted in the identification of 104 "effector" miRNAs and 305 "effector" lncRNAs that passed all filtering criteria and were used for downstream analysis.

After removing shared interactions, a male-specific network remained where 6 upregulated miRNAs, including hsa-miR-335-5p, collectively targeted and suppressed MAPK1, potentially contributing to an immunosuppressive tumor microenvironment.

In male patients, the network centered on a single downregulated mRNA, SOS2, regulated by 24 downregulated lncRNAs and 1 upregulated miRNA.

In female patients, the network was more complex, involving 3 downregulated mRNAs (LAMC3, GLI2, TCF7) and 1 upregulated mRNA (MYC), regulated by numerous ncRNAs including CAHM and CD81-AS1.

Pronounced Sex-Specific Dysregulation of ncRNAs

The analysis revealed significant differences in the expression profiles of ncRNAs between male and female patients with MM.

A greater number of dysregulated ncRNAs were identified in the male patients compared with the female patients. Furthermore, the expression levels of these ncRNAs showed greater variability across male samples, whereas expression in female samples was more concentrated and consistent.

Out of 3458 mRNAs regulated by the identified effector ncRNAs, 530 were controlled by ncRNAs from both sexes. Sex-specific regulation was also prominent, with 126 and 137 mRNAs regulated exclusively by male-specific and female-specific lncRNAs, respectively.

Analysis of ncRNAs located on sex chromosomes identified distinct patterns:

• Both sexes: The lncRNA EIF1AX-AS1 on chromosome X was the only common effector lncRNA shared between sexes.
• Male-specific: 6 lncRNAs and 3 miRNAs were detected on chromosome X. The lncRNA TTTY14 was exclusively found on chromosome Y.
• Female-specific: The miRNA hsa-miR-222-5p was uniquely expressed on chromosome X.

Study Overview and Methodology

The primary objective of the research was to uncover sex-specific differences in MM by investigating the expression patterns of exosomal ncRNAs (miRNAs and lncRNAs) and their interaction with regulatory genes. The study integrated data from patient samples, cell lines, and a large public database.

Exosomes were isolated from 24 patients with bone marrow aspirates (16 males, 8 females) and 7 healthy control samples.

Six MM cell lines (LP1, NCI-H929, JJN-3, U-266, KMS-11, and ANBL-6) were used for comparative analysis.

mRNA expression data were obtained from the MMRF-COMMPASS cohort via the Genomic Data Commons database. This included 451 cancerous and 170 normal bone marrow samples from male patients, and 313 cancerous and 154 normal bone marrow samples from female patients.

Clinical Implications

This study provides comprehensive evidence that the dysregulation of exosomal ncRNAs is a key driver of MM pathogenesis and that these mechanisms are significantly different between male and female patients.

The identified effector ncRNAs, such as CAHM, hsa-miR-335-5p, RAET1E-AS1, and EIF1AX-AS1, represent promising candidates for novel biomarkers and therapeutic targets. By understanding and targeting these sex-specific molecular drivers, it may be possible to enhance treatment efficacy and move toward a more personalized era of medicine for patients with MM.

“Notably, the greater variability observed in males highlights the potential for novel, precise interventions to improve clinical outcomes for both male and female patients [with MM],” concluded Maleknia et al, authors of the study.

REFERENCES

1.Maleknia S, Benam S, Ahmann G et al. Sex-specific dysregulation of exosomal non-coding RNAs drives multiple myeloma progression. Published October 16, 2025. Accessed December 24, 2025. Blood Cancer. 15, 162 (2025). doi: 10.1038/s41408-025-01362-1.

2.Differences revealed in how multiple myeloma develops in men and women. News release. Indiana University School of Medicine. Published December 15, 2025. Accessed December 24, 2025. https://tinyurl.com/3ew45ett