Screening for feature genes and immune infiltration of multiple myeloma: a study based on support vector machine

Shi Lei, Zhang Hongbin

PDF(8673 KB)
PDF(8673 KB)
Journal of Chongqing Medical University ›› 2025, Vol. 50 ›› Issue (01) : 135-144. DOI: 10.13406/j.cnki.cyxb.003710
Clinical research

Screening for feature genes and immune infiltration of multiple myeloma: a study based on support vector machine

Author information +
History +

Abstract

Objective To investigate the genetic heterogeneity of multiple myeloma(MM) and the important regulatory role of immune cells in its pathophysiology by using bioinformatics techniques. Methods The datasets of GSE125364 and GSE72213 associated with MM were obtained from the gene expression omnibus database of National Center for Biotechnology Information,and bioinformatics and machine learning methods were used to identify the key genes for the diagnosis of MM. Pathways associated with the differentially expressed genes in MM were analyzed to calculate immune cell infiltration,and molecular biology experiments were used for validation. Results In this study,a total of 410 differentially expressed genes were obtained by the bioinformatics methods based on the gene microarray data of MM from public databases,among which 259 were downregulated and 151 were upregulated in MM patients compared with controls. The gene ontology enrichment analysis showed that the differentially expressed genes were mainly involved in the biological processes such as DNA replication,chromosome segregation,and mitosis; as for cellular localization,they were mainly enriched in chromosomal region and the spindle apparatus; as for molecular function,they were mainly enriched in single-stranded DNA helicase activity,DNA catalysis,and ATP-dependent activity. The KEGG pathway enrichment analysis showed that the main signaling pathways included cell cycle,the p53 signaling pathway,cellular senescence,and DNA replication. The GSEA analysis showed that in the control group,the genes were mainly enriched in cell cycle,DNA replication,purine metabolism,and ribosomes,while in the MM group,the genes were mainly enriched in the adipokine signaling pathway,cell adhesion molecules,ribonucleic acid polymerase,and ascorbate and aldarate metabolism pathways. Two genes,CPXM1 and UROD,were obtained for the diagnosis of MM by support vector machine-recursive feature elimination algorithm,and the immune infiltration analysis via CIBERSORTx showed that CPXM1 and UROD were associated with immune infiltration; qRT-PCR validation was performed in MM.1S cells (P<0.05). Conclusion Bioinformatics methods can be used to effectively analyze the differentially expressed genes between MM patients and the normal control population,and the key genes CPXM1 and UROD are obtained for the diagnosis of MM and are associated with immune infiltration,which can be used as new targets for subsequent basic and clinical experimental studies on MM.

Key words

multiple myeloma / biomarkers / bioinformatics / immune infiltration

Cite this article

Download Citations
Shi Lei , Zhang Hongbin. Screening for feature genes and immune infiltration of multiple myeloma: a study based on support vector machine. Journal of Chongqing Medical University. 2025, 50(01): 135-144 https://doi.org/10.13406/j.cnki.cyxb.003710

References

1
Cowan AJ Green DJ Kwok M,et al. Diagnosis and management of multiple myeloma:a review[J]. JAMA2022327(5):464-477.
2
Bazarbachi AH Al Hamed R Malard F,et al. Relapsed refractory multiple myeloma:a comprehensive overview[J]. Leukemia201933(10):2343-2357.
3
Kumar SK Rajkumar SV Dispenzieri A,et al. Improved survival in multiple myeloma and the impact of novel therapies[J]. Blood2008111(5):2516-2520.
4
Moreau P Kumar SK Miguel JS,et al. Treatment of relapsed and refractory multiple myeloma:recommendations from the International Myeloma Working Group[J]. Lancet Oncol202122(3):e105-e118.
5
Arron JR Choi Y. Bone versus immune system[J]. Nature2000408(6812):535-536.
6
Huang BH Li J. Advances in the diagnosis and treatment of multiple myeloma[J]. Zhonghua Xue Ye Xue Za Zhi201839(7):605-608.
7
Bakhoum SF Landau DA. Chromosomal instability as a driver of tumor heterogeneity and evolution[J]. Cold Spring Harb Perspect Med20177(6):a029611.
8
Neuse CJ Lomas OC Schliemann C,et al. Genome instability in multiple myeloma[J]. Leukemia202034(11):2887-2897.
9
Manier S Salem KZ Park J,et al. Genomic complexity of multiple myeloma and its clinical implications[J]. Nat Rev Clin Oncol201714(2):100-113.
10
Bergsagel PL Kuehl WM Zhan FH,et al. Cyclin D dysregulation:an early and unifying pathogenic event in multiple myeloma[J]. Blood2005106(1):296-303.
11
Maura F Petljak M Lionetti M,et al. Biological and prognostic impact of APOBEC-induced mutations in the spectrum of plasma cell dyscrasias and multiple myeloma cell lines[J]. Leukemia201832(4):1043-1047.
12
Walker BA Mavrommatis K Wardell CP,et al. A high-risk,Double-Hit,group of newly diagnosed myeloma identified by genomic analysis[J]. Leukemia201933(1):159-170.
13
Chang YT Chiu I Wang QJ,et al. Loss of p53 enhances the tumor-initiating potential and drug resistance of clonogenic multiple myeloma cells[J]. Blood Adv20237(14):3551-3560.
14
Kuilman T Peeper DS. Senescence-messaging secretome:SMS-ing cellular stress[J]. Nat Rev Cancer20099(2):81-94.
15
Acosta JC Gil J. Senescence:a new weapon for cancer therapy[J]. Trends Cell Biol201222(4):211-219.
16
Fairfield H Dudakovic A Khatib CM,et al. Myeloma-modified adipocytes exhibit metabolic dysfunction and a senescence-associated secretory phenotype[J]. Cancer Res202181(3):634-647.
17
Liu H He J Koh SP,et al. Reprogrammed marrow adipocytes contribute to myeloma-induced bone disease[J]. Sci Transl Med201911(494):eaau9087.
18
Sapio MR Fricker LD. Carboxypeptidases in disease:insights from peptidomic studies[J]. Proteomics Clin Appl20148(5/6):327-337.
19
Kim YH O’Neill HM Whitehead JP. Carboxypeptidase X-1 (CPX-1) is a secreted collagen-binding glycoprotein[J]. Biochem Biophys Res Commun2015468(4):894-899.
20
Kim YH Barclay JL He JJ,et al. Identification of carboxypeptidase X(CPX)-1 as a positive regulator of adipogenesis[J]. FASEB J201630(7):2528-2540.
21
Zheng MJ Long JY Chelariu-Raicu A,et al. Identification of a novel tumor microenvironment prognostic signature for advanced-stage serous ovarian cancer[J]. Cancers202113(13):3343.
22
Mao XH Ye Q Zhang GB,et al. Identification of differentially methylated genes as diagnostic and prognostic biomarkers of breast cancer[J]. World J Surg Oncol202119(1):29.
23
Chen Y Li ZY Zhou GQ,et al. An immune-related gene prognostic index for head and neck squamous cell carcinoma[J]. Clin Cancer Res202127(1):330-341.
24
Wang YH Lin CC Yao CY,et al. A 4-gene leukemic stem cell score can independently predict the prognosis of myelodysplastic syndrome patients[J]. Blood Adv20204(4):644-654.
25
Kumar A Bandapalli OR Paramasivam N,et al. Familial Cancer Variant Prioritization Pipeline version 2(FCVPPv2) applied to a papillary thyroid cancer family[J]. Sci Rep20188:11635.
26
Tian LY Long F Hao YJ,et al. A cancer associated fibroblasts-related six-gene panel for anti-PD-1 therapy in melanoma driven by weighted correlation network analysis and supervised machine learning[J]. Front Med20229:880326.
27
Ito E Yue SJ Moriyama EH,et al. Uroporphyrinogen decarboxylase is a radiosensitizing target for head and neck cancer[J]. Sci Transl Med20113(67):e3001922.

Comments

PDF(8673 KB)

Accesses

Citation

Detail

Sections
Recommended

/