Identification of aberrantly expressed lncRNAs and ceRNA networks in multiple myeloma: a combined high-throughput sequencing and microarray analysis

Min-Qiu Lu; Yu-Qin He; Yin Wu; Hui-Xing Zhou; Yuan Jian; Wen Gao; Li Bao; Wen-Ming Chen

doi:10.3389/fonc.2023.1160342

Identification of aberrantly expressed lncRNAs and ceRNA networks in multiple myeloma: a combined high-throughput sequencing and microarray analysis

Front Oncol. 2023 Jun 5:13:1160342. doi: 10.3389/fonc.2023.1160342. eCollection 2023.

Authors

Min-Qiu Lu¹, Yu-Qin He², Yin Wu³, Hui-Xing Zhou³, Yuan Jian³, Wen Gao³, Li Bao¹, Wen-Ming Chen³

Affiliations

¹ Department of Hematology, Beijing Jishuitan Hospital, Beijing, China.
² Department of Emergency, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China.
³ Department of Hematology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China.

Abstract

Background: This study aimed to explore the potential effects of long non-coding RNAs (lncRNAs) in multiple myeloma (MM) patients using two detection methods: high-throughput sequencing and microarray.

Methods: In this study, lncRNAs were detected in 20 newly diagnosed MM patients, with 10 patients analyzed by whole transcriptome-specific RNA sequencing and 10 patients analyzed by microarray (Affymetrix Human Clariom D). The expression levels of lncRNAs, microRNAs, and messenger RNAs (mRNAs) were analyzed, and the differentially expressed lncRNAs identified by both methods were selected. The significant differentially expressed lncRNAs were further validated using PCR.

Results: This study established the aberrant expression of certain lncRNAs involved in the occurrence of MM, with AC007278.2 and FAM157C showing the most significant differences. The top 5 common pathways identified by the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were the chemokine signaling pathway, inflammatory mediator regulation, Th17 cell differentiation, apoptosis, and NF-kappa B signaling pathway. Furthermore, three microRNAs (miRNAs) (miR-4772-3p, miR-617, and miR-618) were found to constitute competing endogenous RNA (ceRNA) networks in both sequencing and microarray analyses.

Conclusions: By the combination analysis, our understanding of lncRNAs in MM will be increased significantly. More overlapping differentially expressed lncRNAs were found to predict therapeutic targets precisely.

Keywords: genomics; high-throughput sequencing; long noncoding RNAs; microarray; multiple myeloma.

Grants and funding

This study was supported by the Yangfan Project Special Foundation of Beijing Hospital Authority (ZXLY201606), Beijing JST Research Funding (IR-202105), and Special Medicine Innovation Scientific Special Project (2018ZX09733003).