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A systems approach to target discovery identifies the role of lncRNA-SPANXA2-OT1 in macrophage chemotaxis
Prabhash K. Jha, … , Shizuka Uchida, Masanori Aikawa
Prabhash K. Jha, … , Shizuka Uchida, Masanori Aikawa
Published October 9, 2025
Citation Information: JCI Insight. 2025;10(21):e191274. https://doi.org/10.1172/jci.insight.191274.
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Research Article Cell biology Inflammation Vascular biology

A systems approach to target discovery identifies the role of lncRNA-SPANXA2-OT1 in macrophage chemotaxis

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Abstract

Coronary artery disease (CAD) is the leading cause of mortality worldwide, with macrophages playing a central role in shaping the inflammatory environment through cytokines, chemokines, and other mediators. Long noncoding RNAs (lncRNAs) are emerging as key regulators of cellular processes owing to their interactions with DNA, RNA, microRNAs, and proteins, which positions them to be promising therapeutic targets. Through integrative transcriptomic analysis, we identified SPANXA2-OT1 as a primate-specific lncRNA with a potential role in macrophage-mediated inflammation in CAD. Functional studies in primary human macrophages demonstrated that SPANXA2-OT1 was induced by inflammatory stimulation, localized to the cytoplasm, and exerted regulatory effects on chemokine expression and macrophage chemotaxis. Mechanistically, SPANXA2-OT1 acted as a molecular sponge for microRNA-338, thereby influencing the expression of IL-8, a critical mediator of monocyte recruitment and inflammatory signaling. Collectively, these findings establish SPANXA2-OT1 as a human-specific regulator of inflammatory pathways in CAD and highlight its translational potential as both a biomarker and therapeutic target.

Authors

Prabhash K. Jha, Sarvesh Chelvanambi, Yuto Nakamura, Lucas Y.U. Itto, Aatira Vijay, Adrien Lupieri, Miguel C. Barbeiro, Thanh-Dat Le, Caio B. Nascimento, Taku Kasai, Mary Whelan, Daiki Hosokawa, Dakota Becker-Greene, Sasha A. Singh, Elena Aikawa, Shizuka Uchida, Masanori Aikawa

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Figure 4

Global transcriptomics and proteomics of SPANXA2-OT1–silenced human primary macrophages found in enrichment of chemotaxis signatures.

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Global transcriptomics and proteomics of SPANXA2-OT1–silenced human prim...
(A) Schematics of global omics on SPANXA2-OT1–silenced human primary macrophages. (B–E) RNA-Seq data. n = 4 PBMC donors. (B) Volcano plot, in which red dots denote the statistically significant overexpressed and underexpressed mRNAs (adjusted P value and log fold change), while the gray dots denote statistically nonsignificant mRNAs. Scr_ASO (scrambled) and SPAN_ASO (SPANXA2-OT1). (C) Bubble plot of KEGG pathway enrichment analysis of DEGs; x axis represents enrichment score. Count indicates the number of DEGs enriched in pathway; P values were corrected by Benjamini-Hochberg method. (D) Heatmap representation of DEGs. Clustering analysis resulted in 2 important clusters that have decreased gene expression in SPANXA2-OT1–silenced group (yellow and green boxes). (E) The clusters were used for STRING database protein-protein interaction (PPI) and pathway analysis and resulted in enrichment of chemokine receptor/ligand (yellow cluster) and chemokine downstream signaling (green cluster), both of which were decreased after SPANXA2-OT1 silencing in human primary macrophages. (F–H) Proteomics data. n = 5 PBMC donors. (F) Heatmap representing the unbiased global proteomics changes after silencing SPANXA2-OT1 in human primary macrophages. Groups included negative control anti-sense oligo– (NC_ASO–) and SPANXA2-OT1 anti-sense oligo–treated (SPAN_ASO–treated) macrophages. (G) Protein abundance clusters showing sum-normalized quantified data on the y axis and macrophage treatment groups on the x axis (average of 5 donors/group). Cluster#6 (n = 37 proteins, highlighted in red) was selected as the important cluster based on the pattern of expression, in which the expression of proteins increased with IL-1β treatment and was maintained in IL-1β+NC ASO, while the expression decreased in IL-1β+SPANXA2-OT1 ASO. (H) Gene ontology biological process analysis of cluster#6 resulted in enrichment of pathways related to monocyte chemotaxis.

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