Multi-Omics Integration-Based Prioritisation of Competing Endogenous RNA Regulation Networks in Small Cell Lung Cancer: Molecular Characteristics and Drug Candidates
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Published on: March 30, 2019
Xiao-Jun Wang1,2, Jing Gao1,2,3,4, Qin Yu2
1Department of Respiratory Medicine, Gansu Provincial Hospital, Lanzhou, China.
Background:
The competing endogenous RNA (ceRNA) network-mediated regulatory mechanisms in small cell lung cancer (SCLC) remain largely unknown. This study aimed to integrate multi-omics profiles, including the transcriptome, regulome, genome and pharmacogenome profiles, to elucidate prioritised ceRNA characteristics, pathways and drug candidates in SCLC.
Method:
We determined the plasma messenger RNA (mRNA), microRNA (miRNA), long noncoding RNA (lncRNA) and circular RNA (circRNA) expression levels using whole-transcriptome sequencing technology in our SCLC plasma cohort. Significantly expressed plasma mRNAs were then overlapped with the Gene Expression Omnibus (GEO) tissue mRNA data (GSE 40275, SCLC tissue cohort). Next, we applied a multistep multi-omics (transcriptome, regulome, genome and pharmacogenome) integration analysis to first construct the network and then to identify the lncRNA/circRNA-miRNA-mRNA ceRNA characteristics, genomic alterations, pathways and drug candidates in SCLC.
Results:
The multi-omics integration-based prioritisation of SCLC ceRNA regulatory networks consisted of downregulated mRNAs (CSF3R/GAA), lncRNAs (AC005005.4-201/DLX6-AS1-201/NEAT1-203) and circRNAs (hsa_HLA-B_1/hsa_VEGFC_8) as well as upregulated miRNAs (hsa-miR-4525/hsa-miR-6747-3p). lncRNAs (lncRNA-AC005005.4-201 and NEAT1-203) and circRNAs (circRNA-hsa_HLA-B_1 and hsa_VEGFC_8) may regulate the inhibited effects of hsa-miR-6747-3p for CSF3R expression in SCLC, while lncRNA-DLX6-AS1-201 or circRNA-hsa_HLA-B_1 may neutralise the negative regulation of hsa-miR-4525 for GAA in SCLC. CSF3R and GAA were present in the genomic alteration, and further identified as targets of FavId and Trastuzumab deruxtecan, respectively. In the SCLC-associated pathway analysis, CSF3R was involved in the autophagy pathways, while GAA was involved in the glucose metabolism pathways.
Conclusions:
We identified potential lncRNA/cirRNA-miRNA-mRNA ceRNA regulatory mechanisms, pathways and promising drug candidates in SCLC, providing novel potential diagnostics and therapeutic targets in SCLC.
Insights
This study reveals competing RNA networks in small cell lung cancer (SCLC), identifying key regulatory RNAs and potential drug targets. These findings offer new avenues for SCLC diagnostics and therapeutics.
Area of Science:
- Oncology
- Genomics
- Molecular Biology
Background:
- Small cell lung cancer (SCLC) regulatory mechanisms involving competing endogenous RNA (ceRNA) networks are poorly understood.
- This study integrates multi-omics data to explore ceRNA networks in SCLC.
Purpose of the Study:
- To elucidate prioritized ceRNA characteristics, pathways, and drug candidates in SCLC.
- To identify novel diagnostic and therapeutic targets for SCLC.
Main Methods:
- Whole-transcriptome sequencing of plasma samples to determine mRNA, miRNA, lncRNA, and circRNA expression.
- Multi-omics integration (transcriptome, regulome, genome, pharmacogenome) to construct ceRNA networks.
- Identification of lncRNA/circRNA-miRNA-mRNA interactions, genomic alterations, pathways, and drug targets.
Main Results:
- Downregulated mRNAs (CSF3R/GAA), lncRNAs (AC005005.4-201/DLX6-AS1-201/NEAT1-203), and circRNAs (hsa_HLA-B_1/hsa_VEGFC_8) were identified.
- Upregulated miRNAs (hsa-miR-4525/hsa-miR-6747-3p) were found to interact with specific lncRNAs and circRNAs, potentially regulating CSF3R and GAA expression.
- CSF3R and GAA were linked to genomic alterations and are targets of FavId and Trastuzumab deruxtecan, respectively.
- CSF3R is involved in autophagy pathways, and GAA is involved in glucose metabolism pathways in SCLC.
Conclusions:
- Novel lncRNA/circRNA-miRNA-mRNA ceRNA regulatory mechanisms were identified in SCLC.
- Potential drug candidates and therapeutic targets, including CSF3R and GAA, were highlighted.
- The findings provide a foundation for developing new diagnostics and therapeutics for SCLC.
