2. Academic Validation
  3. Exploration and validation of ceRNA regulatory networks in colorectal cancer based on associations whole transcriptome sequencing

Exploration and validation of ceRNA regulatory networks in colorectal cancer based on associations whole transcriptome sequencing

  • Sci Rep. 2024 Sep 2;14(1):20446. doi: 10.1038/s41598-024-71465-5.
Lulu Zhang # 1,  Yulei Li # 2,  Chao Fu # 3,  LiXia Yang 1,  Gang Li 3,  Yiyang Wu 3,  Huanjun Tong 2,  Guojiang Tian 3,  Kaifang Wang 4,  Jun Wang 2,  Xiaojiang Ying 5,  Zhenjun Li 6
Affiliations

Affiliations

  • 1 Medical research center, Shaoxing People's Hospital, No. 568, Zhongxing North Road, Shaoxing, 312000, Zhejiang, China.
  • 2 Shaoxing People's Hospital, No. 568, Zhongxing North Road, Shaoxing, 312000, Zhejiang, China.
  • 3 Department of Colorectal and Anal Surgery, Shaoxing People's Hospital, No. 568, Zhongxing North Road, Shaoxing, 312000, Zhejiang, China.
  • 4 Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau Special Adiministrative Region, China.
  • 5 Department of Colorectal and Anal Surgery, Shaoxing People's Hospital, No. 568, Zhongxing North Road, Shaoxing, 312000, Zhejiang, China. J_D_D_water@163.com.
  • 6 Department of Colorectal and Anal Surgery, Shaoxing People's Hospital, No. 568, Zhongxing North Road, Shaoxing, 312000, Zhejiang, China. Lzdx2003@163.com.
  • # Contributed equally.
PMID: 39227669 DOI: 10.1038/s41598-024-71465-5
Abstract

Colorectal Cancer (CRC) is a wide-spread gastrointestinal Cancer that is associated with augmented morbidity and mortality, and we do not yet have a deep understanding of its epidemiology and carcinogenicity. The transcriptome can reveal the complexity and heterogeneity of tumors and uncover new biomarkers or treatment options. In this study, we identified messenger RNAs (mRNAs), long non-coding RNAs (lncRNAs), round RNAs (circRNAs), and MicroRNAs (miRNAs) using whole-transcriptome Sequencing and generated competing endogenous RNA (ceRNA) modulatory axes. We conducted whole transcriptome Sequencing on 10 CRC and para-cancer (CRCP) samples and discovered 2465 differentially expressed (DE) mRNAs (DEmRNAs), 77 DE miRNAs (DEmiRNAs). 2852 DE lncRNAs (DElncRNAs) and 1477 DE circRNAs (DEcircRNAs). In addition, utilizing co-DE analysis, we generated the ceRNA axis. Subsequently, we employed the ceRNA axis to identify essential genes and corresponding associations with lncRNAs, circRNAs, and miRNAs in CRC. ceRNA regulatory network including mRNA-miRNA-lncRNA and mRNA-miRNA-circRNA. These modulatory axes potentially modulate the positive regulation of smooth muscle contraction, melanosome, plasma membrane, integral plasma membrane component and so on. Finally, the results of RNA Sequencing (RNA-SEQ) were combined with the TCGA and GEO databases, and the DEGs strongly correlated with the TCGA-COAD overall survival (OS) as estimated by univariate COX and logarithmic rank analyses were cross-analyzed, and the co-upregulated DEGs were screened. Among the many DEs, KPNA2 was chosen for additional analysis. Using invitro experimentations, western blot, CCK8, EdU and Other experiments were performed to verify the results. We found siRNA-based KPNA2 depletion reduces bladder Cancer cells' viability, migratory, and proliferative activities, which showed that the DEmRNA profiles were comparable to the Sequencing information, confirming that the Sequencing data were very reliable. These evidences highlight the ceRNA regulatory mechanisms in CRC and will aid future research into the molecular mechanisms behind colorectal Cancer prevention and treatment.

Keywords

CRC; Competing endogenous RNA; Expression pattern; Non-coding RNA; Whole transcriptome.

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