Multi-Omics Analysis Based on Integrated Genomics, Epigenomics and Transcriptomics in Pancreatic Cancer

Abstract

Aim: Integrated analysis of genomics, epigenomics, transcriptomics and clinical information contributes to identify specific molecular subgroups and find novel biomarkers for pancreatic cancer. Materials & methods: The DNA copy number variation, the simple nucleotide variation, methylation and mRNA data of pancreatic cancer patients were obtained from The Cancer Genome Atlas. Four molecular subgroups (iC1, iC2, iC3 and iC4) of pancreatic cancer were identified by integrating analysis. Results: The iC1 subgroup harbors better prognosis, higher immune score, lesser DNA copy number variation mutations and better genomic stability compared with iC2, iC3 and iC4 subgroups. Three new genes (GRAP2, ICAM3 and A2ML1) correlated with prognosis were identified. Conclusion: Integrated multi-omics analysis provides fresh insight into molecular classification of pancreatic cancer, which may help discover new prognostic biomarkers and reveal the underlying mechanism of pancreatic cancer.

Keywords::

• A2ML1
• epigenomics
• genomics
• GRAP2
• ICAM3
• molecular subgroup
• multi-omics
• pancreatic cancer
• transcriptomics

Supplementary data

To view the supplementary data that accompany this paper please visit the journal website at: www.tandfonline.com/doi/suppl/10.2217/epi-2019-0374

Acknowledgments

The results published here are in whole or part based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga.

Financial & competing interests disclosure

This work was supported by the National Natural Science Foundation of China (grant numbers: 81902953 and 30973501); Natural Science Foundation of Liaoning Province (grant number: 180530068); the Outstanding Young Doctor Fund of China Medical University (grant number: QGZD2018050); Liaoning BaiQianWan Talents Program (grant number: 3200417003); 345 Talent Project of Shengjing Hospital of China Medical University. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

The writing assistance used in the production of this manuscript was provided by American Journal Experts (AJE). The funding for AJE writing assistance was provided by the 345 Talent Project of Shengjing Hospital of China Medical University.

Ethical conduct of research

The authors state that they have obtained appropriate institutional review board approval or have followed the principles outlined in the Declaration of Helsinki for all human or animal experimental investigations. In addition, for investigations involving human subjects, informed consent has been obtained from the participants involved.

Additional information

Funding

This work was supported by the National Natural Science Foundation of China (grant numbers: 81902953 and 30973501); Natural Science Foundation of Liaoning Province (grant number: 180530068); the Outstanding Young Doctor Fund of China Medical University (grant number: QGZD2018050); Liaoning BaiQianWan Talents Program (grant number: 3200417003); 345 Talent Project of Shengjing Hospital of China Medical University. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. The writing assistance used in the production of this manuscript was provided by American Journal Experts (AJE). The funding for AJE writing assistance was provided by the 345 Talent Project of Shengjing Hospital of China Medical University.