1
|
Zhao G, Jiang R, Shi Y, Gao S, Wang D, Li Z, Zhou Y, Sun J, Wu W, Peng J, Kuang T, Rong Y, Yuan J, Zhu S, Jin G, Wang Y, Lou W. Circulating cell-free DNA methylation-based multi-omics analysis allows early diagnosis of pancreatic ductal adenocarcinoma. Mol Oncol 2024. [PMID: 38561976 DOI: 10.1002/1878-0261.13643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 02/29/2024] [Accepted: 03/15/2024] [Indexed: 04/04/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with a 5-year survival rate of 7.2% in China. However, effective approaches for diagnosis of PDAC are limited. Tumor-originating genomic and epigenomic aberration in circulating free DNA (cfDNA) have potential as liquid biopsy biomarkers for cancer diagnosis. Our study aims to assess the feasibility of cfDNA-based liquid biopsy assay for PDAC diagnosis. In this study, we performed parallel genomic and epigenomic profiling of plasma cfDNA from Chinese PDAC patients and healthy individuals. Diagnostic models were built to distinguish PDAC patients from healthy individuals. Cancer-specific changes in cfDNA methylation landscape were identified, and a diagnostic model based on six methylation markers achieved high sensitivity (88.7% for overall cases and 78.0% for stage I patients) and specificity (96.8%), outperforming the mutation-based model significantly. Moreover, the combination of the methylation-based model with carbohydrate antigen 19-9 (CA19-9) levels further improved the performance (sensitivity: 95.7% for overall cases and 95.5% for stage I patients; specificity: 93.3%). In conclusion, our findings suggest that both methylation-based and integrated liquid biopsy assays hold promise as non-invasive tools for detection of PDAC.
Collapse
Affiliation(s)
- Guochao Zhao
- Department of Pancreatic Surgery, Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | | | - Ying Shi
- Envelope Health Biotechnology Co. Ltd., BGI-Shenzhen, China
| | - Suizhi Gao
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital Affiliated to Navy Medical University, Shanghai, China
| | - Dansong Wang
- Department of Pancreatic Surgery, Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhilong Li
- Envelope Health Biotechnology Co. Ltd., BGI-Shenzhen, China
| | - Yuhong Zhou
- Department of Medical Oncology, Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jianlong Sun
- Envelope Health Biotechnology Co. Ltd., BGI-Shenzhen, China
| | - Wenchuan Wu
- Department of Pancreatic Surgery, Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jiaxi Peng
- Envelope Health Biotechnology Co. Ltd., BGI-Shenzhen, China
| | - Tiantao Kuang
- Department of Pancreatic Surgery, Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yefei Rong
- Department of Pancreatic Surgery, Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jie Yuan
- The Fifth Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Shida Zhu
- BGI Genomics, BGI-Shenzhen, China
- Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics, BGI-Shenzhen, China
| | - Gang Jin
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital Affiliated to Navy Medical University, Shanghai, China
| | - Yuying Wang
- Envelope Health Biotechnology Co. Ltd., BGI-Shenzhen, China
| | - Wenhui Lou
- Department of Pancreatic Surgery, Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| |
Collapse
|
2
|
Murthy D, Attri KS. PTGES Expression Is Associated with Metabolic and Immune Reprogramming in Pancreatic Ductal Adenocarcinoma. Int J Mol Sci 2023; 24:ijms24087304. [PMID: 37108468 PMCID: PMC10138618 DOI: 10.3390/ijms24087304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/18/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Metabolic reprogramming is an established hallmark of multiple cancers, including pancreatic cancer. Dysregulated metabolism is utilized by cancer cells for tumor progression, metastasis, immune microenvironment remodeling, and therapeutic resistance. Prostaglandin metabolites have been shown to be critical for inflammation and tumorigenesis. While the functional role of prostaglandin E2 metabolite has been extensively studied, there is a limited understanding of the PTGES enzyme in pancreatic cancer. Here, we investigated the relationship between expression of prostaglandin E synthase (PTGES) isoforms and the pathogenesis and regulation of pancreatic cancer. Our analysis identified higher expression of PTGES in pancreatic tumors compared to normal pancreatic tissues, suggesting an oncogenic function. Only PTGES1 expression was significantly correlated with worse prognosis of pancreatic cancer patients. Further, utilizing cancer genome atlas data, PTGES was found to be positively correlated with epithelial-mesenchymal transition, metabolic pathways, mucin oncogenic proteins, and immune pathways in cancer cells. PTGES expression was also correlated with higher mutational burden in key driver genes, such as TP53 and KRAS. Furthermore, our analysis indicated that the oncogenic pathway controlled by PTGES1 could be regulated via DNA methylation-dependent epigenetic mechanisms. Notably, the glycolysis pathway was positively correlated with PTGES and may fuel cancer cell growth. PTGES expression was also associated with downregulation of the MHC pathway and negatively correlated with CD8+ T cell activation markers. In summary, our study established an association of PTGES expression with pancreatic cancer metabolism and the immune microenvironment.
Collapse
Affiliation(s)
- Divya Murthy
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kuldeep S Attri
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| |
Collapse
|
3
|
Hu R, Shi M, Xu H, Wu X, He K, Chen Y, Wu L, Ma R. Integrated bioinformatics analysis identifies the effects of Sema3A/NRP1 signaling in oligodendrocytes after spinal cord injury in rats. PeerJ 2022; 10:e13856. [PMID: 35990904 PMCID: PMC9390322 DOI: 10.7717/peerj.13856] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 07/16/2022] [Indexed: 01/18/2023] Open
Abstract
Objective To investigate the effect of Sema3A/NRP1 signaling in oligodendrocytes (OLs) after spinal cord injury. Methods Three analysis strategies, namely differential expression gene analysis, Gene Ontology (GO) enrichment, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, were applied. The protein-protein interaction (PPI) network was constructed using the STRING website to explore the correlation between Sema3A/NRP1 and oligodendrocytes. Then, the T10 spinal cord segment of rats was injured by the Allen method to establish a spinal cord injury (SCI) model. Real-time quantitative PCR, Western blotting, Nissl staining and immunofluorescence staining were used to detect the effect of Sema3A/NRP1 signaling on oligodendrocytes in vivo. Results After the SCI model was established, significantly fewer oligodendrocytes were observed. At the same time, R software was used to analyze the expression of related genes, and NRP1 expression was increased. PCR also demonstrated similar results, and NRP1 ligand Sema3A was also upregulated. KEGG and GO functional enrichment analysis indicated that the SCI model was mainly related to cytokine interaction, cell proliferation, differentiation and maturation. Interestingly, we found that NRP1 was involved in semaphorin-plexin signaling pathway neuronal projection guidance and axon guidance, mediating cell growth and migration. Moreover, Sema3A/NRP1 signaling was closely associated with platelet-derived growth factor receptor α (PDGFRα) in the PPI network. When Sema3A/NRP1 signaling was specifically blocked at early stages, PDGFRα expression was effectively inhibited, and the expression of OLs was promoted. Furthermore, inhibition of Sema3A/NRP1 signaling increased the Basso-Beattie-Bresnahan (BBB) score of lower limb motor function in SCI rats and promoted the survival of motor neurons in the ventral horn of the injured spinal cord. Conclusion Our data suggest that Sema3A/NRP1 signaling may regulate the development of OPCs and OLs after SCI, thereby affecting functional recovery.
Collapse
Affiliation(s)
- Rong Hu
- Zhejiang Chinese Medical University, Key Laboratory of Acupuncture and Neurology of Zhejiang Province, Third School of Clinical Medicine (School of Rehabilitation Medicine), HangZhou, China
| | - Mengting Shi
- Zhejiang Chinese Medical University, Key Laboratory of Acupuncture and Neurology of Zhejiang Province, Third School of Clinical Medicine (School of Rehabilitation Medicine), HangZhou, China
| | - Haipeng Xu
- Zhejiang Chinese Medical University, Key Laboratory of Acupuncture and Neurology of Zhejiang Province, Third School of Clinical Medicine (School of Rehabilitation Medicine), HangZhou, China
| | - Xingying Wu
- Zhejiang Chinese Medical University, Key Laboratory of Acupuncture and Neurology of Zhejiang Province, Third School of Clinical Medicine (School of Rehabilitation Medicine), HangZhou, China
| | - Kelin He
- Zhejiang Chinese Medical University, Key Laboratory of Acupuncture and Neurology of Zhejiang Province, Third School of Clinical Medicine (School of Rehabilitation Medicine), HangZhou, China,Department of Acupuncture and Moxibustion, The Third Affiliated Hospital of Zhejiang Chinese Medical University (Zhongshan Hospital of Zhejiang Province), HangZhou, China
| | - Yi Chen
- Zhejiang Chinese Medical University, Key Laboratory of Acupuncture and Neurology of Zhejiang Province, Third School of Clinical Medicine (School of Rehabilitation Medicine), HangZhou, China
| | - Lei Wu
- Department of Acupuncture and Moxibustion, The Third Affiliated Hospital of Zhejiang Chinese Medical University (Zhongshan Hospital of Zhejiang Province), HangZhou, China
| | - Ruijie Ma
- Zhejiang Chinese Medical University, Key Laboratory of Acupuncture and Neurology of Zhejiang Province, Third School of Clinical Medicine (School of Rehabilitation Medicine), HangZhou, China,Department of Acupuncture and Moxibustion, The Third Affiliated Hospital of Zhejiang Chinese Medical University (Zhongshan Hospital of Zhejiang Province), HangZhou, China
| |
Collapse
|