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Ding Y, Yao J, Wen M, Liu X, Huang J, Zhang M, Zhang Y, Lv Y, Xie Z, Zuo J. The potential, analysis and prospect of ctDNA sequencing in hepatocellular carcinoma. PeerJ 2022; 10:e13473. [PMID: 35602894 PMCID: PMC9121877 DOI: 10.7717/peerj.13473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 04/29/2022] [Indexed: 01/14/2023] Open
Abstract
Background The genome map of hepatocellular carcinoma (HCC) is complex. In order to explore whether circulating tumor cell DNA (ctDNA) can be used as the basis for sequencing and use ctDNA to find tumor related biomarkers, we analyzed the mutant genes of ctDNA in patients with liver cancer by sequencing. Methods We used next-generation targeted sequencing technology to identify mutations in patients with liver cancer. The ctDNA from 10 patients with hepatocellular carcinoma (including eight cases of primary hepatocellular carcinoma and two cases of secondary hepatocellular carcinoma) was sequenced. We used SAMtools to detect and screen single nucleotide polymorphisms (SNPs) and insertion deletion mutations (INDELs) and ANNOVAR to annotate the structure and function of the detected mutations. Screening of pathogenic and possible pathogenic genes was performed using American College of Medical Genetics and Genomics (ACMG) guidelines. GO analysis and KEGG analysis of pathogenic and possible pathogenic genes were performed using the DAVID database, and protein-protein interaction network analysis of pathogenic and possible pathogenic genes was performed using the STRING database. Then, the Kaplan-Meier plotter database, GEPIA database and HPA database were used to analyse the relationship between pathogenic and possible pathogenic genes and patients with liver cancer. Results Targeted capture and deep sequencing of 560 cancer-related genes in 10 liver cancer ctDNA samples revealed 8,950 single nucleotide variation (SNV) mutations and 70 INDELS. The most commonly mutated gene was PDE4DIP, followed by SYNE1, KMT2C, PKHD1 and FN1. We compared these results to the COSMIC database and determined that ctDNA could be used for sequencing. According to the ACMG guidelines, we identified 54 pathogenic and possible pathogenic mutations in 39 genes in exons and splice regions of 10 HCC patients and performed GO analysis, KEGG analysis, and PPI network analysis. Through further analysis, four genes significantly related to the prognosis of liver cancer were identified. Conclusion In this study, our findings indicate that ctDNA can be used for sequencing. Our results provide some molecular data for the mapping of genetic variation in Chinese patients with liver cancer, which enriches the understanding of HCC pathogenesis and provides new ideas for the diagnosis and prognosis of HCC patients.
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Affiliation(s)
- Yubo Ding
- The Affiliated Nanhua Hospital of University of South China, Hengyang, Hunan, China,University of South China, Transformation Research Lab, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Hengyang Medical School, Hengyang, Hunan, China
| | - Jingwei Yao
- The Affiliated Nanhua Hospital of University of South China, Hengyang, Hunan, China,University of South China, Transformation Research Lab, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Hengyang Medical School, Hengyang, Hunan, China
| | - Meiling Wen
- The First Affiliated Hospital, University of South China, Hengyang, China
| | - Xiong Liu
- Department of Otolaryngology-Head and Neck Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jialu Huang
- University of South China, Transformation Research Lab, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Hengyang Medical School, Hengyang, Hunan, China
| | - Minghui Zhang
- University of South China, Transformation Research Lab, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Hengyang Medical School, Hengyang, Hunan, China
| | - Yu Zhang
- University of South China, Transformation Research Lab, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Hengyang Medical School, Hengyang, Hunan, China
| | - Yufan Lv
- The Affiliated Nanhua Hospital of University of South China, Hengyang, Hunan, China
| | - Zhuoyi Xie
- University of South China, Transformation Research Lab, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Hengyang Medical School, Hengyang, Hunan, China
| | - JianHong Zuo
- The Affiliated Nanhua Hospital of University of South China, Hengyang, Hunan, China,University of South China, Transformation Research Lab, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Hengyang Medical School, Hengyang, Hunan, China,Clinical Laboratory, The Third Affiliated Hospital of University of South China, Hengyang, Hunan, China
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Zhang Z, Peng Y, Dang J, Liu X, Zhu D, Zhang Y, Shi Y, Fan H. Identification of key biomarkers related to epithelial-mesenchymal transition and immune infiltration in ameloblastoma using integrated bioinformatics analysis. Oral Dis 2022; 29:1657-1667. [PMID: 35226761 DOI: 10.1111/odi.14173] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/04/2022] [Accepted: 02/19/2022] [Indexed: 01/05/2023]
Abstract
OBJECTIVE This study aimed to elucidate the underlying mechanisms of ameloblastoma (AM) through integrated bioinformatics analysis. METHODS We downloaded two microarrays of AMs from the GEO database and identified differentially expressed genes (DEGs) by integrated bioinformatics analysis. The enrichment analysis of DEGs was conducted to characterize GO and KEGG pathways. Protein-protein interaction (PPI) network and hub genes were screened via STRING and Cytoscape. CIBERSORT algorithm was utilized to analyze immune infiltration in AMs. We also verified the diagnostic and therapeutic value of hub genes. RESULTS Overall, 776 DEGs were identified in AMs through bioinformatics analysis. The function enrichment analysis shed light on pathways involved in AMs. Subsequently, we screened six hub genes via PPI network. Furthermore, we evaluated immune infiltration in AMs and found that macrophages may be participating in the progression of AMs. The upregulated expression of FN1 was related to the macrophages M2 polarization. Finally, ROC analysis indicated that six hub genes had high diagnostic value for AMs and 11 drugs interacted with upregulated hub genes were identified by screening the DGIdb database. CONCLUSION This study revealed the underlying mechanisms of pathogenesis and biological behavior of AMs and provided candidate targets for the diagnosis and treatment of AMs.
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Affiliation(s)
- Zhao Zhang
- Division of Musculoskeletal Cancer Service, Department of Orthopaedic Surgery, Xi-jing Hospital, The Fourth Military Medical University, Shaanxi, China
| | - Ye Peng
- Department of Orthopaedics, Air Force Medical Center, PLA, Beijing, China
| | - Jingyi Dang
- Division of Musculoskeletal Cancer Service, Department of Orthopaedic Surgery, Xi-jing Hospital, The Fourth Military Medical University, Shaanxi, China
| | - Xincheng Liu
- Division of Musculoskeletal Cancer Service, Department of Orthopaedic Surgery, Xi-jing Hospital, The Fourth Military Medical University, Shaanxi, China
| | - Dongze Zhu
- Division of Musculoskeletal Cancer Service, Department of Orthopaedic Surgery, Xi-jing Hospital, The Fourth Military Medical University, Shaanxi, China
| | - Yushen Zhang
- Division of Musculoskeletal Cancer Service, Department of Orthopaedic Surgery, Xi-jing Hospital, The Fourth Military Medical University, Shaanxi, China
| | - Yubo Shi
- Division of Musculoskeletal Cancer Service, Department of Orthopaedic Surgery, Xi-jing Hospital, The Fourth Military Medical University, Shaanxi, China
| | - Hongbin Fan
- Division of Musculoskeletal Cancer Service, Department of Orthopaedic Surgery, Xi-jing Hospital, The Fourth Military Medical University, Shaanxi, China
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