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Cai J, Qiu J, Wang H, Sun J, Ji Y. Identification of potential biomarkers in ovarian carcinoma and an evaluation of their prognostic value. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1472. [PMID: 34734024 PMCID: PMC8506714 DOI: 10.21037/atm-21-4606] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/16/2021] [Indexed: 11/06/2022]
Abstract
Background Ovarian cancer is one of the most common malignant tumors in female genital organs, and its incidence rate is high. However, the pathogenesis and prognostic markers of ovarian cancer are unclear. This study sought to screen potential markers of ovarian cancer and to explore their prognostic value. Methods The Cancer Genome Atlas, Gene Expression Omnibus, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases were used in this study. The least absolute shrinkage and selection operator (LASSO), multivariate Cox regression and stepwise regression analysis were chosen to screen genes and construct risk model. Gene Set Enrichment Analysis (GSEA) and an immune-infiltration analysis were performed. Results One hundred thirty two co-expressed genes were found. They involved in metabolism, protein phosphorylation, mitochondria, and immune signaling pathways. Twelve genes significantly related to the survival of ovarian cancer were identified. Eight risk genes (i.e., CACNB1, FAM120B, HOXB2, MED19, PTPN2, SMU1, WAC.AS1, and BCL2L11) were further screened and used to construct the risk model. The risk status might be an independent prognostic factor of ovarian cancer, and most of the biological functions of genes expressed in high-risk ovarian cancer were related to synapse, adhesion, and immune-related functions. The clusters of CD4+ T cells and M2 macrophages were high in high-risk status samples. Conclusions In ovarian cancer, the abnormal expression of 8 genes, including CACNB1, FAM120B, HOXB2, MED19, PTPN2, SMU1, WAC.AS1, and BCL2L11, is closely related to ovarian cancer progression, and these genes can serve as independent prognosis markers of ovarian cancer.
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Affiliation(s)
- Junyan Cai
- Department of Rehabilitation, Affiliated Hospital of Nantong University, Nantong, China
| | - Jiayi Qiu
- Medical College, Nantong University, Nantong, China
| | - Hongliang Wang
- Department of Neurology, Nantong Sixth People's Hospital, Nantong, China
| | - Jiacheng Sun
- Xinglin College, Nantong University, Nantong, China
| | - Yanan Ji
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Nantong University, Nantong, China
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Jin C, Liu X, Zheng W, Su L, Liu Y, Guo X, Gu X, Li H, Xu B, Wang G, Yu J, Zhang Q, Bao D, Wan S, Xu F, Lai X, Liu J, Xing J. Characterization of fragment sizes, copy number aberrations and 4-mer end motifs in cell-free DNA of hepatocellular carcinoma for enhanced liquid biopsy-based cancer detection. Mol Oncol 2021; 15:2377-2389. [PMID: 34133846 PMCID: PMC8410516 DOI: 10.1002/1878-0261.13041] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/24/2021] [Accepted: 06/15/2021] [Indexed: 02/06/2023] Open
Abstract
Circulating cell‐free DNA (cfDNA) fragmentomics, which encompasses the measurement of cfDNA length and short nucleotide motifs at the ends of cfDNA molecules, is an emerging field for cancer diagnosis. The utilization of cfDNA fragmentomics for the diagnosis of patients with hepatocellular carcinoma (HCC) caused by hepatitis B virus (HBV) is currently limited. In this study, we utilized whole‐genome sequencing data of cfDNA in samples from patients with HCC (n = 197) and HBV (n = 187) to analyze the association of fragment size selection (< 150 bp) with tumor fraction (TF), copy number variation (CNV) alterations and the change in the proportion of 4‐mer end motifs in HCC and HBV samples. Our analyses identified five typical CNV markers (i.e. loss in chr1p, chr4q and chr8p, and gain in chr1q and chr8q) in cfDNA with a cumulatively positive rate of ˜ 95% in HCC samples. Size selection (< 150 bp) significantly enhanced TF and CNV signals in HCC samples. Additionally, three 4‐mer end motifs (CCCA, CCTG and CCAG) were identified as preferred end motifs in HCC samples. We identified 139 end motifs significantly associated with fragment size that showed similar patterns of associations between patients with HCC and HBV, suggesting that end motifs might be inherently coupled with fragment size by a ubiquitous mechanism. Here we conclude that CNV markers, fragment size selection and end‐motif pattern in cfDNA have potential for effective detection of patients with HCC.
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Affiliation(s)
- Chao Jin
- Department of General Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Xiaonan Liu
- Ambulatory Surgery Center of Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Wenyuan Zheng
- Research and Development Division, Oriomics Biotech, Hangzhou, China
| | - Liping Su
- State Key Laboratory of Cancer Biology, Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Yang Liu
- State Key Laboratory of Cancer Biology, Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Xu Guo
- State Key Laboratory of Cancer Biology, Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Xiaoming Gu
- State Key Laboratory of Cancer Biology, Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Hongping Li
- Research and Development Division, Oriomics Biotech, Hangzhou, China
| | - Bo Xu
- Research and Development Division, Oriomics Biotech, Hangzhou, China
| | - Gang Wang
- State Key Laboratory of Cancer Biology, Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Jiyan Yu
- Research and Development Division, Oriomics Biotech, Hangzhou, China
| | - Qiong Zhang
- Research and Development Division, Oriomics Biotech, Hangzhou, China
| | - Dengke Bao
- Laboratory of Cancer Biomarkers and Liquid Biopsy, School of Pharmacy, Henan University, Kaifeng, China
| | - Shaogui Wan
- Center for Molecular Pathology, First Affiliated Hospital, Gannan Medical University, Ganzhou, China
| | - Fei Xu
- Department of Hepatology, The Fifth People's Hospital of Ganzhou, China
| | - Xiaohuan Lai
- Department of Hepatology, The Fifth People's Hospital of Ganzhou, China
| | - Jiayun Liu
- Department of Clinical Laboratory, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Jinliang Xing
- State Key Laboratory of Cancer Biology, Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
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Ponti G, Maccaferri M, Percesepe A, Tomasi A, Ozben T. Liquid biopsy with cell free DNA: new horizons for prostate cancer. Crit Rev Clin Lab Sci 2020; 58:60-76. [PMID: 32805148 DOI: 10.1080/10408363.2020.1803789] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Although prostate cancer (PCa) is one of the most common tumors in European males, the only minimally invasive diagnostic tool in PCa setup is the determination of PSA in serum. Cell-free DNA (cfDNA) has been demonstrated to be helpful for PCa diagnosis but has not yet been integrated into the clinical setting. This review aims to provide a systematic update of cfDNA and its fragmentation patterns in PCa reported in literature published over the last twenty years. Due to the high variability of the scientific methods adopted and a lack of standardized median cfDNA levels, results fluctuate across different studies. These differences may be due to the cfDNA source, the quantification method, or the fragmentation pattern. Blood plasma is the most frequently analyzed biological fluid, but seminal plasma has been reported to contain higher cfDNA concentration due to its vicinity to the tumor origin. CfDNA has been shown to be composed of single-stranded (ssDNA) and double-stranded DNA (dsDNA), so the total cfDNA concentration should be preferred as it corresponds best to the tumor mass. Fluorometry and capillary electrophoresis (CE) may be quick and cost-effective tools for cfDNA assessment in a clinical setting. The greatest future challenge is the elaboration of common guidelines and standardized procedures for diagnostic laboratories performing cfDNA analysis. A multiparametric approach combining the analysis of total cfDNA (both ssDNA and dsDNA), cfDNA fragment length, and specific genetic mutations (ctDNA assessment) is required for optimal future applications of liquid biopsy.
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Affiliation(s)
- Giovanni Ponti
- Division of Clinical Pathology, Department of Surgical, Medical, Dental and Morphological Sciences with Interest in Transplant, Oncological and Regenerative Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - Monia Maccaferri
- Dermatology Unit, Azienda Ospedaliero-Universitaria of Modena, Modena, Italy
| | - Antonio Percesepe
- Medical Genetics Unit, Azienda Ospedaliero-Universitaria of Parma, Parma, Italy
| | - Aldo Tomasi
- Division of Clinical Pathology, Department of Surgical, Medical, Dental and Morphological Sciences with Interest in Transplant, Oncological and Regenerative Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - Tomris Ozben
- Faculty of Medicine, Department of Clinical Biochemistry, Akdeniz University, Antalya, Turkey
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Zhang W. Towards clinical implementation of circulating cell-free DNA in precision medicine. JOURNAL OF TRANSLATIONAL GENETICS AND GENOMICS 2019; 3. [PMID: 31579300 DOI: 10.20517/jtgg.2019.07] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Wei Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
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