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Chitcharoen S, Phokaew C, Mauleekoonphairoj J, Khongphatthanayothin A, Sutjaporn B, Wandee P, Poovorawan Y, Nademanee K, Payungporn S. Metagenomic analysis of viral genes integrated in whole genome sequencing data of Thai patients with Brugada syndrome. Genomics Inform 2022; 20:e44. [PMID: 36617651 PMCID: PMC9847385 DOI: 10.5808/gi.22047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/03/2022] [Accepted: 09/25/2022] [Indexed: 12/31/2022] Open
Abstract
Brugada syndrome (BS) is an autosomal dominant inheritance cardiac arrhythmia disorder associated with sudden death in young adults. Thailand has the highest prevalence of BS worldwide, and over 60% of patients with BS still have unclear disease etiology. Here, we performeda new viral metagenome analysis pipeline called VIRIN and validated it with whole genome sequencing (WGS) data of HeLa cell lines and hepatocellular carcinoma. Then the VIRIN pipelinewas applied to identify viral integration positions from unmapped WGS data of Thai males, including 100 BS patients (case) and 100 controls. Even though the sample preparation had noviral enrichment step, we can identify several virus genes from our analysis pipeline. The predominance of human endogenous retrovirus K (HERV-K) viruses was found in both cases andcontrols by blastn and blastx analysis. This study is the first report on the full-length HERV-Kassembled genomes in the Thai population. Furthermore, the HERV-K integration breakpointpositions were validated and compared between the case and control datasets. Interestingly,Brugada cases contained HERV-K integration breakpoints at promoters five times more oftenthan controls. Overall, the highlight of this study is the BS-specific HERV-K breakpoint positionsthat were found at the gene coding region "NBPF11" (n = 9), "NBPF12" (n = 8) and longnon-coding RNA (lncRNA) "PCAT14" (n = 4) region. The genes and the lncRNA have been reported to be associated with congenital heart and arterial diseases. These findings provide another aspect of the BS etiology associated with viral genome integrations within the humangenome.
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Affiliation(s)
- Suwalak Chitcharoen
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Chureerat Phokaew
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok 10330, Thailand
- Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - John Mauleekoonphairoj
- Department of Medicine, Faculty of Medicine, Center of Excellence in Arrhythmia Research Chulalongkorn University, Chulalongkorn University, Bangkok 10330, Thailand
- Interdisciplinary Program of Biomedical Sciences, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Apichai Khongphatthanayothin
- Department of Medicine, Faculty of Medicine, Center of Excellence in Arrhythmia Research Chulalongkorn University, Chulalongkorn University, Bangkok 10330, Thailand
- Division of Cardiology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Bangkok General Hospital, Bangkok 10330, Thailand
| | - Boosamas Sutjaporn
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok 10330, Thailand
- Department of Medicine, Faculty of Medicine, Center of Excellence in Arrhythmia Research Chulalongkorn University, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pharawee Wandee
- Department of Medicine, Faculty of Medicine, Center of Excellence in Arrhythmia Research Chulalongkorn University, Chulalongkorn University, Bangkok 10330, Thailand
| | - Yong Poovorawan
- Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Koonlawee Nademanee
- Department of Medicine, Faculty of Medicine, Center of Excellence in Arrhythmia Research Chulalongkorn University, Chulalongkorn University, Bangkok 10330, Thailand
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Pacific Rim Electrophysiology Research Institute, Bumrungrad Hospital, Bangkok 10110, Thailand
| | - Sunchai Payungporn
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
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Li L, Chen S, Tang Y, Wu J, He Y, Qiu L. Oncogene or tumor suppressor gene: An integrated pan-cancer analysis of NBPF1. Front Endocrinol (Lausanne) 2022; 13:950326. [PMID: 36060966 PMCID: PMC9428449 DOI: 10.3389/fendo.2022.950326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 07/22/2022] [Indexed: 11/13/2022] Open
Abstract
Neuroblastoma breakpoint family, member 1 (NBPF1), appears to be a double-edged sword with regard to its role in carcinogenesis. On the one hand, the tumor-suppressing functions of NBPF1 have been definitively observed in neuroblastoma, prostate cancer, cutaneous squamous cell carcinoma, and cervical cancer. On the other hand, there is evidence that NBPF1 regulates the colony formation, invasion, and maintenance of liver cancer cells and hence functions as an oncogene. The roles of NBPF1 are strictly dependent on the biological context and type of organization. However, a systematic pan-cancer analysis has thus far not been undertaken, and the significance of NBPF1 in the occurrence and progression of many malignancies is uncertain. In this paper, bioinformatics techniques were employed to analyze NBPF1 expression across different cancers and investigate the relationship between NBPF1 and clinical features, prognosis, genetic alteration, and tumor immune microenvironment, respectively. Our results show that NBPF1 is variably expressed in distinct tumor tissues and is also closely linked to clinical outcomes. In particular, compared to other tumor types, there was a strong negative correlation between NBPF1 expression and various components of the tumor microenvironment in adrenocortical carcinoma (ACC). We thus developed an NBPF1-derived immune risk model based on NBPF1-related immune genes; ACC patients with a high-risk score tended to have a poorer prognosis, accompanied by immune hyporesponsiveness. NBPF1 can be used as a prognostic biomarker for multiple cancers. Moreover, anti-NBPF1 immunotherapy may be suitable for treating ACC patients.
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Affiliation(s)
- Lei Li
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, China
| | - Sen Chen
- Immune Cells and Antibody Engineering Research Center of Guizhou Province, Key Laboratory of Biology and Medical Engineering, School of Biology and Engineering, Guizhou Medical University, Guiyang, China
| | - Yueming Tang
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, China
| | - Jie Wu
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, China
- *Correspondence: Jie Wu, ; Yangzhige He, ; Ling Qiu,
| | - Yangzhige He
- Department of Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- *Correspondence: Jie Wu, ; Yangzhige He, ; Ling Qiu,
| | - Ling Qiu
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, China
- *Correspondence: Jie Wu, ; Yangzhige He, ; Ling Qiu,
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