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Ren N, Dai S, Ma S, Yang F. Strategies for activity analysis of single nucleotide polymorphisms associated with human diseases. Clin Genet 2023; 103:392-400. [PMID: 36527336 DOI: 10.1111/cge.14282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/10/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
Genome-wide association studies (GWAS) have identified a large number of single nucleotide polymorphism (SNP) sites associated with human diseases. In the annotation of human diseases, especially cancers, SNPs, as an important component of genetic factors, have gained increasing attention. Given that most of the SNPs are located in non-coding regions, the functional verification of these SNPs is a great challenge. The key to functional annotation for risk SNPs is to screen SNPs with regulatory activity from thousands of disease associated-SNPs. In this review, we systematically recapitulate the characteristics and functional roles of SNP sites, discuss three parallel reporter screening strategies in detail based on barcode tag classification, and recommend the common in silico strategies to help supplement the annotation of SNP sites with epigenetic activity analysis, prediction of target genes and trans-acting factors. We hope that this review will contribute to this exuberant research field by providing robust activity analysis strategies that can facilitate the translation of GWAS results into personalized diagnosis and prevention measures for human diseases.
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Affiliation(s)
- Naixia Ren
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
| | - Shangkun Dai
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
| | - Shumin Ma
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Fengtang Yang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
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Chen X, Li Y, Paiboonrungruang C, Li Y, Peters H, Kist R, Xiong Z. PAX9 in Cancer Development. Int J Mol Sci 2022; 23:5589. [PMID: 35628401 PMCID: PMC9147292 DOI: 10.3390/ijms23105589] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/12/2022] [Accepted: 05/14/2022] [Indexed: 02/05/2023] Open
Abstract
Paired box 9 (PAX9) is a transcription factor of the PAX family functioning as both a transcriptional activator and repressor. Its functional roles in the embryonic development of various tissues and organs have been well studied. However, its roles and molecular mechanisms in cancer development are largely unknown. Here, we review the current understanding of PAX9 expression, upstream regulation of PAX9, and PAX9 downstream events in cancer development. Promoter hypermethylation, promoter SNP, microRNA, and inhibition of upstream pathways (e.g., NOTCH) result in PAX9 silencing or downregulation, whereas gene amplification and an epigenetic axis upregulate PAX9 expression. PAX9 may contribute to carcinogenesis through dysregulation of its transcriptional targets and related molecular pathways. In summary, extensive studies on PAX9 in its cellular and tissue contexts are warranted in various cancers, in particular, HNSCC, ESCC, lung cancer, and cervical SCC.
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Affiliation(s)
- Xiaoxin Chen
- Cancer Research Program, Julius L. Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, 700 George Street, Durham, NC 27707, USA; (X.C.); (Y.L.); (C.P.); (Y.L.)
| | - Yahui Li
- Cancer Research Program, Julius L. Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, 700 George Street, Durham, NC 27707, USA; (X.C.); (Y.L.); (C.P.); (Y.L.)
| | - Chorlada Paiboonrungruang
- Cancer Research Program, Julius L. Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, 700 George Street, Durham, NC 27707, USA; (X.C.); (Y.L.); (C.P.); (Y.L.)
| | - Yong Li
- Cancer Research Program, Julius L. Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, 700 George Street, Durham, NC 27707, USA; (X.C.); (Y.L.); (C.P.); (Y.L.)
- Department of Thoracic Surgery, National Cancer Center, Cancer Hospital of Chinese Academy of Medical Sciences, 17 Panjiayuan Nanli Road, Beijing 100021, China
| | - Heiko Peters
- Newcastle University Biosciences Institute, Newcastle upon Tyne NE2 4BW, UK;
| | - Ralf Kist
- Newcastle University Biosciences Institute, Newcastle upon Tyne NE2 4BW, UK;
- School of Dental Sciences, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4BW, UK
| | - Zhaohui Xiong
- Cancer Research Program, Julius L. Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, 700 George Street, Durham, NC 27707, USA; (X.C.); (Y.L.); (C.P.); (Y.L.)
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