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Liao X, Lin R, Zhang Z, Tian D, Liu Z, Chen S, Xu G, Su M. Genome-wide DNA methylation and transcriptomic patterns of precancerous gastric cardia lesions. J Natl Cancer Inst 2024; 116:681-693. [PMID: 38258659 DOI: 10.1093/jnci/djad244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/25/2023] [Accepted: 11/15/2023] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Intestinal metaplasia (IM) and intraepithelial neoplasia (IEN) are considered precursors of gastric cardia cancer (GCC). Here, we investigated the histopathologic and molecular profiles of precancerous gastric cardia lesions (PGCLs) and biomarkers for risk stratification of gastric cardia IM. METHODS We conducted a hospital-based evaluation (n = 4578) for PGCL profiles in high-incidence and non-high-incidence regions for GCC in China. We next performed 850K methylation arrays (n = 42) and RNA-seq (n = 44) in tissues with PGCLs. We then examined the protein expression of candidate biomarker using immunohistochemistry. RESULTS Of the 4578 participants, 791 were diagnosed with PGCLs (600 IM, 62 IM with IEN, and 129 IEN). We found that individuals from high-incidence regions (26.7%) were more likely to develop PGCLs than those from non-high-incidence areas (13.5%). DNA methylation and gene expression alterations, indicated by differentially methylated probes (DMPs) and differentially expressed genes (DEGs), exhibited a progressive increase from type I IM (DMP = 210, DEG = 24), type II IM (DMP = 3402, DEG = 129), to type III IM (DMP = 3735, DEG = 328), peaking in IEN (DMP = 47 373, DEG = 2278). Three DEGs with aberrant promoter methylation were identified, shared exclusively by type III IM and IEN. Of these DEGs, we found that OLFM4 expression appears in IMs and increases remarkably in IENs (P < .001). CONCLUSIONS We highlight that type III IM and IEN share similar epigenetic and transcriptional features in gastric cardia and propose biomarkers with potential utility in risk prediction.
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Affiliation(s)
- Xiaoqi Liao
- Department of Pathology, Shantou University Medical College, Shantou, People's Republic of China
| | - Runhua Lin
- Department of Pathology, Shantou University Medical College, Shantou, People's Republic of China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, People's Republic of China
| | - Zhihua Zhang
- Department of Pathology, Shantou University Medical College, Shantou, People's Republic of China
| | - Dongping Tian
- Department of Pathology, Shantou University Medical College, Shantou, People's Republic of China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, People's Republic of China
| | - Zhaohui Liu
- Department of Gastroenterology, Shenzhen Second People's Hospital/The First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, People's Republic of China
| | - Songqin Chen
- Department of Pathology, Jieyang People's Hospital, Jieyang, People's Republic of China
| | - Guohua Xu
- Department of Gastroenterology, Huiyang Sanhe Hospital, Huizhou, People's Republic of China
| | - Min Su
- Department of Pathology, Shantou University Medical College, Shantou, People's Republic of China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, People's Republic of China
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Chen X, Su D, Sun Z, Fu Y, Hu Y, Zhang Y, Zhang X, Wei Q, Zhu W, Ma X, Hu S. Preliminary study on whole genome methylation and transcriptomics in age-related cataracts. Gene 2024; 898:148096. [PMID: 38128790 DOI: 10.1016/j.gene.2023.148096] [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: 09/10/2023] [Revised: 12/10/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
DNA methylation plays an important role in the occurrence and development of age-related cataracts (ARC). This study aims to reveal potential epigenetic biomarkers of ARC by detecting modifications to the DNA methylation patterns of genes shown to be related to ARC by transcriptomics. The MethylationEPIC BeadChip (850 K) was used to analyze the DNA methylation levels in ARC patients and unaffected controls, and the Pearson correlation test was used to perform genome-wide integration analysis of DNA methylation and transcriptome data. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were used to perform functional analysis of the whole genome, promoter regions (TSS1500/TSS200), and the associated differentially methylated genes (DMG). Pyrosequencing was used to verify the methylation levels of the selected genes. The results showed that, compared with the control group, a total of 52,705 differentially methylated sites were detected in the ARC group, of which 13,858 were hypermethylated and 38,847 were hypomethylated. GO and KEGG analyses identified functions related to the cell membrane, the calcium signaling pathway, and their possible molecular mechanisms. Then, 57 DMGs with negative promoter methylation correlations were screened by association analysis. Pyrosequencing verified that the ARC group had higher methylation levels of C3 and CCKAR and lower methylation levels of NLRP3, LEFTY1, and GPR35 compared with the control group. In summary, our study reveals the whole-genome DNA methylation patterns and gene expression profiles in ARC, and the molecular markers of methylation identified herein may aid in the prevention, diagnosis, treatment, and prognosis of ARC.
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Affiliation(s)
- Xiaoya Chen
- Mudanjiang Medical University, Mudanjiang 157011, Heilongjiang, China
| | - Dongmei Su
- Department of Genetics, NHC Key Laboratory of Reproductive Health Engineering Technology Research, National Research Institute for Family Planning, Health Department, Beijing 100081, China; Graduate School, Peking Union Medical College, Beijing 100081, China
| | - Zhaoyi Sun
- Hongqi Hospital of Mudanjiang Medical University, Mudanjiang 157011, Heilongjiang, China
| | - Yanjiang Fu
- Daqing Eye Hospital, Daqing 163000, Heilongjiang, China
| | - Yuzhu Hu
- Mudanjiang Medical University, Mudanjiang 157011, Heilongjiang, China
| | - Yue Zhang
- Mudanjiang Medical University, Mudanjiang 157011, Heilongjiang, China
| | - Xiao Zhang
- Mudanjiang Medical University, Mudanjiang 157011, Heilongjiang, China
| | - Qianqiu Wei
- Hongqi Hospital of Mudanjiang Medical University, Mudanjiang 157011, Heilongjiang, China
| | - Wenna Zhu
- Hongqi Hospital of Mudanjiang Medical University, Mudanjiang 157011, Heilongjiang, China
| | - Xu Ma
- Department of Genetics, NHC Key Laboratory of Reproductive Health Engineering Technology Research, National Research Institute for Family Planning, Health Department, Beijing 100081, China; Graduate School, Peking Union Medical College, Beijing 100081, China.
| | - Shanshan Hu
- Hongqi Hospital of Mudanjiang Medical University, Mudanjiang 157011, Heilongjiang, China.
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