1
|
Hua T, Zhang C, Fu Y, Qin N, Liu S, Chen C, Gong L, Ma H, Ding Y, Wei X, Jin C, Jin C, Zhu M, Zhang E, Dai J, Ma H. Integrative analyses of N6-methyladenosine-associated single-nucleotide polymorphisms (m6A-SNPs) identify tumor suppressor gene AK9 in lung cancer. Mol Carcinog 2024; 63:538-548. [PMID: 38051288 DOI: 10.1002/mc.23669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/21/2023] [Accepted: 11/25/2023] [Indexed: 12/07/2023]
Abstract
N6 -methyladenosine (m6 A) modification has been identified as one of the most important epigenetic regulation mechanisms in the development of human cancers. However, the association between m6 A-associated single-nucleotide polymorphisms (m6 A-SNPs) and lung cancer risk remains largely unknown. Here, we identified m6 A-SNPs and examined the association of these m6 A-SNPs with lung cancer risk in 13,793 lung cancer cases and 14,027 controls. In silico functional annotation was used to identify causal m6 A-SNPs and target genes. Furthermore, methylated RNA immunoprecipitation and quantitative real-time polymerase chain reaction (MeRIP-qPCR) assay was performed to assess the m6 A modification level of different genotypes of the causal SNP. In vitro assays were performed to validate the potential role of the target gene in lung cancer. A total of 8794 m6 A-SNPs were detected, among which 397 SNPs in nine susceptibility loci were associated with lung cancer risk, including six novel loci. Bioinformatics analyses indicated that rs1321328 in 6q21 was located around the m6 A modification site of AK9 and significantly reduced AK9 expression (β = -0.15, p = 2.78 × 10-8 ). Moreover, AK9 was significantly downregulated in lung cancer tissues than that in adjacent normal tissues of samples from the Cancer Genome Atlas and Nanjing Lung Cancer Cohort. MeRIP-qPCR assay suggested that C allele of rs1321328 could significantly decrease the m6 A modification level of AK9 compared with G allele. In vitro assays verified the tumor-suppressing role of AK9 in lung cancer. These findings shed light on the pathogenic mechanism of lung cancer susceptibility loci linked with m6 A modification.
Collapse
Affiliation(s)
- Tingting Hua
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Chang Zhang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou Second People's Hospital, Changzhou Medical Center, Nanjing Medical University, Nanjing, China
| | - Yating Fu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Na Qin
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Su Liu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Congcong Chen
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Linnan Gong
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Huimin Ma
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yue Ding
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xiaoxia Wei
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Chenying Jin
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Chen Jin
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Meng Zhu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Erbao Zhang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Juncheng Dai
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Hongxia Ma
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
- Research Units of Cohort Study on Cardiovascular Diseases and Cancers, Chinese Academy of Medical Sciences, Beijing, China
| |
Collapse
|
2
|
Kleinbielen T, Olasagasti F, Azcarate D, Beristain E, Viguri-Díaz A, Guerra-Merino I, García-Orad Á, de Pancorbo MM. In silico identification and in vitro expression analysis of breast cancer-related m 6A-SNPs. Epigenetics 2022; 17:2144-2156. [PMID: 35971775 PMCID: PMC9665143 DOI: 10.1080/15592294.2022.2111137] [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: 04/05/2022] [Accepted: 08/01/2022] [Indexed: 12/24/2022] Open
Abstract
Research on m6A-associated SNPs (m6A-SNPs) has emerged recently due to their possible critical roles in many key biological processes. In this sense, several investigations have identified m6A-SNPs in different diseases. In order to gain a more complete understanding of the role that m6A-SNPs can play in breast cancer, we performed an in silico analysis to identify the m6A-SNPs associated with breast cancer and to evaluate their possible effects. For this purpose, we downloaded SNPs related to breast cancer and a list of m6A-SNPs from public databases in order to identify which ones appear in both. Subsequently, we assessed the identified m6A-SNPs in silico by expression quantitative trait loci (eQTL) analysis and differential gene expression analysis. We genotyped the m6A-SNPs found in the in silico analysis in 35 patients with breast cancer, and we carried out a gene expression analysis experimentally on those that showed differences. Our results identified 981 m6A-SNPs related to breast cancer. Four m6A-SNPs showed an eQTL effect and only three were in genes that presented an altered gene expression. When the three m6A-SNPs were evaluated in the tissue sample of our breast cancer patients, only the m6A-SNP rs76563149 located in ZNF354A gene presented differences in allele frequencies and a low gene expression in breast cancer tissues, especially in luminal B HER2+ subtype. Future investigations of these m6A-SNPs should expand the study in different ethnic groups and increase the sample sizes to test their association with breast cancer and elucidate their molecular function.
Collapse
Affiliation(s)
- Tamara Kleinbielen
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU. Postal code: 01006. Vitoria-Gasteiz, Araba, Spain
- Department of Zoology and Animal Biology. University of the Basque Country (UPV/EHU). Postal code: 48940. Leioa, Bizkaia, Spain
- Bioaraba Health Research Institute. Postal Code: 01009, Vitoria-Gasteiz, Araba, Spain
| | - Felix Olasagasti
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU. Postal code: 01006. Vitoria-Gasteiz, Araba, Spain
- Bioaraba Health Research Institute. Postal Code: 01009, Vitoria-Gasteiz, Araba, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country, UPV/EHU. Postal code: 01006. Vitoria-Gasteiz, Araba, Spain
| | - Daniel Azcarate
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU. Postal code: 01006. Vitoria-Gasteiz, Araba, Spain
- Department of Zoology and Animal Biology. University of the Basque Country (UPV/EHU). Postal code: 48940. Leioa, Bizkaia, Spain
- Bioaraba Health Research Institute. Postal Code: 01009, Vitoria-Gasteiz, Araba, Spain
| | - Elena Beristain
- Bioaraba Health Research Institute. Postal Code: 01009, Vitoria-Gasteiz, Araba, Spain
- Molecular Genetics Laboratory, Araba University Hospital, Osakidetza Basque Health Service. Postal code: 01009. Vitoria-Gasteiz, Araba, Spain
| | - Amparo Viguri-Díaz
- Pathology Department, Araba University Hospital. Postal code: 01009. Vitoria-Gasteiz, Araba, Spain
| | - Isabel Guerra-Merino
- Bioaraba Health Research Institute. Postal Code: 01009, Vitoria-Gasteiz, Araba, Spain
- Pathology Department, Araba University Hospital. Postal code: 01009. Vitoria-Gasteiz, Araba, Spain
| | - África García-Orad
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU). Postal code: 48940. Leioa, Bizkaia, Spain
- BioCruces Bizkaia Health Research Institute. Postal code: 48903. Barakaldo, Bizkaia, Spain
| | - Marian M. de Pancorbo
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU. Postal code: 01006. Vitoria-Gasteiz, Araba, Spain
- Department of Zoology and Animal Biology. University of the Basque Country (UPV/EHU). Postal code: 48940. Leioa, Bizkaia, Spain
- Bioaraba Health Research Institute. Postal Code: 01009, Vitoria-Gasteiz, Araba, Spain
| |
Collapse
|