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Zhang Y, Lyu Y, Chen L, Cao K, Chen J, He C, Lyu X, Jiang Y, Xiang J, Liu B, Wu C. Exploring the Prognosis-Related Genetic Variation in Gastric Cancer Based on mGWAS. Int J Mol Sci 2023; 24:15259. [PMID: 37894938 PMCID: PMC10607287 DOI: 10.3390/ijms242015259] [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: 08/08/2023] [Revised: 09/30/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
The use of metabolome genome-wide association studies (mGWAS) has been shown to be effective in identifying functional genes in complex diseases. While mGWAS has been applied to biomedical and pharmaceutical studies, its potential in predicting gastric cancer prognosis has yet to be explored. This study aims to address this gap and provide insights into the genetic basis of GC survival, as well as identify vital regulatory pathways in GC cell progression. Genome-wide association analysis of plasma metabolites related to gastric cancer prognosis was performed based on the Generalized Linear Model (GLM). We used a log-rank test, LASSO regression, multivariate Cox regression, GO enrichment analysis, and the Cytoscape software to visualize the complex regulatory network of genes and metabolites and explored in-depth genetic variation in gastric cancer prognosis based on mGWAS. We found 32 genetic variation loci significantly associated with GC survival-related metabolites, corresponding to seven genes, VENTX, PCDH 7, JAKMIP1, MIR202HG, MIR378D1, LINC02472, and LINC02310. Furthermore, this study identified 722 Single nucleotide polymorphism (SNP) sites, suggesting an association with GC prognosis-related metabolites, corresponding to 206 genes. These 206 possible functional genes for gastric cancer prognosis were mainly involved in cellular signaling molecules related to cellular components, which are mainly involved in the growth and development of the body and neurological regulatory functions related to the body. The expression of 23 of these genes was shown to be associated with survival outcome in gastric cancer patients in The Cancer Genome Atlas (TCGA) database. Based on the genome-wide association analysis of prognosis-related metabolites in gastric cancer, we suggest that gastric cancer survival-related genes may influence the proliferation and infiltration of gastric cancer cells, which provides a new idea to resolve the complex regulatory network of gastric cancer prognosis.
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Affiliation(s)
- Yuling Zhang
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Yanping Lyu
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Liangping Chen
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Kang Cao
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Jingwen Chen
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Chenzhou He
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Xuejie Lyu
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Yu Jiang
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Jianjun Xiang
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Baoying Liu
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Chuancheng Wu
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
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Ciceri S, Carenzo A, Iannó MF, Bertolotti A, Morosi C, Luksch R, Spreafico F, Collini P, Radice P, Massimino M, De Cecco L, Perotti D. Gene expression-based dissection of inter-histotypes, intra-histotype and intra-tumor heterogeneity in pediatric tumors. Sci Rep 2022; 12:17837. [PMID: 36284197 PMCID: PMC9596396 DOI: 10.1038/s41598-022-20536-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/14/2022] [Indexed: 02/07/2023] Open
Abstract
Intra-tumor heterogeneity (ITH) fosters tumor evolution, resistance to therapy, and relapse. Recently, many evidence have been accumulated on the occurrence of genetic ITH in pediatric cancers. With this study we aimed to address the downstream effects that genetic and epigenetic ITH, and tumor-microenvironment interactions may produce within a tumor mass. To this aim, we investigated by high-throughput gene expression multiple samples of 5 hepatoblastomas, 5 neuroblastomas, 5 rhabdomyosarcomas, and 5 Wilms tumors. Principal component analysis, single sample hallmark gene sets analysis, and weighted gene co-expression network analysis were performed on gene expression data. We observed that the different tumors clustered by histotype, and then by case, and in addition, a variable degree of ITH was visible in all the investigated cases. The ITH highlighted in this study can represent a challenge in tumor treatment since we demonstrated that different druggable hallmarks and targets may be heterogeneously present within the same tumor mass, and this can potentially lead to therapeutic failure. Despite this heterogeneity, we could highlight some commonalities among the different histotypes investigated, supporting the feasibility to move in the clinic from a histotype-driven to a target-driven, sometimes agnostic, approach at least in some cases.
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Affiliation(s)
- Sara Ciceri
- grid.417893.00000 0001 0807 2568Molecular Bases of Genetic Risk and Genetic Testing Unit, Department of Research, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Venezian 1, 20133 Milano, Italy
| | - Andrea Carenzo
- grid.417893.00000 0001 0807 2568Molecular Mechanisms Unit, Department of Research, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Venezian 1, 20133 Milano, Italy
| | - Maria Federica Iannó
- grid.417893.00000 0001 0807 2568Integrated Biology Platform, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Alessia Bertolotti
- grid.417893.00000 0001 0807 2568Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Carlo Morosi
- grid.417893.00000 0001 0807 2568Department of Radiology, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Roberto Luksch
- grid.417893.00000 0001 0807 2568Pediatric Oncology Unit, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Filippo Spreafico
- grid.417893.00000 0001 0807 2568Pediatric Oncology Unit, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Paola Collini
- grid.417893.00000 0001 0807 2568Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Paolo Radice
- grid.417893.00000 0001 0807 2568Molecular Bases of Genetic Risk and Genetic Testing Unit, Department of Research, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Venezian 1, 20133 Milano, Italy
| | - Maura Massimino
- grid.417893.00000 0001 0807 2568Pediatric Oncology Unit, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Loris De Cecco
- grid.417893.00000 0001 0807 2568Molecular Mechanisms Unit, Department of Research, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Venezian 1, 20133 Milano, Italy
| | - Daniela Perotti
- grid.417893.00000 0001 0807 2568Molecular Bases of Genetic Risk and Genetic Testing Unit, Department of Research, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Venezian 1, 20133 Milano, Italy
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Wu F, Du Y, Hou X, Cheng W. A prognostic model for oral squamous cell carcinoma using 7 genes related to tumor mutational burden. BMC Oral Health 2022; 22:152. [PMID: 35488327 PMCID: PMC9052477 DOI: 10.1186/s12903-022-02193-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 04/14/2022] [Indexed: 02/06/2023] Open
Abstract
Background Oral squamous cell carcinoma (OSCC) is a rising problem in global public health. The traditional physical and imageological examinations are invasive and radioactive. There is a need for less harmful new biomarkers. Tumor mutational burden (TMB) is a novel prognostic biomarker for various cancers. We intended to explore the relationship between TMB-related genes and the prognosis of OSCC and to construct a prognostic model. Methods TMB-related differential expressed genes (DEGs) were screened by differential analysis and optimized via the univariate Cox and LASSO Cox analyses. Risk Score model was constructed by expression values of screened genes multiplying coefficient of LASSO Cox. Results Seven TMB-related DEGs (CTSG, COL6A5, GRIA3, CCL21, ZNF662, TDRD5 and GSDMB) were screened. Patients in high-risk group (Risk Score > − 0.684511507) had worse prognosis compared to the low-risk group (Risk Score < − 0.684511507). Survival rates of patients in the high-risk group were lower in the gender, age and degrees of differentiation subgroups compared to the low-risk group. Conclusions The Risk Score model constructed by 7 TMB-related genes may be a reliable biomarker for predicting the prognosis of OSCC patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12903-022-02193-3.
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Affiliation(s)
- Fei Wu
- Department I of Oral Comprehensive Outpatient, Yantai Stomatological Hospital of Binzhou Medical University, Yantai, 264001, Shandong, China
| | - Yuanyuan Du
- Department of Dental Implant, Yantai Stomatological Hospital of Binzhou Medical University, Yantai, 264001, Shandong, China
| | - Xiujuan Hou
- Department I of Oral Comprehensive Outpatient, Yantai Stomatological Hospital of Binzhou Medical University, Yantai, 264001, Shandong, China
| | - Wei Cheng
- Department of Dental Prosthodontics, Yantai Stomatological Hospital of Binzhou Medical University, No. 142 Zhifu District, Yantai, 264001, Shandong, China.
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