1
|
Qi J, Hong B, Wang S, Wang J, Fang J, Sun R, Nie J, Wang H. Plasma cell-free DNA methylome-based liquid biopsy for accurate gastric cancer detection. Cancer Sci 2024; 115:3426-3438. [PMID: 39038922 PMCID: PMC11447983 DOI: 10.1111/cas.16284] [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: 03/26/2024] [Revised: 07/01/2024] [Accepted: 07/02/2024] [Indexed: 07/24/2024] Open
Abstract
Early detection plays a critical role in mitigating mortality rates linked to gastric cancer. However, current clinical screening methods exhibit suboptimal efficacy. Methylation alterations identified from cell-free DNA (cfDNA) present a promising biomarker for early cancer detection. Our study focused on identifying gastric cancer-specific markers from cfDNA methylation to facilitate early detection. We enrolled 150 gastric cancer patients and 100 healthy controls in this study, and undertook genome-wide methylation profiling of cfDNA using cell-free methylated DNA immunoprecipitation and high-throughput sequencing. We identified 21 differentially methylated regions (DMRs) between the gastric tumor and nontumor groups using multiple algorithms. Subsequently, using the 21 DMRs, we developed a gastric cancer detection model by random forest algorithm in the discovery set, and validated the model in an independent set. The model was able to accurately discriminate gastric cancer with a sensitivity and specificity of 93.90% and 95.15% in the discovery set, respectively, and 88.38% and 94.23% in the validation set, respectively. These results underscore the efficacy and accuracy of cfDNA-derived methylation markers in distinguishing early stage gastric cancer. This study highlighted the significance of cfDNA methylation alterations in early gastric cancer detection.
Collapse
Affiliation(s)
- Jian Qi
- Hefei Cancer Hospital of CAS; Institute of Health and Medical Technology, Hefei Institutes of Physical ScienceChinese Academy of Sciences (CAS)HefeiChina
- Science Island BranchGraduate School of University of Science and Technology of ChinaHefeiChina
| | - Bo Hong
- Hefei Cancer Hospital of CAS; Institute of Health and Medical Technology, Hefei Institutes of Physical ScienceChinese Academy of Sciences (CAS)HefeiChina
- Science Island BranchGraduate School of University of Science and Technology of ChinaHefeiChina
| | - Shujie Wang
- Hefei Cancer Hospital of CAS; Institute of Health and Medical Technology, Hefei Institutes of Physical ScienceChinese Academy of Sciences (CAS)HefeiChina
- Science Island BranchGraduate School of University of Science and Technology of ChinaHefeiChina
| | - Jingyun Wang
- School of MedicineAnhui University of Science and TechnologyHuainanChina
| | - Jinman Fang
- Hefei Cancer Hospital of CAS; Institute of Health and Medical Technology, Hefei Institutes of Physical ScienceChinese Academy of Sciences (CAS)HefeiChina
- Science Island BranchGraduate School of University of Science and Technology of ChinaHefeiChina
| | - Ruifang Sun
- Department of Tumor Biobank, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer HospitalChinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical UniversityTaiyuanChina
| | - Jinfu Nie
- Hefei Cancer Hospital of CAS; Institute of Health and Medical Technology, Hefei Institutes of Physical ScienceChinese Academy of Sciences (CAS)HefeiChina
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and InnovationChinese Academy of SciencesHefeiChina
| | - Hongzhi Wang
- Hefei Cancer Hospital of CAS; Institute of Health and Medical Technology, Hefei Institutes of Physical ScienceChinese Academy of Sciences (CAS)HefeiChina
- Science Island BranchGraduate School of University of Science and Technology of ChinaHefeiChina
| |
Collapse
|
2
|
Xu B, Shi Y, Yuan C, Wang Z, Chen Q, Wang C, Chai J. Integrated gene-metabolite association network analysis reveals key metabolic pathways in gastric adenocarcinoma. Heliyon 2024; 10:e37156. [PMID: 39319160 PMCID: PMC11419903 DOI: 10.1016/j.heliyon.2024.e37156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 07/22/2024] [Accepted: 08/28/2024] [Indexed: 09/26/2024] Open
Abstract
Gastric adenocarcinoma is one of the most death cause cancers worldwide. Metabolomics is an effective approach for investigating the occurrence and progression of cancer and detecting prognostic biomarkers by studying the profiles of small bioactive molecules. To fully decipher the functional roles of the disrupted metabolites that modulate the cellular mechanism of gastric cancer, integrated gene-metabolite association network methods are critical to map the associations between metabolites and genes. In this study, we constructed a knowledge-based gene-metabolite association network of gastric cancer using the dysregulated metabolites and genes between gastric cancer patients and control group. The topological pathway analysis and gene-protein-metabolite-disease association analysis revealed four key gene-metabolite pathways which include eleven metabolites associated with modulated genes. The integrated gene-metabolite association network enables mechanistic investigation and provides a comprehensive overview regarding the investigation of molecular mechanisms of gastric cancer, which facilitates the in-depth understanding of metabolic biomarker roles in gastric cancer.
Collapse
Affiliation(s)
- Botao Xu
- Department of Gastrointestinal Surgery, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Science, Jinan, China
| | - Yuying Shi
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
- National Institute of Health Data Science of China, Shandong University, Jinan, 250000, China
- National Science Library (Chengdu), Chinese Academy of Sciences, Chengdu, 610299, China
| | - Chuang Yuan
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University, Beijing, 100191, China
| | - Zhe Wang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Science, Jinan, Shandong, China
| | - Qitao Chen
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
- National Institute of Health Data Science of China, Shandong University, Jinan, 250000, China
| | - Cheng Wang
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
- National Institute of Health Data Science of China, Shandong University, Jinan, 250000, China
| | - Jie Chai
- Department of Gastrointestinal Surgery, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Science, Jinan, China
| |
Collapse
|
3
|
Poniewierska-Baran A, Sobolak K, Niedźwiedzka-Rystwej P, Plewa P, Pawlik A. Immunotherapy Based on Immune Checkpoint Molecules and Immune Checkpoint Inhibitors in Gastric Cancer-Narrative Review. Int J Mol Sci 2024; 25:6471. [PMID: 38928174 PMCID: PMC11203505 DOI: 10.3390/ijms25126471] [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: 04/30/2024] [Revised: 05/31/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Due to its rapid progression to advanced stages and highly metastatic properties, gastric cancer (GC) is one of the most aggressive malignancies and the fourth leading cause of cancer-related deaths worldwide. The metastatic process includes local invasion, metastasis initiation, migration with colonisation at distant sites, and evasion of the immune response. Tumour growth involves the activation of inhibitory signals associated with the immune response, also known as immune checkpoints, including PD-1/PD-L1 (programmed death 1/programmed death ligand 1), CTLA-4 (cytotoxic T cell antigen 4), TIGIT (T cell immunoreceptor with Ig and ITIM domains), and others. Immune checkpoint molecules (ICPMs) are proteins that modulate the innate and adaptive immune responses. While their expression is prominent on immune cells, mainly antigen-presenting cells (APC) and other types of cells, they are also expressed on tumour cells. The engagement of the receptor by the ligand is crucial for inhibiting or stimulating the immune cell, which is an extremely important aspect of cancer immunotherapy. This narrative review explores immunotherapy, focusing on ICPMs and immune checkpoint inhibitors in GC. We also summarise the current clinical trials that are evaluating ICPMs as a target for GC treatment.
Collapse
Affiliation(s)
- Agata Poniewierska-Baran
- Center of Experimental Immunology and Immunobiology of Infectious and Cancer Diseases, University of Szczecin, 71-417 Szczecin, Poland; (A.P.-B.); (P.N.-R.)
- Institute of Biology, University of Szczecin, 71-412 Szczecin, Poland
- Department of Physiology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Karolina Sobolak
- Students Research Club of Immunobiology of Infectious and Cancer Diseases “NEUTROPHIL”, University of Szczecin, 71-417 Szczecin, Poland; (K.S.); (P.P.)
| | - Paulina Niedźwiedzka-Rystwej
- Center of Experimental Immunology and Immunobiology of Infectious and Cancer Diseases, University of Szczecin, 71-417 Szczecin, Poland; (A.P.-B.); (P.N.-R.)
- Institute of Biology, University of Szczecin, 71-412 Szczecin, Poland
| | - Paulina Plewa
- Students Research Club of Immunobiology of Infectious and Cancer Diseases “NEUTROPHIL”, University of Szczecin, 71-417 Szczecin, Poland; (K.S.); (P.P.)
| | - Andrzej Pawlik
- Department of Physiology, Pomeranian Medical University, 70-111 Szczecin, Poland
| |
Collapse
|
4
|
Hakami ZH. Biomarker discovery and validation for gastrointestinal tumors: A comprehensive review of colorectal, gastric, and liver cancers. Pathol Res Pract 2024; 255:155216. [PMID: 38401376 DOI: 10.1016/j.prp.2024.155216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 02/07/2024] [Accepted: 02/15/2024] [Indexed: 02/26/2024]
Abstract
Gastrointestinal (GI) malignancies, encompassing gastric, hepatic, colonic, and rectal cancers, are prevalent forms of cancer globally and contribute substantially to cancer-related mortality. Although there have been improvements in methods for diagnosing and treating GI cancers, the chances of survival for these types of cancers are still extremely low. According to the World Cancer Research International Fund's most recent figures, stomach cancer was responsible for roughly one million deaths worldwide in 2020. This emphasizes the importance of developing more effective tools for detecting, diagnosing, and predicting the outcome of these cancers at an early stage. Biomarkers, quantitative indications of biological processes or disease states, have emerged as promising techniques for enhancing the diagnosis and prognosis of GI malignancies. Recently, there has been a considerable endeavor to discover and authenticate biomarkers for various GI cancers by the utilization of diverse methodologies, including genomics, proteomics, and metabolomics. This review provides a thorough examination of the current state of biomarker research in the field of gastrointestinal malignancies, with a specific emphasis on colorectal, stomach, and liver cancers. A thorough literature search was performed on prominent databases such as PubMed, Scopus, and Web of Science to find pertinent papers published until November, 2023 for the purpose of compiling this review. The diverse categories of biomarkers, encompassing genetic, epigenetic, and protein-based biomarkers, and their potential utility in the fields of diagnosis, prognosis, and treatment selection, are explored. Recent progress in identifying and confirming biomarkers, as well as the obstacles that persist in employing biomarkers in clinical settings are emphasized. The utilization of biomarkers in GI cancers has significant potential in enhancing patient outcomes. Ongoing research is expected to uncover more efficient biomarkers for the diagnosis and prognosis of these cancers.
Collapse
Affiliation(s)
- Zaki H Hakami
- Department of Medical Laboratory Technology, Faculty of Applied Medical Science, Jazan University, Jazan 45142, Saudi Arabia.
| |
Collapse
|
5
|
Sekaran K, Varghese RP, Zayed H, El Allali A, George Priya Doss C. Single-cell transcriptomic analysis reveals crucial oncogenic signatures and its associative cell types involved in gastric cancer. Med Oncol 2023; 40:305. [PMID: 37740827 DOI: 10.1007/s12032-023-02174-8] [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: 08/01/2023] [Accepted: 08/28/2023] [Indexed: 09/25/2023]
Abstract
The intricate association of oncogenic markers negatively impacts accurate gastric cancer diagnosis and leads to the proliferation of mortality rate. Molecular heterogeneity is inevitable in determining gastric cancer's progression state with multiple cell types involved. Identification of pathogenic gene signatures is imperative to understand the disease's etiology. This study demonstrates a systematic approach to identifying oncogenic gastric cancer genes linked with different cell types. The raw counts of adjacent normal and gastric cancer samples are subjected to a quality control step. The dimensionality reduction and multidimensional clustering are performed using Principal Component Analysis (PCA) and Uniform Manifold Approximation and Projection (UMAP) techniques. The adjacent normal and gastric cancer sample cell clusters are annotated with the Human Primary Cell Atlas database using the "SingleR." Cellular state transition between the distinct groups is characterized using trajectory analysis. The ligand-receptor interaction between Vascular Endothelial Growth Factor (VEGF) and cell clusters unveils crucial molecular pathways in gastric cancer progression. Chondrocytes, Smooth muscle cells, and fibroblast cell clusters contain genes contributing to poor survival rates based on hazard ratio during survival analysis. The GC-related oncogenic signatures are isolated by comparing the gene set with the DisGeNET database. Twelve gastric cancer biomarkers (SPARC, KLF5, HLA-DRB1, IGFBP3, TIMP3, LGALS1, IGFBP6, COL18A1, F3, COL4A1, PDGFRB, COL5A2) are linked with gastric cancer and further validated through gene set enrichment analysis. Drug-gene interaction found PDGFRB, interacting with various anti-cancer drugs, as a potential inhibitor for gastric cancer. Further investigations on these molecular signatures will assist the development of precision therapeutics, promising longevity among gastric cancer patients.
Collapse
Affiliation(s)
- Karthik Sekaran
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India
| | | | - Hatem Zayed
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Achraf El Allali
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - C George Priya Doss
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India.
| |
Collapse
|
6
|
Liu S, Liu X, Lin X, Chen H. Zinc Finger Proteins in the War on Gastric Cancer: Molecular Mechanism and Clinical Potential. Cells 2023; 12:cells12091314. [PMID: 37174714 PMCID: PMC10177130 DOI: 10.3390/cells12091314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 04/30/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
According to the 2020 global cancer data released by the World Cancer Research Fund (WCRF) International, gastric cancer (GC) is the fifth most common cancer worldwide, with yearly increasing incidence and the second-highest fatality rate in malignancies. Despite the contemporary ambiguous molecular mechanisms in GC pathogenesis, numerous in-depth studies have demonstrated that zinc finger proteins (ZFPs) are essential for the development and progression of GC. ZFPs are a class of transcription factors with finger-like domains that bind to Zn2+ extensively and participate in gene replication, cell differentiation and tumor development. In this review, we briefly outline the roles, molecular mechanisms and the latest advances in ZFPs in GC, including eight principal aspects, such as cell proliferation, epithelial-mesenchymal transition (EMT), invasion and metastasis, inflammation and immune infiltration, apoptosis, cell cycle, DNA methylation, cancer stem cells (CSCs) and drug resistance. Intriguingly, the myeloid zinc finger 1 (MZF1) possesses reversely dual roles in GC by promoting tumor proliferation or impeding cancer progression via apoptosis. Therefore, a thorough understanding of the molecular mechanism of ZFPs on GC progression will pave the solid way for screening the potentially effective diagnostic indicators, prognostic biomarkers and therapeutic targets of GC.
Collapse
Affiliation(s)
- Shujie Liu
- Department of Histology and Embryology, Medical College, Nanchang University, Nanchang 330006, China
- Medical Department, Queen Mary School, Nanchang University, Nanchang 330006, China
| | - Xingzhu Liu
- Department of Histology and Embryology, Medical College, Nanchang University, Nanchang 330006, China
- Medical Department, Queen Mary School, Nanchang University, Nanchang 330006, China
| | - Xin Lin
- Department of Histology and Embryology, Medical College, Nanchang University, Nanchang 330006, China
- Medical Department, Queen Mary School, Nanchang University, Nanchang 330006, China
| | - Hongping Chen
- Department of Histology and Embryology, Medical College, Nanchang University, Nanchang 330006, China
| |
Collapse
|