Systems Biology of Gastric Cancer: Perspectives on the Omics-Based Diagnosis and Treatment

Shi, Xiao; Wei, Yongjun; Ji, Boyang

doi:10.3389/fmolb.2020.00203

Cited by 19 publications

(13 citation statements)

References 77 publications

(106 reference statements)

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“…Gastric cancer (GC) is an aggressive solid tumor malignancy with approximately 27600 estimated new cases and 11010 estimated deaths in 2020, which causes a huge socioeconomic burden to patients and their families [ 1 ]. Many lifestyle factors have been researched, with behavioral factors such as tobacco use, alcohol consumption and Helicobacter pylori (HP) infection and are regarded as risk factors contributing to the development of GC [ 2 ]. Currently, the therapeutic strategies for GC include surgery, radiotherapy, neoadjuvant chemotherapy and immunotherapy, and the survival rate for patients with early GC is nearly 90% [ 3 ].…”

Section: Introductionmentioning

confidence: 99%

Identification of pivotal genes associated with the prognosis of gastric carcinoma through integrated analysis

et al. 2021

Bioscience Reports

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Purpose: Detecting and diagnosing gastric cancer (GC) during its early period remains greatly difficult. Our analysis was performed to detect core genes correlated with GC and explore their prognostic values. Methods: Microarray datasets from the GEO (GSE54129) and TCGA-stomach adenocarcinoma (STAD) datasets were applied for common differentially coexpressed genes using differential gene expression analysis and weighted gene coexpression network analysis (WGCNA). Functional enrichment analysis and protein-protein interaction (PPI) network analysis of differentially coexpressed genes were performed. We identified hub genes via the CytoHubba plugin. Prognostic values of hub genes were explored. Afterward, GSEA was used to analyze survival-related hub genes. Finally, the tumor-infiltrating immune cell (TIC) abundance profiles were estimated. Results: Sixty common differentially co-expressed genes were found. Functional enrichment analysis implied that cell−cell junction organization and cell adhesion molecules were primarily enriched. Hub genes were identified using the degree, edge percolated component (EPC), maximal clique centrality (MCC), and maximum neighborhood component (MNC) algorithms, and SERPINE1 was highly associated with the prognosis of GC patients. Moreover, GSEA demonstrated that ECM receptor interactions and pathways in cancers were correlated with SERPINE1 expression. CIBERSORT analysis of the proportion of TICs suggested that CD8+ T cell and T cell regulation were negatively associated with SERPINE1 expression, showing that SERPINE1 may inhibit the immune-dominant status of the tumor microenvironment in GC. Conclusions: Our analysis shows that SERPINE1 is closely correlated with the tumorigenesis and progression of GC. Furthermore, SERPINE1 acts as a candidate therapeutic target and prognostic biomarker of GC.

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Section: Introductionmentioning

confidence: 99%

Identification of pivotal genes associated with the prognosis of gastric carcinoma through integrated analysis

et al. 2021

Bioscience Reports

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“…In the future, isolating the keystone taxa in gastric samples and inoculating them in germ-free mice would provide insights into their functional roles in GC development [20]. Systems-level approaches need to be tried to understand and uncover the mechanisms of GC developments [44].…”

Section: Discussionmentioning

confidence: 99%

Microbial profiling identifies potential key drivers in gastric cancer patients

Wang

et al. 2021

Biotechnology & Biotechnological Equipment

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Gastric cancer (GC) is the fifth most commonly diagnosed cancer and the third leading cause of cancer-related death in the world. Microbiota is believed to be associated with GC. Growing evidences showed Helicobacter pylori played a key role in GC development. However, little was known about the microbiota in gastric juices and tissues in GC patients, and thus it was difficult to understand other potential microbial causation for GC. Here, we collected the gastric juice and surgically removed gastric tissues from GC patients to give insight into GC microbiota. Most microbes identified in the gastric samples were opportunistic pathogens or resident flora of the human microbiota. Further network analyses identified five opportunistic pathogens as keystone species. H. pylori is the direct cause of GC, but other opportunistic microbes might also function in GC development. The microbiota in the gastric juice and gastric tissue of the GC patients were complex, and some dominant opportunistic pathogens contributed to the GC development. This study introduces microbiota in gastric juice, gastric normal tissue and gastric cancer tissue of GC patients, and highlights the potential keystone microbes functioned during GC development.

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“…Therefore, the understanding of interspecies diversity is important for the development of microbiome-based biomarkers linked to human health and disease (Bunyavanich and Berin, 2019). The integration of multi-omics technologies, including genomics, epigenomics, transcriptomics, proteomics, metabolomics, and microbiome, can help in the investigation, characterization, and quantification of microorganisms in human gut microbiota, giving insights into the interactions between host and its gut microbiota (Dhondalay et al, 2018;Shi et al, 2020).…”

Section: Gut Microbiota In Early Childhoodmentioning

confidence: 99%

Advances in the Relationships Between Cow’s Milk Protein Allergy and Gut Microbiota in Infants

Yang

Ying

et al. 2021

Front. Microbiol.

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Cow’s milk protein allergy (CMPA) is an immune response to cow’s milk proteins, which is one of the most common food allergies in infants and young children. It is estimated that 2–3% of infants and young children have CMPA. The diet, gut microbiota, and their interactions are believed to be involved in the alterations of mucosal immune tolerance, which might lead to the development of CMPA and other food allergies. In this review, the potential molecular mechanisms of CMPA, including omics technologies used for analyzing microbiota, impacts of early microbial exposures on CMPA development, and microbiota–host interactions, are summarized. The probiotics, prebiotics, synbiotics, fecal microbiota transplantation, and other modulation strategies for gut microbiota and the potential application of microbiota-based design of diets for the CMPA treatment are also discussed. This review not only summarizes the current studies about the interactions of CMPA with gut microbiota but also gives insights into the possible CMPA treatment strategies by modulating gut microbiota, which might help in improving the life quality of CMPA patients in the future.

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Systems Biology of Gastric Cancer: Perspectives on the Omics-Based Diagnosis and Treatment

Cited by 19 publications

References 77 publications

Identification of pivotal genes associated with the prognosis of gastric carcinoma through integrated analysis

Identification of pivotal genes associated with the prognosis of gastric carcinoma through integrated analysis

Microbial profiling identifies potential key drivers in gastric cancer patients

Advances in the Relationships Between Cow’s Milk Protein Allergy and Gut Microbiota in Infants

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