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Jiang Z, Gu Z, Lu X, Wen W. The role of dysregulated metabolism and associated genes in gastric cancer initiation and development. Transl Cancer Res 2024; 13:3854-3868. [PMID: 39145068 PMCID: PMC11319955 DOI: 10.21037/tcr-23-2244] [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: 12/06/2023] [Accepted: 06/04/2024] [Indexed: 08/16/2024]
Abstract
The review delves into the intricate interplay between metabolic dysregulation and the onset and progression of gastric cancer (GC), shedding light on a pivotal aspect of this prevalent malignancy. GC stands as one of the leading causes of cancer-related mortality worldwide, its trajectory influenced by a multitude of factors, among which metabolic dysregulation and aberrant gene expression play significant roles. The article navigates through the fundamental roles of metabolic dysregulation in the genesis of GC, unveiling phenomena such as aberrant glycolysis, epitomized by the Warburg effect, alongside anomalies in lipid and amino acid metabolism. It delineates how these disruptions fuel the cancerous process, facilitating uncontrolled cell proliferation and survival. Furthermore, the intricate nexus between metabolism and the vitality of GC cells is elucidated, underscoring the profound influence of metabolic reprogramming on tumor energy dynamics and the accrual of metabolic by-products, which further perpetuate malignant growth. A pivotal segment of the review entails an exploration of key metabolic-related genes implicated in GC pathogenesis. MYC and TP53 are spotlighted among others, delineating their pivotal roles in driving tumorigenesis through metabolic pathway modulation. These genetic pathways serve as critical nodes in the intricate network orchestrating GC development, providing valuable targets for therapeutic intervention. This review embarks on a forward-looking trajectory, delineating the potential therapeutic avenues stemming from insights into metabolic dysregulation in GC. It underscores the promise of targeted therapies directed towards specific metabolic pathways implicated in tumor progression, alongside the burgeoning potential of combination therapy strategies leveraging both metabolic and conventional anti-cancer modalities. In essence, this comprehensive review serves as a beacon, illuminating the intricate landscape of metabolic dysregulation in GC pathogenesis. Through its nuanced exploration of metabolic aberrations and their genetic underpinnings, it not only enriches our understanding of GC biology but also unveils novel therapeutic vistas poised to revolutionize its clinical management.
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Affiliation(s)
- Zhengyan Jiang
- Digestive Department, Jiangsu Second Chinese Medicine Hospital, Nanjing, China
| | - Zhengrong Gu
- Digestive Department, Jiangsu Second Chinese Medicine Hospital, Nanjing, China
| | - Xianyan Lu
- Digestive Department, Suzhou Wujiang District Hospital of Traditional Chinese Medicine (Suzhou Wujiang District Second People’s Hospital), Suzhou, China
| | - Wei Wen
- Digestive Department, Jiangsu Second Chinese Medicine Hospital, Nanjing, China
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Lu L, Feng H, Dai G, Liu S, Feng Y, Tan H, Zhang X, Hong G, Lai X. A novel cancer-associated fibroblast signature for kidney renal clear cell carcinoma via integrated analysis of single-cell and bulk RNA-sequencing. Discov Oncol 2024; 15:309. [PMID: 39060620 PMCID: PMC11282037 DOI: 10.1007/s12672-024-01175-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
Cancer-associated fibroblasts (CAFs), integral components of the tumor microenvironment, play a pivotal role in tumor proliferation, metastasis, and clinical outcomes. However, its specific roles in Kidney Renal Clear Cell Carcinoma (KIRC) remain poorly understood. Employing the established Seurat single-cell analysis pipeline, we identified 21 CAFs marker genes. Subsequently, a prognostic signature consisting of 6 CAFs marker genes (RGS5, PGF, TPM2, GJA4, SEPT4, and PLXDC1) was developed in a cohort through univariate and LASSO Cox regression analyses. The model's efficacy was then validated in an external cohort, with a remarkable predictive performance in 1-, 3-, and 5-year. Patients in the high-risk group exhibited significantly inferior survival outcomes (p < 0.001), and the risk score was an independent prognostic factor (p < 0.05). Distinct differences in immune cell profiles and drug susceptibility were observed between the two risk groups. In KIRC, the PGF-VEGFR1 signaling pathway displayed a notable increase. PGF expression was significantly elevated in tumor tissues, as demonstrated by quantitative real-time polymerase chain reaction. In vitro, transwell assays and CCK8 revealed that recombinant-PGF could enhance the capability of cell proliferation, migration, and invasion in 769P and 786-O cells. This study firstly developed a novel predictive model based on 6 CAFs genes for KIRC. Additionally, PGF may present a potential therapeutic target to enhance KIRC treatment.
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Affiliation(s)
- Ling Lu
- Department of Renal Rheumatology Immunology, School of Medicine, Chongqing University Jiangjin Hospital, Chongqing University, Chongqing, China
| | - Huaguo Feng
- Department of Hepatobiliary Surgery, School of Medicine, Chongqing University Jiangjin Hospital, Chongqing University, Chongqing, China
| | - Guohua Dai
- Department of Hepatobiliary Surgery, School of Medicine, Chongqing University Jiangjin Hospital, Chongqing University, Chongqing, China
| | - Shuangquan Liu
- Department of Hepatobiliary Surgery, School of Medicine, Chongqing University Jiangjin Hospital, Chongqing University, Chongqing, China
| | - Yi Feng
- Department of Hepatobiliary Surgery, Jiangjin District Maternal and Child Health Hospital, Chongqing, China
| | - Haoyang Tan
- Department of Hepatobiliary Surgery, School of Medicine, Chongqing University Jiangjin Hospital, Chongqing University, Chongqing, China
| | - Xian Zhang
- Department of Hepatobiliary Surgery, Tongnan District People's Hospital, No. 189, Jianshe Road, Dafo Street, Tongnan District, Chongqing, China
| | - Guoqing Hong
- Department of Hepatobiliary Surgery, Tongnan District People's Hospital, No. 189, Jianshe Road, Dafo Street, Tongnan District, Chongqing, China.
| | - Xing Lai
- Department of Hepatobiliary Surgery, Tongnan District People's Hospital, No. 189, Jianshe Road, Dafo Street, Tongnan District, Chongqing, China.
- Chongqing Traditional Chinese Medicine Hospital, Chongqing, China.
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Zhang J, Li Y, Dai W, Tang F, Wang L, Wang Z, Li S, Ji Q, Zhang J, Liao Z, Yu J, Xu Y, Gong J, Hu J, Li J, Guo X, He F, Han L, Gong Y, Ouyang W, Wang Z, Xie C. Molecular classification reveals the sensitivity of lung adenocarcinoma to radiotherapy and immunotherapy: multi-omics clustering based on similarity network fusion. Cancer Immunol Immunother 2024; 73:71. [PMID: 38430394 PMCID: PMC10908647 DOI: 10.1007/s00262-024-03657-x] [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: 12/01/2023] [Accepted: 02/19/2024] [Indexed: 03/03/2024]
Abstract
BACKGROUND Due to individual differences in tumors and immune systems, the response rate to immunotherapy is low in lung adenocarcinoma (LUAD) patients. Combinations with other therapeutic strategies improve the efficacy of immunotherapy in LUAD patients. Although radioimmunotherapy has been demonstrated to effectively suppress tumors, the underlying mechanisms still need to be investigated. METHODS Total RNA from LUAD cells was sequenced before and after radiotherapy to identify differentially expressed radiation-associated genes. The similarity network fusion (SNF) algorithm was applied for molecular classification based on radiation-related genes, immune-related genes, methylation data, and somatic mutation data. The changes in gene expression, prognosis, immune cell infiltration, radiosensitivity, chemosensitivity, and sensitivity to immunotherapy were assessed for each subtype. RESULTS We used the SNF algorithm and multi-omics data to divide TCGA-LUAD patients into three subtypes. Patients with the CS3 subtype had the best prognosis, while those with the CS1 and CS2 subtypes had poorer prognoses. Among the strains tested, CS2 exhibited the most elevated immune cell infiltration and expression of immune checkpoint genes, while CS1 exhibited the least. Patients in the CS2 subgroup were more likely to respond to PD-1 immunotherapy. The CS2 patients were most sensitive to docetaxel and cisplatin, while the CS1 patients were most sensitive to paclitaxel. Experimental validation of signature genes in the CS2 subtype showed that inhibiting the expression of RHCG and TRPA1 could enhance the sensitivity of lung cancer cells to radiation. CONCLUSIONS In summary, this study identified a risk classifier based on multi-omics data that can guide treatment selection for LUAD patients.
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Affiliation(s)
- Jianguo Zhang
- Department of Pulmonary Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China
| | - Yangyi Li
- Department of Pulmonary Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China
| | - Weijing Dai
- Department of Pulmonary Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China
| | - Fang Tang
- Department of Pulmonary Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China
| | - Lanqing Wang
- Department of Pulmonary Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China
| | - Zhiying Wang
- Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao, 266000, Shandong, China
| | - Siqi Li
- Department of Pulmonary Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China
| | - Qian Ji
- Department of Pulmonary Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China
| | - Junhong Zhang
- Department of Pulmonary Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China
| | - Zhengkai Liao
- Department of Pulmonary Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China
| | - Jing Yu
- Department of Pulmonary Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China
| | - Yu Xu
- Department of Pulmonary Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China
| | - Jun Gong
- Department of Pulmonary Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China
| | - Jing Hu
- Department of Pulmonary Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China
| | - Jie Li
- Department of Pulmonary Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China
| | - Xiuli Guo
- Department of Pulmonary Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China
| | - Fajian He
- Department of Pulmonary Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China
| | - Linzhi Han
- Department of Pulmonary Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China
| | - Yan Gong
- Tumor Precision Diagnosis and Treatment Technology and Translational Medicine, Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China
- Human Genetics Resource Reservation Center, Wuhan University, Wuhan, 430071, Hubei, China
| | - Wen Ouyang
- Department of Pulmonary Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China.
- Hubei Key Laboratory of Tumour Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China.
| | - Zhihao Wang
- Department of Pulmonary Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China.
- Hubei Key Laboratory of Tumour Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China.
| | - Conghua Xie
- Department of Pulmonary Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China.
- Hubei Key Laboratory of Tumour Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China.
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Li J, Chen Z, Li Q, Liu R, Zheng J, Gu Q, Xiang F, Li X, Zhang M, Kang X, Wu R. Study of miRNA and lymphocyte subsets as potential biomarkers for the diagnosis and prognosis of gastric cancer. PeerJ 2024; 12:e16660. [PMID: 38259671 PMCID: PMC10802158 DOI: 10.7717/peerj.16660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 11/21/2023] [Indexed: 01/24/2024] Open
Abstract
Objective The aim of this study was to identify the expression of miRNA and lymphocyte subsets in the blood of gastric cancer (GC) patients, elucidate their clinical significance in GC, and establish novel biomarkers for the early diagnosis and prognosis of GC. Methods The expression of miRNAs in the serum of GC patients was screened using second-generation sequencing and detected using qRT-PCR. The correlation between miRNA expression and clinicopathological characteristics of GC patients was analyzed, and molecular markers for predicting cancer were identified. Additionally, flow cytometry was used to detect the proportion of lymphocyte subsets in GC patients compared to healthy individuals. The correlations between differential lymphocyte subsets, clinicopathological features of GC patients, and their prognosis were analyzed statistically. Results The study revealed that hsa-miR-1306-5p, hsa-miR-3173-5p, and hsa-miR-296-5p were expressed at lower levels in the blood of GC patients, which is consistent with miRNA-seq findings. The AUC values of hsa-miR-1306-5p, hsa-miR-3173-5p, and hsa-miR-296-5p were found to be effective predictors of GC occurrence. Additionally, hsa-miR-296-5p was found to be negatively correlated with CA724. Furthermore, hsa-miR-1306-5p, hsa-miR-3173-5p, and hsa-miR-296-5p were found to be associated with the stage of the disease and were closely linked to the clinical pathology of GC. The lower the levels of these miRNAs, the greater the clinical stage of the tumor and the worse the prognosis of gastric cancer patients. Finally, the study found that patients with GC had lower absolute numbers of CD3+ T cells, CD4+ T cells, CD8+ T cells, CD19+ B cells, and lymphocytes compared to healthy individuals. The quantity of CD4+ T lymphocytes and the level of the tumor marker CEA were shown to be negatively correlated. The ROC curve and multivariate logistic regression analysis demonstrated that lymphocyte subsets can effectively predict gastric carcinogenesis and prognosis. Conclusion These miRNAs such as hsa-miR-1306-5p, hsa-miR-3173-5p, hsa-miR-296-5p and lymphocyte subsets such as the absolute numbers of CD3+ T cells, CD4+ T cells, CD8+ T cells, CD19+ B cells, lymphocytes are down-regulated in GC and are closely related to the clinicopathological characteristics and prognosis of GC patients. They may serve as new molecular markers for predicting the early diagnosis and prognosis of GC patients.
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Affiliation(s)
- Jinpeng Li
- Department of Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zixi Chen
- Department of Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qian Li
- Department of Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Rongrong Liu
- Department of Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jin Zheng
- Department of Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qing Gu
- Department of Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Fenfen Xiang
- Department of Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiaoxiao Li
- Department of Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Mengzhe Zhang
- Department of Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiangdong Kang
- Department of Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Rong Wu
- Department of Laboratory Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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Shen J, Li M. Gastric Cancer Immune Subtypes and Prognostic Modeling: Insights from Aging-Related Gene Analysis. Crit Rev Immunol 2024; 44:1-13. [PMID: 38618724 DOI: 10.1615/critrevimmunol.2024052391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Gastric cancer (GC) is highly heterogeneous and influenced by aging-related factors. This study aimed to improve individualized prognostic assessment of GC by identifying aging-related genes and subtypes. Immune scores of GC samples from GEO and TCGA databases were calculated using ESTIMATE and scored as high immune (IS_high) and low immune (IS_low). ssGSEA was used to analyze immune cell infiltration. Univariate Cox regression was employed to identify prognosis-related genes. LASSO regression analysis was used to construct a prognostic model. GSVA enrichment analysis was applied to determine pathways. CCK-8, wound healing, and Transwell assays tested the proliferation, migration, and invasion of the GC cell line (AGS). Cell cycle and aging were examined using flow cytometry, β-galactosidase staining, and Western blotting. Two aging-related GC subtypes were identified. Subtype 2 was characterized as lower survival probability and higher risk, along with a more immune-responsive tumor microenvironment. Three genes (IGFBP5, BCL11B, and AKR1B1) screened from aging-related genes were used to establish a prognosis model. The AUC values of the model were greater than 0.669, exhibiting strong prognostic value. In vitro, IGFBP5 overexpression in AGS cells was found to decrease viability, migration, and invasion, alter the cell cycle, and increase aging biomarkers (SA-β-galactosidase, p53, and p21). This analysis uncovered the immune characteristics of two subtypes and aging-related prognosis genes in GC. The prognostic model established for three aging-related genes (IGFBP5, BCL11B, and AKR1B1) demonstrated good prognosis performance, providing a foundation for personalized treatment strategies aimed at GC.
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Affiliation(s)
- Jian Shen
- Beijing Chao-Yang Hospital, Capital Medical University
| | - Minzhe Li
- Department of General Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
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Pan D, Chen H, Xu J, Lin X, Li L. Evaluation of vital genes correlated with CD8 + T cell infiltration as prognostic biomarkers in stomach adenocarcinoma. BMC Gastroenterol 2023; 23:399. [PMID: 37978443 PMCID: PMC10656896 DOI: 10.1186/s12876-023-03003-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 10/17/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Infiltration of CD8 + T cells in the tumor microenvironment is correlated with better prognosis in various malignancies. Our study aimed to investigate vital genes correlated with CD8 + T cell infiltration in stomach adenocarcinoma (STAD) and develop a new prognostic model. METHODS Using the STAD dataset, differentially expressed genes (DEGs) were analyzed, and co-expression networks were constructed. Combined with the CIBERSORT algorithm, the most relevant module of WGCNA with CD8 + T cell infiltration was selected for subsequent analysis. The vital genes were screened out by univariate regression analysis to establish the risk score model. The expression of the viral genes was verified by lasso regression analysis and in vitro experiments. RESULTS Four CD8 + T cell infiltration-related genes (CIDEC, EPS8L3, MUC13, and PLEKHS1) were correlated with the prognosis of STAD. Based on these genes, a risk score model was established. We found that the risk score could well predict the prognosis of STAD, and the risk score was positively correlated with CD8 + T cell infiltration. The validation results of the gene expression were consistent with TCGA. Furthermore, the risk score was significantly higher in tumor tissues. The high-risk group had poorer overall survival (OS) in each subgroup. CONCLUSIONS Our study constructed a new risk score model for STAD prognosis, which may provide a new perspective to explore the tumor immune microenvironment mechanism in STAD.
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Affiliation(s)
- Dun Pan
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Fujian Medical University, No.20, ChaZhong Road, TaiJiang District, Fuzhou, 350000, Fujian Province, China
| | - Hui Chen
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Fujian Medical University, No.20, ChaZhong Road, TaiJiang District, Fuzhou, 350000, Fujian Province, China
| | - Jiaxiang Xu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Fujian Medical University, No.20, ChaZhong Road, TaiJiang District, Fuzhou, 350000, Fujian Province, China
| | - Xin Lin
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Fujian Medical University, No.20, ChaZhong Road, TaiJiang District, Fuzhou, 350000, Fujian Province, China
| | - Liangqing Li
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Fujian Medical University, No.20, ChaZhong Road, TaiJiang District, Fuzhou, 350000, Fujian Province, China.
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Hou W, Zhao Y, Zhu H. Predictive Biomarkers for Immunotherapy in Gastric Cancer: Current Status and Emerging Prospects. Int J Mol Sci 2023; 24:15321. [PMID: 37895000 PMCID: PMC10607383 DOI: 10.3390/ijms242015321] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Gastric cancer presents substantial management challenges, and the advent of immunotherapy has ignited renewed hope among patients. Nevertheless, a significant proportion of patients do not respond to immunotherapy, and adverse events associated with immunotherapy also occur on occasion, underscoring the imperative to identify suitable candidates for treatment. Several biomarkers, including programmed death ligand-1 expression, tumor mutation burden, mismatch repair status, Epstein-Barr Virus infection, circulating tumor DNA, and tumor-infiltrating lymphocytes, have demonstrated potential in predicting the effectiveness of immunotherapy in gastric cancer. However, the quest for the optimal predictive biomarker for gastric cancer immunotherapy remains challenging, as each biomarker carries its own limitations. Recently, multi-omics technologies have emerged as promising platforms for discovering novel biomarkers that may help in selecting gastric cancer patients likely to respond to immunotherapy. The identification of reliable predictive biomarkers for immunotherapy in gastric cancer holds the promise of enhancing patient selection and improving treatment outcomes. In this review, we aim to provide an overview of clinically established biomarkers of immunotherapy in gastric cancer. Additionally, we introduce newly reported biomarkers based on multi-omics studies in the context of gastric cancer immunotherapy, thereby contributing to the ongoing efforts to refine patient stratification and treatment strategies.
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Affiliation(s)
- Wanting Hou
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu 610065, China; (W.H.); (Y.Z.)
- Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu 610065, China
| | - Yaqin Zhao
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu 610065, China; (W.H.); (Y.Z.)
- Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu 610065, China
| | - Hong Zhu
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu 610065, China; (W.H.); (Y.Z.)
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Wu W, Chen L, Jia G, Tang Q, Han B, Xia S, Jiang Q, Liu H. Inhibition of FGFR3 upregulates MHC-I and PD-L1 via TLR3/NF-kB pathway in muscle-invasive bladder cancer. Cancer Med 2023; 12:15676-15690. [PMID: 37283287 PMCID: PMC10417096 DOI: 10.1002/cam4.6172] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 05/16/2023] [Accepted: 05/19/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND Improving the potency of immune response is paramount among issues concerning immunotherapy of muscle-invasive bladder cancer (MIBC). METHODS On the basis of immune subtypes, we investigated possible molecular mechanisms involved in tumor immune escape in MIBC. According to the 312 immune-related genes, three MIBC immune subtypes were clustered. RESULTS Cluster 2 subtype is characterized by FGFR3 mutations and has a better clinical prognosis. However, the expression levels of MHC-I and immune checkpoints genes were the lowest, indicating that this subtype is subject to immune escape and has a low response rate to immunotherapy. Bioinformatics analysis and immunofluorescence staining of clinical samples revealed that the FGFR3 is involved in the immune escape in MIBC. Besides, after FGFR3 knockout with siRNA in RT112 and UMUC14 cells, the TLR3/NF-kB pathway was significantly activated and was accompanied by upregulation of MHC-I and PD-L1 gene expression. Furthermore, the use of TLR3 agonists poly(I:C) can further improve the effect. CONCLUSION Together, our results suggest that FGFR3 might involve in immunosuppression by inhibition of NF-kB pathway in BC. Considering that TLR3 agonists are currently approved for clinical treatment as immunoadjuvants, our study might provide more insights for improving the efficacy of immunotherapy in MIBC.
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Affiliation(s)
- WenBo Wu
- Department of UrologyShanghai General HospitalShanghaiChina
- Shanghai JiaoTong University School of MedicineShanghaiChina
| | - Lei Chen
- Department of UrologyShanghai General HospitalShanghaiChina
| | - GaoZhen Jia
- Department of UrologyShanghai General HospitalShanghaiChina
| | - QiLin Tang
- Department of UrologyShanghai General HospitalShanghaiChina
- Shanghai JiaoTong University School of MedicineShanghaiChina
| | - BangMin Han
- Department of UrologyShanghai General HospitalShanghaiChina
| | - ShuJie Xia
- Department of UrologyShanghai General HospitalShanghaiChina
| | - Qi Jiang
- Department of UrologyShanghai General HospitalShanghaiChina
| | - HaiTao Liu
- Department of UrologyShanghai General HospitalShanghaiChina
- Shanghai JiaoTong University School of MedicineShanghaiChina
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Lee M. Deep Learning Techniques with Genomic Data in Cancer Prognosis: A Comprehensive Review of the 2021-2023 Literature. BIOLOGY 2023; 12:893. [PMID: 37508326 PMCID: PMC10376033 DOI: 10.3390/biology12070893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023]
Abstract
Deep learning has brought about a significant transformation in machine learning, leading to an array of novel methodologies and consequently broadening its influence. The application of deep learning in various sectors, especially biomedical data analysis, has initiated a period filled with noteworthy scientific developments. This trend has majorly influenced cancer prognosis, where the interpretation of genomic data for survival analysis has become a central research focus. The capacity of deep learning to decode intricate patterns embedded within high-dimensional genomic data has provoked a paradigm shift in our understanding of cancer survival. Given the swift progression in this field, there is an urgent need for a comprehensive review that focuses on the most influential studies from 2021 to 2023. This review, through its careful selection and thorough exploration of dominant trends and methodologies, strives to fulfill this need. The paper aims to enhance our existing understanding of applications of deep learning in cancer survival analysis, while also highlighting promising directions for future research. This paper undertakes aims to enrich our existing grasp of the application of deep learning in cancer survival analysis, while concurrently shedding light on promising directions for future research in this vibrant and rapidly proliferating field.
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Affiliation(s)
- Minhyeok Lee
- School of Electrical and Electronics Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
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10
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Chen G, Luo D, Qi X, Li D, Zheng J, Luo Y, Zhang C, Ren Q, Lu Y, Chan YT, Chen B, Wu J, Wang N, Feng Y. Characterization of cuproptosis in gastric cancer and relationship with clinical and drug reactions. Front Cell Dev Biol 2023; 11:1172895. [PMID: 37351275 PMCID: PMC10283039 DOI: 10.3389/fcell.2023.1172895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/09/2023] [Indexed: 06/24/2023] Open
Abstract
Gastric cancer (GC) is the fifth most common cancer worldwide. Cuproptosis is associated with cell growth and death as well as tumorigenesis. Aiming to lucubrate the potential influence of CRGs in gastric cancer, we acquired datasets of gastric cancer patients from TCGA and GEO. The identification of molecular subtypes with CRGs expression was achieved through unsupervised learning-cluster analysis. To evaluate the application value of subtypes, the K-M survival analysis was conducted to evaluate the clinical prognostic characteristics. Subsequently, we performed Gene Set Variation Analysis (GSVA) and utilized ssGSEA to quantify the extent of immune infiltration. Further, the K-M survival analysis was used to identify the prognosis-related CRGs. Next, signature genes of diagnostic predictive value were screened using the least absolute shrinkage and selection operator (LASSO) algorithm from the expression matrix for TCGA, as well as the signature gene-related subtype was clustered by the "ConsensusClusterPlus" package. Finally, the immunological and drug sensitivity assessments of the signature gene-related subtypes were conducted. A total of 173 CRGs were identified, most of the CRGs undergo copy number variation in gastric cancer. Under different patient subtypes, immune cell levels differed significantly, and the subtype exhibiting high expression of the CRGs had a better prognosis. Furthermore, we selected 34 CRGs that were highly correlated with the prognosis of gastric cancer. By constructing a multivariate Cox proportional-hazards model and a hazard scoring system, we were able to categorize patients into high- and low-risk groups based on their hazard score. K-M analysis demonstrated a significant survival disadvantage in the high-risk group. Based on Lasso regression analysis, we screened 16 signature genes, a multivariate logistic regression model [cutoff: 0.149 (0.000, 0.974), AUC:0.987] and a prognosis network diagram was constructed and their prediction efficiency for gastric cancer prognostic diagnosis was well validated. According to the signature genes, the patients were separated to two signature subtypes. We found that patients with higher CRGs expression and better prognosis had lower levels of immune infiltration. Finally, according to the results of drug susceptibility analysis, docetaxel, 5-Fluorouracil, gemcitabin, and paclitaxel were found to be more sensitive to gastric cancer.
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Affiliation(s)
- Guoming Chen
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Dongqiang Luo
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiangjun Qi
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Danyun Li
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jiyuan Zheng
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yang Luo
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Cheng Zhang
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Qing Ren
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Yuanjun Lu
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Yau-Tuen Chan
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Bonan Chen
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Sir Y.K. Pao Cancer Center, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Junyu Wu
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Ning Wang
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Yibin Feng
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
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Ning J, Sun K, Fan X, Jia K, Meng L, Wang X, Li H, Ma R, Liu S, Li F, Wang X. Use of machine learning-based integration to develop an immune-related signature for improving prognosis in patients with gastric cancer. Sci Rep 2023; 13:7019. [PMID: 37120631 PMCID: PMC10148812 DOI: 10.1038/s41598-023-34291-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 04/27/2023] [Indexed: 05/01/2023] Open
Abstract
Gastric cancer is one of the most common malignancies. Although some patients benefit from immunotherapy, the majority of patients have unsatisfactory immunotherapy outcomes, and the clinical significance of immune-related genes in gastric cancer remains unknown. We used the single-sample gene set enrichment analysis (ssGSEA) method to evaluate the immune cell content of gastric cancer patients from TCGA and clustered patients based on immune cell scores. The Weighted Correlation Network Analysis (WGCNA) algorithm was used to identify immune subtype-related genes. The patients in TCGA were randomly divided into test 1 and test 2 in a 1:1 ratio, and a machine learning integration process was used to determine the best prognostic signatures in the total cohort. The signatures were then validated in the test 1 and the test 2 cohort. Based on a literature search, we selected 93 previously published prognostic signatures for gastric cancer and compared them with our prognostic signatures. At the single-cell level, the algorithms "Seurat," "SCEVAN", "scissor", and "Cellchat" were used to demonstrate the cell communication disturbance of high-risk cells. WGCNA and univariate Cox regression analysis identified 52 prognosis-related genes, which were subjected to 98 machine-learning integration processes. A prognostic signature consisting of 24 genes was identified using the StepCox[backward] and Enet[alpha = 0.7] machine learning algorithms. This signature demonstrated the best prognostic performance in the overall, test1 and test2 cohort, and outperformed 93 previously published prognostic signatures. Interaction perturbations in cellular communication of high-risk T cells were identified at the single-cell level, which may promote disease progression in patients with gastric cancer. We developed an immune-related prognostic signature with reliable validity and high accuracy for clinical use for predicting the prognosis of patients with gastric cancer.
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Affiliation(s)
- Jingyuan Ning
- Department of Immunology, Immunology Department of Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Keran Sun
- Department of Immunology, Immunology Department of Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Xiaoqing Fan
- Department of Immunology, Immunology Department of Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Keqi Jia
- Department of Pathology, Shijiazhuang People's Hospital, Shijiazhuang, People's Republic of China
| | - Lingtong Meng
- Department of Immunology, Immunology Department of Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Xiuli Wang
- Department of Laboratory, The Second Hospital of Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Hui Li
- Department of Oncology, Shijiazhuang Fourth Hospital, Shijiazhuang, People's Republic of China
| | - Ruixiao Ma
- Department of Oncology, Shijiazhuang Fourth Hospital, Shijiazhuang, People's Republic of China
| | - Subin Liu
- Department of Oncology, Shijiazhuang Fourth Hospital, Shijiazhuang, People's Republic of China
| | - Feng Li
- Department of Oncology, Shijiazhuang Fourth Hospital, Shijiazhuang, People's Republic of China
| | - Xiaofeng Wang
- Department of Immunology, Immunology Department of Hebei Medical University, Shijiazhuang, People's Republic of China.
- Department of Oncology, Shijiazhuang Fourth Hospital, Shijiazhuang, People's Republic of China.
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Chen Y, Shou L, Xia Y, Deng Y, Li Q, Huang Z, Li Y, Li Y, Cai W, Wang Y, Cheng Y, Chen H, Wan L. Artificial intelligence annotated clinical-pathologic risk model to predict outcomes of advanced gastric cancer. Front Oncol 2023; 13:1099360. [PMID: 37056330 PMCID: PMC10086433 DOI: 10.3389/fonc.2023.1099360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
BackgroundGastric cancer with synchronous distant metastases indicates a dismal prognosis. The success in survival improvement mainly relies on our ability to predict the potential benefit of a therapy. Our objective is to develop an artificial intelligence annotated clinical-pathologic risk model to predict its outcomes.MethodsIn participants (n=47553) with gastric cancer of the surveillance, epidemiology, and end results program, we selected patients with distant metastases at first diagnosis, complete clinical-pathologic data and follow-up information. Patients were randomly divided into the training and test cohort at 7:3 ratio. 93 patients with advanced gastric cancer from six other cancer centers were collected as the external validation cohort. Multivariable analysis was used to identify the prognosis-related clinical-pathologic features. Then a survival prediction model was established and validated. Importantly, we provided explanations to the prediction with artificial intelligence SHAP (Shapley additive explanations) method. We also provide novel insights into treatment options.ResultsData from a total 2549 patients were included in model development and internal test (median age, 61 years [range, 53-69 years]; 1725 [67.7%] male). Data from an additional 93 patients were collected as the external validation cohort (median age, 59 years [range, 48-66 years]; 51 [54.8%] male). The clinical-pathologic model achieved a consistently high accuracy for predicting prognosis in the training (C-index: 0.705 [range, 0.690-0.720]), test (C-index: 0.737 [range, 0.717-0.757]), and external validation (C-index: 0.694 [range, 0.562-0.826]) cohorts. Shapley values indicated that undergoing surgery, chemotherapy, young, absence of lung metastases and well differentiated were the top 5 contributors to the high likelihood of survival. A combination of surgery and chemotherapy had the greatest benefit. However, aggressive treatment did not equate to a survival benefit. SHAP dependence plots demonstrated insightful nonlinear interactive associations among predictors in survival benefit prediction. For example, patients who were elderly, or poor differentiated, or presence of lung or bone metastases had a worse prognosis if they undergo surgery or chemotherapy, while patients with metastases to liver alone seemed to gain benefit from surgery and chemotherapy.ConclusionIn this large multicenter cohort study, we developed an artificial intelligence annotated clinical-pathologic risk model to predict outcomes of advanced gastric cancer. It could be used to discuss treatment options.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Li Wan
- *Correspondence: Li Wan, ; Hongzhuan Chen,
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Guo X, Bu X, Yuan L, Ji L. Collagen type V alpha 2 promotes the development of gastric cancer via M2 macrophage polarization. CHINESE J PHYSIOL 2023; 66:93-102. [PMID: 37082997 DOI: 10.4103/cjop.cjop-d-22-00078] [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] [Indexed: 03/29/2023] Open
Abstract
Gastric cancer is a type of digestive tract cancer with a high morbidity and mortality, which leads to a major health burden worldwide. More research into the functions of the immune system will improve therapy and survival in gastric cancer patients. We attempted to identify potential biomarkers or targets in gastric cancer via bioinformatical analysis approaches. Three gene expression profile datasets (GSE79973, GSE103236, and GSE118916) of gastric tissue samples were obtained from the Gene Expression Omnibus database. There were 65 overlapping differentially expressed genes (DEGs) identified from three microarrays. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway were carried out for the key functions and pathways enriched in the DEGs. Then, ten hub genes were identified by protein-protein interaction network. In addition, we observed that collagen type V alpha 2 (COL5A2) was linked to gastric cancer prognosis as well as M2 macrophage infiltration. Furthermore, COL5A2 enhanced gastric cancer cell proliferation through the PI3K-AKT signaling pathway and polarized M2 macrophage cells. Therefore, in this study, we found that COL5A2 was associated with the development of gastric cancer which might function as a potential therapeutic target for the disease.
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Affiliation(s)
- Xin Guo
- Department of Digestive Oncology, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, Shanxi; Department of Digestive Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaoqian Bu
- Department of Digestive Oncology, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, Shanxi; Department of Digestive Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Li Yuan
- Department of Digestive Oncology, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, Shanxi; Department of Digestive Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lina Ji
- Department of Digestive Oncology, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, Shanxi; Department of Digestive Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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Brummel K, Eerkens AL, de Bruyn M, Nijman HW. Tumour-infiltrating lymphocytes: from prognosis to treatment selection. Br J Cancer 2023; 128:451-458. [PMID: 36564565 PMCID: PMC9938191 DOI: 10.1038/s41416-022-02119-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
Tumour-infiltrating lymphocytes (TILs) are considered crucial in anti-tumour immunity. Accordingly, the presence of TILs contains prognostic and predictive value. In 2011, we performed a systematic review and meta-analysis on the prognostic value of TILs across cancer types. Since then, the advent of immune checkpoint blockade (ICB) has renewed interest in the analysis of TILs. In this review, we first describe how our understanding of the prognostic value of TIL has changed over the last decade. New insights on novel TIL subsets are discussed and give a broader view on the prognostic effect of TILs in cancer. Apart from prognostic value, evidence on the predictive significance of TILs in the immune therapy era are discussed, as well as new techniques, such as machine learning that strive to incorporate these predictive capacities within clinical trials.
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Affiliation(s)
- Koen Brummel
- University of Groningen, University Medical Center Groningen, Department of Obstetrics and Gynecology, Groningen, The Netherlands
| | - Anneke L Eerkens
- University of Groningen, University Medical Center Groningen, Department of Obstetrics and Gynecology, Groningen, The Netherlands
| | - Marco de Bruyn
- University of Groningen, University Medical Center Groningen, Department of Obstetrics and Gynecology, Groningen, The Netherlands
| | - Hans W Nijman
- University of Groningen, University Medical Center Groningen, Department of Obstetrics and Gynecology, Groningen, The Netherlands.
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Comprehensive analysis of immune subtypes reveals the prognostic value of cytotoxicity and FAP + fibroblasts in stomach adenocarcinoma. Cancer Immunol Immunother 2023; 72:1763-1778. [PMID: 36650362 DOI: 10.1007/s00262-023-03368-9] [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: 11/09/2022] [Accepted: 01/04/2023] [Indexed: 01/18/2023]
Abstract
BACKGROUND The heterogeneity limits the effective application of immune checkpoint inhibitors for patients with stomach adenocarcinoma (STAD). Precise immunotyping can help select people who may benefit from immunotherapy and guide postoperative management by describing the characteristics of tumor microenvironment. METHODS Gene expression profiles and clinical information of patients were collected from ACRG and TCGA-STAD datasets. The immune subtypes (ISs) were identified by consensus clustering analysis. The tumor immune microenvironments (TIME) of each IS were characterized using a series of immunogenomics methods and further confirmed by multiplex immunohistochemistry (mIHC) staining in clinical samples. Two online datasets and one in-house dataset were utilized to construct and validate a prognostic immune-related gene (IRG) signature. RESULTS STAD patients were stratified into five reproducible ISs. IS1 (immune deserve subtype) had low immune infiltration and the highest degree of HER2 gene mutation. With abundant CD8+ T cells infiltration and activated cytotoxicity reaction, patients in the IS2 (immune-activated subtype) had the best overall survival (OS). IS3 and IS4 subtypes were both in the reactive stroma state and indicated the worst prognosis. However, IS3 (immune-inhibited subtype) was characterized by enrichment of FAP+ fibroblasts and upregulated TGF-β signaling pathway, while IS4 (activated stroma subtype) was characterized by enrichment of ACTA2+ fibroblasts. In addition, mIHC staining confirmed that TGF-β upregulated FAP+ fibroblasts were independent risk factor of OS. IS5 (chronic inflammation subtype) displayed moderate immune cells infiltration and had a relatively good survival. Lastly, we developed a nine-IRG signature model with a robust performance on overall survival prognostication. CONCLUSIONS The immunotyping is indicative for characterize the TIME heterogeneity and the prediction of tumor prognosis for STADs, which may provide valuable stratification for the design of future immunotherapy.
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16
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Development and validation of an artificial neural network model for non-invasive gastric cancer screening and diagnosis. Sci Rep 2022; 12:21795. [PMID: 36526664 PMCID: PMC9758153 DOI: 10.1038/s41598-022-26477-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Non-invasive and cost-effective diagnosis of gastric cancer is essential to improve outcomes. Aim of the study was to establish a neural network model based on patient demographic data and serum biomarker panels to aid gastric cancer diagnosis. A total of 295 patients hospitalized in Nanjing Drum Tower hospital diagnosed with gastric cancer based on tissue biopsy, and 423 healthy volunteers were included in the study. Demographical information and tumor biomarkers were obtained from Hospital Information System (HIS) as original data. Pearson's correlation analysis was applied on 574 individuals' data (training set, 229 patients and 345 healthy volunteers) to analyze the relationship between each variable and the final diagnostic result. And independent sample t test was used to detect the differences of the variables. Finally, a neural network model based on 14 relevant variables was constructed. The model was tested on the validation set (144 individuals including 66 patients and 78 healthy volunteers). The predictive ability of the proposed model was compared with other common machine learning models including logistic regression and random forest. Tumor markers contributing significantly to gastric cancer screening included CA199, CA125, AFP, and CA242 were identified, which might be considered as important inspection items for gastric cancer screening. The accuracy of the model on validation set was 86.8% and the F1-score was 85.0%, which were better than the performance of other models under the same condition. A non-invasive and low-cost artificial neural network model was developed and proved to be a valuable tool to assist gastric cancer diagnosis.
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Xiong S, Jin L, Zeng C, Ma H, Xie L, Liu S. An innovative pyroptosis-related long-noncoding-RNA signature predicts the prognosis of gastric cancer via affecting immune cell infiltration landscape. Pathol Oncol Res 2022; 28:1610712. [PMID: 36567977 PMCID: PMC9767988 DOI: 10.3389/pore.2022.1610712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 11/23/2022] [Indexed: 12/12/2022]
Abstract
Background: Gastric cancer (GC) is a worldwide popular malignant tumor. However, the survival rate of advanced GC remains low. Pyroptosis and long non-coding RNAs (lncRNAs) are important in cancer progression. Thus, we aimed to find out a pyroptosis-related lncRNAs (PRLs) signature and use it to build a practical risk model with the purpose to predict the prognosis of patients with GC. Methods: Univariate Cox regression analysis was used to identify PRLs linked to GC patient's prognosis. Subsequently, to construct a PRLs signature, the least absolute shrinkage and selection operator regression, and multivariate Cox regression analysis were used. Kaplan-Meier analysis, principal component analysis, and receiver operating characteristic curve analysis were performed to assess our novel lncRNA signature. The correlation between risk signature and clinicopathological features was also examined. Finally, the relationship of pyroptosis and immune cells were evaluated through the CIBERSORT tool and single-sample lncRNA set enrichment analysis (ssGSEA). Results: A PRLs signature comprising eight lncRNAs was discerned as a self-determining predictor of prognosis. GC patients were sub-divided into high-risk and low-risk groups via this risk-model. Stratified analysis of different clinical factors also displayed that the PRLs signature was a good prognosis factor. According to the risk score and clinical characteristics, a nomogram was established. Moreover, the difference between the groups is significance in immune cells and immune pathways. Conclusion: This study established an effective prognostic signature consist of eight PRLs in GC, and constructed an efficient nomogram model. Further, the PRLs correlated with immune cells and immune pathways.
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Affiliation(s)
- Siping Xiong
- Department of Pathology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Long Jin
- Department of Pathology, Shengli Clinical Medical College, Fujian Medical University, Fuzhou, Fujian, China
| | - Chao Zeng
- Department of Pathology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Hongmei Ma
- Department of Pathology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Linying Xie
- Department of Pathology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Shuguang Liu
- Department of Pathology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China,*Correspondence: Shuguang Liu,
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Jia B, Liu J, Hu X, Xia L, Han Y. Pan-cancer analysis of DEPDC1 as a candidate prognostic biomarker and associated with immune infiltration. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:1355. [PMID: 36660720 PMCID: PMC9843344 DOI: 10.21037/atm-22-5598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/13/2022] [Indexed: 01/01/2023]
Abstract
Background DEP domain containing 1 (DEPDC1) gene is upregulated in several malignancies and contributes to tumorigenesis. Although the role of DEPDC1 in tumor is becoming increasingly popular, the function of DEPDC1 in pan-cancer still needs to be systematically elucidated. Methods Data were downloaded from Genotype-Tissue Expression Data (GTEx), The Cancer Genome Atlas (TCGA) TIMER2.0, TISIDB, STRING, and CancerSEA databases and analyzed to determine the functionality of the DEPDC1. The results were visualized using tools provided by the databases and the R language. Results The results showed that DEPDC1 was significantly upregulated in 29 of the 33 human cancers analyzed. In addition, there were significant differences in DEPDC1 expression among cancer immune and molecular subtypes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that DEPDC1 was mainly involved in the cell cycle, and CancerSEA analysis showed that DEPDC1 promoted cell cycle, DNA repair, DNA damage, and proliferation in pan-cancer. Receiver operating characteristic (ROC) curve analysis showed high predictive accuracy for pan-cancer. DEPDC1 expression was positively correlated with activated CD4+ T helper 2 cells and common lymphoid progenitor cells, and negatively correlated with natural killer (NK) T cells, CD4+ central memory T cells, and CD4+ effector memory T cells. Furthermore, DEPDC1 was significantly positively correlated with T cell exhaustion marker genes, such as CD274, transforming growth factor beta receptor 1 (TGFBR1), kinase insert domain receptor (KDR), programmed cell death 1 ligand 2 (PDCD1LG2), granzyme B (GZMB), and granulysin (LAG2). Additionally, DEPDC1 was associated with overall survival (OS), disease-specific survival (DSS), and progress-free interval (PFI) prognosis in multiple tumor types. The ROC analysis showed high predictive accuracy for pan-cancer. Conclusions Collectively, DEPDC1 is aberrantly expressed and plays an immune-oncogenic role in pan-cancer, and DEPDC1 may serve as a biomarker for cancer diagnosis and therapy.
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Affiliation(s)
- Boquan Jia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Jun Liu
- Department of Clinical Laboratory, Affiliated Xiaoshan Hospital, Hangzhou Normal University, Hangzhou, China
| | - Xin Hu
- Department of Oral and Maxillofacial Surgery, Center of Stomatology, Xiangya Hospital of Central South University, Changsha, China;,Research Center of Oral and Maxillofacial Tumor, Xiangya Hospital of Central South University, Changsha, China;,Institute of Oral Cancer and Precancerous Lesions, Central South University, Changsha, China
| | - Lu Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Ying Han
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China;,Department of Oral and Maxillofacial Surgery, Center of Stomatology, Xiangya Hospital of Central South University, Changsha, China
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Bu F, Zhao Y, Zhao Y, Yang X, Sun L, Chen Y, Zhu S, Min L. Distinct tumor microenvironment landscapes of rectal cancer for prognosis and prediction of immunotherapy response. Cell Oncol 2022; 45:1363-1381. [PMID: 36251240 DOI: 10.1007/s13402-022-00725-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2022] [Indexed: 12/15/2022] Open
Abstract
PURPOSE Tumor microenvironment (TME) affects the progression of rectal cancer (RC), and the clinical relevance of its immune elements was widely reported. Here we aim to delineate the complete TME landscape, including non-immune features, to improve our understanding of RC heterogeneity and provide a better strategy for precision medicine. METHODS Single-cell analysis of GSE161277 using Seurat and Cellcall was performed to identify cell-cell interactions. The ssGSEA was employed to quantify the TME elements in TCGA patients, which were further clustered into subtypes by hclust. WGCNA and LASSO were combined to construct a degenerated signature for prognosis, and its performance was validated in two GEO datasets. RESULTS We proposed a subtyping strategy based on the abundance of both immune and non-immune components, which divided all RC patients into 4 subtypes (Immune-, Canonical-, Dormant- and Stem-like). Different subtypes exhibited distinct mutation landscapes, biological features, immune characteristics, immunotherapy responses and prognoses. Next, WGCNA and LASSO regression were combined to construct a 10-gene signature based on differentially expressed genes among different subtypes. Subgroups divided by this signature also exhibited different clinical parameters and responses to immune checkpoint blockades. Diverse machine learning algorithms were applied to achieve higher accuracy for survival prediction and a nomogram was further established in combination with M stage and age to provide an accurate and visual prediction of prognosis. CONCLUSIONS We identified four TME-based RC subtypes with distinct biological and clinical features. Based on those subtypes, we also proposed a degenerated 10-gene signature to predict the prognosis and immunotherapy response.
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Affiliation(s)
- Fanqin Bu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, 100050, People's Republic of China
| | - Yu Zhao
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, 100050, People's Republic of China
| | - Yushan Zhao
- The State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Xiaohan Yang
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, 100050, People's Republic of China
| | - Lan Sun
- Innovation Laboratory of Terahertz Biophysics, National Innovation Institute of Defense Technology, Beijing, 100071, People's Republic of China
| | - Yang Chen
- The State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Shengtao Zhu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, 100050, People's Republic of China.
| | - Li Min
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, 100050, People's Republic of China.
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Cao R, Tang L, Fang M, Zhong L, Wang S, Gong L, Li J, Dong D, Tian J. Artificial intelligence in gastric cancer: applications and challenges. Gastroenterol Rep (Oxf) 2022; 10:goac064. [PMID: 36457374 PMCID: PMC9707405 DOI: 10.1093/gastro/goac064] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/27/2022] [Accepted: 10/18/2022] [Indexed: 08/10/2023] Open
Abstract
Gastric cancer (GC) is one of the most common malignant tumors with high mortality. Accurate diagnosis and treatment decisions for GC rely heavily on human experts' careful judgments on medical images. However, the improvement of the accuracy is hindered by imaging conditions, limited experience, objective criteria, and inter-observer discrepancies. Recently, the developments of machine learning, especially deep-learning algorithms, have been facilitating computers to extract more information from data automatically. Researchers are exploring the far-reaching applications of artificial intelligence (AI) in various clinical practices, including GC. Herein, we aim to provide a broad framework to summarize current research on AI in GC. In the screening of GC, AI can identify precancerous diseases and assist in early cancer detection with endoscopic examination and pathological confirmation. In the diagnosis of GC, AI can support tumor-node-metastasis (TNM) staging and subtype classification. For treatment decisions, AI can help with surgical margin determination and prognosis prediction. Meanwhile, current approaches are challenged by data scarcity and poor interpretability. To tackle these problems, more regulated data, unified processing procedures, and advanced algorithms are urgently needed to build more accurate and robust AI models for GC.
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Affiliation(s)
| | | | - Mengjie Fang
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, P. R. China
- CAS Key Laboratory of Molecular Imaging, Beijing Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, P. R. China
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, P. R. China
| | - Lianzhen Zhong
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, P. R. China
- CAS Key Laboratory of Molecular Imaging, Beijing Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, P. R. China
| | - Siwen Wang
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, P. R. China
- CAS Key Laboratory of Molecular Imaging, Beijing Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, P. R. China
| | - Lixin Gong
- College of Medicine and Biological Information Engineering School, Northeastern University, Shenyang, Liaoning, P. R. China
| | - Jiazheng Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Radiology Department, Peking University Cancer Hospital & Institute, Beijing, P. R. China
| | - Di Dong
- Corresponding authors. Di Dong, CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, 95 Zhongguancun East Road, Beijing 100190, P. R. China. Tel: +86-13811833760; ; Jie Tian, Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, P. R. China. Tel: +86-10-82618465;
| | - Jie Tian
- Corresponding authors. Di Dong, CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, 95 Zhongguancun East Road, Beijing 100190, P. R. China. Tel: +86-13811833760; ; Jie Tian, Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, P. R. China. Tel: +86-10-82618465;
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Khvostikov AV, Krylov AS, Mikhailov IA, Malkov PG. Visualization of Whole Slide Histological Images with Automatic Tissue Type Recognition. PATTERN RECOGNITION AND IMAGE ANALYSIS 2022. [DOI: 10.1134/s1054661822030208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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22
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Gastric Cancer Subtypes in Tumour and Nontumour Tissues by Immunologic and Hallmark Gene Sets. JOURNAL OF ONCOLOGY 2022; 2022:7887711. [PMID: 36065314 PMCID: PMC9440817 DOI: 10.1155/2022/7887711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 11/17/2022]
Abstract
A previous research study on differentiating gastric cancer (GC) into distinct subtypes or prognostic models was mostly based on GC tissues, which neglected the role of nontumour tissues in GC subtypes. The purpose of the research was to identify GC subtypes on the basis of tumour and adjacent nontumour tissues to assess the prognosis of GC patients. We characterized three GC subtypes on the basis of the immunologic and hallmark gene sets in GC and adjacent nontumour tissues: among them, the GC patients with subtype I had the longest survival time compared to patients with other subtypes. The classification was closely associated with T stage and pathological stage of GC patients. A prognostic model containing two gene sets was constructed by LASSO analysis. Kaplan–Meier analysis showed that patients in the high-risk group survived longer than those in the low-risk group and the two prognostic genes sets in the model were strongly correlated with survival status. Then, GO and KEGG analyses and PPI network show that nontumour and tumour tissues are influencing the prognosis of GC patients in separate manners. In summary, we emphasized the prognostic value of nontumour tissue in GC patients and proposed a novel insight that both changes in tumour and nontumour tissues should be taken into account when selecting a treatment strategy for GC.
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Sukri A, Hanafiah A, Kosai NR. The Roles of Immune Cells in Gastric Cancer: Anti-Cancer or Pro-Cancer? Cancers (Basel) 2022; 14:cancers14163922. [PMID: 36010915 PMCID: PMC9406374 DOI: 10.3390/cancers14163922] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/05/2022] [Accepted: 08/07/2022] [Indexed: 12/03/2022] Open
Abstract
Simple Summary Gastric cancer is still one of the leading causes of death caused by cancer in developing countries. The emerging role of immunotherapy in cancer treatment has led to more research to elucidate the roles of essential immune cells in gastric cancer prognosis. We reviewed the roles of immune cells including T cells, B cells, dendritic cells, macrophages and natural killer cells in gastric cancer. Although the studies conducted on the roles of immune cells in gastric cancer pathogenesis produced conflicting results, understanding the roles of immune cells in gastric cancer will help us to harness them for application in immunotherapy for better prognosis and management of gastric cancer patients. Abstract Despite the fact that the incidence of gastric cancer has declined over the last decade, it is still the world’s leading cause of cancer-related death. The diagnosis of early gastric cancer is difficult, as symptoms of this cancer only manifest at a late stage of cancer progression. Thus, the prognosis of gastric cancer is poor, and the current treatment for improving patients’ outcomes involves the application of surgery and chemotherapy. Immunotherapy is one of the most recent therapies for gastric cancer, whereby the immune system of the host is programmed to combat cancer cells, and the therapy differs based upon the patient’s immune system. However, an understanding of the role of immune cells, namely the cell-mediated immune response and the humoral immune response, is pertinent for applications of immunotherapy. The roles of immune cells in the prognosis of gastric cancer have yielded conflicting results. This review discusses the roles of immune cells in gastric cancer pathogenesis, specifically, T cells, B cells, macrophages, natural killer cells, and dendritic cells, as well as the evidence presented thus far. Understanding how cancer cells interact with immune cells is of paramount importance in designing treatment options for gastric cancer immunotherapy.
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Affiliation(s)
- Asif Sukri
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM), Bandar Puncak Alam, Shah Alam 43200, Malaysia
| | - Alfizah Hanafiah
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur 56000, Malaysia
- Correspondence:
| | - Nik Ritza Kosai
- Department of Surgery, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur 56000, Malaysia
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Majewski M, Mertowska P, Mertowski S, Smolak K, Grywalska E, Torres K. Microbiota and the Immune System-Actors in the Gastric Cancer Story. Cancers (Basel) 2022; 14:cancers14153832. [PMID: 35954495 PMCID: PMC9367521 DOI: 10.3390/cancers14153832] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/04/2022] [Accepted: 08/06/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Stomach cancer is one of the most commonly diagnosed cancers in the world. Although the number of new cases is decreasing year by year, the death rate for this type of cancer is still high. The heterogeneous course and the lack of symptoms in the early stages of the disease mean that the diagnosis is made late, which translates into a worse prognosis for such patients. That is why it is so important to analyze potential risk factors that may increase the risk of developing gastric cancer and to search for new effective methods of treatment. These requirements are met by the analysis of the composition of the gastric microbiota and its relationship with the immune system, which is a key element in the human anti-cancer fight. This publication was created to systematize the current knowledge on the impact of dysbiosis of human microbiota on the development and progression of gastric cancer. Particular emphasis was placed on taking into account the role of the immune system in this process. Abstract Gastric cancer remains one of the most commonly diagnosed cancers in the world, with a relatively high mortality rate. Due to the heterogeneous course of the disease, its diagnosis and treatment are limited and difficult, and it is associated with a reduced prognosis for patients. That is why it is so important to understand the mechanisms underlying the development and progression of this cancer, with particular emphasis on the role of risk factors. According to the literature data, risk factors include: changes in the composition of the stomach and intestinal microbiota (microbiological dysbiosis and the participation of Helicobacter pylori), improper diet, environmental and genetic factors, and disorders of the body’s immune homeostasis. Therefore, the aim of this review is to systematize the knowledge on the influence of human microbiota dysbiosis on the development and progression of gastric cancer, with particular emphasis on the role of the immune system in this process.
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Affiliation(s)
- Marek Majewski
- 2nd Department of General, Gastrointestinal Surgery and Surgical Oncology of the Alimentary Tract, Medical University of Lublin, 20-081 Lublin, Poland
| | - Paulina Mertowska
- Department of Experimental Immunology, Medical University of Lublin, 20-093 Lublin, Poland
- Correspondence:
| | - Sebastian Mertowski
- Department of Experimental Immunology, Medical University of Lublin, 20-093 Lublin, Poland
| | - Konrad Smolak
- Department of Experimental Immunology, Medical University of Lublin, 20-093 Lublin, Poland
| | - Ewelina Grywalska
- Department of Experimental Immunology, Medical University of Lublin, 20-093 Lublin, Poland
| | - Kamil Torres
- Chair and Department of Didactics and Medical Simulation, Medical University of Lublin, 20-093 Lublin, Poland
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Lin Y, Huang K, Cai Z, Chen Y, Feng L, Gao Y, Zheng W, Fan X, Qiu G, Zhuang J, Feng S. A Novel Exosome-Relevant Molecular Classification Uncovers Distinct Immune Escape Mechanisms and Genomic Alterations in Gastric Cancer. Front Pharmacol 2022; 13:884090. [PMID: 35721114 PMCID: PMC9204030 DOI: 10.3389/fphar.2022.884090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/29/2022] [Indexed: 12/17/2022] Open
Abstract
Objective: Gastric cancer (GC) is a highly heterogeneous malignant carcinoma. This study aimed to conduct an exosome-based classification for assisting personalized therapy for GC.Methods: Based on the expression profiling of prognostic exosome-related genes, GC patients in The Cancer Genome Atlas (TCGA) cohort were classified using the unsupervised consensus clustering approach, and the reproducibility of this classification was confirmed in the GSE84437 cohort. An exosome-based gene signature was developed via Least Absolute Shrinkage and Selection Operator (LASSO) regression analysis. Immunological features, responses to immune checkpoint inhibitors, and genetic alterations were evaluated via computational methods.Results: Two exosome-relevant phenotypes (A and B) were clustered, and this classification was independent of immune subtypes and TCGA subtypes. Exosome-relevant phenotype B had a poorer prognosis and an inflamed tumor microenvironment (TME) relative to phenotype A. Patients with phenotype B presented higher responses to the anti-CTLA4 inhibitor. Moreover, phenotype B occurred at a higher frequency of genetic mutation than phenotype A. The exosome-based gene signature (GPX3, RGS2, MATN3, SLC7A2, and SNCG) could independently and accurately predict GC prognosis, which was linked to stromal activation and immunosuppression.Conclusion: Our findings offer a conceptual frame to further comprehend the roles of exosomes in immune escape mechanisms and genomic alterations of GC. More work is required to evaluate the reference value of exosome-relevant phenotypes for designing immunotherapeutic regimens.
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Affiliation(s)
- Yubiao Lin
- Department of Oncology, Xiamen Haicang Hospital, Xiamen, China
| | - Kaida Huang
- Department of Oncology, Xiamen Haicang Hospital, Xiamen, China
| | - Zhezhen Cai
- Department of General Surgery, Xiamen Haicang Hospital, Xiamen, China
| | - Yide Chen
- Department of Oncology, Xiamen Haicang Hospital, Xiamen, China
| | - Lihua Feng
- Department of Oncology, Xiamen Haicang Hospital, Xiamen, China
| | - Yingqin Gao
- Department of Oncology, Xiamen Haicang Hospital, Xiamen, China
| | - Wenhui Zheng
- Department of Oncology, Xiamen Haicang Hospital, Xiamen, China
| | - Xin Fan
- Department of Oncology, Xiamen Haicang Hospital, Xiamen, China
| | - Guoqin Qiu
- Chenggong Hospital Affiliated to Xiamen University, Xiamen, China
- *Correspondence: Guoqin Qiu, ; Jianmin Zhuang, ; Shuitu Feng,
| | - Jianmin Zhuang
- Department of General Surgery, Xiamen Haicang Hospital, Xiamen, China
- *Correspondence: Guoqin Qiu, ; Jianmin Zhuang, ; Shuitu Feng,
| | - Shuitu Feng
- Department of Oncology, Xiamen Haicang Hospital, Xiamen, China
- *Correspondence: Guoqin Qiu, ; Jianmin Zhuang, ; Shuitu Feng,
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Interpretable tumor differentiation grade and microsatellite instability recognition in gastric cancer using deep learning. J Transl Med 2022; 102:641-649. [PMID: 35177797 DOI: 10.1038/s41374-022-00742-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 01/18/2022] [Accepted: 01/22/2022] [Indexed: 12/13/2022] Open
Abstract
Gastric cancer possesses great histological and molecular diversity, which creates obstacles for rapid and efficient diagnoses. Classic diagnoses either depend on the pathologist's judgment, which relies heavily on subjective experience, or time-consuming molecular assays for subtype diagnosis. Here, we present a deep learning (DL) system to achieve interpretable tumor differentiation grade and microsatellite instability (MSI) recognition in gastric cancer directly using hematoxylin-eosin (HE) staining whole-slide images (WSIs). WSIs from 467 patients were divided into three cohorts: the training cohort with 348 annotated WSIs, the testing cohort with 88 annotated WSIs, and the integration testing cohort with 31 original WSIs without tumor contour annotation. First, the DL models comprehensibly achieved tumor differentiation recognition with an F1 values of 0.8615 and 0.8977 for poorly differentiated adenocarcinoma (PDA) and well-differentiated adenocarcinoma (WDA) classes. Its ability to extract pathological features about the glandular structure formation, which is the key to distinguishing between PDA and WDA, increased the interpretability of the DL models. Second, the DL models achieved MSI status recognition with a patient-level accuracy of 86.36% directly from HE-stained WSIs in the testing cohort. Finally, the integrated end-to-end system achieved patient-level MSI recognition from original HE staining WSIs with an accuracy of 83.87% in the integration testing cohort with no tumor contour annotation. The proposed system, therefore, demonstrated high accuracy and interpretability, which can potentially promote the implementation of artificial intelligence healthcare.
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Gao J, Huo S, Zhang Y, Zhao Z, Pan H, Liu X. Construction of ovarian metastasis-related immune signature predicting prognosis of gastric cancer patients. Cancer Med 2022; 12:913-929. [PMID: 35621244 PMCID: PMC9844635 DOI: 10.1002/cam4.4857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 05/07/2022] [Accepted: 05/15/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Ovarian metastasis (OM) results in poor survival of gastric cancer (GC) patients. While immunotherapy has emerged as a promising approach for late-stage GC, validated immune-related prognostic signatures still remain in need. In this study, we constructed an ovarian metastasis- and immune-related prognostic signature (OMIRPS), characterized the molecular and immune features of OMIRPS-categorized subgroups and predicted their potential response to immunotherapy. METHODS Three individual cohorts were used to construct and evaluate OMIRPS: RNA-seq of matched primary GC and OM from Fudan University Shanghai Cancer Center (FUSCC) (discovery cohort, n = 4), The Cancer Genome Atlas (TCGA) (training cohort, n = 544) and GSE84437 (validation cohort, n = 433). Differentially expressed genes (DEGs) identified between primary GC and OM and immune-related genes (IRGs) from the ImmPort and InnateDB databases were used to identify immune-related prognostic hub genes, which were further used to construct OMIRPS by using LASSO regression analysis. Prognosis, molecular characteristics, immune features, and differential immunotherapy efficacy between different OMIRPS subgroups were analyzed. RESULTS Functional analyses of DEGs revealed the significance of immune-related signatures and pathways in the OM. Immune-related prognostic hub genes including TNFRSF18, CARD11, BCL11B, NRP1, BNIP3L, and ATF3 were utilized to construct OMIRPS, which was identified as an independent prognostic factor. Comprehensive analyses unveiled the distinctive molecular and immune characteristics of OMIRPS-high and -low subgroup in regard to enriched pathways, mutation rate, tumor mutation burden, microsatellite instability status, infiltrated immune cell, immune exclusion score, and the prediction of immunotherapy efficacy. Additionally, OMIRPS was associated with Immune Subtypes with borderline significance. CONCLUSIONS RNA-seq of paired primary and ovarian metastatic tumors unveiled the significance of immune-related pathways and tumor immune microenvironment in OM. OMIRPS served as a promising biomarker to predict the prognosis of GC patients and distinguish the molecular features, immune characteristics, and efficacy of immunotherapy between different subgroups.
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Affiliation(s)
- Jianpeng Gao
- Department of Gastric SurgeryFudan University Shanghai Cancer CenterShanghaiChina,Department of OncologyShanghai Medical College, Fudan UniversityShanghaiChina
| | - Shiying Huo
- Department of Gastric SurgeryFudan University Shanghai Cancer CenterShanghaiChina,Department of OncologyShanghai Medical College, Fudan UniversityShanghaiChina
| | - Yu Zhang
- Department of Gastric SurgeryFudan University Shanghai Cancer CenterShanghaiChina,Department of OncologyShanghai Medical College, Fudan UniversityShanghaiChina
| | - Zhenxiong Zhao
- Department of Gastric SurgeryFudan University Shanghai Cancer CenterShanghaiChina,Department of OncologyShanghai Medical College, Fudan UniversityShanghaiChina
| | - Hongda Pan
- Department of Gastric SurgeryFudan University Shanghai Cancer CenterShanghaiChina,Department of OncologyShanghai Medical College, Fudan UniversityShanghaiChina
| | - Xiaowen Liu
- Department of Gastric SurgeryFudan University Shanghai Cancer CenterShanghaiChina,Department of OncologyShanghai Medical College, Fudan UniversityShanghaiChina
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Chen Y, Sun Z, Wan L, Chen H, Xi T, Jiang Y. Tumor Microenvironment Characterization for Assessment of Recurrence and Survival Outcome in Gastric Cancer to Predict Chemotherapy and Immunotherapy Response. Front Immunol 2022; 13:890922. [PMID: 35572498 PMCID: PMC9101297 DOI: 10.3389/fimmu.2022.890922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/11/2022] [Indexed: 12/24/2022] Open
Abstract
Background The tumor microenvironment (TME) is crucial for tumor recurrence, prognosis, and therapeutic responses. We comprehensively investigated the TME characterization associated with relapse and survival outcomes of gastric cancer (GC) to predict chemotherapy and immunotherapy response. Methods A total of 2,456 GC patients with complete gene-expression data and clinical annotations from twelve cohorts were included. The TME characteristics were evaluated using three proposed computational algorithms. We then developed a TME-classifier, a TME-cluster, and a TME-based risk score for the assessment of tumor recurrence and prognosis in patients with GC to predict chemotherapy and immunotherapy response. Results Patients with tumor recurrence presented with inactive immunogenicity, namely, high infiltration of tumor-associated stromal cells, low infiltration of tumor-associated immunoactivated lymphocytes, high stromal score, and low immune score. The TME-classifier of 4 subtypes with distinct clinicopathology, genomic, and molecular characteristics was significantly associated with tumor recurrence (P = 0.002), disease-free survival (DFS, P <0.001), and overall survival (OS, P <0.001) adjusted by confounding variables in 1,193 stage I–III GC patients who underwent potential radical surgery. The TME cluster and TME-based risk score can also predict DFS (P <0.001) and OS (P <0.001). More importantly, we found that patients in the TMEclassifier-A, TMEclassifier-C, and TMEclassifier-D groups benefited from adjuvant chemotherapy, and patients in the TMEclassifier-B group without chemotherapy benefit responded best to pembrolizumab treatment (PD-1 inhibitor), followed by patients in the TMEclassifier-A, while patients in the C and D groups of the TMEclassifier responded poorly to immunotherapy. Conclusion We determined that TME characterization is significantly associated with tumor recurrence and prognosis. The TME-classifier we proposed can guide individualized chemotherapy and immunotherapy decision-making.
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Affiliation(s)
- Yan Chen
- Shatou Community Health Service Center, Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, The Second People’s Hospital of Bao’an Shenzhen (Group), Shenzhen Bao’an Shajing People’s Hospital, Guangzhou Medical University, Shenzhen, China
- *Correspondence: Yuming Jiang, ; Yan Chen,
| | - Zepang Sun
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Li Wan
- Shatou Community Health Service Center, Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, The Second People’s Hospital of Bao’an Shenzhen (Group), Shenzhen Bao’an Shajing People’s Hospital, Guangzhou Medical University, Shenzhen, China
| | - Hongzhuan Chen
- Shatou Community Health Service Center, Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, The Second People’s Hospital of Bao’an Shenzhen (Group), Shenzhen Bao’an Shajing People’s Hospital, Guangzhou Medical University, Shenzhen, China
| | - Tieju Xi
- Shatou Community Health Service Center, Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, The Second People’s Hospital of Bao’an Shenzhen (Group), Shenzhen Bao’an Shajing People’s Hospital, Guangzhou Medical University, Shenzhen, China
| | - Yuming Jiang
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, United States
- *Correspondence: Yuming Jiang, ; Yan Chen,
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Xiao C, Zhou M, Yang X, Wang H, Tang Z, Zhou Z, Tian Z, Liu Q, Li X, Jiang W, Luo J. Accurate Prediction of Metachronous Liver Metastasis in Stage I-III Colorectal Cancer Patients Using Deep Learning With Digital Pathological Images. Front Oncol 2022; 12:844067. [PMID: 35433467 PMCID: PMC9010865 DOI: 10.3389/fonc.2022.844067] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 03/10/2022] [Indexed: 11/13/2022] Open
Abstract
ObjectivesMetachronous liver metastasis (LM) significantly impacts the prognosis of stage I-III colorectal cancer (CRC) patients. An effective biomarker to predict LM after surgery is urgently needed. We aimed to develop deep learning-based models to assist in predicting LM in stage I-III CRC patients using digital pathological images.MethodsSix-hundred eleven patients were retrospectively included in the study and randomly divided into training (428 patients) and validation (183 patients) cohorts according to the 7:3 ratio. Digital HE images from training cohort patients were used to construct the LM risk score based on a 50-layer residual convolutional neural network (ResNet-50). An LM prediction model was established by multivariable Cox analysis and confirmed in the validation cohort. The performance of the integrated nomogram was assessed with respect to its calibration, discrimination, and clinical application value.ResultsPatients were divided into low- and high-LM risk score groups according to the cutoff value and significant differences were observed in the LM of the different risk score groups in the training and validation cohorts (P<0.001). Multivariable analysis revealed that the LM risk score, VELIPI, pT stage and pN stage were independent predictors of LM. Then, the prediction model was developed and presented as a nomogram to predict the 1-, 2-, and 3-year probability of LM. The integrated nomogram achieved satisfactory discrimination, with C-indexes of 0.807 (95% CI: 0.787, 0.827) and 0.812 (95% CI: 0.773, 0.850) and AUCs of 0.840 (95% CI: 0.795, 0.885) and 0.848 (95% CI: 0.766, 0.931) in the training and validation cohorts, respectively. Favorable calibration of the nomogram was confirmed in the training and validation cohorts. Integrated discrimination improvement and net reclassification index indicated that the integrated nomogram was superior to the traditional clinicopathological model. Decision curve analysis confirmed that the nomogram has clinical application value.ConclusionsThe LM risk score based on ResNet-50 and digital HE images was significantly associated with LM. The integrated nomogram could identify stage I-III CRC patients at high risk of LM after primary colectomy, so it may serve as a potential tool to choose the appropriate treatment to improve the prognosis of stage I-III CRC patients.
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Affiliation(s)
- Chanchan Xiao
- Department of General Surgery, Hunan Provincial People’s Hospital (The First-Affiliated Hospital of Hunan Normal University), Changsha, China
- Department of Microbiology and Immunology, Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, China
| | - Meihua Zhou
- Department of General Surgery, Hunan Provincial People’s Hospital (The First-Affiliated Hospital of Hunan Normal University), Changsha, China
| | - Xihua Yang
- Department of Surgical Oncology, Chenzhou No. 1 People’s Hospital, Chenzhou, China
| | - Haoyun Wang
- Department of Microbiology and Immunology, Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, China
| | - Zhen Tang
- Department of General Surgery, Hunan Provincial People’s Hospital (The First-Affiliated Hospital of Hunan Normal University), Changsha, China
| | - Zheng Zhou
- Department of General Surgery, Hunan Provincial People’s Hospital (The First-Affiliated Hospital of Hunan Normal University), Changsha, China
| | - Zeyu Tian
- Department of General Surgery, Hunan Provincial People’s Hospital (The First-Affiliated Hospital of Hunan Normal University), Changsha, China
| | - Qi Liu
- Department of General Surgery, Hunan Provincial People’s Hospital (The First-Affiliated Hospital of Hunan Normal University), Changsha, China
| | - Xiaojie Li
- Department of Pathology, Chenzhou No. 1 People’s Hospital, Chenzhou, China
| | - Wei Jiang
- Department of General Surgery, Hunan Provincial People’s Hospital (The First-Affiliated Hospital of Hunan Normal University), Changsha, China
- Department of Surgical Oncology, Chenzhou No. 1 People’s Hospital, Chenzhou, China
- *Correspondence: Jihui Luo, ; Wei Jiang,
| | - Jihui Luo
- Department of General Surgery, Hunan Provincial People’s Hospital (The First-Affiliated Hospital of Hunan Normal University), Changsha, China
- *Correspondence: Jihui Luo, ; Wei Jiang,
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