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Liu X, Ou J. The development of prognostic gene markers associated with disulfidptosis in gastric cancer and their application in predicting drug response. Heliyon 2024; 10:e26013. [PMID: 38384541 PMCID: PMC10878937 DOI: 10.1016/j.heliyon.2024.e26013] [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: 11/15/2023] [Revised: 12/24/2023] [Accepted: 02/06/2024] [Indexed: 02/23/2024] Open
Abstract
Background Gastric cancer (GC) is a malignancy known for its high fatality rate. Disulfidptosis, a potentially innovative therapeutic strategy for cancer treatment, has been proposed. Nevertheless, the specific involvement of disulfidptosis in the context of GC remains uncertain. Methods The mRNA expression profiles were obtained from the TCGA and GEO databases. Univariate and LASSO Cox regression analyses were employed to identify differentially expressed genes and develop a risk model for disulfidptosis-related genes. The performance of the model was evaluated using Kaplan-Meier curve, ROC curve, and nomogram. Univariate and multivariate Cox regression analyses were conducted to determine if the risk model could serve as an independent prognostic factor. The biological function of the identified genes was assessed through GO, KEGG, and GSEA analyses. The prediction of drug response was conducted employing the package "pRRophetic". Furthermore, gene expression was determined using qRT-PCR. Results An eight-gene signature were identified and utilized to categorize patients into low- and high-risk groups. Survival, receiver operating characteristic (ROC) curve, and Cox analyses provided clarification that these eight hub genes served as a favorable independent prognostic factor for patients with GC. A nomogram was constructed by integrating clinical parameters with the risk signatures, demonstrating high precision in predicting 1-, 3-, and 5-year survival rates. Additionally, drug sensitivity was different in the high-risk and low-risk groups, and the expression of three genes was verified by qRT-PCR. Conclusion The prognostic risk model developed in this study demonstrates the potential to accurately forecast the prognosis of patients with GC.
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Affiliation(s)
- Xing Liu
- Department of Pharmacy, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Jianghong Ou
- Department of Integrated Chinese and Western Medicine, Changsha Central Hospital, Nanhua University, Changsha, 410000, China
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Huang Y, He J, Duan X, Hou R, Shi J. Prognostic gene HLA-DMA associated with cell cycle and immune infiltrates in LUAD. THE CLINICAL RESPIRATORY JOURNAL 2023; 17:1286-1300. [PMID: 37972401 PMCID: PMC10730455 DOI: 10.1111/crj.13716] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 10/11/2023] [Accepted: 10/19/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND The dominant subclass of non-small-cell lung cancer (NSCLC) is lung adenocarcinoma (LUAD). The tumor microenvironment (TME) is a crucial feature of carcinogenesis and progression in LUAD. Furthermore, immune and stromal components of TME are crucial factors to investigating and curing LUAD. Thus, the study assessed the value of TME-related genes for LUAD prognosis and immune infiltration. METHODS All data were downloaded from TCGA and GEO databases. The immune and stromal scores were downloaded from ESTIMATE, and the association between the scores and prognosis was explored by Kaplan-Meier survival analysis. Protein-protein interaction (PPI) network and univariate Cox regression were used to find TME-related differentially expressed genes (DEGs), and HLA-DMA was regarded as a prognostic hub gene. Western blot analyses, qRT-PCR, and immunofluorescence were applied to verify HLA-DMA expression in clinical samples. NSCLC cell lines were used to verify the effect of HLA-DMA on cell proliferation and cell cycle distribution. At last, the alteration of immunotherapy response and TME transition caused by HLA-DMA different expression were further studied. RESULTS The immune score was positively correlated with survival. The functional analyses suggested that TME-related DEGs may be involved in the immune response. The expression level of HLA-DMA was decreased in LUAD. In addition, HLA-DMA expression was associated with several clinical features and was positively associated with survival. Furthermore, HLA-DMA may suspend cell proliferation by regulating cell cycle. HLA-DMA expression was closely associated with immune infiltration and positively correlated with TMB, indicating that patients with high HLA-DMA level were more suitable for immunotherapy. CONCLUSION These results reveal that HLA-DMA might act as a biomarker for immune infiltration and immunotherapy response.
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Affiliation(s)
- Ya‐jie Huang
- Department of Medical OncologyThe Fourth Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
| | - Jian‐kun He
- Department of PathologyThe Fourth Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
| | - Xiaoyang Duan
- Department of Medical OncologyThe Fourth Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
| | - Ran Hou
- Department of Medical OncologyThe Fourth Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
| | - Jian Shi
- Department of Medical OncologyThe Fourth Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
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Wang Q, Cui L, Li P, Wang Y. Somatic Mutation of FAT Family Genes Implicated Superior Prognosis in Patients With Stomach Adenocarcinoma. Front Med (Lausanne) 2022; 9:873836. [PMID: 35836939 PMCID: PMC9273734 DOI: 10.3389/fmed.2022.873836] [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: 02/11/2022] [Accepted: 06/01/2022] [Indexed: 12/24/2022] Open
Abstract
FAT family genes encode protocadherin, which regulates tumor cell proliferation and migration. Although transcriptional levels of FAT family members had been reported in multiple malignant tumors, the association between mutation and prognosis of the FAT family in stomach adenocarcinoma (STAD) has not been investigated. Herein, we performed a multi-omics integrative bioinformatics analysis using genomic and mRNA expression data to explore the role of gene mutations across the FAT family on clinical outcomes of STAD. The results showed that FAT mutations occurred in 174 of 435 (40%) of the samples. Patients with FAT mutations possessed significantly better progression-free survival (P = 0.019) and overall survival (P = 0.034) than those with non-FAT mutations, and FAT mutations exhibited significantly higher tumor mutational burden (TMB) and microsatellite instability. Notably, FAT mutations had a greater effect on somatic single-nucleotide variation than copy number variation and resulted in more abundant DNA damage repair (DDR) mutations. Further investigation demonstrated that FAT mutations contributed to an inflammatory tumor microenvironment (TME), as indicated by significantly increased numbers of activated CD4 and CD8 T cells, and significantly decreased numbers of mast cell, plasmacytoid dendritic cell, type 2 T helper cell, and high expression of immune-promoting genes. Moreover, biological process antigen processing and presentation, DNA replication, and DDR-related pathways were significantly upregulated in patients with FAT mutations. Collectively, FAT mutations significantly improved the survival of patients with STAD by enhancing tumor immunogenicity (e.g., TMB and DDR mutations) and an inflamed TME, indicating that the FAT family might be a potential prognostic and therapeutic biomarker for STAD.
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Affiliation(s)
- Qingjun Wang
- Department of Clinical Trial, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Liang Cui
- GenePlus-Beijing Institute, Beijing, China
| | - Pansong Li
- GenePlus-Beijing Institute, Beijing, China
| | - Yuanyuan Wang
- Department of Clinical Trial, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
- *Correspondence: Yuanyuan Wang,
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Yin X, Wu Q, Hao Z, Chen L. Identification of novel prognostic targets in glioblastoma using bioinformatics analysis. Biomed Eng Online 2022; 21:26. [PMID: 35436915 PMCID: PMC9014588 DOI: 10.1186/s12938-022-00995-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 04/07/2022] [Indexed: 11/17/2022] Open
Abstract
Background Glioblastoma (GBM) is the most malignant grade of glioma. Highly aggressive characteristics of GBM and poor prognosis cause GBM-related deaths. The potential prognostic biomarkers remain to be demonstrated. This research builds up predictive gene targets of expression alterations in GBM utilizing bioinformatics analysis. Methods and results The microarray datasets (GSE15824 and GSE16011) associated with GBM were obtained from Gene Expression Omnibus (GEO) database to identify the differentially expressed genes (DEGs) between GBM and non-tumor tissues. In total, 719 DEGs were obtained and subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) for function enrichment analysis. Furthermore, we constructed protein–protein Interaction (PPI) network among DEGs utilizing Search Tool for the Retrieval of Interacting Genes (STRING) online tool and Cytoscape software. The DEGs of degree > 10 was selected as hub genes, including 73 upregulated genes and 21 downregulated genes. Moreover, MCODE application in Cytoscape software was employed to identify three key modules involved in GBM development and prognosis. Additionally, we used the Gene expression profiling and interactive analyses (GEPIA) online tool to further confirm four genes involving in poor prognosis of GBM patients, including interferon-gamma-inducible protein 30 (IFI30), major histocompatibility complex class II-DM alpha (HLA-DMA), Prolyl 4-hydroxylase beta polypeptide (P4HB) and reticulocalbin-1 (RCN1). Furthermore, the correlation analysis indicated that the expression of IFI30, an acknowledged biomarker in glioma, was positively correlated with HLA-DMA, P4HB and RCN1. RCN1 expression was positively correlated with P4HB and HLA-DMA. Moreover, qRT-PCR and immunohistochemistry analysis further validated the upregulation of four prognostic markers in GBM tissues. Conclusions Analysis of multiple datasets combined with global network information and experimental verification presents a successful approach to uncover the risk hub genes and prognostic markers of GBM. Our study identified four risk- and prognostic-related gene signatures, including IFI30, HLA-DMA, P4HB and RCN1. This gene sets contribute a new perspective to improve the diagnostic, prognostic, and therapeutic outcomes of GBM.
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Affiliation(s)
- Xiaofeng Yin
- Department of Neurosurgery, Second Hospital of Shanxi Medical University, No.382 Wuyi Road, Taiyuan, 030000, Shanxi, China
| | - Quansheng Wu
- Department of Neurosurgery, Second Hospital of Shanxi Medical University, No.382 Wuyi Road, Taiyuan, 030000, Shanxi, China
| | - Zheng Hao
- Department of Neurosurgery, Second Hospital of Shanxi Medical University, No.382 Wuyi Road, Taiyuan, 030000, Shanxi, China
| | - Laizhao Chen
- Department of Neurosurgery, Second Hospital of Shanxi Medical University, No.382 Wuyi Road, Taiyuan, 030000, Shanxi, China.
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Chai M, Li X, Zhang Y, Tang Y, Shu P, Lin J, Shi K, Wang L, Huang X. A Nomogram Integrating Ferroptosis- and Immune-Related Biomarkers for Prediction of Overall Survival in Lung Adenocarcinoma. Front Genet 2021; 12:706814. [PMID: 34539740 PMCID: PMC8441018 DOI: 10.3389/fgene.2021.706814] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 08/04/2021] [Indexed: 12/25/2022] Open
Abstract
Ferroptosis plays a dual role in cancer, which is known to be affected to antitumor immune responses. However, the association between ferroptosis and antitumor immune responses is uncertain in lung adenocarcinoma (LUAD). In this work, 38 ferroptosis-related genes (FRGs) and 429 immune-related genes (IRGs) were identified as being differentially expressed between tumor and normal samples. Two risk score formulas consisting of seven FRGs and four IRGs, respectively, were developed by Lasso-penalized Cox regression and verified in the GSE13213 dataset. The CIBERSORT algorithm was used to estimate the relative abundance of immune cells in tumors. The correlation between FRGs and immune cells was evaluated using the TIMER database. The results indicated that the development of ferroptosis was synergistic with that of anti-tumor immunity in LUAD. The concordance index and calibration curves showed that the performance of a nomogram that combines clinical staging and risk scores is superior to that of models using a single prognostic factor. In conclusion, ferroptosis might be synergistic with anti-tumor immunity in LUAD. The combined nomogram could reliably predict the probability of overall survival of LUAD patients. These findings may be useful for future investigation of prognostic value and therapeutic potential related to ferroptosis and tumor immunity in LUAD.
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Affiliation(s)
- Mengyu Chai
- Division of Pulmonary Medicine, Key Laboratory of Heart and Lung, The First Affiliated Hospital of Wenzhou Medical University, Zhejiang, China
| | - Xiuchun Li
- Division of Pulmonary Medicine, Key Laboratory of Heart and Lung, The First Affiliated Hospital of Wenzhou Medical University, Zhejiang, China
| | - Yaxin Zhang
- Division of Pulmonary Medicine, Key Laboratory of Heart and Lung, The First Affiliated Hospital of Wenzhou Medical University, Zhejiang, China
| | - Yemeng Tang
- Division of Pulmonary Medicine, Key Laboratory of Heart and Lung, The First Affiliated Hospital of Wenzhou Medical University, Zhejiang, China
| | - Pingping Shu
- Division of Pulmonary Medicine, Key Laboratory of Heart and Lung, The First Affiliated Hospital of Wenzhou Medical University, Zhejiang, China
| | - Jing Lin
- Division of Pulmonary Medicine, Key Laboratory of Heart and Lung, The First Affiliated Hospital of Wenzhou Medical University, Zhejiang, China
| | - Keqing Shi
- Translational Medicine Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Zhejiang, China
| | - Liangxing Wang
- Division of Pulmonary Medicine, Key Laboratory of Heart and Lung, The First Affiliated Hospital of Wenzhou Medical University, Zhejiang, China
| | - Xiaoying Huang
- Division of Pulmonary Medicine, Key Laboratory of Heart and Lung, The First Affiliated Hospital of Wenzhou Medical University, Zhejiang, China
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Cao B, Zhang KC, Wei B, Chen L. Status quo and future prospects of artificial neural network from the perspective of gastroenterologists. World J Gastroenterol 2021; 27:2681-2709. [PMID: 34135549 PMCID: PMC8173384 DOI: 10.3748/wjg.v27.i21.2681] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/29/2021] [Accepted: 04/22/2021] [Indexed: 02/06/2023] Open
Abstract
Artificial neural networks (ANNs) are one of the primary types of artificial intelligence and have been rapidly developed and used in many fields. In recent years, there has been a sharp increase in research concerning ANNs in gastrointestinal (GI) diseases. This state-of-the-art technique exhibits excellent performance in diagnosis, prognostic prediction, and treatment. Competitions between ANNs and GI experts suggest that efficiency and accuracy might be compatible in virtue of technique advancements. However, the shortcomings of ANNs are not negligible and may induce alterations in many aspects of medical practice. In this review, we introduce basic knowledge about ANNs and summarize the current achievements of ANNs in GI diseases from the perspective of gastroenterologists. Existing limitations and future directions are also proposed to optimize ANN’s clinical potential. In consideration of barriers to interdisciplinary knowledge, sophisticated concepts are discussed using plain words and metaphors to make this review more easily understood by medical practitioners and the general public.
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Affiliation(s)
- Bo Cao
- Department of General Surgery & Institute of General Surgery, Chinese People’s Liberation Army General Hospital, Beijing 100853, China
| | - Ke-Cheng Zhang
- Department of General Surgery & Institute of General Surgery, Chinese People’s Liberation Army General Hospital, Beijing 100853, China
| | - Bo Wei
- Department of General Surgery & Institute of General Surgery, Chinese People’s Liberation Army General Hospital, Beijing 100853, China
| | - Lin Chen
- Department of General Surgery & Institute of General Surgery, Chinese People’s Liberation Army General Hospital, Beijing 100853, China
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Bermúdez A, Arranz-Salas I, Mercado S, López-Villodres JA, González V, Ríus F, Ortega MV, Alba C, Hierro I, Bermúdez D. Her2-Positive and Microsatellite Instability Status in Gastric Cancer-Clinicopathological Implications. Diagnostics (Basel) 2021; 11:944. [PMID: 34070574 PMCID: PMC8228707 DOI: 10.3390/diagnostics11060944] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 12/24/2022] Open
Abstract
Gastric cancer (GC) is one of the leading causes of cancer-related death. The combination of new molecular classifications with clinicopathological data could contribute to the individualization of patients and to the development of new therapeutic strategies. We examined the various associations in two molecular types of GC: HER2-positive (human epidermal growth factor receptor 2) and microsatellite instability (MSI), assessing their influence on treatment and prognosis. A retrospective study of 142 GC patients was performed with molecular characterization through HER2 overexpression and DNA repair protein expression for MSI. The percentage of HER2-positive tumors was 13.4%, predominantly in men. Correlations were found with intestinal type, metastases, advanced stages and chemotherapy. Almost 75% of HER2-positive patients died. MSI occurred in 16.2%, associated with advanced age, female sex, distal location and intestinal type. These patients had few metastases and low stages. The percentage of deaths was higher among MSI patients who received perioperative chemotherapy. The determination of HER2 and MSI status in GC is important for their association with specific clinicopathological features and for their prognostic and predictive value.
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Affiliation(s)
- Ana Bermúdez
- Department of Anesthesiology, Nuestra Señora de Valme University Hospital, 41014 Seville, Spain;
| | - Isabel Arranz-Salas
- Department of Human Physiology, Human Histology, Anatomical Pathology and Physical Education, University of Malaga, 29010 Malaga, Spain; (I.A.-S.); (S.M.); (J.A.L.-V.); (M.V.O.); (C.A.)
- Unit of Anatomical Pathology, Virgen de la Victoria University Hospital, 29010 Malaga, Spain;
| | - Silvia Mercado
- Department of Human Physiology, Human Histology, Anatomical Pathology and Physical Education, University of Malaga, 29010 Malaga, Spain; (I.A.-S.); (S.M.); (J.A.L.-V.); (M.V.O.); (C.A.)
| | - Juan A. López-Villodres
- Department of Human Physiology, Human Histology, Anatomical Pathology and Physical Education, University of Malaga, 29010 Malaga, Spain; (I.A.-S.); (S.M.); (J.A.L.-V.); (M.V.O.); (C.A.)
| | - Virginia González
- Unit of Anatomical Pathology; Montilla Hospital, 14550 Montilla, Spain;
| | - Francisca Ríus
- Department of Public Health and Psychiatry, University of Malaga, 29010 Malaga, Spain;
| | - María V. Ortega
- Department of Human Physiology, Human Histology, Anatomical Pathology and Physical Education, University of Malaga, 29010 Malaga, Spain; (I.A.-S.); (S.M.); (J.A.L.-V.); (M.V.O.); (C.A.)
- Unit of Anatomical Pathology, Virgen de la Victoria University Hospital, 29010 Malaga, Spain;
| | - Carmen Alba
- Department of Human Physiology, Human Histology, Anatomical Pathology and Physical Education, University of Malaga, 29010 Malaga, Spain; (I.A.-S.); (S.M.); (J.A.L.-V.); (M.V.O.); (C.A.)
| | - Isabel Hierro
- Unit of Anatomical Pathology, Virgen de la Victoria University Hospital, 29010 Malaga, Spain;
| | - Diego Bermúdez
- Department of Human Physiology, Human Histology, Anatomical Pathology and Physical Education, University of Malaga, 29010 Malaga, Spain; (I.A.-S.); (S.M.); (J.A.L.-V.); (M.V.O.); (C.A.)
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Tian R, Hu J, Ma X, Liang L, Guo S. Immune-related gene signature predicts overall survival of gastric cancer patients with varying microsatellite instability status. Aging (Albany NY) 2020; 13:2418-2435. [PMID: 33316777 PMCID: PMC7880323 DOI: 10.18632/aging.202271] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 11/10/2020] [Indexed: 12/11/2022]
Abstract
Purpose: Gastric cancer (GC) is one of the most common and fatal malignancies globally. While microsatellite instability (MSI) index has earlier been correlated with survival outcome in gastric cancer patients, the present study aims to construct a risk-stratification model based on immune-related genes in GC patients with varying MSI status. Results: The univariate and multivariate Cox regression analyses identified SEMA7A, NUDT6, SCGB3A1, NPR3, PTH1R, and SHC4 as signature genes, which were used to build the prognostic model for GC patients with microsatellite instability-low (MSI-L) and microsatellite stable (MSS). Whereas, for GC patients with microsatellite instability-high (MSI-H), prognostic model was established with three genes (SEMA6A, LTBP1, and BACH2), based on the univariate and multivariate Cox regression, and Kaplan-Meier survival analyses. Conclusion: The prognostic immune-related gene signature identified in this study may offer new targets for personalized treatment and immunotherapy for GC patients with MSI-H or MSI-L/MSS status. Methods: The Cancer Genome Atlas (TCGA) and ImmPort databases were used to extract expression data and to explore prognostic genes from the immune-related genes (IRGs), respectively. Univariate and multivariate Cox regression analysis were applied to identify IRGs correlated with patient prognosis. The regulatory network between prognostic IRGs and TFs were performed using R software.
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Affiliation(s)
- Ruyue Tian
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China.,Department of Ultrasound, Aero Space Central Hospital, Beijing 100050, China
| | - Jiexuan Hu
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Xiao Ma
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Lei Liang
- Department of Ultrasound, Aero Space Central Hospital, Beijing 100050, China
| | - Shuilong Guo
- 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, China
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Chen T, Zhang C, Liu Y, Zhao Y, Lin D, Hu Y, Yu J, Li G. A gastric cancer LncRNAs model for MSI and survival prediction based on support vector machine. BMC Genomics 2019; 20:846. [PMID: 31722674 PMCID: PMC6854775 DOI: 10.1186/s12864-019-6135-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 09/23/2019] [Indexed: 12/12/2022] Open
Abstract
Background Recent studies have shown that long non-coding RNAs (lncRNAs) play a crucial role in the induction of cancer through epigenetic regulation, transcriptional regulation, post-transcriptional regulation and other aspects, thus participating in various biological processes such as cell proliferation, differentiation and apoptosis. As a new nova of anti-tumor therapy, immunotherapy has been shown to be effective in many tumors of which PD-1/PD-L1 monoclonal antibodies has been proofed to increase overall survival rate in advanced gastric cancer (GC). Microsatellite instability (MSI) was known as a biomarker of response to PD-1/PD-L1 monoclonal antibodies therapy. The aim of this study was to identify lncRNAs signatures able to classify MSI status and create a predictive model associated with MSI for GC patients. Methods Using the data of Stomach adenocarcinoma from The Cancer Genome Atlas (TCGA), we developed and validated a lncRNAs model for automatic MSI classification using a machine learning technology – support vector machine (SVM). The C-index was adopted to evaluate its accuracy. The prognostic values of overall survival (OS) and disease-free survival (DFS) were also assessed in this model. Results Using the SVM, a lncRNAs model was established consisting of 16 lncRNA features. In the training cohort with 94 GC patients, accuracy was confirmed with AUC 0.976 (95% CI, 0.952 to 0.999). Veracity was also confirmed in the validation cohort (40 GC patients) with AUC 0.950 (0.889 to 0.999). High predicted score was correlated with better DFS in the patients with stage I-III and lower OS with stage I-IV. Conclusion This study identify 16 LncRNAs signatures able to classify MSI status. The correlation between lncRNAs and MSI status indicates the potential roles of lncRNAs interacting in immunotherapy for GC patients. The pathway of these lncRNAs which might be a target in PD-1/PD-L1 immunotherapy are needed to be further study.
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Affiliation(s)
- Tao Chen
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangdong Provincial Engineering Technology Research Center of Minimally Invasive Surgery, No.1838, North Guangzhou Avenue, Guangzhou, 510515, Guangdong Province, China.
| | - Cangui Zhang
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangdong Provincial Engineering Technology Research Center of Minimally Invasive Surgery, No.1838, North Guangzhou Avenue, Guangzhou, 510515, Guangdong Province, China
| | - Yingqiao Liu
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangdong Provincial Engineering Technology Research Center of Minimally Invasive Surgery, No.1838, North Guangzhou Avenue, Guangzhou, 510515, Guangdong Province, China
| | - Yuyun Zhao
- School of Biomedical Engineering, Southern Medical University, Guangzhou, 510515, Guangdong Province, China
| | - Dingyi Lin
- School of Biomedical Engineering, Southern Medical University, Guangzhou, 510515, Guangdong Province, China
| | - Yanfeng Hu
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangdong Provincial Engineering Technology Research Center of Minimally Invasive Surgery, No.1838, North Guangzhou Avenue, Guangzhou, 510515, Guangdong Province, China
| | - Jiang Yu
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangdong Provincial Engineering Technology Research Center of Minimally Invasive Surgery, No.1838, North Guangzhou Avenue, Guangzhou, 510515, Guangdong Province, China
| | - Guoxin Li
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangdong Provincial Engineering Technology Research Center of Minimally Invasive Surgery, No.1838, North Guangzhou Avenue, Guangzhou, 510515, Guangdong Province, China.
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Yang G, Zheng RY, Jin ZS. Correlations between microsatellite instability and the biological behaviour of tumours. J Cancer Res Clin Oncol 2019; 145:2891-2899. [PMID: 31617076 PMCID: PMC6861542 DOI: 10.1007/s00432-019-03053-4] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/04/2019] [Indexed: 02/07/2023]
Abstract
Purpose Microsatellites are widely distributed repetitive DNA motifs, accounting for approximately 3% of the genome. Due to mismatch repair system deficiency, insertion or deletion of repetitive units often occurs, leading to microsatellite instability. In this review, we aimed to explore the relationship between MSI and biological behaviour of colorectal carcinoma, gastric carcinoma, lymphoma/leukaemia and endometrial carcinoma, as well as the application of frameshift peptide vaccines in cancer therapy. Methods The relevant literature from PubMed and Baidu Xueshu were reviewed in this article. The ClinicalTrials.gov database was searched for clinical trials related to the specific topic. Results Microsatellite instability is divided into three subtypes: high-level, low-level microsatellite instability, and stable microsatellites. The majority of tumour patients with high-level microsatellite instability often show a better efficacy and prognosis than those with low-level microsatellite instability or stable microsatellites. In coding regions, especially for genes involved in tumourigenesis, microsatellite instability often results in inactivation of proteins and contributes to tumourigenesis. Moreover, the occurrence of microsatellite instability in coding regions can also cause the generation of frameshift peptides that are thought to be unknown and novel to the individual immune system. Thus, these frameshift peptides have the potential to be biomarkers to raise tumour-specific immune responses. Conclusion MSI has the potential to become a key predictor for evaluating the degree of malignancy, efficacy and prognosis of tumours. Clinically, MSI patterns will provide more valuable information for clinicians to create optimal individualized treatment strategies based on frameshift peptides vaccines.
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Affiliation(s)
- Guang Yang
- Department of Pathology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Ru-Yi Zheng
- Medical Imaging Center, The Mine Hospital of Xu Zhou, Xuzhou, Jiangsu, China
| | - Zai-Shun Jin
- Mudanjiang Medical University, Mudanjiang, Heilongjiang, 157000, China.
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Machlowska J, Maciejewski R, Sitarz R. The Pattern of Signatures in Gastric Cancer Prognosis. Int J Mol Sci 2018; 19:E1658. [PMID: 29867026 PMCID: PMC6032410 DOI: 10.3390/ijms19061658] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 05/26/2018] [Accepted: 05/30/2018] [Indexed: 02/05/2023] Open
Abstract
Gastric cancer is one of the most common malignancies worldwide and it is a fourth leading cause of cancer-related death. Carcinogenesis is a multistage disease process specified by the gradual procurement of mutations and epigenetic alterations in the expression of different genes, which finally lead to the occurrence of a malignancy. These genes have diversified roles regarding cancer development. Intracellular pathways are assigned to the expression of different genes, signal transduction, cell-cycle supervision, genomic stability, DNA repair, and cell-fate destination, like apoptosis, senescence. Extracellular pathways embrace tumour invasion, metastasis, angiogenesis. Altered expression patterns, leading the different clinical responses. This review highlights the list of molecular biomarkers that can be used for prognostic purposes and provide information on the likely outcome of the cancer disease in an untreated individual.
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Affiliation(s)
- Julita Machlowska
- Department of Human Anatomy, Medical University of Lublin, 20-090 Lublin, Poland.
| | - Ryszard Maciejewski
- Department of Human Anatomy, Medical University of Lublin, 20-090 Lublin, Poland.
| | - Robert Sitarz
- Department of Human Anatomy, Medical University of Lublin, 20-090 Lublin, Poland.
- Department of Surgery, St. John's Cancer Center, 20-090 Lublin, Poland.
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