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Wu Y, Ren L, Tang Y, Zhu Z, Liu S, Jiang Y, Zhang S, Zhuang X, Chen Y. Immunobiological signatures and the emerging role of SPP1 in predicting tumor heterogeneity, malignancy, and clinical outcomes in stomach adenocarcinoma. Aging (Albany NY) 2023; 15:11588-11610. [PMID: 37889539 PMCID: PMC10637809 DOI: 10.18632/aging.205148] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023]
Abstract
BACKGROUND Immunotherapy, as a form of immunobiological therapy, represents a promising approach for enhancing patients' immune responses. This work aims to present innovative ideas and insights for prognostic assessment and clinical treatment of stomach adenocarcinoma (STAD) by leveraging immunobiological signatures. METHODS We employed weighted gene co-expression network analysis (WGCNA) and unsupervised clustering analysis to identify hub genes. These hub genes were utilized to construct a prognostic risk model, and their impact on the tumor microenvironment (TME) and DNA variations was assessed using large-scale STAD patient cohorts. Additionally, we conducted transfection experiments with plasmids to investigate the influence of SPP1 on the malignancy of HGC27 and NCI-N87 cells. RESULTS Unsupervised clustering of 12 immune-related genes (IRGs) revealed three distinct alteration patterns with unique molecular phenotypes, clinicopathological characteristics, prognosis, and TME features. Using LASSO and multivariate Cox regression analyses, we identified three hub genes (MMP12, SPP1, PLAU) from the IRGs to establish a risk signature. This IRG-related risk model significantly stratified the prognosis risk among STAD patients in the training (n = 522), testing (n = 521), and validation (n = 300) cohorts. Notably, there were discernible differences in therapy responses and TME characteristics, such as tumor purity and lymphocyte infiltration, between the risk model groups. Subsequently, a nomogram that incorporates the IRG signature and clinicopathological factors demonstrated superior sensitivity and specificity in predicting outcomes for STAD patients. Furthermore, down-regulation of SPP1, as observed after siRNA transfection, significantly inhibited the proliferation and migration abilities of HGC27 and NCI-N87 cells. CONCLUSIONS In summary, this study highlights the critical role of immune-related signatures in STAD and offers novel insights into prognosis indicators and immunotherapeutic targets for this condition. SPP1 emerges as an independent prognostic factor for STAD and appears to regulate STAD progression by influencing the immune microenvironment.
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Affiliation(s)
- Yanan Wu
- Department of Gastroenterology, Rudong People’s Hospital, Rudong Hospital Affiliated to Nantong University, Nantong, China
| | - Lingyu Ren
- Department of Gastroenterology, Rudong People’s Hospital, Rudong Hospital Affiliated to Nantong University, Nantong, China
| | - Yichun Tang
- Cancer Research Center Nantong, Nantong Tumor Hospital and Affiliated Tumor Hospital of Nantong University, Nantong, China
| | - Zhu Zhu
- Cancer Research Center Nantong, Nantong Tumor Hospital and Affiliated Tumor Hospital of Nantong University, Nantong, China
| | - Shifan Liu
- Department of Medical Imaging, Medical School of Nantong University, Nantong, China
| | - Yan Jiang
- Department of Engineering Training Center, Nantong University, Nantong, China
| | - Siming Zhang
- Cancer Research Center Nantong, Nantong Tumor Hospital and Affiliated Tumor Hospital of Nantong University, Nantong, China
| | - Xiaocan Zhuang
- Department of Gastroenterology, Rudong People’s Hospital, Rudong Hospital Affiliated to Nantong University, Nantong, China
| | - Yuanbiao Chen
- Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
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Ju Y, Choi GE, Lee MW, Jeong M, Kwon H, Kim DH, Kim J, Jin H, Lee KE, Hyun KY, Jang A. Identification of miR-143-3p as a diagnostic biomarker in gastric cancer. BMC Med Genomics 2023; 16:135. [PMID: 37328880 PMCID: PMC10273760 DOI: 10.1186/s12920-023-01554-3] [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: 01/20/2023] [Accepted: 05/19/2023] [Indexed: 06/18/2023] Open
Abstract
BACKGROUND Gastric cancer (GC) is among the most common types of gastrointestinal cancers and has a high incidence and mortality around the world. To suppress the progression of GC, it is essential to develop diagnostic markers. MicroRNAs regulate GC development, but a clearer insight into their role is needed before they can be applied as a molecular markers and targets. METHODS In this study, we assessed the diagnostic value of differentially expressed microRNAs as potential diagnostic biomarkers for GC using data for 389 tissue samples from the Cancer Genome Atlas (TCGA) and 21 plasma samples from GC patients. RESULTS The expression of hsa-miR-143-3p (also known as hsa-miR-143) was significantly downregulated in GC according to the TCGA data and plasma samples. The 228 potential target genes of hsa-miR-143-3p were analyzed using a bioinformatics tool for miRNA target prediction. The target genes correlated with extracellular matrix organization, the cytoplasm, and identical protein binding. Furthermore, the pathway enrichment analysis of target genes showed that they were involved in pathways in cancer, the phosphoinositide 3-kinase (PI3K)-protein kinase B (Akt) signaling pathway, and proteoglycans in cancer. The hub genes in the protein-protein interaction (PPI) network, were matrix metallopeptidase 2 (MMP2), CD44 molecule (CD44), and SMAD family member 3 (SMAD3). CONCLUSIONS This study suggests that hsa-miR-143-3p may be used as a diagnostic marker for GC, contributing via the pathways involved in the development of GC.
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Affiliation(s)
- Yeongdon Ju
- Medical Science Research Center, Pusan National University, Yangsan, 50612, Republic of Korea
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, 46252, Republic of Korea
| | - Go-Eun Choi
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, 46252, Republic of Korea
| | - Moon Won Lee
- Division of Gastroenterology, Pusan National University Hospital, Busan, 49241, Republic of Korea
- Department of Internal Medicine, Pusan National University College of Medicine, Busan, 49241, Republic of Korea
| | - Myeongguk Jeong
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, 46252, Republic of Korea
| | - Hyeokjin Kwon
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, 46252, Republic of Korea
| | - Dong Hyeok Kim
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, 46252, Republic of Korea
| | - Jungho Kim
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, 46252, Republic of Korea
| | - Hyunwoo Jin
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, 46252, Republic of Korea
| | - Kyung Eun Lee
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, 46252, Republic of Korea
| | - Kyung-Yae Hyun
- Department of Clinical Laboratory Science, Dong-Eui University, Busan, 47340, Republic of Korea.
| | - Aelee Jang
- Department of Nursing, University of Ulsan, Ulsan, 44610, Republic of Korea.
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Identification of Prognostic Genes and Immune Landscape Signatures Based on Tumor Microenvironment in Lung Adenocarcinoma. DISEASE MARKERS 2022; 2022:6703053. [PMID: 36033829 PMCID: PMC9411923 DOI: 10.1155/2022/6703053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/14/2022] [Accepted: 07/29/2022] [Indexed: 11/17/2022]
Abstract
Background Lung adenocarcinoma is the most common lung cancer subtype and accounts for the highest proportion of cancer-related deaths. The tumor microenvironment influences prognostic outcomes in lung adenocarcinoma (LUAD). Materials and Methods We used the ESTIMATE algorithm (Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data) to investigate the role of microenvironment-related genes and stromal cells in lung adenocarcinoma prognosis. This analysis was done on lung adenocarcinoma cases from The Cancer Genome Atlas (TCGA). The cases were divided into high and low groups on the basis of immune and stromal scores, respectively. Results There were close correlations between immune scores with prognosis and disease stage. There were 367 differentially expressed genes. Combining the Gene Expression Omnibus (GEO) database, we found 14 prognosis-related genes. Results There were close correlations between immune scores with prognosis and disease stage. There were 367 differentially expressed genes. Combining the Gene Expression Omnibus (GEO) database, we found 14 prognosis-related genes. Results. Based on the enrichment levels of the immune cell types, we clustered LUAD into Immunity_H and Immunity_L subtypes. Most of these genes were upregulated in Immunity_H subtype. Finally, using the Human Protein Atlas (HPA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC) databases, most of the proteins corresponding to prognostic genes were verified to be differentially expressed between the tumor and normal groups. Conclusions The key genes identified in this study are involved in molecular mechanisms of LUAD.
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Wang G, Zheng H, Zhao X, Wang Y, Zeng Y, Du J. The Prognostic Model and Drug Sensitivity of LKB1-Mutant Lung Adenocarcinoma Based on Immune Landscape. Front Mol Biosci 2022; 9:756772. [PMID: 35720127 PMCID: PMC9201220 DOI: 10.3389/fmolb.2022.756772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Lung cancer is the most common cause of cancer-related deaths worldwide. LKB1-mutant lung adenocarcinoma (LUAD) is a unique subtype of this deadly cancer. LKB1 mutations cause functional changes in a variety of cell processes, including immune functions, that affect prognosis. To date, the potential role of immunity in the prognosis of LKB1-mutant LUAD is not well understood.Methods: We systematically analyzed immune-related genes in LUAD samples from The Cancer Genome Atlas (TCGA) database. ESTIMATE and CIBERSORT algorithms were used to explore the immune microenvironment. A prognostic risk model was constructed, and prognostic, immune function, drug sensitivity, and model specificity analyses were performed to identify the effectiveness of the model.Results: Our results showed that LKB1 mutations suppressed immune function in LUAD. A three-gene signature was constructed to stratify patients into two risk groups. The risk score was an independent predictor for overall survival (OS) in multivariate Cox regression analyses [hazard ratio (HR) > 1, p = 0.002]. Receiver operating characteristic (ROC) curve analyses confirmed that the risk score has better performance than clinicopathological characteristics. Functional analysis revealed that the immune status was different between the risk groups. ZM.447439 was an appropriate treatment for the high-risk group of patients. This risk model is only suitable for LKB1-mutant tumors; it performed poorly in LUAD patients with wild-type LKB1.Conclusion: Our findings indicate the potential role of immunity in LKB1-mutant LUAD, providing novel insights into prognosis and guiding effective immunotherapy.
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Affiliation(s)
- Guanghui Wang
- Institute of Oncology, Shandong Provincial Hospital, Shandong University, Jinan, China
- Department of Thoracic Surgery, Shandong Provincial Hospital, Shandong University, Jinan, China
| | - Haotian Zheng
- Institute of Oncology, Shandong Provincial Hospital, Shandong University, Jinan, China
| | - Xiaogang Zhao
- Department of Thoracic Surgery, The Second Hospital of Shandong University, Jinan, China
| | - Yadong Wang
- Institute of Oncology, Shandong Provincial Hospital, Shandong University, Jinan, China
| | - Yukai Zeng
- Institute of Oncology, Shandong Provincial Hospital, Shandong University, Jinan, China
| | - Jiajun Du
- Institute of Oncology, Shandong Provincial Hospital, Shandong University, Jinan, China
- Department of Thoracic Surgery, Shandong Provincial Hospital, Shandong University, Jinan, China
- *Correspondence: Jiajun Du,
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Zeng Y, Zhang X, Li F, Wang Y, Wei M. AFF3 is a novel prognostic biomarker and a potential target for immunotherapy in gastric cancer. J Clin Lab Anal 2022; 36:e24437. [PMID: 35478418 PMCID: PMC9169183 DOI: 10.1002/jcla.24437] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/25/2022] [Accepted: 04/04/2022] [Indexed: 12/26/2022] Open
Abstract
Background Gastric cancer (GC) is one of the most common cancers worldwide with a poor prognosis. The tumor microenvironment (TME) serves a pivotal role in affecting the prognosis and efficacy of immunotherapy. Given the poor prognosis of GC patients and the limitation of immunotherapy, we urged to identify new prognostic and immunotherapeutic biomarkers. Methods The transcriptome data were downloaded from the TCGA, GEO, and GEPIA databases, and performed differential analysis of AFF3 in tumor samples and normal samples. The UALCAN, Kaplan–Meier plotter and GEPIA databases were employed to assess the correlation of AFF3 with clinicopathological characteristics and prognosis. The potential mechanism of AFF3 was explored by the GO and KEGG enrichment. The potential role of AFF3 on tumor‐infiltrating immune cells (TIICs) was explored by TIMER2.0 and TISIDB. TIMER2.0 and SangerBox3.0 databases were, respectively, used to determine the correlation of AFF3 with immune checkpoint (ICs), tumor mutational burden (TMB), and microsatellite instability (MSI) in GC. Results We found significant downregulation of AFF3 in GC tissues as compared with normal tissues. However, GC patients having a higher expression of AFF3 were found to have worse clinicopathological characteristics and prognosis. Moreover, the GO enrichment analysis illustrated that AFF3 might regulate the immune cells in the TME. In addition, the AFF3 was positively correlated with TIICs, ICs, TMB, and MSI. Conclusion Here, we conclude that AFF3 may be a promising potential marker for the diagnosis and prognosis of GC patients, and may influence response to ICIs by affecting TIICs and ICs expression in the TME.
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Affiliation(s)
- Yuling Zeng
- Department of Blood Transfusion, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou City, China
| | - Xueping Zhang
- Department of Hepatobiliary Surgery, Zhengzhou Central Hospital Affiliated of Zhengzhou University, Zhengzhou City, China
| | - Fazhan Li
- Marshall Research Center, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou City, China
| | - Ying Wang
- Department of Blood Transfusion, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou City, China
| | - Ming Wei
- Department of Blood Transfusion, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou City, China
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Wang Y, Guo S, Chen Z, Bai B, Wang S, Gao Y. Re-Clustering and Profiling of Digestive System Tumors According to Microenvironment Components. Front Oncol 2021; 10:607742. [PMID: 33643909 PMCID: PMC7902780 DOI: 10.3389/fonc.2020.607742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/17/2020] [Indexed: 12/24/2022] Open
Abstract
Background Immunotherapy has become the most promising therapy in digestive system tumors besides conventional chemotherapy and radiotherapy. But only a few patients can benefit from different types of immunotherapies, such as immune checkpoint blockade (ICB). To identify these ICB-susceptible patients, methods are urgently needed to screen and profile subgroups of patients with different responsiveness to ICB. Methods This study carried out analysis on patients with digestive system tumors that were obtained from Cancer Genome Atlas (TCGA) cohorts. The analyses were mainly performed using GraphPad Prism 7 and R language. Results We have quantified the microenvironmental components of eight digestive system tumor patients in TCGA cohorts and evaluated their clinical value. We re-clustered patients based on their microenvironment composition and divided these patients into six clusters. The differences between these six clusters were profiled, including survival conditions, enriched biological processes, genomic mutations, and microenvironment traits. Cluster 3 was the most immune-related cluster, exhibiting a high infiltration of non-tumor components and poor survival status, along with an inhibitory immune status, and we found that patients with high stromal score indicated a poor response in ICB cohort. Conclusions Our research provides a new strategy based on the microenvironment components for the reclassification of digestive system tumors, which could provide guidance for prognosis judgment and treatment response prediction like ICB.
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Affiliation(s)
- Yongwei Wang
- Department of Anatomy, Basic Medical Institute, Chengde Medical College, Chengde, China
| | - Sen Guo
- Department of Anatomy, Basic Medical Institute, Chengde Medical College, Chengde, China
| | - Zhihong Chen
- Department of Anatomy, Basic Medical Institute, Chengde Medical College, Chengde, China
| | - Bing Bai
- Department of Immunology, Basic Medical Institute, Chengde Medical College, Chengde, China
| | - Shuo Wang
- Department of Immunology, Basic Medical Institute, Chengde Medical College, Chengde, China
| | - Yaxian Gao
- Department of Immunology, Basic Medical Institute, Chengde Medical College, Chengde, China
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