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Li X, Deng Y, Li Z, Zhao H. A novel angiogenesis-associated risk score predicts prognosis and characterizes the tumor microenvironment in colon cancer. Transl Cancer Res 2024; 13:2094-2107. [PMID: 38881939 PMCID: PMC11170505 DOI: 10.21037/tcr-23-2048] [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: 11/04/2023] [Accepted: 04/24/2024] [Indexed: 06/18/2024]
Abstract
Background Angiogenesis of the tumor microenvironment (TME) can promote the proliferation and metastases of colon cancer (CC). However, there is a lack of bioinformatics analysis to comprehensively clarify the molecular characteristics, immune interaction characteristics and predictive values of angiogenesis characteristics in CC patients. This study aimed to perform a comprehensive elucidation of the correlation between angiogenesis and CC for the purpose of improving the clinical management of CC. Methods Angiogenesis-associated genes (AAGs) were evaluated in the population of CC patients from the Cancer Genome Atlas database and Gene Expression Omnibus dataset. The expression, prognostic role, and immune cell infiltration of AAGs were assessed first. And then we established the AAGs score to further explore the prognosis and treatment response of angiogenesis characteristics in individual patient. Results Totally, we identified two different molecular subtypes of angiogenesis, and there was a significant difference in the background of genome, expression profiles, prognosis, and characteristics of TME between two subtypes. And the AAGs score was independently associated with over survival in CC patients, the prognostic value was significant and confirmed in the entire cohort. And we also constructed a nomogram based on the risk score and clinical parameters to maximize the predictive ability of the risk score. Additionally, the AAGs score was significantly correlated with the tumor mutation burden score, cancer stem cell score and drug sensitivity. Conclusions Our study elucidated the role of angiogenesis characteristics in CC and the AAGs score could help clinicians plan for individual management with chemotherapy agents and promote the development of immunotherapy in CC. Prospective studies need to be conducted to further confirm our findings.
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Affiliation(s)
- Xin Li
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yiqiao Deng
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhiyu Li
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hong Zhao
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Qin R, Ma X, Pu S, Shen C, Hu D, Liu C, Wang K, Wang Y. Identification and validation of a signature based on myofibroblastic cancer-associated fibroblast marker genes for predicting prognosis, immune infiltration, and therapeutic response in bladder cancer. Investig Clin Urol 2024; 65:263-278. [PMID: 38714517 PMCID: PMC11076800 DOI: 10.4111/icu.20230300] [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: 09/02/2023] [Revised: 11/08/2023] [Accepted: 01/02/2024] [Indexed: 05/10/2024] Open
Abstract
PURPOSE Myofibroblastic cancer-associated fibroblasts (myCAFs) are important components of the tumor microenvironment closely associated with tumor stromal remodeling and immunosuppression. This study aimed to explore myCAFs marker gene biomarkers for clinical diagnosis and therapy for patients with bladder cancer (BC). MATERIALS AND METHODS BC single-cell RNA sequencing (scRNA-seq) data were obtained from the National Center for Biotechnology Information Sequence Read Archive. Transcriptome and clinical data were downloaded from The Cancer Genome Atlas and the Gene Expression Omnibus databases. Subsequently, univariate Cox and LASSO (Least Absolute Shrinkage and Selection Operator regression) regression analyses were performed to construct a prognostic signature. Immune cell activity was estimated using single-sample gene set enrichment analysis whilst the TIDE (tumor immune dysfunction and exclusion) method was employed to assess patient response to immunotherapy. The chemotherapy response of patients with BC was evaluated using genomics of drug sensitivity in cancer. Furthermore, Immunohistochemistry was used to verify the correlation between MAP1B expression and immunotherapy efficacy. The scRNA-seq data were analyzed to identify myCAFs marker genes. RESULTS Combined with bulk RNA-sequencing data, we constructed a two-gene (COL6A1 and MAP1B) risk signature. In patients with BC, the signature demonstrated outstanding prognostic value, immune infiltration, and immunotherapy response. This signature served as a crucial guide for the selection of anti-tumor chemotherapy medications. Additionally, immunohistochemistry confirmed that MAP1B expression was significantly correlated with immunotherapy efficacy. CONCLUSIONS Our findings revealed a typical prognostic signature based on myCAF marker genes, which offers patients with BC a novel treatment target alongside theoretical justification.
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Affiliation(s)
- Ruize Qin
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiaocheng Ma
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Shi Pu
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Chengquan Shen
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Ding Hu
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Changxue Liu
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Kongjia Wang
- Department of Urology, Qingdao Municipal Hospital, Qingdao, China
| | - Yonghua Wang
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, China.
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Guan Z, Wang H, Tian M. A Cuproptosis-Related gene Signature as a Prognostic Biomarker in Thyroid Cancer Based on Transcriptomics. Biochem Genet 2024:10.1007/s10528-024-10767-9. [PMID: 38594571 DOI: 10.1007/s10528-024-10767-9] [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: 06/09/2023] [Accepted: 02/28/2024] [Indexed: 04/11/2024]
Abstract
Thyroid cancer (THCA) is the most prevalent endocrine tumor, and its incidence continues to increase every year. However, the processes underlying the aggressive progression of thyroid cancer are unknown. We concentrated on the prognostic and biological importance of thyroid cancer cuproptosis-related genes in this investigation. Genomic and clinical data were obtained from the UCSC XENA website, and cuproptosis-related genes were obtained from the FerrDb website. We performed differential expression analysis and Cox regression analysis to identify possible predictive targets associated with thyroid cancer prognosis. To assess the role of CDKN2A in thyroid cancer and the ability to predict prognosis on the basis of the CDKN2A expression level, we performed immunohistochemical staining, survival analysis, immunological analysis, functional analysis, and clinical analysis with respect to CDKN2A gene expression. CDKN2A expression levels were found to be inversely correlated with thyroid cancer prognosis. Higher levels of CDKN2A expression were associated with higher T, N, and clinicopathological stage and more residual tumor cells. Through univariate and multivariate Cox regression analyses, the CDKN2A expression level was shown to be linked with thyroid cancer patients' overall survival (OS). Moreover, we discovered that CDKN2A expression was linked to a dysfunctional tumor immune microenvironment. The study shows that CDKN2A, a cuproptosis-related gene, can be used as a prognostic marker for thyroid cancer.
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Affiliation(s)
- Zirui Guan
- The Second Hospital of Jilin University, Changchun City, 130022, Jilin Province, People's Republic of China
| | - Hongyong Wang
- The Second Hospital of Jilin University, Changchun City, 130022, Jilin Province, People's Republic of China.
| | - Mingyan Tian
- The Second Hospital of Jilin University, Changchun City, 130022, Jilin Province, People's Republic of China
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Wang F, Wang C, Li B, Wang G, Meng Z, Han J, Guo G, Yu B, Wang G. Identification of angiogenesis-related subtypes, the development of a prognosis model, and features of tumor microenvironment in colon cancer. Biotechnol Appl Biochem 2024; 71:45-60. [PMID: 37881150 DOI: 10.1002/bab.2520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 09/26/2023] [Indexed: 10/27/2023]
Abstract
Angiogenesis is associated with tumor progression, prognosis, and treatment effect. However, the angiogenesis' underlying mechanisms in the tumor microenvironment (TME) still remain unclear. Understanding the dynamic interactions between angiogenesis and TME in colon adenocarcinoma (COAD) is necessary. We downloaded the transcriptome data and corresponding clinical data of colon cancer patients from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases, respectively. We identified two distinct angiogenesis-related molecular subtypes (subtype A and subtype B) and assessed the clinical features, prognosis, and infiltrating immune cells of patients in the two subtypes. According to the prognostic differential genes, we defined two different gene clusters to further explore the correlation between angiogenesis and tumor heterogeneity. Then, we construct the prognostic risk scoring model angiogenesis-related gene (ARG-score) including seven genes (ARMCX2, latent transforming growth factor β binding protein 1, ADAM8, FABP4, CCL11, CXCL11, ITLN1) using Lasso-multivariate cox method. We analyzed the correlation between ARG-score and prognosis, clinicopathological features, TME, molecular feature, cancer stem cells (CSCs), and microsatellite instability (MSI) status. To assess the application value of ARG-score in clinical treatment, immunophenotype score was used to predict patients' immunotherapy response in colon cancer. We found the mutations of ARGs in TCGA-COAD dataset from genetic levels and discussed their expression patterns based on TCGA and GEO datasets. We observed important differences in clinicopathological features, prognosis, immune feature, molecular feature between the two molecular subgroups. Then, we established an ARG-score for predicting OS and validated its predictive capability. A high ARG-score characterized by higher transcription level of ARGs, suggested lower MSI-high (MSI-H), lower immune score, and worse clinical stage and survival outcome. Additionally, the ARG-score was remarkably related to the CSCs index and immunotherapy sensitivity. We found two new molecular subtypes and two gene clusters based on ARGs and established an ARG-score. Multilayered analysis revealed that ARGs were remarkably correlated to the heterogeneity of colon cancer patients and explained the process of tumorigenesis and progression better. The ARG-score can help us better assess patients' survival outcomes and provide guidance for individualized treatment.
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Affiliation(s)
- Feifei Wang
- The Second Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Changjing Wang
- Department of Gastrointestinal Surgery, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Baokun Li
- The Second Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Guanglin Wang
- The Second Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Zesong Meng
- The Second Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Jiachao Han
- The Second Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Ganlin Guo
- The Second Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Bin Yu
- The Second Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Guiying Wang
- Department of Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
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Liu S, He K, Yang L, Xu F, Cui X, Qu L, Li X, Ren BC. Endoplasmic reticulum stress regulators exhibit different prognostic, therapeutic and immune landscapes in pancreatic adenocarcinoma. J Cell Mol Med 2024; 28:e18092. [PMID: 38303549 PMCID: PMC10902308 DOI: 10.1111/jcmm.18092] [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: 05/31/2023] [Revised: 11/24/2023] [Accepted: 12/15/2023] [Indexed: 02/03/2024] Open
Abstract
Endoplasmic reticulum stress (ERS) and unfolded protein response are the critical processes of tumour biology. However, the roles of ERS regulatory genes in pancreatic adenocarcinoma (PAAD) remain elusive. A novel ERS-related risk signature was constructed using the Lasso regression analysis. Its prognostic value, immune effect, metabolic influence, mutational feature and therapeutic correlation were comprehensively analysed through multiple bioinformatic approaches. The biofunctions of KDELR3 and YWHAZ in pancreatic cancer (PC) cells were also investigated through colony formation, Transwell assays, flow cytometric detection and a xenograft model. The upstream miRNA regulatory mechanism of KDELR3 was predicted and validated. ERS risk score was identified as an independent prognostic factor and could improve traditional prognostic model. Meanwhile, it was closely associated with metabolic reprogramming and tumour immune. High ERS risk enhanced glycolysis process and nucleotide metabolism, but was unfavourable for anti-tumour immune response. Moreover, ERS risk score could act as a potential biomarker for predicting the efficacy of ICBs. Overexpression of KDELR3 and YWHAZ stimulated the proliferation, migration and invasion of SW1990 and BxPC-3 cells. Silencing KDELR3 suppressed tumour growth in a xenograft model. miR-137 could weaken the malignant potentials of PC cells through inhibiting KDELR3 (5'-AGCAAUAA-3'). ERS risk score greatly contributed to PAAD clinical assessment. KDELR3 and YWHAZ possessed cancer-promoting capacities, showing promise as a novel treatment target.
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Affiliation(s)
- Shanshan Liu
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Kaini He
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Longbao Yang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Fangshi Xu
- Department of Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Xiaoguang Cui
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Li Qu
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Xueyi Li
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Bin-Cheng Ren
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
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Yin HZ, Zhang MC, Wu H. Clinical and Immunological Significance of ANKRD52 in Pan-Cancer. Biochem Genet 2024:10.1007/s10528-023-10645-w. [PMID: 38296907 DOI: 10.1007/s10528-023-10645-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 12/19/2023] [Indexed: 02/02/2024]
Abstract
Ankyrin repeat domain 52 (ANKRD52) is a regulatory component of the protein phosphatase 6 (PP6) holoenzyme. Evidence has emerged to suggest involvement of ANKRD52 in tumor metastases and cancer cell escape from T cell-mediated elimination and immunotherapy but there has been no research across different cancer types. The current study explored the biological functions of ANKRD52 by combining data from many databases. The aim was to expose new diagnostic or treatment biomarkers for malignant tumors. The roles of ANKRD52 with respect to immunotherapy in 33 human cancer types were analyzed by combining data from The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), Cancer Cell Line Encyclopedia (CCLE), UCSC Xena, the Tumor Immune Estimation Resource (TIMER), TISIDB and Cellminer. Bioinformatics methods were used to analyze the association between ANKRD52 expression and prognosis, immunological indicators (immune cell infiltration, ESTIMATE scores and tumor microenvironment (TME) signatures), tumor mutational burden (TMB), microsatellite instability (MSI) and drug sensitivity. ANKRD52 expression was generally higher in 24 tumor tissues than in normal tissues and was associated with poor prognosis, especially in kidney chromophobe (KICH). Lower expression was observed in advanced cancer. ANKRD52 expression was strongly linked to major immunological indicators, such as immune cell infiltration, ESTIMATE scores, TME signatures, as well as expression of immune and tumor-related genes. Expression was also associated with indicators of immunotherapy efficacy and outcome, such as TMB in 7 cancer types and MSI in 12. In addition, ANKRD52 expression was linked to sensitivity to a number of anticancer drugs. ANKRD52 had a distinct immune function in breast invasive carcinoma (BRCA) that correlated negatively with most immune indicators. Expression was enriched in proliferation-, differentiation- and metabolism-related pathways and linked to other immune cells and TME signatures. A nomogram to predict 3- or 5-year overall survival (OS) of patients with BRCA was constructed. ANKRD52 may have utility as an oncological and immunological biomarker. New insights into oncogenesis are presented and the development of ANKRD52-targeting to increase the therapeutic efficacy of immunotherapy combined with chemotherapy explored.
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Affiliation(s)
- Hui-Zi Yin
- Department of Breast Radiotherapy, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150081, China
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, 157 Baojian Road, Harbin, 150081, China
| | - Meng-Chun Zhang
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, 157 Baojian Road, Harbin, 150081, China
| | - Hao Wu
- Key Laboratory of Tumor Biotherapy, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150081, China.
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, 157 Baojian Road, Harbin, 150081, China.
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Liu S, Zheng Y, Li S, Du Y, Liu X, Tang H, Meng X, Zheng Q. Integrative landscape analysis of prognostic model biomarkers and immunogenomics of disulfidptosis-related genes in breast cancer based on LASSO and WGCNA analyses. J Cancer Res Clin Oncol 2023; 149:16851-16867. [PMID: 37736788 PMCID: PMC10645620 DOI: 10.1007/s00432-023-05372-z] [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: 07/18/2023] [Accepted: 08/29/2023] [Indexed: 09/23/2023]
Abstract
BACKGROUND Disulfidptosis is a novel type of programmed cell death. However, the value of disulfidptosis-related genes (DRGs) in the prediction of breast cancer prognosis is unclear. METHODS RNA-seq data of 1231 patients, together with information on patient clinical characteristics and prognosis, were downloaded from TCGA. DRGs were identified between cancerous and non-cancerous tissues. The LASSO algorithm was used to assign half of the samples to the training set. Risk scores were used for construction of a prognostic model for risk stratification and prognosis prediction, and the clinical applicability was examined using a line diagram. The relationships between risk scores, immune cell infiltration, molecular subtypes, and responses to immunotherapy and chemotherapy were examined. RESULTS We identified and obtained four DRG-related prognostic lncRNAs (AC009097.2, AC133552.5, YTHDF3-AS1, and AC084824.5), which were used for establishing the risk model. Longer survival was associated with low risk. The DRG-associated lncRNAs were found to independently predict patient prognosis. The AUCs under the ROCs for one-, three-, and 5-year survival in the training cohort were 0.720, 0.687, and 0.692, respectively. The model showed that the high-risk patients had reduced overall survival as well as high tumor mutation burdens. Furthermore, high-risk patients showed increased sensitivity to therapeutic drugs, including docetaxel, paclitaxel, and oxaliplatin. CONCLUSION The risk score model was effective for predicting both prognosis and sensitivity to therapeutic drugs, suggesting its possible usefulness for the management of patients with breast cancer.
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Affiliation(s)
- Shuyan Liu
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China
- Department of Breast Surgery, General Surgery, Cancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310053, Zhejiang, China
- Key Laboratory for Diagnosis and Treatment of Upper Limb Edema and Stasis of Breast Cancer, Hangzhou, 310053, Zhejiang, China
| | - Yiwen Zheng
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China
- Department of Breast Surgery, General Surgery, Cancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310053, Zhejiang, China
- Key Laboratory for Diagnosis and Treatment of Upper Limb Edema and Stasis of Breast Cancer, Hangzhou, 310053, Zhejiang, China
| | - Shujin Li
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China
- Department of Breast Surgery, General Surgery, Cancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310053, Zhejiang, China
- Key Laboratory for Diagnosis and Treatment of Upper Limb Edema and Stasis of Breast Cancer, Hangzhou, 310053, Zhejiang, China
| | - Yaoqiang Du
- Laboratory Medicine Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, 310053, Zhejiang, China
| | - Xiaozhen Liu
- Department of Breast Surgery, General Surgery, Cancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310053, Zhejiang, China
- Key Laboratory for Diagnosis and Treatment of Upper Limb Edema and Stasis of Breast Cancer, Hangzhou, 310053, Zhejiang, China
| | - Hongchao Tang
- Department of Breast Surgery, General Surgery, Cancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310053, Zhejiang, China
- Key Laboratory for Diagnosis and Treatment of Upper Limb Edema and Stasis of Breast Cancer, Hangzhou, 310053, Zhejiang, China
| | - Xuli Meng
- Department of Breast Surgery, General Surgery, Cancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310053, Zhejiang, China.
- Key Laboratory for Diagnosis and Treatment of Upper Limb Edema and Stasis of Breast Cancer, Hangzhou, 310053, Zhejiang, China.
| | - Qinghui Zheng
- Department of Breast Surgery, General Surgery, Cancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310053, Zhejiang, China.
- Key Laboratory for Diagnosis and Treatment of Upper Limb Edema and Stasis of Breast Cancer, Hangzhou, 310053, Zhejiang, China.
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Wu H, Wu Z, Ye D, Li H, Dai Y, Wang Z, Bao J, Xu Y, He X, Wang X, Dai X. Prognostic value analysis of cholesterol and cholesterol homeostasis related genes in breast cancer by Mendelian randomization and multi-omics machine learning. Front Oncol 2023; 13:1246880. [PMID: 38023262 PMCID: PMC10661325 DOI: 10.3389/fonc.2023.1246880] [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: 06/24/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction The high incidence of breast cancer (BC) prompted us to explore more factors that might affect its occurrence, development, treatment, and also recurrence. Dysregulation of cholesterol metabolism has been widely observed in BC; however, the detailed role of how cholesterol metabolism affects chemo-sensitivity, and immune response, as well as the clinical outcome of BC is unknown. Methods With Mendelian randomization (MR) analysis, the potential causal relationship between genetic variants of cholesterol and BC risk was assessed first. Then we analyzed 73 cholesterol homeostasis-related genes (CHGs) in BC samples and their expression patterns in the TCGA cohort with consensus clustering analysis, aiming to figure out the relationship between cholesterol homeostasis and BC prognosis. Based on the CHG analysis, we established a CAG_score used for predicting therapeutic response and overall survival (OS) of BC patients. Furthermore, a machine learning method was adopted to accurately predict the prognosis of BC patients by comparing multi-omics differences of different risk groups. Results We observed that the alterations in plasma cholesterol appear to be correlative with the venture of BC (MR Egger, OR: 0.54, 95% CI: 0.35-0.84, p<0.006). The expression patterns of CHGs were classified into two distinct groups(C1 and C2). Notably, the C1 group exhibited a favorable prognosis characterized by a suppressed immune response and enhanced cholesterol metabolism in comparison to the C2 group. In addition, high CHG score were accompanied by high performance of tumor angiogenesis genes. Interestingly, the expression of vascular genes (CDH5, CLDN5, TIE1, JAM2, TEK) is lower in patients with high expression of CHGs, which means that these patients have poorer vascular stability. The CAG_score exhibits robust predictive capability for the immune microenvironment characteristics and prognosis of patients(AUC=0.79). It can also optimize the administration of various first-line drugs, including AKT inhibitors VIII Imatinib, Crizotinib, Saracatinib, Erlotinib, Dasatinib, Rapamycin, Roscovitine and Shikonin in BC patients. Finally, we employed machine learning techniques to construct a multi-omics prediction model(Risklight),with an area under the feature curve (AUC) of up to 0.89. Conclusion With the help of CAG_score and Risklight, we reveal the signature of cholesterol homeostasis-related genes for angiogenesis, immune responses, and the therapeutic response in breast cancer, which contributes to precision medicine and improved prognosis of BC.
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Affiliation(s)
- Haodong Wu
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Department of Burns and Skin Repair Surgery, The Third Affiliated Hospital of Wenzhou Medical University, Ruian, Zhejiang, China
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhixuan Wu
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Department of Burns and Skin Repair Surgery, The Third Affiliated Hospital of Wenzhou Medical University, Ruian, Zhejiang, China
| | - Daijiao Ye
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Hongfeng Li
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yinwei Dai
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Ziqiong Wang
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jingxia Bao
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yiying Xu
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiaofei He
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiaowu Wang
- Department of Burns and Skin Repair Surgery, The Third Affiliated Hospital of Wenzhou Medical University, Ruian, Zhejiang, China
| | - Xuanxuan Dai
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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Zhu Y, Yang Y, Liu Y, Qian H, Qu G, Shi W, Liu J. A novel tetraspanin-related gene signature for predicting prognosis and immune invasion status of lung adenocarcinoma. J Cancer Res Clin Oncol 2023; 149:13631-13643. [PMID: 37516981 PMCID: PMC10590322 DOI: 10.1007/s00432-023-05176-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 07/10/2023] [Indexed: 08/01/2023]
Abstract
BACKGROUND Lung adenocarcinoma (LUAD), the most common subtype of lung cancer, is the primary contributor to cancer-linked fatalities. Dysregulation in the proliferation of cells and death is primarily involved in its development. Recently, tetraspanins, a group of transmembrane proteins, have gained increasing attention for their potential role in the progression of LUAD. Hence, our endeavor involved the development of a novel tetraspanin-based model for the prognostication of lung cancer. METHODS A comprehensive set of bioinformatics tools was utilized to evaluate the expression of tetraspanin-related genes and assess their significance regarding prognosis. Hence, a robust risk signature was established through machine learning. The prognosis-predictive value of the signature was evaluated in terms of clinical application, functional enrichment, and the immune landscape. RESULTS The research first identified differential expression of tetraspanin genes in patients with LUAD via publicly available databases. The resulting data were indicative of the value that nine of them held regarding prognosis. Five distinct elements were utilized in the establishment of a tetraspanin-related model (TSPAN7, TSPAN11, TSPAN14, UPK1B, and UPK1A). Furthermore, as per the median risk scores, the participants were classified into high- and low-risk groups. The model was validated using inner and outer validation sets. Notably, consensus clustering and prognostic score grouping analysis revealed that tetraspanin-related features affect tumor prognosis by modulating tumor immunity. A nomogram based on the tetraspanin gene was constructed with the aim of enhancing the poor prognosis of high-risk groups and facilitating clinical application. CONCLUSION Through machine learning algorithms and in vitro experiments, a novel tetraspanin-associated signature was developed and validated for survival prediction in patients with LUAD that reflects tumor immune infiltration. This could potentially provide new and improved measures for diagnosis and therapeutic interventions for LUAD.
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Affiliation(s)
- Yindong Zhu
- Department of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Ying Yang
- Cancer Research Center Nantong, Nantong Tumor Hospital, The Affiliated Tumor Hospital of Nantong University, Nantong University, Nantong, China
| | - Yuan Liu
- Cancer Research Center Nantong, Nantong Tumor Hospital, The Affiliated Tumor Hospital of Nantong University, Nantong University, Nantong, China
| | - Hongyan Qian
- Cancer Research Center Nantong, Nantong Tumor Hospital, The Affiliated Tumor Hospital of Nantong University, Nantong University, Nantong, China
| | - Ganlin Qu
- Department of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Weidong Shi
- Department of Thoracic Surgery, The Second People Hospital of Nantong, Nantong, China
| | - Jun Liu
- Department of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China.
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Greco F, Panunzio A, Tafuri A, Bernetti C, Pagliarulo V, Beomonte Zobel B, Scardapane A, Mallio CA. Radiogenomic Features of GIMAP Family Genes in Clear Cell Renal Cell Carcinoma: An Observational Study on CT Images. Genes (Basel) 2023; 14:1832. [PMID: 37895181 PMCID: PMC10606653 DOI: 10.3390/genes14101832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/15/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023] Open
Abstract
GTPases of immunity-associated proteins (GIMAP) genes include seven functional genes and a pseudogene. Most of the GIMAPs have a role in the maintenance and development of lymphocytes. GIMAPs could inhibit the development of tumors by increasing the amount and antitumor activity of infiltrating immunocytes. Knowledge of key factors that affect the tumor immune microenvironment for predicting the efficacy of immunotherapy and establishing new targets in ccRCC is of great importance. A computed tomography (CT)-based radiogenomic approach was used to detect the imaging phenotypic features of GIMAP family gene expression in ccRCC. In this retrospective study we enrolled 193 ccRCC patients divided into two groups: ccRCC patients with GIMAP expression (n = 52) and ccRCC patients without GIMAP expression (n = 141). Several imaging features were evaluated on preoperative CT scan. A statistically significant correlation was found with absence of endophytic growth pattern (p = 0.049), tumor infiltration (p = 0.005), advanced age (p = 0.018), and high Fuhrman grade (p = 0.024). This study demonstrates CT imaging features of GIMAP expression in ccRCC. These results could allow the collection of data on GIMAP expression through a CT-approach and could be used for the development of a targeted therapy.
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Affiliation(s)
- Federico Greco
- Department of Radiology, Cittadella Della Salute, Azienda Sanitaria Locale di Lecce, Piazza Filippo Bottazzi, 2, 73100 Lecce, Italy
| | - Andrea Panunzio
- Department of Urology, “Vito Fazzi” Hospital, Piazza Filippo Muratore, 1, 73100 Lecce, Italy; (A.P.); (A.T.); (V.P.)
| | - Alessandro Tafuri
- Department of Urology, “Vito Fazzi” Hospital, Piazza Filippo Muratore, 1, 73100 Lecce, Italy; (A.P.); (A.T.); (V.P.)
| | - Caterina Bernetti
- Department of Medicine and Surgery, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Roma, Italy; (C.B.); (B.B.Z.); (C.A.M.)
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy
| | - Vincenzo Pagliarulo
- Department of Urology, “Vito Fazzi” Hospital, Piazza Filippo Muratore, 1, 73100 Lecce, Italy; (A.P.); (A.T.); (V.P.)
| | - Bruno Beomonte Zobel
- Department of Medicine and Surgery, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Roma, Italy; (C.B.); (B.B.Z.); (C.A.M.)
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy
| | - Arnaldo Scardapane
- Dipartimento Interdisciplinare di Medicina, Sezione di Diagnostica Per Immagini, Università degli Studi di Bari “Aldo Moro”, Piazza Giulio Cesare, 11, 70124 Bari, Italy;
| | - Carlo Augusto Mallio
- Department of Medicine and Surgery, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Roma, Italy; (C.B.); (B.B.Z.); (C.A.M.)
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy
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11
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Tan Z, Chen X, Zuo J, Fu S, Wang J, Wang H. Integrating Bulk and Single-Cell RNA Sequencing Reveals Heterogeneity, Tumor Microenvironment, and Immunotherapeutic Efficacy Based on Sialylation-Related Genes in Bladder Cancer. J Inflamm Res 2023; 16:3399-3417. [PMID: 37600224 PMCID: PMC10438438 DOI: 10.2147/jir.s418433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/24/2023] [Indexed: 08/22/2023] Open
Abstract
Background As known abnormal sialylation exerts crucial roles in the growth, metastasis, and immune evasion of cancers, but the molecular characteristics and roles in bladder cancer (BLCA) remain unclear. This study intends to establish BLCA risk stratification based on sialylation-related genes and elucidate its role in prognosis, tumor microenvironment, and immunotherapy of BLCA. Methods Bulk RNA-seq and scRNA-seq data were downloaded from open-access databases. The scRNA-seq data were processed using the R package "Seurat" to identify the core cell types. The tumor sub-typing of BLCA samples was performed by the R package "ConsensusClusterPlus" in the bulk RNA-seq data. Signature genes were identified by the R package "limma" and univariate regression analysis to calculate risk scores using the R package "GSVA" and establish risk stratification of BLCA patients. Finally, the differences in clinicopathological characteristics, tumor microenvironment, and immunotherapy efficacy between the different groups were investigated. Results 5 core cell types were identified in the scRNA-seq dataset, with monocytes and macrophages presenting the greatest percentage, sialylation-related gene expression, and sialylation scores. The bulk RNA-seq samples were classified into 3 tumor subtypes based on 19 prognosis-related sialylation genes. The 10 differential expressed genes (DEGs) with the smallest p-values were collected as signature genes, and the risk score was calculated, with the samples divided into high and low-risk score groups. The results showed that patients in the high-risk score group exhibited worse survival outcomes, higher tumor grade, more advanced stage, more frequency of gene mutations, higher expression levels of immune checkpoints, and lower immunotherapy response. Conclusion We established a novel risk stratification of BLCA from a glycomics perspective, which demonstrated good accuracy in determining the prognostic outcome, clinicopathological characteristics, immune microenvironment, and immunotherapy efficacy of patients, and we are proposing to apply it to direct the choice of clinical treatment options for patients.
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Affiliation(s)
- Zhiyong Tan
- Department of Urology, the Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People’s Republic of China
- Urological Disease Clinical Medical Center of Yunnan Province, the Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People’s Republic of China
- Scientific and Technological Innovation Team of Basic and Clinical Research of Bladder Cancer in Yunnan Universities, the Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People’s Republic of China
| | - Xiaorong Chen
- Department of Kidney Transplantation, the Third Hospital of Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Jieming Zuo
- Department of Urology, the Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People’s Republic of China
- Urological Disease Clinical Medical Center of Yunnan Province, the Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People’s Republic of China
- Scientific and Technological Innovation Team of Basic and Clinical Research of Bladder Cancer in Yunnan Universities, the Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People’s Republic of China
| | - Shi Fu
- Department of Urology, the Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People’s Republic of China
- Urological Disease Clinical Medical Center of Yunnan Province, the Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People’s Republic of China
- Scientific and Technological Innovation Team of Basic and Clinical Research of Bladder Cancer in Yunnan Universities, the Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People’s Republic of China
| | - Jiansong Wang
- Department of Urology, the Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People’s Republic of China
- Urological Disease Clinical Medical Center of Yunnan Province, the Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People’s Republic of China
- Scientific and Technological Innovation Team of Basic and Clinical Research of Bladder Cancer in Yunnan Universities, the Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People’s Republic of China
| | - Haifeng Wang
- Department of Urology, the Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People’s Republic of China
- Urological Disease Clinical Medical Center of Yunnan Province, the Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People’s Republic of China
- Scientific and Technological Innovation Team of Basic and Clinical Research of Bladder Cancer in Yunnan Universities, the Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, People’s Republic of China
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12
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Xu K, Zhang Y, Yan Z, Wang Y, Li Y, Qiu Q, Du Y, Chen Z, Liu X. Identification of disulfidptosis related subtypes, characterization of tumor microenvironment infiltration, and development of DRG prognostic prediction model in RCC, in which MSH3 is a key gene during disulfidptosis. Front Immunol 2023; 14:1205250. [PMID: 37426643 PMCID: PMC10327482 DOI: 10.3389/fimmu.2023.1205250] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 06/08/2023] [Indexed: 07/11/2023] Open
Abstract
Disulfidptosis is a newly discovered mode of cell death induced by disulfide stress. However, the prognostic value of disulfidptosis-related genes (DRGs) in renal cell carcinoma (RCC) remains to be further elucidated. In this study, consistent cluster analysis was used to classify 571 RCC samples into three DRG-related subtypes based on changes in DRGs expression. Through univariate regression analysis and LASSO-Cox regression analysis of differentially expressed genes (DEGs) among three subtypes, we constructed and validated a DRG risk score to predict the prognosis of patients with RCC, while also identifying three gene subtypes. Analysis of DRG risk score, clinical characteristics, tumor microenvironment (TME), somatic cell mutations, and immunotherapy sensitivity revealed significant correlations between them. A series of studies have shown that MSH3 can be a potential biomarker of RCC, and its low expression is associated with poor prognosis in patients with RCC. Last but not least, overexpression of MSH3 promotes cell death in two RCC cell lines under glucose starvation conditions, indicating that MSH3 is a key gene in the process of cell disulfidptosis. In summary, we identify potential mechanism of RCC progression through DRGs -related tumor microenvironment remodeling. In addition, this study has successfully established a new disulfidptosis-related genes prediction model and discovered a key gene MSH3. They may be new prognostic biomarkers for RCC patients, provide new insights for the treatment of RCC patients, and may inspire new methods for the diagnosis and treatment of RCC patients.
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Affiliation(s)
- Kai Xu
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, Hubei, China
- Institute of Urologic Disease, Renmin Hospital, Wuhan University, Wuhan, Hubei, China
| | - Ye Zhang
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, Hubei, China
- Institute of Urologic Disease, Renmin Hospital, Wuhan University, Wuhan, Hubei, China
| | - Zhiwei Yan
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, Hubei, China
- Institute of Urologic Disease, Renmin Hospital, Wuhan University, Wuhan, Hubei, China
| | - Yuchan Wang
- School of Science, Hubei University of Technology, Wuhan, China
| | - Yanze Li
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, Hubei, China
- Institute of Urologic Disease, Renmin Hospital, Wuhan University, Wuhan, Hubei, China
| | - Qiangmin Qiu
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, Hubei, China
- Institute of Urologic Disease, Renmin Hospital, Wuhan University, Wuhan, Hubei, China
| | - Yang Du
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, Hubei, China
- Institute of Urologic Disease, Renmin Hospital, Wuhan University, Wuhan, Hubei, China
| | - Zhiyuan Chen
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, Hubei, China
- Institute of Urologic Disease, Renmin Hospital, Wuhan University, Wuhan, Hubei, China
| | - Xiuheng Liu
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, Hubei, China
- Institute of Urologic Disease, Renmin Hospital, Wuhan University, Wuhan, Hubei, China
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Lozano-Mendoza J, Ramírez-Montiel F, Rangel-Serrano Á, Páramo-Pérez I, Mendoza-Macías CL, Saavedra-Salazar F, Franco B, Vargas-Maya N, Jeelani G, Saito-Nakano Y, Anaya-Velázquez F, Nozaki T, Padilla-Vaca F. Attenuation of In Vitro and In Vivo Virulence Is Associated with Repression of Gene Expression of AIG1 Gene in Entamoeba histolytica. Pathogens 2023; 12:pathogens12030489. [PMID: 36986411 PMCID: PMC10051847 DOI: 10.3390/pathogens12030489] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/27/2023] [Accepted: 03/02/2023] [Indexed: 03/30/2023] Open
Abstract
Entamoeba histolytica virulence results from complex host-parasite interactions implicating multiple amoebic components (e.g., Gal/GalNAc lectin, cysteine proteinases, and amoebapores) and host factors (microbiota and immune response). UG10 is a strain derived from E. histolytica virulent HM-1:IMSS strain that has lost its virulence in vitro and in vivo as determined by a decrease of hemolytic, cytopathic, and cytotoxic activities, increased susceptibility to human complement, and its inability to form liver abscesses in hamsters. We compared the transcriptome of nonvirulent UG10 and its parental HM-1:IMSS strain. No differences in gene expression of the classical virulence factors were observed. Genes downregulated in the UG10 trophozoites encode for proteins that belong to small GTPases, such as Rab and AIG1. Several protein-coding genes, including iron-sulfur flavoproteins and heat shock protein 70, were also upregulated in UG10. Overexpression of the EhAIG1 gene (EHI_180390) in nonvirulent UG10 trophozoites resulted in augmented virulence in vitro and in vivo. Cocultivation of HM-1:IMSS with E. coli O55 bacteria cells reduced virulence in vitro, and the EhAIG1 gene expression was downregulated. In contrast, virulence was increased in the monoxenic strain UG10, and the EhAIG1 gene expression was upregulated. Therefore, the EhAIG1 gene (EHI_180390) represents a novel virulence determinant in E. histolytica.
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Affiliation(s)
- Janeth Lozano-Mendoza
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36050, Mexico
| | - Fátima Ramírez-Montiel
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36050, Mexico
| | - Ángeles Rangel-Serrano
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36050, Mexico
| | - Itzel Páramo-Pérez
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36050, Mexico
| | | | - Faridi Saavedra-Salazar
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36050, Mexico
| | - Bernardo Franco
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36050, Mexico
| | - Naurú Vargas-Maya
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36050, Mexico
| | - Ghulam Jeelani
- Graduate School of Medicine, The University of Tokyo, Tokyo 113-8654, Japan
| | - Yumiko Saito-Nakano
- Department of Parasitology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo 162-0052, Japan
| | - Fernando Anaya-Velázquez
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36050, Mexico
| | - Tomoyoshi Nozaki
- Graduate School of Medicine, The University of Tokyo, Tokyo 113-8654, Japan
- Department of Parasitology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo 162-0052, Japan
| | - Felipe Padilla-Vaca
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36050, Mexico
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14
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Gao YJ, Li SR, Huang Y. An inflammation-related gene landscape predicts prognosis and response to immunotherapy in virus-associated hepatocellular carcinoma. Front Oncol 2023; 13:1118152. [PMID: 36969014 PMCID: PMC10033597 DOI: 10.3389/fonc.2023.1118152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/14/2023] [Indexed: 03/11/2023] Open
Abstract
BackgroundDue to the viral infection, chronic inflammation significantly increases the likelihood of hepatocellular carcinoma (HCC) development. Nevertheless, an inflammation-based signature aimed to predict the prognosis and therapeutic effect in virus-related HCC has rarely been established.MethodBased on the integrated analysis, inflammation-associated genes (IRGs) were systematically assessed. We comprehensively investigated the correlation between inflammation and transcriptional profiles, prognosis, and immune cell infiltration. Then, an inflammation-related risk model (IRM) to predict the overall survival (OS) and response to treatment for virus-related HCC patients was constructed and verified. Also, the potential association between IRGs and tumor microenvironment (TME) was investigated. Ultimately, hub genes were validated in plasma samples and cell lines via qRT-PCR. After transfection with shCCL20 combined with overSLC7A2, morphological change of SMMC7721 and huh7 cells was observed. Tumorigenicity model in nude mouse was established.ResultsAn inflammatory response-related gene signature model, containing MEP1A, CCL20, ADORA2B, TNFSF9, ICAM4, and SLC7A2, was constructed by conjoint analysis of least absolute shrinkage and selection operator (LASSO) Cox regression and gaussian finite mixture model (GMM). Besides, survival analysis attested that higher IRG scores were positively relevant to worse survival outcomes in virus-related HCC patients, which was testified by external validation cohorts (the ICGC cohort and GSE84337 dataset). Univariate and multivariate Cox regression analyses commonly proved that the IRG was an independent prognostic factor for virus-related HCC patients. Thus, a nomogram with clinical factors and IRG was also constructed to superiorly predict the prognosis of patients. Featured with microsatellite instability-high, mutation burden, and immune activation, lower IRG score verified a superior OS for sufferers. Additionally, IRG score was remarkedly correlated with the cancer stem cell index and drug susceptibility. The measurement of plasma samples further validated that CCL20 upexpression and SLC7A2 downexpression were positively related with virus-related HCC patients, which was in accord with the results in cell lines. Furthermore, CCL20 knockdown combined with SLC7A2 overexpression availably weakened the tumor growth in vivo.ConclusionsCollectively, IRG score, serving as a potential candidate, accurately and stably predicted the prognosis and response to immunotherapy in virus-related HCC patients, which could guide individualized treatment decision-making for the sufferers.
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Affiliation(s)
- Ying-jie Gao
- Department of Biochemistry and Molecular Biology, School of Bioscience and Technology, Chengdu Medical College, Chengdu, Sichuan, China
| | - Shi-rong Li
- Laboratory of Animal Tumor Models, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yuan Huang
- Department of Biochemistry and Molecular Biology, School of Bioscience and Technology, Chengdu Medical College, Chengdu, Sichuan, China
- *Correspondence: Yuan Huang,
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15
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Chen Y, Lu Y, Huang C, Wu J, Shao Y, Wang Z, Zhang H, Fu Z. Subtypes analysis and prognostic model construction based on lysosome-related genes in colon adenocarcinoma. Front Genet 2023; 14:1149995. [PMID: 37168510 PMCID: PMC10166181 DOI: 10.3389/fgene.2023.1149995] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/12/2023] [Indexed: 05/13/2023] Open
Abstract
Background: Lysosomes are essential for the development and recurrence of cancer. The relationship between a single lysosome-related gene and cancer has previously been studied, but the relationship between the lysosome-related genes (LRGs) and colon adenocarcinoma (COAD) remains unknown. This research examined the role of lysosome-related genes in colon adenocarcinoma. Methods: 28 lysosome-related genes associated with prognosis (PLRGs) were found by fusing the gene set that is differently expressed between tumor and non-tumor in colon adenocarcinoma with the gene set that is related to lysosomes. Using consensus unsupervised clustering of PLRGs, the colon adenocarcinoma cohort was divided into two subtypes. Prognostic and tumor microenvironment (TME) comparisons between the two subtypes were then made. The PLRGs_score was constructed using the least absolute shrinkage and selection operator regression (LASSO) method to quantify each patient's prognosis and provide advice for treatment. Lastly, Western Blot and immunohistochemistry (IHC) were used to identify MOGS expression at the protein level in colon adenocarcinoma tissues. Results: PLRGs had more somatic mutations and changes in genetic level, and the outcomes of the two subtypes differed significantly in terms of prognosis, tumor microenvironment, and enrichment pathways. Then, PLRGs_score was established based on two clusters of differential genes in the cancer genome atlas (TCGA) database, and external verification was performed using the gene expression omnibus (GEO) database. Then, we developed a highly accurate nomogram to enhance the clinical applicability of the PLRGs_score. Finally, a higher PLRGs_score was associated with a poorer overall survival (OS), a lower tumor mutation burden (TMB), a lower cancer stem cell (CSC) index, more microsatellite stability (MSS), and a higher clinical stage. MOGS was substantially elevated at the protein level in colon adenocarcinoma as additional confirmation. Conclusion: Overall, based on PLRGs, we identified two subtypes that varied significantly in terms of prognosis and tumor microenvironment. Then, in order to forecast patient prognosis and make treatment suggestions, we developed a diagnostic model with major significance for prognosis, clinical relevance, and immunotherapy. Moreover, we were the first to demonstrate that MOGS is highly expressed in colon adenocarcinoma.
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Affiliation(s)
- Yang Chen
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- The First College of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yunfei Lu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- The First College of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Changzhi Huang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- The First College of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jingyu Wu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- The First College of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yu Shao
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- The First College of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhenling Wang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- The First College of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hongqiang Zhang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- The First College of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zan Fu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- The First College of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- *Correspondence: Zan Fu,
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Xu A, Fan Y, Liu S, Sheng L, Sun Y, Yang H. GIMAP7 induces oxidative stress and apoptosis of ovarian granulosa cells in polycystic ovary syndrome by inhibiting sonic hedgehog signalling pathway. J Ovarian Res 2022; 15:141. [PMID: 36581994 PMCID: PMC9801623 DOI: 10.1186/s13048-022-01092-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022] Open
Abstract
Polycystic ovary syndrome (PCOS) is a gynaecological endocrine disease. The objective of the present study was to investigate the role of GTPase immunity-associated protein (GIMAP) 7 in PCOS. A PCOS rat model was established using dehydroepiandrosterone injection. The data showed that GIMAP7 was mainly located in granulosa cells and was abundantly expressed in the ovarian granulosa cells of PCOS rats. GIMAP7 silencing decreased blood glucose levels, HOMA-IR scores, and number of cystic follicles. In addition, GIMAP7 silencing corrected erratic oestrous cycles, inhibited apoptosis and reduced c-caspase-3 protein expression in the ovarian tissues of PCOS rats. GIMAP7 silencing reduced malondialdehyde (MDA) but increased glutathione (GSH) and superoxide dismutase (SOD) levels in the serum and ovarian tissues of PCOS rats. The effects of GIMAP7 were further investigated in human ovarian granulosa KGN cells. GIMAP7 silencing increased the viability, promoted proliferation, and increased the percentage of S-phase KGN cells. The apoptosis rate was significantly decreased by GIMAP7 silencing. GIMAP7 also inhibited oxidative stress in KGN cells, resulting in decreased levels of reactive oxygen species (ROS) and MDA and increased levels of GSH and SOD. Notably, GIMAP7 inhibited the sonic hedgehog (SHH) signalling pathway, and GIMAP7 silencing increased the expression of the SHH signalling pathway downstream genes SHH, SMO, and Gli1. Inhibition of the SHH signalling pathway using cyclopamine reduced the effect of GIMAP7 silencing on KGN cells. This study proved that GIMAP7 promotes oxidative stress and apoptosis in ovarian granulosa cells in PCOS by inhibiting the SHH signalling pathway.
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Affiliation(s)
- Anran Xu
- grid.27255.370000 0004 1761 1174Center of Reproductive Medicine, Maternity and Child Health Care Hospital of Shandong Province/ Key Laboratory of Birth Regulation and Control Technology of the Health Commission of China, 238 Jiangshuiquan Road, Jinan, 250014 Shandong People’s Republic of China
| | - Yuanyuan Fan
- grid.27255.370000 0004 1761 1174Center of Reproductive Medicine, Maternity and Child Health Care Hospital of Shandong Province/ Key Laboratory of Birth Regulation and Control Technology of the Health Commission of China, 238 Jiangshuiquan Road, Jinan, 250014 Shandong People’s Republic of China
| | - Song Liu
- grid.27255.370000 0004 1761 1174Center of Reproductive Medicine, Maternity and Child Health Care Hospital of Shandong Province/ Key Laboratory of Birth Regulation and Control Technology of the Health Commission of China, 238 Jiangshuiquan Road, Jinan, 250014 Shandong People’s Republic of China
| | - Lianbing Sheng
- grid.27255.370000 0004 1761 1174Center of Reproductive Medicine, Maternity and Child Health Care Hospital of Shandong Province/ Key Laboratory of Birth Regulation and Control Technology of the Health Commission of China, 238 Jiangshuiquan Road, Jinan, 250014 Shandong People’s Republic of China
| | - Yanyan Sun
- grid.27255.370000 0004 1761 1174Center of Reproductive Medicine, Maternity and Child Health Care Hospital of Shandong Province/ Key Laboratory of Birth Regulation and Control Technology of the Health Commission of China, 238 Jiangshuiquan Road, Jinan, 250014 Shandong People’s Republic of China
| | - Huijun Yang
- grid.27255.370000 0004 1761 1174Center of Reproductive Medicine, Maternity and Child Health Care Hospital of Shandong Province/ Key Laboratory of Birth Regulation and Control Technology of the Health Commission of China, 238 Jiangshuiquan Road, Jinan, 250014 Shandong People’s Republic of China
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A Novel Molecular Signature of Cancer-Associated Fibroblasts Predicts Prognosis and Immunotherapy Response in Pancreatic Cancer. Int J Mol Sci 2022; 24:ijms24010156. [PMID: 36613599 PMCID: PMC9820557 DOI: 10.3390/ijms24010156] [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: 10/27/2022] [Revised: 12/15/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
Cancer-associated fibroblasts (CAFs), a prominent population of stromal cells, play a crucial role in tumor progression, prognosis, and treatment response. However, the relationship among CAF-based molecular signatures, clinical outcomes, and tumor microenvironment infiltration remains largely elusive in pancreatic cancer (PC). Here, we collected multicenter PC data and performed integrated analysis to investigate the role of CAF-related genes (CRGs) in PC. Firstly, we demonstrated that α-SMA+ CAFs were the most prominent stromal components and correlated with the poor survival rates of PC patients in our tissue microarrays. Then, we discriminated two diverse molecular subtypes (CAF clusters A and B) and revealed the significant differences in the tumor immune microenvironment (TME), four reported CAF subpopulations, clinical characteristics, and prognosis in PC samples. Furthermore, we analyzed their association with the immunotherapy response of PC patients. Lastly, a CRG score was constructed to predict prognosis, immunotherapy responses, and chemosensitivity in pancreatic cancer patients. In summary, these findings provide insights into further research targeting CAFs and their TME, and they pave a new road for the prognosis evaluation and individualized treatment of PC patients.
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Liu H, Tao T. Prognosis and immune features of pyroptosis-related RNA patterns in low-grade glioma. Front Oncol 2022; 12:1015850. [PMID: 36605437 PMCID: PMC9808047 DOI: 10.3389/fonc.2022.1015850] [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: 08/10/2022] [Accepted: 11/08/2022] [Indexed: 12/24/2022] Open
Abstract
Purpose Low-grade gliomas (LGG), which are malignant primary brain tumors, are more prevalent in young adults. Pyroptosis, an inflammatory form of programmed cell death, has been shown in recent years to be directly associated with tumor growth and tumor microenvironment (TME). However, the correlation between LGG and pyroptosis remained to be explored. In this research, we explored pyroptosis-related gene expression patterns and their prognostic significance based on transcriptome profiles and clinical data in LGG. Methods We identified 31 pyroptosis-related genes differentially expressed at the mRNA level between the data of LGG patients from TCGA and the data of normal brain tissues from GTEx. Univariate Cox regression analysis was used to screen 16 differentially expressed genes (DEGs) based on survival data. Next, the prognostic model was established using LASSO Cox regression, which divided LGG patients into high- and low- risk subgroups and showed an independent prognostic value for overall survival (OS) combined with clinical factors in the CGGA test cohort. Pyroptosis and immune cells were correlated through the CIBERSORT R package and the TIMER database. Results Based on the analyses of 523 LGG and 1152 normal tissues, nine significant differential genes were identified. The AUC remained at about 0.74 when combined with the risk score and clinical factors. Enrichment analyses revealed that DEGs were mainly enriched in cytokine-cytokine receptor interactions, immune response and chemokine signaling pathways. Immune cell enrichment analysis demonstrated that scores for most immune cell types differed significantly between the high-and low-risk groups, and further infiltrating analysis showed obvious differences between these two risk subgroups. Conclusion Pyroptosis-related genes play a pivotal role in LGG and are associated with tumor immunity, which may be beneficial to the prognosis and immunotherapy of LGG.
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Affiliation(s)
- Hanzhang Liu
- Morphology Laboratory, Medical College of Nantong University, Nantong, Jiangsu, China,*Correspondence: Tao Tao, ; Hanzhang Liu,
| | - Tao Tao
- Department of Clinical Medicine, Ningbo College of Health Science, Ningbo, Zhejiang, China,*Correspondence: Tao Tao, ; Hanzhang Liu,
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Cui G, Liu J, Wang M, Shon K, Wang C, Wei F, Sun Z. Crosstalk of angiogenesis-related subtypes, establishment of a prognostic signature and immune infiltration characteristics in colorectal adenocarcinoma. Front Immunol 2022; 13:1049485. [PMID: 36505481 PMCID: PMC9731117 DOI: 10.3389/fimmu.2022.1049485] [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: 09/20/2022] [Accepted: 11/07/2022] [Indexed: 11/25/2022] Open
Abstract
Background Colorectal adenocarcinoma (COAD) is one of the most common malignancies and angiogenesis is vital to the development of cancer. Here, we explored the roles of angiogenesis-related genes (ARGs) that affect the prognosis of COAD and constructed risk models to assess patient prognosis, immune characteristics, and treatment outcomes. Methods We comprehensively characterized the transcriptional and genetic modifications of 48 ARGs in COAD and evaluated the expression patterns. We identified two ARG subgroups using the consensus clustering algorithm. Based on the differentially expressed genes (DEGs) of two ARG subtypes, we calculated risk score, namely ARG_scores, and calssified COAD patients into different risk groups. To investigate the expression of ARG_score-related genes, qRT-PCR was performed. Subsequently, we mapped the nomogram to visually and accurately describe the value of the application of ARG_score. Finally, the correlation between ARG_score and clinical features, immune infiltration along with drug sensitivity were explored. Results We identified two ARG related subgroups and there were great differences in overall survival (OS) and tumor microenvironment. Then, we created an ARG_score for predicting overall survival based on eight DEGs and confirmed its reliable predictive power in COAD patients, with higher ARG_score associated with worse prognosis. Furthermore, eight ARG_score-related genes expression was investigated by qRT-PCR. To make the ARG_score clinically feasible, we created a highly reliable nomogram. We also found a higher proportion of microsatellite instability-high (MSI-H) and higher tumor mutational burden (TMB) in the high-risk group. In addition, ARG_score was notably correlated with cancer stem cell indices and drug sensitivity. Conclusion This scoring model has potential clinical application value in the prognosis, immune microenvironment and therapeutic drug sensitivity of COAD, which provides new insights for personalized treatment.
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Affiliation(s)
- Guoliang Cui
- Department of Gastroenterology, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Jinhui Liu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Manli Wang
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Kinyu Shon
- Department of Gastroenterology, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Can Wang
- Department of Colorectal Surgery, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, China
| | - Fei Wei
- Department of Physiology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China,*Correspondence: Fei Wei, ; Zhiguang Sun,
| | - Zhiguang Sun
- Department of Gastroenterology, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China,The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China,*Correspondence: Fei Wei, ; Zhiguang Sun,
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20
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Wu H, He H, Huang J, Wang C, Dong Y, Lin R, Cheng Z, Qiu Q, Hong L. Identification and validation of transferrin receptor protein 1 for predicting prognosis and immune infiltration in lower grade glioma. Front Mol Neurosci 2022; 15:972308. [PMID: 36483569 PMCID: PMC9723399 DOI: 10.3389/fnmol.2022.972308] [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: 06/18/2022] [Accepted: 10/26/2022] [Indexed: 11/23/2022] Open
Abstract
INTRODUCTION Transferrin receptor protein 1 (TFRC), an ananda molecule associated with ferroptosis, has been identified as affecting a wide spectrum of pathological processes in various cancers, but the prognostic value correlates with the tumor microenvironment of TFRC in lower-grade glioma (LGG) is still unclear. MATERIALS AND METHODS Clinical pathological information and gene expression data of patients with LGG come from The Cancer Genome Atlas (TCGA), Chinese Glioma Genome Atlas (CGGA), GTEx, Oncomine, UCSC Xena, and GEO databases. We then used various bioinformatics methods and mathematical models to analyze those data, aiming to investigate the clinical significance of TFRC in LGG and illustrate its association with tumor immunity. In addition, the molecular function and mechanisms of TFRC were revealed by gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA). Immunohistochemical experiments and single-cell analysis have been performed. RESULTS TFRC expression was highly expressed in many tumors and showed a poor prognosis. Including gliomas, it was significantly associated with several poor clinical prognostic variables, tumor immune microenvironment, tumor mutational burden (TMB), m6a modification, and ferroptosis in LGG. TFRC as a key factor was further used to build a prediction nomogram. The C-index, calibration curve, and decision curve analysis showed the nomogram was clinically useful and calibration was accurate. At the same time, we also demonstrated that promoter hypomethylation of DNA upstream of TFRC could lead to high TFRC expression and poor overall survival. There is a significant correlation between TFRC and CD8 + T cell, macrophage cell infiltration, and several immune checkpoints, such as PD-L1(cd274), CTLA4, and PD1, suggesting a novel direction for future clinical application. Functional and molecular mechanism analysis showed an association of TFRC expression with immune-related pathways through GSEA, GO, and KEGG analysis. Finally, immunohistochemical experiments and single-cell analysis confirmed the expression of TFRC in glioma. CONCLUSION TFRC may be a potential prognostic biomarker and an immunotherapeutic target for glioma.
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Affiliation(s)
- Hongrong Wu
- Department of Pathology, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Haoyang He
- The First Clinical Medical College of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Jiexiong Huang
- Department of Pathology, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Chuan Wang
- Department of Pathology, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Yuejiao Dong
- Department of Pathology, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Ruilin Lin
- Department of Pathology, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Zhuofeng Cheng
- Department of Pathology, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Qiancheng Qiu
- Department of Pathology, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - LiangLi Hong
- Department of Pathology, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
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21
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Shi X, Dong A, Jia X, Zheng G, Wang N, Wang Y, Yang C, Lu J, Yang Y. Integrated analysis of single-cell and bulk RNA-sequencing identifies a signature based on T-cell marker genes to predict prognosis and therapeutic response in lung squamous cell carcinoma. Front Immunol 2022; 13:992990. [PMID: 36311764 PMCID: PMC9614104 DOI: 10.3389/fimmu.2022.992990] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/03/2022] [Indexed: 11/25/2022] Open
Abstract
Cancer immunotherapy is an increasingly successful strategy for treating patients with advanced or conventionally drug-resistant cancers. T cells have been proved to play important roles in anti-tumor and tumor microenvironment shaping, while these roles have not been explained in lung squamous cell carcinoma (LUSC). In this study, we first performed a comprehensive analysis of single-cell RNA sequencing (scRNA-seq) data from the gene expression omnibus (GEO) database to identify 72 T-cell marker genes. Subsequently, we constructed a 5-gene prognostic signature in the training cohort based on the T-cell marker genes from the cancer genome atlas (TCGA) database, which was further validated in the testing cohort and GEO cohort. The areas under the receiver operating characteristic curve at 1-, 3-, and 5-years were 0.614, 0.713 and 0.702 in the training cohort, 0.669, 0.603 and 0.645 in the testing cohort, 0.661, 0.628 and 0.590 in the GEO cohort, respectively. Furthermore, we created a highly reliable nomogram to facilitate clinical application. Gene set enrichment analysis showed that immune-related pathways were mainly enriched in the high-risk group. Tumor immune microenvironment indicated that high-risk group exhibited higher immune score, stromal score, and immune cell infiltration levels. Moreover, genes of the immune checkpoints and human leukocyte antigen family were all overexpressed in high-risk group. Drug sensitivity revealed that low-risk group was sensitive to 8 chemotherapeutic drugs and high-risk group to 4 chemotherapeutic drugs. In short, our study reveals a novel prognostic signature based on T-cell marker genes, which provides a new target and theoretical support for LUSC patients.
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22
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Jiang Z, Pan J, Lu J, Mei J, Xu R, Xia D, Yang X, Wang H, Liu C, Xu J, Ding J. NEUROD1 predicts better prognosis in pancreatic cancer revealed by a TILs-based prognostic signature. Front Pharmacol 2022; 13:1025921. [PMID: 36313290 PMCID: PMC9612957 DOI: 10.3389/fphar.2022.1025921] [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: 08/23/2022] [Accepted: 09/26/2022] [Indexed: 11/29/2022] Open
Abstract
It has been well-defined that tumor-infiltrating lymphocytes (TILs) play critical roles in pancreatic cancer (PaCa) progression. This research aimed to comprehensively explore the composition of TILs in PaCa and their potential clinical significance. A total of 178 samples from the TCGA and 63 samples from the GSE57495 dataset were enrolled in our study. ImmuCellAI was applied to calculate the infiltrating abundance of 24 immune cell types in PaCa and further survival analysis revealed the prognostic values of TILs in PaCa. Moreover, the Hallmark enticement analysis of differentially expressed genes (DEGs) between low- and high-risk groups was performed as well. Immunohistochemistry staining was used to evaluate NEUROD1 expression. As result, different kinds of TILs had distinct infiltrating features. In addition, Specific TILs subsets had notable prognostic values in PaCa. We further established a 6-TILs signature to assess the prognosis of PaCa patients. Kaplan-Meier and Cox regression analyses both suggested the significant prognostic value of the signature in PaCa. Based on the prognostic signature, we screened a great deal of potential prognostic biomarkers and successfully validated NEUROD1 as a novel prognostic biomarker in PaCa. Overall, the current study illuminated the immune cells infiltrating the landscape in PaCa and identified a TILs-dependent signature and NEUROD1 for prognostic prediction in PaCa patients.
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Affiliation(s)
- Zhiyang Jiang
- Department of General Surgery, Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Jiadong Pan
- Department of Gastroenterology, Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Jiahui Lu
- Department of Oncology, Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Jie Mei
- Department of Oncology, Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Rui Xu
- The First College of Clinical Medicine of Nanjing Medical University, Nanjing, China
| | - Dandan Xia
- Department of Oncology, Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Xuejing Yang
- Department of Oncology, Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Huiyu Wang
- Department of Oncology, Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Chaoying Liu
- Department of Oncology, Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Junying Xu
- Department of Oncology, Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
- *Correspondence: Junying Xu, ; Junli Ding,
| | - Junli Ding
- Department of Oncology, Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
- *Correspondence: Junying Xu, ; Junli Ding,
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23
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Ge W, Shentu D, Wang Y, Wang Y, Xue S, Yue M, Mao T, Zhang X, Xu H, Li S, Ma J, Yao J, Cui J, Wang L. A novel angiogenesis-based molecular signature related to prognosis and tumor immune interactions of pancreatic cancer. Front Cell Dev Biol 2022; 10:1001606. [PMID: 36274838 PMCID: PMC9582445 DOI: 10.3389/fcell.2022.1001606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 09/20/2022] [Indexed: 11/25/2022] Open
Abstract
Angiogenesis, a hallmark of cancer, is related to prognosis, tumor progression, and treatment response. Nevertheless, the correlation of angiogenesis-based molecular signature with clinical outcome and immune cell infiltration has not been thoroughly studied in pancreatic cancer. In this study, multiple bioinformatics methods were combined to evaluate prognosis, immune cell infiltration, and the alterations of angiogenesis-related genes (ARGs) in PC samples, and further establish a novel angiogenesis-related gene signature. Moreover, the protein and mRNA expression levels of four angiogenesis risk genes were determined by Human Protein Atlas (HPA) database and qPCR analysis, respectively. Here, we recognized two distinct angiogenesis subtypes and two gene subtypes, and revealed the critical roles of ARGs in the tumor immune microenvironment (TIME), clinical features, and prognosis. Consequently, we established an ARGs score to predict prognosis and therapeutic response of PC patients, and validated its robust predictive ability. Additionally, the ARGs score was markedly associated with clinical outcomes, tumor mutation burden (TMB), and chemotherapeutic drug sensitivity. In brief, our findings imply that the ARGs score is a robust prognostic indicator and may contribute to the development of effective individualized therapies for PC.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Jiujie Cui
- *Correspondence: Jiujie Cui, ; Liwei Wang,
| | - Liwei Wang
- *Correspondence: Jiujie Cui, ; Liwei Wang,
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24
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Li Z, Zhang H, Wang X, Wang Q, Xue J, Shi Y, Wang M, Wang G, Zhang J. Identification of cuproptosis-related subtypes, characterization of tumor microenvironment infiltration, and development of a prognosis model in breast cancer. Front Immunol 2022; 13:996836. [PMID: 36059516 PMCID: PMC9437337 DOI: 10.3389/fimmu.2022.996836] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/02/2022] [Indexed: 01/10/2023] Open
Abstract
Breast cancer (BC) is now the most frequent and lethal cancer among women. Cuproptosis is a newly identified programmed cell death process that has been connected to tumor therapeutic sensitivity, patient outcomes, and the genesis of cancer. Cuproptosis-related genes (CRGs) are involved in breast cancer, although their roles and potential mechanisms are still unclear. First, we examined the effect of gene mutations and copy number changes on overall survival in 1168 breast cancer samples. Breast cancer patients were split into two molecular categories as determined by the variation in CRG based on clinicopathological traits, overall survival, and cell-infiltrating traits in tumor microenvironments. In addition, we created and validated a CRG score to calculate breast cancer patients' OS. Finally, we created a comprehensive nomogram for the clinical use of the CRG score. Patients whose CRG scores were low showed increased odds of developing OS, a larger mutation load, and immunological activation than those with high CRG scores. The CRG score, the cancer stem cell index, and the responsiveness to chemotherapy or targeted therapies were also shown to be statistically significantly correlated. Our thorough examination of CRGs in breast cancer patients demonstrated that they may be useful predictors of prognosis, clinical characteristics, and tumor microenvironment. These findings provide fresh insight into CRGs in breast cancer and might inspire brand-new approaches to both diagnosing and treating patients there.
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Affiliation(s)
- Zhi Li
- Department of General Surgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China,Hubei Key Laboratory of Embryonic Stem Cell Research, Taihe Hospital, Hubei University of Medicine, Shiyan, China,*Correspondence: Jianquan Zhang, ; Zhi Li,
| | - Hua Zhang
- Department of General Surgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Xixi Wang
- Department of General Surgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Qun Wang
- Department of General Surgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Jiapeng Xue
- Department of General Surgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Yun Shi
- Department of General Surgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Minghua Wang
- Department of General Surgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Geng Wang
- Department of General Surgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Jianquan Zhang
- Department of General Surgery, Affiliated Haikou Hospital of Xiangya Medical College, Central South Univesity, Haikou, China,*Correspondence: Jianquan Zhang, ; Zhi Li,
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25
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Song Q, Zhou R, Shu F, Fu W. Cuproptosis scoring system to predict the clinical outcome and immune response in bladder cancer. Front Immunol 2022; 13:958368. [PMID: 35990642 PMCID: PMC9386055 DOI: 10.3389/fimmu.2022.958368] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/08/2022] [Indexed: 12/20/2022] Open
Abstract
Cuproptosis is a novel copper ion-dependent cell death type being regulated in cells, and this is quite different from the common cell death patterns such as apoptosis, pyroptosis, necroptosis, and ferroptosis. Interestingly, like with death patterns, cuproptosis-related genes have recently been reported to regulate the occurrence and progression of various tumors. However, in bladder cancer, the link between cuproptosis and clinical outcome, tumor microenvironment (TME) modification, and immunotherapy is unknown. To determine the role of cuprotosis in the tumor microenvironment, we systematically examined the characteristic patterns of 10 cuproptosis-related genes in bladder cancer (BLCA). By analyzing principal component data, we established a cuproptosis score to determine the degree of cuproptosis among patients. Finally, we evaluated the potential of these values in predicting BLCA prognosis and treatment responses. A comprehensive study of the mutations of cuproptosis-related genes in BLCA specimens was conducted at the genetic level, and their expression and survival patterns were evaluated using The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). Two cuproptosis patterns were constructed based on the transcription level of 10 cuproptosis-related genes, featuring differences in the prognosis and the infiltrating landscape of immune cells (especially T and dendritic cells) with interactions between cuproptosis and the TME. Our study further demonstrated that cuproptosis score may predict prognosis, immunophenotype sensitivity to chemotherapy, and immunotherapy response among bladder cancer patients. The development and progression of bladder cancer are likely to be influenced by cuproptosis, which may involve a diverse and complex TME. The cuproptosis pattern evaluated in our study may enhance understanding of immune infiltrations and guide more potent immunotherapy interventions.
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Affiliation(s)
- Qiang Song
- Department of Urology, Guangzhou Women and Children’s Medical Center, National Children’s Medical Center for South Central Region, Guangzhou Medical University, Guangzhou, China,Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Rui Zhou
- Department of Urology, Guangzhou Women and Children’s Medical Center, National Children’s Medical Center for South Central Region, Guangzhou Medical University, Guangzhou, China
| | - Fangpeng Shu
- Department of Urology, Guangzhou Women and Children’s Medical Center, National Children’s Medical Center for South Central Region, Guangzhou Medical University, Guangzhou, China,*Correspondence: Wen Fu, ; Fangpeng Shu,
| | - Wen Fu
- Department of Urology, Guangzhou Women and Children’s Medical Center, National Children’s Medical Center for South Central Region, Guangzhou Medical University, Guangzhou, China,*Correspondence: Wen Fu, ; Fangpeng Shu,
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Prognostic and Immunological Value of GNB4 in Gastric Cancer by Analyzing TCGA Database. DISEASE MARKERS 2022; 2022:7803642. [PMID: 35756485 PMCID: PMC9225895 DOI: 10.1155/2022/7803642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/09/2022] [Accepted: 05/13/2022] [Indexed: 12/03/2022]
Abstract
Background Gastric cancer (GC) represents a universal malignant tumor of the digestive system. Stromal and immune cells belong to two main nontumor components exerting a vital function in the tumor microenvironment. Methods Based on TCGA database, this study downloaded clinical information and gene profiles of GC. The ESTIMATE algorithm was adopted for evaluating the score of immune-infiltrating cells. This work employed Sangerbox to explore the differentially denoted genes (DEGs) related to stromal, immunity, and prognosis. Besides, the STRING database was involved in order to detect the association among the proteins. The MCODE module of Cytoscape software was used to screen key genes. Oncomine and GEPIA databases were used, aiming to study the differences in key genes in healthy gastric mucosa and GC. At last, we adopted TISDIB and TIMER databases for analyzing the association of guanine nucleotide binding protein subunit-4 (GNB4) between gastric cancer and tumor immune cells. qRT-PCR was applied for exploring differential GNB4 expression between GC and normal gastric mucosa and investigating the relation of GNB4 with tumor-infiltrating lymphocytes (TILs). Results Patients undergoing a great stromal score exhibited worse prognostic outcome, and cases having a low immune score had better prognosis. Overall, altogether 656 genes were upregulated with 5 genes being downregulated, which were matrix immune-related differential genes. Furthermore, 18 genes were screened as hub genes on the basis of the univariate Cox risk model of TCGA database (82 differential genes predicted poor GC survival). Oncomine and GEPIA databases revealed that GNB4 expression in gastric cancer was obviously higher in comparison with that in normal gastric mucosa. The GSEA, TISDIB, and TIMER databases revealed that GNB4 is involved in various tumor signal pathways and immune and metabolic processes. qRT-PCR demonstrated that GNB4 expression in gastric cancer was notably higher in comparison with that in normal gastric mucosa, showing significant association with matrix TILs. Conclusion The selected key gene GNB4 is a potential biomarker to guide the immunotherapy of gastric cancer.
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Zhou K, Yang J, Li X, Xiong W, Zhang P, Zhang X. N7-Methylguanosine Regulatory Genes Profoundly Affect the Prognosis, Progression, and Antitumor Immune Response of Hepatocellular Carcinoma. Front Surg 2022; 9:893977. [PMID: 35784919 PMCID: PMC9246272 DOI: 10.3389/fsurg.2022.893977] [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: 03/11/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is a common abdominal cancer with poor survival outcomes. Although there is growing evidence that N7-methylguanosine (m7G) is closely associated with tumor prognosis, development, and immune response, few studies focus on this topic. Methods The novel m7G risk signature was constructed through the Lasso regression analysis. Its prognostic value was evaluated through a series of survival analyses and was tested in ICGC-LIRI, GSE14520, and GSE116174 cohorts. CIBERSORT, ssGSEA, and ESTIMATE methods were applied to explore the effects of the m7G risk score on tumor immune microenvironment (TIM). The GSEA method was used to evaluate the impacts of the m7G risk score on glycolysis, ferroptosis, and pyroptosis. The human protein atlas (HPA) database was used to clarify the histological expression levels of five m7G signature genes. The biofunctions of NCBP2 in hepatocellular cancer (HC) cells were confirmed through qPCR, CCK8, and transwell assays. Results Five m7G regulatory genes comprised the novel risk signature. The m7G risk score was identified as an independent prognostic factor of HCC and could increase the decision-making benefit of traditional prognostic models. Besides, we established a nomogram containing the clinical stage and m7G risk score to predict the survival rates of HCC patients. The prognostic value of the m7G model was successfully validated in ICGC and GSE116174 cohorts. Moreover, high m7G risk led to a decreased infiltration level of CD8+ T cells, whereas it increased the infiltration levels of Tregs and macrophages. The glycolysis and pyroptosis processes were found to be enriched in the HCC patients with high m7G risk. Finally, overexpression of NCBP2 could promote the proliferation, migration, and invasion of HC cells. Conclusions The m7G risk score was closely related to the prognosis, antitumor immune process, glycolysis, and malignant progression of HCC. NCBP2 has pro-oncogenic abilities, showing promise as a novel treatment target.
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Affiliation(s)
- Kexiang Zhou
- Department of Gastroenterology, The Third Affiliated Hospital of ChongQing Medical University, China
- ChongQing Medical University, Chongqing, China
| | - Jiaqun Yang
- Department of Gastroenterology, The Third Affiliated Hospital of ChongQing Medical University, China
| | - Xiaoyan Li
- Department of Gastroenterology, The Third Affiliated Hospital of ChongQing Medical University, China
| | - Wei Xiong
- Department of Gastroenterology, The Third Affiliated Hospital of ChongQing Medical University, China
| | - Pengbin Zhang
- Department of Gastroenterology, The Third Affiliated Hospital of ChongQing Medical University, China
| | - Xuqing Zhang
- ChongQing Medical University, Chongqing, China
- Department of Infectious Diseases, The Third Affiliated Hospital of ChongQing Medical University, China
- Correspondence: Xuqing Zhang
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28
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Ding R, Prasanna P, Corredor G, Barrera C, Zens P, Lu C, Velu P, Leo P, Beig N, Li H, Toro P, Berezowska S, Baxi V, Balli D, Belete M, Rimm DL, Velcheti V, Schalper K, Madabhushi A. Image analysis reveals molecularly distinct patterns of TILs in NSCLC associated with treatment outcome. NPJ Precis Oncol 2022; 6:33. [PMID: 35661148 PMCID: PMC9166700 DOI: 10.1038/s41698-022-00277-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 04/18/2022] [Indexed: 12/12/2022] Open
Abstract
Despite known histological, biological, and clinical differences between lung adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC), relatively little is known about the spatial differences in their corresponding immune contextures. Our study of over 1000 LUAD and LUSC tumors revealed that computationally derived patterns of tumor-infiltrating lymphocytes (TILs) on H&E images were different between LUAD (N = 421) and LUSC (N = 438), with TIL density being prognostic of overall survival in LUAD and spatial arrangement being more prognostically relevant in LUSC. In addition, the LUAD-specific TIL signature was associated with OS in an external validation set of 100 NSCLC treated with more than six different neoadjuvant chemotherapy regimens, and predictive of response to therapy in the clinical trial CA209-057 (n = 303). In LUAD, the prognostic TIL signature was primarily comprised of CD4+ T and CD8+ T cells, whereas in LUSC, the immune patterns were comprised of CD4+ T, CD8+ T, and CD20+ B cells. In both subtypes, prognostic TIL features were associated with transcriptomics-derived immune scores and biological pathways implicated in immune recognition, response, and evasion. Our results suggest the need for histologic subtype-specific TIL-based models for stratifying survival risk and predicting response to therapy. Our findings suggest that predictive models for response to therapy will need to account for the unique morphologic and molecular immune patterns as a function of histologic subtype of NSCLC.
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Grants
- UL1 TR002548 NCATS NIH HHS
- R01 CA216579 NCI NIH HHS
- UL1 TR001863 NCATS NIH HHS
- R03 CA219603 NCI NIH HHS
- C06 RR012463 NCRR NIH HHS
- U24 CA199374 NCI NIH HHS
- I01 BX004121 BLRD VA
- R43 EB028736 NIBIB NIH HHS
- U54 CA254566 NCI NIH HHS
- U01 CA239055 NCI NIH HHS
- R37 CA245154 NCI NIH HHS
- R01 CA220581 NCI NIH HHS
- P50 CA196530 NCI NIH HHS
- R01 CA202752 NCI NIH HHS
- R01 CA208236 NCI NIH HHS
- Research reported in this publication was supported by the National Cancer Institute under award numbers 1U24CA199374-01, R01CA202752-01A1, R01CA208236-01A1, R01 CA216579-01A1, R01 CA220581-01A1, 1U01 CA239055-01, 1U01CA248226-01, 1U54CA254566-01, National Heart, Lung and Blood Institute, 1R01HL15127701A1, National Institute for Biomedical Imaging and Bioengineering 1R43EB028736-01, National Center for Research Resources under award number 1 C06 RR12463-01, VA Merit Review Award IBX004121A from the United States Department of Veterans Affairs Biomedical Laboratory Research and Development Service, the Office of the Assistant Secretary of Defense for Health Affairs, through the Breast Cancer Research Program (W81XWH-19-1-0668), the Prostate Cancer Research Program (W81XWH-15-1-0558, W81XWH-20-1-0851), the Lung Cancer Research Program (W81XWH-18-1-0440, W81XWH-20-1-0595), the Peer Reviewed Cancer Research Program (W81XWH-18-1-0404), the Kidney Precision Medicine Project (KPMP) Glue Grant, the Ohio Third Frontier Technology Validation Fund, the Clinical and Translational Science Collaborative of Cleveland (UL1TR0002548) from the National Center for Advancing Translational Sciences (NCATS) component of the National Institutes of Health and NIH roadmap for Medical Research, The Wallace H. Coulter Foundation Program in the Department of Biomedical Engineering at Case Western Reserve University, and National Science Foundation Graduate Research Fellowship Program (CON501692).
- A scholarship of the Cancer Research Switzerland (MD-PhD-5088-06-2020).
- the National Cancer Institute under award numbers R03CA219603, R37CA245154, P50CA196530, the Lung Cancer Research Program W81XWH-16-1-0160 and the Stand Up To Cancer – American Cancer Society Lung Cancer Dream Team Translational Research Grants SU2C-AACR-DT1715 and SU2C-AACR-DT22-17
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Affiliation(s)
- Ruiwen Ding
- Case Western Reserve University, Cleveland, OH, USA
| | | | - Germán Corredor
- Case Western Reserve University, Cleveland, OH, USA
- Louis Stokes Cleveland VA Medical Center, Cleveland, OH, USA
| | | | - Philipp Zens
- Institute of Pathology, University of Bern, Bern, Switzerland
- Graduate School for Health Sciences, University of Bern, Bern, Switzerland
| | - Cheng Lu
- Case Western Reserve University, Cleveland, OH, USA
| | - Priya Velu
- Weill Cornell Medical College, New York, NY, USA
| | - Patrick Leo
- Case Western Reserve University, Cleveland, OH, USA
| | - Niha Beig
- Case Western Reserve University, Cleveland, OH, USA
| | - Haojia Li
- Case Western Reserve University, Cleveland, OH, USA
| | - Paula Toro
- Case Western Reserve University, Cleveland, OH, USA
| | - Sabina Berezowska
- Institute of Pathology, University of Bern, Bern, Switzerland
- Department of Laboratory Medicine and Pathology, Institute of Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | | | | | | | | | | | | | - Anant Madabhushi
- Case Western Reserve University, Cleveland, OH, USA.
- Louis Stokes Cleveland VA Medical Center, Cleveland, OH, USA.
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29
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Qing X, Xu W, Liu S, Chen Z, Ye C, Zhang Y. Molecular Characteristics, Clinical Significance, and Cancer Immune Interactions of Angiogenesis-Associated Genes in Gastric Cancer. Front Immunol 2022; 13:843077. [PMID: 35273618 PMCID: PMC8901990 DOI: 10.3389/fimmu.2022.843077] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/03/2022] [Indexed: 12/21/2022] Open
Abstract
Background Immunotherapy has evolved as a critical option to treat diverse cancers. The active response to immunotherapy relies on the unique interaction between cancer and the tumor microenvironment (TME). Angiogenesis is one of the hallmarks of cancer. However, the association between angiogenesis and clinical outcome, immune cell infiltration, and immunotherapy remains unknown in gastric cancer (GC). Methods We systematically assessed 36 angiogenesis-associated genes (AAGs) and comprehensively identified the correlation between angiogenesis and transcriptional patterns, prognosis, and immune cell infiltration. The AAG_score was applied to quantify the angiogenesis subtypes of each patient. We then evaluated their values in prognostic prediction and therapeutic responses in GC. Results We discussed the mutations of AAGs in GC specimens from genetic levels and identified their expression patterns from TCGA and GEO cohorts. We determined two different molecular subtypes and observed that AAG mutations were related to patients’ clinicopathological characteristics, prognosis, and infiltrating TME. Next, an AAG_score for predicting overall survival (OS) was established and its reliable predictive ability in GC patients was confirmed. Furthermore, we created a highly reliable nomogram to facilitate the clinical viability of the AAG_score. A low AAG_score, characterized by elevated microsatellite instability-high, mutation burden, and immune activation, demonstrated a superior OS. Additionally, the AAG_score was remarkedly correlated with the cancer stem cell index and drug susceptibility. Conclusion Collectively, we identified a prognostic AAG signature for GC patients. This signature may contribute to clarifying the characteristics of TME and enable the exploration of more potent immunotherapy strategies.
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Affiliation(s)
- Xin Qing
- School of Medicine, Zhongda Hospital, Southeast University, Nanjing, China
| | - Wenjing Xu
- School of Medicine, Zhongda Hospital, Southeast University, Nanjing, China
| | - Shengli Liu
- Hepatopancreatobiliary Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhencheng Chen
- School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, China
| | - Chunping Ye
- Department of Obstetrics and Gynecology, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, China
| | - Yewei Zhang
- Hepatopancreatobiliary Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
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30
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Hung YH, Chen LT, Hung WC. The Trinity: Interplay among Cancer Cells, Fibroblasts, and Immune Cells in Pancreatic Cancer and Implication of CD8 + T Cell-Orientated Therapy. Biomedicines 2022; 10:biomedicines10040926. [PMID: 35453676 PMCID: PMC9026398 DOI: 10.3390/biomedicines10040926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/15/2022] [Accepted: 04/17/2022] [Indexed: 02/01/2023] Open
Abstract
The microenvironment in tumors is complicated and is constituted by different cell types and stromal proteins. Among the cell types, the abundance of cancer cells, fibroblasts, and immune cells is high and these cells work as the “Trinity” in promoting tumorigenesis. Although unidirectional or bidirectional crosstalk between two independent cell types has been well characterized, the multi-directional interplays between cancer cells, fibroblasts, and immune cells in vitro and in vivo are still unclear. We summarize recent studies in addressing the interaction of the “Trinity” members in the tumor microenvironment and propose a functional network for how these members communicate with each other. In addition, we discuss the underlying mechanisms mediating the interplay. Moreover, correlations of the alterations in the distribution and functionality of cancer cells, fibroblasts, and immune cells under different circumstances are reviewed. Finally, we point out the future application of CD8+ T cell-oriented therapy in the treatment of pancreatic cancer.
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Affiliation(s)
- Yu-Hsuan Hung
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan;
| | - Li-Tzong Chen
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan;
- Division of Hematology & Oncology, Department of Internal Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 804, Taiwan
- Center for Cancer Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- Correspondence: (L.-T.C.); (W.-C.H.)
| | - Wen-Chun Hung
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan;
- Correspondence: (L.-T.C.); (W.-C.H.)
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31
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Zhao Y, Song Q, Xu F, Zhou Y, Zuo X, Zhang Z. Pyroptosis-Related Risk Signature Exhibits Distinct Prognostic, Immune, and Therapeutic Landscapes in Hepatocellular Carcinoma. Front Genet 2022; 13:823443. [PMID: 35368686 PMCID: PMC8965507 DOI: 10.3389/fgene.2022.823443] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/03/2022] [Indexed: 01/26/2023] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is a common abdominal cancer. The existing therapeutic approaches often fail to achieve satisfactory results. Pyroptosis, an inflammatory form of programmed cell death, provides new ideas for anticancer treatment. However, the roles of pyroptosis-related (PR) genes (PRGs) in HCC remain elusive. Methods: Differentially expressed genes (DEGs) (n = 22) were screened out using TCGA and GTEx databases. A novel PR risk signature was constructed through Lasso regression analysis. Its prognostic value was evaluated through a series of survival analyses and was tested in ICGC and GSE14520 cohorts. CIBERSORT, ssGSEA, and ESTIMATE methods were employed to determine the effects of the PR risk score on the tumor immune microenvironment (TIM). The TIDE scoring system, IMvigor210 cohort, GSE109211 dataset, and GSDC database were applied to explore the associations of the PR risk score with therapeutic effects. The biofunctions of WNK1 in hepatocellular cancer (HC) cells were confirmed through qPCR, colony formation, and Transwell assays. Results: Overall, 22 of 45 PRGs (48.9%) were abnormally expressed in HCC samples. Then, a PR risk signature consisting of eight PRGs was constructed. A high PR risk score led to an unfavorable prognosis. The PR risk score was identified as an independent prognostic factor of HCC and could increase the decision-making benefit of the traditional TNM model. In addition, we established a nomogram containing the clinical stage and PR risk score to predict the survival rates of HCC patients. The prognostic value of the PR model was successfully validated in ICGC and GSE14520 cohorts. Moreover, high PR risk conferred the decreased infiltration level of CD8+ T cells and weakened the activities of "cytolytic activity" pathways. As for therapeutic correlation, a high PR risk score seemed to imply a poor efficacy of PD-1/L1 inhibitors and sorafenib. Finally, the overexpression of WNK1 could promote the proliferation, migration, and invasion of HC cells. Conclusions: The PR risk score was closely related to the prognosis, antitumor immune process, therapeutic outcomes, and malignant progression of HCC. WNK1, the core regulator of pyroptosis, possesses pro-oncogenic abilities, showing promise as a novel treatment target.
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Affiliation(s)
- Yidi Zhao
- Department of Emergency, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Qingya Song
- Xi'an Medical Emergency Center, Xi'an, China
| | - Fangshi Xu
- Department of Medicine, Xi'an Jiaotong University, Xi'an, China
| | - Yang Zhou
- Department of Emergency, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiaoli Zuo
- Department of Orthopedics, Second Affiliated Hospital of Xi'a Jiaotong University, Xi'an, China
| | - Zhengliang Zhang
- Department of Emergency, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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32
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Tian Y, Wen C, Zhang Z, Liu Y, Li F, Zhao Q, Yao C, Ni K, Yang S, Zhang Y. CXCL9-modified CAR T cells improve immune cell infiltration and antitumor efficacy. Cancer Immunol Immunother 2022; 71:2663-2675. [PMID: 35352167 DOI: 10.1007/s00262-022-03193-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/14/2022] [Indexed: 12/11/2022]
Abstract
Chimeric antigen receptor (CAR) T cells remain unsatisfactory in treating solid tumors. The frequency of tumor-infiltrating T cells is closely related to the good prognosis of patients. Augmenting T cell accumulation in the tumor microenvironment is essential for tumor clearance. To overcome insufficient immune cell infiltration, innovative CAR designs need to be developed immediately. CXCL9 plays a pivotal role in regulating T cell migration and inhibiting tumor angiogenesis. Therefore, we engineered CAR T cells expressing CXCL9 (CART-CXCL9). The addition of CXCL9 enhanced cytokine secretion and cytotoxicity of CAR T cells and endowed CAR T cells with the ability to recruit activated T cells and antiangiogenic effect. In tumor-bearing mice, CART-CXCL9 cells attracted more T cell trafficking to the tumor site and inhibited angiogenesis than conventional CAR T cells. Additionally, CART-CXCL9 cell therapy slowed tumor growth and prolonged mouse survival, displaying superior antitumor activity. Briefly, modifying CAR T cells to express CXCL9 could effectively improve CAR T cell efficacy against solid tumors.
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Affiliation(s)
- Yonggui Tian
- Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, 450052, Henan, China.,Henan Key Laboratory for Tumor Immunology and Biotherapy, Zhengzhou, 450052, Henan, China
| | - Chunli Wen
- Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, 450052, Henan, China.,Henan Key Laboratory for Tumor Immunology and Biotherapy, Zhengzhou, 450052, Henan, China.,School of Life Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Zhen Zhang
- Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, 450052, Henan, China.,Henan Key Laboratory for Tumor Immunology and Biotherapy, Zhengzhou, 450052, Henan, China
| | - Yanfen Liu
- Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, 450052, Henan, China.,Henan Key Laboratory for Tumor Immunology and Biotherapy, Zhengzhou, 450052, Henan, China
| | - Feng Li
- Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, 450052, Henan, China.,Henan Key Laboratory for Tumor Immunology and Biotherapy, Zhengzhou, 450052, Henan, China
| | - Qitai Zhao
- Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, 450052, Henan, China.,Henan Key Laboratory for Tumor Immunology and Biotherapy, Zhengzhou, 450052, Henan, China
| | - Chang Yao
- Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, 450052, Henan, China.,Henan Key Laboratory for Tumor Immunology and Biotherapy, Zhengzhou, 450052, Henan, China
| | - Kaiyuan Ni
- Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, 450052, Henan, China.,Henan Key Laboratory for Tumor Immunology and Biotherapy, Zhengzhou, 450052, Henan, China
| | - Shengli Yang
- Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China. .,State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, 450052, Henan, China. .,Henan Key Laboratory for Tumor Immunology and Biotherapy, Zhengzhou, 450052, Henan, China.
| | - Yi Zhang
- Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China. .,State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, 450052, Henan, China. .,Henan Key Laboratory for Tumor Immunology and Biotherapy, Zhengzhou, 450052, Henan, China. .,School of Life Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China.
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Song C, Chen J, Zhang C, Dong D. An Integrated Pan-Cancer Analysis of ADAMTS12 and Its Potential Implications in Pancreatic Adenocarcinoma. Front Oncol 2022; 12:849717. [PMID: 35280819 PMCID: PMC8904364 DOI: 10.3389/fonc.2022.849717] [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: 01/06/2022] [Accepted: 01/31/2022] [Indexed: 11/23/2022] Open
Abstract
Background A Disintegrin and Metallopeptidase with Thrombospondin Type 1 Motif 12 (ADAMTS12), a member of the ADAMTS family of multidomain extracellular protease enzymes, is involved in the progression of many tumors. However, a pan-cancer analysis of this gene has not yet been performed. Its role in pancreatic adenocarcinoma (PAAD) also remains unclear. Methods The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression data (GTEx) databases were used to analyze ADAMTS12 expression in pan-cancer. We assessed the expression, clinical characteristics, prognostic significance, copy number alteration, methylation, and mutation of ADAMTS12 and its correlation with the tumor immune microenvironment. qRT-PCR and immunohistochemistry assays were also performed to validate the expression of ADAMTS12 in PAAD. Results Through bioinformatics analysis and preliminary experimental verification, ADAMTS12 was found to be substantially overexpressed in PAAD. High expression level of ADAMTS12 was correlated with worse survival rates in patients with PAAD and high infiltration levels of tumor-associated macrophages, cancer-associated fibroblasts, immune checkpoint proteins, and immunosuppressive genes. Conclusion Our findings suggest ADAMTS12 as a potential prognostic biomarker in PAAD. Elevated ADAMTS12 expression may also indicate an immunosuppressive microenvironment.
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Affiliation(s)
- Caiyun Song
- Department of Gastroenterology, Wenzhou People's Hospital, Wenzhou, China
| | - Jionghuang Chen
- Zhejiang Engineering Research Center of Cognitive Healthcare, School of Medicine, Zhejiang University, Hangzhou, China
| | - Chaolei Zhang
- Zhejiang Engineering Research Center of Cognitive Healthcare, School of Medicine, Zhejiang University, Hangzhou, China
| | - Dapeng Dong
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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34
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Yang J, Wei X, Hu F, Dong W, Sun L. Development and validation of a novel 3-gene prognostic model for pancreatic adenocarcinoma based on ferroptosis-related genes. Cancer Cell Int 2022; 22:21. [PMID: 35033072 PMCID: PMC8760727 DOI: 10.1186/s12935-021-02431-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 12/25/2021] [Indexed: 12/24/2022] Open
Abstract
Background Molecular markers play an important role in predicting clinical outcomes in pancreatic adenocarcinoma (PAAD) patients. Analysis of the ferroptosis-related genes may provide novel potential targets for the prognosis and treatment of PAAD. Methods RNA-sequence and clinical data of PAAD was downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) public databases. The PAAD samples were clustered by a non-negative matrix factorization (NMF) algorithm. The differentially expressed genes (DEGs) between different subtypes were used by “limma_3.42.2” package. The R software package clusterProfiler was used for functional enrichment analysis. Then, a multivariate Cox proportional and LASSO regression were used to develop a ferroptosis-related gene signature for pancreatic adenocarcinoma. A nomogram and corrected curves were constructed. Finally, the expression and function of these signature genes were explored by qRT-PCR, immunohistochemistry (IHC) and proliferation, migration and invasion assays. Results The 173 samples were divided into 3 categories (C1, C2, and C3) and a 3-gene signature model (ALOX5, ALOX12, and CISD1) was constructed. The prognostic model showed good independent prognostic ability in PAAD. In the GSE62452 external validation set, the molecular model also showed good risk prediction. KM-curve analysis showed that there were significant differences between the high and low-risk groups, samples with a high-risk score had a worse prognosis. The predictive efficiency of the 3-gene signature-based nomogram was significantly better than that of traditional clinical features. For comparison with other models, that our model, with a reasonable number of genes, yields a more effective result. The results obtained with qPCR and IHC assays showed that ALOX5 was highly expressed, whether ALOX12 and CISD1 were expressed at low levels in tissue samples. Finally, function assays results suggested that ALOX5 may be an oncogene and ALOX12 and CISD1 may be tumor suppressor genes. Conclusions We present a novel prognostic molecular model for PAAD based on ferroptosis-related genes, which serves as a potentially effective tool for prognostic differentiation in pancreatic cancer patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02431-8.
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Affiliation(s)
- Jihua Yang
- Department of Endocrinology and Metabolism, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, 519000, China
| | - XiaoHong Wei
- Department of Endocrinology and Metabolism, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, 519000, China
| | - Fang Hu
- Department of Endocrinology and Metabolism, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, 519000, China
| | - Wei Dong
- Department of Pathology, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, Shanghai, China.
| | - Liao Sun
- Department of Endocrinology and Metabolism, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, 519000, China.
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35
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Liu T, Chen L, Gao G, Liang X, Peng J, Zheng M, Li J, Ye Y, Shao C. Development of a Gene Risk Signature for Patients of Pancreatic Cancer. JOURNAL OF HEALTHCARE ENGINEERING 2022; 2022:4136825. [PMID: 35035831 PMCID: PMC8759853 DOI: 10.1155/2022/4136825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 10/25/2021] [Indexed: 11/17/2022]
Abstract
BACKGROUND Pancreatic cancer is a highly malignant solid tumor with a high lethality rate, but there is a lack of clinical biomarkers that can assess patient prognosis to optimize treatment. METHODS Gene-expression datasets of pancreatic cancer tissues and normal pancreatic tissues were obtained from the GEO database, and differentially expressed genes analysis and WGCNA analysis were performed after merging and normalizing the datasets. Univariate Cox regression analysis and Lasso Cox regression analysis were used to screen the prognosis-related genes in the modules with the strongest association with pancreatic cancer and construct risk signatures. The performance of the risk signature was subsequently validated by Kaplan-Meier curves, receiver operating characteristic (ROC), and univariate and multivariate Cox analyses. RESULT A three-gene risk signature containing CDKN2A, BRCA1, and UBL3 was established. Based on KM curves, ROC curves, and univariate and multivariate Cox regression analyses in the TRAIN cohort and TEST cohort, it was suggested that the three-gene risk signature had better performance in predicting overall survival. CONCLUSION This study identifies a three-gene risk signature, constructs a nomogram that can be used to predict pancreatic cancer prognosis, and identifies pathways that may be associated with pancreatic cancer prognosis.
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Affiliation(s)
- Tao Liu
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Navy Medical University, Shanghai, China
- Department of Hepatobiliary Surgery, Heze Municipal Hospital, No. 2888, Caozhou Road, Mudan District, Heze 274000, Shandong, China
| | - Long Chen
- Department of Gastrointestinal Surgery, Heze Municipal Hospital, No. 2888, Caozhou Road, Mudan District, Heze 274000, Shandong, China
| | - Guili Gao
- Department of Cardiology, Heze Municipal Hospital, No. 2888, Caozhou Road, Mudan District, Heze 274000, Shandong, China
| | - Xing Liang
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Navy Medical University, Shanghai, China
| | - Junfeng Peng
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Navy Medical University, Shanghai, China
| | - Minghui Zheng
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Navy Medical University, Shanghai, China
| | - Judong Li
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Navy Medical University, Shanghai, China
| | - Yongqiang Ye
- Department of Hepatobiliary Surgery, Heze Municipal Hospital, No. 2888, Caozhou Road, Mudan District, Heze 274000, Shandong, China
| | - Chenghao Shao
- Department of Pancreatic-biliary Surgery, Changzheng Hospital, Navy Medical University, Shanghai, China
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Bai Z, Xu F, Feng X, Wu Y, Lv J, Shi Y, Pei H. Pyroptosis regulators exert crucial functions in prognosis, progression and immune microenvironment of pancreatic adenocarcinoma: a bioinformatic and in vitro research. Bioengineered 2022; 13:1717-1735. [PMID: 35000541 PMCID: PMC8805829 DOI: 10.1080/21655979.2021.2019873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/13/2021] [Indexed: 12/25/2022] Open
Abstract
Pyroptosis is an inflammatory programmed cell death, showing potentials to be a novel anti-cancer approach. However, the roles of pyroptosis-related (PR) genes (PRGs) in pancreatic adenocarcinoma (PAAD) remain elusive. In the present study, we constructed a novel PR risk signature through the lasso regression analysis. The risk signature was greatly conducive to PAAD prognostic assessment. PR risk score was identified as an independent prognostic factor and could distinguish the prognostic differences of most clinical subgroups. Meanwhile, it could improve the traditional prognostic models based on TNM-staging. Next, its prognostic value was also tested in five validation cohorts. Using CIBERSORT, ESTIMATE, and ssGSEA algorithms, the effects of PR risk signature on tumor immune microenvironment (TIM) were explored. High PR risk suppressed antitumor immune through decreasing the infiltrating levels of CD8 T and NK cells. The genomic information and histological expression of risk PRGs were uncovered by USCA and HPA databases. Somatic mutation, methylation alteration, and homozygous CNV of eight PRGs barely occurred in PAAD samples. As for therapeutic correlation, PR risk score may not predict the efficacy of PD-1/L1 inhibitors and was weakly associated with multiple drug susceptibilities. Finally, the biofunctions of toll like receptor 3 (TLR3) in pancreatic cancer (PC) cells were investigated through qPCR, MTT, colony formation, and Transwell assays. Overexpression of TLR3 could promote the proliferation, migration, and invasion of PC cells. In conclusion, PRGs play crucial roles in prognosis, progression, and immune microenvironment of PAAD. TLR3 is expected to be a promising therapeutic target.
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Affiliation(s)
- Zhenghai Bai
- Department of Emergency, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
| | - Fangshi Xu
- Department of Emergency, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
- Department of Medicine, Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
| | - Xiaodan Feng
- Department of Emergency, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
| | - Yuan Wu
- Department of Emergency, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
| | - Junhua Lv
- Department of Emergency, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
| | - Yu Shi
- Department of Emergency, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
| | - Honghong Pei
- Department of Emergency, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
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Yu S, Wang Y, Peng K, Lyu M, Liu F, Liu T. Establishment of a Prognostic Signature of Stromal/Immune-Related Genes for Gastric Adenocarcinoma Based on ESTIMATE Algorithm. Front Cell Dev Biol 2021; 9:752023. [PMID: 34900998 PMCID: PMC8652145 DOI: 10.3389/fcell.2021.752023] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/01/2021] [Indexed: 11/13/2022] Open
Abstract
Different subtypes of gastric cancer differentially respond to immune checkpoint inhibitors (ICI). This study aimed to investigate whether the Estimation of STromal and Immune cells in Malignant Tumor tissues using Expression data (ESTIMATE) algorithm is related to the classification and prognosis of gastric cancer and to establish an ESTIMATE-based gene signature to predict the prognosis for patients. The immune/stromal scores of 388 gastric cancer patients from TCGA were used in this analysis. The upregulated differentially expressed genes (DEGs) in patients with high stromal/immune scores were identified. The immune-related hub DEGs were selected based on protein-protein interaction (PPI) analysis. The prognostic values of the hub DEGs were evaluated in the TCGA dataset and validated in the GSE15460 dataset using the Kaplan-Meier curves. A prognostic signature was built using the hub DEGs by Cox proportional hazards model, and the accuracy was assessed using receiver operating characteristic (ROC) analysis. Different subtypes of gastric cancer had significantly different immune/stromal scores. High stromal scores but not immune scores were significantly associated with short overall survivals of TCGA patients. Nine hub DEGs were identified in PPI analysisThe expression of these hub DEG negatively correlated with the overall survival in the TCGA cohort, which was validated in the GSE15460 cohort. A 9-gene prognostic signature was constructed. The risk factor of patients was calculated by this signature. High-risk patients had significantly shorter overall survival than low-risk patients. ROC analysis showed that the prognostic model accurately identified high-risk individuals within different time frames. We established an effective 9-gene-based risk signature to predict the prognosis of gastric cancer patients, providing guidance for prognostic stratification.
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Affiliation(s)
- Shan Yu
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yan Wang
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ke Peng
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Minzhi Lyu
- Department of Biostatistics, Zhongshan Hospital, Fudan University, Shanghai, China.,Center of Evidence-Based Medicine, Fudan University, Shanghai, China
| | - Fenglin Liu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Tianshu Liu
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China.,Center of Evidence-Based Medicine, Fudan University, Shanghai, China
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Ozhan A, Tombaz M, Konu O. Discovery of Cancer-Specific and Independent Prognostic Gene Subsets of the Slit-Robo Family Using TCGA-PANCAN Datasets. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:782-795. [PMID: 34757814 DOI: 10.1089/omi.2021.0097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The Slit-Robo family of axon guidance molecules works in concert, playing important roles in organ development and cancer. Expressions of individual Slit-Robo genes have been used in calculating univariable hazard ratios (HRuni) for predicting cancer prognosis in the literature. However, Slit-Robo members do not act independently; hence, hazard ratios from multivariable Cox regression (HRmulti) on the whole gene set can further lead to identification of cancer-specific, novel, and independent prognostic gene pairs or modules. Herein, we obtained mRNA expressions of the Slit-Robo family consisting of four Robos (ROBO1/2/3/4) and three Slits (SLIT1/2/3), along with four types of survival outcome across cancers found in the Cancer Genome Atlas (TCGA). We used cluster heat maps to visualize closely associated pairs/modules of prognostic genes across 33 different cancers. We found a smaller number of significant genes in HRmulti than in HRuni, suggesting that the former analysis was less redundant. High ROBO4 expression emerged as relatively protective within the family, in both types of HR analyses. Multivariable Cox regression, on the other hand, revealed significantly more HR signatures containing Slit-Robo pairs acting in opposing directions than those containing Slit-Slit or Robo-Robo pairs for disease-specific survival. Furthermore, we discovered, through the online app SmulTCan's lasso regression, Slit-Robo gene subsets that significantly differentiated between high- versus low-risk prognosis patient groups, particularly for renal cancers and low-grade glioma. The statistical pipeline reported herein can help test independent and significant pairs/modules within a codependent gene family for cancer prognostication, and thus should also prove useful in personalized/precision medicine research.
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Affiliation(s)
- Ayse Ozhan
- UNAM-National Nanotechnology Research Center, Institute of Material Science and Nanotechnology, Bilkent University, Ankara, Turkey
| | - Melike Tombaz
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara, Turkey
| | - Ozlen Konu
- UNAM-National Nanotechnology Research Center, Institute of Material Science and Nanotechnology, Bilkent University, Ankara, Turkey.,Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara, Turkey.,Interdisciplinary Graduate Program in Neuroscience, Aysel Sabuncu Brain Research Center, Bilkent University, Ankara, Turkey
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Ye Y, Chen Z, Shen Y, Qin Y, Wang H. Development and validation of a four-lipid metabolism gene signature for diagnosis of pancreatic cancer. FEBS Open Bio 2021; 11:3153-3170. [PMID: 33386701 PMCID: PMC8564347 DOI: 10.1002/2211-5463.13074] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 12/17/2020] [Accepted: 12/30/2020] [Indexed: 11/11/2022] Open
Abstract
Abnormal lipid metabolism is closely related to the malignant biological behavior of tumor cells. Such abnormal lipid metabolism provides energy for rapid proliferation, and certain genes related to lipid metabolism encode important components of tumor signaling pathways. In this study, we analyzed pancreatic cancer datasets from The Cancer Genome Atlas and searched for prognostic genes related to lipid metabolism in the Molecular Signature Database. A risk score model was built and verified using the GSE57495 dataset and International Cancer Genome Consortium dataset. Four molecular subtypes and 4249 differentially expressed genes (DEGs) were identified. The DEGs obtained by Weighted Gene Coexpression Network Construction analysis were intersected with 4249 DEGs to obtain a total of 1340 DEGs. The final prognosis model included CA8, CEP55, GNB3 and SGSM2, and these had a significant effect on overall survival. The area under the curve at 1, 3 and 5 years was 0.72, 0.79 and 0.87, respectively. These same results were obtained using the validation cohort. Survival analysis data showed that the model could stratify the prognosis of patients with different clinical characteristics, and the model has clinical independence. Functional analysis indicated that the model is associated with multiple cancer-related pathways. Compared with published models, our model has a higher C-index and greater risk value. In summary, this four-gene signature is an independent risk factor for pancreatic cancer survival and may be an effective prognostic indicator.
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Affiliation(s)
- Yanrong Ye
- Department of PharmacyZhongshan HospitalFudan UniversityShanghaiChina
- Department of PharmacyXiamen BranchZhongshan HospitalFudan UniversityXiamenChina
| | - Zhe Chen
- Department of PharmacyZhongshan HospitalFudan UniversityShanghaiChina
| | - Yun Shen
- Department of PharmacyZhongshan HospitalFudan UniversityShanghaiChina
| | - Yan Qin
- Department of PharmacyZhongshan HospitalFudan UniversityShanghaiChina
| | - Hao Wang
- Teaching Center of Experimental MedicineShanghai Medical CollegeFudan UniversityShanghaiChina
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Yuan L, Li F, Wang S, Yi H, Li F, Mao Y. Identification of Tumor Microenvironment-Related Prognostic lncRNAs in Lung Adenocarcinoma. Front Oncol 2021; 11:719812. [PMID: 34408984 PMCID: PMC8366027 DOI: 10.3389/fonc.2021.719812] [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: 06/03/2021] [Accepted: 07/06/2021] [Indexed: 12/19/2022] Open
Abstract
Background Lung adenocarcinoma (LUAD) is the most common type of lung cancer and is a severe threat to human health. Although many therapies have been applied to LUAD, the long-term survival rate of patients remains unsatisfactory. We aim to find reliable immune microenvironment-related lncRNA biomarkers to improve LUAD prognosis. Methods ESTIMATE analysis was performed to evaluate the degree of immune infiltration of each patient in TAGA LUAD cohort. Correlation analysis was used to identify the immune microenvironment-related lncRNAs. Univariate cox regression analysis, LASSO analysis, and Kaplan Meier analysis were used to construct and validate the prognostic model based on microenvironment-related lncRNAs. Results We obtained 1,178 immune microenvironment-related lncRNAs after correlation analysis. One hundred and eighty of them are independent prognostic lncRNAs. Sixteen key lncRNAs were selected by LASSO method. This lncRNA-based model successfully predicted patients’ prognosis in validation cohort, and the risk score was related to pathological stage. Besides, we also found that TP53 had the highest frequency mutation in LUAD, and the mutation of TP53 in the high-risk group, which was identified by our survival model, has a poor prognosis. lncRNA-mRNA co-expression network further suggested that these lncRNAs play a vital role in the prognosis of LUAD. Conclusion Here, we filtered 16 key lncRNAs, which could predict the survival of LUAD and may be potential biomarkers and therapeutic targets.
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Affiliation(s)
- Ligong Yuan
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Feng Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Shuaibo Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Hang Yi
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Fang Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yousheng Mao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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41
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Identification of tumor microenvironment-related prognostic genes in colorectal cancer based on bioinformatic methods. Sci Rep 2021; 11:15040. [PMID: 34294834 PMCID: PMC8298640 DOI: 10.1038/s41598-021-94541-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/13/2021] [Indexed: 02/07/2023] Open
Abstract
Colorectal cancer (CRC) ranks fourth among the deadliest cancers globally, and the progression is highly affected by the tumor microenvironment (TME). This study explores the relationship between TME and colorectal cancer prognosis and identifies prognostic genes related to the CRC microenvironment. We collected the gene expression data from The Cancer Genome Atlas (TCGA) and calculated the scores of stromal/immune cells and their relations to clinical outcomes in colorectal cancer by the ESTIMATE algorithm. Lower immune scores were significantly related to the malignant progression of CRC (metastasis, p = 0.001). We screened 292 differentially expressed genes (DEGs) by dividing CRC cases into high and low stromal/immune score groups. Functional enrichment analyses and protein-protein interaction (PPI) networks illustrated that these DEGs were closely involved in immune response, cytokine-cytokine receptor interaction, and chemokine signaling pathway. Six DEGs (FABP4, MEOX2, MMP12, ERMN, TNFAIP6, and CHST11) with prognostic value were identified by survival analysis and validated in two independent cohorts (GSE17538 and GSE161158). The six DEGs were significantly related to immune cell infiltration levels based on the Tumor Immune Estimation Resource (TIMER). The results might contribute to discovering new diagnostic and prognostic biomarkers and new treatment targets for colorectal cancer.
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Wu H, Zhang Z, Xiao XY, Zhang ZY, Gao SL, Lu C, Zuo L, Zhang LF. Toll-like receptor 2 (TLR2) is a candidate prognostic factor in testicular germ cell tumors as well as an indicator of immune function in the tumor microenvironment. Bioengineered 2021; 12:1939-1951. [PMID: 34002664 PMCID: PMC8806693 DOI: 10.1080/21655979.2021.1927560] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Testicular cancer is the most common malignant tumor in young men, and its incidence has increased in recent years. The tumor microenvironment (TME) plays a crucial role in the development and progression of tumors; however, the TME of testicular germ cell tumor (TGCT) is poorly understood. In this study, we downloaded information for 156 TGCT cases from The Cancer Genome Atlas (TCGA) database, used the ESTIMATE method to determine immune and stromal scores, and used CIBERSORT to calculate the proportion of tumor-infiltrating immune cells (TICs). The differentially expressed genes were subjected to a COX regression analysis and used for the construction of a protein–protein interaction (PPI) network. Toll-like receptor 2 (TLR2) was identified as a predictive marker by combining the results of the Cox regression analysis and PPI network. A survival analysis showed that TLR2 was positively correlated with TGCT survival. A gene set enrichment analysis indicated that genes in the high TLR2 expression group were enriched for cell adhesion molecules (CAMs) and the chemokine signaling pathway, and genes in the low TLR2 expression group were mainly enriched in the spliceosome. Regarding proportions of TICs, naive B cells and follicular helper T cells were negatively correlated with the expression of TLR2. This suggests that as TLR2 expression increases, the immunocompetence of the TME decreases. The expression of TLR2 may affect the prognosis of TGCT, suggesting that this locus can be used as a prognostic factor for TGCT.
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Affiliation(s)
- Hao Wu
- Department of Urology, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China.,Dalian Medical University, Dalian, China
| | - Ze Zhang
- Department of Urology, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China.,Dalian Medical University, Dalian, China
| | | | - Zi-Yi Zhang
- Department of Urology, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China.,Dalian Medical University, Dalian, China
| | - Sheng-Lin Gao
- Department of Urology, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Chao Lu
- Department of Urology, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Li Zuo
- Department of Urology, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Li-Feng Zhang
- Department of Urology, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
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43
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Wang T, Chen B, Meng T, Liu Z, Wu W. Identification and immunoprofiling of key prognostic genes in the tumor microenvironment of hepatocellular carcinoma. Bioengineered 2021; 12:1555-1575. [PMID: 33955820 PMCID: PMC8806269 DOI: 10.1080/21655979.2021.1918538] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Tumor microenvironment (TME) is involved in the occurrence and development of hepatocellular carcinoma (HCC), and immune cells in the TME have been implicated in its progression and treatment. However, the association of genes involved in the TME with HCC prognosis remains unclear. Thus, in this study, we obtained transcriptomic and clinicopathological data of patients with HCC from The Cancer Genome Atlas to identify key genes in TME associated with HCC prognosis. Stromal and immune cell scores were calculated using the ESTIMATE method, and differentially expressed genes (DEGs) were determined. We identified 830 DEGs, which were further subjected to survival analyses and functional enrichment analysis. Next, we identified prognostic TME-associated DEGs, established a protein-protein interaction (PPI) network, and performed Cox analysis.Consequently, four key prognostic genes (CXCL5, CXCL8, IL18RAP, and TREM2) associated with TME, were identified, in which CXCL5 and IL18RAP may be potential independent prognostic factors. Age, clinical stage, N stage, and risk score were also determined as significant prognostic variables. CIBERSORT was used to predict the constitution and relative content of the immune cells, wherein M0 macrophages were the most closely related to the key genes. In conclusion, CXCL5, CXCL8, IL18RAP, and TREM2 were associated with HCC prognosis and were important for immune cell invasion into the TME. Additionally, IL18RAP expression may contribute toward favorable prognosis in patients with HCC. Consequently, these genes may serve as potential biomarkers and immunotherapeutic targets for HCC.
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Affiliation(s)
- Tianbing Wang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Bang Chen
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Tao Meng
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zhiqiang Liu
- Department of General Surgery, Anhui NO.2 Provinicial People's Hospital, Hefei, China
| | - Wenyong Wu
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Department of General Surgery, Anhui NO.2 Provinicial People's Hospital, Hefei, China
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Li C, Liu T, Liu Y, Zhang J, Zuo D. Prognostic value of tumour microenvironment-related genes by TCGA database in rectal cancer. J Cell Mol Med 2021; 25:5811-5822. [PMID: 33949771 PMCID: PMC8184694 DOI: 10.1111/jcmm.16547] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 03/15/2021] [Accepted: 03/30/2021] [Indexed: 12/20/2022] Open
Abstract
Rectal cancer is a common malignant tumour and the progression is highly affected by the tumour microenvironment (TME). This study intended to assess the relationship between TME and prognosis, and explore prognostic genes of rectal cancer. The gene expression profile of rectal cancer was obtained from TCGA and immune/stromal scores were calculated by Estimation of Stromal and Immune cells in Malignant Tumors using Expression data (ESTIMATE) algorithm. The correlation between immune/stromal scores and survival time as well as clinical characteristics were evaluated. Differentially expressed genes (DEGs) were identified according to the stromal/immune scores, and the functional enrichment analyses were conducted to explore functions and pathways of DEGs. The survival analyses were conducted to clarify the DEGs with prognostic value, and the protein‐protein interaction (PPI) network was performed to explore the interrelation of prognostic DEGs. Finally, we validated prognostic DEGs using data from the Gene Expression Omnibus (GEO) database by PrognoScan, and we verified these genes at the protein levels using the Human Protein Atlas (HPA) databases. We downloaded gene expression profiles of 83 rectal cancer patients from The Cancer Genome Atlas (TCGA) database. The Kaplan‐Meier plot demonstrated that low‐immune score was associated with worse clinical outcome (P = .034), metastasis (M1 vs. M0, P = .031) and lymphatic invasion (+ vs. ‐, P < .001). A total of 540 genes were screened as DEGs with 539 up‐regulated genes and 1 down‐regulated gene. In addition, 60 DEGs were identified associated with overall survival. Functional enrichment analyses and PPI networks showed that the DEGs are mainly participated in immune process, and cytokine‐cytokine receptor interaction. Finally, 19 prognostic genes were verified by GSE17536 and GSE17537 from GEO, and five genes (ADAM23, ARHGAP20, ICOS, IRF4,MMRN1) were significantly different in tumour tissues compared with normal tissues at the protein level. In summary, our study demonstrated the associations between TME and prognosis as well as clinical characteristics of rectal cancer. Moreover, we explored and verified microenvironment‐related genes, which may be the potential key prognostic genes of rectal cancer. Further clinical samples and functional studies are needed to validate this finding.
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Affiliation(s)
- Chao Li
- Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, China
| | - Tao Liu
- Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, China
| | - Yi Liu
- Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, China
| | - Jiantao Zhang
- Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, China
| | - Didi Zuo
- Department of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun, China
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Liu X, Chen B, Chen J, Sun S. A novel tp53-associated nomogram to predict the overall survival in patients with pancreatic cancer. BMC Cancer 2021; 21:335. [PMID: 33789615 PMCID: PMC8011162 DOI: 10.1186/s12885-021-08066-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 03/15/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Gene mutations play critical roles in tumorigenesis and cancer development. Our study aimed to screen survival-related mutations and explore a novel gene signature to predict the overall survival in pancreatic cancer. METHODS Somatic mutation data from three cohorts were used to identify the common survival-related gene mutation with Kaplan-Meier curves. RNA-sequencing data were used to explore the signature for survival prediction. First, Weighted Gene Co-expression Network Analysis was conducted to identify candidate genes. Then, the ICGC-PACA-CA cohort was applied as the training set and the TCGA-PAAD cohort was used as the external validation set. A TP53-associated signature calculating the risk score of every patient was developed with univariate Cox, least absolute shrinkage and selection operator, and stepwise regression analysis. Kaplan-Meier and receiver operating characteristic curves were plotted to verify the accuracy. The independence of the signature was confirmed by the multivariate Cox regression analysis. Finally, a prognostic nomogram including 359 patients was constructed based on the combined expression data and the risk scores. RESULTS TP53 mutation was screened to be the robust and survival-related mutation type, and was associated with immune cell infiltration. Two thousand, four hundred fifty-five genes included in the six modules generated in the WGCNA were screened as candidate survival related TP53-associated genes. A seven-gene signature was constructed: Risk score = (0.1254 × ERRFI1) - (0.1365 × IL6R) - (0.4400 × PPP1R10) - (0.3397 × PTOV1-AS2) + (0.1544 × SCEL) - (0.4412 × SSX2IP) - (0.2231 × TXNL4A). Area Under Curves of 1-, 3-, and 5-year ROC curves were 0.731, 0.808, and 0.873 in the training set and 0.703, 0.677, and 0.737 in the validation set. A prognostic nomogram including 359 patients was constructed and well-calibrated, with the Area Under Curves of 1-, 3-, and 5-year ROC curves as 0.713, 0.753, and 0.823. CONCLUSIONS The TP53-associated signature exhibited good prognostic efficacy in predicting the overall survival of PC patients.
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Affiliation(s)
- Xun Liu
- Department of Pancreas and Endocrine Surgery, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, Shenyang, 110004, Liaoning, China
| | - Bobo Chen
- Department of Pancreas and Endocrine Surgery, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, Shenyang, 110004, Liaoning, China
| | - Jiahui Chen
- Department of Pancreas and Endocrine Surgery, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, Shenyang, 110004, Liaoning, China
| | - Shaolong Sun
- Department of Pancreas and Endocrine Surgery, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, Shenyang, 110004, Liaoning, China.
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Huang H, Zhou W, Chen R, Xiang B, Zhou S, Lan L. CXCL10 is a Tumor Microenvironment and Immune Infiltration Related Prognostic Biomarker in Pancreatic Adenocarcinoma. Front Mol Biosci 2021; 8:611508. [PMID: 33681290 PMCID: PMC7930611 DOI: 10.3389/fmolb.2021.611508] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/11/2021] [Indexed: 01/18/2023] Open
Abstract
Pancreatic adenocarcinoma (PAAD) is the 10th most common cancer worldwide and the outcomes for patients with the disease remain extremely poor. Precision biomarkers are urgently needed to increase the efficiency of early diagnosis and to improve the prognosis of patients. The tumor microenvironment (TME) and tumor immune infiltration are thought to impact the occurrence, progression, and prognosis of PAAD. Novel biomarkers excavated originating from the TME and immune infiltration may be effective in predicting the prognosis of PAAD patients. In the current study, the ESTIMATE and CIBERSORT algorithms were applied to estimate the division of immune and stromal components and the proportion of tumor-infiltrating immune cells in 182 PAAD cases downloaded from The Cancer Genome Atlas database. Intersection analyses of the Protein-Protein Interaction networks and Cox regression analysis identified the chemokine (CXC-motif) ligand 10 (CXCL10) as a predictive biomarker. We verified that CXCL10 in the TME negatively correlates with prognosis in PAAD and positively correlates with tumor cell differentiation. GSE62452 from the GEO database and cumulative survival analysis were performed to validate CXCL10 expression as an independent prognostic indicator. We also found that memory B cells, regulatory T cells, and macrophages M0 and M1 were correlated with the expression of CXCL10 indicating that expression of CXCL10 influenced the immune activity of the TME. Our data suggest that CXCL10 is beneficial as a prognostic indicator in PAAD patients and highlights the potential for immune targeted therapy in the treatment of PAAD.
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Affiliation(s)
- Huimin Huang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Wangxiao Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Renpin Chen
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Bingfeng Xiang
- Department of Emergency Intensive Care Unit, The Cangnan Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Shipeng Zhou
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Linhua Lan
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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47
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Fan T, Zhu M, Wang L, Liu Y, Tian H, Zheng Y, Tan F, Sun N, Li C, He J. Immune profile of the tumor microenvironment and the identification of a four-gene signature for lung adenocarcinoma. Aging (Albany NY) 2020; 13:2397-2417. [PMID: 33318300 PMCID: PMC7880407 DOI: 10.18632/aging.202269] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/22/2020] [Indexed: 12/11/2022]
Abstract
The composition and relative abundances of immune cells in the tumor microenvironment are key factors affecting the progression of lung adenocarcinomas (LUADs) and the efficacy of immunotherapy. Using the cancer gene expression dataset from The Cancer Genome Atlas (TCGA) program, we scored stromal and immune cells for tumor purity prediction by CIBERSORT and ESTMATE. Differential expression analysis was employed to identify 374 genes between the high-score group and the low-score group, which were utilized to conduct Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Protein-protein interaction (PPI) and Cox regression analysis were performed on the differentially expressed genes (DEGs) to identify four key tumor microenvironment (TME) -related genes (CCR2, CCR4, P2RY12, and P2RY13). The expression levels of the four DEGs differed significantly among LUAD patients of different ages, genders, and TNM stages. We found that the infiltration of resting memory CD4+ T cells, memory B cells, and M0 macrophages into the TME was co-regulated by these four DEGs. These four genes were closely related to the prognosis of LUAD and affected the infiltration of immune cells into the TME, which had predictive prognostic value in LUAD.
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Affiliation(s)
- Tao Fan
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan 430060, China.,Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Mingchuang Zhu
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan 430060, China.,Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Liyu Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yu Liu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - He Tian
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yujia Zheng
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Fengwei Tan
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Nan Sun
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Chunxiang Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Jie He
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan 430060, China.,Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
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48
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Liu Q, Lan T, Song Y, Cai J, Yu X, Chen W. Oncostatin M expression and TP53 mutation status regulate tumor-infiltration of immune cells and survival outcomes in cholangiocarcinoma. Aging (Albany NY) 2020; 12:21518-21543. [PMID: 33216732 DOI: 10.18632/aging.103936] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 08/01/2020] [Indexed: 11/25/2022]
Abstract
In this study, we used bioinformatics tools to analyze transcriptome data from cholangiocarcinoma (CCA) patients in multiple datasets (Sun Yat-sen University, TCGA and GSE32225 cohorts) to identify mechanisms that regulate tumor infiltration by immune cells and survival outcomes. We identified 96 differentially expressed genes (DEGs), including 13 upregulated and 83 downregulated genes, in CCA tissues as regulatory T cells were significantly higher and the proportions of activated natural killer cells and monocytes were significantly lower in CCA tissues than the precancerous tissues. The survival outcomes of CCA patients were associated with the TP53 gene mutation status, levels of Oncostatin M (OSM) expression, and the proportions of tumor-infiltrating immune cell types, including dendritic cells, monocytes, and T follicular helper cells. Functional enrichment analysis of the DEGs in the high OSM-expressing CCA tissues showed that pathways related to tumor progression and immune response were significantly upregulated. Our study demonstrates that OSM expression and TP53 mutation status regulate the tumor infiltration by immune cells and survival outcomes in CCA. OSM is thus a potential prognostic biomarker and therapeutic target in cholangiocarcinoma.
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Affiliation(s)
- Qi Liu
- Department of Pancreatico-Biliary Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, Guangdong Province, China
| | - Tian Lan
- Department of Pancreatico-Biliary Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, Guangdong Province, China
| | - Yuxuan Song
- Department of Urology, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Jianpeng Cai
- Department of Pancreatico-Biliary Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, Guangdong Province, China
| | - Xi Yu
- Department of Pancreatico-Biliary Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, Guangdong Province, China
| | - Wei Chen
- Department of Pancreatico-Biliary Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, Guangdong Province, China
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49
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Weighted gene correlation network analysis identifies microenvironment-related genes signature as prognostic candidate for Grade II/III glioma. Aging (Albany NY) 2020; 12:22122-22138. [PMID: 33186124 PMCID: PMC7695422 DOI: 10.18632/aging.104075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 09/04/2020] [Indexed: 12/27/2022]
Abstract
Glioma is the most common malignant tumor in the central nervous system. Evidence shows that clinical efficacy of immunotherapy is closely related to the tumor microenvironment. This study aims to establish a microenvironment-related genes (MRGs) model to predict the prognosis of patients with Grade II/III gliomas. Gene expression profile and clinical data of 459 patients with Grade II/III gliomas were extracted from The Cancer Genome Atlas. Then according to the immune/stromal scores generated by the ESTIMATE algorithm, the patients were scored one by one. Weighted gene co-expression network analysis (WGCNA) was used to construct a gene co-expression network to identify potential biomarkers for predicting the prognosis of patients. When adjusting clinical features including age, histology, grading, IDH status, we found that these features were independently associated with survival. The predicted value of the prognostic model was then verified in 440 samples in CGGA part B dataset and 182 samples in CGGA part C dataset by univariate and multivariate cox analysis. The clinical samples of 10 patients further confirmed our signature. Our findings suggested the eight-MRGs signature identified in this study are valuable prognostic predictors for patients with Grade II/III glioma.
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50
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Systemic analyses of expression patterns and clinical features for GIMAPs family members in lung adenocarcinoma. Aging (Albany NY) 2020; 12:20413-20431. [PMID: 33115964 PMCID: PMC7655191 DOI: 10.18632/aging.103836] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/14/2020] [Indexed: 12/22/2022]
Abstract
GTPase of immunity-associated proteins (GIMAPs) are frequently prescribed as important components of immune regulation complexes, which were known to play key roles in lung adenocarcinoma. However, little is known about the function of distinct GIMAPs in lung adenocarcinoma. To address this issue, this study investigated the biological function and pathway of GIMAPs in lung adenocarcinoma using multiple public databases. Absent expression of GIMAPs was found in lung adenocarcinoma at mRNA and protein levels. While a purity-corrected value uncovered that all GIMAPs were positively associated with the immune infiltration of lung adenocarcinoma. Furthermore, the expressions of GIMAPs were considered to be negatively associated with clinical cancer stages, patient’s gender and pathological tumor grades in patients with lung adenocarcinoma. Besides, higher mRNA expression of GIMAPs was significantly associated with longer overall survival of patients with lung adenocarcinoma. Taken together, these results may enable GIMAPs family members as diagnostic and survival biomarker candidates or even potential therapeutic targets for patients with lung adenocarcinoma.
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