1
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Lu J, Rui J, Xu XY, Shen JK. Exploring the Role of Neutrophil-Related Genes in Osteosarcoma via an Integrative Analysis of Single-Cell and Bulk Transcriptome. Biomedicines 2024; 12:1513. [PMID: 39062086 PMCID: PMC11274533 DOI: 10.3390/biomedicines12071513] [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: 05/29/2024] [Revised: 06/29/2024] [Accepted: 07/05/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND The involvement of neutrophil-related genes (NRGs) in patients with osteosarcoma (OS) has not been adequately explored. In this study, we aimed to examine the association between NRGs and the prognosis as well as the tumor microenvironment of OS. METHODS The OS data were obtained from the TARGET-OS and GEO database. Initially, we extracted NRGs by intersecting 538 NRGs from single-cell RNA sequencing (scRNA-seq) data between aneuploid and diploid groups, as well as 161 up-regulated differentially expressed genes (DEGs) from the TARGET-OS datasets. Subsequently, we conducted Least Absolute Shrinkage and Selection Operator (Lasso) analyses to identify the hub genes for constructing the NRG-score and NRG-signature. To assess the prognostic value of the NRG signatures in OS, we performed Kaplan-Meier analysis and generated time-dependent receiver operating characteristic (ROC) curves. Gene enrichment analysis (GSEA) and gene set variation analysis (GSVA) were utilized to ascertain the presence of tumor immune microenvironments (TIMEs) and immunomodulators (IMs). Additionally, the KEGG neutrophil signaling pathway was evaluated using ssGSEA. Subsequently, PCR and IHC were conducted to validate the expression of hub genes and transcription factors (TFs) in K7M2-induced OS mice. RESULTS FCER1G and C3AR1 have been identified as prognostic biomarkers for overall survival. The findings indicate a significantly improved prognosis for OS patients. The effectiveness and precision of the NRG signature in prognosticating OS patients were validated through survival ROC curves and an external validation dataset. The results clearly demonstrate that patients with elevated NRG scores exhibit decreased levels of immunomodulators, stromal score, immune score, ESTIMATE score, and infiltrating immune cell populations. Furthermore, our findings substantiate the potential role of SPI1 as a transcription factor in the regulation of the two central genes involved in osteosarcoma development. Moreover, our analysis unveiled a significant correlation and activation of the KEGG neutrophil signaling pathway with FCER1G and C3AR1. Notably, PCR and IHC demonstrated a significantly higher expression of C3AR1, FCER1G, and SPI1 in Balb/c mice induced with K7M2. CONCLUSIONS Our research emphasizes the significant contribution of neutrophils within the TIME of osteosarcoma. The newly developed NRG signature could serve as a good instrument for evaluating the prognosis and therapeutic approach for OS.
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Affiliation(s)
- Jing Lu
- Department of Radiology, The Second Affiliated Hospital of Soochow University, Suzhou 215025, China;
- Institute of Diagnostic and Interventional Radiology, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200235, China; (J.R.); (X.-Y.X.)
| | - Jiang Rui
- Institute of Diagnostic and Interventional Radiology, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200235, China; (J.R.); (X.-Y.X.)
| | - Xiao-Yu Xu
- Institute of Diagnostic and Interventional Radiology, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200235, China; (J.R.); (X.-Y.X.)
| | - Jun-Kang Shen
- Department of Radiology, The Second Affiliated Hospital of Soochow University, Suzhou 215025, China;
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2
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Peng X, Lu X, Yang D, Liu J, Wu H, Peng H, Zhang Y. A novel CD8+ T cell-related gene signature as a prognostic biomarker in hepatocellular carcinoma. Medicine (Baltimore) 2024; 103:e37496. [PMID: 38489709 PMCID: PMC10939595 DOI: 10.1097/md.0000000000037496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 12/16/2023] [Accepted: 02/14/2024] [Indexed: 03/17/2024] Open
Abstract
CD8+ T cells have great roles in tumor suppression and elimination of various tumors including hepatocellular carcinoma (HCC). Nonetheless, potential prognostic roles of CD8+ T cell-related genes (CD8Gs) in HCC remains unknown. In our study, 416 CD8Gs were identified in HCC, which were enriched in inflammatory and immune signaling pathways. Using The Cancer Genome Atlas dataset, a 5-CD8Gs risk model (KLRB1, FYN, IL2RG, FCER1G, and DGKZ) was constructed, which was verified in International Cancer Genome Consortium and gene expression omnibus datasets. Furthermore, we found that overall survival was independently correlated with the CD8Gs signature, and it was associated with immune- and cancer-related signaling pathways and immune cells infiltration. Finally, drug sensitivity data indicated that 10 chemotherapeutic drugs held promise as therapeutics for HCC patients with high-risk. In conclusion, multi-databases analysis showed that 5-CD8Gs and their signature could be an indicator to predict candidate drugs for HCC therapy.
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Affiliation(s)
- Xiaozhen Peng
- School of Public Health & Laboratory Medicine, Hunan University of Medicine, Huaihua, China
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, Hunan University of Medicine, Huaihua, China
| | - Xingjun Lu
- School of Public Health & Laboratory Medicine, Hunan University of Medicine, Huaihua, China
| | - Daqing Yang
- School of Public Health & Laboratory Medicine, Hunan University of Medicine, Huaihua, China
| | - Jinyan Liu
- Hunan Normal University, Changsha, China
| | - Honglin Wu
- School of Public Health & Laboratory Medicine, Hunan University of Medicine, Huaihua, China
| | - Hong Peng
- Medical School, Huanghe Science & Technology College, Zhengzhou, China
| | - Yiya Zhang
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
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3
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Sun J, Xi L, Zhang D, Gao F, Wang L, Yang G. A novel tumor immunotherapy-related signature for risk stratification, prognosis prediction, and immune status in hepatocellular carcinoma. Sci Rep 2023; 13:18709. [PMID: 37907783 PMCID: PMC10618198 DOI: 10.1038/s41598-023-46252-3] [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: 06/13/2023] [Accepted: 10/30/2023] [Indexed: 11/02/2023] Open
Abstract
Immunotherapy as a strategy to deal with cancer is increasingly being used clinically, especially in hepatocellular carcinoma (HCC). We aim to create an immunotherapy-related signature that can play a role in predicting HCC patients' survival and therapeutic outcomes. Immunotherapy-related genes were discovered first. Clinical information and gene expression data were extracted from GSE140901. By a series of bioinformatics methods to analyze, overlapping genes were used to build an immunotherapy-related signature that could contribute to predict both the prognosis of people with hepatocellular carcinoma and responder to immune checkpoint blockade therapy of them in TCGA database. Differences of the two groups in immune cell subpopulations were then compared. Furthermore, A nomogram was constructed, based on the immunotherapy-related signature and clinicopathological features, and proved to be highly predictive. Finally, immunohistochemistry assays were performed in HCC tissue and normal tissue adjacent tumors to verify the differences of the four genes expression. As a result of this study, a prognostic protein profile associated with immunotherapy had been created, which could be applied to predict patients' response to immunotherapy and may provide a new perspective as clinicians focus on non-apoptotic treatment for patients with HCC.
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Affiliation(s)
- Jianping Sun
- Department of Pathology, Zhengzhou YIHE Hospital, Zhengzhou, 450000, Henan Province, China
| | - Lefeng Xi
- Department of Pathology, Zhengzhou YIHE Hospital, Zhengzhou, 450000, Henan Province, China
| | - Dechen Zhang
- Department of Pathology, Zhengzhou YIHE Hospital, Zhengzhou, 450000, Henan Province, China
| | - Feipei Gao
- Department of Pathology, Zhengzhou YIHE Hospital, Zhengzhou, 450000, Henan Province, China
| | - Liqin Wang
- Department of Pathology, Zhengzhou YIHE Hospital, Zhengzhou, 450000, Henan Province, China
| | - Guangying Yang
- Department of Pathology, Zhengzhou YIHE Hospital, Zhengzhou, 450000, Henan Province, China.
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4
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Muccioli S, Brillo V, Varanita T, Rossin F, Zaltron E, Velle A, Alessio G, Angi B, Severin F, Tosi A, D'Eletto M, Occhigrossi L, Falasca L, Checchetto V, Ciaccio R, Fascì A, Chieregato L, Rebelo AP, Giacomello M, Rosato A, Szabò I, Romualdi C, Piacentini M, Leanza L. Transglutaminase Type 2-MITF axis regulates phenotype switching in skin cutaneous melanoma. Cell Death Dis 2023; 14:704. [PMID: 37898636 PMCID: PMC10613311 DOI: 10.1038/s41419-023-06223-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 10/30/2023]
Abstract
Skin cutaneous melanoma (SKCM) is the deadliest form of skin cancer due to its high heterogeneity that drives tumor aggressiveness. Melanoma plasticity consists of two distinct phenotypic states that co-exist in the tumor niche, the proliferative and the invasive, respectively associated with a high and low expression of MITF, the master regulator of melanocyte lineage. However, despite efforts, melanoma research is still far from exhaustively dissecting this phenomenon. Here, we discovered a key function of Transglutaminase Type-2 (TG2) in regulating melanogenesis by modulating MITF transcription factor expression and its transcriptional activity. Importantly, we demonstrated that TG2 expression affects melanoma invasiveness, highlighting its positive value in SKCM. These results suggest that TG2 may have implications in the regulation of the phenotype switching by promoting melanoma differentiation and impairing its metastatic potential. Our findings offer potential perspectives to unravel melanoma vulnerabilities via tuning intra-tumor heterogeneity.
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Affiliation(s)
- Silvia Muccioli
- Department of Biology, University of Padua, Padua, Italy
- Laboratory of Translational Research, Azienda USL - IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | | | | | - Federica Rossin
- Department of Biology, University of Rome 'Tor Vergata', Rome, Italy
| | | | - Angelo Velle
- Department of Biology, University of Padua, Padua, Italy
| | | | - Beatrice Angi
- Department of Biology, University of Padua, Padua, Italy
| | | | - Anna Tosi
- Immunology and Molecular Oncology Diagnostics, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Manuela D'Eletto
- Department of Biology, University of Rome 'Tor Vergata', Rome, Italy
| | - Luca Occhigrossi
- Department of Biology, University of Rome 'Tor Vergata', Rome, Italy
| | - Laura Falasca
- National Institute for Infectious Diseases IRCCS "Lazzaro Spallanzani", Rome, Italy
| | | | | | - Amelia Fascì
- Department of Biology, University of Padua, Padua, Italy
| | | | | | | | - Antonio Rosato
- Immunology and Molecular Oncology Diagnostics, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
- Department of Surgery, Oncology and Gastroenterology (DiSCOG), University of Padua, Padua, Italy
| | - Ildikò Szabò
- Department of Biology, University of Padua, Padua, Italy
| | | | - Mauro Piacentini
- Department of Biology, University of Rome 'Tor Vergata', Rome, Italy
- National Institute for Infectious Diseases IRCCS "Lazzaro Spallanzani", Rome, Italy
| | - Luigi Leanza
- Department of Biology, University of Padua, Padua, Italy.
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5
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Dong W, Wang N, Qi Z. Advances in the application of neuroinflammatory molecular imaging in brain malignancies. Front Immunol 2023; 14:1211900. [PMID: 37533851 PMCID: PMC10390727 DOI: 10.3389/fimmu.2023.1211900] [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: 04/25/2023] [Accepted: 06/27/2023] [Indexed: 08/04/2023] Open
Abstract
The prevalence of brain cancer has been increasing in recent decades, posing significant healthcare challenges. The introduction of immunotherapies has brought forth notable diagnostic imaging challenges for brain tumors. The tumor microenvironment undergoes substantial changes in induced immunosuppression and immune responses following the development of primary brain tumor and brain metastasis, affecting the progression and metastasis of brain tumors. Consequently, effective and accurate neuroimaging techniques are necessary for clinical practice and monitoring. However, patients with brain tumors might experience radiation-induced necrosis or other neuroinflammation. Currently, positron emission tomography and various magnetic resonance imaging techniques play a crucial role in diagnosing and evaluating brain tumors. Nevertheless, differentiating between brain tumors and necrotic lesions or inflamed tissues remains a significant challenge in the clinical diagnosis of the advancements in immunotherapeutics and precision oncology have underscored the importance of clinically applicable imaging measures for diagnosing and monitoring neuroinflammation. This review summarizes recent advances in neuroimaging methods aimed at enhancing the specificity of brain tumor diagnosis and evaluating inflamed lesions.
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Affiliation(s)
- Wenxia Dong
- Department of Radiology, The First People’s Hospital of Linping District, Hangzhou, China
| | - Ning Wang
- Department of Medical Imaging, Jining Third People’s Hospital, Jining, Shandong, China
| | - Zhe Qi
- Department of Radiology, Zibo Central Hospital, Zibo, Shandong, China
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6
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Yang R, Chen Z, Liang L, Ao S, Zhang J, Chang Z, Wang Z, Zhou Y, Duan X, Deng T. Fc Fragment of IgE Receptor Ig (FCER1G) acts as a key gene involved in cancer immune infiltration and tumour microenvironment. Immunology 2023; 168:302-319. [PMID: 36054819 DOI: 10.1111/imm.13557] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 07/07/2022] [Indexed: 01/17/2023] Open
Abstract
Although recent studies have revealed the relationship between Fc Fragment of IgE Receptor Ig (FCER1G) and human tumours, there is still a lack of a more comprehensive pan-cancer analysis of FCER1G as an immune-related gene. In this study, we investigated the expression pattern and prognostic value of FCER1G based on multiple databases. Subsequently, we further explored the role of FCER1G in tumour proliferation and metastasis, as well as its genomic alterations and DNA methylation levels, we next assessed the association between FCER1G and the immune infiltrating cells of the tumour microenvironment in different cancers and verified it by immunohistochemical staining. The correlation between FCER1G and immune checkpoint genes expression and its predictive power in the immune checkpoint blockade treatment cohorts were used to evaluate the importance of FCER1G in immunotherapy. Enrichment analysis of FCER1G-associated partners was also performed. In addition, we substantiated the expression of FCER1G in specific cell types of different tumours using single-cell RNA sequencing data from different databases. Our research results showed that FCER1G is up-regulated in most tumour. Positive associations were found between FCER1G expression and tumour prognosis, proliferation, and metastasis, we also found that FCER1G is closely related to the tumour microenvironment and tumour immunity. Moreover, FCER1G-associated partners were enriched in pathways associated with neutrophils activation. Finally, we confirmed that FCER1G was mainly expressed in monocyte/macrophages of the tumour microenvironment. In conclusion, our findings provided a comprehensive understanding of FCER1G in oncogenesis and tumour immunology among various tumours and demonstrated its potential value in prognosis prediction and tumour immunotherapy.
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Affiliation(s)
- Riwei Yang
- Department of Urology and Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Zude Chen
- Department of Urology and Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Leqi Liang
- Department of Urology and Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Shan Ao
- Department of Urology and Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Jinhu Zhang
- Department of Urology and Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Zhenglin Chang
- Department of Urology and Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Zuomin Wang
- Department of Urology and Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Yuhao Zhou
- Department of Urology and Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Xiaolu Duan
- Department of Urology and Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Tuo Deng
- Department of Urology and Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
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7
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Li T, Liu T, Zhao Z, Pan Y, Xu X, Zhang Y, Zhan S, Zhou S, Zhu W, Guo H, Yang R. Antifungal immunity mediated by C-type lectin receptors may be a novel target in immunotherapy for urothelial bladder cancer. Front Immunol 2022; 13:911325. [PMID: 36131933 PMCID: PMC9483128 DOI: 10.3389/fimmu.2022.911325] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 07/18/2022] [Indexed: 11/29/2022] Open
Abstract
Immunotherapies, such as immune-checkpoint blockade and adoptive T-cell therapy, offer novel treatment options with good efficacy for patients with urothelial bladder cancer. However, heterogeneity and therapeutic resistance have limited the use of immunotherapy. Further research into immune-regulatory mechanisms in bladder cancer is urgently required. Emerging evidence demonstrates that the commensal microbiota and its interactions with host immunity play pivotal roles in a variety of physiological and pathological processes, including in cancer. The gut microbiota has been identified as a potentially effective target of treatment that can be synergized with immunotherapy. The urothelial tract is also a key site for multiple microbes, although the immune-regulatory role of the urinary microbiome in the process of carcinogenesis of bladder cancer remains to be elucidated. We performed a comprehensive analysis of the expression and biological functions of C-type lectin receptors (CLRs), which have been recognized as innate pathogen-associated receptors for fungal microbiota, in bladder cancer. In line with previous research on fungal colonization of the urothelial tract, we found that CLRs, including Dectin-1, Dectin-2, Dectin-3, and macrophage-inducible Ca2+-dependent lectin receptor (Mincle), had a significant association with immune infiltration in bladder cancer. Multiple innate and adaptive pathways are positively correlated with the upregulation of CLRs. In addition, we found a significant correlation between the expression of CLRs and a range of immune-checkpoint proteins in bladder cancer. Based on previous studies and our findings, we hypothesize that the urinary mycobiome plays a key role in the pathogenesis of bladder cancer and call for more research on CLR-mediated anti-fungal immunity against bladder cancer as a novel target for immunotherapy in urothelial bladder cancer.
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Affiliation(s)
- Tianhang Li
- Department of Urology, Affiliated Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Tianyao Liu
- Department of Urology, Affiliated Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Zihan Zhao
- Department of Urology, Affiliated Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Yuchen Pan
- State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School, Nanjing University, Nanjing, China
| | - Xinyan Xu
- Department of Urology, Affiliated Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Yulin Zhang
- Department of Urology, Affiliated Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Shoubin Zhan
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Shengkai Zhou
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Wenjie Zhu
- Department of Urology, Affiliated Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Hongqian Guo
- Department of Urology, Affiliated Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
- *Correspondence: Rong Yang, ; Hongqian Guo,
| | - Rong Yang
- Department of Urology, Affiliated Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
- *Correspondence: Rong Yang, ; Hongqian Guo,
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8
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Li R, Zhao W, Liang R, Jin C, Xiong H. Identification and Validation of a Novel Tumor Microenvironment-Related Prognostic Signature of Patients With Hepatocellular Carcinoma. Front Mol Biosci 2022; 9:917839. [PMID: 35847972 PMCID: PMC9280086 DOI: 10.3389/fmolb.2022.917839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/05/2022] [Indexed: 12/12/2022] Open
Abstract
Background: In recent years, immunotherapy has changed the therapeutic landscape of hepatocellular carcinoma (HCC). Since the efficacy of immunotherapy is closely related to the tumor microenvironment (TME), in this study, we constructed a prognostic model based on TME to predict the prognosis and immunotherapy effect of HCC patients. Methods: Transcriptome and follow-up data of 374 HCC patients were acquired from the TCGA Cancer Genome Atlas (TCGA) database. The immune/stromal/estimate scores (TME scores) and tumor purity were calculated using the ESTIMATE algorithm and the module most associated with TME scores were screened by the weighted gene co-expression network analysis (WGCNA). A TME score-related prognostic model was constructed and patients were divided into a high-risk group and a low-risk group. Kaplan-Meier survival curves and receiver operator characteristic curve (ROC) were used to evaluate the performance of the TME risk prognostic model and validated with the external database International Cancer Genome Consortium (ICGC) cohort. Combined with clinicopathologic factors, a prognostic nomogram was established. The nomogram’s ability to predict prognosis was assessed by ROC, calibration curve, and the decision curve analysis (DCA). Gene Set Enrichment Analyses (GSEA) were conducted to explore the underlying biological functions and pathways of this risk signature. Moreover, the possible correlation of risk signature with TME immune cell infiltration, immune checkpoint inhibitor (ICI) treatment response, single-nucleotide polymorphisms (SNPs), and drug sensitivity were assessed. Finally, real-time PCR was used to verify the gene expression levels in normal liver cells and cancer cells. Results: KM survival analysis results indicated that high immune/stromal/estimate score groups were closely associated with a better prognosis, while the tumor purity showed a reverse trend (p < 0.01). WGCNA demonstrated that the yellow module was significantly correlated with the TME score. The 5-genes TME risk signature was built to predict the prognosis of patients with HCC including DAB2, IL18RAP, RAMP3, FCER1G, and LHFPL2. Patients with a low-risk score have higher levels of tumor-infiltrating immune cells and higher expression of immune checkpoints, which may be more sensitive to immunotherapy. Conclusion: It provided a theoretical basis for predicting the prognosis and personalized treatment of patients with HCC.
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Affiliation(s)
- Rui Li
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Weiheng Zhao
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Rui Liang
- Biological Engineering Academy, Chongqing University, Chongqing, China
| | - Chen Jin
- Department of Epidemiology and Biostatistics, School of Public Health and Management, Wenzhou Medical University, Wenzhou, China
- *Correspondence: Chen Jin, ; Huihua Xiong,
| | - Huihua Xiong
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Chen Jin, ; Huihua Xiong,
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9
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Promising prognostic value of Transglutaminase type 2 and its correlation with tumor-infiltrating immune cells in skin cutaneous melanoma. Cell Death Dis 2022; 8:294. [PMID: 35725560 PMCID: PMC9209462 DOI: 10.1038/s41420-022-01087-1] [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: 04/20/2022] [Revised: 06/05/2022] [Accepted: 06/09/2022] [Indexed: 12/03/2022]
Abstract
Tissue Transglutaminases (TGs) are crosslinking enzymes with pleiotropic functions that have been linked to the development and progression of numerous cancers, with a recent focus on their ability to remodel the tumor microenvironment. Although several pieces of evidence demonstrated their importance in the regulation of the major signaling pathways that control oncogenesis, the correlation between TGs with clinical and pathological features remains controversial and to be further explored. Moreover, an assessment of the TGs alterations together with a functional analysis associated with clinical features and prognostic values are still lacking and would help to understand these intricacies, particularly in human cancers. In the present study, we processed data from numerous public datasets to investigate TGs distribution and prognostic signature in cancer patients. Here, we found that skin cutaneous melanoma (SKCM) shows the highest abundance of TGs mutations among the other human cancers. Interestingly, among all the TGs, TG2 is the only member whose expression is associated with a better overall survival in SKCM, although its expression increases with the worsening of the tumor phenotype. Our analysis revealed a strong positive association between TG2 expression and anti-tumoral immune response, which would explain the relationship between high mRNA levels and better overall survival. Our data suggest that TG2 may be presented as a new promising immune biomarker of prognosis in SKCM, which may contribute to identifying patients who would benefit the most from adjuvant immunotherapy.
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10
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Xiang X, Gao LM, Zhang Y, Tang Y, Zhao S, Liu W, Ye Y, Zhang W. Identification of FCER1G related to Activated Memory CD4 + T Cells Infiltration by Gene Co-expression Network and Construction of a Risk Prediction Module in Diffuse Large B-Cell Lymphoma. Front Genet 2022; 13:849422. [PMID: 35711924 PMCID: PMC9196638 DOI: 10.3389/fgene.2022.849422] [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: 04/26/2022] [Indexed: 02/05/2023] Open
Abstract
Diffuse large B cell lymphoma (DLBCL) is a group of biologically heterogeneous tumors with different prognoses. The tumor microenvironment plays a vital role in the tumorigenesis and development of DLBCL, and activated memory CD4+ T cells are an essential component of immunological cells in the lymphoma microenvironment. So far, there are few reports about activated memory CD4+T cells infiltration and related genes in the DLBCL tumor microenvironment. This study obtained the mRNA expression profile information of the testing GSE87371 dataset and another six validation datasets (GSE53786, GSE181063, GSE10846, GSE32918, GSE32018, GSE9327, GSE3892, TCGA-DLBC) from the GEO and TCGA databases. Weighted Gene Co-expression Network Analysis (WGCNA) screened gene module associated with activated memory CD4+ T cells infiltration. CIBERSORT and TIMER (immune cells infiltrating estimation analysis tools) were used to identify the relationship between activated memory CD4+ T cells and genes associated with immune infiltrating cells in the tumor microenvironment. The least absolute shrinkage and selection operator (LASSO) built the risk prediction model and verified it using nomogram and Kaplan-Meier analysis. Further functional characterization includes Gene Ontology, KEGG pathway analysis and Gene Set Enrichment Analysis (GSEA) to investigate the role and underlying mechanisms of these genes. These results suggest that the expression of FCER1G can reflect the invasion of activated memory CD4+ T cells in DLBCL, which provides a new idea for studying the tumor microenvironment and may become a potential predictive biomarker for the assessment of DLBCL.
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Affiliation(s)
- Xiaoyu Xiang
- Department of Pathology, West China Hospital of Sichuan University, Chengdu, China
| | - Li-Min Gao
- Department of Pathology, West China Hospital of Sichuan University, Chengdu, China
| | - Yuehua Zhang
- Department of Pathology, West China Hospital of Sichuan University, Chengdu, China
| | - Yuan Tang
- Department of Pathology, West China Hospital of Sichuan University, Chengdu, China
| | - Sha Zhao
- Department of Pathology, West China Hospital of Sichuan University, Chengdu, China
| | - Weiping Liu
- Department of Pathology, West China Hospital of Sichuan University, Chengdu, China
| | - Yunxia Ye
- Department of Pathology, West China Hospital of Sichuan University, Chengdu, China
| | - Wenyan Zhang
- Department of Pathology, West China Hospital of Sichuan University, Chengdu, China
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Immunotherapeutic Approaches for Glioblastoma Treatment. Biomedicines 2022; 10:biomedicines10020427. [PMID: 35203636 PMCID: PMC8962267 DOI: 10.3390/biomedicines10020427] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 02/05/2022] [Accepted: 02/08/2022] [Indexed: 11/17/2022] Open
Abstract
Glioblastoma remains a challenging disease to treat, despite well-established standard-of-care treatments, with a median survival consistently of less than 2 years. In this review, we delineate the unique disease-specific challenges for immunotherapies, both brain-related and non-brain-related, which will need to be adequately overcome for the development of effective treatments. We also review current immunotherapy treatments, with a focus on clinical applications, and propose future directions for the field of GBM immunotherapy.
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Yearley AG, Iorgulescu JB, Chiocca EA, Peruzzi PP, Smith TR, Reardon DA, Mooney MA. The current state of glioma data registries. Neurooncol Adv 2022; 4:vdac099. [DOI: 10.1093/noajnl/vdac099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
The landscape of glioma research has evolved in the past 20 years to include numerous large, multi-institutional, database efforts compiling either clinical data on glioma patients, molecular data on glioma specimens, or a combination of both. While these strategies can provide a wealth of information for glioma research, obtaining information regarding data availability and access specifications can be challenging.
Methods
We reviewed the literature for ongoing clinical, molecular, and combined database efforts related to glioma research to provide researchers with a curated overview of the current state of glioma database resources.
Results
We identified and reviewed a total of 20 databases with data collection spanning from 1975 to 2022. Surveyed databases included both low- and high-grade gliomas, and data elements included over 100 clinical variables and 12 molecular data types. Select database strengths included large sample sizes and a wide variety of variables available, while limitations of some databases included complex data access requirements and a lack of glioma-specific variables.
Conclusions
This review highlights current databases and registries and their potential utility in clinical and genomic glioma research. While many high-quality resources exist, the fluid nature of glioma taxonomy makes it difficult to isolate a large cohort of patients with a pathologically confirmed diagnosis. Large, well-defined, and publicly available glioma datasets have the potential to expand the reach of glioma research and drive the field forward.
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Affiliation(s)
- Alexander G Yearley
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School , Boston, Massachusetts , USA
| | - Julian Bryan Iorgulescu
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School , Boston, Massachusetts , USA
- Department of Medical Oncology, Dana-Farber Cancer Institute , Boston, Massachusetts , USA
| | - Ennio Antonio Chiocca
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School , Boston, Massachusetts , USA
| | - Pier Paolo Peruzzi
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School , Boston, Massachusetts , USA
| | - Timothy R Smith
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School , Boston, Massachusetts , USA
| | - David A Reardon
- Center for Neuro-Oncology, Dana-Farber Cancer Institute , Boston, Massachusetts , USA
| | - Michael A Mooney
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School , Boston, Massachusetts , USA
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Fan Y, Hou J, Liu X, Han B, Meng Y, Liu B, Chen F, Shang Y, Cao P, Tan K. Integrated Bioinformatics Analysis Identifies Heat Shock Factor 2 as a Prognostic Biomarker Associated With Immune Cell Infiltration in Hepatocellular Carcinoma. Front Genet 2021; 12:668516. [PMID: 34917120 PMCID: PMC8669829 DOI: 10.3389/fgene.2021.668516] [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: 03/05/2021] [Accepted: 11/10/2021] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common malignancies and ranks as the second leading cause of cancer-related mortality worldwide. Heat shock factor 2 (HSF2) is a transcription factor that plays a critical role in development, particularly corticogenesis and spermatogenesis. However, studies examining the expression and prognostic value of HSF2 and its association with tumor-infiltrating immune cells in HCC are still rare. In the present study, we found that HSF2 expression was significantly upregulated in HCC tissues compared with normal liver tissues using the TCGA, ICGC, GEO, UALCAN, HCCDB and HPA databases. High HSF2 expression was associated with shorter survival of patients with HCC. Cox regression analyses and nomogram were used to evaluate the association of HSF2 expression with the prognosis of patients with HCC. Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and gene set enrichment analysis (GSEA) revealed that HSF2 was associated with various signaling pathways, including the immune response. Notably, HSF2 expression was significantly correlated with the infiltration levels of different immune cells using the TIMER database and CIBERSORT algorithm. HSF2 expression also displayed a significant correlation with multiple immune marker sets in HCC tissues. Knockdown of HSF2 significantly inhibited the proliferation, migration, invasion and colony formation ability of HCC cells. In summary, we explored the clinical significance of HSF2 and provided a therapeutic basis for the early diagnosis, prognostic judgment, and immunotherapy of HCC.
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Affiliation(s)
- Yumei Fan
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Jiajie Hou
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Xiaopeng Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China.,Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Bihui Han
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Yanxiu Meng
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Bing Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Fei Chen
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Yanan Shang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Pengxiu Cao
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Ke Tan
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
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14
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Zhang A, Xu H, Zhang Z, Liu Y, Han X, Yuan L, Ni Y, Gao S, Xu Y, Chen S, Jiang J, Chen Y, Zhang X, Lou M, Zhang J. Establishment of a nomogram with EMP3 for predicting clinical outcomes in patients with glioma: A bi-center study. CNS Neurosci Ther 2021; 27:1238-1250. [PMID: 34268874 PMCID: PMC8446216 DOI: 10.1111/cns.13701] [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: 03/03/2021] [Revised: 06/10/2021] [Accepted: 06/16/2021] [Indexed: 12/20/2022] Open
Abstract
Aim To demonstrate the clinical value of epithelial membrane protein 3 (EMP3) with bioinformatic analysis and clinical data, and then to establish a practical nomogram predictive model with bicenter validation. Methods The data from CGGA and TCGA database were used to analyze the expression of EMP3 and its correlation with clinical prognosis. Then, we analyzed EMP3 expression in samples from 179 glioma patients from 2013 to 2017. Univariate and multivariate cox regression were used to predict the prognosis with multiple factors. Finally, a nomogram to predict poor outcomes was formulated. The accuracy and discrimination of nomograms were determined with ROC curve and calibration curve in training and validation cohorts. Results EMP3 was significantly higher in higher‐grade glioma and predicted poor prognosis. In multivariate analysis, high expression of EMP3 (HR = 2.842, 95% CI 1.984–4.071), WHO grade (HR = 1.991, 95% CI 1.235–3.212), and IDH1 mutant (HR = 0.503, 95% CI 0.344–0.737) were included. The nomogram was constructed based on the above features, which represented great predictive value in clinical outcomes. Conclusion This study demonstrated EMP3 as a novel predictor for clinical progression and clinical outcomes in glioma. Moreover, the nomogram with EMP3 expression represented a practical approach to provide individualized risk assessment for glioma patients.
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Affiliation(s)
- Anke Zhang
- Department of Neurosurgery, School of Medicine, The Second Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Houshi Xu
- Department of Neurosurgery, School of Medicine, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Zeyu Zhang
- Department of Neurosurgery, School of Medicine, The Second Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Yibo Liu
- Department of Neurosurgery, School of Medicine, The Second Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Xiaying Han
- Department of Orthopedics, School of Medicine, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
| | | | - Yunjia Ni
- Department of Neurosurgery, School of Medicine, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Shiqi Gao
- Department of Neurosurgery, School of Medicine, The Second Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Yuanzhi Xu
- Department of Neurosurgery, School of Medicine, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Sheng Chen
- Department of Neurosurgery, School of Medicine, The Second Affiliated Hospital, Zhejiang University, Hangzhou, China
| | | | - Yike Chen
- Department of Neurosurgery, School of Medicine, The Second Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Xiaotao Zhang
- Department of Neurosurgery, School of Medicine, The Second Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Meiqing Lou
- Department of Neurosurgery, School of Medicine, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jianmin Zhang
- Department of Neurosurgery, School of Medicine, The Second Affiliated Hospital, Zhejiang University, Hangzhou, China
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