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Lin WR, Liu WQ, Meng XY, Liu XT, Kou ZY, Li WL, Yang J. Identification of driving genes of familial adenomatous polyposis by differential gene expression analysis and weighted gene co-expression network analysis. Technol Health Care 2024; 32:1675-1696. [PMID: 38073344 PMCID: PMC11091565 DOI: 10.3233/thc-230719] [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: 06/01/2023] [Accepted: 10/07/2023] [Indexed: 05/12/2024]
Abstract
BACKGROUND Despite the advancement of new screening strategies and the advances in pharmacological therapies, the cancerization rates of familial adenomatous polyposis (FAP) are stable and even increased in the last years. Therefore, it necessitates additional research to characterize and understand the underlying mechanisms of FAP. OBJECTIVE To determine the genes that drive the pathogenesis of familial adenomatous polyposis (FAP). METHODS We performed on a cohort (GSE111156) gene profile, which consist of four group of gene expressions (the gene expressions of cancer, adenoma and normal tissue of duodenal cancer from patients with FAP were defined as Case N, Case A and Case C respectively, while that of adenoma tissue from patients with FAP who did not have duodenal cancer was Ctrl A). Tracking Tumor Immunophenotype (TIP) website was applied to reveal immune infiltration profile and signature genes of FAP. We merged the genes of key module (pink and midnight module) with signature genes to obtained the biomarkers related with FAP pathogenesis. The expression of these five biomarkers in FAP intratumoral region (IT) and tumor rim (TR) was detected with Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR). RESULTS In total, 220, 23 and 63 DEGs were determined in Cases C, A and N, in comparison to Ctrl A. In total, 196 and 10 DEGs were determined in Cases C and A, separately, as compared to Case N. A total of four biomarkers including CCL5, CD3G, CD2 and TLR3 were finally identified associated with pink module, while only one biomarker (KLF2) associated with midnight module was identified. All biomarkers were evidently raised in FAP IT tissues utilizing qRT-PCR. CONCLUSION We identified five potential biomarkers for pathogenesis of FAP to understand the fundamental mechanisms of FAP progression and revealed some probable targets for the diagnosis or treatment of FAP.
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Affiliation(s)
- Wan-Rong Lin
- Department of Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Wei-Qing Liu
- Department of Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Department of Internal Medicine-Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Xuan-Yu Meng
- Department of Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Xiao-Ting Liu
- Department of Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Zhi-Yong Kou
- Department of Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Wen-Liang Li
- Colorectal Cancer Clinical Research Center, Third Affiliated Hospital, Kunming Medical University, Kunming, Yunnan, China
| | - Jun Yang
- Department of Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
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Chaudhary B, Kumar P, Arya P, Singla D, Kumar V, Kumar D, S R, Wadhwa S, Gulati M, Singh SK, Dua K, Gupta G, Gupta MM. Recent Developments in the Study of the Microenvironment of Cancer and Drug Delivery. Curr Drug Metab 2023; 23:CDM-EPUB-128715. [PMID: 36627789 DOI: 10.2174/1389200224666230110145513] [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: 07/16/2022] [Revised: 09/20/2022] [Accepted: 11/29/2022] [Indexed: 01/12/2023]
Abstract
Cancer is characterized by disrupted molecular variables caused by cells that deviate from regular signal transduction. The uncontrolled segment of such cancerous cells annihilates most of the tissues that contact them. Gene therapy, immunotherapy, and nanotechnology advancements have resulted in novel strategies for anticancer drug delivery. Furthermore, diverse dispersion of nanoparticles in normal stroma cells adversely affects the healthy cells and disrupts the crosstalk of tumour stroma. It can contribute to cancer cell progression inhibition and, conversely, to acquired resistance, enabling cancer cell metastasis and proliferation. The tumour's microenvironment is critical in controlling the dispersion and physiological activities of nano-chemotherapeutics which is one of the targeted drug therapy. As it is one of the methods of treating cancer that involves the use of medications or other substances to specifically target and kill off certain subsets of malignant cells. A targeted therapy may be administered alone or in addition to more conventional methods of care like surgery, chemotherapy, or radiation treatment. The tumour microenvironment, stromatogenesis, barriers and advancement in the drug delivery system across tumour tissue are summarised in this review.
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Affiliation(s)
- Benu Chaudhary
- Guru Gobind Singh College of Pharmacy, Yamunanagar, Haryana, India
| | - Parveen Kumar
- Shri Ram College of Pharmacy, Karnal, Haryana, India
| | - Preeti Arya
- Guru Gobind Singh College of Pharmacy, Yamunanagar, Haryana, India
| | - Deepak Singla
- Guru Gobind Singh College of Pharmacy, Yamunanagar, Haryana, India
| | - Virender Kumar
- Swami Dayanand post graduate institute of Pharmaceutical Sciences, Rohtak, Haryana, India
| | - Davinder Kumar
- Swami Dayanand post graduate institute of Pharmaceutical Sciences, Rohtak, Haryana, India
| | - Roshan S
- Deccan College of Pharmacy, Hyderabad, India
| | - Sheetu Wadhwa
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Monica Gulati
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, 144411, India
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, Australia
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, NSW 2007, Australia
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, Australia
| | - Gaurav Gupta
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura, Mahal Road, Jaipur, India
- Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | - Madan Mohan Gupta
- School of Pharmacy, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad &Tobago, WI
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Xiao B, Li M, Cui M, Yin C, Zhang B. A large-scale screening and functional sorting of tumour microenvironment prognostic genes for breast cancer patients. Front Endocrinol (Lausanne) 2023; 14:1131525. [PMID: 36936167 PMCID: PMC10014861 DOI: 10.3389/fendo.2023.1131525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 02/14/2023] [Indexed: 03/04/2023] Open
Abstract
PURPOSE The aim of this study was to systematically establish a comprehensive tumour microenvironment (TME)-relevant prognostic gene and target miRNA network for breast cancer patients. METHODS Based on a large-scale screening of TME-relevant prognostic genes (760 genes) for breast cancer patients, the prognostic model was established. The primary TME prognostic genes were selected from the constructing database and verified in the testing database. The internal relationships between the potential TME prognostic genes and the prognosis of breast cancer patients were explored in depth. The associated miRNAs for the TME prognostic genes were generated, and the functions of each primary TME member were investigated in the breast cancer cell line. RESULTS Compared with sibling controls, breast cancer patients showed 55 differentially expressed TME prognostic genes, of which 31 were considered as protective genes, while the remaining 24 genes were considered as risk genes. According to the lambda values of the LASSO Cox analysis, the 15 potential TME prognostic genes were as follows: ENPEP, CCDC102B, FEZ1, NOS2, SCG2, RPLP2, RELB, RGS3, EMP1, PDLIM4, EPHA3, PCDH9, VIM, GFI1, and IRF1. Among these, there was a remarkable linear internal relationship for CCDC102B but non-linear relationships for others with breast cancer patient prognosis. Using the siRNA technique, we silenced the expression of each TME prognostic gene. Seven of the 15 TME prognostic genes (NOS2, SCG2, RGS3, EMP1, PDLIM4, PCDH9, and GFI1) were involved in enhancing cell proliferation, destroying cell apoptosis, promoting cell invasion, or migration in breast cancer. Six of them (CCDC102B, RPLP2, RELB, EPHA3, VIM, and IRF1) were favourable for maintaining cell invasion or migration. Only two of them (ENPEP and FEZ1) were favourable for the processes of cell proliferation and apoptosis. CONCLUSIONS This integrated study hypothesised an innovative TME-associated genetic functional network for breast cancer patients. The external relationships between these TME prognostic genes and the disease were measured. Meanwhile, the internal molecular mechanisms were also investigated.
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Affiliation(s)
- Bo Xiao
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Mingwei Li
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Mingxuan Cui
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Chengliang Yin
- Faculty of Medicine, Macau University of Science and Technology, Macau, Macau SAR, China
- *Correspondence: Bo Zhang, ; Chengliang Yin,
| | - Bo Zhang
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- *Correspondence: Bo Zhang, ; Chengliang Yin,
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Liu J, Yu F, Liu Z, Wang X, Li J. A Robust Prognostic Signature of Tumor Microenvironment in Colorectal Cancer. Cancer Biother Radiopharm 2022; 37:963-975. [PMID: 34551265 DOI: 10.1089/cbr.2021.0171] [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] [Indexed: 12/16/2022] Open
Abstract
Background: Colorectal cancer (CRC) has been a major public health problem. Tumor microenvironment (TME) greatly contributes to the heterogeneity of CRC and is crucial for the regulation of CRC progression. The authors' study aimed to develop a robust prognostic signature for CRC patients based on TME-related genes. Materials and Methods: Gene expression data and clinicopathologic information of CRC patients were collected from Gene Expression Omnibus and The Cancer Genome Atlas databases. TME-related genes with prognostic value were identified by Cox regression and bootstrap method. The authors used the prognostic genes to construct a robust prognostic model using the least absolute shrinkage and selection operator (LASSO) regression method. The immune and stromal cell abundance of CRC samples were estimated by a microenvironment cell populations-counter method. Results: Based on a training set that comprised 893 CRC samples and 4775 TME-related genes, they established a prognostic model consisting of 25 TME-related genes. With specific risk score formulae, the prognostic model divided CRC patients into high-risk and low-risk subgroups with significantly different survival, which were further confirmed in validation cohorts consisting of other 473 CRC cases or subpopulation of specific stages. The result of time-dependent receiver operating characteristic analysis demonstrated strong predictive accuracy of the prognostic model both in training and validation cohorts. Multivariate Cox regression analysis showed that the 25-gene signature was an independent prognostic factor for overall survival, which was validated through clinical subgroups analysis. Further analysis revealed that CRC samples of high-risk group was abundant of stromal-relevant processes and had a significantly higher proportion of fibroblasts and endothelial cells infiltration. Conclusion: The authors established a robust prognostic signature of 25 TME-related genes which may be an effective tool for prognostic prediction and CRC patient stratification to assist in making treatment decisions.
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Affiliation(s)
- Jingwen Liu
- Department of Pathology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, P.R. China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, P.R. China.,RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Fei Yu
- Emergency Department, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, P.R. China
| | - Zhao Liu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Xiaojing Wang
- Clinical Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China.,Department of Geriatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Jianming Li
- Department of Pathology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, P.R. China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, P.R. China.,RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, P.R. China
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Tiwari A, Trivedi R, Lin SY. Tumor microenvironment: barrier or opportunity towards effective cancer therapy. J Biomed Sci 2022; 29:83. [PMID: 36253762 PMCID: PMC9575280 DOI: 10.1186/s12929-022-00866-3] [Citation(s) in RCA: 84] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/01/2022] [Indexed: 12/24/2022] Open
Abstract
Tumor microenvironment (TME) is a specialized ecosystem of host components, designed by tumor cells for successful development and metastasis of tumor. With the advent of 3D culture and advanced bioinformatic methodologies, it is now possible to study TME’s individual components and their interplay at higher resolution. Deeper understanding of the immune cell’s diversity, stromal constituents, repertoire profiling, neoantigen prediction of TMEs has provided the opportunity to explore the spatial and temporal regulation of immune therapeutic interventions. The variation of TME composition among patients plays an important role in determining responders and non-responders towards cancer immunotherapy. Therefore, there could be a possibility of reprogramming of TME components to overcome the widely prevailing issue of immunotherapeutic resistance. The focus of the present review is to understand the complexity of TME and comprehending future perspective of its components as potential therapeutic targets. The later part of the review describes the sophisticated 3D models emerging as valuable means to study TME components and an extensive account of advanced bioinformatic tools to profile TME components and predict neoantigens. Overall, this review provides a comprehensive account of the current knowledge available to target TME.
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Affiliation(s)
- Aadhya Tiwari
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Rakesh Trivedi
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shiaw-Yih Lin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Zhao J, Galvez C, Beckermann KE, Johnson DB, Sosman JA. Novel insights into the pathogenesis and treatment of NRAS mutant melanoma. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2021; 6:281-294. [PMID: 34485698 PMCID: PMC8415440 DOI: 10.1080/23808993.2021.1938545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
INTRODUCTION NRAS was the first mutated oncogene identified in melanoma and is currently the second most common driver mutation in this malignancy. For patients with NRASmutant advanced stage melanoma refractory to immunotherapy or with contraindications to immune-based regimens, there are few therapeutic options including low-efficacy chemotherapy regimens and binimetinib monotherapy. Here, we review recent advances in preclinical studies of molecular targets for NRAS mutant melanoma as well as the failures and successes of early-phase clinical trials. While there are no targeted therapies for NRAS-driven melanoma, there is great promise in approaches combining MEK inhibition with inhibitors of the focal adhesion kinase (FAK), inhibitors of autophagy pathways, and pan-RAF inhibitors. AREAS COVERED This review surveys new developments in all aspects of disease pathogenesis and potential treatment - including those that have failed, stalled, or progressed through various phases of preclinical and clinical development. EXPERT OPINION There are no currently approved targeted therapies for BRAF wild-type melanoma patients harboring NRAS driver mutations though an array of agents are in early phase clinical trials. The diverse strategies taken exploit combined MAP kinase signaling blockade with inhibition of cell cycle mediators, inhibition of the autophagy pathway, and alteration of kinases involved in actin cytoskeleton signaling. Future advances of developmental therapeutics into late stage trials may yield new options beyond immunotherapy for patients with advanced stage disease and NRAS mutation status.
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Affiliation(s)
- Jeffrey Zhao
- Northwestern University Feinberg School of Medicine
| | - Carlos Galvez
- Northwestern Medicine, Division of Hematology and Oncology.,Robert H. Lurie Comprehensive Cancer Center
| | - Kathryn Eby Beckermann
- Vanderbilt University Medical Center, Department of Medicine, Division of Hematology and Oncology, 1301 Medical Center Drive, Nashville, 37232, USA
| | - Douglas B Johnson
- Vanderbilt University Medical Center, Department of Medicine, Division of Hematology and Oncology, 1301 Medical Center Drive, Nashville, 37232, USA
| | - Jeffrey A Sosman
- Northwestern Medicine, Division of Hematology and Oncology.,Robert H. Lurie Comprehensive Cancer Center
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7
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Farc O, Cristea V. An overview of the tumor microenvironment, from cells to complex networks (Review). Exp Ther Med 2021; 21:96. [PMID: 33363607 PMCID: PMC7725019 DOI: 10.3892/etm.2020.9528] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 09/29/2020] [Indexed: 01/13/2023] Open
Abstract
For a long period, cancer has been believed to be a gene disease, in which oncogenic and suppressor mutations accumulate gradually, finally leading to the malignant transformation of cells. This vision has changed in the last few years, the involvement of the tumor microenvironment, the non-malignant part of the tumors, as an important contributor to the malignant growth being now largely recognized. There is a consensus according to which the understanding of the tumor microenvironment is important as a means to develop new approaches in the therapy of cancer. In this context, the present study is a review of the different types of non-malignant cells that can be found in tumors, with their pro or antitumoral actions, presence in tumors and therapeutic targeting. These cells establish complex relations between them, through cytokines, exosomes, cell adhesion, co-stimulation and co-inhibition; these relations will also be examined in the present work.
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Affiliation(s)
- Ovidiu Farc
- Immunology Department, ‘Iuliu Hatieganu’ University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Victor Cristea
- Immunology Department, ‘Iuliu Hatieganu’ University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
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8
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Zhuang G, Zeng Y, Tang Q, He Q, Luo G. Identifying M1 Macrophage-Related Genes Through a Co-expression Network to Construct a Four-Gene Risk-Scoring Model for Predicting Thyroid Cancer Prognosis. Front Genet 2020; 11:591079. [PMID: 33193731 PMCID: PMC7658400 DOI: 10.3389/fgene.2020.591079] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/28/2020] [Indexed: 12/18/2022] Open
Abstract
Macrophages are key innate immune cells in the tumor microenvironment that regulate primary tumor growth, vascularization, metastatic spread and response to therapies. Macrophages can polarize into two different states (M1 and M2) with distinct phenotypes and functions. To investigate the known tumoricidal effects of M1 macrophages, we obtained RNA expression profiles and clinical data from The Cancer Genome Atlas Thyroid Cancer (TCGA-THCA). The proportions of immune cells in tumor samples were assessed using CIBERSORT, and weighted gene co-expression network analysis (WGCNA) was used to identify M1 macrophage-related modules. Univariate Cox analysis and LASSO-Cox regression analysis were performed, and four genes (SPP1, DHRS3, SLC11A1, and CFB) with significant differential expression were selected through GEPIA. These four genes can be considered hub genes. The four-gene risk-scoring model may be an independent prognostic factor for THCA patients. The validation cohort and the entire cohort confirmed the results. Univariate and multivariate Cox analysis was performed to identify independent prognostic factors for THCA. Finally, a prognostic nomogram was built based on the entire cohort, and the nomogram combining the risk score and clinical prognostic factors was superior to the nomogram with individual clinical prognostic factors in predicting overall survival. Time-dependent ROC curves and DCA confirmed that the combined nomogram is useful. Gene set enrichment analysis (GSEA) was used to elucidate the potential molecular functions of the high-risk group. Our study identified four genes associated with M1 macrophages and established a prognostic nomogram that predicts overall survival for patients with THCA, which may help determine clinical treatment options for different patients.
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Affiliation(s)
- Gaojian Zhuang
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
| | - Yu Zeng
- Department of Thyroid and Neck Tumor, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Qun Tang
- Department of Pathology, Hunan University of Chinese Medicine, Changsha, China
| | - Qian He
- Department of Neurosurgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Guoqing Luo
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
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Li Y, Gu J, Xu F, Zhu Q, Chen Y, Ge D, Lu C. Molecular characterization, biological function, tumor microenvironment association and clinical significance of m6A regulators in lung adenocarcinoma. Brief Bioinform 2020; 22:5916941. [PMID: 33003204 DOI: 10.1093/bib/bbaa225] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/03/2020] [Accepted: 08/19/2020] [Indexed: 12/17/2022] Open
Abstract
N6-methyladenosine (m6A) modification can regulate a variety of biological processes. However, the implications of m6A modification in lung adenocarcinoma (LUAD) remain largely unknown. Here, we systematically evaluated the m6A modification features in more than 2400 LUAD samples by analyzing the multi-omics features of 23 m6A regulators. We depicted the genetic variation features of m6A regulators, and found mutations of FTO and YTHDF3 were linked to worse overall survival. Many m6A regulators were aberrantly expressed in tumors, among which FTO, IGF2BP3, YTHDF1 and RBM15 showed consistent alteration features across 11 independent cohorts. Besides, the regulator-pathway interaction network demonstrated that m6A modification was associated with various biological pathways, including immune-related pathways. The correlation between m6A regulators and tumor microenvironment was also assessed. We found that LRPPRC was negatively correlated with most tumor-infiltrating immune cells. On the other hand, we established a scoring tool named m6Sig, which was positively correlated with PD-L1 expression and could reflect both the tumor microenvironment characterization and prognosis of LUAD patients. Comparison of CNV between high and low m6Sig groups revealed differences on chromosome 7. Application of m6Sig on an anti-PD-L1 immunotherapy cohort confirmed that the high m6Sig group demonstrated therapeutic advantages and clinical benefits. Our study indicated that m6A modification is involved in many aspects of LUAD and contributes to tumor microenvironment formation. A better understanding of m6A modification will provide more insights into the molecular mechanisms of LUAD and facilitate developing more effective personalized treatment strategies. A web application was built along with this study (http://www.bioinfo-zs.com/luadexpress/).
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Affiliation(s)
- Yin Li
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University
| | - Jie Gu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University
| | - Fengkai Xu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University
| | - Qiaoliang Zhu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University
| | - Yiwei Chen
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University
| | - Di Ge
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University
| | - Chunlai Lu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University
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Hao Shi, Yan KK, Ding L, Qian C, Chi H, Yu J. Network Approaches for Dissecting the Immune System. iScience 2020; 23:101354. [PMID: 32717640 PMCID: PMC7390880 DOI: 10.1016/j.isci.2020.101354] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/21/2020] [Accepted: 07/08/2020] [Indexed: 02/06/2023] Open
Abstract
The immune system is a complex biological network composed of hierarchically organized genes, proteins, and cellular components that combat external pathogens and monitor the onset of internal disease. To meet and ultimately defeat these challenges, the immune system orchestrates an exquisitely complex interplay of numerous cells, often with highly specialized functions, in a tissue-specific manner. One of the major methodologies of systems immunology is to measure quantitatively the components and interaction levels in the immunologic networks to construct a computational network and predict the response of the components to perturbations. The recent advances in high-throughput sequencing techniques have provided us with a powerful approach to dissecting the complexity of the immune system. Here we summarize the latest progress in integrating omics data and network approaches to construct networks and to infer the underlying signaling and transcriptional landscape, as well as cell-cell communication, in the immune system, with a focus on hematopoiesis, adaptive immunity, and tumor immunology. Understanding the network regulation of immune cells has provided new insights into immune homeostasis and disease, with important therapeutic implications for inflammation, cancer, and other immune-mediated disorders.
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Affiliation(s)
- Hao Shi
- Departments of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Koon-Kiu Yan
- Departments of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Liang Ding
- Departments of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Chenxi Qian
- Departments of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hongbo Chi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jiyang Yu
- Departments of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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Li Z, Hu J, Qin Z, Tao Y, Lai Z, Wang Q, Li T. High-dimensional single-cell proteomics analysis reveals the landscape of immune cells and stem-like cells in renal tumors. J Clin Lab Anal 2019; 34:e23155. [PMID: 31855296 PMCID: PMC7246380 DOI: 10.1002/jcla.23155] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/29/2019] [Accepted: 11/02/2019] [Indexed: 12/16/2022] Open
Abstract
Background Renal tumors are highly heterogeneous, and identification of tumor heterogeneity is an urgent clinical need for effective treatment. Mass cytometry (MC) can be used to perform high‐dimensional single‐cell proteomics analysis of heterogeneous samples via cytometry by time‐of‐flight (CyTOF), in order to achieve more accurate observation and classification of phenotypes within a cell population. This study aimed to develop a high‐dimensional MC method for the detection and analysis of heterogeneity in renal tumors. Materials and Methods We collected tissue samples from 8 patients with different types of renal tumors. Single‐cell suspensions were prepared and stained using a panel of 28 immune cell‐centric antibodies and a panel of 21 stem‐like cell‐centric antibodies. The stained cells were detected using CyTOF. Result Renal tumors were divided into 25 immune cell subsets (4 CD4+ T cells, 7 CD8+ T cells, 1 B cells, 8 macrophages, 1 dendritic cells, 2 natural killer (NK) cells, 1 granulocyte, and 1 other subset) and 7 stem‐like cells subsets (based on positivity of vimentin, CD326, CD34, CD90, CD13, CD44, and CD47). Different types of renal tumors have different cell subsets with significantly different characteristics. Conclusion High‐dimensional single‐cell proteomics analysis using MC aids in the discovery and analysis of renal tumors heterogeneity. Additionally, it can be used to accurately classify the immune cell population and analyze the expression of stem cell‐related markers in renal tumors. Our findings provide a valuable resource for deciphering tumor heterogeneity and might improve the clinical management of patients with renal tumors.
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Affiliation(s)
- Zhijian Li
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
| | - Jiaxin Hu
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
| | - Zhao Qin
- Department of Plastic and Aesthetic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yuting Tao
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
| | - Zhiyong Lai
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China.,Guangxi key laboratory for genomic and personalized medicine, Guangxi collaborative innovation center for genomic and personalized medicine, Nanning, China
| | - Qiuyan Wang
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China.,Guangxi key laboratory for genomic and personalized medicine, Guangxi collaborative innovation center for genomic and personalized medicine, Nanning, China
| | - Tianyu Li
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China.,Guangxi key laboratory for genomic and personalized medicine, Guangxi collaborative innovation center for genomic and personalized medicine, Nanning, China.,Department of Urology and Nephrology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
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12
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Lin S, Zhou R, Zeng D, Wu J, Wu J, Zhang J, Sun H, Zhu S, Shi M, Bin J, Liao Y, Liao W. A novel assessing system for predicting the prognosis of gastric cancer. Epigenomics 2019; 11:1251-1266. [PMID: 31364879 DOI: 10.2217/epi-2019-0151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Aim: To develop novel diagnostic tools that can predict the prognosis of gastric cancer. Material & methods: Using RNA expression data from The Cancer Genome Atlas and Gene Expression Omnibus, we established protein-coding RNAs-noncoding RNAs-tumor microenvironment type (PNM) scores, which contain signatures of tumor protein coding genes (P), tumor noncoding genes (N) and immune/stroma cells in tumor microenvironment (M) to predict the prognosis of gastric cancer. Results & conclusion: Based on PNM scores, gastric cancer patients were divided into three subgroups and Kaplan-Meier survival curves revealed significant differences among the subgroups (p < 0.001). Our study showed that the PNM scores could be used as a robust predicting tool for the prognosis of gastric cancer.
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Affiliation(s)
- Siheng Lin
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, PR China
| | - Rui Zhou
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, PR China
| | - Dongqiang Zeng
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, PR China
| | - Jiani Wu
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, PR China
| | - Jianhua Wu
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, PR China
| | - Jingwen Zhang
- Department of Medicine Ultrasonics, Nanfang Hospital, Southern Medical University, Guangzhou, PR China
| | - Huiying Sun
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, PR China
| | - Shaowei Zhu
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, PR China
| | - Min Shi
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, PR China
| | - Jianping Bin
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, PR China
| | - Yulin Liao
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, PR China
| | - Wangjun Liao
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, PR China
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13
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Cursons J, Souza-Fonseca-Guimaraes F, Foroutan M, Anderson A, Hollande F, Hediyeh-Zadeh S, Behren A, Huntington ND, Davis MJ. A Gene Signature Predicting Natural Killer Cell Infiltration and Improved Survival in Melanoma Patients. Cancer Immunol Res 2019; 7:1162-1174. [PMID: 31088844 DOI: 10.1158/2326-6066.cir-18-0500] [Citation(s) in RCA: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 01/31/2019] [Accepted: 05/07/2019] [Indexed: 12/14/2022]
Abstract
Natural killer (NK) cell activity is essential for initiating antitumor responses and may be linked to immunotherapy success. NK cells and other innate immune components could be exploitable for cancer treatment, which drives the need for tools and methods that identify therapeutic avenues. Here, we extend our gene-set scoring method singscore to investigate NK cell infiltration by applying RNA-seq analysis to samples from bulk tumors. Computational methods have been developed for the deconvolution of immune cell types within solid tumors. We have taken the NK cell gene signatures from several such tools, then curated the gene list using a comparative analysis of tumors and immune cell types. Using a gene-set scoring method to investigate RNA-seq data from The Cancer Genome Atlas (TCGA), we show that patients with metastatic cutaneous melanoma have an improved survival rate if their tumor shows evidence of NK cell infiltration. Furthermore, these survival effects are enhanced in tumors that show higher expression of genes that encode NK cell stimuli such as the cytokine IL15 Using this signature, we then examine transcriptomic data to identify tumor and stromal components that may influence the penetrance of NK cells into solid tumors. Our results provide evidence that NK cells play a role in the regulation of human tumors and highlight potential survival effects associated with increased NK cell activity. Our computational analysis identifies putative gene targets that may be of therapeutic value for boosting NK cell antitumor immunity.
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Affiliation(s)
- Joseph Cursons
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Fernando Souza-Fonseca-Guimaraes
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
- Division of Molecular Immunology, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Momeneh Foroutan
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Clinical Pathology, The University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne, Victoria, Australia
| | - Ashley Anderson
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Frédéric Hollande
- Department of Clinical Pathology, The University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne, Victoria, Australia
| | - Soroor Hediyeh-Zadeh
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Andreas Behren
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
| | - Nicholas D Huntington
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia.
- Division of Molecular Immunology, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Biomedicine Discovery Institute and the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Melissa J Davis
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
- Department of Biochemistry, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
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14
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Zhou R, Zeng D, Zhang J, Sun H, Wu J, Li N, Liang L, Shi M, Bin J, Liao Y, Huang N, Liao W. A robust panel based on tumour microenvironment genes for prognostic prediction and tailoring therapies in stage I-III colon cancer. EBioMedicine 2019; 42:420-430. [PMID: 30917936 PMCID: PMC6491960 DOI: 10.1016/j.ebiom.2019.03.043] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 02/18/2019] [Accepted: 03/15/2019] [Indexed: 12/29/2022] Open
Abstract
Background Tumour microenvironment (TME) is critical for the regulation of cancer development as well as therapy. The objective of the current study was the development of a robust prognostic model based on TME-relevant genes. Methods Five public microarray datasets providing clinical information were obtained. The least absolute shrinkage and selection operator regression method was used to reduce the dimensionality of robust prognostic genes identified via the bootstrap method. Findings We established a prognostic panel, designated as tumour microenvironment risk score (TMRS), consisting of 100 genes. With specific risk score formulae, the TMRS panel possesses a strong ability to predict relapse-free survival and overall survival through both univariate and multivariate analyses. Compared with the TNM stage, the TMRS panel showed much higher predictive accuracy. Further analysis revealed that patients with higher TMRS scores exhibited no therapeutic benefits from adjuvant chemotherapy, probably due to the activation of stromal relevant pathways and infiltration of stromal cells. Besides colon cancer, the TMRS panel was also revealed to be a reliable tool for prognostic prediction and chemotherapeutic decision-making in gastric cancer. Its value in predicting immunotherapy outcomes was also confirmed in two other cohorts consisting of metastatic urothelial carcinoma patients and melanoma patients. Interpretation Our TMRS panel may be an effective tool for survival prediction and treatment guidance in patients with stage I–III colon cancer. Fund This work was supported by the National Natural Science Foundation of China (No. 81772580) and Guangzhou Planed Project of Science and Technology (No. 201803010070).
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Affiliation(s)
- Rui Zhou
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, PR China
| | - Dongqiang Zeng
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, PR China
| | - Jingwen Zhang
- Department of Medicine Ultrasonics, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, PR China
| | - Huiying Sun
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, PR China
| | - Jianhua Wu
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, PR China
| | - Nailin Li
- Department of Medicine-Solna, Clinical Pharmacology Group, Karolinska University Hospital-Solna, Karolinska Institutet, Stockholm, Sweden
| | - Li Liang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, PR China; Department of Pathology, Southern Medical University, Guangzhou, Guangdong, PR China; Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, PR China
| | - Min Shi
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, PR China
| | - Jianping Bin
- Department of Cardiology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, PR China
| | - Yulin Liao
- Department of Cardiology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, PR China
| | - Na Huang
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, PR China
| | - Wangjun Liao
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, PR China.
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15
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Antohe M, Nedelcu RI, Nichita L, Popp CG, Cioplea M, Brinzea A, Hodorogea A, Calinescu A, Balaban M, Ion DA, Diaconu C, Bleotu C, Pirici D, Zurac SA, Turcu G. Tumor infiltrating lymphocytes: The regulator of melanoma evolution. Oncol Lett 2019; 17:4155-4161. [PMID: 30944610 DOI: 10.3892/ol.2019.9940] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 09/27/2018] [Indexed: 02/06/2023] Open
Abstract
Melanoma is the most severe type of skin cancer and its incidence has increased in the last decades. In the United States, it is the 6th most common cancer in both men and women. Prognosis for patients with melanoma depends on the stage of the disease at the time of diagnosis and it can be influenced by the immunologic response. Melanoma has been historically considered an immunogenic malignancy. It often contains great amount of immune cells (different subsets of T-cells, dendritic cells, macrophages, neutrophils, mast cells, B lymphocytes), which may reflect a continuous intercommunication between host and tumor. It is not established if tumor-infiltrating lymphocytes (TILs) are induced by tumor cells or by other components of the microenvironment or when they are a host direct immunologic reaction. It has been observed that in many cases, the presence of a dense TIL is associated with good prognosis. The pattern and activation state of the cells which constitute TIL is variable and modulates the clinical outcome. An important step in the understanding of tumor immunobiology is the analysis of the populations and subsets of immune cells that form TIL. Besides its prognostic significance, after approval of cytotoxic T lymphocyte antigen 4, programmed cell death-1 and programmed death-1 ligand antibodies for the treatment of melanoma, the assessment of immune infiltrate composition has become even more captivating, as it could provide new target molecules and new biomarkers for predicting the effect of the treatment and disease outcome in patients treated with immunotherapy. In this review we discuss current state of knowledge in the field of immune cells that infiltrate melanoma, resuming the potential of TIL components to become prognostic markers for natural evolution, for response to drugs or valuable targets for new medication.
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Affiliation(s)
- Mihaela Antohe
- Department of Pathophysiology, 'Carol Davila' University of Medicine and Pharmacy, 050474 Bucharest, Romania.,Department of Dermatology, Derma 360° Clinic, 011274 Bucharest, Romania
| | - Roxana Ioana Nedelcu
- Department of Pathophysiology, 'Carol Davila' University of Medicine and Pharmacy, 050474 Bucharest, Romania.,Department of Dermatology, Derma 360° Clinic, 011274 Bucharest, Romania
| | - Luciana Nichita
- Department of Pathology, Colentina Clinical Hospital, 021103 Bucharest, Romania
| | | | - Mirela Cioplea
- Department of Pathology, Colentina Clinical Hospital, 021103 Bucharest, Romania
| | - Alice Brinzea
- Department of Pathophysiology, 'Carol Davila' University of Medicine and Pharmacy, 050474 Bucharest, Romania.,National Institute for Infectious Diseases 'Prof. Dr. Matei Balș', Ambulatory Service, 021105 Bucharest, Romania
| | - Anastasia Hodorogea
- Department of Pathophysiology, 'Carol Davila' University of Medicine and Pharmacy, 050474 Bucharest, Romania.,Department of Dermatology, Colentina Clinical Hospital, 021103 Bucharest, Romania
| | - Andreea Calinescu
- Department of Dermatology, Colentina Clinical Hospital, 021103 Bucharest, Romania.,Department of Physiology, 'Carol Davila' University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Mihaela Balaban
- Department of Dermatology, Derma 360° Clinic, 011274 Bucharest, Romania.,Department of Biochemistry, 'Carol Davila' University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Daniela Adriana Ion
- Department of Pathophysiology, 'Carol Davila' University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Carmen Diaconu
- Department of Cellular and Molecular Pathology, 'Stefan S. Nicolau' Institute of Virology, 030304 Bucharest, Romania
| | - Coralia Bleotu
- Department of Cellular and Molecular Pathology, 'Stefan S. Nicolau' Institute of Virology, 030304 Bucharest, Romania
| | - Daniel Pirici
- Department of Pathology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | - Sabina Andrada Zurac
- Department of Pathology, Colentina Clinical Hospital, 021103 Bucharest, Romania.,Department of Pathology, 'Carol Davila' University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Gabriela Turcu
- Department of Dermatology, Derma 360° Clinic, 011274 Bucharest, Romania.,Department of Dermatology, Colentina Clinical Hospital, 021103 Bucharest, Romania.,Department of Dermatology, 'Carol Davila' University of Medicine and Pharmacy, 050474 Bucharest, Romania
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16
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Alban TJ, Alvarado AG, Sorensen MD, Bayik D, Volovetz J, Serbinowski E, Mulkearns-Hubert EE, Sinyuk M, Hale JS, Onzi GR, McGraw M, Huang P, Grabowski MM, Wathen CA, Ahluwalia MS, Radivoyevitch T, Kornblum HI, Kristensen BW, Vogelbaum MA, Lathia JD. Global immune fingerprinting in glioblastoma patient peripheral blood reveals immune-suppression signatures associated with prognosis. JCI Insight 2018; 3:122264. [PMID: 30385717 DOI: 10.1172/jci.insight.122264] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 10/02/2018] [Indexed: 12/17/2022] Open
Abstract
Glioblastoma (GBM) remains uniformly lethal, and despite a large accumulation of immune cells in the microenvironment, there is limited antitumor immune response. To overcome these challenges, a comprehensive understanding of GBM systemic immune response during disease progression is required. Here, we integrated multiparameter flow cytometry and mass cytometry TOF (CyTOF) analysis of patient blood to determine changes in the immune system among tumor types and over disease progression. Utilizing flow cytometry analysis in a cohort of 259 patients ranging from benign to malignant primary and metastatic brain tumors, we found that GBM patients had a significant elevation in myeloid-derived suppressor cells (MDSCs) in peripheral blood but not immunosuppressive Tregs. In GBM patient tissue, we found that increased MDSC levels in recurrent GBM portended poor prognosis. CyTOF analysis of peripheral blood from newly diagnosed GBM patients revealed that reduced MDSCs over time were accompanied by a concomitant increase in DCs. GBM patients with extended survival also had reduced MDSCs, similar to the levels of low-grade glioma (LGG) patients. Our findings provide a rationale for developing strategies to target MDSCs, which are elevated in GBM patients and predict poor prognosis.
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Affiliation(s)
- Tyler J Alban
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case, Western Reserve University, Cleveland, Ohio, USA
| | - Alvaro G Alvarado
- Department of Psychiatry and Biobehavioral Sciences and Semel Institute for Neuroscience, UCLA, USA
| | - Mia D Sorensen
- Department of Pathology, Odense University Hospital, Odense, Denmark.,Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Defne Bayik
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Josephine Volovetz
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case, Western Reserve University, Cleveland, Ohio, USA
| | - Emily Serbinowski
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Erin E Mulkearns-Hubert
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Maksim Sinyuk
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - James S Hale
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Giovana R Onzi
- Department of Psychiatry and Biobehavioral Sciences and Semel Institute for Neuroscience, UCLA, USA.,Department of Biophysics and Center of Biotechnology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS-Brazil
| | - Mary McGraw
- Rose Ella Burkhardt Brain Tumor and Neuro-Oncology Center and
| | - Pengjing Huang
- Rose Ella Burkhardt Brain Tumor and Neuro-Oncology Center and
| | - Matthew M Grabowski
- Rose Ella Burkhardt Brain Tumor and Neuro-Oncology Center and.,Department of Neurosurgery, Cleveland Clinic, Cleveland, Ohio, USA
| | - Connor A Wathen
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case, Western Reserve University, Cleveland, Ohio, USA.,Rose Ella Burkhardt Brain Tumor and Neuro-Oncology Center and
| | - Manmeet S Ahluwalia
- Rose Ella Burkhardt Brain Tumor and Neuro-Oncology Center and.,Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, USA
| | - Tomas Radivoyevitch
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Harley I Kornblum
- Department of Psychiatry and Biobehavioral Sciences and Semel Institute for Neuroscience, UCLA, USA
| | - Bjarne W Kristensen
- Department of Pathology, Odense University Hospital, Odense, Denmark.,Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Michael A Vogelbaum
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case, Western Reserve University, Cleveland, Ohio, USA.,Rose Ella Burkhardt Brain Tumor and Neuro-Oncology Center and.,Department of Neurosurgery, Cleveland Clinic, Cleveland, Ohio, USA.,Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, USA
| | - Justin D Lathia
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case, Western Reserve University, Cleveland, Ohio, USA.,Rose Ella Burkhardt Brain Tumor and Neuro-Oncology Center and.,Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, USA
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17
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Cari L, Nocentini G, Migliorati G, Riccardi C. Potential effect of tumor-specific Treg-targeted antibodies in the treatment of human cancers: A bioinformatics analysis. Oncoimmunology 2017; 7:e1387705. [PMID: 29308313 DOI: 10.1080/2162402x.2017.1387705] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 09/28/2017] [Accepted: 09/29/2017] [Indexed: 12/27/2022] Open
Abstract
One of the mechanisms of tumor rejection in immune-modulatory treatments is antibody-dependent cell-mediated cytotoxicity (ADCC) of regulatory T cells (Tregs) that infiltrate tumors in which cells expressing activating Fcγ receptors (FcγRs) are present. Our objective was to identify, through a bioinformatics analysis, Treg marker(s) expressed at the highest levels in nine types of human cancers, in order to determine the best targets for ADCC-inducing antitumor antibodies. We analyzed the mRNA levels of 24 surface Treg markers evaluated by the Affymetrix Human Genome U133 Plus 2.0 Array in 5728 cancer samples obtained via the Genevestigator v3 suite. Our analysis was based on overexpression of markers in tumors as compared to healthy tissues (HTs) and correlation between overexpression of the markers and the tumor suppressive microenvironment. Moreover, we evaluated tumoral infiltration of activating FcγR-expressing cells and calculated the ADCC index for each overexpressed marker, as an indicator of whether the marker was a good target for ADCC induction in tumor-infiltrating Tregs. The results demonstrated that the ADCC strategy is unlikely to succeed in colorectal, liver, prostate and ovarian cancers. Moreover, we identified nine Treg markers that could be targeted in the other tumors: 4-1BB, CD39, galectin-9, GITR, IL-21R, LAP, neuropilin-1, TIGIT and TNFR2. GITR and TIGIT were the only markers that could be potentially useful as targets for the treatment of three cancers: non-squamous and squamous NSCLC and breast infiltrating ductal carcinoma. LAP, neuropilin-1 and CD39 presented as good targets in the treatment of renal cell carcinoma. Our findings may have value for the development of new anti-tumor antibodies.
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Affiliation(s)
- Luigi Cari
- Section of Pharmacology, Department of Medicine, University of Perugia, Perugia, Italy
| | - Giuseppe Nocentini
- Section of Pharmacology, Department of Medicine, University of Perugia, Perugia, Italy
| | - Graziella Migliorati
- Section of Pharmacology, Department of Medicine, University of Perugia, Perugia, Italy
| | - Carlo Riccardi
- Section of Pharmacology, Department of Medicine, University of Perugia, Perugia, Italy
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18
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Boespflug A, Caramel J, Dalle S, Thomas L. Treatment of NRAS-mutated advanced or metastatic melanoma: rationale, current trials and evidence to date. Ther Adv Med Oncol 2017; 9:481-492. [PMID: 28717400 PMCID: PMC5502949 DOI: 10.1177/1758834017708160] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/13/2017] [Indexed: 12/19/2022] Open
Abstract
The disease course of BRAF (v-raf murine sarcoma viral oncogene homolog B1)-mutant melanoma has been drastically improved by the arrival of targeted therapies. NRAS (neuroblastoma RAS viral oncogene homolog)-mutated melanoma represents 15–25% of all metastatic melanoma patients. It currently does not have an approved targeted therapy. Metastatic patients receive immune-based therapies as first-line treatments, then cytotoxic chemotherapy like carboplatin/paclitaxel (C/P), dacarbazine (DTIC) or temozolomide (TMZ) as a second-line treatment. We will review current preclinical and clinical developments in NRAS-mutated melanoma, and analyze ongoing clinical trials that are evaluating the benefit of different targeted and immune-based therapies, either tested as single agents or in combination, in NRAS-mutant melanoma.
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Affiliation(s)
| | - Julie Caramel
- Cancer Research Center of Lyon, Claude Bernard Lyon-1 University, INSERM1052, CNRS 5286, Lyon, France
| | | | - Luc Thomas
- Service de Dermatologie, CH Lyon Sud, 165 Chemin du Grand Revoyet, 69495 Pierre Bénite, Cedex, France
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