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Wei W, Ye B, Huang Z, Mu X, Qiao J, Zhao P, Jiang Y, Wu J, Zhan X. Prediction of Prognosis, Immunotherapy and Chemotherapy with an Immune-Related Risk Score Model for Endometrial Cancer. Cancers (Basel) 2023; 15:3673. [PMID: 37509334 PMCID: PMC10377799 DOI: 10.3390/cancers15143673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
Endometrial cancer (EC) is the most common gynecologic cancer. The overall survival remains unsatisfying due to the lack of effective treatment screening approaches. Immunotherapy as a promising therapy has been applied for EC treatment, but still fails in many cases. Therefore, there is a strong need to optimize the screening approach for clinical treatment. In this study, we employed co-expression network (GCN) analysis to mine immune-related GCN modules and key genes and further constructed an immune-related risk score model (IRSM). The IRSM was proved effective as an independent predictor of poor prognosis. The roles of IRSM-related genes in EC were confirmed by IHC. The molecular basis, tumor immune microenvironment and clinical characteristics of the IRSM were revealed. Moreover, the IRSM effectiveness was associated with immunotherapy and chemotherapy. Patients in the low-risk group were more sensitive to immunotherapy and chemotherapy than those in the high-risk group. Interestingly, the patients responding to immunotherapy were also more sensitive to chemotherapy. Overall, we developed an IRSM which could be used to predict the prognosis, immunotherapy response and chemotherapy sensitivity of EC patients. Our analysis not only improves the treatment of EC but also offers targets for personalized therapeutic interventions.
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Affiliation(s)
- Wei Wei
- Department of Bioinformatics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Bo Ye
- Department of Bioinformatics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Zhenting Huang
- Department of Pathology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Xiaoling Mu
- Department of Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Jing Qiao
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Peng Zhao
- School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Yuehang Jiang
- Department of Pathology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Jingxian Wu
- Department of Pathology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
- Department of Pathology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Molecular Medicine Diagnostic and Testing Center, Chongqing Medical University, Chongqing 400016, China
| | - Xiaohui Zhan
- Department of Bioinformatics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
- Center for Medical Epigenetics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
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Analysis of rainbow trout TCRαβ/CD3 complex: An in-silico modeling approach. Mol Immunol 2022; 144:35-43. [DOI: 10.1016/j.molimm.2022.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 11/18/2022]
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Saiz-Ladera C, Baliu-Piqué M, Cimas FJ, Manzano A, García-Barberán V, Camarero SC, Hinojal GF, Pandiella A, Győrffy B, Stewart D, Cruz-Hernández JJ, Pérez-Segura P, Ocana A. Transcriptomic Correlates of Immunologic Activation in Head and Neck and Cervical Cancer. Front Oncol 2021; 11:714550. [PMID: 34692491 PMCID: PMC8527851 DOI: 10.3389/fonc.2021.714550] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 09/13/2021] [Indexed: 12/31/2022] Open
Abstract
Targeting the immune system has emerged as an effective therapeutic strategy for the treatment of various tumor types, including Head and Neck Squamous Cell Carcinoma (HNSCC) and Non-small-Cell Lung Cancer (NSCLC), and checkpoint inhibitors have shown to improve patient survival in these tumor types. Unfortunately, not all cancers respond to these agents, making it necessary to identify responsive tumors. Several biomarkers of response have been described and clinically tested. As of yet what seems to be clear is that a pre-activation state of the immune system is necessary for these agents to be efficient. In this study, using established transcriptomic signatures, we identified a group of gene combination associated with favorable outcome in HNSCC linked to a higher presence of immune effector cells. CD2, CD3D, CD3E, and CXCR6 combined gene expression is associated with improved outcome of HNSCC patients and an increase of infiltrating immune effector cells. This new signature also identifies a subset of cervical squamous cell carcinoma (CSCC) patients with favorable prognosis, who show an increased presence of immune effector cells in the tumor, which outcome shows similarities with the HP-positive HNSCC cohort of patients. In addition, CD2, CD3D, CD3E, and CXCR6 signature is able to predict the best favorable prognosis in terms of overall survival of CSSC patients. Of note, these findings were not reproduced in other squamous cell carcinomas like esophageal SCC or lung SCC. Prospective confirmatory studies should be employed to validate these findings.
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Affiliation(s)
- Cristina Saiz-Ladera
- Experimental Therapeutics Unit, Medical Oncology Department, Hospital Clínico Universitario San Carlos (HCSC), Instituto de Investigación Sanitaria (IdISSC), Madrid, Spain
| | - Mariona Baliu-Piqué
- Experimental Therapeutics Unit, Medical Oncology Department, Hospital Clínico Universitario San Carlos (HCSC), Instituto de Investigación Sanitaria (IdISSC), Madrid, Spain
| | - Francisco J Cimas
- Translational Oncology Laboratory, Centro Regional de Investigaciones Biomedicas, Castilla-La Mancha University (CRIB-UCLM), Albacete, Spain
| | - Aránzazu Manzano
- Experimental Therapeutics Unit, Medical Oncology Department, Hospital Clínico Universitario San Carlos (HCSC), Instituto de Investigación Sanitaria (IdISSC), Madrid, Spain
| | - Vanesa García-Barberán
- Experimental Therapeutics Unit, Medical Oncology Department, Hospital Clínico Universitario San Carlos (HCSC), Instituto de Investigación Sanitaria (IdISSC), Madrid, Spain
| | - Santiago Cabezas Camarero
- Experimental Therapeutics Unit, Medical Oncology Department, Hospital Clínico Universitario San Carlos (HCSC), Instituto de Investigación Sanitaria (IdISSC), Madrid, Spain
| | - Gonzalo Fernández Hinojal
- Experimental Therapeutics Unit, Medical Oncology Department, Hospital Clínico Universitario San Carlos (HCSC), Instituto de Investigación Sanitaria (IdISSC), Madrid, Spain
| | - Atanasio Pandiella
- Instituto de Biología Molecular y Celular del Cáncer and Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Centro Superior de Investigaciones Científicas (CSIC), Salamanca, Spain
| | - Balázs Győrffy
- Department of Bioinformatics, Faculty of Medicine, Semmelweis University, Budapest, Hungary.,2nd Department of Pediatrics, Faculty of Medicine, Semmelweis University, Budapest, Hungary.,Institute of Enzymology, Research Centre of Nature Sciences, Budapest, Hungary
| | - David Stewart
- Ottawa University Hospital, University of Ottawa, Ottawa, ON, Canada
| | - Juan J Cruz-Hernández
- Instituto de Biología Molecular y Celular del Cáncer and Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Centro Superior de Investigaciones Científicas (CSIC), Salamanca, Spain
| | - Pedro Pérez-Segura
- Experimental Therapeutics Unit, Medical Oncology Department, Hospital Clínico Universitario San Carlos (HCSC), Instituto de Investigación Sanitaria (IdISSC), Madrid, Spain
| | - Alberto Ocana
- Experimental Therapeutics Unit, Medical Oncology Department, Hospital Clínico Universitario San Carlos (HCSC), Instituto de Investigación Sanitaria (IdISSC), Madrid, Spain.,Translational Oncology Laboratory, Centro Regional de Investigaciones Biomedicas, Castilla-La Mancha University (CRIB-UCLM), Albacete, Spain
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Schrum AG, Gil D, Turka LA, Palmer E. Physical and functional bivalency observed among TCR/CD3 complexes isolated from primary T cells. THE JOURNAL OF IMMUNOLOGY 2011; 187:870-8. [PMID: 21666056 DOI: 10.4049/jimmunol.1100538] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Unlike BCR and secreted Ig, TCR expression is not thought to occur in a bivalent form. The conventional monovalent model of TCR/CD3 is supported by published studies of complexes solubilized in the detergent digitonin, in which bivalency was not observed. We revisited the issue of TCR valency by examining complexes isolated from primary αβ T cells after solubilization in digitonin. Using immunoprecipitation followed by flow cytometry, we unexpectedly observed TCR/CD3 complexes that contained two TCRs per complex. Standard anti-TCR Abs, being bivalent themselves, tended to bind with double occupancy to bivalent TCRs; this property masked the presence of the second TCR per complex in certain Ab binding assays, which may partially explain why previous data did not reveal these bivalent complexes. We also found that the prevalence of bivalency among fully assembled, mature TCR/CD3 complexes was sufficient to impact the functional performance of immunoprecipitated TCRs in binding antigenic peptide/MHC-Ig fusion proteins. Both TCR positions per bivalent complex required an Ag-specific TCR to effect optimal binding to these soluble ligands. Therefore, we conclude that in primary T cells, TCR/CD3 complexes can be found that are physically and functionally bivalent. The expression of bivalent TCR/CD3 complexes has implications regarding potential mechanisms by which Ag may trigger signaling. It also suggests the possibility that the potential for bivalent expression could represent a general feature of Ag receptors.
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Affiliation(s)
- Adam G Schrum
- Department of Immunology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
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Riveros C, Mellor D, Gandhi KS, McKay FC, Cox MB, Berretta R, Vaezpour SY, Inostroza-Ponta M, Broadley SA, Heard RN, Vucic S, Stewart GJ, Williams DW, Scott RJ, Lechner-Scott J, Booth DR, Moscato P. A transcription factor map as revealed by a genome-wide gene expression analysis of whole-blood mRNA transcriptome in multiple sclerosis. PLoS One 2010; 5:e14176. [PMID: 21152067 PMCID: PMC2995726 DOI: 10.1371/journal.pone.0014176] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Accepted: 10/20/2010] [Indexed: 12/03/2022] Open
Abstract
Background Several lines of evidence suggest that transcription factors are involved in the pathogenesis of Multiple Sclerosis (MS) but complete mapping of the whole network has been elusive. One of the reasons is that there are several clinical subtypes of MS and transcription factors that may be involved in one subtype may not be in others. We investigate the possibility that this network could be mapped using microarray technologies and contemporary bioinformatics methods on a dataset derived from whole blood in 99 untreated MS patients (36 Relapse Remitting MS, 43 Primary Progressive MS, and 20 Secondary Progressive MS) and 45 age-matched healthy controls. Methodology/Principal Findings We have used two different analytical methodologies: a non-standard differential expression analysis and a differential co-expression analysis, which have converged on a significant number of regulatory motifs that are statistically overrepresented in genes that are either differentially expressed (or differentially co-expressed) in cases and controls (e.g., V$KROX_Q6, p-value <3.31E-6; V$CREBP1_Q2, p-value <9.93E-6, V$YY1_02, p-value <1.65E-5). Conclusions/Significance Our analysis uncovered a network of transcription factors that potentially dysregulate several genes in MS or one or more of its disease subtypes. The most significant transcription factor motifs were for the Early Growth Response EGR/KROX family, ATF2, YY1 (Yin and Yang 1), E2F-1/DP-1 and E2F-4/DP-2 heterodimers, SOX5, and CREB and ATF families. These transcription factors are involved in early T-lymphocyte specification and commitment as well as in oligodendrocyte dedifferentiation and development, both pathways that have significant biological plausibility in MS causation.
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Affiliation(s)
- Carlos Riveros
- Centre for Bioinformatics, Biomarker Discovery & Information-Based Medicine, University of Newcastle, and Hunter Medical Research Institute, Newcastle, Australia
| | - Drew Mellor
- Centre for Bioinformatics, Biomarker Discovery & Information-Based Medicine, University of Newcastle, and Hunter Medical Research Institute, Newcastle, Australia
- School of Computer Science and Software Engineering, The University of Western Australia, Crawley, Australia
| | - Kaushal S. Gandhi
- Westmead Millennium Institute, University of Sydney, Westmead, Australia
| | - Fiona C. McKay
- Westmead Millennium Institute, University of Sydney, Westmead, Australia
| | - Mathew B. Cox
- Centre for Bioinformatics, Biomarker Discovery & Information-Based Medicine, University of Newcastle, and Hunter Medical Research Institute, Newcastle, Australia
- Hunter Medical Research Institute, Newcastle, Australia
| | - Regina Berretta
- Centre for Bioinformatics, Biomarker Discovery & Information-Based Medicine, University of Newcastle, and Hunter Medical Research Institute, Newcastle, Australia
| | - S. Yahya Vaezpour
- Centre for Bioinformatics, Biomarker Discovery & Information-Based Medicine, University of Newcastle, and Hunter Medical Research Institute, Newcastle, Australia
- Department of Computer Engineering, Amirkabir University of Technology, Tehran, Iran
| | - Mario Inostroza-Ponta
- Centre for Bioinformatics, Biomarker Discovery & Information-Based Medicine, University of Newcastle, and Hunter Medical Research Institute, Newcastle, Australia
- Departamento de Ingeniería Informática, Universidad de Santiago de Chile, Santiago, Chile
| | - Simon A. Broadley
- School of Medicine, Griffith University, Brisbane, Australia
- Department of Neurology, Gold Coast Hospital, Southport, Australia
| | - Robert N. Heard
- Westmead Millennium Institute, University of Sydney, Westmead, Australia
| | - Stephen Vucic
- Westmead Millennium Institute, University of Sydney, Westmead, Australia
| | - Graeme J. Stewart
- Westmead Millennium Institute, University of Sydney, Westmead, Australia
| | | | - Rodney J. Scott
- Centre for Bioinformatics, Biomarker Discovery & Information-Based Medicine, University of Newcastle, and Hunter Medical Research Institute, Newcastle, Australia
| | - Jeanette Lechner-Scott
- Centre for Bioinformatics, Biomarker Discovery & Information-Based Medicine, University of Newcastle, and Hunter Medical Research Institute, Newcastle, Australia
| | - David R. Booth
- Westmead Millennium Institute, University of Sydney, Westmead, Australia
| | - Pablo Moscato
- Centre for Bioinformatics, Biomarker Discovery & Information-Based Medicine, University of Newcastle, and Hunter Medical Research Institute, Newcastle, Australia
- Australian Research Council Centre of Excellence in Bioinformatics, St Lucia, Australia
- * E-mail:
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Brodeur JF, Li S, Martins MDS, Larose L, Dave VP. Critical and Multiple Roles for the CD3ε Intracytoplasmic Tail in Double Negative to Double Positive Thymocyte Differentiation. THE JOURNAL OF IMMUNOLOGY 2009; 182:4844-53. [DOI: 10.4049/jimmunol.0803679] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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