1
|
Pourjafar M, Saidijam M, Miehe M, Najafi R, Soleimani M, Spillner E. Surfaceome Profiling Suggests Potential of Anti-MUC1×EGFR Bispecific Antibody for Breast Cancer Targeted Therapy. J Immunother 2023; 46:245-261. [PMID: 37493044 DOI: 10.1097/cji.0000000000000482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 06/16/2023] [Indexed: 07/27/2023]
Abstract
Breast cancer (BC) treatment has traditionally been challenging due to tumor heterogeneity. Bispecific antibodies (bsAbs) offer a promising approach for overcoming these challenges by targeting multiple specific epitopes. In the current study, we designed a new bsAb against the most common BC cell surface proteins (SPs). To achieve this, we analyzed RNA-sequencing data to identify differentially expressed genes, which were further evaluated using Gene Ontology enrichment, Hidden Markov Models, clinical trial data, and survival analysis to identify druggable gene-encoding cell SPs. Based on these analyses, we constructed and expressed a bsAb targeting the mucin 1 (MUC1) and epidermal growth factor receptor (EGFR) proteins, which are the dominant druggable gene-encoding cell SPs in BC. The recombinant anti-MUC1×EGFR bsAb demonstrated efficient production and high specificity for MUC1 and EGFR + cell lines and BC tissue. Furthermore, the bsAb significantly reduced the proliferation and migration of BC cells. Our results suggested that simultaneous targeting with bsAbs could be a promising targeted therapy for improving the overall efficacy of BC treatment.
Collapse
Affiliation(s)
- Mona Pourjafar
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences
- Department of Biological and Chemical Engineering, Immunological Biotechnology, Aarhus University, Aarhus, Denmark
| | - Massoud Saidijam
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences
| | - Michaela Miehe
- Department of Biological and Chemical Engineering, Immunological Biotechnology, Aarhus University, Aarhus, Denmark
| | - Rezvan Najafi
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences
| | - Meysam Soleimani
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Edzard Spillner
- Department of Biological and Chemical Engineering, Immunological Biotechnology, Aarhus University, Aarhus, Denmark
| |
Collapse
|
2
|
Grass GD, Ercan D, Obermayer AN, Shaw T, Stewart PA, Chahoud J, Dhillon J, Lopez A, Johnstone PAS, Rogatto SR, Spiess PE, Eschrich SA. An Assessment of the Penile Squamous Cell Carcinoma Surfaceome for Biomarker and Therapeutic Target Discovery. Cancers (Basel) 2023; 15:3636. [PMID: 37509297 PMCID: PMC10377392 DOI: 10.3390/cancers15143636] [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: 06/01/2023] [Revised: 07/01/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Penile squamous cell carcinoma (PSCC) is a rare malignancy in most parts of the world and the underlying mechanisms of this disease have not been fully investigated. About 30-50% of cases are associated with high-risk human papillomavirus (HPV) infection, which may have prognostic value. When PSCC becomes resistant to upfront therapies there are limited options, thus further research is needed in this venue. The extracellular domain-facing protein profile on the cell surface (i.e., the surfaceome) is a key area for biomarker and drug target discovery. This research employs computational methods combined with cell line translatomic (n = 5) and RNA-seq transcriptomic data from patient-derived tumors (n = 18) to characterize the PSCC surfaceome, evaluate the composition dependency on HPV infection, and explore the prognostic impact of identified surfaceome candidates. Immunohistochemistry (IHC) was used to validate the localization of select surfaceome markers. This analysis characterized a diverse surfaceome within patient tumors with 25% and 18% of the surfaceome represented by the functional classes of receptors and transporters, respectively. Significant differences in protein classes were noted by HPV status, with the most change being seen in transporter proteins (25%). IHC confirmed the robust surface expression of select surfaceome targets in the top 85% of expression and a superfamily immunoglobulin protein called BSG/CD147 was prognostic of survival. This study provides the first description of the PSCC surfaceome and its relation to HPV infection and sets a foundation for novel biomarker and drug target discovery in this rare cancer.
Collapse
Affiliation(s)
- George Daniel Grass
- Department of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Dalia Ercan
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Alyssa N Obermayer
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Timothy Shaw
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Paul A Stewart
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Jad Chahoud
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Jasreman Dhillon
- Department of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Alex Lopez
- Department of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Peter A S Johnstone
- Department of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Silvia Regina Rogatto
- Department of Clinical Genetics, University Hospital of Southern Denmark-Vejle, Beriderbakken 4, 7100 Vejle, Denmark
| | - Philippe E Spiess
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Steven A Eschrich
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| |
Collapse
|
3
|
Data-Driven Identification of Targets for Fluorescence-Guided Surgery in Non-Small Cell Lung Cancer. Mol Imaging Biol 2023; 25:228-239. [PMID: 36575340 DOI: 10.1007/s11307-022-01791-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 12/28/2022]
Abstract
PURPOSE Intraoperative identification of lung tumors can be challenging. Tumor-targeted fluorescence-guided surgery can provide surgeons with a tool for real-time intraoperative tumor detection. This study evaluated cell surface biomarkers, partially selected via data-driven selection software, as potential targets for fluorescence-guided surgery in non-small cell lung cancers: adenocarcinomas (ADC), adenocarcinomas in situ (AIS), and squamous cell carcinomas (SCC). PROCEDURES Formalin-fixed paraffin-embedded tissue slides of resection specimens from 15 patients with ADC and 15 patients with SCC were used and compared to healthy tissue. Molecular targets were selected based on two strategies: (1) a data-driven selection using > 275 multi-omics databases, literature, and experimental evidence; and (2) the availability of a fluorescent targeting ligand in advanced stages of clinical development. The selected targets were carbonic anhydrase 9 (CAIX), collagen type XVII alpha 1 chain (collagen XVII), glucose transporter 1 (GLUT1), G protein-coupled receptor 87 (GPR87), transmembrane protease serine 4 (TMPRSS4), carcinoembryonic antigen (CEA), epithelial cell adhesion molecule (EpCAM), folate receptor alpha (FRα), integrin αvβ6 (αvβ6), and urokinase-type plasminogen activator receptor (uPAR). Tumor expression of these targets was assessed by immunohistochemical staining. A total immunostaining score (TIS, range 0-12), combining the percentage and intensity of stained cells, was calculated. The most promising targets in ADC were explored in six AIS tissue slides to explore its potential in non-palpable lesions. RESULTS Statistically significant differences in TIS between healthy lung and tumor tissue for ADC samples were found for CEA, EpCAM, FRα, αvβ6, CAIX, collagen XVII, GLUT-1, and TMPRSS4, and of these, CEA, CAIX, and collagen XVII were also found in AIS. For SCC, EpCAM, uPAR, CAIX, collagen XVII, and GLUT-1 were found to be overexpressed. CONCLUSIONS EpCAM, CAIX, and Collagen XVII were identified using concomitant use of data-driven selection software and clinical evidence as promising targets for intraoperative fluorescence imaging for both major subtypes of non-small cell lung carcinomas.
Collapse
|
4
|
Saha SS, Samanas NB, Miralda I, Shubin NJ, Niino K, Bhise G, Acharya M, Seo AJ, Camp N, Deutsch GH, James RG, Piliponsky AM. Mast cell surfaceome characterization reveals CD98 heavy chain is critical for optimal cell function. J Allergy Clin Immunol 2022; 149:685-697. [PMID: 34324892 PMCID: PMC8792104 DOI: 10.1016/j.jaci.2021.07.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/07/2021] [Accepted: 07/14/2021] [Indexed: 02/03/2023]
Abstract
BACKGROUND Mast cells are involved in many distinct pathologic conditions, suggesting that they recognize and respond to various stimuli and thus require a rich repertoire of cell surface proteins. However, mast cell surface proteomes have not been comprehensively characterized. OBJECTIVE We aimed to further characterize the mast cell surface proteome to obtain a better understanding of how mast cells function in health and disease. METHODS We enriched for glycosylated surface proteins expressed in mouse bone marrow-derived cultured mast cells (BMCMCs) and identified them using mass spectrometry analysis. The presence of novel surface proteins in mast cells was validated by real-time quantitative PCR and flow cytometry analysis in BMCMCs and peritoneal mast cells (PMCs). We developed a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) gene editing approach to disrupt genes of interest in BMCMCs. RESULTS The glycoprotein enrichment approach resulted in the identification of 1270 proteins in BMCMCs, 378 of which were localized to the plasma membrane. The most common protein classes among plasma membrane proteins were small GTPases, receptors, and transporters. One such cell surface protein was CD98 heavy chain (CD98hc), encoded by the Slc3a2 gene. Slc3a2 gene disruption resulted in a significant reduction in CD98hc expression, adhesion, and proliferation. CONCLUSIONS Glycoprotein enrichment coupled with mass spectrometry can be used to identify novel surface molecules in mast cells. Moreover, CD98hc plays an important role in mast cell function.
Collapse
Affiliation(s)
- Siddhartha S. Saha
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Nyssa B. Samanas
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Irina Miralda
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Nicholas J. Shubin
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Kerri Niino
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Gauri Bhise
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Manasa Acharya
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Albert J. Seo
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Nathan Camp
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Gail H. Deutsch
- Department of Laboratories, Seattle Children’s Research Institute, Seattle, Washington, United States of America,Department of Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Richard G. James
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, United States of America,Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Adrian M. Piliponsky
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, United States of America,Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, United States of America,Department of Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America,Department of Global Health, University of Washington School of Medicine, Seattle, Washington, United States of America,Corresponding author: Adrian M. Piliponsky, Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, 1900 9th Ave, Room 721, , Phone number: 206-884-7226, Fax number: 206-987-7310
| |
Collapse
|
5
|
Wojtowicz WM, Vielmetter J, Fernandes RA, Siepe DH, Eastman CL, Chisholm GB, Cox S, Klock H, Anderson PW, Rue SM, Miller JJ, Glaser SM, Bragstad ML, Vance J, Lam AW, Lesley SA, Zinn K, Garcia KC. A Human IgSF Cell-Surface Interactome Reveals a Complex Network of Protein-Protein Interactions. Cell 2021; 182:1027-1043.e17. [PMID: 32822567 PMCID: PMC7440162 DOI: 10.1016/j.cell.2020.07.025] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/19/2020] [Accepted: 07/17/2020] [Indexed: 12/17/2022]
Abstract
Cell-surface protein-protein interactions (PPIs) mediate cell-cell communication, recognition, and responses. We executed an interactome screen of 564 human cell-surface and secreted proteins, most of which are immunoglobulin superfamily (IgSF) proteins, using a high-throughput, automated ELISA-based screening platform employing a pooled-protein strategy to test all 318,096 PPI combinations. Screen results, augmented by phylogenetic homology analysis, revealed ∼380 previously unreported PPIs. We validated a subset using surface plasmon resonance and cell binding assays. Observed PPIs reveal a large and complex network of interactions both within and across biological systems. We identified new PPIs for receptors with well-characterized ligands and binding partners for “orphan” receptors. New PPIs include proteins expressed on multiple cell types and involved in diverse processes including immune and nervous system development and function, differentiation/proliferation, metabolism, vascularization, and reproduction. These PPIs provide a resource for further biological investigation into their functional relevance and may offer new therapeutic drug targets. Human IgSF interactome reveals complex network of cell-surface protein interactions Phylogenetic homology analysis predicts protein-protein interactions ∼380 previously unknown protein-protein interactions identified Deorphanization of receptors and new binding partners for well-studied receptors
Collapse
Affiliation(s)
- Woj M Wojtowicz
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Jost Vielmetter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ricardo A Fernandes
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Dirk H Siepe
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Catharine L Eastman
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gregory B Chisholm
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Sarah Cox
- The Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Heath Klock
- The Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Paul W Anderson
- The Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Sarah M Rue
- The Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Jessica J Miller
- The Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Scott M Glaser
- The Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Melisa L Bragstad
- The Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Julie Vance
- The Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Annie W Lam
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Scott A Lesley
- The Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Kai Zinn
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| |
Collapse
|
6
|
Zhang Y, Liu T, Wang J, Zou B, Li L, Yao L, Chen K, Ning L, Wu B, Zhao X, Wang D. Cellinker: a platform of ligand-receptor interactions for intercellular communication analysis. Bioinformatics 2021; 37:btab036. [PMID: 33471060 PMCID: PMC7929259 DOI: 10.1093/bioinformatics/btab036] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/10/2020] [Accepted: 01/14/2020] [Indexed: 12/18/2022] Open
Abstract
MOTIVATION Ligand-receptor (L-R) interactions mediate cell adhesion, recognition and communication and play essential roles in physiological and pathological signaling. With the rapid development of single-cell RNA sequencing (scRNA-seq) technologies, systematically decoding the intercellular communication network involving L-R interactions has become a focus of research. Therefore, construction of a comprehensive, high-confidence and well-organized resource to retrieve L-R interactions in order to study the functional effects of cell-cell communications would be of great value. RESULTS In this study, we developed Cellinker, a manually curated resource of literature-supported L-R interactions that play roles in cell-cell communication. We aimed to provide a useful platform for studies on cell-cell communication mediated by L-R interactions. The current version of Cellinker documents over 3,700 human and 3,200 mouse L-R protein-protein interactions (PPIs) and embeds a practical and convenient webserver with which researchers can decode intercellular communications based on scRNA-seq data. And over 400 endogenous small molecule (sMOL) related L-R interactions were collected as well. Moreover, to help with research on coronavirus (CoV) infection, Cellinker collects information on 16 L-R PPIs involved in CoV-human interactions (including 12 L-R PPIs involved in SARS-CoV-2 infection). In summary, Cellinker provides a user-friendly interface for querying, browsing and visualizing L-R interactions as well as a practical and convenient web tool for inferring intercellular communications based on scRNA-seq data. We believe this platform could promote intercellular communication research and accelerate the development of related algorithms for scRNA-seq studies. AVAILABILITY Cellinker is available at http://www.rna-society.org/cellinker/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Yang Zhang
- Shunde Hospital, Southern Medical University (The First People’s Hospital of Shunde Foshan), Foshan 528308, China
| | - Tianyuan Liu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jing Wang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Bohao Zou
- Department of Statistics, University of California Davis, Davis, CA 95616, USA
| | - Le Li
- Department of Pathology, Harbin Medical University, Harbin 150081, China
| | - Linhui Yao
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Kechen Chen
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Lin Ning
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Bingyi Wu
- Shunde Hospital, Southern Medical University (The First People’s Hospital of Shunde Foshan), Foshan 528308, China
| | - Xiaoyang Zhao
- Shunde Hospital, Southern Medical University (The First People’s Hospital of Shunde Foshan), Foshan 528308, China
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Dong Wang
- Shunde Hospital, Southern Medical University (The First People’s Hospital of Shunde Foshan), Foshan 528308, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| |
Collapse
|
7
|
He X, Lei S, Zhang Q, Ma L, Li N, Wang J. Deregulation of cell adhesion molecules is associated with progression and poor outcomes in endometrial cancer: Analysis of The Cancer Genome Atlas data. Oncol Lett 2020; 19:1906-1914. [PMID: 32194686 PMCID: PMC7039152 DOI: 10.3892/ol.2020.11295] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 11/15/2019] [Indexed: 01/14/2023] Open
Abstract
Cell adhesion molecules (CAMs) determine the behavior of cancer cells during metastasis. Although some CAMs are dysregulated in certain types of cancer and are associated with cancer progression, to the best of our knowledge, a comprehensive study of CAMs has not been undertaken, particularly in endometrial cancer (EC). In the present study the expression of 225 CAMs in EC patients with various clinicopathological phenotypes were evaluated by statistical analysis using publicly available data from The Cancer Genome Atlas database. The Kaplan-Meier method, and univariate and multivariate Cox proportional hazards regression models were used for survival analyses. Among the differentially expressed CAMs that were associated with aggressive clinicopathological phenotypes, 10 CAM genes were independent prognostic factors compared with other clinicopathological prognostic factors, including stage, grade, age, lymph node status, peritoneal cytology and histological subtype. A total of six genes (L1 cell adhesion molecule, mucin 15, cell surface associated, cell adhesion associated, oncogene regulated, immunoglobulin superfamily member 9B, protocadherin 9 and protocadherin β1) were selected for integrative analysis. The six-gene signature was demonstrated to be an independent prognostic factor and could effectively stratify patients with different risks. Patients with more high-expression CAMs had a higher risk of poor overall survival (OS) rate. The mortality risk for patients with elevation of >4 CAMs was 11 times of that in those without elevation of these 6 CAMs. Similar results were obtained when relapse-free survival (RFS) time was used during the analysis. Prognostic reliability of the six-gene model was validated using data of an independent cohort from the International Cancer Genome Consortium. In conclusion, a combination of CAM alterations contributed to progression and aggressiveness of EC. The six-gene signature was effective for predicting worse OS and RFS in patients with EC and could be complementary to the present clinical prognostic criteria.
Collapse
Affiliation(s)
- Xiangjun He
- Central Laboratory and Institute of Clinical Molecular Biology, Peking University People's Hospital, Beijing 100044, P.R. China
| | - Shu Lei
- Central Laboratory and Institute of Clinical Molecular Biology, Peking University People's Hospital, Beijing 100044, P.R. China.,Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing 100044, P.R. China
| | - Qi Zhang
- Central Laboratory and Institute of Clinical Molecular Biology, Peking University People's Hospital, Beijing 100044, P.R. China
| | - Liping Ma
- Central Laboratory and Institute of Clinical Molecular Biology, Peking University People's Hospital, Beijing 100044, P.R. China
| | - Na Li
- Central Laboratory and Institute of Clinical Molecular Biology, Peking University People's Hospital, Beijing 100044, P.R. China
| | - Jianliu Wang
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing 100044, P.R. China
| |
Collapse
|
8
|
Identification of Key Genes and Prognostic Value Analysis in Hepatocellular Carcinoma by Integrated Bioinformatics Analysis. Int J Genomics 2019; 2019:3518378. [PMID: 31886163 PMCID: PMC6893264 DOI: 10.1155/2019/3518378] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/07/2019] [Accepted: 08/20/2019] [Indexed: 01/17/2023] Open
Abstract
Emerging evidence indicates that various functional genes with altered expression are involved in the tumor progression of human cancers. This study is aimed at identifying novel key genes that may be used for hepatocellular carcinoma (HCC) diagnosis, prognosis, and targeted therapy. This study included 3 expression profiles (GSE45267, GSE74656, and GSE84402), which were obtained from the Gene Expression Omnibus (GEO). GEO2R was used to analyze the differentially expressed genes (DEGs) between HCC and normal samples. The functional and pathway enrichment analysis was performed by the Database for Annotation, Visualization and Integrated Discovery. A protein-protein interaction (PPI) network of the identified DEGs was constructed using the Search Tool for the Retrieval of Interacting Gene, and hub genes were identified. ONCOMINE and CCLE databases were used to verify the expression of the hub genes in HCC tissues and cells. Kaplan-Meier plotter was used to assess the effects of the hub genes on the overall survival of HCC patients. A total of 99 DEGs were identified from the 3 expression profiles. These DEGs were enriched with functional processes and pathways related to HCC pathogenesis. From the PPI network, 5 hub genes were identified. The expression of the 5 hub genes was all upregulated in HCC tissues and cells compared with the control tissues and cells. Kaplan-Meier survival curves indicated that high expression of cyclin-dependent kinase (CDK1), cyclin B1 (CCNB1), cyclin B2 (CCNB2), MAD2 mitotic arrest deficient-like 1 (MAD2L1), and topoisomerase IIα (TOP2A) predicted poor overall survival in HCC patients (all log-rank P < 0.01). These results revealed that the DEGs may serve as candidate key genes during HCC pathogenesis. The 5 hub genes, including CDK1, CCNB1, CCNB2, MAD2L1, and TOP2A, may serve as promising prognostic biomarkers in HCC.
Collapse
|
9
|
Bausch-Fluck D, Goldmann U, Müller S, van Oostrum M, Müller M, Schubert OT, Wollscheid B. The in silico human surfaceome. Proc Natl Acad Sci U S A 2018; 115:E10988-E10997. [PMID: 30373828 PMCID: PMC6243280 DOI: 10.1073/pnas.1808790115] [Citation(s) in RCA: 188] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Cell-surface proteins are of great biomedical importance, as demonstrated by the fact that 66% of approved human drugs listed in the DrugBank database target a cell-surface protein. Despite this biomedical relevance, there has been no comprehensive assessment of the human surfaceome, and only a fraction of the predicted 5,000 human transmembrane proteins have been shown to be located at the plasma membrane. To enable analysis of the human surfaceome, we developed the surfaceome predictor SURFY, based on machine learning. As a training set, we used experimentally verified high-confidence cell-surface proteins from the Cell Surface Protein Atlas (CSPA) and trained a random forest classifier on 131 features per protein and, specifically, per topological domain. SURFY was used to predict a human surfaceome of 2,886 proteins with an accuracy of 93.5%, which shows excellent overlap with known cell-surface protein classes (i.e., receptors). In deposited mRNA data, we found that between 543 and 1,100 surfaceome genes were expressed in cancer cell lines and maximally 1,700 surfaceome genes were expressed in embryonic stem cells and derivative lines. Thus, the surfaceome diversity depends on cell type and appears to be more dynamic than the nonsurface proteome. To make the predicted surfaceome readily accessible to the research community, we provide visualization tools for intuitive interrogation (wlab.ethz.ch/surfaceome). The in silico surfaceome enables the filtering of data generated by multiomics screens and supports the elucidation of the surfaceome nanoscale organization.
Collapse
Affiliation(s)
- Damaris Bausch-Fluck
- Institute of Molecular Systems Biology at the Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
- Biomedical Proteomics Platform, Department of Health Sciences and Technology, ETH Zurich, 8093 Zurich, Switzerland
| | - Ulrich Goldmann
- Institute of Molecular Systems Biology at the Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Sebastian Müller
- Institute of Molecular Systems Biology at the Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Marc van Oostrum
- Institute of Molecular Systems Biology at the Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
- Biomedical Proteomics Platform, Department of Health Sciences and Technology, ETH Zurich, 8093 Zurich, Switzerland
| | - Maik Müller
- Institute of Molecular Systems Biology at the Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
- Biomedical Proteomics Platform, Department of Health Sciences and Technology, ETH Zurich, 8093 Zurich, Switzerland
| | - Olga T Schubert
- Institute of Molecular Systems Biology at the Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Bernd Wollscheid
- Institute of Molecular Systems Biology at the Department of Biology, ETH Zurich, 8093 Zurich, Switzerland;
- Biomedical Proteomics Platform, Department of Health Sciences and Technology, ETH Zurich, 8093 Zurich, Switzerland
| |
Collapse
|
10
|
Wang Y, Wang Y, Liu F. A 44-gene set constructed for predicting the prognosis of clear cell renal cell carcinoma. Int J Mol Med 2018; 42:3105-3114. [PMID: 30272265 PMCID: PMC6202093 DOI: 10.3892/ijmm.2018.3899] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 09/07/2018] [Indexed: 12/14/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most frequent type of renal cell carcinoma (RCC). The present study aimed to examine prognostic markers and construct a prognostic prediction system for ccRCC. The mRNA sequencing data of ccRCC was downloaded from The Cancer Genome Atlas (TCGA) database, and the GSE40435 dataset was obtained from the Gene Expression Omnibus database. Using the Limma package, the differentially expressed genes (DEGs) in the TCGA dataset and GSE40435 dataset were obtained, respectively, and the overlapped DEGs were selected. Subsequently, Cox regression analysis was applied for screening prognosis-associated genes. Following visualization of the co-expression network using Cytoscape software, the network modules were examined using the GraphWeb tool. Functional annotation for genes in the network was performed using the clusterProfiler package. Finally, a prognostic prediction system was constructed through Bayes discriminant analysis and confirmed with the GSE29609 validation dataset. The results revealed a total of 263 overlapped DEGs and 161 prognosis-associated genes. Following construction of the co-expression network, 16 functional terms and three pathways were obtained for genes in the network. In addition, red, yellow (Involving chemokine ligand 10 (CXCL10), CD27 molecule (CD27) and runt-related transcription factor 3 (RUNX3)], green (Involving angiopoietin-like 4 (ANGPTL4), stannio-calcin 2 (STC2), and sperm associated antigen 4 (SPAG4)], and cyan modules were extracted from the co-expression network. Additionally, the prognostic prediction system involving 44 signature genes, including ANGPTL4, STC2, CXCL10, SPAG4, CD27, matrix metalloproteinase (MMP9) and RUNX3, was identified and confirmed. In conclusion, the 44-gene prognostic prediction system involving ANGPTL4, STC2, CXCL10, SPAG4, CD27, MMP9 and RUNX3 may be utilized for predicting the prognosis of patients with ccRCC.
Collapse
Affiliation(s)
- Yonggang Wang
- Department of Urology, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Yao Wang
- Department of Urology, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Feng Liu
- Department of Urology, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| |
Collapse
|
11
|
Ajina A, Maher J. Prospects for combined use of oncolytic viruses and CAR T-cells. J Immunother Cancer 2017; 5:90. [PMID: 29157300 PMCID: PMC5696728 DOI: 10.1186/s40425-017-0294-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/17/2017] [Indexed: 12/18/2022] Open
Abstract
With the approval of talimogene laherparepvec (T-VEC) for inoperable locally advanced or metastatic malignant melanoma in the USA and Europe, oncolytic virotherapy is now emerging as a viable therapeutic option for cancer patients. In parallel, following the favourable results of several clinical trials, adoptive cell transfer using chimeric antigen receptor (CAR)-redirected T-cells is anticipated to enter routine clinical practice for the management of chemotherapy-refractory B-cell malignancies. However, CAR T-cell therapy for patients with advanced solid tumours has proved far less successful. This Review draws upon recent advances in the design of novel oncolytic viruses and CAR T-cells and provides a comprehensive overview of the synergistic potential of combination oncolytic virotherapy with CAR T-cell adoptive cell transfer for the management of solid tumours, drawing particular attention to the methods by which recombinant oncolytic viruses may augment CAR T-cell trafficking into the tumour microenvironment, mitigate or reverse local immunosuppression and enhance CAR T-cell effector function and persistence.
Collapse
Affiliation(s)
- Adam Ajina
- Department of Oncology, Royal Free London NHS Foundation Trust, London, UK
| | - John Maher
- King’s College London, CAR Mechanics Group, School of Cancer and Pharmaceutical Sciences, Guy’s Hospital Campus, Great Maze Pond, London, SE1 9RT UK
- Department of Clinical Immunology and Allergy, King’s College Hospital NHS Foundation Trust, London, UK
- Department of Immunology, Eastbourne Hospital, East Sussex, UK
| |
Collapse
|
12
|
da Silva VL, Fonseca AF, Fonseca M, da Silva TE, Coelho AC, Kroll JE, de Souza JES, Stransky B, de Souza GA, de Souza SJ. Genome-wide identification of cancer/testis genes and their association with prognosis in a pan-cancer analysis. Oncotarget 2017; 8:92966-92977. [PMID: 29190970 PMCID: PMC5696236 DOI: 10.18632/oncotarget.21715] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 08/17/2017] [Indexed: 11/29/2022] Open
Abstract
Cancer/testis (CT) genes are excellent candidates for cancer immunotherapies because of their restrict expression in normal tissues and the capacity to elicit an immune response when expressed in tumor cells. In this study, we provide a genome-wide screen for CT genes with the identification of 745 putative CT genes. Comparison with a set of known CT genes shows that 201 new CT genes were identified. Integration of gene expression and clinical data led us to identify dozens of CT genes associated with either good or poor prognosis. For the CT genes related to good prognosis, we show that there is a direct relationship between CT gene expression and a signal for CD8+ cells infiltration for some tumor types, especially melanoma.
Collapse
Affiliation(s)
- Vandeclecio Lira da Silva
- Instituto do Cérebro, UFRN, Natal, Brazil.,Ph.D. Program in Bioinformatics, UFRN, Natal, Brazil.,Bioinformatics Multidisciplinary Environment (BioME), Digital Metropolis Institute, UFRN, Natal, Brazil
| | - André Faustino Fonseca
- Instituto do Cérebro, UFRN, Natal, Brazil.,Ph.D. Program in Bioinformatics, UFRN, Natal, Brazil.,Bioinformatics Multidisciplinary Environment (BioME), Digital Metropolis Institute, UFRN, Natal, Brazil
| | | | | | - Ana Carolina Coelho
- Instituto do Cérebro, UFRN, Natal, Brazil.,Bioinformatics Multidisciplinary Environment (BioME), Digital Metropolis Institute, UFRN, Natal, Brazil
| | - José Eduardo Kroll
- Instituto do Cérebro, UFRN, Natal, Brazil.,Bioinformatics Multidisciplinary Environment (BioME), Digital Metropolis Institute, UFRN, Natal, Brazil.,Instituto de Bioinformática e Biotecnologia, Natal, Brazil
| | - Jorge Estefano Santana de Souza
- Bioinformatics Multidisciplinary Environment (BioME), Digital Metropolis Institute, UFRN, Natal, Brazil.,Instituto Metrópole Digital, UFRN, Natal, Brazil
| | - Beatriz Stransky
- Bioinformatics Multidisciplinary Environment (BioME), Digital Metropolis Institute, UFRN, Natal, Brazil.,Departmento de Engenharia Biomédica, UFRN, Natal, Brazil
| | - Gustavo Antonio de Souza
- Instituto do Cérebro, UFRN, Natal, Brazil.,Bioinformatics Multidisciplinary Environment (BioME), Digital Metropolis Institute, UFRN, Natal, Brazil
| | - Sandro José de Souza
- Instituto do Cérebro, UFRN, Natal, Brazil.,Bioinformatics Multidisciplinary Environment (BioME), Digital Metropolis Institute, UFRN, Natal, Brazil
| |
Collapse
|