1
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Chen Q, Zhou Q. Identification of exosome-related gene signature as a promising diagnostic and therapeutic tool for breast cancer. Heliyon 2024; 10:e29551. [PMID: 38665551 PMCID: PMC11043961 DOI: 10.1016/j.heliyon.2024.e29551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Background Exosomes are promising tools for the development of new diagnostic and therapeutic approaches. Exosomes possess the ability to activate signaling pathways that contribute to the remodeling of the tumor microenvironment, angiogenesis, and the regulation of immune responses. We aimed to develop a prognostic score based on exosomes derived from breast cancer. Materials and methods Training was conducted on the TCGA-BRCA dataset, while validation was conducted on GSE20685, GSE5764, GSE7904, and GSE29431. A total of 121 genes related to exosomes were retrieved from the ExoBCD database. The Cox proportional hazards model is used to develop risk score model. The GSVA package was utilized to analyze single-sample gene sets and identify exosome signatures, while the WGCNA package was utilized to identify gene modules associated with clinical outcomes. The clusterProfiler and GSVA R packages facilitated gene set enrichment and variation analyses. Furthermore, CIBERSORT quantified immune infiltration, and a correlation between gene expression and drug sensitivity was assessed using the TIDE algorithm. Results An exosome-related prognostic score was established using the following selected genes: ABCC9, PIGR, CXCL13, DOK7, CD24, and IVL. Various immune cells that promote cancer immune evasion were associated with a high-risk prognostic score, which was an independent predictor of outcome. High-risk and low-risk groups exhibited significantly different infiltration abundances (p < 0.05). By conducting a sensitivity comparison, we found that patients with high-risk scores exhibited more favorable responses to immunotherapy than those with low-risk scores. Conclusion The exosome-related gene signature exhibits outstanding performance in predicting the prognosis and cancer status of patients with breast cancer and guiding immunotherapy.
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Affiliation(s)
- Qitong Chen
- Department of General Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Research Center for Breast Disease in Hunan Province, Changsha, Hunan, China
| | - Qin Zhou
- Department of General Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Research Center for Breast Disease in Hunan Province, Changsha, Hunan, China
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2
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Zhu G, Wang W, Yao H, Li H, Zhang C, Meng Y, Wang J, Zhu M, Zheng H. Identification and validation of novel prognostic signatures based on m5C methylation patterns and tumor EMT profiles in head and neck squamous cell carcinoma. Sci Rep 2023; 13:18763. [PMID: 37907576 PMCID: PMC10618291 DOI: 10.1038/s41598-023-45976-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/26/2023] [Indexed: 11/02/2023] Open
Abstract
The role of 5-methylcytosine (m5C) in tumor initiation and progression has been increasingly recognized. However, the precise association between the regulation of m5C and the progression, metastasis, and prognosis of head and neck squamous cell carcinoma (HNSCC) has not yet been fully explored. Data from 545 HNSCC patients obtained from The Cancer Genome Atlas (TCGA) database were analyzed. Unsupervised cluster analysis was conducted using the expression levels of m5C regulatory genes. Additionally, gene set variation analysis (GSVA), single-sample gene set enrichment analysis (ssGSEA), and Cox regression analysis were utilized. Quantitative reverse transcription polymerase chain reaction (RT-qPCR), colony formation assay, transwell experiments and western blots were performed in the HNSCC cell line UM-SCC-17B to assess the expression and functional role of one of the novel signatures, CNFN. Significant expression differences were found in m5C regulatory genes between tumor and normal tissues in HNSCC. Two distinct m5C modification patterns, characterized by substantial prognostic differences, were identified. Cluster-2, which exhibited a strong association with epithelial-mesenchymal transition (EMT), was found to be associated with a poorer prognosis. Based on the m5C clusters and EMT status, differentially expressed genes (DEGs) were identified. Using DEGs, an 8-gene signature (CAMK2N1, WNT7A, F2RL1, AREG, DEFB1, CNFN, TGFBI, and CAV1) was established to develop a prognostic model. The performance of this signature was validated in both the training and external validation datasets, demonstrating its promising efficacy. Furthermore, additional investigations using RT-qPCR on clinical specimens and experimental assays in cell lines provided compelling evidence suggesting that CNFN, one of the genes in the signature, could play a role in HNSCC progression and metastasis through the EMT pathway. This study highlighted the role of m5C in HNSCC progression and metastasis. The relationship between m5C and EMT has been elucidated for the first time. A robust prognostic model was developed for accurately predicting HNSCC patients' survival outcomes. Potential molecular mechanisms underlying these associations have been illuminated through this research.
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Affiliation(s)
- Guanghao Zhu
- Department of Otolaryngology Head and Neck Surgery, Shanghai Changhai Hospital, The Second Military Medical University, Shanghai, China
| | - Wei Wang
- Department of Otolaryngology Head and Neck Surgery, Shanghai Changhai Hospital, The Second Military Medical University, Shanghai, China
| | - Hui Yao
- Department of Otolaryngology Head and Neck Surgery, Shanghai Changhai Hospital, The Second Military Medical University, Shanghai, China
| | - Haopu Li
- Department of Otolaryngology Head and Neck Surgery, Shanghai Changhai Hospital, The Second Military Medical University, Shanghai, China
| | - Caiyun Zhang
- Department of Otolaryngology Head and Neck Surgery, Shanghai Changhai Hospital, The Second Military Medical University, Shanghai, China
| | - Yindi Meng
- Department of Otolaryngology Head and Neck Surgery, Shanghai Changhai Hospital, The Second Military Medical University, Shanghai, China
| | - Jingjie Wang
- Department of Otolaryngology Head and Neck Surgery, Shanghai Changhai Hospital, The Second Military Medical University, Shanghai, China
| | - Minhui Zhu
- Department of Otolaryngology Head and Neck Surgery, Shanghai Changhai Hospital, The Second Military Medical University, Shanghai, China.
| | - Hongliang Zheng
- Department of Otolaryngology Head and Neck Surgery, Shanghai Changhai Hospital, The Second Military Medical University, Shanghai, China.
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3
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Warrick JI, Hu W, Yamashita H, Walter V, Shuman L, Craig JM, Gellert LL, Castro MAA, Robertson AG, Kuo F, Ostrovnaya I, Sarungbam J, Chen YB, Gopalan A, Sirintrapun SJ, Fine SW, Tickoo SK, Kim K, Thomas J, Karan N, Gao SP, Clinton TN, Lenis AT, Chan TA, Chen Z, Rao M, Hollman TJ, Li Y, Socci ND, Chavan S, Viale A, Mohibullah N, Bochner BH, Pietzak EJ, Teo MY, Iyer G, Rosenberg JE, Bajorin DF, Kaag M, Merrill SB, Joshi M, Adam R, Taylor JA, Clark PE, Raman JD, Reuter VE, Chen Y, Funt SA, Solit DB, DeGraff DJ, Al-Ahmadie HA. FOXA1 repression drives lineage plasticity and immune heterogeneity in bladder cancers with squamous differentiation. Nat Commun 2022; 13:6575. [PMID: 36323682 PMCID: PMC9630410 DOI: 10.1038/s41467-022-34251-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
Cancers arising from the bladder urothelium often exhibit lineage plasticity with regions of urothelial carcinoma adjacent to or admixed with regions of divergent histomorphology, most commonly squamous differentiation. To define the biologic basis for and clinical significance of this morphologic heterogeneity, here we perform integrated genomic analyses of mixed histology bladder cancers with separable regions of urothelial and squamous differentiation. We find that squamous differentiation is a marker of intratumoral genomic and immunologic heterogeneity in patients with bladder cancer and a biomarker of intrinsic immunotherapy resistance. Phylogenetic analysis confirms that in all cases the urothelial and squamous regions are derived from a common shared precursor. Despite the presence of marked genomic heterogeneity between co-existent urothelial and squamous differentiated regions, no recurrent genomic alteration exclusive to the urothelial or squamous morphologies is identified. Rather, lineage plasticity in bladder cancers with squamous differentiation is associated with loss of expression of FOXA1, GATA3, and PPARG, transcription factors critical for maintenance of urothelial cell identity. Of clinical significance, lineage plasticity and PD-L1 expression is coordinately dysregulated via FOXA1, with patients exhibiting morphologic heterogeneity pre-treatment significantly less likely to respond to immune checkpoint inhibitors.
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Affiliation(s)
- Joshua I Warrick
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Wenhuo Hu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hironobu Yamashita
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, Hershey, PA, USA
- Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Vonn Walter
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Lauren Shuman
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, Hershey, PA, USA
- Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Jenna M Craig
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, Hershey, PA, USA
- Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Lan L Gellert
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mauro A A Castro
- Bioinformatics and Systems Biology Laboratory, Federal University of Parana, Curitiba, Paraná, Brazil
| | - A Gordon Robertson
- BC Cancer, Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Fengshen Kuo
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Irina Ostrovnaya
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Judy Sarungbam
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ying-Bei Chen
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anuradha Gopalan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sahussapont J Sirintrapun
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samson W Fine
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Satish K Tickoo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kwanghee Kim
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jasmine Thomas
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nagar Karan
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sizhi Paul Gao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timothy N Clinton
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew T Lenis
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ziyu Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Manisha Rao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Travis J Hollman
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yanyun Li
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicholas D Socci
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shweta Chavan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Agnes Viale
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Neeman Mohibullah
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bernard H Bochner
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eugene J Pietzak
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Min Yuen Teo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gopa Iyer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jonathan E Rosenberg
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dean F Bajorin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew Kaag
- Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Suzanne B Merrill
- Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Monika Joshi
- Department of Medicine, Division of Hematology-Oncology, Penn State Cancer Institute, Hershey, PA, USA
| | - Rosalyn Adam
- Department of Urology, Boston Children's Hospital, Boston, MA, USA
| | - John A Taylor
- Department of Urology, University of Kansas Medical Center, Kansas City, MO, USA
| | - Peter E Clark
- Levine Cancer Institute, Atrium Health, Charlotte, NC, USA
| | - Jay D Raman
- Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Victor E Reuter
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yu Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samuel A Funt
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David B Solit
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David J DeGraff
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, Hershey, PA, USA.
- Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, USA.
- Deparment of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, USA.
| | - Hikmat A Al-Ahmadie
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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4
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Suprabasin: Role in human cancers and other diseases. Mol Biol Rep 2021; 49:1453-1461. [PMID: 34775572 DOI: 10.1007/s11033-021-06897-7] [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: 08/06/2021] [Accepted: 10/29/2021] [Indexed: 10/19/2022]
Abstract
Suprabasin (SBSN), a gene with unknown function located in q13 region of chromosome 19, was first found to be expressed in the basal layer of the stratified epithelium in mouse and human tissues and was thought to be a potential precursor of keratinized capsules. However, in recent years, significant progress has been made in the study of SBSN in a variety of human diseases. One common theme appears to be the effect of SBSN on tumor progression, such as invasion, metastasis and resistance. However, the function and mechanism of action of SBSN is still elusive. In this study, we reviewed the literature on SBSN in the PubMed database to identify the basic characteristics, biological functions, and roles of SBSN in cancer and other diseases. In particular, we focused on the potential mechanisms of SBSN activity, to improve our understanding of the complex function of this protein and provide a theoretical basis for further research on the role of SBSN in cancer and other diseases.
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5
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Li W, Zhao Y, Wang D, Ding Z, Li C, Wang B, Xue X, Ma J, Deng Y, Liu Q, Zhang G, Zhang Y, Wang K, Yuan B. Transcriptome research identifies four hub genes related to primary myelofibrosis: a holistic research by weighted gene co-expression network analysis. Aging (Albany NY) 2021; 13:23284-23307. [PMID: 34633991 PMCID: PMC8544335 DOI: 10.18632/aging.203619] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 09/29/2021] [Indexed: 01/14/2023]
Abstract
Objectives: This study aimed to identify specific diagnostic as well as predictive targets of primary myelofibrosis (PMF). Methods: The gene expression profiles of GSE26049 were obtained from Gene Expression Omnibus (GEO) dataset, WGCNA was constructed to identify the most related module of PMF. Subsequently, Gene Ontology (GO), Kyoto Encyclopedia Genes and Genomes (KEGG), Gene Set Enrichment Analysis (GSEA) and Protein-Protein interaction (PPI) network were conducted to fully understand the detailed information of the interested green module. Machine learning, Principal component analysis (PCA), and expression pattern analysis including immunohistochemistry and immunofluorescence of genes and proteins were performed to validate the reliability of these hub genes. Results: Green module was strongly correlated with PMF disease after WGCNA analysis. 20 genes in green module were identified as hub genes responsible for the progression of PMF. GO, KEGG revealed that these hub genes were primarily enriched in erythrocyte differentiation, transcription factor binding, hemoglobin complex, transcription factor complex and cell cycle, etc. Among them, EPB42, CALR, SLC4A1 and MPL had the most correlations with PMF. Machine learning, Principal component analysis (PCA), and expression pattern analysis proved the results in this study. Conclusions: EPB42, CALR, SLC4A1 and MPL were significantly highly expressed in PMF samples. These four genes may be considered as candidate prognostic biomarkers and potential therapeutic targets for early stage of PMF. The effects are worth expected whether in the diagnosis at early stage or as therapeutic target.
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Affiliation(s)
- Weihang Li
- Department of Orthopaedics, Xijing Hospital, The Fourth Military Medical University, Xi'an 710032, People's Republic of China
| | - Yingjing Zhao
- Department of Intensive Care Unit, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu Province, China
| | - Dong Wang
- Department of Orthopaedics, Xijing Hospital, The Fourth Military Medical University, Xi'an 710032, People's Republic of China
| | - Ziyi Ding
- Department of Orthopaedics, Xijing Hospital, The Fourth Military Medical University, Xi'an 710032, People's Republic of China
| | - Chengfei Li
- Department of Aerospace Medical Training, School of Aerospace Medicine, Fourth Military Medical University, Xi'an 710032, Shaanxi, China
| | - Bo Wang
- Department of Spine Surgery, Daxing Hospital, Xi'an 710016, Shaanxi, China
| | - Xiong Xue
- Department of Spine Surgery, Daxing Hospital, Xi'an 710016, Shaanxi, China
| | - Jun Ma
- Department of Spine Surgery, Daxing Hospital, Xi'an 710016, Shaanxi, China
| | - Yajun Deng
- Department of Spine Surgery, Daxing Hospital, Xi'an 710016, Shaanxi, China
| | - Quancheng Liu
- Department of Spine Surgery, Daxing Hospital, Xi'an 710016, Shaanxi, China
| | - Guohua Zhang
- Department of Spine Surgery, Daxing Hospital, Xi'an 710016, Shaanxi, China
| | - Ying Zhang
- Department of Spine Surgery, Daxing Hospital, Xi'an 710016, Shaanxi, China
| | - Kai Wang
- Department of Hematology, Daxing Hospital, Xi'an 710016, Shaanxi, China
| | - Bin Yuan
- Department of Spine Surgery, Daxing Hospital, Xi'an 710016, Shaanxi, China
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Liu YQ, Zou HY, Xie JJ, Fang WK. Paradoxical Roles of Desmosomal Components in Head and Neck Cancer. Biomolecules 2021; 11:biom11060914. [PMID: 34203070 PMCID: PMC8234459 DOI: 10.3390/biom11060914] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/14/2021] [Accepted: 06/16/2021] [Indexed: 02/05/2023] Open
Abstract
Desmosomes are intercellular adhesion complexes involved in various aspects of epithelial pathophysiology, including tissue homeostasis, morphogenesis, and disease development. Recent studies have reported that the abnormal expression of various desmosomal components correlates with tumor progression and poor survival. In addition, desmosomes have been shown to act as a signaling platform to regulate the proliferation, invasion, migration, morphogenesis, and apoptosis of cancer cells. The occurrence and progression of head and neck cancer (HNC) is accompanied by abnormal expression of desmosomal components and loss of desmosome structure. However, the role of desmosomal components in the progression of HNC remains controversial. This review aims to provide an overview of recent developments showing the paradoxical roles of desmosomal components in tumor suppression and promotion. It offers valuable insights for HNC diagnosis and therapeutics development.
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Affiliation(s)
- Yin-Qiao Liu
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China; (Y.-Q.L.); (H.-Y.Z.)
| | - Hai-Ying Zou
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China; (Y.-Q.L.); (H.-Y.Z.)
| | - Jian-Jun Xie
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China; (Y.-Q.L.); (H.-Y.Z.)
- Precision Medicine Research Center, Shantou University Medical College, Shantou 515041, China
- Correspondence: (J.-J.X.); (W.-K.F.)
| | - Wang-Kai Fang
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China; (Y.-Q.L.); (H.-Y.Z.)
- Precision Medicine Research Center, Shantou University Medical College, Shantou 515041, China
- Correspondence: (J.-J.X.); (W.-K.F.)
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7
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Xu Y, Xu F, Lv Y, Wang S, Li J, Zhou C, Jiang J, Xie B, He F. A ceRNA-associated risk model predicts the poor prognosis for head and neck squamous cell carcinoma patients. Sci Rep 2021; 11:6374. [PMID: 33737696 PMCID: PMC7973582 DOI: 10.1038/s41598-021-86048-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 03/09/2021] [Indexed: 02/06/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is one of the most malignant cancers with poor prognosis worldwide. Emerging evidence indicates that competing endogenous RNAs (ceRNAs) are involved in various diseases, however, the regulatory mechanisms of ceRNAs underlying HNSCC remain unclear. In this study, we retrieved differentially expressed long non-coding RNAs (DElncRNAs), messenger RNAs (DEmRNAs) and microRANs (DEmiRNAs) from The Cancer Genome Atlas database and constructed a ceRNA-based risk model in HNSCC by integrated bioinformatics approaches. Functional enrichment analyses showed that DEmRNAs might be involved in extracellular matrix related biological processes, and protein–protein interaction network further selected out prognostic genes, including MYL1 and ACTN2. Importantly, co-expressed RNAs identified by weighted co-expression gene network analysis constructed the ceRNA networks. Moreover, AC114730.3, AC136375.3, LAT and RYR3 were highly correlated to overall survival of HNSCC by Kaplan–Meier method and univariate Cox regression analysis, which were subsequently implemented multivariate Cox regression analysis to build the risk model. Our study provides a deeper understanding of ceRNAs on the regulatory mechanisms, which will facilitate the expansion of the roles on the ceRNAs in the tumorigenesis, development and treatment of HNSCC.
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Affiliation(s)
- Yuzi Xu
- Department of Oral Implantology and Prosthodontics, The Affiliated Hospital of Stomatology, School of Stomatology, Zhejiang University School of Medicine, and Key Laboratory of Oral Biomedical Research of Zhejiang Province, 395# Yanan Road, Hangzhou, 310006, Zhejiang, People's Republic of China
| | - Fengqin Xu
- The First Affiliated Hospital of Kangda College of Nanjing Medical University, The First People's Hospital of Lianyungang, The Affiliated Lianyungang Hospital of Xuzhou Medical University, Lianyungang, 222000, Jiangsu, People's Republic of China
| | - Yiming Lv
- Department of Colorectal Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, Zhejiang, People's Republic of China
| | - Siyuan Wang
- Department of Oral Implantology and Prosthodontics, The Affiliated Hospital of Stomatology, School of Stomatology, Zhejiang University School of Medicine, and Key Laboratory of Oral Biomedical Research of Zhejiang Province, 395# Yanan Road, Hangzhou, 310006, Zhejiang, People's Republic of China
| | - Jia Li
- Department of Oral Implantology and Prosthodontics, The Affiliated Hospital of Stomatology, School of Stomatology, Zhejiang University School of Medicine, and Key Laboratory of Oral Biomedical Research of Zhejiang Province, 395# Yanan Road, Hangzhou, 310006, Zhejiang, People's Republic of China
| | - Chuan Zhou
- Department of Oral Implantology and Prosthodontics, The Affiliated Hospital of Stomatology, School of Stomatology, Zhejiang University School of Medicine, and Key Laboratory of Oral Biomedical Research of Zhejiang Province, 395# Yanan Road, Hangzhou, 310006, Zhejiang, People's Republic of China
| | - Jimin Jiang
- Department of Oral Implantology and Prosthodontics, The Affiliated Hospital of Stomatology, School of Stomatology, Zhejiang University School of Medicine, and Key Laboratory of Oral Biomedical Research of Zhejiang Province, 395# Yanan Road, Hangzhou, 310006, Zhejiang, People's Republic of China
| | - Binbin Xie
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3# East Qingchun Road, Hangzhou, 310016, Zhejiang, People's Republic of China.
| | - Fuming He
- Department of Oral Implantology and Prosthodontics, The Affiliated Hospital of Stomatology, School of Stomatology, Zhejiang University School of Medicine, and Key Laboratory of Oral Biomedical Research of Zhejiang Province, 395# Yanan Road, Hangzhou, 310006, Zhejiang, People's Republic of China.
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8
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Xiong Y, Ju L, Yuan L, Chen L, Wang G, Xu H, Peng T, Luo Y, Xiao Y, Wang X. KNSTRN promotes tumorigenesis and gemcitabine resistance by activating AKT in bladder cancer. Oncogene 2021; 40:1595-1608. [PMID: 33452459 DOI: 10.1038/s41388-020-01634-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 01/29/2023]
Abstract
KNSTRN is a component of the mitotic spindle, which was rarely investigated in tumorigenesis. AKT plays an essential role in tumorigenesis by modulating the phosphorylation of various substrates. The activation of AKT is regulated by PTEN and PIP3. Here, we prove KNSTRN is positively correlated with malignancy of bladder cancer and KNSTRN activates AKT phosphorylation at Thr308 and Ser473. More importantly, our study reveals that both KNSTRN and PTEN interact with PH domain of AKT at cell membrane. The amount of KNSTRN interacted with AKT is negatively related to PTEN. Furthermore, PIP3 pull-down assay proves that KNSTRN promoted AKT movement to PIP3. These data suggest KNSTRN may activate AKT phosphorylation by promoting AKT movement to PIP3 and alleviating PTEN suppression. Based on the activation of AKT phosphorylation, our study demonstrates that KNSTRN promotes bladder cancer metastasis and gemcitabine resistance in vitro and in vivo. Meanwhile, the effect of KNSTRN on tumorigenesis and gemcitabine resistance could be restored by AKT specific inhibitor MK2206 or AKT overexpression. In conclusion, we identify an oncogene KNSTRN that promotes tumorigenesis and gemcitabine resistance by activating AKT phosphorylation and may serve as a therapeutic target in bladder cancer.
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Affiliation(s)
- Yaoyi Xiong
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Lingao Ju
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Human Genetic Resource Preservation Center of Hubei Province, Wuhan, China.,Research Center of Wuhan for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
| | - Lushun Yuan
- Division of Nephrology, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Liang Chen
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, USA
| | - Gang Wang
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Human Genetic Resource Preservation Center of Hubei Province, Wuhan, China.,Research Center of Wuhan for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
| | - Huimin Xu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Tianchen Peng
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yongwen Luo
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yu Xiao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China. .,Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China. .,Human Genetic Resource Preservation Center of Hubei Province, Wuhan, China. .,Research Center of Wuhan for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China. .,Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China.
| | - Xinghuan Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China. .,Research Center of Wuhan for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China. .,Medical Research Institute, Wuhan University, Wuhan, China.
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9
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Abstract
Among the ~22,000 human genes, very few remain that have unknown functions. One such example is suprabasin (SBSN). Originally described as a component of the cornified envelope, the function of stratified epithelia-expressed SBSN is unknown. Both the lack of knowledge about the gene role under physiological conditions and the emerging link of SBSN to various human diseases, including cancer, attract research interest. The association of SBSN expression with poor prognosis of patients suffering from oesophageal carcinoma, glioblastoma multiforme, and myelodysplastic syndromes suggests that SBSN may play a role in human tumourigenesis. Three SBSN isoforms code for the secreted proteins with putative function as signalling molecules, yet with poorly described effects. In this first review about SBSN, we summarised the current knowledge accumulated since its original description, and we discuss the potential mechanisms and roles of SBSN in both physiology and pathology.
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10
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WFDC2 suppresses prostate cancer metastasis by modulating EGFR signaling inactivation. Cell Death Dis 2020; 11:537. [PMID: 32678075 PMCID: PMC7366654 DOI: 10.1038/s41419-020-02752-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 07/01/2020] [Accepted: 07/06/2020] [Indexed: 11/09/2022]
Abstract
WAP four-disulfide core domain 2 (WFDC2) is a small secretory protein that has been widely studied in ovarian cancer. It has been proven that WFDC2 promotes proliferation and metastasis in ovarian cancer, and serves as a diagnostic biomarker. However, the specific function of WFDC2 in prostate cancer has not been reported. Here, we first screened the diagnostic marker and favorable prognostic factor WFDC2 in prostate cancer by bioinformatics. WFDC2 expression was negatively correlated with Gleason score and metastasis in prostate cancer. Then, we revealed that overexpression of WFDC2, and addition of recombinant protein HE4 can significantly inhibit prostate cancer metastasis in vivo and in vitro. By co-immunoprecipitation and co-localization assays, we proved that WFDC2 binds to the extracellular domain of epidermal growth factor receptor (EGFR). Immunoblot showed that WFDC2 overexpression and recombinant protein HE4 addition inactivated the EGFR/AKT/GSK3B/Snail signaling pathway, and then restrained the progression of epithelial-mesenchymal transition. In conclusion, our study identified that the tumor suppressor WFDC2 can suppress prostate cancer metastasis by inactivating EGFR signaling.
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11
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Identification of Hub Genes as Biomarkers Correlated with the Proliferation and Prognosis in Lung Cancer: A Weighted Gene Co-Expression Network Analysis. BIOMED RESEARCH INTERNATIONAL 2020; 2020:3416807. [PMID: 32596300 PMCID: PMC7305540 DOI: 10.1155/2020/3416807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 01/27/2020] [Accepted: 02/03/2020] [Indexed: 12/24/2022]
Abstract
Lung cancer is one of the most malignant tumors in the world. Early diagnosis and treatment of lung cancer are vitally important to reduce the mortality of lung cancer patients. In the present study, we attempt to identify the candidate biomarkers for lung cancer by weighted gene co-expression network analysis (WGCNA). Gene expression profile of GSE30219 was downloaded from the gene expression omnibus (GEO) database. The differentially expressed genes (DEGs) were analyzed by the limma package, and the co-expression modules of genes were built by WGCNA. UALCAN was used to analyze the relative expression of normal group and tumor subgroups based on tumor individual cancer stages. Survival analysis for the hub genes was performed by Kaplan–Meier plotter analysis with the TCGA database. A total of 2176 genes (745 upregulated and 1431 downregulated genes) were obtained from the GSE30219 database. Seven gene co-expression modules were conducted by WGCNA and the blue module might be inferred as the most crucial module in the pathogenesis of lung cancer. In the pathway enrichment analysis of KEGG, the candidate genes were enriched in the “DNA replication,” “Cell cycle,” and “P53 signaling pathway” pathways. Among these, the cell cycle pathway was the most significant pathway in the blue module with four hub genes CCNB1, CCNE2, MCM7, and PCNA which were selected in our study. Kaplan–Meier plotter analysis indicated that the high expressions of four hub genes were correlated with a worse overall survival (OS) and advanced tumors. qRT-PCR showed that mRNA expression levels of MCM7 (p = 0.038) and CCNE2 (0.003) were significantly higher in patients with the TNM stage. In summary, the high expression of the MCM7 and CCNE2 were significantly related with advanced tumors and worse OS in lung cancer. Thus, the MCM7 and CCNE2 genes can be good indicators for cellular proliferation and prognosis in lung cancer.
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12
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Hu X, Sun G, Shi Z, Ni H, Jiang S. Identification and validation of key modules and hub genes associated with the pathological stage of oral squamous cell carcinoma by weighted gene co-expression network analysis. PeerJ 2020; 8:e8505. [PMID: 32117620 PMCID: PMC7006519 DOI: 10.7717/peerj.8505] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 01/03/2020] [Indexed: 12/18/2022] Open
Abstract
Background Oral squamous cell carcinoma (OSCC) is a major lethal malignant cancer of the head and neck region, yet its molecular mechanisms of tumourigenesis are still unclear. Patients and methods We performed weighted gene co-expression network analysis (WGCNA) on RNA-sequencing data with clinical information obtained from The Cancer Genome Atlas (TCGA) database. The relationship between co-expression modules and clinical traits was investigated by Pearson correlation analysis. Furthermore, the prognostic value and expression level of the hub genes of these modules were validated based on data from the TCGA database and other independent datasets from the Gene Expression Omnibus (GEO) database and the Human Protein Atlas database. The significant modules and hub genes were also assessed by functional analysis and gene set enrichment analysis (GSEA). Results We found that the turquoise module was strongly correlated with pathologic T stage and significantly enriched in critical functions and pathways related to tumourigenesis. PPP1R12B, CFD, CRYAB, FAM189A2 and ANGPTL1 were identified and statistically validated as hub genes in the turquoise module and were closely implicated in the prognosis of OSCC. GSEA indicated that five hub genes were significantly involved in many well-known cancer-related biological functions and signaling pathways. Conclusion In brief, we systematically discovered a co-expressed turquoise module and five hub genes associated with the pathologic T stage for the first time, which provided further insight that WGCNA may reveal the molecular regulatory mechanism involved in the carcinogenesis and progression of OSCC. In addition, the five hub genes may be considered candidate prognostic biomarkers and potential therapeutic targets for the precise early diagnosis, clinical treatment and prognosis of OSCC in the future.
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Affiliation(s)
- Xuegang Hu
- Department of Stomatology, Shenzhen Hospital, University of Chinese Academy of Sciences, Shenzhen, Guangdong, China.,Department of Endodontics and Operative Dentistry, School and Hospital of Stomatology, Fujian Medical University, Fuhou, Fujian, China
| | - Guanwen Sun
- Department of Endodontics and Operative Dentistry, School and Hospital of Stomatology, Fujian Medical University, Fuhou, Fujian, China.,Department of Stomatology, Ningbo Medical Center Lihuili Eastern Hospital, Ningbo, Zhejiang, China
| | - Zhiqiang Shi
- Department of Stomatology, Shenzhen Hospital, University of Chinese Academy of Sciences, Shenzhen, Guangdong, China
| | - Hui Ni
- Department of Stomatology, Shenzhen Hospital, University of Chinese Academy of Sciences, Shenzhen, Guangdong, China
| | - Shan Jiang
- Restorative Dental Sciences, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
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13
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Xiong Y, Yuan L, Xiong J, Xu H, Luo Y, Wang G, Ju L, Xiao Y, Wang X. An outcome model for human bladder cancer: A comprehensive study based on weighted gene co-expression network analysis. J Cell Mol Med 2019; 24:2342-2355. [PMID: 31883309 PMCID: PMC7011142 DOI: 10.1111/jcmm.14918] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/22/2019] [Accepted: 11/29/2019] [Indexed: 01/01/2023] Open
Abstract
The precision evaluation of prognosis is crucial for clinical treatment decision of bladder cancer (BCa). Therefore, establishing an effective prognostic model for BCa has significant clinical implications. We performed WGCNA and DEG screening to initially identify the candidate genes. The candidate genes were applied to construct a LASSO Cox regression analysis model. The effectiveness and accuracy of the prognostic model were tested by internal/external validation and pan‐cancer validation and time‐dependent ROC. Additionally, a nomogram based on the parameter selected from univariate and multivariate cox regression analysis was constructed. Eight genes were eventually screened out as progression‐related differentially expressed candidates in BCa. LASSO Cox regression analysis identified 3 genes to build up the outcome model in E‐MTAB‐4321 and the outcome model had good performance in predicting patient progress free survival of BCa patients in discovery and test set. Subsequently, another three datasets also have a good predictive value for BCa patients' OS and DFS. Time‐dependent ROC indicated an ideal predictive accuracy of the outcome model. Meanwhile, the nomogram showed a good performance and clinical utility. In addition, the prognostic model also exhibits good performance in pan‐cancer patients. Our outcome model was the first prognosis model for human bladder cancer progression prediction via integrative bioinformatics analysis, which may aid in clinical decision‐making.
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Affiliation(s)
- Yaoyi Xiong
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Lushun Yuan
- Division of Nephrology, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Jing Xiong
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Department of Urology, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, China
| | - Huimin Xu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yongwen Luo
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Gang Wang
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Human Genetics Resource Preservation Center of Hubei Province, Wuhan, China
| | - Lingao Ju
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Human Genetics Resource Preservation Center of Hubei Province, Wuhan, China
| | - Yu Xiao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Human Genetics Resource Preservation Center of Hubei Province, Wuhan, China.,Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xinghuan Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Medical Research Institute, Wuhan University, Wuhan, China
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14
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Fagan V, Johansson C, Gileadi C, Monteiro O, Dunford JE, Nibhani R, Philpott M, Malzahn J, Wells G, Faram R, Cribbs AP, Halidi N, Li F, Chau I, Greschik H, Velupillai S, Allali-Hassani A, Bennett J, Christott T, Giroud C, Lewis AM, Huber KVM, Athanasou N, Bountra C, Jung M, Schüle R, Vedadi M, Arrowsmith C, Xiong Y, Jin J, Fedorov O, Farnie G, Brennan PE, Oppermann U. A Chemical Probe for Tudor Domain Protein Spindlin1 to Investigate Chromatin Function. J Med Chem 2019; 62:9008-9025. [PMID: 31550156 DOI: 10.1021/acs.jmedchem.9b00562] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Modifications of histone tails, including lysine/arginine methylation, provide the basis of a "chromatin or histone code". Proteins that contain "reader" domains can bind to these modifications and form specific effector complexes, which ultimately mediate chromatin function. The spindlin1 (SPIN1) protein contains three Tudor methyllysine/arginine reader domains and was identified as a putative oncogene and transcriptional coactivator. Here we report a SPIN1 chemical probe inhibitor with low nanomolar in vitro activity, exquisite selectivity on a panel of methyl reader and writer proteins, and with submicromolar cellular activity. X-ray crystallography showed that this Tudor domain chemical probe simultaneously engages Tudor domains 1 and 2 via a bidentate binding mode. Small molecule inhibition and siRNA knockdown of SPIN1, as well as chemoproteomic studies, identified genes which are transcriptionally regulated by SPIN1 in squamous cell carcinoma and suggest that SPIN1 may have a role in cancer related inflammation and/or cancer metastasis.
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Affiliation(s)
- Vincent Fagan
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Target Discovery Institute, Nuffield Department of Medicine , University of Oxford , OX3 7FZ Oxford , U.K
| | - Catrine Johansson
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Carina Gileadi
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Octovia Monteiro
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Target Discovery Institute, Nuffield Department of Medicine , University of Oxford , OX3 7FZ Oxford , U.K
| | - James E Dunford
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Reshma Nibhani
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Martin Philpott
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Jessica Malzahn
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Graham Wells
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Ruth Faram
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Adam P Cribbs
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Nadia Halidi
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Fengling Li
- Structural Genomics Consortium , University of Toronto , 101 College Street , Toronto , Ontario M5G 1L7 , Canada
| | - Irene Chau
- Structural Genomics Consortium , University of Toronto , 101 College Street , Toronto , Ontario M5G 1L7 , Canada
| | - Holger Greschik
- Department of Urology, Center for Clinical Research, Medical Center, Signalling Research Centres BIOSS and CIBSS , University of Freiburg , D-79106 Freiburg , Germany
| | - Srikannathasan Velupillai
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
| | - Abdellah Allali-Hassani
- Structural Genomics Consortium , University of Toronto , 101 College Street , Toronto , Ontario M5G 1L7 , Canada
| | - James Bennett
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Target Discovery Institute, Nuffield Department of Medicine , University of Oxford , OX3 7FZ Oxford , U.K
| | - Thomas Christott
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Target Discovery Institute, Nuffield Department of Medicine , University of Oxford , OX3 7FZ Oxford , U.K
| | - Charline Giroud
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Target Discovery Institute, Nuffield Department of Medicine , University of Oxford , OX3 7FZ Oxford , U.K
| | - Andrew M Lewis
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Target Discovery Institute, Nuffield Department of Medicine , University of Oxford , OX3 7FZ Oxford , U.K
| | - Kilian V M Huber
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Target Discovery Institute, Nuffield Department of Medicine , University of Oxford , OX3 7FZ Oxford , U.K
| | - Nick Athanasou
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Chas Bountra
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
| | - Manfred Jung
- FRIAS-Freiburg Institute of Advanced Studies , University of Freiburg , 79104 Freiburg , Germany
- Institute of Pharmaceutical Sciences , University of Freiburg , Albertstraße 25 , 79104 Freiburg , Germany
| | - Roland Schüle
- Department of Urology, Center for Clinical Research, Medical Center, Signalling Research Centres BIOSS and CIBSS , University of Freiburg , D-79106 Freiburg , Germany
| | - Masoud Vedadi
- Structural Genomics Consortium , University of Toronto , 101 College Street , Toronto , Ontario M5G 1L7 , Canada
| | - Cheryl Arrowsmith
- Structural Genomics Consortium , University of Toronto , 101 College Street , Toronto , Ontario M5G 1L7 , Canada
| | - Yan Xiong
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences , Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai , New York , New York 10029 , United States
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences , Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai , New York , New York 10029 , United States
| | - Oleg Fedorov
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Target Discovery Institute, Nuffield Department of Medicine , University of Oxford , OX3 7FZ Oxford , U.K
| | - Gillian Farnie
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
| | - Paul E Brennan
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Target Discovery Institute, Nuffield Department of Medicine , University of Oxford , OX3 7FZ Oxford , U.K
- Alzheimer's Research UK Oxford Drug Discovery Institute, Nuffield Department of Medicine , University of Oxford , OX3 7FZ Oxford , U.K
| | - Udo Oppermann
- Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K
- FRIAS-Freiburg Institute of Advanced Studies , University of Freiburg , 79104 Freiburg , Germany
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