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Freyer G, Floquet A, Tredan O, Carrot A, Langlois-Jacques C, Lopez J, Selle F, Abdeddaim C, Leary A, Dubot-Poitelon C, Fabbro M, Gladieff L, Lamuraglia M. Bevacizumab, olaparib, and durvalumab in patients with relapsed ovarian cancer: a phase II clinical trial from the GINECO group. Nat Commun 2024; 15:1985. [PMID: 38443333 PMCID: PMC10914754 DOI: 10.1038/s41467-024-45974-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 02/08/2024] [Indexed: 03/07/2024] Open
Abstract
Most patients with advanced ovarian cancer (AOC) ultimately relapse after platinum-based chemotherapy. Combining bevacizumab, olaparib, and durvalumab likely drives synergistic activity. This open-label phase 2 study (NCT04015739) aimed to assess activity and safety of this triple combination in female patients with relapsed high-grade AOC following prior platinum-based therapy. Patients were treated with olaparib (300 mg orally, twice daily), the bevacizumab biosimilar FKB238 (15 mg/kg intravenously, once-every-3-weeks), and durvalumab (1.12 g intravenously, once-every-3-weeks) in nine French centers. The primary endpoint was the non-progression rate at 3 months for platinum-resistant relapse or 6 months for platinum-sensitive relapse per RECIST 1.1 and irRECIST. Secondary endpoints were CA-125 decline with CA-125 ELIMination rate constant K (KELIM-B) per CA-125 longitudinal kinetics over 100 days, progression free survival and overall survival, tumor response, and safety. Non-progression rates were 69.8% (90%CI 55.9%-80.0%) at 3 months for platinum-resistant relapse patients (N = 41), meeting the prespecified endpoint, and 43.8% (90%CI 29.0%-57.4%) at 6 months for platinum-sensitive relapse (N = 33), not meeting the prespecified endpoint. Median progression-free survival was 4.1 months (95%CI 3.5-5.9) and 4.9 months (95%CI 2.9-7.0) respectively. Favorable KELIM-B was associated with better survival. No toxic deaths or major safety signals were observed. Here we show that further investigation of this triple combination may be considered in AOC patients with platinum-resistant relapse.
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Affiliation(s)
- Gilles Freyer
- Department of Medical Oncology, Lyon 1 University, Lyon, France.
- GINECO (Groupe d'Investigateurs Nationaux pour l'Etude des Cancers de l'Ovaire, Paris, France.
- Institut de Cancérologie des HCL, Lyon, France.
| | - Anne Floquet
- GINECO (Groupe d'Investigateurs Nationaux pour l'Etude des Cancers de l'Ovaire, Paris, France
- Department of Medical Oncology - Gynecological Tumors, Institut Bergonié, Bordeaux, France
| | - Olivier Tredan
- GINECO (Groupe d'Investigateurs Nationaux pour l'Etude des Cancers de l'Ovaire, Paris, France
- Medical Oncology, Centre Léon Bérard, Lyon, France
| | - Aurore Carrot
- GINECO (Groupe d'Investigateurs Nationaux pour l'Etude des Cancers de l'Ovaire, Paris, France
- EMR 3738, UFR Lyon-Sud, Université Lyon1, Lyon, France
| | - Carole Langlois-Jacques
- GINECO (Groupe d'Investigateurs Nationaux pour l'Etude des Cancers de l'Ovaire, Paris, France
- Biostatistics and Bioinformatics Department, Hospices Civils de Lyon, Lyon, France
| | - Jonathan Lopez
- GINECO (Groupe d'Investigateurs Nationaux pour l'Etude des Cancers de l'Ovaire, Paris, France
- Department of Biochemistry and Molecular Biology, Hospices Civils de Lyon, Lyon, France
| | - Frédéric Selle
- GINECO (Groupe d'Investigateurs Nationaux pour l'Etude des Cancers de l'Ovaire, Paris, France
- Department of Medical Oncology, Groupe Hospitalier Diaconesses Croix Saint-Simon, Paris, France
| | - Cyril Abdeddaim
- GINECO (Groupe d'Investigateurs Nationaux pour l'Etude des Cancers de l'Ovaire, Paris, France
- Gynecologic Oncology Department, Centre Oscar Lambret, Lille, France
| | - Alexandra Leary
- GINECO (Groupe d'Investigateurs Nationaux pour l'Etude des Cancers de l'Ovaire, Paris, France
- Oncology Department, Institut Gustave Roussy, Villejuif, France
| | - Coraline Dubot-Poitelon
- GINECO (Groupe d'Investigateurs Nationaux pour l'Etude des Cancers de l'Ovaire, Paris, France
- Medical Oncology, Institut Curie Saint Cloud, Paris, France
| | - Michel Fabbro
- GINECO (Groupe d'Investigateurs Nationaux pour l'Etude des Cancers de l'Ovaire, Paris, France
- Department of Medical Oncology, Institut du Cancer de Montpellier, Montpellier, France
| | - Laurence Gladieff
- GINECO (Groupe d'Investigateurs Nationaux pour l'Etude des Cancers de l'Ovaire, Paris, France
- Medical Oncology, Institut Claudius Regaud IUCT-Oncopole, Toulouse, France
| | - Michele Lamuraglia
- GINECO (Groupe d'Investigateurs Nationaux pour l'Etude des Cancers de l'Ovaire, Paris, France
- Medical Oncology, Institut de Cancérologie du CHUSE, Saint-Etienne, France
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Liu Y, Liu G. Targeting NEAT1 Affects the Sensitivity to PARPi in Serous Ovarian Cancer by Regulating the Homologous Recombination Repair Pathway. J Cancer 2024; 15:1397-1413. [PMID: 38356722 PMCID: PMC10861825 DOI: 10.7150/jca.91896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 12/16/2023] [Indexed: 02/16/2024] Open
Abstract
Objective: Patients initially sensitive to PARPi (PARP inhibitor) regain resistance because of homologous recombination (HR) restoration, although PARPi has a synthetic lethality effect on serous ovarian cancer cells with BRCA1/2 mutations. This study aimed to investigate the role of NEAT1 in HR function and whether targeting NEAT1 in serous ovarian cancer cells could increase PARPi sensitivity. Methods: Ovarian cancer patients' clinical information and the expression of NEAT1 were collected from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC). Ovarian cancer (OC) cells HeyA8 and SKOV3 were silenced by transfecting NEAT1 ASO. QRT-PCR confirmed the mRNA expression of RAD51, FOXM1, NEAT1_1 and NEAT1_2. We assessed the expression of RAD51, FOXM1, and γ-H2AX by Western blotting and Immunofluorescence. Comet Assays were used to detect DNA double-strand damage levels. In OC cells transfected with NEAT1 ASO or co-transfected overexpression RAD51/empty vector and si-NEAT1/si-ctrl, the sensitivity to Olaparib was determined using CCK8 assay. The Kaplan-Meier survival curves assessed the prognostic and predictive roles of NEAT1 in OC. Results: NEAT1 was an independent prognostic marker of ovarian cancer. NEAT1 knockdown reduced the expression of NEAT1_1, NEAT1_2, RAD51, and FOXM1 and increased the expression of γ-H2AX. In addition, Olaparib increased the expression of RAD51, representing HR repair efficiency, which was inhibited by NEAT1 knockdown. Moreover, the knockdown of NEAT1 increased the DNA damage caused by Olaparib, demonstrated by increased nuclear γ-H2AX foci, DNA in the tail, and expression of γ-H2AX. NEAT1 knockdown sensitized ovarian cancer cells to Olaparib by targeting RAD51-HR. NEAT1 expression could predict response to chemotherapy for ovarian cancer. Conclusions: NEAT1 knockdown inhibited HR capacity and increased DNA damage caused by Olaparib in serous ovarian cancer cells, making them more sensitive to Olaparib and providing a crucial therapeutic advantage of increasing sensitivity to Olaparib.
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Affiliation(s)
- Yang Liu
- Departments of Obstetrics and Gynecology, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Guoyan Liu
- Correspondence to: Dr. Guoyan Liu, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Department of Gynecologic Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Huanhuxi Road, Hexi District, Tianjin, 300060, China
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3
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Huan Q, Cheng S, Ma H, Zhao M, Chen Y, Yuan X. Machine learning-derived identification of prognostic signature for improving prognosis and drug response in patients with ovarian cancer. J Cell Mol Med 2024; 28:e18021. [PMID: 37994489 PMCID: PMC10805490 DOI: 10.1111/jcmm.18021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/18/2023] [Accepted: 10/19/2023] [Indexed: 11/24/2023] Open
Abstract
Clinical assessments relying on pathology classification demonstrate limited effectiveness in predicting clinical outcomes and providing optimal treatment for patients with ovarian cancer (OV). Consequently, there is an urgent requirement for an ideal biomarker to facilitate precision medicine. To address this issue, we selected 15 multicentre cohorts, comprising 12 OV cohorts and 3 immunotherapy cohorts. Initially, we identified a set of robust prognostic risk genes using data from the 12 OV cohorts. Subsequently, we employed a consensus cluster analysis to identify distinct clusters based on the expression profiles of the risk genes. Finally, a machine learning-derived prognostic signature (MLDPS) was developed based on differentially expressed genes and univariate Cox regression genes between the clusters by using 10 machine-learning algorithms (101 combinations). Patients with high MLDPS had unfavourable survival rates and have good prediction performance in all cohorts and in-house cohorts. The MLDPS exhibited robust and dramatically superior capability than 21 published signatures. Of note, low MLDIS have a positive prognostic impact on patients treated with anti-PD-1 immunotherapy by driving changes in the level of infiltration of immune cells. Additionally, patients suffering from OV with low MLDIS were more sensitive to immunotherapy. Meanwhile, patients with low MLDIS might benefit from chemotherapy, and 19 compounds that may be potential agents for patients with low MLDIS were identified. MLDIS presents an appealing instrument for the identification of patients at high/low risk. This could enhance the precision treatment, ultimately guiding the clinical management of OV.
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Affiliation(s)
- Qing Huan
- Shandong Key Laboratory of Reproductive Medicine, Department of Obstetrics and GynecologyShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanShandongChina
| | - Shuchao Cheng
- Bidding Management OfficeThe Second Affiliated Hospital of Shandong University of Traditional Chinese MedicineJinanShandongChina
| | - Hui‐Fen Ma
- School of Medical ManagementShandong First Medical UniversityJinanShandongChina
| | - Min Zhao
- Mianyang Central Hospital, School of MedicineUniversity of Electronic Science and Technology of ChinaMianyangSichuanChina
| | - Yu Chen
- School of ScienceWuhan University of TechnologyWuhanHubeiChina
| | - Xiaolu Yuan
- Department of PathologyMaoming People's HospitalMaomingGuangdongChina
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Wang H, Han X, Ren J, Cheng H, Li H, Li Y, Li X. A prognostic prediction model for ovarian cancer using a cross-modal view correlation discovery network. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2024; 21:736-764. [PMID: 38303441 DOI: 10.3934/mbe.2024031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Ovarian cancer is a tumor with different clinicopathological and molecular features, and the vast majority of patients have local or extensive spread at the time of diagnosis. Early diagnosis and prognostic prediction of patients can contribute to the understanding of the underlying pathogenesis of ovarian cancer and the improvement of therapeutic outcomes. The occurrence of ovarian cancer is influenced by multiple complex mechanisms, including the genome, transcriptome and proteome. Different types of omics analysis help predict the survival rate of ovarian cancer patients. Multi-omics data of ovarian cancer exhibit high-dimensional heterogeneity, and existing methods for integrating multi-omics data have not taken into account the variability and inter-correlation between different omics data. In this paper, we propose a deep learning model, MDCADON, which utilizes multi-omics data and cross-modal view correlation discovery network. We introduce random forest into LASSO regression for feature selection on mRNA expression, DNA methylation, miRNA expression and copy number variation (CNV), aiming to select important features highly correlated with ovarian cancer prognosis. A multi-modal deep neural network is used to comprehensively learn feature representations of each omics data and clinical data, and cross-modal view correlation discovery network is employed to construct the multi-omics discovery tensor, exploring the inter-relationships between different omics data. The experimental results demonstrate that MDCADON is superior to the existing methods in predicting ovarian cancer prognosis, which enables survival analysis for patients and facilitates the determination of follow-up treatment plans. Finally, we perform Gene Ontology (GO) term analysis and biological pathway analysis on the genes identified by MDCADON, revealing the underlying mechanisms of ovarian cancer and providing certain support for guiding ovarian cancer treatments.
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Affiliation(s)
- Huiqing Wang
- College of Computer Science and Technology (College of Data Science), Taiyuan University of Technology, Taiyuan 030024, China
| | - Xiao Han
- College of Computer Science and Technology (College of Data Science), Taiyuan University of Technology, Taiyuan 030024, China
| | - Jianxue Ren
- College of Computer Science and Technology (College of Data Science), Taiyuan University of Technology, Taiyuan 030024, China
| | - Hao Cheng
- College of Computer Science and Technology (College of Data Science), Taiyuan University of Technology, Taiyuan 030024, China
| | - Haolin Li
- College of Computer Science and Technology (College of Data Science), Taiyuan University of Technology, Taiyuan 030024, China
| | - Ying Li
- College of Computer Science and Technology (College of Data Science), Taiyuan University of Technology, Taiyuan 030024, China
| | - Xue Li
- College of Computer Science and Technology (College of Data Science), Taiyuan University of Technology, Taiyuan 030024, China
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Salamini-Montemurri M, Lamas-Maceiras M, Lorenzo-Catoira L, Vizoso-Vázquez Á, Barreiro-Alonso A, Rodríguez-Belmonte E, Quindós-Varela M, Cerdán ME. Identification of lncRNAs Deregulated in Epithelial Ovarian Cancer Based on a Gene Expression Profiling Meta-Analysis. Int J Mol Sci 2023; 24:10798. [PMID: 37445988 PMCID: PMC10341812 DOI: 10.3390/ijms241310798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/19/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023] Open
Abstract
Epithelial ovarian cancer (EOC) is one of the deadliest gynecological cancers worldwide, mainly because of its initially asymptomatic nature and consequently late diagnosis. Long non-coding RNAs (lncRNA) are non-coding transcripts of more than 200 nucleotides, whose deregulation is involved in pathologies such as EOC, and are therefore envisaged as future biomarkers. We present a meta-analysis of available gene expression profiling (microarray and RNA sequencing) studies from EOC patients to identify lncRNA genes with diagnostic and prognostic value. In this meta-analysis, we include 46 independent cohorts, along with available expression profiling data from EOC cell lines. Differential expression analyses were conducted to identify those lncRNAs that are deregulated in (i) EOC versus healthy ovary tissue, (ii) unfavorable versus more favorable prognosis, (iii) metastatic versus primary tumors, (iv) chemoresistant versus chemosensitive EOC, and (v) correlation to specific histological subtypes of EOC. From the results of this meta-analysis, we established a panel of lncRNAs that are highly correlated with EOC. The panel includes several lncRNAs that are already known and even functionally characterized in EOC, but also lncRNAs that have not been previously correlated with this cancer, and which are discussed in relation to their putative role in EOC and their potential use as clinically relevant tools.
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Affiliation(s)
- Martín Salamini-Montemurri
- Centro Interdisciplinar de Química e Bioloxía (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Facultade de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
| | - Mónica Lamas-Maceiras
- Centro Interdisciplinar de Química e Bioloxía (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Facultade de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
| | - Lidia Lorenzo-Catoira
- Centro Interdisciplinar de Química e Bioloxía (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Facultade de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
| | - Ángel Vizoso-Vázquez
- Centro Interdisciplinar de Química e Bioloxía (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Facultade de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
| | - Aida Barreiro-Alonso
- Centro Interdisciplinar de Química e Bioloxía (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Facultade de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
| | - Esther Rodríguez-Belmonte
- Centro Interdisciplinar de Química e Bioloxía (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Facultade de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
| | - María Quindós-Varela
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
- Complexo Hospitalario Universitario de A Coruña (CHUAC), Servizo Galego de Saúde (SERGAS), 15006 A Coruña, Spain
| | - M Esperanza Cerdán
- Centro Interdisciplinar de Química e Bioloxía (CICA), As Carballeiras, s/n, Campus de Elviña, Universidade da Coruña, 15071 A Coruña, Spain
- Facultade de Ciencias, A Fraga, s/n, Campus de A Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), As Xubias de Arriba 84, 15006 A Coruña, Spain
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6
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Shutta KH, Balzer LB, Scholtens DM, Balasubramanian R. SpiderLearner: An ensemble approach to Gaussian graphical model estimation. Stat Med 2023; 42:2116-2133. [PMID: 37004994 DOI: 10.1002/sim.9714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 12/10/2022] [Accepted: 03/07/2023] [Indexed: 04/04/2023]
Abstract
Gaussian graphical models (GGMs) are a popular form of network model in which nodes represent features in multivariate normal data and edges reflect conditional dependencies between these features. GGM estimation is an active area of research. Currently available tools for GGM estimation require investigators to make several choices regarding algorithms, scoring criteria, and tuning parameters. An estimated GGM may be highly sensitive to these choices, and the accuracy of each method can vary based on structural characteristics of the network such as topology, degree distribution, and density. Because these characteristics are a priori unknown, it is not straightforward to establish universal guidelines for choosing a GGM estimation method. We address this problem by introducing SpiderLearner, an ensemble method that constructs a consensus network from multiple estimated GGMs. Given a set of candidate methods, SpiderLearner estimates the optimal convex combination of results from each method using a likelihood-based loss function.K $$ K $$ -fold cross-validation is applied in this process, reducing the risk of overfitting. In simulations, SpiderLearner performs better than or comparably to the best candidate methods according to a variety of metrics, including relative Frobenius norm and out-of-sample likelihood. We apply SpiderLearner to publicly available ovarian cancer gene expression data including 2013 participants from 13 diverse studies, demonstrating our tool's potential to identify biomarkers of complex disease. SpiderLearner is implemented as flexible, extensible, open-source code in the R package ensembleGGM at https://github.com/katehoffshutta/ensembleGGM.
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Affiliation(s)
- Katherine H Shutta
- Department of Biostatistics and Epidemiology, University of Massachusetts-Amherst, Amherst, Massachusetts, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Laura B Balzer
- Division of Biostatistics, University of California-Berkeley, Berkeley, California, USA
| | - Denise M Scholtens
- Division of Biostatistics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Raji Balasubramanian
- Department of Biostatistics and Epidemiology, University of Massachusetts-Amherst, Amherst, Massachusetts, USA
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7
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Sensitivity Analysis for Survival Prognostic Prediction with Gene Selection: A Copula Method for Dependent Censoring. Biomedicines 2023; 11:biomedicines11030797. [PMID: 36979776 PMCID: PMC10045003 DOI: 10.3390/biomedicines11030797] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/20/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Prognostic analysis for patient survival often employs gene expressions obtained from high-throughput screening for tumor tissues from patients. When dealing with survival data, a dependent censoring phenomenon arises, and thus the traditional Cox model may not correctly identify the effect of each gene. A copula-based gene selection model can effectively adjust for dependent censoring, yielding a multi-gene predictor for survival prognosis. However, methods to assess the impact of various types of dependent censoring on the multi-gene predictor have not been developed. In this article, we propose a sensitivity analysis method using the copula-graphic estimator under dependent censoring, and implement relevant methods in the R package “compound.Cox”. The purpose of the proposed method is to investigate the sensitivity of the multi-gene predictor to a variety of dependent censoring mechanisms. In order to make the proposed sensitivity analysis practical, we develop a web application. We apply the proposed method and the web application to a lung cancer dataset. We provide a template file so that developers can modify the template to establish their own web applications.
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8
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Rae S, Spillane C, Blackshields G, Madden SF, Keenan J, Stordal B. The EMT-activator ZEB1 is unrelated to platinum drug resistance in ovarian cancer but is predictive of survival. Hum Cell 2022; 35:1547-1559. [PMID: 35794446 PMCID: PMC9374625 DOI: 10.1007/s13577-022-00744-y] [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: 04/19/2022] [Accepted: 06/24/2022] [Indexed: 11/30/2022]
Abstract
The IGROVCDDP cisplatin-resistant ovarian cancer cell line is an unusual model, as it is also cross-resistant to paclitaxel. IGROVCDDP, therefore, models the resistance phenotype of serous ovarian cancer patients who have failed frontline platinum/taxane chemotherapy. IGROVCDDP has also undergone epithelial-mesenchymal transition (EMT). We aim to determine if alterations in EMT-related genes are related to or independent from the drug-resistance phenotypes. EMT gene and protein markers, invasion, motility and morphology were investigated in IGROVCDDP and its parent drug-sensitive cell line IGROV-1. ZEB1 was investigated by qPCR, Western blotting and siRNA knockdown. ZEB1 was also investigated in publicly available ovarian cancer gene-expression datasets. IGROVCDDP cells have decreased protein levels of epithelial marker E-cadherin (6.18-fold, p = 1.58e-04) and higher levels of mesenchymal markers vimentin (2.47-fold, p = 4.43e-03), N-cadherin (4.35-fold, p = 4.76e-03) and ZEB1 (3.43-fold, p = 0.04). IGROVCDDP have a spindle-like morphology consistent with EMT. Knockdown of ZEB1 in IGROVCDDP does not lead to cisplatin sensitivity but shows a reversal of EMT-gene signalling and an increase in cell circularity. High ZEB1 gene expression (HR = 1.31, n = 2051, p = 1.31e-05) is a marker of poor overall survival in high-grade serous ovarian-cancer patients. In contrast, ZEB1 is not predictive of overall survival in high-grade serous ovarian-cancer patients known to be treated with platinum chemotherapy. The increased expression of ZEB1 in IGROVCDDP appears to be independent of the drug-resistance phenotypes. ZEB1 has the potential to be used as biomarker of overall prognosis in ovarian-cancer patients but not of platinum/taxane chemoresistance.
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Affiliation(s)
- Sophie Rae
- Department of Natural Sciences, Middlesex University London, London, UK
| | - Cathy Spillane
- Department of Histopathology, St James' Hospital and Trinity College Dublin, Dublin, Ireland
| | - Gordon Blackshields
- Department of Histopathology, St James' Hospital and Trinity College Dublin, Dublin, Ireland
| | - Stephen F Madden
- Data Science Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Joanne Keenan
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Britta Stordal
- Department of Natural Sciences, Middlesex University London, London, UK.
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9
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Dogan B, Gumusoglu E, Ulgen E, Sezerman OU, Gunel T. Integrated bioinformatics analysis of validated and circulating miRNAs in ovarian cancer. Genomics Inform 2022; 20:e20. [PMID: 35794700 PMCID: PMC9299562 DOI: 10.5808/gi.21067] [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: 11/04/2021] [Accepted: 01/03/2022] [Indexed: 11/20/2022] Open
Abstract
Recent studies have focused on the early detection of ovarian cancer (OC) using tumor materials by liquid biopsy. The mechanisms of microRNAs (miRNAs) to impact OC and signaling pathways are still unknown. This study aims to reliably perform functional analysis of previously validated circulating miRNAs' target genes by using pathfindR. Also, overall survival and pathological stage analyses were evaluated with miRNAs' target genes which are common in the The Cancer Genome Atlas and GTEx datasets. Our previous studies have validated three downregulated miRNAs (hsa-miR-885-5p, hsa-miR-1909-5p, and hsalet7d-3p) having a diagnostic value in OC patients' sera, with high-throughput techniques. The predicted target genes of these miRNAs were retrieved from the miRDB database (v6.0). Active-subnetwork-oriented Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was conducted by pathfindR using the target genes. Enrichment of KEGG pathways assessed by the analysis of pathfindR indicated that 24 pathways were related to the target genes. Ubiquitin-mediated proteolysis, spliceosome and Notch signaling pathway were the top three pathways with the lowest p-values (p < 0.001). Ninety-three common genes were found to be differentially expressed (p < 0.05) in the datasets. No significant genes were found to be significant in the analysis of overall survival analyses, but 24 genes were found to be significant with pathological stages analysis (p < 0.05). The findings of our study provide in-silico evidence that validated circulating miRNAs' target genes and enriched pathways are related to OC and have potential roles in theranostics applications. Further experimental investigations are required to validate our results which will ultimately provide a new perspective for translational applications in OC management.
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Affiliation(s)
- Berkcan Dogan
- Department of Medical Genetics, Faculty of Medicine, Bursa Uludag University, Bursa 16059, Turkey.,Department of Translational Medicine, Institute of Health Sciences, Bursa Uludag University, Bursa 16059, Turkey
| | - Ece Gumusoglu
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Istanbul 34134, Turkey
| | - Ege Ulgen
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul 34750, Turkey
| | - Osman Ugur Sezerman
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul 34750, Turkey
| | - Tuba Gunel
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Istanbul 34134, Turkey
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10
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Dynamic Risk Prediction via a Joint Frailty-Copula Model and IPD Meta-Analysis: Building Web Applications. ENTROPY 2022; 24:e24050589. [PMID: 35626474 PMCID: PMC9140593 DOI: 10.3390/e24050589] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/11/2022] [Accepted: 04/21/2022] [Indexed: 12/17/2022]
Abstract
Clinical risk prediction formulas for cancer patients can be improved by dynamically updating the formulas by intermediate events, such as tumor progression. The increased accessibility of individual patient data (IPD) from multiple studies has motivated the development of dynamic prediction formulas accounting for between-study heterogeneity. A joint frailty-copula model for overall survival and time to tumor progression has the potential to develop a dynamic prediction formula of death from heterogenous studies. However, the process of developing, validating, and publishing the prediction formula is complex, which has not been sufficiently described in the literature. In this article, we provide a tutorial in order to build a web-based application for dynamic risk prediction for cancer patients on the basis of the R packages joint.Cox and Shiny. We demonstrate the proposed methods using a dataset of breast cancer patients from multiple clinical studies. Following this tutorial, we demonstrate how one can publish web applications available online, which can be manipulated by any user through a smartphone or personal computer. After learning this tutorial, developers acquire the ability to build an online web application using their own datasets.
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11
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Berkel C, Cacan E. Copy number and expression of CEP89, a protein required for ciliogenesis, are increased and predict poor prognosis in patients with ovarian cancer. Cell Biochem Funct 2022; 40:298-309. [PMID: 35285957 DOI: 10.1002/cbf.3694] [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: 12/29/2021] [Revised: 02/12/2022] [Accepted: 02/21/2022] [Indexed: 11/10/2022]
Abstract
CEP89 (centrosomal protein 89) is required for ciliogenesis and mitochondrial metabolism, but its role in cancer has yet to be clarified. We report that CEP89 is overexpressed in ovarian cancer (OC) compared to normal ovaries. Likewise, its expression is higher in malignant ovarian tumors than in borderline ovarian tumors with low malignant potential. More than a quarter of patients with OC have copy number gains in the CEP89 gene, and patients with high expression have more than a year shorter overall survival compared to those with low expression. Moreover, we found that CEP89 can be considered as a prognostic marker for poor overall survival in patients with OC, after adjusting for tumor stage and residual tumor. Nine out of the top 10 protein interactors of CEP89 have the highest percentage of total copy number variation (CNV) events in OC among all other cancer types. Furthermore, CEP89 messenger RNA (mRNA) levels are higher in OC patients with disease recurrence compared to those with no recurrence. We also analyzed CEP89 levels in OC cell lines in terms of CNV, mRNA, and protein levels; and observed that the FUOV-1 cell line has the highest levels among cell lines that originated from primary sites. Our study suggests that CEP89 may be a valuable prognostic predictor for the overall survival of patients with OC, and it could also be a novel therapeutic target in this malignancy.
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Affiliation(s)
- Caglar Berkel
- Department of Molecular Biology and Genetics, Tokat Gaziosmanpasa University, Tokat, Turkey
| | - Ercan Cacan
- Department of Molecular Biology and Genetics, Tokat Gaziosmanpasa University, Tokat, Turkey
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12
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Zhou L, Wang H. A Combined Feature Screening Approach of Random Forest and Filter-based Methods for Ultra-high Dimensional Data. Curr Bioinform 2022. [DOI: 10.2174/1574893617666220221120618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Various feature (variable) screening approaches have been proposed in the past decade to mitigate the impact of ultra-high dimensionality in classification and regression problems, including filter based methods such as sure indepen¬dence screening, and wrapper based methods such random forest. However, the former type of methods rely heavily on strong modelling assumptions while the latter ones requires an adequate sample size to make the data speak for themselves. These require¬ments can seldom be met in biochemical studies in cases where we have only access to ultra-high dimensional data with a complex structure and a small number of observations.
Objective:
In this research, we want to investigate the possibility of combing both filter based screening methods and random forest based screening methods in the regression context.
Method:
We have combined four state-of-art filter approaches, namely, sure independence screening (SIS) , robust rank corre¬lation based screening (RRCS), high dimensional ordinary least squares projection (HOLP) and a model free sure independence screening procedure based on the distance correlation (DCSIS) from the statistical community with a random forest based Boruta screening method from the machine learning community for regression problems.
Result:
Among all combined methods, RF-DCSIS performs better than the other methods in terms of screening accuracy and prediction capability on the simulated scenarios and real benchmark datasets.
Conclusion:
By empirical study from both extensive simulation and real data, we have shown that both filter based screening and random forest based screening have their pros and cons while a combination of both may lead to a better feature screening result and prediction capability
Keywords:
feature screening, filter-based method, ultra-high dimensional data, variable selection, random forest,RF-DCSIS
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Affiliation(s)
- Lifeng Zhou
- School of Economics and Management, Changsha University, China
| | - Hong Wang
- School of Mathematics and Statistics, Central South University, China
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13
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Pawar A, Chowdhury OR, Chauhan R, Talole S, Bhattacharjee A. Identification of key gene signatures for the overall survival of ovarian cancer. J Ovarian Res 2022; 15:12. [PMID: 35057823 PMCID: PMC8780391 DOI: 10.1186/s13048-022-00942-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 12/31/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The five-year overall survival (OS) of advanced-stage ovarian cancer remains nearly 25-35%, although several treatment strategies have evolved to get better outcomes. A considerable amount of heterogeneity and complexity has been seen in ovarian cancer. This study aimed to establish gene signatures that can be used in better prognosis through risk prediction outcome for the survival of ovarian cancer patients. Different studies' heterogeneity into a single platform is presented to explore the penetrating genes for poor or better survival. The integrative analysis of multiple data sets was done to determine the genes that influence poor or better survival. A total of 6 independent data sets was considered. The Cox Proportional Hazard model was used to obtain significant genes that had an impact on ovarian cancer patients. The gene signatures were prepared by splitting the over-expressed and under-expressed genes parallelly by the variable selection technique. The data visualisation techniques were prepared to predict the overall survival, and it could support the therapeutic regime. RESULTS We preferred to select 20 genes in each data set as upregulated and downregulated. Irrespective of the selection of multiple genes, not even a single gene was found common among data sets for the survival of ovarian cancer patients. However, the same analytical approach adopted. The chord plot was presented to make a comprehensive understanding of the outcome. CONCLUSIONS This study helps us to understand the results obtained from different studies. It shows the impact of the heterogeneity from one study to another. It shows the requirement of integrated studies to make a holistic view of the gene signature for ovarian cancer survival.
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Affiliation(s)
- Akash Pawar
- Section of Biostatistics, Center for Cancer Epidemiology, Tata Memorial Centre, Mumbai, India
| | - Oindrila Roy Chowdhury
- Section of Biostatistics, Center for Cancer Epidemiology, Tata Memorial Centre, Mumbai, India
| | - Ruby Chauhan
- Section of Biostatistics, Center for Cancer Epidemiology, Tata Memorial Centre, Mumbai, India
| | - Sanjay Talole
- Section of Biostatistics, Center for Cancer Epidemiology, Tata Memorial Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Atanu Bhattacharjee
- Section of Biostatistics, Center for Cancer Epidemiology, Tata Memorial Centre, Mumbai, India.
- Homi Bhabha National Institute, Mumbai, India.
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14
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Li Y, Gong X, Hu T, Chen Y. Two novel prognostic models for ovarian cancer respectively based on ferroptosis and necroptosis. BMC Cancer 2022; 22:74. [PMID: 35039008 PMCID: PMC8764839 DOI: 10.1186/s12885-021-09166-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 12/30/2021] [Indexed: 12/01/2022] Open
Abstract
Background Platinum-resistant cases account for 25% of ovarian cancer patients. Our aim was to construct two novel prognostic models based on gene expression data respectively from ferroptosis and necroptosis, for predicting the prognosis of advanced ovarian cancer patients with platinum treatment. Methods According to the different overall survivals, we screened differentially expressed genes (DEGs) from 85 ferroptosis-related and 159 necroptosis-related gene expression data in the GSE32062 cohort, to establish two ovarian cancer prognostic models based on calculating risk factors of DEGs, and log-rank test was used for statistical significance test of survival data. Subsequently, we validated the two models in the GSE26712 cohort and the GSE17260 cohort. In addition, we took gene enrichment and microenvironment analyses respectively using limma package and GSVA software to compare the differences between high- and low-risk ovarian cancer patients. Results We constructed two ovarian cancer prognostic models: a ferroptosis-related model based on eight-gene expression signature and a necroptosis-related model based on ten-gene expression signature. The two models performed well in the GSE26712 cohort, but the performance of necroptosis-related model was not well in the GSE17260 cohort. Gene enrichment and microenvironment analyses indicated that the main differences between high- and low- risk ovarian cancer patients occurred in the immune-related indexes, including the specific immune cells abundance and overall immune indexes. Conclusion In this study, ovarian cancer prognostic models based on ferroptosis and necroptosis have been preliminarily validated in predicting prognosis of advanced patients treated with platinum drugs. And the risk score calculated by these two models reflected immune microenvironment. Future work is needed to find out other gene signatures and clinical characteristics to affect the accuracy and applicability of the two ovarian cancer prognostic models. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-09166-9.
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Affiliation(s)
- Yang Li
- Department of Obstetrics and Gynecology, Tianjin Hospital, Tianjin, 300211, China
| | - Xiaojin Gong
- Department of Obstetrics and Gynecology, Tianjin Hospital, Tianjin, 300211, China
| | - Tongxiu Hu
- Department of Obstetrics and Gynecology, Tianjin Hospital, Tianjin, 300211, China
| | - Yurong Chen
- Department of Oncology, Zhuji People's Hospital of Zhejiang Province, Zhuji, 311800, Zhejiang, China.
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15
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OSov: An Interactive Web Server to Evaluate Prognostic Biomarkers for Ovarian Cancer. BIOLOGY 2021; 11:biology11010023. [PMID: 35053021 PMCID: PMC8773055 DOI: 10.3390/biology11010023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/17/2021] [Accepted: 12/21/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary The OSov web server incorporates gene expression profiles with clinical risk factors to estimate the ovarian cancers patients’ survival, and provides a tool for multiple analysis, such as forest-plot, uni/multi-variate survival analysis, Kaplan-Meier plot and nomogram construction. Abstract Ovarian cancer is one of the most aggressive and highly lethal gynecological cancers. The purpose of our study is to build a free prognostic web server to help researchers discover potential prognostic biomarkers by integrating gene expression profiling data and clinical follow-up information of ovarian cancer. We construct a prognostic web server OSov (Online consensus Survival analysis for Ovarian cancer) based on RNA expression profiles. OSov is a user-friendly web server which could present a Kaplan–Meier plot, forest plot, nomogram and survival summary table of queried genes in each individual cohort to evaluate the prognostic potency of each queried gene. To assess the performance of OSov web server, 163 previously published prognostic biomarkers of ovarian cancer were tested and 72% of them had their prognostic values confirmed in OSov. It is a free and valuable prognostic web server to screen and assess survival-associated biomarkers for ovarian cancer.
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16
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Duraiswamy J, Turrini R, Minasyan A, Barras D, Crespo I, Grimm AJ, Casado J, Genolet R, Benedetti F, Wicky A, Ioannidou K, Castro W, Neal C, Moriot A, Renaud-Tissot S, Anstett V, Fahr N, Tanyi JL, Eiva MA, Jacobson CA, Montone KT, Westergaard MCW, Svane IM, Kandalaft LE, Delorenzi M, Sorger PK, Färkkilä A, Michielin O, Zoete V, Carmona SJ, Foukas PG, Powell DJ, Rusakiewicz S, Doucey MA, Dangaj Laniti D, Coukos G. Myeloid antigen-presenting cell niches sustain antitumor T cells and license PD-1 blockade via CD28 costimulation. Cancer Cell 2021; 39:1623-1642.e20. [PMID: 34739845 PMCID: PMC8861565 DOI: 10.1016/j.ccell.2021.10.008] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 07/06/2021] [Accepted: 10/15/2021] [Indexed: 12/15/2022]
Abstract
The mechanisms regulating exhaustion of tumor-infiltrating lymphocytes (TIL) and responsiveness to PD-1 blockade remain partly unknown. In human ovarian cancer, we show that tumor-specific CD8+ TIL accumulate in tumor islets, where they engage antigen and upregulate PD-1, which restrains their functions. Intraepithelial PD-1+CD8+ TIL can be, however, polyfunctional. PD-1+ TIL indeed exhibit a continuum of exhaustion states, with variable levels of CD28 costimulation, which is provided by antigen-presenting cells (APC) in intraepithelial tumor myeloid niches. CD28 costimulation is associated with improved effector fitness of exhausted CD8+ TIL and is required for their activation upon PD-1 blockade, which also requires tumor myeloid APC. Exhausted TIL lacking proper CD28 costimulation in situ fail to respond to PD-1 blockade, and their response may be rescued by local CTLA-4 blockade and tumor APC stimulation via CD40L.
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Affiliation(s)
- Jaikumar Duraiswamy
- Ovarian Cancer Research Center, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Riccardo Turrini
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Aspram Minasyan
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - David Barras
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland; Bioinformatics Core Facility, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Isaac Crespo
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Alizée J Grimm
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Julia Casado
- Research Program of Systems Oncology, University of Helsinki, 00014 Helsinki, Finland
| | - Raphael Genolet
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Fabrizio Benedetti
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Alexandre Wicky
- Center for Precision Oncology, Department of Oncology, CHUV, 1011 Lausanne, Switzerland
| | - Kalliopi Ioannidou
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Wilson Castro
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Christopher Neal
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Amandine Moriot
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Stéphanie Renaud-Tissot
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland; Center of Experimental Therapeutics, Department of Oncology, CHUV, 1011 Lausanne, Switzerland
| | - Victor Anstett
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Noémie Fahr
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Janos L Tanyi
- Ovarian Cancer Research Center, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Monika A Eiva
- Ovarian Cancer Research Center, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Connor A Jacobson
- Harvard Ludwig Center, Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Kathleen T Montone
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Inge Marie Svane
- National Center for Cancer Immune Therapy, Copenhagen University Hospital, 2730 Herlev, Denmark
| | - Lana E Kandalaft
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland; Center of Experimental Therapeutics, Department of Oncology, CHUV, 1011 Lausanne, Switzerland
| | - Mauro Delorenzi
- Bioinformatics Core Facility, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; Department of Oncology, UNIL, 1011 Lausanne, Switzerland
| | - Peter K Sorger
- Harvard Ludwig Center, Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Anniina Färkkilä
- Research Program of Systems Oncology, University of Helsinki, 00014 Helsinki, Finland; Department of Obstetrics and Gynecology, Helsinki University Hospital, 00014 Helsinki, Finland
| | - Olivier Michielin
- Center for Precision Oncology, Department of Oncology, CHUV, 1011 Lausanne, Switzerland
| | - Vincent Zoete
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Santiago J Carmona
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Periklis G Foukas
- 2nd Department of Pathology, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Daniel J Powell
- Ovarian Cancer Research Center, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sylvie Rusakiewicz
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland; Center of Experimental Therapeutics, Department of Oncology, CHUV, 1011 Lausanne, Switzerland
| | - Marie-Agnès Doucey
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Denarda Dangaj Laniti
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - George Coukos
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland.
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Construction of a Macrophage Infiltration Regulatory Network and Related Prognostic Model of High-Grade Serous Ovarian Cancer. JOURNAL OF ONCOLOGY 2021; 2021:1331031. [PMID: 34868310 PMCID: PMC8635947 DOI: 10.1155/2021/1331031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/27/2021] [Accepted: 11/02/2021] [Indexed: 01/31/2023]
Abstract
Background High-grade serous ovarian cancer (HGSOC) carries the highest mortality in the gynecological cancers; however, therapeutic outcomes have not significantly improved in recent decades. Macrophages play an essential role in the occurrence and development of ovarian cancer, so the mechanisms of macrophage infiltration should be elucidated. Method We downloaded transcriptome data of ovarian cancers from the Gene Expression Omnibus and The Cancer Genome Atlas. After rigorous screening, 1566 HGSOC were used for data analysis. CIBERSORT was used to estimate the level of macrophage infiltration and WGCNA was used to identify macrophage-related modules. We constructed a macrophage-related prognostic model using machine learning LASSO algorithm and verified it using multiple HGSOC cohorts. Results In the GPL570-OV cohort, high infiltration level of M1 macrophages was associated with a good outcome, while high infiltration level of M2 macrophages was associated with poor outcomes. We used WGCNA to select genes correlated with macrophage infiltration. These genes were used to construct protein-protein interaction maps of macrophage infiltration. IFL44L, RSAD2, IFIT3, MX1, IFIH1, IFI44, and ISG15 were the hub genes in the network. We then constructed a macrophage-related prognostic model composed of CD38, ACE2, BATF2, HLA-DOB, and WARS. The model had the ability to predict the overall survival rate of HGSOC patients in GPL570-OV, GPL6480-OV, TCGA-OV, GSE50088, and GSE26712. In exploring the immune microenvironment, we found that CD4 memory T cells and activated mast cells showed that the degree of infiltration was higher in the high-risk group, while M1 macrophages were the opposite, and HLA molecules were overexpressed in the high-risk group. Conclusion We constructed a macrophage infiltration-related protein interaction network that provides a basis for studying macrophages in HGSOC. Our macrophage-related prognostic model is robust and widely applicable. It predicts overall survival in HGSOC patients and may improve HGSOC treatment.
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18
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Xu M, Huang S, Chen J, Xu W, Xiang R, Piao Y, Zhao S. Cytotoxic lymphocytes-related gene ITK from a systematic CRISPR screen could predict prognosis of ovarian cancer patients with distant metastasis. J Transl Med 2021; 19:447. [PMID: 34702300 PMCID: PMC8549276 DOI: 10.1186/s12967-021-03119-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 10/15/2021] [Indexed: 11/10/2022] Open
Abstract
Background Ovarian cancer, a highly metastatic malignancy, has benefited tremendously from advances in modern human genomics. However, the genomic variations related to the metastasis remains unclear. Methods We filtered various significant genes (n = 6722) associated with metastasis within a large-scale functional genomic CRISPR/Cas9 knock-out library including 122,756 single guide RNAs, and identified ITK (IL2 Inducible T Cell Kinase) as a potential cancer suppressor gene for ovarian cancer metastasis. Downstream bioinformatic analysis was performed for ITK using public databases. Results We found that patients in low-ITK group had poor prognosis and more distant metastasis than those in high-ITK group in TCGA and GEO databases. We also demonstrated that ITK combined with the clinical factors could accurately predict prognosis through multiple Cox regression analysis and ROC analysis. Moreover, alterations correlated with distant metastasis emereged with significantly increased expression in SAMRCD1 in low-ITK group, but CD244 and SOCS1 in high-ITK group. Integrated analysis revealed dysregulated molecular processes including predominantly oncogenic signaling pathways in low-ITK group but immune related pathways in high-ITK group, which suggested ITK might inhibit distant metastasis in ovarian cancer. Furtherly, deconvolution of the cellular composition of all samples validated the close correlation between ITK and immune related function especially for cytotoxic lymphocytes. Conclusions Together, these data provide insights into the potential role of ITK, with implications for the future development of tansformative ovarian cancer therapeutics. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-03119-3.
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Affiliation(s)
- Mengyao Xu
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Shan Huang
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Jiahui Chen
- Department of Nuclear Medicine and PET/CT-MRI Center, The First Affiliated Hospital of Jinan University, Tianhe District, 613 West Huangpu Road, Guangzhou, 510630, China
| | - Wanxue Xu
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Rong Xiang
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Yongjun Piao
- School of Medicine, Nankai University, Tianjin, 300071, China. .,Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University Affiliated Hospital of Obstetrics and Gynecology, Tianjin, China.
| | - Shuangtao Zhao
- Department of Thoracic Surgery, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China.
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19
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Zheng J, Guo J, Zhang H, Cao B, Xu G, Zhang Z, Tong J. Four Prognosis-Associated lncRNAs Serve as Biomarkers in Ovarian Cancer. Front Genet 2021; 12:672674. [PMID: 34367239 PMCID: PMC8336869 DOI: 10.3389/fgene.2021.672674] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/31/2021] [Indexed: 12/15/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play crucial roles in ovarian cancer (OC) development. However, prognosis-associated lncRNAs (PALs) for OC have not been completely elucidated. Our study aimed to identify the PAL signature of OC. A total of 663 differentially expressed lncRNAs were identified in the databases. According to the weighted gene coexpression analysis, the highly correlated genes were clustered into seven modules related to the clinical phenotype of OC. A total of 25 lncRNAs that were significantly related to overall survival were screened based on univariate Cox regression analysis. The prognostic risk model constructed contained seven PALs based on the parameter λmin, which could stratify OC patients into two risk groups. The results showed that the risk groups had different overall survival rates in both The Cancer Genome Atlas (TCGA) and two verified Gene Expression Omnibus (GEO) databases. Univariate and multivariate Cox regression analyses confirmed that the risk model was an independent risk factor for OC. Gene enrichment analysis revealed that the identified genes were involved in some pathways of malignancy. The competitive endogenous RNA (ceRNA) network included five PALs, of which four were selected for cell function assays. The four PALs were downregulated in 33 collected OC tissues and 3 OC cell lines relative to the control. They were shown to regulate the proliferative, migratory, and invasive potential of OC cells via Cell Counting Kit-8 (CCK-8) and transwell assays. Our study fills the gaps of the four PALs in OC, which are worthy of further study.
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Affiliation(s)
- Jianfeng Zheng
- Department of Obstetrics and Gynecology, Affiliated Hangzhou Hospital, Nanjing Medical University, Hangzhou, China.,Department of Obstetrics and Gynecology, Hangzhou Women's Hospital, Hangzhou, China
| | - Jialu Guo
- Department of Fourth Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Huizhi Zhang
- Department of Fourth Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Benben Cao
- Department of Fourth Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Guomin Xu
- Department of Obstetrics and Gynecology, Haining Second People's Hospital, Haining, China
| | - Zhifen Zhang
- Department of Obstetrics and Gynecology, Hangzhou Women's Hospital, Hangzhou, China
| | - Jinyi Tong
- Department of Obstetrics and Gynecology, Affiliated Hangzhou Hospital, Nanjing Medical University, Hangzhou, China.,Department of Obstetrics and Gynecology, Hangzhou Women's Hospital, Hangzhou, China
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20
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Qiu Y, Pan M, Chen X. A Liquid-Liquid Phase Separation-Related Gene Signature as Prognostic Biomarker for Epithelial Ovarian Cancer. Front Oncol 2021; 11:671892. [PMID: 34168991 PMCID: PMC8217755 DOI: 10.3389/fonc.2021.671892] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/12/2021] [Indexed: 02/04/2023] Open
Abstract
Objective The aim of the present study was to construct and test a liquid-liquid phase separation (LLPS)-related gene signature as a prognostic tool for epithelial ovarian cancer (EOC). Materials and Methods The data set GSE26712 was used to screen the differentially expressed LLPS-related genes. Functional enrichment analysis was performed to reveal the potential biological functions. GSE17260 and GSE32062 were combined as the discovery to construct an LLPS-related gene signature through a three-step analysis (univariate Cox, least absolute shrinkage and selection operator, and multivariate Cox analyses). The EOC data set from The Cancer Genome Atlas as the test set was used to test the LLPS-related gene signature. Results The differentially expressed LLPS-related genes involved in several cancer-related pathways, such as MAPK signaling pathway, cell cycle, and DNA replication. Eleven genes were selected to construct the LLPS-related gene signature risk index as prognostic biomarker for EOC. The risk index could successfully divide patients with EOC into high- and low-risk groups. The patients in high-risk group had significantly shorter overall survival than those with in low-risk group. The LLPS-related gene signature was validated in the test set and may be an independent prognostic factor compared to routine clinical features. Conclusion We constructed and validated an LLPS-related gene signature as a prognosis tool in EOC through integrated analysis of multiple data sets.
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Affiliation(s)
- Yan Qiu
- Department of Gynecology, Maoming People's Hospital, Maoming, China
| | - Min Pan
- Department of Gynecology, Maoming People's Hospital, Maoming, China
| | - Xuemei Chen
- Department of Gynecology, Maoming People's Hospital, Maoming, China
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21
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He P, Zhang C, Chen G, Shen S. Loss of lncRNA SNHG8 promotes epithelial-mesenchymal transition by destabilizing CDH1 mRNA. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1858-1867. [PMID: 33754289 DOI: 10.1007/s11427-020-1895-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/22/2021] [Indexed: 10/21/2022]
Abstract
Long non-coding RNAs (lncRNAs) are widely involved in a variety of biological processes, including epithelial-mesenchymal transition (EMT). In the current study, we found that lncRNA small nucleolar RNA host gene 8 (SNHG8) was tightly correlated with EMT-associated gene signatures, and was down-regulated by Zinc finger E-box-binding homeobox 1 (ZEB1) during EMT progress. Functionally, knockdown of SNHG8 induced EMT in epithelial cells, through destabilizing the CDH1 mRNA dependent on a 17-nucleotide sequence shared by SNHG8 and CDH1. In addition, analysis with public database showed that SNHG8 tended to be down-regulated in different cancer types and the lower expression of SNHG8 predicted poorer prognosis. Taken together, our study reports a ZEB1-repressed lncRNA SNHG8 which is important for stabilizing CDH1 mRNA, thereby maintaining the epithelial status of epithelial cells.
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Affiliation(s)
- Ping He
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, State Key Laboratory of Oncogenes and Related Genes and Chinese Academy of Medical Sciences Research Unit (NO.2019RU043), Shanghai Cancer Institute, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Cheng Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, State Key Laboratory of Oncogenes and Related Genes and Chinese Academy of Medical Sciences Research Unit (NO.2019RU043), Shanghai Cancer Institute, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Guoqiang Chen
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, State Key Laboratory of Oncogenes and Related Genes and Chinese Academy of Medical Sciences Research Unit (NO.2019RU043), Shanghai Cancer Institute, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Shaoming Shen
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, State Key Laboratory of Oncogenes and Related Genes and Chinese Academy of Medical Sciences Research Unit (NO.2019RU043), Shanghai Cancer Institute, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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22
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Ye W, Luo C, Liu F, Liu Z, Chen F. CD96 Correlates With Immune Infiltration and Impacts Patient Prognosis: A Pan-Cancer Analysis. Front Oncol 2021; 11:634617. [PMID: 33680972 PMCID: PMC7935557 DOI: 10.3389/fonc.2021.634617] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 01/05/2021] [Indexed: 01/08/2023] Open
Abstract
Background Immunotherapy has significantly improved patient outcomes, but encountered obstacles recently. CD96, a novel immune checkpoint expressed on T cells and natural killer (NK) cells, is essential for regulating immune functions. However, how CD96 correlating with immune infiltration and patient prognosis in pan-cancer remains unclear. Methods HPA, TCGA, GEO, GTEx, Oncomine, TIMER2.0, PrognoScan, Linkedomics, Metascape, and GEPIA2 databases were used to analyze CD96 in cancers. Visualization of data was mostly achieved by R language, version 4.0.2. Results In general, CD96 was differentially expressed between most cancer and adjacent normal tissues. CD96 significantly impacted the prognosis of diverse cancers. Especially, high CD96 expression was associated with poorer overall survival (OS) and disease-specific survival (DSS) in the TCGA lower grade glioma (LGG) cohort (OS, HR = 2.18, 95% CI = 1.79–2.66, P < 0.001). The opposite association was significantly observed in skin cutaneous melanoma (SKCM) cohort (OS, HR = 0.96, 95% CI = 0.94–0.98, P < 0.001). Notably, SKCM samples demonstrated the highest CD96 mutation frequency among all cancer types. Furthermore, in most cancers, CD96 expression level was significantly correlated with expression levels of recognized immune checkpoints and abundance of multiple immune infiltrates including CD8+ T cells, dendric cells (DCs), macrophages, monocytes, NK cells, neutrophils, regulatory T cells (Tregs), and follicular helper T cells (Tfh). CD96 was identified as a risk factor, protective factor, and irrelevant variable in LGG, SKCM and adrenocortical carcinoma (ACC), respectively. CD96 related genes were involved in negative regulation of leukocyte in LGG, however, involved in multiple positive immune processes in SKCM. Furthermore, CD96 was significantly associated with particular immune marker subsets. Importantly, it strongly correlated with markers of type 1 helper T cell (Th1) in SKCM, but not in LGG or ACC either. Conclusions CD96 participates in diverse immune responses, governs immune cell infiltration, and impacts malignant properties of various cancer types, thus standing as a potential biomarker for determining patient prognosis and immune infiltration in multiple cancers, especially in glioma and melanoma.
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Affiliation(s)
- Wenrui Ye
- Department of Neurosurgery, Xiangya Hospital, Central South University (CSU), Changsha, China.,Clinical Medicine Eight-year Program, Xiangya Medical School of Central South University, Changsha, China
| | - Cong Luo
- Clinical Medicine Eight-year Program, Xiangya Medical School of Central South University, Changsha, China.,Department of Urology, Xiangya Hospital, Central South University (CSU), Changsha, China
| | - Fangkun Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University (CSU), Changsha, China
| | - Zhixiong Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University (CSU), Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University (CSU), Changsha, China
| | - Fenghua Chen
- Department of Neurosurgery, Xiangya Hospital, Central South University (CSU), Changsha, China
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23
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Lin J, Xu X, Sun D, Li T. Development and Validation of an Immune-Related Gene-Pair Model of High-Grade Serous Ovarian Cancer After Platinum-Based Chemotherapy. Front Oncol 2021; 10:626555. [PMID: 33680950 PMCID: PMC7928280 DOI: 10.3389/fonc.2020.626555] [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: 11/06/2020] [Accepted: 12/29/2020] [Indexed: 11/28/2022] Open
Abstract
Background High-grade serous ovarian cancer (HGSOC) is a common cause of death from gynecological cancer, with an overall survival rate that has not significantly improved in decades. Reliable bio-markers are needed to identify high-risk HGSOC to assist in the selection and development of treatment options. Method The study included ten HGSOC cohorts, which were merged into four separate cohorts including a total of 1,526 samples. We used the relative expression of immune genes to construct the gene-pair matrix, and the least absolute shrinkage and selection operator regression was performed to build the prognosis model using the training set. The prognosis of the model was verified in the training set (363 cases) and three validation sets (of 251, 354, and 558 cases). Finally, the differences in immune cell infiltration and gene enrichment pathways between high and low score groups were identified. Results A prognosis model of HGSOC overall survival rate was constructed in the training set, and included data for 35 immune gene-related gene pairs and the regression coefficients. The risk stratification of HGSOC patients was successfully performed using the training set, with a p-value of Kaplan-Meier of < 0.001. A score from this model is an independent prognostic factor of HGSOC, and prognosis was evaluated in different clinical subgroups. This model was also successful for the other three validation sets, and the results of Kaplan-Meier analysis were statistically significant (p < 0.05). The model can also predict patient progression-free survival with HGSOC to reflect tumor growth status. There was a lower infiltration level of M1 macrophages in the high-risk group compared to that in the low-risk group (p < 0.001). Finally, the immune-related pathways were enriched in the low-risk group. Conclusion The prognostic model based on immune-related gene pairs developed is a potential prognostic marker for high-grade serous ovarian cancer treated with platinum. The model has robust prognostic ability and wide applicability. More prospective studies will be needed to assess the practical application of this model for precision therapy.
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Affiliation(s)
- Jiaxing Lin
- Department of Urology, The First Hospital of China Medical University, Shenyang, China
| | - Xiao Xu
- Department of Pediatric Intensive Care Unit, The Shengjing Hospital of China Medical University, Shenyang, China
| | - Dan Sun
- Department of Urology, The First Hospital of China Medical University, Shenyang, China
| | - Tianren Li
- Department of Gynaecology, The First Hospital of China Medical University, Shenyang, China
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24
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Mysona DP, Tran L, Bai S, dos Santos B, Ghamande S, Chan J, She JX. Tumor-intrinsic and -extrinsic (immune) gene signatures robustly predict overall survival and treatment response in high grade serous ovarian cancer patients. Am J Cancer Res 2021; 11:181-199. [PMID: 33520368 PMCID: PMC7840710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 09/14/2020] [Indexed: 06/12/2023] Open
Abstract
In the present study, we developed a transcriptomic signature capable of predicting prognosis and response to primary therapy in high grade serous ovarian cancer (HGSOC). Proportional hazard analysis was performed on individual genes in the TCGA RNAseq data set containing 229 HGSOC patients. Ridge regression analysis was performed to select genes and develop multigenic models. Survival analysis identified 120 genes whose expression levels were associated with overall survival (OS) (HR = 1.49-2.46 or HR = 0.48-0.63). Ridge regression modeling selected 38 of the 120 genes for development of the final Ridge regression models. The consensus model based on plurality voting by 68 individual Ridge regression models classified 102 (45%) as low, 23 (10%) as moderate and 104 patients (45%) as high risk. The median OS was 31 months (HR = 7.63, 95% CI = 4.85-12.0, P < 1.0-10) and 77 months (HR = ref) in the high and low risk groups, respectively. The gene signature had two components: intrinsic (proliferation, metastasis, autophagy) and extrinsic (immune evasion). Moderate/high risk patients had more partial and non-responses to primary therapy than low risk patients (odds ratio = 4.54, P < 0.001). We concluded that the overall survival and response to primary therapy in ovarian cancer is best assessed using a combination of gene signatures. A combination of genes which combines both tumor intrinsic and extrinsic functions has the best prediction. Validation studies are warranted in the future.
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Affiliation(s)
- David P Mysona
- University of North CarolinaChapel Hill, NC 27517, USA
- Jinfiniti Precision Medicine, Inc.Augusta, GA 30907, USA
| | - Lynn Tran
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia at Augusta UniversityAugusta, GA 30912, USA
| | - Shan Bai
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia at Augusta UniversityAugusta, GA 30912, USA
| | | | - Sharad Ghamande
- Department of OBGYN, Medical College of Georgia at Augusta UniversityAugusta, GA 30912, USA
| | - John Chan
- Palo Alto Medical Foundation Research InstitutePalo Alto, CA 94301, USA
| | - Jin-Xiong She
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia at Augusta UniversityAugusta, GA 30912, USA
- Department of OBGYN, Medical College of Georgia at Augusta UniversityAugusta, GA 30912, USA
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25
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Robust ridge M-estimators with pretest and Stein-rule shrinkage for an intercept term. JAPANESE JOURNAL OF STATISTICS AND DATA SCIENCE 2020. [DOI: 10.1007/s42081-020-00089-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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26
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Hensler M, Kasikova L, Fiser K, Rakova J, Skapa P, Laco J, Lanickova T, Pecen L, Truxova I, Vosahlikova S, Moserova I, Praznovec I, Drochytek V, Rehackova M, Brtnicky T, Rob L, Benes V, Pistolic J, Sojka L, Ryska A, Sautes-Fridman C, Fridman WH, Galluzzi L, Spisek R, Fucikova J. M2-like macrophages dictate clinically relevant immunosuppression in metastatic ovarian cancer. J Immunother Cancer 2020; 8:jitc-2020-000979. [PMID: 32819974 PMCID: PMC7443306 DOI: 10.1136/jitc-2020-000979] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2020] [Indexed: 02/07/2023] Open
Abstract
Background The immunological microenvironment of primary high-grade serous carcinomas (HGSCs) has a major impact on disease outcome. Conversely, little is known on the microenvironment of metastatic HGSCs and its potential influence on patient survival. Here, we explore the clinical relevance of the immunological configuration of HGSC metastases. Methods RNA sequencing was employed on 24 paired primary tumor microenvironment (P-TME) and metastatic tumor microenvironment (M-TME) chemotherapy-naive HGSC samples. Immunohistochemistry was used to evaluate infiltration by CD8+ T cells, CD20+ B cells, DC-LAMP+ (lysosomal-associated membrane protein 3) dendritic cells (DCs), NKp46+ (natural killer) cells and CD68+CD163+ M2-like tumor-associated macrophages (TAMs), abundance of PD-1+ (programmed cell death 1), LAG-3+ (lymphocyte-activating gene 3) cells, and PD-L1 (programmed death ligand 1) expression in 80 samples. Flow cytometry was used for functional assessments on freshly resected HGSC samples. Results 1468 genes were differentially expressed in the P-TME versus M-TME of HGSCs, the latter displaying signatures of extracellular matrix remodeling and immune infiltration. M-TME infiltration by immune effector cells had little impact on patient survival. Accordingly, M-TME-infiltrating T cells were functionally impaired, but not upon checkpoint activation. Conversely, cytokine signaling in favor of M2-like TAMs activity appeared to underlie inhibited immunity in the M-TME and poor disease outcome. Conclusions Immunosuppressive M2-like TAM infiltrating metastatic sites limit clinically relevant immune responses against HGSCs.
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Affiliation(s)
| | - Lenka Kasikova
- Sotio, Prague, Czech Republic.,Department of Immunology, Charles University, 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Karel Fiser
- CLIP-Childhood Leukemia Investigation Prague, Department of Pediatric Hematology and Oncology, 2nd Faculty of Medicine, Charles University Prague and University Hospital Motol, Prague, Czech Republic
| | | | - Petr Skapa
- Department of Pathology and Molecular Medicine, Charles University, 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Jan Laco
- The Fingerland Department of Pathology, Charles University, Faculty of Medicine and University Hospital, Hradec Kralove, Czech Republic
| | - Tereza Lanickova
- Sotio, Prague, Czech Republic.,Department of Immunology, Charles University, 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | | | | | | | | | - Ivan Praznovec
- Department of Gynecology and Obstetrics, Charles University, Faculty of Medicine and University Hospital, Hradec Kralove, Czech Republic
| | - Vit Drochytek
- Department of Gynecology and Obstetrics, Charles University, 3rd Faculty of Medicine and University Hospital Kralovske Vinohrady, Prague, Czech Republic
| | - Martina Rehackova
- Department of Gynecology and Obstetrics, Charles University, 3rd Faculty of Medicine and University Hospital Kralovske Vinohrady, Prague, Czech Republic
| | - Tomas Brtnicky
- Department of Gynecology and Obstetrics, Charles University, 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Lukas Rob
- Department of Gynecology and Obstetrics, Charles University, 3rd Faculty of Medicine and University Hospital Kralovske Vinohrady, Prague, Czech Republic
| | | | | | - Ludek Sojka
- Sotio, Prague, Czech Republic.,Department of Immunology, Charles University, 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Ales Ryska
- The Fingerland Department of Pathology, Charles University, Faculty of Medicine and University Hospital, Hradec Kralove, Czech Republic
| | - Catherine Sautes-Fridman
- INSERM, U1138, Centre de Recherche des Cordeliers, Paris, France.,Sorbonne Université, Paris, France
| | - Wolf Herve Fridman
- INSERM, U1138, Centre de Recherche des Cordeliers, Paris, France.,Sorbonne Université, Paris, France
| | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York City, New York, USA.,Sandra and Edward Meyer Cancer Center, New York City, New York, USA.,Caryl and Israel Englander Institute for Precision Medicine, New York City, New York, USA.,Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut, USA.,Université de Paris, Paris, France
| | - Radek Spisek
- Sotio, Prague, Czech Republic.,Department of Immunology, Charles University, 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Jitka Fucikova
- Sotio, Prague, Czech Republic .,Department of Immunology, Charles University, 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
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Bioinformatics analysis of gene expression profile of serous ovarian carcinomas to screen key genes and pathways. J Ovarian Res 2020; 13:82. [PMID: 32693821 PMCID: PMC7374965 DOI: 10.1186/s13048-020-00680-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/07/2020] [Indexed: 12/19/2022] Open
Abstract
Background Serous ovarian carcinomas (SCA) are the most common and most aggressive ovarian carcinoma subtype which etiology remains unclear. To investigate the prospective role of mRNAs in the tumorigenesis and progression of SCA, the aberrantly expressed mRNAs were calculated based on the NCBI-GEO RNA-seq data. Results Of 21,755 genes with 89 SCA and SBOT cases from 3 independent laboratories, 59 mRNAs were identified as differentially expressed genes (DEGs) (|log2Fold Change| > 1.585, also |FoldChange| > 3 and adjusted P < 0.05) by DESeq R. There were 26 up-regulated DEGs and 33 down-regulated DEGs screened. The hierarchical clustering analysis, functional analysis and pathway enrichment analysis were performed on all DEGs and found that Polo-like kinase (PLK) signaling events are important. PPI network constructed with different filtration conditions screened out 4 common hub genes (KIF11, CDC20, PBK and TOP2A). Mutual exclusivity or co-occurrence analysis of 4 hub genes identified a tendency towards co-occurrence between KIF11 and CDC20 or TOP2A in SCA (p < 0.05). To analyze further the potential role of KIF11 in SCA, the co-expression profiles of KIF11 in SCA were identified and we found that CDC20 co-expressed with KIF11 also is DEG that we screened out before. To verify our previous results in this paper, we assessed the expression levels of 4 hub DEGs (all up-regulated) and 4 down-regulated DEGs in Oncomine database. And the results were consistent with previous conclusions obtained from GEO series. The survival curves showed that KIF11, CDC20 and TOP2A expression are significantly related to prognosis of SCA patients. Conclusions From all the above results, we speculate that KIF11, CDC20 and TOP2A played an important role in SCA.
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Høgdall E, Høgdall C, Vo T, Zhou W, Huang L, Marton M, Keefe SM, Busch-Sørensen M, Sørensen SM, Georgsen J, Mejlgaard E, Nedergaard L, Steiniche T. Impact of PD-L1 and T-cell inflamed gene expression profile on survival in advanced ovarian cancer. Int J Gynecol Cancer 2020; 30:1034-1042. [PMID: 32527769 DOI: 10.1136/ijgc-2019-001109] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 04/16/2020] [Accepted: 04/23/2020] [Indexed: 01/23/2023] Open
Abstract
OBJECTIVE Programmed death ligand 1 (PD-L1) expression affects tumor evasion of immune surveillance. The prognostic value and relationship of PD-L1 expression to T-cell-inflamed immune signatures in ovarian cancer are unclear. The purpose of this study is to evaluate the impact of PD-L1 on overall survival and its correlation with an immune-mediated gene expression profile in patients with advanced ovarian cancer. METHODS PD-L1 expression in tumor and immune cells was assessed by immunohistochemistry, and PD-L1-positive expression was defined as a combined positive score ≥1; a T-cell-inflamed gene expression profile containing interferon γ response genes was evaluated using extracted RNA from surgical samples. Associations between PD-L1 expression, gene expression profile status, and overall survival were analyzed using the Kaplan-Meier method, log-rank test, and multivariate Cox proportional hazards regression models. RESULTS A total of 376 patients with advanced epithelial ovarian, primary peritoneal, or fallopian tube cancer treated by cytoreductive surgery and platinum-based therapy were included. PD-L1-positive expression was observed in 50.5% of patients and associated with more advanced stage (p=0.047), more aggressive histologic subtype (p=0.001), and platinum sensitivity defined by increasing treatment-free interval from first platinum-based chemotherapy to next systemic treatment (p=0.027). PD-L1-positive expression was associated with longer overall survival in multivariate analyses (adjusted HR 0.72, 95% CI 0.56 to 0.93). In subgroup analyses, this association was most pronounced in patients with partially platinum-sensitive disease (treatment-free interval ≥6 to <12 months). T-cell-inflamed gene expression profile status correlated with PD-L1 expression (Spearman, ρ=0.712) but was not an independent predictor of overall survival. CONCLUSION PD-L1 expression is associated with longer overall survival among advanced ovarian cancer patients. PD-L1 expression may be an independent prognostic biomarker.
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Affiliation(s)
- Estrid Høgdall
- Department of Pathology, Herlev and Gentofte Hospital, University of Copenhagen, Herlev, Denmark
| | - Claus Høgdall
- Department of Gynecology and Obstetrics, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Thao Vo
- Merck & Co., Inc, Kenilworth, New Jersey, USA
| | - Wei Zhou
- Merck & Co., Inc, Kenilworth, New Jersey, USA
| | | | | | | | | | - Sarah M Sørensen
- Department of Gynecology and Obstetrics, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Jeanette Georgsen
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Else Mejlgaard
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Lotte Nedergaard
- Department of Pathology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Torben Steiniche
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
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Links between cancer metabolism and cisplatin resistance. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2020; 354:107-164. [PMID: 32475471 DOI: 10.1016/bs.ircmb.2020.01.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Cisplatin is one of the most potent and widely used chemotherapeutic agent in the treatment of several solid tumors, despite the high toxicity and the frequent relapse of patients due to the onset of drug resistance. Resistance to chemotherapeutic agents, either intrinsic or acquired, is currently one of the major problems in oncology. Thus, understanding the biology of chemoresistance is fundamental in order to overcome this challenge and to improve the survival rate of patients. Studies over the last 30 decades have underlined how resistance is a multifactorial phenomenon not yet completely understood. Recently, tumor metabolism has gained a lot of interest in the context of chemoresistance; accumulating evidence suggests that the rearrangements of the principal metabolic pathways within cells, contributes to the sensitivity of tumor to the drug treatment. In this review, the principal metabolic alterations associated with cisplatin resistance are highlighted. Improving the knowledge of the influence of metabolism on cisplatin response is fundamental to identify new possible metabolic targets useful for combinatory treatments, in order to overcome cisplatin resistance.
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30
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Hu Z, Artibani M, Alsaadi A, Wietek N, Morotti M, Shi T, Zhong Z, Santana Gonzalez L, El-Sahhar S, Carrami EM, Mallett G, Feng Y, Masuda K, Zheng Y, Chong K, Damato S, Dhar S, Campo L, Garruto Campanile R, Soleymani Majd H, Rai V, Maldonado-Perez D, Jones S, Cerundolo V, Sauka-Spengler T, Yau C, Ahmed AA. The Repertoire of Serous Ovarian Cancer Non-genetic Heterogeneity Revealed by Single-Cell Sequencing of Normal Fallopian Tube Epithelial Cells. Cancer Cell 2020; 37:226-242.e7. [PMID: 32049047 DOI: 10.1016/j.ccell.2020.01.003] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 10/30/2019] [Accepted: 01/09/2020] [Indexed: 02/08/2023]
Abstract
The inter-differentiation between cell states promotes cancer cell survival under stress and fosters non-genetic heterogeneity (NGH). NGH is, therefore, a surrogate of tumor resilience but its quantification is confounded by genetic heterogeneity. Here we show that NGH in serous ovarian cancer (SOC) can be accurately measured when informed by the molecular signatures of the normal fallopian tube epithelium (FTE) cells, the cells of origin of SOC. Surveying the transcriptomes of ∼6,000 FTE cells, predominantly from non-ovarian cancer patients, identified 6 FTE subtypes. We used subtype signatures to deconvolute SOC expression data and found substantial intra-tumor NGH. Importantly, NGH-based stratification of ∼1,700 tumors robustly correlated with survival. Our findings lay the foundation for accurate prognostic and therapeutic stratification of SOC.
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Affiliation(s)
- Zhiyuan Hu
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford OX3 9DU, UK; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Mara Artibani
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford OX3 9DU, UK; Gene Regulatory Networks in Development and Disease Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Abdulkhaliq Alsaadi
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford OX3 9DU, UK
| | - Nina Wietek
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford OX3 9DU, UK; Department of Gynecological Oncology, Churchill Hospital, Oxford University Hospitals, Oxford OX3 7LE, UK
| | - Matteo Morotti
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford OX3 9DU, UK; Department of Gynecological Oncology, Churchill Hospital, Oxford University Hospitals, Oxford OX3 7LE, UK
| | - Tingyan Shi
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford OX3 9DU, UK
| | - Zhe Zhong
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford OX3 9DU, UK
| | - Laura Santana Gonzalez
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford OX3 9DU, UK
| | - Salma El-Sahhar
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford OX3 9DU, UK
| | - Eli M Carrami
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford OX3 9DU, UK
| | - Garry Mallett
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford OX3 9DU, UK
| | - Yun Feng
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Kenta Masuda
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford OX3 9DU, UK
| | - Yiyan Zheng
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford OX3 9DU, UK
| | - Kay Chong
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford OX3 9DU, UK
| | - Stephen Damato
- Department of Histopathology, Oxford University Hospitals, Oxford OX3 9DU, UK
| | - Sunanda Dhar
- Department of Histopathology, Oxford University Hospitals, Oxford OX3 9DU, UK
| | - Leticia Campo
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Riccardo Garruto Campanile
- Department of Gynecological Oncology, Churchill Hospital, Oxford University Hospitals, Oxford OX3 7LE, UK
| | - Hooman Soleymani Majd
- Department of Gynecological Oncology, Churchill Hospital, Oxford University Hospitals, Oxford OX3 7LE, UK
| | - Vikram Rai
- Department of Gynaecology, Oxford University Hospitals NHS Trust, Oxford OX3 9DU, UK
| | - David Maldonado-Perez
- Oxford Radcliffe Biobank, Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK; NIHR Oxford Biomedical Research Centre, Second Floor, Unipart House Business Centre, Oxford OX4 2PG, UK
| | - Stephanie Jones
- Oxford Radcliffe Biobank, Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK
| | - Vincenzo Cerundolo
- Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Tatjana Sauka-Spengler
- Gene Regulatory Networks in Development and Disease Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Christopher Yau
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; Centre for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK; Division of Informatics, Imaging and Data Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester M13 9PT, UK; Alan Turing Institute, London NW1 2DB, UK.
| | - Ahmed Ashour Ahmed
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford OX3 9DU, UK; Department of Gynecological Oncology, Churchill Hospital, Oxford University Hospitals, Oxford OX3 7LE, UK.
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Siamakpour-Reihani S, Cobb LP, Jiang C, Zhang D, Previs RA, Owzar K, Nixon AB, Alvarez Secord A. Differential expression of immune related genes in high-grade ovarian serous carcinoma. Gynecol Oncol 2020; 156:662-668. [PMID: 31918995 DOI: 10.1016/j.ygyno.2019.12.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/11/2019] [Accepted: 12/16/2019] [Indexed: 01/23/2023]
Abstract
OBJECTIVE To identify novel immunologic targets and biomarkers associated with overall survival (OS) in high-grade serous ovarian cancer (HGSC). METHODS In this retrospective study, microarray data from 51 HGSC specimens were analyzed (Affymetrix HG-U133A). A panel of 183 immune/inflammatory response related genes linked to 279 probe sets was constructed a priori and screened. Associations between gene expression and OS were assessed using logrank tests. Multiple testing was addressed within the False Discovery Rate (FDR) framework. For external validation, TCGA Ovarian dataset and five GSE publicly available HGSC datasets were evaluated. RESULTS In Duke data, 110 probe sets linked to 83 immunologic/inflammatory-related genes were differentially expressed in tumors from long versus short-term HGSC survivors (adjusted p < 0.05). In TCGA, concordant with the results from the Duke discovery cohort, high expression of one probe (IL6R) demonstrated a consistent significance and concordant association with higher expression in long-term HGSC survivors (Duke q-value = 0.022) and improved OS in the TCGA dataset (p-value = 0.015, HR = 0.8). Thirteen genes in GSE14764 (N = 4) and GSE26712 (N = 9) datasets had significant p-values and consistent concordant with Duke Data. Despite the significant associations of gene expression and OS in the individual GSE datasets, in the GSE meta-analysis no genes were consistently concordant and significantly associated with survival. CONCLUSIONS Evaluation of IL6R expression may be warranted based on higher expression in long-term survivors and association with improved survival in advanced HGSC. The other candidate genes may also be of worthy of further exploration to enhance immuno-oncology drug discovery.
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Affiliation(s)
- Sharareh Siamakpour-Reihani
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, Duke University Medical Center, United States.
| | - Lauren Patterson Cobb
- Division of Gynecology Oncology, Department of Obstetrics and Gynecology, Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, United States
| | - Chen Jiang
- Bioinformatics Shared Resource, Duke Cancer Institute, United States.
| | - Dadong Zhang
- Bioinformatics Shared Resource, Duke Cancer Institute, United States.
| | - Rebecca A Previs
- Division of Gynecology Oncology, Department of Obstetrics and Gynecology, Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, United States.
| | - Kouros Owzar
- Duke Department of Biostatistics and Bioinformatics, Duke University Medical Center, United States; Bioinformatics Shared Resource, Duke Cancer Institute, United States.
| | - Andrew B Nixon
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, Duke University Medical Center, United States.
| | - Angeles Alvarez Secord
- Division of Gynecology Oncology, Department of Obstetrics and Gynecology, Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, United States.
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Integrated pan-cancer gene expression and drug sensitivity analysis reveals SLFN11 mRNA as a solid tumor biomarker predictive of sensitivity to DNA-damaging chemotherapy. PLoS One 2019; 14:e0224267. [PMID: 31682620 PMCID: PMC6827986 DOI: 10.1371/journal.pone.0224267] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 10/09/2019] [Indexed: 12/14/2022] Open
Abstract
Background Precision oncology seeks to integrate multiple layers of data from a patient’s cancer to effectively tailor therapy. Conventional chemotherapies are sometimes effective but accompanied by adverse events, warranting the identification of a biomarker of chemosensitivity. Objective Identify an mRNA biomarker that predicts chemosensitivity across solid tumor subtypes. Methods We performed a pan-solid tumor analysis integrating gene expression and drug sensitivity profiles from 3 cancer cell line datasets to identify transcripts correlated with sensitivity to a panel of chemotherapeutics. We then tested the ability of an mRNA biomarker to predictive clinical outcomes in cohorts of patients with breast, lung, or ovarian cancer. Results Expression levels of several mRNA transcripts were significantly correlated with sensitivity or resistance chemotherapeutics in cancer cell line datasets. The only mRNA transcript significantly correlated with sensitization to multiple classes of DNA-damaging chemotherapeutics in all 3 cell line datasets was encoded by Schlafen Family Member 11 (SLFN11). Analyses of multiple breast, lung, and ovarian cancer patient cohorts treated with chemotherapy confirmed SLFN11 mRNA expression as a predictive biomarker of longer overall survival and improved tumor response. Conclusions Tumor SLFN11 mRNA expression is a biomarker of sensitivity to an array of DNA-damaging chemotherapeutics across solid tumor subtypes.
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33
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Bing Z, Yao Y, Xiong J, Tian J, Guo X, Li X, Zhang J, Shi X, Zhang Y, Yang K. Novel Model for Comprehensive Assessment of Robust Prognostic Gene Signature in Ovarian Cancer Across Different Independent Datasets. Front Genet 2019; 10:931. [PMID: 31681404 PMCID: PMC6798149 DOI: 10.3389/fgene.2019.00931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 09/05/2019] [Indexed: 12/31/2022] Open
Abstract
Different analytical methods or models can often find completely different prognostic biomarkers for the same cancer. In the study of prognostic molecular biomarkers of ovarian cancer (OvCa), different studies have reported a variety of prognostic gene signatures. In the current study, based on geometric concepts, the linearity-clustering phase diagram with integrated P-value (LCP) method was used to comprehensively consider three indicators that are commonly employed to estimate the quality of a prognostic gene signature model. The three indicators, namely, concordance index, area under the curve, and level of the hazard ratio were determined via calculation of the prognostic index of various gene signatures from different datasets. As evaluation objects, we selected 13 gene signature models (Cox regression model) and 16 OvCa genomic datasets (including gene expression information and follow-up data) from published studies. The results of LCP showed that three models were universal and better than other models. In addition, combining the three models into one model showed the best performance in all datasets by LCP calculation. The combination gene signature model provides a more reliable model and could be validated in various datasets of OvCa. Thus, our method and findings can provide more accurate prognostic biomarkers and effective reference for the precise clinical treatment of OvCa.
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Affiliation(s)
- Zhitong Bing
- Evidence Based Medicine Center, School of Basic Medical Science of Lanzhou University, Lanzhou, China.,Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, Lanzhou, China.,Department of Computational Physics, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Yuxiang Yao
- School of Physical Science and Technology, Lanzhou University, Lanzhou, China
| | - Jie Xiong
- Department of Applied Mathematics, Changsha University, Changsha, China
| | - Jinhui Tian
- Evidence Based Medicine Center, School of Basic Medical Science of Lanzhou University, Lanzhou, China.,Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, Lanzhou, China
| | - Xiangqian Guo
- Medical Bioinformatics Institute, School of Basic Medicine, Henan University, Henan, China
| | - Xiuxia Li
- Evidence Based Medicine Center, School of Basic Medical Science of Lanzhou University, Lanzhou, China.,Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, Lanzhou, China.,School of Public Health, Lanzhou University, Lanzhou, China
| | - Jingyun Zhang
- Evidence Based Medicine Center, School of Basic Medical Science of Lanzhou University, Lanzhou, China.,Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, Lanzhou, China
| | - Xiue Shi
- Institute for Evidence Based Rehabilitation Medicine of Gansu Province, Lanzhou, China
| | - Yanying Zhang
- Department of Pharmacology and Toxicology of Traditional Chinese Medicine, Gansu University of Chinese Medicine, Lanzhou, China
| | - Kehu Yang
- Evidence Based Medicine Center, School of Basic Medical Science of Lanzhou University, Lanzhou, China.,Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, Lanzhou, China.,Institute for Evidence Based Rehabilitation Medicine of Gansu Province, Lanzhou, China.,Department of Pharmacology and Toxicology of Traditional Chinese Medicine, Gansu University of Chinese Medicine, Lanzhou, China
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Zhao Q, Fan C. A novel risk score system for assessment of ovarian cancer based on co-expression network analysis and expression level of five lncRNAs. BMC MEDICAL GENETICS 2019; 20:103. [PMID: 31182053 PMCID: PMC6558878 DOI: 10.1186/s12881-019-0832-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 05/23/2019] [Indexed: 02/07/2023]
Abstract
Background Ovarian cancer (OC) is the most deadly gynaecological cancer, contributing significantly to female cancer-related deaths worldwide. Improving the outlook for OC patients depends on the identification of more reliable prognostic biomarkers for early diagnosis and survival prediction. The various roles of long non-coding RNAs (lncRNAs) in OC have attracted increasing attention. This study aimed to identify a lncRNA-based signature for survival prediction in OC patients. Methods RNA expression data and clinical information from a large number of OC patients were downloaded from a public database. These data were regarded as a training set to construct a weighed gene co-expression network analysis (WGCNA) network, mine stable modules, and screen differentially expressed lncRNAs. The prognostic lncRNAs were screened using univariate Cox regression analysis and the optimal prognosis lncRNA combination was screened using a Cox-PH model. The finalised lncRNA combination was used to construct the risk score system, which was validated and assessed for effectiveness using other independent datasets. Further functional pathway enrichment was performed using gene set enrichment analysis (GSEA). Results A co-expression network was constructed and four stable modules with OC-related biological functions were obtained. A total of 19 lncRNAs significantly related to prognosis of ovarian cancer were obtained using univariate Cox regression analysis, and the 5 prognostic signature lncRNAs GAS5, HCP5, PART1, SNHG11, and SNHG5 were used to establish a risk assessment system. The reliability of the prognostic scoring system was further confirmed using validation sets, which indicated that the risk assessment system could be used as an independent prognostic factor. Pathway enrichment analysis revealed that the network modules related to the above five prognostic genes were significantly associated with cell local adhesion, cancer signaling pathways, JAK-STAT signalling, and endogenous cell receptor interaction. Conclusions The risk score system established in this study could provide a novel reliable method to identify individuals at high risk of OC. In addition, the five prognostic lncRNAs identified here are promising potential prognostic biomarkers that could help to elucidate the pathogenesis of OC.
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Affiliation(s)
- Qian Zhao
- Department of Gynecology & Obstetrics, Chengdu Women's & Children's Central Hospital, No.1617 Riyue Avenue, Chengdu, 610091, Sichuan Province, China.
| | - Conghong Fan
- Department of Gynecology & Obstetrics, Chengdu Women's & Children's Central Hospital, No.1617 Riyue Avenue, Chengdu, 610091, Sichuan Province, China
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Cui L, Zhou F, Chen C, Wang CC. Overexpression of CCDC69 activates p14 ARF/MDM2/p53 pathway and confers cisplatin sensitivity. J Ovarian Res 2019; 12:4. [PMID: 30651135 PMCID: PMC6334460 DOI: 10.1186/s13048-019-0479-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 01/03/2019] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVES The aim of the study is to explore the relationship between CCDC69 expression and resistance of ovarian cancer cells to cisplatin and reveal the underlying mechanism. METHODS One hundred thirty five ovarian cancer patients with intact chemo-response information from The Cancer Genome Atlas (TCGA) database were included and analyzed. Stable CCDC69 overexpressing 293 and ovarian cancer A2780 cell lines were established and subjected to examine cell apoptosis and cell cycle distribution using CCK-8 assay and flow cytometry. Cell cycle and apoptosis pathway were evaluated by immunoblots. Stability of p14ARF/MDM2/p53 pathway related proteins were determined by half-life analysis and ubiquitination experiments. RESULTS We found that CCDC69 expression was significantly higher in chemo-sensitive groups compared with chemo-resistant groups from TCGA database. High CCDC69 expression was associated longer survival. CCDC69 overexpressing 293 and A2780 cells with wildtype p53 and contributes to cisplatin sensitivity following treatment with cisplatin. We further found over-expression of CCDC69 activated p14ARF/MDM2/p53 pathway. Importantly, we also demonstrated that CCDC69 expression extended p53 and p14ARF protein half-life and shortened MDM2 protein half-life. Ubiquitination assay revealing a decrease in p14 ubiquitination in CCDC69 over-expression cells comparing to cells expressing empty vector. CONCLUSIONS It is tempting to conclude that targeting CCDC69 may play a role in cisplatin resistance.
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Affiliation(s)
- Long Cui
- Department of Obstetrics and Gynaecology, Guangzhou Women and Children Hospital, Guangzhou, 511400, Guangdong, China. .,Department of Obstetrics and Gynecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, SAR, China.
| | - Fang Zhou
- School of Nursing, The First Affiliated Hospital, Xuzhou Medical University, Xuzhou, China
| | - Cui Chen
- Intensive Care Unit, The First Affiliated Hospital, Xuzhou Medical University, Xuzhou, China
| | - Chi Chiu Wang
- Department of Obstetrics and Gynecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, SAR, China.,Reproduction and Development Laboratory, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, Shatin, China
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36
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Jeong S, Mok L, Kim SI, Ahn T, Song YS, Park T. Ovarian Cancer Prognostic Prediction Model Using RNA Sequencing Data. Genomics Inform 2019; 16:e32. [PMID: 30602093 PMCID: PMC6440672 DOI: 10.5808/gi.2018.16.4.e32] [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: 12/10/2018] [Accepted: 12/16/2018] [Indexed: 11/20/2022] Open
Abstract
Ovarian cancer is one of the leading causes of cancer-related deaths in gynecologic malignancies. Over 70 % of ovarian cancer cases are high-grade serous ovarian cancers (HGSC) and have high death rates due to their resistance to chemotherapy. Despite advances in surgical and pharmaceutical therapies, overall survival rates are not good and accurate prediction of prognosis is not easy because of the highly heterogeneous nature of ovarian cancer. To improve patient's prognosis through proper treatment, we present a prognostic prediction model by integrating the high dimensional RNA sequencing data with their clinical data through the following steps: (1) gene filtration, (2) pre-screening, (3) gene marker selection (4) integrated study of selected gene markers and prediction model building. These steps of the prognostic prediction model can be applied to other types of cancer besides ovarian cancer.
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Affiliation(s)
- Seokho Jeong
- Department of Statistics, Seoul National University, Seoul 08826, Korea
| | - Lydia Mok
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea
| | - Se Ik Kim
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - TaeJin Ahn
- Department of Life Science, Handong Global University, Pohang 37554, Korea
| | - Yong-Sang Song
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Taesung Park
- Department of Statistics, Seoul National University, Seoul 08826, Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea
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37
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Emura T, Matsui S, Chen HY. compound.Cox: Univariate feature selection and compound covariate for predicting survival. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2019; 168:21-37. [PMID: 30527130 DOI: 10.1016/j.cmpb.2018.10.020] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 09/26/2018] [Accepted: 10/26/2018] [Indexed: 05/15/2023]
Abstract
BACKGROUND AND OBJECTIVE Univariate feature selection is one of the simplest and most commonly used techniques to develop a multigene predictor for survival. Presently, there is no software tailored to perform univariate feature selection and predictor construction. METHODS We develop the compound.Cox R package that implements univariate significance tests (via the Wald tests or score tests) for feature selection. We provide a cross-validation algorithm to measure predictive capability of selected genes and a permutation algorithm to assess the false discovery rate. We also provide three algorithms for constructing a multigene predictor (compound covariate, compound shrinkage, and copula-based methods), which are tailored to the subset of genes obtained from univariate feature selection. We demonstrate our package using survival data on the lung cancer patients. We examine the predictive capability of the developed algorithms by the lung cancer data and simulated data. RESULTS The developed R package, compound.Cox, is available on the CRAN repository. The statistical tools in compound.Cox allow researchers to determine an optimal significance level of the tests, thus providing researchers an optimal subset of genes for prediction. The package also allows researchers to compute the false discovery rate and various prediction algorithms.
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Affiliation(s)
- Takeshi Emura
- Graduate Institute of Statistics, National Central University, Zhongda Road, Zhongli District, Taoyuan 32001, Taiwan.
| | - Shigeyuki Matsui
- Department of Biostatistics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Hsuan-Yu Chen
- Institute of Statistical Science, Academia Sinica, 128 Academia Road Sec.2, Nankang Taipei 115, Taiwan
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38
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Tan TZ, Heong V, Ye J, Lim D, Low J, Choolani M, Scott C, Tan DSP, Huang RYJ. Decoding transcriptomic intra-tumour heterogeneity to guide personalised medicine in ovarian cancer. J Pathol 2018; 247:305-319. [PMID: 30374975 DOI: 10.1002/path.5191] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 10/17/2018] [Accepted: 10/25/2018] [Indexed: 01/24/2023]
Abstract
The evaluation of intra-tumour heterogeneity (ITH) from a transcriptomic point of view is limited. Single-cell cancer studies reveal significant genomic and transcriptomic ITH within a tumour and it is no longer adequate to employ single-subtype assignment as this does not acknowledge the ITH that exists. Molecular assessment of subtype heterogeneity (MASH) was developed to comprehensively report on the composition of all transcriptomic subtypes within a tumour lesion. Using MASH on 3431 ovarian cancer samples, correlation and association analyses with survival, metastasis and clinical outcomes were performed to assess the impact of subtype composition as a surrogate for ITH. The association was validated on two independent cohorts. We identified that 30% of ovarian tumours consist of two or more subtypes. When biological features of the subtype constituents were examined, we identified significant impact on clinical outcomes with the presence of poor prognostic subtypes (Mes or Stem-A). Poorer outcomes correlated with having higher degrees of poor prognostic subtype populations within the tumour. Subtype prediction in several independent datasets reflected a similar prognostic trend. In addition, paired analysis of primary and recurrent/metastatic tumours demonstrated Mes and/or Stem-A subtypes predominated in recurrent and metastatic tumours regardless of the original primary subtype. Given the biological and prognostic value in delineating individual subtypes within a tumour, a clinically applicable MASH assay using NanoString® technology was developed as a classification tool to comprehensively describe constituents of molecular subtypes. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Tuan Zea Tan
- Cancer Science Institute of Singapore, National University of Singapore, Center for Translational Medicine, Singapore
| | - Valerie Heong
- Cancer Science Institute of Singapore, National University of Singapore, Center for Translational Medicine, Singapore.,Department of Haematology-Oncology, National University Cancer Institute Singapore, Level 8 NUH Medical Center, Singapore.,Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Jieru Ye
- Cancer Science Institute of Singapore, National University of Singapore, Center for Translational Medicine, Singapore
| | - Diana Lim
- Department of Pathology, National University Health System, Singapore.,Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jeffrey Low
- Department of Obstetrics and Gynecology, National University Health System, Singapore
| | - Mahesh Choolani
- Department of Obstetrics and Gynecology, National University Health System, Singapore
| | - Clare Scott
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - David Shao Peng Tan
- Cancer Science Institute of Singapore, National University of Singapore, Center for Translational Medicine, Singapore.,Department of Haematology-Oncology, National University Cancer Institute Singapore, Level 8 NUH Medical Center, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Ruby Yun-Ju Huang
- Cancer Science Institute of Singapore, National University of Singapore, Center for Translational Medicine, Singapore.,Department of Obstetrics and Gynecology, National University Health System, Singapore.,Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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39
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Chen GM, Kannan L, Geistlinger L, Kofia V, Safikhani Z, Gendoo DMA, Parmigiani G, Birrer M, Haibe-Kains B, Waldron L. Consensus on Molecular Subtypes of High-Grade Serous Ovarian Carcinoma. Clin Cancer Res 2018. [PMID: 30084834 DOI: 10.1158/1078-0432.ccr-18-0784] [] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Purpose: The majority of ovarian carcinomas are of high-grade serous histology, which is associated with poor prognosis. Surgery and chemotherapy are the mainstay of treatment, and molecular characterization is necessary to lead the way to targeted therapeutic options. To this end, various computational methods for gene expression-based subtyping of high-grade serous ovarian carcinoma (HGSOC) have been proposed, but their overlap and robustness remain unknown.Experimental Design: We assess three major subtype classifiers by meta-analysis of publicly available expression data, and assess statistical criteria of subtype robustness and classifier concordance. We develop a consensus classifier that represents the subtype classifications of tumors based on the consensus of multiple methods, and outputs a confidence score. Using our compendium of expression data, we examine the possibility that a subset of tumors is unclassifiable based on currently proposed subtypes.Results: HGSOC subtyping classifiers exhibit moderate pairwise concordance across our data compendium (58.9%-70.9%; P < 10-5) and are associated with overall survival in a meta-analysis across datasets (P < 10-5). Current subtypes do not meet statistical criteria for robustness to reclustering across multiple datasets (prediction strength < 0.6). A new subtype classifier is trained on concordantly classified samples to yield a consensus classification of patient tumors that correlates with patient age, survival, tumor purity, and lymphocyte infiltration.Conclusions: A new consensus ovarian subtype classifier represents the consensus of methods and demonstrates the importance of classification approaches for cancer that do not require all tumors to be assigned to a distinct subtype. Clin Cancer Res; 24(20); 5037-47. ©2018 AACR.
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Affiliation(s)
- Gregory M Chen
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Lavanya Kannan
- City University of New York School of Public Health, New York, New York.,Institute for Implementation Science in Population Health, City University of New York, New York, New York
| | - Ludwig Geistlinger
- City University of New York School of Public Health, New York, New York.,Institute for Implementation Science in Population Health, City University of New York, New York, New York
| | - Victor Kofia
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Zhaleh Safikhani
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Deena M A Gendoo
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Giovanni Parmigiani
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts
| | - Michael Birrer
- University of Alabama Comprehensive Cancer Center, Birmingham, Alabama
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute of Cancer Research, Toronto, Ontario, Canada
| | - Levi Waldron
- City University of New York School of Public Health, New York, New York. .,Institute for Implementation Science in Population Health, City University of New York, New York, New York
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40
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Chen GM, Kannan L, Geistlinger L, Kofia V, Safikhani Z, Gendoo DMA, Parmigiani G, Birrer M, Haibe-Kains B, Waldron L. Consensus on Molecular Subtypes of High-Grade Serous Ovarian Carcinoma. Clin Cancer Res 2018; 24:5037-5047. [PMID: 30084834 PMCID: PMC6207081 DOI: 10.1158/1078-0432.ccr-18-0784] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/01/2018] [Accepted: 06/26/2018] [Indexed: 01/19/2023]
Abstract
Purpose: The majority of ovarian carcinomas are of high-grade serous histology, which is associated with poor prognosis. Surgery and chemotherapy are the mainstay of treatment, and molecular characterization is necessary to lead the way to targeted therapeutic options. To this end, various computational methods for gene expression-based subtyping of high-grade serous ovarian carcinoma (HGSOC) have been proposed, but their overlap and robustness remain unknown.Experimental Design: We assess three major subtype classifiers by meta-analysis of publicly available expression data, and assess statistical criteria of subtype robustness and classifier concordance. We develop a consensus classifier that represents the subtype classifications of tumors based on the consensus of multiple methods, and outputs a confidence score. Using our compendium of expression data, we examine the possibility that a subset of tumors is unclassifiable based on currently proposed subtypes.Results: HGSOC subtyping classifiers exhibit moderate pairwise concordance across our data compendium (58.9%-70.9%; P < 10-5) and are associated with overall survival in a meta-analysis across datasets (P < 10-5). Current subtypes do not meet statistical criteria for robustness to reclustering across multiple datasets (prediction strength < 0.6). A new subtype classifier is trained on concordantly classified samples to yield a consensus classification of patient tumors that correlates with patient age, survival, tumor purity, and lymphocyte infiltration.Conclusions: A new consensus ovarian subtype classifier represents the consensus of methods and demonstrates the importance of classification approaches for cancer that do not require all tumors to be assigned to a distinct subtype. Clin Cancer Res; 24(20); 5037-47. ©2018 AACR.
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Affiliation(s)
- Gregory M Chen
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Lavanya Kannan
- City University of New York School of Public Health, New York, New York
- Institute for Implementation Science in Population Health, City University of New York, New York, New York
| | - Ludwig Geistlinger
- City University of New York School of Public Health, New York, New York
- Institute for Implementation Science in Population Health, City University of New York, New York, New York
| | - Victor Kofia
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Zhaleh Safikhani
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Deena M A Gendoo
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Giovanni Parmigiani
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts
| | - Michael Birrer
- University of Alabama Comprehensive Cancer Center, Birmingham, Alabama
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Ontario Institute of Cancer Research, Toronto, Ontario, Canada
| | - Levi Waldron
- City University of New York School of Public Health, New York, New York.
- Institute for Implementation Science in Population Health, City University of New York, New York, New York
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41
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Feng M, Marjon KD, Zhu F, Weissman-Tsukamoto R, Levett A, Sullivan K, Kao KS, Markovic M, Bump PA, Jackson HM, Choi TS, Chen J, Banuelos AM, Liu J, Gip P, Cheng L, Wang D, Weissman IL. Programmed cell removal by calreticulin in tissue homeostasis and cancer. Nat Commun 2018; 9:3194. [PMID: 30097573 PMCID: PMC6086865 DOI: 10.1038/s41467-018-05211-7] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Accepted: 06/19/2018] [Indexed: 02/05/2023] Open
Abstract
Macrophage-mediated programmed cell removal (PrCR) is a process essential for the clearance of unwanted (damaged, dysfunctional, aged, or harmful) cells. The detection and recognition of appropriate target cells by macrophages is a critical step for successful PrCR, but its molecular mechanisms have not been delineated. Here using the models of tissue turnover, cancer immunosurveillance, and hematopoietic stem cells, we show that unwanted cells such as aging neutrophils and living cancer cells are susceptible to "labeling" by secreted calreticulin (CRT) from macrophages, enabling their clearance through PrCR. Importantly, we identified asialoglycans on the target cells to which CRT binds to regulate PrCR, and the availability of such CRT-binding sites on cancer cells correlated with the prognosis of patients in various malignancies. Our study reveals a general mechanism of target cell recognition by macrophages, which is the key for the removal of unwanted cells by PrCR in physiological and pathophysiological processes.
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Affiliation(s)
- Mingye Feng
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA.
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA, 91010, USA.
| | - Kristopher D Marjon
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University, Stanford, CA, 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, CA, 94305, USA
| | - Fangfang Zhu
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University, Stanford, CA, 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, CA, 94305, USA
| | - Rachel Weissman-Tsukamoto
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University, Stanford, CA, 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, CA, 94305, USA
| | - Aaron Levett
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University, Stanford, CA, 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, CA, 94305, USA
| | - Katie Sullivan
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University, Stanford, CA, 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, CA, 94305, USA
| | - Kevin S Kao
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University, Stanford, CA, 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, CA, 94305, USA
| | - Maxim Markovic
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University, Stanford, CA, 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, CA, 94305, USA
| | - Paul A Bump
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University, Stanford, CA, 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, CA, 94305, USA
| | - Hannah M Jackson
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University, Stanford, CA, 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, CA, 94305, USA
| | - Timothy S Choi
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University, Stanford, CA, 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, CA, 94305, USA
| | - Jing Chen
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA, 91010, USA
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Allison M Banuelos
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University, Stanford, CA, 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, CA, 94305, USA
| | - Jie Liu
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University, Stanford, CA, 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, CA, 94305, USA
| | - Phung Gip
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University, Stanford, CA, 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, CA, 94305, USA
| | - Lei Cheng
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Denong Wang
- SRI International, Menlo Park, CA, 94025, USA
| | - Irving L Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA.
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University, Stanford, CA, 94305, USA.
- Stanford Cancer Institute, Stanford University, Stanford, CA, 94305, USA.
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA.
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42
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Zhou J, Li L, Wang L, Li X, Xing H, Cheng L. Establishment of a SVM classifier to predict recurrence of ovarian cancer. Mol Med Rep 2018; 18:3589-3598. [PMID: 30106117 PMCID: PMC6131358 DOI: 10.3892/mmr.2018.9362] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 04/23/2018] [Indexed: 02/02/2023] Open
Abstract
Gene expression data using retrieved ovarian cancer (OC) samples were used to identify genes of interest and a support vector machine (SVM) classifier was subsequently established to predict the recurrence of OC. Three datasets (GSE17260, GSE44104 and GSE51088) investigating OC gene expression were downloaded from the Gene Expression Omnibus. Differentially expressed genes (DEGs) in samples from patients with non-recurrent and recurrent OC were revealed via a homogeneity test and quality control analysis. A protein-protein interaction (PPI) network was subsequently established for the DEGs using data from Biological General Repository for Interaction Datasets, Human Protein Reference Database and Database of Interacting Proteins. Degrees of interaction and betweenness centrality (BC) scores were calculated for each node in the PPI network. The top 100 genes ranked by BC scores were selected to identify feature genes via recursive feature elimination using the GSE17260 dataset. Following this, a SVM classifier was constructed and further validated using the GSE44104 and GSE51088 datasets and independent gene expression data obtained from the Cancer Genome Atlas (TCGA). A total of 639 DEGs were identified from the three gene expression datasets, and a PPI network including 249 nodes and 354 edges was constructed. A SVM classifier consisting of 39 feature genes (including cullin 3, mouse double minute 2 homolog, aurora kinase A, WW domain containing oxidoreducatase, large tumor suppressor kinase 2, sirtuin 6, staphylococcal nuclease and tudor domain containing 1, leucine rich repeats and immunoglobulin like domains 1 and aurora kinase 1 interacting protein 1) was subsequently constructed. The prediction accuracies of the SVM classifier for GSE17260, GSE44104 and GSE51088 datasets as well as data downloaded from TCGA were revealed to be 92.7, 93.3, 96.6 and 90.4%, respectively. Furthermore, the results of the present study revealed that patients with predicted non-recurrent OC survived significantly longer compared with the patients with predicted recurrent OC (P=6.598×10−6). A SVM classifier consisting of 39 feature genes was established for predicting the recurrence and prognosis of OC. Therefore, the results of the present study suggested that the 39 feature genes may serve important roles in the development of OC and may represent therapeutic biomarkers of OC.
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Affiliation(s)
- Jinting Zhou
- Department of Obstetrics and Gynecology, Xiangyang Central Hospital Affiliated to The Hubei University of Arts and Science, Xiangyang, Hubei 441021, P.R. China
| | - Lin Li
- Department of Obstetrics and Gynecology, Xiangyang Central Hospital Affiliated to The Hubei University of Arts and Science, Xiangyang, Hubei 441021, P.R. China
| | - Liling Wang
- Department of Obstetrics and Gynecology, Xiangyang Central Hospital Affiliated to The Hubei University of Arts and Science, Xiangyang, Hubei 441021, P.R. China
| | - Xiaofang Li
- Department of Obstetrics and Gynecology, Xiangyang Central Hospital Affiliated to The Hubei University of Arts and Science, Xiangyang, Hubei 441021, P.R. China
| | - Hui Xing
- Department of Obstetrics and Gynecology, Xiangyang Central Hospital Affiliated to The Hubei University of Arts and Science, Xiangyang, Hubei 441021, P.R. China
| | - Li Cheng
- Department of Obstetrics and Gynecology, Xiangyang Central Hospital Affiliated to The Hubei University of Arts and Science, Xiangyang, Hubei 441021, P.R. China
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43
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Stoll G, Pol J, Soumelis V, Zitvogel L, Kroemer G. Impact of chemotactic factors and receptors on the cancer immune infiltrate: a bioinformatics study revealing homogeneity and heterogeneity among patient cohorts. Oncoimmunology 2018; 7:e1484980. [PMID: 30288345 PMCID: PMC6169589 DOI: 10.1080/2162402x.2018.1484980] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 05/29/2018] [Accepted: 05/30/2018] [Indexed: 01/19/2023] Open
Abstract
Multiple soluble factors including proteins (in particular chemokines), non-proteinaceous factors released by dead cells, as well as receptors for such factors (in particular chemokine receptors, formyl peptide receptors and purinergic receptors), influence the recruitment of distinct cell subsets into the tumor microenvironment. We performed an extensive bioinformatic analysis on tumor specimens from 5953 cancer patients to correlate the mRNA expression levels of chemotactic factors/receptors with the density of immune cell types infiltrating the malignant lesions. This meta-analysis, which included specimens from breast, colorectal, lung, ovary and head and neck carcinomas as well as melanomas, revealed that a subset of chemotactic factors/receptors exhibited a positive and reproducible correlation with several infiltrating cell types across various solid cancers, revealing a universal pattern of association. Hence, this meta-analysis distinguishes between homogeneous associations that occur across different cancer types and heterogeneous correlations, that are specific of one organ. Importantly, in four out of five breast cancer cohorts for which clinical data were available, the levels of expression of chemotactic factors/receptors that exhibited universal (rather than organ-specific) positive correlations with the immune infiltrate had a positive impact on the response to neoadjuvant chemotherapy. These results support the notion that general (rather than organ-specific) rules governing the recruitment of immune cells into the tumor bed are particularly important in determining local immunosurveillance and response to therapy.
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Affiliation(s)
- Gautier Stoll
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,Institut National de la Santé et de la Recherche Médicale, U1138, Paris, France.,Université Pierre et Marie Curie, Paris, France.,Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France
| | - Jonathan Pol
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,Institut National de la Santé et de la Recherche Médicale, U1138, Paris, France.,Université Pierre et Marie Curie, Paris, France.,Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France
| | - Vassili Soumelis
- pôle de biopathologie, Institut Curie, Paris, France.,Institut National de la Santé et de la Recherche Médicale, U932, Paris, France.,CIC IGR-Curie 1428, Paris, France.,PSL, Paris, France
| | - Laurence Zitvogel
- Equipe labellisée Ligue Nationale Contre le Cancer, Institut National de la Santé et de la Recherche Médicale, U1015, Villejuif, France.,Institut Gustave Roussy Cancer Campus, Villejuif, France.,Faculty of Medicine, University of Paris Sud, Kremlin-Bicêtre, France.,Center of Clinical Investigations in Biotherapies of Cancer (CICBT), Villejuif, France
| | - Guido Kroemer
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,Institut National de la Santé et de la Recherche Médicale, U1138, Paris, France.,Université Pierre et Marie Curie, Paris, France.,Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France.,Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France.,Department of Women's and Children's Health, Karolinska University Hospital, Stockholm, Sweden
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44
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Miller KR, Patel JN, Zhang Q, Norris EJ, Symanowski J, Michener C, Sehouli J, Braicu I, Destephanis DD, Sutker AP, Jones W, Livasy CA, Biscotti C, Ganapathi RN, Tait DL, Ganapathi MK. HOXA4/HOXB3 gene expression signature as a biomarker of recurrence in patients with high-grade serous ovarian cancer following primary cytoreductive surgery and first-line adjuvant chemotherapy. Gynecol Oncol 2018; 149:155-162. [PMID: 29402501 DOI: 10.1016/j.ygyno.2018.01.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 01/18/2018] [Accepted: 01/21/2018] [Indexed: 01/14/2023]
Abstract
OBJECTIVES Aberrant homeobox (HOX) gene expression is reported in high-grade serous ovarian carcinoma (HGSOC), however, its prognostic significance remains unclear. METHODS HOX genes associated with progression-free survival (PFS) in a discovery cohort of primary HGSOC samples with RNA sequencing data, and those previously reported to be associated with clinical outcomes, were selected for qPCR testing in an independent training cohort of primary HGSOC samples (n=71). A prognostic model for PFS was developed using univariate and multivariate Cox regression. Patients were stratified into risk groups that optimized the test statistic. The model was tested in an independent HGSOC cohort from The Cancer Genome Atlas (TCGA) (n=320). The effect of selected HOX genes on drug sensitivity and reactive oxygen species (ROS) accumulation was examined in vitro. RESULTS Of 23 HOX genes tested in the training cohort, HOXA4 (HR=1.20, 95% CI=1.07-1.34, P=0.002) and HOXB3 (HR=1.09, 95% CI=1.01-1.17, P=0.027) overexpression were significantly associated with shorter PFS in multivariate analysis. Based on the optimal cutoff of the HOXA4/HOXB3 risk score, median PFS was 16.9months (95% CI=14.6-21.2months) and not reached (>80months) for patients with high and low risk scores, respectively (HR=8.89, 95% CI=2.09-37.74, P<0.001). In TCGA, the HOXA4/HOXB3 risk score was significantly associated with disease-free survival (HR=1.44, 95% CI=1.00-2.09, P=0.048). HOXA4 or HOXB3 overexpression in ovarian cancer cells decreased sensitivity to cisplatin and attenuated the generation of cisplatin-induced ROS (P<0.05). CONCLUSIONS HOXA4/HOXB3 gene expression-based risk score may be useful for prognostic risk stratification and warrants prospective validation in HGSOC patients.
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Affiliation(s)
- Katherine R Miller
- Department of Cancer Pharmacology, Levine Cancer Institute, Carolinas HealthCare System, Charlotte, NC, USA
| | - Jai N Patel
- Department of Cancer Pharmacology, Levine Cancer Institute, Carolinas HealthCare System, Charlotte, NC, USA
| | - Qing Zhang
- Department of Biostatistics, Levine Cancer Institute, Carolinas HealthCare System, Charlotte, NC, USA
| | - Eric J Norris
- Department of Cancer Pharmacology, Levine Cancer Institute, Carolinas HealthCare System, Charlotte, NC, USA
| | - James Symanowski
- Department of Biostatistics, Levine Cancer Institute, Carolinas HealthCare System, Charlotte, NC, USA
| | - Chad Michener
- Women's Health and Obstetrics/Gynecology Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jalid Sehouli
- Department of Gynecology, Charité Medical University of Berlin, Berlin, Germany
| | - Ioana Braicu
- Department of Gynecology, Charité Medical University of Berlin, Berlin, Germany
| | - Darla D Destephanis
- Department of Cancer Pharmacology, Levine Cancer Institute, Carolinas HealthCare System, Charlotte, NC, USA
| | - Ashley P Sutker
- Department of Cancer Pharmacology, Levine Cancer Institute, Carolinas HealthCare System, Charlotte, NC, USA
| | - Wendell Jones
- Bioinformatics and Clinical Systems, Q(2) Solutions - EA Genomics, 5927 S. Miami Blvd., Suite 100, Morrisville, NC 27560, USA
| | - Chad A Livasy
- Carolinas Pathology Group, Carolinas HealthCare System, Charlotte, NC, USA
| | - Charles Biscotti
- Department of Anatomic Pathology, Cleveland Clinic, Cleveland, OH, USA
| | - Ram N Ganapathi
- Department of Cancer Pharmacology, Levine Cancer Institute, Carolinas HealthCare System, Charlotte, NC, USA.
| | - David L Tait
- Division of Gynecologic Oncology, Levine Cancer Institute, Carolinas HealthCare System, Charlotte, NC 28204, USA.
| | - Mahrukh K Ganapathi
- Department of Cancer Pharmacology, Levine Cancer Institute, Carolinas HealthCare System, Charlotte, NC, USA.
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45
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Pearce OMT, Delaine-Smith RM, Maniati E, Nichols S, Wang J, Böhm S, Rajeeve V, Ullah D, Chakravarty P, Jones RR, Montfort A, Dowe T, Gribben J, Jones JL, Kocher HM, Serody JS, Vincent BG, Connelly J, Brenton JD, Chelala C, Cutillas PR, Lockley M, Bessant C, Knight MM, Balkwill FR. Deconstruction of a Metastatic Tumor Microenvironment Reveals a Common Matrix Response in Human Cancers. Cancer Discov 2018; 8:304-319. [PMID: 29196464 PMCID: PMC5837004 DOI: 10.1158/2159-8290.cd-17-0284] [Citation(s) in RCA: 218] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/08/2017] [Accepted: 11/28/2017] [Indexed: 12/21/2022]
Abstract
We have profiled, for the first time, an evolving human metastatic microenvironment by measuring gene expression, matrisome proteomics, cytokine and chemokine levels, cellularity, extracellular matrix organization, and biomechanical properties, all on the same sample. Using biopsies of high-grade serous ovarian cancer metastases that ranged from minimal to extensive disease, we show how nonmalignant cell densities and cytokine networks evolve with disease progression. Multivariate integration of the different components allowed us to define, for the first time, gene and protein profiles that predict extent of disease and tissue stiffness, while also revealing the complexity and dynamic nature of matrisome remodeling during development of metastases. Although we studied a single metastatic site from one human malignancy, a pattern of expression of 22 matrisome genes distinguished patients with a shorter overall survival in ovarian and 12 other primary solid cancers, suggesting that there may be a common matrix response to human cancer.Significance: Conducting multilevel analysis with data integration on biopsies with a range of disease involvement identifies important features of the evolving tumor microenvironment. The data suggest that despite the large spectrum of genomic alterations, some human malignancies may have a common and potentially targetable matrix response that influences the course of disease. Cancer Discov; 8(3); 304-19. ©2017 AACR.This article is highlighted in the In This Issue feature, p. 253.
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Affiliation(s)
- Oliver M T Pearce
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK
| | - Robin M Delaine-Smith
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK
- School of Engineering and Materials Science, Queen Mary University of London, London, UK
| | - Eleni Maniati
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK
| | - Sam Nichols
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK
| | - Jun Wang
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK
| | - Steffen Böhm
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK
| | - Vinothini Rajeeve
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK
| | - Dayem Ullah
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK
| | | | - Roanne R Jones
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK
| | - Anne Montfort
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK
| | - Tom Dowe
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK
| | - John Gribben
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK
| | - J Louise Jones
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK
| | - Hemant M Kocher
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK
| | - Jonathan S Serody
- UNC Lineberger Comprehensive Cancer Centre, Chapel Hill, North Carolina
| | | | - John Connelly
- Institute of Bioengineering, Queen Mary University of London, London, UK
- Blizard Institute, Queen Mary University of London, London, UK
| | - James D Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
| | - Claude Chelala
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK
| | - Pedro R Cutillas
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK
| | - Michelle Lockley
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK
| | - Conrad Bessant
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Martin M Knight
- School of Engineering and Materials Science, Queen Mary University of London, London, UK
- Bioinformatics Core, The Francis Crick Institute, London, UK
| | - Frances R Balkwill
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK.
- Bioinformatics Core, The Francis Crick Institute, London, UK
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46
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Wang XV, Parmigiani G. Integrative factor analysis — An unsupervised method for quantifying cross-study consistency of gene expression data. Genomics 2018; 110:80-88. [DOI: 10.1016/j.ygeno.2017.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 08/28/2017] [Accepted: 08/30/2017] [Indexed: 11/30/2022]
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47
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Xiong J, Xiong K, Bing Z. Clinical and RNA expression integrated signature for urothelial bladder cancer prognosis. Cancer Biomark 2018; 21:535-546. [DOI: 10.3233/cbm-170314] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jie Xiong
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, Hunan, China
| | - Ke Xiong
- School of Medicine, Tongji University, Shanghai, China
| | - Zhitong Bing
- Department of Computational Physics, Institute of Modern Physics of Chinese Academy of Sciences, Lanzhou, Gansu, China
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Comprehensive analysis of lncRNA expression profiles reveals a novel lncRNA signature to discriminate nonequivalent outcomes in patients with ovarian cancer. Oncotarget 2018; 7:32433-48. [PMID: 27074572 PMCID: PMC5078024 DOI: 10.18632/oncotarget.8653] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 03/28/2016] [Indexed: 02/01/2023] Open
Abstract
There is growing evidence of dysregulated long non-coding RNAs (lncRNAs) serving as potential biomarkers for cancer prognosis. However, systematic efforts of searching for an expression-based lncRNA signature for prognosis prediction in ovarian cancer (OvCa) have not been made yet. Here, we performed comprehensive analysis for lncRNA expression profiles and clinical data of 544 OvCa patients from The Cancer Genome Atlas (TCGA), and identified an eight-lncRNA signature with ability to classify patients of the training cohort into high-risk group showing poor outcome and low-risk group showing significantly improved outcome, which was further validated in the validation cohort and entire TCGA cohort. Multivariate Cox regression analysis and stratified analysis demonstrated that the prognostic value of this signature was independent of other clinicopathological factors. Associating the outcome prediction with BRCA1 and/or BRCA2 mutation revealed a superior prognosis performance both in BRCA1/2-mutated and BRCA1/2 wild-type tumors. Finally, a significantly correlation was found between the lncRNA signature and the complete response rate of chemotherapy, suggesting that this eight-lncRNA signature may be a measure to predict chemotherapy response and identify platinum-resistant patients who might benefit from other more efficacious therapies. With further prospective validation, this eight-lncRNA signature may have important implications for outcome prediction and therapy decisions.
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Hudson CD, Savadelis A, Nagaraj AB, Joseph P, Avril S, DiFeo A, Avril N. Altered glutamine metabolism in platinum resistant ovarian cancer. Oncotarget 2018; 7:41637-41649. [PMID: 27191653 PMCID: PMC5173084 DOI: 10.18632/oncotarget.9317] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 04/10/2016] [Indexed: 01/21/2023] Open
Abstract
Ovarian cancer is characterized by an increase in cellular energy metabolism, which is predominantly satisfied by glucose and glutamine. Targeting metabolic pathways is an attractive approach to enhance the therapeutic effectiveness and to potentially overcome drug resistance in ovarian cancer. In platinum-sensitive ovarian cancer cell lines the metabolism of both, glucose and glutamine was initially up-regulated in response to platinum treatment. In contrast, platinum-resistant cells revealed a significant dependency on the presence of glutamine, with an upregulated expression of glutamine transporter ASCT2 and glutaminase. This resulted in a higher oxygen consumption rate compared to platinum-sensitive cell lines reflecting the increased dependency of glutamine utilization through the tricarboxylic acid cycle. The important role of glutamine metabolism was confirmed by stable overexpression of glutaminase, which conferred platinum resistance. Conversely, shRNA knockdown of glutaminase in platinum resistant cells resulted in re-sensitization to platinum treatment. Importantly, combining the glutaminase inhibitor BPTES with platinum synergistically inhibited platinum sensitive and resistant ovarian cancers in vitro. Apoptotic induction was significantly increased using platinum together with BPTES compared to either treatment alone. Our findings suggest that targeting glutamine metabolism together with platinum based chemotherapy offers a potential treatment strategy particularly in drug resistant ovarian cancer.
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Affiliation(s)
- Chantelle D Hudson
- Department of Radiology, Case Center for Imaging Research, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Alyssa Savadelis
- Department of Radiology, Case Center for Imaging Research, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Anil Belur Nagaraj
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Peronne Joseph
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Stefanie Avril
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Analisa DiFeo
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Norbert Avril
- Department of Radiology, Case Center for Imaging Research, Case Western Reserve University, Cleveland, OH 44106, USA
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Previs RA, Sood AK, Mills GB, Westin SN. The rise of genomic profiling in ovarian cancer. Expert Rev Mol Diagn 2017; 16:1337-1351. [PMID: 27828713 DOI: 10.1080/14737159.2016.1259069] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Next-generation sequencing and advances in 'omics technology have rapidly increased our understanding of the molecular landscape of epithelial ovarian cancers. Areas covered: Once characterized only by histologic appearance and clinical behavior, we now understand many of the molecular phenotypes that underlie the different ovarian cancer subtypes. While the current approach to treatment involves standard cytotoxic therapies after cytoreductive surgery for all ovarian cancers regardless of histologic or molecular characteristics, focus has shifted beyond a 'one size fits all' approach to ovarian cancer. Expert commentary: Genomic profiling offers potentially 'actionable' opportunities for development of targeted therapies and a more individualized approach to treatment with concomitant improved outcomes and decreased toxicity.
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Affiliation(s)
- Rebecca A Previs
- a Department of Gynecologic Oncology and Reproductive Medicine , The University of Texas MD Anderson Cancer Center , Houston , TX , USA
| | - Anil K Sood
- a Department of Gynecologic Oncology and Reproductive Medicine , The University of Texas MD Anderson Cancer Center , Houston , TX , USA
| | - Gordon B Mills
- b Department of Systems Biology , The University of Texas MD Anderson Cancer , Houston , TX , USA
| | - Shannon N Westin
- a Department of Gynecologic Oncology and Reproductive Medicine , The University of Texas MD Anderson Cancer Center , Houston , TX , USA
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