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Berglund AE, Puskas J, Yoder SJ, Smith AT, Marchion DC, Qin D, Mulé JJ, Torres-Roca JF, Eschrich SA. Evaluating the Radiation Sensitivity Index and 12-Chemokine Gene Expression Signature for Clinical Use in a CLIA Laboratory. CANCER RESEARCH COMMUNICATIONS 2025; 5:389-397. [PMID: 39932296 PMCID: PMC11873780 DOI: 10.1158/2767-9764.crc-24-0534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2024] [Revised: 01/22/2025] [Accepted: 02/06/2025] [Indexed: 02/19/2025]
Abstract
SIGNIFICANCE The RSI and 12CK GES are two GESs that predict tumor radiation sensitivity or the presence of tertiary lymphoid structures in tumors, respectively. These GESs were assessed within the CLIA process for future clinical use. We established proficiency, reproducibility, and reliability characteristics for both signatures in a controlled setting, indicating these GESs are suitable for validation within future clinical trials.
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Affiliation(s)
- Anders E. Berglund
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center & Research Institute, Tampa, Florida
- Department of Quantitative Health Sciences, Mayo Clinic Florida, Jacksonville, Florida
| | - John Puskas
- Advanced Diagnostic Laboratory, Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Sean J. Yoder
- Molecular Genomics Core, Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Andrew T. Smith
- Molecular Genomics Core, Moffitt Cancer Center & Research Institute, Tampa, Florida
| | | | - Dahui Qin
- Advanced Diagnostic Laboratory, Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - James J. Mulé
- Department of Immunology, Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Javier F. Torres-Roca
- Department of Radiation Oncology, Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Steven A. Eschrich
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center & Research Institute, Tampa, Florida
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2
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Ye C, Sun Q, Yan J, Xue D, Xu J, Ma H, Li F. Development of fatty acid metabolism score based on gene signature for predicting prognosis and immunotherapy response in colon cancer. Clin Transl Oncol 2024; 26:630-643. [PMID: 37480430 DOI: 10.1007/s12094-023-03282-7] [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: 06/11/2023] [Accepted: 07/11/2023] [Indexed: 07/24/2023]
Abstract
PURPOSE Metabolic reprogramming is a novel hallmark and therapeutic target of cancer. Our study aimed to establish fatty acid metabolism-associated scores based on gene signature and investigated its effects on immunotherapy in colon cancer. METHODS Gene expression and clinical information were collected from Gene Expression Omnibus (GEO) database to identify a gene signature by non-negative matrix factorization (NMF) clustering and Cox regression analysis. Subsequently, we constructed the fatty acid metabolism score (FA-score) model by principal component analysis (PCA) and explored its relativity of prognosis and the response to immunotherapy in colon cancer. Finally, the Cancer Genome Atlas (TCGA) database was introduced and in vitro study was performed for verification. RESULTS The FA-score-high group had a higher level of fatty acid metabolism and was associated with worse patient overall survival. Significantly, FA-score correlated closely with the biomarkers of immunotherapy, and the FA-score-high group had a poorer therapeutic efficacy of immune checkpoint blockade. In vitro experiments demonstrated that ACSL5 may be a critical metabolic regulatory target. CONCLUSIONS Our study provided a comprehensive analysis of the heterogeneity of fatty acid metabolism in colon cancer. We highlighted the potential clinical utility of fatty acid metabolism-related genes to be biomarkers of colon cancer prognosis and targets to improve the effect of immunotherapy.
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Affiliation(s)
- Changchun Ye
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Qi Sun
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jun Yan
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Dong Xue
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jiarui Xu
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Haiyun Ma
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Fanni Li
- Department of Talent Highland, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, Shaanxi, China.
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3
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Watts J, Allen E, Mitoubsi A, Khojandi A, Eales J, Papamarkou T. Towards Faster Gene Expression Prediction via Dimensionality Reduction and Feature Selection. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2023; 2023:1-4. [PMID: 38083578 DOI: 10.1109/embc40787.2023.10340962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
The majority of genes have a genetic component to their expression. Elastic nets have been shown effective at predicting tissue-specific, individual-level gene expression from genotype data. We apply principal component analysis (PCA), linkage disequilibrium pruning, or the combination of the two to reduce, or generate, a lower-dimensional representation of the genetic variants used as inputs to the elastic net models for the prediction of gene expression. Our results show that, in general, elastic nets attain their best performance when all genetic variants are included as inputs; however, a relatively low number of principal components can effectively summarize the majority of genetic variation while reducing the overall computation time. Specifically, 100 principal components reduce the computational time of the models by over 80% with only an 8% loss in R2. Finally, linkage disequilibrium pruning does not effectively reduce the genetic variants for predicting gene expression. As predictive models are commonly made for over 27,000 genes for more than 50 tissues, PCA may provide an effective method for reducing the computational burden of gene expression analysis.
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4
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Li P, Chen C, Li J, Yang L, Wang Y, Dong Z, Mi J, Zhang Y, Wang J, Wang H, Rodriguez R, Tian J, Wang Z. Homologous Recombination Related Signatures Predict Prognosis and Immunotherapy Response in Metastatic Urothelial Carcinoma. Front Genet 2022; 13:875128. [PMID: 35559013 PMCID: PMC9086193 DOI: 10.3389/fgene.2022.875128] [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: 02/14/2022] [Accepted: 04/05/2022] [Indexed: 11/13/2022] Open
Abstract
Objective: This study used homologous recombination (HR) related signatures to develop a clinical prediction model for screening immune checkpoint inhibitors (ICIs) advantaged populations and identify hub genes in advanced metastatic urothelial carcinoma. Methods: The single-sample gene enrichment analysis and weighted gene co-expression network analysis were applied to identify modules associated with immune response and HR in IMvigor210 cohort samples. The principal component analysis was utilized to determine the differences in HR-related module gene signature scores across different tissue subtypes and clinical variables. Risk prediction models and nomograms were developed using differential gene expression analysis associated with HR scores, least absolute shrinkage and selection operator, and multivariate proportional hazards model regression. Additionally, hub genes were identified by analyzing the contribution of HR-related genes to principal components and overall survival analysis. Finally, clinical features from GSE133624, GSE13507, the TCGA, and other data sets were analyzed to validate the relationship between hub genes and tumor growth and mutation. Results: The HR score was significantly higher in the complete/partial response group than in the stable/progressive disease group. The majority of genes associated with HR were discovered to be involved in the cell cycle and others. Genomically unstable, high tumor level, and high immune level samples all exhibited significantly higher HR score than other sample categories, and higher HR scores were related to improved survival following ICIs treatment. The risk scores for AUNIP, SEPT, FAM72D, CAMKV, CXCL9, and FOXN4 were identified, and the training and verification groups had markedly different survival times. The risk score, tumor neoantigen burden, mismatch repair, and cell cycle regulation were discovered to be independent predictors of survival time following immunotherapy. Patients with a high level of expression of hub genes such as EME1, RAD51AP1, and RAD54L had a greater chance of surviving following immunotherapy. These genes are expressed at significantly higher levels in tumors, high-grade cancer, and invasive cancer than other categories, and are associated with TP53 and RB1 mutations. Conclusion: HR-related genes are upregulated in genomically unstable samples, the survival time of mUC patients after treatment with ICIs can be predicted using a normogram model based on HR signature.
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Affiliation(s)
- Pan Li
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China
| | - Chaohu Chen
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China
| | - Jianpeng Li
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China
| | - Li Yang
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China.,Key Laboratory of Gansu Province for Urological Diseases, Lanzhou, China.,Clinical Center of Gansu Province for Nephron-Urology, Lanzhou, China
| | - Yuhan Wang
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China
| | - Zhilong Dong
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China.,Key Laboratory of Gansu Province for Urological Diseases, Lanzhou, China.,Clinical Center of Gansu Province for Nephron-Urology, Lanzhou, China
| | - Jun Mi
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China.,Key Laboratory of Gansu Province for Urological Diseases, Lanzhou, China.,Clinical Center of Gansu Province for Nephron-Urology, Lanzhou, China
| | - Yunxin Zhang
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China.,Key Laboratory of Gansu Province for Urological Diseases, Lanzhou, China.,Clinical Center of Gansu Province for Nephron-Urology, Lanzhou, China
| | - Juan Wang
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China
| | - Hanzhang Wang
- Department of Urology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Ronald Rodriguez
- Department of Urology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Junqiang Tian
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China.,Key Laboratory of Gansu Province for Urological Diseases, Lanzhou, China.,Clinical Center of Gansu Province for Nephron-Urology, Lanzhou, China
| | - Zhiping Wang
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China.,Key Laboratory of Gansu Province for Urological Diseases, Lanzhou, China.,Clinical Center of Gansu Province for Nephron-Urology, Lanzhou, China
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5
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Fernandez MR, Schaub FX, Yang C, Li W, Yun S, Schaub SK, Dorsey FC, Liu M, Steeves MA, Ballabio A, Tzankov A, Chen Z, Koomen JM, Berglund AE, Cleveland JL. Disrupting the MYC-TFEB Circuit Impairs Amino Acid Homeostasis and Provokes Metabolic Anergy. Cancer Res 2022; 82:1234-1250. [PMID: 35149590 DOI: 10.1158/0008-5472.can-21-1168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 12/07/2021] [Accepted: 02/08/2022] [Indexed: 11/16/2022]
Abstract
MYC family oncoproteins are regulators of metabolic reprogramming that sustains cancer cell anabolism. Normal cells adapt to nutrient-limiting conditions by activating autophagy, which is required for amino acid (AA) homeostasis. Here we report that the autophagy pathway is suppressed by Myc in normal B cells, in premalignant and neoplastic B cells of Eμ-Myc transgenic mice, and in human MYC-driven Burkitt lymphoma. Myc suppresses autophagy by antagonizing the expression and function of transcription factor EB (TFEB), a master regulator of autophagy. Mechanisms that sustained AA pools in MYC-expressing B cells include coordinated induction of the proteasome and increases in AA transport. Reactivation of the autophagy-lysosomal pathway by TFEB disabled the malignant state by disrupting mitochondrial functions, proteasome activity, amino acid transport, and amino acid and nucleotide metabolism, leading to metabolic anergy, growth arrest and apoptosis. This phenotype provides therapeutic opportunities to disable MYC-driven malignancies, including AA restriction and treatment with proteasome inhibitors.
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Affiliation(s)
- Mario R Fernandez
- Department of Tumor Biology, Moffitt Cancer Center and Research Institute
| | - Franz X Schaub
- Department of Tumor Biology, Moffitt Cancer Center and Research Institute
| | - Chunying Yang
- Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute
| | - Weimin Li
- Department of Tumor Biology, Moffitt Cancer Center and Research Institute
| | | | | | | | - Min Liu
- Proteomics Core, Moffitt Cancer Center
| | | | | | | | - Zhihua Chen
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center
| | - John M Koomen
- Department of Molecular Oncology, Moffitt Cancer Center
| | - Anders E Berglund
- Department of Biostatistics and Bioinformatics, Division of Population Sciences, H. Lee Moffitt Cancer Center & Research Institute
| | - John L Cleveland
- Department of Tumor Biology, Moffitt Cancer Center and Research Institute
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6
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Kreis J, Nedić B, Mazur J, Urban M, Schelhorn SE, Grombacher T, Geist F, Brors B, Zühlsdorf M, Staub E. RosettaSX: Reliable gene expression signature scoring of cancer models and patients. Neoplasia 2021; 23:1069-1077. [PMID: 34583245 PMCID: PMC8479477 DOI: 10.1016/j.neo.2021.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/28/2021] [Accepted: 08/30/2021] [Indexed: 11/29/2022]
Abstract
Gene expression signatures have proven their potential to characterize important cancer phenomena like oncogenic signaling pathway activities, cellular origins of tumors, or immune cell infiltration into tumor tissues. Large collections of expression signatures provide the basis for their application to data sets, but the applicability of each signature in a new experimental context must be reassessed. We apply a methodology that utilizes the previously developed concept of coherent expression of genes in signatures to identify translatable signatures before scoring their activity in single tumors. We present a web interface (www.rosettasx.com) that applies our methodology to expression data from the Cancer Cell Line Encyclopaedia and The Cancer Genome Atlas. Configurable heat maps visualize per-cancer signature scores for 293 hand-curated literature-derived gene sets representing a wide range of cancer-relevant transcriptional modules and phenomena. The platform allows users to complement heatmaps of signature scores with molecular information on SNVs, CNVs, gene expression, gene dependency, and protein abundance or to analyze own signatures. Clustered heatmaps and further plots to drill-down results support users in studying oncological processes in cancer subtypes, thereby providing a rich resource to explore how mechanisms of cancer interact with each other as demonstrated by exemplary analyses of 2 cancer types.
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Affiliation(s)
- Julian Kreis
- Department of Translational Medicine, Oncology Bioinformatics, Merck KGaA, Darmstadt, Germany; Faculty of Bioscience, University of Heidelberg, Heidelberg, Germany
| | - Boro Nedić
- Department of Translational Medicine, Oncology Bioinformatics, Merck KGaA, Darmstadt, Germany
| | - Johanna Mazur
- Department of Translational Medicine, Oncology Bioinformatics, Merck KGaA, Darmstadt, Germany
| | - Miriam Urban
- Department of Translational Medicine, Oncology Bioinformatics, Merck KGaA, Darmstadt, Germany
| | - Sven-Eric Schelhorn
- Department of Translational Medicine, Oncology Bioinformatics, Merck KGaA, Darmstadt, Germany
| | - Thomas Grombacher
- Department of Translational Medicine, Oncology Bioinformatics, Merck KGaA, Darmstadt, Germany
| | - Felix Geist
- Therapeutic Innovation Platform Oncology & Immuno-Oncology, Merck KGaA, Darmstadt, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Core Center, Heidelberg, Germany
| | - Michael Zühlsdorf
- Therapeutic Innovation Platform Oncology & Immuno-Oncology, Merck KGaA, Darmstadt, Germany
| | - Eike Staub
- Department of Translational Medicine, Oncology Bioinformatics, Merck KGaA, Darmstadt, Germany.
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7
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Chao KH, Hsiao YW, Lee YF, Lee CY, Lai LC, Tsai MH, Lu TP, Chuang EY. RNASeqR: An R Package for Automated Two-Group RNA-Seq Analysis Workflow. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:2023-2031. [PMID: 31796413 DOI: 10.1109/tcbb.2019.2956708] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
RNA-Seq analysis has revolutionized researchers' understanding of the transcriptome in biological research. Assessing the differences in transcriptomic profiles between tissue samples or patient groups enables researchers to explore the underlying biological impact of transcription. RNA-Seq analysis requires multiple processing steps and huge computational capabilities. There are many well-developed R packages for individual steps; however, there are few R/Bioconductor packages that integrate existing software tools into a comprehensive RNA-Seq analysis and provide fundamental end-to-end results in pure R environment so that researchers can quickly and easily get fundamental information in big sequencing data. To address this need, we have developed the open source R/Bioconductor package, RNASeqR. It allows users to run an automated RNA-Seq analysis with only six steps, producing essential tabular and graphical results for further biological interpretation. The features of RNASeqR include: six-step analysis, comprehensive visualization, background execution version, and the integration of both R and command-line software. RNASeqR provides fast, light-weight, and easy-to-run RNA-Seq analysis pipeline in pure R environment. It allows users to efficiently utilize popular software tools, including both R/Bioconductor and command-line tools, without predefining the resources or environments. RNASeqR is freely available for Linux and macOS operating systems from Bioconductor (https://bioconductor.org/packages/release/bioc/html/RNASeqR.html).
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8
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Epigenetic dysregulation of immune-related pathways in cancer: bioinformatics tools and visualization. Exp Mol Med 2021; 53:761-771. [PMID: 33963293 PMCID: PMC8178403 DOI: 10.1038/s12276-021-00612-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 02/15/2021] [Indexed: 12/14/2022] Open
Abstract
Cancer immune evasion is one of the hallmarks of carcinogenesis. Cancer cells employ multiple mechanisms to avoid immune recognition and suppress antitumor immune responses. Recently, accumulating evidence has indicated that immune-related pathways are epigenetically dysregulated in cancer. Most importantly, the epigenetic footprint of immune-related pathways is associated with the patient outcome, underscoring the crucial need to understand this process. In this review, we summarize the current evidence for epigenetic regulation of immune-related pathways in cancer and describe bioinformatics tools, informative visualization techniques, and resources to help decipher the cancer epigenome. Abnormal patterns of genomic chemical modification help tumors elude immunological destruction, but sophisticated computational tools could help identify and overcome these survival mechanisms. Immunotherapy can be a potent weapon against cancer, but many tumors evolve the ability to protect themselves by subduing the immune response. Sungjune Kim and colleagues at the Moffitt Cancer Center, Tampa, USA, have reviewed efforts to study how chemical alterations to DNA that affect gene expression contribute to this process. Considerable evidence indicates a role for a modification called methylation in this immune evasion, and researchers now have access to vast repositories of tumor-specific gene methylation profiles. The authors describe these data resources, and highlight some of the software tools that are helping oncologists to identify patterns in the data that might lead to better therapies.
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9
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Yun S, Vincelette ND, Yu X, Watson GW, Fernandez MR, Yang C, Hitosugi T, Cheng CH, Freischel AR, Zhang L, Li W, Hou H, Schaub FX, Vedder AR, Cen L, McGraw KL, Moon J, Murphy DJ, Ballabio A, Kaufmann SH, Berglund AE, Cleveland JL. TFEB links MYC signaling to epigenetic control of myeloid differentiation and acute myeloid leukemia. Blood Cancer Discov 2021; 2:162-185. [PMID: 33860275 PMCID: PMC8043621 DOI: 10.1158/2643-3230.bcd-20-0029] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 10/30/2020] [Accepted: 12/15/2020] [Indexed: 12/20/2022] Open
Abstract
MYC oncoproteins regulate transcription of genes directing cell proliferation, metabolism and tumorigenesis. A variety of alterations drive MYC expression in acute myeloid leukemia (AML) and enforced MYC expression in hematopoietic progenitors is sufficient to induce AML. Here we report that AML and myeloid progenitor cell growth and survival rely on MYC-directed suppression of Transcription Factor EB (TFEB), a master regulator of the autophagy-lysosome pathway. Notably, although originally identified as an oncogene, TFEB functions as a tumor suppressor in AML, where it provokes AML cell differentiation and death. These responses reflect TFEB control of myeloid epigenetic programs, by inducing expression of isocitrate dehydrogenase-1 (IDH1) and IDH2, resulting in global hydroxylation of 5-methycytosine. Finally, activating the TFEB-IDH1/IDH2-TET2 axis is revealed as a targetable vulnerability in AML. Thus, epigenetic control by a MYC-TFEB circuit dictates myeloid cell fate and is essential for maintenance of AML.
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Affiliation(s)
- Seongseok Yun
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Nicole D Vincelette
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Xiaoqing Yu
- Department of Bioinformatics and Biostatistics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Gregory W Watson
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Mario R Fernandez
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Chunying Yang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Taro Hitosugi
- Department of Molecular Pharmacology and Experimental Therapeutics, and Department of Oncology, Mayo Clinic, Rochester, Minnesota
| | - Chia-Ho Cheng
- Department of Bioinformatics and Biostatistics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Audrey R Freischel
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Ling Zhang
- Department of Pathology and Laboratory Medicine, Tampa, Florida
| | - Weimin Li
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Hsinan Hou
- Department of Internal Medicine, National Taiwan University, Taipei, Taiwan
| | - Franz X Schaub
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Alexis R Vedder
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Ling Cen
- Department of Bioinformatics and Biostatistics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Kathy L McGraw
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jungwon Moon
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Daniel J Murphy
- University of Glasgow, Institute of Cancer Sciences, Cancer Research UK Beatson Institute, Garscube Estate, Glasgow, United Kingdom
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Naples, Italy
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas
- SSM School for Advanced Studies, Federico II University, Naples, Italy
| | - Scott H Kaufmann
- Department of Molecular Pharmacology and Experimental Therapeutics, and Department of Oncology, Mayo Clinic, Rochester, Minnesota
| | - Anders E Berglund
- Department of Bioinformatics and Biostatistics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - John L Cleveland
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.
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10
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Doultsinos D, Mills IG. Derivation and Application of Molecular Signatures to Prostate Cancer: Opportunities and Challenges. Cancers (Basel) 2021; 13:495. [PMID: 33525365 PMCID: PMC7865812 DOI: 10.3390/cancers13030495] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 12/15/2022] Open
Abstract
Prostate cancer is a high-incidence cancer that requires improved patient stratification to ensure accurate predictions of risk and treatment response. Due to the significant contributions of transcription factors and epigenetic regulators to prostate cancer progression, there has been considerable progress made in developing gene signatures that may achieve this. Some of these are aligned to activities of key drivers such as the androgen receptor, whilst others are more agnostic. In this review, we present an overview of these signatures, the strategies for their derivation, and future perspectives on their continued development and evolution.
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Affiliation(s)
- Dimitrios Doultsinos
- Nuffield Department of Surgical Sciences, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK;
| | - Ian G. Mills
- Nuffield Department of Surgical Sciences, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK;
- Patrick G Johnston Centre for Cancer Research, Queen’s University of Belfast, Belfast BT9 7AE, UK
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11
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Ohandjo AQ, Liu Z, Dammer EB, Dill CD, Griffen TL, Carey KM, Hinton DE, Meller R, Lillard JW. Transcriptome Network Analysis Identifies CXCL13-CXCR5 Signaling Modules in the Prostate Tumor Immune Microenvironment. Sci Rep 2019; 9:14963. [PMID: 31628349 PMCID: PMC6802083 DOI: 10.1038/s41598-019-46491-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 06/26/2019] [Indexed: 12/12/2022] Open
Abstract
The tumor immune microenvironment (TIME) consists of multiple cell types that contribute to the heterogeneity and complexity of prostate cancer (PCa). In this study, we sought to understand the gene-expression signature of patients with primary prostate tumors by investigating the co-expression profiles of patient samples and their corresponding clinical outcomes, in particular “disease-free months” and “disease reoccurrence”. We tested the hypothesis that the CXCL13-CXCR5 axis is co-expressed with factors supporting TIME and PCa progression. Gene expression counts, with clinical attributes from PCa patients, were acquired from TCGA. Profiles of PCa patients were used to identify key drivers that influence or regulate CXCL13-CXCR5 signaling. Weighted gene co-expression network analysis (WGCNA) was applied to identify co-expression patterns among CXCL13-CXCR5, associated genes, and key genetic drivers within the CXCL13-CXCR5 signaling pathway. The processing of downloaded data files began with quality checks using NOISeq, followed by WGCNA. Our results confirmed the quality of the TCGA transcriptome data, identified 12 co-expression networks, and demonstrated that CXCL13, CXCR5 and associated genes are members of signaling networks (modules) associated with G protein coupled receptor (GPCR) responsiveness, invasion/migration, immune checkpoint, and innate immunity. We also identified top canonical pathways and upstream regulators associated with CXCL13-CXCR5 expression and function.
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Affiliation(s)
- Adaugo Q Ohandjo
- Department of Microbiology, Biochemistry & Immunology, Morehouse School of Medicine, Atlanta, GA, 30310, USA
| | - Zongzhi Liu
- R & D Bioinformatics, Sema4, Stamford, CT, 06902, USA
| | - Eric B Dammer
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Courtney D Dill
- Department of Microbiology, Biochemistry & Immunology, Morehouse School of Medicine, Atlanta, GA, 30310, USA
| | - Tiara L Griffen
- Department of Microbiology, Biochemistry & Immunology, Morehouse School of Medicine, Atlanta, GA, 30310, USA
| | - Kaylin M Carey
- Department of Microbiology, Biochemistry & Immunology, Morehouse School of Medicine, Atlanta, GA, 30310, USA
| | - Denise E Hinton
- Department of Microbiology, Biochemistry & Immunology, Morehouse School of Medicine, Atlanta, GA, 30310, USA
| | - Robert Meller
- Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA, 30310, USA
| | - James W Lillard
- Department of Microbiology, Biochemistry & Immunology, Morehouse School of Medicine, Atlanta, GA, 30310, USA.
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12
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Wu Q, Berglund AE, Wang D, MacAulay RJ, Mulé JJ, Etame AB. Paradoxical epigenetic regulation of XAF1 mediates plasticity towards adaptive resistance evolution in MGMT-methylated glioblastoma. Sci Rep 2019; 9:14072. [PMID: 31575897 PMCID: PMC6773736 DOI: 10.1038/s41598-019-50489-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 09/11/2019] [Indexed: 12/19/2022] Open
Abstract
Epigenetic regulation of O6-alkylguanine DNA alkyltransferase (MGMT) is surrogate of intrinsic resistance to temozolomide (TMZ). However, mechanisms associated with adaptive resistance evolution of glioblastoma (GBM) relative to MGMT methylation remain unclear. We hereby report a paradoxical yet translational epigenetic regulation of plasticity towards adaptive resistance in GBM. Based on an adaptive resistance model of GBM cells with differential MGMT methylation profiles, MGMT-hypermethylation enhanced genetic and phenotypic plasticity towards adaptive resistance to TMZ while MGMT hypomethylation limited plasticity. The resulting model-associated adaptive resistance gene signature negatively correlated with GBM patient survival. XAF1, a tumor suppressor protein, paradoxically emerged as a mediator of differential plasticities towards adaptive resistance to TMZ through epigenetic regulation. XAF1 promoted resistance both in-vitro and in-vivo. Furthermore, XAF1 expression negatively correlated with XAF1 promoter methylation status, and negatively correlate with GBM patient survival. Collectively, XAF1 appears to have a pradoxical yet translational role in GBM.
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Affiliation(s)
- Qiong Wu
- Departments of Neuro-Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Anders E Berglund
- Departments of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Dapeng Wang
- Departments of Neuro-Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Robert J MacAulay
- Departments of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - James J Mulé
- Departments of Immunology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Arnold B Etame
- Departments of Neuro-Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA.
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13
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Dhawan A, Barberis A, Cheng WC, Domingo E, West C, Maughan T, Scott JG, Harris AL, Buffa FM. Guidelines for using sigQC for systematic evaluation of gene signatures. Nat Protoc 2019; 14:1377-1400. [PMID: 30971781 DOI: 10.1038/s41596-019-0136-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 01/11/2019] [Indexed: 11/09/2022]
Abstract
With the increased use of next-generation sequencing generating large amounts of genomic data, gene expression signatures are becoming critically important tools for the interpretation of these data, and are poised to have a substantial effect on diagnosis, management, and prognosis for a number of diseases. It is becoming crucial to establish whether the expression patterns and statistical properties of sets of genes, or gene signatures, are conserved across independent datasets. Conversely, it is necessary to compare established signatures on the same dataset to better understand how they capture different clinical or biological characteristics. Here we describe how to use sigQC, a tool that enables a streamlined, systematic approach for the evaluation of previously obtained gene signatures across multiple gene expression datasets. We implemented sigQC in an R package, making it accessible to users who have knowledge of file input/output and matrix manipulation in R and a moderate grasp of core statistical principles. SigQC has been adopted in basic biology and translational studies, including, but not limited to, the evaluation of multiple gene signatures for potential clinical use as cancer biomarkers. This protocol uses a previously obtained signature for breast cancer metastasis as an example to illustrate the critical quality control steps involved in evaluating its expression, variability, and structure in breast tumor RNA-sequencing data, a different dataset from that in which the signature was originally derived. We demonstrate how the outputs created from sigQC can be used for the evaluation of gene signatures on large-scale gene expression datasets.
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Affiliation(s)
- Andrew Dhawan
- Computational Biology and Integrative Genomics Lab, MRC/CRUK Oxford Institute and Department of Oncology, University of Oxford, Oxford, UK
| | - Alessandro Barberis
- Computational Biology and Integrative Genomics Lab, MRC/CRUK Oxford Institute and Department of Oncology, University of Oxford, Oxford, UK
| | - Wei-Chen Cheng
- Computational Biology and Integrative Genomics Lab, MRC/CRUK Oxford Institute and Department of Oncology, University of Oxford, Oxford, UK
| | - Enric Domingo
- Computational Biology and Integrative Genomics Lab, MRC/CRUK Oxford Institute and Department of Oncology, University of Oxford, Oxford, UK
| | - Catharine West
- Division of Cancer Studies, University of Manchester, Manchester, UK
| | - Tim Maughan
- Computational Biology and Integrative Genomics Lab, MRC/CRUK Oxford Institute and Department of Oncology, University of Oxford, Oxford, UK
| | - Jacob G Scott
- Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - Adrian L Harris
- Computational Biology and Integrative Genomics Lab, MRC/CRUK Oxford Institute and Department of Oncology, University of Oxford, Oxford, UK
| | - Francesca M Buffa
- Computational Biology and Integrative Genomics Lab, MRC/CRUK Oxford Institute and Department of Oncology, University of Oxford, Oxford, UK.
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14
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The JAK-STAT1 transcriptional signature in peripheral immune cells reveals alterations related to illness duration and acuity in psychosis. Brain Behav Immun 2019; 77:37-45. [PMID: 30503835 PMCID: PMC8521437 DOI: 10.1016/j.bbi.2018.11.317] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 10/18/2018] [Accepted: 11/28/2018] [Indexed: 11/22/2022] Open
Abstract
Multiple lines of inquiry demonstrate alterations to immune function in psychosis. Clinically, this is reflected by elevated proinflammatory cytokines in serum, indicating activation of circulating immune cells. Data from isolated cells in clinical populations support the presence of altered activity of pertinent intracellular signaling pathways. Here, we focus on the well-characterized IFN-γ mediated JAK-STAT1 signaling pathway, which is involved in multiple aspects of immunity, including activation of circulating immune cells to a proinflammatory phenotype. By measuring a transcriptional signature characteristic of activation of this pathway, we demonstrate that JAK-STAT1 signature gene expression is suppressed in participants with psychosis who are early in illness and in participants who are hospitalized with an acute exacerbation of psychosis. Furthermore, we find that this expression signature normalizes in participants who have a longer illness duration and chronic, but not acute, psychopathology. This relationship of JAK-STAT1 signature gene expression with clinical characteristics highlights the temporal and contextual complexity of alterations to immune activity in psychosis and provides important insight into the functional state of circulating immune cells. These findings are of particular interest given recent research illustrating the importance of peripherally derived immune cells and the effectors they secrete in mediating neurophysiological processes of relevance for psychiatric illness.
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15
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Gordian E, Welsh EA, Gimbrone N, Siegel EM, Shibata D, Creelan BC, Cress WD, Eschrich SA, Haura EB, Muñoz-Antonia T. Transforming growth factor β-induced epithelial-to-mesenchymal signature predicts metastasis-free survival in non-small cell lung cancer. Oncotarget 2019; 10:810-824. [PMID: 30783512 PMCID: PMC6368226 DOI: 10.18632/oncotarget.26574] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 12/29/2018] [Indexed: 12/20/2022] Open
Abstract
Transforming growth factor beta (TGFβ) plays a key role in regulating epithelial-to-mesenchymal transition (EMT). A gene expression signature (TGFβ-EMT) associated with TGFβ-induced EMT activities was developed using human Non-Small Cell Lung Carcinoma (NSCLC) cells treated with TGFβ-1 and subjected to Affymetrix microarray analysis. The final 105-probeset TGFβ-EMT signature covers 77 genes, and a NanoString assay utilized a subset of 60 of these genes (TGFβ-EMTN signature). We found that the TGFβ-EMT and TGFβ-EMTN gene signatures predicted overall survival (OS) and metastasis-free survival (MFS). The TGFβ-EMT signature was validated as prognostic of 5-year MFS in 3 cohorts: a 133 NSCLC tumor dataset (P = 0.0002), a NanoString assays of RNA isolated from formalin-fixed paraffin-embedded samples from these same tumors (P = 0.0015), and a previously published NSCLC MFS dataset (P = 0.0015). The separation between high and low metastasis signature scores was higher at 3 years (ΔMFS TGFβ-EMT = −28.6%; ΔMFS TGFβ-EMTN = −25.2%) than at 5 years (ΔMFS TGFβ-EMT = −18.6%; ΔMFS TGFβ-EMTN = −11.8%). In addition, the TGFβ-EMT signature correlated with whether the cancer had already metastasized or not at time of surgery in a colon cancer cohort. The results show that the TGFβ-EMT signature successfully discriminated lung cancer cell lines capable of undergoing EMT in response to TGFβ-1 and predicts MFS in lung adenocarcinomas. Thus, the TGFβ-EMT signature has the potential to be developed as a clinically relevant predictive biomarker, for example to identify those patients with resected early stage lung cancer who may benefit from adjuvant therapy.
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Affiliation(s)
- Edna Gordian
- Tumor Biology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Eric A Welsh
- Cancer Informatics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Nicholas Gimbrone
- Molecular Oncology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Erin M Siegel
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - David Shibata
- Department of Surgery, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ben C Creelan
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - William Douglas Cress
- Molecular Oncology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Steven A Eschrich
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Eric B Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Teresita Muñoz-Antonia
- Tumor Biology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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16
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Berglund AE, Rounbehler RJ, Gerke T, Awasthi S, Cheng CH, Takhar M, Davicioni E, Alshalalfa M, Erho N, Klein EA, Freedland SJ, Ross AE, Schaeffer EM, Trock BJ, Den RB, Cleveland JL, Park JY, Dhillon J, Yamoah K. Distinct transcriptional repertoire of the androgen receptor in ETS fusion-negative prostate cancer. Prostate Cancer Prostatic Dis 2018; 22:292-302. [PMID: 30367117 PMCID: PMC6760558 DOI: 10.1038/s41391-018-0103-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/27/2018] [Accepted: 09/08/2018] [Indexed: 12/21/2022]
Abstract
Background Prostate cancer (PCa) tumors harboring translocations of ETS family genes with the androgen responsive TMPRSS2 gene (ETS+ tumors) provide a robust biomarker for detecting PCa in approximately 70% of patients. ETS+ PCa express high levels of the androgen receptor (AR), yet PCa tumors lacking ETS fusions (ETS−) also express AR and demonstrate androgen-regulated growth. In this study, we evaluate the differences in the AR-regulated transcriptomes between ETS+ and ETS− PCa tumors. Methods 10,608 patient tumors from three independent PCa datasets classified as ETS+ (samples overexpressing ERG or other ETS family members) or ETS− (all other PCa) were analyzed for differential gene expression using false-discovery-rate adjusted methods and gene-set enrichment analysis (GSEA). Results Based on the expression of AR-dependent genes and an unsupervised Principal Component Analysis (PCA) model, AR-regulated gene expression alone was able to separate PCa samples into groups based on ETS status in all PCa databases. ETS status distinguished several differentially expressed genes in both TCGA (6.9%) and GRID (6.6%) databases, with 413 genes overlapping in both databases. Importantly, GSEA showed enrichment of distinct androgen-responsive genes in both ETS− and ETS+ tumors, and AR ChIP-seq data identified 131 direct AR-target genes that are regulated in an ETS-specific fashion. Notably, dysregulation of ETS-dependent AR-target genes within the metabolic and non-canonical WNT pathways was associated with clinical outcomes. Conclusions ETS status influences the transcriptional repertoire of the AR, and ETS− PCa tumors appear to rely on distinctly different AR-dependent transcriptional programs to drive and sustain tumorigenesis.
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Affiliation(s)
- Anders E Berglund
- Department of Biostatistics & Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Robert J Rounbehler
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA.,Department of Oncological Sciences, University of South Florida, Tampa, FL, USA
| | - Travis Gerke
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Shivanshu Awasthi
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Chia-Ho Cheng
- Department of Biostatistics & Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | | | | | | | | | - Eric A Klein
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Stephen J Freedland
- Department of Surgery, Division of Urology, Center for Integrated Research on Cancer and Lifestyle, Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | | | - Bruce J Trock
- Department of Urology, Johns Hopkins, Baltimore, MD, USA
| | - Robert B Den
- Department of Radiation Oncology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - John L Cleveland
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Jong Y Park
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Jasreman Dhillon
- Department of Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Kosj Yamoah
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA. .,Department of Radiation Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA.
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17
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Shao Z, Wang H, Zhou X, Guo B, Gao X, Xiao Z, Liu M, Sha J, Jiang C, Luo Y, Liu Z, Li S. Spontaneous generation of a novel foetal human retinal pigment epithelium (RPE) cell line available for investigation on phagocytosis and morphogenesis. Cell Prolif 2017; 50. [PMID: 28924976 PMCID: PMC6529143 DOI: 10.1111/cpr.12386] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 08/18/2017] [Indexed: 12/16/2022] Open
Abstract
Objectives Primary retinal pigment epithelium (RPE) cells have a limited capacity to re‐establish epithelial morphology and to maintain native RPE function in vitro, and all commercially available RPE cell lines have drawbacks of morphology or function; therefore, the establishment of new RPE cell lines with typical characteristics of RPE would be helpful in further understanding of their physiological and pathological mechanisms. Here, we firstly report a new spontaneously generated RPE line, fhRPE‐13A, from a 13‐week aborted foetus. We aimed to investigate its availability as a RPE model. Materials and methods RNA‐seq data were mapped to the human genome assembly hg19. Global transcriptional data were analysed by Weighted Gene Co‐expression Network Analysis (WGCNA) and differentially expressed genes (DEGs). The morphology and molecular characteristics were examined by immunofluorescence, transmission electron micrographs, PCR and western blot. Photoreceptor outer segments (POS) phagocytosis assay and transepithelial resistance measurement (TER) were performed to assess phagocytic activity and barrier function, respectively. Results The fhRPE‐13A cells showed typical polygonal morphology and normal biological processes of RPE. Meanwhile they were capable of POS phagocytosis in vitro, and the expression level of TYR and TYRP1 were significantly higher than that in ARPE‐19 cells. Conclusions The foetal human RPE line fhRPE‐13A is a valuable system for researching phagocytosis and morphogenesis of RPE in vitro.
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Affiliation(s)
- Zhihua Shao
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Haiyun Wang
- Shanghai First Maternity and Infant Health Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xuejian Zhou
- Department of Regenerative Medicine, Tongji University School of Medicine, Shanghai, China
| | - Baosen Guo
- College of Life Sciences, Nanchang University, Nanchang, China
| | - Xuehu Gao
- College of Life Sciences, Nanchang University, Nanchang, China
| | - Zengrong Xiao
- College of Life Sciences, Nanchang University, Nanchang, China
| | - Meng Liu
- College of Life Sciences, Nanchang University, Nanchang, China
| | - Jihong Sha
- Department of Regenerative Medicine, Tongji University School of Medicine, Shanghai, China
| | - Chunlian Jiang
- College of Life Sciences, Nanchang University, Nanchang, China
| | - Yuping Luo
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhixue Liu
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Siguang Li
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
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