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Zhu Y, Zhang S, Shao Y, Tang L, Zhang C, Tang S, Lu H. Regulatory role of oxidative stress in retrorsine - Induced apoptosis and autophagy in primary rat hepatocytes. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 279:116515. [PMID: 38810283 DOI: 10.1016/j.ecoenv.2024.116515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 05/31/2024]
Abstract
Pyrrolizidine alkaloids (PAs) are a group of naturally occurring alkaloids widely present in plants. PAs are highly hepatotoxic and have been documented to cause many incidents of human and animal poisoning. Retrorsine (RTS) is a pyrrolizidine alkaloid (PA) derived from the Compositae Senecio, which has been shown to cause hepatotoxicity. Human liver poisoning occurs through the consumption of RTS-contaminated food, and animals can also be poisoned by ingesting RTS-containing toxic plants. The mechanism of RTS-induced liver toxicity is not fully understood. In this study, we demonstrated that RTS-induced oxidative stress plays a pivotal role in RTS-induced liver toxicity involving apoptosis and autophagy. The results showed that RTS treatment in the cultured Primary rat hepatocytes caused cytotoxicity and release of aspartate aminotransferase (AST) and alanine aminotransferase (ALT) in a time- and dose-dependent manner. Our study showed that treatment of RTS induced ROS and MDA (malondialdehyde, a lipid peroxidation marker) in the hepatocytes, and reduced antioxidant capacity (GSH content, SOD activity), suggesting RTS treatment caused oxidative stress response in the hepatocytes. Furthermore, we found that RTS induced apoptosis and autophagy in the hepatocytes, and RTS-induced apoptosis and autophagy could be alleviated by ROS scavenger N-acetylcysteine (NAC) and the MAPK pathway inhibitors suggesting ROS/MAPK signaling pathway plays a role in RTS induced apoptosis and autophagy. Collectively, this study reveals the regulatory mechanism of oxidative stress in RTS-induced apoptosis and autophagy in the hepatocytes, providing important insights of molecular mechanisms of hepatotoxicity induced by RTS and related pyrrolizidine alkaloids in liver. This mechanism provides a basis for the prevention and treatment of PA poisoning in humans and animals.
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Affiliation(s)
- Yanli Zhu
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shuhang Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yin Shao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lihui Tang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Congcheng Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shiyu Tang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hao Lu
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China.
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2
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Rezaei Z, Tahmasebi A, Pourabbas B. Using meta-analysis and machine learning to investigate the transcriptional response of immune cells to Leishmania infection. PLoS Negl Trop Dis 2024; 18:e0011892. [PMID: 38190401 PMCID: PMC10798641 DOI: 10.1371/journal.pntd.0011892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 01/19/2024] [Accepted: 12/29/2023] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND Leishmaniasis is a parasitic disease caused by the Leishmania protozoan affecting millions of people worldwide, especially in tropical and subtropical regions. The immune response involves the activation of various cells to eliminate the infection. Understanding the complex interplay between Leishmania and the host immune system is crucial for developing effective treatments against this disease. METHODS This study collected extensive transcriptomic data from macrophages, dendritic, and NK cells exposed to Leishmania spp. Our objective was to determine the Leishmania-responsive genes in immune system cells by applying meta-analysis and feature selection algorithms, followed by co-expression analysis. RESULTS As a result of meta-analysis, we discovered 703 differentially expressed genes (DEGs), primarily associated with the immune system and cellular metabolic processes. In addition, we have substantiated the significance of transcription factor families, such as bZIP and C2H2 ZF, in response to Leishmania infection. Furthermore, the feature selection techniques revealed the potential of two genes, namely G0S2 and CXCL8, as biomarkers and therapeutic targets for Leishmania infection. Lastly, our co-expression analysis has unveiled seven hub genes, including PFKFB3, DIAPH1, BSG, BIRC3, GOT2, EIF3H, and ATF3, chiefly related to signaling pathways. CONCLUSIONS These findings provide valuable insights into the molecular mechanisms underlying the response of immune system cells to Leishmania infection and offer novel potential targets for the therapeutic goals.
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Affiliation(s)
- Zahra Rezaei
- Professor Alborzi Clinical Microbiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ahmad Tahmasebi
- Professor Alborzi Clinical Microbiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Bahman Pourabbas
- Professor Alborzi Clinical Microbiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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3
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Lesage R, Ferrao Blanco MN, Narcisi R, Welting T, van Osch GJVM, Geris L. An integrated in silico-in vitro approach for identifying therapeutic targets against osteoarthritis. BMC Biol 2022; 20:253. [DOI: 10.1186/s12915-022-01451-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 10/27/2022] [Indexed: 11/11/2022] Open
Abstract
Abstract
Background
Without the availability of disease-modifying drugs, there is an unmet therapeutic need for osteoarthritic patients. During osteoarthritis, the homeostasis of articular chondrocytes is dysregulated and a phenotypical transition called hypertrophy occurs, leading to cartilage degeneration. Targeting this phenotypic transition has emerged as a potential therapeutic strategy. Chondrocyte phenotype maintenance and switch are controlled by an intricate network of intracellular factors, each influenced by a myriad of feedback mechanisms, making it challenging to intuitively predict treatment outcomes, while in silico modeling can help unravel that complexity. In this study, we aim to develop a virtual articular chondrocyte to guide experiments in order to rationalize the identification of potential drug targets via screening of combination therapies through computational modeling and simulations.
Results
We developed a signal transduction network model using knowledge-based and data-driven (machine learning) modeling technologies. The in silico high-throughput screening of (pairwise) perturbations operated with that network model highlighted conditions potentially affecting the hypertrophic switch. A selection of promising combinations was further tested in a murine cell line and primary human chondrocytes, which notably highlighted a previously unreported synergistic effect between the protein kinase A and the fibroblast growth factor receptor 1.
Conclusions
Here, we provide a virtual articular chondrocyte in the form of a signal transduction interactive knowledge base and of an executable computational model. Our in silico-in vitro strategy opens new routes for developing osteoarthritis targeting therapies by refining the early stages of drug target discovery.
Graphical Abstract
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4
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A Novel Approach for the Discovery of Biomarkers of Radiotherapy Response in Breast Cancer. J Pers Med 2021; 11:jpm11080796. [PMID: 34442440 PMCID: PMC8399231 DOI: 10.3390/jpm11080796] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/09/2021] [Accepted: 08/11/2021] [Indexed: 01/08/2023] Open
Abstract
Radiotherapy (RT) is an important treatment modality for the local control of breast cancer (BC). Unfortunately, not all patients that receive RT will obtain a therapeutic benefit, as cancer cells that either possess intrinsic radioresistance or develop resistance during treatment can reduce its efficacy. For RT treatment regimens to become personalised, there is a need to identify biomarkers that can predict and/or monitor a tumour's response to radiation. Here we describe a novel method to identify such biomarkers. Liquid chromatography-mass spectrometry (LC-MS) was used on conditioned media (CM) samples from a radiosensitive oestrogen receptor positive (ER+) BC cell line (MCF-7) to identify cancer-secreted biomarkers which reflected a response to radiation. A total of 33 radiation-induced secreted proteins that had higher (up to 12-fold) secretion levels at 24 h post-2 Gy radiation were identified. Secretomic results were combined with whole-transcriptome gene expression experiments, using both radiosensitive and radioresistant cells, to identify a signature related to intrinsic radiosensitivity. Gene expression analysis assessing the levels of the 33 proteins showed that 5 (YBX3, EIF4EBP2, DKK1, GNPNAT1 and TK1) had higher expression levels in the radiosensitive cells compared to their radioresistant derivatives; 3 of these proteins (DKK1, GNPNAT1 and TK1) underwent in-lab and initial clinical validation. Western blot analysis using CM samples from cell lines confirmed a significant increase in the release of each candidate biomarker from radiosensitive cells 24 h after treatment with a 2 Gy dose of radiation; no significant increase in secretion was observed in the radioresistant cells after radiation. Immunohistochemistry showed that higher intracellular protein levels of the biomarkers were associated with greater radiosensitivity. Intracellular levels were further assessed in pre-treatment biopsy tissues from patients diagnosed with ER+ BC that were subsequently treated with breast-conserving surgery and RT. High DKK1 and GNPNAT1 intracellular levels were associated with significantly increased recurrence-free survival times, indicating that these two candidate biomarkers have the potential to predict sensitivity to RT. We suggest that the methods highlighted in this study could be utilised for the identification of biomarkers that may have a potential clinical role in personalising and optimising RT dosing regimens, whilst limiting the administration of RT to patients who are unlikely to benefit.
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5
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Jeon YS, Shivakumar M, Kim D, Kim CS, Lee JS. Reliability of microarray analysis for studying periodontitis: low consistency in 2 periodontitis cohort data sets from different platforms and an integrative meta-analysis. J Periodontal Implant Sci 2021; 51:18-29. [PMID: 33634612 PMCID: PMC7920837 DOI: 10.5051/jpis.2002120106] [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: 03/30/2020] [Revised: 07/14/2020] [Accepted: 09/24/2020] [Indexed: 11/08/2022] Open
Abstract
PURPOSE The aim of this study was to compare the characteristic expression patterns of advanced periodontitis in 2 cohort data sets analyzed using different microarray platforms, and to identify differentially expressed genes (DEGs) through a meta-analysis of both data sets. METHODS Twenty-two patients for cohort 1 and 40 patients for cohort 2 were recruited with the same inclusion criteria. The 2 cohort groups were analyzed using different platforms: Illumina and Agilent. A meta-analysis was performed to increase reliability by removing statistical differences between platforms. An integrative meta-analysis based on an empirical Bayesian methodology (ComBat) was conducted. DEGs for the integrated data sets were identified using the limma package to adjust for age, sex, and platform and compared with the results for cohorts 1 and 2. Clustering and pathway analyses were also performed. RESULTS This study detected 557 and 246 DEGs in cohorts 1 and 2, respectively, with 146 and 42 significantly enriched gene ontology (GO) terms. Overlapping between cohorts 1 and 2 was present in 59 DEGs and 18 GO terms. However, only 6 genes from the top 30 enriched DEGs overlapped, and there were no overlapping GO terms in the top 30 enriched pathways. The integrative meta-analysis detected 34 DEGs, of which 10 overlapped in all the integrated data sets of cohorts 1 and 2. CONCLUSIONS The characteristic expression pattern differed between periodontitis and the healthy periodontium, but the consistency between the data sets from different cohorts and metadata was too low to suggest specific biomarkers for identifying periodontitis.
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Affiliation(s)
- Yoon Seon Jeon
- Department of Periodontology, Research Institute for Periodontal Regeneration, Yonsei University College of Dentistry, Seoul, Korea
| | - Manu Shivakumar
- Department of Biostatistics, Epidemiology and Informatics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dokyoon Kim
- Department of Biostatistics, Epidemiology and Informatics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Chang Sung Kim
- Department of Periodontology, Research Institute for Periodontal Regeneration, Yonsei University College of Dentistry, Seoul, Korea
| | - Jung Seok Lee
- Department of Periodontology, Research Institute for Periodontal Regeneration, Yonsei University College of Dentistry, Seoul, Korea.
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6
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Lykhenko O. СONSECUTIVE INTEGRATION OF AVAILABLE MICROARRAY DATA FOR ANALYSIS OF DIFFERENTIAL GENE EXPRESSION IN HUMAN PLACENTA. BIOTECHNOLOGIA ACTA 2021. [DOI: 10.15407/biotech14.01.38] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The purpose of the study was to provide the pipeline for processing of publicly available unprocessed data on gene expression via integration and differential gene expression analysis. Data collection from open gene expression databases, normalization and integration into a single expression matrix in accordance with metadata and determination of differentially expressed genes were fulfilled. To demonstrate all stages of data processing and integrative analysis, there were used the data from gene expression in the human placenta from the first and second trimesters of normal pregnancy. The source code for the integrative analysis was written in the R programming language and publicly available as a repository on GitHub. Four clusters of functionally enriched differentially expressed genes were identified for the human placenta in the interval between the first and second trimester of pregnancy. Immune processes, developmental processes, vasculogenesis and angiogenesis, signaling and the processes associated with zinc ions varied in the considered interval between the first and second trimester of placental development. The proposed sequence of actions for integrative analysis could be applied to any data obtained by microarray technology.
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7
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Gray M, Turnbull AK, Meehan J, Martínez-Pérez C, Kay C, Pang LY, Argyle DJ. Comparative Analysis of the Development of Acquired Radioresistance in Canine and Human Mammary Cancer Cell Lines. Front Vet Sci 2020; 7:439. [PMID: 32851022 PMCID: PMC7396503 DOI: 10.3389/fvets.2020.00439] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 06/16/2020] [Indexed: 01/09/2023] Open
Abstract
Research using in vitro canine mammary cancer cell lines and naturally-occurring canine mammary tumors are not only fundamental models used to advance the understanding of cancer in veterinary patients, but are also regarded as excellent translational models of human breast cancer. Human breast cancer is commonly treated with radiotherapy; however, tumor response depends on both innate radiosensitivity and on tumor repopulation by cells that develop radioresistance. Comparative canine and human studies investigating the mechanisms of radioresistance may lead to novel cancer treatments that benefit both species. In this study, we developed a canine mammary cancer (REM-134) radioresistant (RR) cell line and investigated the cellular mechanisms related to the development of acquired radioresistance. We performed a comparative analysis of this resistant model with our previously developed human breast cancer radioresistant cell lines (MCF-7 RR, ZR-751 RR, and MDA-MB-231 RR), characterizing inherent differences through genetic, molecular, and cell biology approaches. RR cells demonstrated enhanced invasion/migration capabilities, with phenotypic evidence suggestive of epithelial-to-mesenchymal transition. Similarities were identified between the REM-134 RR, MCF-7 RR, and ZR-751 RR cell lines in relation to the pattern of expression of both epithelial and mesenchymal genes, in addition to WNT, PI3K, and MAPK pathway activation. Following the development of radioresistance, transcriptomic data indicated that parental MCF-7 and ZR-751 cell lines changed from a luminal A classification to basal/HER2-overexpressing (MCF-7 RR) and normal-like/HER2-overexpressing (ZR-751 RR). These radioresistant subtypes were similar to the REM-134 and REM-134 RR cell lines, which were classified as HER2-overexpressing. To our knowledge, our study is the first to generate a canine mammary cancer RR cell line model and provide a comparative genetic and phenotypic analysis of the mechanisms of acquired radioresistance between canine and human cancer cell lines. We demonstrate that the cellular processes that occur with the development of acquired radioresistance are similar between the human and canine cell lines; our results therefore suggest that the canine model is appropriate to study both human and canine radioresistant mammary cancers, and that treatment strategies used in human medicine may also be applicable to veterinary patients.
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Affiliation(s)
- Mark Gray
- The Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Arran K Turnbull
- Translational Oncology Research Group, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, United Kingdom.,Breast Cancer Now Edinburgh Research Team, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, United Kingdom
| | - James Meehan
- Translational Oncology Research Group, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, United Kingdom
| | - Carlos Martínez-Pérez
- Translational Oncology Research Group, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, United Kingdom.,Breast Cancer Now Edinburgh Research Team, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, United Kingdom
| | - Charlene Kay
- Translational Oncology Research Group, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, United Kingdom.,Breast Cancer Now Edinburgh Research Team, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, United Kingdom
| | - Lisa Y Pang
- The Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - David J Argyle
- The Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
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8
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Toms D, Al-Ani A, Sunba S, Tong QYV, Workentine M, Ungrin M. Automated Hypothesis Generation to Identify Signals Relevant in the Development of Mammalian Cell and Tissue Bioprocesses, With Validation in a Retinal Culture System. Front Bioeng Biotechnol 2020; 8:534. [PMID: 32582664 PMCID: PMC7287043 DOI: 10.3389/fbioe.2020.00534] [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: 04/16/2019] [Accepted: 05/04/2020] [Indexed: 12/13/2022] Open
Abstract
We have developed an accessible software tool (receptoR) to predict potentially active signaling pathways in one or more cell type(s) of interest from publicly available transcriptome data. As proof-of-concept, we applied it to mouse photoreceptors, yielding the previously untested hypothesis that activin signaling pathways are active in these cells. Expression of the type 2 activin receptor (Acvr2a) was experimentally confirmed by both RT-qPCR and immunochemistry, and activation of this signaling pathway with recombinant activin A significantly enhanced the survival of magnetically sorted photoreceptors in culture. Taken together, we demonstrate that our approach can be easily used to mine publicly available transcriptome data and generate hypotheses around receptor expression that can be used to identify novel signaling pathways in specific cell types of interest. We anticipate that receptoR (available at https://www.ucalgary.ca/ungrinlab/receptoR) will enable more efficient use of limited research resources.
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Affiliation(s)
- Derek Toms
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Abdullah Al-Ani
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada.,Biomedical Engineering Graduate Program, University of Calgary, Calgary, AB, Canada.,Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada.,Leaders in Medicine Program, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Saud Sunba
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Qing Yun Victor Tong
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Matthew Workentine
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Mark Ungrin
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada.,Biomedical Engineering Graduate Program, University of Calgary, Calgary, AB, Canada.,Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
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9
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Ghosheh N, Küppers-Munther B, Asplund A, Andersson CX, Björquist P, Andersson TB, Carén H, Simonsson S, Sartipy P, Synnergren J. Human Pluripotent Stem Cell-Derived Hepatocytes Show Higher Transcriptional Correlation with Adult Liver Tissue than with Fetal Liver Tissue. ACS OMEGA 2020; 5:4816-4827. [PMID: 32201767 PMCID: PMC7081255 DOI: 10.1021/acsomega.9b03514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 02/14/2020] [Indexed: 06/10/2023]
Abstract
Human pluripotent stem cell-derived hepatocytes (hPSC-HEP) display many properties of mature hepatocytes, including expression of important genes of the drug metabolizing machinery, glycogen storage, and production of multiple serum proteins. To this date, hPSC-HEP do not, however, fully recapitulate the complete functionality of in vivo mature hepatocytes. In this study, we applied versatile bioinformatic algorithms, including functional annotation and pathway enrichment analyses, transcription factor binding-site enrichment, and similarity and correlation analyses, to datasets collected from different stages during hPSC-HEP differentiation and compared these to developmental stages and tissues from fetal and adult human liver. Our results demonstrate a high level of similarity between the in vitro differentiation of hPSC-HEP and in vivo hepatogenesis. Importantly, the transcriptional correlation of hPSC-HEP with adult liver (AL) tissues was higher than with fetal liver (FL) tissues (0.83 and 0.70, respectively). Functional data revealed mature features of hPSC-HEP including cytochrome P450 enzymes activities and albumin secretion. Moreover, hPSC-HEP showed expression of many genes involved in drug absorption, distribution, metabolism, and excretion. Despite the high similarities observed, we identified differences of specific pathways and regulatory players by analyzing the gene expression between hPSC-HEP and AL. These findings will aid future intervention and improvement of in vitro hepatocyte differentiation protocol in order to generate hepatocytes displaying the complete functionality of mature hepatocytes. Finally, on the transcriptional level, our results show stronger correlation and higher similarity of hPSC-HEP to AL than to FL. In addition, potential targets for further functional improvement of hPSC-HEP were also identified.
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Affiliation(s)
- Nidal Ghosheh
- School
of Bioscience, Systems Biology Research Center, University of Skövde, 541 28 Skövde, Sweden
| | | | - Annika Asplund
- Takara
Bio Europe AB, Arvid Wallgrens Backe 20, 413 46 Gothenburg, Sweden
| | | | - Petter Björquist
- VeriGraft
AB, Arvid Wallgrens Backe
20, 413 46 Gothenburg, Sweden
| | - Tommy B. Andersson
- Cardiovascular
Renal and Metabolism, Innovative Medicines and Early Development Biotech
Unit, AstraZeneca, Pepparedsleden 1, Mölndal 431 83, Sweden
- Department
of Physiology and Pharmacology, Section of Pharmacogenetics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Helena Carén
- Sahlgrenska
Cancer Center, Department of Pathology, Institute of Biomedicine,
Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Stina Simonsson
- Institute
of Biomedicine, Department of Clinical Chemistry and Transfusion Medicine,
Sahlgrenska Academy, University of Gothenburg, 413 45 Gothenburg, Sweden
| | - Peter Sartipy
- School
of Bioscience, Systems Biology Research Center, University of Skövde, 541 28 Skövde, Sweden
- Late
Stage Cardiovascular, Renal, and Metabolism, R&D BioPharmaceuticals, AstraZeneca, Pepparedsleden 1, Mölndal 431 83, Sweden
| | - Jane Synnergren
- School
of Bioscience, Systems Biology Research Center, University of Skövde, 541 28 Skövde, Sweden
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10
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Turnbull AK, Selli C, Martinez-Perez C, Fernando A, Renshaw L, Keys J, Figueroa JD, He X, Tanioka M, Munro AF, Murphy L, Fawkes A, Clark R, Coutts A, Perou CM, Carey LA, Dixon JM, Sims AH. Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: comparison of gene expression profiling approaches. BMC Bioinformatics 2020; 21:30. [PMID: 31992186 PMCID: PMC6988223 DOI: 10.1186/s12859-020-3365-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 01/14/2020] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND High-throughput transcriptomics has matured into a very well established and widely utilised research tool over the last two decades. Clinical datasets generated on a range of different platforms continue to be deposited in public repositories provide an ever-growing, valuable resource for reanalysis. Cost and tissue availability normally preclude processing samples across multiple technologies, making it challenging to directly evaluate performance and whether data from different platforms can be reliably compared or integrated. METHODS This study describes our experiences of nine new and established mRNA profiling techniques including Lexogen QuantSeq, Qiagen QiaSeq, BioSpyder TempO-Seq, Ion AmpliSeq, Nanostring, Affymetrix Clariom S or U133A, Illumina BeadChip and RNA-seq of formalin-fixed paraffin embedded (FFPE) and fresh frozen (FF) sequential patient-matched breast tumour samples. RESULTS The number of genes represented and reliability varied between the platforms, but overall all methods provided data which were largely comparable. Crucially we found that it is possible to integrate data for combined analyses across FFPE/FF and platforms using established batch correction methods as required to increase cohort sizes. However, some platforms appear to be better suited to FFPE samples, particularly archival material. CONCLUSIONS Overall, we illustrate that technology selection is a balance between required resolution, sample quality, availability and cost.
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Affiliation(s)
- Arran K Turnbull
- Applied Bioinformatics of Cancer, Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, Edinburgh, UK.,Edinburgh Breast Unit, Western General Hospital, Edinburgh, UK
| | - Cigdem Selli
- Applied Bioinformatics of Cancer, Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, Edinburgh, UK.,Department of Pharmacology, Faculty of Pharmacy, Ege University, 35040, Izmir, Turkey
| | - Carlos Martinez-Perez
- Applied Bioinformatics of Cancer, Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, Edinburgh, UK.,Edinburgh Breast Unit, Western General Hospital, Edinburgh, UK
| | - Anu Fernando
- Applied Bioinformatics of Cancer, Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, Edinburgh, UK.,Edinburgh Breast Unit, Western General Hospital, Edinburgh, UK
| | - Lorna Renshaw
- Edinburgh Breast Unit, Western General Hospital, Edinburgh, UK
| | - Jane Keys
- Edinburgh Breast Unit, Western General Hospital, Edinburgh, UK
| | - Jonine D Figueroa
- Usher Institute of Population Health Sciences and Informatics, Old Medical School, Teviot Place, Edinburgh, UK
| | - Xiaping He
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Maki Tanioka
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Alison F Munro
- Applied Bioinformatics of Cancer, Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, Edinburgh, UK
| | - Lee Murphy
- Host and Tumour Profiling Unit, Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Angie Fawkes
- Edinburgh Clinical Research Facility, Western General Hospital, Edinburgh, UK
| | - Richard Clark
- Edinburgh Clinical Research Facility, Western General Hospital, Edinburgh, UK
| | - Audrey Coutts
- Edinburgh Clinical Research Facility, Western General Hospital, Edinburgh, UK
| | - Charles M Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Lisa A Carey
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - J Michael Dixon
- Edinburgh Breast Unit, Western General Hospital, Edinburgh, UK
| | - Andrew H Sims
- Applied Bioinformatics of Cancer, Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, Edinburgh, UK.
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11
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Sibai M, Parlayan C, Tuğlu P, Öztürk G, Demircan T. Integrative Analysis of Axolotl Gene Expression Data from Regenerative and Wound Healing Limb Tissues. Sci Rep 2019; 9:20280. [PMID: 31889169 PMCID: PMC6937273 DOI: 10.1038/s41598-019-56829-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 12/09/2019] [Indexed: 01/08/2023] Open
Abstract
Axolotl (Ambystoma mexicanum) is a urodele amphibian endowed with remarkable regenerative capacities manifested in scarless wound healing and restoration of amputated limbs, which makes it a powerful experimental model for regenerative biology and medicine. Previous studies have utilized microarrays and RNA-Seq technologies for detecting differentially expressed (DE) genes in different phases of the axolotl limb regeneration. However, sufficient consistency may be lacking due to statistical limitations arising from intra-laboratory analyses. This study aims to bridge such gaps by performing an integrative analysis of publicly available microarray and RNA-Seq data from axolotl limb samples having comparable study designs using the “merging” method. A total of 351 genes were found DE in regenerative samples compared to the control in data of both technologies, showing an adjusted p-value < 0.01 and log fold change magnitudes >1. Downstream analyses illustrated consistent correlations of the directionality of DE genes within and between data of both technologies, as well as concordance with the literature on regeneration related biological processes. qRT-PCR analysis validated the observed expression level differences of five of the top DE genes. Future studies may benefit from the utilized concept and approach for enhanced statistical power and robust discovery of biomarkers of regeneration.
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Affiliation(s)
- Mustafa Sibai
- Graduate School of Engineering and Natural Sciences, Istanbul Medipol University, Istanbul, Turkey
| | - Cüneyd Parlayan
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul Medipol University, Istanbul, Turkey. .,Department of Biomedical Engineering, Faculty of Engineering, İstanbul Medipol University, Istanbul, Turkey.
| | - Pelin Tuğlu
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul Medipol University, Istanbul, Turkey
| | - Gürkan Öztürk
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul Medipol University, Istanbul, Turkey.,Department of Physiology, International School of Medicine, İstanbul Medipol University, Istanbul, Turkey
| | - Turan Demircan
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul Medipol University, Istanbul, Turkey. .,Department of Medical Biology, School of Medicine, Mugla Sitki Kocman University, Mugla, Turkey.
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12
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Paquette AG, Brockway HM, Price ND, Muglia LJ. Comparative transcriptomic analysis of human placentae at term and preterm delivery. Biol Reprod 2019; 98:89-101. [PMID: 29228154 PMCID: PMC5803773 DOI: 10.1093/biolre/iox163] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 11/30/2017] [Indexed: 12/11/2022] Open
Abstract
Preterm birth affects 1 out of every 10 infants in the United States, resulting in substantial neonatal morbidity and mortality. Currently, there are few predictive markers and few treatment options to prevent preterm birth. A healthy, functioning placenta is essential to positive pregnancy outcomes. Previous studies have suggested that placental pathology may play a role in preterm birth etiology. Therefore, we tested the hypothesis that preterm placentae may exhibit unique transcriptomic signatures compared to term samples reflective of their abnormal biology leading to this adverse outcome. We aggregated publicly available placental villous microarray data to generate a preterm and term sample dataset (n = 133, 55 preterm placentae and 78 normal term placentae). We identified differentially expressed genes using the linear regression for microarray (LIMMA) package and identified perturbations in known biological networks using Differential Rank Conservation (DIRAC). We identified 129 significantly differentially expressed genes between term and preterm placenta with 96 genes upregulated and 33 genes downregulated (P-value <0.05). Significant changes in gene expression in molecular networks related to Tumor Protein 53 and phosphatidylinositol signaling were identified using DIRAC. We have aggregated a uniformly normalized transcriptomic dataset and have identified novel and established genes and pathways associated with developmental regulation of the placenta and potential preterm birth pathology. These analyses provide a community resource to integrate with other high-dimensional datasets for additional insights in normal placental development and its disruption.
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Affiliation(s)
| | - Heather M Brockway
- Division of Human Genetics, Center for Prevention of Preterm Birth, Cincinnati Children's, Hospital Medical Center, Cincinnati, Ohio, USA
| | | | - Louis J Muglia
- Division of Human Genetics, Center for Prevention of Preterm Birth, Cincinnati Children's, Hospital Medical Center, Cincinnati, Ohio, USA
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13
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Gray M, Turnbull AK, Ward C, Meehan J, Martínez-Pérez C, Bonello M, Pang LY, Langdon SP, Kunkler IH, Murray A, Argyle D. Development and characterisation of acquired radioresistant breast cancer cell lines. Radiat Oncol 2019; 14:64. [PMID: 30987655 PMCID: PMC6466735 DOI: 10.1186/s13014-019-1268-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 04/02/2019] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Radiotherapy plays an important role in the multimodal treatment of breast cancer. The response of a breast tumour to radiation depends not only on its innate radiosensitivity but also on tumour repopulation by cells that have developed radioresistance. Development of effective cancer treatments will require further molecular dissection of the processes that contribute to resistance. METHODS Radioresistant cell lines were established by exposing MDA-MB-231, MCF-7 and ZR-751 parental cells to increasing weekly doses of radiation. The development of radioresistance was evaluated through proliferation and colony formation assays. Phenotypic characterisation included migration and invasion assays and immunohistochemistry. Transcriptomic data were also generated for preliminary hypothesis generation involving pathway-focused analyses. RESULTS Proliferation and colony formation assays confirmed radioresistance. Radioresistant cells exhibited enhanced migration and invasion, with evidence of epithelial-to-mesenchymal-transition. Significantly, acquisition of radioresistance in MCF-7 and ZR-751 cell lines resulted in a loss of expression of both ERα and PgR and an increase in EGFR expression; based on transcriptomic data they changed subtype classification from their parental luminal A to HER2-overexpressing (MCF-7 RR) and normal-like (ZR-751 RR) subtypes, indicating the extent of phenotypic changes and cellular plasticity involved in this process. Radioresistant cell lines derived from ER+ cells also showed a shift from ER to EGFR signalling pathways with increased MAPK and PI3K activity. CONCLUSIONS This is the first study to date that extensively describes the development and characterisation of three novel radioresistant breast cancer cell lines through both genetic and phenotypic analysis. More changes were identified between parental cells and their radioresistant derivatives in the ER+ (MCF-7 and ZR-751) compared with the ER- cell line (MDA-MB-231) model; however, multiple and likely interrelated mechanisms were identified that may contribute to the development of acquired resistance to radiotherapy.
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Affiliation(s)
- Mark Gray
- The Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Edinburgh, Scotland. .,Cancer Research UK Edinburgh Centre and Division of Pathology Laboratories, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, Scotland.
| | - Arran K Turnbull
- Cancer Research UK Edinburgh Centre and Division of Pathology Laboratories, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, Scotland.,Breast Cancer Now Edinburgh Research Team, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, Scotland
| | - Carol Ward
- The Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Edinburgh, Scotland.,Cancer Research UK Edinburgh Centre and Division of Pathology Laboratories, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, Scotland
| | - James Meehan
- Cancer Research UK Edinburgh Centre and Division of Pathology Laboratories, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, Scotland.,Institute of Sensors, Signals and Systems, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, Scotland
| | - Carlos Martínez-Pérez
- Cancer Research UK Edinburgh Centre and Division of Pathology Laboratories, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, Scotland.,Breast Cancer Now Edinburgh Research Team, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, Scotland
| | - Maria Bonello
- Cancer Research UK Edinburgh Centre and Division of Pathology Laboratories, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, Scotland
| | - Lisa Y Pang
- The Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Edinburgh, Scotland
| | - Simon P Langdon
- Cancer Research UK Edinburgh Centre and Division of Pathology Laboratories, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, Scotland
| | - Ian H Kunkler
- Cancer Research UK Edinburgh Centre and Division of Pathology Laboratories, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, Scotland
| | - Alan Murray
- School of Engineering, Faraday Building, The King's Buildings, University of Edinburgh, Edinburgh, Scotland
| | - David Argyle
- The Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Edinburgh, Scotland
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14
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Selli C, Turnbull AK, Pearce DA, Li A, Fernando A, Wills J, Renshaw L, Thomas JS, Dixon JM, Sims AH. Molecular changes during extended neoadjuvant letrozole treatment of breast cancer: distinguishing acquired resistance from dormant tumours. Breast Cancer Res 2019; 21:2. [PMID: 30616553 PMCID: PMC6323855 DOI: 10.1186/s13058-018-1089-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 12/19/2018] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND The risk of recurrence for endocrine-treated breast cancer patients persists for many years or even decades following surgery and apparently successful adjuvant therapy. This period of dormancy and acquired resistance is inherently difficult to investigate; previous efforts have been limited to in-vitro or in-vivo approaches. In this study, sequential tumour samples from patients receiving extended neoadjuvant aromatase inhibitor therapy were characterised as a novel clinical model. METHODS Consecutive tumour samples from 62 patients undergoing extended (4-45 months) neoadjuvant aromatase inhibitor therapy with letrozole were subjected to transcriptomic and proteomic analysis, representing before (≤ 0), early (13-120 days), and long-term (> 120 days) neoadjuvant aromatase inhibitor therapy with letrozole. Patients with at least a 40% initial reduction in tumour size by 4 months of treatment were included. Of these, 42 patients with no subsequent progression were classified as "dormant", and the remaining 20 patients as "acquired resistant". RESULTS Changes in gene expression in dormant tumours begin early and become more pronounced at later time points. Therapy-induced changes in resistant tumours were common features of treatment, rather than being specific to the resistant phenotype. Comparative analysis of long-term treated dormant and resistant tumours highlighted changes in epigenetics pathways including DNA methylation and histone acetylation. The DNA methylation marks 5-methylcytosine and 5-hydroxymethylcytosine were significantly reduced in resistant tumours compared with dormant tissues after extended letrozole treatment. CONCLUSIONS This is the first patient-matched gene expression study investigating long-term aromatase inhibitor-induced dormancy and acquired resistance in breast cancer. Dormant tumours continue to change during treatment whereas acquired resistant tumours more closely resemble their diagnostic samples. Global loss of DNA methylation was observed in resistant tumours under extended treatment. Epigenetic alterations may lead to escape from dormancy and drive acquired resistance in a subset of patients, supporting a potential role for therapy targeted at these epigenetic alterations in the management of resistance to oestrogen deprivation therapy.
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Affiliation(s)
- Cigdem Selli
- Applied Bioinformatics of Cancer, University of Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, Edinburgh, UK.,Department of Pharmacology, Faculty of Pharmacy, Ege University, 35040, Izmir, Turkey
| | - Arran K Turnbull
- Applied Bioinformatics of Cancer, University of Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, Edinburgh, UK.,Edinburgh Breast Unit, Western General Hospital, Edinburgh, UK
| | - Dominic A Pearce
- Applied Bioinformatics of Cancer, University of Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, Edinburgh, UK
| | - Ang Li
- Applied Bioinformatics of Cancer, University of Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, Edinburgh, UK
| | - Anu Fernando
- Applied Bioinformatics of Cancer, University of Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, Edinburgh, UK.,Edinburgh Breast Unit, Western General Hospital, Edinburgh, UK
| | - Jimi Wills
- Mass Spectrometry Unit, MRC Institute of Genetics and Molecular Medicine, Edinburgh, UK
| | - Lorna Renshaw
- Edinburgh Breast Unit, Western General Hospital, Edinburgh, UK
| | - Jeremy S Thomas
- Edinburgh Breast Unit, Western General Hospital, Edinburgh, UK
| | - J Michael Dixon
- Edinburgh Breast Unit, Western General Hospital, Edinburgh, UK
| | - Andrew H Sims
- Applied Bioinformatics of Cancer, University of Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, Edinburgh, UK.
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15
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Al–Taie Z, Thanintorn N, Ersoy I, Kholod O, Taylor K, Hammer R, Shin D. REDESIGN: RDF-based Differential Signaling Framework for Precision Medicine Analytics. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE PROCEEDINGS. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE 2018; 2017:35-44. [PMID: 29888036 PMCID: PMC5961787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pathway-based analysis holds promise to be instrumental in precision and personalized medicine analytics. However, the majority of pathway-based analysis methods utilize "fixed" or "rigid" data sets that limit their ability to account for complex biological inter-dependencies. Here, we present REDESIGN: RDF-based Differential Signaling Pathway informatics framework. The distinctive feature of the REDESIGN is that it is designed to run on "flexible" ontology-enabled data sets of curated signal transduction pathway maps to uncover high explanatory differential pathway mechanisms on gene-to-gene level. The experiments on two morphoproteomic cases demonstrated REDESIGN's capability to generate actionable hypotheses in precision/personalized medicine analytics.
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Affiliation(s)
- Zainab Al–Taie
- MU Informatics Institute, University of Missouri, Columbia, MO,Department of Pathology and Anatomical Sciences, University of Missouri, Columbia, MO
| | - Nattapon Thanintorn
- Department of Pathology and Anatomical Sciences, University of Missouri, Columbia, MO
| | - Ilker Ersoy
- MU Informatics Institute, University of Missouri, Columbia, MO,Department of Pathology and Anatomical Sciences, University of Missouri, Columbia, MO
| | - Olha Kholod
- MU Informatics Institute, University of Missouri, Columbia, MO,Department of Pathology and Anatomical Sciences, University of Missouri, Columbia, MO
| | - Kristen Taylor
- Department of Pathology and Anatomical Sciences, University of Missouri, Columbia, MO
| | - Richard Hammer
- MU Informatics Institute, University of Missouri, Columbia, MO,Department of Pathology and Anatomical Sciences, University of Missouri, Columbia, MO
| | - Dmitriy Shin
- MU Informatics Institute, University of Missouri, Columbia, MO,Department of Pathology and Anatomical Sciences, University of Missouri, Columbia, MO
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16
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Irigoyen A, Jimenez-Luna C, Benavides M, Caba O, Gallego J, Ortuño FM, Guillen-Ponce C, Rojas I, Aranda E, Torres C, Prados J. Integrative multi-platform meta-analysis of gene expression profiles in pancreatic ductal adenocarcinoma patients for identifying novel diagnostic biomarkers. PLoS One 2018; 13:e0194844. [PMID: 29617451 PMCID: PMC5884535 DOI: 10.1371/journal.pone.0194844] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 03/09/2018] [Indexed: 01/16/2023] Open
Abstract
Applying differentially expressed genes (DEGs) to identify feasible biomarkers in diseases can be a hard task when working with heterogeneous datasets. Expression data are strongly influenced by technology, sample preparation processes, and/or labeling methods. The proliferation of different microarray platforms for measuring gene expression increases the need to develop models able to compare their results, especially when different technologies can lead to signal values that vary greatly. Integrative meta-analysis can significantly improve the reliability and robustness of DEG detection. The objective of this work was to develop an integrative approach for identifying potential cancer biomarkers by integrating gene expression data from two different platforms. Pancreatic ductal adenocarcinoma (PDAC), where there is an urgent need to find new biomarkers due its late diagnosis, is an ideal candidate for testing this technology. Expression data from two different datasets, namely Affymetrix and Illumina (18 and 36 PDAC patients, respectively), as well as from 18 healthy controls, was used for this study. A meta-analysis based on an empirical Bayesian methodology (ComBat) was then proposed to integrate these datasets. DEGs were finally identified from the integrated data by using the statistical programming language R. After our integrative meta-analysis, 5 genes were commonly identified within the individual analyses of the independent datasets. Also, 28 novel genes that were not reported by the individual analyses (‘gained’ genes) were also discovered. Several of these gained genes have been already related to other gastroenterological tumors. The proposed integrative meta-analysis has revealed novel DEGs that may play an important role in PDAC and could be potential biomarkers for diagnosing the disease.
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Affiliation(s)
- Antonio Irigoyen
- Department of Medical Oncology, Virgen de la Salud Hospital, Toledo, Spain
| | - Cristina Jimenez-Luna
- Institute of Biopathology and Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, Granada, Spain
| | - Manuel Benavides
- Department of Medical Oncology, Virgen de la Victoria Hospital, Malaga, Spain
| | - Octavio Caba
- Department of Health Sciences, University of Jaen, Jaen, Spain
- * E-mail:
| | - Javier Gallego
- Department of Medical Oncology, University General Hospital of Elche, Alicante, Spain
| | - Francisco Manuel Ortuño
- Department of Computer Architecture and Computer Technology, Research Center for Information and Communications Technologies, University of Granada, Granada, Spain
| | | | - Ignacio Rojas
- Department of Computer Architecture and Computer Technology, Research Center for Information and Communications Technologies, University of Granada, Granada, Spain
| | - Enrique Aranda
- Maimonides Institute of Biomedical Research (IMIBIC), Reina Sofia Hospital, University of Cordoba, Cordoba, Spain
| | - Carolina Torres
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, Granada, Spain
| | - Jose Prados
- Institute of Biopathology and Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, Granada, Spain
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17
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Pearce DA, Arthur LM, Turnbull AK, Renshaw L, Sabine VS, Thomas JS, Bartlett JMS, Dixon JM, Sims AH. Tumour sampling method can significantly influence gene expression profiles derived from neoadjuvant window studies. Sci Rep 2016; 6:29434. [PMID: 27384960 PMCID: PMC4935948 DOI: 10.1038/srep29434] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 06/17/2016] [Indexed: 01/09/2023] Open
Abstract
Patient-matched transcriptomic studies using tumour samples before and after treatment allow inter-patient heterogeneity to be controlled, but tend not to include an untreated comparison. Here, Illumina BeadArray technology was used to measure dynamic changes in gene expression from thirty-seven paired diagnostic core and surgically excised breast cancer biopsies obtained from women receiving no treatment prior to surgery, to determine the impact of sampling method and tumour heterogeneity. Despite a lack of treatment and perhaps surprisingly, consistent changes in gene expression were identified during the diagnosis-surgery interval (48 up, 2 down; Siggenes FDR 0.05) in a manner independent of both subtype and sampling-interval length. Instead, tumour sampling method was seen to directly impact gene expression, with similar effects additionally identified in six published breast cancer datasets. In contrast with previous findings, our data does not support the concept of a significant wounding or immune response following biopsy in the absence of treatment and instead implicates a hypoxic response following the surgical biopsy. Whilst sampling-related gene expression changes are evident in treated samples, they are secondary to those associated with response to treatment. Nonetheless, sampling method remains a potential confounding factor for neoadjuvant study design.
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Affiliation(s)
- Dominic A Pearce
- Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Laura M Arthur
- Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Arran K Turnbull
- Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Lorna Renshaw
- Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Vicky S Sabine
- Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jeremy S Thomas
- Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - John M S Bartlett
- Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - J Michael Dixon
- Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Andrew H Sims
- Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
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18
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Müller C, Schillert A, Röthemeier C, Trégouët DA, Proust C, Binder H, Pfeiffer N, Beutel M, Lackner KJ, Schnabel RB, Tiret L, Wild PS, Blankenberg S, Zeller T, Ziegler A. Removing Batch Effects from Longitudinal Gene Expression - Quantile Normalization Plus ComBat as Best Approach for Microarray Transcriptome Data. PLoS One 2016; 11:e0156594. [PMID: 27272489 PMCID: PMC4896498 DOI: 10.1371/journal.pone.0156594] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 05/17/2016] [Indexed: 12/13/2022] Open
Abstract
Technical variation plays an important role in microarray-based gene expression studies, and batch effects explain a large proportion of this noise. It is therefore mandatory to eliminate technical variation while maintaining biological variability. Several strategies have been proposed for the removal of batch effects, although they have not been evaluated in large-scale longitudinal gene expression data. In this study, we aimed at identifying a suitable method for batch effect removal in a large study of microarray-based longitudinal gene expression. Monocytic gene expression was measured in 1092 participants of the Gutenberg Health Study at baseline and 5-year follow up. Replicates of selected samples were measured at both time points to identify technical variability. Deming regression, Passing-Bablok regression, linear mixed models, non-linear models as well as ReplicateRUV and ComBat were applied to eliminate batch effects between replicates. In a second step, quantile normalization prior to batch effect correction was performed for each method. Technical variation between batches was evaluated by principal component analysis. Associations between body mass index and transcriptomes were calculated before and after batch removal. Results from association analyses were compared to evaluate maintenance of biological variability. Quantile normalization, separately performed in each batch, combined with ComBat successfully reduced batch effects and maintained biological variability. ReplicateRUV performed perfectly in the replicate data subset of the study, but failed when applied to all samples. All other methods did not substantially reduce batch effects in the replicate data subset. Quantile normalization plus ComBat appears to be a valuable approach for batch correction in longitudinal gene expression data.
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Affiliation(s)
- Christian Müller
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Hamburg, 20246, Germany
- Institute of Medical Biometry and Statistics, University Medical Center Schleswig-Holstein, Campus Luebeck, Lübeck, 23562, Germany
- German Center for Cardiovascular Research (DZHK e.V.), partner site Hamburg, Lübeck, Kiel, 20246, Germany
| | - Arne Schillert
- Institute of Medical Biometry and Statistics, University Medical Center Schleswig-Holstein, Campus Luebeck, Lübeck, 23562, Germany
- German Center for Cardiovascular Research (DZHK e.V.), partner site Hamburg, Lübeck, Kiel, 20246, Germany
| | - Caroline Röthemeier
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Hamburg, 20246, Germany
| | - David-Alexandre Trégouët
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche(UMR) enSanté 1166, F-75013, Paris, France
- Institute for Cardiometabolism and Nutrition (ICAN), F-75013 Paris, France
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC Univ Paris 06), UMR_S1166, Team Genomics & Pathophysiology of Cardiovascular Diseases, F-75013, Paris, France
| | - Carole Proust
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche(UMR) enSanté 1166, F-75013, Paris, France
- Institute for Cardiometabolism and Nutrition (ICAN), F-75013 Paris, France
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC Univ Paris 06), UMR_S1166, Team Genomics & Pathophysiology of Cardiovascular Diseases, F-75013, Paris, France
| | - Harald Binder
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI) at the University Medical Center of the Johannes Gutenberg University Mainz, Mainz, 55131, Germany
| | - Norbert Pfeiffer
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center of the Johannes Gutenberg University, Mainz, 55131, Germany
| | - Manfred Beutel
- Department of Psychosomatic Medicine and Psychotherapy, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Karl J. Lackner
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Mainz, Germany
| | - Renate B. Schnabel
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Hamburg, 20246, Germany
- German Center for Cardiovascular Research (DZHK e.V.), partner site Hamburg, Lübeck, Kiel, 20246, Germany
| | - Laurence Tiret
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche(UMR) enSanté 1166, F-75013, Paris, France
- Institute for Cardiometabolism and Nutrition (ICAN), F-75013 Paris, France
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC Univ Paris 06), UMR_S1166, Team Genomics & Pathophysiology of Cardiovascular Diseases, F-75013, Paris, France
| | - Philipp S. Wild
- Preventive Cardiology and Preventive Medicine, Center for Cardiology, University Medical Center Mainz, Mainz, 55131, Germany
- Center for Thrombosis and Hemostasis, University Medical Center Mainz, Mainz, 55131, Germany
- German Center for Cardiovascular Research (DZHK e.V.), partner site Rhine Main, Mainz, 55131, Germany
| | - Stefan Blankenberg
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Hamburg, 20246, Germany
- German Center for Cardiovascular Research (DZHK e.V.), partner site Hamburg, Lübeck, Kiel, 20246, Germany
| | - Tanja Zeller
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Hamburg, 20246, Germany
- German Center for Cardiovascular Research (DZHK e.V.), partner site Hamburg, Lübeck, Kiel, 20246, Germany
| | - Andreas Ziegler
- Institute of Medical Biometry and Statistics, University Medical Center Schleswig-Holstein, Campus Luebeck, Lübeck, 23562, Germany
- German Center for Cardiovascular Research (DZHK e.V.), partner site Hamburg, Lübeck, Kiel, 20246, Germany
- Center for Clinical Trials, University of Lübeck, Lübeck, 23562, Germany
- * E-mail:
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19
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Martínez-Pérez C, Ward C, Turnbull AK, Mullen P, Cook G, Meehan J, Jarman EJ, Thomson PIT, Campbell CJ, McPhail D, Harrison DJ, Langdon SP. Antitumour activity of the novel flavonoid Oncamex in preclinical breast cancer models. Br J Cancer 2016; 114:905-16. [PMID: 27031849 PMCID: PMC4984802 DOI: 10.1038/bjc.2016.6] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 11/17/2015] [Accepted: 12/16/2015] [Indexed: 12/28/2022] Open
Abstract
Background: The natural polyphenol myricetin induces cell cycle arrest and apoptosis in preclinical cancer models. We hypothesised that myricetin-derived flavonoids with enhanced redox properties, improved cell uptake and mitochondrial targeting might have increased potential as antitumour agents. Methods: We studied the effect of a second-generation flavonoid analogue Oncamex in a panel of seven breast cancer cell lines, applying western blotting, gene expression analysis, fluorescence microscopy and immunohistochemistry of xenograft tissue to investigate its mechanism of action. Results: Proliferation assays showed that Oncamex treatment for 8 h reduced cell viability and induced cytotoxicity and apoptosis, concomitant with increased caspase activation. Microarray analysis showed that Oncamex was associated with changes in the expression of genes controlling cell cycle and apoptosis. Fluorescence microscopy showed the compound's mitochondrial targeting and reactive oxygen species-modulating properties, inducing superoxide production at concentrations associated with antiproliferative effects. A preliminary in vivo study in mice implanted with the MDA-MB-231 breast cancer xenograft showed that Oncamex inhibited tumour growth, reducing tissue viability and Ki-67 proliferation, with no signs of untoward effects on the animals. Conclusions: Oncamex is a novel flavonoid capable of specific mitochondrial delivery and redox modulation. It has shown antitumour activity in preclinical models of breast cancer, supporting the potential of this prototypic candidate for its continued development as an anticancer agent.
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Affiliation(s)
- Carlos Martínez-Pérez
- Division of Pathology Laboratories, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Carol Ward
- Division of Pathology Laboratories, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Arran K Turnbull
- Division of Pathology Laboratories, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Peter Mullen
- School of Medicine, University of St Andrews, St Andrews KY16 9TF, UK
| | - Graeme Cook
- Antoxis Limited, IMS Building, Foresterhill Health and Research Complex, Aberdeen AB25 2ZD, UK
| | - James Meehan
- Division of Pathology Laboratories, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Edward J Jarman
- Division of Pathology Laboratories, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Patrick I T Thomson
- EaSTCHEM, School of Chemistry, University of Edinburgh, Joseph Black Building, Edinburgh EH9 3FJ, UK
| | - Colin J Campbell
- EaSTCHEM, School of Chemistry, University of Edinburgh, Joseph Black Building, Edinburgh EH9 3FJ, UK
| | - Donald McPhail
- Antoxis Limited, IMS Building, Foresterhill Health and Research Complex, Aberdeen AB25 2ZD, UK
| | - David J Harrison
- School of Medicine, University of St Andrews, St Andrews KY16 9TF, UK
| | - Simon P Langdon
- Division of Pathology Laboratories, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
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Maimari N, Pedrigi RM, Russo A, Broda K, Krams R. Integration of flow studies for robust selection of mechanoresponsive genes. Thromb Haemost 2016; 115:474-83. [PMID: 26842798 DOI: 10.1160/th15-09-0704] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 11/13/2015] [Indexed: 11/05/2022]
Abstract
Blood flow is an essential contributor to plaque growth, composition and initiation. It is sensed by endothelial cells, which react to blood flow by expressing > 1000 genes. The sheer number of genes implies that one needs genomic techniques to unravel their response in disease. Individual genomic studies have been performed but lack sufficient power to identify subtle changes in gene expression. In this study, we investigated whether a systematic meta-analysis of available microarray studies can improve their consistency. We identified 17 studies using microarrays, of which six were performed in vivo and 11 in vitro. The in vivo studies were disregarded due to the lack of the shear profile. Of the in vitro studies, a cross-platform integration of human studies (HUVECs in flow cells) showed high concordance (> 90 %). The human data set identified > 1600 genes to be shear responsive, more than any other study and in this gene set all known mechanosensitive genes and pathways were present. A detailed network analysis indicated a power distribution (e. g. the presence of hubs), without a hierarchical organisation. The average cluster coefficient was high and further analysis indicated an aggregation of 3 and 4 element motifs, indicating a high prevalence of feedback and feed forward loops, similar to prokaryotic cells. In conclusion, this initial study presented a novel method to integrate human-based mechanosensitive studies to increase its power. The robust network was large, contained all known mechanosensitive pathways and its structure revealed hubs, and a large aggregate of feedback and feed forward loops.
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Affiliation(s)
| | | | | | | | - Rob Krams
- Prof. Rob Krams, Chair in Molecular Bioengineering, Dept. Bioengineering, Imperial College London, Room 3.15, Royal School of Mines, Exhibition Road, SW7 2AZ London, UK, Tel.:+44 2075941473, E-mail:
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21
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Varešlija D, McBryan J, Fagan A, Redmond AM, Hao Y, Sims AH, Turnbull A, Dixon JM, Ó Gaora P, Hudson L, Purcell S, Hill ADK, Young LS. Adaptation to AI Therapy in Breast Cancer Can Induce Dynamic Alterations in ER Activity Resulting in Estrogen-Independent Metastatic Tumors. Clin Cancer Res 2016; 22:2765-77. [PMID: 26763249 DOI: 10.1158/1078-0432.ccr-15-1583] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 12/20/2015] [Indexed: 11/16/2022]
Abstract
PURPOSE Acquired resistance to aromatase inhibitor (AI) therapy is a major clinical problem in the treatment of breast cancer. The detailed mechanisms of how tumor cells develop this resistance remain unclear. Here, the adapted function of estrogen receptor (ER) to an estrogen-depleted environment following AI treatment is reported. EXPERIMENTAL DESIGN Global ER chromatin immuno-precipitation (ChIP)-seq analysis of AI-resistant cells identified steroid-independent ER target genes. Matched patient tumor samples, collected before and after AI treatment, were used to assess ER activity. RESULTS Maintained ER activity was observed in patient tumors following neoadjuvant AI therapy. Genome-wide ER-DNA-binding analysis in AI-resistant cell lines identified a subset of classic ligand-dependent ER target genes that develop steroid independence. The Kaplan-Meier analysis revealed a significant association between tumors, which fail to decrease this steroid-independent ER target gene set in response to neoadjuvant AI therapy, and poor disease-free survival and overall survival (n = 72 matched patient tumor samples, P = 0.00339 and 0.00155, respectively). The adaptive ER response to AI treatment was highlighted by the ER/AIB1 target gene, early growth response 3 (EGR3). Elevated levels of EGR3 were detected in endocrine-resistant local disease recurrent patient tumors in comparison with matched primary tissue. However, evidence from distant metastatic tumors demonstrates that the ER signaling network may undergo further adaptations with disease progression as estrogen-independent ER target gene expression is routinely lost in established metastatic tumors. CONCLUSIONS Overall, these data provide evidence of a dynamic ER response to endocrine treatment that may provide vital clues for overcoming the clinical issue of therapy resistance. Clin Cancer Res; 22(11); 2765-77. ©2016 AACR.
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Affiliation(s)
- Damir Varešlija
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Jean McBryan
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Ailís Fagan
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Aisling M Redmond
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Yuan Hao
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Andrew H Sims
- University of Edinburgh Cancer Research Centre, Carrington Crescent, Edinburgh, EH4 2XU, United Kingdom
| | - Arran Turnbull
- University of Edinburgh Cancer Research Centre, Carrington Crescent, Edinburgh, EH4 2XU, United Kingdom
| | - J M Dixon
- University of Edinburgh Cancer Research Centre, Carrington Crescent, Edinburgh, EH4 2XU, United Kingdom
| | - Peadar Ó Gaora
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Lance Hudson
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Siobhan Purcell
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Arnold D K Hill
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Leonie S Young
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin 2, Ireland.
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Microarray Meta-Analysis and Cross-Platform Normalization: Integrative Genomics for Robust Biomarker Discovery. MICROARRAYS 2015; 4:389-406. [PMID: 27600230 PMCID: PMC4996376 DOI: 10.3390/microarrays4030389] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 08/16/2015] [Accepted: 08/17/2015] [Indexed: 01/24/2023]
Abstract
The diagnostic and prognostic potential of the vast quantity of publicly-available microarray data has driven the development of methods for integrating the data from different microarray platforms. Cross-platform integration, when appropriately implemented, has been shown to improve reproducibility and robustness of gene signature biomarkers. Microarray platform integration can be conceptually divided into approaches that perform early stage integration (cross-platform normalization) versus late stage data integration (meta-analysis). A growing number of statistical methods and associated software for platform integration are available to the user, however an understanding of their comparative performance and potential pitfalls is critical for best implementation. In this review we provide evidence-based, practical guidance to researchers performing cross-platform integration, particularly with an objective to discover biomarkers.
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Turnbull AK, Arthur LM, Renshaw L, Larionov AA, Kay C, Dunbier AK, Thomas JS, Dowsett M, Sims AH, Dixon JM. Accurate Prediction and Validation of Response to Endocrine Therapy in Breast Cancer. J Clin Oncol 2015; 33:2270-8. [PMID: 26033813 DOI: 10.1200/jco.2014.57.8963] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
PURPOSE Aromatase inhibitors (AIs) have an established role in the treatment of breast cancer. Response rates are only 50% to 70% in the neoadjuvant setting and lower in advanced disease. Accurate biomarkers are urgently needed to predict response in these settings and to determine which individuals will benefit from adjuvant AI therapy. PATIENTS AND METHODS Pretreatment and on-treatment (after 2 weeks and 3 months) biopsies were obtained from 89 postmenopausal women who had estrogen receptor-alpha positive breast cancer and were receiving neoadjuvant letrozole for transcript profiling. Dynamic clinical response was assessed with use of three-dimensional ultrasound measurements. RESULTS The molecular response to letrozole was characterized and a four-gene classifier of clinical response was established (accuracy of 96%) on the basis of the level of two genes before treatment (one gene [IL6ST] was associated with immune signaling, and the other [NGFRAP1] was associated with apoptosis) and the level of two proliferation genes (ASPM, MCM4) after 2 weeks of therapy. The four-gene signature was found to be 91% accurate in a blinded, completely independent validation data set of patients treated with anastrozole. Matched 2-week on-treatment biopsies were associated with improved predictive power as compared with pretreatment biopsies alone. This signature also significantly predicted recurrence-free survival (P = .029) and breast cancer -specific survival (P = .009). We demonstrate that the test can also be performed with use of quantitative polymerase chain reaction or immunohistochemistry. CONCLUSION A four-gene predictive model of clinical response to AIs by 2 weeks has been generated and validated. Deregulated immune and apoptotic responses before treatment and cell proliferation that is not reduced 2 weeks after initiation of treatment are functional characteristics of breast tumors that do not respond to AIs.
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Affiliation(s)
- Arran K Turnbull
- Arran K. Turnbull, Laura M. Arthur, Lorna Renshaw, Alexey A. Larionov, Charlene Kay, Jeremy S. Thomas, Andrew H. Sims, J. Michael Dixon, University of Edinburgh Cancer Research UK Centre, Edinburgh; Anita K. Dunbier, Mitch Dowsett, Institute of Cancer Research, London, United Kingdom; and Anita K. Dunbier, University of Otago, Dunedin, New Zealand
| | - Laura M Arthur
- Arran K. Turnbull, Laura M. Arthur, Lorna Renshaw, Alexey A. Larionov, Charlene Kay, Jeremy S. Thomas, Andrew H. Sims, J. Michael Dixon, University of Edinburgh Cancer Research UK Centre, Edinburgh; Anita K. Dunbier, Mitch Dowsett, Institute of Cancer Research, London, United Kingdom; and Anita K. Dunbier, University of Otago, Dunedin, New Zealand
| | - Lorna Renshaw
- Arran K. Turnbull, Laura M. Arthur, Lorna Renshaw, Alexey A. Larionov, Charlene Kay, Jeremy S. Thomas, Andrew H. Sims, J. Michael Dixon, University of Edinburgh Cancer Research UK Centre, Edinburgh; Anita K. Dunbier, Mitch Dowsett, Institute of Cancer Research, London, United Kingdom; and Anita K. Dunbier, University of Otago, Dunedin, New Zealand
| | - Alexey A Larionov
- Arran K. Turnbull, Laura M. Arthur, Lorna Renshaw, Alexey A. Larionov, Charlene Kay, Jeremy S. Thomas, Andrew H. Sims, J. Michael Dixon, University of Edinburgh Cancer Research UK Centre, Edinburgh; Anita K. Dunbier, Mitch Dowsett, Institute of Cancer Research, London, United Kingdom; and Anita K. Dunbier, University of Otago, Dunedin, New Zealand
| | - Charlene Kay
- Arran K. Turnbull, Laura M. Arthur, Lorna Renshaw, Alexey A. Larionov, Charlene Kay, Jeremy S. Thomas, Andrew H. Sims, J. Michael Dixon, University of Edinburgh Cancer Research UK Centre, Edinburgh; Anita K. Dunbier, Mitch Dowsett, Institute of Cancer Research, London, United Kingdom; and Anita K. Dunbier, University of Otago, Dunedin, New Zealand
| | - Anita K Dunbier
- Arran K. Turnbull, Laura M. Arthur, Lorna Renshaw, Alexey A. Larionov, Charlene Kay, Jeremy S. Thomas, Andrew H. Sims, J. Michael Dixon, University of Edinburgh Cancer Research UK Centre, Edinburgh; Anita K. Dunbier, Mitch Dowsett, Institute of Cancer Research, London, United Kingdom; and Anita K. Dunbier, University of Otago, Dunedin, New Zealand
| | - Jeremy S Thomas
- Arran K. Turnbull, Laura M. Arthur, Lorna Renshaw, Alexey A. Larionov, Charlene Kay, Jeremy S. Thomas, Andrew H. Sims, J. Michael Dixon, University of Edinburgh Cancer Research UK Centre, Edinburgh; Anita K. Dunbier, Mitch Dowsett, Institute of Cancer Research, London, United Kingdom; and Anita K. Dunbier, University of Otago, Dunedin, New Zealand
| | - Mitch Dowsett
- Arran K. Turnbull, Laura M. Arthur, Lorna Renshaw, Alexey A. Larionov, Charlene Kay, Jeremy S. Thomas, Andrew H. Sims, J. Michael Dixon, University of Edinburgh Cancer Research UK Centre, Edinburgh; Anita K. Dunbier, Mitch Dowsett, Institute of Cancer Research, London, United Kingdom; and Anita K. Dunbier, University of Otago, Dunedin, New Zealand
| | - Andrew H Sims
- Arran K. Turnbull, Laura M. Arthur, Lorna Renshaw, Alexey A. Larionov, Charlene Kay, Jeremy S. Thomas, Andrew H. Sims, J. Michael Dixon, University of Edinburgh Cancer Research UK Centre, Edinburgh; Anita K. Dunbier, Mitch Dowsett, Institute of Cancer Research, London, United Kingdom; and Anita K. Dunbier, University of Otago, Dunedin, New Zealand.
| | - J Michael Dixon
- Arran K. Turnbull, Laura M. Arthur, Lorna Renshaw, Alexey A. Larionov, Charlene Kay, Jeremy S. Thomas, Andrew H. Sims, J. Michael Dixon, University of Edinburgh Cancer Research UK Centre, Edinburgh; Anita K. Dunbier, Mitch Dowsett, Institute of Cancer Research, London, United Kingdom; and Anita K. Dunbier, University of Otago, Dunedin, New Zealand
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Sfakianakis S, Bei ES, Zervakis M, Vassou D, Kafetzopoulos D. On the identification of circulating tumor cells in breast cancer. IEEE J Biomed Health Inform 2015; 18:773-82. [PMID: 24808221 DOI: 10.1109/jbhi.2013.2295262] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Breast cancer is a highly heterogeneous disease and very common among western women. The main cause of death is not the primary tumor but its metastases at distant sites, such as lymph nodes and other organs (preferentially lung, liver, and bones). The study of circulating tumor cells (CTCs) in peripheral blood resulting from tumor cell invasion and intravascular filtration highlights their crucial role concerning tumor aggressiveness and metastasis. Genomic research regarding CTCs monitoring for breast cancer is limited due to the lack of indicative genes for their detection and isolation. Instead of direct CTC detection, in our study, we focus on the identification of factors in peripheral blood that can indirectly reveal the presence of such cells. Using selected publicly available breast cancer and peripheral blood microarray datasets, we follow a two-step elimination procedure for the identification of several discriminant factors. Our procedure facilitates the identification of major genes involved in breast cancer pathology, which are also indicative of CTCs presence.
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25
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Zimmermann P, Bleuler S, Laule O, Martin F, Ivanov NV, Campanoni P, Oishi K, Lugon-Moulin N, Wyss M, Hruz T, Gruissem W. ExpressionData - A public resource of high quality curated datasets representing gene expression across anatomy, development and experimental conditions. BioData Min 2014; 7:18. [PMID: 25228922 PMCID: PMC4165432 DOI: 10.1186/1756-0381-7-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 08/13/2014] [Indexed: 11/18/2022] Open
Abstract
Reference datasets are often used to compare, interpret or validate experimental data and analytical methods. In the field of gene expression, several reference datasets have been published. Typically, they consist of individual baseline or spike-in experiments carried out in a single laboratory and representing a particular set of conditions. Here, we describe a new type of standardized datasets representative for the spatial and temporal dimensions of gene expression. They result from integrating expression data from a large number of globally normalized and quality controlled public experiments. Expression data is aggregated by anatomical part or stage of development to yield a representative transcriptome for each category. For example, we created a genome-wide expression dataset representing the FDA tissue panel across 35 tissue types. The proposed datasets were created for human and several model organisms and are publicly available at http://www.expressiondata.org.
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Affiliation(s)
| | | | - Oliver Laule
- NEBION AG, Hohlstrasse 515, 8048 Zurich, Switzerland
| | - Florian Martin
- Philip Morris International R&D, Quai Jeanrenaud 5, 2003 Neuchatel, Switzerland
| | - Nikolai V Ivanov
- Philip Morris International R&D, Quai Jeanrenaud 5, 2003 Neuchatel, Switzerland
| | - Prisca Campanoni
- Philip Morris International R&D, Quai Jeanrenaud 5, 2003 Neuchatel, Switzerland
| | - Karen Oishi
- Philip Morris International R&D, Quai Jeanrenaud 5, 2003 Neuchatel, Switzerland
| | | | - Markus Wyss
- NEBION AG, Hohlstrasse 515, 8048 Zurich, Switzerland
| | - Tomas Hruz
- Institute of Theoretical Computer Science, ETH Zurich, 8092 Zurich, Switzerland
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26
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Arthur LM, Turnbull AK, Webber VL, Larionov AA, Renshaw L, Kay C, Thomas JS, Dixon JM, Sims AH. Molecular Changes in Lobular Breast Cancers in Response to Endocrine Therapy. Cancer Res 2014; 74:5371-6. [DOI: 10.1158/0008-5472.can-14-0620] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Bundela S, Sharma A, Bisen PS. Potential therapeutic targets for oral cancer: ADM, TP53, EGFR, LYN, CTLA4, SKIL, CTGF, CD70. PLoS One 2014; 9:e102610. [PMID: 25029526 PMCID: PMC4110113 DOI: 10.1371/journal.pone.0102610] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 06/20/2014] [Indexed: 12/16/2022] Open
Abstract
In India, oral cancer has consistently ranked among top three causes of cancer-related deaths, and it has emerged as a top cause for the cancer-related deaths among men. Lack of effective therapeutic options is one of the main challenges in clinical management of oral cancer patients. We interrogated large pool of samples from oral cancer gene expression studies to identify potential therapeutic targets that are involved in multiple cancer hallmark events. Therapeutic strategies directed towards such targets can be expected to effectively control cancer cells. Datasets from different gene expression studies were integrated by removing batch-effects and was used for downstream analyses, including differential expression analysis. Dependency network analysis was done to identify genes that undergo marked topological changes in oral cancer samples when compared with control samples. Causal reasoning analysis was carried out to identify significant hypotheses, which can explain gene expression profiles observed in oral cancer samples. Text-mining based approach was used to detect cancer hallmarks associated with genes significantly expressed in oral cancer. In all, 2365 genes were detected to be differentially expressed genes, which includes some of the highly differentially expressed genes like matrix metalloproteinases (MMP-1/3/10/13), chemokine (C-X-C motif) ligands (IL8, CXCL-10/-11), PTHLH, SERPINE1, NELL2, S100A7A, MAL, CRNN, TGM3, CLCA4, keratins (KRT-3/4/13/76/78), SERPINB11 and serine peptidase inhibitors (SPINK-5/7). XIST, TCEAL2, NRAS and FGFR2 are some of the important genes detected by dependency and causal network analysis. Literature mining analysis annotated 1014 genes, out of which 841 genes were statistically significantly annotated. The integration of output of various analyses, resulted in the list of potential therapeutic targets for oral cancer, which included targets such as ADM, TP53, EGFR, LYN, CTLA4, SKIL, CTGF and CD70.
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Affiliation(s)
- Saurabh Bundela
- Defence Research Development Establishment, Defence Research Development Organization, Ministry of Defence, Govt. of India, Gwalior, Madhya Pradesh, India
- Department of Postgraduate Studies & Research in Biological Sciences, Rani Durgavati University, Jabalpur, Madhya Pradesh, India
| | - Anjana Sharma
- Department of Postgraduate Studies & Research in Biological Sciences, Rani Durgavati University, Jabalpur, Madhya Pradesh, India
| | - Prakash S. Bisen
- Defence Research Development Establishment, Defence Research Development Organization, Ministry of Defence, Govt. of India, Gwalior, Madhya Pradesh, India
- School of Studies in Biotechnology, Jiwaji University, Gwalior, Madhya Pradesh, India
- * E-mail:
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Lê Cao KA, Rohart F, McHugh L, Korn O, Wells CA. YuGene: A simple approach to scale gene expression data derived from different platforms for integrated analyses. Genomics 2014; 103:239-51. [DOI: 10.1016/j.ygeno.2014.03.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 03/14/2014] [Accepted: 03/16/2014] [Indexed: 01/09/2023]
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29
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Emmert-Streib F, Zhang SD, Hamilton P. Dry computational approaches for wet medical problems. J Transl Med 2014; 12:26. [PMID: 24460894 PMCID: PMC3905162 DOI: 10.1186/1479-5876-12-26] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 01/23/2014] [Indexed: 11/10/2022] Open
Abstract
This is a report on the 4th international conference in 'Quantitative Biology and Bioinformatics in Modern Medicine' held in Belfast (UK), 19-20 September 2013. The aim of the conference was to bring together leading experts from a variety of different areas that are key for Systems Medicine to exchange novel findings and promote interdisciplinary ideas and collaborations.
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Affiliation(s)
- Frank Emmert-Streib
- Computational Biology and Machine Learning Laboratory, Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Lisburn Road 97, Belfast, UK.
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