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Guan Q, Song X, Zhang Z, Zhang Y, Chen Y, Li J. Identification of Tamoxifen-Resistant Breast Cancer Cell Lines and Drug Response Signature. Front Mol Biosci 2020; 7:564005. [PMID: 33344500 PMCID: PMC7746845 DOI: 10.3389/fmolb.2020.564005] [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: 05/20/2020] [Accepted: 10/15/2020] [Indexed: 11/30/2022] Open
Abstract
Breast cancer cell lines are frequently used to elucidate the molecular mechanisms of the disease. However, a large proportion of cell lines are affected by problems such as mislabeling and cross-contamination. Therefore, it is of great clinical significance to select optimal breast cancer cell lines models. Using tamoxifen survival-related genes from breast cancer tissues as the gold standard, we selected the optimal cell line model to represent the characteristics of clinical tissue samples. Moreover, using relative expression orderings of gene pairs, we developed a gene pair signature that could predict tamoxifen therapy outcomes. Based on 235 consistently identified survival-related genes from datasets GSE17705 and GSE6532, we found that only the differentially expressed genes (DEGs) from the cell line dataset GSE26459 were significantly reproducible in tissue samples (binomial test, p = 2.13E-07). Finally, using the consistent DEGs from cell line dataset GSE26459 and tissue samples, we used the transcriptional qualitative feature to develop a two-gene pair (TOP2A, SLC7A5; NMU, PDSS1) for predicting clinical tamoxifen resistance in the training data (logrank p = 1.98E-07); this signature was verified using an independent dataset (logrank p = 0.009909). Our results indicate that the cell line model from dataset GSE26459 provides a good representation of the characteristics of clinical tissue samples; thus, it will be a good choice for the selection of drug-resistant and drug-sensitive breast cancer cell lines in the future. Moreover, our signature could predict tamoxifen treatment outcomes in breast cancer patients.
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Affiliation(s)
- Qingzhou Guan
- Co-construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan & Education Ministry of P.R. China, Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, China
| | - Xuekun Song
- College of Information Technology, Henan University of Chinese Medicine, Zhengzhou, China
| | - Zhenzhen Zhang
- Co-construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan & Education Ministry of P.R. China, Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, China
| | - Yizhi Zhang
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Yating Chen
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Jing Li
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
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2
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Abstract
A central tenet in support of research reproducibility is the ability to uniquely identify research resources, i.e., reagents, tools, and materials that are used to perform experiments. However, current reporting practices for research resources are insufficient to identify the exact resources that are reported or to answer basic questions such as "How did other studies use resource X?" To address this issue, the Resource Identification Initiative was launched as a pilot project to improve the reporting standards for research resources in the methods sections of papers and thereby improve identifiability and scientific reproducibility. The pilot engaged over 25 biomedical journal editors from most major publishers, as well as scientists and funding officials. Authors were asked to include Research Resource Identifiers (RRIDs) in their manuscripts prior to publication for three resource types: antibodies, model organisms, and tools (i.e., software and databases). RRIDs are assigned by an authoritative database, for example a model organism database, for each type of resource. To make it easier for authors to obtain RRIDs, resources were aggregated from the appropriate databases and their RRIDs made available in a central web portal ( http://scicrunch.org/resources ). RRIDs meet three key criteria: they are machine readable, free to generate and access, and are consistent across publishers and journals. The pilot was launched in February of 2014 and over 300 papers have appeared that report RRIDs. The number of journals participating has expanded from the original 25 to more than 40 with RRIDs appearing in 62 different journals to date. Here, we present an overview of the pilot project and its outcomes to date. We show that authors are able to identify resources and are supportive of the goals of the project. Identifiability of the resources post-pilot showed a dramatic improvement for all three resource types, suggesting that the project has had a significant impact on identifiability of research resources.
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Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan SC, Washington N, Zudilova-Seinstra E, Vasilevsky N. The Resource Identification Initiative: A Cultural Shift in Publishing. J Comp Neurol 2016; 524:8-22. [PMID: 26599696 PMCID: PMC4684178 DOI: 10.1002/cne.23913] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 10/12/2015] [Indexed: 01/10/2023]
Abstract
A central tenet in support of research reproducibility is the ability to uniquely identify research resources, i.e., reagents, tools, and materials that are used to perform experiments. However, current reporting practices for research resources are insufficient to identify the exact resources that are reported or to answer basic questions such as “How did other studies use resource X?” To address this issue, the Resource Identification Initiative was launched as a pilot project to improve the reporting standards for research resources in the Methods sections of articles and thereby improve identifiability and scientific reproducibility. The pilot engaged over 25 biomedical journal editors from most major publishers, as well as scientists and funding officials. Authors were asked to include Research Resource Identifiers (RRIDs) in their articles prior to publication for three resource types: antibodies, model organisms, and tools (i.e., software and databases). RRIDs are assigned by an authoritative database, for example, a model organism database for each type of resource. To make it easier for authors to obtain RRIDs, resources were aggregated from the appropriate databases and their RRIDs made available in a central Web portal (http://scicrunch.org/resources). RRIDs meet three key criteria: they are machine‐readable, free to generate and access, and are consistent across publishers and journals. The pilot was launched in February of 2014 and over 300 articles have appeared that report RRIDs. The number of journals participating has expanded from the original 25 to more than 40, with RRIDs appearing in 62 different journals to date. Here we present an overview of the pilot project and its outcomes to date. We show that authors are able to identify resources and are supportive of the goals of the project. Identifiability of the resources post‐pilot showed a dramatic improvement for all three resource types, suggesting that the project has had a significant impact on identifiability of research resources. J. Comp. Neurol. 524:8–22, 2016. © 2015 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Anita Bandrowski
- Center for Research in Biological Systems, UCSD, La Jolla, California, USA
| | - Matthew Brush
- Oregon Health & Science University (OHSU) Library, Department of Medical Informatics & Clinical Epidemiology, Portland, Oregon, USA
| | - Jeffery S Grethe
- Center for Research in Biological Systems, UCSD, La Jolla, California, USA
| | - Melissa A Haendel
- Oregon Health & Science University (OHSU) Library, Department of Medical Informatics & Clinical Epidemiology, Portland, Oregon, USA
| | - David N Kennedy
- University of Massachusetts Medical School, Department of Psychiatry, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Sean Hill
- Karolinska Institutet, Stockholm, Sweden
| | - Patrick R Hof
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Maryann E Martone
- Center for Research in Biological Systems, UCSD, La Jolla, California, USA
| | | | | | | | | | - Nicole Vasilevsky
- Oregon Health & Science University (OHSU) Library, Department of Medical Informatics & Clinical Epidemiology, Portland, Oregon, USA
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4
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Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan SC, Washington N, Zudilova-Seinstra E, Vasilevsky N. The Resource Identification Initiative: a cultural shift in publishing. Brain Behav 2016; 6:e00417. [PMID: 27110440 PMCID: PMC4834942 DOI: 10.1002/brb3.417] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
A central tenet in support of research reproducibility is the ability to uniquely identify research resources, that is, reagents, tools, and materials that are used to perform experiments. However, current reporting practices for research resources are insufficient to identify the exact resources that are reported or to answer basic questions such as "How did other studies use resource X?" To address this issue, the Resource Identification Initiative was launched as a pilot project to improve the reporting standards for research resources in the methods sections of papers and thereby improve identifiability and scientific reproducibility. The pilot engaged over 25 biomedical journal editors from most major publishers, as well as scientists and funding officials. Authors were asked to include Research Resource Identifiers (RRIDs) in their manuscripts prior to publication for three resource types: antibodies, model organisms, and tools (i.e., software and databases). RRIDs are assigned by an authoritative database, for example, a model organism database for each type of resource. To make it easier for authors to obtain RRIDs, resources were aggregated from the appropriate databases and their RRIDs made available in a central web portal ( http://scicrunch.org/resources). RRIDs meet three key criteria: they are machine readable, free to generate and access, and are consistent across publishers and journals. The pilot was launched in February of 2014 and over 300 papers have appeared that report RRIDs. The number of journals participating has expanded from the original 25 to more than 40 with RRIDs appearing in 62 different journals to date. Here, we present an overview of the pilot project and its outcomes to date. We show that authors are able to identify resources and are supportive of the goals of the project. Identifiability of the resources post-pilot showed a dramatic improvement for all three resource types, suggesting that the project has had a significant impact on identifiability of research resources.
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Affiliation(s)
- Anita Bandrowski
- Center for Research in Biological Systems UCSD 9500 Gillman Dr.#0446 la Jolla California 92093-0446
| | - Matthew Brush
- Department of Medical Informatics & Clinical Epidemiology OHSU Library Oregon Health and Science University 3181 SW Sam Jackson Park Road Portland, Oregon 97239 USA
| | - Jeffery S Grethe
- Center for Research in Biological Systems UCSD 9500 Gillman Dr.#0446 la Jolla California 92093-0446
| | - Melissa A Haendel
- Department of Medical Informatics & Clinical Epidemiology OHSU Library Oregon Health and Science University 3181 SW Sam Jackson Park Road Portland, Oregon 97239 USA
| | - David N Kennedy
- Department of Psychiatry University of Massachusetts Medical School 365 Plantation Street Biotech One Worcester Massachusetts 01605
| | - Sean Hill
- INCF Karolinska Institutet Nobels väg 15A 171 77 Stockholm Sweden
| | - Patrick R Hof
- Department of Neuroscience Hess CSM Building Floor 10 Room 118 1470 Madison Avenue New York City New York 10029
| | - Maryann E Martone
- Center for Research in Biological Systems UCSD 9500 Gillman Dr.#0446 la Jolla California 92093-0446
| | - Maaike Pols
- Scientific Outreach Executive Faculty of 1000 Ltd Middlesex House 34-42, Cleveland Street London W1T 4LB UK
| | - Serena C Tan
- John Wiley and Sons 11 River St Hoboken New Jersey 07030
| | - Nicole Washington
- Lawrence Berkeley National Laboratory 1 Cyclotron Road Berkeley California 94720
| | | | - Nicole Vasilevsky
- Department of Medical Informatics & Clinical Epidemiology OHSU Library Oregon Health and Science University 3181 SW Sam Jackson Park Road Portland, Oregon 97239 USA
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Wu X, Deng L, Tang D, Ying G, Yao X, Liu F, Liang G. miR-615-5p prevents proliferation and migration through negatively regulating serine hydromethyltransferase 2 (SHMT2) in hepatocellular carcinoma. Tumour Biol 2015; 37:6813-21. [PMID: 26662310 DOI: 10.1007/s13277-015-4506-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 11/24/2015] [Indexed: 01/13/2023] Open
Abstract
It has been reported that miR-615-5p was upregulated in hepatocellular carcinoma (HCC) preventing both growth and migration. However, the underlying mechanism by which miR-615-5p played a role in HCC remains unknown. Here, in our present study, to investigate the mechanism of miR-615-5p, bioinformatic prediction and luciferase reporter assay were employed to ascertain the downstream target of miR-615-5p finding that the serine hydromethyltransferase 2 (SHMT2) was the direct downstream target. Knockdown or overexpression of miR-615-5p can lead to increasing or decreasing expression of SHMT2 in HCC cells. Besides, knockdown or overexpression of SHMT2 can suppress or promote both proliferation and migration of HCC cells, indicating that miR-615-5p can directly and negatively regulate the SHMT2 in HCC cells. In addition, to understand the clinicopathological significance of SHMT2 expression in HCC, immunohistochemistry was performed. It was found that SHMT2 expression was significantly associated with poor prognosis and TNM stage. Together, our results for the first time showed that miR-615-5p prevents proliferation and migration through negatively regulating SHMT2 in HCC.
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Affiliation(s)
- Xiaoyu Wu
- Department of Surgical Oncology, Affiliated Hospital of Nanjing University of Traditional Chinese Medicine, 155 Hanzhong Road, Nanjing, 210029, China
| | - Liang Deng
- Department of Hepatobiliary Surgery, the Eastern Hospital of the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510700, China., Sun Yat-sen University, Guangzhou, 510700, People's Republic of China
| | - Decai Tang
- Nanjing University of Traditional Chinese Medicine, 282 Hanzhong Road, Nanjing, 210029, China
| | - Gang Ying
- Nanjing University of Traditional Chinese Medicine, 282 Hanzhong Road, Nanjing, 210029, China
| | - Xuequan Yao
- Nanjing University of Traditional Chinese Medicine, 282 Hanzhong Road, Nanjing, 210029, China
| | - Fukun Liu
- Nanjing University of Traditional Chinese Medicine, 282 Hanzhong Road, Nanjing, 210029, China
| | - Gui Liang
- Department of General Surgery, Jiangsu Cancer Hospital, The Affiliated Cancer Hospital of Nanjing Medical University, 42 Baiziting, Nanjing, 210009, China.
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6
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Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan S, Washington N, Zudilova-Seinstra E, Vasilevsky N. The Resource Identification Initiative: A cultural shift in publishing. F1000Res 2015; 4:134. [PMID: 26594330 DOI: 10.12688/f1000research.6555.1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/26/2015] [Indexed: 01/10/2023] Open
Abstract
A central tenet in support of research reproducibility is the ability to uniquely identify research resources, i.e., reagents, tools, and materials that are used to perform experiments. However, current reporting practices for research resources are insufficient to allow humans and algorithms to identify the exact resources that are reported or answer basic questions such as "What other studies used resource X?" To address this issue, the Resource Identification Initiative was launched as a pilot project to improve the reporting standards for research resources in the methods sections of papers and thereby improve identifiability and reproducibility. The pilot engaged over 25 biomedical journal editors from most major publishers, as well as scientists and funding officials. Authors were asked to include Research Resource Identifiers (RRIDs) in their manuscripts prior to publication for three resource types: antibodies, model organisms, and tools (including software and databases). RRIDs represent accession numbers assigned by an authoritative database, e.g., the model organism databases, for each type of resource. To make it easier for authors to obtain RRIDs, resources were aggregated from the appropriate databases and their RRIDs made available in a central web portal ( www.scicrunch.org/resources). RRIDs meet three key criteria: they are machine readable, free to generate and access, and are consistent across publishers and journals. The pilot was launched in February of 2014 and over 300 papers have appeared that report RRIDs. The number of journals participating has expanded from the original 25 to more than 40. Here, we present an overview of the pilot project and its outcomes to date. We show that authors are generally accurate in performing the task of identifying resources and supportive of the goals of the project. We also show that identifiability of the resources pre- and post-pilot showed a dramatic improvement for all three resource types, suggesting that the project has had a significant impact on reproducibility relating to research resources.
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Affiliation(s)
- Anita Bandrowski
- Center for Research in Biological Systems, UCSD, la Jolla, CA, 92093, USA
| | - Matthew Brush
- Department of Medical Informatics & Clinical Epidemiology, OHSU, Portland, Oregon, 97239, USA
| | - Jeffery S Grethe
- Center for Research in Biological Systems, UCSD, la Jolla, CA, 92093, USA
| | - Melissa A Haendel
- Department of Medical Informatics & Clinical Epidemiology, OHSU, Portland, Oregon, 97239, USA
| | - David N Kennedy
- Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Sean Hill
- Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Patrick R Hof
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Maryann E Martone
- Center for Research in Biological Systems, UCSD, la Jolla, CA, 92093, USA
| | - Maaike Pols
- Scientific Outreach, Faculty of 1000 Ltd, London, W1T 4LB, UK
| | - Serena Tan
- John Wiley and Sons, Hoboken, NJ, 07030, USA
| | - Nicole Washington
- Lawrence Berkeley National Laboratory, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | | | - Nicole Vasilevsky
- Department of Medical Informatics & Clinical Epidemiology, OHSU, Portland, Oregon, 97239, USA
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7
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Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan S, Washington N, Zudilova-Seinstra E, Vasilevsky N. The Resource Identification Initiative: A cultural shift in publishing. F1000Res 2015; 4:134. [PMID: 26594330 PMCID: PMC4648211 DOI: 10.12688/f1000research.6555.2] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/25/2015] [Indexed: 11/20/2022] Open
Abstract
A central tenet in support of research reproducibility is the ability to uniquely identify research resources, i.e., reagents, tools, and materials that are used to perform experiments. However, current reporting practices for research resources are insufficient to allow humans and algorithms to identify the exact resources that are reported or answer basic questions such as “What other studies used resource X?” To address this issue, the Resource Identification Initiative was launched as a pilot project to improve the reporting standards for research resources in the methods sections of papers and thereby improve identifiability and reproducibility. The pilot engaged over 25 biomedical journal editors from most major publishers, as well as scientists and funding officials. Authors were asked to include Research Resource Identifiers (RRIDs) in their manuscripts prior to publication for three resource types: antibodies, model organisms, and tools (including software and databases). RRIDs represent accession numbers assigned by an authoritative database, e.g., the model organism databases, for each type of resource. To make it easier for authors to obtain RRIDs, resources were aggregated from the appropriate databases and their RRIDs made available in a central web portal (
www.scicrunch.org/resources). RRIDs meet three key criteria: they are machine readable, free to generate and access, and are consistent across publishers and journals. The pilot was launched in February of 2014 and over 300 papers have appeared that report RRIDs. The number of journals participating has expanded from the original 25 to more than 40. Here, we present an overview of the pilot project and its outcomes to date. We show that authors are generally accurate in performing the task of identifying resources and supportive of the goals of the project. We also show that identifiability of the resources pre- and post-pilot showed a dramatic improvement for all three resource types, suggesting that the project has had a significant impact on reproducibility relating to research resources.
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Affiliation(s)
- Anita Bandrowski
- Center for Research in Biological Systems, UCSD, la Jolla, CA, 92093, USA
| | - Matthew Brush
- Department of Medical Informatics & Clinical Epidemiology, OHSU, Portland, Oregon, 97239, USA
| | - Jeffery S Grethe
- Center for Research in Biological Systems, UCSD, la Jolla, CA, 92093, USA
| | - Melissa A Haendel
- Department of Medical Informatics & Clinical Epidemiology, OHSU, Portland, Oregon, 97239, USA
| | - David N Kennedy
- Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Sean Hill
- Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Patrick R Hof
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Maryann E Martone
- Center for Research in Biological Systems, UCSD, la Jolla, CA, 92093, USA
| | - Maaike Pols
- Scientific Outreach, Faculty of 1000 Ltd, London, W1T 4LB, UK
| | - Serena Tan
- John Wiley and Sons, Hoboken, NJ, 07030, USA
| | - Nicole Washington
- Lawrence Berkeley National Laboratory, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | | | - Nicole Vasilevsky
- Department of Medical Informatics & Clinical Epidemiology, OHSU, Portland, Oregon, 97239, USA
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