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Huang J, Demmler R, Mohamed Abdou M, Thoma OM, Weigmann B, Waldner MJ, Stürzl M, Naschberger E. Rapid qPCR-based quantitative immune cell phenotyping in mouse tissues. J Investig Med 2024; 72:47-56. [PMID: 37858974 DOI: 10.1177/10815589231210497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
The immune microenvironment plays an important role in the regulation of diseases. The characterization of the cellular composition of immune cell infiltrates in diseases and respective models is a major task in pathogenesis research and diagnostics. For the assessment of immune cell populations in tissues, fluorescence-activated cell sorting (FACS) or immunohistochemistry (IHC) are the two most common techniques presently applied, but they are cost intensive, laborious, and sometimes limited by the availability of suitable antibodies. Complementary rapid qPCR-based approaches exist for the human situation but are lacking for experimental mouse models. Accordingly, we developed a robust, rapid RT-qPCR-based approach to determine and quantify the abundance of prominent immune cell populations such as T cells, helper T (Th) cells, cytotoxic T cells, Th1 cells, B cells, and macrophages in mouse tissues. The results were independently validated by the gold standards IHC and FACS in corresponding tissues and showed high concordance.
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Affiliation(s)
- Jinghao Huang
- Division of Molecular and Experimental Surgery, Translational Research Center, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Richard Demmler
- Division of Molecular and Experimental Surgery, Translational Research Center, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Mariam Mohamed Abdou
- Division of Molecular and Experimental Surgery, Translational Research Center, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Oana-Maria Thoma
- Department of Medicine 1, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Benno Weigmann
- Department of Medicine 1, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
- Medical Immunology Campus Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Maximilian J Waldner
- Department of Medicine 1, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Michael Stürzl
- Division of Molecular and Experimental Surgery, Translational Research Center, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Elisabeth Naschberger
- Division of Molecular and Experimental Surgery, Translational Research Center, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN, Universitätsklinikum Erlangen, Erlangen, Germany
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2
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Iwasaki T, Tokumori M, Matsubara M, Ojima F, Kamigochi K, Aizawa S, Ogoshi M, Kimura AP, Takeuchi S, Takahashi S. A regulatory mechanism of mouse kallikrein 1 gene expression by estrogen. Mol Cell Endocrinol 2023; 577:112044. [PMID: 37580010 DOI: 10.1016/j.mce.2023.112044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 08/16/2023]
Abstract
Tissue kallikrein 1 (Klk1) is a serine protease that degrades several proteins including insulin-like growth factor binding protein-3 and extracellular matrix molecules. Klk1 mRNA expression in the mouse uterus was increased by estradiol-17β (E2). The present study aimed to clarify the regulatory mechanism for Klk1 expression by estrogen. The promoter analysis of the 5'-flanking region of Klk1 showed that the minimal promoter of Klk1 existed in the -136/+24 region, and the estrogen-responsive region in the -433/-136 region. Tamoxifen increased Klk1 mRNA expression and the promoter activity, suggesting the involvement of AP-1 sites. Site-directed mutagenesis for the putative AP-1 sites in the -433/-136 region showed that the two putative AP-1 sites were involved in the regulation of Klk1 expression. Binding of estrogen receptor α (ERα) to the -433/-136 region was revealed by Chip assay. These results indicated that ERα bound the two putative AP-1 sites and transactivated Klk1 in the mouse uterus.
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Affiliation(s)
- Takumi Iwasaki
- Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Megumi Tokumori
- Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Misaki Matsubara
- Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Fumiya Ojima
- Department of Natural Sciences and Biology, Kawasaki Medical School, Kurashiki, 701-0192, Japan
| | - Kana Kamigochi
- Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Sayaka Aizawa
- Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Maho Ogoshi
- Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Atsushi P Kimura
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Sakae Takeuchi
- Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Sumio Takahashi
- Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan.
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3
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Sultana A, Alam MS, Liu X, Sharma R, Singla RK, Gundamaraju R, Shen B. Single-cell RNA-seq analysis to identify potential biomarkers for diagnosis, and prognosis of non-small cell lung cancer by using comprehensive bioinformatics approaches. Transl Oncol 2022; 27:101571. [PMID: 36401966 PMCID: PMC9676382 DOI: 10.1016/j.tranon.2022.101571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 10/12/2022] [Accepted: 10/24/2022] [Indexed: 11/18/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) is the most common type of lung cancer and the leading cause of cancer-related deaths worldwide. Identification of gene biomarkers and their regulatory factors and signaling pathways is very essential to reveal the molecular mechanisms of NSCLC initiation and progression. Thus, the goal of this study is to identify gene biomarkers for NSCLC diagnosis and prognosis by using scRNA-seq data through bioinformatics techniques. scRNA-seq data were obtained from the GEO database to identify DEGs. A total of 158 DEGs (including 48 upregulated and 110 downregulated) were detected after gene integration. Gene Ontology enrichment and KEGG pathway analysis of DEGs were performed by FunRich software. A PPI network of DEGs was then constructed using the STRING database and visualized by Cytoscape software. We identified 12 key genes (KGs) including MS4A1, CCL5, and GZMB, by using two topological methods based on the PPI networking results. The diagnostic, expression, and prognostic potentials of the identified 12 key genes were assessed using the receiver operating characteristics (ROC) curve and a web-based tool, SurvExpress. From the regulatory network analysis, we extracted the 7 key transcription factors (TFs) (FOXC1, YY1, CEBPB, TFAP2A, SREBF2, RELA, and GATA2), and 8 key miRNAs (hsa-miR-124-3p, hsa-miR-34a-5p, hsa-miR-21-5p, hsa-miR-155-5p, hsa-miR-449a, hsa-miR-24-3p, hsa-let-7b-5p, and hsa-miR-7-5p) associated with the KGs were evaluated. Functional enrichment and pathway analysis, survival analysis, ROC analysis, and regulatory network analysis highlighted crucial roles of the key genes. Our findings might play a significant role as candidate biomarkers in NSCLC diagnosis and prognosis.
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Affiliation(s)
- Adiba Sultana
- School of Biology and Basic Medical Sciences, Soochow University Medical College, 199 Ren'ai Road, Suzhou 215123, China; Center for Systems Biology, Soochow University, Suzhou 215006, China; Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Xinchuan Road 2222, Chengdu, Sichuan, China
| | - Md Shahin Alam
- School of Biology and Basic Medical Sciences, Soochow University Medical College, 199 Ren'ai Road, Suzhou 215123, China
| | - Xingyun Liu
- Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Xinchuan Road 2222, Chengdu, Sichuan, China
| | - Rohit Sharma
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India.
| | - Rajeev K Singla
- Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Xinchuan Road 2222, Chengdu, Sichuan, China; School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab 144411, India.
| | - Rohit Gundamaraju
- ER Stress and Mucosal Immunology Lab, School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, Tasmania, TAS 7248, Australia
| | - Bairong Shen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Xinchuan Road 2222, Chengdu, Sichuan, China.
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Dynamic Expression of the Homeobox Factor PBX1 during Mouse Testis Development. ENDOCRINES 2022. [DOI: 10.3390/endocrines3010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Members of the pre-B-cell leukemia transcription factor (PBX) family of homeoproteins are mainly known for their involvement in hematopoietic cell differentiation and in the development of leukemia. The four PBX proteins, PBX1, PBX2, PBX3 and PBX4, belong to the three amino acid loop extension (TALE) superfamily of homeoproteins which are important transcriptional cofactors in several developmental processes involving homeobox (HOX) factors. Mutations in the human PBX1 gene are responsible for cases of gonadal dysgenesis with absence of male sex differentiation while Pbx1 inactivation in the mouse causes a failure in Leydig cell differentiation and function. However, no data is available regarding the expression profile of this transcription factor in the testis. To fill this knowledge gap, we have characterized PBX1 expression during mouse testicular development. Real time PCRs and Western blots confirmed the presence Pbx1 mRNA and PBX1 protein in different Leydig and Sertoli cell lines. The cellular localization of the PBX1 protein was determined by immunohistochemistry and immunofluorescence on mouse testis sections at different embryonic and postnatal developmental stages. PBX1 was detected in interstitial cells and in peritubular myoid cells from embryonic life until puberty. Most interstitial cells expressing PBX1 do not express the Leydig cell marker CYP17A1, indicating that they are not differentiated and steroidogenically active Leydig cells. In adults, PBX1 was mainly detected in Sertoli cells. The presence of PBX1 in different somatic cell populations during testicular development further supports a direct role for this transcription factor in testis cell differentiation and in male reproductive function.
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García-Pérez O, Melgar-Vilaplana L, Córdoba-Lanús E, Fernández-de-Misa R. Gene Expression Studies in Formalin-Fixed Paraffin-Embedded Samples of Cutaneous Cancer: The Need for Reference Genes. Curr Issues Mol Biol 2021; 43:2167-2176. [PMID: 34940125 PMCID: PMC8928935 DOI: 10.3390/cimb43030151] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/27/2021] [Accepted: 11/29/2021] [Indexed: 01/02/2023] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) tumour samples may provide crucial data regarding biomarkers for neoplasm progression. Analysis of gene expression is frequently used for this purpose. Therefore, mRNA expression needs to be normalized through comparison to reference genes. In this study, we establish which of the usually reported reference genes is the most reliable one in cutaneous malignant melanoma (MM) and cutaneous squamous cell carcinoma (CSCC). ACTB, TFRC, HPRT1 and TBP expression was quantified in 123 FFPE samples (74 MM and 49 CSCC biopsies) using qPCR. Expression stability was analysed by NormFinder and Bestkeeper softwares, and the direct comparison method between means and SD. The in-silico analysis with BestKeeper indicated that HPRT1 was more stable than ACTB and TFRC in MM (1.85 vs. 2.15) and CSCC tissues (2.09 vs. 2.33). The best option to NormFinder was ACTB gene (0.56) in MM and TFRC (0.26) in CSCC. The direct comparison method showed lower SD means of ACTB expression in MM (1.17) and TFRC expression in CSCC samples (1.00). When analysing the combination of two reference genes for improving stability, NormFinder indicated HPRT1 and ACTB to be the best for MM samples, and HPRT1 and TFRC genes for CSCC. In conclusion, HPRT1 and ACTB genes in combination are the most appropriate choice for normalization in gene expression studies in MM FFPE tissue, while the combination of HPRT1 and TFRC genes are the best option in analysing CSCC FFPE samples. These may be used consistently in forthcoming studies on gene expression in both tumours.
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Affiliation(s)
- Omar García-Pérez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Ctra. Gral. del Rosario, 145, 38010 Santa Cruz de Tenerife, Spain;
- Universidad de La Laguna, Calle Padre Herrera, s/n, 38200 San Cristóbal de La Laguna, Spain
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC), 38296 San Cristóbal de La Laguna, Spain
| | - Leticia Melgar-Vilaplana
- Pathology Department, Hospital Universitario Nuestra Señora de Candelaria, Ctra. Gral. del Rosario, 145, 38010 Santa Cruz de Tenerife, Spain;
| | - Elizabeth Córdoba-Lanús
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Ctra. Gral. del Rosario, 145, 38010 Santa Cruz de Tenerife, Spain;
- Universidad de La Laguna, Calle Padre Herrera, s/n, 38200 San Cristóbal de La Laguna, Spain
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC), 38296 San Cristóbal de La Laguna, Spain
- Correspondence: (E.C.-L.); (R.F.-d.-M.)
| | - Ricardo Fernández-de-Misa
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Ctra. Gral. del Rosario, 145, 38010 Santa Cruz de Tenerife, Spain;
- Universidad de La Laguna, Calle Padre Herrera, s/n, 38200 San Cristóbal de La Laguna, Spain
- Dermatology Department, Hospital Universitario Nuestra Señora de Candelaria, Ctra. Gral. del Rosario, 145, 38010 Santa Cruz de Tenerife, Spain
- Correspondence: (E.C.-L.); (R.F.-d.-M.)
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6
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Systematic Identification and Validation of Housekeeping and Tissue-Specific Genes in Allotetraploid Chenopodium quinoa. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7080235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Quinoa is a gluten-free food crop that contains all the essential amino acids and vitamins. The selection of proper housekeeping and tissue-specific genes is the crucial prerequisite for gene expression analysis using the common approach, real-time quantitative PCR (RT-qPCR). In this study, we identified 40 novel candidate housekeeping genes by the minimum transcript per million (TPM), coefficient of variation (CV) and maximum fold change (MFC) methods and 19 candidate tissue-specific genes by the co-expression network method based on an RNA-seq dataset that included 53 stem, leaf, flower and seed samples, as well as additional shoot and root samples under different stresses. The expression stability of 12 housekeeping and tissue-specific genes, as well as that of another two traditionally used housekeeping genes, was further evaluated using qPCR and ranked using NormFinder, BestKeeper and the comparative delta-Ct method. The results demonstrated that MIF, RGGA, VATE and UBA2B were ranked as the top four most stable candidate housekeeping genes. qPCR analysis also revealed three leaf-specific genes and five root-specific genes, but no stem-specific gene was identified. Gene Ontology (GO) enrichment analysis identified that housekeeping genes were mainly enriched in the small molecule metabolic process, organonitrogen compound metabolic process, NAD binding and ligase activity. In addition, tissue-specific genes are closely associated with the major functions of a specific tissue. Specifically, GO terms “photosynthesis” and “thylakoid” were most significantly overrepresented in candidate leaf-specific genes. The novel housekeeping and tissue-specific genes in our study will enable better normalization and quantification of transcript levels in quinoa.
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Huang CY, Liao KW, Chou CH, Shrestha S, Yang CD, Chiew MY, Huang HT, Hong HC, Huang SH, Chang TH, Huang HD. Pilot Study to Establish a Novel Five-Gene Biomarker Panel for Predicting Lymph Node Metastasis in Patients With Early Stage Endometrial Cancer. Front Oncol 2020; 9:1508. [PMID: 32039004 PMCID: PMC6985442 DOI: 10.3389/fonc.2019.01508] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 12/16/2019] [Indexed: 12/27/2022] Open
Abstract
Introduction: In the United States and Europe, endometrial endometrioid carcinoma (EEC) is the most prevalent gynecologic malignancy. Lymph node metastasis (LNM) is the key determinant of the prognosis and treatment of EEC. A biomarker that predicts LNM in patients with EEC would be beneficial, enabling individualized treatment. Current preoperative assessment of LNM in EEC is not sufficiently accurate to predict LNM and prevent overtreatment. This pilot study established a biomarker signature for the prediction of LNM in early stage EEC. Methods: We performed RNA sequencing in 24 clinically early stage (T1) EEC tumors (lymph nodes positive and negative in 6 and 18, respectively) from Cathay General Hospital and analyzed the RNA sequencing data of 289 patients with EEC from The Cancer Genome Atlas (lymph node positive and negative in 33 and 256, respectively). We analyzed clinical data including tumor grade, depth of tumor invasion, and age to construct a sequencing-based prediction model using machine learning. For validation, we used another independent cohort of early stage EEC samples (n = 72) and performed quantitative real-time polymerase chain reaction (qRT-PCR). Finally, a PCR-based prediction model and risk score formula were established. Results: Eight genes (ASRGL1, ESR1, EYA2, MSX1, RHEX, SCGB2A1, SOX17, and STX18) plus one clinical parameter (depth of myometrial invasion) were identified for use in a sequencing-based prediction model. After qRT-PCR validation, five genes (ASRGL1, RHEX, SCGB2A1, SOX17, and STX18) were identified as predictive biomarkers. Receiver operating characteristic curve analysis revealed that these five genes can predict LNM. Combined use of these five genes resulted in higher diagnostic accuracy than use of any single gene, with an area under the curve of 0.898, sensitivity of 88.9%, and specificity of 84.1%. The accuracy, negative, and positive predictive values were 84.7, 98.1, and 44.4%, respectively. Conclusion: We developed a five-gene biomarker panel associated with LNM in early stage EEC. These five genes may represent novel targets for further mechanistic study. Our results, after corroboration by a prospective study, may have useful clinical implications and prevent unnecessary elective lymph node dissection while not adversely affecting the outcome of treatment for early stage EEC.
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Affiliation(s)
- Chia-Yen Huang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan.,Department of Obstetrics and Gynecology, Gynecologic Cancer Center, Cathay General Hospital, Taipei, Taiwan.,School of Medicine, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Kuang-Wen Liao
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan.,Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, Taiwan
| | - Chih-Hung Chou
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan.,Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Chiao Tung University, Hsinchu, Taiwan.,Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Sirjana Shrestha
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | - Chi-Dung Yang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan.,School of Life and Health Sciences, Chinese University of Hong Kong, Shenzhen, China.,Warshel Institute for Computational Biology, Chinese University of Hong Kong, Shenzhen, China
| | - Men-Yee Chiew
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | - Hsin-Tzu Huang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | - Hsiao-Chin Hong
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan.,Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan.,School of Life and Health Sciences, Chinese University of Hong Kong, Shenzhen, China.,Warshel Institute for Computational Biology, Chinese University of Hong Kong, Shenzhen, China
| | - Shih-Hung Huang
- Department of Pathology, Cathay General Hospital, Taipei, Taiwan
| | - Tzu-Hao Chang
- International Center for Health Information Technology, Taipei Medical University, Taipei, Taiwan.,Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Hsien-Da Huang
- School of Life and Health Sciences, Chinese University of Hong Kong, Shenzhen, China.,Warshel Institute for Computational Biology, Chinese University of Hong Kong, Shenzhen, China
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8
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Desul S, N. MM, Venkatesh T, Gunta V, R. G, Sai Baba M. Method for automatic key concepts extraction. ELECTRONIC LIBRARY 2018. [DOI: 10.1108/el-01-2018-0012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Purpose
Ontology of a domain mainly consists of a set of concepts and their semantic relations. It is typically constructed and maintained by using ontology editors with substantial human intervention. It is desirable to perform the task automatically, which has led to the development of ontology learning techniques. One of the main challenges of ontology learning from the text is to identify key concepts from the documents. A wide range of techniques for key concept extraction have been proposed but are having the limitations of low accuracy, poor performance, not so flexible and applicability to a specific domain. The propose of this study is to explore a new method to extract key concepts and to apply them to literature in the nuclear domain.
Design/methodology/approach
In this article, a novel method for key concept extraction is proposed and applied to the documents from the nuclear domain. A hybrid approach was used, which includes a combination of domain, syntactic name entity knowledge and statistical based methods. The performance of the developed method has been evaluated from the data obtained using two out of three voting logic from three domain experts by using 120 documents retrieved from SCOPUS database.
Findings
The work reported pertains to extracting concepts from the set of selected documents and aids the search for documents relating to given concepts. The results of a case study indicated that the method developed has demonstrated better metrics than Text2Onto and CFinder. The method described has the capability of extracting valid key concepts from a set of candidates with long phrases.
Research limitations/implications
The present study is restricted to literature coming out in the English language and applied to the documents from nuclear domain. It has the potential to extend to other domains also.
Practical implications
The work carried out in the current study has the potential of leading to updating International Nuclear Information System thesaurus for ontology in the nuclear domain. This can lead to efficient search methods.
Originality/value
This work is the first attempt to automatically extract key concepts from the nuclear documents. The proposed approach will address and fix the most of the problems that are existed in the current methods and thereby increase the performance.
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9
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Schulze F, Malhan D, El Khassawna T, Heiss C, Seckinger A, Hose D, Rösen-Wolff A. A tissue-based approach to selection of reference genes for quantitative real-time PCR in a sheep osteoporosis model. BMC Genomics 2017; 18:975. [PMID: 29258442 PMCID: PMC5735898 DOI: 10.1186/s12864-017-4356-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 11/29/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In order to better understand the multifactorial nature of osteoporosis, animal models are utilized and compared to healthy controls. Female sheep are well established as a model for osteoporosis induced by ovariectomy, calcium and vitamin D low diet, application of steroids, or a combination of these treatments. Transcriptional studies can be performed by applying quantitative real time PCR (RT-qPCR). RT-qPCR estimates mRNA-levels of target genes in relation to reference genes. A chosen set of reference genes should not show variation under experimental conditions. Currently, no standard reference genes are accepted for all tissue types and experimental conditions. Studies examining reference genes for sheep are rare and only one study described stable reference in mandibular bone. However, this type of bone differs from trabecular bone where most osteoporotic fractures occur. The present study aimed at identifying a set of reference genes for relative quantification of transcriptional activity of ovine spine bone and ovine in vitro differentiated mesenchymal stromal cells (MSC) for reliable comparability. METHODS Twelve candidate reference genes belonging to different functional classes were selected and their expression was measured from cultured ovMSCs (n = 18) and ovine bone samples (n = 16), respectively. RefFinder was used to rank the candidate genes. RESULTS We identified B2M, GAPDH, RPL19 and YWHAZ as the best combination of reference genes for normalization of RT-qPCR results for transcriptional analyses of these ovine samples. CONCLUSION This study demonstrates the importance of applying a set of reference genes for RT-qPCR analysis in sheep. Based on our data we recommend using four identified reference genes for relative quantification of gene expression studies in ovine bone or for in vitro experiments with osteogenically differentiated ovine MSCs.
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Affiliation(s)
- Felix Schulze
- Department of Pediatrics, University Hospital Carl Gustav Carus, TU Dresden, Fetscherstraße 74, 01307, Dresden, Germany
| | - Deeksha Malhan
- Experimental Trauma Surgery, Justus-Liebig University, Aulweg 128, 35392, Giessen, Germany
| | - Thaqif El Khassawna
- Experimental Trauma Surgery, Justus-Liebig University, Aulweg 128, 35392, Giessen, Germany
| | - Christian Heiss
- Experimental Trauma Surgery, Justus-Liebig University, Aulweg 128, 35392, Giessen, Germany.,Department of Trauma, Hand and Reconstructive Surgery, University Hospital of Giessen-Marburg, Rudolf-Buchheim-Strasse 7, 35385, Giessen, Germany
| | - Anja Seckinger
- Labor für Myelomforschung, Medizinische Klinik V, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
| | - Dirk Hose
- Labor für Myelomforschung, Medizinische Klinik V, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
| | - Angela Rösen-Wolff
- Department of Pediatrics, University Hospital Carl Gustav Carus, TU Dresden, Fetscherstraße 74, 01307, Dresden, Germany.
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10
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Hoang VLT, Tom LN, Quek XC, Tan JM, Payne EJ, Lin LL, Sinnya S, Raphael AP, Lambie D, Frazer IH, Dinger ME, Soyer HP, Prow TW. RNA-seq reveals more consistent reference genes for gene expression studies in human non-melanoma skin cancers. PeerJ 2017; 5:e3631. [PMID: 28852586 PMCID: PMC5572537 DOI: 10.7717/peerj.3631] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 07/11/2017] [Indexed: 11/20/2022] Open
Abstract
Identification of appropriate reference genes (RGs) is critical to accurate data interpretation in quantitative real-time PCR (qPCR) experiments. In this study, we have utilised next generation RNA sequencing (RNA-seq) to analyse the transcriptome of a panel of non-melanoma skin cancer lesions, identifying genes that are consistently expressed across all samples. Genes encoding ribosomal proteins were amongst the most stable in this dataset. Validation of this RNA-seq data was examined using qPCR to confirm the suitability of a set of highly stable genes for use as qPCR RGs. These genes will provide a valuable resource for the normalisation of qPCR data for the analysis of non-melanoma skin cancer.
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Affiliation(s)
- Van L T Hoang
- Dermatology Research Centre, Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, The University of Queensland, Brisbane, Queensland, Australia
| | - Lisa N Tom
- Dermatology Research Centre, Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, The University of Queensland, Brisbane, Queensland, Australia
| | - Xiu-Cheng Quek
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia.,St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Jean-Marie Tan
- Dermatology Research Centre, Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, The University of Queensland, Brisbane, Queensland, Australia
| | - Elizabeth J Payne
- Dermatology Research Centre, Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, The University of Queensland, Brisbane, Queensland, Australia
| | - Lynlee L Lin
- Dermatology Research Centre, Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, The University of Queensland, Brisbane, Queensland, Australia
| | - Sudipta Sinnya
- Dermatology Research Centre, Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, The University of Queensland, Brisbane, Queensland, Australia
| | - Anthony P Raphael
- Dermatology Research Centre, Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, The University of Queensland, Brisbane, Queensland, Australia.,Wellman Center for Photomedicine, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - Duncan Lambie
- Department of Anatomical Pathology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Ian H Frazer
- Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, The University of Queensland, Brisbane, Queensland, Australia
| | - Marcel E Dinger
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia.,St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - H Peter Soyer
- Dermatology Research Centre, Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, The University of Queensland, Brisbane, Queensland, Australia
| | - Tarl W Prow
- Dermatology Research Centre, Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, The University of Queensland, Brisbane, Queensland, Australia.,Biomaterials Engineering and Nanomedicine Strand, Future Industries Institute, University of South Australia, Mawson Lakes, Australia
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11
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Peng H, Wei D, Chen G, Chen F. Transcriptome analysis reveals global regulation in response to CO2 supplementation in oleaginous microalga Coccomyxa subellipsoidea C-169. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:151. [PMID: 27453726 PMCID: PMC4957332 DOI: 10.1186/s13068-016-0571-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 07/12/2016] [Indexed: 05/05/2023]
Abstract
BACKGROUND Microalgae are emerging as suitable feedstock for renewable biofuel production and providing a promising way to alleviate green house gas CO2. Characterizing the metabolic pathways involved in the biosynthesis of energy-rich compounds and their global regulation upon elevated CO2 is necessary to explore the mechanism underlying rapid growth and lipid accumulation, so as to realize the full potential of these organisms as energy resources. RESULTS In the present study, 2 and 5 % CO2 increased growth rate and lipid accumulation in autotrophically cultured green alga Coccomyxa subellipsoidea C-169. Overall biomass productivity as 222 mg L(-1) day(-1) and fatty acid content as 48.5 % dry cell weight were attained in 2 % CO2, suggesting C-169 as a great candidate for lipid production via CO2 supplementation. Transcriptomic analysis of 2 % against 0.04 % CO2-cultured C-169 unveiled the global regulation of important metabolic processes. Other than enhancing gene expression in the Calvin cycle, C-169 upregulated the expression of phosphoenolpyruvate carboxylase, pyruvate carboxylase and carbamoyl-phosphate synthetase II to enhance the anaplerotic carbon assimilation reactions upon elevated CO2. Upregulation of ferredoxin and ferredoxin-NADP(+) reductase implied that plentiful energy captured through photosynthesis was transferred through ferredoxin to sustain rapid growth and lipid accumulation. Genes involved in the glycolysis, TCA cycle and oxidative phosphorylation were predominantly upregulated presumably to provide abundant intermediates and metabolic energy for anabolism. Coordinated upregulation of nitrogen acquisition and assimilation genes, together with activation of specific carbamoyl-phosphate synthetase and ornithine pathway genes, might help C-169 to maintain carbon/nitrogen balance upon elevated CO2. Significant downregulation of fatty acid degradation genes, as well as the upregulation of fatty acid synthesis genes at the later stage might contribute to the tremendous lipid accumulation. CONCLUSION Global and collaborative regulation was employed by C-169 to assimilate more carbon and maintain carbon/nitrogen balance upon elevated CO2, which provide abundant carbon skeleton and affluent metabolic energy to sustain rapid growth and lipid accumulation. Data here for the first time bring significant insights into the regulatory profile of metabolism and acclimation to elevated CO2 in C-169, which provide important information for future metabolic engineering in the development of sustainable microalgae-based biofuels.
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Affiliation(s)
- Huifeng Peng
- />School of Food Science and Engineering, South China University of Technology, Guangzhou, 510640 People’s Republic of China
| | - Dong Wei
- />School of Food Science and Engineering, South China University of Technology, Guangzhou, 510640 People’s Republic of China
| | - Gu Chen
- />School of Food Science and Engineering, South China University of Technology, Guangzhou, 510640 People’s Republic of China
| | - Feng Chen
- />School of Food Science and Engineering, South China University of Technology, Guangzhou, 510640 People’s Republic of China
- />Institute for Food and Bioresource Engineering, College of Engineering, Peking University, Beijing, 100871 People’s Republic of China
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12
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Expression of Ribonucleotide Reductase Subunit-2 and Thymidylate Synthase Correlates with Poor Prognosis in Patients with Resected Stages I-III Non-Small Cell Lung Cancer. DISEASE MARKERS 2015; 2015:302649. [PMID: 26663950 PMCID: PMC4664813 DOI: 10.1155/2015/302649] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/05/2015] [Accepted: 10/07/2015] [Indexed: 12/12/2022]
Abstract
Biomarkers can help to identify patients with early-stages or locally advanced non-small cell lung cancer (NSCLC) who have high risk of relapse and poor prognosis. To correlate the expression of seven biomarkers involved in DNA synthesis and repair and in cell division with clinical outcome, we consecutively collected 82 tumour tissues from radically resected NSCLC patients. The following biomarkers were investigated using IHC and qRT-PCR: excision repair cross-complementation group 1 (ERCC1), breast cancer 1 (BRCA1), ribonucleotide reductase subunits M1 and M2 (RRM1 and RRM2), subunit p53R2, thymidylate synthase (TS), and class III beta-tubulin (TUBB3). Gene expression levels were also validated in an available NSCLC microarray dataset. Multivariate analysis identified the protein overexpression of RRM2 and TS as independent prognostic factors of shorter overall survival (OS). Kaplan-Meier analysis showed a trend in shorter OS for patients with RRM2, TS, and ERCC1, BRCA1 overexpressed tumours. For all of the biomarkers except TUBB3, the OS trends relative to the gene expression levels were in agreement with those relative to the protein expression levels. The NSCLC microarray dataset showed RRM2 and TS as biomarkers significantly associated with OS. This study suggests that high expression levels of RRM2 and TS might be negative prognostic factors for resected NSCLC patients.
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13
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Clemente-Vicario F, Alvarez CE, Rowell JL, Roy S, London CA, Kisseberth WC, Lorch G. Human Genetic Relevance and Potent Antitumor Activity of Heat Shock Protein 90 Inhibition in Canine Lung Adenocarcinoma Cell Lines. PLoS One 2015; 10:e0142007. [PMID: 26560147 PMCID: PMC4641597 DOI: 10.1371/journal.pone.0142007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 10/15/2015] [Indexed: 12/22/2022] Open
Abstract
Background It has been an open question how similar human and canine lung cancers are. This has major implications in availability of human treatments for dogs and in establishing translational models to test new therapies in pet dogs. The prognosis for canine advanced lung cancer is poor and new treatments are needed. Heat shock protein 90 (HSP90) is an ATPase-dependent molecular chaperone ubiquitously expressed in eukaryotic cells. HSP90 is essential for posttranslational conformational maturation and stability of client proteins including protein kinases and transcription factors, many of which are important for the proliferation and survival of cancer cells. We investigated the activity of STA-1474, a HSP90 inhibitor, in two canine lung cancer cell lines, BACA and CLAC. Results Comparative genomic hybridization analysis of both cell lines revealed genetic relevance to human non-small cell lung cancer. STA-1474 inhibited growth and induced apoptosis of both cell lines in a dose- and time-dependent manner. The ICs50 after 72 h treatment with STA-1474 were 0.08 and 0.11 μM for BACA and CLAC, respectively. When grown as spheroids, the IC50 of STA-1474 for BACA cells was approximately two-fold higher than when grown as a monolayer (0.348 μM vs. 0.168 μM), whereas CLAC spheroids were relatively drug resistant. Treatment of tumor-stromal fibroblasts with STA-1474 resulted in a dose-dependent decrease in their relative cell viability with a low IC50 of 0.28 μM. Conclusions Here we first established that lung adenocarcinoma in people and dogs are genetically and biochemically similar. STA1474 demonstrated biological activity in both canine lung cancer cell lines and tumor-stromal fibroblasts. As significant decreases in relative cell viability can be achieved with nanomolar concentrations of STA-1474, investigation into the clinical efficacy of this drug in canine lung cancer patients is warranted.
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Affiliation(s)
- Francisco Clemente-Vicario
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Carlos E. Alvarez
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Jennie L. Rowell
- College of Nursing, The Ohio State University, Columbus, Ohio, United States of America
| | - Satavisha Roy
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Cheryl A. London
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - William C. Kisseberth
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Gwendolen Lorch
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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Sharan RN, Vaiphei ST, Nongrum S, Keppen J, Ksoo M. Consensus reference gene(s) for gene expression studies in human cancers: end of the tunnel visible? Cell Oncol (Dordr) 2015; 38:419-31. [PMID: 26384826 DOI: 10.1007/s13402-015-0244-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2015] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Gene expression studies are increasingly used to provide valuable information on the diagnosis and prognosis of human cancers. Also, for in vitro and in vivo experimental cancer models gene expression studies are widely used. The complex algorithms of differential gene expression analyses require normalization of data against a reference or normalizer gene, or a set of such genes. For this purpose, mostly invariant housekeeping genes are used. Unfortunately, however, there are no consensus (housekeeping) genes that serve as reference or normalizer for different human cancers. In fact, scientists have employed a wide range of reference genes across different types of cancer for normalization of gene expression data. As a consequence, comparisons of these data and/or data harmonizations are difficult to perform and challenging. In addition, an inadequate choice for a reference gene may obscure genuine changes and/or result in erroneous gene expression data comparisons. METHODS In our effort to highlight the importance of selecting the most appropriate reference gene(s), we have screened the literature for gene expression studies published since the turn of the century on thirteen of the most prevalent human cancers worldwide. CONCLUSIONS Based on the analysis of the data at hand, we firstly recommend that in each study the suitability of candidate reference gene(s) should carefully be evaluated in order to yield reliable differential gene expression data. Secondly, we recommend that a combination of PPIA and either GAPDH, ACTB, HPRT and TBP, or appropriate combinations of two or three of these genes, should be employed in future studies, to ensure that results from different studies on different human cancers can be harmonized. This approach will ultimately increase the depth of our understanding of gene expression signatures across human cancers.
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Affiliation(s)
- R N Sharan
- Radiation and Molecular Biology Unit, Department of Biochemistry, North-Eastern Hill University (NEHU), Shillong, 793022, India.
| | - S Thangminlal Vaiphei
- Radiation and Molecular Biology Unit, Department of Biochemistry, North-Eastern Hill University (NEHU), Shillong, 793022, India
| | - Saibadaiahun Nongrum
- Radiation and Molecular Biology Unit, Department of Biochemistry, North-Eastern Hill University (NEHU), Shillong, 793022, India
| | - Joshua Keppen
- Radiation and Molecular Biology Unit, Department of Biochemistry, North-Eastern Hill University (NEHU), Shillong, 793022, India
| | - Mandahakani Ksoo
- Radiation and Molecular Biology Unit, Department of Biochemistry, North-Eastern Hill University (NEHU), Shillong, 793022, India
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Jiang X, Xue Y, Zhou H, Li S, Zhang Z, Hou R, Ding Y, Hu K. Evaluation of reference gene suitability for quantitative expression analysis by quantitative polymerase chain reaction in the mandibular condyle of sheep. Mol Med Rep 2015; 12:5633-40. [PMID: 26238421 PMCID: PMC4581798 DOI: 10.3892/mmr.2015.4128] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 05/08/2015] [Indexed: 11/29/2022] Open
Abstract
Reference genes are commonly used as a reliable approach to normalize the results of quantitative polymerase chain reaction (qPCR), and to reduce errors in the relative quantification of gene expression. Suitable reference genes belonging to numerous functional classes have been identified for various types of species and tissue. However, little is currently known regarding the most suitable reference genes for bone, specifically for the sheep mandibular condyle. Sheep are important for the study of human bone diseases, particularly for temporomandibular diseases. The present study aimed to identify a set of reference genes suitable for the normalization of qPCR data from the mandibular condyle of sheep. A total of 12 reference genes belonging to various functional classes were selected, and the expression stability of the reference genes was determined in both the normal and fractured area of the sheep mandibular condyle. RefFinder, which integrates the following currently available computational algorithms: geNorm, NormFinder, BestKeeper, and the comparative ΔCt method, was used to compare and rank the candidate reference genes. The results obtained from the four methods demonstrated a similar trend: RPL19, ACTB, and PGK1 were the most stably expressed reference genes in the sheep mandibular condyle. As determined by RefFinder comprehensive analysis, the results of the present study suggested that RPL19 is the most suitable reference gene for studies associated with the sheep mandibular condyle. In addition, ACTB and PGK1 may be considered suitable alternatives.
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Affiliation(s)
- Xin Jiang
- State Key Laboratory of Military Stomatology, Department of Oral and Maxillofacial Surgery, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Yang Xue
- State Key Laboratory of Military Stomatology, Department of Oral Biology, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Hongzhi Zhou
- State Key Laboratory of Military Stomatology, Department of Oral and Maxillofacial Surgery, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Shouhong Li
- Department of Oral and Maxillofacial Surgery, Dongfeng Hospital, Hubei University of Medicine, Shiyan, Hubei 442008, P.R. China
| | - Zongmin Zhang
- State Key Laboratory of Military Stomatology, Department of Oral and Maxillofacial Surgery, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Rui Hou
- State Key Laboratory of Military Stomatology, Department of Oral and Maxillofacial Surgery, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Yuxiang Ding
- State Key Laboratory of Military Stomatology, Department of Oral and Maxillofacial Surgery, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Kaijin Hu
- State Key Laboratory of Military Stomatology, Department of Oral and Maxillofacial Surgery, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
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Aithal MGS, Rajeswari N. Validation of housekeeping genes for gene expression analysis in glioblastoma using quantitative real-time polymerase chain reaction. Brain Tumor Res Treat 2015; 3:24-9. [PMID: 25977903 PMCID: PMC4426273 DOI: 10.14791/btrt.2015.3.1.24] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 03/23/2015] [Accepted: 04/02/2015] [Indexed: 11/21/2022] Open
Abstract
Background Quantitative real-time polymerase chain reaction (qPCR) is the most reliable tool for gene expression studies. Selection of housekeeping genes (HKGs) that are having most stable expression is critical to carry out accurate gene expression profiling. There is no 'universal' HKG having stable expression in all kinds of tissues under all experimental conditions. Methods The present study aims to identify most appropriate HKGs for gene expression analysis in glioblastoma (GBM) samples. Based on literature survey, six most commonly used HKGs that are invariant in GBM were chosen. We performed qPCR using RNA from formalin fixed paraffin embedded GBM samples and normal brain samples to investigate the expression pattern of HPRT, GAPDH, TBP, B2M, B2M, RPL13A, and RN18S1 with different abundance. A simple Δcycle threshold approach was employed to calculate the fold change. Results Our study shows that the expression of RPL13A and TBP were found to be most stable across all the samples and are thus suitable for gene expression analysis in human GBM. Except for TBP, none of the other conventionally used HKGs in GBM studies e.g., HPRT and GAPDH were found to be suitable as they showed variation in RNA expression. Conclusion Validation of HKGs is therefore immensely specific for a particular experimental setup and is crucial in assessing any new setup.
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Affiliation(s)
- Madhuri G S Aithal
- Department of Biotechnology, Dayananda Sagar College of Engineering, Bangalore, India
| | - Narayanappa Rajeswari
- Department of Biotechnology, Dayananda Sagar College of Engineering, Bangalore, India
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Reference genes in real-time PCR. J Appl Genet 2014; 54:391-406. [PMID: 24078518 PMCID: PMC3825189 DOI: 10.1007/s13353-013-0173-x] [Citation(s) in RCA: 597] [Impact Index Per Article: 59.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 09/09/2013] [Accepted: 09/11/2013] [Indexed: 10/31/2022]
Abstract
This paper aims to discuss various aspects of the use of reference genes in qPCR technique used in the thousands of present studies. Most frequently, these are housekeeping genes and they must meet several criteria so that they can lay claim to the name. Lots of papers report that in different conditions, for different organisms and even tissues the basic assumption—the constant level of the expression is not maintained for many genes that seem to be perfect candidates. Moreover, their transcription can not be affected by experimental factors. Sounds simple and clear but a great number of designed protocols and lack of consistency among them brings confusion on how to perform experiment properly. Since during selection of the most stable normalizing gene we can not use any reference gene, different ways and algorithms for their selection were developed. Such methods, including examples of best normalizing genes in some specific cases and possible mistakes are presented based on available sources. Numerous examples of reference genes applications, which are usually in too few numbers in relevant articles not allowing to make a solid fundament for a reader, will be shown along with instructive compilations to make an evidence for presented statements and an arrangement of future qPCR experiments. To include all the pitfalls and problems associated with the normalization methods there is no way not to begin from sample preparation and its storage going through candidate gene selection, primer design and statistical analysis. This is important because numerous short reviews available cover the topic only in lesser extent at the same time giving the reader false conviction of complete topic recognition.
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18
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Amini-Nik S, Cambridge E, Yu W, Guo A, Whetstone H, Nadesan P, Poon R, Hinz B, Alman BA. β-Catenin-regulated myeloid cell adhesion and migration determine wound healing. J Clin Invest 2014; 124:2599-610. [PMID: 24837430 DOI: 10.1172/jci62059] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 03/27/2014] [Indexed: 01/28/2023] Open
Abstract
A β-catenin/T cell factor-dependent transcriptional program is critical during cutaneous wound repair for the regulation of scar size; however, the relative contribution of β-catenin activity and function in specific cell types in the granulation tissue during the healing process is unknown. Here, cell lineage tracing revealed that cells in which β-catenin is transcriptionally active express a gene profile that is characteristic of the myeloid lineage. Mice harboring a macrophage-specific deletion of the gene encoding β-catenin exhibited insufficient skin wound healing due to macrophage-specific defects in migration, adhesion to fibroblasts, and ability to produce TGF-β1. In irradiated mice, only macrophages expressing β-catenin were able to rescue wound-healing deficiency. Evaluation of scar tissue collected from patients with hypertrophic and normal scars revealed a correlation between the number of macrophages within the wound, β-catenin levels, and cellularity. Our data indicate that β-catenin regulates myeloid cell motility and adhesion and that β-catenin-mediated macrophage motility contributes to the number of mesenchymal cells and ultimate scar size following cutaneous injury.
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Main Histologic Types of Non–Small-Cell Lung Cancer Differ in Expression of Prognosis-related Genes. Clin Lung Cancer 2013; 14:666-673.e2. [DOI: 10.1016/j.cllc.2013.04.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 04/17/2013] [Accepted: 04/22/2013] [Indexed: 11/19/2022]
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20
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Pikor LA, Lockwood WW, Thu KL, Vucic EA, Chari R, Gazdar AF, Lam S, Lam WL. YEATS4 is a novel oncogene amplified in non-small cell lung cancer that regulates the p53 pathway. Cancer Res 2013; 73:7301-12. [PMID: 24170126 DOI: 10.1158/0008-5472.can-13-1897] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genetic analyses of lung cancer have helped found new treatments in this disease. We conducted an integrative analysis of gene expression and copy number in 261 non-small cell lung cancers (NSCLC) relative to matched normal tissues to define novel candidate oncogenes, identifying 12q13-15 and more specifically the YEATS4 gene as amplified and overexpressed in ~20% of the NSCLC cases examined. Overexpression of YEATS4 abrogated senescence in human bronchial epithelial cells. Conversely, RNAi-mediated attenuation of YEATS4 in human lung cancer cells reduced their proliferation and tumor growth, impairing colony formation and inducing cellular senescence. These effects were associated with increased levels of p21WAF1 and p53 and cleavage of PARP, implicating YEATS4 as a negative regulator of the p21-p53 pathway. We also found that YEATS4 expression affected cellular responses to cisplastin, with increased levels associated with resistance and decreased levels with sensitivity. Taken together, our findings reveal YEATS4 as a candidate oncogene amplified in NSCLC, and a novel mechanism contributing to NSCLC pathogenesis.
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Affiliation(s)
- Larissa A Pikor
- Authors' Affiliations: Integrative Oncology, BC Cancer Research Center, Vancouver, BC, Canada; National Institutes of Health, Bethesda, Maryland; Department of Genetics, Harvard Medical School, Boston, Massachusetts; and Hamon Center of Therapeutics, University of Texas South Western, Dallas, Texas
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Coe BP, Thu KL, Aviel-Ronen S, Vucic EA, Gazdar AF, Lam S, Tsao MS, Lam WL. Genomic deregulation of the E2F/Rb pathway leads to activation of the oncogene EZH2 in small cell lung cancer. PLoS One 2013; 8:e71670. [PMID: 23967231 PMCID: PMC3744458 DOI: 10.1371/journal.pone.0071670] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 07/02/2013] [Indexed: 01/15/2023] Open
Abstract
Small cell lung cancer (SCLC) is a highly aggressive lung neoplasm with extremely poor clinical outcomes and no approved targeted treatments. To elucidate the mechanisms responsible for driving the SCLC phenotype in hopes of revealing novel therapeutic targets, we studied copy number and methylation profiles of SCLC. We found disruption of the E2F/Rb pathway was a prominent feature deregulated in 96% of the SCLC samples investigated and was strongly associated with increased expression of EZH2, an oncogene and core member of the polycomb repressive complex 2 (PRC2). Through its catalytic role in the PRC2 complex, EZH2 normally functions to epigenetically silence genes during development, however, it aberrantly silences genes in human cancers. We provide evidence to support that EZH2 is functionally active in SCLC tumours, exerts pro-tumourigenic functions in vitro, and is associated with aberrant methylation profiles of PRC2 target genes indicative of a “stem-cell like” hypermethylator profile in SCLC tumours. Furthermore, lentiviral-mediated knockdown of EZH2 demonstrated a significant reduction in the growth of SCLC cell lines, suggesting EZH2 has a key role in driving SCLC biology. In conclusion, our data confirm the role of EZH2 as a critical oncogene in SCLC, and lend support to the prioritization of EZH2 as a potential therapeutic target in clinical disease.
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Affiliation(s)
- Bradley P. Coe
- Integrative Oncology Department, BC Cancer Research Centre, Vancouver, Canada
| | - Kelsie L. Thu
- Integrative Oncology Department, BC Cancer Research Centre, Vancouver, Canada
- * E-mail:
| | | | - Emily A. Vucic
- Integrative Oncology Department, BC Cancer Research Centre, Vancouver, Canada
| | - Adi F. Gazdar
- Hamon Center for Therapeutic Oncology Research and Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Stephen Lam
- Integrative Oncology Department, BC Cancer Research Centre, Vancouver, Canada
| | - Ming-Sound Tsao
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Department of Pathology, Princess Margaret Hospital University Health Network, Toronto, Canada
| | - Wan L. Lam
- Integrative Oncology Department, BC Cancer Research Centre, Vancouver, Canada
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Ealba EL, Schneider RA. A simple PCR-based strategy for estimating species-specific contributions in chimeras and xenografts. Development 2013; 140:3062-8. [PMID: 23785056 PMCID: PMC3699287 DOI: 10.1242/dev.092676] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2013] [Indexed: 11/20/2022]
Abstract
Many tissue-engineering approaches for repair and regeneration involve transplants between species. Yet a challenge is distinguishing donor versus host effects on gene expression. This study provides a simple molecular strategy to quantify species-specific contributions in chimeras and xenografts. Species-specific primers for reverse transcription quantitative real-time PCR (RT-qPCR) were designed by identifying silent mutations in quail, duck, chicken, mouse and human ribosomal protein L19 (RPL19). cDNA from different pairs of species was mixed in a dilution series and species-specific RPL19 primers were used to generate standard curves. Then quail cells were transplanted into transgenic-GFP chick and resulting chimeras were analyzed with species-specific primers. Fluorescence-activated cell sorting (FACS) confirmed that donor- and host-specific levels of RPL19 expression represent actual proportions of cells. To apply the RPL19 strategy, we measured Runx2 expression in quail-duck chimeras. Elevated Runx2 levels correlated with higher percentages of donor cells. Finally, RPL19 primers also discriminated mouse from human and chick. Thus, this strategy enables chimeras and/or xenografts to be screened rapidly at the molecular level.
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Affiliation(s)
- Erin L. Ealba
- Department of Orofacial Sciences, University of California at San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Richard A. Schneider
- Department of Orthopaedic Surgery, University of California at San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
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Meyer FRL, Grausgruber H, Binter C, Mair GE, Guelly C, Vogl C, Steinborn R. Cross-platform microarray meta-analysis for the mouse jejunum selects novel reference genes with highly uniform levels of expression. PLoS One 2013; 8:e63125. [PMID: 23671661 PMCID: PMC3650031 DOI: 10.1371/journal.pone.0063125] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 03/28/2013] [Indexed: 11/18/2022] Open
Abstract
Reference genes (RGs) with uniform expression are used for normalization of reverse transcription quantitative PCR (RT-qPCR) data. Their optimization for a specific biological context, e.g. a specific tissue, has been increasingly considered. In this article, we compare RGs identified by expression data meta-analysis restricted to the context tissue, the jejunum of Mus musculus domesticus, i) to traditional RGs, ii) to expressed interspersed repeated DNA elements, and iii) to RGs identified by meta-analysis of expression data from diverse tissues and conditions. To select the set of candidate RGs, we developed a novel protocol for the cross-platform meta-analysis of microarray data. The expression stability of twenty-four putative RGs was analysed by RT-qPCR in at least 14 jejunum samples of the mouse strains C57Bl/6N, CD1, and OF1. Across strains, the levels of expression of the novel RGs Plekha7, Zfx, and Ube2v1 as well as of Oaz1 varied less than two-fold irrespective of genotype, sex or their combination. The gene set consisting of Plekha7 and Oaz1 showed superior expression stability analysed with the tool RefFinder. The novel RGs are functionally diverse. This facilitates expression studies over a wide range of conditions. The highly uniform expression of the optimized RGs in the jejunum points towards their involvement in tightly regulated pathways in this tissue. We also applied our novel protocol of cross-microarray platform meta-analysis to the identification of RGs in the duodenum, the ileum and the entire small intestine. The selection of RGs with improved expression stability in a specific biological context can reduce the number of RGs for the normalization step of RT-qPCR expression analysis, thus reducing the number of samples and experimental costs.
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Affiliation(s)
- Florian R. L. Meyer
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Vienna, Austria
- Institute of Anatomy, Histology and Embryology, University of Veterinary Medicine, Vienna, Austria
| | - Heinrich Grausgruber
- Department of Crop Sciences, University of Natural Resources and Life Sciences, Tulln, Austria
| | - Claudia Binter
- Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, Vienna, Austria
| | - Georg E. Mair
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Vienna, Austria
| | - Christian Guelly
- Center for Medical Research, Medical University of Graz, Graz, Austria
| | - Claus Vogl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Ralf Steinborn
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Vienna, Austria
- * E-mail:
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Aberrant expression of long noncoding RNAs in cervical intraepithelial neoplasia. Int J Gynecol Cancer 2013; 22:1557-63. [PMID: 23095774 DOI: 10.1097/igc.0b013e318272f2c9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
OBJECTIVE Long noncoding RNAs (lncRNAs) are a unique class of messenger RNA-like transcripts of at least 200 nucleotides in length with no significant protein-coding capacity. Aberrant lncRNA expression is emerging as a major component of the cancer transcriptome. Here, we sought to determine if differential lncRNA expression is a feature of the human cervical intraepithelial neoplasia (CIN) transcriptome. METHODS Sequence data were derived from 16 long serial analyses of gene expression (L-SAGE) libraries constructed from cervical specimens representing mild (CIN1), moderate (CIN2), and severe (CIN3) histopathologic grades of CIN. A novel lncRNA discovery pipeline was developed to query the expression of lncRNAs within the SAGE data sets. RESULTS A total of 2,230,370 sequence tags were delineated from the 16 SAGE libraries, representing the expression of 367,482 unique tags at varying abundance. Using a novel stepwise filtering strategy, we analyzed the cervical SAGE libraries and identified the expression profiles of 1056 lncRNAs in the human cervix. We present the first lncRNA expression profile derived from nonneoplastic cervical tissue and establish that changes in lncRNA expression do occur in cervical intraepithelial lesions. Our analysis also shows statistically significant aberrant expression of lncRNAs in the 3 CIN grades, suggesting that these unique noncoding RNA transcripts may contribute to the development and progression of precursor lesions. CONCLUSIONS Through the analysis of L-SAGE libraries constructed from cervical specimens, we provide the first lncRNA expression profile of the cervix and demonstrate aberrant expression in early-stage neoplasia.
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Boyarskikh UA, Bondar NP, Filipenko ML, Kudryavtseva NN. Downregulation of serotonergic gene expression in the Raphe nuclei of the midbrain under chronic social defeat stress in male mice. Mol Neurobiol 2013; 48:13-21. [PMID: 23392607 DOI: 10.1007/s12035-013-8413-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Accepted: 01/24/2013] [Indexed: 12/11/2022]
Abstract
There is ample experimental evidence supporting the hypothesis that the brain serotonergic system is involved in the control of chronic social defeat stress (CSDS), depression, and anxiety. The study aimed to analyze mRNA levels of the serotonergic genes in the raphe nuclei of midbrain that may be associated with chronic social defeats consistently shown by male mice in special experimental settings. The serotonergic genes were the Tph2, Sert, Maoa, and Htr1a. The Bdnf and Creb genes were also studied. The experimental groups were composed of male mice with experience of defeats in 21 daily encounters and male mice with the same track record of defeats followed by a no-defeat period without agonistic interactions (relative rest for 14 days). It has been shown that mRNA levels of the Tph2, Maoa, Sert, Htr1a, Bdnf, and Creb genes in the raphe nuclei of defeated mice are decreased as compared with the controls. The expression of the serotonergic genes as well as the Creb gene is not restored to the control level after the 2 weeks of relative rest. mRNA levels of Bdnf gene are not recovered to the control levels, although some upregulation was observed in rested losers. CSDS experience inducing the development of mixed anxiety/depression-like state in male mice downregulates the expression of serotonergic genes associated with the synthesis, inactivation, and reception of serotonin. The Bdnf and Creb genes in the midbrain raphe nuclei are also downregulated under CSDS. Period of relative rest is not enough for most serotonergic genes to recover expression to the control levels.
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Affiliation(s)
- Ul'yana A Boyarskikh
- Institute of Chemical Biology and Basic Medicine SD RAS, pr. Ac. Lavrentjeva, 8, Novosibirsk, 630090, Russia
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Guo C, Liu S, Wang J, Sun MZ, Greenaway FT. ACTB in cancer. Clin Chim Acta 2012; 417:39-44. [PMID: 23266771 DOI: 10.1016/j.cca.2012.12.012] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 11/27/2012] [Accepted: 12/01/2012] [Indexed: 01/27/2023]
Abstract
Beta-actin (ACTB) has traditionally been regarded as an endogenous housekeeping gene and has been widely used as a reference gene/protein in quantifying expression levels in tumors. However, ACTB is closely associated with a variety of cancers and accumulating evidence indicates that ACTB is de-regulated in liver, melanoma, renal, colorectal, gastric, pancreatic, esophageal, lung, breast, prostate, ovarian cancers, leukemia and lymphoma. ACTB is generally found to be up-regulated in the majority of tumor cells and tissues. The abnormal expression and polymerization of ACTB and the resulting changes to the cytoskeleton are revealed to be associated with the invasiveness and metastasis of cancers. The current review explores relevant mechanisms, integrates current understandings, and provides suggestions for future studies of the roles of ACTB in tumors.
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Affiliation(s)
- Chunmei Guo
- Department of Biotechnology, Dalian Medical University, Dalian 116044, China
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MacLellan SA, Lawson J, Baik J, Guillaud M, Poh CFY, Garnis C. Differential expression of miRNAs in the serum of patients with high-risk oral lesions. Cancer Med 2012; 1:268-74. [PMID: 23342275 PMCID: PMC3544450 DOI: 10.1002/cam4.17] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 06/05/2012] [Accepted: 06/13/2012] [Indexed: 12/15/2022] Open
Abstract
Oral cancer is one of the most commonly diagnosed cancers worldwide. Disease is often diagnosed at later stages, which is associated with a poor 5-year survival rate and a high rate of local recurrence. MicroRNAs (miRNAs), a group of small, noncoding RNAs, can be isolated from blood serum samples and have demonstrated utility as biomarkers in multiple cancer types. The aim of this study was to examine the expression profiles of circulating miRNAs in the serum of patients with high-risk oral lesions (HRLs; oral cancer or carcinoma in situ) and to explore their utility as potential oral cancer biomarkers. Global serum miRNA profiles were generated using quantitative PCR method from 1) patients diagnosed with HRLs and undergoing intent-to-cure surgical treatment (N = 30) and 2) a demographically matched, noncancer control group (N = 26). We next honed our list of serum miRNAs associated with disease by reducing the effects of interpatient variability; we compared serum miRNA profiles from samples taken both before and after tumor resections (N = 10). Based on these analyses, fifteen miRNAs were significantly upregulated and five were significantly downregulated based on presence of disease (minimum fold-change >2 in at least 50% of samples, P < 0.05, permutation). Five of these miRNAs (miR-16, let-7b, miR-338-3p, miR-223, and miR-29a) yielded an area under the ROC curve (AUC) >0.8, suggesting utility as noninvasive biomarkers for detection of oral cancer or high-grade lesions. Combining these serum miRNA profiles with other screening techniques could greatly improve the sensitivity in oral cancer detection.
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Affiliation(s)
- Sara Ann MacLellan
- Department of Integrative Oncology, British Columbia Cancer Research CentreVancouver, BC, Canada
| | - James Lawson
- Department of Integrative Oncology, British Columbia Cancer Research CentreVancouver, BC, Canada
| | - Jonathan Baik
- Department of Integrative Oncology, British Columbia Cancer Research CentreVancouver, BC, Canada
| | - Martial Guillaud
- Department of Integrative Oncology, British Columbia Cancer Research CentreVancouver, BC, Canada
| | - Catherine Fang-Yeu Poh
- Department of Integrative Oncology, British Columbia Cancer Research CentreVancouver, BC, Canada
- Oral Biological and Medical Sciences, University of British ColumbiaVancouver, BC, Canada
| | - Cathie Garnis
- Department of Integrative Oncology, British Columbia Cancer Research CentreVancouver, BC, Canada
- Division of Otolaryngology, Department of Surgery, University of British ColumbiaVancouver, BC, Canada
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Reference genes for measuring mRNA expression. Theory Biosci 2012; 131:215-23. [PMID: 22588998 DOI: 10.1007/s12064-012-0152-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 04/26/2012] [Indexed: 12/29/2022]
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29
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Amini-Nik S, Glancy D, Boimer C, Whetstone H, Keller C, Alman BA. Pax7 expressing cells contribute to dermal wound repair, regulating scar size through a β-catenin mediated process. Stem Cells 2012; 29:1371-9. [PMID: 21739529 DOI: 10.1002/stem.688] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
During skin wound healing, fibroblast-like cells reconstitute the dermal compartment of the repaired skin filling the wound gap. A subset of these cells are transcriptionally active for β-catenin/T-cell factor (TCF) signaling during the proliferative phase of the repair process, and β-catenin levels control the size of the scar that ultimately forms by regulating the number of dermal fibroblasts. Here, we performed cell lineage studies to reveal a source of the dermal cells in which β-catenin signaling is activated during wound repair. Using a reporter mouse, we found that cells in the early wound in which TCF-dependent transcription is activated express genes involved in muscle development. Using mice in which cells express Pax7 (muscle progenitors) or Mck (differentiated myocytes) are permanently labeled, we showed that one quarter of dermal cells in the healing wound are Pax7 expressing progeny, but none are Mck progeny. Removing one allele of β-catenin in Pax7 expressing progeny resulted in a significantly smaller scar size with fewer Pax7 expressing progeny cell contributing to wound repair. During wound healing, β-catenin activation causes muscle satellite cells to adopt a fibrotic phenotype and this is a source of dermal cells in the repair process.
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Affiliation(s)
- Saeid Amini-Nik
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
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Gibb EA, Enfield KSS, Stewart GL, Lonergan KM, Chari R, Ng RT, Zhang L, MacAulay CE, Rosin MP, Lam WL. Long non-coding RNAs are expressed in oral mucosa and altered in oral premalignant lesions. Oral Oncol 2011; 47:1055-61. [PMID: 21835683 DOI: 10.1016/j.oraloncology.2011.07.008] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Revised: 06/17/2011] [Accepted: 07/09/2011] [Indexed: 01/01/2023]
Abstract
Oral epithelial dysplasias are believed to progress through a series of histopathological stages; from mild to severe dysplasia, to carcinoma in situ, and finally to invasive OSCC. Underlying this change in histopathological grade are gross chromosome alterations and changes in gene expression of both protein-coding genes and non-coding RNAs. Recent papers have described associations of aberrant expression of microRNAs, one class of non-coding RNAs, with oral cancer. However, expression profiling of long non-coding RNAs (lncRNAs) has not been reported. Long non-coding RNAs are a novel class of mRNA-like transcripts with no protein coding capacity, but with a variety of functions including roles in epigenetics and gene regulation. In recent reports, the aberrant expression of lncRNAs has been associated with human cancers, suggesting a critical role in tumorigenesis. Here, we present the first long non-coding RNA expression map for the human oral mucosa. We describe the expression of 325 long non-coding RNAs, suggesting lncRNA expression contributes significantly to the oral transcriptome. Intriguingly, ∼60% of the detected lncRNAs show aberrant expression in oral premalignant lesions. A number of these lncRNAs have been previously associated with other human cancers.
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Affiliation(s)
- Ewan A Gibb
- British Columbia Cancer Agency Research Centre, Vancouver, Canada V5Z 1L3.
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Patel RK, Jain M. PlantRGS: a web server for the identification of most suitable candidate reference genes for quantitative gene expression studies in plants. DNA Res 2011; 18:463-70. [PMID: 21987088 PMCID: PMC3223078 DOI: 10.1093/dnares/dsr032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Normalization of quantitative gene expression data with a suitable reference gene is essential for accurate and reliable results. However, the availability and choice of most suitable reference gene(s) showing uniform expression across all the experimental conditions remain a drawback. We have developed a web server, PlantRGS (http://www.nipgr.res.in/PlantRGS), for the identification of most suitable candidate reference gene(s) at the whole-genome level using microarray data for quantitative gene expression studies in plants. Microarray data from more than 11 000 tissue samples for nine plant species have been included in the PlantRGS for meta-analysis. The web server provides a user-friendly graphical user interface-based analysis tool for the identification of most suitable reference genes in the selected plant species under user-defined experimental conditions. Various parameter options and output formats will help users to investigate desired number of most suitable reference genes with wide range of expression levels. Validation of results revealed that novel reference genes identified by the PlantRGS outperforms the traditionally used reference genes in terms of expression stability. We anticipate that the PlantRGS will provide a platform for the identification of most suitable reference gene(s) under given experimental conditions and facilitate quantitative gene expression studies in plants.
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Affiliation(s)
- Ravi K Patel
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
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Abstract
Once thought to be a part of the 'dark matter' of the genome, long non-coding RNAs (lncRNAs) are emerging as an integral functional component of the mammalian transcriptome. LncRNAs are a novel class of mRNA-like transcripts which, despite no known protein-coding potential, demonstrate a wide range of structural and functional roles in cellular biology. However, the magnitude of the contribution of lncRNA expression to normal human tissues and cancers has not been investigated in a comprehensive manner. In this study, we compiled 272 human serial analysis of gene expression (SAGE) libraries to delineate lncRNA transcription patterns across a broad spectrum of normal human tissues and cancers. Using a novel lncRNA discovery pipeline we parsed over 24 million SAGE tags and report lncRNA expression profiles across a panel of 26 different normal human tissues and 19 human cancers. Our findings show extensive, tissue-specific lncRNA expression in normal tissues and highly aberrant lncRNA expression in human cancers. Here, we present a first generation atlas for lncRNA profiling in cancer.
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Bee A, Brewer D, Beesley C, Dodson A, Forootan S, Dickinson T, Gerard P, Lane B, Yao S, Cooper CS, Djamgoz MBA, Gosden CM, Ke Y, Foster CS. siRNA knockdown of ribosomal protein gene RPL19 abrogates the aggressive phenotype of human prostate cancer. PLoS One 2011; 6:e22672. [PMID: 21799931 PMCID: PMC3142177 DOI: 10.1371/journal.pone.0022672] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Accepted: 07/04/2011] [Indexed: 12/15/2022] Open
Abstract
We provide novel functional data that posttranscriptional silencing of gene RPL19 using RNAi not only abrogates the malignant phenotype of PC-3M prostate cancer cells but is selective with respect to transcription and translation of other genes. Reducing RPL19 transcription modulates a subset of genes, evidenced by gene expression array analysis and Western blotting, but does not compromise cell proliferation or apoptosis in-vitro. However, growth of xenografted tumors containing the knocked-down RPL19 in-vivo is significantly reduced. Analysis of the modulated genes reveals induction of the non-malignant phenotype principally to involve perturbation of networks of transcription factors and cellular adhesion genes. The data provide evidence that extra-ribosomal regulatory functions of RPL19, beyond protein synthesis, are critical regulators of cellular phenotype. Targeting key members of affected networks identified by gene expression analysis raises the possibility of therapeutically stabilizing a benign phenotype generated by modulating the expression of an individual gene and thereafter constraining a malignant phenotype while leaving non-malignant tissues unaffected.
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Affiliation(s)
- Alix Bee
- Section of Cellular Pathology and Molecular Genetics, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Daniel Brewer
- Molecular Carcinogenesis Group, Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | - Carol Beesley
- Section of Cellular Pathology and Molecular Genetics, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Andrew Dodson
- Section of Cellular Pathology and Molecular Genetics, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Shiva Forootan
- Section of Cellular Pathology and Molecular Genetics, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Timothy Dickinson
- Section of Cellular Pathology and Molecular Genetics, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Patricia Gerard
- Section of Cellular Pathology and Molecular Genetics, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Brian Lane
- Liverpool Microarray Facility, Centre for Genomic Research, University of Liverpool, Liverpool, United Kingdom
| | - Sheng Yao
- Section of Cellular Pathology and Molecular Genetics, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Colin S. Cooper
- Molecular Carcinogenesis Group, Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | - Mustafa B. A. Djamgoz
- Division of Cell and Molecular Biology, Imperial College London, London, United Kingdom
| | - Christine M. Gosden
- Section of Cellular Pathology and Molecular Genetics, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Youqiang Ke
- Section of Cellular Pathology and Molecular Genetics, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Christopher S. Foster
- Section of Cellular Pathology and Molecular Genetics, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
- * E-mail:
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Conover CA, Boldt HB, Bale LK, Clifton KB, Grell JA, Mader JR, Mason EJ, Powell DR. Pregnancy-associated plasma protein-A2 (PAPP-A2): tissue expression and biological consequences of gene knockout in mice. Endocrinology 2011; 152:2837-44. [PMID: 21586553 DOI: 10.1210/en.2011-0036] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Pregnancy-associated plasma protein-A2 (PAPP-A2) is a novel homolog of PAPP-A in the metzincin superfamily. However, compared with the accumulating data on PAPP-A, very little is known about PAPP-A2. In this study, we determined the tissue expression pattern of PAPP-A2 mRNA in wild-type (WT) mice and characterized the phenotype of mice with global PAPP-A2 deficiency. Tissues expressing PAPP-A2 in WT mice were more limited than those expressing PAPP-A. The highest PAPP-A2 mRNA expression was found in the placenta, with abundant expression in fetal, skeletal, and reproductive tissues. Heterozygous breeding produced the expected Mendelian distribution for the pappa2 gene and viable homozygous PAPP-A2 knockout (KO) mice that were normal size at birth. The most striking phenotype of the PAPP-A2 KO mouse was postnatal growth retardation. Male and female PAPP-A2 KO mice had 10 and 25-30% lower body weight, respectively, than WT littermates. Adult femur and body length were also reduced in PAPP-A2 KO mice, but without significant effects on bone mineral density. PAPP-A2 KO mice were fertile, but with compromised fecundity. PAPP-A expression was not altered to compensate for the loss of PAPP-A2 expression, and proteolysis of PAPP-A2's primary substrate, IGF-binding protein-5, was not altered in fibroblasts from PAPP-A2 KO embryos. In conclusion, tissue expression patterns and biological consequences of gene KO indicate distinct physiological roles for PAPP-A2 and PAPP-A in mice.
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Affiliation(s)
- Cheryl A Conover
- Endocrine Research Unit, Division of Endocrinology, Metabolism, and Nutrition, College of Medicine Mayo Clinic, 200 First Street SW, 5-194 Joseph, Rochester, Minnesota 55905, USA.
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Cernak I, Merkle AC, Koliatsos VE, Bilik JM, Luong QT, Mahota TM, Xu L, Slack N, Windle D, Ahmed FA. The pathobiology of blast injuries and blast-induced neurotrauma as identified using a new experimental model of injury in mice. Neurobiol Dis 2010; 41:538-51. [PMID: 21074615 DOI: 10.1016/j.nbd.2010.10.025] [Citation(s) in RCA: 202] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Revised: 10/05/2010] [Accepted: 10/27/2010] [Indexed: 12/24/2022] Open
Abstract
Current experimental models of blast injuries used to study blast-induced neurotrauma (BINT) vary widely, which makes the comparison of the experimental results extremely challenging. Most of the blast injury models replicate the ideal Friedländer type of blast wave, without the capability to generate blast signatures with multiple shock fronts and refraction waves as seen in real-life conditions; this significantly reduces their clinical and military relevance. Here, we describe the pathophysiological consequences of graded blast injuries and BINT generated by a newly developed, highly controlled, and reproducible model using a modular, multi-chamber shock tube capable of tailoring pressure wave signatures and reproducing complex shock wave signatures seen in theater. While functional deficits due to blast exposure represent the principal health problem for today's warfighters, the majority of available blast models induces tissue destruction rather than mimic functional deficits. Thus, the main goal of our model is to reliably reproduce long-term neurological impairments caused by blast. Physiological parameters, functional (motor, cognitive, and behavioral) outcomes, and underlying molecular mechanisms involved in inflammation measured in the brain over the 30 day post-blast period showed this model is capable of reproducing major neurological changes of clinical BINT.
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Affiliation(s)
- Ibolja Cernak
- Biomedicine Business Area, National Security Technology Department, Johns Hopkins University Applied Physics Laboratory (JHU/APL), Laurel, MD 20723, USA.
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