1
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Aracena KA, Lin YL, Luo K, Pacis A, Gona S, Mu Z, Yotova V, Sindeaux R, Pramatarova A, Simon MM, Chen X, Groza C, Lougheed D, Gregoire R, Brownlee D, Boye C, Pique-Regi R, Li Y, He X, Bujold D, Pastinen T, Bourque G, Barreiro LB. Epigenetic variation impacts individual differences in the transcriptional response to influenza infection. Nat Genet 2024; 56:408-419. [PMID: 38424460 DOI: 10.1038/s41588-024-01668-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 01/16/2024] [Indexed: 03/02/2024]
Abstract
Humans display remarkable interindividual variation in their immune response to identical challenges. Yet, our understanding of the genetic and epigenetic factors contributing to such variation remains limited. Here we performed in-depth genetic, epigenetic and transcriptional profiling on primary macrophages derived from individuals of European and African ancestry before and after infection with influenza A virus. We show that baseline epigenetic profiles are strongly predictive of the transcriptional response to influenza A virus across individuals. Quantitative trait locus (QTL) mapping revealed highly coordinated genetic effects on gene regulation, with many cis-acting genetic variants impacting concomitantly gene expression and multiple epigenetic marks. These data reveal that ancestry-associated differences in the epigenetic landscape can be genetically controlled, even more than gene expression. Lastly, among QTL variants that colocalized with immune-disease loci, only 7% were gene expression QTL, while the remaining genetic variants impact epigenetic marks, stressing the importance of considering molecular phenotypes beyond gene expression in disease-focused studies.
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Affiliation(s)
| | - Yen-Lung Lin
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Kaixuan Luo
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Alain Pacis
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada
| | - Saideep Gona
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Zepeng Mu
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Vania Yotova
- Department of Genetics, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Renata Sindeaux
- Department of Genetics, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | | | | | - Xun Chen
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Cristian Groza
- Quantitative Life Sciences, McGill University, Montreal, Quebec, Canada
| | - David Lougheed
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Romain Gregoire
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada
| | - David Brownlee
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada
| | - Carly Boye
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
| | - Yang Li
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Xin He
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - David Bujold
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada
- McGill Genome Centre, Montreal, Quebec, Canada
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Genomic Medicine Center, Children's Mercy, Kansas City, MO, USA
| | - Guillaume Bourque
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada.
- McGill Genome Centre, Montreal, Quebec, Canada.
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.
| | - Luis B Barreiro
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA.
- Committee on Immunology, University of Chicago, Chicago, IL, USA.
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2
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Yoshida H. Dissecting the Immune System through Gene Regulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1444:219-235. [PMID: 38467983 DOI: 10.1007/978-981-99-9781-7_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
The immune system plays a dual role in human health, functioning both as a protector against pathogens and, at times, as a contributor to disease. This feature emphasizes the importance to uncover the underlying causes of its malfunctions, necessitating an in-depth analysis in both pathological and physiological conditions to better understand the immune system and immune disorders. Recent advances in scientific technology have enabled extensive investigations into gene regulation, a crucial mechanism governing cellular functionality. Studying gene regulatory mechanisms within the immune system is a promising avenue for enhancing our understanding of immune cells and the immune system as a whole. The gene regulatory mechanisms, revealed through various methodologies, and their implications in the field of immunology are discussed in this chapter.
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Affiliation(s)
- Hideyuki Yoshida
- YCI Laboratory for Immunological Transcriptomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
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3
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Jayachandran SK, Anusuyadevi M, Essa MM, Qoronfleh MW. Decoding information on COVID-19: Ontological approach towards design possible therapeutics. INFORMATICS IN MEDICINE UNLOCKED 2020; 22:100486. [PMID: 33263073 PMCID: PMC7691137 DOI: 10.1016/j.imu.2020.100486] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/20/2020] [Accepted: 11/20/2020] [Indexed: 12/23/2022] Open
Abstract
To date, no effective preventive or curative medical interventions exist against COVID-19, caused by Severe Acute Respiratory Syndrome corona virus 2 (SARS CoV-2). The available interventions are only supportive and palliative in nature. Popular among the emerging explanations for the mortality from COVID-19 is "cytokine storm", attributed to the body's aggressive immune response to this novel pathogen. In less than a year the disease has spread to almost all countries, though the mortality rates have varied significantly from country to country based on factors such as the demographical mix of the population, prevalence of comorbidities, as well as prior exposure to viruses from the corona family. This review examines the current literature on mortality rates across the globe, explores the possible reasons, thereby decoding variations. COVID-19 researchers have noted unique characteristics in the structural and host-pathogen interaction and identified several possible target proteins and sites that could exhibit control over the entry of SARS CoV-2 into the host, which this paper reviews in detail. Identification of new targets, both in the virus and the host, may accelerate the search for effective vaccines and curative drugs against COVID-19. Further, the ontological approach of this review is likely to provide insights for researchers to anticipate and be ready for future mutant viruses that may emerge in future.
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Affiliation(s)
- Swaminathan K Jayachandran
- Drug Discovery and Molecular Cardiology Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, 620204, India
| | - Muthuswamy Anusuyadevi
- Molecular Gerontology Lab, Department of Biochemistry, School of Life Sciences, Bharathidasan University, Tiruchirappalli, 620204, India
| | - Musthafa Mohamed Essa
- Department of Food Science and Nutrition, CAMS, Sultan Qaboos University, Muscat, Oman
- Ageing and Dementia Research Group, Sultan Qaboos University, Muscat, Oman
| | - M Walid Qoronfleh
- Research & Policy Department, World Innovation Summit for Health (WISH), Qatar Foundation, P.O. Box 5825, Doha, Qatar
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4
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Zeng W, Liu Y, Li WT, Li Y, Zhu JF. CircFNDC3B sequestrates miR-937-5p to derepress TIMP3 and inhibit colorectal cancer progression. Mol Oncol 2020; 14:2960-2984. [PMID: 32896063 PMCID: PMC7607164 DOI: 10.1002/1878-0261.12796] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/29/2020] [Accepted: 09/01/2020] [Indexed: 12/18/2022] Open
Abstract
Circular RNA (circRNA) are single‐stranded RNA with covalently closed 3′ and 5′ ends, with many recognized to be involved in human diseases as gene regulators, typically by interacting with other RNA. CircFNDC3B is a circRNA formed by back‐splicing of exons 5 and 6 of the FNDC3B gene. CircFNDC3B was recently implicated in renal carcinoma, gastric and bladder cancer. However, the expression levels of circFNDC3B and its role in colorectal cancer (CRC) remain unclear. Expression of circFNDC3B and TIMP3 levels in CRC tissues and cell lines were found to be low, whereas microRNA (miR)‐937‐5p expression was high in CRC. MicroRNA‐937‐5p downregulated TIMP3, thereby promoting tumor cell proliferation, invasion, migration and angiogenesis. Moreover, CircFNDC3B was shown to bind to miR‐937‐5p. CircFNDC3B and circFNDC3B‐enriched exosomes inhibited tumorigenic, metastatic and angiogenic properties of CRC, and miR‐937‐5p overexpression or TIMP3 knockdown could reverse these effects. In vivo CRC tumor growth, angiogenesis and liver metastasis were suppressed by circFNDC3B overexpression, circFNDC3B‐enriched exosomes or miR‐937‐5p knockdown. In conclusion, our work reports a tumor‐suppressing role for the circFNDC3B–miR‐97‐5p–TIMP3 pathway and suggests that circFNDC3B‐enriched exosomes can inhibit angiogenesis and CRC progression.
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Affiliation(s)
- Wei Zeng
- Department of Hematology and Oncology, Shenzhen University General Hospital, Shenzhen, China.,Shenzhen University International Cancer Center, China
| | - Yi Liu
- Department of Cardiothoracic Surgery, Shenzhen University General Hospital, Shenzhen, China
| | - Wen-Ting Li
- Department of Pathology, Shenzhen University General Hospital, Shenzhen, China
| | - Yi Li
- Department of Hematology and Oncology, Shenzhen University General Hospital, Shenzhen, China.,Shenzhen University International Cancer Center, China
| | - Jin-Feng Zhu
- Department of General Surgery, Shenzhen University General Hospital, Shenzhen, China
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5
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Harding SD, Faccenda E, Southan C, Pawson AJ, Maffia P, Alexander SPH, Davenport AP, Fabbro D, Levi‐Schaffer F, Spedding M, Davies JA. The IUPHAR Guide to Immunopharmacology: connecting immunology and pharmacology. Immunology 2020; 160:10-23. [PMID: 32020584 PMCID: PMC7160657 DOI: 10.1111/imm.13175] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/17/2020] [Accepted: 01/27/2020] [Indexed: 12/19/2022] Open
Abstract
Given the critical role that the immune system plays in a multitude of diseases, having a clear understanding of the pharmacology of the immune system is crucial to new drug discovery and development. Here we describe the International Union of Basic and Clinical Pharmacology (IUPHAR) Guide to Immunopharmacology (GtoImmuPdb), which connects expert-curated pharmacology with key immunological concepts and aims to put pharmacological data into the hands of immunologists. In the pursuit of new therapeutics, pharmacological databases are a vital resource to researchers through providing accurate information on the fundamental science underlying drug action. This extension to the existing IUPHAR/British Pharmacological Society Guide to Pharmacology supports research into the development of drugs targeted at modulating immune, inflammatory or infectious components of disease. To provide a deeper context for how the resource can support research we show data in GtoImmuPdb relating to a case study on the targeting of vascular inflammation.
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Affiliation(s)
- Simon D. Harding
- Deanery of Biomedical SciencesUniversity of EdinburghEdinburghUK
| | - Elena Faccenda
- Deanery of Biomedical SciencesUniversity of EdinburghEdinburghUK
| | - Christopher Southan
- Deanery of Biomedical SciencesUniversity of EdinburghEdinburghUK
- Present address:
TW2Informatics LtdGöteborg42166Sweden
| | - Adam J. Pawson
- Deanery of Biomedical SciencesUniversity of EdinburghEdinburghUK
| | - Pasquale Maffia
- Centre for ImmunobiologyInstitute of Infection, Immunity and InflammationCollege of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
- Institute of Cardiovascular and Medical SciencesCollege of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
- Department of PharmacyUniversity of Naples Federico IINaplesItaly
| | | | | | - Doriano Fabbro
- Cellestia Biotech SABaselSwitzerland
- TargImmune Therapeutics AGBaselSwitzerland
| | | | | | - Jamie A. Davies
- Deanery of Biomedical SciencesUniversity of EdinburghEdinburghUK
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6
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Fry M. Ontologically simple theories do not indicate the true nature of complex biological systems: three test cases. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2020; 42:17. [PMID: 32346811 DOI: 10.1007/s40656-020-00310-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/13/2020] [Indexed: 06/11/2023]
Abstract
A longstanding philosophical premise perceives simplicity as a desirable attribute of scientific theories. One of several raised justifications for this notion is that simple theories are more likely to indicate the true makeup of natural systems. Qualitatively parsimonious hypotheses and theories keep to a minimum the number of different postulated entities within a system. Formulation of such ontologically simple working hypotheses proved to be useful in the experimental probing of narrowly defined bio systems. It is less certain, however, whether qualitatively parsimonious theories are effective indicators of the true nature of complex biological systems. This paper assesses the success of ontologically simple theories in envisaging the makeup of three complex systems in bacteriology, immunology, and molecular biology. Evidence shows that parsimonious theories completely misconstrued the actual ontologically complex constitutions of the three examined systems. Since evolution and selective pressures typically produce ontologically intricate rather than simple bio systems, qualitatively parsimonious theories are mostly inapt indicators of the true nature of complex biological systems.
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Affiliation(s)
- Michael Fry
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, POB 9649, 31096, Bat Galim, Haifa, Israel.
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7
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Kuznetsova I, Lugmayr A, Siira SJ, Rackham O, Filipovska A. CirGO: an alternative circular way of visualising gene ontology terms. BMC Bioinformatics 2019; 20:84. [PMID: 30777018 PMCID: PMC6380029 DOI: 10.1186/s12859-019-2671-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 02/07/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Prioritisation of gene ontology terms from differential gene expression analyses in a two-dimensional format remains a challenge with exponentially growing data volumes. Typically, gene ontology terms are represented as tree-maps that enclose all data into defined space. However, large datasets make this type of visualisation appear cluttered and busy, and often not informative as some labels are omitted due space limits, especially when published in two-dimensional (2D) figures. RESULTS Here we present an open source CirGO (Circular Gene Ontology) software that visualises non-redundant two-level hierarchically structured ontology terms from gene expression data in a 2D space. Gene ontology terms based on statistical significance were summarised with a semantic similarity algorithm and grouped by hierarchical clustering. This software visualises the most enriched gene ontology terms in an informative, comprehensive and intuitive format that is achieved by organising data from the most relevant to the least, as well as the appropriate use of colours and supporting information. Additionally, CirGO is an easy to use software that supports researchers with little computational background to present their gene ontology data in a publication ready format. CONCLUSIONS Our easy to use open source CirGO Python software package provides biologists with a succinct presentation of terms and functions that are most represented in a specific gene expression data set in a visually appealing 2D format (e.g. for reporting research results in scientific articles). CirGO is freely available at https://github.com/IrinaVKuznetsova/CirGO.git .
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Affiliation(s)
- Irina Kuznetsova
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia, 6009, Australia.
| | - Artur Lugmayr
- Visualisation and Interactive Media (VisLab), Curtin University, Perth, 6102, Australia
| | - Stefan J Siira
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia, 6009, Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia, 6009, Australia.,School of Molecular Sciences, University of Western Australia, Nedlands, 6009, Australia
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia, 6009, Australia. .,School of Molecular Sciences, University of Western Australia, Nedlands, 6009, Australia.
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8
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Chen F, Wang RJ, Li GZ, Zhang Y, Yu S, Liu YF, Chen XY, Hou SK. miRNA array analysis of plasma miRNA alterations in rats exposed to a high altitude hypoxic environment. Mol Med Rep 2018; 18:5502-5510. [PMID: 30365091 PMCID: PMC6236226 DOI: 10.3892/mmr.2018.9570] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 03/20/2017] [Indexed: 11/06/2022] Open
Abstract
In the present study, the microRNA (miRNA) expression profiles of rats exposed to high altitude hypoxia and normal conditions were obtained from miRNA array analysis. Bioinformatics analyses, including the use of the Gene Oncology and Kyoto Encyclopedia of Genes and Genomes databases, were used to identify the genes and pathways, which were specifically associated with high altitude hypoxic environment‑associated miRNAs. A total of 26 miRNAs were differentially expressed in the two groups, comprising six upregulated and 20 downregulated miRNAs. In the present study, a novel pattern of upregulated miRNAs and their associated pathways were constructed, including proteoglycans in cancer, spliceosome, gluamatergic synapse, glycolysis/gluconeogenesis, Foxo, cGMP‑PKG and p53 signaling pathways, which may provide novel targets for diagnosing and understanding the mechanism of high altitude hypoxia‑induced disease.
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Affiliation(s)
- Feng Chen
- Graduate School, Tianjin Medical University, Tianjin 300070, P.R. China
| | - Ren-Jie Wang
- Department of Neurosurgery, Logistics University of Chinese People's Armed Police Force, Tianjin 300162, P.R. China
| | - Guang-Zong Li
- Key Laboratory of Disaster and Emergency Rescue Medicine in People's Liberation Army, Logistics University of Chinese People's Armed Police Force, Tianjin 300162, P.R. China
| | - Yi Zhang
- Key Laboratory of Disaster and Emergency Rescue Medicine in People's Liberation Army, Logistics University of Chinese People's Armed Police Force, Tianjin 300162, P.R. China
| | - Shuo Yu
- Key Laboratory of Disaster and Emergency Rescue Medicine in People's Liberation Army, Logistics University of Chinese People's Armed Police Force, Tianjin 300162, P.R. China
| | - Ying-Fu Liu
- Department of Cell Biology, Logistics University of Chinese People's Armed Police Forces, Tianjin 300309, P.R. China
| | - Xiao-Yi Chen
- Department of Cell Biology, Logistics University of Chinese People's Armed Police Forces, Tianjin 300309, P.R. China
| | - Shi-Ke Hou
- Graduate School, Tianjin Medical University, Tianjin 300070, P.R. China
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9
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Cui XW, Qian ZL, Li C, Cui SC. Identification of miRNA and mRNA expression profiles by PCR microarray in hepatitis B virus‑associated hepatocellular carcinoma. Mol Med Rep 2018; 18:5123-5132. [PMID: 30272372 DOI: 10.3892/mmr.2018.9516] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 08/23/2018] [Indexed: 02/07/2023] Open
Abstract
The present study aimed to identify differentially expressed microRNAs (miRNAs) and mRNAs in hepatitis B virus‑associated hepatocellular carcinoma (HCC). A total of five HCC tissues and paired adjacent non‑tumor tissues were screened to identify the differentially expressed miRNAs and target mRNAs using polymerase chain reaction microarrays. The interaction between differential miRNA and mRNA expression was concurrently analyzed using bioinformatics methods. A total of 32 differentially expressed miRNAs (four upregulated miRNAs and 28 downregulated miRNAs) and 16 differentially expressed mRNAs (11 upregulated mRNAs and five downregulated mRNAs) were identified. Among these, upregulated hsa‑miRNA (miR)‑96‑5p and hsa‑miR‑18b‑5p suppressed their target mRNAs forkhead box O1 and MET transcriptional regulator MACC1 (MACC1). Downregulation of hsa‑miR‑199a‑5p led to upregulation of its target mRNAs, cyclin dependent kinase 4 and insulin like growth factor 2 (IGF2). The high‑level expression of IGF2 mRNA and cyclin E1 mRNA was due to the low‑level expression of hsa‑miR‑145‑5p, hsa‑miR‑181a‑5p, hsa‑miR‑199a‑5p and hsa‑miR‑223a‑3p, and hsa‑miR‑26a‑5p and hsa‑miR‑26b‑5p, respectively. The low‑level expression of coronin 1A mRNA and MACC1 mRNA was due to overexpression of hsa‑miR‑517a‑3p and hsa‑miR‑18a‑5p, and hsa‑miR‑18b‑5p, respectively. Numerous gene ontology terms were associated with oncogenesis. The most enriched pathways targeted by the dysregulated miRNAs and mRNAs were associated with cancer and oncogenesis pathways. The present data suggested that differential miRNA and mRNA expression is present in HCC. Thus, interactions between certain miRNAs and mRNAs may be involved in the pathogenesis of HCC.
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Affiliation(s)
- Xiong-Wei Cui
- Interventional Center for Oncology, Beijing Youan Hospital, Capital Medical University, Beijing 100069, P.R. China
| | - Zhi-Ling Qian
- Interventional Center for Oncology, Beijing Youan Hospital, Capital Medical University, Beijing 100069, P.R. China
| | - Cong Li
- Interventional Center for Oncology, Beijing Youan Hospital, Capital Medical University, Beijing 100069, P.R. China
| | - Shi-Chang Cui
- Interventional Center for Oncology, Beijing Youan Hospital, Capital Medical University, Beijing 100069, P.R. China
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10
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Harding SD, Sharman JL, Faccenda E, Southan C, Pawson AJ, Ireland S, Gray AJG, Bruce L, Alexander SPH, Anderton S, Bryant C, Davenport AP, Doerig C, Fabbro D, Levi-Schaffer F, Spedding M, Davies JA. The IUPHAR/BPS Guide to PHARMACOLOGY in 2018: updates and expansion to encompass the new guide to IMMUNOPHARMACOLOGY. Nucleic Acids Res 2018; 46:D1091-D1106. [PMID: 29149325 PMCID: PMC5753190 DOI: 10.1093/nar/gkx1121] [Citation(s) in RCA: 1455] [Impact Index Per Article: 242.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 10/25/2017] [Indexed: 02/06/2023] Open
Abstract
The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb, www.guidetopharmacology.org) and its precursor IUPHAR-DB, have captured expert-curated interactions between targets and ligands from selected papers in pharmacology and drug discovery since 2003. This resource continues to be developed in conjunction with the International Union of Basic and Clinical Pharmacology (IUPHAR) and the British Pharmacological Society (BPS). As previously described, our unique model of content selection and quality control is based on 96 target-class subcommittees comprising 512 scientists collaborating with in-house curators. This update describes content expansion, new features and interoperability improvements introduced in the 10 releases since August 2015. Our relationship matrix now describes ∼9000 ligands, ∼15 000 binding constants, ∼6000 papers and ∼1700 human proteins. As an important addition, we also introduce our newly funded project for the Guide to IMMUNOPHARMACOLOGY (GtoImmuPdb, www.guidetoimmunopharmacology.org). This has been 'forked' from the well-established GtoPdb data model and expanded into new types of data related to the immune system and inflammatory processes. This includes new ligands, targets, pathways, cell types and diseases for which we are recruiting new IUPHAR expert committees. Designed as an immunopharmacological gateway, it also has an emphasis on potential therapeutic interventions.
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Affiliation(s)
- Simon D Harding
- Deanery of Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Joanna L Sharman
- Deanery of Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Elena Faccenda
- Deanery of Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Chris Southan
- Deanery of Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Adam J Pawson
- Deanery of Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Sam Ireland
- Department of Structural & Molecular Biology, University College London, London WC1E 6BT, UK
| | - Alasdair J G Gray
- School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Liam Bruce
- School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Stephen P H Alexander
- School of Life Sciences, University of Nottingham Medical School, Nottingham NG7 2UH, UK
| | - Stephen Anderton
- MRC Centre for inflammation Research, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Clare Bryant
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Anthony P Davenport
- Experimental Medicine and Immunotherapeutics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Christian Doerig
- Department of Microbiology, Monash University, Clayton 3800, Australia
| | | | - Francesca Levi-Schaffer
- Pharmacology and Experimental Therapeutics Unit, School of Pharmacy, Institute for Drug Research, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | | | - Jamie A Davies
- Deanery of Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
- To whom correspondence should be addressed. Tel: +44 131 650 2999;
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11
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Kang SW, Patnaik BB, Park SY, Hwang HJ, Chung JM, Sang MK, Min HR, Park JE, Seong J, Jo YH, Noh MY, Lee JD, Jung KY, Park HS, Han YS, Lee JS, Lee YS. Transcriptome analysis of the threatened snail Ellobium chinense reveals candidate genes for adaptation and identifies SSRs for conservation genetics. Genes Genomics 2017; 40:333-347. [PMID: 29892840 DOI: 10.1007/s13258-017-0620-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/26/2017] [Indexed: 11/29/2022]
Abstract
Ellobium chinense (Pfeiffer, 1854) is a brackish pulmonate species that inhabits the bases of mangrove trees and is most commonly found in salt grass meadows. Threats to mangrove ecosystems due to habitat degradation and overexploitation have threatened the species with extinction. In South Korea, E. chinense has been assessed as vulnerable, but there are limited data on its population structure and distribution. The nucleotide and protein sequences for this species are not available in databases, which limits the understanding of adaptation-related traits. We sequenced an E. chinense cDNA library using the Illumina platform, and the subsequent bioinformatics analysis yielded 227,032 unigenes. Of these unigenes, 69,088 were annotated to matched protein and nucleotide sequences in databases, for an annotation rate of 30.42%. Among the predominant gene ontology terms, cellular and metabolic processes (under the biological process category), membrane and cell (under the cellular component category), and binding and catalytic activity (under the molecular function category) were noteworthy. In addition, 4850 unigenes were distributed to 15 Kyoto Encyclopaedia of Genes and Genomes based enrichment categories. Among the candidate genes related to adaptation, angiotensin I converting enzyme, adenylate cyclase activating polypeptide, and AMP-activated protein kinase were the most prominent. A total of 15,952 simple sequence repeats (SSRs) were identified in sequences of > 1 kb in length. The di- and trinucleotide repeat motifs were the most common. Among the repeat motif types, AG/CT, AC/GT, and AAC/GTT dominated. Our study provides the first comprehensive genomics dataset for E. chinense, which favors conservation programs for the restoration of the species and provides sufficient evidence for genetic variability among the wild populations.
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Affiliation(s)
- Se Won Kang
- Biological Resources Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181, Ipsin-gil, Jungeup-si, Jeollabuk-do, 56212, South Korea
| | - Bharat Bhusan Patnaik
- Trident School of Biotech Sciences, Trident Academy of Creative Technology (TACT), Chandaka Industrial Estate, Chandrasekharpur, Bhubaneswar, Odisha, 751024, India
| | - So Young Park
- Nakdonggang National Institute of Biological Resources, Biodiversity Conservation and Climate Change Division, 137, Donam-2-gil, Sangju-si, Gyeongsangbuk-do, 37242, South Korea
| | - Hee-Ju Hwang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do, 31538, South Korea
| | - Jong Min Chung
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do, 31538, South Korea
| | - Min Kyu Sang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do, 31538, South Korea
| | - Hye Rin Min
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do, 31538, South Korea
| | - Jie Eun Park
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do, 31538, South Korea
| | - Jiyeon Seong
- Genomic Informatics Center, Hankyong National University, 327 Chungang-ro, Anseong-si, Kyonggi-do, 17579, South Korea
| | - Yong Hun Jo
- Division of Plant Biotechnology, Institute of Environmentally-Friendly (IEFA), College of Agriculture and Life Sciences, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, 61186, South Korea
| | - Mi Young Noh
- Division of Plant Biotechnology, Institute of Environmentally-Friendly (IEFA), College of Agriculture and Life Sciences, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, 61186, South Korea
| | - Jong Dae Lee
- Department of Environmental Health Science, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do, 31538, South Korea
| | - Ki Yoon Jung
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do, 31538, South Korea
| | - Hong Seog Park
- Research Institute, GnC BIO Co., LTD., 621-6 Banseok-dong, Yuseong-gu, Daejeon, 34069, South Korea
| | - Yeon Soo Han
- Division of Plant Biotechnology, Institute of Environmentally-Friendly (IEFA), College of Agriculture and Life Sciences, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, 61186, South Korea
| | - Jun Sang Lee
- Institute of Environmental Research, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 243341, South Korea
| | - Yong Seok Lee
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do, 31538, South Korea.
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12
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Zhu H, Dai M, Chen X, Chen X, Qin S, Dai S. Integrated analysis of the potential roles of miRNA‑mRNA networks in triple negative breast cancer. Mol Med Rep 2017. [PMID: 28627677 PMCID: PMC5561991 DOI: 10.3892/mmr.2017.6750] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Triple negative breast cancer (TNBC) is a type of breast cancer where the tumor cells are negative for the estrogen, progesterone and human epidermal growth factor 2 receptors. To date, expression profiling of microRNA (miRNA/miR) and mRNA sequences have been widely applied for the diagnosis of TNBC. In the present study, an integrated analysis of miRNA‑mRNA profiling arrays was performed. A total of five dysregulated miRNAs in patients with TNBC were identified, including upregulated miR‑558 expression and downregulated miR‑320d‑1, miR‑548v, miR‑99a and miR‑21 expression. In addition, 49 potential target mRNA sequences were identified. Bioinformatics analyses were performed on the identified miRNAs and mRNAs, including gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes pathway and miRNA‑mRNA network analyses. A total of 31 GO terms and three signaling pathways were identified. The results indicated that the differentially expressed miRNAs and their potential target mRNAs may affect the pathogenesis of TNBC, and may therefore be considered as promising biomarkers for the early diagnosis and targeted therapy of patients with TNBC.
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Affiliation(s)
- Huiru Zhu
- Department of Galactophore, The Third Affiliated Hospital of Guangxi University of Chinese Medicine, Liuzhou, Guangxi 545001, P.R. China
| | - Meiyu Dai
- Department of Clinical Laboratory, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, Guangxi 545005, P.R. China
| | - Xiaoli Chen
- Department of Clinical Laboratory, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, Guangxi 545005, P.R. China
| | - Xiang Chen
- Department of Clinical Laboratory, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, Guangxi 545005, P.R. China
| | - Shini Qin
- Department of Clinical Laboratory, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, Guangxi 545005, P.R. China
| | - Shengming Dai
- Department of Clinical Laboratory, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, Guangxi 545005, P.R. China
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13
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Bocuk D, Wolff A, Krause P, Salinas G, Bleckmann A, Hackl C, Beissbarth T, Koenig S. The adaptation of colorectal cancer cells when forming metastases in the liver: expression of associated genes and pathways in a mouse model. BMC Cancer 2017; 17:342. [PMID: 28525976 PMCID: PMC5437520 DOI: 10.1186/s12885-017-3342-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 05/11/2017] [Indexed: 01/28/2023] Open
Abstract
Background Colorectal cancer (CRC) is the second leading cause of cancer-related death in men and women. Systemic disease with metastatic spread to distant sites such as the liver reduces the survival rate considerably. The aim of this study was to investigate the changes in gene expression that occur on invasion and expansion of CRC cells when forming metastases in the liver. Methods The livers of syngeneic C57BL/6NCrl mice were inoculated with 1 million CRC cells (CMT-93) via the portal vein, leading to the stable formation of metastases within 4 weeks. RNA sequencing performed on the Illumina platform was employed to evaluate the expression profiles of more than 14,000 genes, utilizing the RNA of the cell line cells and liver metastases as well as from corresponding tumour-free liver. Results A total of 3329 differentially expressed genes (DEGs) were identified when cultured CMT-93 cells propagated as metastases in the liver. Hierarchical clustering on heat maps demonstrated the clear changes in gene expression of CMT-93 cells on propagation in the liver. Gene ontology analysis determined inflammation, angiogenesis, and signal transduction as the top three relevant biological processes involved. Using a selection list, matrix metallopeptidases 2, 7, and 9, wnt inhibitory factor, and chemokine receptor 4 were the top five significantly dysregulated genes. Conclusion Bioinformatics assists in elucidating the factors and processes involved in CRC liver metastasis. Our results support the notion of an invasion-metastasis cascade involving CRC cells forming metastases on successful invasion and expansion within the liver. Furthermore, we identified a gene expression signature correlating strongly with invasiveness and migration. Our findings may guide future research on novel therapeutic targets in the treatment of CRC liver metastasis. Electronic supplementary material The online version of this article (doi:10.1186/s12885-017-3342-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Derya Bocuk
- Department of General, Visceral and Paediatric Surgery, University Medical Centre, Georg - August - University Goettingen, Göttingen, Germany
| | - Alexander Wolff
- Statistical Bioinformatics, Department of Medical Statistics, University Medical Centre, Georg - August - University Goettingen, Göttingen, Germany
| | - Petra Krause
- Department of General, Visceral and Paediatric Surgery, University Medical Centre, Georg - August - University Goettingen, Göttingen, Germany
| | - Gabriela Salinas
- Microarray and Deep-Sequencing Core Facility, Institute for Developmental Biochemistry, University Medical Centre, Georg - August - University Goettingen, Göttingen, Germany
| | - Annalen Bleckmann
- Statistical Bioinformatics, Department of Medical Statistics, University Medical Centre, Georg - August - University Goettingen, Göttingen, Germany.,Department of Haematology and Medical Oncology, University Medical Centre, Georg - August - University Goettingen, Göttingen, Germany
| | - Christina Hackl
- Department of Surgery, University Hospital Regensburg, Regensburg, Germany
| | - Tim Beissbarth
- Statistical Bioinformatics, Department of Medical Statistics, University Medical Centre, Georg - August - University Goettingen, Göttingen, Germany
| | - Sarah Koenig
- Department of General, Visceral and Paediatric Surgery, University Medical Centre, Georg - August - University Goettingen, Göttingen, Germany. .,Medical Teaching and Medical Education Research, University Hospital Wuerzburg, Julius-Maximilians-University Wuerzburg, Josef-Schneider-Str. 2/D6, 97080, Wuerzburg, Germany.
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14
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Abstract
The Gene Ontology (GO) project is the largest resource for cataloguing gene function. The combination of solid conceptual underpinnings and a practical set of features have made the GO a widely adopted resource in the research community and an essential resource for data analysis. In this chapter, we provide a concise primer for all users of the GO. We briefly introduce the structure of the ontology and explain how to interpret annotations associated with the GO.
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Affiliation(s)
- Pascale Gaudet
- CALIPHO group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 Michel-Servet, 1211, Geneva, Switzerland. .,Department of Human Protein Sciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
| | - Nives Škunca
- Department of Computer Science, ETH Zurich, Universitätstrasse 19, 8092, Zurich, Switzerland.,SIB Swiss Institute of Bioinformatics, Universitätstr. 19, 8092, Zurich, Switzerland.,University College London, Gower St, London, WC1E 6BT, UK
| | - James C Hu
- Department of Biochemistry and Biophysics, Texas A&M University and Texas AgriLife Research, College Station, TX, USA
| | - Christophe Dessimoz
- Department of Genetics, Evolution & Environment, University College London, Gower St, London, WC1E 6BT, UK.,Swiss Institute of Bioinformatics, Biophore, 1015, Lausanne, Switzerland.,Department of Ecology and Evolution, University of Lausanne, Street Biophore, 1015, Lausanne, Switzerland.,Center of Integrative Genomics, University of Lausanne, Biophore, 1015, Lausanne, Switzerland.,Department of Computer Science, University College London, Gower St, Lausanne, WC1E 6BT, UK
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15
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Transcriptomic Analysis of the Endangered Neritid Species Clithon retropictus: De Novo Assembly, Functional Annotation, and Marker Discovery. Genes (Basel) 2016; 7:genes7070035. [PMID: 27455329 PMCID: PMC4962005 DOI: 10.3390/genes7070035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 07/05/2016] [Accepted: 07/06/2016] [Indexed: 11/25/2022] Open
Abstract
An aquatic gastropod belonging to the family Neritidae, Clithon retropictus is listed as an endangered class II species in South Korea. The lack of information on its genomic background limits the ability to obtain functional data resources and inhibits informed conservation planning for this species. In the present study, the transcriptomic sequencing and de novo assembly of C. retropictus generated a total of 241,696,750 high-quality reads. These assembled to 282,838 unigenes with mean and N50 lengths of 736.9 and 1201 base pairs, respectively. Of these, 125,616 unigenes were subjected to annotation analysis with known proteins in Protostome DB, COG, GO, and KEGG protein databases (BLASTX; E ≤ 0.00001) and with known nucleotides in the Unigene database (BLASTN; E ≤ 0.00001). The GO analysis indicated that cellular process, cell, and catalytic activity are the predominant GO terms in the biological process, cellular component, and molecular function categories, respectively. In addition, 2093 unigenes were distributed in 107 different KEGG pathways. Furthermore, 49,280 simple sequence repeats were identified in the unigenes (>1 kilobase sequences). This is the first report on the identification of transcriptomic and microsatellite resources for C. retropictus, which opens up the possibility of exploring traits related to the adaptation and acclimatization of this species.
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16
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Liao J, Chen Z, He Q, Liu Y, Wang J. Differential gene expression analysis and network construction of recurrent cardiovascular events. Mol Med Rep 2015; 13:1746-64. [PMID: 26708382 DOI: 10.3892/mmr.2015.4707] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Accepted: 11/02/2015] [Indexed: 11/06/2022] Open
Abstract
Recurrent cardiovascular events are vital to the prevention and treatment strategies in patients who have experienced primary cardiovascular events. However, the susceptibility of recurrent cardiovascular events varies among patients. Personalized treatment and prognosis prediction are urged. Microarray profiling of samples from patients with acute myocardial infarction (AMI), with or without recurrent cardiovascular events, were obtained from the Gene Expression Omnibus database. Bioinformatics analysis, including Gene Oncology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), were used to identify genes and pathways specifically associated with recurrent cardiovascular events. A protein-protein interaction (PPI) network was constructed and visualized. A total of 1,329 genes were differentially expressed in the two group samples. Among them, 1,023 differentially expressed genes (DEGs; 76.98%) were upregulated in the recurrent cardiovascular events group and 306 DEGs (23.02%) were downregulated. Significantly enriched GO terms for molecular functions were nucleotide binding and nucleic acid binding, for biological processes were signal transduction and regulation of transcription (DNA-dependent), and for cellular component were cytoplasm and nucleus. The most significant pathway in our KEGG analysis was Pathways in cancer (P=0.000336681), and regulation of actin cytoskeleton was also significantly enriched (P=0.00165229). In the PPI network, the significant hub nodes were GNG4, MAPK8, PIK3R2, EP300, CREB1 and PIK3CB. The present study demonstrated the underlying molecular differences between patients with AMI, with and without recurrent cardiovascular events, including DEGs, their biological function, signaling pathways and key genes in the PPI network. With the use of bioinformatics and genomics these findings can be used to investigate the pathological mechanism, and improve the prevention and treatment of recurrent cardiovascular events.
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Affiliation(s)
- Jiangquan Liao
- Department of Cardiology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, P.R. China
| | - Zhong Chen
- Department of Cardiology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, P.R. China
| | - Qinghong He
- Department of Cardiology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, P.R. China
| | - Yongmei Liu
- Department of Cardiology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, P.R. China
| | - Jie Wang
- Department of Cardiology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, P.R. China
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17
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Yang Y, Li D, Yang Y, Jiang G. An integrated analysis of the effects of microRNA and mRNA on esophageal squamous cell carcinoma. Mol Med Rep 2015; 12:945-52. [PMID: 25823933 PMCID: PMC4438920 DOI: 10.3892/mmr.2015.3557] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 03/16/2015] [Indexed: 01/29/2023] Open
Abstract
Esophageal squamous cell cancer (ESCC) is an aggressive type of cancer with poor prognosis and leading to decreased quality of life. The identification of patients at increased risk of esophageal squamous cell cancer may improve current understanding of the role of micro (mi)RNA in tumorigenesis, since the miRNA pattern of these patients may be associated with tumorigenesis. In the present study, the miRNA and mRNA expression profiles of ESCC tissue samples and adjacent normal control tissue samples were obtained from two dependent GEO series. Bioinformatics analyses, including the use of the Gene Oncology and Kyoto Encyclopedia of Genes and Genomes databases, were used to identify genes and pathways, which were specifically associated with miRNA-associated ESCC oncology. A total of 17 miRNAs and 1,670 probes were differentially expressed in the two groups, and the differentially expressed miRNA and target interactions were analyzed. The mRNA of miRNA target genes were found to be involve 49 GO terms and 14 pathways. Of the genes differentially expressed between the two groups, miRNA-181a, miRNA-202, miRNA-155, FNDC3B, BNC2 and MBD2 were the most significantly altered and may be important in the regulatory network. In the present study, a novel pattern of differential miRNA-target expression was constructed, which with further investigation, may provide novel targets for diagnosing and understanding the mechanism of ESCC.
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Affiliation(s)
- Yong Yang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital Affiliated Tongji University, Shanghai 200433, P.R. China
| | - Dianbo Li
- Department of Thoracic Surgery, Linyi Tumor Hospital, Linyi, Shandong 276001, P.R. China
| | - Yang Yang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital Affiliated Tongji University, Shanghai 200433, P.R. China
| | - Gening Jiang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital Affiliated Tongji University, Shanghai 200433, P.R. China
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18
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Zhou XL, Wu JH, Wang XJ, Guo FJ. Integrated microRNA-mRNA analysis revealing the potential roles of microRNAs in tongue squamous cell cancer. Mol Med Rep 2015; 12:885-94. [PMID: 25760063 PMCID: PMC4438953 DOI: 10.3892/mmr.2015.3467] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Accepted: 02/02/2015] [Indexed: 01/21/2023] Open
Abstract
Tongue squamous cell carcinoma (TSCC) is a rare and aggressive type of cancer, which is associated with a poor prognosis. Identification of patients at high risk of TSCC tumorigenesis may provide information for the early detection of metastases, and for potential treatment strategies. MicroRNA (miRNA; miR) and mRNA expression profiling of TSCC tissue samples and normal control tissue samples were obtained from three Gene Expression Omnibus (GEO) data series. Bioinformatics analyses, including the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes were used to identify genes and pathways specifically associated with miRNA-associated TSCC oncology. A total of 25 miRNAs and 769 mRNAs were differentially expressed in the two groups assessed, and all the differentially expressed miRNA and mRNA target interactions were analyzed. The miRNA target genes were predominantly associated with 38 GO terms and 13 pathways. Of the genes differentially expressed between the two groups, and confirmed in another GEO series, miRNA-494, miRNA-96, miRNA-183, runt-related transcription factor 1, programmed cell death protein 4 and membrane-associated guanylate kinase were the most significantly altered, and may be central in the regulation of TSCC. Bioinformatics may be used to analyze large quantities of data in microarrays through rigorous experimental planning, statistical analysis and the collection of complete data on TSCC. In the present study, a novel differential miRNA-mRNA expression network was constructed, and further investigation may provide novel targets for the diagnosis of TSCC.
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Affiliation(s)
- Xiao-Li Zhou
- Department of Stomatology, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, Henan 471003, P.R. China
| | - Jun-Hua Wu
- Department of Prosthodontics, School of Stomatology, Tongji University, Shanghai 200072, P.R. China
| | - Xin-Juan Wang
- Department of Stomatology, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, Henan 471003, P.R. China
| | - Fu-Jun Guo
- Department of Stomatology, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, Henan 471003, P.R. China
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19
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Veskimäe K, Staff S, Tabaro F, Nykter M, Isola J, Mäenpää J. Microarray analysis of differentially expressed genes in ovarian and fallopian tube epithelium from risk-reducing salpingo-oophorectomies. Genes Chromosomes Cancer 2015; 54:276-87. [PMID: 25706666 DOI: 10.1002/gcc.22241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Accepted: 01/02/2015] [Indexed: 11/11/2022] Open
Abstract
Mutations in the BRCA1 and BRCA2 genes confer an increased lifetime risk for breast and ovarian cancer. Ovarian cancer risk can be decreased by risk-reducing salpingo-oophorectomy (RRSO). Studies on RRSO material have altered the paradigm of serous ovarian cancer pathogenesis. The purpose of this study was to identify candidate genes possibly involved in the pathogenesis of serous ovarian cancer by carrying out a microarray analysis of differentially expressed genes in BRCA1/2- mutation positive ovarian and fallopian tube epithelium derived from RRSO surgery. Freshly frozen ovarian and fallopian tube samples from nine BRCA1/2 mutation carriers scheduled for RRSO were prospectively collected together with five mutation-negative control patients undergoing salpingo-oophorectomy for benign indications. Microarray analysis of genome-wide gene expression was performed on ovarian and fallopian tube samples from the BRCA1/2 and control patients. The validation of microarray data was performed by quantitative real-time polymerase chain reaction (qRT-PCR) in selected cases of RRSO samples and also in high grade serous carcinoma samples collected from patients with a BRCA phenotype. From 22,733 genes, 454 transcripts were identified that were differentially expressed in BRCA1/2 mutation carriers when compared with controls, pooling all ovarian and fallopian tube samples together. Of these, 299 genes were statistically significantly downregulated and 155 genes upregulated. Differentially expressed genes in BRCA1/2 samples reported here might be involved in serous ovarian carcinogenesis and provide interesting targets for further studies.
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Affiliation(s)
- Kristina Veskimäe
- Department of Obstetrics and Gynecology, Tampere University Hospital, Tampere, Finland
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20
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Zhang Y, Yang Y, Chen L, Zhang J. Expression analysis of genes and pathways associated with liver metastases of the uveal melanoma. BMC MEDICAL GENETICS 2014; 15:29. [PMID: 24597767 PMCID: PMC4015751 DOI: 10.1186/1471-2350-15-29] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Accepted: 02/12/2014] [Indexed: 12/25/2022]
Abstract
Background Uveal melanoma is an aggressive cancer which has a high percentage metastasizing to the liver, with a worse prognosis. Identification of patients at high risk of metastases may provide information for early detection of metastases and treatment. Methods Expression profiling of ocular tumor tissues from 46 liver metastatic uveal melanoma samples and 45 non-metastatic uveal melanoma samples were got from GEO database. Bioinformatic analyses such as the Gene Oncology and Kyoto Encyclopedia of Genes and Genomes were used to identify genes and pathways specifically associated with liver metastases of the uveal melanoma. Results A total of 1138 probes were differentially expressed in two group samples. All differential gene interactions in the Signal-Net were analyzed. Of them, 768 probes were up-regulated and 370 down-regulated. They mainly participated in 125 GO terms and 16 pathways. Of the genes differentially expressed between two group cancers, HTR2B, CHL1, the ZNF family, YWHAZ and FYN were the most significantly altered. Conclusions Bioinformatics may help excavate and analyze large amounts of data in microarrays by means of rigorous experimental planning, scientific statistical analysis and collection of complete data about liver metastases of uveal melanoma patients. In the present study, a novel differential gene expression pattern was constructed and advanced study will provide new targets for diagnosis and mechanism of uveal melanoma liver metastases.
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Affiliation(s)
| | | | - Lei Chen
- Department of Ophthalmology, The branch of the first people's hospital of Shanghai, Shanghai 200081, China.
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21
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Gu S, Su P, Yan J, Zhang X, An X, Gao J, Xin R, Liu Y. Comparison of gene expression profiles and related pathways in chronic thromboembolic pulmonary hypertension. Int J Mol Med 2013; 33:277-300. [PMID: 24337368 PMCID: PMC3896458 DOI: 10.3892/ijmm.2013.1582] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 12/03/2013] [Indexed: 01/08/2023] Open
Abstract
Chronic thromboembolic pulmonary hypertension (CTEPH) is one of the main causes of severe pulmonary hypertension. However, despite treatment (pulmonary endarterectomy), in approximately 15–20% of patients, pulmonary vascular resistance and pulmonary arterial pressure continue to increase. To date, little is known about the changes that occur in gene expression in CTEPH. The identification of genes associated with CTEPH may provide insight into the pathogenesis of CTEPH and may aid in diagnosis and treatment. In this study, we analyzed the gene expresion profiles of pulmonary artery endothelial cells from 5 patients with CTEPH and 5 healthy controls using oligonucleotide microarrays. Bioinformatics analyses using the Gene Ontology (GO) and KEGG databases were carried out to identify the genes and pathways specifically associated with CTEPH. Signal transduction networks were established to identify the core genes regulating the progression of CTEPH. A number of genes were found to be differentially expressed in the pulmonary artery endothelial cells from patients with CTEPH. In total, 412 GO terms and 113 pathways were found to be associated with our list of genes. All differential gene interactions in the Signal-Net network were analyzed. JAK3, GNA15, MAPK13, ARRB2 and F2R were the most significantly altered. Bioinformatics analysis may help gather and analyze large amounts of data in microarrays by means of rigorous experimental planning, scientific statistical analysis and the collection of complete data. In this study, a novel differential gene expression pattern was constructed. However, further studies are required to identify novel targets for the diagnosis and treatment of CTEPH.
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Affiliation(s)
- Song Gu
- Department of Cardiac Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, P.R. China
| | - Pixiong Su
- Department of Cardiac Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, P.R. China
| | - Jun Yan
- Department of Cardiac Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, P.R. China
| | - Xitao Zhang
- Department of Cardiac Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, P.R. China
| | - Xiangguang An
- Department of Cardiac Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, P.R. China
| | - Jie Gao
- Department of Cardiac Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, P.R. China
| | - Rui Xin
- Department of Cardiac Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, P.R. China
| | - Yan Liu
- Department of Cardiac Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, P.R. China
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22
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Yang Y, Li H, Hou S, Hu B, Liu J, Wang J. Differences in gene expression profiles and carcinogenesis pathways involved in cisplatin resistance of four types of cancer. Oncol Rep 2013; 30:596-614. [PMID: 23733047 DOI: 10.3892/or.2013.2514] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Accepted: 03/04/2013] [Indexed: 11/06/2022] Open
Abstract
Cisplatin-based chemotherapy is the standard therapy used for the treatment of several types of cancer. However, its efficacy is largely limited by the acquired drug resistance. To date, little is known about the RNA expression changes in cisplatin-resistant cancers. Identification of the RNAs related to cisplatin resistance may provide specific insight into cancer therapy. In the present study, expression profiling of 7 cancer cell lines was performed using oligonucleotide microarray analysis data obtained from the GEO database. Bioinformatic analyses such as the Gene Ontology (GO) and KEGG pathway were used to identify genes and pathways specifically associated with cisplatin resistance. A signal transduction network was established to identify the core genes in regulating cancer cell cisplatin resistance. A number of genes were differentially expressed in 7 groups of cancer cell lines. They mainly participated in 85 GO terms and 11 pathways in common. All differential gene interactions in the Signal-Net were analyzed. CTNNB1, PLCG2 and SRC were the most significantly altered. With the use of bioinformatics, large amounts of data in microarrays were retrieved and analyzed by means of thorough experimental planning, scientific statistical analysis and collection of complete data on cancer cell cisplatin resistance. In the present study, a novel differential gene expression pattern was constructed and further study will provide new targets for the diagnosis and mechanisms of cancer cisplatin resistance.
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Affiliation(s)
- Yong Yang
- Beijing Key Laboratory of Respiratory and Pulmonary Circulation, Capital Medical University, Beijing 100069, PR China
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Long X, Li Y, Qi Y, Xu J, Wang Z, Zhang X, Zhang D, Zhang L, Huang J. XAF1 contributes to dengue virus-induced apoptosis in vascular endothelial cells. FASEB J 2012. [PMID: 23207547 DOI: 10.1096/fj.12-213967] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The mechanism of vascular leakage in severe dengue infection remains unclear. Here, we used primary human umbilical vein endothelial cells (HUVECs) and the EA.hy926 cell line to study the molecular events that occur after dengue virus serotype 2 (DENV2) infection. DENV2-induced apoptosis was confirmed using nuclear staining, TUNEL assay, and electron microscopy. A genome-wide transcriptome analysis was performed using a microarray of DENV2-infected HUVECs. Notably, interferon-inducible genes were differentially expressed after DENV2 infection. Prominent among these genes was the X chromosome-linked inhibitor of apoptosis protein (XIAP)-associated factor 1 (XAF1; up-regulated 1.2-fold in the microarray analysis and ∼8-fold by qRT-PCR after DENV2 infection). XAF1 protein levels were up-regulated after DENV2 infection in both HUVECs and EA.hy926 cells. Evidence indicated interaction between XAF1 and XIAP during DENV2 infection based on their cellular localization, as observed by confocal microscopy and the coimmunoprecipitation of XIAP with an anti-XAF1 antibody. Next, recombinant EA.hy926 cell lines in which XAF1 was either knocked down or overexpressed were constructed. The expression levels of the apoptosis-related genes caspase 3, caspase 8, caspase 9, and poly-(ADP-ribose) polymerase (PARP) were down-regulated in the XAF1 knockdown (24-48 h postinfection) but were up-regulated in XAF1 overexpressing cells (36 h postinfection). This is the first study of the role of XAF1 in promoting apoptosis in vascular endothelial cells after DENV2 infection.
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Affiliation(s)
- Xigui Long
- Institute of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
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24
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Zhao Z, Liu Y, He H, Chen X, Chen J, Lu YC. Candidate genes influencing sensitivity and resistance of human glioblastoma to Semustine. Brain Res Bull 2011; 86:189-94. [PMID: 21807073 DOI: 10.1016/j.brainresbull.2011.07.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 07/07/2011] [Accepted: 07/13/2011] [Indexed: 12/28/2022]
Abstract
OBJECTIVE The prognosis of glioblastoma (GBM) is poor. The therapeutic outcome of conventional surgical and adjuvant treatments remains unsatisfactory, and therefore individualized adjuvant chemotherapy has aroused more attention. Microarrays have been applied to study mechanism of GBM development and progression but it has difficulty in determining responsible genes from the plethora of genes on microarrays unrelated to outcome. The present study was attempted to use bioinformatics method to investigate candidate genes that may influence chemosensitivity of GBM to Semustine (Me-CCNU). METHODS Clinical data of 4 GBM patients in Affymetrix microarray were perfected through long-term follow-up study. Differential expression genes between the long- and short-survival groups were picked out, GO-analysis and pathway-analysis of the differential expression genes were performed. Me-CCNU-related signal transduction networks were constructed. The methods combined three steps before were used to screen core genes that influenced Me-CCNU chemosensitivity in GBM. RESULTS In Affymetrix microarray there were altogether 2018 differential expression genes that influenced survival duration of GBM. Of them, 934 genes were up-regulated and 1084 down-regulated. They mainly participated in 94 pathways. Me-CCNU-related signal transduction networks were constructed. The total number of genes in the networks was 466, of which 66 were also found in survival duration-related differential expression genes. Studied key genes through GO-analysis, pathway-analysis and in the Me-CCNU-related signal transduction networks, 25 core genes that influenced chemosensitivity of GBM to Me-CCNU were obtained, including TP53, MAP2K2, EP300, PRKCA, TNF, CCND1, AKT2, RBL1, CDC2, ID2, RAF1, CDKN2C, FGFR1, SP1, CDK6, IGFBP3, MDM4, PDGFD, SOCS2, CCNG2, CDK2, SDC2, STMN1, TCF7L1, TUBB. CONCLUSION Bioinformatics may help excavate and analyze large amounts of data in microarrays by means of rigorous experimental planning, scientific statistical analysis and collection of complete data about survival of GBM patients. In the present study, a novel differential gene expression pattern was constructed and advanced study will provide new targets for chemosensitivity of GBM.
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Affiliation(s)
- Zhenyu Zhao
- Department of Neurosurgery, ChangZheng Hospital, Second Military Medical University, Shanghai, China
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25
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du Plessis L, Skunca N, Dessimoz C. The what, where, how and why of gene ontology--a primer for bioinformaticians. Brief Bioinform 2011; 12:723-35. [PMID: 21330331 PMCID: PMC3220872 DOI: 10.1093/bib/bbr002] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
With high-throughput technologies providing vast amounts of data, it has become more important to provide systematic, quality annotations. The Gene Ontology (GO) project is the largest resource for cataloguing gene function. Nonetheless, its use is not yet ubiquitous and is still fraught with pitfalls. In this review, we provide a short primer to the GO for bioinformaticians. We summarize important aspects of the structure of the ontology, describe sources and types of functional annotations, survey measures of GO annotation similarity, review typical uses of GO and discuss other important considerations pertaining to the use of GO in bioinformatics applications.
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Affiliation(s)
- Louis du Plessis
- ETH Zurich, Computer Science, Universitätstr. 6, 8092 Zurich, Switzerland
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Lockstone HE, Sanderson S, Kulakova N, Baban D, Leonard A, Kok WL, McGowan S, McMichael AJ, Ho LP. Gene set analysis of lung samples provides insight into pathogenesis of progressive, fibrotic pulmonary sarcoidosis. Am J Respir Crit Care Med 2010; 181:1367-75. [PMID: 20194811 DOI: 10.1164/rccm.200912-1855oc] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
RATIONALE Approximately 60 to 70% of patients with pulmonary sarcoidosis have disease that resolves spontaneously; the rest follow a chronic course with varying levels of fibrosis. It is unclear why some patients progress and if treatment affects outcome. OBJECTIVES To determine differential gene expression profile in lungs of patients with self-limiting sarcoidosis compared to those with progressive-fibrotic disease, and to analyze the biological relevance of these differentially expressed genes. METHODS We examined microarray expression of 26,626 genes in transbronchial biopsies of granulomatous areas in lungs of patients with active but self-limiting (n = 8) versus those with active, progressive (+/- fibrotic) pulmonary disease (n = 7). MEASUREMENTS AND MAIN RESULTS Three hundred thirty-four genes were differentially expressed between the two groups (P < 0.01, Bayesian moderated t test). Gene Set Enrichment Analysis showed over-representation of gene-sets (defined by Gene Ontology) related to host immune activation, proliferation, and defense, among genes up-regulated in the progressive-fibrotic group (FDR q < 0.0001 for the top 43 gene sets), and a marked enrichment of, and similarity in gene expression profiles between, progressive-fibrotic sarcoidosis and hypersensitivity pneumonitis (HP), (q < 0.001), but not idiopathic pulmonary fibrosis (IPF). CONCLUSIONS The findings suggest that patients with progressive/fibrotic pulmonary sarcoidosis have intense immune activity related to host defense in their lungs, with processes more similar to HP than IPF. The study also demonstrates that transbronchial lung biopsy samples can provide good-quality RNA for gene expression profiling, supporting its potential use as a prognostic classifier for pulmonary sarcoidosis.
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Affiliation(s)
- Helen E Lockstone
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
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